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4288696877,4290822336,4287090411,4285160141,4285563024,4294966010,4278255487,4282811060,4291998860,4278222976,4292394968,4294927175,4282441936,4293821166,4294303411,4294967295,4294309365,4294967040,4288335154,4289714175,4281240407,4288217011,4286611584,4286611584,4294945723,4294919424,4294375029]);b.mapJavaScriptColors=new java.util.Hashtable;for(b=JU.CU.colorNames.length;0<=--b;)JU.CU.mapJavaScriptColors.put(JU.CU.colorNames[b],Integer.$valueOf(JU.CU.colorArgbs[b]))});n("JU");z(null,"JU.DF",["JU.PT",
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"~N");c(b,"removeObj",function(a){return this._removeObject(a)},"~O")});n("JU");var P=r(function(){this.m22=this.m21=this.m20=this.m12=this.m11=this.m10=this.m02=this.m01=this.m00=0;u(this,arguments)},JU,"M34",null);c(P,"setAA33",function(b){var a=b.x,d=b.y,h=b.z;b=b.angle;var q=Math.sqrt(a*a+d*d+h*h),q=1/q,a=a*q,d=d*q,h=h*q,c=Math.cos(b);b=Math.sin(b);q=1-c;this.m00=c+a*a*q;this.m11=c+d*d*q;this.m22=c+h*h*q;var c=a*d*q,g=h*b;this.m01=c-g;this.m10=c+g;c=a*h*q;g=d*b;this.m02=c+g;this.m20=c-g;c=d*h*
q;g=a*b;this.m12=c-g;this.m21=c+g},"JU.A4");c(P,"rotate",function(b){this.rotate2(b,b)},"JU.T3");c(P,"rotate2",function(b,a){a.set(this.m00*b.x+this.m01*b.y+this.m02*b.z,this.m10*b.x+this.m11*b.y+this.m12*b.z,this.m20*b.x+this.m21*b.y+this.m22*b.z)},"JU.T3,JU.T3");c(P,"setM33",function(b){this.m00=b.m00;this.m01=b.m01;this.m02=b.m02;this.m10=b.m10;this.m11=b.m11;this.m12=b.m12;this.m20=b.m20;this.m21=b.m21;this.m22=b.m22},"JU.M34");c(P,"clear33",function(){this.m00=this.m01=this.m02=this.m10=this.m11=
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case 1:switch(a){case 0:return this.m10;case 1:return this.m11;case 2:return this.m12}break;case 2:switch(a){case 0:return this.m20;case 1:return this.m21;case 2:return this.m22}}this.err();return 0},"~N,~N");c(P,"setRow33",function(b,a){switch(b){case 0:this.m00=a[0];this.m01=a[1];this.m02=a[2];break;case 1:this.m10=a[0];this.m11=a[1];this.m12=a[2];break;case 2:this.m20=a[0];this.m21=a[1];this.m22=a[2];break;default:this.err()}},"~N,~A");c(P,"getRow33",function(b,a){switch(b){case 0:a[0]=this.m00;
a[1]=this.m01;a[2]=this.m02;return;case 1:a[0]=this.m10;a[1]=this.m11;a[2]=this.m12;return;case 2:a[0]=this.m20;a[1]=this.m21;a[2]=this.m22;return}this.err()},"~N,~A");c(P,"setColumn33",function(b,a){switch(b){case 0:this.m00=a[0];this.m10=a[1];this.m20=a[2];break;case 1:this.m01=a[0];this.m11=a[1];this.m21=a[2];break;case 2:this.m02=a[0];this.m12=a[1];this.m22=a[2];break;default:this.err()}},"~N,~A");c(P,"getColumn33",function(b,a){switch(b){case 0:a[0]=this.m00;a[1]=this.m10;a[2]=this.m20;break;
case 1:a[0]=this.m01;a[1]=this.m11;a[2]=this.m21;break;case 2:a[0]=this.m02;a[1]=this.m12;a[2]=this.m22;break;default:this.err()}},"~N,~A");c(P,"add33",function(b){this.m00+=b.m00;this.m01+=b.m01;this.m02+=b.m02;this.m10+=b.m10;this.m11+=b.m11;this.m12+=b.m12;this.m20+=b.m20;this.m21+=b.m21;this.m22+=b.m22},"JU.M34");c(P,"sub33",function(b){this.m00-=b.m00;this.m01-=b.m01;this.m02-=b.m02;this.m10-=b.m10;this.m11-=b.m11;this.m12-=b.m12;this.m20-=b.m20;this.m21-=b.m21;this.m22-=b.m22},"JU.M34");c(P,
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this.m00=a;this.m01=0;this.m02=b;this.m10=0;this.m11=1;this.m12=0;this.m20=-b;this.m21=0;this.m22=a},"~N");c(P,"setZRot",function(b){var a=Math.cos(b);b=Math.sin(b);this.m00=a;this.m01=-b;this.m02=0;this.m10=b;this.m11=a;this.m21=this.m20=this.m12=0;this.m22=1},"~N");c(P,"determinant3",function(){return this.m00*(this.m11*this.m22-this.m21*this.m12)-this.m01*(this.m10*this.m22-this.m20*this.m12)+this.m02*(this.m10*this.m21-this.m20*this.m11)});c(P,"err",function(){throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");
});n("JU");z(["JU.M34"],"JU.M3",["JU.T3"],function(){var b=G(JU,"M3",JU.M34,java.io.Serializable);b.newA9=c(b,"newA9",function(a){var d=new JU.M3;d.setA(a);return d},"~A");b.newM3=c(b,"newM3",function(a){var d=new JU.M3;if(null==a)return d.setScale(1),d;d.m00=a.m00;d.m01=a.m01;d.m02=a.m02;d.m10=a.m10;d.m11=a.m11;d.m12=a.m12;d.m20=a.m20;d.m21=a.m21;d.m22=a.m22;return d},"JU.M3");c(b,"setScale",function(a){this.clear33();this.m00=this.m11=this.m22=a},"~N");c(b,"setM3",function(a){this.setM33(a)},"JU.M34");
c(b,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m10=a[3];this.m11=a[4];this.m12=a[5];this.m20=a[6];this.m21=a[7];this.m22=a[8]},"~A");c(b,"setElement",function(a,d,h){this.set33(a,d,h)},"~N,~N,~N");c(b,"getElement",function(a,d){return this.get33(a,d)},"~N,~N");c(b,"setRow",function(a,d,h,b){switch(a){case 0:this.m00=d;this.m01=h;this.m02=b;break;case 1:this.m10=d;this.m11=h;this.m12=b;break;case 2:this.m20=d;this.m21=h;this.m22=b;break;default:this.err()}},"~N,~N,~N,~N");c(b,
"setRowV",function(a,d){switch(a){case 0:this.m00=d.x;this.m01=d.y;this.m02=d.z;break;case 1:this.m10=d.x;this.m11=d.y;this.m12=d.z;break;case 2:this.m20=d.x;this.m21=d.y;this.m22=d.z;break;default:this.err()}},"~N,JU.T3");c(b,"setRowA",function(a,d){this.setRow33(a,d)},"~N,~A");f(b,"getRow",function(a,d){this.getRow33(a,d)},"~N,~A");c(b,"setColumn3",function(a,d,h,b){switch(a){case 0:this.m00=d;this.m10=h;this.m20=b;break;case 1:this.m01=d;this.m11=h;this.m21=b;break;case 2:this.m02=d;this.m12=h;
this.m22=b;break;default:this.err()}},"~N,~N,~N,~N");c(b,"setColumnV",function(a,d){switch(a){case 0:this.m00=d.x;this.m10=d.y;this.m20=d.z;break;case 1:this.m01=d.x;this.m11=d.y;this.m21=d.z;break;case 2:this.m02=d.x;this.m12=d.y;this.m22=d.z;break;default:this.err()}},"~N,JU.T3");c(b,"getColumnV",function(a,d){switch(a){case 0:d.x=this.m00;d.y=this.m10;d.z=this.m20;break;case 1:d.x=this.m01;d.y=this.m11;d.z=this.m21;break;case 2:d.x=this.m02;d.y=this.m12;d.z=this.m22;break;default:this.err()}},
"~N,JU.T3");c(b,"setColumnA",function(a,d){this.setColumn33(a,d)},"~N,~A");c(b,"getColumn",function(a,d){this.getColumn33(a,d)},"~N,~A");c(b,"add",function(a){this.add33(a)},"JU.M3");c(b,"sub",function(a){this.sub33(a)},"JU.M3");c(b,"transpose",function(){this.transpose33()});c(b,"transposeM",function(a){this.setM33(a);this.transpose33()},"JU.M3");c(b,"invertM",function(a){this.setM33(a);this.invert()},"JU.M3");c(b,"invert",function(){var a=this.determinant3();0!=a&&(a=1/a,this.set9(this.m11*this.m22-
this.m12*this.m21,this.m02*this.m21-this.m01*this.m22,this.m01*this.m12-this.m02*this.m11,this.m12*this.m20-this.m10*this.m22,this.m00*this.m22-this.m02*this.m20,this.m02*this.m10-this.m00*this.m12,this.m10*this.m21-this.m11*this.m20,this.m01*this.m20-this.m00*this.m21,this.m00*this.m11-this.m01*this.m10),this.scale(a))});c(b,"setAsXRotation",function(a){this.setXRot(a);return this},"~N");c(b,"setAsYRotation",function(a){this.setYRot(a);return this},"~N");c(b,"setAsZRotation",function(a){this.setZRot(a);
return this},"~N");c(b,"scale",function(a){this.mul33(a)},"~N");c(b,"mul",function(a){this.mul2(this,a)},"JU.M3");c(b,"mul2",function(a,d){this.set9(a.m00*d.m00+a.m01*d.m10+a.m02*d.m20,a.m00*d.m01+a.m01*d.m11+a.m02*d.m21,a.m00*d.m02+a.m01*d.m12+a.m02*d.m22,a.m10*d.m00+a.m11*d.m10+a.m12*d.m20,a.m10*d.m01+a.m11*d.m11+a.m12*d.m21,a.m10*d.m02+a.m11*d.m12+a.m12*d.m22,a.m20*d.m00+a.m21*d.m10+a.m22*d.m20,a.m20*d.m01+a.m21*d.m11+a.m22*d.m21,a.m20*d.m02+a.m21*d.m12+a.m22*d.m22)},"JU.M3,JU.M3");f(b,"equals",
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c(b,"setZero",function(){this.clear33()});c(b,"set9",function(a,d,h,b,c,g,j,k,l){this.m00=a;this.m01=d;this.m02=h;this.m10=b;this.m11=c;this.m12=g;this.m20=j;this.m21=k;this.m22=l},"~N,~N,~N,~N,~N,~N,~N,~N,~N");f(b,"toString",function(){return"[\n  ["+this.m00+"\t"+this.m01+"\t"+this.m02+"]\n  ["+this.m10+"\t"+this.m11+"\t"+this.m12+"]\n  ["+this.m20+"\t"+this.m21+"\t"+this.m22+"] ]"});c(b,"setAA",function(a){this.setAA33(a);return this},"JU.A4");c(b,"setAsBallRotation",function(a,d,h){var b=Math.sqrt(d*
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c(b,"setZero",function(){this.clear33();this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=this.m33=0});c(b,"setIdentity",function(){this.setZero();this.m00=this.m11=this.m22=this.m33=1});c(b,"setM4",function(a){this.setM33(a);this.m03=a.m03;this.m13=a.m13;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;this.m33=a.m33;return this},"JU.M4");c(b,"setMV",function(a,d){this.setM33(a);this.setTranslation(d);this.m33=1},"JU.M3,JU.T3");c(b,"setToM3",function(a){this.setM33(a);this.m03=this.m13=
this.m23=this.m30=this.m31=this.m32=0;this.m33=1},"JU.M34");c(b,"setToAA",function(a){this.setIdentity();this.setAA33(a)},"JU.A4");c(b,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m03=a[3];this.m10=a[4];this.m11=a[5];this.m12=a[6];this.m13=a[7];this.m20=a[8];this.m21=a[9];this.m22=a[10];this.m23=a[11];this.m30=a[12];this.m31=a[13];this.m32=a[14];this.m33=a[15]},"~A");c(b,"setTranslation",function(a){this.m03=a.x;this.m13=a.y;this.m23=a.z},"JU.T3");c(b,"setElement",function(a,
d,h){if(3>a&&3>d)this.set33(a,d,h);else{(3<a||3<d)&&this.err();switch(a){case 0:this.m03=h;return;case 1:this.m13=h;return;case 2:this.m23=h;return}switch(d){case 0:this.m30=h;break;case 1:this.m31=h;break;case 2:this.m32=h;break;case 3:this.m33=h}}},"~N,~N,~N");c(b,"getElement",function(a,d){if(3>a&&3>d)return this.get33(a,d);if(3<a||3<d)return this.err(),0;switch(a){case 0:return this.m03;case 1:return this.m13;case 2:return this.m23;default:switch(d){case 0:return this.m30;case 1:return this.m31;
case 2:return this.m32;default:return this.m33}}},"~N,~N");c(b,"getTranslation",function(a){a.x=this.m03;a.y=this.m13;a.z=this.m23},"JU.T3");c(b,"getRotationScale",function(a){a.m00=this.m00;a.m01=this.m01;a.m02=this.m02;a.m10=this.m10;a.m11=this.m11;a.m12=this.m12;a.m20=this.m20;a.m21=this.m21;a.m22=this.m22},"JU.M3");c(b,"setRotationScale",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m10=a.m10;this.m11=a.m11;this.m12=a.m12;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M3");
c(b,"setRowA",function(a,d){3>a&&this.setRow33(a,d);switch(a){case 0:this.m03=d[3];return;case 1:this.m13=d[3];return;case 2:this.m23=d[3];return;case 3:this.m30=d[0];this.m31=d[1];this.m32=d[2];this.m33=d[3];return}this.err()},"~N,~A");f(b,"getRow",function(a,d){3>a&&this.getRow33(a,d);switch(a){case 0:d[3]=this.m03;return;case 1:d[3]=this.m13;return;case 2:d[3]=this.m23;return;case 3:d[0]=this.m30;d[1]=this.m31;d[2]=this.m32;d[3]=this.m33;return}this.err()},"~N,~A");c(b,"setColumn4",function(a,
d,h,b,c){0==a?(this.m00=d,this.m10=h,this.m20=b,this.m30=c):1==a?(this.m01=d,this.m11=h,this.m21=b,this.m31=c):2==a?(this.m02=d,this.m12=h,this.m22=b,this.m32=c):3==a?(this.m03=d,this.m13=h,this.m23=b,this.m33=c):this.err()},"~N,~N,~N,~N,~N");c(b,"setColumnA",function(a,d){3>a&&this.setColumn33(a,d);switch(a){case 0:this.m30=d[3];break;case 1:this.m31=d[3];break;case 2:this.m32=d[3];break;case 3:this.m03=d[0];this.m13=d[1];this.m23=d[2];this.m33=d[3];break;default:this.err()}},"~N,~A");c(b,"getColumn",
function(a,d){3>a&&this.getColumn33(a,d);switch(a){case 0:d[3]=this.m30;break;case 1:d[3]=this.m31;break;case 2:d[3]=this.m32;break;case 3:d[0]=this.m03;d[1]=this.m13;d[2]=this.m23;d[3]=this.m33;break;default:this.err()}},"~N,~A");c(b,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31;this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(b,"add",function(a){this.m03+=a.x;this.m13+=a.y;this.m23+=a.z},"JU.T3");c(b,"transpose",function(){this.transpose33();
var a=this.m03;this.m03=this.m30;this.m30=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(b,"invert",function(){var a=this.determinant4();if(0==a)return this;a=1/a;this.set(this.m11*(this.m22*this.m33-this.m23*this.m32)+this.m12*(this.m23*this.m31-this.m21*this.m33)+this.m13*(this.m21*this.m32-this.m22*this.m31),this.m21*(this.m02*this.m33-this.m03*this.m32)+this.m22*(this.m03*this.m31-this.m01*this.m33)+this.m23*(this.m01*this.m32-this.m02*this.m31),this.m31*
(this.m02*this.m13-this.m03*this.m12)+this.m32*(this.m03*this.m11-this.m01*this.m13)+this.m33*(this.m01*this.m12-this.m02*this.m11),this.m01*(this.m13*this.m22-this.m12*this.m23)+this.m02*(this.m11*this.m23-this.m13*this.m21)+this.m03*(this.m12*this.m21-this.m11*this.m22),this.m12*(this.m20*this.m33-this.m23*this.m30)+this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22*(this.m00*this.m33-this.m03*this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+
this.m20*(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*
this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-
this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*this.m10)+this.m32*(this.m01*this.m10-this.m00*this.m11),this.m00*(this.m11*this.m22-this.m12*this.m21)+this.m01*(this.m12*this.m20-this.m10*this.m22)+this.m02*(this.m10*this.m21-this.m11*this.m20));this.scale(a);return this});c(b,"set",function(a,d,h,b,c,g,
j,k,l,f,m,p,x,A,H,M){this.m00=a;this.m01=d;this.m02=h;this.m03=b;this.m10=c;this.m11=g;this.m12=j;this.m13=k;this.m20=l;this.m21=f;this.m22=m;this.m23=p;this.m30=x;this.m31=A;this.m32=H;this.m33=M},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(b,"determinant4",function(){return(this.m00*this.m11-this.m01*this.m10)*(this.m22*this.m33-this.m23*this.m32)-(this.m00*this.m12-this.m02*this.m10)*(this.m21*this.m33-this.m23*this.m31)+(this.m00*this.m13-this.m03*this.m10)*(this.m21*this.m32-this.m22*
this.m31)+(this.m01*this.m12-this.m02*this.m11)*(this.m20*this.m33-this.m23*this.m30)-(this.m01*this.m13-this.m03*this.m11)*(this.m20*this.m32-this.m22*this.m30)+(this.m02*this.m13-this.m03*this.m12)*(this.m20*this.m31-this.m21*this.m30)});c(b,"scale",function(a){this.mul33(a);this.m03*=a;this.m13*=a;this.m23*=a;this.m30*=a;this.m31*=a;this.m32*=a;this.m33*=a},"~N");c(b,"mul",function(a){this.mul2(this,a)},"JU.M4");c(b,"mul2",function(a,d){this.set(a.m00*d.m00+a.m01*d.m10+a.m02*d.m20+a.m03*d.m30,
a.m00*d.m01+a.m01*d.m11+a.m02*d.m21+a.m03*d.m31,a.m00*d.m02+a.m01*d.m12+a.m02*d.m22+a.m03*d.m32,a.m00*d.m03+a.m01*d.m13+a.m02*d.m23+a.m03*d.m33,a.m10*d.m00+a.m11*d.m10+a.m12*d.m20+a.m13*d.m30,a.m10*d.m01+a.m11*d.m11+a.m12*d.m21+a.m13*d.m31,a.m10*d.m02+a.m11*d.m12+a.m12*d.m22+a.m13*d.m32,a.m10*d.m03+a.m11*d.m13+a.m12*d.m23+a.m13*d.m33,a.m20*d.m00+a.m21*d.m10+a.m22*d.m20+a.m23*d.m30,a.m20*d.m01+a.m21*d.m11+a.m22*d.m21+a.m23*d.m31,a.m20*d.m02+a.m21*d.m12+a.m22*d.m22+a.m23*d.m32,a.m20*d.m03+a.m21*d.m13+
a.m22*d.m23+a.m23*d.m33,a.m30*d.m00+a.m31*d.m10+a.m32*d.m20+a.m33*d.m30,a.m30*d.m01+a.m31*d.m11+a.m32*d.m21+a.m33*d.m31,a.m30*d.m02+a.m31*d.m12+a.m32*d.m22+a.m33*d.m32,a.m30*d.m03+a.m31*d.m13+a.m32*d.m23+a.m33*d.m33)},"JU.M4,JU.M4");c(b,"transform",function(a){this.transform2(a,a)},"JU.T4");c(b,"transform2",function(a,d){d.set4(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03*a.w,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13*a.w,this.m20*a.x+this.m21*a.y+this.m22*a.z+this.m23*a.w,this.m30*a.x+this.m31*
a.y+this.m32*a.z+this.m33*a.w)},"JU.T4,JU.T4");c(b,"rotTrans",function(a){this.rotTrans2(a,a)},"JU.T3");c(b,"rotTrans2",function(a,d){d.set(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13,this.m20*a.x+this.m21*a.y+this.m22*a.z+this.m23);return d},"JU.T3,JU.T3");c(b,"setAsXYRotation",function(a){this.setIdentity();var d=Math.cos(a);a=Math.sin(a);this.m22=d;this.m23=-a;this.m32=a;this.m33=d;return this},"~N");c(b,"setAsYZRotation",function(a){this.setIdentity();
var d=Math.cos(a);a=Math.sin(a);this.m00=d;this.m03=-a;this.m30=a;this.m33=d;return this},"~N");c(b,"setAsXZRotation",function(a){this.setIdentity();var d=Math.cos(a);a=Math.sin(a);this.m11=d;this.m13=-a;this.m31=a;this.m33=d;return this},"~N");f(b,"equals",function(a){return!C(a,"JU.M4")?!1:this.m00==a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m03==a.m03&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m13==a.m13&&this.m20==a.m20&&this.m21==a.m21&&this.m22==a.m22&&this.m23==a.m23&&this.m30==
a.m30&&this.m31==a.m31&&this.m32==a.m32&&this.m33==a.m33},"~O");f(b,"hashCode",function(){return JU.T3.floatToIntBits(this.m00)^JU.T3.floatToIntBits(this.m01)^JU.T3.floatToIntBits(this.m02)^JU.T3.floatToIntBits(this.m03)^JU.T3.floatToIntBits(this.m10)^JU.T3.floatToIntBits(this.m11)^JU.T3.floatToIntBits(this.m12)^JU.T3.floatToIntBits(this.m13)^JU.T3.floatToIntBits(this.m20)^JU.T3.floatToIntBits(this.m21)^JU.T3.floatToIntBits(this.m22)^JU.T3.floatToIntBits(this.m23)^JU.T3.floatToIntBits(this.m30)^JU.T3.floatToIntBits(this.m31)^
JU.T3.floatToIntBits(this.m32)^JU.T3.floatToIntBits(this.m33)});f(b,"toString",function(){return"[\n  ["+this.m00+"\t"+this.m01+"\t"+this.m02+"\t"+this.m03+"]\n  ["+this.m10+"\t"+this.m11+"\t"+this.m12+"\t"+this.m13+"]\n  ["+this.m20+"\t"+this.m21+"\t"+this.m22+"\t"+this.m23+"]\n  ["+this.m30+"\t"+this.m31+"\t"+this.m32+"\t"+this.m33+"] ]"});c(b,"round",function(a){this.m00=this.rnd(this.m00,a);this.m01=this.rnd(this.m01,a);this.m02=this.rnd(this.m02,a);this.m03=this.rnd(this.m03,a);this.m10=this.rnd(this.m10,
a);this.m11=this.rnd(this.m11,a);this.m12=this.rnd(this.m12,a);this.m13=this.rnd(this.m13,a);this.m20=this.rnd(this.m20,a);this.m21=this.rnd(this.m21,a);this.m22=this.rnd(this.m22,a);this.m23=this.rnd(this.m23,a);this.m30=this.rnd(this.m30,a);this.m31=this.rnd(this.m31,a);this.m32=this.rnd(this.m32,a);this.m33=this.rnd(this.m33,a);return this},"~N");c(b,"rnd",function(a,d){return Math.abs(a)<d?0:a},"~N,~N")});n("JU");z(["java.io.OutputStream","javajs.api.GenericOutputChannel"],"JU.OC",["java.io.BufferedWriter",
"$.ByteArrayOutputStream","$.OutputStreamWriter","JU.Base64","$.SB"],function(){var b=r(function(){this.bw=this.fileName=this.bytePoster=null;this.isLocalFile=!1;this.byteCount=0;this.closed=this.isCanceled=!1;this.type=this.sb=this.os=null;this.$isBase64=!1;this.bytes=this.os0=null;this.bigEndian=!0;u(this,arguments)},JU,"OC",java.io.OutputStream,javajs.api.GenericOutputChannel);y(b,function(){I(this,JU.OC,[])});y(b,function(a){I(this,JU.OC,[]);this.setParams(null,a,!1,null)},"~S");c(b,"setParams",
function(a,d,h,b){this.bytePoster=a;if(this.$isBase64=";base64,".equals(d))d=null,this.os0=b,b=null;this.fileName=d;this.os=b;this.isLocalFile=null!=d&&!JU.OC.isRemote(d);h&&(!this.$isBase64&&null!=b)&&(this.bw=new java.io.BufferedWriter(new java.io.OutputStreamWriter(b)));return this},"javajs.api.BytePoster,~S,~B,java.io.OutputStream");f(b,"isBigEndian",function(){return this.bigEndian});c(b,"setBigEndian",function(a){this.bigEndian=a},"~B");c(b,"setBytes",function(a){this.bytes=a;return this},"~A");
c(b,"getFileName",function(){return this.fileName});c(b,"getName",function(){return null==this.fileName?null:this.fileName.substring(this.fileName.lastIndexOf("/")+1)});c(b,"getByteCount",function(){return this.byteCount});c(b,"setType",function(a){this.type=a},"~S");c(b,"getType",function(){return this.type});c(b,"append",function(a){try{if(null!=this.bw)this.bw.write(a);else if(null==this.os)null==this.sb&&(this.sb=new JU.SB),this.sb.append(a);else{var d=a.getBytes();this.os.write(d,0,d.length);
this.byteCount+=d.length;return this}}catch(h){if(!D(h,"java.io.IOException"))throw h;}this.byteCount+=a.length;return this},"~S");f(b,"reset",function(){this.sb=null;this.initOS()});c(b,"initOS",function(){if(null!=this.sb){var a=this.sb.toString();this.reset();this.append(a)}else{try{this.os=null,null==this.os&&(this.os=new java.io.ByteArrayOutputStream),null!=this.bw&&(this.bw.close(),this.bw=new java.io.BufferedWriter(new java.io.OutputStreamWriter(this.os)))}catch(d){if(D(d,Exception))System.out.println(d.toString());
else throw d;}this.byteCount=0}});f(b,"writeByteAsInt",function(a){null==this.os&&this.initOS();this.os.writeByteAsInt(a);this.byteCount++},"~N");f(b,"write",function(a,d,h){null==this.os&&this.initOS();0>h&&(h=a.length-d);try{this.os.write(a,d,h)}catch(b){if(!D(b,"java.io.IOException"))throw b;}this.byteCount+=h},"~A,~N,~N");f(b,"writeShort",function(a){this.isBigEndian()?(this.writeByteAsInt(a>>8),this.writeByteAsInt(a)):(this.writeByteAsInt(a),this.writeByteAsInt(a>>8))},"~N");f(b,"writeLong",
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-1;return d}var h=d=null,d=self.J2S||Jmol,h="function"==typeof this.fileName?this.fileName:null;if(null!=d){var b=null==this.sb?this.toByteArray():this.sb.toString();null==h?d.doAjax(this.fileName,null,b,null==this.sb):d.applyFunc(this.fileName,b)}return null});c(b,"isBase64",function(){return this.$isBase64});c(b,"getBase64",function(){return JU.Base64.getBase64(this.toByteArray()).toString()});c(b,"toByteArray",function(){return null!=this.bytes?this.bytes:C(this.os,"java.io.ByteArrayOutputStream")?
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function(){var b=G(JU,"V3d",JU.T3d);c(b,"cross",function(a,d){this.set(a.y*d.z-a.z*d.y,a.z*d.x-a.x*d.z,a.x*d.y-a.y*d.x)},"JU.V3d,JU.V3d");c(b,"normalize",function(){var a=this.length();this.x/=a;this.y/=a;this.z/=a});c(b,"angle",function(a){var d=this.y*a.z-this.z*a.y,h=this.z*a.x-this.x*a.z,b=this.x*a.y-this.y*a.x,d=Math.sqrt(d*d+h*h+b*b);return Math.abs(Math.atan2(d,this.dot(a)))},"JU.V3d");c(b,"dot",function(a){return this.x*a.x+this.y*a.y+this.z*a.z},"JU.V3d");c(b,"lengthSquared",function(){return this.x*
this.x+this.y*this.y+this.z*this.z});c(b,"length",function(){return Math.sqrt(this.lengthSquared())})});n("J.adapter.readers.molxyz");z(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.MolReader","java.util.Hashtable JU.BS $.Lst $.PT J.adapter.smarter.Atom J.api.JmolAdapter JU.Logger".split(" "),function(){var b=r(function(){this.haveAtomSerials=!1;this.allow2D=!0;this.iatom0=0;this.vr=null;this.atomCount=0;this.bsDeleted=this.atomData=null;this.is3D=this.fixN=this.haveNonzeroZ=
!1;this.nC=this.nH=this.nDouble=0;u(this,arguments)},J.adapter.readers.molxyz,"MolReader",J.adapter.smarter.AtomSetCollectionReader);f(b,"initializeReader",function(){this.fixN=this.checkFilterKey("FIXN")});f(b,"checkLine",function(){var a=this.line.startsWith("$MDL");if(a){if(this.discardLinesUntilStartsWith("$HDR"),this.rd(),null==this.line)return JU.Logger.warn("$HDR not found in MDL RG file"),this.continuing=!1}else if(this.line.equals("M  END"))return!0;if(this.doGetModel(++this.modelNumber,
null)&&(this.iatom0=this.asc.ac,this.processMolSdHeader(),this.processCtab(a),this.vr=null,this.isLastModel(this.modelNumber)))return this.continuing=!1;null!=this.line&&0>this.line.indexOf("$$$$")&&this.discardLinesUntilStartsWith("$$$$");return!0});f(b,"finalizeSubclassReader",function(){this.finalizeReaderMR()});c(b,"finalizeReaderMR",function(){this.fixN&&this.addJmolScript("{search('[Nv4+0,nv4+0]')}.formalCharge=1;{search('{[Ov1-0]}[Nv4+1,nv4+1]')}.formalCharge=-1;");this.check2D3D();null!=this.bsDeleted&&
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this.vr=this.getInterface("J.adapter.readers.molxyz.V3000Rdr").set(this),this.discardLinesUntilContains("COUNTS"),this.vr.readAtomsAndBonds(this.getTokens())):this.readAtomsAndBonds(this.parseIntRange(this.line,0,3),this.parseIntRange(this.line,3,6)),this.applySymmetryAndSetTrajectory())},"~B");c(b,"readAtomsAndBonds",function(a,d){this.atomCount=a;for(var h=0;h<a;++h){this.rd();var b=this.line.length,c,g,j,k,l=0,f=0,m=-2147483648;g=this.parseFloatRange(this.line,0,10);j=this.parseFloatRange(this.line,
10,20);k=this.parseFloatRange(this.line,20,30);34>b?c=this.line.substring(31).trim():(c=this.line.substring(31,34).trim(),c.equals("H1")&&(c="H",f=1),39<=b&&(b=this.parseIntRange(this.line,36,39),1<=b&&7>=b&&(l=4-b),b=this.parseIntRange(this.line,34,36),0!=b&&(-3<=b&&4>=b)&&(f=J.api.JmolAdapter.getNaturalIsotope(J.api.JmolAdapter.getElementNumber(c))+b),-2147483648==m&&this.haveAtomSerials&&(m=h+1)));this.addMolAtom(m,f,c,l,g,j,k)}this.asc.setModelInfoForSet("dimension",this.is2D?"2D":"3D",this.asc.iSet);
this.rd();this.line.startsWith("V  ")&&this.readAtomValues();0==d&&this.asc.setNoAutoBond();for(h=0;h<d;++h){0<h&&this.rd();j=0;c=this.line.substring(0,3).trim();g=this.line.substring(3,6).trim();k=this.parseIntRange(this.line,6,9);if((this.is2D||!this.is3D)&&1==k&&12<=this.line.length)j=this.parseIntRange(this.line,9,12);0!=j&&!this.is3D&&(this.is2D=!0);k=this.fixOrder(k,j);this.haveAtomSerials?this.asc.addNewBondFromNames(c,g,k):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(c)-1,this.iatom0+
this.parseIntStr(g)-1,k)}h=new java.util.Hashtable;c=new JU.Lst;for(this.rd();null!=this.line&&0!=this.line.indexOf("$$$$");)0==this.line.indexOf(">")?this.readMolData(h,c):this.line.startsWith("M  ISO")?this.readIsotopes():this.rd();null!=this.atomData&&(g=h.get("atom_value_name"),h.put(null==g?"atom_values":g.toString(),this.atomData));h.isEmpty()||(this.asc.setCurrentModelInfo("molDataKeys",c),this.asc.setCurrentModelInfo("molData",h))},"~N,~N");c(b,"readAtomValues",function(){this.atomData=Array(this.atomCount);
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b+4),b=b+8,k=JU.PT.replaceAllCharacters(g.elementSymbol,"0123456789","");17==j&&k.equals("C")?g.elementSymbol="N":5==j&&k.equals("H")?this.deleteAtom(g):g.elementSymbol=""+j+k}}catch(l){}this.rd()});c(b,"deleteAtom",function(a){null==this.bsDeleted&&(this.bsDeleted=new JU.BS);this.bsDeleted.set(a.index)},"J.adapter.smarter.Atom");c(b,"readMolData",function(a,d){for(var h=this.asc.atoms,b=JU.PT.trim(this.line,"> <").toLowerCase(),c="",g=null;null!=this.rd()&&!this.line.equals("$$$$")&&0<this.line.length;)c+=
81==this.line.length&&"+"==this.line.charAt(80)?this.line.substring(0,80):this.line+"\n";c=JU.PT.trim(c,"\n");JU.Logger.info(b+":"+JU.PT.esc(c));a.put(b,c);d.addLast(b);var j=0;if(b.toUpperCase().contains("_PARTIAL_CHARGES")){try{for(var g=JU.PT.parseFloatArray(c),k=this.asc.getLastAtomSetAtomIndex(),l=this.asc.ac;k<l;k++)h[k].partialCharge=0;for(var f=0,k=F(g[f++]);0<=--k;){var m=F(g[f++])+this.iatom0-1,p=g[f++];h[m].partialCharge=p;j++}}catch(x){k=this.asc.getLastAtomSetAtomIndex();for(l=this.asc.ac;k<
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c(b,"addMolAtom",function(a,d,h,b,c,g,j){"H".equals(h)?this.nH++:"C".equals(h)&&this.nC++;this.haveNonzeroZ=(new Boolean(this.haveNonzeroZ|0!=j)).valueOf();switch(d){case 0:break;case 1:h="1H";break;case 2:h="2H";break;case 3:h="3H";break;default:h=d+h}d=new J.adapter.smarter.Atom;d.elementSymbol=h;d.formalCharge=b;this.setAtomCoordXYZ(d,c,g,j);-2147483648==a?this.asc.addAtom(d):(this.haveAtomSerials=!0,d.atomSerial=a,this.asc.addAtomWithMappedSerialNumber(d));return d},"~N,~N,~S,~N,~N,~N,~N");c(b,
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d,h):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(a)-1,this.iatom0+this.parseIntStr(d)-1,h)},"~S,~S,~N,~N")});n("J.adapter.readers.molxyz");z(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["JU.Logger"],function(){var b=G(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);f(b,"checkLine",function(){var a=this.parseIntStr(this.line);if(-2147483648==a)return this.continuing=!1;this.vibrationNumber=++this.modelNumber;if(0>=
this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):this.doGetVibration(this.vibrationNumber)){this.rd();this.checkCurrentLineForScript();this.asc.newAtomSet();var d=this.line.trim();this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.asc.setAtomSetName(d);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();return!1});f(b,"finalizeSubclassReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});
c(b,"skipAtomSet",function(a){for(this.rd();0<=--a;)this.rd()},"~N");c(b,"readAtoms",function(a){for(var d=0;d<a;++d){this.rd();var h=this.getTokens();if(4>h.length)JU.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var b=this.addAtomXYZSymName(h,1,null,null);this.setElementAndIsotope(b,h[0]);var c=4;switch(h.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=h[4].indexOf("."))b.partialCharge=this.parseFloatStr(h[4]);else{var g=this.parseIntStr(h[4]);-2147483648!=g&&(b.formalCharge=
g)}switch(h.length){case 5:continue;case 6:b.radius=this.parseFloatStr(h[5]);continue;case 9:b.atomSerial=this.parseIntStr(h[8])}c++;default:var g=this.parseFloatStr(h[c++]),j=this.parseFloatStr(h[c++]),h=this.parseFloatStr(h[c++]);if(Float.isNaN(g)||Float.isNaN(j)||Float.isNaN(h))continue;this.asc.addVibrationVector(b.index,g,j,h)}}}},"~N")});n("J.adapter.smarter");z(["JU.P3"],"J.adapter.smarter.Atom",["JU.AU","$.Lst","$.V3"],function(){var b=r(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=
null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=null;this.formalCharge=-2147483648;this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.bondingRadius=NaN;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.tensors=this.anisoBorU=null;this.isNegDisorder=!1;this.typeSymbol=null;u(this,arguments)},J.adapter.smarter,"Atom",
JU.P3,Cloneable);y(b,function(){I(this,J.adapter.smarter.Atom,[]);this.set(NaN,NaN,NaN)});c(b,"addTensor",function(a,d,h){if(null==a)return null;if(h||null==this.tensors)this.tensors=new JU.Lst;this.tensors.addLast(a);null!=d&&a.setType(d);return a},"JU.Tensor,~S,~B");c(b,"getClone",function(){var a;try{a=this.clone()}catch(d){if(D(d,"CloneNotSupportedException"))return null;throw d;}null!=this.vib&&(a.vib=C(this.vib,"JU.Vibration")?this.vib.clone():JU.V3.newV(a.vib));null!=this.anisoBorU&&(a.anisoBorU=
JU.AU.arrayCopyF(this.anisoBorU,-1));if(null!=this.tensors){a.tensors=new JU.Lst;for(var h=this.tensors.size();0<=--h;)a.tensors.addLast(this.tensors.get(h).copyTensor())}return a});c(b,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=this.atomName){for(var a=this.atomName.length,d=0,h=String.fromCharCode(0);d<a&&!J.adapter.smarter.Atom.isValidSymChar1(h=this.atomName.charAt(d));)++d;switch(a-d){case 0:break;default:if(a=this.atomName.charAt(d+1),J.adapter.smarter.Atom.isValidSymNoCase(h,
a)){this.elementSymbol=""+h+a;break}case 1:J.adapter.smarter.Atom.isValidSym1(h)&&(this.elementSymbol=""+h)}}return this.elementSymbol});b.isValidSym1=c(b,"isValidSym1",function(a){return"A"<=a&&"Z">=a&&0>J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");b.isValidSym2=c(b,"isValidSym2",function(a,d){return"A"<=a&&"Z">=a&&"a"<=d&&"z">=d&&0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>d.charCodeAt(0)-97&1)},"~S,~S");b.isValidSymNoCase=c(b,"isValidSymNoCase",function(a,
d){return J.adapter.smarter.Atom.isValidSym2(a,"a">d?String.fromCharCode(d.charCodeAt(0)+32):d)},"~S,~S");b.isValidSymChar1=c(b,"isValidSymChar1",function(a){return"A"<=a&&"Z">=a&&0!=J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c(b,"copyTo",function(a,d){var h=d.newCloneAtom(this);h.setT(a);return h},"JU.P3,J.adapter.smarter.AtomSetCollection");b.elementCharMasks=E(-1,[1972292,-2147351151,-2146019271,-2130706430,1441792,-2147348464,25,-2147205008,-2147344384,0,-2147352576,1179905,
548936,-2147434213,-2147221504,-2145759221,0,1056947,-2147339946,-2147477097,-2147483648,-2147483648,-2147483648,8388624,-2147483646,139264])});n("J.adapter.smarter");z(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["J.api.JmolAdapter"],function(){var b=r(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;u(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);y(b,function(a){this.ac=a.ac;this.atoms=a.atoms;this.bsAtoms=
a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");f(b,"hasNext",function(){if(this.iatom==this.ac)return!1;for(;null==(this.atom=this.atoms[this.iatom++])||null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==this.ac)return!1;this.atoms[this.iatom-1]=null;return!0});f(b,"getAtomSetIndex",function(){return this.atom.atomSetIndex});f(b,"getSymmetry",function(){return this.atom.bsSymmetry});f(b,"getAtomSite",function(){return this.atom.atomSite+1});f(b,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});
f(b,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});f(b,"getAtomName",function(){return this.atom.atomName});f(b,"getFormalCharge",function(){return-2147483648==this.atom.formalCharge?0:this.atom.formalCharge});f(b,"getPartialCharge",function(){return this.atom.partialCharge});f(b,"getTensors",function(){return this.atom.tensors});f(b,"getRadius",function(){return this.atom.radius});f(b,"getBondRadius",
function(){return this.atom.bondingRadius});f(b,"getVib",function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});f(b,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1094713365!=this.atom.vib.z?0:F(this.atom.vib.x)});f(b,"getBfactor",function(){return this.atom.bfactor});f(b,"getOccupancy",function(){return 100*this.atom.foccupancy});f(b,"getIsHetero",function(){return this.atom.isHetero});f(b,"getSerial",function(){return this.atom.atomSerial});
f(b,"getChainID",function(){return this.atom.chainID});f(b,"getAltLoc",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});f(b,"getGroup3",function(){return this.atom.group3});f(b,"getSequenceNumber",function(){return this.atom.sequenceNumber});f(b,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});f(b,"getXYZ",function(){return this.atom});f(b,"getElement",function(){return this.getElementNumber()&127});f(b,"getIsotope",
function(){return this.getElementNumber()>>7})});n("J.adapter.smarter");z(["java.util.Hashtable"],"J.adapter.smarter.AtomSetCollection","java.util.Collections $.Properties JU.AU $.BS $.Lst $.P3 $.V3 J.adapter.smarter.Atom $.Bond $.SmarterJmolAdapter J.api.Interface JU.BSUtil $.Logger JV.JC".split(" "),function(){var b=r(function(){this.atoms=this.atomSetInfo=this.collectionName=this.fileTypeName=this.bsAtoms=this.reader=null;this.ac=0;this.bonds=null;this.bondCount=0;this.structures=null;this.atomSetCount=
this.structureCount=0;this.iSet=-1;this.errorMessage=this.atomSetAuxiliaryInfo=this.atomSetBondCounts=this.atomSetAtomCounts=this.atomSetAtomIndexes=this.atomSetNumbers=null;this.isTrajectory=this.coordinatesAreFractional=!1;this.trajectoryStepCount=0;this.trajectoryNames=this.vibrationSteps=this.trajectorySteps=null;this.allowMultiple=this.doFixPeriodic=!1;this.readerList=null;this.atomMapAnyCase=!1;this.fixedSite=0;this.bsStructuredModels=null;this.haveAnisou=!1;this.baseSymmetryAtomCount=0;this.crystalReaderLatticeOpsOnly=
!1;this.xtalSymmetry=null;this.bondIndex0=0;this.atomSymbolicMap=null;this.haveUnitCell=!1;this.vibScale=0;this.firstAtomToBond=-1;u(this,arguments)},J.adapter.smarter,"AtomSetCollection",null);N(b,function(){this.atomSetInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=E(16,0);this.atomSetAtomIndexes=E(16,0);this.atomSetAtomCounts=E(16,0);this.atomSetBondCounts=E(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});
y(b,function(a,d,h,b){this.fileTypeName=a;this.reader=d;this.allowMultiple=null==d||0>d.desiredVibrationNumber;a=new java.util.Properties;a.put("PATH_KEY",".PATH");a.put("PATH_SEPARATOR",J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);this.setInfo("properties",a);null!=d&&(a=d.htParams.get("appendToModelIndex"),null!=a&&this.setInfo("appendToModelIndex",a),a=d.htParams.get("fixedSite"),null!=a&&(this.fixedSite=a.intValue()));if(null!=h){d=0;this.readerList=new JU.Lst;for(b=0;b<h.length;b++)null!=
h[b]&&(0<h[b].ac||null!=h[b].reader&&h[b].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(d++,h[b]);1<d&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=b&&(this.setInfo("isMultiFile",Boolean.TRUE),this.appendAtomSetCollectionList(b))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");c(b,"setCollectionName",function(a){if(null!=a&&0<(a=a.trim()).length)this.collectionName=a},"~S");c(b,"clearGlobalBoolean",function(a){this.atomSetInfo.remove(JV.JC.getBoolName(a))},"~N");c(b,
"setGlobalBoolean",function(a){this.setInfo(JV.JC.getBoolName(a),Boolean.TRUE)},"~N");c(b,"getGlobalBoolean",function(a){return this.atomSetInfo.get(JV.JC.getBoolName(a))===Boolean.TRUE},"~N");c(b,"appendAtomSetCollectionList",function(a){var d=a.size();if(0==d)this.errorMessage="No file found!";else for(var h=0;h<d;h++){var b=a.get(h);C(b,"JU.Lst")?this.appendAtomSetCollectionList(b):this.appendAtomSetCollection(h,b)}},"JU.Lst");c(b,"setTrajectory",function(){this.isTrajectory||(this.trajectorySteps=
new JU.Lst);this.isTrajectory=!0;var a=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(!(1>=a)){for(var d=Array(a),h=0<a&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),a=h?Array(a):null,b=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,g=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var j=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=b&&(j=J.adapter.smarter.AtomSetCollection.fixPeriodic(j,b[c]));d[g]=j;h&&(a[g]=this.atoms[c].vib);
g++}if(h){if(null==this.vibrationSteps){this.vibrationSteps=new JU.Lst;for(c=0;c<this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(a)}this.trajectorySteps.addLast(d);this.trajectoryStepCount++}});c(b,"appendAtomSetCollection",function(a,d){null!=d.reader&&d.reader.mustFinalizeModelSet&&this.readerList.addLast(d.reader);var h=this.ac;this.setInfo("loadState",d.atomSetInfo.get("loadState"));if(null!=d.bsAtoms){this.getBSAtoms(0);for(var b=d.bsAtoms.nextSetBit(0);0<=
b;b=d.bsAtoms.nextSetBit(b+1))this.bsAtoms.set(h+b)}for(var b=0,c=this.atomSetCount,g=0;g<d.atomSetCount;g++){this.newAtomSet();var j=(this.atomSetAuxiliaryInfo[this.iSet]=d.atomSetAuxiliaryInfo[g]).get("PDB_CONECT_firstAtom_count_max");null!=j&&(j[0]+=h);this.setCurrentModelInfo("title",d.collectionName);this.setAtomSetName(d.getAtomSetName(g));for(j=0;j<d.atomSetAtomCounts[g];j++)null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(d.atoms[b]),b++;this.atomSetNumbers[this.iSet]=0>a?this.iSet+
1:1E6*(a+1)+d.atomSetNumbers[g]}for(b=0;b<d.bondCount;b++)g=d.bonds[b],this.addNewBondWithOrder(g.atomIndex1+h,g.atomIndex2+h,g.order);for(b=JV.JC.globalBooleans.length;0<=--b;)d.getGlobalBoolean(b)&&this.setGlobalBoolean(b);for(b=0;b<d.structureCount;b++)h=d.structures[b],this.addStructure(h),h.modelStartEnd[0]+=c,h.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(b,"setNoAutoBond",function(){this.setInfo("noAutoBond",Boolean.TRUE)});c(b,"freeze",function(a){1==this.atomSetCount&&
null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setModelInfoForSet("initialAtomCount",Integer.$valueOf(this.atomSetAtomCounts[a]),a),this.setModelInfoForSet("initialBondCount",Integer.$valueOf(this.atomSetBondCounts[a]),a)},"~B");c(b,"reverseAtomSets",function(){this.reverseArray(this.atomSetAtomIndexes);
this.reverseArray(this.atomSetNumbers);this.reverseArray(this.atomSetAtomCounts);this.reverseArray(this.atomSetBondCounts);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectorySteps);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectoryNames);J.adapter.smarter.AtomSetCollection.reverseList(this.vibrationSteps);this.reverseObject(this.atomSetAuxiliaryInfo);for(var a=0;a<this.ac;a++)this.atoms[a].atomSetIndex=this.atomSetCount-1-this.atoms[a].atomSetIndex;for(a=0;a<this.structureCount;a++){var d=
this.structures[a].modelStartEnd[0];0<=d&&(this.structures[a].modelStartEnd[0]=this.atomSetCount-1-this.structures[a].modelStartEnd[1],this.structures[a].modelStartEnd[1]=this.atomSetCount-1-d)}for(a=0;a<this.bondCount;a++)this.bonds[a].atomSetIndex=this.atomSetCount-1-this.atoms[this.bonds[a].atomIndex1].atomSetIndex;this.reverseSets(this.bonds,this.bondCount);for(var h=JU.AU.createArrayOfArrayList(this.atomSetCount),a=0;a<this.atomSetCount;a++)h[a]=new JU.Lst;for(a=0;a<this.ac;a++)h[this.atoms[a].atomSetIndex].addLast(this.atoms[a]);
for(var d=E(this.ac,0),b=this.ac,a=this.atomSetCount;0<=--a;)for(var c=h[a].size();0<=--c;){var g=this.atoms[--b]=h[a].get(c);d[g.index]=b;g.index=b}for(a=0;a<this.bondCount;a++)this.bonds[a].atomIndex1=d[this.bonds[a].atomIndex1],this.bonds[a].atomIndex2=d[this.bonds[a].atomIndex2];for(a=0;a<this.atomSetCount;a++)h=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),null!=h&&(h[0]=d[h[0]],h[1]=this.atomSetAtomCounts[a])});c(b,"reverseSets",function(a,d){for(var h=JU.AU.createArrayOfArrayList(this.atomSetCount),
b=0;b<this.atomSetCount;b++)h[b]=new JU.Lst;for(b=0;b<d;b++){if(0>a[b].atomSetIndex)return;h[a[b].atomSetIndex].addLast(a[b])}for(b=this.atomSetCount;0<=--b;)for(var c=h[b].size();0<=--c;)a[--d]=h[b].get(c)},"~A,~N");c(b,"reverseObject",function(a){for(var d=this.atomSetCount,h=v(d/2);0<=--h;)JU.AU.swap(a,h,d-1-h)},"~A");b.reverseList=c(b,"reverseList",function(a){null!=a&&java.util.Collections.reverse(a)},"JU.Lst");c(b,"reverseArray",function(a){for(var d=this.atomSetCount,h=v(d/2);0<=--h;)JU.AU.swapInt(a,
h,d-1-h)},"~A");c(b,"getList",function(a){var d;for(d=this.ac;0<=--d&&!(null!=this.atoms[d]&&"\x00"!=(a?this.atoms[d].altLoc:this.atoms[d].insertionCode)););if(!(0>d)){var h=Array(this.atomSetCount);for(d=0;d<this.atomSetCount;d++)h[d]="";var b;for(d=0;d<this.ac;d++)if(null!=this.atoms[d]){var c=a?this.atoms[d].altLoc:this.atoms[d].insertionCode;if("\x00"!=c&&0>h[b=this.atoms[d].atomSetIndex].indexOf(c))h[b]+=c}a=a?"altLocs":"insertionCodes";for(d=0;d<this.atomSetCount;d++)0<h[d].length&&this.setModelInfoForSet(a,
h[d],d)}},"~B");c(b,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=E(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=E(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=
Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(b,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.clearMap();this.atomSetCount=0;this.iSet=-1;for(a=this.atomSetAuxiliaryInfo.length;0<=--a;)this.atomSetAtomCounts[a]=0,this.atomSetBondCounts[a]=0,this.atomSetAuxiliaryInfo[a]=null});c(b,"removeCurrentAtomSet",function(){if(!(0>this.iSet)){var a=this.atomSetAtomIndexes[this.iSet];null!=this.bsAtoms&&this.bsAtoms.clearBits(a,
this.ac);this.ac=a;this.atomSetAtomCounts[this.iSet]=0;this.iSet--;this.atomSetCount--;this.reader.doCheckUnitCell=!1}});c(b,"getHydrogenAtomCount",function(){for(var a=0,d=0;d<this.ac;d++)(1==this.atoms[d].elementNumber||this.atoms[d].elementSymbol.equals("H"))&&a++;return a});c(b,"newCloneAtom",function(a){a=a.getClone();this.addAtom(a);return a},"J.adapter.smarter.Atom");c(b,"cloneFirstAtomSet",function(a){if(!this.allowMultiple)return 0;this.newAtomSet();0==a&&(a=this.atomSetAtomCounts[0]);for(var d=
0;d<a;++d)this.newCloneAtom(this.atoms[d]);return this.ac},"~N");c(b,"cloneAtomSetWithBonds",function(a){var d=this.atomSetBondCounts[a?this.iSet:0];a=a?this.cloneLastAtomSet():this.cloneFirstAtomSet(0);if(0<a)for(var h=0;h<d;h++){var b=this.bonds[this.bondCount-d];this.addNewBondWithOrder(b.atomIndex1+a,b.atomIndex2+a,b.order)}},"~B");c(b,"cloneLastAtomSet",function(){return this.cloneLastAtomSetFromPoints(0,null)});c(b,"cloneLastAtomSetFromPoints",function(a,d){if(!this.allowMultiple)return 0;var h=
0<a?a:this.getLastAtomSetAtomCount(),b=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<h;++c){var g=this.newCloneAtom(this.atoms[b++]);null!=d&&g.setT(d[c])}return h},"~N,~A");c(b,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.iSet]});c(b,"getLastAtomSetAtomIndex",function(){return this.ac-this.atomSetAtomCounts[this.iSet]});c(b,"addNewAtom",function(){return this.addAtom(new J.adapter.smarter.Atom)});c(b,"addAtom",function(a){this.ac==this.atoms.length&&(this.atoms=
2E5<this.ac?JU.AU.ensureLength(this.atoms,this.ac+5E4):JU.AU.doubleLength(this.atoms));0==this.atomSetCount&&this.newAtomSet();a.index=this.ac;this.atoms[this.ac++]=a;a.atomSetIndex=this.iSet;a.atomSite=0<this.fixedSite?this.fixedSite-1:this.atomSetAtomCounts[this.iSet]++;return a},"J.adapter.smarter.Atom");c(b,"addAtomWithMappedName",function(a){var d=this.addAtom(a).atomName;null!=d&&this.atomSymbolicMap.put(d,a)},"J.adapter.smarter.Atom");c(b,"addAtomWithMappedSerialNumber",function(a){var d=this.addAtom(a).atomSerial;
-2147483648!=d&&this.atomSymbolicMap.put(""+d,a)},"J.adapter.smarter.Atom");c(b,"getAtomFromName",function(a){return this.atomSymbolicMap.get(a)},"~S");c(b,"setAtomMapAnyCase",function(){this.atomMapAnyCase=!0;var a=new java.util.Hashtable;a.putAll(this.atomSymbolicMap);for(var d,h=this.atomSymbolicMap.entrySet().iterator();h.hasNext()&&((d=h.next())||1);){var b=d.getKey(),c=b.toUpperCase();c.equals(b)||a.put(c,d.getValue())}this.atomSymbolicMap=a});c(b,"getAtomIndex",function(a){var d=this.atomSymbolicMap.get(a);
null==d&&this.atomMapAnyCase&&(d=this.atomSymbolicMap.get(a.toUpperCase()));return null==d?-1:d.index},"~S");c(b,"addNewBondWithOrder",function(a,d,h){var b=null;0<=a&&(a<this.ac&&0<=d&&d<this.ac&&a!=d)&&(b=new J.adapter.smarter.Bond(a,d,h),this.addBond(b));return b},"~N,~N,~N");c(b,"addNewBondFromNames",function(a,d,h){return this.addNewBondWithOrderA(this.getAtomFromName(a),this.getAtomFromName(d),h)},"~S,~S,~N");c(b,"addNewBondWithOrderA",function(a,d,h){return null!=a&&null!=d?this.addNewBondWithOrder(a.index,
d.index,h):null},"J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");c(b,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||a.atomIndex1==a.atomIndex2||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?JU.Logger.debugging&&JU.Logger.debug(">>>>>>BAD BOND:"+a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):this.addBondNoCheck(a))},"J.adapter.smarter.Bond");c(b,"addBondNoCheck",function(a){this.bondCount==this.bonds.length&&(this.bonds=
JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024));this.bonds[this.bondCount++]=a;this.atomSetBondCounts[this.iSet]++},"J.adapter.smarter.Bond");c(b,"finalizeStructures",function(){if(0!=this.structureCount){this.bsStructuredModels=new JU.BS;for(var a=new java.util.Hashtable,d=0;d<this.structureCount;d++){var h=this.structures[d];-1==h.modelStartEnd[0]&&(h.modelStartEnd[0]=0,h.modelStartEnd[1]=this.atomSetCount-1);this.bsStructuredModels.setBits(h.modelStartEnd[0],h.modelStartEnd[1]+1);if(0!=
h.strandCount){var h=h.structureID+" "+h.modelStartEnd[0],b=a.get(h),b=(null==b?0:b.intValue())+1;a.put(h,Integer.$valueOf(b))}}for(d=0;d<this.structureCount;d++)h=this.structures[d],1==h.strandCount&&(h.strandCount=a.get(h.structureID+" "+h.modelStartEnd[0]).intValue())}});c(b,"addStructure",function(a){this.structureCount==this.structures.length&&(this.structures=JU.AU.arrayCopyObject(this.structures,this.structureCount+32));this.structures[this.structureCount++]=a},"J.adapter.smarter.Structure");
c(b,"addVibrationVectorWithSymmetry",function(a,d,h,b,c){if(c){c=this.atoms[a].atomSite;for(var g=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==g;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,d,h,b)}else this.addVibrationVector(a,d,h,b)},"~N,~N,~N,~N,~B");c(b,"addVibrationVector",function(a,d,h,b){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(d,h,b)},"~N,~N,~N,~N");c(b,"setCoordinatesAreFractional",function(a){this.coordinatesAreFractional=a;this.setCurrentModelInfo("coordinatesAreFractional",
Boolean.$valueOf(a));a&&this.setGlobalBoolean(0)},"~B");c(b,"setAnisoBorU",function(a,d,h){this.haveAnisou=!0;a.anisoBorU=d;d[6]=h},"J.adapter.smarter.Atom,~A,~N");c(b,"setU",function(a,d,h){var b=a.anisoBorU;null==b&&this.setAnisoBorU(a,b=L(8,0),8);b[d]=h},"J.adapter.smarter.Atom,~N,~N");c(b,"getXSymmetry",function(){null==this.xtalSymmetry&&(this.xtalSymmetry=J.api.Interface.getOption("adapter.smarter.XtalSymmetry",this.reader.vwr,"file").set(this.reader));return this.xtalSymmetry});c(b,"getSymmetry",
function(){return this.getXSymmetry().getSymmetry()});c(b,"setSymmetry",function(a){return null==a?null:this.getXSymmetry().setSymmetry(a)},"J.api.SymmetryInterface");c(b,"setTensors",function(){this.haveAnisou&&this.getXSymmetry().setTensors()});c(b,"setInfo",function(a,d){null==d?this.atomSetInfo.remove(a):this.atomSetInfo.put(a,d)},"~S,~O");c(b,"setAtomSetCollectionPartialCharges",function(a){if(!this.atomSetInfo.containsKey(a))return!1;for(var d=this.atomSetInfo.get(a),h=d.size(),b=this.ac;0<=
--b;)this.atoms[b].partialCharge=d.get(b%h).floatValue();JU.Logger.info("Setting partial charges type "+a);return!0},"~S");c(b,"mapPartialCharge",function(a,d){this.getAtomFromName(a).partialCharge=d},"~S,~N");b.fixPeriodic=c(b,"fixPeriodic",function(a,d){a.x=J.adapter.smarter.AtomSetCollection.fixPoint(a.x,d.x);a.y=J.adapter.smarter.AtomSetCollection.fixPoint(a.y,d.y);a.z=J.adapter.smarter.AtomSetCollection.fixPoint(a.z,d.z);return a},"JU.P3,JU.P3");b.fixPoint=c(b,"fixPoint",function(a,d){for(;0.9<
a-d;)a-=1;for(;-0.9>a-d;)a+=1;return a},"~N,~N");c(b,"finalizeTrajectoryAs",function(a,d){this.trajectorySteps=a;this.vibrationSteps=d;this.trajectoryStepCount=a.size();this.finalizeTrajectory()},"JU.Lst,JU.Lst");c(b,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),d=null==this.vibrationSteps?null:this.vibrationSteps.get(0),h=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=d&&d.length<h||a.length<h)this.errorMessage=
"File cannot be loaded as a trajectory";else{for(var h=new JU.V3,b=0,c=0;b<this.ac;b++)if(null==this.bsAtoms||this.bsAtoms.get(b))null!=this.vibrationSteps&&(this.atoms[b].vib=null==d?h:d[c]),null!=a[c]&&this.atoms[b].setT(a[c]),c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps);0==this.ac&&(this.ac=a.length)}}});c(b,"newAtomSet",function(){this.newAtomSetClear(!0)});c(b,"newAtomSetClear",function(a){!this.allowMultiple&&
0<=this.iSet&&this.reader.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.reader.discardPreviousAtoms();this.iSet=this.atomSetCount++;this.atomSetCount>this.atomSetNumbers.length&&(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));this.atomSetAtomIndexes[this.iSet]=
this.ac;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?this.atomSetNumbers[this.iSet+this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:this.atomSetNumbers[this.iSet]=this.atomSetCount;a&&this.clearMap();this.setCurrentModelInfo("title",this.collectionName)},"~B");c(b,"clearMap",function(){this.atomSymbolicMap.clear();this.atomMapAnyCase=!1});c(b,"getAtomSetAtomIndex",function(a){return this.atomSetAtomIndexes[a]},
"~N");c(b,"getAtomSetAtomCount",function(a){return this.atomSetAtomCounts[a]},"~N");c(b,"getAtomSetBondCount",function(a){return this.atomSetBondCounts[a]},"~N");c(b,"setAtomSetName",function(a){if(null!=a)if(this.isTrajectory)this.setTrajectoryName(a);else{var d=0>this.iSet?null:this.getAtomSetName(this.iSet);this.setModelInfoForSet("name",a,this.iSet);null!=this.reader&&(0<a.length&&!a.equals(d))&&this.reader.appendLoadNote(a);this.allowMultiple||this.setCollectionName(a)}},"~S");c(b,"setTrajectoryName",
function(a){if(0!=this.trajectoryStepCount){null==this.trajectoryNames&&(this.trajectoryNames=new JU.Lst);for(var d=this.trajectoryNames.size();d<this.trajectoryStepCount;d++)this.trajectoryNames.addLast(null);this.trajectoryNames.set(this.trajectoryStepCount-1,a)}},"~S");c(b,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.iSet+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(b,"setAtomSetNumber",function(a,d){this.atomSetNumbers[a]=d},"~N,~N");c(b,"setAtomSetModelProperty",
function(a,d){this.setAtomSetModelPropertyForSet(a,d,this.iSet)},"~S,~S");c(b,"setAtomSetModelPropertyForSet",function(a,d,h){var b=this.getAtomSetAuxiliaryInfoValue(h,"modelProperties");null==b&&this.setModelInfoForSet("modelProperties",b=new java.util.Properties,h);b.put(a,d);a.startsWith(".")&&b.put(a.substring(1),d)},"~S,~S,~N");c(b,"setAtomProperties",function(a,d,h){"string"==typeof d&&!d.endsWith("\n")&&(d+="\n");0>h&&(h=this.iSet);var b=this.getAtomSetAuxiliaryInfoValue(h,"atomProperties");
null==b&&this.setModelInfoForSet("atomProperties",b=new java.util.Hashtable,h);b.put(a,d)},"~S,~O,~N,~B");c(b,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;a=this.getAtomSetAuxiliaryInfoValue(this.iSet,a);for(var d=a.size();0<=--d;)this.atoms[d].partialCharge=a.get(d).floatValue();return!0},"~S");c(b,"getAtomSetAuxiliaryInfoValue",function(a,d){return this.atomSetAuxiliaryInfo[0<=a?a:this.iSet].get(d)},"~N,~S");c(b,"setCurrentModelInfo",function(a,
d){this.setModelInfoForSet(a,d,this.iSet)},"~S,~O");c(b,"setModelInfoForSet",function(a,d,h){0>h||(null==this.atomSetAuxiliaryInfo[h]&&(this.atomSetAuxiliaryInfo[h]=new java.util.Hashtable),null==d?this.atomSetAuxiliaryInfo[h].remove(a):this.atomSetAuxiliaryInfo[h].put(a,d))},"~S,~O,~N");c(b,"getAtomSetNumber",function(a){return this.atomSetNumbers[a>=this.atomSetCount?0:a]},"~N");c(b,"getAtomSetName",function(a){if(null!=this.trajectoryNames&&a<this.trajectoryNames.size())return this.trajectoryNames.get(a);
a>=this.atomSetCount&&(a=this.atomSetCount-1);return this.getAtomSetAuxiliaryInfoValue(a,"name")},"~N");c(b,"getAtomSetAuxiliaryInfo",function(a){a=a>=this.atomSetCount?this.atomSetCount-1:a;return 0>a?null:this.atomSetAuxiliaryInfo[a]},"~N");c(b,"setAtomSetEnergy",function(a,d){0>this.iSet||(JU.Logger.info("Energy for model "+(this.iSet+1)+" = "+a),this.setCurrentModelInfo("EnergyString",a),this.setCurrentModelInfo("Energy",Float.$valueOf(d)),this.setAtomSetModelProperty("Energy",""+d))},"~S,~N");
c(b,"setAtomSetFrequency",function(a,d,h,b,c){this.setAtomSetModelProperty("FreqValue",b);b+=" "+(null==c?"cm^-1":c);c=(null==h?"":h+" ")+b;this.setAtomSetName(c);this.setAtomSetModelProperty("Frequency",b);this.setAtomSetModelProperty("Mode",""+a);this.setModelInfoForSet("vibrationalMode",Integer.$valueOf(a),this.iSet);null!=h&&this.setAtomSetModelProperty("FrequencyLabel",h);this.setAtomSetModelProperty(".PATH",(null==d?"":d+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+"Frequencies")+"Frequencies");
return c},"~N,~S,~S,~S,~S");c(b,"getBondList",function(){for(var a=Array(this.bondCount),d=0;d<this.bondCount;d++)a[d]=B(-1,[this.atoms[this.bonds[d].atomIndex1].atomName,this.atoms[this.bonds[d].atomIndex2].atomName,""+this.bonds[d].order]);return a});c(b,"centralize",function(){for(var a=new JU.P3,d=0;d<this.atomSetCount;d++){var h=this.atomSetAtomCounts[d],b=this.atomSetAtomIndexes[d];a.set(0,0,0);for(var c=b+h;--c>=b;)a.add(this.atoms[c]);a.scale(1/h);for(c=b+h;--c>=b;)this.atoms[c].sub(a)}});
c(b,"mergeTrajectories",function(a){if(this.isTrajectory&&a.isTrajectory&&null==this.vibrationSteps){for(var d=0;d<a.trajectoryStepCount;d++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(d));this.setInfo("trajectorySteps",this.trajectorySteps);this.setInfo("ignoreUnitCell",a.atomSetInfo.get("ignoreUnitCell"))}},"J.adapter.smarter.AtomSetCollection");c(b,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=JU.BSUtil.newBitSet2(0,this.ac));var d=this.atomSetAtomIndexes[a],
h=d+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(d,h);for(d=h;d<this.ac;d++)this.atoms[d].atomSetIndex--;for(d=a+1;d<this.atomSetCount;d++)this.atomSetAuxiliaryInfo[d-1]=this.atomSetAuxiliaryInfo[d],this.atomSetAtomIndexes[d-1]=this.atomSetAtomIndexes[d],this.atomSetBondCounts[d-1]=this.atomSetBondCounts[d],this.atomSetAtomCounts[d-1]=this.atomSetAtomCounts[d],this.atomSetNumbers[d-1]=this.atomSetNumbers[d];for(d=0;d<this.bondCount;d++)this.bonds[d].atomSetIndex=this.atoms[this.bonds[d].atomIndex1].atomSetIndex;
this.atomSetAuxiliaryInfo[--this.atomSetCount]=null;for(d=h=0;d<this.structureCount;d++){var b=this.structures[d];b.modelStartEnd[0]==a&&b.modelStartEnd[1]==a&&(this.structures[d]=null,h++)}if(0<h){a=Array(this.structureCount-h);for(h=d=0;d<this.structureCount;d++)null!=this.structures[d]&&(a[h++]=this.structures[d]);this.structures=a}},"~N");c(b,"removeLastUnselectedAtoms",function(){for(var a=this.ac,d=0,h=this.getLastAtomSetAtomIndex(),b=0,c=h;c<a;c++)this.bsAtoms.get(c)?(0<d&&(this.atoms[this.atoms[c].index=
c-d]=this.atoms[c],this.atoms[c]=null),b++):(d++,this.ac--,this.atoms[c]=null);this.atomSetAtomCounts[this.iSet]=b;0==b?(this.iSet--,this.atomSetCount--):this.bsAtoms.setBits(h,h+b)});c(b,"checkNoEmptyModel",function(){for(;0<this.atomSetCount&&0==this.atomSetAtomCounts[this.atomSetCount-1];)this.atomSetCount--});c(b,"getBSAtoms",function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,0!=a&&this.bsAtoms.setBits(0,0>a?this.ac:a));return this.bsAtoms},"~N");c(b,"setBSAtomsForSet",function(a){if(null!=
this.bsAtoms){0>a&&(a=this.iSet);var d=this.atomSetAtomIndexes[a];0>this.bsAtoms.nextSetBit(d)&&this.bsAtoms.setBits(d,d+this.atomSetAtomCounts[a])}},"~N");c(b,"fix2Stereo",function(){this.getBSAtoms(-1);for(var a=this.bondCount;0<=--a;){var d=this.bonds[a];this.atoms[d.atomIndex2].elementSymbol.equals("H")&&1025!=d.order&&1041!=d.order&&this.atoms[d.atomIndex1].elementSymbol.equals("C")?this.bsAtoms.clear(d.atomIndex2):this.atoms[d.atomIndex1].elementSymbol.equals("H")&&this.atoms[d.atomIndex2].elementSymbol.equals("C")&&
this.bsAtoms.clear(d.atomIndex1)}})});n("J.adapter.smarter");z(["javajs.api.GenericLineReader","JU.SB","JV.Viewer"],"J.adapter.smarter.AtomSetCollectionReader","JU.BS $.Lst $.M3 $.P3 $.PT $.Quat $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter JU.BSUtil $.Logger $.SimpleUnitCell JV.FileManager $.JC".split(" "),function(){var b=r(function(){this.requiresBSFilter=this.debugging=this.isBinary=!1;this.dssr=this.validation=this.domains=this.trajectorySteps=this.htParams=this.readerName=
this.binaryDoc=this.reader=this.asc=this.primitiveToCrystal=null;this.isConcatenated=!1;this.lstNCS=this.thisBiomolecule=this.addedDataKey=this.addedData=null;this.floatifyJavaDouble=!0;this.next=this.prevline=this.line=null;this.ptLine=0;this.checkNearAtoms=!0;this.fillRange=this.latticeCells=this.latticeType=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=this.doProcessLines=!1;this.continuing=!0;this.vwr=null;this.isMolecular=this.is2D=this.noMinimize=this.noHydrogens=this.optimize2D=this.isSequential=
this.getHeader=this.doCheckUnitCell=this.applySymmetryToBonds=this.isTrajectory=this.ignoreFileSymmetryOperators=this.doApplySymmetry=!1;this.vibrationNumber=this.modelNumber=this.templateAtomCount=0;this.desiredVibrationNumber=-2147483648;this.bsModels=null;this.havePartialChargeFilter=this.useFileModelNumbers=!1;this.calculationType="?";this.sgName=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=!1;this.unitCellParams=null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;
this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.packingRange=null;this.cellSlop=1E-4;this.isPrimitive=this.rotateHexCell=!1;this.modDim=0;this.highprecision0=this.lowPrecision=!1;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=this.doConvertToFractional=!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;this.desiredSpaceGroupIndex=-1;this.latticeScaling=NaN;this.unitCellOffset=
null;this.unitCellOffsetFractional=!1;this.paramsLattice=this.moreUnitCellInfo=null;this.paramsPacked=this.paramsCentroid=!1;this.fileName=this.filePath=this.fileOffsetFractional=this.fileOffset=this.fileScaling=null;this.baseBondIndex=this.baseAtomIndex=0;this.stateScriptVersionInt=2147483647;this.noPack=this.isFinalized=!1;this.precision=0;this.haveModel=!1;this.previousUnitCell=this.previousSpaceGroup=null;this.nMatrixElements=0;this.filterCased=this.filter=this.bsFilter=this.matUnitCellOrientation=
this.ucItems=null;this.filterAtomType=this.filterAtomName=this.filterChain=this.filterGroup3=this.filterAltLoc=this.haveAtomFilter=!1;this.filterAtomTypeStr=null;this.filterAtomNameTerminator=";";this.filterEveryNth=this.filterAllHetero=this.filterHetero=this.filterElement=!1;this.filterSymop=null;this.nFiltered=this.filterN=0;this.reverseModels=this.doReadMolecularOrbitals=this.allowPDBFilter=this.isDSSP1=this.ignoreStructure=this.useAltNames=this.addVibrations=this.doCentralize=this.doSetOrientation=
!1;this.nameRequired=null;this.centroidPacked=this.doCentroidUnitCell=!1;this.strSupercell=null;this.filteredPrecision=this.fixUnitCell=this.polymerX=this.slabXY=this.allow_a_len_1=!1;this.ms=this.matRot=this.filter2Cased=this.filter1Cased=this.filter2=this.filter1=null;this.vibsFractional=!1;this.siteScript=this.previousScript=null;u(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);N(b,function(){this.next=E(1,0);this.highprecision0=JV.Viewer.isHighPrecision;
this.loadNote=new JU.SB});c(b,"getPackingRangeValue",function(a){return null!=this.packingRange?this.packingRange.floatValue():0!=a?a:0.02},"~N");c(b,"setup",function(a,d,h){this.setupASCR(a,d,h)},"~S,java.util.Map,~O");c(b,"setupASCR",function(a,d,h){null!=a&&(this.debugging=JU.Logger.debugging,this.htParams=d,this.filePath=JV.FileManager.stripTypePrefix(""+d.get("fullPathName")),a=this.filePath.lastIndexOf("/"),this.fileName=this.filePath.substring(a+1),C(h,"java.io.BufferedReader")?this.reader=
h:C(h,"javajs.api.GenericBinaryDocument")&&(this.binaryDoc=h))},"~S,java.util.Map,~O");c(b,"readData",function(){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);try{this.initializeReader();if(null==this.binaryDoc)for(null==this.line&&this.continuing&&this.rd();null!=this.line&&this.continuing;)this.checkLine()&&this.rd();else this.binaryDoc.setOutputChannel(this.out),this.processBinaryDocument();this.finalizeSubclassReader();this.isFinalized||this.finalizeReaderASCR()}catch(a){JU.Logger.info("Reader error: "+
a),a.printStackTrace(),this.setError(a)}null!=this.reader&&this.reader.close();null!=this.binaryDoc&&this.binaryDoc.close();return this.finish()});c(b,"fixBaseIndices",function(){try{var a=this.htParams.get("baseModelIndex");if(null!=a){var d=a.intValue();this.baseAtomIndex+=this.asc.ac;this.baseBondIndex+=this.asc.bondCount;d+=this.asc.atomSetCount;this.htParams.put("baseAtomIndex",Integer.$valueOf(this.baseAtomIndex));this.htParams.put("baseBondIndex",Integer.$valueOf(this.baseBondIndex));this.htParams.put("baseModelIndex",
Integer.$valueOf(d))}}catch(h){if(!D(h,Exception))throw h;}});c(b,"readDataObject",function(a){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(b,"processDOM",function(){},"~O");c(b,"processBinaryDocument",function(){});c(b,"initializeReader",function(){});c(b,"checkLine",function(){return!0});c(b,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=
this.doProcessLines=!1;this.doProcessLines=!1;return!0});c(b,"isLastModel",function(a){return 0<this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(b,"appendLoadNote",function(a){null==a?this.loadNote=new JU.SB:(this.loadNote.append(a).append("\n"),JU.Logger.info(a))},"~S");c(b,"initializeTrajectoryFile",function(){this.asc.addAtom(new J.adapter.smarter.Atom);this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=
new JU.Lst)});c(b,"finalizeSubclassReader",function(){});c(b,"finalizeReaderASCR",function(){this.isFinalized=!0;if(0<this.asc.atomSetCount){1==this.asc.atomSetCount&&(this.asc.setCurrentModelInfo("dbName",this.htParams.get("dbName")),this.asc.setCurrentModelInfo("auxFiles",this.htParams.get("auxFiles")));this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();this.doCentralize&&this.asc.centralize();null!=this.fillRange&&this.asc.setInfo("boundbox",this.fillRange);var a=this.asc.getAtomSetAuxiliaryInfo(0);
if(null!=a){if(null!=this.domains){this.asc.setGlobalBoolean(5);var d=this.domains.getMapKeys(2,!0),h=d.indexOf("{ ",2);0<=h&&(d=d.substring(h+2));h=d.indexOf("_metadata");0>h&&(h=d.indexOf("metadata"));0<=h&&(d=d.substring(0,h));d=JU.PT.rep(JU.PT.replaceAllCharacters(d,"{}","").trim(),"\n","\n  ")+"\n\nUse SHOW DOMAINS for details.";this.appendLoadNote("\nDomains loaded:\n   "+d);for(d=this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("domains",this.domains)}if(null!=this.validation)for(d=
this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("validation",this.validation);if(null!=this.dssr){a.put("dssrJSON",Boolean.TRUE);for(d=this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("dssr",this.dssr)}}}this.floatifyJavaDouble||this.asc.setInfo("highPrecision",Boolean.TRUE);this.setLoadNote()});c(b,"setLoadNote",function(){var a=this.loadNote.toString();0<this.loadNote.length()&&this.asc.setInfo("modelLoadNote",a);return a});c(b,"setIsPDB",function(){this.asc.setGlobalBoolean(4);
null!=this.htParams.get("pdbNoHydrogens")&&this.asc.setInfo("pdbNoHydrogens",this.htParams.get("pdbNoHydrogens"));this.checkFilterKey("ADDHYDROGENS")&&this.asc.setInfo("pdbAddHydrogens",Boolean.TRUE)});c(b,"setModelPDB",function(a){a?this.asc.setGlobalBoolean(4):this.asc.clearGlobalBoolean(4);this.asc.setCurrentModelInfo(JV.JC.getBoolName(4),a?Boolean.TRUE:null)},"~B");c(b,"finish",function(){!0!=this.highprecision0&&this.vwr.setBooleanPropertyTok("doubleprecision",603979831,this.highprecision0);
var a=this.htParams.get("loadState");this.asc.setInfo("loadState",null==a?"":a);a=this.htParams.get("smilesString");null!=a&&this.asc.setInfo("smilesString",a);this.htParams.containsKey("templateAtomCount")||this.htParams.put("templateAtomCount",Integer.$valueOf(this.asc.ac));null!=this.bsFilter&&(this.htParams.put("filteredAtomCount",Integer.$valueOf(JU.BSUtil.cardinalityOf(this.bsFilter))),this.htParams.put("bsFilter",this.bsFilter));this.calculationType.equals("?")||this.asc.setInfo("calculationType",
this.calculationType);var d=a=this.asc.fileTypeName;0<=d.indexOf("(")&&(d=d.substring(0,d.indexOf("(")));for(var h=this.asc.atomSetCount;0<=--h;)this.asc.setModelInfoForSet("fileName",this.filePath,h),this.asc.setModelInfoForSet("fileType",d,h);this.asc.freeze(this.reverseModels);if(null!=this.asc.errorMessage)return this.asc.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if(!this.merging&&(null==this.asc.bsAtoms?0==this.asc.ac:0>this.asc.bsAtoms.nextSetBit(0))&&0>d.indexOf("DataOnly")&&null==
this.asc.atomSetInfo.get("dataOnly"))return"No atoms found\nfor file "+this.filePath+"\ntype "+a;this.fixBaseIndices();return this.asc});c(b,"setError",function(a){var d=a.getMessage();this.asc.errorMessage=null==this.line?"Error reading file at end of file \n"+d:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+d;a.printStackTrace()},"Throwable");c(b,"initialize",function(){this.htParams.containsKey("baseAtomIndex")&&(this.baseAtomIndex=this.htParams.get("baseAtomIndex").intValue());
this.htParams.containsKey("baseBondIndex")&&(this.baseBondIndex=this.htParams.get("baseBondIndex").intValue());this.initializeSymmetry();this.vwr=this.htParams.remove("vwr");this.htParams.containsKey("stateScriptVersionInt")&&(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());this.packingRange=this.htParams.get("packingRange");var a=null!=this.htParams.get("highPrecision");null==this.packingRange&&a&&(this.floatifyJavaDouble=!1,this.packingRange=Float.$valueOf(1E-4));
this.merging=this.htParams.containsKey("merging");this.getHeader=this.htParams.containsKey("getHeader");this.isSequential=this.htParams.containsKey("isSequential");this.readerName=this.htParams.get("readerName");this.htParams.containsKey("outputChannel")&&(this.out=this.htParams.get("outputChannel"));this.htParams.containsKey("vibrationNumber")?this.desiredVibrationNumber=this.htParams.get("vibrationNumber").intValue():this.htParams.containsKey("modelNumber")&&(this.desiredModelNumber=this.htParams.get("modelNumber").intValue());
this.applySymmetryToBonds=this.htParams.containsKey("applySymmetryToBonds");this.bsFilter=this.requiresBSFilter?this.htParams.get("bsFilter"):null;this.setFilter(null);this.fillRange=this.htParams.get("fillRange");this.paramsLattice=this.htParams.get("lattice");a=this.htParams.get("supercell");this.noPack=this.checkFilterKey("NOPACK");null!=this.strSupercell&&!this.noPack&&(this.forcePacked=!0);C(a,"JU.P3")?(a=this.ptSupercell=a,1!=a.length()&&(this.strSupercell=F(a.x)+"a,"+F(a.y)+"b,"+F(a.z)+"c")):
"string"==typeof a&&(this.strSupercell=a);a=this.htParams.containsKey("ptFile")?this.htParams.get("ptFile").intValue():-1;this.isTrajectory=this.htParams.containsKey("isTrajectory");0<a&&this.htParams.containsKey("firstLastSteps")?(a=this.htParams.get("firstLastSteps").get(a-1),C(a,"JU.BS")?this.bsModels=a:this.firstLastStep=a):this.htParams.containsKey("firstLastStep")?this.firstLastStep=this.htParams.get("firstLastStep"):this.htParams.containsKey("bsModels")&&(this.bsModels=this.htParams.get("bsModels"));
this.useFileModelNumbers=this.htParams.containsKey("useFileModelNumbers")||this.checkFilterKey("USEFILEMODELNUMBERS");this.htParams.containsKey("templateAtomCount")&&(this.templateAtomCount=this.htParams.get("templateAtomCount").intValue());if(null!=this.bsModels||null!=this.firstLastStep)this.desiredModelNumber=-2147483648;if(null==this.bsModels&&null!=this.firstLastStep){0>this.firstLastStep[0]&&(this.firstLastStep[0]=0);if(0==this.firstLastStep[2]||this.firstLastStep[1]<this.firstLastStep[0])this.firstLastStep[1]=
-1;1>this.firstLastStep[2]&&(this.firstLastStep[2]=1);this.bsModels=JU.BSUtil.newAndSetBit(this.firstLastStep[0]);if(this.firstLastStep[1]>this.firstLastStep[0])for(a=this.firstLastStep[0];a<=this.firstLastStep[1];a+=this.firstLastStep[2])this.bsModels.set(a)}if(null!=this.bsModels&&(null==this.firstLastStep||-1!=this.firstLastStep[1]))this.lastModelNumber=this.bsModels.length();this.symmetryRange=this.htParams.containsKey("symmetryRange")?this.htParams.get("symmetryRange").floatValue():0;this.paramsCentroid=
this.htParams.containsKey("centroid");this.paramsPacked=this.htParams.containsKey("packed");this.initializeSymmetryOptions();this.htParams.containsKey("spaceGroupIndex")&&(this.desiredSpaceGroupIndex=this.htParams.get("spaceGroupIndex").intValue(),-2==this.desiredSpaceGroupIndex&&(this.sgName=this.htParams.get("spaceGroupName")),this.ignoreFileSpaceGroupName=-2==this.desiredSpaceGroupIndex||0<=this.desiredSpaceGroupIndex,this.ignoreFileSymmetryOperators=-1!=this.desiredSpaceGroupIndex);this.htParams.containsKey("unitCellOffset")&&
(this.fileScaling=JU.P3.new3(1,1,1),this.fileOffset=this.htParams.get("unitCellOffset"),this.fileOffsetFractional=JU.P3.newP(this.fileOffset),this.unitCellOffsetFractional=this.htParams.containsKey("unitCellOffsetFractional"));this.htParams.containsKey("unitcell")&&(a=this.htParams.get("unitcell"),this.merging&&this.setFractionalCoordinates(!0),9==a.length?(this.addExplicitLatticeVector(0,a,0),this.addExplicitLatticeVector(1,a,3),this.addExplicitLatticeVector(2,a,6)):this.setUnitCell(a[0],a[1],a[2],
a[3],a[4],a[5]),this.ignoreFileUnitCell=this.iHaveUnitCell,this.merging&&!this.iHaveUnitCell&&this.setFractionalCoordinates(!1));this.domains=this.htParams.get("domains");this.validation=this.htParams.get("validation");this.dssr=this.htParams.get("dssr");this.isConcatenated=this.htParams.containsKey("concatenate")});c(b,"parsePrecision",function(a){if(!this.filteredPrecision){var d=a.indexOf(".")+1;if(0<=d){var h=a.indexOf("(");this.precision=Math.max(this.precision,(0>h?a.length:h)-d)}}return this.parseFloatStr(a)},
"~S");c(b,"setLowPrecision",function(){this.lowPrecision=!0;this.cellSlop=1E-4;null==this.packingRange&&(this.packingRange=Double.$valueOf(1E-4))});c(b,"setPrecision",function(){var a;if(this.lowPrecision)a=!1,this.precision=4;else if(this.precision=1E3<this.precision?this.precision-1E3:Math.min(12,Math.max(4,this.precision)),a=7<=this.precision)this.vwr.setBooleanProperty("doubleprecision",!0),JV.Viewer.isHighPrecision?(this.cellSlop=1E-12,this.paramsPacked||(this.packingRange=Double.$valueOf(this.cellSlop)),
this.asc.setInfo("highPrecision",Boolean.TRUE)):(a=!1,this.precision=6,this.appendLoadNote("Structure read has high precision but this version of Jmol uses float precision.\nUse JmolD.jar or JavaScript for full precision."));!a&&10>this.precision&&(this.cellSlop=Math.pow(10,-this.precision));this.symmetry.setPrecision(this.cellSlop);this.unitCellParams[26]=this.cellSlop;if(this.fileCoordinatesAreFractional){a=this.asc.ac;for(var d=this.asc.getLastAtomSetAtomIndex();--a>=d;)this.symmetry.twelfthify(this.asc.atoms[a])}this.appendLoadNote("Precision set to "+
this.precision+"; packing set to "+(null==this.packingRange?0.02:this.packingRange.floatValue()))});c(b,"initializeSymmetryOptions",function(){this.latticeCells=E(4,0);this.doApplySymmetry=!1;var a=this.paramsLattice;if(null==a||0==a.length()){if(!this.forcePacked&&null==this.strSupercell)return;a=JU.P3.new3(1,1,1)}this.latticeCells[0]=F(a.x);this.latticeCells[1]=F(a.y);this.latticeCells[2]=F(a.z);C(a,"JU.T4")&&(this.latticeCells[3]=F(a.w));if((this.doCentroidUnitCell=this.paramsCentroid)&&(-1==this.latticeCells[2]||
0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.paramsPacked;this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2]);this.doApplySymmetry=0<this.latticeCells[0]&&0<this.latticeCells[1];this.doApplySymmetry||(this.latticeCells=E(3,0))});c(b,"doGetModel",function(a,d){if(null!=d&&null!=this.nameRequired&&0<this.nameRequired.length&&0>d.toUpperCase().indexOf(this.nameRequired))return!1;var h=null==this.bsModels?
1>this.desiredModelNumber||a==this.desiredModelNumber:a>this.lastModelNumber?!1:0<a&&this.bsModels.get(a-1)||this.haveModel&&null!=this.firstLastStep&&0>this.firstLastStep[1]&&(2>this.firstLastStep[2]||0==(a-1-this.firstLastStep[0])%this.firstLastStep[2]);h&&0==this.desiredModelNumber&&this.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|h)).valueOf();h&&(this.doProcessLines=!0);return h},"~N,~S");c(b,"discardPreviousAtoms",function(){this.asc.discardPreviousAtoms()});c(b,"initializeSymmetry",
function(){this.previousSpaceGroup=this.sgName;this.previousUnitCell=this.unitCellParams;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.unitCellParams=L(27,0);for(var a=27;0<=--a;)this.unitCellParams[a]=NaN;this.unitCellParams[25]=this.latticeScaling;this.unitCellParams[26]=this.cellSlop;this.symmetry=null}this.ignoreFileSpaceGroupName||(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(b,"newAtomSet",function(a){0<=this.asc.iSet?(this.asc.newAtomSet(),this.asc.setCollectionName("<collection of "+
(this.asc.iSet+1)+" models>")):this.asc.setCollectionName(a);this.asc.setModelInfoForSet("name",a,Math.max(0,this.asc.iSet));this.asc.setAtomSetName(a)},"~S");c(b,"cloneLastAtomSet",function(a,d){var h=this.asc.getLastAtomSetAtomCount();this.asc.cloneLastAtomSetFromPoints(a,d);this.asc.haveUnitCell&&(this.doCheckUnitCell=this.iHaveUnitCell=!0,this.sgName=this.previousSpaceGroup,this.unitCellParams=this.previousUnitCell);return h},"~N,~A");c(b,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||
null==a||(a=a.trim(),0==a.length||(a.equals("HM:")||a.equals(this.sgName))||(a.equals("P1")||JU.Logger.info("Setting space group name to "+a),this.sgName=a))},"~S");c(b,"setSymmetryOperator",function(a){if(this.ignoreFileSymmetryOperators)return-1;var d=this.asc.getXSymmetry().addSpaceGroupOperation(a,!0);0>d&&JU.Logger.warn("Skippings symmetry operation "+a);this.iHaveSymmetryOperators=!0;return d},"~S");c(b,"initializeCartesianToFractional",function(){for(var a=0;16>a;a++)if(!Float.isNaN(this.unitCellParams[6+
a]))return;for(a=0;16>a;a++)this.unitCellParams[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(b,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=6;22>a;a++)this.unitCellParams[a]=NaN;this.checkUnitCell(6)}});c(b,"setUnitCellItem",function(a,d){this.ignoreFileUnitCell||(0==a&&1==d&&!this.allow_a_len_1||3==a&&0==d?(null==this.ucItems&&(this.ucItems=L(6,0)),this.ucItems[a]=d):(null!=this.ucItems&&6>a&&(this.ucItems[a]=d),!Float.isNaN(d)&&(6<=a&&Float.isNaN(this.unitCellParams[6]))&&this.initializeCartesianToFractional(),
this.unitCellParams[a]=d,this.debugging&&JU.Logger.debug("setunitcellitem "+a+" "+d),6>a||Float.isNaN(d)?this.iHaveUnitCell=this.checkUnitCell(6):12==++this.nMatrixElements&&(this.iHaveUnitCell=this.checkUnitCell(22))))},"~N,~N");c(b,"setUnitCell",function(a,d,h,b,c,g){this.ignoreFileUnitCell||(this.clearUnitCell(),this.unitCellParams[0]=a,this.unitCellParams[1]=d,this.unitCellParams[2]=h,0!=b&&(this.unitCellParams[3]=b),0!=c&&(this.unitCellParams[4]=c),0!=g&&(this.unitCellParams[5]=g),this.iHaveUnitCell=
this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(b,"addExplicitLatticeVector",function(a,d,h){if(!this.ignoreFileUnitCell){if(0==a)for(var b=0;6>b;b++)this.unitCellParams[b]=0;a=6+3*a;this.unitCellParams[a++]=d[h++];this.unitCellParams[a++]=d[h++];this.unitCellParams[a]=d[h];if(Float.isNaN(this.unitCellParams[0]))for(a=0;6>a;a++)this.unitCellParams[a]=-1;if(this.iHaveUnitCell=this.checkUnitCell(15)){if(this.slabXY||this.polymerX)this.unitCellParams[2]=-1;this.polymerX&&(this.unitCellParams[1]=-1)}}},
"~N,~A,~N");c(b,"checkUnitCell",function(a){for(var d=0;d<a;d++)if(Float.isNaN(this.unitCellParams[d]))return!1;this.fixFloatA(this.unitCellParams);if(22==a&&1==this.unitCellParams[0]&&1==this.unitCellParams[1]&&1==this.unitCellParams[2]&&1==this.unitCellParams[6]&&1==this.unitCellParams[11]&&1==this.unitCellParams[16])return!1;6==a&&Float.isNaN(this.unitCellParams[6])&&(this.slabXY&&0<this.unitCellParams[2]?(JU.SimpleUnitCell.addVectors(this.unitCellParams),this.unitCellParams[2]=-1):this.polymerX&&
0<this.unitCellParams[1]&&(JU.SimpleUnitCell.addVectors(this.unitCellParams),this.unitCellParams[1]=this.unitCellParams[2]=-1));this.doApplySymmetry&&(this.getSymmetry(),this.doConvertToFractional=!this.fileCoordinatesAreFractional);return!0},"~N");c(b,"getSymmetry",function(){if(!this.iHaveUnitCell)return null;null==this.symmetry&&(this.getNewSymmetry().setUnitCellFromParams(this.unitCellParams,!1,this.cellSlop),this.checkUnitCellOffset());null==this.symmetry?this.iHaveUnitCell=!1:this.symmetry.setSpaceGroupName(this.sgName);
return this.symmetry});c(b,"checkUnitCellOffset",function(){null==this.fileOffsetFractional||null==this.symmetry||(this.fileOffset.setT(this.fileOffsetFractional),this.unitCellOffsetFractional!=this.fileCoordinatesAreFractional&&(this.unitCellOffsetFractional?this.symmetry.toCartesian(this.fileOffset,!1):this.symmetry.toFractional(this.fileOffset,!1)))});c(b,"fractionalizeCoordinates",function(a){if(null!=this.getSymmetry()){var d=this.asc.atoms;if(a)for(var h=this.asc.ac;0<=--h;)this.symmetry.toFractional(d[h],
!1);else for(h=this.asc.ac;0<=--h;)this.symmetry.toCartesian(d[h],!1);this.setFractionalCoordinates(a)}},"~B");c(b,"getNewSymmetry",function(){return this.symmetry=this.getInterface("JS.Symmetry")});c(b,"setFractionalCoordinates",function(a){this.iHaveFractionalCoordinates=this.fileCoordinatesAreFractional=a;this.checkUnitCellOffset()},"~B");c(b,"setFilterAtomTypeStr",function(a){this.filterAtomTypeStr=a;this.filterAtomNameTerminator="\x00"},"~S");c(b,"setFilter",function(a){null==a?a=this.htParams.get("filter"):
this.filterCased=this.bsFilter=null;null==this.filterCased&&(this.filterCased=null==a?null:a+";");null!=a&&(a=a.toUpperCase());this.filter=a;this.doSetOrientation=!this.checkFilterKey("NOORIENT");this.doCentralize=!this.checkFilterKey("NOCENTER")&&this.checkFilterKey("CENTER");this.addVibrations=!this.checkFilterKey("NOVIB");this.ignoreStructure=this.checkFilterKey("DSSP");this.isDSSP1=this.checkFilterKey("DSSP1");this.doReadMolecularOrbitals=!this.checkFilterKey("NOMO");this.useAltNames=this.checkFilterKey("ALTNAME");
this.reverseModels=this.checkFilterKey("REVERSEMODELS");this.allow_a_len_1=this.checkFilterKey("TOPOS");this.slabXY=this.checkFilterKey("SLABXY");this.polymerX=!this.slabXY&&this.checkFilterKey("POLYMERX");this.noHydrogens=this.checkFilterKey("NOH");this.noMinimize=this.checkFilterKey("NOMIN");this.optimize2D=this.checkFilterKey("2D")&&!this.noHydrogens&&!this.noMinimize;if(null!=this.filter){this.fixUnitCell=this.checkFilterKey("FIXUNITCELL");this.checkFilterKey("LOWPRECISION")&&this.setLowPrecision();
this.checkFilterKey("HETATM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"HETATM","HETATM-Y"),this.filterCased=JU.PT.rep(this.filterCased,"HETATM","HETATM-Y"));this.checkFilterKey("ATOM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"ATOM","HETATM-N"),this.filterCased=JU.PT.rep(this.filterCased,"ATOM","HETATM-N"));this.checkFilterKey("CELL=")&&(this.strSupercell=this.filter.substring(this.filter.indexOf("CELL=")+5).toLowerCase());this.nameRequired=JU.PT.getQuotedAttribute(this.filter,
"NAME");null!=this.nameRequired&&(this.nameRequired.startsWith("'")?this.nameRequired=JU.PT.split(this.nameRequired,"'")[1]:this.nameRequired.startsWith('"')&&(this.nameRequired=JU.PT.split(this.nameRequired,'"')[1]),this.filter=JU.PT.rep(this.filter,this.nameRequired,""),this.filter=JU.PT.rep(this.filter,"NAME=",""));this.filterAtomName=this.checkFilterKey("*.")||this.checkFilterKey("!.");if(this.filter.startsWith("_")||this.filter.startsWith("!_")||0<=this.filter.indexOf(";_"))this.filterElement=
this.checkFilterKey("_");this.filterGroup3=this.checkFilterKey("[");this.filterChain=this.checkFilterKey(":");this.filterAltLoc=this.checkFilterKey("%");this.filterEveryNth=this.checkFilterKey("/=");this.filterAllHetero=this.checkFilterKey("ALLHET");if(this.filterEveryNth)this.filterN=this.parseIntAt(this.filter,this.filter.indexOf("/=")+2);else if(this.filter.startsWith("=")||0<=this.filter.indexOf(";="))this.filterAtomType=this.checkFilterKey("=");-2147483648==this.filterN&&(this.filterEveryNth=
!1);this.haveAtomFilter=this.filterAtomName||this.filterAtomType||this.filterElement||this.filterGroup3||this.filterChain||this.filterAltLoc||this.filterHetero||this.filterEveryNth||this.checkFilterKey("/=");if(null==this.bsFilter&&(this.bsFilter=new JU.BS,this.htParams.put("bsFilter",this.bsFilter),this.filter=(";"+this.filter+";").$replace(",",";"),a=this.getFilter("PRECISION="),null!=a&&(a=JU.PT.parseInt(a),0<a&&16>=a&&(this.precision=1E3+a,this.filteredPrecision=!0)),a=this.getFilter("LATTICESCALING="),
null!=a&&25<this.unitCellParams.length&&(this.unitCellParams[25]=this.latticeScaling=this.parseFloatStr(a)),a=this.getFilter("SYMOP="),null!=a&&(this.filterSymop=" "+a+" "),JU.Logger.info("filtering with "+this.filter),this.haveAtomFilter)){this.filter1Cased=this.filterCased;this.filter2Cased="";if(0<=(a=this.filter.indexOf("|")))this.filter1Cased=this.filter.substring(0,a).trim()+";",this.filter2Cased=";"+this.filter.substring(a).trim();this.filter1=this.filter1Cased.toUpperCase();this.filter2=0==
this.filter2Cased.length?null:this.filter2Cased.toUpperCase()}}},"~S");c(b,"getFilterWithCase",function(a){var d=null==this.filterCased?-1:this.filterCased.toUpperCase().indexOf(a.toUpperCase());return 0>d?null:this.filterCased.substring(d+a.length,this.filterCased.indexOf(";",d))},"~S");c(b,"getFilter",function(a){var d=null==this.filter?-1:this.filter.indexOf(a);return 0>d?null:this.filter.substring(d+a.length,this.filter.indexOf(";",d))},"~S");c(b,"checkFilterKey",function(a){return null!=this.filter&&
0<=this.filter.indexOf(a)},"~S");c(b,"checkAndRemoveFilterKey",function(a){if(!this.checkFilterKey(a))return!1;this.filter=JU.PT.rep(this.filter,a,"");3>this.filter.length&&(this.filter=null);return!0},"~S");c(b,"filterAtom",function(a,d){if(!this.haveAtomFilter)return!0;var h=this.checkFilter(a,this.filter1,this.filter1Cased);null!=this.filter2&&(h=(new Boolean(h|this.checkFilter(a,this.filter2,this.filter2Cased))).valueOf());if(h&&this.filterEveryNth&&(!a.isHetero||!this.filterAllHetero))h=0==this.nFiltered++%
this.filterN;this.bsFilter.setBitTo(0<=d?d:this.asc.ac,h);return h},"J.adapter.smarter.Atom,~N");c(b,"checkFilter",function(a,d,h){return a.isHetero&&this.filterAllHetero?!0:(!this.filterGroup3||null==a.group3||!this.filterReject(d,"[",a.group3.toUpperCase()+"]"))&&(!this.filterAtomName||this.allowAtomName(a.atomName,d))&&(null==this.filterAtomTypeStr||null==a.atomName||0<=a.atomName.toUpperCase().indexOf("\x00"+this.filterAtomTypeStr))&&(!this.filterElement||null==a.elementSymbol||!this.filterReject(d,
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l,A+l,H+l),x=M|f|m|l;this.clipped=0!=x;if(!(-1==x||0!=(M&l&f&m))){this.dxBf=j.x-g.x;this.dyBf=j.y-g.y;this.dzBf=j.z-g.z;0<c&&(this.diameter=c,this.xAf=g.x,this.yAf=g.y,this.zAf=g.z);g=0==h&&(this.clipped||2==b||0==b);this.xA=F(this.xAf);this.yA=F(this.yAf);this.zA=F(this.zAf);this.dxB=F(this.dxBf);this.dyB=F(this.dyBf);this.dzB=F(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=d);this.endcaps=b;this.calcArgbEndcap(!0,!0);x=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);
2==b&&this.renderFlatEndcap(!0,!0,x);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;j=x[0];M=x[1];l=x[2];x=x[3];for(A=this.rasterCount;0<=--A;){var H=x[A]>>8,f=H>>1,m=j[A],p=M[A],n=l[A];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-n-1,a,d,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+n-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,
this.xEndcap+m,this.yEndcap+p,this.zEndcap-n-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+n-1,a,d,c)));this.ptA0.set(this.xA+m,this.yA+p,this.zA-n);this.ptB0.setT(this.ptA0);this.ptB0.x+=this.dxB;this.ptB0.y+=this.dyB;this.ptB0.z+=this.dzB;this.line3d.plotLineDeltaABitsFloat(this.shadesA,this.shadesB,H,this.ptA0,this.ptB0,h,this.clipped);g&&(this.ptA0.set(this.xA-m,this.yA-p,this.zA+n),this.ptB0.setT(this.ptA0),this.ptB0.x+=this.dxB,this.ptB0.y+=this.dyB,
this.ptB0.z+=this.dzB,this.line3d.plotLineDeltaABitsFloat(this.shadesA,this.shadesB,f,this.ptA0,this.ptB0,h,this.clipped))}k.setZMargin(0);3==b&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}},"~N,~N,~N,~N,~N,JU.P3,JU.P3");c(b,"renderBits",function(a,d,h,b,c,g,j){var k=this.g3d;if(0==c||1==c)this.line3d.plotLineBits(k.getColorArgbOrGray(a),k.getColorArgbOrGray(d),g,j,0,0,!1);else{this.ptA0i.setT(g);var l=v(c/2)+1,f=g.x,m=g.y,p=g.z,x=j.x,A=j.y,H=j.z,M=k.clipCode3(f-
l,m-l,p-l),f=k.clipCode3(f+l,m+l,p+l),m=k.clipCode3(x-l,A-l,H-l),l=k.clipCode3(x+l,A+l,H+l),x=M|f|m|l;this.clipped=0!=x;if(!(-1==x||0!=(M&l&f&m))){this.dxBf=j.x-g.x;this.dyBf=j.y-g.y;this.dzBf=j.z-g.z;0<c&&(this.diameter=c,this.xAf=g.x,this.yAf=g.y,this.zAf=g.z);g=0==h&&(this.clipped||2==b||0==b);this.xA=F(this.xAf);this.yA=F(this.yAf);this.zA=F(this.zAf);this.dxB=F(this.dxBf);this.dyB=F(this.dyBf);this.dzB=F(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=
d);this.endcaps=b;this.calcArgbEndcap(!0,!0);x=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==b&&this.renderFlatEndcap(!0,!0,x);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;j=x[0];M=x[1];l=x[2];x=x[3];for(A=this.rasterCount;0<=--A;){var H=x[A]>>8,f=H>>1,m=j[A],p=M[A],n=l[A];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-n-1,a,d,c),k.plotPixelClippedArgb(this.argbEndcap,
this.xEndcap-m,this.yEndcap-p,this.zEndcap+n-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+m,this.yEndcap+p,this.zEndcap-n-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-m,this.yEndcap-p,this.zEndcap+n-1,a,d,c)));this.ptA0i.set(this.xA+m,this.yA+p,this.zA-n);this.ptB0i.setT(this.ptA0i);this.ptB0i.x+=this.dxB;this.ptB0i.y+=this.dyB;this.ptB0i.z+=this.dzB;this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,H,this.ptA0i,this.ptB0i,h,this.clipped);g&&(this.ptA0i.set(this.xA-
m,this.yA-p,this.zA+n),this.ptB0i.setT(this.ptA0i),this.ptB0i.x+=this.dxB,this.ptB0i.y+=this.dyB,this.ptB0i.z+=this.dzB,this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,f,this.ptA0i,this.ptB0i,h,this.clipped))}k.setZMargin(0);3==b&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}}},"~N,~N,~N,~N,~N,JU.P3i,JU.P3i");c(b,"renderConeOld",function(a,d,h,b,c,g,j,k,l,f,m){this.dxBf=j-(this.xAf=b);this.dyBf=k-(this.yAf=c);this.dzBf=l-(this.zAf=g);this.xA=
v(Math.floor(this.xAf));this.yA=v(Math.floor(this.yAf));this.zA=v(Math.floor(this.zAf));this.dxB=v(Math.floor(this.dxBf));this.dyB=v(Math.floor(this.dyBf));this.dzB=v(Math.floor(this.dzBf));this.xTip=j;this.yTip=k;this.zTip=l;this.shadesA=this.g3d.getShades(this.colixA=a);var p=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB);a=this.g3d;b=a.pixel;c=a.width;g=a.zbuf;a.plotPixelClippedArgb(this.shadesA[p],F(j),F(k),F(l),c,g,b);this.diameter=h;if(1>=h)1==h&&this.line3d.plotLineDeltaOld(this.colixA,
this.colixA,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=d;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(m);!m&&2==this.endcaps&&this.renderFlatEndcap(!1,!0,this.xyzfRaster);a.setZMargin(5);d=this.xyztRaster[0];h=this.xyztRaster[1];j=this.xyztRaster[2];k=this.xyzfRaster[3];l=this.shadesA;for(var p=this.endCapHidden&&0!=this.argbEndcap,x=this.rasterCount;0<=--x;){var A=d[x],H=h[x],M=j[x],n=k[x]>>8,u=this.xAf+A,r=this.yAf+H,w=this.zAf-M,A=this.xAf-
A,H=this.yAf-H,M=this.zAf+M,B=l[0];p&&(a.plotPixelClippedArgb(this.argbEndcap,F(u),F(r),F(w),c,g,b),a.plotPixelClippedArgb(this.argbEndcap,F(A),F(H),F(M),c,g,b));0!=B&&(this.line3d.plotLineDeltaAOld(l,l,0,n,F(u),F(r),F(w),v(Math.ceil(this.xTip-u)),v(Math.ceil(this.yTip-r)),v(Math.ceil(this.zTip-w)),!0),f&&(this.line3d.plotLineDeltaAOld(l,l,0,n,F(u),F(r)+1,F(w),v(Math.ceil(this.xTip-u)),v(Math.ceil(this.yTip-r))+1,v(Math.ceil(this.zTip-w)),!0),this.line3d.plotLineDeltaAOld(l,l,0,n,F(u)+1,F(r),F(w),
v(Math.ceil(this.xTip-u))+1,v(Math.ceil(this.yTip-r)),v(Math.ceil(this.zTip-w)),!0)),!m&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDeltaOld(B,B,F(A),F(H),F(M),v(Math.ceil(this.xTip-A)),v(Math.ceil(this.yTip-H)),v(Math.ceil(this.zTip-M)),!0))}a.setZMargin(0)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(b,"generateBaseEllipsePrecisely",function(a){this.calcCosSin(this.dxBf,this.dyBf,this.dzBf);this.calcPoints(a?2:3,!0);this.interpolatePrecisely(0,1,this.xyzfRaster,this.xyztRaster);a||this.interpolatePrecisely(1,
2,this.xyzfRaster,this.xyztRaster);for(a=3;0<=--a;)for(var d=this.rasterCount;0<=--d;)this.xyzfRaster[a][d]=v(Math.floor(this.xyztRaster[a][d]))},"~B");c(b,"calcPoints",function(a,d){this.calcRotatedPoint(0,0,d,this.xyzfRaster,this.xyztRaster);this.calcRotatedPoint(0.5,1,d,this.xyzfRaster,this.xyztRaster);3==(this.rasterCount=a)&&this.calcRotatedPoint(1,2,d,this.xyzfRaster,this.xyztRaster)},"~N,~B");c(b,"calcCosSin",function(a,d,h){var b=a*a+d*d;if(0==b)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var c=
Math.sqrt(b),b=Math.sqrt(b+h*h);this.cosTheta=h/b;this.cosPhi=a/c;this.sinPhi=d/c}},"~N,~N,~N");c(b,"calcRotatedPoint",function(a,d,h,b,c){c[3][d]=a;a*=3.141592653589793;var g=Math.sin(a)*this.cosTheta,j=Math.cos(a);a=this.radius*(g*this.cosPhi-j*this.sinPhi);g=this.radius*(g*this.sinPhi+j*this.cosPhi);j=this.radius2-(a*a+g*g);j=0<j?Math.sqrt(j):0;h?(c[0][d]=a,c[1][d]=g,c[2][d]=j):(this.tEvenDiameter?(b[0][d]=v(a-0.5),b[1][d]=v(g-0.5)):(b[0][d]=v(a),b[1][d]=v(g)),b[2][d]=v(j+0.5));b[3][d]=this.shader.getShadeFp8(a,
g,j)},"~N,~N,~B,~A,~A");c(b,"allocRaster",function(a,d,h){if(this.rasterCount>=d[0].length)for(;this.rasterCount>=d[0].length;){for(var b=4;0<=--b;)d[b]=JU.AU.doubleLengthI(d[b]);h[3]=JU.AU.doubleLengthF(h[3])}if(a)for(;this.rasterCount>=h[0].length;)for(b=3;0<=--b;)h[b]=JU.AU.doubleLengthF(h[b]);return this.rasterCount++},"~B,~A,~A");c(b,"interpolate",function(a,d,h,b){var c=h[0],g=h[1],c=c[d]-c[a];0>c&&(c=-c);g=g[d]-g[a];0>g&&(g=-g);if(!(1>=c+g)){for(var j=this.allocRaster(!1,h,b),c=h[0],g=h[1],
k=h[3],l=b[3][a],f=b[3][d],m=4;0<=--m;){var p=(l+f)/2;this.calcRotatedPoint(p,j,!1,h,b);if(c[j]==c[a]&&g[j]==g[a])k[a]=k[a]+k[j]>>>1,l=p;else if(c[j]==c[d]&&g[j]==g[d])k[d]=k[d]+k[j]>>>1,f=p;else{this.interpolate(a,j,h,b);this.interpolate(j,d,h,b);return}}c[j]=c[a];g[j]=g[d]}},"~N,~N,~A,~A");c(b,"interpolatePrecisely",function(a,d,h,b){var c=b[0],g=b[1],j=v(Math.floor(c[d]))-v(Math.floor(c[a]));0>j&&(j=-j);g=v(Math.floor(g[d]))-v(Math.floor(g[a]));0>g&&(g=-g);if(!(1>=j+g)){for(var g=b[3],j=g[a],k=
g[d],l=this.allocRaster(!0,h,b),c=b[0],g=b[1],f=h[3],m=4;0<=--m;){var p=(j+k)/2;this.calcRotatedPoint(p,l,!0,h,b);if(v(Math.floor(c[l]))==v(Math.floor(c[a]))&&v(Math.floor(g[l]))==v(Math.floor(g[a])))f[a]=f[a]+f[l]>>>1,j=p;else if(v(Math.floor(c[l]))==v(Math.floor(c[d]))&&v(Math.floor(g[l]))==v(Math.floor(g[d])))f[d]=f[d]+f[l]>>>1,k=p;else{this.interpolatePrecisely(a,l,h,b);this.interpolatePrecisely(l,d,h,b);return}}c[l]=c[a];g[l]=g[d]}},"~N,~N,~A,~A");c(b,"renderFlatEndcap",function(a,d,h){var b,
c;if(d){if(0==this.dzBf||0==this.colixEndcap||!this.g3d.setC(this.colixEndcap))return;d=this.xAf;b=this.yAf;c=this.zAf;a&&0>this.dzBf&&(d+=this.dxBf,b+=this.dyBf,c+=this.dzBf);d=F(d);b=F(b);c=F(c)}else{if(0==this.dzB||0==this.colixEndcap||!this.g3d.setC(this.colixEndcap))return;d=this.xAend;b=this.yAend;c=this.zAend;a&&0>this.dzB&&(d+=this.dxB,b+=this.dyB,c+=this.dzB)}var g=h[1][0];a=h[1][0];var j=0,k=0,l=h[0],f=h[1];h=h[2];for(var m=this.rasterCount;0<--m;){var p=f[m];p<g?g=p:p>a?a=p:(p=-p,p<g?g=
p:p>a&&(a=p))}for(p=g;p<=a;++p){for(var g=2147483647,x=-2147483648,m=this.rasterCount;0<=--m;){if(f[m]==p){var A=l[m];A<g&&(g=A,j=h[m]);A>x&&(x=A,k=h[m])}f[m]==-p&&(A=-l[m],A<g&&(g=A,j=-h[m]),A>x&&(x=A,k=-h[m]))}m=x-g+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(m,d+g,b+p,c-j-1,c-k-1,null,null)}},"~B,~B,~A");c(b,"renderSphericalEndcaps",function(){0!=this.colixA&&this.g3d.setC(this.colixA)&&this.g3d.fillSphereXYZ(this.diameter,this.xA,this.yA,this.zA+1);0!=this.colixB&&
this.g3d.setC(this.colixB)&&this.g3d.fillSphereXYZ(this.diameter,this.xA+this.dxB,this.yA+this.dyB,this.zA+this.dzB+1)});c(b,"calcArgbEndcap",function(a,d){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;this.endCapHidden=!1;var h=d?this.dzBf:this.dzB;if(!(3==this.endcaps||0==h)){this.xEndcap=this.xAend=this.xA;this.yEndcap=this.yAend=this.yA;this.zEndcap=this.zAend=this.zA;var b=d?this.dxBf:this.dxB,c=d?this.dyBf:this.dyB;0<=h||!a?(this.endcapShadeIndex=
this.shader.getShadeIndex(-b,-c,h),0==this.colixA?(this.xAend+=v(this.dxB/2),this.yAend+=v(this.dyB/2),this.zAend+=v(this.dzB/2),this.colixEndcap=this.colixB):this.colixEndcap=this.colixA):(this.endcapShadeIndex=this.shader.getShadeIndex(b,c,-h),0==this.colixB?(this.colixEndcap=this.colixA,this.xAend-=v(this.dxB/2),this.yAend-=v(this.dyB/2),this.zAend-=v(this.dzB/2)):(this.colixEndcap=this.colixB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB));h=this.colixEndcap==this.colixA?
this.shadesA:this.shadesB;56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=h[this.endcapShadeIndex];this.endCapHidden=1==this.endcaps}},"~B,~B")});n("J.g3d");K(J.g3d,"G3DRenderer");n("J.g3d");z(["J.api.JmolRendererInterface","JU.GData","JU.P3i","$.V3"],"J.g3d.Graphics3D","java.util.Arrays JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.LineRenderer $.Pixelator $.PixelatorScreened $.PixelatorShaded $.PixelatorT $.Platform3D $.SphereRenderer $.TextRenderer $.TextString JU.C $.Normix".split(" "),
function(){var b=r(function(){this.hermite3d=this.circle3d=this.triangle3d=this.cylinder3d=this.sphere3d=this.line3d=this.platform=null;this.antialias2=this.isFullSceneAntialiasingEnabled=!1;this.strings=null;this.stringCount=0;this.anaglyphChannelBytes=null;this.$haveTranslucentObjects=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.pixelShaded=this.pixelScreened=this.pixelT0=this.pixel0=this.pixel=
null;this.zMargin=0;this.aobuf=null;this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.wasScreened=!1;this.saveDiffuse=this.saveAmbient=0;this.shadeIndexes2Sided=this.shadeIndexes=this.vectorNormal=this.vectorAC=this.vectorAB=this.sC=this.sB=this.sA=null;this.pass2Flag01=0;u(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);N(b,function(){this.sA=new JU.P3i;this.sB=new JU.P3i;this.sC=new JU.P3i;this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=
new JU.V3;this.shadeIndexes=O(JU.GData.normixCount,0);this.shadeIndexes2Sided=O(JU.GData.normixCount,0)});y(b,function(){I(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3});f(b,"isWebGL",function(){return!1});f(b,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});f(b,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.pixelScreened=this.pixelT0=this.pixel=this.pixel0=this.pixelShaded=
this.platform=null});c(b,"setZMargin",function(a){this.zMargin=a},"~N");f(b,"initialize",function(a,d){this.vwr=a;this.apiPlatform=d;this.platform=new J.g3d.Platform3D(d);this.pixel=this.pixel0=new J.g3d.Pixelator(this);this.graphicsForMetrics=this.platform.getGraphicsForMetrics();this.line3d=new J.g3d.LineRenderer(this);this.sphere3d=new J.g3d.SphereRenderer(this);this.cylinder3d=new J.g3d.CylinderRenderer(this)},"JV.Viewer,J.api.GenericPlatform");f(b,"addRenderer",function(a){switch(a){case 1073741880:null==
this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648143:null==this.hermite3d&&(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"),this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth)}},"~N");c(b,"getRenderer",function(a){a=J.api.Interface.getOption("g3d."+a+"Renderer",this.vwr,"render");if(null==a)throw new NullPointerException("Interface");a.set(this,this);return a},"~S");f(b,"setWindowParameters",
function(a,d,h){this.setWinParams(a,d,h);this.currentlyRendering&&this.endRendering()},"~N,~N,~B");f(b,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.isPass2==a},"~B");f(b,"beginRendering",function(a,d,h,b){this.currentlyRendering&&this.endRendering();this.renderLow=b;if(this.windowWidth!=this.newWindowWidth||this.windowHeight!=this.newWindowHeight||this.newAntialiasing!=this.isFullSceneAntialiasingEnabled)this.windowWidth=this.newWindowWidth,
this.windowHeight=this.newWindowHeight,this.isFullSceneAntialiasingEnabled=this.newAntialiasing,this.releaseBuffers();this.setRotationMatrix(a);this.line3d.isOrthographic=!this.vwr.tm.perspectiveDepth;null!=this.triangle3d&&(this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth);this.antialiasEnabled=this.antialiasThisFrame=this.newAntialiasing;this.currentlyRendering=!0;if(null!=this.strings)for(a=Math.min(this.strings.length,this.stringCount);0<=--a;)this.strings[a]=null;this.stringCount=
0;this.twoPass=!0;this.isPass2=!1;this.colixCurrent=this.pass2Flag01=0;this.$haveTranslucentObjects=this.wasScreened=!1;this.pixel=this.pixel0;this.pixel.bgcolor=this.bgcolor;this.translucentCoverOnly=!d;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,h),this.pbuf=this.platform.pBuffer,this.zbuf=this.platform.zBuffer,this.aobuf=null,this.pixel0.setBuf(),null!=this.pixelT0&&this.pixelT0.setBuf(),null!=this.pixelShaded&&this.pixelShaded.setBuf());
this.setWidthHeight(this.antialiasThisFrame);null!=this.pixelScreened&&(this.pixelScreened.width=this.width);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0);this.textY=0},"JU.M3,~B,~B,~B");f(b,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(b,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=this.pbuf=null;this.platform.releaseBuffers();
this.line3d.clearLineCache()});f(b,"setPass2",function(a){if(!this.$haveTranslucentObjects||!this.currentlyRendering)return!1;this.isPass2=!0;this.pass2Flag01=1;this.colixCurrent=0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();null==this.pixelT0&&(this.pixelT0=new J.g3d.PixelatorT(this));
null==this.pixel.p0?this.pixel=this.pixelT0:this.pixel.p0=this.pixelT0;return!0},"~B");f(b,"endRendering",function(){if(this.currentlyRendering){if(null!=this.pbuf){if(this.isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)this.pbuf[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pbuf[a],this.pbufT[a],this.bgcolor);this.pixel===this.pixelShaded&&0==this.pixelShaded.zShadePower&&this.pixelShaded.showZBuffer();this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);
this.platform.notifyEndOfRendering();this.currentlyRendering=this.isPass2=!1}});b.mergeBufferPixel=c(b,"mergeBufferPixel",function(a,d,h){if(0==d||a==d)return a;0==a&&(a=h);h=a&16711935;a&=65280;var b=d&16711935,c=d&65280;switch(d>>24&15){case 0:h=b;a=c;break;case 1:h=(b<<2)+(b<<1)+b+h>>3&16711935;a=(c<<2)+ +(c<<1)+c+a>>3&65280;break;case 2:h=(b<<1)+b+h>>2&16711935;a=(c<<1)+c+a>>2&65280;break;case 3:h=(b<<2)+b+(h<<1)+h>>3&16711935;a=(c<<2)+c+(a<<1)+a>>3&65280;break;case 4:h=h+b>>1&16711935;a=a+c>>
1&65280;break;case 5:h=(b<<1)+b+(h<<2)+h>>3&16711935;a=(c<<1)+c+(a<<2)+a>>3&65280;break;case 6:h=(h<<1)+h+b>>2&16711935;a=(a<<1)+a+c>>2&65280;break;case 7:h=(h<<2)+(h<<1)+h+b>>3&16711935,a=(a<<2)+(a<<1)+a+c>>3&65280}return 4278190080|h|a},"~N,~N,~N");f(b,"getScreenImage",function(a){var d=this.platform.bufferedImage;a&&this.releaseBuffers();return d},"~B");f(b,"applyAnaglygh",function(a,d){switch(a){case J.c.STER.REDCYAN:for(var h=this.anaglyphLength;0<=--h;){var b=this.anaglyphChannelBytes[h]&255;
this.pbuf[h]=this.pbuf[h]&4294901760|b<<8|b}break;case J.c.STER.CUSTOM:for(var b=d[0],c=d[1]&16777215,h=this.anaglyphLength;0<=--h;){var g=this.anaglyphChannelBytes[h]&255,g=(g|(g|g<<8)<<8)&c;this.pbuf[h]=this.pbuf[h]&b|g}break;case J.c.STER.REDBLUE:for(h=this.anaglyphLength;0<=--h;)b=this.anaglyphChannelBytes[h]&255,this.pbuf[h]=this.pbuf[h]&4294901760|b;break;case J.c.STER.REDGREEN:for(h=this.anaglyphLength;0<=--h;)this.pbuf[h]=this.pbuf[h]&4294901760|(this.anaglyphChannelBytes[h]&255)<<8}},"J.c.STER,~A");
f(b,"snapshotAnaglyphChannelBytes",function(){if(this.currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=O(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});f(b,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});f(b,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});
f(b,"setSlabAndZShade",function(a,d,h,b,c){this.setSlab(a);this.setDepth(d);h<b?(null==this.pixelShaded&&(this.pixelShaded=new J.g3d.PixelatorShaded(this)),this.pixel=this.pixelShaded.set(h,b,c)):this.pixel=this.pixel0},"~N,~N,~N,~N,~N");c(b,"downsampleFullSceneAntialiasing",function(a){var d=this.bgcolor;a&&(d+=255==(d&255)?-1:1);J.g3d.Graphics3D.downsample2d(this.pbuf,this.windowWidth,this.windowHeight,d);a&&(J.g3d.Graphics3D.downsample2dZ(this.pbuf,this.zbuf,this.windowWidth,this.windowHeight,
d),this.antialiasThisFrame=!1,this.setWidthHeight(!1))},"~B");b.downsample2d=c(b,"downsample2d",function(a,d,h,b){var c=d<<1;if(0!=b){b&=16777215;for(var g=a.length;0<=--g;)0==a[g]&&(a[g]=b)}for(var j=(b>>2&1061109567)<<2,j=j+((j&3233857728)>>6),k=0,l=0,g=h;0<=--g;l+=c)for(h=d;0<=--h;++k){var f=(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567)+(a[l]>>2&1061109567)+(a[l++ +c]>>2&1061109567),f=f+((f&3233857728)>>6);f==j&&(f=b);a[k]=f&16777215|4278190080}},"~A,~N,~N,~N");b.downsample2dZ=c(b,"downsample2dZ",
function(a,d,h,b,c){for(var g=h<<1,j=0,k=0;0<=--b;k+=g)for(var l=h;0<=--l;++j,++k){var f=Math.min(d[k],d[k+g]),f=Math.min(f,d[++k]),f=Math.min(f,d[k+g]);2147483647!=f&&(f>>=1);d[j]=a[j]==c?2147483647:f}},"~A,~A,~N,~N,~N");c(b,"hasContent",function(){return this.platform.hasContent()});f(b,"setC",function(a){var d=JU.C.isColixLastAvailable(a);if(!d&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var h=a&30720;if(16384==h)return!1;this.renderLow&&(h=0);var b=0!=h,c=b&&30720==h;this.setScreened(c);
if(!this.checkTranslucent(b&&!c))return!1;this.isPass2?(this.translucencyMask=h<<13|16777215,this.translucencyLog=h>>11):this.translucencyLog=0;this.colixCurrent=a;d&&this.argbCurrent!=this.lastRawColor&&(0==this.argbCurrent&&(this.argbCurrent=4294967295),this.lastRawColor=this.argbCurrent,this.shader.setLastColix(this.argbCurrent,this.inGreyscaleMode));this.shadesCurrent=this.getShades(a);this.currentShadeIndex=-1;this.setColor(this.getColorArgbOrGray(a));return!0},"~N");c(b,"setScreened",function(a){this.wasScreened!=
a&&((this.wasScreened=a)?(null==this.pixelScreened&&(this.pixelScreened=new J.g3d.PixelatorScreened(this,this.pixel0)),null==this.pixel.p0?this.pixel=this.pixelScreened:this.pixel.p0=this.pixelScreened):null==this.pixel.p0||this.pixel===this.pixelScreened?this.pixel=this.isPass2?this.pixelT0:this.pixel0:this.pixel.p0=this.isPass2?this.pixelT0:this.pixel0);return this.pixel},"~B");f(b,"drawFilledCircle",function(a,d,h,b,c,g){if(!this.isClippedZ(g)){var j=v((h+1)/2),j=b<j||b+j>=this.width||c<j||c+j>=
this.height;if(!j||!this.isClippedXY(h,b,c))0!=a&&this.setC(a)&&(j?this.isClippedXY(h,b,c)||this.circle3d.plotCircleCenteredClipped(b,c,g,h):this.circle3d.plotCircleCenteredUnclipped(b,c,g,h)),0!=d&&this.setC(d)&&(j?this.circle3d.plotFilledCircleCenteredClipped(b,c,g,h):this.circle3d.plotFilledCircleCenteredUnclipped(b,c,g,h))}},"~N,~N,~N,~N,~N,~N");f(b,"volumeRender4",function(a,d,h,b){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,d,h,b,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(b)){var c=
v((a+1)/2),c=d<c||d+c>=this.width||h<c||h+c>=this.height;if(!c||!this.isClippedXY(a,d,h))c?this.circle3d.plotFilledCircleCenteredClipped(d,h,b,a):this.circle3d.plotFilledCircleCenteredUnclipped(d,h,b,a)}},"~N,~N,~N,~N");f(b,"fillSphereXYZ",function(a,d,h,b){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,h,b,this.width,this.zbuf,this.pixel);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,a,d,h,b,null,null,null,-1,null)},"~N,~N,~N,~N");
f(b,"volumeRender",function(a){a?(this.saveAmbient=this.getAmbientPercent(),this.saveDiffuse=this.getDiffusePercent(),this.setAmbientPercent(100),this.setDiffusePercent(0),this.addRenderer(1073741880)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},"~B");f(b,"fillSphereI",function(a,d){this.fillSphereXYZ(a,d.x,d.y,d.z)},"~N,JU.P3i");f(b,"fillSphereBits",function(a,d){this.fillSphereXYZ(a,Math.round(d.x),Math.round(d.y),Math.round(d.z))},"~N,JU.P3");f(b,"fillEllipsoid",
function(a,d,h,b,c,g,j,k,l,f,m){switch(g){case 1:this.plotPixelClippedArgb(this.argbCurrent,h,b,c,this.width,this.zbuf,this.pixel);return;case 0:return}g<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,g,h,b,c,j,k,l,f,m)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");f(b,"drawRect",function(a,d,h,b,c,g){if(!(0!=b&&this.isClippedZ(b))){b=c-1;g-=1;c=a+b;var j=d+g;0<=d&&d<this.height&&this.drawHLine(a,d,h,b);0<=j&&j<this.height&&this.drawHLine(a,j,h,b);0<=a&&a<this.width&&
this.drawVLine(a,d,h,g);0<=c&&c<this.width&&this.drawVLine(c,d,h,g)}},"~N,~N,~N,~N,~N,~N");c(b,"drawHLine",function(a,d,h,b){0>b&&(a+=b,b=-b);0>a&&(b+=a,a=0);a+b>=this.width&&(b=this.width-1-a);var c=this.pixel,g=this.argbCurrent;a+=this.width*d;for(d=0;d<=b;d++)h<this.zbuf[a]&&c.addPixel(a,h,g),a++},"~N,~N,~N,~N");c(b,"drawVLine",function(a,d,h,b){0>b&&(d+=b,b=-b);0>d&&(b+=d,d=0);d+b>=this.height&&(b=this.height-1-d);a+=this.width*d;d=this.pixel;for(var c=this.argbCurrent,g=0;g<=b;g++)h<this.zbuf[a]&&
d.addPixel(a,h,c),a+=this.width},"~N,~N,~N,~N");f(b,"fillTextRect",function(a,d,h,b,c,g){if(!this.isClippedZ(b)){b=this.width;if(0>a){c+=a;if(0>=c)return;a=0}if(a+c>b&&(c=b-a,0>=c))return;if(0>d){g+=d;if(0>=g)return;d=0}d+g>this.height&&(g=this.height-d);var j=this.argbCurrent;this.isAntialiased()&&(j=J.g3d.Graphics3D.fixTextImageRGB(j));for(var k=this.zbuf,l=this.pixel;0<=--g;)this.plotPixelsUnclippedCount(j,c,a,d++,h,b,k,l)}},"~N,~N,~N,~N,~N,~N");f(b,"drawString",function(a,d,h,b,c,g,j){this.currentShadeIndex=
0;null!=a&&(this.isClippedZ(g)||this.drawStringNoSlab(a,d,h,b,c,j))},"~S,JU.Font,~N,~N,~N,~N,~N");f(b,"drawStringNoSlab",function(a,d,h,b,c,g){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var j=new J.g3d.TextString;j.setText(a,null==d?this.currentFont:this.currentFont=d,this.argbCurrent,JU.C.isColixTranslucent(g)?this.getColorArgbOrGray(g)&16777215|(g&30720)<<13:0,h,b,c);this.strings[this.stringCount++]=
j}},"~S,JU.Font,~N,~N,~N,~N");f(b,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&(J.g3d.Graphics3D.sort=new J.g3d.TextString),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var d=0;d<this.stringCount;d++){var h=this.strings[d];this.plotText(h.x,h.y,h.z,h.argb,h.bgargb,h.text,h.font,a)}this.strings=null;this.stringCount=0}},"~O");f(b,"plotText",function(a,d,h,b,c,g,j,k){J.g3d.TextRenderer.plot(a,d,h,b,c,g,j,this,k,this.antialiasThisFrame)},
"~N,~N,~N,~N,~N,~S,JU.Font,J.api.JmolRendererInterface");f(b,"drawImage",function(a,d,h,b,c,g,j,k){null!=a&&(0<j&&0<k&&!this.isClippedZ(c))&&this.plotImage(d,h,b,a,null,g,j,k)},"~O,~N,~N,~N,~N,~N,~N,~N");f(b,"plotImage",function(a,d,h,b,c,g,j,k){this.setC(g);this.isPass2||(this.translucencyMask=-1);0==g&&(this.argbCurrent=0);var l=-2147483648==a;g=l?this.bgcolor:this.argbCurrent;l&&(a=0,h=2147483646,j=this.width,k=this.height);if(!(0>=a+j||a>=this.width||0>=d+k||d>=this.height))if(b=this.apiPlatform.drawImageToBuffer(null,
this.platform.offscreenImage,b,j,k,l?g:0),null!=b){var l=this.zbuf,f=this.width,m=this.pixel,p=this.height,x=this.translucencyLog;if(null==c&&0<=a&&a+j<=f&&0<=d&&d+k<=p){var A=0,H=0;for(a=d*f+a;A<k;A++,a+=f-j)for(var M=0;M<j;M++,H++,a++)if(h<l[a]){var n=b[H];-16777216==(n&4278190080)&&m.addPixel(a,h,n)}}else{null==c&&(c=this);for(H=A=0;A<k;A++)for(M=0;M<j;M++)n=b[H++],-16777216==(n&4278190080)&&c.plotImagePixel(n,a+M,d+A,h,8,g,f,p,l,m,x)}}},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");f(b,
"setFont",function(a){this.currentFont=a},"JU.Font");f(b,"drawPixel",function(a,d,h){this.plotPixelClippedArgb(this.argbCurrent,a,d,h,this.width,this.zbuf,this.pixel)},"~N,~N,~N");f(b,"drawPoints",function(a,d,h){if(1<h)for(var b=0.8*h*h,c=-h;c<h;c++)for(var g=-h;g<h;g++)c*c+g*g>b||(this.plotPoints(a,d,c,g),this.plotPoints(a,d,c,g));else this.plotPoints(a,d,0,0)},"~N,~A,~N");f(b,"drawDashedLineBits",function(a,d,h,b){this.isAntialiased()&&(a+=a,d+=d);this.setScreeni(h,this.sA);this.setScreeni(b,this.sB);
this.drawLineABBits(a,d,!0)},"~N,~N,JU.P3,JU.P3");c(b,"drawLineABBits",function(a,d,h){this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,d,h);Math.abs(this.sA.x-this.sB.x)<Math.abs(this.sA.y-this.sB.y)?(this.sA.x+=1,this.sB.x+=1):(this.sA.y+=1,this.sB.y+=1);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,d,h)},"~N,~N,~B");c(b,"setScreeni",function(a,d){d.x=Math.round(a.x);d.y=Math.round(a.y);d.z=Math.round(a.z)},"JU.P3,JU.P3i");f(b,"drawLineXYZ",
function(a,d,h,b,c,g){this.line3d.plotLineOld(this.argbCurrent,this.argbCurrent,a,d,h,b,c,g)},"~N,~N,~N,~N,~N,~N");f(b,"drawLine",function(a,d,h,b,c,g,j,k){this.setC(a)||(a=0);var l=this.argbCurrent;this.setC(d)||(d=0);(0!=a||0!=d)&&this.line3d.plotLineOld(l,this.argbCurrent,h,b,c,g,j,k)},"~N,~N,~N,~N,~N,~N,~N,~N");f(b,"drawLineBits",function(a,d,h,b){this.setC(a)||(a=0);var c=this.argbCurrent;this.setC(d)||(d=0);if(0!=a||0!=d)this.setScreeni(h,this.sA),this.setScreeni(b,this.sB),this.line3d.plotLineBits(c,
this.argbCurrent,this.sA,this.sB,0,0,!1)},"~N,~N,JU.P3,JU.P3");f(b,"drawLinePixels",function(a,d,h,b){this.sA.setT(a);this.sB.setT(d);this.sA.z=this.sB.z=h;a=this.slab;-2147483648==b&&(this.slab=0);this.drawLineABBits(0,0,!1);this.slab=a},"JU.P3i,JU.P3i,~N,~N");f(b,"drawLineAB",function(a,d){this.setScreeni(a,this.sA);this.setScreeni(d,this.sB);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,0,0,!1)},"JU.P3,JU.P3");f(b,"fillCylinderXYZ",function(a,d,h,b,c,g,j,k,l,f){if(!(b>
this.ht3)){var m=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(m=2);this.setC(a)||(a=0);this.wasScreened&&(m+=1);0==a&&0==d||this.cylinder3d.renderOld(a,d,m,h,b,c,g,j,k,l,f)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");f(b,"fillCylinderScreen3I",function(a,d,h,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,this.colixCurrent,0,a,d,F(h.x),F(h.y),F(h.z),F(b.x),F(b.y),F(b.z))},"~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");f(b,"fillCylinder",function(a,d,h,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,
this.colixCurrent,0,a,d,h.x,h.y,h.z,b.x,b.y,b.z)},"~N,~N,JU.P3i,JU.P3i");f(b,"fillCylinderBits",function(a,d,h,b){d<=this.ht3&&(1!=h.z&&1!=b.z)&&(0==d||1==d?(this.setScreeni(h,this.sA),this.setScreeni(b,this.sB),this.line3d.plotLineBits(this.getColorArgbOrGray(this.colixCurrent),this.getColorArgbOrGray(this.colixCurrent),this.sA,this.sB,0,0,!1)):this.cylinder3d.renderBitsFloat(this.colixCurrent,this.colixCurrent,0,a,d,h,b))},"~N,~N,JU.P3,JU.P3");f(b,"fillCylinderBits2",function(a,d,h,b,c,g){if(!(b>
this.ht3)){var j=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(j=2);this.setC(a)||(a=0);this.wasScreened&&(j+=1);0==a&&0==d||(this.setScreeni(c,this.sA),this.setScreeni(g,this.sB),this.cylinder3d.renderBits(a,d,j,h,b,this.sA,this.sB))}},"~N,~N,~N,~N,JU.P3,JU.P3");f(b,"fillConeScreen3f",function(a,d,h,b,c){d<=this.ht3&&this.cylinder3d.renderConeOld(this.colixCurrent,a,d,h.x,h.y,h.z,b.x,b.y,b.z,!0,c)},"~N,~N,JU.P3,JU.P3,~B");f(b,"drawHermite4",function(a,d,h,b,c){this.hermite3d.renderHermiteRope(!1,
a,0,0,0,d,h,b,c)},"~N,JU.P3,JU.P3,JU.P3,JU.P3");f(b,"drawHermite7",function(a,d,h,b,c,g,j,k,l,f,m,p,x){if(0==x)this.hermite3d.renderHermiteRibbon(a,d,h,b,c,g,j,k,l,f,m,p,0);else{this.hermite3d.renderHermiteRibbon(a,d,h,b,c,g,j,k,l,f,m,p,1);var A=this.colixCurrent;this.setC(x);this.hermite3d.renderHermiteRibbon(a,d,h,b,c,g,j,k,l,f,m,p,-1);this.setC(A)}},"~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");f(b,"fillHermite",function(a,d,h,b,c,g,j,k){this.hermite3d.renderHermiteRope(!0,
a,d,h,b,c,g,j,k)},"~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");f(b,"drawTriangle3C",function(a,d,h,b,c,g,j){1==(j&1)&&this.drawLine(d,b,a.x,a.y,a.z,h.x,h.y,h.z);2==(j&2)&&this.drawLine(b,g,h.x,h.y,h.z,c.x,c.y,c.z);4==(j&4)&&this.drawLine(d,g,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");f(b,"fillTriangleTwoSided",function(a,d,h,b){this.setColorNoisy(this.getShadeIndex(a));this.fillTriangleP3f(d,h,b,!1)},"~N,JU.P3,JU.P3,JU.P3");c(b,"fillTriangleP3f",function(a,d,h,b){this.setScreeni(a,this.sA);
this.setScreeni(d,this.sB);this.setScreeni(h,this.sC);this.triangle3d.fillTriangle(this.sA,this.sB,this.sC,b)},"JU.P3,JU.P3,JU.P3,~B");f(b,"fillTriangle3f",function(a,d,h,b){var c=this.getShadeIndexP3(a,d,h,b);0>c||(b?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]),this.fillTriangleP3f(a,d,h,!1))},"JU.P3,JU.P3,JU.P3,~B");f(b,"fillTriangle3i",function(a,d,h,b,c,g,j){j&&(b=this.vectorAB,b.set(d.x-a.x,d.y-a.y,d.z-a.z),null==h?b=this.shader.getShadeIndex(-b.x,-b.y,b.z):(this.vectorAC.set(h.x-
a.x,h.y-a.y,h.z-a.z),b.cross(b,this.vectorAC),b=0<=b.z?this.shader.getShadeIndex(-b.x,-b.y,b.z):this.shader.getShadeIndex(b.x,b.y,-b.z)),56<b&&(b=56),this.setColorNoisy(b));this.fillTriangleP3f(a,d,h,!1)},"JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");f(b,"fillTriangle3CN",function(a,d,h,b,c,g,j,k,l){this.triangle3d.fillTriangle(a,b,j,this.checkGouraud(d,c,k,h,g,l))},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");f(b,"fillTriangle3CNBits",function(a,d,h,b,c,g,j,k,l){this.fillTriangleP3f(a,b,j,this.checkGouraud(d,
c,k,h,g,l))},"JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");c(b,"checkGouraud",function(a,d,h,b,c,g){if(!this.isPass2&&b==c&&b==g&&a==d&&a==h){d=this.getShadeIndex(b);if(a!=this.colixCurrent||this.currentShadeIndex!=d)this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(d);return!1}this.setTriangleTranslucency(a,d,h);this.triangle3d.setGouraud(this.getShades(a)[this.getShadeIndex(b)],this.getShades(d)[this.getShadeIndex(c)],this.getShades(h)[this.getShadeIndex(g)]);return!0},"~N,~N,~N,~N,~N,~N");
c(b,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");c(b,"setTriangleTranslucency",function(a,d,h){this.isPass2&&(a&=14336,d&=14336,h&=14336,this.translucencyMask=(JU.GData.roundInt(v((a+d+h)/3))&30720)<<13|16777215)},"~N,~N,~N");f(b,"fillQuadrilateral",function(a,d,h,b,c){c=this.getShadeIndexP3(a,d,h,c);0>c||(this.setColorNoisy(c),this.fillTriangleP3f(a,d,h,!1),this.fillTriangleP3f(a,h,b,!1))},"JU.P3,JU.P3,JU.P3,JU.P3,~B");
f(b,"drawSurface",function(){},"JU.MeshSurface,~N");f(b,"plotPixelClippedP3i",function(a){this.plotPixelClippedArgb(this.argbCurrent,a.x,a.y,a.z,this.width,this.zbuf,this.pixel)},"JU.P3i");c(b,"plotPixelClippedArgb",function(a,d,h,b,c,g,j){this.isClipped3(d,h,b)||(d=h*c+d,b<g[d]&&j.addPixel(d,b,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPixelUnclipped",function(a,d,h,b,c,g,j){d=h*c+d;b<g[d]&&j.addPixel(d,b,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotImagePixel",function(a,d,h,b,c,g,
j,k,l,f,m){0>d||(d>=j||0>h||h>=k)||f.addImagePixel(c,m,h*j+d,b,a,g)},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");c(b,"plotPixelsClippedRaster",function(a,d,h,b,c,g,j){var k,l;if(!(0>=a||0>h||h>=this.height||d>=this.width||b<(l=this.slab)&&c<l||b>(k=this.depth)&&c>k)){var f=this.zbuf,m=(d<<16)+(h<<1)^858993459,p=(b<<10)+512;b=c-b;c=v(a/2);b=JU.GData.roundInt(v(((b<<10)+(0<=b?c:-c))/a));if(0>d){d=-d;p+=b*d;a-=d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);d=h*this.width+d;h=this.pixel;if(null==g){g=
this.argbNoisyDn;c=this.argbNoisyUp;for(var x=this.argbCurrent;0<=--a;){j=p>>10;if(j>=l&&j<=k&&j<f[d]){var m=(m<<16)+(m<<1)+m&2147483647,A=m>>16&7;h.addPixel(d,j,0==A?g:1==A?c:x)}++d;p+=b}}else{m=g.r<<8;c=v((j.r-g.r<<8)/a);x=g.g;A=v((j.g-x)/a);g=g.b;for(var H=v((j.b-g)/a);0<=--a;)j=p>>10,j>=l&&(j<=k&&j<f[d])&&h.addPixel(d,j,4278190080|m&16711680|x&65280|g>>8&255),++d,p+=b,m+=c,x+=A,g+=H}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsUnclippedRaster",function(a,d,h,b,c,g,j){if(!(0>=a)){var k=
((d<<16)+(h<<1)^858993459)&2147483647,l=(b<<10)+512;b=c-b;c=v(a/2);b=JU.GData.roundInt(v(((b<<10)+(0<=b?c:-c))/a));d=h*this.width+d;h=this.zbuf;c=this.pixel;if(null==g){g=this.argbNoisyDn;for(var f=this.argbNoisyUp,m=this.argbCurrent;0<=--a;){j=l>>10;if(j<h[d]){var k=(k<<16)+(k<<1)+k&2147483647,p=k>>16&7;c.addPixel(d,j,0==p?g:1==p?f:m)}++d;l+=b}}else{k=g.r<<8;f=JU.GData.roundInt(v((j.r-g.r<<8)/a));m=g.g;p=JU.GData.roundInt(v((j.g-m)/a));g=g.b;for(var x=JU.GData.roundInt(v((j.b-g)/a));0<=--a;)j=l>>
10,j<h[d]&&c.addPixel(d,j,4278190080|k&16711680|m&65280|g>>8&255),++d,l+=b,k+=f,m+=p,g+=x}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsClippedRasterBits",function(a,d,h,b,c,g,j,k,l){var f,m;if(!(0>=a||0>h||h>=this.height||d>=this.width||b<(m=this.slab)&&c<m||b>(f=this.depth)&&c>f)){b=this.zbuf;var p=(d<<16)+(h<<1)^858993459;if(0>d){a-=-d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);h=h*this.width+d;c=this.pixel;if(null==g){g=this.argbNoisyDn;for(var x=this.argbNoisyUp,A=this.argbCurrent;0<=
--a;){j=this.line3d.getZCurrent(k,l,d++);if(j>=m&&j<=f&&j<b[h]){var p=(p<<16)+(p<<1)+p&2147483647,H=p>>16&7;c.addPixel(h,j,2>H?g:6>H?x:A)}++h}}else{p=g.r<<8;x=v((j.r-g.r<<8)/a);A=g.g;H=v((j.g-A)/a);g=g.b;for(var M=v((j.b-g)/a);0<=--a;)j=this.line3d.getZCurrent(k,l,d++),j>=m&&(j<=f&&j<b[h])&&c.addPixel(h,j,4278190080|p&16711680|A&65280|g>>8&255),++h,p+=x,A+=H,g+=M}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedRasterBits",function(a,d,h,b,c,g,j){if(!(0>=a)){var k=((d<<16)+(h<<
1)^858993459)&2147483647;h=h*this.width+d;var l=this.zbuf,f=this.pixel;if(null==b)for(var m=this.argbNoisyDn,p=this.argbNoisyUp,x=this.argbCurrent;0<=--a;)c=this.line3d.getZCurrent(g,j,d++),c<l[h]&&(k=(k<<16)+(k<<1)+k&2147483647,b=k>>16&7,f.addPixel(h,c,0==b?m:1==b?p:x)),++h;else{k=b.r<<8;m=JU.GData.roundInt(v((c.r-b.r<<8)/a));p=b.g;x=JU.GData.roundInt(v((c.g-p)/a));b=b.b;for(var A=JU.GData.roundInt(v((c.b-b)/a));0<=--a;)c=this.line3d.getZCurrent(g,j,d++),c<l[h]&&f.addPixel(h,c,4278190080|k&16711680|
p&65280|b>>8&255),++h,k+=m,p+=x,b+=A}}},"~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedCount",function(a,d,h,b,c,g,j,k){for(h=b*g+h;0<=--d;)c<j[h]&&k.addPixel(h,c,a),++h},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPoints",function(a,d,h,b){var c=this.pixel,g=this.argbCurrent,j=this.zbuf,k=this.width,l=this.antialiasThisFrame;for(a*=3;0<a;){var f=d[--a],m=d[--a]+b,p=d[--a]+h;if(!this.isClipped3(p,m,f)){var x=m*k+p++;f<j[x]&&c.addPixel(x,f,g);l&&(x=m*k+p,!this.isClipped3(p,m,f)&&
f<j[x]&&c.addPixel(x,f,g),x=++m*k+p,!this.isClipped3(p,m,f)&&f<j[x]&&c.addPixel(x,f,g),x=m*k+--p,!this.isClipped3(p,m,f)&&f<j[x]&&c.addPixel(x,f,g))}}},"~N,~A,~N,~N");c(b,"setColorNoisy",function(a){this.currentShadeIndex=a;this.argbCurrent=this.shadesCurrent[a];this.argbNoisyUp=this.shadesCurrent[63>a?a+1:63];this.argbNoisyDn=this.shadesCurrent[0<a?a-1:0]},"~N");c(b,"getShadeIndexP3",function(a,d,h,b){this.vectorAB.sub2(d,a);this.vectorAC.sub2(h,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);
return 0>a.z?this.shader.getShadeIndex(a.x,a.y,-a.z):b?-1:this.shader.getShadeIndex(-a.x,-a.y,a.z)},"JU.P3,JU.P3,JU.P3,~B");f(b,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");f(b,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom,~N");f(b,"getExportType",function(){return 0});f(b,"getExportName",function(){return null});c(b,"canDoTriangles",function(){return!0});
c(b,"isCartesianExport",function(){return!1});f(b,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");f(b,"finalizeOutput",function(){return null});f(b,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");f(b,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(b,"getPrivateKey",function(){return 0});f(b,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});c(b,"setRotationMatrix",function(a){for(var d=JU.Normix.getVertexVectors(),h=JU.GData.normixCount;0<=
--h;){var b=this.transformedVectors[h];a.rotate2(d[h],b);this.shadeIndexes[h]=this.shader.getShadeB(b.x,-b.y,b.z);this.shadeIndexes2Sided[h]=0<=b.z?this.shadeIndexes[h]:this.shader.getShadeB(-b.x,b.y,-b.z)}},"JU.M3");f(b,"renderCrossHairs",function(a,d,h,b,c){d=this.isAntialiased();this.setC(0>c?10:100<c?11:23);c=Math.max(Math.min(this.width,Math.round(b.x)),0);h=Math.max(Math.min(this.height,Math.round(b.y)),0);var g=Math.round(b.z)+1,j=d?8:4,k=d?20:10;d=d?2:1;this.drawRect(c-j,h,g,0,k,d);this.drawRect(c,
h-j,g,0,d,k);this.drawRect(c-j,h-j,g,0,k,k);j=k;k>>=1;this.setC(a[1]<b.x?21:11);this.drawRect(c-j,h,g,0,k,d);this.setC(a[0]>b.x?21:11);this.drawRect(c+k,h,g,0,k,d);this.setC(a[3]<b.y?21:11);this.drawRect(c,h-j,g,0,d,k);this.setC(a[2]>b.y?21:11);this.drawRect(c,h+k,g,0,d,k)},"~A,~N,~N,JU.P3,~N");f(b,"initializeOutput",function(){return!1},"JV.Viewer,~N,java.util.Map");b.fixTextImageRGB=c(b,"fixTextImageRGB",function(a){return 0==(a&12632256)?a|263172:a},"~N");b.sort=null;b.nullShadeIndex=50});n("J.g3d");
z(["J.g3d.PrecisionRenderer","java.util.Hashtable"],"J.g3d.LineRenderer",["JU.BS"],function(){var b=r(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nBits=0;this.slopeKey=this.lineCache=null;this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;u(this,arguments)},J.g3d,"LineRenderer",J.g3d.PrecisionRenderer);N(b,function(){this.lineCache=new java.util.Hashtable});y(b,function(a){I(this,J.g3d.LineRenderer,[]);this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");
c(b,"setLineBits",function(a,d){this.slope=0!=a?d/a:0<=d?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.width:this.g3d.height;this.slopeKey=Float.$valueOf(this.slope);if(this.lineCache.containsKey(this.slopeKey))this.lineBits=this.lineCache.get(this.slopeKey);else{this.lineBits=JU.BS.newN(this.nBits);d=Math.abs(d);a=Math.abs(a);if(d>a){var h=a;a=d;d=h}for(var h=0,b=a+a,c=d+d,g=0;g<this.nBits;g++)h+=c,h>a&&(this.lineBits.set(g),h-=b);this.lineCache.put(this.slopeKey,
this.lineBits)}},"~N,~N");c(b,"clearLineCache",function(){this.lineCache.clear()});c(b,"plotLineOld",function(a,d,h,b,c,g,j,k){this.x1t=h;this.x2t=g;this.y1t=b;this.y2t=j;this.z1t=c;this.z2t=k;var l=!0;switch(this.getTrimmedLineImpl()){case 0:l=!1;break;case 2:return}this.plotLineClippedOld(a,d,h,b,c,g-h,j-b,k-c,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N");c(b,"plotLineDeltaOld",function(a,d,h,b,c,g,j,k,l){this.x1t=h;this.x2t=h+g;this.y1t=b;this.y2t=b+j;this.z1t=c;this.z2t=c+k;if(l)switch(this.getTrimmedLineImpl()){case 2:return;
case 0:l=!1}this.plotLineClippedOld(a,d,h,b,c,g,j,k,l,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaAOld",function(a,d,h,b,c,g,j,k,l,f,m){this.x1t=c;this.x2t=c+k;this.y1t=g;this.y2t=g+l;this.z1t=j;this.z2t=j+f;if(m)switch(this.getTrimmedLineImpl()){case 2:return;case 0:m=!1}var p=this.g3d.zbuf,x=this.g3d.width,A=0,H=g*x+c,M=this.g3d.bufferSize,n=63>b?b+1:b,u=0<b?b-1:b,r=a[n],w=a[u],B=d[b],n=d[n];d=d[u];a=a[b];b=this.g3d.pixel;0!=h&&(b=this.g3d.setScreened(1==(h&1)),this.g3d.currentShadeIndex=
0);0!=a&&(!m&&0<=H&&H<M&&j<p[H])&&b.addPixel(H,j,a);if(!(0==k&&0==l)){m=1;u=x;c+=k;var y=g+l;0>k&&(k=-k,m=-1);0>l&&(l=-l,u=-x);x=k+k;g=l+l;j<<=10;if(l<=k){var z=k-1;0>f&&(z=-z);f=v(((f<<10)+z)/k);l=0;z=Math.abs(c-this.x2t)-1;c=Math.abs(c-this.x1t)-1;for(var y=k-1,C=v(y/2);--y>=z;){if(y==C){a=B;if(0==a)break;r=n;w=d;0!=h%3&&(b=this.g3d.setScreened(2==(h&2)),this.g3d.currentShadeIndex=0)}H+=m;j+=f;l+=g;l>k&&(H+=u,l-=x);if(0!=a&&y<c&&0<=H&&H<M&&2147483647>A){var E=j>>10;if(E<p[H]){var D=this.shader.nextRandom8Bit();
b.addPixel(H,E,85>D?w:170<D?r:a)}}A=(A+1)%1}}else{z=l-1;0>f&&(z=-z);f=v(((f<<10)+z)/l);k=0;z=Math.abs(y-this.y2t)-1;c=Math.abs(y-this.y1t)-1;y=l-1;for(C=v(y/2);--y>=z;){if(y==C){a=B;if(0==a)break;r=n;w=d;0!=h%3&&(b=this.g3d.setScreened(2==(h&2)),this.g3d.currentShadeIndex=0)}H+=u;j+=f;k+=x;k>l&&(H+=m,k-=g);0!=a&&(y<c&&0<=H&&H<M&&2147483647>A)&&(E=j>>10,E<p[H]&&(D=this.g3d.shader.nextRandom8Bit(),b.addPixel(H,E,85>D?w:170<D?r:a)));A=(A+1)%1}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaABitsFloat",
function(a,d,h,b,c,g,j){var k=Math.round(b.x),l=Math.round(b.y),f=Math.round(b.z),m=Math.round(c.x),p=Math.round(c.y),x=Math.round(c.z),A=m-k,H=p-l;this.x1t=k;this.x2t=m;this.y1t=l;this.y2t=p;this.z1t=f;this.z2t=x;if(!(j&&2==this.getTrimmedLineImpl())){j=this.g3d.zbuf;var M=this.g3d.width,m=0,x=63>h?h+1:h,p=0<h?h-1:h,n=a[h],u=a[x],r=a[p];h=d[h];a=d[x];d=d[p];var p=l*M+k,x=this.g3d.bufferSize,w,y,B,z;this.lineTypeX?(w=k,y=this.x1t,B=this.x2t,k+=v(A/2),z=l=0<=A?1:-1,A=0<=H?M:-M,this.setRastABFloat(b.x,
b.z,c.x,c.z)):(w=l,y=this.y1t,B=this.y2t,k=l+v(H/2),l=0<=H?1:-1,z=0<=H?M:-M,A=0<=A?1:-1,this.setRastABFloat(b.y,b.z,c.y,c.z));b=f;c=n;f=u;H=r;u=!1;r=this.g3d.pixel;0!=g&&(r=this.g3d.setScreened(1==(g&1)),this.g3d.currentShadeIndex=0);for(n=w;;n+=l,w+=l){n==y&&(u=!0);if(n==k){c=h;if(0==c)break;f=a;H=d;0!=g%3&&(r=this.g3d.setScreened(2==(g&2)),this.g3d.currentShadeIndex=0)}0!=c&&(u&&0<=p&&p<x&&2147483647>m)&&(b=this.getZCurrent(this.a,this.b,n),b<j[p]&&(M=this.shader.nextRandom8Bit(),r.addPixel(p,F(b),
85>M?H:170<M?f:c)));if(n==B)break;m=(m+1)%1;for(p+=z;0>w;)w+=this.nBits;this.lineBits.get(w%this.nBits)&&(p+=A)}}},"~A,~A,~N,JU.P3,JU.P3,~N,~B");c(b,"plotLineDeltaABitsInt",function(a,d,h,b,c,g,j){var k=b.x,l=b.y,f=b.z,m=c.x,p=c.y,x=c.z,A=m-k,H=p-l;this.x1t=k;this.x2t=m;this.y1t=l;this.y2t=p;this.z1t=f;this.z2t=x;if(!(j&&2==this.getTrimmedLineImpl())){j=this.g3d.zbuf;var M=this.g3d.width,m=0,x=63>h?h+1:h,p=0<h?h-1:h,n=a[h],u=a[x],r=a[p];h=d[h];a=d[x];d=d[p];var p=l*M+k,x=this.g3d.bufferSize,w,y,B,
z;this.lineTypeX?(w=k,y=this.x1t,B=this.x2t,k+=v(A/2),z=l=0<=A?1:-1,A=0<=H?M:-M,this.setRastAB(b.x,b.z,c.x,c.z)):(w=l,y=this.y1t,B=this.y2t,k=l+v(H/2),l=0<=H?1:-1,z=0<=H?M:-M,A=0<=A?1:-1,this.setRastAB(b.y,b.z,c.y,c.z));b=f;c=n;f=u;H=r;u=!1;r=this.g3d.pixel;0!=g&&(r=this.g3d.setScreened(1==(g&1)),this.g3d.currentShadeIndex=0);for(n=w;;n+=l,w+=l){n==y&&(u=!0);if(n==k){c=h;if(0==c)break;f=a;H=d;0!=g%3&&(r=this.g3d.setScreened(2==(g&2)),this.g3d.currentShadeIndex=0)}0!=c&&(u&&0<=p&&p<x&&2147483647>m)&&
(b=this.getZCurrent(this.a,this.b,n),b<j[p]&&(M=this.shader.nextRandom8Bit(),r.addPixel(p,F(b),85>M?H:170<M?f:c)));if(n==B)break;m=(m+1)%1;for(p+=z;0>w;)w+=this.nBits;this.lineBits.get(w%this.nBits)&&(p+=A)}}},"~A,~A,~N,JU.P3i,JU.P3i,~N,~B");c(b,"plotLineBits",function(a,d,h,b,c,g,j){if(!(1>=h.z||1>=b.z)){var k=!0;this.x1t=h.x;this.y1t=h.y;this.z1t=h.z;this.x2t=b.x;this.y2t=b.y;this.z2t=b.z;switch(this.getTrimmedLineImpl()){case 2:return;case 0:k=!1;break;default:j&&(h.set(this.x1t,this.y1t,this.z1t),
b.set(this.x2t,this.y2t,this.z2t))}j=this.g3d.zbuf;var l=this.g3d.width,f=0;0==c&&(g=2147483647,c=1);var m=h.x,p=h.y,x=h.z,A=b.x-m,H=m+A,n=b.y-p,u=p+n,r=p*l+m,w=this.g3d.bufferSize,y=this.g3d.pixel;0!=a&&(!k&&0<=r&&r<w&&x<j[r])&&y.addPixel(r,x,a);if(!(0==A&&0==n)){var B=k=1,x=l;0>A&&(A=-A,k=-1);0>n&&(n=-n,x=-l,B=-1);var l=A+A,z=n+n;if(n<=A){this.setRastAB(h.x,h.z,b.x,b.z);p=0;h=Math.abs(H-this.x2t)-1;H=Math.abs(H-this.x1t)-1;u=A-1;for(b=v(u/2);--u>=h&&!(u==b&&(a=d,0==a));){r+=k;m+=k;p+=z;p>A&&(r+=
x,p-=l);if(0!=a&&u<H&&0<=r&&r<w&&f<g){var C=this.getZCurrent(this.a,this.b,m);C<j[r]&&y.addPixel(r,C,a)}f=(f+1)%c}}else{this.setRastAB(h.y,h.z,b.y,b.z);m=0;h=Math.abs(u-this.y2t)-1;H=Math.abs(u-this.y1t)-1;u=n-1;for(b=v(u/2);--u>=h&&!(u==b&&(a=d,0==a));)r+=x,p+=B,m+=l,m>n&&(r+=k,m-=z),0!=a&&(u<H&&0<=r&&r<w&&f<g)&&(C=this.getZCurrent(this.a,this.b,p),C<j[r]&&y.addPixel(r,C,a)),f=(f+1)%c}}}},"~N,~N,JU.P3i,JU.P3i,~N,~N,~B");c(b,"getTrimmedLineImpl",function(){var a=this.g3d.clipCode3(this.x1t,this.y1t,
this.z1t),d=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(a|d))return 0;if(-1==(a|d))return 2;var h=this.g3d.xLast,b=this.g3d.yLast,c=this.g3d.slab,g=this.g3d.depth;do{if(0!=(a&d))return 2;var j=this.x2t-this.x1t,k=this.y2t-this.y1t,l=this.z2t-this.z1t;0!=a?(0!=(a&8)?(this.y1t+=F(-this.x1t*k/j),this.z1t+=F(-this.x1t*l/j),this.x1t=0):0!=(a&4)?(this.y1t+=F((h-this.x1t)*k/j),this.z1t+=F((h-this.x1t)*l/j),this.x1t=h):0!=(a&2)?(this.x1t+=F(-this.y1t*j/k),this.z1t+=F(-this.y1t*l/k),this.y1t=0):
0!=(a&1)?(this.x1t+=F((b-this.y1t)*j/k),this.z1t+=F((b-this.y1t)*l/k),this.y1t=b):0!=(a&32)?(this.x1t+=F((c-this.z1t)*j/l),this.y1t+=F((c-this.z1t)*k/l),this.z1t=c):(this.x1t+=F((g-this.z1t)*j/l),this.y1t+=F((g-this.z1t)*k/l),this.z1t=g),a=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(d&8)?(this.y2t+=F(-this.x2t*k/j),this.z2t+=F(-this.x2t*l/j),this.x2t=0):0!=(d&4)?(this.y2t+=F((h-this.x2t)*k/j),this.z2t+=F((h-this.x2t)*l/j),this.x2t=h):0!=(d&2)?(this.x2t+=F(-this.y2t*j/k),this.z2t+=F(-this.y2t*
l/k),this.y2t=0):0!=(d&1)?(this.x2t+=F((b-this.y2t)*j/k),this.z2t+=F((b-this.y2t)*l/k),this.y2t=b):0!=(d&32)?(this.x2t+=F((c-this.z2t)*j/l),this.y2t+=F((c-this.z2t)*k/l),this.z2t=c):(this.x2t+=F((g-this.z2t)*j/l),this.y2t+=F((g-this.z2t)*k/l),this.z2t=g),d=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(a|d));return 1});c(b,"plotLineClippedOld",function(a,d,h,b,c,g,j,k,l,f,m){var p=this.g3d.zbuf,x=this.g3d.width,A=0;0==f&&(m=2147483647,f=1);var H=b*x+h,n=this.g3d.bufferSize,u=this.g3d.pixel;
0!=a&&(!l&&0<=H&&H<n&&c<p[H])&&u.addPixel(H,c,a);if(!(0==g&&0==j)){l=1;var r=x;h+=g;var w=b+j;0>g&&(g=-g,l=-1);0>j&&(j=-j,r=-x);x=g+g;b=j+j;c<<=10;if(j<=g){var y=g-1;0>k&&(y=-y);k=v(((k<<10)+y)/g);j=0;y=Math.abs(h-this.x2t)-1;h=Math.abs(h-this.x1t)-1;for(var w=g-1,B=v(w/2);--w>=y&&!(w==B&&(a=d,0==a));){H+=l;c+=k;j+=b;j>g&&(H+=r,j-=x);if(0!=a&&w<h&&0<=H&&H<n&&A<m){var z=c>>10;z<p[H]&&u.addPixel(H,z,a)}A=(A+1)%f}}else{y=j-1;0>k&&(y=-y);k=v(((k<<10)+y)/j);g=0;y=Math.abs(w-this.y2t)-1;h=Math.abs(w-this.y1t)-
1;w=j-1;for(B=v(w/2);--w>=y&&!(w==B&&(a=d,0==a));)H+=r,c+=k,g+=x,g>j&&(H+=l,g-=b),0!=a&&(w<h&&0<=H&&H<n&&A<m)&&(z=c>>10,z<p[H]&&u.addPixel(H,z,a)),A=(A+1)%f}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N")});n("J.g3d");z(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){var b=r(function(){this.pb=this.zb=this.p0=this.g=null;this.bgcolor=this.width=0;u(this,arguments)},J.g3d,"Pixelator",null);y(b,function(a){this.g=a;this.bgcolor=this.g.bgcolor;this.setBuf()},"J.g3d.Graphics3D");c(b,"setBuf",function(){this.zb=
this.g.zbuf;this.pb=this.g.pbuf});c(b,"clearPixel",function(a,d){this.zb[a]>d&&(this.zb[a]=2147483647)},"~N,~N");c(b,"addPixel",function(a,d,h){this.zb[a]=d;this.pb[a]=h},"~N,~N,~N");c(b,"addImagePixel",function(a,d,h,b,c,g){if(b<this.zb[h])switch(a){case 0:break;case 8:this.addPixel(h,b,c);break;default:a+=d,7>=a&&(d=this.pb[h],0!=g&&(d=J.g3d.Graphics3D.mergeBufferPixel(d,g,g)),d=J.g3d.Graphics3D.mergeBufferPixel(d,c&16777215|a<<24,this.bgcolor),this.addPixel(h,b,d))}},"~N,~N,~N,~N,~N,~N")});n("J.g3d");
z(["J.g3d.Pixelator"],"J.g3d.PixelatorT",["J.g3d.Graphics3D"],function(){var b=G(J.g3d,"PixelatorT",J.g3d.Pixelator);f(b,"clearPixel",function(){},"~N,~N");f(b,"addPixel",function(a,d,h){var b=this.g.zbufT[a];if(d<b){var c=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=c&&b-d>this.g.zMargin)&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],c,this.g.bgcolor));this.g.zbufT[a]=d;this.g.pbufT[a]=h&this.g.translucencyMask}else d!=b&&!this.g.translucentCoverOnly&&d-b>this.g.zMargin&&(this.pb[a]=
J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],h&this.g.translucencyMask,this.g.bgcolor))},"~N,~N,~N")});n("J.g3d");z(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){var b=r(function(){this.tmp=this.bgRGB=null;this.zShadePower=this.zDepth=this.zSlab=0;u(this,arguments)},J.g3d,"PixelatorShaded",J.g3d.Pixelator);y(b,function(a){I(this,J.g3d.PixelatorShaded,[a]);this.tmp=E(3,0)},"J.g3d.Graphics3D");c(b,"set",function(a,d,h){this.bgcolor=this.g.bgcolor;this.bgRGB=E(-1,[this.bgcolor&255,this.bgcolor>>
8&255,this.g.bgcolor>>16&255]);this.zSlab=0>a?0:a;this.zDepth=0>d?0:d;this.zShadePower=h;this.p0=this.g.pixel0;return this},"~N,~N,~N");f(b,"addPixel",function(a,d,h){if(!(d>this.zDepth)){if(d>=this.zSlab&&0<this.zShadePower){var b=this.tmp,c=this.bgRGB;b[0]=h;b[1]=h>>8;b[2]=h>>16;var g=(this.zDepth-d)/(this.zDepth-this.zSlab);if(1<this.zShadePower)for(var j=0;j<this.zShadePower;j++)g*=g;for(j=0;3>j;j++)b[j]=c[j]+F(g*((b[j]&255)-c[j]));h=b[2]<<16|b[1]<<8|b[0]|h&4278190080}this.p0.addPixel(a,d,h)}},
"~N,~N,~N");c(b,"showZBuffer",function(){for(var a=this.p0.zb.length;0<=--a;)if(0!=this.p0.pb[a]){var d=F(Math.min(255,Math.max(0,255*(this.zDepth-this.p0.zb[a])/(this.zDepth-this.zSlab))));this.p0.pb[a]=4278190080|d|d<<8|d<<16}})});n("J.g3d");z(["J.g3d.Pixelator"],"J.g3d.PixelatorScreened",null,function(){var b=G(J.g3d,"PixelatorScreened",J.g3d.Pixelator);y(b,function(a,d){I(this,J.g3d.PixelatorScreened,[a]);this.width=a.width;this.p0=d},"J.g3d.Graphics3D,J.g3d.Pixelator");f(b,"addPixel",function(a,
d,h){a%this.width%2==v(a/this.width)%2&&this.p0.addPixel(a,d,h)},"~N,~N,~N")});n("J.g3d");var Z=r(function(){this.bufferSizeT=this.bufferSize=this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=this.graphicsForTextOrImage=this.offscreenImage=null;u(this,arguments)},J.g3d,"Platform3D",null);y(Z,function(b){this.apiPlatform=b},
"J.api.GenericPlatform");c(Z,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(Z,"allocateTBuffers",function(b){this.bufferSizeT=b?this.bufferSize:this.windowSize;this.zBufferT=E(this.bufferSizeT,0);this.pBufferT=E(this.bufferSizeT,0)},"~B");c(Z,"allocateBuffers",function(b,a,d,h){this.windowWidth=b;this.windowHeight=a;this.windowSize=b*a;d&&(b*=2,a*=2);this.bufferWidth=b;this.bufferHeight=a;this.bufferSize=this.bufferWidth*this.bufferHeight;
this.zBuffer=E(this.bufferSize,0);this.pBuffer=E(this.bufferSize,0);this.bufferedImage=this.apiPlatform.allocateRgbImage(this.windowWidth,this.windowHeight,this.pBuffer,this.windowSize,J.g3d.Platform3D.backgroundTransparent,h)},"~N,~N,~B,~B");c(Z,"releaseBuffers",function(){this.windowWidth=this.windowHeight=this.bufferWidth=this.bufferHeight=this.bufferSize=-1;null!=this.bufferedImage&&(this.apiPlatform.flushImage(this.bufferedImage),this.bufferedImage=null);this.zBufferT=this.pBufferT=this.zBuffer=
this.pBuffer=null});c(Z,"hasContent",function(){for(var b=this.bufferSize;0<=--b;)if(2147483647!=this.zBuffer[b])return!0;return!1});c(Z,"clearScreenBuffer",function(){for(var b=this.bufferSize;0<=--b;)this.zBuffer[b]=2147483647,this.pBuffer[b]=0});c(Z,"setBackgroundColor",function(b){if(null!=this.pBuffer)for(var a=this.bufferSize;0<=--a;)0==this.pBuffer[a]&&(this.pBuffer[a]=b)},"~N");c(Z,"clearTBuffer",function(){for(var b=this.bufferSizeT;0<=--b;)this.zBufferT[b]=2147483647,this.pBufferT[b]=0});
c(Z,"clearBuffer",function(){this.clearScreenBuffer()});c(Z,"clearScreenBufferThreaded",function(){});c(Z,"notifyEndOfRendering",function(){this.apiPlatform.notifyEndOfRendering()});c(Z,"getGraphicsForTextOrImage",function(b,a){if(b>this.widthOffscreen||a>this.heightOffscreen)null!=this.offscreenImage&&(this.apiPlatform.disposeGraphics(this.graphicsForTextOrImage),this.apiPlatform.flushImage(this.offscreenImage)),b>this.widthOffscreen&&(this.widthOffscreen=b),a>this.heightOffscreen&&(this.heightOffscreen=
a),this.offscreenImage=this.allocateOffscreenImage(this.widthOffscreen,this.heightOffscreen),this.graphicsForTextOrImage=this.apiPlatform.getStaticGraphics(this.offscreenImage,J.g3d.Platform3D.backgroundTransparent);return this.graphicsForTextOrImage},"~N,~N");c(Z,"allocateOffscreenImage",function(b,a){return this.apiPlatform.newOffScreenImage(b,a)},"~N,~N");c(Z,"setBackgroundTransparent",function(b){J.g3d.Platform3D.backgroundTransparent=b},"~B");Z.backgroundTransparent=!1;n("J.g3d");var La=r(function(){this.b=
this.a=0;this.isOrthographic=!1;u(this,arguments)},J.g3d,"PrecisionRenderer",null);c(La,"getZCurrent",function(b,a,d){return Math.round(1.4E-45==b?a:this.isOrthographic?b*d+a:b/(a-d))},"~N,~N,~N");c(La,"setRastABFloat",function(b,a,d,h){var c=h-a,e=d-b;0==c||0==e?(this.a=1.4E-45,this.b=a):this.isOrthographic?(this.a=c/e,this.b=a-this.a*b):(this.a=e*a*(h/c),this.b=(d*h-b*a)/c)},"~N,~N,~N,~N");c(La,"setRastAB",function(b,a,d,h){var c=h-a,e=d-b;1.4E-45==b||0==c||0==e?(this.a=1.4E-45,this.b=h):this.isOrthographic?
(this.a=c/e,this.b=a-this.a*b):(this.a=e*a*(h/c),this.b=(d*h-b*a)/c)},"~N,~N,~N,~N");n("J.g3d");z(["JU.P3"],"J.g3d.SphereRenderer",null,function(){var b=r(function(){this.mDeriv=this.coef=this.mat=this.zroot=this.shader=this.g3d=null;this.planeShade=this.selectedOctant=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.dxyz=this.planeShades=this.ptTemp=null;u(this,arguments)},J.g3d,"SphereRenderer",null);N(b,function(){this.zroot=R(2,0);this.ptTemp=new JU.P3;
this.planeShades=E(3,0);this.dxyz=L(3,3,0)});y(b,function(a){this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");c(b,"render",function(a,d,h,b,c,g,j,k,l,f){if(1!=c&&(49<d&&(d&=-2),!this.g3d.isClippedXY(d,h,b))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var m=d+1>>1,p=c-m;if(!(c+m<this.slab||p>this.depth)){var x=h-m,A=h+m,H=b-m,n=b+m;this.shader.nOut=this.shader.nIn=0;this.zbuf=this.g3d.zbuf;this.height=this.g3d.height;this.width=this.g3d.width;this.offsetPbufBeginLine=this.width*b+h;var u=
this.shader;this.mat=g;if(null!=g&&(this.coef=j,this.mDeriv=k,this.selectedOctant=l,null==u.ellipsoidShades&&u.createEllipsoidShades(),null!=f)){this.planeShade=-1;for(j=0;3>j;j++)if(m=this.dxyz[j][0]=f[j].x-h,k=this.dxyz[j][1]=f[j].y-b,l=this.dxyz[j][2]=f[j].z-c,this.planeShades[j]=u.getShadeIndex(m,k,-l),0==m&&0==k){this.planeShade=this.planeShades[j];break}}if(null!=g||128<d)this.renderQuadrant(-1,-1,h,b,c,d,a),this.renderQuadrant(-1,1,h,b,c,d,a),this.renderQuadrant(1,-1,h,b,c,d,a),this.renderQuadrant(1,
1,h,b,c,d,a),null!=g&&(this.mDeriv=this.coef=this.mat=null);else{var r=u.sphereShapeCache[d-1];if(null==r){r=0;g=0!=(d&1);f=d/2;k=f*f;m=v((d+1)/2);l=g?0:0.5;for(j=0;j<m;++j,++l)for(var w=l*l,y=g?0:0.5,B=0;B<m;++B,++y){var z=y*y,z=k-w-z;0<=z&&++r}var r=E(r,0),C=0;l=g?0:0.5;for(j=0;j<m;++j,++l){w=l*l;y=g?0:0.5;for(B=0;B<m;++B,++y)if(z=y*y,z=k-w-z,0<=z){var D=Math.sqrt(z),z=F(D),G=u.getShadeN(y,l,D,f),I=u.getShadeN(-y,l,D,f),L=u.getShadeN(y,-l,D,f),D=u.getShadeN(-y,-l,D,f),z=z|G<<7|I<<13|L<<19|D<<25;
r[C++]=z}r[C-1]|=2147483648}u.sphereShapeCache[d-1]=r}0>x||A>=this.width||0>H||n>=this.height||p<this.slab||c>this.depth?this.renderSphereClipped(r,h,b,c,d,a):this.renderSphereUnclipped(r,c,d,a)}this.zbuf=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(b,"renderSphereUnclipped",function(a,d,h,b){var c=0,g=1-(h&1),j=this.offsetPbufBeginLine,k=j-g*this.width;h=v((h+1)/2);var l=this.zbuf,f=this.width,m=this.g3d.pixel;do{var p=j,x=j-g,A=k,H=k-g,n;do{n=a[c++];var r=d-(n&127);r<l[p]&&m.addPixel(p,r,b[n>>
7&63]);r<l[x]&&m.addPixel(x,r,b[n>>13&63]);r<l[A]&&m.addPixel(A,r,b[n>>19&63]);r<l[H]&&m.addPixel(H,r,b[n>>25&63]);++p;--x;++A;--H}while(0<=n);j+=f;k-=f}while(0<--h)},"~A,~N,~N,~A");c(b,"renderSphereClipped",function(a,d,h,b,c,g){var j=this.width,k=this.height,l=0,f=1-(c&1),m=this.offsetPbufBeginLine,p=m-f*j;c=v((c+1)/2);var x=h,A=h-f;h=(d<<16)+(h<<1)^858993459;var H=this.zbuf,n=this.g3d.pixel,r=this.slab,u=this.depth;do{var w=0<=x&&x<k,y=0<=A&&A<k,B=m,z=m-f,C=p,D=p-f,E,F=d,G=d-f;do{var I=0<=G&&G<
j,L=0<=F&&F<j;E=a[l++];var K;K=E&127;var N;b<r?(N=b+K,K=N>=r):(N=b-K,K=N<r);K&&(N=r);if(N>=r&&N<=u){if(w){if(L&&N<H[B]){var O=K?44+(h>>7&7):E>>7&63;n.addPixel(B,N,g[O])}I&&N<H[z]&&(O=K?44+(h>>13&7):E>>13&63,n.addPixel(z,N,g[O]))}y&&(L&&N<H[C]&&(O=K?44+(h>>19&7):E>>19&63,n.addPixel(C,N,g[O])),I&&N<H[D]&&(O=K?44+(h>>25&7):E>>25&63,n.addPixel(D,N,g[O])))}++B;--z;++C;--D;++F;--G;K&&(h=(h<<16)+(h<<1)+h&2147483647)}while(0<=E);m+=j;p-=j;++x;--A}while(0<--c)},"~A,~N,~N,~N,~N,~A");c(b,"renderQuadrant",function(a,
d,h,b,c,g,j){g=v(g/2);var k=h+g*a,l=(0>h?-1:h<this.width?0:1)+(0>k?-2:k<this.width?0:2);-3==l||3==l||(k=b+g*d,k=(0>b?-1:b<this.height?0:1)+(0>k?-2:k<this.height?0:2),-3==k||3==k||(null==this.mat&&0==l&&0==k&&c-g>=this.slab&&c<=this.depth?this.renderQuadrantUnclipped(g,a,d,c,j):this.renderQuadrantClipped(g,a,d,h,b,c,j)))},"~N,~N,~N,~N,~N,~N,~A");c(b,"renderQuadrantUnclipped",function(a,d,h,b,c){for(var g=a*a,j=2*a+1,k=0>h?-this.width:this.width,l=this.offsetPbufBeginLine,f=this.zbuf,m=this.g3d.pixel,
p=this.shader.sphereShadeIndexes,x=0,A=0;A<=g;A+=x+ ++x,l+=k)for(var H=l,n=g-A,r=b-a,u=v((x*h+a<<8)/j),w=0,y=0;y<=n;y+=w+ ++w,H+=d)if(!(f[H]<=r)&&(r=v(Math.sqrt(n-y)),r=b-r,!(f[H]<=r))){var B=v((w*d+a<<8)/j);m.addPixel(H,r,c[p[(u<<8)+B]])}},"~N,~N,~N,~N,~A");c(b,"renderQuadrantClipped",function(a,d,h,b,c,g,j){for(var k=null!=this.mat,l=0<=this.selectedOctant,f=a*a,m=2*a+1,p=0>h?-this.width:this.width,x=this.offsetPbufBeginLine,A=(b<<16)+(c<<1)^858993459,H=0,n=0,r=this.g3d.pixel,u=0,w=this.height,
y=this.width,B=this.zbuf,z=this.dxyz,C=this.slab,D=this.depth,E=this.ptTemp,F=this.coef,G=this.zroot,I=this.selectedOctant,K=this.shader,L=this.planeShades,N=K.sphereShadeIndexes,O=this.planeShade,R=this.mat,T=0,V=0,Q=c;V<=f;V+=T+ ++T,x+=p,Q+=h)if(0>Q){if(0>h)break}else if(Q>=w){if(0<h)break}else{var Y=f-(k?0:V);k||(H=v((T*h+a<<8)/m));for(var A=(A<<16)+(A<<1)+A&2147483647,P=b,X=0,W=0,$=-1,U=1,Z=x;W<=Y;W+=X+ ++X,Z+=d,P+=d)if(0>P){if(0>d)break}else if(P>=y){if(0<d)break}else{var S;if(k){S=(F[4]*P+F[5]*
Q+F[8])/F[2]/2;var aa=S*S-(F[0]*P*P+F[1]*Q*Q+F[3]*P*Q+F[6]*P+F[7]*Q-1)/F[2];if(0>aa){if(0<=$)break;continue}aa=Math.sqrt(aa);G[0]=-S-aa;G[1]=-S+aa;$=g<C?1:0;if(0==(S=v(G[$])))S=g;U=2;u=S;if(l){E.set(P-b,Q-c,S-g);R.rotate(E);aa=0;0>E.x&&(aa|=1);0>E.y&&(aa|=2);0>E.z&&(aa|=4);if(aa==I){if(0<=O)n=O;else{U=3;n=3.4028235E38;for(S=0;3>S;S++)if(0!=(aa=z[S][2]))aa=g+(-z[S][0]*(P-b)-z[S][1]*(Q-c))/aa,aa<n&&(n=aa,U=S);3==U&&(U=0,n=g);G[0]=n;n=L[U]}S=v(G[0]);U=3}if(aa=g<C?S>=C:S<C)u=S=C,U=0}if(S<C||S>D||B[Z]<=
u)continue}else{S=v(Math.sqrt(Y-W));S=g+(g<C?S:-S);if(aa=g<C?S>=C:S<C)S=C,U=0;if(S<C||S>D||B[Z]<=S)continue}switch(U){case 0:n=44+(A>>8&7);A=(A<<16)+(A<<1)+A&2147483647;U=1;break;case 2:n=K.getEllipsoidShade(P,Q,G[$],a,this.mDeriv);break;case 3:r.clearPixel(Z,u);break;default:n=v((X*d+a<<8)/m),n=N[(H<<8)+n]}r.addPixel(Z,S,j[n])}A=(A+P+Q|1)&2147483647}},"~N,~N,~N,~N,~N,~N,~A")});n("J.g3d");z(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU","J.g3d.Graphics3D"],function(){var b=r(function(){this.size=
this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=null;this.isInvalid=!1;u(this,arguments)},J.g3d,"TextRenderer",null);y(b,function(a,d){this.ascent=d.getAscent();this.height=d.getHeight();this.width=d.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,JU.Font");b.clearFontCache=c(b,"clearFontCache",function(){J.g3d.TextRenderer.working||(J.g3d.TextRenderer.htFont3d.clear(),J.g3d.TextRenderer.htFont3dAntialias.clear())});b.plot=c(b,"plot",
function(a,d,h,b,c,g,j,k,l,f){if(0==g.length)return 0;if(0<=g.indexOf("<su")||0<=g.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,d,h,b,c,g,j,k,l,f);var m=j.getAscent();d-=m;g=J.g3d.TextRenderer.getPlotText3D(a,d,k,g,j,f);if(g.isInvalid)return g.width;f&&(b=J.g3d.Graphics3D.fixTextImageRGB(b));f=g.height;j=g.width;var m=g.tmap,p=k.width,x=k.height,A=k.zbuf,n=k.pixel,r=k.translucencyLog;if(null!=l||(0>a||a+g.width>p||0>d||d+g.height>x)&&null!=(l=k))for(var u=k=0;u<f;u++)for(var v=0;v<
j;v++){var w=m[k++];0!=w&&l.plotImagePixel(b,a+v,d+u,h,w,c,p,x,A,n,r)}else{k=u=0;for(a=d*p+a;u<f;u++,a+=p-j)for(v=0;v<j;v++)n.addImagePixel(m[k++],r,a++,h,b,c)}return g.width},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");b.plotByCharacter=c(b,"plotByCharacter",function(a,d,h,b,c,g,j,k,l,f){for(var m=0,p=g.length,x=Math.round(0.25*j.getHeight()),A=-Math.round(0.3*j.getHeight()),n=0,r=0;r<p;r++){if("<"==g.charAt(r)){if(r+5<p&&g.substring(r,r+6).equals("<color")){var n=
b,u=g.indexOf(">",r);if(0>u)continue;b=JU.CU.getArgbFromString(g.substring(r+7,u).trim());r=u;continue}if(r+7<p&&g.substring(r,r+8).equals("</color>")){r+=7;b=n;continue}if(r+4<p&&g.substring(r,r+5).equals("<sub>")){r+=4;d+=x;continue}if(r+4<p&&g.substring(r,r+5).equals("<sup>")){r+=4;d+=A;continue}if(r+5<p&&g.substring(r,r+6).equals("</sub>")){r+=5;d-=x;continue}if(r+5<p&&g.substring(r,r+6).equals("</sup>")){r+=5;d-=A;continue}}u=J.g3d.TextRenderer.plot(a+m,d,h,b,c,g.substring(r,r+1),j,k,l,f);m+=
u}return m},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");b.getPlotText3D=c(b,"getPlotText3D",function(a,d,h,b,c,g){J.g3d.TextRenderer.working=!0;g=g?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var j=g.get(c),k=null,l=!1,f=!1;null!=j?k=j.get(b):(j=new java.util.Hashtable,l=!0);null==k&&(k=new J.g3d.TextRenderer(b,c),f=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=h.width||0>=d+k.height||d>=h.height;if(k.isInvalid)return k;l&&g.put(c,j);f&&(k.setTranslucency(b,
c,h),j.put(b,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,JU.Font,~B");c(b,"setTranslucency",function(a,d,b){a=b.apiPlatform.getTextPixels(a,d,b.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),b.platform.offscreenImage,this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=O(this.size,0);for(d=a.length;0<=--d;)b=a[d]&255,0!=b&&(this.tmap[d]=J.g3d.TextRenderer.translucency[b>>5])}},"~S,JU.Font,J.g3d.Graphics3D");b.translucency=O(-1,[7,6,5,4,3,2,1,8]);b.working=
!1;b.htFont3d=new java.util.Hashtable;b.htFont3dAntialias=new java.util.Hashtable});n("J.g3d");z(["JU.P3i"],"J.g3d.TextString",null,function(){var b=r(function(){this.font=this.text=null;this.bgargb=this.argb=0;u(this,arguments)},J.g3d,"TextString",JU.P3i,java.util.Comparator);c(b,"setText",function(a,d,b,c,e,g,j){this.text=a;this.font=d;this.argb=b;this.bgargb=c;this.x=e;this.y=g;this.z=j},"~S,JU.Font,~N,~N,~N,~N,~N");f(b,"compare",function(a,d){return null==a||null==d?0:a.z>d.z?-1:a.z<d.z?1:0},
"J.g3d.TextString,J.g3d.TextString");f(b,"toString",function(){return this.asString()+" "+this.text})});n("J.g3d");z(["J.g3d.G3DRenderer","$.PrecisionRenderer","JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){var b=r(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.bb=this.aa=this.az=this.ay=this.ax=this.g3d=null;u(this,arguments)},J.g3d,"TriangleRenderer",J.g3d.PrecisionRenderer,J.g3d.G3DRenderer);N(b,function(){this.ax=
E(3,0);this.ay=E(3,0);this.az=E(3,0);this.aa=L(64,0);this.bb=L(64,0);this.axW=E(64,0);this.azW=E(64,0);this.axE=E(64,0);this.azE=E(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});y(b,function(){I(this,J.g3d.TriangleRenderer,[])});f(b,"set",function(a){try{this.rgb16sW=Array(64);this.rgb16sE=Array(64);for(var d=64;0<=--d;)this.rgb16sW[d]=new JU.Rgb16,this.rgb16sE[d]=new JU.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(d=3;0<=--d;)this.rgb16sGouraud[d]=new JU.Rgb16}catch(b){if(!D(b,Exception))throw b;
}return this},"J.api.JmolRendererInterface,JU.GData");c(b,"reallocRgb16s",function(a,d){var b=Array(d);System.arraycopy(a,0,b,0,a.length);for(var c=a.length;c<d;++c)b[c]=new JU.Rgb16;return b},"~A,~N");c(b,"setGouraud",function(a,d,b){this.rgb16sGouraud[0].setInt(a);this.rgb16sGouraud[1].setInt(d);this.rgb16sGouraud[2].setInt(b)},"~N,~N,~N");c(b,"fillTriangle",function(a,d,b,c){this.ax[0]=a.x;this.ax[1]=d.x;this.ax[2]=b.x;this.ay[0]=a.y;this.ay[1]=d.y;this.ay[2]=b.y;this.az[0]=a.z;this.az[1]=d.z;
this.az[2]=b.z;if(!(1>=this.az[0]||1>=this.az[1]||1>=this.az[2])){d=this.g3d.clipCode3(this.ax[0],this.ay[0],this.az[0]);b=this.g3d.clipCode3(this.ax[1],this.ay[1],this.az[1]);var e=this.g3d.clipCode3(this.ax[2],this.ay[2],this.az[2]),g=d|b|e;a=0!=g;if(!a||!(-1==g||0!=(d&b&e))){e=0;this.ay[1]<this.ay[e]&&(e=1);this.ay[2]<this.ay[e]&&(e=2);var g=(e+1)%3,j=(e+2)%3;if(this.ay[g]>this.ay[j])var k=g,g=j,j=k;d=this.ay[e];var l=this.ay[g],f=this.ay[j];b=f-d+1;if(!(b>3*this.g3d.height)){if(b>this.axW.length){var m=
b+31&-32;this.axW=E(m,0);this.azW=E(m,0);this.axE=E(m,0);this.azE=E(m,0);this.aa=L(m,0);this.bb=L(m,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,m);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,m)}var p;c?(m=this.rgb16sW,p=this.rgb16sE):m=p=null;k=l-d;0==k?(this.ax[g]<this.ax[e]&&(k=g,g=e,e=k),this.generateRaster(b,e,j,this.axW,this.azW,0,m),this.generateRaster(b,g,j,this.axE,this.azE,0,p)):l==f?(this.ax[j]<this.ax[g]&&(k=g,g=j,j=k),this.generateRaster(b,e,g,this.axW,this.azW,0,m),this.generateRaster(b,
e,j,this.axE,this.azE,0,p)):(l=this.ax[j]-this.ax[e],f=JU.GData.roundInt(v(b/2)),0>l&&(f=-f),this.ax[e]+v((l*k+f)/b)<this.ax[g]?(this.generateRaster(b,e,j,this.axW,this.azW,0,m),this.generateRaster(k+1,e,g,this.axE,this.azE,0,p),this.generateRaster(b-k,g,j,this.axE,this.azE,k,p)):(this.generateRaster(k+1,e,g,this.axW,this.azW,0,m),this.generateRaster(b-k,g,j,this.axW,this.azW,k,m),this.generateRaster(b,e,j,this.axE,this.azE,0,p)));this.g3d.setZMargin(5);e=this.g3d.pass2Flag01;g=1-e;j=0;0>d&&(b+=d,
j-=d,d=0);d+b>this.g3d.height&&(b=this.g3d.height-d);if(c)if(a)for(;--b>=e;++d,++j)a=this.axE[j]-(c=this.axW[j])+g,0<a&&this.g3d.plotPixelsClippedRaster(a,c,d,this.azW[j],this.azE[j],this.rgb16sW[j],this.rgb16sE[j]);else for(;--b>=e;++d,++j)a=this.axE[j]-(c=this.axW[j])+g,1==e&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRaster(a,c,d,this.azW[j],this.azE[j],this.rgb16sW[j],this.rgb16sE[j]);else if(a)for(;--b>=e;++d,++j)a=this.axE[j]-(c=this.axW[j])+g,0<a&&this.g3d.plotPixelsClippedRasterBits(a,
c,d,this.azW[j],this.azE[j],null,null,this.aa[j],this.bb[j]);else for(;--b>=e;++d,++j)a=this.axE[j]-(c=this.axW[j])+g,1==e&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRasterBits(a,c,d,null,null,this.aa[j],this.bb[j]);this.g3d.setZMargin(0)}}}},"JU.P3i,JU.P3i,JU.P3i,~B");c(b,"generateRaster",function(a,d,b,c,e,g,j){var k=this.ax[d],l=this.ax[b]-k,f,m,p;0<=l?(f=1,m=l,p=0):(f=-1,m=-l,p=1-a);var x;m<=a?x=0:(x=JU.GData.roundInt(v(l/a)),m%=a);this.setRastAB(this.ay[d],this.az[d],this.ay[b],this.az[b]);
for(var A=this.a,n=this.b,r=c===this.axE,u=0,w=this.ay[d],y=a-1,l=g;u<=y;++l,++u,++w){if(0==l||l>g)c[l]=u==y?this.ax[b]:k,e[l]=this.getZCurrent(A,n,w),r&&(this.setRastAB(this.axW[l],this.azW[l],c[l],e[l]),this.aa[l]=this.a,this.bb[l]=this.b);k+=x;p+=m;0<p&&(k+=f,p-=a)}if(null!=j){c=this.rgb16t1;c.setRgb(this.rgb16sGouraud[d]);d=this.rgb16t2;d.diffDiv(this.rgb16sGouraud[b],c,a);l=g;for(a=g+a;l<a;++l)j[l].setAndIncrement(c,d)}},"~N,~N,~N,~A,~A,~N,~A")});n("J.i18n");z("J.api.Translator java.text.MessageFormat java.util.Hashtable JU.PT J.i18n.Language $.Resource".split(" "),
"J.i18n.GT",["JU.Logger"],function(){var b=r(function(){this.resources=null;this.resourceCount=0;this.doTranslate=!0;this.language=null;u(this,arguments)},J.i18n,"GT",null,J.api.Translator);y(b,function(a,d){this.resources=null;this.resourceCount=0;J.i18n.GT.$getTextWrapper=this;null!=d&&0==d.length&&(d="none");null!=d&&(this.language=d);"none".equals(this.language)&&(this.language=null);null==this.language&&(this.language=J.i18n.Resource.getLanguage());null==this.language&&(this.language="en");var b=
this.language,c=null,e=null,g=this.language.indexOf("_");if(0<=g&&(b=b.substring(0,g),c=this.language,0<=(g=c.indexOf("_",++g))))c=c.substring(0,g),e=this.language;if(null==(this.language=this.getSupported(e))&&null==(this.language=this.getSupported(c))&&null==(this.language=this.getSupported(b)))this.language="en",System.out.println(this.language+" not supported -- using en");else{c=e=null;switch(this.language.length){default:e=this.language;c=this.language.substring(0,5);b=this.language.substring(0,
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this.tickAs.z;0>b&&(b=1);this.vectorT2.set(-this.vectorT2.y,this.vectorT2.x,0);this.vectorT2.scale(d/this.vectorT2.length());d=this.tickInfo.reference;null==d?(this.pointT3.setT(this.vwr.getBoundBoxCenter()),603979809==this.vwr.g.axesMode&&this.pointT3.add3(1,1,1)):this.pointT3.setT(d);this.tm.transformPtScr(this.pointT3,this.pt2i);d=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var f=!d,m=!d&&0>this.vectorT2.x,p=null!=c&&0<c.length,x,A,n=Array(1),r=this.draw000?0:-1;k<j;){if(k>=this.tickInfo.first&&
(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,this.pointT2),this.drawLine(v(Math.floor(this.pointT2.x)),v(Math.floor(this.pointT2.y)),F(l),x=v(Math.floor(this.pointT2.x+this.vectorT2.x)),A=v(Math.floor(this.pointT2.y+this.vectorT2.y)),F(l),b),p&&(this.draw000||0!=k))){n[0]=Float.$valueOf(0==k?0:k*e);var u=JU.PT.sprintf(c[r%c.length],"f",n);this.drawString(x,A,F(l),4,m,d,f,v(Math.floor(this.pointT2.y)),u)}this.pointT.add(this.vectorT);k+=a;l+=g;r++}}}},"~N,~N,~N,~A");c(b,"drawLine",
function(a,d,b,c,e,g,j){return this.drawLine2(this.g3d,a,d,b,c,e,g,j)},"~N,~N,~N,~N,~N,~N,~N");c(b,"drawLine2",function(a,d,b,c,e,g,j,k){this.pt0.set(d,b,c);this.pt1.set(e,g,j);if(this.dotsOrDashes)null!=this.dashDots&&J.render.FontLineShapeRenderer.drawDashedCylinder(a,d,b,c,e,g,j,this.dashDots,this.width,this.colixA,this.colixB,!this.isExport||1==this.mad?this.width:this.mad,this.asLineOnly,this.s1);else{if(0>k)return a.drawDashedLineBits(8,4,this.pt0,this.pt1),1;a.fillCylinderBits(2,k,this.pt0,
this.pt1)}return v((k+1)/2)},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~N");c(b,"drawString",function(a,d,b,c,e,g,j,k,l){if(null!=l){var f=this.font3d.stringWidth(l),m=this.font3d.getAscent();a=e?a-(v(c/2)+2+f):g?a-(v(c/2)+2+v(f/2)):a+(v(c/2)+2);e=d;e=j?e+v(m/2):0==k||k<d?e+m:e-v(c/2);d=b-c-2;1>d&&(d=1);this.g3d.drawString(l,this.font3d,a,e,d,d,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");b.drawDashedCylinder=c(b,"drawDashedCylinder",function(a,d,b,c,e,g,j,k,l,f,m,p,x,A){if(!(null==k||0>l)){var n=k[0];
e-=d;g-=b;j-=c;var r=0,u=k===J.render.FontLineShapeRenderer.ndots,w=u||k===J.render.FontLineShapeRenderer.sixdots;if(w){null==A&&(A=new JU.P3i);var y=(e*e+g*g)/(l*l);u?(n=Math.sqrt(y)/1.5,r=F(n)+2):8>y?k=J.render.FontLineShapeRenderer.twodots:32>y&&(k=J.render.FontLineShapeRenderer.fourdots)}var y=k[1],B=k[2],z=f,C=0==B?m:f;0==r&&(r=k.length);for(var D=0,E=3;E<r;E++){var D=u?D+1:k[E],G=v(Math.floor(d+e*D/n)),I=v(Math.floor(b+g*D/n)),K=v(Math.floor(c+j*D/n));if(w)A.set(G,I,K),E==y?a.setC(f):E==B&&
a.setC(m),a.fillSphereI(l,A);else{E==y&&(z=m);D=k[++E];E==B&&(C=m);var L=v(Math.floor(d+e*D/n)),N=v(Math.floor(b+g*D/n)),O=v(Math.floor(c+j*D/n));J.render.FontLineShapeRenderer.fillCylinder(a,z,C,2,G,I,K,L,N,O,p,x)}}}},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~A,~N,~N,~N,~N,~B,JU.P3i");b.fillCylinder=c(b,"fillCylinder",function(a,d,b,c,e,g,j,k,l,f,m,p){p?a.drawLine(d,b,e,g,j,k,l,f):a.fillCylinderXYZ(d,b,c,m,e,g,j,k,l,f)},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");b.dashes=
E(-1,[12,0,0,2,5,7,10]);b.hDashes=E(-1,[10,7,6,1,3,4,6,7,9]);b.ndots=E(-1,[0,3,1E3]);b.sixdots=E(-1,[12,3,6,1,3,5,7,9,11]);b.fourdots=E(-1,[13,3,5,2,5,8,11]);b.twodots=E(-1,[12,3,4,3,9])});n("J.render");z(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JV.Viewer"],function(){var b=G(J.render,"FrankRenderer",J.render.ShapeRenderer);f(b,"render",function(){var a=this.shape,d=this.vwr.getBooleanProperty("allowKeyStrokes"),b=this.vwr.getBoolean(603983903);this.colix=b?20:this.vwr.isSignedApplet?
d||(JV.Viewer.isJS||JV.Viewer.isSwingJS)&&!this.vwr.isWebGL?5:10:d?7:12;if(this.isExport||!this.vwr.getShowFrank()||!this.g3d.setC(this.colix))return!1;if(this.vwr.frankOn&&!this.vwr.noFrankEcho)return this.vwr.noFrankEcho;this.vwr.noFrankEcho=!0;d=this.vwr.imageFontScaling;a.getFont(d);d=F(a.frankWidth+4*d);this.g3d.drawStringNoSlab(a.frankString,a.font3d,this.vwr.gdata.width-d,this.vwr.gdata.height-a.frankDescent,0,0);a=b?this.vwr.getModelkit(!1):null;b&&!a.isHidden()&&(this.g3d.setC(12),this.g3d.fillTextRect(0,
0,1,0,10,104),b=a.getActiveMenu(),null!=b&&("atomMenu".equals(b)?(this.g3d.setC(21),this.g3d.fillTextRect(0,0,0,0,10,26)):"bondMenu".equals(b)?(this.g3d.setC(7),this.g3d.fillTextRect(0,26,0,0,10,26)):"xtalMenu".equals(b)&&(this.g3d.setC(8),this.g3d.fillTextRect(0,52,0,0,10,26))));return!1})});n("J.render");z(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.api.Interface","JU.Logger","JV.JC","$.Viewer"],function(){var b=r(function(){this.bsTranslucent=this.renderers=this.shapeManager=
this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;u(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);N(b,function(){this.bsTranslucent=JU.BS.newN(37)});y(b,function(){});f(b,"set",function(a,d){this.vwr=a;this.shapeManager=d},"JV.Viewer,JV.ShapeManager");f(b,"isRepaintPending",function(){return this.repaintPending});f(b,"pushHoldRepaint",function(){++this.holdRepaint},"~S");f(b,"popHoldRepaint",function(a,d){null!=d&&d.startsWith("CLEAR HOLD")&&(this.holdRepaint=0,a=
!0);--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(d)))},"~B,~S");f(b,"requestRepaintAndWait",function(a){var d=null;JV.Viewer.isJS&&!JV.Viewer.isSwingJS&&(d=self.Jmol&&Jmol.repaint?Jmol:null);if(null==d)try{this.repaintNow(a),JV.Viewer.isJS||this.wait(this.vwr.g.repaintWaitMs),this.repaintPending&&(JU.Logger.error("repaintManager requestRepaintAndWait timeout"),this.repaintDone())}catch(b){if(D(b,"InterruptedException"))System.out.println("repaintManager requestRepaintAndWait interrupted thread="+
Thread.currentThread().getName());else throw b;}else d.repaint(this.vwr.html5Applet,!1),this.repaintDone()},"~S");f(b,"repaintIfReady",function(a){if(this.repaintPending)return!1;this.repaintPending=!0;0==this.holdRepaint&&this.repaintNow(a);return!0},"~S");c(b,"repaintNow",function(){this.vwr.haveDisplay&&this.vwr.apiPlatform.repaint(this.vwr.display)},"~S");f(b,"repaintDone",function(){this.repaintPending=!1});f(b,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=
0;37>a;++a)this.renderers[a]=null},"~N");c(b,"getRenderer",function(a){if(null!=this.renderers[a])return this.renderers[a];var d=JV.JC.getShapeClassName(a,!0)+"Renderer";if(null==(d=J.api.Interface.getInterface(d,this.vwr,"render")))return null;d.setViewerG3dShapeID(this.vwr,a);return this.renderers[a]=d},"~N");f(b,"render",function(a,d,b,c){null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();try{var e=this.vwr.getBoolean(603979934);a.renderBackground(null);if(b){this.bsTranslucent.clearAll();
null!=c&&a.renderCrossHairs(c,this.vwr.getScreenWidth(),this.vwr.getScreenHeight(),this.vwr.tm.getNavigationOffset(),this.vwr.tm.navigationDepthPercent);var g=this.vwr.getRubberBandSelection();null!=g&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(g.x,g.y,0,0,g.width,g.height);this.vwr.noFrankEcho=!0}c=null;for(g=0;37>g&&a.currentlyRendering;++g){var j=this.shapeManager.getShape(g);null!=j&&(e&&(c="rendering "+JV.JC.getShapeClassName(g,!1),JU.Logger.startTimer(c)),(b||this.bsTranslucent.get(g))&&
this.getRenderer(g).renderShape(a,d,j)&&this.bsTranslucent.set(g),e&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(D(k,Exception)){k.printStackTrace();if(this.vwr.async&&"Interface".equals(k.getMessage()))throw new NullPointerException;JU.Logger.error("rendering error? "+k)}else throw k;}},"JU.GData,JM.ModelSet,~B,~A");c(b,"getAllRenderers",function(){for(var a=!0,d=0;37>d;++d)null==this.shapeManager.getShape(d)||null!=this.getRenderer(d)||(a=this.repaintPending=!this.vwr.async);
if(!a)throw new NullPointerException;});f(b,"renderExport",function(a,d,b){this.shapeManager.finalizeAtoms(null,!0);a=this.vwr.initializeExporter(b);if(null==a)return JU.Logger.error("Cannot export "+b.get("type")),null;null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();b=null;try{var c=this.vwr.getBoolean(603979934);a.renderBackground(a);for(var e=0;37>e;++e){var g=this.shapeManager.getShape(e);null!=g&&(c&&(b="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(b)),
this.getRenderer(e).renderShape(a,d,g),c&&JU.Logger.checkTimer(b,!1))}a.renderAllStrings(a);b=a.finalizeOutput()}catch(j){if(D(j,Exception))j.printStackTrace(),JU.Logger.error("rendering error? "+j);else throw j;}return b},"JU.GData,JM.ModelSet,java.util.Map")});n("J.render");z(null,"J.render.ShapeRenderer",["JV.JC"],function(){var b=r(function(){this.shape=this.ms=this.g3d=this.tm=this.vwr=null;this.exportType=this.mad=this.colix=this.shapeID=this.myVisibilityFlag=0;this.isExport=!1;u(this,arguments)},
J.render,"ShapeRenderer",null);c(b,"initRenderer",function(){});c(b,"setViewerG3dShapeID",function(a,d){this.vwr=a;this.tm=a.tm;this.shapeID=d;this.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(d);this.initRenderer()},"JV.Viewer,~N");c(b,"renderShape",function(a,d,b){this.setup(a,d,b);a=this.render();this.exportType=0;this.isExport=!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(b,"setup",function(a,d,b){this.g3d=a;this.ms=d;this.shape=b;this.exportType=a.getExportType();this.isExport=
0!=this.exportType},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(b,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});n("J.render");z(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["JU.A4","$.M3","J.c.PAL","JU.C","$.Edge"],function(){var b=r(function(){this.showMultipleBonds=!1;this.multipleBondRadiusFactor=this.multipleBondSpacing=0;this.useBananas=this.bondsPerp=!1;this.modeMultipleBond=0;this.isCartesian=!1;
this.endcaps=0;this.hbondsSolid=this.bondsBackbone=this.hbondsBackbone=this.ssbondsBackbone=!1;this.bond=this.b=this.a=null;this.bondOrder=this.mag2d=this.dy=this.dx=this.zB=this.yB=this.xB=this.zA=this.yA=this.xA=0;this.slabByAtom=this.slabbing=this.isAntialiased=this.wireframeOnly=!1;this.bsForPass2=this.p2=this.p1=this.z=this.y=this.x=null;this.isPass2=!1;this.dyStep=this.dxStep=this.yAxis2=this.xAxis2=this.yAxis1=this.xAxis1=0;this.a4=this.rot=null;u(this,arguments)},J.render,"SticksRenderer",
J.render.FontLineShapeRenderer);N(b,function(){this.x=new JU.V3;this.y=new JU.V3;this.z=new JU.V3;this.p1=new JU.P3;this.p2=new JU.P3;this.bsForPass2=JU.BS.newN(64)});f(b,"render",function(){var a=this.ms.bo;if(null==a)return!1;(this.isPass2=this.vwr.gdata.isPass2)||this.bsForPass2.clearAll();this.slabbing=this.tm.slabEnabled;this.slabByAtom=this.vwr.getBoolean(603979939);this.endcaps=3;this.dashDots=this.vwr.getBoolean(603979893)?J.render.FontLineShapeRenderer.sixdots:J.render.FontLineShapeRenderer.dashes;
this.isCartesian=1==this.exportType;this.getMultipleBondSettings(!1);this.wireframeOnly=!this.vwr.checkMotionRendering(1677721602);this.ssbondsBackbone=this.vwr.getBoolean(603979952);this.hbondsBackbone=this.vwr.getBoolean(603979852);this.bondsBackbone=(new Boolean(this.hbondsBackbone|this.ssbondsBackbone)).valueOf();this.hbondsSolid=this.vwr.getBoolean(603979854);this.isAntialiased=this.g3d.isAntialiased();var d=!1;if(this.isPass2){if(!this.isExport)for(var b=this.bsForPass2.nextSetBit(0);0<=b;b=
this.bsForPass2.nextSetBit(b+1))this.bond=a[b],this.renderBond()}else for(b=this.ms.bondCount;0<=--b;)this.bond=a[b],0!=(this.bond.shapeVisibilityFlags&this.myVisibilityFlag)&&this.renderBond()&&(d=!0,this.bsForPass2.set(b));return d});c(b,"getMultipleBondSettings",function(a){this.useBananas=this.vwr.getBoolean(603979886)&&!a;this.multipleBondSpacing=a?0.15:this.vwr.getFloat(570425370);this.multipleBondRadiusFactor=a?0.4:this.vwr.getFloat(570425369);this.bondsPerp=this.useBananas||0<this.multipleBondSpacing&&
0>this.multipleBondRadiusFactor;this.useBananas&&(this.multipleBondSpacing=0>this.multipleBondSpacing?0.4*-this.multipleBondSpacing:this.multipleBondSpacing);this.multipleBondRadiusFactor=Math.abs(this.multipleBondRadiusFactor);0==this.multipleBondSpacing&&this.isCartesian&&(this.multipleBondSpacing=0.2);this.modeMultipleBond=this.vwr.g.modeMultipleBond;this.showMultipleBonds=0!=this.multipleBondSpacing&&0!=this.modeMultipleBond&&this.vwr.getBoolean(603979928)},"~B");c(b,"renderBond",function(){var a,
d;this.a=a=this.bond.atom1;this.b=d=this.bond.atom2;var b=this.bond.order&131071;this.bondsBackbone&&(this.ssbondsBackbone&&0!=(b&256)?(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.getLeadAtomOr(this.b)):this.hbondsBackbone&&JU.Edge.isOrderH(b)&&(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.getLeadAtomOr(this.b)));if(!this.isPass2&&(!this.a.isVisible(9)||!this.b.isVisible(9)||!this.g3d.isInDisplayRange(this.a.sX,this.a.sY)||!this.g3d.isInDisplayRange(this.b.sX,this.b.sY)))return!1;
if(this.slabbing){var c=this.vwr.gdata.isClippedZ(this.a.sZ);if(c&&this.vwr.gdata.isClippedZ(this.b.sZ)||this.slabByAtom&&(c||this.vwr.gdata.isClippedZ(this.b.sZ)))return!1}this.zA=this.a.sZ;this.zB=this.b.sZ;if(1==this.zA||1==this.zB)return!1;this.colixA=a.colixAtom;this.colixB=d.colixAtom;2==((this.colix=this.bond.colix)&-30721)?(this.colix&=30720,this.colixA=JU.C.getColixInherited(this.colix|this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id),this.colixA),this.colixB=JU.C.getColixInherited(this.colix|
this.vwr.cm.getColixAtomPalette(d,J.c.PAL.CPK.id),this.colixB)):(this.colixA=JU.C.getColixInherited(this.colix,this.colixA),this.colixB=JU.C.getColixInherited(this.colix,this.colixB));a=!1;if(!this.isExport&&!this.isPass2&&(d=!JU.C.renderPass2(this.colixA),c=!JU.C.renderPass2(this.colixB),!d||!c)){if(!d&&!c&&!a)return this.g3d.setC(!d?this.colixA:this.colixB),!0;a=!0}this.bondOrder=b&131071;if(0==(this.bondOrder&224)&&(0!=(this.bondOrder&256)&&(this.bondOrder&=-257),0!=(this.bondOrder&1023)&&(!this.showMultipleBonds||
2==this.modeMultipleBond&&500<this.mad||65536==(this.bondOrder&98304))))this.bondOrder=1;d=0;switch(this.bondOrder){case 1025:case 1041:case 1057:this.bondOrder=1;case 1:case 2:case 3:case 4:case 5:case 6:break;case 17:case 513:this.bondOrder=1;d=513==b?0:1;break;case 515:case 514:this.bondOrder=2;d=515==b?this.getAromaticDottedBondMask():0;break;default:0!=(this.bondOrder&224)?(this.bondOrder=JU.Edge.getPartialBondOrder(b),d=JU.Edge.getPartialBondDotted(b)):JU.Edge.isOrderH(this.bondOrder)?(this.bondOrder=
1,this.hbondsSolid||(d=-1)):32768==this.bondOrder?this.bondOrder=1:98304==(this.bondOrder&98304)&&(this.getMultipleBondSettings(!0),this.bondOrder&=3,d=-2)}this.xA=this.a.sX;this.yA=this.a.sY;this.xB=this.b.sX;this.yB=this.b.sY;this.mad=this.bond.mad;0<this.multipleBondRadiusFactor&&1<this.bondOrder&&(this.mad*=this.multipleBondRadiusFactor);this.dx=this.xB-this.xA;this.dy=this.yB-this.yA;this.width=F(this.vwr.tm.scaleToScreen(v((this.zA+this.zB)/2),this.mad));this.wireframeOnly&&0<this.width&&(this.width=
1);if(!this.isCartesian&&(this.asLineOnly=1>=this.width)&&this.isAntialiased)this.width=3,this.asLineOnly=!1;b=!this.isExport||1==this.mad?this.width:this.mad;switch(d){case -2:this.drawBond(0);this.getMultipleBondSettings(!1);break;case -1:J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,J.render.FontLineShapeRenderer.hDashes,this.width,this.colixA,this.colixB,b,this.asLineOnly,this.s1);break;default:switch(this.bondOrder){case 4:this.bondOrder=
2;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=v(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.3);this.drawBond(d);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.drawBond(d>>2);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;case 5:this.bondOrder=3;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=v(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.2);this.drawBond(d);this.bondsPerp=!this.bondsPerp;
this.bondOrder=2;this.multipleBondSpacing*=1.5;this.drawBond(d>>3);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;case 6:this.bondOrder=4;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=v(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.15);this.drawBond(d);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.multipleBondSpacing*=1.5;this.drawBond(d>>4);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;default:this.drawBond(d)}}return a});
c(b,"drawBond",function(a){var d=0!=(a&1),b=16384==(this.colixA&30720)||16384==(this.colixB&30720)?2:this.endcaps;if(this.isCartesian&&1==this.bondOrder&&!d)this.g3d.drawBond(this.a,this.b,this.colixA,this.colixB,b,this.mad,-1);else{var c=0==this.dx&&0==this.dy;if(!c||!this.asLineOnly||this.isCartesian){var e=!this.isExport||1==this.mad?this.width:this.mad,g=1<this.bondOrder&&0<this.multipleBondSpacing,j=g&&(null!=this.vwr.getHybridizationAndAxes(this.a.i,this.z,this.x,"pz")||null!=this.vwr.getHybridizationAndAxes(this.b.i,
this.z,this.x,"pz"))&&!Float.isNaN(this.x.x);if(c&&!g){a=v(this.width/8)+3;a=this.width+a;d=this.yA-v((this.bondOrder-1)*a/2);do J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xA,d,this.zA,this.xB,d,this.zB,e,this.asLineOnly),d+=a;while(0<--this.bondOrder)}else if(1==this.bondOrder)d?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,this.dashDots,this.width,this.colixA,this.colixB,e,this.asLineOnly,this.s1):
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JS.SV.getVariableAF(b):1>d||d>j?JS.SV.newV(4,""):JS.SV.newV(3,Float.$valueOf(b[d-1]))}0>=e&&(e=j+e);g||(1>e&&(e=1),0==d?d=j:0>d&&(d=j+d),d<e&&(d=e));switch(a.tok){case 10:l.value=b;if(k){1<e&&b.clearAll();break}if(g){e==j?d=b.length()-1:1==e&&(d=b.nextSetBit(0));if(-1<=d){b.clearAll();0<=d&&b.set(d);break}d=e}j=0;for(g=b.nextSetBit(0);0<=g;g=b.nextSetBit(g+1))(++j<e||j>d)&&b.clear(g);break;case 4:l.value=0>--e||e>=j?"":g?c.substring(e,e+1):c.substring(e,Math.min(d,j));break;case 7:if(0>--e||e>=j)return JS.SV.newV(4,
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b.isLike=c(b,"isLike",function(a,d){return null!=a&&null!=d&&4==a.tok&&4==d.tok&&JU.PT.isLike(a.value,d.value)},"JS.SV,JS.SV");c(b,"sortOrReverse",function(a){var d=this.getList();if(null!=d&&1<d.size())if(-2147483648==a){a=d.size();for(var b=0;b<a;b++){var c=d.get(b);d.set(b,d.get(--a));d.set(a,c)}}else java.util.Collections.sort(this.getList(),Y(JS.SV.Sort,this,null,--a,null));return this},"~N");c(b,"pushPop",function(a,d){if(null==a){if(4==this.tok){if(null==d){var b=this.value,c=b.length-1;if(0>
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j.length+")"),System.exit(1));e=a.length;for(g=0;g<e;g++)h=a[g],q=h.toLowerCase(),d=j[g],d=b=-1==d?b:JS.T.o(d,h),null!=JS.T.tokenMap.get(q)&&JU.Logger.error("duplicate token definition:"+q),JS.T.tokenMap.put(q,d);j=a=null});n("J.shape");z(["J.shape.Shape"],"J.shape.AtomShape","JU.AU $.BS J.atomdata.RadiusData J.c.PAL $.VDW JU.BSUtil $.C".split(" "),function(){var b=r(function(){this.mad=-1;this.paletteIDs=this.colixes=this.mads=null;this.isActive=!1;this.rd=null;this.isSet=!1;this.monomerCount=0;
this.bsSizeDefault=null;u(this,arguments)},J.shape,"AtomShape",J.shape.Shape);f(b,"initShape",function(){});f(b,"initModelSet",function(){this.isSet=!0;var a=this.ms.ac;null!=this.mads&&(this.mads=JU.AU.arrayCopyShort(this.mads,a));null!=this.colixes&&(this.colixes=JU.AU.arrayCopyShort(this.colixes,a));null!=this.paletteIDs&&(this.paletteIDs=JU.AU.arrayCopyByte(this.paletteIDs,a))});f(b,"getSize",function(a){return null==this.mads?0:this.mads[a]},"~N");f(b,"setSize",function(a,d){this.setSize2(a,
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a,b)}},"J.atomdata.RadiusData,JU.BS");c(b,"setSizeRD2",function(a,d,b){var c=this.ms.at[a];this.mads[a]=c.calculateMad(this.vwr,d);this.bsSizeSet.setBitTo(a,b);c.setShapeVisibility(this.vf,b)},"~N,J.atomdata.RadiusData,~B");c(b,"setPropAS",function(a,d,b){if("color"===a){this.isActive=!0;var c=JU.C.getColixO(d),e=J.c.PAL.pidOf(d);d=this.checkColixLength(c,b.length());for(a=b.nextSetBit(0);0<=a&&a<d;a=b.nextSetBit(a+1))this.setColixAndPalette(c,e,a)}else if("params"===a){this.isActive=!0;var e=d[0],
g=d[1],j=d[2],k=new J.atomdata.RadiusData(null,0,J.atomdata.RadiusData.EnumType.FACTOR,J.c.VDW.AUTO);null==this.bsColixSet&&(this.bsColixSet=new JU.BS);null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS);a=b.nextSetBit(0);null==this.mads&&0<=a&&(this.mads=U(this.ms.ac,0));d=this.checkColixLength(null==e?0:4,b.length());for(var l=0;0<=a&&a<d;a=b.nextSetBit(a+1),l++){var c=null==e?0:e[l],f=null==g?0:g[l];0.01<f&&(c=JU.C.getColixTranslucent3(c,!0,f));this.setColixAndPalette(c,J.c.PAL.UNKNOWN.id,a);null!=
j&&(c=0<(k.value=j[l]),this.setSizeRD2(a,k,c))}}else if("translucency"===a){this.isActive=!0;d=d.equals("translucent");this.checkColixLength(4,this.ms.ac);for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1))this.colixes[a]=JU.C.getColixTranslucent3(this.colixes[a],d,this.translucentLevel),d&&this.bsColixSet.set(a)}else"deleteModelAtoms"===a?(a=d[2],d=a[1],a=a[2],this.mads=JU.AU.deleteElements(this.mads,d,a),this.colixes=JU.AU.deleteElements(this.colixes,d,a),this.paletteIDs=JU.AU.deleteElements(this.paletteIDs,
d,a),JU.BSUtil.deleteBits(this.bsSizeSet,b),JU.BSUtil.deleteBits(this.bsColixSet,b)):this.setPropS(a,d,b)},"~S,~O,JU.BS");c(b,"checkColixLength",function(a,d){d=Math.min(this.ms.ac,d);if(0==a)return null==this.colixes?0:this.colixes.length;if(null==this.colixes||d>this.colixes.length)this.colixes=JU.AU.ensureLengthShort(this.colixes,d),this.paletteIDs=JU.AU.ensureLengthByte(this.paletteIDs,d);null==this.bsColixSet&&(this.bsColixSet=JU.BS.newN(this.ms.ac));return d},"~N,~N");c(b,"setColixAndPalette",
function(a,d,b){null==this.colixes&&this.checkColixLength(-1,this.ms.ac);this.colixes[b]=a=this.getColixI(a,d,b);this.bsColixSet.setBitTo(b,0!=a||0==this.shapeID);this.paletteIDs[b]=d},"~N,~N,~N");f(b,"setAtomClickability",function(){if(this.isActive)for(var a=this.ms.at,d=this.ms.ac;0<=--d;){var b=a[d];null==b||(0==(b.shapeVisibilityFlags&this.vf)||this.ms.isAtomHidden(d))||b.setClickable(this.vf)}});f(b,"getShapeState",function(){return null})});n("J.shape");z(["J.shape.AtomShape"],"J.shape.Balls",
["JU.BS","J.c.PAL","JU.C"],function(){var b=G(J.shape,"Balls",J.shape.AtomShape);f(b,"setSize",function(a,d){2147483647==a?(this.isActive=!0,null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS),this.bsSizeSet.or(d)):this.setSize2(a,d)},"~N,JU.BS");f(b,"setSizeRD",function(a,d){this.isActive=!0;null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS);for(var b=Math.min(this.ms.at.length,d.length()),c=d.nextSetBit(0);0<=c&&c<b;c=d.nextSetBit(c+1))this.ms.at[c].setMadAtom(this.vwr,a),this.bsSizeSet.set(c)},"J.atomdata.RadiusData,JU.BS");
f(b,"setProperty",function(a,d,b){if("color"===a){var c=JU.C.getColixO(d);0==c&&(c=2);null==this.bsColixSet&&(this.bsColixSet=new JU.BS);var e=J.c.PAL.pidOf(d);for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1)){var g=this.ms.at[a];g.colixAtom=this.getColixA(c,e,g);this.bsColixSet.setBitTo(a,2!=c||e!=J.c.PAL.NONE.id);g.paletteID=e}this.vwr.setModelkitPropertySafely("key",b)}else if("colorValues"===a){if(0!=d.length){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);var j=0,e=null;for(a=b.nextSetBit(0);0<=
a&&!(j>=d.length);a=b.nextSetBit(a+1))e=Integer.$valueOf(d[j++]),c=JU.C.getColixO(e),0==c&&(c=2),e=J.c.PAL.pidOf(e),g=this.ms.at[a],g.colixAtom=this.getColixA(c,e,g),this.bsColixSet.setBitTo(a,2!=c||e!=J.c.PAL.NONE.id),g.paletteID=e}}else if("colors"===a){j=d[0];null==this.bsColixSet&&(this.bsColixSet=new JU.BS);d=this.ms.at;for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1))if(!(a>=j.length||0==(c=j[a])))d[a].colixAtom=c,d[a].paletteID=J.c.PAL.UNKNOWN.id,this.bsColixSet.set(a)}else if("translucency"===
a){c=d.equals("translucent");null==this.bsColixSet&&(this.bsColixSet=new JU.BS);d=this.ms.at;for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1))d[a].setTranslucent(c,this.translucentLevel),c&&this.bsColixSet.set(a)}else a.startsWith("ball")&&(a=a.substring(4).intern()),this.setPropAS(a,d,b)},"~S,~O,JU.BS");f(b,"setAtomClickability",function(){for(var a=this.vwr.slm.bsDeleted,d=this.ms.ac;0<=--d;){var b=this.ms.at[d];null!=b&&(b.setClickable(0),null!=a&&a.get(d)||(0==(b.shapeVisibilityFlags&this.vf)||
this.ms.isAtomHidden(d))||b.setClickable(this.vf))}})});n("J.shape");z(["J.shape.Shape"],"J.shape.FontLineShape",null,function(){var b=r(function(){this.font3d=this.tickInfos=null;u(this,arguments)},J.shape,"FontLineShape",J.shape.Shape);N(b,function(){this.tickInfos=Array(4)});f(b,"initShape",function(){this.translucentAllowed=!1});c(b,"setPropFLS",function(a,d){if("tickInfo"===a){var b=d;if(null==b.ticks){if(b.type.equals(" ")){this.tickInfos[0]=this.tickInfos[1]=this.tickInfos[2]=this.tickInfos[3]=
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function(){this.myType="frank";this.baseFont3d=this.font3d=this.vwr.gdata.getFont3DFSS("SansSerif","Plain",16);this.calcMetrics()});f(b,"setProperty",function(a,d){"font"===a&&10<=d.fontSize&&(this.baseFont3d=d,this.scaling=0)},"~S,~O,JU.BS");f(b,"wasClicked",function(a,d){var b=this.vwr.getScreenWidth(),c=this.vwr.getScreenHeight();return 0<b&&0<c&&a>b-this.frankWidth-4&&d>c-this.frankAscent-4},"~N,~N");f(b,"checkObjectHovered",function(a,d){if(!this.vwr.getShowFrank()||!this.wasClicked(a,d)||!this.vwr.menuEnabled())return!1;
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new JU.BS);for(var b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,d);b.hasNext();)this.bsSizeSet.set(b.nextIndex()),b.next().setMad(a)}},"~N,JU.BS");f(b,"setProperty",function(a,d,b){if("type"===a)this.myMask=d.intValue();else if("reportAll"===a)this.reportAll=!0;else if("reset"===a)this.selectedBonds=this.bsColixSet=this.bsSizeSet=this.bsOrderSet=null;else if("bondOrder"===a){null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS);a=d.intValue();
for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(65535,b);b.hasNext();)this.bsOrderSet.set(b.nextIndex()),b.next().setOrder(a)}else if("color"===a)if(null==this.bsColixSet&&(this.bsColixSet=new JU.BS),a=JU.C.getColixO(d),d=C(d,"J.c.PAL")?d:null,d===J.c.PAL.TYPE||d===J.c.PAL.ENERGY){var c=d===J.c.PAL.ENERGY;for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,b);b.hasNext();){this.bsColixSet.set(b.nextIndex());
var e=b.next();e.colix=c?this.getColixB(a,d.id,e):JU.C.getColix(JU.Edge.getArgbHbondType(e.order))}}else{if(!(2==a&&d!==J.c.PAL.CPK))for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,b);b.hasNext();)d=b.nextIndex(),b.next().colix=a,this.bsColixSet.setBitTo(d,0!=a&&2!=a)}else if("translucency"===a){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);a=d.equals("translucent");for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):
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this.triggered&&(this.triggered=!1,this.$name.equals("_SET_IN_MOTION_")?this.vwr.checkInMotion(2):this.vwr.evalStringQuiet(a?this.script+';\ntimeout ID "'+this.$name+'";':this.script));a=a?0:-2;break;case -2:this.vwr.timeouts.remove(this.$name);return}},"~N");b.clear=c(b,"clear",function(a){for(var d,b=a.values().iterator();b.hasNext()&&((d=b.next())||1);){var c=d;c.script.equals("exitJmol")||c.interrupt()}a.clear()},"java.util.Map");b.setTimeout=c(b,"setTimeout",function(a,d,b,c,e){var g=d.get(b);
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this.bonds[c];for(;c<d;++c)b[c]=this.bonds[c+1];this.bonds=b}},"~N");f(b,"getBondedAtomIndex",function(a){return this.bonds[a].getOtherAtom(this).i},"~N");c(b,"setMadAtom",function(a,d){this.madAtom=this.calculateMad(a,d)},"JV.Viewer,J.atomdata.RadiusData");c(b,"calculateMad",function(a,d){if(null==d)return 0;var b=d.value;if(0==b)return 0;switch(d.factorType){case J.atomdata.RadiusData.EnumType.SCREEN:return sa(b);case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:var c=
0;switch(d.vdwType){case J.c.VDW.TEMP:c=a.ms.getBfactor100Hi();c=0<c?this.getBfactor100()/c:0;break;case J.c.VDW.HYDRO:c=Math.abs(this.getHydrophobicity());break;case J.c.VDW.BONDING:c=this.getBondingRadius();break;case J.c.VDW.ADPMIN:case J.c.VDW.ADPMAX:c=this.getADPMinMax(d.vdwType===J.c.VDW.ADPMAX);break;default:c=this.getVanderwaalsRadiusFloat(a,d.vdwType)}b=d.factorType===J.atomdata.RadiusData.EnumType.FACTOR?b*c:b+c;break;case J.atomdata.RadiusData.EnumType.ABSOLUTE:if(16.1==b)return JM.Atom.MAD_GLOBAL}c=
sa(0>b?b:2E3*b);0>c&&0<b&&(c=0);return c},"JV.Viewer,J.atomdata.RadiusData");c(b,"getADPMinMax",function(a){var d=this.getTensors();if(null==d)return 0;var b=d[0];if(null==b||1!=b.iType)return 0;this.group.chain.model.ms.isModulated(this.i)&&b.isUnmodulated&&(b=d[1]);return b.getFactoredValue(a?2:1)},"~B");c(b,"getTensors",function(){return this.group.chain.model.ms.getAtomTensorList(this.i)});c(b,"getRasMolRadius",function(){return Math.abs(v(this.madAtom/8))});f(b,"getEdges",function(){return null==
this.bonds?[]:this.bonds});f(b,"getBondCount",function(){return null==this.bonds?0:this.bonds.length});c(b,"setTranslucent",function(a,d){this.colixAtom=JU.C.getColixTranslucent3(this.colixAtom,a,d)},"~B,~N");f(b,"getElementNumber",function(){return JU.Elements.getElementNumber(this.atomNumberFlags)});f(b,"getIsotopeNumber",function(){return JU.Elements.getIsotopeNumber(this.atomNumberFlags)});f(b,"getAtomicAndIsotopeNumber",function(){return this.atomNumberFlags});c(b,"setAtomicAndIsotopeNumber",
function(a){if(0>a||(a&127)>=JU.Elements.elementNumberMax||32767<a)a=0;this.atomNumberFlags=a},"~N");c(b,"getElementSymbolIso",function(a){return JU.Elements.elementSymbolFromNumber(a?this.atomNumberFlags:this.atomNumberFlags&127)},"~B");c(b,"getElementSymbol",function(){return this.getElementSymbolIso(!0)});c(b,"isHetero",function(){return 0!=(this.formalChargeAndFlags&2)});c(b,"hasVibration",function(){return 0!=(this.formalChargeAndFlags&1)});c(b,"setFormalCharge",function(a){this.formalChargeAndFlags=
this.formalChargeAndFlags&15|(-2147483648==a?0:7<a?7:-3>a?-3:a)<<24},"~N");c(b,"setVibrationVector",function(){this.formalChargeAndFlags|=1});f(b,"getFormalCharge",function(){return this.formalChargeAndFlags>>24});c(b,"getOccupancy100",function(){var a=this.group.chain.model.ms.occupancies;return null==a?100:Math.round(a[this.i])});c(b,"isOccupied",function(){var a=this.group.chain.model.ms.occupancies;return null==a||50<=a[this.i]});c(b,"getBfactor100",function(){var a=this.group.chain.model.ms.bfactor100s;
return null==a?0:a[this.i]});c(b,"getHydrophobicity",function(){var a=this.group.chain.model.ms.hydrophobicities;return null==a?JU.Elements.getHydrophobicity(this.group.groupID):a[this.i]});c(b,"setRadius",function(a){return!Float.isNaN(this.userDefinedVanDerWaalRadius=0<a?a:NaN)},"~N");c(b,"$delete",function(a){this.valence=-1;if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;){var b=this.bonds[d];b.getOtherAtom(this).deleteBond(b);a.set(b.index)}this.bonds=null},"JU.BS");f(b,"isDeleted",function(){return 0>
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this.bonds)return 0;for(var a=0,d=this.bonds.length;0<=--d;){var b=this.bonds[d];b.isCovalentNotPartial0()&&!b.getOtherAtom(this).isDeleted()&&++a}return a});c(b,"getCovalentOrPartialBondCount",function(){if(null==this.bonds)return 0;for(var a=0,d=this.bonds.length;0<=--d;){var b=this.bonds[d];b.isCovalent()&&!b.getOtherAtom(this).isDeleted()&&++a}return a});f(b,"getCovalentHydrogenCount",function(){if(null==this.bonds)return 0;for(var a=0,d=this.bonds.length;0<=--d;)if(this.bonds[d].isCovalentNotPartial0()){var b=
this.bonds[d].getOtherAtom(this);0<=b.valence&&1==b.getElementNumber()&&++a}return a});f(b,"getImplicitHydrogenCount",function(){return this.group.chain.model.ms.getMissingHydrogenCount(this,!1)});f(b,"getTotalHydrogenCount",function(){return this.getCovalentHydrogenCount()+this.getImplicitHydrogenCount()});f(b,"getTotalValence",function(){var a=this.getValence();if(0>a)return a;var d=this.getImplicitHydrogenCount();return a+d+this.group.chain.model.ms.aaRet[4]});f(b,"getCovalentBondCountPlusMissingH",
function(){return this.getCovalentBondCount()+this.getImplicitHydrogenCount()});c(b,"getTargetValence",function(){switch(this.getElementNumber()){case 6:case 14:case 32:return 4;case 5:case 7:case 15:return 3;case 8:case 16:return 2;case 1:case 9:case 17:case 35:case 53:return 1}return-1});c(b,"getDimensionValue",function(a){return 0==a?this.x:1==a?this.y:this.z},"~N");c(b,"getVanderwaalsRadiusFloat",function(a,d){return Float.isNaN(this.userDefinedVanDerWaalRadius)?a.getVanderwaalsMarType(this.atomNumberFlags,
this.getVdwType(d))/1E3:this.userDefinedVanDerWaalRadius},"JV.Viewer,J.c.VDW");c(b,"getVdwType",function(a){switch(a){case J.c.VDW.AUTO:a=this.group.chain.model.ms.getDefaultVdwType(this.mi);break;case J.c.VDW.NOJMOL:a=this.group.chain.model.ms.getDefaultVdwType(this.mi),a===J.c.VDW.AUTO_JMOL&&(a=J.c.VDW.AUTO_BABEL)}return a},"J.c.VDW");c(b,"getBondingRadius",function(){var a=this.group.chain.model.ms.bondingRadii,a=null==a||this.i>=a.length?0:a[this.i];return 0==a?JU.Elements.getBondingRadius(this.atomNumberFlags,
this.getFormalCharge()):a});c(b,"getVolume",function(a,d){var b=null==d?this.userDefinedVanDerWaalRadius:NaN;Float.isNaN(b)&&(b=a.getVanderwaalsMarType(this.getElementNumber(),this.getVdwType(d))/1E3);var c=0;if(null!=this.bonds)for(var e=0;e<this.bonds.length;e++)if(this.bonds[e].isCovalent()){var g=this.bonds[e].getOtherAtom(this),j=null==d?g.userDefinedVanDerWaalRadius:NaN;Float.isNaN(j)&&(j=a.getVanderwaalsMarType(g.getElementNumber(),g.getVdwType(d))/1E3);g=this.distance(g);if(!(g>b+j)){if(g+
b<=j)return 0;j=b-(b*b+g*g-j*j)/(2*g);c-=1.0471975511965976*j*j*(3*b-j)}}return c+4.1887902047863905*b*b*b},"JV.Viewer,J.c.VDW");c(b,"getCurrentBondCount",function(){return null==this.bonds?0:this.bonds.length});c(b,"getRadius",function(){return Math.abs(this.madAtom/2E3)});f(b,"getIndex",function(){return this.i});f(b,"getAtomSite",function(){return this.atomSite});f(b,"getGroupBits",function(a){this.group.setAtomBits(a)},"JU.BS");f(b,"getAtomName",function(){return 0<this.atomID?JM.Group.specialAtomNames[this.atomID]:
null==this.group.chain.model.ms.atomNames?"":this.group.chain.model.ms.atomNames[this.i]});f(b,"getAtomType",function(){var a=this.group.chain.model.ms.atomTypes,a=null==a?null:a[this.i];return null==a?this.getAtomName():a});f(b,"getAtomNumber",function(){var a=this.group.chain.model.ms.atomSerials;return null==a?this.i:a[this.i]});c(b,"getSeqID",function(){var a=this.group.chain.model.ms.atomSeqIDs;return null==a?0:a[this.i]});c(b,"isVisible",function(a){return(this.shapeVisibilityFlags&a)==a},"~N");
c(b,"getPartialCharge",function(){var a=this.group.chain.model.ms.partialCharges;return null==a?0:a[this.i]});c(b,"getSymmetryTranslation",function(a,d,b){for(var c=0;c<d.length;c++)if(this.atomSymmetry.get(a+=b))return d[c];return 0},"~N,~A,~N");c(b,"getCellTranslation",function(a,d,b){for(var c=b,e=0;e<d.length;e++)for(var g=0;g<b;g++,c++)if(this.atomSymmetry.get(c)&&d[e]==a)return d[e];return 0},"~N,~A,~N");c(b,"getSymmetryOperatorList",function(a){var d="",b=this.group.chain.model.ms,c=b.getModelSymmetryCount(this.mi);
if(0==c||null==this.atomSymmetry)return"";for(var b=b.getModelCellRange(this.mi),e=c,g=null==b?1:b.length,j=a?null:new JU.BS,k=0;k<g;k++)for(var l=0;l<c;l++)this.atomSymmetry.get(e++)&&(a?d+=","+(l+1)+b[k]:j.set(l+1));if(!a)for(k=j.nextSetBit(0);0<=k;k=j.nextSetBit(k+1))d+=","+k;return 0==d.length?"":d.substring(1)},"~B");f(b,"getModelIndex",function(){return this.mi});f(b,"getMoleculeNumber",function(a){return this.group.chain.model.ms.getMoleculeIndex(this.i,a)+1},"~B");c(b,"getFractionalCoord",
function(a,d,b,c){c=this.getFractionalCoordPt(a,b,c);return"X"==d?c.x:"Y"==d?c.y:c.z},"~B,~S,~B,JU.P3");f(b,"getXYZ",function(){return this});c(b,"getFractionalCoordPt",function(a,d,b){var c=this.getUnitCell();null==b?b=JU.P3.newP(this):b.setT(this);null!=c&&(c=c.getUnitCellMultiplied(),c.toFractional(b,d),a&&JU.PT.fixPtFloats(b,1E5));return b},"~B,~B,JU.P3");c(b,"getUnitCell",function(){return this.group.chain.model.ms.getUnitCellForAtom(this.i)});c(b,"getFractionalUnitCoord",function(a,d,b){b=this.getFractionalUnitCoordPt(a,
!1,b);return"X"==d?b.x:"Y"==d?b.y:b.z},"~B,~S,JU.P3");c(b,"getFractionalUnitCoordPt",function(a,d,b){var c=this.getUnitCell();null==b?b=JU.P3.newP(this):b.setT(this);if(null==c)return b;c=c.getUnitCellMultiplied();this.group.chain.model.isJmolDataFrame?(c.toFractional(b,!1),d&&c.toCartesian(b,!1)):(c.toUnitCell(b,null),d||c.toFractional(b,!1));a&&JU.PT.fixPtFloats(b,d?1E4:1E5);return b},"~B,~B,JU.P3");c(b,"getFractionalUnitDistance",function(a,d,b){var c=this.getUnitCell();if(null==c)return this.distance(a);
d.setT(this);b.setT(a);this.group.chain.model.isJmolDataFrame?(c.toFractional(d,!0),c.toFractional(b,!0)):(c.toUnitCell(d,null),c.toUnitCell(b,null));return d.distance(b)},"JU.T3,JU.T3,JU.T3");c(b,"setFractionalCoord",function(a,d,b){var c=this.getUnitCell();null!=c&&c.toFractional(this,b);switch(a){case 1111492615:case 1111492612:this.x=d;break;case 1111492616:case 1111492613:this.y=d;break;case 1111492617:case 1111492614:this.z=d}null!=c&&c.toCartesian(this,b)},"~N,~N,~B");c(b,"setFractionalCoordTo",
function(a,d){this.setFractionalCoordPt(this,a,d)},"JU.P3,~B");c(b,"setFractionalCoordPt",function(a,d,b){a.setT(d);d=this.getUnitCell();null!=d&&d.toCartesian(a,b&&!this.group.chain.model.isJmolDataFrame)},"JU.P3,JU.P3,~B");c(b,"isCursorOnTopOf",function(a,d,b,c){var e=v(this.sD/2);e<b&&(e=b);b=e*e;e=this.sX-a;e*=e;if(e>b)return!1;var g=this.sY-d;b-=e+g*g;if(0>b)return!1;if(null==c)return!0;var e=this.sZ,g=c.sZ,j=v(c.sD/2);if(e<g-j)return!0;a=c.sX-a;d=c.sY-d;d=j*j-(a*a+d*d);return e-Math.sqrt(b)<
g-Math.sqrt(d)},"~N,~N,~N,JM.Atom");c(b,"getInfo",function(){return this.getIdentity(2)});c(b,"getIdentityXYZ",function(a,d){a=3==d||this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!this.group.chain.model.ms.vwr.g.legacyJavaFloat,!1,a):this;return(3==d?"":this.getIdentity(d)+" ")+JU.PT.formatF(a.x,0,3,!0,!0)+" "+JU.PT.formatF(a.y,0,3,!0,!0)+" "+JU.PT.formatF(a.z,0,3,!0,!0)},"JU.P3,~N");c(b,"getIdentity",function(a){var d=new JU.SB,b=this.getGroup3(!0);if(null!=b&&0<b.length&&(!b.equals("UNK")||
this.group.chain.model.isBioModel)){d.append("[");d.append(b);d.append("]");b=this.group.getSeqcodeString();null!=b&&d.append(b);b=this.group.chain.chainID;if(0!=b&&32!=b){d.append(":");var c=this.getChainIDStr();256<=b&&(c=JU.PT.esc(c));d.append(c)}if(2!=a&&5!=a)return d.toString();d.append(".")}d.append(this.getAtomName());0==d.length()&&(d.append(this.getElementSymbolIso(!1)),d.append(" "),d.appendI(this.getAtomNumber()));2==a&&("\x00"!=this.altloc&&(d.append("%"),d.appendC(this.altloc)),1<this.group.chain.model.ms.mc&&
!this.group.chain.model.isJmolDataFrame&&(d.append("/"),d.append(this.getModelNumberForLabel())),d.append(" #"),d.appendI(this.getAtomNumber()));return d.toString()},"~N");f(b,"getGroup3",function(a){var d=this.group.getGroup3();return a||null!=d&&0<d.length?d:"UNK"},"~B");f(b,"getGroup1",function(a){var d=this.group.getGroup1();return"\x00"!=d?""+d:"\x00"!=a?""+a:""},"~S");f(b,"getBioSmilesType",function(){return this.group.isProtein()?"p":this.group.isDna()?"d":this.group.isRna()?"r":this.group.isCarbohydrate()?
"c":" "});f(b,"isPurine",function(){return this.group.isPurine()});f(b,"isPyrimidine",function(){return this.group.isPyrimidine()});f(b,"getResno",function(){return this.group.getResno()});c(b,"isClickable",function(){return this.checkVisible()&&0!=this.clickabilityFlags&&0!=((this.shapeVisibilityFlags|this.group.shapeVisibilityFlags)&this.clickabilityFlags)});c(b,"setClickable",function(a){0==a?this.clickabilityFlags=0:(this.clickabilityFlags|=a,1040384!=a&&(this.shapeVisibilityFlags|=a))},"~N");
c(b,"checkVisible",function(){if(this.isVisible(2))return this.isVisible(4);var a=this.isVisible(9);if(a){a=this.shapeVisibilityFlags;if(0!=this.group.shapeVisibilityFlags&&(8192!=this.group.shapeVisibilityFlags||this.isLeadAtom()))a|=this.group.shapeVisibilityFlags;a&=-10;32==a&&0==this.clickabilityFlags&&(a=0);if(a=0!=a)this.shapeVisibilityFlags|=4}this.shapeVisibilityFlags|=2;return a});f(b,"isLeadAtom",function(){return this.group.isLeadAtom(this.i)});f(b,"getChainID",function(){return this.group.chain.chainID});
f(b,"getChainIDStr",function(){return this.group.chain.getIDStr()});c(b,"getSurfaceDistance100",function(){return this.group.chain.model.ms.getSurfaceDistance100(this.i)});c(b,"getVibrationVector",function(){return this.group.chain.model.ms.getVibration(this.i,!1)});c(b,"getModulation",function(){return this.group.chain.model.ms.getModulation(this.i)});c(b,"getModelNumberForLabel",function(){return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi)});c(b,"getModelNumber",function(){return this.group.chain.model.ms.getModelNumber(this.mi)%
1E6});f(b,"getBioStructureTypeName",function(){return this.group.getProteinStructureType().getBioStructureTypeName(!0)});f(b,"equals",function(a){return this===a},"~O");f(b,"hashCode",function(){return this.i});c(b,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var d=this.bonds.length;0<=--d;){var b=this.bonds[d],c=b.getOtherAtom(this);if(b.isAromatic()&&c.i!=a)return c}return null},"~N");c(b,"atomPropertyInt",function(a){switch(a){case 1094715393:return this.getAtomNumber();
case 1094713365:return this.getSeqID();case 1094713346:return this.atomID;case 1094713368:return Math.max(0,this.altloc.charCodeAt(0)-32);case 1094713347:return this.i;case 1228931586:return this.getCovalentBondCount();case 1094713351:return this.group.chain.chainNo;case 1765808134:return this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom);case 1086326789:case 1094715402:return this.getElementNumber();case 1094713353:return this.atomNumberFlags;case 1228935687:return this.group.chain.model.fileIndex+
1;case 1631586315:return this.getFormalCharge();case 1094713356:return this.group.groupID;case 1094713357:return this.group.groupIndex;case 1094717454:return this.getModelNumber();case -1094717454:return this.group.chain.model.ms.modelFileNumbers[this.mi];case 1094713359:return this.mi;case 1094713360:return this.getMoleculeNumber(!0);case 1094713361:return this.group.getMonomerIndex()+1;case 1128269825:return this.getOccupancy100();case 1094713362:return this.group.getBioPolymerIndexInModel()+1;
case 1094713363:return this.group.getBioPolymerLength();case 1665140738:return this.getRasMolRadius();case 1094715412:return this.getResno();case 1094713366:return this.getAtomSite();case 1639976963:return this.group.getProteinStructureType().getId();case 1237320707:return this.group.getProteinStructureSubType().getId();case 1094713367:return this.group.getStrucNo();case 1296041985:return this.getSymOp();case 1094715418:return this.getValence()}return 0},"~N");c(b,"getSymOp",function(){return null==
this.atomSymmetry?0:this.atomSymmetry.nextSetBit(0)+1});c(b,"atomPropertyFloat",function(a,d,b){switch(d){case 1111490561:return this.getADPMinMax(!0);case 1111490562:return this.getADPMinMax(!1);case 1111492609:case 1111492629:return this.x;case 1111492610:case 1111492630:return this.y;case 1111492611:case 1111492631:return this.z;case 1111490587:return this.group.chain.model.ms.getAtomicDSSRData(this.i);case 1114249217:case 1112152066:case 1112150019:case 1112150020:case 1112150021:case 1112152070:case 1112152071:case 1112152073:case 1112152074:case 1112152076:case 1649022989:case 1112152078:return a.shm.getAtomShapeValue(d,
this.group,this.i);case 1111492618:return this.getBondingRadius();case 1111490563:return a.getNMRCalculation().getChemicalShift(this);case 1111490564:return JU.Elements.getCovalentRadius(this.atomNumberFlags);case 1111490565:case 1111490576:case 1111490574:return this.group.getGroupParameter(d);case 1111492615:case 1111492612:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!1,b);case 1111492616:case 1111492613:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,b);case 1111492617:case 1111492614:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"Z",!1,b);case 1113589786:return this.getHydrophobicity();case 1111490566:return a.getNMRCalculation().getMagneticShielding(this);case 1111490567:return this.getMass();case 1128269825:return this.getOccupancy100()/100;case 1111492619:return this.getPartialCharge();case 1111490569:case 1111490570:case 1111490568:if(this.group.chain.model.isJmolDataFrame&&this.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(d){case 1111490569:return this.getFractionalCoord(!a.g.legacyJavaFloat,
"X",!1,b);case 1111490570:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,b);case 1111490568:return a=this.getFractionalCoord(!a.g.legacyJavaFloat,"Z",!1,b)-180,-180>a?360+a:a}return this.group.getGroupParameter(d);case 1665140738:case 1112152075:return this.getRadius();case 1111490571:return a.antialiased?v(this.sX/2):this.sX;case 1111490572:return a.getScreenHeight()-(a.antialiased?v(this.sY/2):this.sY);case 1111490573:return a.antialiased?v(this.sZ/2):this.sZ;case 1113589787:return a.slm.isAtomSelected(this.i)?
1:0;case 1111490575:return a.ms.getSurfaceDistanceMax(),this.getSurfaceDistance100()/100;case 1111492620:return this.getBfactor100()/100;case 1111490577:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"X",b);case 1111490578:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Y",b);case 1111490579:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Z",b);case 1648363544:return this.getVanderwaalsRadiusFloat(a,J.c.VDW.AUTO);case 1648361473:return d=this.getVibrationVector(),null==
d?0:d.length()*a.getFloat(1648361473);case 1111492626:return this.getVib("x");case 1111492627:return this.getVib("y");case 1111492628:return this.getVib("z");case 1111490583:return this.getVib("X");case 1111490584:return this.getVib("Y");case 1111490585:return this.getVib("Z");case 1111490586:return this.getVib("O");case 1111490580:return this.getVib("1");case 1111490581:return this.getVib("2");case 1111490582:return this.getVib("3");case 1312817669:return this.getVolume(a,J.c.VDW.AUTO);case 1145047051:case 1145047053:case 1145045006:case 1145047052:case 1145047055:case 1145045008:case 1145047050:return a=
this.atomPropertyTuple(a,d,b),null==a?-1:a.length()}return this.atomPropertyInt(d)},"JV.Viewer,~N,JU.P3");c(b,"getVib",function(a){return this.group.chain.model.ms.getVibCoord(this.i,a)},"~S");c(b,"getNominalMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getNaturalIsotope(this.getElementNumber())});f(b,"getMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getAtomicMass(this.getElementNumber())});c(b,"atomPropertyString",function(a,d){var b;switch(d){case 1153433601:return this.getIdentity(5);
case 1086324739:return b=this.altloc,"\x00"==b?"":""+b;case 1086326786:return this.getAtomName();case 1086326785:return this.getAtomType();case 1086326788:return this.getChainIDStr();case 1086324752:return this.getCIPChirality(!0);case 1086324753:return this.getCIPChiralityRule();case 1086324754:return this.getWyckoffPosition();case 1086324744:return this.getGroup1("?");case 1086324747:return b=this.group.getSeqcodeString(),null==b?"":b;case 1086324743:return this.getGroup1("\x00");case 1086324742:return this.getGroup3(!1);
case 1086326789:return this.getElementSymbolIso(!0);case 1086324745:return this.getIdentity(2);case 1086324746:return b=this.group.getInsertionCode(),"\x00"==b?"":""+b;case 1825200146:case 1287653388:return b=a.shm.getShapePropertyIndex(5,"label",this.i),null==b&&(b=""),b;case 1639976963:return this.group.getProteinStructureType().getBioStructureTypeName(!1);case 1237320707:return this.group.getProteinStructureSubType().getBioStructureTypeName(!1);case 1086324749:return this.group.getStructureId();
case 1086324748:return a.getHybridizationAndAxes(this.i,null,null,"d");case 1086326798:return this.getElementSymbolIso(!1);case 1088421903:return this.getSymmetryOperatorList(!0)}return""},"JV.Viewer,~N");c(b,"getWyckoffPosition",function(){var a=this.group.chain.model.ms,d=a.getBasisAtom(this.i,!0).getSeqID();if(0!=d)return""+String.fromCharCode(d);var d=this.getUnitCell(),b;if(null==d||null==(b=d.getWyckoffPosition(a.vwr,this,null)))return"?";a.setAtomSeqID(this.i,0+b.charAt(0).charCodeAt(0));return b});
f(b,"getCIPChirality",function(a){var d=(this.formalChargeAndFlags&496)>>4;0==d&&(1<this.atomNumberFlags&&a)&&(d=this.group.chain.model.ms.getAtomCIPChiralityCode(this),this.formalChargeAndFlags|=(0==d?3:d)<<4);return JV.JC.getCIPChiralityName(d)},"~B");c(b,"getCIPChiralityRule",function(){var a=0==this.getCIPChirality(!0).length?-1:(this.formalChargeAndFlags&3584)>>9;return JV.JC.getCIPRuleName(a+1)});f(b,"setCIPChirality",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&-4081|a<<
4},"~N");f(b,"getCIPChiralityCode",function(){return(this.formalChargeAndFlags&496)>>4});f(b,"getInsertionCode",function(){return this.group.getInsertionCode()});c(b,"atomPropertyTuple",function(a,d,b){switch(d){case 1073742329:return JU.P3.newP(this);case 1145047051:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,b);case 1145047053:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,b);case 1145045006:return this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!a.g.legacyJavaFloat,
!1,b):this.getFractionalUnitCoordPt(!a.g.legacyJavaFloat,!1,b);case 1145047052:return JU.P3.new3(a.antialiased?v(this.sX/2):this.sX,a.getScreenHeight()-(a.antialiased?v(this.sY/2):this.sY),a.antialiased?v(this.sZ/2):this.sZ);case 1145047055:return this.getVibrationVector();case 1145045008:return a=this.getModulation(),null==a?null:a.getV3();case 1145047050:return this;case 1765808134:return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom),b)}return null},
"JV.Viewer,~N,JU.P3");f(b,"getOffsetResidueAtom",function(a,d){return this.group.getAtomIndex(a,d)},"~S,~N");f(b,"isCrossLinked",function(a){return this.group.isCrossLinked(a.group)},"JU.Node");f(b,"getCrossLinkVector",function(a,d,b){return this.group.getCrossLinkVector(a,d,b)},"JU.Lst,~B,~B");f(b,"toString",function(){return this.getInfo()});f(b,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");c(b,"getUnitID",function(a){var d=this.group.chain.model;return d.isBioModel?
d.getUnitID(this,a):""},"~N");f(b,"getFloatProperty",function(a){a=this.group.chain.model.ms.vwr.getDataObj(a,null,1);var d=NaN;if(null!=a)try{d=a[this.i]}catch(b){if(!D(b,Exception))throw b;}return d},"~S");f(b,"modelIsRawPDB",function(){var a=this.group.chain.model;return a.isBioModel&&!a.isPdbWithMultipleBonds&&0==a.hydrogenCount});c(b,"setSymop",function(a,d){null==this.atomSymmetry&&(this.atomSymmetry=new JU.BS);d&&this.atomSymmetry.clearAll();0<a&&this.atomSymmetry.set(a-1)},"~N,~B");f(b,"getExplicitHydrogenCount",
function(){return 0});b.MAD_GLOBAL=32200});n("JM");z(["JU.V3"],"JM.AtomCollection","java.util.Arrays $.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.Measure $.P3 $.PT J.api.Interface J.atomdata.RadiusData J.c.PAL $.VDW JM.Group JS.T JU.BSUtil $.Elements $.Logger $.Parser $.Vibration".split(" "),function(){var b=r(function(){this.at=this.bioModelset=this.g3d=this.vwr=null;this.ac=0;this.labeler=this.pointGroup=this.trajectory=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=
!1;this.bfactor100Hi=this.bfactor100Lo=0;this.haveBSClickable=this.haveBSVisible=!1;this.bsSurface=null;this.surfaceDistanceMax=this.nSurfaceAtoms=0;this.haveChirality=!1;this.bspf=null;this.canSkipLoad=this.preserveState=!0;this.haveStraightness=!1;this.aaRet=this.bsPartialCharges=this.hydrophobicities=this.bondingRadii=this.partialCharges=this.bfactor100s=this.occupancies=this.vibrations=this.dssrData=this.atomSeqIDs=this.atomResnos=this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.surfaceDistance100s=
this.atomTensors=this.atomTensorList=this.bsModulated=this.bsClickable=this.bsVisible=this.bsHidden=null;W("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();this.atomCapacity=0;u(this,arguments)},JM,"AtomCollection",null);c(b,"getAtom",function(a){return 0<=a&&a<this.at.length?this.at[a]:null},"~N");c(b,"setupAC",function(){this.bsHidden=new JU.BS;this.bsVisible=new JU.BS;this.bsClickable=new JU.BS;null==JM.AtomCollection.userSettableValues&&(JM.AtomCollection.userSettableValues=
"atomName atomType coord element formalCharge hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals vibrationVector atomNo seqID resNo chain site".$plit(" "))});c(b,"releaseModelSetAC",function(){this.ac=0;this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=this.atomSerials=this.dssrData=this.atomResnos=this.atomTypes=this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=this.bspf=this.g3d=this.vwr=this.at=null;this.resetPartialCharges();this.atomTensors=
this.bondingRadii=null});c(b,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomResnos=a.atomResnos;this.dssrData=a.dssrData;this.atomSerials=a.atomSerials;this.atomSeqIDs=a.atomSeqIDs;this.vibrations=a.vibrations;this.occupancies=a.occupancies;this.bfactor100s=a.bfactor100s;this.bondingRadii=a.bondingRadii;this.partialCharges=a.partialCharges;this.bsPartialCharges=a.bsPartialCharges;this.atomTensors=a.atomTensors;this.atomTensorList=
a.atomTensorList;this.bsModulated=a.bsModulated;this.haveStraightness=!1;this.surfaceDistance100s=null},"JM.AtomCollection");c(b,"getAtomPointVector",function(a){var d=new JU.Lst,b=this.ac;if(null!=a)for(var c=a.nextSetBit(0);0<=c&&c<b;c=a.nextSetBit(c+1))d.addLast(this.at[c]);return d},"JU.BS");c(b,"modelSetHasVibrationVectors",function(){return null!=this.vibrations});c(b,"getAtomTypes",function(){return this.atomTypes});c(b,"getPartialCharges",function(){return this.partialCharges});c(b,"getBondingRadii",
function(){return this.bondingRadii});c(b,"getBFactors",function(){return this.bfactor100s});c(b,"getHydrophobicity",function(){return this.hydrophobicities});c(b,"setBsHidden",function(a){this.bsHidden=a},"JU.BS");c(b,"isAtomHidden",function(a){return this.bsHidden.get(a)},"~N");c(b,"getLabeler",function(){return null==this.labeler?this.labeler=J.api.Interface.getInterface("JM.LabelToken",this.vwr,"ms"):this.labeler});c(b,"getAtomInfo",function(a,d,b){return null==d?this.at[a].getInfo():this.getLabeler().formatLabel(this.vwr,
this.at[a],d,b)},"~N,~S,JU.P3");c(b,"getElementName",function(a){return JU.Elements.elementNameFromNumber(this.at[a].getAtomicAndIsotopeNumber())},"~N");c(b,"getQuaternion",function(a,d){return 0>a?null:this.at[a].group.getQuaternion(d)},"~N,~S");c(b,"getFirstAtomIndexFromAtomNumber",function(a,d){for(var b=0;b<this.ac;b++){var c=this.at[b];if(!JM.AtomCollection.isDeleted(c)&&c.getAtomNumber()==a&&d.get(c.mi))return b}return-1},"~N,JU.BS");c(b,"setFormalCharges",function(a,d){if(null!=a){this.resetPartialCharges();
for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.at[b].setFormalCharge(d),this.taintAtom(b,4)}},"JU.BS,~N");c(b,"getAtomicCharges",function(){for(var a=L(this.ac,0),d=this.ac;0<=--d;)a[d]=JM.AtomCollection.isDeleted(this.at[d])?0:this.at[d].getElementNumber();return a});c(b,"getRadiusVdwJmol",function(a){return JU.Elements.getVanderwaalsMar(a.getElementNumber(),J.c.VDW.JMOL)/1E3},"JM.Atom");c(b,"getMaxVanderwaalsRadius",function(){1.4E-45==this.maxVanderwaalsRadius&&this.findMaxRadii();return this.maxVanderwaalsRadius});
c(b,"findMaxRadii",function(){for(var a,d=this.ac;0<=--d;){var b=this.at[d];if(!JM.AtomCollection.isDeleted(b)){if((a=b.getBondingRadius())>this.maxBondingRadius)this.maxBondingRadius=a;if((a=b.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO))>this.maxVanderwaalsRadius)this.maxVanderwaalsRadius=a}}});c(b,"clearBfactorRange",function(){this.hasBfactorRange=!1});c(b,"calcBfactorRange",function(a){if(!this.hasBfactorRange){this.bfactor100Lo=2147483647;this.bfactor100Hi=-2147483648;if(null==a)for(var d=
0;d<this.ac;d++)this.setBf(d);else for(d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.setBf(d);this.hasBfactorRange=!0}},"JU.BS");c(b,"setBf",function(a){JM.AtomCollection.isDeleted(this.at[a])||(a=this.at[a].getBfactor100(),a<this.bfactor100Lo?this.bfactor100Lo=a:a>this.bfactor100Hi&&(this.bfactor100Hi=a))},"~N");c(b,"getBfactor100Lo",function(){this.hasBfactorRange||(this.vwr.g.rangeSelected?this.calcBfactorRange(this.vwr.bsA()):this.calcBfactorRange(null));return this.bfactor100Lo});c(b,"getBfactor100Hi",
function(){this.getBfactor100Lo();return this.bfactor100Hi});c(b,"getSurfaceDistanceMax",function(){null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistanceMax});c(b,"calculateVolume",function(a,d){var b=0;if(null!=a)for(var c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))b+=this.at[c].getVolume(this.vwr,d);return b},"JU.BS,J.c.VDW");c(b,"getSurfaceDistance100",function(a){if(0==this.nSurfaceAtoms)return-1;null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistance100s[a]},
"~N");c(b,"calcSurfaceDistances",function(){this.calculateSurface(null,-1)});c(b,"calculateSurface",function(a,d){0>d&&(d=3);var b=J.api.Interface.getOption("geodesic.EnvelopeCalculation",this.vwr,"ms").set(this.vwr,this.ac,null);b.calculate(new J.atomdata.RadiusData(null,d,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,JU.BSUtil.copyInvert(a,this.ac),!1,!1,!1,!0);var c=b.getPoints();this.surfaceDistanceMax=0;this.bsSurface=b.getBsSurfaceClone();this.surfaceDistance100s=E(this.ac,0);
this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var b=3.4028235E38==d?0:d,e=0;e<this.ac;e++)if(this.bsSurface.get(e)||JM.AtomCollection.isDeleted(this.at[e]))this.surfaceDistance100s[e]=0;else{for(var g=3.4028235E38,j=this.at[e],k=c.length;0<=--k;)g=Math.min(Math.abs(c[k].distance(j)-b),g);g=this.surfaceDistance100s[e]=v(Math.floor(100*g));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,g)}return c},"JU.BS,~N");c(b,"setAtomCoord2",
function(a,d,b){var c=null,e=null,g=null,j=0,k=1;if(C(b,"JU.P3"))c=b;else if(C(b,"JU.Lst")){g=b;if(0==(k=g.size()))return;j=1}else if(JU.AU.isAP(b)){e=b;if(0==(k=e.length))return;j=2}else return;b=0;if(null!=a)for(var l=a.nextSetBit(0);0<=l;l=a.nextSetBit(l+1)){switch(j){case 1:if(b>=k)return;c=g.get(b++);break;case 2:if(b>=k)return;c=e[b++]}if(null!=c)switch(d){case 1145047050:this.setAtomCoord(l,c.x,c.y,c.z);break;case 1145047051:case 1145047053:this.at[l].setFractionalCoordTo(c,!1);this.taintAtom(l,
2);break;case 1145047055:this.setAtomVibrationVector(l,c)}}},"JU.BS,~N,~O");c(b,"setAtomVibrationVector",function(a,d){this.setVibrationVector(a,d);this.taintAtom(a,12)},"~N,JU.T3");c(b,"setAtomCoord",function(a,d,b,c){if(!(0>a||a>=this.ac)){var e=this.at[a];e.set(d,b,c);this.fixTrajectory(e);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(b,"fixTrajectory",function(a){this.isTrajectory(a.mi)&&this.trajectory.fixAtom(a)},"JM.Atom");c(b,"setAtomCoordRelative",function(a,d,b,c){if(!(0>a||a>=this.ac)){var e=
this.at[a];e.add3(d,b,c);this.fixTrajectory(e);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(b,"setAtomsCoordRelative",function(a,d,b,c){if(null!=a)for(var e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))this.setAtomCoordRelative(e,d,b,c)},"JU.BS,~N,~N,~N");c(b,"setAPa",function(a,d,b,c,e,g,j){var k=0;if(!(null!=g&&0==g.length||null==a)){for(var l=null!=g&&g.length==this.ac||null!=j&&j.length==this.ac,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){l&&(k=f);if(null!=g){if(k>=g.length)return;c=g[k++];if(Float.isNaN(c))continue;
b=F(c)}else if(null!=j){if(k>=j.length)return;e=j[k++]}var m=this.at[f],p;switch(d){case 1086326786:this.setAtomName(f,e,!0);break;case 1086326785:this.setAtomType(f,e);break;case 1086326788:this.setChainID(f,e);break;case 1094715393:this.setAtomNumber(f,b,!0);break;case 1094713365:this.setAtomSeqID(f,b);break;case 1111492609:case 1111492629:this.setAtomCoord(f,c,m.y,m.z);break;case 1111492610:case 1111492630:this.setAtomCoord(f,m.x,c,m.z);break;case 1111492611:case 1111492631:this.setAtomCoord(f,
m.x,m.y,c);break;case 1111492626:case 1111492627:case 1111492628:this.setVibrationVector2(f,d,c);break;case 1111492612:case 1111492613:case 1111492614:case 1111492615:case 1111492616:case 1111492617:m.setFractionalCoord(d,c,!1);this.taintAtom(f,2);break;case 1094715402:case 1086326789:this.setElement(m,b,!0);break;case 1631586315:this.resetPartialCharges();m.setFormalCharge(b);this.taintAtom(f,4);break;case 1113589786:this.setHydrophobicity(f,c);break;case 1128269825:p=2>c&&0.01<=c?100*c:c;this.setOccupancy(f,
p,!0);break;case 1111492619:this.setPartialCharge(f,c,!0);break;case 1111492618:this.setBondingRadius(f,c);break;case 1111492620:this.setBFactor(f,c,!0);break;case 1094715412:this.setAtomResno(f,b);break;case 1825200146:case 1287653388:this.vwr.shm.setAtomLabel(e,f);break;case 1665140738:case 1112152075:p=c;0>p?p=0:16<p&&(p=16.1);m.madAtom=sa(2E3*p);break;case 1113589787:this.vwr.slm.setSelectedAtom(m.i,0!=c);break;case 1094715418:m.setValence(b);this.taintAtom(f,10);break;case 1648363544:m.setRadius(c)?
this.taintAtom(f,11):this.untaint(f,11);break;default:JU.Logger.error("unsettable atom property: "+JS.T.nameOf(d));return}}switch(d){case 1113589787:this.vwr.slm.setSelectedAtom(-1,!1);break;case 1665140738:case 1112152075:this.vwr.setShapeSize(0,2147483647,a)}}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"getVibCoord",function(a,d){var b=null,c=null;switch(d.charCodeAt(0)){case 120:case 121:case 122:c=this.getVibration(a,!1);break;default:b=this.getModulation(a),null!=b&&(c=b.getVibration(!1),null==c&&(c=b))}if(null==
c&&null==b)return NaN;switch(d.charCodeAt(0)){case 120:case 88:return c.x;case 121:case 89:return c.y;case 122:case 90:return c.z;case 79:return b.getModulation("O",null,!0).floatValue();case 49:case 50:case 51:return b=b.getModulation("T",null,!0),b="1"==d?b.x:"2"==d?b.y:b.z,b-Math.floor(b);default:return NaN}},"~N,~S");c(b,"getVibration",function(a,d){var b=null==this.vibrations?null:this.vibrations[a];return C(b,"J.api.JmolModulationSet")?b.getVibration(d):null==b&&d?new JU.Vibration:b},"~N,~B");
c(b,"getModulation",function(a){a=null==this.vibrations?null:this.vibrations[a];return null!=a&&0<a.modDim?a:null},"~N");c(b,"setVibrationVector",function(a,d){if(null==d)null!=this.vibrations&&this.vibrations.length>a&&(this.vibrations[a]=null);else if(!Double.isNaN(d.x)&&!Double.isNaN(d.y)&&!Double.isNaN(d.z)){if(null==this.vibrations||this.vibrations.length<=a)this.vibrations=Array(this.at.length);C(d,"JU.Vibration")?this.vibrations[a]=d:(null==this.vibrations[a]&&(this.vibrations[a]=new JU.Vibration),
this.vibrations[a].setXYZ(d));this.at[a].setVibrationVector()}},"~N,JU.T3");c(b,"setVibrationVector2",function(a,d,b){var c=this.getVibration(a,!0);if(null!=c){switch(d){case 1111492626:c.x=b;break;case 1111492627:c.y=b;break;case 1111492628:c.z=b}this.setAtomVibrationVector(a,c)}},"~N,~N,~N");c(b,"setAtomName",function(a,d,b){if(!b||!d.equals(this.at[a].getAtomName())){var c=this.am[this.at[a].mi].isBioModel?this.vwr.getJBR().lookupSpecialAtomID(d):0;this.at[a].atomID=c;0>=c&&(null==this.atomNames&&
(this.atomNames=Array(this.at.length)),this.atomNames[a]=d);b&&this.taintAtom(a,0)}},"~N,~S,~B");c(b,"setAtomType",function(a,d){d.equals(this.at[a].getAtomType())||(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[a]=d)},"~N,~S");c(b,"setChainID",function(a,d){if(!d.equals(this.at[a].getChainIDStr())){var b=this.at[a].getChainID(),b=this.getChainBits(b);this.at[a].group.chain.chainID=this.vwr.getChainID(d,!0);for(var c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))this.taintAtom(c,
16)}},"~N,~S");c(b,"setAtomNumber",function(a,d,b){b&&d==this.at[a].getAtomNumber()||(null==this.atomSerials&&(this.atomSerials=E(this.at.length,0)),this.atomSerials[a]=d,b&&this.taintAtom(a,13))},"~N,~N,~B");c(b,"setElement",function(a,d,b){b&&a.getElementNumber()==d||(a.setAtomicAndIsotopeNumber(d),a.paletteID=J.c.PAL.CPK.id,a.colixAtom=this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id),this.resetPartialCharges(),b&&this.taintAtom(a.i,3))},"JM.Atom,~N,~B");c(b,"setSite",function(a,d,b){a.atomSite!=
d&&(a.atomSite=d,b&&this.taintAtom(a.i,17))},"JM.Atom,~N,~B");c(b,"resetPartialCharges",function(){this.bsPartialCharges=this.partialCharges=null});c(b,"setAtomResno",function(a,d){d!=this.at[a].getResno()&&(this.at[a].group.setResno(d),null==this.atomResnos&&(this.atomResnos=E(this.at.length,0)),this.atomResnos[a]=d,this.taintAtom(a,15))},"~N,~N");c(b,"setAtomSeqID",function(a,d){d!=this.at[a].getSeqID()&&(null==this.atomSeqIDs&&(this.atomSeqIDs=E(this.at.length,0)),this.atomSeqIDs[a]=d,this.taintAtom(a,
14))},"~N,~N");c(b,"setOccupancy",function(a,d,b){if(!(b&&d==this.at[a].getOccupancy100())){if(null==this.occupancies){if(100==d)return;this.occupancies=L(this.at.length,0);for(var c=this.at.length;0<=--c;)this.occupancies[c]=100}this.occupancies[a]=d;b&&this.taintAtom(a,7)}},"~N,~N,~B");c(b,"getOccupancyFloat",function(a){return null==this.occupancies||a>=this.occupancies.length?100:this.occupancies[a]},"~N");c(b,"setPartialCharge",function(a,d,b){if(!Float.isNaN(d)){if(null==this.partialCharges){this.bsPartialCharges=
new JU.BS;if(0==d)return;this.partialCharges=L(this.at.length,0)}this.bsPartialCharges.set(a);this.partialCharges[a]=d;b&&this.taintAtom(a,8)}},"~N,~N,~B");c(b,"setBondingRadius",function(a,d){Float.isNaN(d)||d==this.at[a].getBondingRadius()||(null==this.bondingRadii?this.bondingRadii=L(this.at.length,0):this.bondingRadii.length<this.at.length&&(this.bondingRadii=JU.AU.ensureLengthA(this.bondingRadii,this.at.length)),this.bondingRadii[a]=d,this.taintAtom(a,6))},"~N,~N");c(b,"setBFactor",function(a,
d,b){if(!(Float.isNaN(d)||b&&d==this.at[a].getBfactor100())){if(null==this.bfactor100s){if(0==d)return;this.bfactor100s=U(this.at.length,0)}this.bfactor100s[a]=cb(100*(-327.68>d?-327.68:327.67<d?327.67:d)+(0>d?-0.5:0.5));b&&this.taintAtom(a,9)}},"~N,~N,~B");c(b,"setHydrophobicity",function(a,d){if(!(Float.isNaN(d)||d==this.at[a].getHydrophobicity())){if(null==this.hydrophobicities){this.hydrophobicities=L(this.at.length,0);for(var b=0;b<this.at.length;b++)this.hydrophobicities[b]=JU.Elements.getHydrophobicity(this.at[b].group.groupID)}this.hydrophobicities[a]=
d;this.taintAtom(a,5)}},"~N,~N");c(b,"setAtomData",function(a,d,b,c){var e=null,g=null;switch(a){case 2:this.loadCoordinates(b,!1,!c);return;case 12:this.loadCoordinates(b,!0,!0);return;case 18:e=L(this.ac,0),g=JU.BS.newN(this.ac)}c=JU.Parser.markLines(b,";");var j=0;try{for(var k=JU.PT.parseInt(b.substring(0,c[0]-1)),l=1;l<=k;l++){var f=JU.PT.getTokens(JU.PT.parseTrimmed(b.substring(c[l],c[l+1]-1))),m=JU.PT.parseInt(f[0])-1;if(!(0>m||m>=this.ac)){var p=this.at[m];j++;var x=f.length-1,A=JU.PT.parseFloat(f[x]);
switch(a){case 18:e[m]=A;g.set(m);continue;case 0:this.setAtomName(m,f[x],!0);break;case 13:this.setAtomNumber(m,F(A),!0);break;case 15:this.setAtomResno(m,F(A));break;case 14:this.setAtomSeqID(m,F(A));break;case 1:this.setAtomType(m,f[x]);break;case 16:this.setChainID(m,f[x]);break;case 17:p.atomSite=F(A);break;case 3:p.setAtomicAndIsotopeNumber(F(A));p.paletteID=J.c.PAL.CPK.id;p.colixAtom=this.vwr.cm.getColixAtomPalette(p,J.c.PAL.CPK.id);break;case 4:p.setFormalCharge(F(A));break;case 5:this.setHydrophobicity(m,
A);break;case 6:this.setBondingRadius(m,A);break;case 8:this.setPartialCharge(m,A,!0);break;case 9:this.setBFactor(m,A,!0);break;case 10:p.setValence(F(A));break;case 11:p.setRadius(A)}this.taintAtom(m,a)}}18==a&&0<j&&this.vwr.setData(d,B(-1,[d,e,g,Integer.$valueOf(1)]),0,0,0,0,0)}catch(n){if(D(n,Exception))JU.Logger.error("loadData error: "+n);else throw n;}},"~N,~S,~S,~B");c(b,"loadCoordinates",function(a,d,b){var c=JU.Parser.markLines(a,";"),e=d?new JU.V3:null;try{for(var g=JU.PT.parseInt(a.substring(0,
c[0]-1)),j=1;j<=g;j++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[j],c[j+1]))),l=JU.PT.parseInt(k[0])-1,f=k[3].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[3]),m=k[4].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[4]),p=JU.PT.parseFloat(k[5]);d?(e.set(f,m,p),this.setAtomVibrationVector(l,e)):(this.setAtomCoord(l,f,m,p),b||this.untaint(l,2))}}catch(x){if(D(x,Exception))JU.Logger.error("Frame.loadCoordinate error: "+x);else throw x;}},"~S,~B,~B");c(b,"validateBspf",function(a){null!=
this.bspf&&(this.bspf.isValid=a)},"~B");c(b,"validateBspfForModel",function(a,d){null!=this.bspf&&this.bspf.validateModel(a,d)},"~N,~B");c(b,"setPreserveState",function(a){this.preserveState=a},"~B");b.getUserSettableType=c(b,"getUserSettableType",function(a){var d=0==a.indexOf("property_");a=d?a.substring(9):a;for(var b=0;18>b;b++)if(JM.AtomCollection.userSettableValues[b].equalsIgnoreCase(a))return b;return d?18:-1},"~S");c(b,"getTaintedAtoms",function(a){return null==this.tainted?null:this.tainted[a]},
"~N");c(b,"taintAtoms",function(a,d){this.canSkipLoad=!1;if(this.preserveState)for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.taintAtom(b,d)},"JU.BS,~N");c(b,"taintAtom",function(a,d){this.preserveState&&(null==this.tainted&&(this.tainted=Array(18)),null==this.tainted[d]&&(this.tainted[d]=JU.BS.newN(this.ac)),this.tainted[d].set(a));2==d&&this.taintModelCoord(a)},"~N,~N");c(b,"taintModelCoord",function(a){a=this.am[this.at[a].mi];this.validateBspfForModel(a.trajectoryBaseIndex,!1);a.isBioModel&&
a.resetDSSR(!0);this.pointGroup=null},"~N");c(b,"untaint",function(a,d){this.preserveState&&(null==this.tainted||null==this.tainted[d]||this.tainted[d].clear(a))},"~N,~N");c(b,"setTaintedAtoms",function(a,d){if(this.preserveState){if(null==a){if(null==this.tainted)return;this.tainted[d]=null;return}null==this.tainted&&(this.tainted=Array(18));null==this.tainted[d]&&(this.tainted[d]=JU.BS.newN(this.ac));JU.BSUtil.copy2(a,this.tainted[d])}if(2==d){var b=a.nextSetBit(0);0<=b&&this.taintModelCoord(b)}},
"JU.BS,~N");c(b,"unTaintAtoms",function(a,d){if(!(null==this.tainted||null==this.tainted[d])){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.tainted[d].clear(b);0>this.tainted[d].nextSetBit(0)&&(this.tainted[d]=null)}},"JU.BS,~N");c(b,"findNearest2",function(a,d,b,c,e){for(var g=null,j,k=this.ac;0<=--k;)if(!(null!=c&&c.get(k)||null==(j=this.at[k])))j.isClickable()&&this.isCursorOnTopOf(j,a,d,e,g)&&(g=j);b[0]=g},"~N,~N,~A,JU.BS,~N");c(b,"isCursorOnTopOf",function(a,d,b,c,e){return 1<a.sZ&&
!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(d,b,c,e)},"JM.Atom,~N,~N,~N,JM.Atom");c(b,"fillADa",function(a,d){a.xyz=a.atoms=this.at;a.ac=this.ac;a.atomicNumber=E(this.ac,0);var b=0!=(d&2);b&&(a.atomRadius=L(this.ac,0));for(var c=0!=(d&16),e=0;e<this.ac;e++){var g=this.at[e];JM.AtomCollection.isDeleted(g)||!c&&0<=a.modelIndex&&g.mi!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(e)):(a.atomicNumber[e]=g.getElementNumber(),a.lastModelIndex=
g.mi,b&&(a.atomRadius[e]=this.getWorkingRadius(g,a)))}},"J.atomdata.AtomData,~N");c(b,"getWorkingRadius",function(a,d){var b=0,c=d.radiusData;switch(c.factorType){case J.atomdata.RadiusData.EnumType.ABSOLUTE:b=c.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:switch(c.vdwType){case J.c.VDW.BONDING:b=a.getBondingRadius();break;case J.c.VDW.ADPMAX:b=a.getADPMinMax(!0);break;case J.c.VDW.ADPMIN:b=a.getADPMinMax(!1);break;default:b=a.getVanderwaalsRadiusFloat(this.vwr,
d.radiusData.vdwType)}b=c.factorType===J.atomdata.RadiusData.EnumType.FACTOR?b*c.value:b+c.value}return b+c.valueExtended},"JM.Atom,J.atomdata.AtomData");c(b,"calculateHydrogens",function(a,d,b,c){var e=256==(c&256),g=512==(c&512),j=8==(c&8),k=2048==(c&2048);c=4096==(c&4096);var l=new JU.V3,f=new JU.V3,m=Array(this.ac),p=this.vwr.slm.bsDeleted,x,A=d[0]=0;if(null==a)return m;var n=this.vwr.getOperativeSymmetry();null!=n&&0==this.vwr.getObjectMad10(5)&&(n=null);for(var r=null==n?null:new JU.P3,u=a.nextSetBit(0);0<=
u;u=a.nextSetBit(u+1))if(!(null!=p&&p.get(u))){var v=this.at[u],w=v.getElementNumber();if(!(g&&6!=w)){var y=6>=w?1.1:10>=w?1:1.3;switch(w){case 7:case 8:y=1}var B=e||k||c?v.getCovalentHydrogenCount():0;if(!(e&&0<B||k&&0==B)){var z=this.getMissingHydrogenCount(v,!1);if(!(e&&0==z)){k||(B=z);var C=this.aaRet[0];x=this.aaRet[2];var D=this.aaRet[3]-(k?B:0);if(!(0==D&&v.isHetero())){m[u]=Array(B);z=0;if(0==D)switch(B){case 4:l.set(0.635,0.635,0.635),x=JU.P3.newP(l),x.add(v),z=JM.AtomCollection.addH(m[u],
z,x,v,b,n,r);case 3:l.set(-0.635,-0.635,0.635),x=JU.P3.newP(l),x.add(v),z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);case 2:l.set(-0.635,0.635,-0.635),x=JU.P3.newP(l),x.add(v),z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);case 1:l.set(0.635,-0.635,-0.635),x=JU.P3.newP(l),x.add(v),z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r)}else switch(B){case 3:this.getHybridizationAndAxes(u,w,l,f,"sp3b",!1,!0,j,null);x=new JU.P3;x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,
w,l,f,"sp3c",!1,!0,j,null);x=new JU.P3;x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,w,l,f,"sp3d",!1,!0,j,null);x=new JU.P3;x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);break;case 2:D=2==x||5==w||1==D&&4==C||7==w&&this.isAdjacentSp2(v);this.getHybridizationAndAxes(u,w,l,f,D?"sp2b":3==C?"sp3c":"lpa",!1,!0,j,null);x=JU.P3.newP(l);x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,w,l,f,D?"sp2c":
3==C?"sp3d":"lpb",!1,!0,j,null);x=JU.P3.newP(l);x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);break;case 1:switch(C-D){case 1:if(8==w&&v===v.group.getCarbonylOxygenAtom()){m[u]=null;continue}if(null!=this.getHybridizationAndAxes(u,w,l,f,2==x||5==w||6==w&&1==this.aaRet[1]||7==w&&(new Boolean((new Boolean(v.group.getNitrogenAtom()===v&0==v.getFormalCharge())).valueOf()||this.isAdjacentSp2(v))).valueOf()?"sp2c":"sp3d",!0,!1,j,null))x=JU.P3.newP(l),x.scaleAdd2(y,l,v),z=JM.AtomCollection.addH(m[u],
z,x,v,b,n,r);break;case 2:this.getHybridizationAndAxes(u,w,l,f,4==C?"sp2c":"sp2b",!1,!1,j,null);x=JU.P3.newP(l);x.scaleAdd2(y,l,v);z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r);break;case 3:this.getHybridizationAndAxes(u,w,l,f,"spb",!1,!0,j,null),x=JU.P3.newP(l),x.scaleAdd2(y,l,v),z=JM.AtomCollection.addH(m[u],z,x,v,b,n,r)}}if(z<B){v=Array(z);for(w=0;w<z;w++)v[w]=m[u][w];m[u]=v}A+=z}}}}}d[0]=A;return m},"JU.BS,~A,JU.Lst,~N");b.addH=c(b,"addH",function(a,d,b,c,e,g,j){if(null!=g&&(j.setT(b),g.toFractional(j,
!1),!g.isWithinUnitCell(j,1,1,1)))return d;a[d++]=b;null!=e&&e.addLast(c);return d},"~A,~N,JU.P3,JM.Atom,JU.Lst,J.api.SymmetryInterface,JU.P3");c(b,"isAdjacentSp2",function(a){for(var d=a.bonds,b=0;b<d.length;b++)for(var c=d[b].getOtherAtom(a).bonds,e=0;e<c.length;e++)switch(c[e].getCovalentOrder()){case 2:case 3:return!0}return!1},"JM.Atom");c(b,"getMissingHydrogenCount",function(a,d){null==this.aaRet&&(this.aaRet=E(5,0));var b=a.getTargetValence();if(0>b)return 0;var c=a.getFormalCharge(),e=a.getValence(),
g=this.am[a.mi],g=g.isBioModel&&!g.isPdbWithMultipleBonds?a.group.getGroup3():null;this.aaRet[0]=b;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();this.aaRet[4]=null==g?0:e;null!=g&&0==c&&this.bioModelset.getAminoAcidValenceAndCharge(g,a.getAtomName(),this.aaRet)&&(b=this.aaRet[0],c=this.aaRet[1]);0!=c&&(b+=4==b?-Math.abs(c):c,this.aaRet[0]=b);b-=e;return 0>b&&!d?0:b},"JM.Atom,~B");c(b,"fixFormalCharges",function(a){for(var d=0,b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1)){var c=
this.at[b],e=this.getMissingHydrogenCount(c,!0);if(0!=e){var g=c.getFormalCharge(),e=g-e;c.setFormalCharge(e);this.taintAtom(b,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+g+" -> "+e);d++}}return d},"JU.BS");c(b,"getHybridizationAndAxes",function(a,d,b,c,e,g,j,k,f){var s=0<e.length&&"-"==e.charAt(0)?e.substring(1):e;if(0<=e.indexOf("d")&&!e.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,b,c,s);e=this.at[a];0==d&&(d=e.getElementNumber());var m=this.getAttached(e,4,g,
k),p=m.length,x=s.charAt(s.length-1).charCodeAt(0)-97;if(0>x||6<x)x=0;b.set(0,0,0);c.set(0,0,0);for(var A=Array(4),n=0;n<p;n++){var r=m[n];if(null==r){p=n;break}A[n]=JU.V3.newVsub(e,r);A[n].normalize();b.add(A[n])}0<p&&c.setT(A[0]);n=!1;a=new JU.V3;if(3<=p){2.9845130209103035>c.angle(A[1])?a.cross(c,A[1]):a.cross(c,A[2]);a.normalize();var u=new JU.V3;2.9845130209103035>A[1].angle(A[2])?u.cross(A[1],A[2]):u.cross(c,A[2]);u.normalize();n=0.95<=Math.abs(u.dot(a))}var v=0==s.indexOf("sp3"),r=!v&&0==s.indexOf("sp2"),
w=!v&&!r&&0==s.indexOf("sp"),y=0==s.indexOf("p"),z=0==s.indexOf("lp"),u=null;if(g){if(0==p)return null;if(v){if(3<x||4<p)return null}else if(r){if(2<x||3<p)return null}else if(w&&(1<x||2<p))return null;switch(p){case 1:if(1==d&&!v)return null;if(v){u="sp3";break}switch(m[0].getCovalentBondCount()){case 1:if(2!=m[0].getValence()){u="sp";break}case 2:u=w?"sp":"sp2";break;case 3:if(!r&&!y)return null;u="sp2"}break;case 2:if(0.1>b.length()){if(0<=s.indexOf("2")||0<=s.indexOf("3"))return null;u="sp";break}u=
v?"sp3":"sp2";if(0==s.indexOf("sp"))break;if(z){u="lp";break}u=s;break;default:if(n&&!k)u="sp2";else{n&&b.setT(a);if(z&&3==p){u="lp";break}u="sp3"}}if(null==u)return null;if(0==s.indexOf("p")){if("sp3"===u)return null}else if(0>s.indexOf(u))return null}if(x<p&&!s.startsWith("p")&&!s.startsWith("l"))return b.sub2(m[x],e),b.normalize(),u;switch(p){case 0:s.equals("sp3c")||s.equals("sp2d")||s.equals("lpa")?b.set(-0.5,-0.7,1):s.equals("sp3b")||s.equals("lpb")?b.set(0.5,-0.7,-1):s.equals("sp3a")?b.set(0,
1,0):b.set(0,0,1);c.set(1,0,0);break;case 1:a.setT(JM.AtomCollection.vRef);c.cross(a,b);if(v){for(n=m[0].getBondCount();0<=--n;)if(m[0].bonds[n].isCovalentNotPartial0()&&m[0].getBondedAtomIndex(n)!=e.i&&(c.sub2(m[0],m[0].bonds[n].getOtherAtom(m[0])),c.cross(b,c),0!=c.length())){c.cross(c,b);break}c.normalize();Float.isNaN(c.x)&&(c.setT(JM.AtomCollection.vRef),c.cross(c,b));a.cross(b,c);a.normalize();b.normalize();c.scaleAdd2(2.828,c,b);3!=x&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(b.x,b.y,b.z,
2.09439507*(2==x?1:-1))).rotate(c));b.setT(c);c.cross(a,b);break}a.cross(c,b);s=m[0].getCovalentBondCount();switch(s){case 3:if(f!==m[0]){this.getHybridizationAndAxes(m[0].i,0,c,a,"pz",!1,j,k,e);a.setT(c);r?(c.cross(c,b),1==x&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,b,c)):w||(a.setT(b),b.setT(c));c.cross(a,b);break}s=2;case 1:if(1==s&&2!=m[0].getValence())break;case 2:j=m[0];c.setT(b);for(a.setT(JM.AtomCollection.vRef);null!=j&&2==j.getCovalentBondCount();){k=j.bonds;r=null;
for(n=0;n<k.length;n++)if(k[n].isCovalentNotPartial0()&&(r=k[n].getOtherAtom(j),r!==e)){a.sub2(r,j);break}a.cross(a,c);if(0.1<a.length()||2!=r.getCovalentBondCount())break;e=j;j=r}w||(0.1<a.length()?(b.cross(a,c),b.normalize(),1==x&&b.scale(-1),b.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,c,b),y&&(a.cross(b,c),b.setT(a),a.setT(c)),c.cross(a,b)):(b.setT(c),c.cross(JM.AtomCollection.vRef,c)))}break;case 2:if(0.1>b.length()){if(!s.equals("pz")){r=m[0];(f=3==r.getCovalentBondCount())||(f=3==(r=
m[1]).getCovalentBondCount());if(f){this.getHybridizationAndAxes(r.i,0,c,b,"pz",!1,j,k,null);s.equals("px")&&c.scale(-1);b.setT(A[0]);break}a.setT(JM.AtomCollection.vRef);b.cross(a,c);a.cross(b,c)}b.setT(c);c.cross(a,b);break}a.cross(b,c);if(r){c.cross(b,a);break}if(v||z){a.normalize();b.normalize();s.equals("lp")||(0==x||2==x?b.scaleAdd2(-1.2,a,b):b.scaleAdd2(1.2,a,b));c.cross(b,a);break}c.cross(b,a);b.setT(a);0>b.z&&(b.scale(-1),c.scale(-1));break;default:if(v)break;if(!n){c.cross(b,c);break}b.setT(a);
0>b.z&&j&&(b.scale(-1),c.scale(-1))}c.normalize();b.normalize();return u},"~N,~N,JU.V3,JU.V3,~S,~B,~B,~B,JU.T3");c(b,"getHybridizationAndAxesD",function(a,d,b,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&(c="dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var e=c.startsWith("dsp3"),g=c.charAt(c.length-1).charCodeAt(0)-97;if(null!=d&&(!e&&(5<g||!c.startsWith("d2sp3"))||e&&4<g))return null;a=this.at[a];c=this.getAttached(a,
6,!0,!1);if(null==c)return null==d?null:"?";var j=c.length;if(3>j&&null!=d)return null;for(var k=g>=j,f=v(j*(j-1)/2),s=JU.AU.newInt2(f),m=E(3,0),f=E(3,f,0),p=0,x=0,A=0;A<j-1;A++)for(var n=A+1;n<j;n++){var r=JU.Measure.computeAngleABC(c[A],a,c[n],!0),r=105>r?0:150<=r?2:1;f[r][m[r]]=p;m[r]++;s[p++]=E(-1,[A,n]);0==A&&1==r&&x++}p=100*m[0]+10*m[1]+m[2];if(null==d)switch(p){default:return"";case 0:return"";case 1:return"linear";case 100:case 10:return"bent";case 111:case 201:return"T-shaped";case 30:case 120:case 210:case 300:return 162<
Math.abs(JU.Measure.computeTorsion(c[0],a,c[1],c[2],!0))?"trigonal planar":"trigonal pyramidal";case 330:return 1==x%2?"tetrahedral":"uncapped trigonal pyramid";case 60:case 150:case 240:return"tetrahedral";case 402:return"square planar";case 411:case 501:return"see-saw";case 631:return"trigonal bipyramidal";case 802:return"uncapped square pyramid";case 1203:return"octahedral"}switch(p){default:return null;case 201:break;case 210:case 330:case 411:case 631:if(!e)return null;break;case 300:case 402:case 501:case 802:case 1203:if(e)return null}if(k)if(e)switch(m[1]){case 0:d.sub2(c[s[f[0][0]][0]],
a);b.sub2(c[s[f[0][0]][1]],a);d.cross(d,b);d.normalize();4==g&&d.scale(-1);m=this.findNotAttached(j,s,f[2],m[2]);A=m.nextSetBit(0);b.sub2(c[A],a);b.normalize();b.scale(0.5);d.scaleAdd2(JM.AtomCollection.sqrt3_2,d,b);g=-1;break;case 1:4==g?(b=s[f[1][0]],d.add2(c[b[0]],c[b[1]]),d.scaleAdd2(-2,a,d),g=-1):(m=this.findNotAttached(j,s,f[1],m[1]),g=m.nextSetBit(0));break;default:m=this.findNotAttached(j,s,f[1],m[1]),g=m.nextSetBit(0)}else{p=!1;if(4==j)switch(m[2]){case 1:m=this.findNotAttached(j,s,f[2],
m[2]);A=m.nextSetBit(0);g=4==g?A:m.nextSetBit(A+1);break;default:p=!0}else{m=this.findNotAttached(j,s,f[2],m[2]);A=m.nextSetBit(0);for(n=j;n<g&&0<=A;n++)A=m.nextSetBit(A+1);-1==A?p=!0:g=A}p&&(d.sub2(c[s[f[0][0]][0]],a),b.sub2(c[s[f[0][0]][1]],a),d.cross(d,b),4==g&&d.scale(-1),g=-1)}0<=g&&d.sub2(c[g],a);k&&d.scale(-1);d.normalize();return e?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(b,"getAttached",function(a,d,b,c){var e=a.getCovalentBondCount();if(e>d)return null;d=Array(e);if(0<e){for(var e=a.bonds,
g=0,j=0;j<e.length;j++)if(e[j].isCovalentNotPartial0()){var k=e[j].getOtherAtom(a);if(!c||1!=k.getAtomicAndIsotopeNumber())d[g++]=k}b&&!c&&java.util.Arrays.sort(d,Y(JM.AtomCollection.AtomSorter,this,null))}return d},"JM.Atom,~N,~B,~B");c(b,"findNotAttached",function(a,d,b,c){var e=JU.BS.newN(a);e.setBits(0,a);for(var g=0;g<a;g++)for(var j=0;j<c;j++){var k=d[b[j]];(k[0]==g||k[1]==g)&&e.clear(g)}return e},"~N,~A,~A,~N");c(b,"getAtomBitsMDa",function(a,d,b){var c=C(d,Integer)?d.intValue():0;switch(a){case 1086326786:case 1086326785:var e=
1086326785==a,g=","+d+",";for(a=this.ac;0<=--a;)JM.AtomCollection.isDeleted(this.at[a])||(d=e?this.at[a].getAtomType():this.at[a].getAtomName(),0<=g.indexOf(","+d+",")&&b.set(a));return b;case 1094715393:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getAtomNumber()==c&&b.set(a);return b;case 2097155:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&0<this.at[a].getCovalentBondCount()&&b.set(a);return b;case 2097188:case 2097156:case 136314895:case 2097166:case 2097168:case 2097170:case 2097172:case 2097174:case 2097184:return this.haveBioModels?
this.bioModelset.getAtomBitsBS(a,null,b):b;case 1612709900:c=1;case 1094715402:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getElementNumber()==c&&b.set(a);return b;case 1612709894:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isHetero()&&b.set(a);return b;case 1073741824:return this.getIdentifierOrNull(d);case 2097165:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isLeadAtom()&&b.set(a);return b;case 1094713362:case 1639976963:return this.haveBioModels?
this.bioModelset.getAtomBitsBS(a,d,b):b;case 1094715412:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getResno()==c&&b.set(a);return b;case 1612709912:d=E(2,0);for(a=this.ac;0<=--a;)if(!JM.AtomCollection.isDeleted(this.at[a]))if(c=this.at[a].group.groupID,42<=c&&45>c)b.set(a);else if(8==(e=this.at[a]).getElementNumber()&&2==e.getCovalentBondCount()){for(var c=e.bonds,j=0,k=c.length;0<=--k&&3>j;)if(c[k].isCovalentNotPartial0()&&1==(g=c[k].getOtherAtom(e)).getElementNumber())d[j++%
2]=g.i;2==j&&(b.set(d[1]),b.set(d[0]),b.set(a))}return b;case 1073742355:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.isAltLoc(this.at[a].altloc,d)&&b.set(a);return b;case 1073742356:e=d.toUpperCase();0<=e.indexOf("\\?")&&(e=JU.PT.rep(e,"\\?","\u0001"));(g=e.startsWith("?*"))&&(e=e.substring(1));for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.isAtomNameMatch(this.at[a],e,g,g)&&b.set(a);return b;case 1073742357:return JU.BSUtil.copy(this.getChainBits(c));
case 1073742360:return this.getSpecName(d);case 1073742361:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].group.groupID==c&&b.set(a);return b;case 1073742362:return JU.BSUtil.copy(this.getSeqcodeBits(c,!0));case 5:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].group.getInsCode()==c&&b.set(a);return b;case 1296041985:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getSymOp()==c&&b.set(a);return b}g=d.nextSetBit(0);if(0>
g)return b;switch(a){case 1094717454:e=JU.BSUtil.copy(d);for(a=g;0<=a;a=e.nextSetBit(a+1))b.or(this.am[this.at[a].mi].bsAtoms),e.andNot(b);return b;case 1086326788:e=JU.BSUtil.copy(d);for(a=g;0<=a;a=e.nextSetBit(a+1))this.at[a].group.chain.setAtomBits(b),e.andNot(b);return b;case 1086326789:e=new JU.BS;for(a=g;0<=a;a=d.nextSetBit(a+1))e.set(this.at[a].getElementNumber());for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&e.get(this.at[a].getElementNumber())&&b.set(a);return b;case 1086324742:e=
JU.BSUtil.copy(d);for(a=g;0<=a;a=e.nextSetBit(a+1))this.at[a].group.setAtomBits(b),e.andNot(b);return b;case 1094713366:e=new JU.BS;for(a=g;0<=a;a=d.nextSetBit(a+1))e.set(this.at[a].atomSite);for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&e.get(this.at[a].atomSite)&&b.set(a);return b}JU.Logger.error("MISSING getAtomBits entry for "+JS.T.nameOf(a));return b},"~N,~O,JU.BS");c(b,"getChainBits",function(a){var d=this.vwr.getBoolean(603979822);d?97<=a&&122>=a&&(a+=159):0<=a&&300>a&&(a=
this.chainToUpper(a));for(var b=new JU.BS,c=JU.BS.newN(this.ac),e,g=c.nextClearBit(0);g<this.ac;g=c.nextClearBit(g+1))if(!JM.AtomCollection.isDeleted(this.at[g])){var j=this.at[g].group.chain;a==(e=j.chainID)||!d&&0<=e&&300>e&&a==this.chainToUpper(e)?(j.setAtomBits(b),c.or(b)):j.setAtomBits(c)}return b},"~N");c(b,"chainToUpper",function(a){return 97<=a&&122>=a?a-32:256<=a&&300>a?a-191:a},"~N");c(b,"isAltLoc",function(a,d){if(null==d)return"\x00"==a;if(1!=d.length)return!1;var b=d.charAt(0);return"*"==
b||"?"==b&&"\x00"!=a||a==b},"~S,~S");c(b,"getSeqcodeBits",function(a,d){var b=new JU.BS,c=JM.Group.getSeqNumberFor(a),e=2147483647!=c,g=!0,j=JM.Group.getInsertionCodeChar(a);switch(j.charCodeAt(0)){case 63:for(var k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])){var f=this.at[k].group.seqcode;if((!e||c==JM.Group.getSeqNumberFor(f))&&0!=JM.Group.getInsertionCodeFor(f))b.set(k),g=!1}break;default:for(k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])&&(f=this.at[k].group.seqcode,
a==f||!e&&a==JM.Group.getInsertionCodeFor(f)||"*"==j&&c==JM.Group.getSeqNumberFor(f)))b.set(k),g=!1}return!g||d?b:null},"~N,~B");c(b,"getIdentifierOrNull",function(a){var d=this.getSpecNameOrNull(a,!1);0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));return null!=d||0<a.indexOf("?")?d:0<a.indexOf("*")?this.getSpecNameOrNull(a,!0):this.haveBioModels?this.bioModelset.getIdentifierOrNull(a):null},"~S");c(b,"getSpecName",function(a){var d=this.getSpecNameOrNull(a,!1);if(null!=d)return d;0<a.indexOf("*")&&
(d=this.getSpecNameOrNull(a,!0));return null==d?new JU.BS:d},"~S");c(b,"getSpecNameOrNull",function(a,d){var b=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));var c=a.startsWith("?*");c&&(a=a.substring(1));for(var e=this.ac;0<=--e;)if(!JM.AtomCollection.isDeleted(this.at[e])){var g=this.at[e].getGroup3(!0);if(null!=g&&0<g.length){if(JU.PT.isMatch(g,a,d,!0)){null==b&&(b=JU.BS.newN(e+1));for(b.set(e);0<=--e;)!JM.AtomCollection.isDeleted(this.at[e])&&this.at[e].getGroup3(!0).equals(g)&&
b.set(e);e++}}else this.isAtomNameMatch(this.at[e],a,d,c)&&(null==b&&(b=JU.BS.newN(e+1)),b.set(e))}return b},"~S,~B");c(b,"isAtomNameMatch",function(a,d,b,c){return JU.PT.isMatch(a.getAtomName().toUpperCase(),d,b,c)},"JM.Atom,~S,~B,~B");c(b,"getAtomIndices",function(a){for(var d=0,b=E(this.ac,0),c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))b[c]=++d;return b},"JU.BS");c(b,"getAtomsNearPlane",function(a,d){for(var b=new JU.BS,c=this.ac;0<=--c;){var e=this.at[c];if(!JM.AtomCollection.isDeleted(e)){var g=
JU.Measure.distanceToPlane(d,e);(0<a&&-0.1<=g&&g<=a||0>a&&0.1>=g&&g>=a||0==a&&0.01>Math.abs(g))&&b.set(e.i)}}return b},"~N,JU.P4");c(b,"clearVisibleSets",function(){this.haveBSClickable=this.haveBSVisible=!1});c(b,"getAtomsInFrame",function(a){this.clearVisibleSets();a.clearAll();for(var d=this.ac;0<=--d;)!JM.AtomCollection.isDeleted(this.at[d])&&this.at[d].isVisible(1)&&a.set(d)},"JU.BS");c(b,"getVisibleSet",function(a){if(a)this.vwr.setModelVisibility(),this.vwr.shm.finalizeAtoms(null,!0);else if(this.haveBSVisible)return this.bsVisible;
this.bsVisible.clearAll();for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].checkVisible()&&this.bsVisible.set(a);null!=this.vwr.shm.bsSlabbedInternal&&this.bsVisible.andNot(this.vwr.shm.bsSlabbedInternal);this.haveBSVisible=!0;return this.bsVisible},"~B");c(b,"getClickableSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSClickable)return this.bsClickable;this.bsClickable.clearAll();for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isClickable()&&
this.bsClickable.set(a);this.haveBSClickable=!0;return this.bsClickable},"~B");c(b,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(b,"deleteModelAtoms",function(a,d,b){this.at=JU.AU.deleteElements(this.at,a,d);this.ac=this.at.length;for(var c=a;c<this.ac;c++)this.at[c].i=c,this.at[c].mi--;null!=this.bsModulated&&JU.BSUtil.deleteBits(this.bsModulated,b);this.deleteAtomTensors(b);this.atomNames=JU.AU.deleteElements(this.atomNames,a,d);this.atomTypes=JU.AU.deleteElements(this.atomTypes,
a,d);this.atomResnos=JU.AU.deleteElements(this.atomResnos,a,d);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,d);this.atomSeqIDs=JU.AU.deleteElements(this.atomSeqIDs,a,d);this.dssrData=JU.AU.deleteElements(this.dssrData,a,d);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,d);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,d);this.resetPartialCharges();this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,d);this.vibrations=JU.AU.deleteElements(this.vibrations,
a,d);this.nSurfaceAtoms=0;this.surfaceDistance100s=this.bsSurface=null;if(null!=this.tainted)for(a=0;18>a;a++)JU.BSUtil.deleteBits(this.tainted[a],b)},"~N,~N,JU.BS");c(b,"getAtomIdentityInfo",function(a,d,b){d.put("_ipt",Integer.$valueOf(a));d.put("atomIndex",Integer.$valueOf(a));d.put("atomno",Integer.$valueOf(this.at[a].getAtomNumber()));d.put("info",this.getAtomInfo(a,null,b));d.put("sym",this.at[a].getElementSymbol())},"~N,java.util.Map,JU.P3");c(b,"getAtomTensorList",function(a){return 0>a||
null==this.atomTensorList||a>=this.atomTensorList.length?null:this.atomTensorList[a]},"~N");c(b,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var d=new JU.Lst,b,c=this.atomTensors.keySet().iterator();c.hasNext()&&((b=c.next())||1);){for(var e=this.atomTensors.get(b),g=e.size();0<=--g;){var j=e.get(g);(a.get(j.atomIndex1)||0<=j.atomIndex2&&a.get(j.atomIndex2))&&e.removeItemAt(g)}0==e.size()&&d.addLast(b)}for(g=d.size();0<=--g;)this.atomTensors.remove(d.get(g))}},"JU.BS");c(b,"setCapacity",
function(a){this.atomCapacity+=a},"~N");c(b,"setAtomTensors",function(a,d){if(!(null==d||0==d.size())){null==this.atomTensors&&(this.atomTensors=new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.at.length));this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.at.length);this.atomTensorList[a]=JM.AtomCollection.getTensorList(d);for(var b=d.size();0<=--b;){var c=d.get(b);c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=
c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c(b,"addTensor",function(a,d){d=d.toLowerCase();var b=this.atomTensors.get(d);null==b&&(this.atomTensors.put(d,b=new JU.Lst),b.ensureCapacity(this.atomCapacity));b.addLast(a)},"JU.Tensor,~S");b.getTensorList=c(b,"getTensorList",function(a){for(var d=-1,b=!1,c=a.size(),e=c;0<=--e;){var g=a.get(e);g.forThermalEllipsoid?d=e:2==g.iType&&(b=!0)}var j=Array((0<=d||!b?0:1)+c);if(0<=d&&(j[0]=a.get(d),1==a.size()))return j;if(b){d=0;for(e=c;0<=--e;)g=
a.get(e),g.forThermalEllipsoid||(j[++d]=g)}else for(e=0;e<c;e++)j[e]=a.get(e);return j},"JU.Lst");c(b,"getAtomTensor",function(a,d){var b=this.getAtomTensorList(a);if(null!=b&&null!=d){d=d.toLowerCase();for(var c=0;c<b.length;c++){var e=b[c];if(null!=e&&(d.equals(e.type)||d.equals(e.altType)))return e}}return null},"~N,~S");c(b,"getAllAtomTensors",function(a){if(null==this.atomTensors)return null;if(null!=a)return this.atomTensors.get(a.toLowerCase());a=new JU.Lst;for(var d,b=this.atomTensors.entrySet().iterator();b.hasNext()&&
((d=b.next())||1);)a.addAll(d.getValue());return a},"~S");c(b,"scaleVectorsToMax",function(a){if(null!=this.vibrations){for(var d=0,b=JU.BS.newN(this.ac),c=this.vibrations.length;0<=--c;){var e=this.getVibration(c,!1);if(null!=e&&(-1==e.modDim||-2==e.modDim))d=Math.max(d,e.length()),b.set(c)}if(!(d==a||0==d)){d=a/d;a=!1;for(c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1)){var e=this.getVibration(c,!1),g=this.getModulation(c);if(null==g){if(0==d)return;e.scale(d)}else g.scaleVibration(d);a||(this.taintAtom(c,
12),a=!0)}this.tainted[12].or(b)}}},"~N");c(b,"getAtomsFromAtomNumberInFrame",function(a){for(var d=this.vwr.getFrameAtoms(),b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))this.at[b].getAtomNumber()!=a&&d.clear(b);return d},"~N");c(b,"generateCrystalClass",function(a,d){var b=0>a||a>=this.ac?this.vwr.getOperativeSymmetry():this.at[a].getUnitCell(),c=null!=d&&Float.isNaN(d.x);return null==b?new JU.Lst:b.generateCrystalClass(c?null:null!=d?d:this.at[a])},"~N,JU.P3");b.isDeleted=c(b,"isDeleted",function(a){return null==
a||a.isDeleted()},"JM.Atom");c(b,"getWyckoffPosition",function(a){return 0>a||a>=this.ac||JM.AtomCollection.isDeleted(this.at[a])?"?":this.at[a].getWyckoffPosition()},"~N");b.$AtomCollection$AtomSorter$=function(){var a=r(function(){fa(this,arguments);u(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);f(a,"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom")};b.sqrt3_2=Math.sqrt(3)/2;b.vRef=JU.V3.new3(3.14159,2.71828,1.41421);b.userSettableValues=null});
n("JM");z(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){var b=r(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=0;this.isVdw=!1;this.vwr=this.atoms=null;this.iNext=0;u(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);
c(b,"initialize",function(a,d,b,c,e,g){this.bspf=a;this.bsSelected=d;this.isGreaterOnly=b;this.isZeroBased=c;this.hemisphereOnly=e;this.threadSafe=g;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");f(b,"setModel",function(a,d,b,c,e,g,j){this.threadSafe&&(d=-1-d);if(d!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=this.bspf.getCubeIterator(d),this.modelIndex=d;this.zeroBase=this.isZeroBased?b:0;if(-2147483648!=g){this.atomIndex=0>g?-1:c;if(this.isVdw=null!=j)this.radiusData=j,
this.atoms=a.at,this.vwr=a.vwr,g=j.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+j.value:5*j.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,j.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(e,g)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");f(b,"setCenter",function(a,d){this.setCenter2(a,d)},"JU.T3,~N");c(b,"setCenter2",function(a,d){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,d,this.hemisphereOnly),this.distanceSquared=
d*d)},"JU.T3,~N");f(b,"hasNext",function(){return this.hasNext2()});c(b,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});f(b,"next",function(){return this.iNext-
this.zeroBase});f(b,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});f(b,"addAtoms",function(a){for(var d;this.hasNext();)if(0<=(d=this.next())){var b;if(this.isVdw){b=this.atoms[d].getVanderwaalsRadiusFloat(this.vwr,this.radiusData.vdwType)+this.vdw1;switch(this.radiusData.factorType){case J.atomdata.RadiusData.EnumType.OFFSET:b+=2*this.radiusData.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:b*=this.radiusData.value}b*=b}else b=this.distanceSquared;
this.foundDistance2()<=b&&a.set(d)}},"JU.BS");f(b,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)});f(b,"getPosition",function(){return null})});n("JM");z(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){var b=r(function(){this.center=this.bsModels=null;this.distance=0;u(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);y(b,function(a){I(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=
a},"JU.BS");f(b,"setCenter",function(a,d){this.center=a;this.distance=d;this.set(0)},"JU.T3,~N");c(b,"set",function(a){if(0>(this.modelIndex=this.bsModels.nextSetBit(a))||null==(this.cubeIterator=this.bspf.getCubeIterator(this.modelIndex)))return!1;this.setCenter2(this.center,this.distance);return!0},"~N");f(b,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});n("JM");z(["JU.Edge","JV.JC"],"JM.Bond",["JU.C"],function(){var b=r(function(){this.atom2=this.atom1=
null;this.shapeVisibilityFlags=this.colix=this.mad=0;u(this,arguments)},JM,"Bond",JU.Edge);y(b,function(a,d,b,c,e){I(this,JM.Bond,[]);this.atom1=a;this.atom2=d;this.colix=e;this.setOrder(b);this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(b,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(b,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,
a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(b,"getIdentity",function(){return this.index+1+" "+JU.Edge.getBondOrderNumberFromOrder(this.order)+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});f(b,"isCovalent",function(){return 0!=(this.order&1023)});f(b,"isHydrogen",function(){return JU.Edge.isOrderH(this.order)});c(b,"isStereo",function(){return 0!=(this.order&
1024)});f(b,"isPartial",function(){return 0!=(this.order&224)});c(b,"isAromatic",function(){return 0!=(this.order&512)});c(b,"getEnergy",function(){return 0});c(b,"getValence",function(){return!this.isCovalent()||33==this.order?0:this.is(515)?1:this.order&7});c(b,"deleteAtomReferences",function(){null!=this.atom1&&this.atom1.deleteBond(this);null!=this.atom2&&this.atom2.deleteBond(this);this.atom1=this.atom2=null});c(b,"setTranslucent",function(a,d){this.colix=JU.C.getColixTranslucent3(this.colix,
a,d)},"~B,~N");c(b,"setOrder",function(a){16==this.atom1.getElementNumber()&&16==this.atom2.getElementNumber()&&(a|=256);512==a&&(a=515);this.order=a|this.order&131072},"~N");f(b,"getAtomIndex1",function(){return this.atom1.i});f(b,"getAtomIndex2",function(){return this.atom2.i});f(b,"getCovalentOrder",function(){return JU.Edge.getCovalentBondOrder(this.order)});c(b,"getOtherAtom",function(a){return this.atom1===a?this.atom2:this.atom2===a?this.atom1:null},"JM.Atom");c(b,"is",function(a){return(this.order&
131071)==a},"~N");f(b,"getOtherNode",function(a){return this.atom1===a?this.atom2:this.atom2===a||null==a?this.atom1:null},"JU.SimpleNode");c(b,"setAtropisomerOptions",function(){var a,d=2147483647,b=this.atom1.bonds;for(a=0;a<b.length;a++){var c=b[a].getOtherAtom(this.atom1);if(c!==this.atom2)break}if(a<b.length){b=this.atom2.bonds;for(d=0;d<b.length&&!(c=b[d].getOtherAtom(this.atom2),c!==this.atom1);d++);}this.order=2<a||d>=b.length||2<d?1:JU.Edge.getAtropismOrder(a+1,d+1)});f(b,"getCIPChirality",
function(){return""},"~B");f(b,"setCIPChirality",function(){},"~N");f(b,"toString",function(){return this.atom1+" - "+this.atom2});f(b,"getAtom",function(a){return 1==a?this.atom2:this.atom1},"~N");c(b,"isCovalentNotPartial0",function(){return 0!=(this.order&1023)&&33!=this.order});b.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(1)});n("JM");z(["JM.AtomCollection","JU.V3"],"JM.BondCollection","JU.AU $.BS $.Measure JM.Bond $.BondIteratorSelected $.BondSet $.HBond JU.BSUtil $.C $.Edge".split(" "),function(){var b=
r(function(){this.bo=null;this.bondCount=0;this.molecules=this.freeBonds=this.numCached=null;this.defaultCovalentMad=this.moleculeCount=0;this.bsAromatic=this.bsAromaticDouble=this.bsAromaticSingle=null;this.haveHiddenBonds=!1;this.v2=this.v1=null;this.haveAtropicBonds=!1;u(this,arguments)},JM,"BondCollection",JM.AtomCollection);N(b,function(){this.v1=new JU.V3;this.v2=new JU.V3});c(b,"setupBC",function(){this.bsAromatic=new JU.BS;this.numCached=E(5,0);this.freeBonds=Array(5);for(var a=5;0<--a;)this.freeBonds[a]=
Array(200);this.setupAC()});c(b,"releaseModelSetBC",function(){this.freeBonds=this.bo=null;this.releaseModelSetAC()});c(b,"getBondIteratorForType",function(a,d){return new JM.BondIteratorSelected(this.bo,this.bondCount,a,d,this.vwr.getBoolean(603979812))},"~N,JU.BS");c(b,"getBondIterator",function(a){return new JM.BondIteratorSelected(this.bo,this.bondCount,131071,a,!1)},"JU.BS");c(b,"getBondColix1",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom1.colixAtom)},"~N");c(b,
"getBondColix2",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom2.colixAtom)},"~N");c(b,"getBondCountInModel",function(a){for(var d=0,b=this.bondCount;0<=--b;)this.bo[b].atom1.mi==a&&d++;return d},"~N");c(b,"getBondsForSelectedAtoms",function(a,d){var b=new JU.BS,c=a.cardinality();switch(c){case 0:return b;case 1:case 2:var e=this.at[a.nextSetBit(0)],g=2==c?this.at[a.nextSetBit(e.i+1)]:null;if(1==c||d){for(c=e.getBondCount();0<=--c;)b.set(e.bonds[c].index);if(null!=g)for(c=
g.getBondCount();0<=--c;)b.set(g.bonds[c].index)}else e=e.getBond(g),null!=g&&b.set(e.index);return b}for(g=0;g<this.bondCount;++g)e=this.bo[g],c=a.get(e.atom1.i),e=a.get(e.atom2.i),(d?c||e:c&&e)&&b.set(g);return b},"JU.BS,~B");c(b,"bondAtoms",function(a,d,b,c,e,g,j,k){b=this.getOrAddBond(a,d,b,c,e,g,!0);k&&(b.order|=131072,j&&(a.group=d.group,a.group.addAtoms(a.i)));return b},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B,~B");c(b,"getOrAddBond",function(a,d,b,c,e,g,j){if(131071==b||65535==b)b=1;a.isBonded(d)?
(a=a.getBond(d).index,j&&(this.bo[a].setOrder(b),this.bo[a].setMad(c),C(this.bo[a],"JM.HBond")&&(this.bo[a].energy=g))):(this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250)),a=this.setBond(this.bondCount++,this.bondMutually(a,d,b,c,g)).index);null!=e&&e.set(a);return this.bo[a]},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B");c(b,"setBond",function(a,d){return this.bo[d.index=a]=d},"~N,JM.Bond");c(b,"bondMutually",function(a,d,b,c,e){b=JU.Edge.isOrderH(b)?new JM.HBond(a,
d,b,c,0,e):new JM.Bond(a,d,b,c,0);this.addBondToAtom(a,b);this.addBondToAtom(d,b);return b},"JM.Atom,JM.Atom,~N,~N,~N");c(b,"addBondToAtom",function(a,d){null==a.bonds?(a.bonds=Array(1),a.bonds[0]=d):a.bonds=this.addToBonds(d,a.bonds)},"JM.Atom,JM.Bond");c(b,"addToBonds",function(a,d){var b;if(null==d)b=0<this.numCached[1]?this.freeBonds[1][--this.numCached[1]]:Array(1),b[0]=a;else{var c=d.length;b=c+1;b=5>b&&0<this.numCached[b]?this.freeBonds[b][--this.numCached[b]]:Array(b);b[c]=a;for(var e=c;0<=
--e;)b[e]=d[e];5>c&&200>this.numCached[c]&&(this.freeBonds[c][this.numCached[c]++]=d)}return b},"JM.Bond,~A");c(b,"addHBond",function(a,d,b,c){this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250));return this.setBond(this.bondCount++,this.bondMutually(a,d,b,1,c)).index},"JM.Atom,JM.Atom,~N,~N");c(b,"deleteAllBonds2",function(){this.vwr.setShapeProperty(1,"reset",null);for(var a=this.bondCount;0<=--a;)this.bo[a].deleteAtomReferences(),this.bo[a]=null;this.bondCount=
0});c(b,"getDefaultMadFromOrder",function(a){return JU.Edge.isOrderH(a)?1:32768==a?v(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(b,"deleteConnections",function(a,d,b,c,e,g,j){var k=0>a,f=0>d,s=k||f;a=this.fixD(a,k);d=this.fixD(d,f);var m=new JU.BS,p=0,x=b|=131072;!j&&JU.Edge.isOrderH(b)&&(b=30720);if(g)g=c;else{g=new JU.BS;for(var A=c.nextSetBit(0);0<=A;A=c.nextSetBit(A+1)){var n=this.at[A];if(null!=n.bonds)for(var r=n.bonds.length;0<=--r;)e.get(n.getBondedAtomIndex(r))&&
g.set(n.bonds[r].index)}}for(A=g.nextSetBit(0);A<this.bondCount&&0<=A;A=g.nextSetBit(A+1))if(c=this.bo[A],this.isInRange(c.atom1,c.atom2,a,d,k,f,s)&&(j||x==(c.order&-257|131072)||0!=(b&c.order&30720)))m.set(A),p++;0<p&&this.deleteBonds(m,!1);return E(-1,[0,p])},"~N,~N,~N,JU.BS,JU.BS,~B,~B");c(b,"fixD",function(a,d){return d?-a:a*a},"~N,~B");c(b,"isInRange",function(a,d,b,c,e,g,j){var k=a.distanceSquared(d);return j?(j=Math.sqrt(k),a=a.getBondingRadius()+d.getBondingRadius(),(e?j>=a*b:k>=b)&&(g?j<=
a*c:k<=c)):k>=b&&k<=c},"JM.Atom,JM.Atom,~N,~N,~B,~B,~B");c(b,"dBb",function(a,d){var b=a.nextSetBit(0);if(!(0>b)){this.resetMolecules();for(var c=-1,e=a.cardinality(),g=b;g<this.bondCount;++g){var j=this.bo[g];if(0<e&&a.get(g)){e--;if(!d){var k=j.atom1.mi;k!=c&&this.am[c=k].resetBoundCount()}j.deleteAtomReferences()}else this.setBond(b++,j)}for(c=this.bondCount;--c>=b;)this.bo[c]=null;this.bondCount=b;b=this.vwr.getShapeProperty(1,"sets");if(null!=b)for(c=0;c<b.length;c++)JU.BSUtil.deleteBits(b[c],
a);JU.BSUtil.deleteBits(this.bsAromatic,a)}},"JU.BS,~B");c(b,"resetAromatic",function(){for(var a=this.bondCount;0<=--a;){var d=this.bo[a];d.isAromatic()&&d.setOrder(515)}});c(b,"assignAromaticBondsBs",function(a,d){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var b=null==d,c=b?this.bondCount-1:d.nextSetBit(0),e=c;0<=e;e=b?e-1:d.nextSetBit(e+1)){var g=this.bo[e];this.bsAromatic.get(e)&&g.setOrder(515);switch(g.order&131071){case 515:if(!this.assignAromaticMustBeSingle(g.atom1)&&
!this.assignAromaticMustBeSingle(g.atom2)){this.bsAromatic.set(e);break}g.order=513;case 513:this.bsAromaticSingle.set(e);break;case 514:this.bsAromaticDouble.set(e)}}for(var c=(b=null==d)?this.bondCount-1:d.nextSetBit(0),j=new JU.BS,e=c;0<=e;e=b?e-1:d.nextSetBit(e+1))if(g=this.bo[e],g.is(515)&&(!this.bsAromaticDouble.get(e)&&!this.bsAromaticSingle.get(e))&&(j.set(e),8==g.atom1.getElementNumber()||8==g.atom2.getElementNumber()))this.assignAromaticDouble(g)||this.assignAromaticSingle(g);for(e=j.nextSetBit(0);0<=
e;e=j.nextSetBit(e+1))this.assignAromaticDouble(g=this.bo[e])||this.assignAromaticSingle(g);j=new JU.BS;for(e=c;0<=e;e=b?e-1:d.nextSetBit(e+1))if(g=this.bo[e],this.bsAromaticDouble.get(e))g.is(514)||(this.bsAromatic.set(e),j.set(g.atom1.mi),g.setOrder(this.isLinear(g,this.v1,this.v2)?3:514));else if((this.bsAromaticSingle.get(e)||g.isAromatic())&&!g.is(513))this.bsAromatic.set(e),g.setOrder(513);b=this.am;for(e=j.nextSetBit(0);0<=e;e=j.nextSetBit(e+1))b[e].isBioModel&&(b[e].isPdbWithMultipleBonds=
!0);this.assignAromaticNandO(d);this.bsAromaticDouble=this.bsAromaticSingle=null},"~B,JU.BS");c(b,"isLinear",function(a,d,b){if(3==a.order)return!0;if(2!=a.atom1.getCovalentBondCount()||2!=a.atom2.getCovalentBondCount())return!1;for(var c=a.atom1.getEdges(),e=c.length;0<=-e;)if(c[e]!==a&&c[e].isCovalent()){if(175>JU.Measure.computeAngle(c[e].getOtherNode(a.atom1),a.atom1,a.atom2,d,b,!0))return!1;break}c=a.atom2.getEdges();for(e=c.length;0<=-e;)if(c[e]!==a&&c[e].isCovalent()){if(175>JU.Measure.computeAngle(c[e].getOtherNode(a.atom2),
a.atom2,a.atom1,d,b,!0))return!1;break}return!0},"JM.Bond,JU.V3,JU.V3");c(b,"assignAromaticDouble",function(a){var d=a.index;if(this.bsAromaticSingle.get(d))return!1;if(this.bsAromaticDouble.get(d))return!0;this.bsAromaticDouble.set(d);return!this.assignAromaticSingleForAtom(a.atom1,d)||!this.assignAromaticSingleForAtom(a.atom2,d)?(this.bsAromaticDouble.clear(d),!1):!0},"JM.Bond");c(b,"assignAromaticSingle",function(a){var d=a.index;if(this.bsAromaticDouble.get(d))return!1;if(this.bsAromaticSingle.get(d))return!0;
this.bsAromaticSingle.set(d);return!this.assignAromaticDoubleForAtom(a.atom1)||!this.assignAromaticDoubleForAtom(a.atom2)?(this.bsAromaticSingle.clear(d),!1):!0},"JM.Bond");c(b,"assignAromaticSingleForAtom",function(a,d){var b=a.bonds;if(null==b)return!1;for(var c=b.length;0<=--c;){var e=b[c],g=e.index;if(!(g==d||!e.isAromatic()||this.bsAromaticSingle.get(g)))if(this.bsAromaticDouble.get(g)||!this.assignAromaticSingle(e))return!1}return!0},"JM.Atom,~N");c(b,"assignAromaticDoubleForAtom",function(a){a=
a.bonds;if(null==a)return!1;for(var d=!1,b=-1,c=a.length;0<=--c;)this.bsAromaticDouble.get(a[c].index)&&(d=!0),a[c].isAromatic()&&(b=c);for(c=a.length;0<=--c;){var e=a[c],g=e.index;if(e.isAromatic()&&!this.bsAromaticDouble.get(g)&&!this.bsAromaticSingle.get(g))if(!d&&this.assignAromaticDouble(e))d=!0;else if((d||c<b)&&!this.assignAromaticSingle(e))return!1}return d},"JM.Atom");c(b,"allowAromaticBond",function(a){if(this.assignAromaticMustBeSingle(a.atom1)||this.assignAromaticMustBeSingle(a.atom2))return!1;
switch(a.getCovalentOrder()){case 1:case 2:return 3>=a.atom1.getCovalentBondCount()&&3>=a.atom2.getCovalentBondCount();default:return!1}},"JM.Bond");c(b,"assignAromaticMustBeSingle",function(a){var d=a.getElementNumber();switch(d){case 6:case 7:case 8:case 16:break;default:return!0}var b=a.getValenceAromatic(!1);switch(d){case 6:return 4==b;case 7:return a.group.getNitrogenAtom()===a||3==b&&1>a.getFormalCharge();case 8:return a.group.getCarbonylOxygenAtom()!==a&&2==b&&1>a.getFormalCharge();case 16:return 5==
a.group.groupID||2==b&&1>a.getFormalCharge()}return!1},"JM.Atom");c(b,"assignAromaticNandO",function(a){for(var d,b=null==a,c=b?this.bondCount-1:a.nextSetBit(0);0<=c;c=b?c-1:a.nextSetBit(c+1))if(d=this.bo[c],d.is(513)){var e,g=d.atom2,j,k=g.getElementNumber();7==k||8==k?(j=k,e=g,g=d.atom1,k=g.getElementNumber()):(e=d.atom1,j=e.getElementNumber());if(!(7!=j&&8!=j)){var f=e.getValence();if(!(0>f)){var s=e.getCovalentBondCount();e=e.getFormalCharge();switch(j){case 7:3==f&&(3==s&&1>e&&6==k&&3==g.getValence())&&
d.setOrder(514);break;case 8:1==f&&(0==e&&(14==k||16==k))&&d.setOrder(514)}}}}},"JU.BS");c(b,"getAtomBitsMDb",function(a,d){var b=new JU.BS;switch(a){default:return this.getAtomBitsMDa(a,d,b);case 1677721602:for(var c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))c<this.bondCount?(b.set(this.bo[c].atom1.i),b.set(this.bo[c].atom2.i)):d.clear(c);return b;case 1073742331:for(c=this.bondCount;0<=--c;)this.bo[c].isAromatic()&&(b.set(this.bo[c].atom1.i),b.set(this.bo[c].atom2.i));return b}},"~N,~O");c(b,"removeUnnecessaryBonds",
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b.getBondLabelValues=c(b,"getBondLabelValues",function(){var a=new java.util.Hashtable;a.put("#","");a.put("ORDER","");a.put("TYPE","");a.put("LENGTH",Float.$valueOf(0));a.put("ENERGY",Float.$valueOf(0));return a});b.formatLabelBond=c(b,"formatLabelBond",function(a,d,b,c,e,g){c.put("#",""+(d.index+1));c.put("ORDER",""+JU.Edge.getBondOrderNumberFromOrder(d.order));c.put("TYPE",JU.Edge.getBondOrderNameFromOrder(d.order));c.put("LENGTH",Float.$valueOf(d.atom1.distance(d.atom2)));c.put("ENERGY",Float.$valueOf(d.getEnergy()));
JM.LabelToken.setValues(b,c);JM.LabelToken.formatLabelAtomArray(a,d.atom1,b,"1",e,g);JM.LabelToken.formatLabelAtomArray(a,d.atom2,b,"2",e,g);return JM.LabelToken.getLabel(b)},"JV.Viewer,JM.Bond,~A,java.util.Map,~A,JU.P3");b.formatLabelMeasure=c(b,"formatLabelMeasure",function(a,d,b,c,e){var g=new java.util.Hashtable;g.put("#",""+(d.index+1));g.put("VALUE",Float.$valueOf(c));g.put("UNITS",e);b=JM.LabelToken.compile(a,b,"\u0001",g);if(null==b)return"";JM.LabelToken.setValues(b,g);g=d.ms.at;d=d.countPlusIndices;
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b.text.length-1),d);if(null==s)System.out.println("?? o is null ??");else if(1==s.size())k=s.get(0).floatValue();else{k=NaN;j="";a=0;for(var m=s.size();a<m;a++)j+=","+s.get(a);1<j.length&&(j=j.substring(1))}}break;case 1715472409:var p=a.ms.getInfo(d.mi,b.data),x=d.i-a.ms.am[d.mi].firstAtomIndex,s=null;if(0<=x)if(C(p,Array))var A=p,s=x<A.length?A[x]:null;else C(p,"JU.Lst")&&(s=x<p.size()?JS.SV.oValue(p.get(x)):null);null==s?j="":C(s,Float)?k=s.floatValue():C(s,Integer)?k=s.intValue():C(s,"JU.T3")?
f=s:j=s.toString();break;case 1275068418:null!=b.data&&(A=b.data,j=d.i<A.length?A[d.i]:"");break;case 1631586315:var n=d.getFormalCharge(),j=0<n?""+n+"+":0>n?""+-n+"-":"";break;case 1094717454:j=d.getModelNumberForLabel();break;case 1128269825:j=""+d.atomPropertyInt(b.tok);break;case 1665140738:k=d.atomPropertyFloat(a,b.tok,g);break;case 1086324749:j=d.group.getStructureId();break;case 1094713367:var r=d.group.getStrucNo(),j=0>=r?"":""+r;break;case 1111490574:if(Float.isNaN(k=d.group.getGroupParameter(1111490574)))j=
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r(function(){this.thisID=this.ms=null;this.index=0;this.isVisible=!0;this.isTrajectory=this.isHidden=!1;this.$isValid=!0;this.colix=0;this.labelColix=-1;this.mad=0;this.tickInfo=null;this.traceX=-2147483648;this.count=this.traceY=0;this.pts=this.countPlusIndices=null;this.value=0;this.type=this.strMeasurement=this.vwr=this.text=this.units=this.strFormat=this.property=null;this.tainted=!1;this.newUnits=this.renderArc=this.renderAxis=null;this.fixedValue=NaN;this.useDefaultLabel=this.inFront=this.isPending=
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this.count?this.countPlusIndices[this.count]:-1});c(b,"getString",function(){return this.strMeasurement});f(b,"toString",function(){return this.getString()});c(b,"getStringUsing",function(a,d,b){this.vwr=a;this.value=this.getMeasurement(null);this.formatMeasurementAs(d,b,!0);return null==d?this.getInfoAsString(b):this.strMeasurement},"JV.Viewer,~S,~S");c(b,"getStringDetail",function(){return(2==this.count?"Distance":3==this.count?"Angle":"Torsion")+this.getMeasurementScript(" - ",!1)+" : "+this.value});
c(b,"refresh",function(a){this.value=this.getMeasurement(a);this.isTrajectory=this.ms.isTrajectoryMeasurement(this.countPlusIndices);this.formatMeasurement(null)},"~A");c(b,"getMeasurementScript",function(a,d){for(var b=new JU.SB,c=a.equals(" "),e=1;e<=this.count;e++)b.append(1<e?a:" ").append(this.getLabel(e,c,d));return b.toString()},"~S,~B");c(b,"formatMeasurementAs",function(a,d,b){null!=a&&0==a.length&&(a=null);if(b||!(null!=a&&0!=a.indexOf(this.countPlusIndices[0]+":")))this.strFormat=a,this.formatMeasurement(d)},
"~S,~S,~B");c(b,"formatMeasurement",function(a){this.tainted=!0;switch(Float.isNaN(this.value)?0:this.count){default:this.strMeasurement=null;break;case 2:this.strMeasurement=this.formatDistance(a);break;case 3:case 4:this.strMeasurement=this.formatAngle(this.value)}},"~S");c(b,"reformatDistanceIfSelected",function(a){if(2==this.count&&this.vwr.slm.isSelected(this.countPlusIndices[1])&&this.vwr.slm.isSelected(this.countPlusIndices[2])){var d;if(this.useDefaultLabel&&null!=this.strFormat&&0<=(d=this.strFormat.indexOf("//")))this.strFormat=
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a=this.fixValue(a,0<=d.indexOf("%V"));return this.formatString(a,this.newUnits,d)},"~S");c(b,"fixValue",function(a,d){this.checkJ(a);null!=a&&a.startsWith("+")&&(this.isPending||(this.value=Math.abs(this.value)),a=a.substring(1));this.newUnits=a;if(2!=this.count)return this.value;var b=this.value;null==a&&null!=this.property&&(a="");if(null!=a){var c=a.equals("%");if(null==this.property&&(c||a.endsWith("hz"))){var e=this.getAtomIndex(1),g=this.getAtomIndex(2);if(0<=e&&0<=g){var e=this.getAtom(1),
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e,g,a,null);this.$isValid=!Float.isNaN(b);c&&(a="pm")}}return JM.Measurement.toUnits(b,a,d)}return d?Math.round(100*b)/100:b},"~S,~B");c(b,"checkJ",function(a){null!=this.property||(null!=a||null!=this.units)||(a=this.vwr.g.measureDistanceUnits,"+hz".equals(a)&&(this.property="property_J",this.units=a))},"~S");b.nmrType=c(b,"nmrType",function(a){return 0>a.indexOf("hz")?0:a.equals("noe_hz")?3:a.startsWith("dc_")||a.equals("khz")?1:2},"~S");c(b,"formatAngle",function(a){var d=this.getLabelString();
0<=d.indexOf("%V")&&(a=Math.round(10*a)/10);return this.formatString(a,"\u00b0",d)},"~N");c(b,"getLabelString",function(){var a=this.countPlusIndices[0]+":",d=null;if(null!=this.strFormat){if(0==this.strFormat.length)return null;d=2<this.strFormat.length&&0==this.strFormat.indexOf(a)?this.strFormat:null}this.useDefaultLabel=!1;null==d&&(this.strFormat=null,d=this.vwr.getDefaultMeasurementLabel(this.countPlusIndices[0]),this.useDefaultLabel=null==this.units);0==d.indexOf(a)&&(d=d.substring(2));null==
this.strFormat&&(this.strFormat=a+d);return d});c(b,"formatString",function(a,d,b){return JM.LabelToken.formatLabelMeasure(this.vwr,this,b,a,d)},"~N,~S,~S");c(b,"sameAsPoints",function(a,d){if(this.count!=a[0])return!1;for(var b=!0,c=1;c<=this.count&&b;c++)b=this.countPlusIndices[c]==a[c];if(b)for(c=0;c<this.count&&b;c++)null!=d[c]&&(b=0.01>this.pts[c].distance(d[c]));if(b)return!0;switch(this.count){default:return!0;case 2:return this.sameAsIJ(a,d,1,2)&&this.sameAsIJ(a,d,2,1);case 3:return this.sameAsIJ(a,
d,1,3)&&this.sameAsIJ(a,d,2,2)&&this.sameAsIJ(a,d,3,1);case 4:return this.sameAsIJ(a,d,1,4)&&this.sameAsIJ(a,d,2,3)&&this.sameAsIJ(a,d,3,2)&&this.sameAsIJ(a,d,4,1)}},"~A,~A");c(b,"sameAsIJ",function(a,d,b,c){b=this.countPlusIndices[b];a=a[c];return 0<=b||0<=a?b==a:0.01>this.pts[-2-b].distance(d[-2-a])},"~A,~A,~N,~N");c(b,"sameAs",function(a,d){return this.sameAsIJ(this.countPlusIndices,this.pts,a,d)},"~N,~N");c(b,"getPropMeasurement",function(a){if(null==this.countPlusIndices||2!=this.count)return NaN;
for(var d=this.count;0<=--d;)if(0>this.countPlusIndices[d+1])return NaN;try{var b=null==a?this.getAtom(1):a[0],c=null==a?this.getAtom(2):a[1],e=this.vwr.getDataObj(this.property,null,2),g=b.i,j=c.i;return null==e||j>=e.length||g>=e.length?NaN:e[g][j]}catch(k){return NaN}},"~A");c(b,"getMeasurement",function(a){this.checkJ(null);if(!Float.isNaN(this.fixedValue))return this.fixedValue;if(null!=this.property)return this.getPropMeasurement(a);if(null==this.countPlusIndices||2>this.count)return NaN;for(var d=
this.count;0<=--d;)if(-1==this.countPlusIndices[d+1])return NaN;var d=null==a?this.getAtom(1):a[0],b=null==a?this.getAtom(2):a[1],c;switch(this.count){case 2:return d.distance(b);case 3:return c=null==a?this.getAtom(3):a[2],JU.Measure.computeAngleABC(d,b,c,!0);case 4:return c=null==a?this.getAtom(3):a[2],a=null==a?this.getAtom(4):a[3],JU.Measure.computeTorsion(d,b,c,a,!0);default:return NaN}},"~A");c(b,"getLabel",function(a,d,b){var c=this.countPlusIndices[a];return 0>c?(b?"modelIndex "+this.getAtom(a).mi+
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function(a,d){for(var b=-1,c=1;c<=d;c++){var e=this.getAtomIndex(c);if(!(0>e)){if(0<=b&&!a[e].isBonded(a[b]))return!1;b=e}}return!0},"~A,~N");c(b,"getInfoAsString",function(a){var d=this.fixValue(a,!0);a=new JU.SB;a.append(2==this.count?null!=this.property?this.property:null==this.type?"distance":this.type:3==this.count?"angle":"dihedral");a.append(" \t").appendF(d);a.append(" \t").append(JU.PT.esc(this.strMeasurement));for(d=1;d<=this.count;d++)a.append(" \t").append(this.getLabel(d,!1,!1));null!=
this.thisID&&a.append(" \t").append(this.thisID);return a.toString()},"~S");c(b,"isInRange",function(a,d){if(a.factorType===J.atomdata.RadiusData.EnumType.FACTOR){var b=this.getAtom(1),c=this.getAtom(2),b=(b.getVanderwaalsRadiusFloat(this.vwr,a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return d<=b}return 3.4028235E38==a.values[0]||d>=a.values[0]&&d<=a.values[1]},"J.atomdata.RadiusData,~N");c(b,"isIntramolecular",function(a,d){for(var b=-1,c=1;c<=d;c++){var e=this.getAtomIndex(c);
if(!(0>e))if(e=a[e].getMoleculeNumber(!1),0>b)b=e;else if(e!=b)return!1}return!0},"~A,~N");c(b,"isMin",function(a){var d=this.getAtom(1),b=this.getAtom(2),c=F(100*b.distanceSquared(d)),d=d.getAtomName(),b=b.getAtomName(),b=0>d.compareTo(b)?d+b:b+d;a=a.get(b);return null!=a&&c==a.intValue()},"java.util.Map");b.isUnits=c(b,"isUnits",function(a){return JU.PT.isOneOf((a.startsWith("+")?a.substring(1):a).toLowerCase(),";nm;nanometers;pm;picometers;angstroms;angstroms;ang;\u00c5;au;vanderwaals;vdw;%;noe;")||
0>a.indexOf(" ")&&a.endsWith("hz")},"~S");b.toUnits=c(b,"toUnits",function(a,d,b){return Float.isNaN(a)?NaN:d.equals("hz")?b?Math.round(10*a)/10:a:d.equals("nm")?b?Math.round(100*a)/1E3:a/10:d.equals("pm")?b?Math.round(1E3*a)/10:100*a:d.equals("au")?b?Math.round(1E3*(a/0.5291772))/1E3:a/0.5291772:d.endsWith("khz")?b?Math.round(a/10)/100:a/1E3:b?Math.round(100*a)/100:a},"~N,~S,~B");b.fromUnits=c(b,"fromUnits",function(a,d){return d.equals("nm")?10*a:d.equals("pm")?a/100:d.equals("au")?0.5291772*a:
d.equals("\u00c5")?a:0},"~N,~S");b.fixUnits=c(b,"fixUnits",function(a){var d=a.endsWith("s")?a.substring(0,a.length-1):a;return d.equals("nanometer")?"nm":d.equals("bohr")||d.equals("atomicunits")||d.equals("atomic")?"au":d.equals("picometer")?"pm":d.equals("\u00e5")||d.equals("angstrom")||d.equals("a")||d.equals("ang")?"\u00c5":d.equals("vanderwaal")||d.equals("vdw")?"%":a},"~S");c(b,"getDistanceFormatForState",function(){return this.useDefaultLabel?null:this.strFormat});c(b,"setFromMD",function(a){null!=
a.thisID&&(this.thisID=a.thisID,this.mad=a.mad,0!=a.colix&&(this.colix=a.colix),this.strFormat=a.strFormat,this.text=a.text);this.units="default".equals(a.units)?null:a.units;this.property=a.property;this.fixedValue=a.fixedValue;0!=a.colix&&(this.colix=a.colix);0!=a.mad&&(this.mad=a.mad);null!=a.strFormat&&(this.strFormat=(null==this.strFormat?a.strFormat:this.strFormat.substring(0,2))+a.strFormat.substring(2));null!=a.text&&(null==this.text?this.text=a.text:(null!=a.text.font&&(this.text.setFont(a.text.font,
!1),this.text.fontScale=a.text.font.fontSize/a.text.font.fontSizeNominal),this.text.text=null,0!=a.text.align&&(this.text.align=a.text.align),0!=a.colix&&(this.labelColix=this.text.colix=a.text.colix)));this.formatMeasurement(null)},"JM.MeasurementData,~B")});n("JM");z(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["JU.Lst","JM.Measurement"],function(){var b=r(function(){this.points=this.measurements=this.measurementStrings=this.bsSelected=this.client=null;this.mustNotBeConnected=this.mustBeConnected=
!1;this.tickInfo=null;this.tokAction=12290;this.note=this.property=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=null;this.mad=0;this.units=this.text=this.thisID=null;this.fixedValue=0;this.ms=this.minArray=this.atoms=null;this.allowSelf=!1;this.vwr=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;u(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);c(b,"init",function(a,d,b){this.vwr=d;this.points=b;this.thisID=a;return this},"~S,JV.Viewer,JU.Lst");
c(b,"setModelSet",function(a){this.ms=a;return this},"JM.ModelSet");c(b,"set",function(a,d,b,c,e,g,j,k,f,s,m,p,x,A,n,r){this.ms=this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(C(this.points.get(0),"JU.BS")&&C(this.points.get(1),"JU.BS"))&&(this.justOneModel=this.vwr.ms.getModelBS(this.points.get(0),!1).equals(this.vwr.ms.getModelBS(this.points.get(1),!1)));this.bsSelected=r;this.htMin=d;this.radiusData=b;this.property=c;this.strFormat=e;this.units=g;this.tickInfo=j;this.mustBeConnected=k;this.mustNotBeConnected=
f;this.intramolecular=s;this.isAll=m;this.mad=p;this.colix=x;this.text=A;this.fixedValue=n;return this},"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text,~N,JU.BS");c(b,"processNextMeasure",function(a,d){var b=d.getMeasurement(null);if(!(null!=this.htMin&&!d.isMin(this.htMin)||null!=this.radiusData&&!d.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var c=this.minArray[this.iFirstAtom];d.value=b;b=d.fixValue(this.units,
!1);this.minArray[this.iFirstAtom]=-Infinity==1/c?b:Math.min(c,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(d.getStringUsing(this.vwr,this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(d.getMeasurement(null)))},"JM.MeasurementData,JM.Measurement");c(b,"getMeasurements",function(a,d){if(d){this.minArray=L(this.points.get(0).cardinality(),0);for(var b=0;b<this.minArray.length;b++)this.minArray[b]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.allowSelf=
!0,this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");c(b,"define",function(a,d){this.client=null==a?this:a;this.atoms=d.at;var b=this.points.size();if(!(2>b)){var c=-1,e=Array(4),g=E(5,0),j=(new JM.Measurement).setPoints(d,g,e,null);j.setCount(b);j.property=this.property;j.strFormat=this.strFormat;j.units=this.units;j.fixedValue=this.fixedValue;for(var k=-1,f=0;f<b;f++){var s=
this.points.get(f);if(C(s,"JU.BS")){k=s.cardinality();if(0==k)return;1<k&&(c=0);k=f;0==f&&(this.iFirstAtom=0);g[f+1]=s.nextSetBit(0)}else e[f]=s,g[f+1]=-2-f}this.nextMeasure(0,k,j,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(b,"nextMeasure",function(a,d,b,c){if(a>d)(this.allowSelf&&!this.mustBeConnected&&!this.mustNotBeConnected||b.isValid())&&((!this.mustBeConnected||b.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!b.isConnected(this.atoms,a))&&(null==this.intramolecular||b.isIntramolecular(this.atoms,
a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(this,b);else{var e=this.points.get(a),g=b.countPlusIndices,j=0==a?2147483647:g[a];if(0>j)this.nextMeasure(a+1,d,b,c);else{for(var k=!1,f=e.nextSetBit(0),s=0;0<=f;f=e.nextSetBit(f+1),s++)if(f!=j||this.allowSelf){var m=this.atoms[f].mi;if(0<=c&&this.justOneModel)if(0==a)c=m;else if(c!=m)continue;g[a+1]=f;0==a&&(this.iFirstAtom=s);k=!0;this.nextMeasure(a+1,d,b,c)}k||this.nextMeasure(a+1,d,b,c)}}},"~N,~N,JM.Measurement,~N")});n("JM");
z(["JM.Measurement"],"JM.MeasurementPending",null,function(){var b=r(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;u(this,arguments)},JM,"MeasurementPending",JM.Measurement);c(b,"set",function(a){return this.setM(a,null,NaN,0,null,0)},"JM.ModelSet");c(b,"checkPoint",function(a){for(var d=1;d<=this.numSet;d++)if(this.countPlusIndices[d]==-1-d&&0.01>this.pts[d-1].distance(a))return!1;return!0},"JU.Point3fi");c(b,"getIndexOf",function(a){for(var d=1;d<=this.numSet;d++)if(this.countPlusIndices[d]==
a)return d;return 0},"~N");f(b,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(b,"addPoint",function(a,d,b){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==d){if(0<this.getIndexOf(a))return b&&(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(d))return b&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=
!0;this.count=this.numSet+1;this.pts[a]=d;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;b&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);return this.count},"~N,JU.Point3fi,~B")});n("JM");z(null,"JM.Model","java.util.Hashtable JU.AU $.BS $.SB JU.BSUtil JV.FileManager".split(" "),function(){var b=r(function(){this.mat4=this.ms=null;this.fileIndex=this.modelIndex=0;this.isModelKit=this.isPdbWithMultipleBonds=
this.isBioModel=!1;this.translation=this.dataFrames=this.biosymmetry=this.properties=this.auxiliaryInfo=this.orientation=this.dssrCache=this.simpleCage=this.chains=null;this.dataSourceFrame=-1;this.loadState="";this.loadScript=null;this.isTrajectory=this.isJmolDataFrame=this.structureTainted=this.hasRasmolHBonds=!1;this.act=this.insertionCount=this.altLocCount=this.trajectoryBaseIndex=0;this.bondCount=-1;this.chainCount=0;this.groupCount=-1;this.firstMoleculeIndex=this.firstAtomIndex=this.biosymmetryCount=
this.moleculeCount=this.hydrogenCount=0;this.bsAtomsDeleted=this.bsAtoms=null;this.frameDelay=this.defaultRotationRadius=0;this.selectedTrajectory=-1;this.bsCheck=this.pdbID=this.jmolFrameType=this.jmolData=null;this.hasChirality=!1;this.isOrderly=!0;this.bsAsymmetricUnit=null;u(this,arguments)},JM,"Model",null);y(b,function(){this.setupArrays()});c(b,"setupArrays",function(){this.chains=Array(8);this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS});c(b,"set",function(a,
d,b,c,e,g){this.ms=a;this.dataSourceFrame=this.modelIndex=d;this.trajectoryBaseIndex=(this.isTrajectory=0<=b)?b:d;null==g&&(g=new java.util.Hashtable);this.auxiliaryInfo=g;a=g.get("biosymmetryCount");null!=a&&(this.biosymmetryCount=a.intValue(),this.biosymmetry=g.get("biosymmetry"));a=g.get("fileName");null!=a&&g.put("fileName",JV.FileManager.stripTypePrefix(a));this.properties=e;null==c?this.jmolFrameType="modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,g.put("jmolData",c),g.put("title",c),this.jmolFrameType=
0<=c.indexOf("ramachandran")?"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data");return this},"JM.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(b,"getTrueAtomCount",function(){return JU.BSUtil.andNot(this.bsAtoms,this.bsAtomsDeleted).cardinality()});c(b,"isContainedIn",function(a){null==this.bsCheck&&(this.bsCheck=new JU.BS);this.bsCheck.clearAll();this.bsCheck.or(a);a=JU.BSUtil.andNot(this.bsAtoms,this.bsAtomsDeleted);this.bsCheck.and(a);return this.bsCheck.equals(a)},"JU.BS");
c(b,"resetBoundCount",function(){this.bondCount=-1});c(b,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;var a=this.ms.bo;this.bondCount=0;for(var d=this.ms.bondCount;0<=--d;)a[d].atom1.mi==this.modelIndex&&this.bondCount++;return this.bondCount});c(b,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(b,"calcSelectedGroupsCount",function(a){for(var d=this.chainCount;0<=
--d;)this.chains[d].calcSelectedGroupsCount(a)},"JU.BS");c(b,"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].groupCount}return this.groupCount});c(b,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(b,"getChain",function(a){for(var d=this.chainCount;0<=--d;){var b=this.chains[d];if(b.chainID==a)return b}return null},"~N");c(b,"resetDSSR",function(a){this.dssrCache=null;a&&this.auxiliaryInfo.remove("dssr")},
"~B");c(b,"fixIndices",function(a,d,b){this.fixIndicesM(a,d,b)},"~N,~N,JU.BS");c(b,"fixIndicesM",function(a,d,b){this.dataSourceFrame>a&&this.dataSourceFrame--;this.trajectoryBaseIndex>a&&this.trajectoryBaseIndex--;this.firstAtomIndex-=d;for(a=0;a<this.chainCount;a++)this.chains[a].fixIndices(d,b);JU.BSUtil.deleteBits(this.bsAtoms,b);JU.BSUtil.deleteBits(this.bsAtomsDeleted,b)},"~N,~N,JU.BS");c(b,"freeze",function(){this.freezeM();return!1});c(b,"freezeM",function(){for(var a=0;a<this.chainCount;a++)if(0==
this.chains[a].groupCount){for(var d=a+1;d<this.chainCount;d++)this.chains[d-1]=this.chains[d];this.chainCount--}this.chains=JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=-1;this.getGroupCount();for(a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)});c(b,"setSimpleCage",function(a){this.simpleCage=a;null!=a&&this.auxiliaryInfo.put("unitCellParams",a.getUnitCellParams())},"J.api.SymmetryInterface")});n("JM");
z(["java.util.Hashtable","JU.BS"],"JM.ModelLoader","java.util.Arrays JU.AU $.Lst $.P3 $.PT $.SB $.V3 J.api.Interface JM.AtomCollection $.Chain $.Group $.Model $.ModelSet JS.T JU.BSUtil $.Elements $.JmolMolecule $.Logger JV.JC".split(" "),function(){var b=r(function(){this.modelSet0=this.ms=this.vwr=null;this.appendNew=this.merging=!1;this.specialAtomIndexes=this.group3Counts=this.group3Lists=this.jmolData=null;this.doAddPDBHydrogens=this.doMinimize=this.isPyMOLsession=this.isTrajectory=this.isMutate=
this.isMOL2D=this.is2D=this.someModelsAreModulated=this.someModelsHaveUnitcells=!1;this.groups=this.jbr=this.fileHeader=null;this.groupCount=0;this.modulationTUV=null;this.noH=!1;this.firstAtomIndexes=this.seqcodes=this.group3Of=this.chainOf=this.htAtomMap=null;this.iModel=0;this.model=null;this.currentChainID=0;this.isNewChain=!1;this.currentChain=null;this.currentGroupSequenceNumber=0;this.currentGroupInsertionCode="\x00";this.nullGroup=this.currentGroup3=null;this.adapterTrajectoryCount=this.adapterModelCount=
this.baseTrajectoryCount=this.baseGroupIndex=this.baseAtomIndex=this.baseModelCount=this.baseModelIndex=0;this.modulationOn=this.noAutoBond=!1;this.$mergeGroups=this.appendToModelIndex=this.htGroup1=null;this.iChain=0;this.vStereo=null;this.lastModel=-1;this.structuresDefinedInFile=null;this.stereodir=1;u(this,arguments)},JM,"ModelLoader",null);N(b,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});y(b,function(a,d,b,c,e,g){this.vwr=a;this.ms=new JM.ModelSet(a,
d);var j=a.getModelAdapter();this.modelSet0=e;(this.merging=null!=e&&(0<e.ac||null!=e.vwr.getOperativeSymmetry()))?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==g?(this.initializeInfo(d,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),d=j.getAtomSetCollectionAuxiliaryInfo(c),d.put("loadScript",b),this.initializeInfo(j.getFileTypeName(c).toLowerCase().intern(),
d),this.createModelSet(j,c,g),null!=d.get("lowPrecision")&&a.setBooleanPropertyTok("doublePrecision",603979831,!1),null!=this.jbr&&this.jbr.setLoader(null),this.jbr=null)},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");c(b,"initializeInfo",function(a,d){this.ms.g3d=this.vwr.gdata;this.ms.modelSetTypeName=a;this.ms.isXYZ="xyz"===a;this.ms.msInfo=d;this.ms.modelSetProperties=this.ms.getInfoM("properties");this.ms.haveBioModels=this.ms.getMSInfoB(JV.JC.getBoolName(4));this.isMutate=this.ms.getMSInfoB("isMutate");
this.ms.haveBioModels&&(this.jbr=this.vwr.getJBR().setLoader(this));this.jmolData=0==this.adapterModelCount?this.ms.getInfoM("jmolData"):null;this.fileHeader=this.ms.getInfoM("fileHeader");var b=this.ms.getInfoM("trajectorySteps");if(this.isTrajectory=null!=b)this.ms.trajectory=this.newTrajectory(this.ms,b);this.isPyMOLsession=this.ms.getMSInfoB("isPyMOL");this.doAddPDBHydrogens=null!=this.jbr&&!this.isTrajectory&&!this.isPyMOLsession&&!this.ms.getMSInfoB("pdbNoHydrogens")&&(this.ms.getMSInfoB("pdbAddHydrogens")||
this.vwr.getBoolean(603979894));null!=d&&(d.remove("pdbNoHydrogens"),d.remove("pdbAddHydrogens"),d.remove("trajectorySteps"),this.isTrajectory&&(this.ms.vibrationSteps=d.remove("vibrationSteps")),d.containsKey("highPrecision")&&this.vwr.setBooleanProperty("legacyJavaFloat",!0));this.htGroup1=this.ms.getInfoM("htGroup1");b=this.ms.getInfoM("modulationOn");null!=b&&(this.modulationOn=!0,this.modulationTUV=b===Boolean.TRUE?null:b);this.noAutoBond=this.ms.getMSInfoB("noAutoBond");this.noH=this.ms.getMSInfoB("noHydrogen");
this.doMinimize=((this.is2D=this.ms.getMSInfoB("is2D"))&&!this.noH||this.ms.getMSInfoB("minimize3D"))&&this.ms.getMSInfoB("doMinimize");this.adapterTrajectoryCount=this.isTrajectory?this.ms.trajectory.steps.size():0;this.ms.someModelsHaveSymmetry=this.ms.getMSInfoB(JV.JC.getBoolName(1));this.someModelsHaveUnitcells=this.ms.getMSInfoB(JV.JC.getBoolName(2));this.someModelsAreModulated=this.ms.getMSInfoB(JV.JC.getBoolName(9));this.ms.someModelsHaveFractionalCoordinates=this.ms.getMSInfoB(JV.JC.getBoolName(1));
this.merging&&(this.ms.haveBioModels=(new Boolean(this.ms.haveBioModels|this.modelSet0.haveBioModels)).valueOf(),this.ms.bioModelset=this.modelSet0.bioModelset,null!=this.ms.bioModelset&&this.ms.bioModelset.set(this.vwr,this.ms),this.ms.someModelsHaveSymmetry=(new Boolean(this.ms.someModelsHaveSymmetry|this.modelSet0.getMSInfoB(JV.JC.getBoolName(1)))).valueOf(),this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.modelSet0.getMSInfoB(JV.JC.getBoolName(2)))).valueOf(),this.ms.someModelsHaveFractionalCoordinates=
(new Boolean(this.ms.someModelsHaveFractionalCoordinates|this.modelSet0.getMSInfoB(JV.JC.getBoolName(0)))).valueOf(),this.ms.someModelsHaveAromaticBonds=(new Boolean(this.ms.someModelsHaveAromaticBonds|this.modelSet0.someModelsHaveAromaticBonds)).valueOf(),this.ms.msInfo.put(JV.JC.getBoolName(1),Boolean.$valueOf(this.ms.someModelsHaveSymmetry)),this.ms.msInfo.put(JV.JC.getBoolName(2),Boolean.$valueOf(this.someModelsHaveUnitcells)),this.ms.msInfo.put(JV.JC.getBoolName(0),Boolean.$valueOf(this.ms.someModelsHaveFractionalCoordinates)),
this.ms.msInfo.put(JV.JC.getBoolName(8),Boolean.$valueOf(this.ms.someModelsHaveAromaticBonds)))},"~S,java.util.Map");c(b,"newTrajectory",function(a,d){return J.api.Interface.getInterface("JM.Trajectory",this.vwr,"load").set(this.vwr,a,d)},"JM.ModelSet,JU.Lst");c(b,"getGroup3",function(a){return a>=this.group3Of.length?null:this.group3Of[a]},"~N");c(b,"getFirstAtomIndex",function(a){return this.firstAtomIndexes[a]},"~N");c(b,"getAtomCount",function(){return this.ms.ac});c(b,"createModelSet",function(a,
d,b){var c=null==a?0:a.getAtomCount(d,-1);0<c&&JU.Logger.info("reading "+c+" atoms");this.adapterModelCount=null==a?1:a.getAtomSetCount(d);this.appendToModelIndex=null==this.ms.msInfo?null:this.ms.msInfo.get("appendToModelIndex");this.appendNew=!this.isMutate&&(!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||this.vwr.getBoolean(603979792)&&null==this.appendToModelIndex);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=E(32,0);this.firstAtomIndexes=
E(32,0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.iModel=-1;this.model=null;this.merging&&this.mergeTrajAndVib(this.modelSet0,this.ms);this.initializeAtomBondModelCounts(c);!this.noH&&(null!=b&&(this.doMinimize||this.is2D))&&b.setBits(this.baseAtomIndex,this.baseAtomIndex+a.getAtomCount(d,0));if(null==a)this.setModelNameNumberProperties(0,-1,"",1,null,null,null);else{0<this.adapterModelCount&&(JU.Logger.info("ModelSet: haveSymmetry:"+
this.ms.someModelsHaveSymmetry+" haveUnitcells:"+this.someModelsHaveUnitcells+" haveFractionalCoord:"+this.ms.someModelsHaveFractionalCoordinates),JU.Logger.info(this.adapterModelCount+" model"+(1==this.ms.mc?"":"s")+' in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.'));b=this.ms.getInfoM("defaultOrientationQuaternion");null!=b&&(JU.Logger.info("defaultOrientationQuaternion = "+b),JU.Logger.info('Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.'));
this.iterateOverAllNewModels(a,d);b=a.getBondIterator(d);c=null!=b;this.iterateOverAllNewAtoms(a,d,c);var e=this.vwr.getMadBond();c&&(this.ms.defaultCovalentMad=null==this.jmolData?e:0,this.iterateOverAllNewBonds(b));this.ms.defaultCovalentMad=e;this.merging&&!this.appendNew&&(b=a.getAtomSetAuxiliaryInfo(d,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",b.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",b.get("initialBondCount")));this.initializeUnitCellAndSymmetry();
this.initializeBonding()}this.finalizeGroupBuild();this.is2D&&this.doMinimize&&this.setupMinimization();this.doAddPDBHydrogens&&this.jbr.finalizeHydrogens();null!=a&&(this.ms.calculatePolymers(this.groups,this.groupCount,this.baseGroupIndex,null),null!=this.jbr&&this.jbr.iterateOverAllNewStructures(a,d));this.setDefaultRendering(this.vwr.getInt(553648170));var g=this.vwr.rd;b=this.ms.ac;c=this.ms.at;for(e=this.baseAtomIndex;e<b;e++)c[e].setMadAtom(this.vwr,g);g=this.ms.am;for(e=g[this.baseModelIndex].firstAtomIndex;e<
b;e++)null!=c[e]&&g[c[e].mi].bsAtoms.set(e);this.freeze();this.finalizeShapes();this.vwr.setModelSet(this.ms);this.setAtomProperties();null!=a&&a.finish(d);null!=this.modelSet0&&this.modelSet0.releaseModelSet();this.modelSet0=null},"J.api.JmolAdapter,~O,JU.BS");c(b,"mergeTrajAndVib",function(a,d){this.baseModelCount=a.mc;this.baseTrajectoryCount=0;null==a.trajectory&&this.isTrajectory&&this.newTrajectory(a,new JU.Lst);if(!(null==a.trajectory||0==a.mc)){this.baseTrajectoryCount=a.mc;for(var b=a.trajectory.steps.size(),
c=b;c<this.baseTrajectoryCount;c++)a.trajectory.steps.addLast(null);if(this.isTrajectory){if(null==a.vibrationSteps){a.vibrationSteps=new JU.Lst;for(c=b;0<=--c;)a.vibrationSteps.addLast(null)}b=d.trajectory.steps.size();for(c=0;c<b;c++)a.trajectory.steps.addLast(d.trajectory.steps.get(c)),a.vibrationSteps.addLast(null==d.vibrationSteps?null:d.vibrationSteps.get(c))}else d.trajectory=this.newTrajectory(d,null);d.vibrationSteps=a.vibrationSteps;d.trajectory.steps=a.trajectory.steps;a.trajectory=null}},
"JM.ModelSet,JM.ModelSet");c(b,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var d=new JU.SB,b=this.ms.mc,c=this.ms.am,e=this.baseModelIndex;e<b;e++)c[e].isBioModel&&c[e].getDefaultLargePDBRendering(d,a);0!=d.length()&&(d.append("select *;"),a=this.ms.getInfoM("jmolscript"),null==a&&(a=""),d.append(a),this.ms.msInfo.put("jmolscript",d.toString()))}},"~N");c(b,"setAtomProperties",function(){for(var a=this.ms.mc,d=this.baseModelIndex;d<a;d++){var b=this.ms.getInfo(d,"atomProperties");
null!=this.jmolData&&this.addJmolDataProperties(this.ms.am[d],this.ms.getInfo(d,"jmolDataProperties"));var c=this.ms.getInfo(d,"groupPropertyList");this.ms.am[d].isBioModel&&null!=this.ms.getInfo(d,"dssr")&&this.vwr.getAnnotationParser(!0).setGroup1(this.ms,d);if(null!=b){for(var e,b=b.entrySet().iterator();b.hasNext()&&((e=b.next())||1);){var g=e.getKey(),j=e.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(d,!0);if(this.doAddPDBHydrogens)var f=null!=c&&JU.PT.isOneOf(g,c),j=this.jbr.fixPropertyValue(k,
j,f);g="property_"+g.toLowerCase();JU.Logger.info("creating "+g+" for model "+this.ms.getModelName(d));this.vwr.setData(g,B(-1,[g,j,k,Integer.$valueOf(-1),Boolean.FALSE,e]),this.ms.ac,0,0,2147483647,0)}this.ms.setInfo(d,"atomProperties",null)}}});c(b,"initializeAtomBondModelCounts",function(a){var d=this.adapterTrajectoryCount;if(this.merging){if(this.appendNew)this.baseModelIndex=this.baseModelCount,this.ms.mc=this.baseModelCount+this.adapterModelCount;else{this.baseModelIndex=null==this.appendToModelIndex?
this.vwr.am.cmi:this.appendToModelIndex.intValue();if(0>this.baseModelIndex||this.baseModelIndex>=this.baseModelCount)this.baseModelIndex=this.baseModelCount-1;this.ms.mc=this.baseModelCount}this.ms.ac=this.baseAtomIndex=this.modelSet0.ac;this.ms.bondCount=this.modelSet0.bondCount;this.$mergeGroups=this.modelSet0.getGroups();this.groupCount=this.baseGroupIndex=this.$mergeGroups.length;this.ms.mergeModelArrays(this.modelSet0);this.ms.growAtomArrays(this.ms.ac+a)}else this.ms.mc=this.adapterModelCount,
this.ms.ac=0,this.ms.bondCount=0,this.ms.at=Array(a),this.ms.bo=Array(250+a);this.doAddPDBHydrogens&&this.jbr.initializeHydrogenAddition();1<d&&(this.ms.mc+=d-1);this.ms.am=JU.AU.arrayCopyObject(this.ms.am,this.ms.mc);this.ms.modelFileNumbers=JU.AU.arrayCopyI(this.ms.modelFileNumbers,this.ms.mc);this.ms.modelNumbers=JU.AU.arrayCopyI(this.ms.modelNumbers,this.ms.mc);this.ms.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.ms.modelNumbersForAtomLabel,this.ms.mc);this.ms.modelNames=JU.AU.arrayCopyS(this.ms.modelNames,
this.ms.mc);this.ms.frameTitles=JU.AU.arrayCopyS(this.ms.frameTitles,this.ms.mc);if(this.merging)for(a=0;a<this.modelSet0.mc;a++)(this.ms.am[a]=this.modelSet0.am[a]).ms=this.ms},"~N");c(b,"mergeGroups",function(){var a=this.modelSet0.getModelSetAuxiliaryInfo(null),d=a.get("group3Lists"),a=a.get("group3Counts");if(null!=d){for(var b=0;b<this.baseModelCount;b++)this.group3Lists[b+1]=d[b+1],this.group3Counts[b+1]=a[b+1],this.structuresDefinedInFile.set(b);this.group3Lists[0]=d[0];this.group3Counts[0]=
a[0]}!this.appendNew&&this.ms.haveBioModels&&this.structuresDefinedInFile.clear(this.baseModelIndex)});c(b,"iterateOverAllNewModels",function(a,d){this.group3Lists=Array(this.ms.mc+1);this.group3Counts=JU.AU.newInt2(this.ms.mc+1);this.structuresDefinedInFile=new JU.BS;this.merging&&this.mergeGroups();for(var b=this.isTrajectory?this.baseTrajectoryCount:-1,c=this.baseModelIndex,e=0;e<this.adapterModelCount;++e,++c){var g=a.getAtomSetNumber(d,e),j=a.getAtomSetName(d,e),k=a.getAtomSetAuxiliaryInfo(d,
e);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var f=k.get("modelProperties");if(!this.merging||this.appendNew){var s=k.get("fileType");this.vwr.setStringProperty("_fileType",s);this.vwr.fm.setFileType(s)}null==j&&(j=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?""+g%1E6:"");this.setModelNameNumberProperties(c,b,j,g,f,k,this.jmolData)}b=this.ms.am[null==this.appendToModelIndex?this.baseModelIndex:
this.ms.mc-1];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));e=this.ms.msInfo.remove("loadState");g=this.ms.msInfo.remove("loadScript");if(0>g.indexOf("Viewer.AddHydrogens")||!b.isModelKit){j=JU.PT.split(e,"\n");k=new JU.SB;for(e=0;e<j.length;e++)f=b.loadState.indexOf(j[e]),(0>f||f!=b.loadState.lastIndexOf(j[e]))&&k.append(j[e]).appendC("\n");b.loadState+=b.loadScript.toString()+k.toString();b.loadScript=new JU.SB;if(0<=g.indexOf("load append ")||0<=g.indexOf('data "append '))g.insert(0,
";var anew = appendNew;"),g.append(";set appendNew anew");b.loadScript.append("  ").appendSB(g).append(";\n")}if(this.isTrajectory){e=this.ms.mc-c+1;JU.Logger.info(e+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(e));b=this.adapterModelCount;for(e=c;e<this.ms.mc;e++,b++)this.ms.am[e]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[e]=a.getAtomSetNumber(d,b),this.ms.modelNames[e]=a.getAtomSetName(d,b),this.structuresDefinedInFile.set(e)}this.finalizeModels(this.baseModelCount)},
"J.api.JmolAdapter,~O");c(b,"setModelNameNumberProperties",function(a,d,b,c,e,g,j){if(this.appendNew){var k=null!=g&&Boolean.TRUE===g.get(JV.JC.getBoolName(4));this.ms.am[a]=k?this.jbr.getBioModel(a,d,j,e,g):(new JM.Model).set(this.ms,a,d,j,e,g);this.ms.modelNumbers[a]=c;this.ms.modelNames[a]=b;k&&this.jbr.setGroupLists(a)}else d=g.get("PDB_CONECT_firstAtom_count_max"),null!=d&&this.ms.setInfo(a,"PDB_CONECT_firstAtom_count_max",d);d=this.ms.am;c=this.ms.at;d[a].bsAtoms.set(c.length+1);d[a].bsAtoms.clear(c.length+
1);c=this.ms.getInfo(a,"altLocs");d[a].altLocCount=null==c?0:c.length;null!=c&&(c=c.toCharArray(),java.util.Arrays.sort(c),c=String.valueOf(c),this.ms.setInfo(a,"altLocs",c));c=this.ms.getInfo(a,"insertionCodes");d[a].insertionCount=null==c?0:c.length;b=null!=this.ms.modelSetName&&this.ms.modelSetName.startsWith("Jmol Model Kit")||b.startsWith("Jmol Model Kit")||"Jme".equals(this.ms.getInfo(a,"fileType"))&&this.is2D;d[a].isModelKit=b},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(b,"finalizeModels",
function(a){var d=this.ms.mc;if(d!=a){var b,c=0,e=-1,g=this.ms.modelNumbers,j=this.ms.modelNames;if(this.isTrajectory)for(var k=a;++k<this.ms.mc;)g[k]=g[k-1]+1;if(0<a){if(1E6>g[0])for(k=0;k<a;k++)0==j[k].length&&(j[k]=""+g[k]),g[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var f=g[a-1],f=f-f%1E6;1E6>g[a]&&(f+=1E6);for(k=a;k<d;k++)g[k]+=f}for(var s=this.ms.am,k=a;k<d;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),
f=v(g[k]/1E6),f!=e&&(c=0,e=f),c++,0==f?(b=""+this.ms.getModelNumber(k),f=1):b=f+"."+c,this.ms.modelNumbersForAtomLabel[k]=b,s[k].fileIndex=f-1,this.ms.modelFileNumbers[k]=1E6*f+c,null==j[k]||0==j[k].length)j[k]=b;if(this.merging)for(k=0;k<a;k++)s[k].ms=this.ms;for(k=0;k<d;k++)this.ms.setInfo(k,"modelName",j[k]),this.ms.setInfo(k,"modelNumber",Integer.$valueOf(g[k]%1E6)),this.ms.setInfo(k,"modelFileNumber",Integer.$valueOf(this.ms.modelFileNumbers[k])),this.ms.setInfo(k,"modelNumberDotted",this.ms.getModelNumberDotted(k)),
a=this.ms.getInfo(k,"altLocs"),null!=a&&JU.Logger.info("model "+this.ms.getModelNumberDotted(k)+" alternative locations: "+a)}},"~N");c(b,"iterateOverAllNewAtoms",function(a,d,b){var c=-1,e=0,g=!1,j=!1,k=a.getAtomIterator(d),f=a.getAtomCount(d,-1);this.ms.setCapacity(a.getAtomCount(d,-1));d=0;var s=this.ms.am;0<this.ms.mc&&(this.nullGroup=(new JM.Group).setGroup(new JM.Chain(this.ms.am[this.baseModelIndex],32,0),"",0,-1,-1));for(;k.hasNext();){d++;var m=k.getAtomSetIndex()+this.baseModelIndex;m!=
c&&(this.iChain=0,this.iModel=m,this.model=s[m],c=this.model.bsAtoms,this.merging&&(!this.appendNew&&null!=this.vwr.getOperativeSymmetry())&&(e=this.getAtomSiteBase(c)),this.currentChainID=2147483647,this.isNewChain=!0,c.set(this.ms.ac+f),c.clearAll(),this.model.isOrderly=null==this.appendToModelIndex,g=this.model.isBioModel,c=m,j=g&&this.doAddPDBHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var m=k.getGroup3(),p=k.getChainID();this.checkNewGroup(a,p,m,k.getSequenceNumber(),k.getInsertionCode(),
j,!1);p=k.getElementNumber();j&&1==JU.Elements.getElementNumber(p)&&this.jbr.setHaveHsAlready(!0);var x=k.getAtomName(),A=j?this.getPdbCharge(m,x):k.getFormalCharge(),m=this.addAtom(g,k.getSymmetry(),k.getAtomSite()+e,p,x,A,k.getPartialCharge(),k.getTensors(),k.getOccupancy(),k.getBfactor(),k.getXYZ(),k.getIsHetero(),k.getSerial(),k.getSeqID(),m,k.getVib(),k.getAltLoc(),k.getRadius(),k.getBondRadius());b&&this.htAtomMap.put(k.getUniqueID(),m)}0<this.groupCount&&j&&this.jbr.addImplicitHydrogenAtoms(a,
this.groupCount-1,this.isNewChain?1:0);c=-1;a=null;b=this.ms.at;for(e=s[0].firstAtomIndex=0;e<this.ms.ac;e++)null!=b[e]&&b[e].mi>c&&(c=b[e].mi,k=s[c],k.firstAtomIndex=e,k.isOrderly=k.act==k.bsAtoms.length(),k=this.ms.getDefaultVdwType(c),k!==a&&(JU.Logger.info("Default Van der Waals type for model set to "+k.getVdwLabel()),a=k));JU.Logger.info(d+" atoms created")},"J.api.JmolAdapter,~O,~B");c(b,"getAtomSiteBase",function(a){for(var d=0,b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1)){var c=this.ms.at[b];
!JM.AtomCollection.isDeleted(c)&&c.atomSite>d&&(d=c.atomSite)}return d},"JU.BS");c(b,"addJmolDataProperties",function(a,d){if(null!=d)for(var b=a.bsAtoms,c=b.cardinality(),e,g=d.entrySet().iterator();g.hasNext()&&((e=g.next())||1);){var j=e.getKey(),k=e.getValue();if(k.length!=c)break;var f=j.startsWith("property_")?1715472409:JS.T.getTokFromName(j);switch(f){default:if(JS.T.tokAttr(f,2048)){this.vwr.setAtomProperty(b,f,0,0,null,k,null);break}case 1111492629:case 1111492630:case 1111492631:j="property_"+
j;case 1715472409:this.vwr.setData(j,B(-1,[j,k,b,Integer.$valueOf(1)]),0,0,0,0,0)}}},"JM.Model,java.util.Map");c(b,"getPdbCharge",function(a,d){return a.equals("ARG")&&d.equals("NH1")||a.equals("LYS")&&d.equals("NZ")||a.equals("HIS")&&d.equals("ND1")?1:0},"~S,~S");c(b,"addAtom",function(a,d,b,c,e,g,j,k,f,s,m,p,x,A,n,r,u,v,w){var y=0,z=null;if(null!=e){var B;if(0<=(B=e.indexOf("\x00")))z=e.substring(B+1),e=e.substring(0,B);a&&(0<=e.indexOf("*")&&(e=e.$replace("*","'")),y=this.vwr.getJBR().lookupSpecialAtomID(e),
2==y&&"CA".equalsIgnoreCase(n)&&(y=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,c,e,z,x,A,b,m,v,r,g,j,f,s,k,p,y,d,w);a.altloc=u;return a},"~B,JU.BS,~N,~N,~S,~N,~N,JU.Lst,~N,~N,JU.P3,~B,~N,~N,~S,JU.V3,~S,~N,~N");c(b,"checkNewGroup",function(a,d,b,c,e,g,j){d!=this.currentChainID&&(this.currentChainID=d,this.currentChain=this.getOrAllocateChain(this.model,d),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=-1,this.currentGroup3="xxxx",this.isNewChain=!0);d=null==b?null:b.intern();
if(c!=this.currentGroupSequenceNumber||e!=this.currentGroupInsertionCode||d!==this.currentGroup3){0<this.groupCount&&g&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!j?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=e;for(this.currentGroup3=d;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),
this.firstAtomIndexes=JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.ms.ac;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=b;this.seqcodes[this.groupCount]=JM.Group.getSeqcodeFor(c,e);++this.groupCount}},"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");c(b,"getOrAllocateChain",function(a,d){var b=a.getChain(d);if(null!=b)return b;a.chainCount==a.chains.length&&(a.chains=0==a.chainCount?Array(2):JU.AU.doubleLength(a.chains));return a.chains[a.chainCount++]=
new JM.Chain(a,d,0==d||32==d?0:++this.iChain)},"JM.Model,~N");c(b,"iterateOverAllNewBonds",function(a){for(var d=this.isMutate&&!this.vwr.getBoolean(603979894),b=!1;a.hasNext();){var c=a.getEncodedOrder(),e=d?1:c,g=this.bondAtoms(a.getAtomUniqueID1(),a.getAtomUniqueID2(),e);null!=g&&(1<e&&(1025!=e&&1041!=e)&&(b=!0),e=a.getRadius(),0<e&&g.setMad(sa(2E3*e)),e=a.getColix(),0<=e&&(g.colix=e),g.order|=c&98304)}b&&(this.ms.someModelsHaveSymmetry&&!this.vwr.getBoolean(603979794))&&JU.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.')},
"J.api.JmolAdapterBondIterator");c(b,"bondAtoms",function(a,d,b){var c=this.htAtomMap.get(a);if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(d);if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+d),null;if(c.isBonded(a))return null;1025==b||1041==b?(d=c.getModelIndex(),d!=this.lastModel&&(this.lastModel=d,d=this.ms.getModelAuxiliaryInfo(d),this.isMOL2D=this.is2D||null!=d&&"2D".equals(d.get("dimension"))),b=this.ms.bondMutually(c,
a,this.isMOL2D?b:513,this.ms.getDefaultMadFromOrder(1),0),this.isMOL2D&&(null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(b))):(b=this.ms.bondMutually(c,a,b,this.ms.getDefaultMadFromOrder(b),0),b.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,b);return b},"~O,~O,~N");c(b,"initializeUnitCellAndSymmetry",function(){this.someModelsAreModulated&&
null==this.ms.bsModulated&&(this.ms.bsModulated=new JU.BS);var a=null!=this.modelSet0&&null!=this.modelSet0.unitCells;if(this.someModelsHaveUnitcells||a){this.ms.unitCells=Array(this.ms.mc);this.ms.haveUnitCells=!0;for(var d=0,b=0;d<this.ms.mc;d++)if(a&&d<this.baseModelCount)this.ms.unitCells[d]=this.modelSet0.unitCells[d];else{this.ms.unitCells[d]=J.api.Interface.getSymmetry(this.vwr,"file");var c=null;if(this.isTrajectory){var e=this.ms.getInfoM("unitCells");null!=e&&(c=e.get(b++))}this.ms.unitCells[d].setSymmetryInfo(d,
this.ms.getModelAuxiliaryInfo(d),c)}}if(this.appendNew&&this.ms.someModelsHaveSymmetry){this.ms.getAtoms(1088421903,null);a=this.ms.at;d=this.baseAtomIndex;b=-1;for(c=0;d<this.ms.ac;d++){if(a[d].mi!=b){b=a[d].mi;c=this.baseAtomIndex+this.ms.getInfoI(b,"presymmetryAtomIndex");if(0>c)break;e=this.ms.getInfoI(b,"presymmetryAtomCount");this.ms.am[b].auxiliaryInfo.put("presymmetryAtomIndex",Integer.$valueOf(c));this.ms.setInfo(b,"asymmetricUnit",this.ms.am[b].bsAsymmetricUnit=JU.BSUtil.newBitSet2(c,c+
e));c+=e}d>=c&&this.ms.bsSymmetry.set(d)}}if(this.appendNew&&this.ms.someModelsHaveFractionalCoordinates){a=this.ms.at;b=-1;c=null;e=!1;for(d=this.baseAtomIndex;d<this.ms.ac;d++)if(a[d].mi!=b&&(b=a[d].mi,c=this.ms.getUnitCell(b),e=null!=c&&c.getCoordinatesAreFractional()),e){var g=null==this.ms.getModulation(d)?c:a[d].getUnitCell();g.toCartesian(g.toSupercell(a[d]),!1)}for(d=this.baseModelIndex;d<this.ms.mc;d++)this.ms.isTrajectory(d)&&this.ms.trajectory.setUnitCell(d)}});c(b,"initializeBonding",
function(){var a=this.ms.mc,d=this.ms.am,b=0,c=this.ms.getInfoM("bsExcludeBonding");null==c&&(c=null==this.ms.getInfoM(JV.JC.getBoolName(3))?null:new JU.BS,null!=c&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,c));var e=this.vwr.getBoolean(603979794),g=this.vwr.getBoolean(603979798),j=this.vwr.getBoolean(603979847),k=null,f=!1;if(!this.noAutoBond)for(var s=this.baseModelIndex;s<a;s++){var b=d[s].bsAtoms.cardinality(),m=this.ms.getInfoI(s,"initialBondCount"),p=d[s].isBioModel;
0>m&&(m=this.ms.bondCount);if(j||g&&(0==m||p&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||m<v(b/2))||this.ms.getInfoB(s,"hasSymmetry")&&!e&&!this.ms.getInfoB(s,"hasBonds")))if(f=!0,this.merging||1<a)null==k&&(k=JU.BS.newN(this.ms.ac)),(s==this.baseModelIndex||!this.isTrajectory)&&k.or(d[s].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);f?(this.ms.autoBondBs4(k,k,c,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979872),null),JU.Logger.info("ModelSet: autobonding; use  autobond=false  to not generate bonds automatically")):
JU.Logger.info("ModelSet: not autobonding; use  forceAutobond=true  to force automatic bond creation")});c(b,"finalizeGroupBuild",function(){this.groups=Array(this.groupCount);if(this.merging)for(var a=0;a<this.$mergeGroups.length;a++)(this.groups[a]=this.$mergeGroups[a]).chain.model.ms=this.ms;for(a=this.baseGroupIndex;a<this.groupCount;++a)this.distinguishAndPropagateGroup(a,this.chainOf[a],this.group3Of[a],this.seqcodes[a],this.firstAtomIndexes[a],(a==this.groupCount-1?this.ms.ac:this.firstAtomIndexes[a+
1])-1);if(null!=this.group3Lists){this.ms.msInfo.put("group3Lists",this.group3Lists);this.ms.msInfo.put("group3Counts",this.group3Counts);for(a=0;a<this.group3Counts.length;a++)null==this.group3Counts[a]&&(this.group3Counts[a]=E(0,0))}});c(b,"distinguishAndPropagateGroup",function(a,d,b,c,e,g){if(g<e)throw new NullPointerException;var j=null==b||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(d,b,c,e,g,this.specialAtomIndexes,this.ms.at);null==j?(j=(new JM.Group).setGroup(d,b,c,e,g),null!=
this.jbr&&(j.groupID=this.jbr.getGroupID(b)),c="o>"):c=j.isProtein()?"p>":j.isNucleic()?"n>":j.isCarbohydrate()?"c>":"o>";null!=b&&(this.countGroup(this.ms.at[e].mi,c,b),j.isNucleic()&&(b=null==this.htGroup1?null:this.htGroup1.get(b),null!=b&&(j.group1=b.charAt(0))));this.addGroup(d,j);this.groups[a]=j;j.groupIndex=a;for(a=g+1;--a>=e;)this.ms.at[a].group=j},"~N,JM.Chain,~S,~N,~N,~N");c(b,"addGroup",function(a,d){a.groupCount==a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));a.groups[a.groupCount++]=
d},"JM.Chain,JM.Group");c(b,"countGroup",function(a,d,b){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var e=(b+"   ").substring(0,3),g=this.group3Lists[c].indexOf(e);0>g&&(this.group3Lists[c]+=",["+e+"]",g=this.group3Lists[c].indexOf(e),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][v(g/6)]++;g=this.group3Lists[c].indexOf(",["+e);0<=g&&(this.group3Lists[c]=this.group3Lists[c].substring(0,g)+d+this.group3Lists[c].substring(g+
2));0<=a&&this.countGroup(-1,d,b)}},"~N,~S,~S");c(b,"freeze",function(){this.htAtomMap.clear();this.ms.ac<this.ms.at.length&&this.ms.growAtomArrays(this.ms.ac);this.ms.bondCount<this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount));for(var a=5;0<--a;){this.ms.numCached[a]=0;for(var d=this.ms.freeBonds[a],b=d.length;0<=--b;)d[b]=null}this.ms.setAtomNamesAndNumbers(0,this.baseAtomIndex,this.modelSet0,!1);this.findElementsPresent();this.ms.resetMolecules();this.currentChain=
this.model=null;!this.ms.haveBioModels||this.isPyMOLsession||this.isMutate?this.ms.freezeModels():(a=this.vwr.getBoolean(603979826),a=this.ms.calculateStructuresAllExcept(this.structuresDefinedInFile,a,!1,!0,!0,a,1405E3<=JV.JC.versionInt&&null==this.ms.getInfoM("DSSP1")?2:1),0<a.length&&JU.Logger.info(a))});c(b,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var d=this.ms.at[a];
if(null!=d){var b=d.getAtomicAndIsotopeNumber();b>=JU.Elements.elementNumberMax&&(b=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(b));this.ms.elementsPresent[d.mi].set(b)}}});c(b,"setupMinimization",function(){this.initialize2DMin();var a=new JU.V3;if(null!=this.vStereo){var d=this.vStereo.size();a:for(;0<=--d;)for(var b=this.vStereo.get(d),c=b.atom1,e=c.bonds,g=c.getBondCount();0<=--g;){var j=e[g];if(j!==b&&(j=j.getOtherAtom(c),a.sub2(j,c),0.1>Math.abs(a.x))){1025==b.order==
0>a.y&&(this.stereodir=-1);break a}}}this.set2dZ(a);if(null!=this.vStereo){a=JU.BSUtil.newBitSet2(this.baseAtomIndex,this.vwr.ms.ac);for(d=this.vStereo.size();0<=--d;){b=this.vStereo.get(d);c=1025==b.order?3:-3;b.order=1;6>b.atom1.getBondCount()&&(b.atom2.z!=b.atom1.z&&0>c==b.atom2.z<b.atom1.z)&&(c/=3);e=JU.JmolMolecule.getBranchBitSet(this.ms.at,b.atom2.i,a,null,b.atom1.i,!1,!0);e.set(b.atom2.i);for(g=e.nextSetBit(0);0<=g;g=e.nextSetBit(g+1))this.ms.at[g].z+=c;b.atom2.x=(b.atom1.x+b.atom2.x)/2;b.atom2.y=
(b.atom1.y+b.atom2.y)/2}this.vStereo=null}this.is2D=!1});c(b,"initialize2DMin",function(){for(var a=0,d=0,b=-1,c=this.baseAtomIndex,e=this.vwr.ms.ac,g=c;g<e;g++){var j=this.ms.at[g],k=j.getModelIndex();k!=b&&(b=k,this.ms.setInfo(k,"dimension","3D"));k=j.bonds;if(null!=k)for(var f=k.length;0<=--f;)if(null!=k[f]){var s=k[f].getOtherAtom(j);1!=s.getAtomNumber()&&s.getIndex()>g&&(a+=s.distance(j),d++)}}if(0!=d){a=1.45/(a/d);for(g=c;g<e;g++)this.ms.at[g].scale(a)}});c(b,"set2dZ",function(a){var d=this.baseAtomIndex,
b=this.vwr.ms.ac,c=JU.BS.newN(b),e=new JU.BS,g=JU.V3.new3(0,1,0),j=new JU.V3,k=new JU.BS;for(k.setBits(d,b);d<b;d++)!c.get(d)&&!e.get(d)&&(e=this.getBranch2dZ(d,-1,k,e,a,g,j,this.stereodir),c.or(e))},"JU.V3");c(b,"getBranch2dZ",function(a,d,b,c,e,g,j,k){c=JU.BS.newN(this.ms.ac);if(0>a)return c;b=JU.BSUtil.copy(b);0<=d&&b.clear(d);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,b,e,g,j,k);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");b.setBranch2dZ=c(b,"setBranch2dZ",function(a,d,b,c,e,g,j){var k=
a.i;if(b.get(k)&&(b.clear(k),d.set(k),null!=a.bonds))for(k=a.bonds.length;0<=--k;){var f=a.bonds[k];f.isHydrogen()||(f=f.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,f,c,e,g,j),JM.ModelLoader.setBranch2dZ(f,d,b,c,e,g,j))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");b.setAtom2dZ=c(b,"setAtom2dZ",function(a,d,b,c,e,g){b.sub2(d,a);b.z=0;b.normalize();e.cross(c,b);b=Math.acos(b.dot(c));g=0.4*-g*Math.sin(4*b);d.z=a.z+g},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3,~N");c(b,"finalizeShapes",function(){this.ms.sm=
this.vwr.shm;this.ms.sm.setModelSet(this.ms);this.ms.setBsHidden(this.vwr.slm.getHiddenSet());this.merging||this.ms.sm.resetShapes(!1);this.ms.sm.loadDefaultShapes(this.ms);this.ms.someModelsHaveAromaticBonds&&this.vwr.getBoolean(603979944)&&this.ms.assignAromaticBondsBs(!1,null);this.merging&&1==this.baseModelCount&&this.ms.sm.setShapePropertyBs(6,"clearModelIndex",null,null)});c(b,"undeleteAtom",function(a){this.ms.at[a].valence=0},"~N");b.createAtomDataSet=c(b,"createAtomDataSet",function(a,d,
b,c,e){if(null==c)return null;var g=a.getModelAdapter(),j=new JU.P3,k=d.at,f=a.getFloat(570425363);if(null!=d.unitCells)for(var s=e.nextSetBit(0);0<=s;s=e.nextSetBit(s+1))if(null!=k[s].atomSymmetry){f=-f;break}for(var s=-1,m=0,p=JU.BSUtil.cardinalityOf(e)==a.ms.ac,x=g.getAtomIterator(c);x.hasNext();){var A=x.getXYZ();if(!Float.isNaN(A.x+A.y+A.z))if(1145047050==b){s=e.nextSetBit(s+1);if(0>s)break;m++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+s+": "+k[s]+" --\x3e ("+A.x+","+A.y+","+A.z);d.setAtomCoord(s,
A.x,A.y,A.z)}else{j.setT(A);A=JU.BS.newN(d.ac);d.getAtomsWithin(f,j,A,-1);A.and(e);if(p)if(m=JU.BSUtil.cardinalityOf(A),0==m){JU.Logger.warn("createAtomDataSet: no atom found at position "+j);continue}else 1<m&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+m+" atoms found at position "+j);switch(b){case 1145047055:var n=x.getVib();if(null==n)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+j+" vib: "+n);d.setAtomCoords(A,1145047055,n);break;case 1128269825:d.setAtomProperty(A,b,
0,x.getOccupancy(),null,null,null);break;case 1111492619:d.setAtomProperty(A,b,0,x.getPartialCharge(),null,null,null);break;case 1111492620:d.setAtomProperty(A,b,0,x.getBfactor(),null,null,null)}}}switch(b){case 1145047055:d=g.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+d);a.setStringProperty("_vibrationName",d);break;case 1145047050:if(JU.Logger.info(m+" atom positions read"),d.recalculateLeadMidpointsAndWingVectors(-1),m==d.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS")});
n("JM");z(["JM.BondCollection"],"JM.ModelSet","java.util.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.M4 $.Measure $.P3 $.P4 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.bspt.Bspf J.c.PAL $.VDW JM.Atom $.AtomIteratorWithinModel $.AtomIteratorWithinModelSet $.HBond $.Model $.StateScript JS.ScriptCompiler JU.BSUtil $.BoxInfo $.Edge $.Elements $.Escape $.JmolMolecule $.Logger JV.JC".split(" "),function(){var b=r(function(){this.haveBioModels=!1;this.am=this.modelSetName=this.bsSymmetry=null;
this.mc=0;this.unitCells=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=this.closest=null;this.isXYZ=!1;this.msInfo=this.modelSetProperties=null;this.isBbcageDefault=this.someModelsHaveFractionalCoordinates=this.someModelsHaveAromaticBonds=this.someModelsHaveSymmetry=!1;this.stateScripts=this.boxInfo=this.bboxAtoms=this.bboxModels=null;this.thisStateModel=0;this.selectedMolecules=this.vibrationSteps=
null;this.showRebondTimes=!0;this.sm=this.bsAll=null;this.proteinStructureTainted=!1;this.vTemp=this.mat4t=this.mat4=this.matInv=this.matTemp=this.ptTemp2=this.ptTemp1=this.ptTemp=this.vOrientations=this.htPeaks=null;this.echoShapeActive=!1;this.defaultBBox=this.translations=this.modelSetTypeName=null;this.maxBondWarned=!1;u(this,arguments)},JM,"ModelSet",JM.BondCollection);y(b,function(a,d){I(this,JM.ModelSet,[]);this.vwr=a;this.modelSetName=d;this.selectedMolecules=new JU.BS;this.stateScripts=new JU.Lst;
this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.am=Array(1);this.modelNumbers=E(1,0);this.modelFileNumbers=E(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.closest=Array(1);this.ptTemp=new JU.P3;this.ptTemp1=new JU.P3;this.ptTemp2=new JU.P3;this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=new JU.M4;this.vTemp=new JU.V3;this.setupBC()},
"JV.Viewer,~S");c(b,"getBoxInfo",function(){return this.boxInfo});c(b,"releaseModelSet",function(){this.am=null;this.mc=0;this.unitCells=this.bsAll=this.bsSymmetry=this.am=this.closest[0]=null;this.releaseModelSetBC()});c(b,"getEchoStateActive",function(){return this.echoShapeActive});c(b,"setEchoStateActive",function(a){this.echoShapeActive=a},"~B");c(b,"getModelSetTypeName",function(){return this.modelSetTypeName});c(b,"getModelNumberIndex",function(a,d,b){if(d){for(d=0;d<this.mc;d++)if(this.modelNumbers[d]==
a||1E6>a&&this.modelNumbers[d]==1E6+a)return d;return-1}if(1E6>a)return a;for(d=0;d<this.mc;d++)if(this.modelFileNumbers[d]==a)return b&&this.isTrajectory(d)&&this.setTrajectory(d),d;return-1},"~N,~B,~B");c(b,"getModelDataBaseName",function(a){for(var d=0;d<this.mc;d++)if(a.equals(this.am[d].bsAtoms))return this.getInfo(d,"dbName");return null},"JU.BS");c(b,"setTrajectory",function(a){0<=a&&(this.isTrajectory(a)&&this.at[this.am[a].firstAtomIndex].mi!=a)&&this.trajectory.setModel(a)},"~N");c(b,"getBitSetTrajectories",
function(){return null==this.trajectory?null:this.trajectory.getModelsSelected()});c(b,"setTrajectoryBs",function(a){if(null!=this.trajectory)for(var d=0;d<this.mc;d++)a.get(d)&&this.setTrajectory(d)},"JU.BS");c(b,"morphTrajectories",function(a,d,b){0<=a&&(0<=d&&this.isTrajectory(a)&&this.isTrajectory(d))&&this.trajectory.morph(a,d,b)},"~N,~N,~N");c(b,"getTranslation",function(a){return null==this.translations||a>=this.translations.length?null:this.translations[a]},"~N");c(b,"translateModel",function(a,
d){if(null==d){var b=this.getTranslation(a);null!=b&&(d=JU.P3.newP(b),d.scale(-1),this.translateModel(a,d),this.translations[a]=null)}else{if(null==this.translations||this.translations.length<=a)this.translations=Array(this.mc);null==this.translations[a]&&(this.translations[a]=new JU.P3);this.translations[a].add(d);for(var b=this.am[a].bsAtoms,c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))this.at[c].add(d)}},"~N,JU.T3");c(b,"getFrameOffsets",function(a,d){if(null==a){if(d)for(var b=this.mc;0<=--b;){var c=
this.am[b];!c.isJmolDataFrame&&!c.isTrajectory&&this.translateModel(c.modelIndex,null)}return null}if(0>a.nextSetBit(0))return null;if(d){for(var e=JU.BSUtil.copy(a),g=null,j=new JU.P3,b=0;b<this.mc;b++){c=this.am[b];if(!c.isJmolDataFrame&&!c.isTrajectory){var k=e.nextSetBit(0);c.bsAtoms.get(k)&&(null==g?g=JU.P3.newP(this.at[k]):(j.sub2(g,this.at[k]),this.translateModel(b,j)))}e.andNot(c.bsAtoms)}return null}e=Array(this.mc);for(b=this.mc;0<=--b;)e[b]=new JU.P3;for(var j=g=0,k=null,f=null!=this.trajectory&&
this.trajectory.steps.size()==this.mc,s=f?this.mc:1,c=0;c<s;c++){f&&this.setTrajectory(c);for(b=0;b<=this.ac;b++)if(!(b<this.ac&&JM.AtomCollection.isDeleted(this.at[b]))){if(b==this.ac||this.at[b].mi!=g){0<j&&(k.scale(-1/j),0!=g&&k.sub(e[0]),j=0);if(b==this.ac)break;g=this.at[b].mi;k=e[g]}a.get(b)&&(k.add(this.at[b]),j++)}}e[0].set(0,0,0);return e},"JU.BS,~B");c(b,"getAtoms",function(a,d){switch(a){default:return JU.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,d),this.vwr.slm.bsDeleted);case 1073742358:var b=
d.intValue(),c=this.getModelNumberIndex(b,!0,!0);return 0>c&&0<b?new JU.BS:this.vwr.getModelUndeletedAtomsBitSet(c);case 1275203608:return b=B(-1,[null,null,null]),this.vwr.shm.getShapePropertyData(21,"getCenters",b),null==b[1]?new JU.BS:b[1]}},"~N,~O");c(b,"findNearestAtomIndex",function(a,d,b,c){if(0==this.ac)return-1;this.closest[0]=null;this.g3d.isAntialiased()&&(a<<=1,d<<=1);this.findNearest2(a,d,this.closest,b,c);this.sm.findNearestShapeAtomIndex(a,d,this.closest,b);a=null==this.closest[0]?
-1:this.closest[0].i;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(b,"calculatePointGroup",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,null,0,0,null,null,null)},"JU.BS");c(b,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!0,null,0,0,null,null,null)},"JU.BS");c(b,"getPointGroupAsString",function(a,d,b,c,e,g,j){return this.calculatePointGroupForFirstModel(a,!0,!1,d,b,c,e,g,j)},"JU.BS,~S,~N,~N,~A,JU.P3,~S");c(b,"calculatePointGroupForFirstModel",
function(a,d,b,c,e,g,j,k,f){var s=this.pointGroup,m=J.api.Interface.getSymmetry(this.vwr,"ms"),p=null,x=!1,A=!1,n=!1,r=null!=j,u=this.vwr.am.cmi;if(!r)if(j=null==a?-1:a.nextSetBit(0),0>u&&0<=j&&(u=this.at[j].mi),0>u&&(u=this.vwr.getVisibleFramesBitSet().nextSetBit(0),a=null),p=this.vwr.getModelUndeletedAtomsBitSet(u),n=null!=a&&p.cardinality()!=a.cardinality(),null!=a&&p.and(a),j=p.nextSetBit(0),0>j&&(p=this.vwr.getModelUndeletedAtomsBitSet(u),j=p.nextSetBit(0)),A=this.vwr.shm.getShapePropertyIndex(18,
"mad",j),x=null!=A&&0!=A.intValue()||this.vwr.tm.vibrationOn,A=null!=c&&0<=c.toUpperCase().indexOf(":POLY")){s=B(-1,[Integer.$valueOf(j),null]);this.vwr.shm.getShapePropertyData(21,"points",s);j=s[1];if(null==j)return null;p=null;x=!1;s=null}else j=this.at;var v;if(null!=c&&0<=(v=c.indexOf(":")))c=c.substring(0,v);if(null!=c&&0<=(v=c.indexOf(".")))e=JU.PT.parseInt(c.substring(v+1)),0>e&&(e=0),c=c.substring(0,v);s=m.setPointGroup(s,k,j,p,x,r?0:this.vwr.getFloat(570425382),this.vwr.getFloat(570425384),
null==p?j.length:p.cardinality(),n);!A&&!r&&(this.pointGroup=s);if(!d&&!b)return s.getPointGroupName();d=s.getPointGroupInfo(u,f,b,c,e,g);return b?d:(1<this.mc?"frame "+this.getModelNumberDotted(u)+"; ":"")+d},"JU.BS,~B,~B,~S,~N,~N,~A,JU.P3,~S");c(b,"getDefaultStructure",function(a,d){return this.haveBioModels?this.bioModelset.getAllDefaultStructures(a,d):""},"JU.BS,JU.BS");c(b,"deleteModelBonds",function(a){a=this.getModelAtomBitSetIncludingDeleted(a,!1);this.makeConnections(0,3.4028235E38,131071,
12291,a,a,null,!1,!1,0)},"~N");c(b,"makeConnections",function(a,d,b,c,e,g,j,k,f,s){this.moleculeCount=0;var m=1073741852==c&&2048!=b?new JU.SB:null;a=this.makeConnections2(a,d,b,c,e,g,j,k,f,s,m);null!=m&&this.addStateScript(m.toString(),null,null,null,null,!1,!0);return a},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(b,"setPdbConectBonding",function(a,d,b){for(var c=this.vwr.getMadBond();d<this.mc;d++){var e=this.getInfo(d,"PDB_CONECT_bonds");if(null!=e){var g=e.size();this.setInfo(d,"initialBondCount",
Integer.$valueOf(g));var j=this.getInfo(d,"PDB_CONECT_firstAtom_count_max"),k=j[0]+a,f=k+j[1];f>this.atomSerials.length&&(f=this.atomSerials.length);for(var j=j[2],s=E(j+1,0),m=k;m<f;m++)if(0<(k=this.atomSerials[m]))s[k]=m+1;for(f=0;f<g;f++){var k=e.get(f),m=k[0],p=k[1],k=k[2];if(!(0>m||0>p||m>j||p>j))if(m=s[m]-1,p=s[p]-1,!(0>m||0>p)){var x=this.at[m],A=this.at[p];null!=b&&(x.isHetero()&&b.set(m),A.isHetero()&&b.set(p));if(x.altloc==A.altloc||"\x00"==x.altloc||"\x00"==A.altloc)this.getOrAddBond(x,
A,k,2048==k?1:c,null,0,!1)}}}}},"~N,~N,JU.BS");c(b,"deleteAllBonds",function(){this.moleculeCount=0;for(var a=this.stateScripts.size();0<=--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.removeItemAt(a);this.deleteAllBonds2()});c(b,"includeAllRelatedFrames",function(a){for(var d=0,b=0;b<this.mc;b++){var c=this.isTrajectory(b),e=c&&a.get(d=this.am[b].trajectoryBaseIndex);if(a.get(b)){if(c&&!e){a.set(d);this.includeAllRelatedFrames(a);break}}else(c||this.isJmolDataFrameForModel(b)&&a.get(this.am[b].dataSourceFrame))&&
a.set(b)}},"JU.BS");c(b,"deleteModels",function(a){this.includeAllRelatedFrames(a);var d=a.cardinality();if(0==d)return null;this.moleculeCount=0;null!=this.msInfo&&this.msInfo.remove("models");for(var b=new JU.BS,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.clearDataFrameReference(c),b.or(this.am[c].bsAtoms);var e;if(d==this.mc)return e=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),e;this.validateBspf(!1);e=new JU.BS;for(var g=!0,j=!1,k=new JU.BS,f=b.nextSetBit(0),c=0;c<
this.mc;c++)b=this.am[c],c<this.mc-1&&(g=(new Boolean(g&(b.isOrderly||b.bsAtoms.length()<=f))).valueOf()),a.get(c)?(0<=b.fileIndex&&k.set(b.fileIndex),e.or(this.getModelAtomBitSetIncludingDeleted(c,!1))):0<=b.fileIndex&&k.get(b.fileIndex)&&(j=!0);if(!g||j)return this.vwr.deleteAtoms(e,!1),null;d=Array(this.mc-d);g=this.am;for(j=c=0;c<this.mc;c++)a.get(c)||(b=this.am[c],b.modelIndex=j,d[j++]=b);this.am=d;b=this.mc;k=this.getBondsForSelectedAtoms(e,!0);this.deleteBonds(k,!0);for(j=c=0;c<b;c++)if(a.get(c)){var s=
g[c],f=s.act;if(0!=f){var m=s.bsAtoms,s=s.firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,m);this.deleteModel(j,m,k);this.deleteModelAtoms(s,f,m);this.vwr.deleteModelAtoms(j,s,f,m);for(var p=b;--p>c;)g[p].fixIndices(j,f,m);this.vwr.shm.deleteShapeAtoms(B(-1,[d,this.at,E(-1,[j,s,f])]),m);this.mc--}}else j++;this.haveBioModels=!1;for(c=this.mc;0<=--c;)this.am[c].isBioModel&&(this.haveBioModels=!0,this.bioModelset.set(this.vwr,this));this.validateBspf(!1);this.bsAll=null;this.resetMolecules();this.isBbcageDefault=
!1;this.calcBoundBoxDimensions(null,1);return e},"JU.BS");c(b,"resetMolecules",function(){this.molecules=this.bsAll=null;this.moleculeCount=0;this.resetChirality()});c(b,"resetChirality",function(){if(this.haveChirality)for(var a=-1,d=this.ac;0<=--d;){var b=this.at[d];null!=b&&(b.setCIPChirality(0),b.mi!=a&&b.mi<this.am.length&&(this.am[a=b.mi].hasChirality=!1))}});c(b,"deleteModel",function(a,d,b){if(!(0>a)){this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,
a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var c=this.getInfoM("group3Lists"),e=this.getInfoM("group3Counts"),g=a+1;if(null!=c&&null!=c[g])for(var j=v(c[g].length/6);0<=--j;)0<e[g][j]&&(e[0][j]-=e[g][j],0==e[0][j]&&(c[0]=c[0].substring(0,6*j)+",["+c[0].substring(6*j+2)));null!=c&&(this.msInfo.put("group3Lists",
JU.AU.deleteElements(c,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(e,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(j=this.stateScripts.size();0<=--j;)this.stateScripts.get(j).deleteAtoms(a,b,d)||this.stateScripts.removeItemAt(j)}},"~N,JU.BS,JU.BS");c(b,"setAtomProperty",function(a,d,b,c,e,g,j){switch(d){case 1114249217:case 1112152066:case 1112152071:case 1112152073:case 1112152074:case 1649022989:case 1112152078:if(4<c&&(c=4),null!=g){b=
L(this.ac,0);try{var k=a.nextSetBit(0);for(e=0;0<=k;k=a.nextSetBit(k+1))b[k]=g[e++]}catch(f){if(D(f,Exception))return;throw f;}g=b}case 1112152070:case 1112152076:k=null;b=0;null==g?(16<c&&(c=16.1),0>c&&(c=0),b=v(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(g,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(d),b,k,a);return}this.setAPm(a,d,b,c,e,g,j)},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"getFileData",function(a){if(0>a)return"";var d=this.getInfo(a,"fileData");if(null!=d)return d;if(!this.getInfoB(a,
"isCIF"))return this.getPDBHeader(a);d=this.vwr.getCifData(a);this.setInfo(a,"fileData",d);return d},"~N");c(b,"addHydrogens",function(a,d){var b=a.get(0).mi,c=new JU.BS;if(this.isTrajectory(b)||1<this.am[b].getGroupCount())return c;this.growAtomArrays(this.ac+d.length);var e=this.vwr.rd,g=this.getDefaultMadFromOrder(1);this.am[b].resetDSSR(!1);for(var j=0,k=this.am[b].act+1;j<a.size();j++,k++){var f=a.get(j),s=this.addAtom(b,f.group,1,"H"+k,null,k,f.getSeqID(),k,d[j],NaN,null,0,0,100,NaN,null,!1,
0,null,NaN);s.setMadAtom(this.vwr,e);c.set(s.i);this.bondAtoms(f,s,1,g,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(b,"mergeModelArrays",function(a){this.at=a.at;this.bo=a.bo;this.stateScripts=a.stateScripts;this.proteinStructureTainted=a.proteinStructureTainted;this.thisStateModel=-1;this.bsSymmetry=a.bsSymmetry;this.modelFileNumbers=a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=a.modelNumbers;
this.frameTitles=a.frameTitles;this.haveChirality=a.haveChirality;this.boxInfo.setBoundBox(a.boxInfo.bbCorner0,a.boxInfo.bbCorner1,!0,1);null!=this.msInfo&&this.msInfo.remove("models");this.mergeAtomArrays(a)},"JM.ModelSet");c(b,"getUnitCell",function(a){return 0>a||a>=this.mc?null:null!=this.am[a].simpleCage?this.am[a].simpleCage:null!=this.unitCells&&a<this.unitCells.length&&null!=this.unitCells[a]&&this.unitCells[a].haveUnitCell()?this.unitCells[a]:null!=this.getInfo(a,"unitCellParams")?(null==
this.unitCells&&(this.unitCells=Array(this.mc)),this.haveUnitCells=!0,this.unitCells[a]=this.vwr.getSymTemp().setSymmetryInfo(a,this.am[a].auxiliaryInfo,null)):null},"~N");c(b,"getModelName",function(a){return 1>this.mc?"":0<=a?this.modelNames[a]:this.modelNumbersForAtomLabel[-1-a]},"~N");c(b,"getModelTitle",function(a){return this.getInfo(a,"title")},"~N");c(b,"getModelFileName",function(a){return this.getInfo(a,"fileName")},"~N");c(b,"getModelFileType",function(a){return this.getInfo(a,"fileType")},
"~N");c(b,"setFrameTitle",function(a,d){if("string"==typeof d)for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.frameTitles[b]=d;else for(var b=a.nextSetBit(0),c=0;0<=b;b=a.nextSetBit(b+1))c<d.length&&(this.frameTitles[b]=d[c++])},"JU.BS,~O");c(b,"getFrameTitle",function(a){return 0<=a&&a<this.mc?this.frameTitles[a]:""},"~N");c(b,"getModelNumberForAtomLabel",function(a){return this.modelNumbersForAtomLabel[a]},"~N");c(b,"getGroups",function(){for(var a=0,d=0;d<this.mc;d++)a+=this.am[d].getGroupCount();
for(var a=Array(a),b=d=0;d<this.mc;d++)for(var c=0;c<this.am[d].chainCount;c++)for(var e=0;e<this.am[d].chains[c].groupCount;e++)a[b]=this.am[d].chains[c].groups[e],a[b].groupIndex=b,b++;return a});c(b,"getUnitCellParams",function(){var a=this.getUnitCell(0);return null==a?null:a.getUnitCellParams()});c(b,"setCrystallographicDefaults",function(){return!this.haveBioModels&&this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates});c(b,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?
new JU.P3:(null==this.getDefaultBoundBox()?this.boxInfo:this.defaultBBox).getBoundBoxCenter()},"~N");c(b,"getBoundBoxCornerVector",function(){return this.boxInfo.getBoundBoxCornerVector()});c(b,"getBBoxVertices",function(){return this.boxInfo.getBoundBoxVertices()});c(b,"setBoundBox",function(a,d,b,c){0==c&&null!=this.msInfo&&(this.msInfo.remove("boundbox"),this.defaultBBox=null,this.isBbcageDefault=!1,this.calcBoundBoxDimensions(null,c=1));this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;
this.boxInfo.setBoundBox(a,d,b,c)},"JU.T3,JU.T3,~B,~N");c(b,"getBoundBoxCommand",function(a){if(!a&&null!=this.bboxAtoms)return"boundbox "+JU.Escape.eBS(this.bboxAtoms);this.ptTemp.setT(this.boxInfo.getBoundBoxCenter());var d=this.boxInfo.getBoundBoxCornerVector();a=a?"boundbox "+JU.Escape.eP(this.ptTemp)+" "+JU.Escape.eP(d)+"\n#or\n":"";this.ptTemp.sub(d);a+="boundbox corners "+JU.Escape.eP(this.ptTemp)+" ";this.ptTemp.scaleAdd2(2,d,this.ptTemp);d=Math.abs(8*d.x*d.y*d.z);return a+=JU.Escape.eP(this.ptTemp)+
" # volume = "+d},"~B");c(b,"findAtomsInRectangle",function(a){for(var d=this.vwr.getVisibleFramesBitSet(),b=new JU.BS,c=this.ac;0<=--c;){var e=this.at[c];JM.AtomCollection.isDeleted(e)||(d.get(e.mi)?e.checkVisible()&&a.contains(e.sX,e.sY)&&b.set(c):c=this.am[e.mi].firstAtomIndex)}return b},"JU.Rectangle");c(b,"getDefaultVdwType",function(a){return!this.am[a].isBioModel?J.c.VDW.AUTO_BABEL:0==this.am[a].hydrogenCount?J.c.VDW.AUTO_JMOL:J.c.VDW.AUTO_BABEL},"~N");c(b,"setRotationRadius",function(a,d){return this.isJmolDataFrameForModel(a)?
(this.am[a].defaultRotationRadius=d,!1):!0},"~N,~N");c(b,"calcRotationRadius",function(a,d,b){if(this.isJmolDataFrameForModel(a))return a=this.am[a].defaultRotationRadius,0==a?10:a;if(b&&null!=this.getDefaultBoundBox())return 1.2*(this.defaultBBox.getMaxDim()/2);if(0==this.ac)return 10;a=-2;b=0;for(var c=this.ac;0<=--c;){var e=this.at[c];if(!JM.AtomCollection.isDeleted(e))if(this.isJmolDataFrameForAtom(e)){for(a=e.mi;0<=c&&null!=this.at[c]&&this.at[c].mi==a;)c--;c++}else{if(e.mi!=a){a=e.mi;var g=
this.am[a].isBioModel?null:this.getUnitCell(a);if(null!=g)for(var j=g.getUnitCellVerticesNoOffset(),g=g.getCartesianOffset(),k=0;8>k;k++)this.ptTemp.setT(j[k]),this.ptTemp.add(g),b=Math.max(b,d.distance(this.ptTemp))}e=d.distance(e)+this.getRadiusVdwJmol(e);e>b&&(b=e)}}return 0==b?10:b},"~N,JU.P3,~B");c(b,"calcBoundBoxDimensions",function(a,d){null!=a&&0>a.nextSetBit(0)&&(a=null);if(!(null==a&&this.isBbcageDefault||0==this.ac)){if(null==this.getDefaultBoundBox())this.bboxModels=this.getModelBS(this.bboxAtoms=
JU.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.ac&&(this.isBbcageDefault=!0),null==a&&null!=this.unitCells&&this.calcUnitCellMinMax();else{var b=this.defaultBBox.getBoundBoxVertices();this.boxInfo.reset();for(var c=0;8>c;c++)this.boxInfo.addBoundBoxPoint(b[c])}this.boxInfo.setBbcage(d)}},"JU.BS,~N");c(b,"getDefaultBoundBox",function(){var a=this.getInfoM("boundbox");null==a?this.defaultBBox=null:(null==this.defaultBBox&&(this.defaultBBox=new JU.BoxInfo),this.defaultBBox.setBoundBoxFromOABC(a));
return this.defaultBBox});c(b,"getBoxInfo",function(a,d){if(null==a)return this.boxInfo;var b=new JU.BoxInfo;this.calcAtomsMinMax(a,b);b.setBbcage(d);return b},"JU.BS,~N");c(b,"calcAtomsMinMax",function(a,d){d.reset();for(var b=0,c=null==a,e=c?this.ac-1:a.nextSetBit(0);0<=e;e=c?e-1:a.nextSetBit(e+1)){b++;var g=this.at[e];null!=g&&!this.isJmolDataFrameForAtom(g)&&d.addBoundBoxPoint(g)}return b},"JU.BS,JU.BoxInfo");c(b,"calcUnitCellMinMax",function(){for(var a=new JU.P3,d=0;d<this.mc;d++)if(this.unitCells[d].getCoordinatesAreFractional())for(var b=
this.unitCells[d].getUnitCellVerticesNoOffset(),c=this.unitCells[d].getCartesianOffset(),e=0;8>e;e++)a.add2(c,b[e]),this.boxInfo.addBoundBoxPoint(a)});c(b,"calcRotationRadiusBs",function(a){for(var d=this.getAtomSetCenter(a),b=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var e=this.at[c],e=d.distance(e)+this.getRadiusVdwJmol(e);e>b&&(b=e)}return 0==b?10:b},"JU.BS");c(b,"getCenterAndPoints",function(a,d){for(var b,c,e=d?1:0,g=a.size();0<=--g;){var j=a.get(g);b=j[0];C(j[1],"JU.BS")?(c=j[1],e+=Math.min(b.cardinality(),
c.cardinality())):e+=Math.min(b.cardinality(),j[1].length)}var k=B(2,e,null);d&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(g=a.size();0<=--g;)if(j=a.get(g),b=j[0],C(j[1],"JU.BS")){c=j[1];for(var j=b.nextSetBit(0),f=c.nextSetBit(0);0<=j&&0<=f;j=b.nextSetBit(j+1),f=c.nextSetBit(f+1))k[0][--e]=this.at[j],k[1][e]=this.at[f],d&&(k[0][0].add(this.at[j]),k[1][0].add(this.at[f]))}else{c=j[1];j=b.nextSetBit(0);for(f=0;0<=j&&f<c.length;j=b.nextSetBit(j+1),f++)k[0][--e]=this.at[j],k[1][e]=c[f],d&&(k[0][0].add(this.at[j]),
k[1][0].add(c[f]))}d&&(k[0][0].scale(1/(k[0].length-1)),k[1][0].scale(1/(k[1].length-1)));return k},"JU.Lst,~B");c(b,"getAtomSetCenter",function(a){for(var d=new JU.P3,b=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||(b++,d.add(this.at[c]));1<b&&d.scale(1/b);return d},"JU.BS");c(b,"getAverageAtomPoint",function(){return this.getAtomSetCenter(this.vwr.bsA())});c(b,"setAPm",function(a,d,b,c,e,g,j){this.setAPa(a,d,b,c,e,g,j);switch(d){case 1094715418:case 1631586315:this.vwr.getBoolean(603979944)&&
this.assignAromaticBondsBs(!0,null)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"addStateScript",function(a,d,b,c,e,g,j){var k=this.vwr.am.cmi;g?(this.thisStateModel!=k&&(a="frame "+(0>k?"all #"+k:this.getModelNumberDotted(k))+";\n  "+a),this.thisStateModel=k):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,d,b,c,e,j);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(b,"freezeModels",function(){this.haveBioModels=!1;for(var a=this.mc;0<=--a;)this.haveBioModels=
(new Boolean(this.haveBioModels|this.am[a].freeze())).valueOf()});c(b,"getStructureList",function(){return this.vwr.getStructureList()});c(b,"getInfoM",function(a){return null==this.msInfo?null:this.msInfo.get(a)},"~S");c(b,"getMSInfoB",function(a){a=this.getInfoM(a);return C(a,Boolean)&&a.booleanValue()},"~S");c(b,"isTrajectory",function(a){return this.am[a].isTrajectory},"~N");c(b,"isTrajectorySubFrame",function(a){return this.am[a].trajectoryBaseIndex!=a},"~N");c(b,"isTrajectoryMeasurement",function(a){return null!=
this.trajectory&&this.trajectory.hasMeasure(a)},"~A");c(b,"getModelBS",function(a,d){var b=new JU.BS,c=0,e=null==a;d=(new Boolean(d&null!=this.trajectory)).valueOf();for(var g=e?0:a.nextSetBit(0);0<=g&&g<this.ac;g=e?g+1:a.nextSetBit(g+1))JM.AtomCollection.isDeleted(this.at[g])||(b.set(c=this.at[g].mi),d&&this.trajectory.getModelBS(c,b),c=this.am[c],c.isOrderly&&(g=c.firstAtomIndex+c.act-1));return b},"JU.BS,~B");c(b,"getIterativeModels",function(a){for(var d=new JU.BS,b=0;b<this.mc;b++)if(a||!this.isJmolDataFrameForModel(b))this.isTrajectorySubFrame(b)||
d.set(b);return d},"~B");c(b,"fillAtomData",function(a,d){if(0!=(d&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=E(this.ac,0);for(var b,c=0;c<this.molecules.length;c++){b=a.bsMolecules[c]=this.molecules[c].atomList;for(var e=b.nextSetBit(0);0<=e;e=b.nextSetBit(e+1))a.atomMolecule[e]=c}}0!=(d&8)?(b=E(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,b,null,512),a.hydrogenAtomCount=b[0]):(a.firstAtomIndex=0>a.modelIndex?
null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,d))},"J.atomdata.AtomData,~N");c(b,"getModelNumberDotted",function(a){return 1>this.mc||a>=this.mc||0>a?"":JU.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(b,"getModelNumber",function(a){return this.modelNumbers[2147483647==a?this.mc-1:a]},
"~N");c(b,"getModelProperty",function(a,d){var b=this.am[a].properties;return null==b?null:b.getProperty(d)},"~N,~S");c(b,"getModelAuxiliaryInfo",function(a){return 0>a?null:this.am[a].auxiliaryInfo},"~N");c(b,"setInfo",function(a,d,b){0<=a&&a<this.mc&&(null==b?this.am[a].auxiliaryInfo.remove(d):this.am[a].auxiliaryInfo.put(d,b))},"~N,~O,~O");c(b,"getInfo",function(a,d){return 0>a?null:this.am[a].auxiliaryInfo.get(d)},"~N,~S");c(b,"getInfoB",function(a,d){var b=this.am[a].auxiliaryInfo;return null!=
b&&b.containsKey(d)&&b.get(d).booleanValue()},"~N,~S");c(b,"getInfoI",function(a,d){var b=this.am[a].auxiliaryInfo;return null!=b&&b.containsKey(d)?b.get(d).intValue():-2147483648},"~N,~S");c(b,"getInsertionCountInModel",function(a){return this.am[a].insertionCount},"~N");b.modelFileNumberFromFloat=c(b,"modelFileNumberFromFloat",function(a){var d=v(Math.floor(a));for(a=v(Math.floor(1E4*(a-d+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*d+a},"~N");c(b,"getChainCountInModelWater",function(a,d){if(0>a){for(var b=
0,c=this.mc;0<=--c;)b+=this.am[c].getChainCount(d);return b}return this.am[a].getChainCount(d)},"~N,~B");c(b,"getGroupCountInModel",function(a){if(0>a){a=0;for(var d=this.mc;0<=--d;)a+=this.am[d].getGroupCount();return a}return this.am[a].getGroupCount()},"~N");c(b,"calcSelectedGroupsCount",function(){for(var a=this.vwr.bsA(),d=this.mc;0<=--d;)this.am[d].calcSelectedGroupsCount(a)});c(b,"isJmolDataFrameForModel",function(a){return null!=this.am&&0<=a&&a<this.mc&&this.am[a].isJmolDataFrame},"~N");
c(b,"isJmolDataFrameForAtom",function(a){return this.am[a.mi].isJmolDataFrame},"JM.Atom");c(b,"setJmolDataFrame",function(a,d,b){var c=this.am[null==a?this.am[b].dataSourceFrame:d];null==a&&(a=this.am[b].jmolFrameType);0<=d&&(null==c.dataFrames&&(c.dataFrames=new java.util.Hashtable),this.am[b].dataSourceFrame=d,this.am[b].jmolFrameType=a,c.dataFrames.put(a,Integer.$valueOf(b)));a.startsWith("quaternion")&&0>a.indexOf("deriv")&&(a=a.substring(0,a.indexOf(" ")),c.dataFrames.put(a,Integer.$valueOf(b)))},
"~S,~N,~N");c(b,"getJmolDataFrameIndex",function(a,d){if(null==this.am[a].dataFrames)return-1;var b=this.am[a].dataFrames.get(d);return null==b?-1:b.intValue()},"~N,~S");c(b,"clearDataFrameReference",function(a){for(var d=0;d<this.mc;d++){var b=this.am[d].dataFrames;if(null!=b)for(b=b.values().iterator();b.hasNext();)b.next().intValue()==a&&b.remove()}},"~N");c(b,"getJmolFrameType",function(a){return 0<=a&&a<this.mc?this.am[a].jmolFrameType:"modelSet"},"~N");c(b,"getJmolDataSourceFrame",function(a){return 0<=
a&&a<this.mc?this.am[a].dataSourceFrame:-1},"~N");c(b,"saveModelOrientation",function(a,d){this.am[a].orientation=d},"~N,JM.Orientation");c(b,"getModelOrientation",function(a){return this.am[a].orientation},"~N");c(b,"getPDBHeader",function(a){return this.am[a].isBioModel?this.am[a].getFullPDBHeader():this.getFileHeader(a)},"~N");c(b,"getFileHeader",function(a){if(0>a)return"";if(this.am[a].isBioModel)return this.getPDBHeader(a);a=this.getInfo(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=
a?a:"no header information found"},"~N");c(b,"getAltLocCountInModel",function(a){return this.am[a].altLocCount},"~N");c(b,"getAltLocIndexInModel",function(a,d){if("\x00"==d)return 0;var b=this.getAltLocListInModel(a);return 0==b.length?0:b.indexOf(d)+1},"~N,~S");c(b,"getInsertionCodeIndexInModel",function(a,d){if("\x00"==d)return 0;var b=this.getInsertionListInModel(a);return 0==b.length?0:b.indexOf(d)+1},"~N,~S");c(b,"getAltLocListInModel",function(a){a=this.getInfo(a,"altLocs");return null==a?"":
a},"~N");c(b,"getInsertionListInModel",function(a){a=this.getInfo(a,"insertionCodes");return null==a?"":a},"~N");c(b,"getModelSymmetryCount",function(a){return 0<this.am[a].biosymmetryCount?this.am[a].biosymmetryCount:null==this.unitCells||null==this.unitCells[a]?0:this.unitCells[a].getSpaceGroupOperationCount()},"~N");c(b,"getModelCellRange",function(a){return null==this.unitCells?null:this.unitCells[a].getCellRange()},"~N");c(b,"getLastVibrationVector",function(a,d){if(null!=this.vibrations&&a<
this.vwr.ms.mc)for(var b,c=0>a||this.isTrajectory(a)||a>=this.mc-1?this.ac:this.am[a+1].firstAtomIndex,e=0>=a?0:this.am[a].firstAtomIndex;--c>=e;)if((0>a||null!=this.at[c]&&this.at[c].mi==a)&&((1275072532==d||0==d)&&null!=(b=this.getModulation(c))||(4166==d||0==d)&&null!=(b=this.getVibration(c,!1)))&&b.isNonzero())return c;return-1},"~N,~N");c(b,"getModulationList",function(a,d,b){var c=new JU.Lst;if(null!=this.vibrations)for(var e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))C(this.vibrations[e],"J.api.JmolModulationSet")?
c.addLast(this.vibrations[e].getModulation(d,b,!1)):c.addLast(Float.$valueOf("O"==d?NaN:-1));return c},"JU.BS,~S,JU.P3");c(b,"getElementsPresentBitSet",function(a){if(0<=a)return this.elementsPresent[a];a=new JU.BS;for(var d=0;d<this.mc;d++)a.or(this.elementsPresent[d]);return a},"~N");c(b,"getMoleculeIndex",function(a,d){0==this.moleculeCount&&this.getMolecules();for(var b=0;b<this.moleculeCount;b++)if(this.molecules[b].atomList.get(a))return d?this.molecules[b].indexInModel:b;return 0},"~N,~B");
c(b,"getMoleculeBitSet",function(a){0==this.moleculeCount&&this.getMolecules();var d=JU.BSUtil.copy(a);a=JU.BSUtil.copy(a);for(var b=0,c=new JU.BS;0<=(b=a.length()-1);)c=this.getMoleculeBitSetForAtom(b),null==c?(a.clear(b),d.clear(b)):(a.andNot(c),d.or(c));return d},"JU.BS");c(b,"getMoleculeBitSetForAtom",function(a){0==this.moleculeCount&&this.getMolecules();for(var d=0;d<this.moleculeCount;d++)if(this.molecules[d].atomList.get(a))return this.molecules[d].atomList;return null},"~N");c(b,"getModelDipole",
function(a){if(0>a)return null;var d=this.getInfo(a,"dipole");null==d&&(d=this.getInfo(a,"DIPOLE_VEC"));return d},"~N");c(b,"calculateMolecularDipole",function(a,d){if(null!=d){var b=d.nextSetBit(0);if(0>b)return null;a=this.at[b].mi}if(0>a)return null;var c=b=0,e=0,g=0,j=new JU.V3,k=new JU.V3;null==d&&(d=this.getModelAtomBitSetIncludingDeleted(-1,!1));this.vwr.getOrCalcPartialCharges(this.am[a].bsAtoms,null);for(var f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+1))if(!(JM.AtomCollection.isDeleted(this.at[f])||
this.at[f].mi!=a)){var s=this.partialCharges[f];0>s?(c++,g+=s,k.scaleAdd2(s,this.at[f],k)):0<s&&(b++,e+=s,j.scaleAdd2(s,this.at[f],j))}if(0.015<Math.abs(e+g))return JU.Logger.info("Dipole calculation requires balanced charges: "+e+" "+g),null;if(0==c||0==b)return null;j.add(k);j.scale(4.8);return j},"~N,JU.BS");c(b,"getMoleculeCountInModel",function(a){var d=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var b=0;b<this.mc;b++)a==b&&(d+=this.am[b].moleculeCount);
return d},"~N");c(b,"calcSelectedMoleculesCount",function(){var a=this.vwr.bsA();0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var d=new JU.BS,b=0;b<this.moleculeCount;b++)JU.BSUtil.copy2(a,d),d.and(this.molecules[b].atomList),0<d.length()&&this.selectedMolecules.set(b)});c(b,"setCentroid",function(a,d){var b=this.getNotInCentroid(a,d);null!=b&&0<=b.nextSetBit(0)&&this.vwr.deleteAtoms(b,!1)},"JU.BS,~A");c(b,"getNotInCentroid",function(a,d){var b=
a.nextSetBit(0);if(0>b)return null;b=this.getUnitCell(this.at[b].mi);return null==b?null:b.notInCentroid(this,a,d)},"JU.BS,~A");c(b,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=null,d=Array(this.mc),b=null,c=0;c<this.mc;c++)d[c]=this.vwr.getModelUndeletedAtomsBitSet(c),a=this.am[c],a.moleculeCount=0,b=a.isBioModel?a.getBioBranches(b):null;this.molecules=JU.JmolMolecule.getMolecules(this.at,d,
b,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(b,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isValid)){this.showRebondTimes&&JU.Logger.startTimer("build bspf");var a=new J.bspt.Bspf(3);JU.Logger.debugging&&JU.Logger.debug("sequential bspt order");for(var d=JU.BS.newN(this.mc),b=this.ac;0<=--b;){var c=this.at[b];!JM.AtomCollection.isDeleted(c)&&!this.isTrajectorySubFrame(c.mi)&&
(a.addTuple(this.am[c.mi].trajectoryBaseIndex,c),d.set(c.mi))}this.showRebondTimes&&(JU.Logger.checkTimer("build bspf",!1),a.stats());for(b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))a.validateModel(b,!0);a.isValid=!0;this.bspf=a}});c(b,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||this.bspf.initialize(a,this.at,this.vwr.getModelUndeletedAtomsBitSet(a))},"~N");c(b,"setIteratorForPoint",function(a,d,b,c){0>d?a.setCenter(b,c):(this.initializeBspt(d),a.setModel(this,
d,this.am[d].firstAtomIndex,2147483647,b,c,null))},"J.api.AtomIndexIterator,~N,JU.T3,~N");c(b,"setIteratorForAtom",function(a,d,b,c,e){0>d&&(d=this.at[b].mi);d=this.am[d].trajectoryBaseIndex;this.initializeBspt(d);a.setModel(this,d,this.am[d].firstAtomIndex,b,this.at[b],c,e)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(b,"getSelectedAtomIterator",function(a,d,b,c,e){this.initializeBspf();if(e){e=this.getModelBS(a,!1);for(var g=e.nextSetBit(0);0<=g;g=e.nextSetBit(g+1))this.initializeBspt(g);
e=new JM.AtomIteratorWithinModelSet(e)}else e=new JM.AtomIteratorWithinModel;e.initialize(this.bspf,a,d,b,c,this.vwr.isParallel());return e},"JU.BS,~B,~B,~B,~B");f(b,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.am[a].getBondCount()},"~N");c(b,"getAtomCountInModel",function(a){return 0>a?this.ac:this.am[a].act},"~N");c(b,"getModelAtomBitSetIncludingDeletedBs",function(a){var d=new JU.BS;null==a&&null==this.bsAll&&(this.bsAll=JU.BSUtil.setAll(this.ac));if(null==a)d.or(this.bsAll);
else for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))d.or(this.getModelAtomBitSetIncludingDeleted(b,!1));return d},"JU.BS");c(b,"getModelAtomBitSetIncludingDeleted",function(a,d){var b=0>a?this.bsAll:this.am[a].bsAtoms;null==b&&(b=this.bsAll=JU.BSUtil.setAll(this.ac));return d?JU.BSUtil.copy(b):b},"~N,~B");c(b,"getAtomBitsMaybeDeleted",function(a,d){var b;switch(a){default:return this.getAtomBitsMDa(a,d,new JU.BS);case 1073741925:case 1073742189:case 1111490587:case 1073742128:case 1073741863:case 1086324744:return b=
new JU.BS,this.haveBioModels?this.bioModelset.getAtomBitsStr(a,d,b):b;case 1677721602:case 1073742331:return this.getAtomBitsMDb(a,d);case 1812599299:var c=this.getBoxInfo(d,1);b=this.getAtomsWithin(c.getBoundBoxCornerVector().length()+1E-4,c.getBoundBoxCenter(),null,-1);for(var e=b.nextSetBit(0);0<=e;e=b.nextSetBit(e+1))c.isWithin(this.at[e])||b.clear(e);return b;case 1094713350:b=JU.BSUtil.newBitSet2(0,this.ac);c=E(-1,[F(d.x)-1,F(d.y)-1,F(d.z)-1,F(d.x),F(d.y),F(d.z),0]);for(e=this.mc;0<=--e;){var g=
this.getUnitCell(e);null==g?JU.BSUtil.andNot(b,this.am[e].bsAtoms):b.andNot(g.notInCentroid(this,this.am[e].bsAtoms,c))}return b;case 1094713360:return this.getMoleculeBitSet(d);case 1073742363:return this.getSelectCodeRange(d);case 2097196:b=JU.BS.newN(this.ac);c=-1;g=0;for(e=this.ac;0<=--e;){var j=this.at[e];if(!JM.AtomCollection.isDeleted(j)){var k=j.atomSymmetry;if(null!=k){if(j.mi!=c){c=j.mi;if(null==this.getModelCellRange(c))continue;g=this.getModelSymmetryCount(c)}for(var j=0,f=g;0<=--f;)if(k.get(f)&&
1<++j){b.set(e);break}}}}return b;case 1088421903:return JU.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);case 1094713349:b=new JU.BS;c=this.vwr.getSymTemp();g=-1;for(e=this.ac;0<=--e;)JM.AtomCollection.isDeleted(this.at[e])||(k=this.at[e].getModelIndex(),g!=k&&(g=k,c=this.getUnitCell(g)),null!=c&&(this.ptTemp.setT(this.at[e]),c.toFractional(this.ptTemp,!1),c.isWithinUnitCell(this.ptTemp,d.x,d.y,d.z)&&b.set(e)));return b;case 1814695966:b=new JU.BS;g=C(d,"J.api.SymmetryInterface")?
d:this.vwr.getCurrentUnitCell();if(null==g)return b;g=g.getUnitCellMultiplied();for(e=this.ac;0<=--e;)null!=this.at[e]&&(this.ptTemp1.setT(this.at[e]),g.toFractional(this.ptTemp1,!1),g.checkPeriodic(this.ptTemp1)&&b.set(e));return b}},"~N,~O");c(b,"getSelectCodeRange",function(a){var d=new JU.BS,b=a[0],c=a[1];a=a[2];var e=this.vwr.getBoolean(603979822);0<=a&&(300>a&&!e)&&(a=this.chainToUpper(a));for(var g=this.mc;0<=--g;)if(this.am[g].isBioModel)for(var j=this.am[g],k,f=j.chainCount;0<=--f;){var s=
j.chains[f];if(-1==a||a==(k=s.chainID)||!e&&0<k&&300>k&&a==this.chainToUpper(k))for(var m=s.groups,s=s.groupCount,p=0;0<=p;)p=JM.ModelSet.selectSeqcodeRange(m,s,p,b,c,d)}return d},"~A");b.selectSeqcodeRange=c(b,"selectSeqcodeRange",function(a,d,b,c,e,g){var j,k,f,s=!1;for(k=b;k<d&&a[k].seqcode!=c;k++);if(k==d){if(0<b)return-1;s=!0;f=2147483647;for(var m=d;0<=--m;)if((j=a[m].seqcode)>c&&j-c<f)k=m,f=j-c;if(2147483647==f)return-1}if(2147483647==e)c=d-1,s=!0;else{for(c=k;c<d&&a[c].seqcode!=e;c++);if(c==
d){if(0<b)return-1;s=!0;f=2147483647;for(m=k;m<d;m++)if((j=a[m].seqcode)<e&&e-j<f)c=m,f=e-j;if(2147483647==f)return-1}}for(m=k;m<=c;++m)a[m].setAtomBits(g);return s?-1:c+1},"~A,~N,~N,~N,~N,JU.BS");c(b,"getAtomsWithinRadius",function(a,d,b,c,e){var g=new JU.BS;d=JU.BSUtil.andNot(d,this.vwr.slm.bsDeleted);var j=this.getSelectedAtomIterator(e,!1,!1,!1,!1);if(b){b=!this.vwr.g.legacyJavaFloat;var k=new JU.P3;e=null==e?JU.BSUtil.newBitSet2(0,this.mc):this.getModelBS(e,!1);e.and(this.getIterativeModels(!1));
for(var f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+1))for(var s=e.nextSetBit(0);0<=s;s=e.nextSetBit(s+1))0>a?this.getAtomsWithin(a,this.at[f].getFractionalUnitCoordPt(b,!0,k),g,s):(this.setIteratorForAtom(j,s,f,a,c),j.addAtoms(g))}else{null==e&&g.or(d);for(f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+1))0>a?this.getAtomsWithin(a,this.at[f],g,this.at[f].mi):(this.setIteratorForAtom(j,-1,f,a,c),j.addAtoms(g))}j.release();return g},"~N,JU.BS,~B,J.atomdata.RadiusData,JU.BS");c(b,"getAtomsWithin",function(a,d,
b,c){null==b&&(b=new JU.BS);if(0>a){a=-a;for(var e=this.ac;0<=--e;){var g=this.at[e];JM.AtomCollection.isDeleted(g)||0<=c&&g.mi!=c||!b.get(e)&&g.getFractionalUnitDistance(d,this.ptTemp1,this.ptTemp2)<=a&&b.set(g.i)}return b}for(var g=this.getSelectedAtomIterator(null,!1,!1,!1,!1),j=0<=c?JU.BSUtil.newAndSetBit(c):this.getIterativeModels(!0),k=j.nextSetBit(0);0<=k;k=j.nextSetBit(k+1))e=this.am[k].bsAtoms.nextSetBit(0),0>e||(this.setIteratorForAtom(g,c,e,-1,null),g.setCenter(d,a),g.addAtoms(b));g.release();
return b},"~N,JU.T3,JU.BS,~N");c(b,"deleteBonds",function(a,d){if(!d)for(var b=new JU.BS,c=new JU.BS,e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1)){var g=this.bo[e].atom1;this.am[g.mi].isModelKit||(b.clearAll(),c.clearAll(),b.set(g.i),c.set(this.bo[e].getAtomIndex2()),this.addStateScript("connect ",null,b,c,"delete",!1,!0))}this.dBb(a,d)},"JU.BS,~B");c(b,"makeConnections2",function(a,d,b,c,e,g,j,k,f,s,m){null==j&&(j=new JU.BS);var p=65535==b,x=131071==b,A=65537==b;x&&(b=1);var n=JU.Edge.isOrderH(b),
r=!1,u=!1,v=!1,w=!1;switch(c){case 12291:return this.deleteConnections(a,d,b,e,g,k,x);case 603979872:case 1073741852:if(515!=b){if(k){a=e;e=new JU.BS;g=new JU.BS;for(var y=a.nextSetBit(0);0<=y;y=a.nextSetBit(y+1))e.set(this.bo[y].atom1.i),g.set(this.bo[y].atom2.i)}return E(-1,[n?this.autoHbond(e,g,!1):this.autoBondBs4(e,g,null,j,this.vwr.getMadBond(),603979872==c,m),0])}u=w=!0;break;case 1086324745:r=u=!0;break;case 1073742025:u=!0;break;case 1073741904:v=!0}c=!r&&!p;this.defaultCovalentMad=this.vwr.getMadBond();
m=0>a;var x=0>d,z=m||x,B=!k||0.1!=a||1E8!=d;B&&(a=this.fixD(a,m),d=this.fixD(d,x));var C=this.getDefaultMadFromOrder(b),F=0,G=0,I=null,K=null,L=null,N="\x00",O=b|131072,Q=65535!=b&&0!=(b&512);try{for(y=e.nextSetBit(0);0<=y;y=e.nextSetBit(y+1)){if(k)I=this.bo[y],K=I.atom1,L=I.atom2;else{K=this.at[y];if(K.isDeleted())continue;N=this.isModulated(y)?"\x00":K.altloc}for(var P=k?0:g.nextSetBit(0);0<=P;P=g.nextSetBit(P+1)){if(k)P=2147483646;else{if(P==y)continue;L=this.at[P];if(null==L||K.mi!=L.mi||L.isDeleted())continue;
if("\x00"!=N&&N!=L.altloc&&"\x00"!=L.altloc)continue;I=K.getBond(L)}if(!(null==I?u:v)&&!(B&&!this.isInRange(K,L,a,d,m,x,z)||Q&&null!=I&&!this.allowAromaticBond(I)))if(null==I)j.set(this.bondAtoms(K,L,b,C,j,s,f,!0).index),F++;else if(c&&(I.setOrder(b),A&&(this.haveAtropicBonds=!0,I.setAtropisomerOptions()),this.bsAromatic.clear(I.index)),p||b==I.order||O==I.order||n&&I.isHydrogen())j.set(I.index),G++}}}catch(R){if(!D(R,Exception))throw R;}w&&this.assignAromaticBondsBs(!0,j);r||this.sm.setShapeSizeBs(1,
-2147483648,null,j);return E(-1,[F,G])},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N,JU.SB");c(b,"autoBondBs4",function(a,d,b,c,e,g,j){if(g)return this.autoBond_Pre_11_9_24(a,d,b,c,e);if(0==this.ac)return 0;0==e&&(e=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();g=this.vwr.getFloat(570425348);var k=this.vwr.getFloat(570425364),k=k*k,f=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var s=-1,m=null==a,p,x;m?(x=0,p=null):(a.equals(d)?p=a:(p=JU.BSUtil.copy(a),p.or(d)),x=p.nextSetBit(0));
for(var A=this.getSelectedAtomIterator(null,!1,!1,!0,!1),n=!1;0<=x&&x<this.ac;x=m?x+1:p.nextSetBit(x+1)){var r=m||a.get(x),u=m||d.get(x),v=this.at[x];if(!JM.AtomCollection.isDeleted(v)){var w=v.mi;if(w!=s){s=w;if(this.isJmolDataFrameForModel(w)){x=this.am[w].firstAtomIndex+this.am[w].act-1;continue}n=this.getInfoB(w,"autoBondUsingOccupation")}w=v.getBondingRadius();if(0!=w){var y=v.getFormalCharge(),z=0!=y;z&&(y=Math.signum(y));var B=null!=b&&b.get(x);for(this.setIteratorForAtom(A,-1,x,w+this.maxBondingRadius+
g,null);A.hasNext();){var C=this.at[A.next()];if(!C.isDeleted()){var D=C.i,E=m||a.get(D),F=m||d.get(D);!E&&!F||(!(r&&F||u&&E)||B&&b.get(D)||n&&null!=this.occupancies&&50>this.occupancies[x]!=50>this.occupancies[D]||z&&Math.signum(C.getFormalCharge())==y)||(E=this.isBondable(w,C.getBondingRadius(),A.foundDistance2(),k,g)?1:0,0<E&&this.autoBondCheck(v,C,E,e,c)&&(f++,null!=j&&j.append("connect ({"+x+"}) ({"+D+"});")))}}A.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return f},
"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B,JU.SB");c(b,"isBondable",function(a,d,b,c,e){if(0==a||0==d||b<c)return!1;a=a+d+e;return b<=a*a},"~N,~N,~N,~N,~N");c(b,"autoBondCheck",function(a,d,b,c,e){if(20<a.getCurrentBondCount()||20<d.getCurrentBondCount())return this.maxBondWarned||JU.Logger.warn("maximum auto bond count reached"),this.maxBondWarned=!0,!1;var g=a.getFormalCharge();if(0!=g){var j=d.getFormalCharge();if(0>g&&0>j||0<g&&0<j)return!1}if(a.altloc!=d.altloc&&"\x00"!=a.altloc&&"\x00"!=d.altloc&&null==
this.getModulation(a.i))return!1;this.getOrAddBond(a,d,b,c,e,0,!1);return!0},"JM.Atom,JM.Atom,~N,~N,JU.BS");c(b,"autoBond_Pre_11_9_24",function(a,d,b,c,e){if(0==this.ac)return 0;0==e&&(e=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var g=this.vwr.getFloat(570425348),j=this.vwr.getFloat(570425364),j=j*j,k=0;this.initializeBspf();for(var f=-1,s=this.ac;0<=--s;){var m=this.at[s];if(!JM.AtomCollection.isDeleted(m)){var p=null==a||a.get(s),x=null==d||d.get(s);if((p||x)&&!m.isDeleted()){var A=
m.mi;if(A!=f&&(f=A,this.isJmolDataFrameForModel(A))){for(;0<=--s&&!(JM.AtomCollection.isDeleted(this.at[s])||this.at[s].mi!=A););s++;continue}var n=m.getBondingRadius();if(0!=n){var r=n+this.maxBondingRadius+g;this.initializeBspt(A);A=this.bspf.getCubeIterator(A);for(A.initialize(m,r,!0);A.hasMoreElements();)if(r=A.nextElement(),!(r===m||r.isDeleted())){var u=r.i,v=null==a||a.get(u),w=null==d||d.get(u);if(!(!v&&!w||null!=b&&b.get(u)&&b.get(s)))if(p&&w||x&&v)u=this.isBondable(n,r.getBondingRadius(),
A.foundDistance2(),j,g)?1:0,0<u&&this.autoBondCheck(m,r,u,e,c)&&k++}A.release()}}}}return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(b,"autoHbond",function(a,d,b){if(b){for(var c=this.getModelBS(a,!1),e=c.nextSetBit(0);0<=e&&b;e=c.nextSetBit(e+1))b=!this.am[e].hasRasmolHBonds;if(b)return 0}b=!1;for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))if(1==this.at[e].getElementNumber()){b=!0;break}c=new JU.BS;e=this.vwr.getBoolean(603979853);if(null==d||e&&!b)return JU.Logger.info((null==d?"DSSP/DSSR ":"RasMol")+" pseudo-hbond calculation"),
this.calcRasmolHydrogenBonds(a,d,null,!1,2147483647,!1,c),-c.cardinality();JU.Logger.info(b?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var g=null;if(!b){g=new JU.BS;for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))switch(this.at[e].atomID){case 64:case 4:case 14:case 15:case 16:case 17:g.set(e)}}var j,k;b?(j=this.vwr.getFloat(570425361),k=1):(j=this.vwr.getFloat(570425360),k=JM.ModelSet.hbondMinRasmol*JM.ModelSet.hbondMinRasmol);var f=j*j,s=3.141592653589793*this.vwr.getFloat(570425359)/
180,m=0,p=0;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var x=null,A=null;d=this.getSelectedAtomIterator(d,!1,!1,!1,!1);for(e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1)){var n=this.at[e],r=n.getElementNumber(),u=1==r;if(!(u?!b:b||7!=r&&8!=r)){if(u){r=!1;x=n.bonds;if(null==x)continue;for(var v=!1,A=0;!v&&A<x.length;A++)v=x[A].getOtherAtom(n).getElementNumber(),v=7==v||8==v;if(!v)continue}else r=g.get(e);for(this.setIteratorForAtom(d,-1,n.i,j,null);d.hasNext();)if(v=this.at[d.next()],
x=v.getElementNumber(),!(v===n||(u?1==x:7!=x&&8!=x)||(p=d.foundDistance2())<k||p>f||r&&g.get(v.i)||n.isBonded(v)))if(this.v1.sub2(n,v),null!=(A=JM.ModelSet.checkMinAttachedAngle(n,s,this.v1,this.v2,b)))if(this.v1.scale(-1),null!=(x=JM.ModelSet.checkMinAttachedAngle(v,s,this.v1,this.v2,b))){var w=0,y;u&&!Float.isNaN(x.x)&&!Float.isNaN(A.x)?(y=4096,w=JM.HBond.calcEnergy(Math.sqrt(p),x.distance(n),x.distance(A),v.distance(A))/1E3):y=2048;c.set(this.addHBond(n,v,y,w));m++}}}d.release();this.sm.setShapeSizeBs(1,
-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return b?m:-m},"JU.BS,JU.BS,~B");b.checkMinAttachedAngle=c(b,"checkMinAttachedAngle",function(a,d,b,c,e){var g=a.bonds,j=!0,k=null;if(null!=g&&0<g.length)for(var f=3.4028235E38,s=g.length;0<=--s;)if(g[s].isCovalent()){var j=!1,m=g[s].getOtherAtom(a);if(e||1!=m.getElementNumber()){c.sub2(a,m);var p=c.angle(b);if(p<d)return null;p<f&&(k=m,f=p)}}return j?JU.P3.new3(NaN,0,0):k},"JM.Atom,~N,JU.V3,JU.V3,~B");c(b,"setStructureIndexes",
function(){for(var a,d=0,b=-1,c=-1,e=-1,g=0;g<this.ac;g++)if(!JM.AtomCollection.isDeleted(this.at[g])){if((c=this.at[g].mi)!=e)d=0,e=c,b=-1;if((a=this.at[g].group.getStrucNo())!=b&&0!=a)this.at[g].group.setStrucNo(++d),b=d}});c(b,"getModelInfoAsString",function(){var a=(new JU.SB).append('<models count="');a.appendI(this.mc).append('" modelSetHasVibrationVectors="').append(this.modelSetHasVibrationVectors()+'">\n<properties>');if(null!=this.modelSetProperties){for(var d=this.modelSetProperties.propertyNames();d.hasMoreElements();){var b=
d.nextElement();a.append('\n <property name="').append(b).append('" value=').append(JU.PT.esc(this.modelSetProperties.getProperty(b))).append(" />")}a.append("\n</properties>")}for(d=0;d<this.mc;++d)a.append('\n<model index="').appendI(d).append('" n="').append(this.getModelNumberDotted(d)).append('" id=').append(JU.PT.esc(""+this.getInfo(d,"modelID"))),b=this.vwr.getJDXBaseModelIndex(d),b!=d&&a.append(" baseModelId=").append(JU.PT.esc(this.getInfo(b,"jdxModelID"))),a.append(" name=").append(JU.PT.esc(this.getModelName(d))).append(" title=").append(JU.PT.esc(this.getModelTitle(d))).append(' hasVibrationVectors="').appendB(this.vwr.modelHasVibrationVectors(d)).append('" />');
a.append("\n</models>");return a.toString()});c(b,"getSymmetryInfoAsString",function(){for(var a=(new JU.SB).append("Symmetry Information:"),d=0;d<this.mc;++d){a.append("\nmodel #").append(this.getModelNumberDotted(d)).append("; name=").append(this.getModelName(d)).append("\n");var b=this.getUnitCell(d);a.append(null==b?"no symmetry information":b.getSymmetryInfoStr())}return a.toString()});c(b,"createModels",function(a){a=this.mc+a;var d=JU.AU.arrayCopyObject(this.am,a);this.validateBspf(!1);this.modelNumbers=
JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,a);for(var b=v(this.modelFileNumbers[this.mc-1]/1E6)+1,c=this.mc,e=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*b+ ++e,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=b+"."+e;this.thisStateModel=
-1;b=this.getInfoM("group3Lists");null!=b&&(c=this.getInfoM("group3Counts"),b=JU.AU.arrayCopyS(b,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",b),this.msInfo.put("group3Counts",c));this.unitCells=JU.AU.arrayCopyObject(this.unitCells,a);for(c=this.mc;c<a;c++)d[c]=(new JM.Model).set(this,c,-1,null,null,null),d[c].loadState=" model create #"+c+";";this.am=d;this.mc=a},"~N");c(b,"deleteAtoms",function(a){if(null!=a){for(var d=this.getModelBS(a,!1),b=new JU.BS,c=a.nextSetBit(0);0<=c&&c<this.ac;c=
a.nextSetBit(c+1))JM.AtomCollection.isDeleted(this.at[c])||this.at[c].$delete(b);for(var e=JU.BSUtil.copy(a),c=0;c<this.mc;c++){var g=this.am[c];g.resetDSSR(!1);g.bsAtomsDeleted.or(a);g.bsAtomsDeleted.and(g.bsAtoms);null!=g.bsAsymmetricUnit&&g.bsAsymmetricUnit.andNot(a);d.get(g.modelIndex)&&this.updateBasisFromSite(g.modelIndex);a=JU.BSUtil.andNot(g.bsAtoms,g.bsAtomsDeleted);g.firstAtomIndex=a.nextSetBit(0);g.act=a.cardinality();g.isOrderly=g.act==g.bsAtoms.length()}this.deleteBonds(b,!1);a=this.vwr.shm.getShape(6);
null!=a&&a.setProperty("deleteAtoms",null,e);this.validateBspf(!1);this.vwr.setModelkitPropertySafely("modelkeys",d)}},"JU.BS");c(b,"clearDB",function(a){this.getModelAuxiliaryInfo(this.at[a].mi).remove("dbName")},"~N");c(b,"adjustAtomArrays",function(a,d,b){this.ac=b;for(var c=d;c<b;c++){this.at[c]=this.at[a[c]];this.at[c].i=c;var e=this.am[this.at[c].mi];e.firstAtomIndex==a[c]&&(e.firstAtomIndex=c);e.bsAtoms.set(c)}if(null!=this.vibrations)for(c=d;c<b;c++)this.vibrations[c]=this.vibrations[a[c]];
if(null!=this.atomTensorList)for(c=d;c<b;c++)if(e=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=e)for(var g=e.length;0<=--g;){var j=e[g];null!=j&&(j.atomIndex1=c)}if(null!=this.atomNames)for(c=d;c<b;c++)this.atomNames[c]=this.atomNames[a[c]];if(null!=this.atomTypes)for(c=d;c<b;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomResnos)for(c=d;c<b;c++)this.atomResnos[c]=this.atomResnos[a[c]];if(null!=this.atomSerials)for(c=d;c<b;c++)this.atomSerials[c]=this.atomSerials[a[c]];if(null!=
this.atomSeqIDs)for(c=d;c<b;c++)this.atomSeqIDs[c]=this.atomSeqIDs[a[c]];if(null!=this.bfactor100s)for(c=d;c<b;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.occupancies)for(c=d;c<b;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.partialCharges)for(c=d;c<b;c++)this.partialCharges[c]=this.partialCharges[a[c]]},"~A,~N,~N");c(b,"growAtomArrays",function(a){this.at=JU.AU.arrayCopyObject(this.at,a);null!=this.vibrations&&(this.vibrations=JU.AU.arrayCopyObject(this.vibrations,
a));null!=this.occupancies&&(this.occupancies=JU.AU.arrayCopyF(this.occupancies,a));null!=this.bfactor100s&&(this.bfactor100s=JU.AU.arrayCopyShort(this.bfactor100s,a));null!=this.partialCharges&&(this.partialCharges=JU.AU.arrayCopyF(this.partialCharges,a));null!=this.atomTensorList&&(this.atomTensorList=JU.AU.arrayCopyObject(this.atomTensorList,a));null!=this.atomNames&&(this.atomNames=JU.AU.arrayCopyS(this.atomNames,a));null!=this.atomTypes&&(this.atomTypes=JU.AU.arrayCopyS(this.atomTypes,a));null!=
this.atomResnos&&(this.atomResnos=JU.AU.arrayCopyI(this.atomResnos,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a));null!=this.atomSeqIDs&&(this.atomSeqIDs=JU.AU.arrayCopyI(this.atomSeqIDs,a))},"~N");c(b,"addAtom",function(a,d,b,c,e,g,j,k,f,s,m,p,x,A,n,r,u,v,w,y){k=(new JM.Atom).setAtom(a,this.ac,f,s,w,k,b,p,u);this.am[a].act++;this.am[a].bsAtoms.set(this.ac);JU.Elements.isElement(b,1)&&this.am[a].hydrogenCount++;this.ac>=this.at.length&&this.growAtomArrays(this.ac+
100);this.at[this.ac]=k;this.setBFactor(this.ac,n,!1);this.setOccupancy(this.ac,A,!1);this.setPartialCharge(this.ac,x,!1);null!=r&&this.setAtomTensors(this.ac,r);k.group=d;k.colixAtom=this.vwr.cm.getColixAtomPalette(k,J.c.PAL.CPK.id);null!=c&&(null!=e&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=e),k.atomID=v,0==v&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=g&&(null==this.atomSerials&&(this.atomSerials=
E(this.at.length,0)),this.atomSerials[this.ac]=g);0!=j&&(null==this.atomSeqIDs&&(this.atomSeqIDs=E(this.at.length,0)),this.atomSeqIDs[this.ac]=j);null!=m&&this.setVibrationVector(this.ac,m);Float.isNaN(y)||this.setBondingRadius(this.ac,y);this.ac++;return k},"~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~N,JU.BS,~N");c(b,"getInlineData",function(a){var d=null;if(0<=a)d=this.am[a].loadScript;else for(a=this.mc;0<=--a&&!(0<(d=this.am[a].loadScript).length()););a=d.lastIndexOf('data "');
if(0>a)return d=JU.PT.getQuotedStringAt(d.toString(),0),JS.ScriptCompiler.unescapeString(d,0,d.length);a=d.indexOf2('"',a+7);var b=d.lastIndexOf('end "');return b<a||0>a?null:d.substring2(a+2,b)},"~N");c(b,"isAtomPDB",function(a){return 0<=a&&this.am[this.at[a].mi].isBioModel},"~N");c(b,"setAtomNamesAndNumbers",function(a,d,b,c){var e=-1;c&&(e=this.at[a].mi,a=this.am[e].firstAtomIndex);null==this.atomSerials&&(this.atomSerials=E(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var g=
this.isXYZ&&this.vwr.getBoolean(603979978),j=2147483647,k=1;a<this.ac;++a){var f=this.at[a];if(!JM.AtomCollection.isDeleted(f)){if(f.mi!=j){if(c&&2147483647!=j&&f.mi!=e)continue;j=f.mi;k=g?0:1}var s=this.atomSerials[a];if(a>=-d){if(0==s||c)this.atomSerials[a]=a<d?b.atomSerials[a]:k;if(null==this.atomNames[a]||c)this.atomNames[a]=(f.getElementSymbol()+this.atomSerials[a]).intern()}else s>k&&(k=s),c&&(this.atomNames[a]=(f.getElementSymbol()+s).intern());(!this.am[j].isModelKit||0<f.getElementNumber())&&
k++}}},"~N,~N,JM.AtomCollection,~B");b.setUnitCellOffset=c(b,"setUnitCellOffset",function(a,d,b){null!=a&&(null==d?a.setOffset(b):a.setOffsetPt(d))},"J.api.SymmetryInterface,JU.T3,~N");c(b,"connect",function(a){this.resetMolecules();for(var d=new JU.BS,b=0;b<a.length;b++){var c=a[b];if(!(null==c||2>c.length)){var e=F(c[0]),g=0>e;g&&(e=-1-e);var j=F(c[1]);if(!(0>j||e>=this.ac||j>=this.ac)){var k=2<c.length?F(c[2]):1;0>k&&(k&=65535);var f=3<c.length?sa(1E3*a[b][3]):this.getDefaultMadFromOrder(k);0==
k||0==f&&32768!=k&&!JU.Edge.isOrderH(k)?(c=this.at[e].getBond(this.at[j]),null!=c&&d.set(c.index)):this.bondAtoms(this.at[e],this.at[j],k,f,null,4<c.length?c[4]:0,g,!0)}}}0<=d.nextSetBit(0)&&this.deleteBonds(d,!1)},"~A");c(b,"setFrameDelayMs",function(a,d){for(var b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))this.am[this.am[b].trajectoryBaseIndex].frameDelay=a},"~N,JU.BS");c(b,"getFrameDelayMs",function(a){return a<this.am.length&&0<=a?this.am[this.am[a].trajectoryBaseIndex].frameDelay:0},"~N");c(b,
"getModelIndexFromId",function(a){var d=0<=a.indexOf("#"),b=a.toLowerCase().endsWith(".basemodel");b&&(a=a.substring(0,a.length-10));for(var c=-1,e=null,g=0;g<this.mc;g++){var j=this.getInfo(g,"modelID"),k=a.startsWith("~")?"~"+this.getModelNumberDotted(g):null;if(!(null==k&&null==j&&null==(j=this.getModelTitle(g)))){d&&(e=this.getModelFileName(g),e.endsWith("#molfile")?j=e:(e+="#",j=e+j));if(a.equalsIgnoreCase(j)||a.equalsIgnoreCase(k))return b?this.vwr.getJDXBaseModelIndex(g):g;null!=e&&a.startsWith(e)&&
(c=-2)}}return null==e&&!d?-2:c},"~S");c(b,"getModelSetAuxiliaryInfo",function(a){var d=this.msInfo;null==d&&(d=new java.util.Hashtable);if(null!=a||!d.containsKey("models")){for(var b=new JU.Lst,c=0;c<this.mc;++c)if(null==a||a.get(c)){var e=this.getModelAuxiliaryInfo(c);e.put("modelIndex",Integer.$valueOf(c));b.addLast(e)}d.put("models",b)}return d},"JU.BS");c(b,"getDihedralMap",function(a){for(var d=new JU.Lst,b=a.length,c=null,e=null,g=null,j=null,k=b-1;0<=--k;)for(var f=b;--f>k;)if(c=this.at[a[k]],
e=this.at[a[f]],c.isBonded(e))for(var s=b;0<=--s;)if(s!=k&&s!=f&&(g=this.at[a[s]]).isBonded(c))for(var m=b;0<=--m;)if(m!=k&&m!=f&&m!=s&&(j=this.at[a[m]]).isBonded(e)){var p=E(4,0);p[0]=g.i;p[1]=c.i;p[2]=e.i;p[3]=j.i;d.addLast(p)}b=d.size();a=JU.AU.newInt2(b);for(k=b;0<=--k;)a[b-k-1]=d.get(k);return a},"~A");c(b,"setModulation",function(a,d,b,c){if(null==this.bsModulated)if(d)this.bsModulated=new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var e=this.vwr.getFloat(1275072532),
g=!1,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){var k=this.getModulation(j);null!=k&&(k.setModTQ(this.at[j],d,b,c,e),null!=this.bsModulated&&this.bsModulated.setBitTo(j,d),g=!0)}g||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(b,"getBoundBoxOrientation",function(a,d,b){var c=0,e=0,g=0,j=null,k=null,f=d.nextSetBit(0),s=0;if(0<=f){e=null==this.vOrientations?0:this.vOrientations.length;if(0==e){j=Array(3375);e=0;s=new JU.P4;for(c=-7;7>=c;c++)for(g=-7;7>=g;g++)for(var m=0;14>=m;m++,e++)1<(j[e]=JU.V3.new3(c/
7,g/7,m/14)).length()&&--e;this.vOrientations=Array(e);for(c=e;0<=--c;)m=Math.sqrt(1-j[c].lengthSquared()),Float.isNaN(m)&&(m=0),s.set4(j[c].x,j[c].y,j[c].z,m),this.vOrientations[c]=JU.Quat.newP4(s)}var m=new JU.P3,s=3.4028235E38,p=null,x=new JU.BoxInfo;x.setMargin(1312817669==a?0:0.1);for(c=0;c<e;c++){j=this.vOrientations[c];x.reset();if(null==b)for(g=f;0<=g;g=d.nextSetBit(g+1))x.addBoundBoxPoint(j.transform2(this.at[g],m));else for(g=b.length;0<=--g;)x.addBoundBoxPoint(j.transform2(b[g],m));switch(a){default:case 1312817669:case 1073741864:case 1814695966:g=
(x.bbCorner1.x-x.bbCorner0.x)*(x.bbCorner1.y-x.bbCorner0.y)*(x.bbCorner1.z-x.bbCorner0.z);break;case 1111492629:g=x.bbCorner1.x-x.bbCorner0.x;break;case 1111492630:g=x.bbCorner1.y-x.bbCorner0.y;break;case 1111492631:g=x.bbCorner1.z-x.bbCorner0.z}g<s&&(k=j,p=x,x=new JU.BoxInfo,x.setMargin(0.1),s=g)}switch(a){default:return k;case 1814695966:a=p.getBoundBoxVertices();a=B(-1,[a[0],a[4],a[2],a[1]]);k=k.inv();for(c=0;4>c;c++)k.transform2(a[c],a[c]),0<c&&a[c].sub(a[0]);return a;case 1312817669:case 1073741864:j=
JU.Quat.newQ(k),c=p.bbCorner1.x-p.bbCorner0.x,e=p.bbCorner1.y-p.bbCorner0.y,g=p.bbCorner1.z-p.bbCorner0.z,c<e&&(m.set(0,0,1),j=JU.Quat.newVA(m,90).mulQ(j),k=c,c=e,e=k),e<g&&(g>c&&(m.set(0,1,0),j=JU.Quat.newVA(m,90).mulQ(j),k=c,c=g,g=k),m.set(1,0,0),j=JU.Quat.newVA(m,90).mulQ(j),k=e,e=g,g=k)}}return 1312817669==a?s+"\t{"+c+" "+e+" "+g+"}\t"+d:1814695966==a?null:null==j||0==j.getTheta()?new JU.Quat:j},"~N,JU.BS,~A");c(b,"getUnitCellForAtom",function(a){if(0>a||a>this.ac||null==this.at[a])return null;
if(null!=this.bsModulated){var d=this.getModulation(a),d=null==d?null:d.getSubSystemUnitCell();if(null!=d)return d}return this.getUnitCell(this.at[a].mi)},"~N");c(b,"clearCache",function(){for(var a=this.mc;0<=--a;)this.am[a].resetDSSR(!1)});c(b,"getSymMatrices",function(a){var d=this.getModelSymmetryCount(a);if(0==d)return null;var b=Array(d),c=this.am[a].biosymmetry;null==c&&(c=this.getUnitCell(a));for(a=d;0<=--a;)b[a]=c.getSpaceGroupOperation(a);return b},"~N");c(b,"getSymmetryInvariant",function(a){a=
this.getBasisAtom(a,!0);return null==a?E(0,0):this.getUnitCellForAtom(a.i).getInvariantSymops(a,null)},"~N");c(b,"getBsBranches",function(a){for(var d=v(a.length/6),b=Array(d),c=new java.util.Hashtable,e=0,g=0;e<d;e++,g+=6)if(!(1>Math.abs(a[g+5]-a[g+4]))){var j=F(a[g+1]),k=F(a[g+2]),f=""+j+"_"+k;if(!c.containsKey(f)){c.put(f,Boolean.TRUE);for(var f=this.vwr.getBranchBitSet(k,j,!0),s=this.at[j].bonds,j=this.at[j],m=0;m<s.length;m++){var p=s[m];if(p.isCovalent()&&(p=p.getOtherAtom(j).i,p!=k&&f.get(p))){f=
null;break}}b[e]=f}}return b},"~A");c(b,"recalculatePositionDependentQuantities",function(a,d){null!=this.vwr.shm.getShape(21)&&this.vwr.shm.getShapePropertyData(21,"move",B(-1,[a,d]));this.haveStraightness&&this.calculateStraightnessAll();this.recalculateLeadMidpointsAndWingVectors(-1);for(var b=this.getModelBS(a,!1),c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))if(this.sm.notifyAtomPositionsChanged(c,a,d),null!=d){var e=this.am[c];e.isContainedIn(a)&&(null==e.mat4&&(e.mat4=JU.M4.newM4(null)),e.mat4.mul2(d,
e.mat4))}},"JU.BS,JU.M4");c(b,"moveAtoms",function(a,d,b,c,e,g,j,k){if(null!=a){for(d=e.nextSetBit(0);0<=d;d=e.nextSetBit(d+1))a.rotTrans(this.at[d]),this.taintAtom(d,2);this.mat4.setM4(a);c=null}else if(k)j||(this.matInv.setM3(b),this.matInv.invert(),this.matInv.rotate(c));else{null==d?this.matTemp.setM3(b):(this.ptTemp.set(0,0,0),this.matInv.setM3(b),this.matInv.invert(),this.matTemp.mul2(d,b),this.matTemp.mul2(this.matInv,this.matTemp));j?(this.vTemp.setT(g),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),
this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);for(d=e.nextSetBit(0);0<=d;d=e.nextSetBit(d+1))j?this.mat4.rotTrans(this.at[d]):(this.ptTemp.add(this.at[d]),this.mat4.rotTrans(this.at[d]),this.ptTemp.sub(this.at[d])),this.taintAtom(d,2);j||(this.ptTemp.scale(1/e.cardinality()),null==c&&(c=new JU.V3),c.add(this.ptTemp))}if(null!=c){for(d=e.nextSetBit(0);0<=
d;d=e.nextSetBit(d+1))this.at[d].add(c),this.taintAtom(d,2);k||(this.mat4t.setIdentity(),this.mat4t.setTranslation(c),this.mat4.mul2(this.mat4t,this.mat4))}this.recalculatePositionDependentQuantities(e,this.mat4)},"JU.M4,JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(b,"setDihedrals",function(a,d,b){var c=v(a.length/6);1<b&&(b=1);for(var e=0,g=0;e<c;e++,g+=6){var j=d[e];if(!(null==j||j.isEmpty())){var k=this.at[F(a[g+1])],f=JU.V3.newVsub(this.at[F(a[g+2])],k),f=JU.A4.newVA(f,-((a[g+5]-a[g+4])*b)/57.29577951308232);
this.matTemp.setAA(f);this.ptTemp.setT(k);for(k=j.nextSetBit(0);0<=k;k=j.nextSetBit(k+1))this.at[k].sub(this.ptTemp),this.matTemp.rotate(this.at[k]),this.at[k].add(this.ptTemp),this.taintAtom(k,2)}}},"~A,~A,~N");c(b,"setAtomCoordsRelative",function(a,d){this.setAtomsCoordRelative(d,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(d,this.mat4)},"JU.T3,JU.BS");c(b,"setAtomCoords",function(a,d,b){this.setAtomCoord2(a,
d,b);switch(d){case 1111492626:case 1111492627:case 1111492628:case 1145047055:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(b,"invertSelected",function(a,d,b,c){this.resetChirality();if(null!=a)for(var e=c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1)){var g=2*(a.x-this.at[e].x);b=2*(a.y-this.at[e].y);var j=2*(a.z-this.at[e].z);this.setAtomCoordRelative(e,g,b,j)}else if(null!=d){a=JU.V3.new3(d.x,d.y,d.z);a.normalize();for(var k=Math.sqrt(d.x*d.x+d.y*d.y+d.z*d.z),e=
c.nextSetBit(0);0<=e;e=c.nextSetBit(e+1))j=2*-JU.Measure.distanceToPlaneD(d,k,this.at[e]),g=a.x*j,b=a.y*j,j*=a.z,this.setAtomCoordRelative(e,g,b,j)}else if(0<=b&&(d=this.at[b],a=d.bonds,null!=a)){g=new JU.BS;j=new JU.Lst;k=this.vwr.getModelUndeletedAtomsBitSet(d.mi);for(e=0;e<a.length;e++){var f=a[e].getOtherAtom(d);c.get(f.i)?g.or(JU.JmolMolecule.getBranchBitSet(this.at,f.i,k,null,b,!0,!0)):j.addLast(f)}0!=j.size()&&(a=JU.Measure.getCenterAndPoints(j)[0],c=JU.V3.newVsub(d,a),c=JU.Quat.newVA(c,180),
this.moveAtoms(null,null,c.getMatrix(),null,g,d,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS");c(b,"getCellWeights",function(a){var d=null,b=a.nextSetBit(0),c=-1,e;if(0<=b&&null!=(e=this.getUnitCell(c=this.at[b].mi))){e=e.getUnitCellMultiplied();this.getModelAtomBitSetIncludingDeleted(c,!0).and(a);for(var d=L(a.cardinality(),0),g=new JU.P3,j=0;0<=b;b=a.nextSetBit(b+1))c=this.at[b],g.setT(c),e.toFractional(g,!1),e.unitize(g),d[j++]=e.getCellWeight(g)}return d},"JU.BS");c(b,"getAtomGroupQuaternions",function(a,
d,b){var c=0,e=new JU.Lst;a=JU.BSUtil.copy(a);for(var g=new JU.BS,j=a.nextSetBit(0);0<=j&&c<d;j=a.nextSetBit(j+1)){var k=this.at[j].group;k.setAtomBits(g);a.andNot(g);var f=k.getQuaternion(b);if(null==f&&(this.am[this.at[j].mi].isBioModel||(f=k.getQuaternionFrame(this.at)),null==f))continue;c++;e.addLast(f)}return e.toArray(Array(e.size()))},"JU.BS,~N,~S");c(b,"getConformation",function(a,d,b,c){for(var e=new JU.BS,g=this.mc;0<=--g;)if(!(0<=a&&g!=a)){var j=this.am[g],k=this.vwr.getModelUndeletedAtomsBitSet(a);
null!=c&&k.and(c);if(!(0>k.nextSetBit(0)))if(d>j.altLocCount)1==d&&e.or(k);else{if(this.am[g].isBioModel){if(-1E3>d){var j=1E3+d,f=this.getAltLocListInModel(g);-32!=j&&0>f.indexOf(String.fromCharCode(-j))&&(j=-2147483648)}else 0>d?(f=this.getAltLocListInModel(g),j=-1-d,j=j>=f.length?-2147483648:-f.charAt(j).charCodeAt(0)):j=d;if(-2147483648==j)continue;this.am[g].getConformation(j,b,k,e)}else{var s=this.getAltLocCountInModel(g),f=this.getAltLocListInModel(g),m=new JU.BS;if(-1E3>d)var p=String.fromCharCode(-1E3-
d),j=f.indexOf(p);else j=Math.abs(d)-1;if(0>j||j>=s)continue;for(p=s;0<=--p;)p!=j&&k.andNot(this.getAtomBitsMDa(1073742355,f.substring(p,p+1),m))}e.or(k)}}return e},"~N,~N,~B,JU.BS");c(b,"getSequenceBits",function(a,d,b){return this.haveBioModels?this.bioModelset.getAllSequenceBits(a,d,b):b},"~S,JU.BS,JU.BS");c(b,"getBioPolymerCountInModel",function(a){return this.haveBioModels?this.bioModelset.getBioPolymerCountInModel(a):0},"~N");c(b,"getPolymerPointsAndVectors",function(a,d,b,c){this.haveBioModels&&
this.bioModelset.getAllPolymerPointsAndVectors(a,d,b,c)},"JU.BS,JU.Lst,~B,~N");c(b,"recalculateLeadMidpointsAndWingVectors",function(a){this.haveBioModels&&this.bioModelset.recalculatePoints(a)},"~N");c(b,"calcRasmolHydrogenBonds",function(a,d,b,c,e,g,j){this.haveBioModels&&this.bioModelset.calcAllRasmolHydrogenBonds(a,d,b,c,e,g,j,2)},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(b,"calculateStraightnessAll",function(){this.haveBioModels&&!this.haveStraightness&&this.bioModelset.calculateStraightnessAll()});
c(b,"calculateStruts",function(a,d){return this.haveBioModels?this.bioModelset.calculateStruts(a,d):0},"JU.BS,JU.BS");c(b,"getGroupsWithin",function(a,d){return this.haveBioModels?this.bioModelset.getGroupsWithinAll(a,d):new JU.BS},"~N,JU.BS");c(b,"getProteinStructureState",function(a,d){return this.haveBioModels?this.bioModelset.getFullProteinStructureState(a,d):""},"JU.BS,~N");c(b,"calculateStructures",function(a,d,b,c,e,g){return this.haveBioModels?this.bioModelset.calculateAllStuctures(a,d,b,
c,e,g):""},"JU.BS,~B,~B,~B,~B,~N");c(b,"calculateStructuresAllExcept",function(a,d,b,c,e,g,j){this.freezeModels();return this.haveBioModels?this.bioModelset.calculateAllStructuresExcept(a,d,b,c,e,g,j):""},"JU.BS,~B,~B,~B,~B,~B,~N");c(b,"recalculatePolymers",function(a){this.bioModelset.recalculateAllPolymers(a,this.getGroups())},"JU.BS");c(b,"calculatePolymers",function(a,d,b,c){null!=this.bioModelset&&this.bioModelset.calculateAllPolymers(a,d,b,c)},"~A,~N,~N,JU.BS");c(b,"calcSelectedMonomersCount",
function(){this.haveBioModels&&this.bioModelset.calcSelectedMonomersCount()});c(b,"setProteinType",function(a,d){this.haveBioModels&&this.bioModelset.setAllProteinType(a,d)},"JU.BS,J.c.STR");c(b,"setStructureList",function(a){this.haveBioModels&&this.bioModelset.setAllStructureList(a)},"java.util.Map");c(b,"setConformation",function(a){this.haveBioModels&&this.bioModelset.setAllConformation(a);return JU.BSUtil.copy(a)},"JU.BS");c(b,"getHeteroList",function(a){a=this.haveBioModels?this.bioModelset.getAllHeteroList(a):
null;return null==a?this.getInfoM("hetNames"):a},"~N");c(b,"getUnitCellPointsWithin",function(a,d,b,c){var e=new JU.Lst,g=null,j=null;c&&(g=new java.util.Hashtable,j=new JU.Lst,g.put("atoms",j),g.put("points",e));var k=null==d?-1:d.nextSetBit(0);d=this.vwr.getModelUndeletedAtomsBitSet(0>k?this.vwr.am.cmi:this.at[k].mi);0>k&&(k=d.nextSetBit(0));if(0<=k){var f=this.getUnitCellForAtom(k);if(null!=f){d=f.getIterator(this.vwr,this.at[k],d,a);for(null!=b&&d.setCenter(b,a);d.hasNext();)k=d.next(),b=d.getPosition(),
e.addLast(b),c&&j.addLast(Integer.$valueOf(k))}}return c?g:e},"~N,JU.BS,JU.P3,~B");c(b,"calculateDssrProperty",function(a){if(null!=a){if(null==this.dssrData||this.dssrData.length<this.ac)this.dssrData=L(this.ac,0);for(var d=0;d<this.ac;d++)this.dssrData[d]=NaN;for(d=this.mc;0<=--d;)this.am[d].isBioModel&&this.am[d].getAtomicDSSRData(this.dssrData,a)}},"~S");c(b,"getAtomicDSSRData",function(a){return null==this.dssrData||this.dssrData.length<=a?NaN:this.dssrData[a]},"~N");c(b,"getAtomCIPChiralityCode",
function(a){this.haveChirality=!0;var d=this.am[a.mi];d.hasChirality||(this.calculateChiralityForAtoms(d.bsAtoms,!1),d.hasChirality=!0);return a.getCIPChiralityCode()},"JM.Atom");c(b,"calculateChiralityForAtoms",function(a,d){this.haveChirality=!0;for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.at[b].setCIPChirality(0);J.api.Interface.getSymmetry(this.vwr,"ms").calculateCIPChiralityForAtoms(this.vwr,a);if(!d)return null;for(var c="",b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))c+=this.at[b].getCIPChirality(!1);
return c},"JU.BS,~B");c(b,"getPointTransf",function(a,d,b,c){this.isTrajectory(0<=a?a:d.mi)?this.trajectory.getFractional(d,c):c.setT(d);null!=b&&b.transform2(c,c)},"~N,JM.Atom,JU.Quat,JU.P3");c(b,"getSymmetryEquivAtoms",function(a,d,b){a=JU.BS.copy(a);var c=JU.BS.copy(a),e=a.nextSetBit(0);null==d&&(d=this.getUnitCellForAtom(e));if(null!=d){null==b&&(b=this.vwr.getModelUndeletedAtomsBitSet(this.at[e].mi));d=JU.BSUtil.copy(b);for(b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.getSymmetryEquivAtomsForAtom(b,
a,d,c)}return c},"JU.BS,J.api.SymmetryInterface,JU.BS");c(b,"getSymmetryEquivAtomsForAtom",function(a,d,b,c){a=this.at[a].getAtomSite();if(0<a)for(var e=b.nextSetBit(0);0<=e;e=b.nextSetBit(e+1))this.at[e].getAtomSite()==a&&(c.set(e),null!=d&&(d.clear(e),b.clear(e)))},"~N,JU.BS,JU.BS,JU.BS");c(b,"setSpaceGroup",function(a,d,b){null==this.unitCells&&(this.unitCells=Array(this.mc));this.unitCells[a]=d;this.haveUnitCells=!0;var c=1==d.getSpaceGroupOperationCount();d.setFinalOperations(3,null,null,-1,
-1,!1,null);var e=d.getSpaceGroupOperationCount();this.am[a].bsAsymmetricUnit=b;null==this.bsSymmetry&&(this.bsSymmetry=JU.BS.newN(this.ac));var g=this.vwr.getModelUndeletedAtomsBitSet(a);this.bsSymmetry.or(g);this.bsSymmetry.andNot(b);1<e&&this.setModelCage(a,null);var j=JU.P3.newP(d.getCartesianOffset());0==j.length()?j=null:(d.setOffsetPt(new JU.P3),this.setTaintedAtoms(g,2));if(c)this.fixP1AtomSites(d,g);else for(var k=0,f=g.nextSetBit(0);0<=f;f=g.nextSetBit(f+1)){null!=j&&this.at[f].sub(j);var s=
b.get(f);this.at[f].setSymop(s?1:0,!0);s&&this.setSite(this.at[f],++k,!0)}g.andNot(b);if(!c)for(var c=null!=this.occupancies,j=d.getSymmetryOperations(),k=new JU.P3,s=new JU.P3,m=new JU.P3,p=b.nextSetBit(0);0<=p;p=b.nextSetBit(p+1)){f=this.at[p];s.setT(f);d.toFractional(s,!0);d.unitize(s);var x=f.atomSite,A=c?this.occupancies[p]:0,f=g.nextSetBit(0);a:for(;0<=f;f=g.nextSetBit(f+1)){var n=this.at[f];if(!(n.atomNumberFlags!=n.atomNumberFlags||c&&A!=this.occupancies[f])){k.setT(n);d.toFractional(k,!0);
d.unitize(k);for(var r=0;r<e;r++)if(m.setT(s),j[r].rotTrans(m),d.unitize(m),1.96E-6>m.distanceSquared(k)){this.setSite(n,x,!0);g.clear(f);continue a}}}}g.isEmpty()||System.err.println("Model basis atoms not found for "+g);this.setInfo(a,"unitCellParams",d.getUnitCellParams());b=this.getInfo(a,"spaceGroup");null==this.getInfo(a,"spaceGroupOriginal")&&null!=b&&this.setInfo(a,"spaceGroupOriginal",b);this.setInfo(a,"spaceGroupAssigned",Boolean.TRUE);this.setInfo(a,"spaceGroup",d.getSpaceGroupName());
this.setInfo(a,"spaceGroupInfo",null);null!=this.am[a].simpleCage&&(d.getUnitCell(this.am[a].simpleCage.getUnitCellVectors(),!1,null),this.setInfo(a,"unitCellParams",d.getUnitCellParams()));this.setModelCage(a,null)},"~N,J.api.SymmetryInterface,JU.BS");c(b,"setModelCage",function(a,d){0<=a&&a<this.mc&&(this.am[a].setSimpleCage(d),this.haveUnitCells=!0)},"~N,J.api.SymmetryInterface");c(b,"fixP1AtomSites",function(a,d){if(!(null==a||1!=a.getSpaceGroupOperationCount()))for(var b=d.cardinality(),b=Array(b),
c=0,e=a.getPrecision(),e=e*e,g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1)){var j=this.at[g],k=new JU.A4;k.setT(j);a.toFractional(k,!0);a.unitize(k);for(var f=!1,s=0;s<c;s++){var m=b[s];if(j.atomNumberFlags==m.angle&&m.distanceSquared(k)<e){f=!0;this.setSite(j,s+1,!0);break}}f||(k.angle=j.atomNumberFlags,b[c]=k,this.setSite(j,++c,!0))}},"J.api.SymmetryInterface,JU.BS");c(b,"getBasisAtom",function(a,d){var b=this.at[a];if(!d||null!=this.getUnitCellForAtom(a)){var c=b.atomSite;if(0<c){var e=this.am[b.mi].bsAsymmetricUnit;
if(null!=e)for(var g=e.nextSetBit(0);0<=g;g=e.nextSetBit(g+1))if(this.at[g].atomSite==c)return this.at[g]}}return b},"~N,~B");c(b,"updateBasisFromSite",function(a){if(null!=this.getUnitCell(a)){var d=this.am[a].bsAsymmetricUnit;if(null!=d){d.clearAll();var b=new JU.BS;a=this.am[a].bsAtoms;for(var c=E(this.ac,0),e=0,g=a.nextSetBit(0);0<=g;g=a.nextSetBit(g+1))if(!JM.AtomCollection.isDeleted(this.at[g])){var j=this.at[g].atomSite;if(!b.get(j)){b.set(j);if(j>=c.length)continue;c[j]=++e;d.set(g)}this.setSite(this.at[g],
-1,!1);this.setSite(this.at[g],c[j],!0)}null==this.bsSymmetry&&(this.bsSymmetry=JU.BS.newN(this.ac));this.bsSymmetry.or(a);this.bsSymmetry.andNot(d)}}},"~N");c(b,"getConnectingAtoms",function(a,d){for(var b=new JU.BS,c=new JU.BS,e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))for(var g=this.at[e],j=g.bonds,k=0,f=g.getBondCount();0<=--f;)if(j[f].isCovalent()&&!a.get(k=j[f].getOtherAtom(g).i))b.set(e),c.set(k);a.or(c);d.or(c);return b},"JU.BS,JU.BS");c(b,"saveAtomPositions",function(){for(var a=Array(this.at.length),
d=a.length;0<=--d;){var b=this.at[d];JM.AtomCollection.isDeleted(b)||(a[d]=JU.P3.newP(b))}return a});c(b,"restoreAtomPositions",function(a){for(var d=a.length;0<=--d;){var b=this.at[d];JM.AtomCollection.isDeleted(b)||b.setT(a[d])}},"~A");b.hbondMinRasmol=2.5});n("JM");z(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){var b=r(function(){this.rotationMatrix=this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=
this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;u(this,arguments)},JM,"Orientation",null);N(b,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});y(b,function(a,d,b){this.vwr=a;null!=b?(this.pymolView=b,this.moveToText="moveTo -1.0 PyMOL "+JU.Escape.eAF(b)):(a.finalizeTransformParameters(),d?(d=a.ms.getInfoM("defaultOrientationMatrix"),null==d?this.rotationMatrix.setScale(1):
this.rotationMatrix.setM3(d)):a.tm.getRotation(this.rotationMatrix),this.xTrans=a.tm.getTranslationXPercent(),this.yTrans=a.tm.getTranslationYPercent(),this.zoom=a.tm.getZoomSetting(),this.center.setT(a.tm.fixedRotationCenter),this.windowCenteredFlag=a.tm.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=a.getBoolean(603979889),this.moveToText=a.tm.getMoveToText(-1,!1),this.navigationMode&&(this.xNav=a.tm.getNavigationOffsetPercent("X"),this.yNav=a.tm.getNavigationOffsetPercent("Y"),
this.navDepth=a.tm.navigationDepthPercent,this.navCenter=JU.P3.newP(a.tm.navigationCenter)),0!=a.tm.camera.z&&(this.cameraDepth=a.tm.getCameraDepth(),this.cameraX=a.tm.camera.x,this.cameraY=a.tm.camera.y))},"JV.Viewer,~B,~A");c(b,"getMoveToText",function(a){return a?"   "+this.moveToText+"\n  save orientation "+JU.PT.esc(this.saveName.substring(12))+";\n":this.moveToText},"~B");c(b,"restore",function(a,d){d?(this.vwr.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.vwr.setBooleanProperty("navigationMode",
this.navigationMode),null==this.pymolView?this.vwr.moveTo(this.vwr.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.vwr.tm.moveToPyMOL(this.vwr.eval,a,this.pymolView)):this.vwr.tm.setRotation(this.rotationMatrix);return!0},"~N,~B")});n("JM");z(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){var b=r(function(){this.modelIndex=0;this.script2=
this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;u(this,arguments)},JM,"StateScript",null);y(b,function(a,d,b,c,e,g,j){this.modelIndex=a;this.script1=d;this.bsBonds=JU.BSUtil.copy(b);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(e);this.script2=g;this.inDefinedStateBlock=j},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");c(b,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||
0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});f(b,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(JU.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms1));null!=this.bsAtoms2&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms2));null!=this.script2&&a.append(" ").append(this.script2);a=a.toString();a.endsWith(";")||(a+=";");return a});c(b,
"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(b,"deleteAtoms",function(a,d,b){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;JU.BSUtil.deleteBits(this.bsBonds,d);JU.BSUtil.deleteBits(this.bsAtoms1,b);JU.BSUtil.deleteBits(this.bsAtoms2,b);return this.isValid()},"~N,JU.BS,JU.BS");c(b,"setModelIndex",function(a){this.modelIndex=a},"~N")});n("JM");K(JM,"Structure");n("JM");var pb=r(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;
this.first=0;this.signFactor=1;this.reference=null;u(this,arguments)},JM,"TickInfo",null);y(pb,function(b){this.ticks=b},"JU.P3");n("JU");z(["JU.P3","$.V3"],"JU.BoxInfo",["java.util.Hashtable","JU.Measure","$.P4","JU.Point3fi"],function(){var b=r(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;u(this,arguments)},JU,"BoxInfo",null);N(b,function(){this.bbCorner0=new JU.P3;this.bbCorner1=new JU.P3;this.bbCenter=new JU.P3;this.bbVector=
new JU.V3;this.bbVertices=Array(8);for(var a=0;8>a;a++)JU.BoxInfo.unitBboxPoints[a]=JU.P3.new3(-1,-1,-1),JU.BoxInfo.unitBboxPoints[a].scaleAdd2(2,JU.BoxInfo.unitCubePoints[a],JU.BoxInfo.unitBboxPoints[a])});y(b,function(){for(var a=8;0<=--a;)this.bbVertices[a]=new JU.Point3fi;this.reset()});c(b,"reset",function(){this.isScaleSet=!1;this.bbCorner0.set(3.4028235E38,3.4028235E38,3.4028235E38);this.bbCorner1.set(-3.4028235E38,-3.4028235E38,-3.4028235E38)});b.scaleBox=c(b,"scaleBox",function(a,d){if(!(0==
d||1==d)){for(var b=new JU.P3,c=new JU.V3,e=0;8>e;e++)b.add(a[e]);b.scale(0.125);for(e=0;8>e;e++)c.sub2(a[e],b),c.scale(d),a[e].add2(b,c)}},"~A,~N");b.getVerticesFromOABC=c(b,"getVerticesFromOABC",function(a){for(var d=Array(8),b=0;7>=b;b++)d[b]=JU.P3.newP(a[0]),4==(b&4)&&d[b].add(a[1]),2==(b&2)&&d[b].add(a[2]),1==(b&1)&&d[b].add(a[3]);return d},"~A");b.getCanonicalCopy=c(b,"getCanonicalCopy",function(a,d){for(var b=Array(8),c=0;8>c;c++)b[JU.BoxInfo.toCanonical[c]]=JU.P3.newP(a[c]);JU.BoxInfo.scaleBox(b,
d);return b},"~A,~N");b.toOABC=c(b,"toOABC",function(a,d){var b=JU.P3.newP(a[0]),c=JU.P3.newP(a[4]),e=JU.P3.newP(a[2]),g=JU.P3.newP(a[1]);c.sub(b);e.sub(b);g.sub(b);null!=d&&b.add(d);return B(-1,[b,c,e,g])},"~A,JU.T3");c(b,"getBoundBoxCenter",function(){this.isScaleSet||this.setBbcage(1);return this.bbCenter});c(b,"getBoundBoxCornerVector",function(){this.isScaleSet||this.setBbcage(1);return this.bbVector});c(b,"getBoundBoxPoints",function(a){this.isScaleSet||this.setBbcage(1);return a?B(-1,[this.bbCenter,
JU.P3.newP(this.bbVector),this.bbCorner0,this.bbCorner1]):B(-1,[this.bbCorner0,this.bbCorner1])},"~B");c(b,"getBoundBoxVertices",function(){this.isScaleSet||this.setBbcage(1);return this.bbVertices});c(b,"setBoundBoxFromOABC",function(a){for(var d=JU.P3.newP(a[0]),b=new JU.P3,c=0;4>c;c++)b.add(a[c]);this.setBoundBox(d,b,!0,1)},"~A");c(b,"setBoundBox",function(a,d,b,c){if(null!=a){if(0==c)return;if(b){if(0==a.distance(d))return;this.bbCorner0.set(Math.min(a.x,d.x),Math.min(a.y,d.y),Math.min(a.z,d.z));
this.bbCorner1.set(Math.max(a.x,d.x),Math.max(a.y,d.y),Math.max(a.z,d.z))}else{if(0==d.x||0==d.y&&0==d.z)return;this.bbCorner0.set(a.x-d.x,a.y-d.y,a.z-d.z);this.bbCorner1.set(a.x+d.x,a.y+d.y,a.z+d.z)}}this.setBbcage(c)},"JU.T3,JU.T3,~B,~N");c(b,"setMargin",function(a){this.margin=a},"~N");c(b,"addBoundBoxPoint",function(a){this.isScaleSet=!1;JU.BoxInfo.addPoint(a,this.bbCorner0,this.bbCorner1,this.margin)},"JU.T3");b.addPoint=c(b,"addPoint",function(a,d,b,c){a.x-c<d.x&&(d.x=a.x-c);a.x+c>b.x&&(b.x=
a.x+c);a.y-c<d.y&&(d.y=a.y-c);a.y+c>b.y&&(b.y=a.y+c);a.z-c<d.z&&(d.z=a.z-c);a.z+c>b.z&&(b.z=a.z+c)},"JU.T3,JU.T3,JU.T3,~N");b.addPointXYZ=c(b,"addPointXYZ",function(a,d,b,c,e,g){a-g<c.x&&(c.x=a-g);a+g>e.x&&(e.x=a+g);d-g<c.y&&(c.y=d-g);d+g>e.y&&(e.y=d+g);b-g<c.z&&(c.z=b-g);b+g>e.z&&(e.z=b+g)},"~N,~N,~N,JU.P3,JU.P3,~N");c(b,"setBbcage",function(a){this.isScaleSet=!0;this.bbCenter.add2(this.bbCorner0,this.bbCorner1);this.bbCenter.scale(0.5);this.bbVector.sub2(this.bbCorner1,this.bbCenter);0<a?this.bbVector.scale(a):
(this.bbVector.x-=a/2,this.bbVector.y-=a/2,this.bbVector.z-=a/2);for(var d=8;0<=--d;){var b=this.bbVertices[d];b.setT(JU.BoxInfo.unitBboxPoints[d]);b.x*=this.bbVector.x;b.y*=this.bbVector.y;b.z*=this.bbVector.z;b.add(this.bbCenter)}1!=a&&(this.bbCorner0.setT(this.bbVertices[0]),this.bbCorner1.setT(this.bbVertices[7]))},"~N");c(b,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&a.y>=this.bbCorner0.y&&a.y<=this.bbCorner1.y&&a.z>=this.bbCorner0.z&&
a.z<=this.bbCorner1.z},"JU.P3");c(b,"getMaxDim",function(){return 2*this.bbVector.length()});c(b,"getInfo",function(a){var d=Double.$valueOf(Math.abs(8*this.bbVector.x*this.bbVector.y*this.bbVector.z));if("volume".equals(a))return d;var b=JU.P3.newP(this.bbCenter);return"center".equals(a)?b:null==a||"info".equals(a)?(a=new java.util.Hashtable,a.put("center",b),b=JU.V3.newVsub(this.bbCorner1,this.bbCorner0),a.put("dimensions",b),a.put("girth",Double.$valueOf(b.x+b.y+b.z)),a.put("area",Double.$valueOf(2*
(b.x*b.y+b.x*b.z+b.z*b.y))),a.put("volume",d),a):null},"~S");f(b,"toString",function(){return""+this.bbCorner0+this.bbCorner1});b.getBoxFacesFromOABC=c(b,"getBoxFacesFromOABC",function(a){var d=Array(6),b=new JU.V3,c=new JU.V3,e=new JU.P3,g=new JU.P3,j=new JU.P3;a=null==a?JU.BoxInfo.unitCubePoints:JU.BoxInfo.getVerticesFromOABC(a);for(var k=0;6>k;k++)e.setT(a[JU.BoxInfo.facePoints[k][0]]),g.setT(a[JU.BoxInfo.facePoints[k][1]]),j.setT(a[JU.BoxInfo.facePoints[k][2]]),d[k]=JU.Measure.getPlaneThroughPoints(e,
g,j,b,c,new JU.P4);return d},"~A");b.bbcageTickEdges=ba(-1,"z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""));b.uccageTickEdges=ba(-1,"zyx\x00\x00\x00\x00\x00\x00\x00\x00\x00".split(""));b.edges=O(-1,[0,1,0,2,0,4,1,3,1,5,2,3,2,6,3,7,4,5,4,6,5,7,6,7]);b.faceOrder=E(-1,[0,3,5,2,1,4]);b.facePoints=B(-1,[E(-1,[4,0,6]),E(-1,[4,6,5]),E(-1,[5,7,1]),E(-1,[1,3,0]),E(-1,[6,2,7]),E(-1,[1,0,5]),E(-1,[0,2,6]),E(-1,[6,7,5]),E(-1,[7,3,1]),E(-1,[3,2,0]),E(-1,[2,3,7]),E(-1,[0,4,5])]);b.unitCubePoints=B(-1,[JU.P3.new3(0,
0,0),JU.P3.new3(0,0,1),JU.P3.new3(0,1,0),JU.P3.new3(0,1,1),JU.P3.new3(1,0,0),JU.P3.new3(1,0,1),JU.P3.new3(1,1,0),JU.P3.new3(1,1,1)]);b.toCanonical=E(-1,[0,3,4,7,1,2,5,6]);b.unitBboxPoints=Array(8)});n("JU");z(["JU.BS"],"JU.BSUtil",null,function(){var b=G(JU,"BSUtil",null);b.newAndSetBit=c(b,"newAndSetBit",function(a){var d=JU.BS.newN(a+1);d.set(a);return d},"~N");b.areEqual=c(b,"areEqual",function(a,d){return null==a||null==d?null==a&&null==d:a.equals(d)},"JU.BS,JU.BS");b.haveCommon=c(b,"haveCommon",
function(a,d){return null==a||null==d?!1:a.intersects(d)},"JU.BS,JU.BS");b.cardinalityOf=c(b,"cardinalityOf",function(a){return null==a?0:a.cardinality()},"JU.BS");b.newBitSet2=c(b,"newBitSet2",function(a,d){var b=JU.BS.newN(d);b.setBits(a,d);return b},"~N,~N");b.setAll=c(b,"setAll",function(a){var d=JU.BS.newN(a);d.setBits(0,a);return d},"~N");b.andNot=c(b,"andNot",function(a,d){null!=d&&null!=a&&a.andNot(d);return a},"JU.BS,JU.BS");b.copy=c(b,"copy",function(a){return null==a?null:a.clone()},"JU.BS");
b.copy2=c(b,"copy2",function(a,d){if(null==a||null==d)return null;d.clearAll();d.or(a);return d},"JU.BS,JU.BS");b.copyInvert=c(b,"copyInvert",function(a,d){return null==a?null:JU.BSUtil.andNot(JU.BSUtil.setAll(d),a)},"JU.BS,~N");b.invertInPlace=c(b,"invertInPlace",function(a,d){return JU.BSUtil.copy2(JU.BSUtil.copyInvert(a,d),a)},"JU.BS,~N");b.toggleInPlace=c(b,"toggleInPlace",function(a,d){a.equals(d)?a.clearAll():0==JU.BSUtil.andNot(JU.BSUtil.copy(d),a).length()?JU.BSUtil.andNot(a,d):a.or(d);return a},
"JU.BS,JU.BS");b.deleteBits=c(b,"deleteBits",function(a,d){if(null==a||null==d)return a;var b=d.nextSetBit(0);if(0>b)return a;var c=a.length(),e=Math.min(c,d.length()),g;for(g=d.nextClearBit(b);g<e&&0<=g;g=d.nextClearBit(g+1))a.setBitTo(b++,a.get(g));for(g=e;g<c;g++)a.setBitTo(b++,a.get(g));b<c&&a.clearBits(b,c);return a},"JU.BS,JU.BS");b.shiftBits=c(b,"shiftBits",function(a,d,b,c){if(!(null==a||null==d)){for(var e=d.length(),g=JU.BS.newN(e),j=!1,k=!1,f=b,s=0,m=0;s<e&&m<c;s++)d.get(s)?(k&&g.set(s),
f=b,j=!1):a.get(m++)?(g.set(s),f&&(f=!1,k=j=!0)):f&&!j&&(k=!1);a.clearAll();a.or(g)}},"JU.BS,JU.BS,~B,~N");b.offset=c(b,"offset",function(a,d,b){if(null!=a){for(var c=JU.BS.newN(a.length()+b),e=a.nextSetBit(0);e>=d;e=a.nextSetBit(e+1))c.set(e+b);JU.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");b.setMapBitSet=c(b,"setMapBitSet",function(a,d,b,c){var e;a.containsKey(c)?e=a.get(c):a.put(c,e=new JU.BS);e.setBits(d,b+1)},"java.util.Map,~N,~N,~S");b.emptySet=new JU.BS});n("JU");z(["JU.Int2IntHash"],"JU.C","JU.AU $.CU $.PT $.SB J.c.PAL JU.Escape $.Logger".split(" "),
function(){var b=G(JU,"C",null);b.getColix=c(b,"getColix",function(a){if(0==a)return 0;var b=0;-16777216!=(a&4278190080)&&(b=JU.C.getTranslucentFlag(a>>24&255),a|=4278190080);var c=JU.C.colixHash.get(a);3==(c&3)&&(b=0);return(0<c?c:JU.C.allocateColix(a,!1))|b},"~N");b.allocateColix=c(b,"allocateColix",function(a,b){var c;if(b)c=2047;else{for(c=JU.C.colixMax;4<=--c;)if((a&16777215)==(JU.C.argbs[c]&16777215))return c;c=JU.C.colixMax}if(c>=JU.C.argbs.length){var e=b?c+1:2*JU.C.colixMax;2048<e&&(e=2048);
JU.C.argbs=JU.AU.arrayCopyI(JU.C.argbs,e);null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale=JU.AU.arrayCopyI(JU.C.argbsGreyscale,e))}JU.C.argbs[c]=a;null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale[c]=JU.CU.toFFGGGfromRGB(a));JU.C.colixHash.put(a,c);return 2047>c?JU.C.colixMax++:JU.C.colixMax},"~N,~B");b.setLastGrey=c(b,"setLastGrey",function(a){JU.C.calcArgbsGreyscale();JU.C.argbsGreyscale[2047]=JU.CU.toFFGGGfromRGB(a)},"~N");b.calcArgbsGreyscale=c(b,"calcArgbsGreyscale",function(){if(null==JU.C.argbsGreyscale){for(var a=
E(JU.C.argbs.length,0),b=JU.C.argbs.length;4<=--b;)a[b]=JU.CU.toFFGGGfromRGB(JU.C.argbs[b]);JU.C.argbsGreyscale=a}});b.getArgbGreyscale=c(b,"getArgbGreyscale",function(a){null==JU.C.argbsGreyscale&&JU.C.calcArgbsGreyscale();return JU.C.argbsGreyscale[a&-30721]},"~N");b.getColixO=c(b,"getColixO",function(a){if(null==a)return 0;if(C(a,"J.c.PAL"))return a===J.c.PAL.NONE?0:2;if(C(a,Integer))return JU.C.getColix(a.intValue());if("string"==typeof a)return JU.C.getColixS(a);if(C(a,Byte))return 0==a.byteValue()?
0:2;JU.Logger.debugging&&JU.Logger.debug("?? getColix("+a+")");return 22},"~O");b.getTranslucentFlag=c(b,"getTranslucentFlag",function(a){return 0==a?0:0>a?30720:Float.isNaN(a)||255<=a||1==a?16384:(v(Math.floor(1>a?256*a:15<=a?a:9>=a?v(Math.floor(a-1))<<5:256))>>5&15)<<11},"~N");b.isColixLastAvailable=c(b,"isColixLastAvailable",function(a){return 0<a&&2047==(a&2047)},"~N");b.getArgb=c(b,"getArgb",function(a){return JU.C.argbs[a&-30721]},"~N");b.isColixColorInherited=c(b,"isColixColorInherited",function(a){switch(a){case 0:case 1:return!0;
default:return 1==(a&-30721)}},"~N");b.getColixInherited=c(b,"getColixInherited",function(a,b){switch(a){case 0:return b;case 1:return b&-30721;default:return 1==(a&-30721)?b&-30721|a&30720:a}},"~N,~N");b.renderPass2=c(b,"renderPass2",function(a){a&=30720;return 0!=a&&30720!=a},"~N");b.isColixTranslucent=c(b,"isColixTranslucent",function(a){return 0!=(a&30720)},"~N");b.getChangeableColixIndex=c(b,"getChangeableColixIndex",function(a){return 0<=a?-1:a&2047},"~N");b.getColixTranslucent3=c(b,"getColixTranslucent3",
function(a,b,c){a&=-30721;0==a&&(a=1);return b?a|JU.C.getTranslucentFlag(c):a},"~N,~B,~N");b.copyColixTranslucency=c(b,"copyColixTranslucency",function(a,b){return JU.C.getColixTranslucent3(b,JU.C.isColixTranslucent(a),JU.C.getColixTranslucencyLevel(a))},"~N,~N");b.getColixTranslucencyFractional=c(b,"getColixTranslucencyFractional",function(a){a=JU.C.getColixTranslucencyLevel(a);return-1==a?0.5:0==a?0:255==a?1:a/256},"~N");b.getColixTranslucencyLabel=c(b,"getColixTranslucencyLabel",function(a){return"translucent "+
(30720==(a&30720)?-1:JU.C.getColixTranslucencyFractional(a))},"~N");b.getColixTranslucencyLevel=c(b,"getColixTranslucencyLevel",function(a){a=a>>11&15;switch(a){case 0:return 0;case 1:case 2:case 3:case 4:case 5:case 6:case 7:return a<<5;case 15:return-1;default:return 255}},"~N");b.getColixS=c(b,"getColixS",function(a){var b=JU.CU.getArgbFromString(a);return 0!=b?JU.C.getColix(b):"none".equalsIgnoreCase(a)?0:"opaque".equalsIgnoreCase(a)?1:2},"~S");b.getColixArray=c(b,"getColixArray",function(a){if(null==
a||0==a.length)return null;a=JU.PT.getTokens(a);for(var b=U(a.length,0),c=0;c<a.length;c++)if(b[c]=JU.C.getColix(JU.CU.getArgbFromString(a[c])),0==b[c])return null;return b},"~S");b.getHexCode=c(b,"getHexCode",function(a){return JU.Escape.escapeColor(JU.C.getArgb(a))},"~N");b.getHexCodes=c(b,"getHexCodes",function(a){if(null==a)return null;for(var b=new JU.SB,c=0;c<a.length;c++)b.append(0==c?"":" ").append(JU.C.getHexCode(a[c]));return b.toString()},"~A");b.getColixTranslucent=c(b,"getColixTranslucent",
function(a){var b=a>>24&255;return 255==b?JU.C.getColix(a):JU.C.getColixTranslucent3(JU.C.getColix(a),!0,b/255)},"~N");b.getBgContrast=c(b,"getBgContrast",function(a){return 128>(JU.CU.toFFGGGfromRGB(a)&255)?8:4},"~N");b.colixMax=4;b.argbs=E(128,0);b.argbsGreyscale=null;b.colixHash=new JU.Int2IntHash(256);for(var b=E(-1,[4278190080,4294944E3,4294951115,4278190335,4294967295,4278255615,4294901760,4278222848,4286611584,4290822336,4278255360,4286578688,4278190208,4286611456,4286578816,4278222976,4294902015,
4294967040,4294928820,4294956800]),a=0;a<b.length;++a)JU.C.getColix(b[a])});n("JU");z(null,"JU.ColorEncoder","java.util.Hashtable JU.AU $.CU $.Lst $.PT $.Rdr J.c.PAL JU.C $.Escape $.Logger JV.FileManager $.JC".split(" "),function(){var b=r(function(){this.argbsNucleic=this.argbsAmino=this.argbsShapely=this.argbsRwb=this.argbsRoygb=this.argbsCpk=this.paletteFriendly=this.paletteWB=this.paletteBW=this.vwr=null;this.ihalf=0;this.schemes=null;this.currentPalette=0;this.currentSegmentCount=1;this.isTranslucent=
!1;this.hi=this.lo=0;this.isReversed=!1;this.thisScale=this.userScale=null;this.thisName="scheme";this.isColorIndex=!1;this.ce=null;u(this,arguments)},JU,"ColorEncoder",null);N(b,function(){this.userScale=E(-1,[-8355712]);this.thisScale=E(-1,[-8355712])});y(b,function(a,d){null==a?(this.vwr=d,this.schemes=new java.util.Hashtable,this.argbsCpk=J.c.PAL.argbsCpk,this.argbsRoygb=JV.JC.argbsRoygbScale,this.argbsRwb=JV.JC.argbsRwbScale,this.argbsAmino=this.argbsNucleic=this.argbsShapely=null,this.ihalf=
v(JV.JC.argbsRoygbScale.length/3),this.ce=this):(this.ce=a,this.vwr=a.vwr,this.schemes=a.schemes)},"JU.ColorEncoder,JV.Viewer");c(b,"clearCache",function(){this.schemes.clear()});b.getSchemeIndex=c(b,"getSchemeIndex",function(a){for(var d=0;d<JU.ColorEncoder.colorSchemes.length;d++)if(JU.ColorEncoder.colorSchemes[d].equalsIgnoreCase(a))return 16<=d?d-16:13>d?d:-d;return-1},"~S");b.fixName=c(b,"fixName",function(a){if(a.equalsIgnoreCase("byelement"))return"byelement_jmol";var d=JU.ColorEncoder.getSchemeIndex(a);
return 0<=d?JU.ColorEncoder.colorSchemes[d]:0<=a.indexOf("/")?a:a.toLowerCase()},"~S");c(b,"makeColorScheme",function(a,d,b){a=JU.ColorEncoder.fixName(a);if(null==d){this.schemes.remove(a);a=this.createColorScheme(a,!1,b);if(b)switch(a){case 2147483647:return 0;case 12:this.paletteFriendly=this.getPaletteAC();break;case 10:this.paletteBW=this.getPaletteBW();break;case 11:this.paletteWB=this.getPaletteWB();break;case 0:case 1:this.argbsRoygb=JV.JC.argbsRoygbScale;break;case 6:case 7:this.argbsRwb=
JV.JC.argbsRwbScale;break;case 2:this.argbsCpk=J.c.PAL.argbsCpk;break;case 3:JU.ColorEncoder.getRasmolScale();break;case 17:this.getNucleic();break;case 5:this.getAmino();break;case 4:this.getShapely()}return a}this.schemes.put(a,d);this.setThisScheme(a,d);a=this.createColorScheme(a,!1,b);if(b)switch(a){case 10:this.paletteBW=this.thisScale;break;case 11:this.paletteWB=this.thisScale;break;case 0:case 1:this.argbsRoygb=this.thisScale;this.ihalf=v(this.argbsRoygb.length/3);break;case 6:case 7:this.argbsRwb=
this.thisScale;break;case 2:this.argbsCpk=this.thisScale;break;case 5:this.argbsAmino=this.thisScale;break;case 17:this.argbsNucleic=this.thisScale;break;case 4:this.argbsShapely=this.thisScale}return-1},"~S,~A,~B");c(b,"getShapely",function(){return null==this.argbsShapely?this.argbsShapely=this.vwr.getJBR().getArgbs(1073742144):this.argbsShapely});c(b,"getAmino",function(){return null==this.argbsAmino?this.argbsAmino=this.vwr.getJBR().getArgbs(2097154):this.argbsAmino});c(b,"getNucleic",function(){return null==
this.argbsNucleic?this.argbsNucleic=this.vwr.getJBR().getArgbs(2097166):this.argbsNucleic});c(b,"createColorScheme",function(a,d,b){if(a.equalsIgnoreCase("inherit"))return 15;var c=a.lastIndexOf("="),e=a.indexOf("/"),g=Math.max(c,a.indexOf("[")),c=JU.ColorEncoder.fixName(a),j=JU.ColorEncoder.getSchemeIndex(c);if(-1==j&&(0>g||0<e)){b=a;e=this.schemes.get(c);if(null==e)try{var k="~"==b.charAt(1);k&&(b=b.substring(1));for(c=null;;){if(0>b.indexOf("/")){0>b.indexOf(".")&&(b+=".lut.txt");var f=Array(1);
try{JU.Logger.info("ColorEncoder opening colorschemes/"+b),JU.Rdr.readAllAsString(JV.FileManager.getBufferedReaderForResource(this.vwr,new JU.C,"JU/","colorschemes/"+b),-1,!1,f,0)}catch(s){if(D(s,"java.io.IOException")){JU.Logger.info("ColorEncoder "+s);break}else throw s;}b=f[0]}else{b=JU.PT.rep(b," ","%20");JU.Logger.info("ColorEncoder opening "+b);var m=this.vwr.fm.getFileAsBytes(b,null);if("string"==typeof m){JU.Logger.info("ColorEncoder "+m);break}c=m;JU.Logger.info("ColorEncoder read "+c.length+
" bytes");var f=0,p=c.length;if(800==p||802==p)f=32;if(768==p-f||770==p-f)for(var e=E(256,0),p=256+f,x=0;256>x;x++)e[x]=JU.CU.rgb(c[x+f]&255,c[x+f+256]&255,c[x+f+512]&255);else b=String.instantialize(c)}if(null==e)for(var A=JU.PT.split(b.trim(),"\n"),p=A.length,e=E(p,0),n=0<p&&0>A[0].indexOf("."),x=0;x<p;x++){var r=JU.PT.getTokens(A[x]);if(3>r.length){e=null;break}var u=r.length;e[x]=n?JU.CU.rgb(JU.PT.parseInt(r[u-3]),JU.PT.parseInt(r[u-2]),JU.PT.parseInt(r[u-1])):JU.CU.colorTriadToFFRGB(JU.PT.parseFloat(r[u-
3]),JU.PT.parseFloat(r[u-2]),JU.PT.parseFloat(r[u-1]))}if(null!=e&&k){x=0;p=e.length-1;for(k=p+1>>1;x<k;x++){var v=e[x];e[x]=e[p-x];e[p-x]=v}}break}}catch(w){if(D(w,Exception))JU.Logger.info("ColorEncoder "+w),e=null;else throw w;}null==e&&(e=E(-1,[-1]));this.schemes.put(a,e);this.setThisScheme(a,e);return-1}if(0<=g){a=a.toLowerCase();c=JU.PT.replaceAllCharacters(a.substring(0,g)," =","");0<c.length&&(b=!0);p=0;a.length>g+1&&!a.contains("[")&&(a="["+a.substring(g+1).trim()+"]",a=JU.PT.rep(a.$replace("\n",
" "),"  "," "),a=JU.PT.rep(a,", ",",").$replace(" ",","),a=JU.PT.rep(a,",","]["));for(g=-1;0<=(g=a.indexOf("[",g+1));)p++;if(0==p)return this.makeColorScheme(c,null,b);e=E(p,0);for(p=0;0<=(g=a.indexOf("[",g+1));){x=a.indexOf("]",g);0>x&&(x=a.length-1);v=JU.CU.getArgbFromString(a.substring(g,x+1));0==v&&(v=JU.CU.getArgbFromString(a.substring(g+1,x).trim()));if(0==v)return JU.Logger.error("error in color value: "+a.substring(g,x+1)),0;e[p++]=v}return c.equals("user")?(this.setUserScale(e),-13):this.makeColorScheme(c,
e,b)}e=this.schemes.get(c);return null!=e?(this.setThisScheme(c,e),j):-1!=j?j:d?0:2147483647},"~S,~B,~B");c(b,"setUserScale",function(a){this.ce.userScale=a;this.makeColorScheme("user",a,!1)},"~A");c(b,"getColorSchemeArray",function(a){switch(a){case -1:return this.thisScale;case 0:return this.ce.argbsRoygb;case 1:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRoygb,0,-1);case 8:return JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,0,this.ce.ihalf);case 9:var d=JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,this.ce.argbsRoygb.length-
2*this.ce.ihalf,-1);a=E(this.ce.ihalf,0);for(var b=a.length,c=d.length;0<=--b&&0<=--c;)a[b]=d[c--];return a;case 12:return this.getPaletteAC();case 10:return this.getPaletteBW();case 11:return this.getPaletteWB();case 6:return this.ce.argbsRwb;case 7:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRwb,0,-1);case 2:return this.ce.argbsCpk;case 3:return JU.ColorEncoder.getRasmolScale();case 4:return this.ce.getShapely();case 17:return this.ce.getNucleic();case 5:return this.ce.getAmino();case -13:return this.ce.userScale;
case -14:return JU.AU.arrayCopyRangeRevI(this.ce.userScale,0,-1);default:return null}},"~N");c(b,"getColorIndexFromPalette",function(a,d,b,c,e){c=JU.C.getColix(this.getArgbFromPalette(a,d,b,c));e&&(a=(b-a)/(b-d),1<a?a=1:0.125>a&&(a=0.125),c=JU.C.getColixTranslucent3(c,!0,a));return c},"~N,~N,~N,~N,~B");c(b,"getPaletteColorCount",function(a){switch(a){case -1:return this.thisScale.length;case 10:case 11:return this.getPaletteBW().length;case 0:case 1:return this.ce.argbsRoygb.length;case 8:case 9:return this.ce.ihalf;
case 6:case 7:return this.ce.argbsRwb.length;case -13:case -14:return this.ce.userScale.length;case 2:return this.ce.argbsCpk.length;case 3:return JU.ColorEncoder.getRasmolScale().length;case 4:return this.ce.getShapely().length;case 17:return this.ce.getNucleic().length;case 5:return this.ce.getAmino().length;case 12:return this.getPaletteAC().length;default:return 0}},"~N");c(b,"getArgbFromPalette",function(a,d,b,c){if(Float.isNaN(a))return-8355712;var e=this.getPaletteColorCount(c);switch(c){case -1:return this.isColorIndex&&
(d=0,b=this.thisScale.length),this.thisScale[JU.ColorEncoder.quantize4(a,d,b,e)];case 10:return this.getPaletteBW()[JU.ColorEncoder.quantize4(a,d,b,e)];case 11:return this.getPaletteWB()[JU.ColorEncoder.quantize4(a,d,b,e)];case 0:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,d,b,e)];case 1:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(-a,-b,-d,e)];case 8:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,d,b,e)];case 9:return this.ce.argbsRoygb[this.ce.ihalf+2*JU.ColorEncoder.quantize4(a,
d,b,e)];case 6:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(a,d,b,e)];case 7:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(-a,-b,-d,e)];case -13:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(a,d,b,e)];case -14:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(-a,-b,-d,e)];case 2:return this.ce.argbsCpk[JU.ColorEncoder.colorIndex(a,e)];case 3:return JU.ColorEncoder.getRasmolScale()[JU.ColorEncoder.colorIndex(a,
e)];case 4:return this.ce.getShapely()[JU.ColorEncoder.colorIndex(a,e)];case 5:return this.ce.getAmino()[JU.ColorEncoder.colorIndex(a,e)];case 17:return this.ce.getNucleic()[JU.ColorEncoder.colorIndex(a-24+2,e)];case 12:return this.getPaletteAC()[JU.ColorEncoder.colorIndexRepeat(a,e)];default:return-8355712}},"~N,~N,~N,~N");c(b,"setThisScheme",function(a,d){this.thisName=a;this.thisScale=d;a.equals("user")&&(this.userScale=d);this.isColorIndex=0==a.indexOf("byelement")||0==a.indexOf("byresidue")},
"~S,~A");c(b,"getArgb",function(a){return this.isReversed?this.getArgbFromPalette(-a,-this.hi,-this.lo,this.currentPalette):this.getArgbFromPalette(a,this.lo,this.hi,this.currentPalette)},"~N");c(b,"getArgbMinMax",function(a,d,b){return this.isReversed?this.getArgbFromPalette(-a,-b,-d,this.currentPalette):this.getArgbFromPalette(a,d,b,this.currentPalette)},"~N,~N,~N");c(b,"getColorIndex",function(a){return this.isReversed?this.getColorIndexFromPalette(-a,-this.hi,-this.lo,this.currentPalette,this.isTranslucent):
this.getColorIndexFromPalette(a,this.lo,this.hi,this.currentPalette,this.isTranslucent)},"~N");c(b,"getColorKey",function(){for(var a=new java.util.Hashtable,d=this.getPaletteColorCount(this.currentPalette),b=new JU.Lst,c=L(d+1,0),e=(this.hi-this.lo)/d,g=e*(this.isReversed?-0.5:0.5),j=0;j<d;j++)c[j]=this.isReversed?this.hi-j*e:this.lo+j*e,b.addLast(JU.CU.colorPtFromInt(this.getArgb(c[j]+g),null));c[d]=this.isReversed?this.lo:this.hi;a.put("values",c);a.put("colors",b);a.put("min",Float.$valueOf(this.lo));
a.put("max",Float.$valueOf(this.hi));a.put("reversed",Boolean.$valueOf(this.isReversed));a.put("name",this.getCurrentColorSchemeName());return a});c(b,"getColorScheme",function(){return(this.isTranslucent?"translucent ":"")+(0>this.currentPalette?JU.ColorEncoder.getColorSchemeList(this.getColorSchemeArray(this.currentPalette)):this.getColorSchemeName(this.currentPalette))});c(b,"setColorScheme",function(a,d){this.isTranslucent=d;null!=a&&(this.currentPalette=this.createColorScheme(a,!0,!1))},"~S,~B");
c(b,"setRange",function(a,d,b){3.4028235E38==d&&(a=1,d=this.getPaletteColorCount(this.currentPalette)+1);this.lo=Math.min(a,d);this.hi=Math.max(a,d);this.isReversed=b},"~N,~N,~B");c(b,"getCurrentColorSchemeName",function(){return this.getColorSchemeName(this.currentPalette)});c(b,"getColorSchemeName",function(a){var d=Math.abs(a);return-1==a?this.thisName:d<JU.ColorEncoder.colorSchemes.length&&0<=d?JU.ColorEncoder.colorSchemes[d]:null},"~N");b.getColorSchemeList=c(b,"getColorSchemeList",function(a){if(null==
a)return"";for(var d="",b=0;b<a.length;b++)d+=(0==b?"":" ")+JU.Escape.escapeColor(a[b]);return d},"~A");b.getRasmolScale=c(b,"getRasmolScale",function(){if(null!=JU.ColorEncoder.rasmolScale)return JU.ColorEncoder.rasmolScale;JU.ColorEncoder.rasmolScale=E(J.c.PAL.argbsCpk.length,0);for(var a=J.c.PAL.argbsCpkRasmol[0]|4278190080,d=JU.ColorEncoder.rasmolScale.length;0<=--d;)JU.ColorEncoder.rasmolScale[d]=a;for(d=J.c.PAL.argbsCpkRasmol.length;0<=--d;)a=J.c.PAL.argbsCpkRasmol[d],JU.ColorEncoder.rasmolScale[a>>
24]=a|4278190080;return JU.ColorEncoder.rasmolScale});c(b,"getPaletteAC",function(){return null==this.ce.paletteFriendly?this.ce.paletteFriendly=E(-1,[8421504,1067945,11141282,13235712,16753152,2640510,8331387,10467374,12553008,339310,7209065,8626176,10906112,4488148,13907405,14219839,16759360,6984660,13918415,14809713,16764019]):this.ce.paletteFriendly});c(b,"getPaletteWB",function(){if(null!=this.ce.paletteWB)return this.ce.paletteWB;for(var a=E(JV.JC.argbsRoygbScale.length,0),d=0;d<a.length;d++){var b=
1/a.length*(a.length-d);a[d]=JU.CU.colorTriadToFFRGB(b,b,b)}return this.ce.paletteWB=a});b.getPaletteAtoB=c(b,"getPaletteAtoB",function(a,d,b){2>b&&(b=JV.JC.argbsRoygbScale.length);var c=E(b,0),e=L(3,0),g=L(3,0);JU.CU.toRGB3f(a,e);JU.CU.toRGB3f(d,g);a=(g[0]-e[0])/(b-1);d=(g[1]-e[1])/(b-1);for(var g=(g[2]-e[2])/(b-1),j=0;j<b;j++)c[j]=JU.CU.colorTriadToFFRGB(e[0]+a*j,e[1]+d*j,e[2]+g*j);return c},"~N,~N,~N");c(b,"getPaletteBW",function(){if(null!=this.ce.paletteBW)return this.ce.paletteBW;for(var a=
E(JV.JC.argbsRoygbScale.length,0),d=0;d<a.length;d++){var b=1/a.length*d;a[d]=JU.CU.colorTriadToFFRGB(b,b,b)}return this.ce.paletteBW=a});c(b,"quantize",function(a,d){var b=this.getPaletteColorCount(this.currentPalette);a=(F(a*b)+(d?0:1))/b;return 0>=a?this.lo:1<=a?this.hi:this.lo+(this.hi-this.lo)*a},"~N,~B");b.quantize4=c(b,"quantize4",function(a,d,b,c){b-=d;if(0>=b||Float.isNaN(a))return v(c/2);a-=d;if(0>=a)return 0;a=F(a/(b/c)+1E-4);a>=c&&(a=c-1);return a},"~N,~N,~N,~N");b.colorIndex=c(b,"colorIndex",
function(a,d){return v(Math.floor(0>=a||a>=d?0:a))},"~N,~N");b.colorIndexRepeat=c(b,"colorIndexRepeat",function(a,d){return v(Math.floor(0>=a?0:a))%d},"~N,~N");b.colorSchemes=B(-1,"roygb bgyor byelement_jmol byelement_rasmol byresidue_shapely byresidue_amino rwb bwr low high bw wb friendly user resu inherit rgb bgr jmol rasmol byresidue byresidue_nucleic".split(" "));b.rasmolScale=null;b.argbsChainAtom=null;b.argbsChainHetero=null});n("JU");z(null,"JU.CommandHistory",["JU.Lst"],function(){var b=r(function(){this.commandList=
null;this.maxSize=100;this.cursorPos=this.nextCommand=0;this.isOn=!0;this.lstStates=null;u(this,arguments)},JU,"CommandHistory",null);y(b,function(){this.reset(100)});c(b,"clear",function(){this.reset(this.maxSize)});c(b,"reset",function(a){this.maxSize=a;this.commandList=new JU.Lst;this.nextCommand=0;this.commandList.addLast("");this.cursorPos=0},"~N");c(b,"setMaxSize",function(a){if(a!=this.maxSize){for(2>a&&(a=2);this.nextCommand>a;)this.commandList.removeItemAt(0),this.nextCommand--;this.nextCommand>
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(null!=this.b$.get(J.c.CBK.MESSAGE)||null!=this.statusForm||null!=this.statusText))this.doTranslate&&null==this.getValue("doTranslate",null)&&(this.doTranslate=!1,JU.Logger.warn("Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet()")),this.doTranslate&&JU.Logger.warn("Note -- Automatic language translation may affect parsing of message callbacks messages; use scriptCallback or errorCallback to process errors");
this.doTranslate||(J.i18n.GT.setDoTranslate(!1),JU.Logger.warn("Note -- language translation disabled"));this.getBooleanValue("popupMenu",!0)||this.viewer.getProperty("DATA_API","disablePopupMenu",null);d=this.getJmolParameter("menuFile");null!=d&&this.viewer.setMenu(d,!0);d=this.getValue("script","");a=this.getValue("loadInline",null);if(null==a){if(null!=(a=this.getValue("load",null)))d='load "'+a+'";'+d;a=null}this.viewer.popHoldRepaint("applet init");null!=a&&null!=this.viewer.loadInline(a)&&
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default:return this.viewer.script(a)}},"~S,~S,~N");f(b,"register",function(a,d){JU.GenericApplet.checkIn(a,d)},"~S,J.api.JmolSyncInterface");f(b,"getJSpecViewProperty",function(){return null},"~S");c(b,"syncScript",function(a){this.viewer.syncScript(a,"~",0)},"~S");f(b,"handleEvent",function(a){return null==this.viewer?!1:this.viewer.processMouseEvent(a.id,a.x,a.y,a.modifiers,a.when)},"java.awt.Event");f(b,"getAppletInfo",function(){return J.i18n.GT.o(J.i18n.GT.$("Jmol Applet version {0} {1}.\n\nAn OpenScience project.\n\nSee http://www.jmol.org for more information"),
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a,d).toString()},"~S,~S");f(b,"loadInlineString",function(a,d,b){a=this.viewer.loadInlineAppend(a,b);null==a&&this.script(d);return a},"~S,~S,~B");f(b,"loadInlineArray",function(a,d,b){if(null==a||0==a.length)return null;a=this.viewer.loadInline(a,b);null==a&&this.script(d);return a},"~A,~S,~B");f(b,"loadDOMNode",function(a){return this.viewer.openDOM(a)},"~O");c(b,"loadInline",function(a){return this.loadInlineString(a,"",!1)},"~S");c(b,"loadInline",function(a,d){return this.loadInlineString(a,d,
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null!=b&&(this.loading||b!==J.c.CBK.EVAL)?null==d?this.b$.remove(b):this.b$.put(b,d):this.consoleMessage("Available callbacks include: "+J.c.CBK.getNameList().$replace(";"," ").trim())}},"~S,~S");c(b,"consoleMessage",function(a){this.notifyCallback(J.c.CBK.ECHO,B(-1,["",a]))},"~S");f(b,"notifyEnabled",function(a){switch(a){case J.c.CBK.SYNC:if(!JU.GenericApplet.isJS)return!1;case J.c.CBK.ANIMFRAME:case J.c.CBK.DRAGDROP:case J.c.CBK.ECHO:case J.c.CBK.ERROR:case J.c.CBK.EVAL:case J.c.CBK.IMAGE:case J.c.CBK.LOADSTRUCT:case J.c.CBK.MEASURE:case J.c.CBK.MESSAGE:case J.c.CBK.PICK:case J.c.CBK.SCRIPT:return!0}return null!=
this.b$.get(a)},"J.c.CBK");c(b,"notifyCallback",function(a,d){var b=null==a?null:this.b$.get(a),c=null==a||null!=b&&(null==d||null==d[0]),e=!1;null!=d&&(d[0]=this.htmlName);var g=null==d||null==d[1]?null:d[1].toString();if(null!=a)switch(a){case J.c.CBK.APPLETREADY:d[3]=this.appletObject;break;case J.c.CBK.CLICK:"alert".equals(b)&&(g="x="+d[1]+" y="+d[2]+" action="+d[3]+" clickCount="+d[4]);break;case J.c.CBK.ANIMFRAME:var j=d[1],k=j[0],f=j[1],s=j[2],m=j[3],j=j[4],p=-2>=k,x=0>m?-1:1,A=0>j?-1:1;c&&
(d=B(-1,[this.htmlName,Integer.$valueOf(Math.max(k,-2-k)),Integer.$valueOf(f),Integer.$valueOf(s),Integer.$valueOf(Math.abs(m)),Integer.$valueOf(Math.abs(j)),Integer.$valueOf(p?1:0),Integer.$valueOf(x),Integer.$valueOf(A),d[2],d[3]]));break;case J.c.CBK.ECHO:f=(k=2==d.length)||1==d[2].intValue();c||(f&&(e=!0),c=!k&&null!=(b=this.b$.get(a=J.c.CBK.MESSAGE)));e||this.output(g);break;case J.c.CBK.LOADSTRUCT:k=d[4];if(null!=k){k=(0<=k.indexOf("NOTE:")?"":J.i18n.GT.$("File Error:"))+k;this.doShowStatus(k);
this.notifyCallback(J.c.CBK.MESSAGE,B(-1,["",k]));return}break;case J.c.CBK.MEASURE:c||(c=null!=(b=this.b$.get(a=J.c.CBK.MESSAGE)));k=d[3];0<=k.indexOf("Picked")||0<=k.indexOf("Sequence")?(this.doShowStatus(g),e=!0):0<=k.indexOf("Completed")&&(g=k+": "+g,e=!0);break;case J.c.CBK.MESSAGE:e=!c;c=(new Boolean(c&null!=g)).valueOf();e||this.output(g);break;case J.c.CBK.PICK:this.doShowStatus(g);e=!0;break;case J.c.CBK.SCRIPT:!(0<d[3].intValue())&&!c&&(c=null!=(b=this.b$.get(a=J.c.CBK.MESSAGE)));this.output(g);
this.doShowStatus(g);break;case J.c.CBK.SYNC:this.sendScript(g,d[2],!0,c);return}e&&(e=this.viewer.getProperty("DATA_API","getAppConsole",null),null!=e&&(e.notifyCallback(a,d),this.output(g)));if(c&&this.mayScript)try{this.doSendCallback(a,b,d,g)}catch(n){if(D(n,Exception))this.haveNotifiedError||JU.Logger.debugging&&JU.Logger.debug(a.name()+"Callback call error to "+b+": "+n),this.haveNotifiedError=!0;else throw n;}},"J.c.CBK,~A");c(b,"sendScript",function(a,d,b,c){if(!JU.GenericApplet.isJS||c&&
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d},"JU.P4,~N,JU.P3");b.distanceToPlaneV=c(b,"distanceToPlaneV",function(a,d,b){return null==a?NaN:(a.dot(b)+d)/Math.sqrt(a.dot(a))},"JU.V3,~N,JU.P3");b.calcNormalizedNormal=c(b,"calcNormalizedNormal",function(a,d,b,c,e){e.sub2(d,a);c.sub2(b,a);c.cross(e,c);c.normalize()},"JU.T3,JU.T3,JU.T3,JU.T3,JU.T3");b.getDirectedNormalThroughPoints=c(b,"getDirectedNormalThroughPoints",function(a,d,b,c,e,g){d=JU.Measure.getNormalThroughPoints(a,d,b,e,g);null!=c&&(b=JU.P3.newP(a),b.add(e),g=b.distance(c),b.sub2(a,
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c(b,"getNormalFromCenter",function(a,d,b,c,e,g,j){d=JU.Measure.getNormalThroughPoints(d,b,c,g,j);a=0<JU.Measure.distanceToPlaneV(g,d,a);a==e&&g.scale(-1);return!a},"JU.P3,JU.P3,JU.P3,JU.P3,~B,JU.V3,JU.V3");b.getNormalToLine=c(b,"getNormalToLine",function(a,d,b){b.sub2(a,d);b.cross(b,JU.Measure.axisY);b.normalize();Float.isNaN(b.x)&&b.set(1,0,0)},"JU.P3,JU.P3,JU.V3");b.getBisectingPlane=c(b,"getBisectingPlane",function(a,d,b,c,e){b.scaleAdd2(0.5,d,a);c.setT(d);c.normalize();JU.Measure.getPlaneThroughPoint(b,
c,e)},"JU.P3,JU.V3,JU.T3,JU.V3,JU.P4");b.projectOntoAxis=c(b,"projectOntoAxis",function(a,d,b,c){c.sub2(a,d);var e=c.dot(b);a.scaleAdd2(e,b,d);c.sub2(a,d);return e},"JU.P3,JU.P3,JU.V3,JU.V3");b.calcBestAxisThroughPoints=c(b,"calcBestAxisThroughPoints",function(a,d,b,c,e,g){b.setT(a[0]);c.sub2(a[d-1],b);c.normalize();JU.Measure.calcAveragePointN(a,d,b);for(var j=0;j++<g&&0.001<JU.Measure.findAxis(a,d,b,c,e););a=JU.P3.newP(a[0]);JU.Measure.projectOntoAxis(a,b,c,e);b.setT(a)},"~A,~N,JU.P3,JU.V3,JU.V3,~N");
b.findAxis=c(b,"findAxis",function(a,d,b,c,e){for(var g=new JU.V3,j=new JU.V3,k=new JU.P3,f=new JU.P3,s=JU.V3.newV(c),m=0;0<=--d;)k.setT(a[d]),f.setT(k),JU.Measure.projectOntoAxis(f,b,c,e),j.sub2(k,f),j.cross(e,j),g.add(j),m+=e.lengthSquared();a=JU.V3.newV(g);a.scale(1/m);j.cross(a,c);c.add(j);c.normalize();j.sub2(c,s);return j.length()},"~A,~N,JU.P3,JU.V3,JU.V3");b.calcAveragePoint=c(b,"calcAveragePoint",function(a,d,b){b.set((a.x+d.x)/2,(a.y+d.y)/2,(a.z+d.z)/2)},"JU.P3,JU.P3,JU.P3");b.calcAveragePointN=
c(b,"calcAveragePointN",function(a,d,b){b.setT(a[0]);for(var c=1;c<d;c++)b.add(a[c]);b.scale(1/d)},"~A,~N,JU.P3");b.transformPoints=c(b,"transformPoints",function(a,d,b){for(var c=new JU.Lst,e=0;e<a.size();e++){var g=JU.P3.newP(a.get(e));g.sub(b);d.rotTrans(g);g.add(b);c.addLast(g)}return c},"JU.Lst,JU.M4,JU.P3");b.isInTetrahedron=c(b,"isInTetrahedron",function(a,d,b,c,e,g,j,k,f){var s=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(c,e,d,j,k,g),a);if(s!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(d,
e,b,j,k,g),a)||s!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(b,e,c,j,k,g),a))return!1;a=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(d,b,c,j,k,g),a);if(f)return s==0<=a;e=JU.Measure.distanceToPlane(g,e);return 0>=e*a||Math.abs(e)>Math.abs(a)},"JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P4,JU.V3,JU.V3,~B");b.getIntersectionPP=c(b,"getIntersectionPP",function(a,d){var b=a.x,c=a.y,e=a.z,g=a.w,j=d.x,k=d.y,f=d.z,s=d.w,m=JU.V3.new3(b,c,e),p=JU.V3.new3(j,k,f),x=new JU.V3;x.cross(m,
p);var m=Math.abs(x.x),p=Math.abs(x.y),A=Math.abs(x.z);switch(m>p?m>A?1:3:p>A?2:3){case 1:m=0;p=c*f-k*e;if(0.01>Math.abs(p))return null;e=(e*s-f*g)/p;b=(k*g-s*c)/p;break;case 2:p=b*f-j*e;if(0.01>Math.abs(p))return null;m=(e*s-f*g)/p;e=0;b=(j*g-s*b)/p;break;default:p=b*k-j*c;if(0.01>Math.abs(p))return null;m=(c*s-k*g)/p;e=(j*g-s*b)/p;b=0}c=new JU.Lst;c.addLast(JU.P3.new3(m,e,b));x.normalize();c.addLast(x);return c},"JU.P4,JU.P4");b.getIntersection=c(b,"getIntersection",function(a,d,b,c,e,g){JU.Measure.getPlaneProjection(a,
b,c,e);e.set(b.x,b.y,b.z);e.normalize();null==d&&(d=JU.V3.newV(e));b=d.dot(e);if(0.01>Math.abs(b))return null;g.sub2(c,a);c.scaleAdd2(g.dot(e)/b,d,a);return c},"JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");b.calculateQuaternionRotation=c(b,"calculateQuaternionRotation",function(a,d){d[1]=NaN;var b=new JU.Quat,c=a[0],e=a[1],g=c.length-1;if(2>g||c.length!=e.length)return b;for(var j=0,k=0,f=0,s=0,m=0,p=0,x=0,A=0,n=0,r=new JU.P3,u=new JU.P3,v=c[0],w=e[0],g=g+1;1<=--g;)r.sub2(c[g],v),u.sub2(e[g],w),j+=r.x*u.x,
k+=r.x*u.y,f+=r.x*u.z,s+=r.y*u.x,m+=r.y*u.y,p+=r.y*u.z,x+=r.z*u.x,A+=r.z*u.y,n+=r.z*u.z;d[0]=JU.Measure.getRmsd(a,b);b=R(4,4,0);b[0][0]=j+m+n;b[0][1]=b[1][0]=p-A;b[0][2]=b[2][0]=x-f;b[0][3]=b[3][0]=k-s;b[1][1]=j-m-n;b[1][2]=b[2][1]=k+s;b[1][3]=b[3][1]=x+f;b[2][2]=-j+m-n;b[2][3]=b[3][2]=p+A;b[3][3]=-j-m+n;j=javajs.api.Interface.getInterface("JU.Eigen").setM(b).getEigenvectorsFloatTransposed()[3];b=JU.Quat.newP4(JU.P4.new4(j[1],j[2],j[3],j[0]));d[1]=JU.Measure.getRmsd(a,b);return b},"~A,~A");b.getTransformMatrix4=
c(b,"getTransformMatrix4",function(a,d,b,c){a=JU.Measure.getCenterAndPoints(a);var e=JU.Measure.getCenterAndPoints(d);d=L(2,0);var g=JU.Measure.calculateQuaternionRotation(B(-1,[a,e]),d).getMatrix();null==c?g.rotate(a[0]):c.setT(a[0]);c=JU.V3.newVsub(e[0],a[0]);b.setMV(g,c);return d[1]},"JU.Lst,JU.Lst,JU.M4,JU.P3");b.getCenterAndPoints=c(b,"getCenterAndPoints",function(a){var d=a.size(),b=Array(d+1);b[0]=new JU.P3;if(0<d){for(var c=0;c<d;c++)b[0].add(b[c+1]=a.get(c));b[0].scale(1/d)}return b},"JU.Lst");
b.getRmsd=c(b,"getRmsd",function(a,d){for(var b=0,c=a[0],e=a[1],g=c[0],j=e[0],k=c.length-1,f=new JU.P3,s=k+1;1<=--s;)f.sub2(c[s],g),d.transform2(f,f).add(j),b+=f.distanceSquared(e[s]);return Math.sqrt(b/k)},"~A,JU.Quat");b.getBestLineThroughPoints=c(b,"getBestLineThroughPoints",function(a,d){0>=d&&(d=a.length);if(2>=d)return a;var b=new JU.P3,c=new JU.V3,e=new JU.V3;JU.Measure.calcBestAxisThroughPoints(a,d,b,c,e,8);return JU.Measure.getProjectedLineSegment(a,d,b,c,e)},"~A,~N");b.getProjectedLineSegment=
c(b,"getProjectedLineSegment",function(a,d,b,c,e){null==e&&(e=new JU.V3);for(var g=d=null,j,k=3.4028235E38,f=-3.4028235E38,s=0;s<a.length;s++){JU.Measure.projectOntoAxis(j=JU.P3.newP(a[s]),b,c,e);var m=c.dot(e);m<k&&(k=m,d=j);m>f&&(f=m,g=j)}return B(-1,[d,g])},"~A,~N,JU.P3,JU.V3,JU.V3");b.isInTriangle=c(b,"isInTriangle",function(a,d,b,c,e,g,j){e.sub2(c,d);g.sub2(b,d);j.sub2(a,d);a=e.dot(e);d=e.dot(g);e=e.dot(j);b=g.dot(g);g=g.dot(j);j=1/(a*b-d*d);b=(b*e-d*g)*j;g=(a*g-d*e)*j;return 0<=b&&0<=g&&1>=
b+g},"JU.P3,JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");b.calcBestPlaneThroughPoints=c(b,"calcBestPlaneThroughPoints",function(a,d,b){0>=d&&(d=a.length);if(3==d)return JU.Measure.getPlaneThroughPoints(a[0],a[1],a[2],null,null,b),0;var c=b,e=new JU.P4,g=JU.Measure.calcPlaneForMode(a,d,b,"z");if(1E-6>g)return g;var j=JU.Measure.calcPlaneForMode(a,d,e,"y");j<g&&(g=j,c=e,e=b);1E-6<=g&&(j=JU.Measure.calcPlaneForMode(a,d,e,"x"),j<g&&(g=j,c=e));c!==b&&(b.setT(c),b.w=c.w);return g},"~A,~N,JU.P4");b.calcPlaneForMode=
c(b,"calcPlaneForMode",function(a,d,b,c){for(var e=R(d,3,0),g=R(3,d,0),j=R(3,d,0),k=R(3,3,0),f=R(d,0),s=d;0<=--s;){var m=a[s];e[s][0]=g[0][s]="x"==c?m.z:m.x;e[s][1]=g[1][s]="y"==c?m.z:m.y;e[s][2]=g[2][s]=1;f[s]=-("y"==c?m.y:"x"==c?m.x:m.z)}for(var p=new JU.M3,s=3;0<=--s;)for(m=3;0<=--m;){for(var x=0,A=d;0<=--A;)x+=g[s][A]*e[A][m];p.set33(s,m,x)}p.invert();for(s=3;0<=--s;)for(m=3;0<=--m;)k[s][m]=p.get33(s,m);for(s=3;0<=--s;)for(A=d;0<=--A;){x=0;for(m=3;0<=--m;)x+=k[s][m]*g[m][A];j[s][A]=x}switch(c.charCodeAt(0)){case 120:b.x=
1;break;case 121:b.y=1;break;case 122:b.z=1}s=1;for(m=3;0<=--m;){e=0;for(A=d;0<=--A;)e+=j[m][A]*f[A];switch(m){case 0:s+=e*e;"x"==c?b.z=e:b.x=e;break;case 1:s+=e*e;"y"==c?b.z=e:b.y=e;break;case 2:b.w=e}}c=Math.sqrt(s);b.scale4((0<1/b.w?1:-1)/c);for(s=c=0;s<d;s++)x=JU.Measure.distanceToPlane(b,a[s]),c+=x*x;return Math.sqrt(c/d)},"~A,~N,JU.P4,~S");b.rndPt=c(b,"rndPt",function(){return JU.P3.new3(20*Math.random(),20*Math.random(),20*Math.random())});b.testRnd=c(b,"testRnd",function(){var a=JU.P4.new4(20*
Math.random(),20*Math.random(),20*Math.random(),20*Math.random());a.scale4(1/a.length());System.out.println("\n==========\n ");System.out.println("plane is "+a);for(var d=new JU.P3,b=new JU.V3,c=Array(4),e=0;e<c.length;e++){c[e]=new JU.P3;var g=JU.Measure.rndPt();JU.Measure.getPlaneProjection(g,a,d,b);c[e].setT(d);g=0.1*Math.random();c[e].scaleAdd2(g,b,d);System.out.println(c[e]+" d="+g)}a=new JU.P4;c=JU.Measure.calcBestPlaneThroughPoints(c,-1,a);System.out.println("found "+a+" rmsd = "+c)});b.test=
c(b,"test",function(){for(var a=0;10>a;a++)JU.Measure.testRnd();System.exit(0)});b.getPointsOnPlane=c(b,"getPointsOnPlane",function(a,d){for(var b=new JU.Lst,c=a.length;0<=--c;)0.001>Math.abs(JU.Measure.distanceToPlane(d,a[c]))&&b.addLast(a[c]);return b},"~A,JU.P4");b.getLatticePoints=c(b,"getLatticePoints",function(a,d,b,c){a.addLast(new JU.P3);d=0==d?1:Math.abs(d);b=0==b?1:Math.abs(b);c=0==c?1:Math.abs(c);for(var e=a.size(),g=-d;g<=d;g++)for(var j=-b;j<=b;j++)for(var k=-c;k<=c;k++)for(var f=0;f<
e;f++){var s=JU.P3.new3(g,j,k);s.add(a.get(f));a.addLast(s)}for(f=e;0<=--f;)a.removeItemAt(0);return a},"JU.Lst,~N,~N,~N");b.computeHelicalAxis=c(b,"computeHelicalAxis",function(a,d,b){var c=new JU.V3;c.sub2(d,a);var e=b.getTheta(),g=b.getNormal(),j=c.dot(g);1E-4>Math.abs(j)&&(j=0);var k=new JU.V3;k.cross(c,g);0!=k.dot(k)&&k.normalize();var f=new JU.V3,s=JU.V3.newV(g);0==j&&(j=1.4E-45);s.scale(j);f.sub2(s,c);f.scale(0.5);k.scale(0==e?0:f.length()/Math.tan(3.141592653589793*(e/2/180)));c=JU.V3.newV(k);
0!=e&&c.add(f);f=JU.P3.newP(a);f.sub(c);1.4E-45!=j&&g.scale(j);k=JU.P3.newP(f);k.add(g);e=JU.Measure.computeTorsion(a,f,k,d,!0);if(Float.isNaN(e)||1E-4>c.length())e=b.getThetaDirectedV(g);a=Math.abs(0==e?0:360/e);j=Math.abs(1.4E-45==j?0:g.length()*(0==e?1:360/e));return B(-1,[f,g,c,JU.P3.new3(e,j,a),k])},"JU.P3,JU.P3,JU.Quat");b.axisY=JU.V3.new3(0,1,0)});n("JU");z(null,"JU.MeshSurface","JU.AU $.P3 J.api.Interface JU.BoxInfo $.C $.Geodesic $.TempArray".split(" "),function(){var b=r(function(){this.meshType=
this.oabc=this.slicer=this.vwr=null;this.vc=0;this.surfaceAtoms=this.vertexSource=this.vvs=this.vs=null;this.pc=0;this.pis=null;this.haveQuads=this.isDrawPolygon=this.colorsExplicit=!1;this.colixBack=this.colix=0;this.isColorSolid=!0;this.normalsTemp=this.normals=this.vcs=this.pcs=this.altVertices=this.offset=null;this.normixCount=this.normalCount=0;this.vertexSets=this.surfaceSet=this.mat4=this.bsPolygons=null;this.nSets=0;this.dataOnly=!1;this.vertexCount0=this.polygonCount0=this.iC=this.iB=this.iA=
this.lastColix=this.lastColor=0;this.bsSlabGhost=this.bsSlabDisplay=null;this.slabColix=this.slabMeshType=0;this.slabOptions=this.bsDisplay=null;this.mergePolygonCount0=this.mergeVertexCount0=0;this.isMerged=!1;u(this,arguments)},JU,"MeshSurface",null);c(b,"getMeshSlicer",function(){return null==this.slicer?this.slicer=J.api.Interface.getInterface("JU.MeshSlicer",this.vwr,"script").set(this):this.slicer});b.newMesh=c(b,"newMesh",function(a,d,b,c,e,g){var j=new JU.MeshSurface;j.pis=c;a?j.altVertices=
d:j.vs=d;j.vc=0==b?d.length:b;j.normals=e;j.normalCount=0==g&&null!=e?e.length:g;return j},"~B,~A,~N,~A,~A,~N");c(b,"getVertices",function(){return null==this.altVertices?this.vs:this.altVertices});c(b,"getFaces",function(){return this.pis});c(b,"setColix",function(a){this.colix=a},"~N");c(b,"setColixBack",function(a){this.colixBack=a},"~N");c(b,"addV",function(a,d){0==this.vc?this.vs=Array(25):this.vc==this.vs.length&&(this.vs=JU.AU.doubleLength(this.vs));this.vs[this.vc]=d?JU.P3.newP(a):a;return this.vc++},
"JU.T3,~B");c(b,"addTriangle",function(a,d,b){this.addPolygon(E(-1,[a,d,b]),null)},"~N,~N,~N");c(b,"addQuad",function(a,d,b,c){this.haveQuads=!0;this.addPolygon(E(-1,[a,d,b,c]),null)},"~N,~N,~N,~N");c(b,"setPolygonCount",function(a){this.pc=a;if(!(0>a)&&(null==this.pis||a>this.pis.length))this.pis=JU.AU.newInt2(a)},"~N");c(b,"addVCVal",function(a,d,b){0==this.vc?this.vvs=L(25,0):this.vc>=this.vvs.length&&(this.vvs=JU.AU.doubleLengthF(this.vvs));this.vvs[this.vc]=d;return this.addV(a,b)},"JU.T3,~N,~B");
c(b,"addTriangleCheck",function(a,d,b,c,e,g){return null==this.vs||null!=this.vvs&&(Float.isNaN(this.vvs[a])||Float.isNaN(this.vvs[d])||Float.isNaN(this.vvs[b]))||Float.isNaN(this.vs[a].x)||Float.isNaN(this.vs[d].x)||Float.isNaN(this.vs[b].x)?-1:this.addPolygonV3(a,d,b,c,e,g,null)},"~N,~N,~N,~N,~N,~N");c(b,"addPolygonV3",function(a,d,b,c,e,g,j){return this.dataOnly?this.addPolygon(E(-1,[a,d,b,c]),j):this.addPolygonC(E(-1,[a,d,b,c,e]),g,j,0>e)},"~N,~N,~N,~N,~N,~N,JU.BS");c(b,"addPolygonC",function(a,
d,b,c){if(0!=d){if(null==this.pcs||0==this.pc)this.lastColor=0;c?this.colorsExplicit=!0:(null==this.pcs?this.pcs=U(25,0):this.pc>=this.pcs.length&&(this.pcs=JU.AU.doubleLengthShort(this.pcs)),this.pcs[this.pc]=c?2047:d==this.lastColor?this.lastColix:this.lastColix=JU.C.getColix(this.lastColor=d))}return this.addPolygon(a,b)},"~A,~N,JU.BS,~B");c(b,"addPolygon",function(a,d){var b=this.pc;0==b?this.pis=JU.AU.newInt2(25):b==this.pis.length&&(this.pis=JU.AU.doubleLength(this.pis));null!=d&&d.set(b);this.pis[this.pc++]=
a;return b},"~A,JU.BS");c(b,"invalidatePolygons",function(){for(var a=this.pc;--a>=this.mergePolygonCount0;)if((null==this.bsSlabDisplay||this.bsSlabDisplay.get(a))&&null==this.setABC(a))this.pis[a]=null});c(b,"setABC",function(a){if(null!=this.bsSlabDisplay&&!this.bsSlabDisplay.get(a)&&(null==this.bsSlabGhost||!this.bsSlabGhost.get(a)))return null;a=this.pis[a];if(null==a||3>a.length)return null;this.iA=a[0];this.iB=a[1];this.iC=a[2];return null==this.vvs||!Float.isNaN(this.vvs[this.iA])&&!Float.isNaN(this.vvs[this.iB])&&
!Float.isNaN(this.vvs[this.iC])?a:null},"~N");c(b,"setTranslucentVertices",function(){},"JU.BS");c(b,"getSlabColor",function(){return null==this.bsSlabGhost?null:JU.C.getHexCode(this.slabColix)});c(b,"getSlabType",function(){return null!=this.bsSlabGhost&&1073742018==this.slabMeshType?"mesh":null});c(b,"resetSlab",function(){null!=this.slicer&&this.slicer.slabPolygons(JU.TempArray.getSlabObjectType(1073742333,null,!1,null),!1)});c(b,"slabPolygonsList",function(a,d){this.getMeshSlicer();for(var b=
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0<this.c&&(d=!0,this.gamma=120);26<a.length&&(Float.isNaN(a[26])?a[26]=this.slop:this.slop=a[26]);var b=this.na=Math.max(1,24<a.length&&!Float.isNaN(a[22])?F(a[22]):1),c=this.nb=Math.max(1,24<a.length&&!Float.isNaN(a[23])?F(a[23]):1),e=this.nc=Math.max(1,24<a.length&&!Float.isNaN(a[24])?F(a[24]):1);if(25<a.length&&!Float.isNaN(a[25])){var g=a[25];0<g&&(b*=g,c*=g,e*=g)}else b=c=e=1;if(0>=this.a&&0>=this.c){var g=JU.V3.new3(a[6],a[7],a[8]),j=JU.V3.new3(a[9],a[10],a[11]),k=JU.V3.new3(a[12],a[13],a[14]);
this.setABC(g,j,k);0>this.c&&(a=JU.AU.arrayCopyF(a,-1),0>this.b&&(j.set(0,0,1),j.cross(j,g),0.001>j.length()&&j.set(0,1,0),j.normalize(),a[9]=j.x,a[10]=j.y,a[11]=j.z),0>this.c&&(k.cross(g,j),k.normalize(),a[12]=k.x,a[13]=k.y,a[14]=k.z))}this.a*=b;0>=this.b?this.b=this.c=1:0>=this.c?(this.c=1,this.b*=c):(this.b*=c,this.c*=e);this.setCellParams();if(21<a.length&&!Float.isNaN(a[21])){d=L(16,0);for(g=0;16>g;g++){switch(g%4){case 0:j=b;break;case 1:j=c;break;case 2:j=e;break;default:j=1}d[g]=a[6+g]*j}this.matrixCartesianToFractional=
JU.M4.newA16(d);this.matrixCartesianToFractional.getTranslation(this.fractionalOrigin);this.matrixFractionalToCartesian=JU.M4.newM4(this.matrixCartesianToFractional).invert();1==a[0]&&this.setParamsFromMatrix()}else 14<a.length&&!Float.isNaN(a[14])?(g=this.matrixFractionalToCartesian=new JU.M4,g.setColumn4(0,a[6]*b,a[7]*b,a[8]*b,0),g.setColumn4(1,a[9]*c,a[10]*c,a[11]*c,0),g.setColumn4(2,a[12]*e,a[13]*e,a[14]*e,0),17<a.length&&!Float.isNaN(a[17])?g.setColumn4(3,a[15],a[16],a[17],1):g.setColumn4(3,
0,0,0,1)):(g=this.matrixFractionalToCartesian=new JU.M4,d?(g.setColumn4(0,-this.b*this.cosGamma,-this.b*this.sinGamma,0,0),g.setColumn4(1,-this.b*this.cosGamma,this.b*this.sinGamma,0,0)):(g.setColumn4(0,this.a,0,0,0),g.setColumn4(1,this.b*this.cosGamma,this.b*this.sinGamma,0,0)),g.setColumn4(2,this.c*this.cosBeta,this.c*(this.cosAlpha-this.cosBeta*this.cosGamma)/this.sinGamma,this.volume/(this.a*this.b*this.sinGamma),0),g.setColumn4(3,0,0,0,1)),this.matrixCartesianToFractional=JU.M4.newM4(this.matrixFractionalToCartesian).invert();
this.matrixCtoFNoOffset=this.matrixCartesianToFractional;this.matrixFtoCNoOffset=this.matrixFractionalToCartesian}},"~A");b.newParams=c(b,"newParams",function(a,d){for(var b=L(27,0),c=a.length,e=0;27>e;e++)b[e]=e<c?a[e]:NaN;27>c&&(b[26]=d);return b},"~A,~N");b.addVectors=c(b,"addVectors",function(a){for(var d=JU.SimpleUnitCell.newA(a).matrixFractionalToCartesian,b=0;9>b;b++)a[6+b]=d.getElement(b%3,v(b/3))},"~A");c(b,"setParamsFromMatrix",function(){var a=JU.V3.new3(1,0,0),d=JU.V3.new3(0,1,0),b=JU.V3.new3(0,
0,1);this.matrixFractionalToCartesian.rotate(a);this.matrixFractionalToCartesian.rotate(d);this.matrixFractionalToCartesian.rotate(b);this.setABC(a,d,b);this.setCellParams()});c(b,"setABC",function(a,d,b){this.a=a.length();this.b=d.length();this.c=b.length();0!=this.a&&(0==this.b?this.b=this.c=-1:0==this.c&&(this.c=-1),this.alpha=0>this.b||0>this.c?90:d.angle(b)/0.017453292519943295,this.beta=0>this.c?90:a.angle(b)/0.017453292519943295,this.gamma=0>this.b?90:a.angle(d)/0.017453292519943295,a=this.unitCellParams,
a[0]=this.a,a[1]=this.b,a[2]=this.c,a[3]=this.alpha,a[4]=this.beta,a[5]=this.gamma)},"JU.V3,JU.V3,JU.V3");c(b,"setCellParams",function(){this.cosAlpha=Math.cos(0.017453292519943295*this.alpha);this.sinAlpha=Math.sin(0.017453292519943295*this.alpha);this.cosBeta=Math.cos(0.017453292519943295*this.beta);this.sinBeta=Math.sin(0.017453292519943295*this.beta);this.cosGamma=Math.cos(0.017453292519943295*this.gamma);this.sinGamma=Math.sin(0.017453292519943295*this.gamma);var a=Math.sqrt(this.sinAlpha*this.sinAlpha+
this.sinBeta*this.sinBeta+this.sinGamma*this.sinGamma+2*this.cosAlpha*this.cosBeta*this.cosGamma-2);this.volume=this.a*this.b*this.c*a;this.cA_=(this.cosAlpha-this.cosBeta*this.cosGamma)/this.sinGamma;this.cB_=a/this.sinGamma;this.a_=this.b*this.c*this.sinAlpha/this.volume;this.b_=this.a*this.c*this.sinBeta/this.volume;this.c_=this.a*this.b*this.sinGamma/this.volume});c(b,"getFractionalOrigin",function(){return this.fractionalOrigin});c(b,"toSupercell",function(a){a.x/=this.na;a.y/=this.nb;a.z/=this.nc;
return a},"JU.P3");c(b,"toCartesian",function(a,d){null!=this.matrixFractionalToCartesian&&(d?this.matrixFtoCNoOffset:this.matrixFractionalToCartesian).rotTrans(a)},"JU.T3,~B");c(b,"toFractionalM",function(a){null!=this.matrixCartesianToFractional&&(a.mul(this.matrixFractionalToCartesian),a.mul2(this.matrixCartesianToFractional,a))},"JU.M4");c(b,"toFractional",function(a,d){null!=this.matrixCartesianToFractional&&(d?this.matrixCtoFNoOffset:this.matrixCartesianToFractional).rotTrans(a)},"JU.T3,~B");
c(b,"isPolymer",function(){return 1==this.dimension});c(b,"isSlab",function(){return 2==this.dimension});c(b,"getUnitCellParams",function(){return this.unitCellParams});c(b,"getUnitCellAsArray",function(a){var d=this.matrixFractionalToCartesian;return a?L(-1,[d.m00,d.m10,d.m20,d.m01,d.m11,d.m21,d.m02,d.m12,d.m22]):L(-1,[this.a,this.b,this.c,this.alpha,this.beta,this.gamma,d.m00,d.m10,d.m20,d.m01,d.m11,d.m21,d.m02,d.m12,d.m22,this.dimension,this.volume])},"~B");c(b,"getInfo",function(a){switch(a){case 0:return this.a;
case 1:return this.b;case 2:return this.c;case 3:return this.alpha;case 4:return this.beta;case 5:return this.gamma;case 6:return this.dimension;case 7:return JU.SimpleUnitCell.isHexagonal(this.unitCellParams)?1:0;case 8:return JU.SimpleUnitCell.isRhombohedral(this.unitCellParams)?1:0}return NaN},"~N");b.getReciprocal=c(b,"getReciprocal",function(a,d,b){var c=4==a.length?1:0,e=Array(4);e[0]=1==c?JU.P3.newP(a[0]):new JU.P3;0==b&&(b=6.283185307179586);for(var g=0;3>g;g++){var j=e[g+1]=new JU.P3;j.cross(a[(g+
1)%3+c],a[(g+2)%3+c]);var k=a[g+c].dot(j);-1==b&&(b=Math.sqrt(k));j.scale(b/k)}if(null==d)return e;for(g=0;4>g;g++)d[g]=e[g];return d},"~A,~A,~N");b.setAbc=c(b,"setAbc",function(a,d,b){if(null!=a&&(null==d&&(d=L(6,0)),a=JU.PT.split(a.$replace(",","="),"="),12<=a.length))for(var c=0;6>c;c++)d[c]=JU.PT.parseFloat(a[2*c+1]);return null==b?null:JU.SimpleUnitCell.setAbcFromParams(d,b)},"~S,~A,~A");b.setAbcFromParams=c(b,"setAbcFromParams",function(a,d){var b=JU.SimpleUnitCell.newA(a).getUnitCellAsArray(!0);
d[1].set(b[0],b[1],b[2]);d[2].set(b[3],b[4],b[5]);d[3].set(b[6],b[7],b[8]);return d},"~A,~A");c(b,"unitizeDim",function(a,d){switch(a){case 3:d.z=JU.SimpleUnitCell.unitizeX(d.z,this.slop);case 2:d.y=JU.SimpleUnitCell.unitizeX(d.y,this.slop);case 1:d.x=JU.SimpleUnitCell.unitizeX(d.x,this.slop)}},"~N,JU.T3");b.unitizeDimRnd=c(b,"unitizeDimRnd",function(a,d,b){switch(a){case 3:d.z=JU.SimpleUnitCell.unitizeXRnd(d.z,b);case 2:d.y=JU.SimpleUnitCell.unitizeXRnd(d.y,b);case 1:d.x=JU.SimpleUnitCell.unitizeXRnd(d.x,
b)}},"~N,JU.T3,~N");b.unitizeX=c(b,"unitizeX",function(a,d){a-=Math.floor(a);if(a>1-d||a<d)a=0;return a},"~N,~N");b.unitizeXRnd=c(b,"unitizeXRnd",function(a,d){a-=Math.floor(a);if(a>1-d||a<d)a=0;return a},"~N,~N");c(b,"twelfthsOf",function(a){if(0==a)return 0;a=Math.abs(12*a);var d=Math.round(a);return 12>=d&&Math.abs(a-d)<12*this.slop?d:-1},"~N");c(b,"twelfthify",function(a){switch(this.dimension){case 3:a.z=this.setTwelfths(a.z);case 2:a.y=this.setTwelfths(a.y);case 1:a.x=this.setTwelfths(a.x)}},
"JU.P3");c(b,"setTwelfths",function(a){var d=this.twelfthsOf(a);return 0<=d?d/12:a},"~N");b.ijkToPoint3f=c(b,"ijkToPoint3f",function(a,d,b,c){var e=1E9<a?1E3:1E6<a?100:10,g=e*e;b-=0<=b?v(5*e/10):b;d.x=v(a/g)%e+b;d.y=v(a%g/e)+b;d.z=(0==c?a%e:(-500==b?v(c/e):c)%e)+b},"~N,JU.P3,~N,~N");b.ptToIJK=c(b,"ptToIJK",function(a,d){return 5>=a.x&&5>=a.y&&5>=a.z?JU.P4.new4(555,100*(a.x+4)+10*(a.y+4)+a.z+4,d,0):JU.P4.new4(1500500500,1500500500+1E6*a.x+1E3*a.y+a.z,d,1500500+a.z)},"JU.T3,~N");b.escapeMultiplier=
c(b,"escapeMultiplier",function(a){if(C(a,"JU.P4")){var d=1E3*v(Math.floor(a.x/1E3))+v(Math.floor(a.w/1E3))-1E3,b=1E3*v(Math.floor(a.y/1E3))+v(Math.floor(a.w))%1E3;return"{"+d+" "+b+" "+a.z+"}"}return JU.Escape.eP(a)},"JU.T3");b.setMinMaxLatticeParameters=c(b,"setMinMaxLatticeParameters",function(a,d,b,c){if(b.x<=b.y&&555<=b.y){var e=new JU.P3;JU.SimpleUnitCell.ijkToPoint3f(b.x,e,0,c);d.x=F(e.x);d.y=F(e.y);d.z=F(e.z);JU.SimpleUnitCell.ijkToPoint3f(b.y,e,1,c);b.x=F(e.x);b.y=F(e.y);b.z=F(e.z)}switch(a){case 1:d.y=
0,b.y=1;case 2:d.z=0,b.z=1}},"~N,JU.P3i,JU.P3i,~N");b.isHexagonal=c(b,"isHexagonal",function(a){return JU.SimpleUnitCell.approx0(a[0]-a[1])&&JU.SimpleUnitCell.approx0(a[3]-90)&&JU.SimpleUnitCell.approx0(a[4]-90)&&(JU.SimpleUnitCell.approx0(a[5]-120)||-1==a[5])},"~A");b.isRhombohedral=c(b,"isRhombohedral",function(a){return JU.SimpleUnitCell.approx0(a[0]-a[1])&&JU.SimpleUnitCell.approx0(a[1]-a[2])&&!JU.SimpleUnitCell.approx0(a[3]-90)&&JU.SimpleUnitCell.approx0(a[3]-a[4])&&JU.SimpleUnitCell.approx0(a[4]-
a[5])},"~A");b.approx0=c(b,"approx0",function(a){return 0.001>Math.abs(a)},"~N");f(b,"toString",function(){return"["+this.a+" "+this.b+" "+this.c+" "+this.alpha+" "+this.beta+" "+this.gamma+"]"})});n("JU");z(null,"JU.TempArray",["JU.P3","$.P3i"],function(){var b=r(function(){this.freeEnum=this.lengthsFreeEnum=this.freeScreens=this.lengthsFreeScreens=this.freePoints=this.lengthsFreePoints=null;u(this,arguments)},JU,"TempArray",null);N(b,function(){this.lengthsFreePoints=E(6,0);this.freePoints=Array(6);
this.lengthsFreeScreens=E(6,0);this.freeScreens=Array(6);this.lengthsFreeEnum=E(2,0);this.freeEnum=Array(2)});y(b,function(){});c(b,"clear",function(){this.clearTempPoints();this.clearTempScreens()});b.findBestFit=c(b,"findBestFit",function(a,d){for(var b=-1,c=2147483647,e=d.length;0<=--e;){var g=d[e];g>=a&&g<c&&(c=g,b=e)}0<=b&&(d[b]=0);return b},"~N,~A");b.findShorter=c(b,"findShorter",function(a,d){for(var b=d.length;0<=--b;)if(0==d[b])return d[b]=a,b;for(var c=0,e=d[0],b=d.length;0<--b;)d[b]<e&&
(e=d[b],c=b);return e<a?(d[c]=a,c):-1},"~N,~A");c(b,"clearTempPoints",function(){for(var a=0;6>a;a++)this.lengthsFreePoints[a]=0,this.freePoints[a]=null});c(b,"allocTempPoints",function(a){var d;d=JU.TempArray.findBestFit(a,this.lengthsFreePoints);if(0<d)d=this.freePoints[d];else for(d=Array(a);0<=--a;)d[a]=new JU.P3;return d},"~N");c(b,"freeTempPoints",function(a){for(var d=0;d<this.freePoints.length;d++)if(this.freePoints[d]===a){this.lengthsFreePoints[d]=a.length;return}d=JU.TempArray.findShorter(a.length,
this.lengthsFreePoints);0<=d&&(this.freePoints[d]=a)},"~A");c(b,"clearTempScreens",function(){for(var a=0;6>a;a++)this.lengthsFreeScreens[a]=0,this.freeScreens[a]=null});c(b,"allocTempScreens",function(a){var d;d=JU.TempArray.findBestFit(a,this.lengthsFreeScreens);if(0<d)d=this.freeScreens[d];else for(d=Array(a);0<=--a;)d[a]=new JU.P3i;return d},"~N");c(b,"freeTempScreens",function(a){for(var d=0;d<this.freeScreens.length;d++)if(this.freeScreens[d]===a){this.lengthsFreeScreens[d]=a.length;return}d=
JU.TempArray.findShorter(a.length,this.lengthsFreeScreens);0<=d&&(this.freeScreens[d]=a)},"~A");c(b,"allocTempEnum",function(a){var d=JU.TempArray.findBestFit(a,this.lengthsFreeEnum);return 0<d?this.freeEnum[d]:Array(a)},"~N");c(b,"freeTempEnum",function(a){for(var d=0;d<this.freeEnum.length;d++)if(this.freeEnum[d]===a){this.lengthsFreeEnum[d]=a.length;return}d=JU.TempArray.findShorter(a.length,this.lengthsFreeEnum);0<=d&&(this.freeEnum[d]=a)},"~A");b.getSlabWithinRange=c(b,"getSlabWithinRange",function(a,
d){return B(-1,[Integer.$valueOf(1073742114),B(-1,[Float.$valueOf(a),Float.$valueOf(d)]),Boolean.FALSE,null])},"~N,~N");b.getSlabObjectType=c(b,"getSlabObjectType",function(a,d,b,c){return B(-1,[Integer.$valueOf(a),d,Boolean.$valueOf(b),c])},"~N,~O,~B,~O")});n("JU");G(JU,"Txt",null);n("JU");z(["JU.V3"],"JU.Vibration",["JU.P3"],function(){var b=r(function(){this.modDim=-1;this.modScale=NaN;this.showTrace=!1;this.trace=null;this.tracePt=0;u(this,arguments)},JU,"Vibration",JU.V3);c(b,"setCalcPoint",
function(a,d,b){switch(this.modDim){case -2:case -3:break;default:a.scaleAdd2(Math.cos(6.283185307179586*d.x)*b,this,a)}return a},"JU.T3,JU.T3,~N,~N");c(b,"getInfo",function(a){a.put("vibVector",JU.V3.newV(this));a.put("vibType",-2==this.modDim?"spin":-1==this.modDim?"vib":"mod")},"java.util.Map");f(b,"clone",function(){var a=new JU.Vibration;a.setT(this);a.modDim=this.modDim;return a});c(b,"setXYZ",function(a){this.setT(a)},"JU.T3");c(b,"setType",function(a){this.modDim=a;return this},"~N");c(b,
"isNonzero",function(){return 0!=this.x||0!=this.y||0!=this.z});c(b,"getOccupancy100",function(){return-2147483648},"~B");c(b,"startTrace",function(a){this.trace=Array(a);this.tracePt=a},"~N");c(b,"addTracePt",function(a,d){(null==this.trace||0==a||a!=this.trace.length)&&this.startTrace(a);if(null!=d&&2<a){if(0>=--this.tracePt){for(var b=this.trace[this.trace.length-1],c=this.trace.length;1<=--c;)this.trace[c]=this.trace[c-1];this.trace[1]=b;this.tracePt=1}b=this.trace[this.tracePt];null==b&&(b=this.trace[this.tracePt]=
new JU.P3);b.setT(d)}return this.trace},"~N,JU.Point3fi")});n("JV");z(["J.api.EventManager","JU.Rectangle","JV.MouseState"],["JV.MotionPoint","$.ActionManager","$.Gesture"],"JU.AU $.PT J.api.Interface J.i18n.GT JS.SV $.ScriptEval J.thread.HoverWatcherThread JU.BSUtil $.Escape $.Logger $.Point3fi JV.Viewer JV.binding.Binding $.JmolBinding".split(" "),function(){var b=r(function(){this.vwr=null;this.isMultiTouch=this.haveMultiTouchInput=!1;this.predragBinding=this.rasmolBinding=this.dragBinding=this.pfaatBinding=
this.jmolBinding=this.b=null;this.LEFT_DRAGGED=0;this.hoverable=!1;this.dragGesture=this.hoverWatcherThread=null;this.apm=1;this.pickingStyleSelect=this.pickingStyle=this.bondPickingMode=0;this.pickingStyleMeasure=5;this.rootPickingStyle=0;this.mouseDragFactor=this.gestureSwipeFactor=1;this.mouseWheelFactor=1.15;this.dragged=this.pressed=this.clicked=this.moved=this.current=null;this.clickedCount=this.pressedCount=0;this.dragSelectedMode=this.labelMode=this.drawMode=!1;this.measuresEnabled=!0;this.hoverActive=
this.haveSelection=!1;this.mp=null;this.dragAtomIndex=-1;this.rubberbandSelectionMode=this.mkBondPressed=!1;this.rectRubber=null;this.isAltKeyReleased=!0;this.isMultiTouchServer=this.isMultiTouchClient=this.keyProcessing=!1;this.clickAction=this.dragAction=this.pressAction=0;this.measurementQueued=null;this.selectionWorking=this.zoomTrigger=!1;u(this,arguments)},JV,"ActionManager",null,J.api.EventManager);N(b,function(){this.current=new JV.MouseState("current");this.moved=new JV.MouseState("moved");
this.clicked=new JV.MouseState("clicked");this.pressed=new JV.MouseState("pressed");this.dragged=new JV.MouseState("dragged");this.rectRubber=new JU.Rectangle});c(b,"setViewer",function(a){this.vwr=a;JV.Viewer.isJS||this.createActions();this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.LEFT_DRAGGED=JV.binding.Binding.getMouseAction(1,16,1);this.dragGesture=new JV.Gesture(20,a)},"JV.Viewer,~S");c(b,"isHoverable",function(){return this.hoverable});c(b,"checkHover",function(){if(this.zoomTrigger)this.zoomTrigger=
!1,8==this.vwr.currentCursor&&this.vwr.setCursor(0),this.vwr.setInMotion(!1);else if(!this.vwr.getInMotion(!0)&&!this.vwr.tm.spinOn&&!this.vwr.tm.navOn&&!this.vwr.checkObjectHovered(this.current.x,this.current.y)){var a=this.vwr.findNearestAtomIndex(this.current.x,this.current.y);if(!(0>a)){var d=2==this.apm&&this.bnd(JV.binding.Binding.getMouseAction(this.clickedCount,this.moved.modifiers,1),[10]);this.vwr.hoverOn(a,d)}}});c(b,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(b,"bind",
function(a,d){var b=JV.ActionManager.getActionFromName(d),c=JV.binding.Binding.getMouseActionStr(a);0!=c&&(0<=b?this.b.bindAction(c,b):this.b.bindName(c,d))},"~S,~S");c(b,"clearBindings",function(){this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.rasmolBinding=this.dragBinding=this.pfaatBinding=null});c(b,"unbindAction",function(a,d){if(null==a&&null==d)this.clearBindings();else{var b=JV.ActionManager.getActionFromName(d),c=JV.binding.Binding.getMouseActionStr(a);0<=b?this.b.unbindAction(c,
b):0!=c&&this.b.unbindName(c,d);null==d&&this.b.unbindUserAction(a)}},"~S,~S");b.newAction=c(b,"newAction",function(a,d,b){JV.ActionManager.actionInfo[a]=b;JV.ActionManager.actionNames[a]=d},"~N,~S,~S");c(b,"createActions",function(){null==JV.ActionManager.actionInfo[0]&&(JV.ActionManager.newAction(0,"_assignNew",J.i18n.GT.o(J.i18n.GT.$("assign/new atom or bond (requires {0})"),"set picking assignAtom_??/assignBond_?")),JV.ActionManager.newAction(1,"_center",J.i18n.GT.$("center")),JV.ActionManager.newAction(2,
"_clickFrank",J.i18n.GT.$("pop up recent context menu (click on Jmol frank)")),JV.ActionManager.newAction(4,"_deleteAtom",J.i18n.GT.o(J.i18n.GT.$("delete atom (requires {0})"),"set picking DELETE ATOM")),JV.ActionManager.newAction(5,"_deleteBond",J.i18n.GT.o(J.i18n.GT.$("delete bond (requires {0})"),"set picking DELETE BOND")),JV.ActionManager.newAction(6,"_depth",J.i18n.GT.o(J.i18n.GT.$("adjust depth (back plane; requires {0})"),"SLAB ON")),JV.ActionManager.newAction(7,"_dragAtom",J.i18n.GT.o(J.i18n.GT.$("move atom (requires {0})"),
"set picking DRAGATOM")),JV.ActionManager.newAction(8,"_dragDrawObject",J.i18n.GT.o(J.i18n.GT.$("move whole DRAW object (requires {0})"),"set picking DRAW")),JV.ActionManager.newAction(9,"_dragDrawPoint",J.i18n.GT.o(J.i18n.GT.$("move specific DRAW point (requires {0})"),"set picking DRAW")),JV.ActionManager.newAction(10,"_dragLabel",J.i18n.GT.o(J.i18n.GT.$("move label (requires {0})"),"set picking LABEL")),JV.ActionManager.newAction(11,"_dragMinimize",J.i18n.GT.o(J.i18n.GT.$("move atom and minimize molecule (requires {0})"),
"set picking DRAGMINIMIZE")),JV.ActionManager.newAction(12,"_dragMinimizeMolecule",J.i18n.GT.o(J.i18n.GT.$("move and minimize molecule (requires {0})"),"set picking DRAGMINIMIZEMOLECULE")),JV.ActionManager.newAction(13,"_dragSelected",J.i18n.GT.o(J.i18n.GT.$("move selected atoms (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(14,"_dragZ",J.i18n.GT.o(J.i18n.GT.$("drag atoms in Z direction (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(15,"_multiTouchSimulation",J.i18n.GT.$("simulate multi-touch using the mouse)")),
JV.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT.$("translate navigation point (requires {0} and {1})"),B(-1,["set NAVIGATIONMODE","set picking NAVIGATE"]))),JV.ActionManager.newAction(17,"_pickAtom",J.i18n.GT.$("pick an atom")),JV.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT.$("connect atoms (requires {0})"),"set picking CONNECT")),JV.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT.$("pick an ISOSURFACE point (requires {0}"),"set DRAWPICKING")),
JV.ActionManager.newAction(19,"_pickLabel",J.i18n.GT.o(J.i18n.GT.$("pick a label to toggle it hidden/displayed (requires {0})"),"set picking LABEL")),JV.ActionManager.newAction(20,"_pickMeasure",J.i18n.GT.o(J.i18n.GT.$("pick an atom to include it in a measurement (after starting a measurement or after {0})"),"set picking DISTANCE/ANGLE/TORSION")),JV.ActionManager.newAction(21,"_pickNavigate",J.i18n.GT.o(J.i18n.GT.$("pick a point or atom to navigate to (requires {0})"),"set NAVIGATIONMODE")),JV.ActionManager.newAction(22,
"_pickPoint",J.i18n.GT.o(J.i18n.GT.$("pick a DRAW point (for measurements) (requires {0}"),"set DRAWPICKING")),JV.ActionManager.newAction(23,"_popupMenu",J.i18n.GT.$("pop up the full context menu")),JV.ActionManager.newAction(24,"_reset",J.i18n.GT.$("reset (when clicked off the model)")),JV.ActionManager.newAction(25,"_rotate",J.i18n.GT.$("rotate")),JV.ActionManager.newAction(26,"_rotateBranch",J.i18n.GT.o(J.i18n.GT.$("rotate branch around bond (requires {0})"),"set picking ROTATEBOND")),JV.ActionManager.newAction(27,
"_rotateSelected",J.i18n.GT.o(J.i18n.GT.$("rotate selected atoms (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(28,"_rotateZ",J.i18n.GT.$("rotate Z")),JV.ActionManager.newAction(29,"_rotateZorZoom",J.i18n.GT.$("rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse)")),JV.ActionManager.newAction(30,"_select",J.i18n.GT.o(J.i18n.GT.$("select an atom (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(31,"_selectAndDrag",J.i18n.GT.o(J.i18n.GT.$("select and drag atoms (requires {0})"),
"set DRAGSELECTED")),JV.ActionManager.newAction(32,"_selectAndNot",J.i18n.GT.o(J.i18n.GT.$("unselect this group of atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(33,"_selectNone",J.i18n.GT.o(J.i18n.GT.$("select NONE (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(34,"_selectOr",J.i18n.GT.o(J.i18n.GT.$("add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(35,
"_selectToggle",J.i18n.GT.o(J.i18n.GT.$("toggle selection (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL")),JV.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT.$("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG")),JV.ActionManager.newAction(37,"_setMeasure",J.i18n.GT.$("pick an atom to initiate or conclude a measurement")),JV.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT.$("adjust slab (front plane; requires {0})"),
"SLAB ON")),JV.ActionManager.newAction(39,"_slabAndDepth",J.i18n.GT.o(J.i18n.GT.$("move slab/depth window (both planes; requires {0})"),"SLAB ON")),JV.ActionManager.newAction(40,"_slideZoom",J.i18n.GT.$("zoom (along right edge of window)")),JV.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis counterclockwise (requires {0})"),"set picking SPIN")),JV.ActionManager.newAction(42,"_spinDrawObjectCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis clockwise (requires {0})"),
"set picking SPIN")),JV.ActionManager.newAction(43,"_stopMotion",J.i18n.GT.o(J.i18n.GT.$("stop motion (requires {0})"),"set waitForMoveTo FALSE")),JV.ActionManager.newAction(44,"_swipe",J.i18n.GT.$("spin model (swipe and release button and stop motion simultaneously)")),JV.ActionManager.newAction(45,"_translate",J.i18n.GT.$("translate")),JV.ActionManager.newAction(46,"_wheelZoom",J.i18n.GT.$("zoom")))});b.getActionName=c(b,"getActionName",function(a){return a<JV.ActionManager.actionNames.length?JV.ActionManager.actionNames[a]:
null},"~N");b.getActionFromName=c(b,"getActionFromName",function(a){for(var d=0;d<JV.ActionManager.actionNames.length;d++)if(JV.ActionManager.actionNames[d].equalsIgnoreCase(a))return d;return-1},"~S");c(b,"getBindingInfo",function(a){return this.b.getBindingInfo(JV.ActionManager.actionInfo,JV.ActionManager.actionNames,a)},"~S");c(b,"setBinding",function(a){this.b=a},"JV.binding.Binding");c(b,"bnd",function(a,d){for(var b=d.length;0<=--b;)if(this.b.isBound(a,d[b]))return!0;return!1},"~N,~A");c(b,
"isDrawOrLabelAction",function(a){return this.drawMode&&this.bnd(a,[8,9])||this.labelMode&&this.bnd(a,[10])},"~N");c(b,"getBondPickingMode",function(){return this.bondPickingMode});b.getPickingModeName=c(b,"getPickingModeName",function(a){return 0>a||a>=JV.ActionManager.pickingModeNames.length?"off":JV.ActionManager.pickingModeNames[a]},"~N");b.getPickingMode=c(b,"getPickingMode",function(a){for(var d=JV.ActionManager.pickingModeNames.length;0<=--d;)if(a.equalsIgnoreCase(JV.ActionManager.pickingModeNames[d]))return d;
return-1},"~S");b.getPickingStyleName=c(b,"getPickingStyleName",function(a){return 0>a||a>=JV.ActionManager.pickingStyleNames.length?"toggle":JV.ActionManager.pickingStyleNames[a]},"~N");b.getPickingStyleIndex=c(b,"getPickingStyleIndex",function(a){for(var d=JV.ActionManager.pickingStyleNames.length;0<=--d;)if(a.equalsIgnoreCase(JV.ActionManager.pickingStyleNames[d]))return d;return-1},"~S");c(b,"getAtomPickingMode",function(){return this.apm});c(b,"setPickingMode",function(a){var d=!1;switch(a){case -1:d=
!0;this.bondPickingMode=35;a=1;this.vwr.setStringProperty("pickingStyle","toggle");this.vwr.setBooleanProperty("bondPicking",!1);break;case 34:case 33:case 8:this.vwr.getModelkit(!1);case 35:this.vwr.setBooleanProperty("bondPicking",!0);this.bondPickingMode=a;this.resetMeasurement();return}d=(new Boolean(d|this.apm!=a)).valueOf();this.apm=a;d&&this.resetMeasurement()},"~N");c(b,"getPickingState",function(){var a=";set modelkitMode "+this.vwr.getBoolean(603983903)+";set picking "+JV.ActionManager.getPickingModeName(this.apm);
32==this.apm&&(a+="_"+this.vwr.getModelkitPropertySafely("atomType"));a+=";";0!=this.bondPickingMode&&(a+="set picking "+JV.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.vwr.getModelkitPropertySafely("bondType"));return a+";"});c(b,"getPickingStyle",function(){return this.pickingStyle});c(b,"setPickingStyle",function(a){this.pickingStyle=a;4<=a?(this.pickingStyleMeasure=a,this.resetMeasurement()):(3>a&&(this.rootPickingStyle=a),this.pickingStyleSelect=
a);this.rubberbandSelectionMode=!1;switch(this.pickingStyleSelect){case 2:this.b.name.equals("extendedSelect")||this.setBinding(null==this.pfaatBinding?this.pfaatBinding=JV.binding.Binding.newBinding(this.vwr,"Pfaat"):this.pfaatBinding);break;case 3:this.b.name.equals("drag")||this.setBinding(null==this.dragBinding?this.dragBinding=JV.binding.Binding.newBinding(this.vwr,"Drag"):this.dragBinding);this.rubberbandSelectionMode=!0;break;case 1:this.b.name.equals("selectOrToggle")||this.setBinding(null==
this.rasmolBinding?this.rasmolBinding=JV.binding.Binding.newBinding(this.vwr,"Rasmol"):this.rasmolBinding);break;default:this.b!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.b.name.equals("drag")||(this.predragBinding=this.b)},"~N");c(b,"setGestureSwipeFactor",function(a){this.gestureSwipeFactor=a},"~N");c(b,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(b,"setMouseWheelFactor",function(a){this.mouseWheelFactor=a},"~N");c(b,"setCurrent",function(a,d,b,c){this.vwr.hoverOff();
this.current.set(a,d,b,c)},"~N,~N,~N,~N");c(b,"getCurrentX",function(){return this.current.x});c(b,"getCurrentY",function(){return this.current.y});c(b,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=this.vwr.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.vwr.getModelkit(!1).isPickAtomAssignCharge();return;case 4:this.drawMode=!0;this.measuresEnabled=!1;break;
case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(b,"clearMouseInfo",function(){this.pressedCount=this.clickedCount=0;this.dragGesture.setAction(0,0);this.exitMeasurementMode(null)});c(b,"setDragAtomIndex",function(a){this.dragAtomIndex=a;this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a)},"~N");c(b,"isMTClient",function(){return this.isMultiTouchClient});
c(b,"isMTServer",function(){return this.isMultiTouchServer});c(b,"dispose",function(){this.clear()});c(b,"clear",function(){this.startHoverWatcher(!1);null!=this.predragBinding&&(this.b=this.predragBinding);this.vwr.setPickingStyle(null,this.rootPickingStyle);this.isAltKeyReleased=!0});c(b,"startHoverWatcher",function(a){if(!this.vwr.isPreviewOnly)try{a?null==this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread=new J.thread.HoverWatcherThread(this,this.current,this.moved,this.vwr)):
null!=this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread.interrupt(),this.hoverWatcherThread=null)}catch(d){if(!D(d,Exception))throw d;}},"~B");c(b,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");f(b,"keyPressed",function(a,d){if(this.keyProcessing)return!1;this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelectedXY(-2147483648,0,d);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.moved.keybuf=
0;this.dragged.modifiers|=1;this.moved.modifiers|=1;break;case 17:this.moved.modifiers|=2;break;case 27:this.vwr.hoverOff();this.exitMeasurementMode("escape");break;default:this.vwr.hoverOff()}var b=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(b)&&this.checkMotionRotateZoom(b,this.current.x,0,0,!1);if(this.vwr.getBoolean(603979889))switch(a){case 38:case 40:case 37:case 39:case 32:case 46:this.vwr.navigate(a,d)}this.keyProcessing=!1;return!0},"~N,~N");f(b,"keyTyped",function(){return!1},
"~N,~N");f(b,"keyReleased",function(a){switch(a){case 18:this.moved.modifiers&=-9;this.dragSelectedMode&&this.vwr.moveSelectedXY(2147483647,0,this.moved.modifiers);this.isAltKeyReleased=!0;break;case 16:this.moved.modifiers&=-2;0<this.moved.keybuf&&this.vwr.isModelKitOpen()&&this.checkKeyBuf(0);break;case 17:this.moved.modifiers&=-3}0==this.moved.modifiers&&this.vwr.setCursor(0);if(65<=a&&this.vwr.isModelKitOpen()&&(this.dragAtomIndex=this.vwr.findNearestAtomIndex(this.current.x,this.current.y),0<=
this.dragAtomIndex)){this.checkKeyBuf(a);return}if(this.vwr.getBoolean(603979889))switch(a){case 38:case 40:case 37:case 39:this.vwr.navigate(0,0)}this.moved.keybuf=0},"~N");c(b,"checkKeyBuf",function(a){var d=0!=(this.moved.modifiers&1);if(0!=a)if(0==this.moved.keybuf){if(this.moved.keybuf=a,d)return}else this.moved.keybuf+=a<<8;0<this.moved.keybuf&&(this.assignNew(this.moved.keybuf),this.moved.keybuf=0)},"~N");f(b,"mouseEnterExit",function(a,d,b,c){this.vwr.tm.stereoDoubleDTI&&(d<<=1);this.setCurrent(a,
d,b,0);c&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(b,"setMouseActions",function(a,d,b){this.pressAction=JV.binding.Binding.getMouseAction(a,d,b?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,d,1);this.clickAction=JV.binding.Binding.getMouseAction(a,d,2)},"~N,~N,~B");f(b,"mouseAction",function(a,d,b,c,e,g){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&(0!=a&&this.vwr.getBoolean(603979960))&&this.vwr.showString("mouse action: "+a+" "+g+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(e,
g,a),!1),!1),this.vwr.tm.stereoDoubleDTI&&(b<<=1),a){case 0:this.hoverable||(JU.Logger.info("ActionManager: mouse move detected"),this.hoverable=!0);this.setCurrent(d,b,c,g);this.moved.setCurrent(this.current,0);this.moved.keybuf=0;if(null!=this.mp||this.hoverActive){this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,g,0);this.checkClickAction(b,c,d,0);break}if(this.isZoomArea(b)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.vwr.currentCursor&&this.vwr.setCursor(0);
break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(20,b,c,g,d,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(d,b,c,g));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,g,4);this.vwr.setCursor(12);this.pressed.setCurrent(this.current,1);this.dragged.setCurrent(this.current,1);this.vwr.setFocus();this.dragGesture.setAction(this.dragAction,d);this.checkPressedAction(b,c,d);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,
g,!1);a=b-this.dragged.x;e=c-this.dragged.y;this.setCurrent(d,b,c,g);this.dragged.setCurrent(this.current,-1);this.dragGesture.add(this.dragAction,b,c,d);this.checkDragWheelAction(this.dragAction,b,c,a,e,d,1);break;case 5:this.setMouseActions(this.pressedCount,g,!0);this.setCurrent(d,b,c,g);this.vwr.spinXYBy(0,0,0);g=!this.pressed.check(10,b,c,g,d,9223372036854775E3);this.checkReleaseAction(b,c,d,g);break;case 3:if(this.vwr.isApplet&&!this.vwr.hasFocus())break;this.setCurrent(d,this.current.x,this.current.y,
g);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,g,3),this.current.x,this.current.y,0,c,d,3);break;case 2:this.setMouseMode();this.clickedCount=1<e?e:this.clicked.check(10,0,0,g,d,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(d,b,c,g);this.setMouseActions(this.clickedCount,g,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,g,4),[31]))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,
g,2);this.checkClickAction(b,c,d,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(b,"checkPressedAction",function(a,d,b){var c=JV.binding.Binding.getButtonMods(this.pressAction),e=this.bnd(JV.binding.Binding.getMouseAction(1,c,4),[31]);if(0!=c){this.pressAction=this.vwr.notifyMouseClicked(a,d,this.pressAction,4);if(0==this.pressAction)return;c=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,c,!1);JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,
!1));if(!this.isDrawOrLabelAction(this.dragAction)||!this.vwr.checkObjectDragged(-2147483648,0,a,d,this.dragAction)){this.checkUserAction(this.pressAction,a,d,0,0,b,4);b=!1;switch(this.apm){case 32:b=this.bnd(this.clickAction,[0]);break;case 28:b=this.bnd(this.dragAction,[7,14]);break;case 26:case 36:case 37:case 27:b=this.bnd(this.dragAction,[7,14,27]);break;case 29:b=this.bnd(this.dragAction,[11,14]);break;case 30:b=this.bnd(this.dragAction,[11,14,27]);break;default:b=34==this.bondPickingMode}if(b){this.dragAtomIndex=
this.vwr.findNearestAtomIndexMovable(a,d,!0);a=34==this.bondPickingMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1;if(0<=this.dragAtomIndex&&(0<=a||32==this.apm||31==this.apm))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1),0<=a&&this.updateModelkitBranch(a,!0);a=this.vwr.getModelkitPropertySafely("screenXY");this.mkBondPressed=null!=a&&this.pressed.inRange(10,a[0],a[1])}else this.bnd(this.pressAction,[23])?this.doPopup(a,d):this.dragSelectedMode?(this.haveSelection=
!e||0<=this.vwr.findNearestAtomIndexMovable(a,d,!0))&&this.bnd(this.dragAction,[13,14])&&this.vwr.moveSelectedXY(-2147483648,0,c):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(b,"checkDragWheelAction",function(a,d,b,c,e,g,j){var k=JV.binding.Binding.getButtonMods(a);if(0!=k){var f=this.vwr.notifyMouseClicked(d,b,JV.binding.Binding.getMouseAction(this.pressedCount,k,j),j);if(0==f)return;0<f&&(a=f)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");
else if(!this.checkUserAction(a,d,b,c,e,g,j))if(g=34==this.bondPickingMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1,0<=g&&(0<=this.dragAtomIndex||this.mkBondPressed||this.bnd(a,[26])))0<=this.dragAtomIndex&&this.updateModelkitBranch(g,!1),this.vwr.moveSelected(c,e,-2147483648,d,b,null,null,null,!1,!1,0<=this.dragAtomIndex?0:16);else{g=null;if(0<=this.dragAtomIndex&&2!=this.apm)switch(this.apm){case 26:this.dragSelected(a,c,e,!0);return;case 36:case 37:case 27:case 30:g=this.vwr.ms.getAtoms(37==
this.apm?1094717454:1094713360,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&g.and(this.vwr.getAtomBitSet("ligand"));case 28:case 29:1==this.dragGesture.getPointCount()&&this.vwr.undoMoveActionClear(this.dragAtomIndex,2,!0);this.setMotion(13,!0);if(this.bnd(a,[27]))this.vwr.rotateSelected(this.getDegrees(c,!0),this.getDegrees(e,!1),g);else{switch(this.apm){case 36:case 37:case 27:case 30:this.vwr.selectStatus(g,!1,0,!0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,c,e,this.bnd(a,
[14])?-e:-2147483648,null,g);this.vwr.checkCoordinatesChanged()}return}if(0<=this.dragAtomIndex&&1==j&&this.bnd(this.clickAction,[0])&&32==this.apm)a=this.vwr.findNearestAtomIndexMovable(d,b,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),null!=this.mp&&(this.vwr.antialiased&&(d<<=1,b<<=1),this.mp.traceX=d,this.mp.traceY=b,this.vwr.refresh(3,"assignNew"));
else if(!this.drawMode&&!this.labelMode&&this.bnd(a,[45]))this.vwr.translateXYBy(c,e);else if(this.dragSelectedMode&&this.haveSelection&&this.bnd(a,[13,27]))d=this.vwr.bsA().nextSetBit(0),0>d||(1==this.dragGesture.getPointCount()?this.vwr.undoMoveActionClear(d,2,!0):this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,null,null,!1,!1,k),this.dragSelected(a,c,e,!1));else{if(this.isDrawOrLabelAction(a)&&(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,
d,b,a)))return;if(this.checkMotionRotateZoom(a,d,c,e,!0))this.vwr.tm.slabEnabled&&this.bnd(a,[39])?this.vwr.slabDepthByPixels(e):this.vwr.zoomBy(e);else if(this.bnd(a,[25]))this.vwr.rotateXYBy(this.getDegrees(c,!0),this.getDegrees(e,!1));else if(this.bnd(a,[29]))0==c&&1<Math.abs(e)?(this.setMotion(8,!0),this.vwr.zoomBy(e+(0<e?-1:1))):0==e&&1<Math.abs(c)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c+(0<c?1:-1),2147483647,2147483647));else{if(this.vwr.tm.slabEnabled){if(this.bnd(a,[6])){this.vwr.depthByPixels(e);
return}if(this.bnd(a,[38])){this.vwr.slabByPixels(e);return}if(this.bnd(a,[39])){this.vwr.slabDepthByPixels(e);return}}this.bnd(a,[46])?this.zoomByFactor(e,2147483647,2147483647):this.bnd(a,[28])&&(this.setMotion(13,!0),this.vwr.rotateZBy(-c,2147483647,2147483647))}}}},"~N,~N,~N,~N,~N,~N,~N");c(b,"updateModelkitBranch",function(a,d){this.vwr.setModelkitPropertySafely(d?"branchAtomClicked":"branchAtomDragged",Integer.$valueOf(this.dragAtomIndex));null==this.measurementQueued||0==this.measurementQueued.numSet||
null==this.mp?this.vwr.setPendingMeasurement(this.vwr.getModelkit(!1).setBondMeasure(a,this.measurementQueued=this.mp=this.getMP())):this.measurementQueued.refresh(null)},"~N,~B");c(b,"dragSelected",function(a,d,b,c){this.setMotion(13,!0);this.bnd(a,[27])&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(d,!0),this.getDegrees(b,!1),null):this.vwr.moveSelected(d,b,c&&this.bnd(a,[14])?-b:-2147483648,-2147483648,-2147483648,null,null,null,!0,!1,this.dragged.modifiers)},"~N,~N,~N,~B");
c(b,"checkReleaseAction",function(a,d,b,c){JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,d,b);0<=this.dragAtomIndex&&!this.vwr.isModelkitPickingRotateBond()&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==this.apm&&this.bnd(this.clickAction,[0]))null==this.mp||0>this.dragAtomIndex?this.exitMeasurementMode(null):
34==this.bondPickingMode?(this.vwr.setModelkitPropertySafely("bondAtomIndex",Integer.$valueOf(this.dragAtomIndex)),this.exitMeasurementMode(null)):this.assignNew(-1);else if(this.dragAtomIndex=-1,this.mkBondPressed=!1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,c&&this.vwr.notifyMouseClicked(a,d,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.isDrawOrLabelAction(this.dragAction))this.vwr.checkObjectDragged(2147483647,
0,a,d,this.dragAction);else if(this.haveSelection&&(this.dragSelectedMode&&this.bnd(this.dragAction,[13]))&&this.vwr.moveSelectedXY(2147483647,0,this.dragged.modifiers),(!c||!this.checkUserAction(this.pressAction,a,d,0,0,b,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,[44]))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");
c(b,"checkClickAction",function(a,d,b,c){if(0<c){if(this.checkUserAction(this.clickAction,a,d,0,0,b,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,d,this.clickAction,32768);if(0==this.clickAction)return}JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.bnd(this.clickAction,[2])){if(this.vwr.frankClicked(a,d)){this.vwr.popupMenu(-a,d,"j");return}if(this.vwr.frankClickedModelKit(a,d)){this.vwr.popupMenu(10,
0,"m");return}}b=null;var e=!1,g=!1,j=null;if(!this.drawMode&&(j=this.vwr.checkObjectClicked(a,d,this.clickAction),null!=j)){if(this.labelMode){this.pickLabel(j.get("atomIndex").intValue());return}e="bond".equals(j.get("type"));g="isosurface".equals(j.get("type"));b=this.getPoint(j);e&&this.vwr.isModelkitPickingRotateBond()&&this.vwr.highlightBond(j.get("index").intValue(),-1,a,d)}e&&(c=1);if(!(null!=b&&Float.isNaN(b.x))){var f=this.findNearestAtom(a,d,b,0<c);if(this.bnd(this.clickAction,[23]))this.doPopup(a,
d);else if(0==c&&32!=this.apm&&!this.vwr.isModelkitPickingRotateBond()){if(null!=this.mp){if(null!=b||0==this.mp.getIndexOf(f))try{this.mp.addPoint(f,b,!1)}catch(l){if(D(l,Exception)){this.exitMeasurementMode(null);return}throw l;}this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp);this.vwr.refresh(3,"measurementPending")}}else if(this.setMouseMode(),this.bnd(this.clickAction,[43])&&this.vwr.tm.stopMotion(),this.vwr.getBoolean(603979889)&&23==this.apm&&this.bnd(this.clickAction,[21]))this.vwr.navTranslatePercent(100*
a/this.vwr.getScreenWidth()-50,100*d/this.vwr.getScreenHeight()-50);else{if(e){if(this.bnd(this.clickAction,[34==this.bondPickingMode||33==this.bondPickingMode?0:5])){this.bondPicked(j.get("index").intValue());this.vwr.refresh(1,"bondpicked");return}}else{if(g)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,[20])){this.atomOrPointPicked(f,b);4==this.addToMeasurement(f,b,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,[37])){null!=this.mp?(this.addToMeasurement(f,
b,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(f),this.addToMeasurement(f,b,!0));this.atomOrPointPicked(f,b);return}}this.isSelectAction(this.clickAction)?g||this.atomOrPointPicked(f,b):this.bnd(this.clickAction,[24])&&0>f&&this.reset()}}},"~N,~N,~N,~N");c(b,"doPopup",function(a,d){this.vwr.popupMenu(a,d,this.vwr.getBoolean(603983903)?"m":"j")},"~N,~N");c(b,"pickLabel",function(a){var d=this.vwr.ms.at[a].atomPropertyString(this.vwr,
1825200146);2==this.pressedCount?(d=this.vwr.apiPlatform.prompt("Set label for atomIndex="+a,d,null,!1),null!=d&&(this.vwr.shm.setAtomLabel(d,a),this.vwr.refresh(1,"label atom"))):this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a+": "+d)},"~N");c(b,"checkUserAction",function(a,d,b,c,e,g,j){if(!this.b.isUserAction(a))return!1;for(var f=!1,l,s=this.b.getBindings(),m=a+"\t",p,x=s.keySet().iterator();x.hasNext()&&((p=x.next())||1);)if(0==p.indexOf(m)&&JU.AU.isAS(l=s.get(p))){var n=
l[1],r=null;if(0<=n.indexOf("_ATOM")){var u=this.findNearestAtom(d,b,null,!0),n=JU.PT.rep(n,"_ATOM","({"+(0<=u?""+u:"")+"})");0<=u&&(n=JU.PT.rep(n,"_POINT",JU.Escape.eP(this.vwr.ms.at[u])))}if(!this.drawMode&&(0<=n.indexOf("_POINT")||0<=n.indexOf("_OBJECT")||0<=n.indexOf("_BOND"))){u=this.vwr.checkObjectClicked(d,b,a);if(null!=u&&null!=(r=u.get("pt")))u.get("type").equals("bond")&&(n=JU.PT.rep(n,"_BOND","[{"+u.get("index")+"}]")),n=JU.PT.rep(n,"_POINT",JU.Escape.eP(r)),n=JU.PT.rep(n,"_OBJECT",JU.Escape.escapeMap(u));
n=JU.PT.rep(n,"_BOND","[{}]");n=JU.PT.rep(n,"_OBJECT","{}")}n=JU.PT.rep(n,"_POINT","{}");n=JU.PT.rep(n,"_ACTION",""+a);n=JU.PT.rep(n,"_X",""+d);n=JU.PT.rep(n,"_Y",""+(this.vwr.getScreenHeight()-b));n=JU.PT.rep(n,"_DELTAX",""+c);n=JU.PT.rep(n,"_DELTAY",""+e);n=JU.PT.rep(n,"_TIME",""+g);n=JU.PT.rep(n,"_MODE",""+j);n.startsWith("+:")&&(f=!0,n=n.substring(2));this.vwr.evalStringQuiet(n)}return!f},"~N,~N,~N,~N,~N,~N,~N");c(b,"checkMotionRotateZoom",function(a,d,b,c,e){d=this.bnd(a,[40])&&this.isZoomArea(this.pressed.x);
var g=this.bnd(a,[25]),j=this.bnd(a,[29]);if(!d&&!g&&!j)return!1;a=(b=j&&(0==b||Math.abs(c)>5*Math.abs(b)))||this.isZoomArea(this.moved.x)||this.bnd(a,[46])?8:g||j?13:this.bnd(a,[1])?12:0;this.setMotion(a,e);return b||d},"~N,~N,~N,~N,~B");c(b,"getExitRate",function(){var a=this.dragGesture.getTimeDifference(2);return this.isMultiTouch?80<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(2,1):10<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(4,2)});c(b,"isRubberBandSelect",function(a){return this.rubberbandSelectionMode&&
this.bnd(a&-8193|32768,[35,34,32])},"~N");c(b,"getRubberBand",function(){return this.rubberbandSelectionMode&&2147483647!=this.rectRubber.x?this.rectRubber:null});c(b,"calcRectRubberBand",function(){var a=this.vwr.antialiased?2:1;this.current.x<this.pressed.x?(this.rectRubber.x=this.current.x*a,this.rectRubber.width=(this.pressed.x-this.current.x)*a):(this.rectRubber.x=this.pressed.x*a,this.rectRubber.width=(this.current.x-this.pressed.x)*a);this.current.y<this.pressed.y?(this.rectRubber.y=this.current.y*
a,this.rectRubber.height=(this.pressed.y-this.current.y)*a):(this.rectRubber.y=this.pressed.y*a,this.rectRubber.height=(this.current.y-this.pressed.y)*a)});c(b,"getDegrees",function(a,d){return 180*(a/Math.min(500,d?this.vwr.getScreenWidth():this.vwr.getScreenHeight()))*this.mouseDragFactor},"~N,~B");c(b,"isZoomArea",function(a){return a>98*this.vwr.getScreenWidth()*(this.vwr.tm.stereoDoubleFull||this.vwr.tm.stereoDoubleDTI?2:1)/100},"~N");c(b,"getPoint",function(a){var d=new JU.Point3fi;d.setT(a.get("pt"));
d.mi=a.get("modelIndex").intValue();return d},"java.util.Map");c(b,"findNearestAtom",function(a,d,b,c){a=this.drawMode||null!=b?-1:this.vwr.findNearestAtomIndexMovable(a,d,!1);return 0<=a&&(c||null==this.mp)&&!this.vwr.slm.isInSelectionSubset(a)?-1:a},"~N,~N,JU.Point3fi,~B");c(b,"isSelectAction",function(a){return this.bnd(a,[17])||!this.drawMode&&!this.labelMode&&1==this.apm&&this.bnd(a,[1])||this.dragSelectedMode&&this.bnd(this.dragAction,[27,13])||this.bnd(a,[22,35,32,34,36,30])},"~N");c(b,"enterMeasurementMode",
function(a){this.vwr.setPicked(a,!0);this.vwr.setCursor(1);this.vwr.setPendingMeasurement(this.mp=this.getMP());this.measurementQueued=this.mp},"~N");c(b,"getMP",function(){return J.api.Interface.getInterface("JM.MeasurementPending",this.vwr,"mouse").set(this.vwr.ms)});c(b,"addToMeasurement",function(a,d,b){if(-1==a&&null==d||null==this.mp)return this.exitMeasurementMode(null),0;var c=this.mp.count;-2147483648!=this.mp.traceX&&2==c&&this.mp.setCount(c=1);return 4==c&&!b?c:this.mp.addPoint(a,d,!0)},
"~N,JU.Point3fi,~B");c(b,"resetMeasurement",function(){this.exitMeasurementMode(null);this.measurementQueued=this.getMP()});c(b,"exitMeasurementMode",function(a){null!=this.mp&&(this.vwr.setPendingMeasurement(this.mp=null),this.vwr.setCursor(0),null!=a&&this.vwr.refresh(3,a))},"~S");c(b,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),d=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>d))try{var b=this.vwr.getSmilesOpt(null,a,d,1048576,null);this.vwr.setStatusMeasuring("measureSequence",
-2,b,0)}catch(c){if(D(c,Exception))JU.Logger.error(c.toString());else throw c;}});c(b,"minimize",function(a){var d=this.dragAtomIndex;a&&(this.dragAtomIndex=-1,this.mkBondPressed=!1);this.vwr.dragMinimizeAtom(d)},"~B");c(b,"queueAtom",function(a,d){var b=this.measurementQueued.addPoint(a,d,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+b+":"+this.vwr.getAtomInfo(a),null,!1);return b},"~N,JU.Point3fi");c(b,"setMotion",function(a,d){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}d&&
this.vwr.setInMotion(!0)},"~N,~B");c(b,"zoomByFactor",function(a,d,b){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),d,b),this.moved.setCurrent(this.current,0),this.vwr.setInMotion(!0),this.zoomTrigger=!0,this.startHoverWatcher(!0))},"~N,~N,~N");c(b,"runScript",function(a){this.vwr.evalStringGUI(a)},"~S");c(b,"atomOrPointPicked",function(a,d){if(0>a){this.resetMeasurement();if(this.bnd(this.clickAction,[33])){this.runScript("select none");return}if(5!=this.apm&&
6!=this.apm)return}var b=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var b=8==this.apm,c=25==this.apm;if(!this.bnd(this.clickAction,[b?5:3]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,d,!0);if(2!=this.queueAtom(a,d))return;b=b||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":c?"STRUTS":"";this.runScript("connect "+
this.measurementQueued.getMeasurementScript(" ",!0)+b);this.resetMeasurement();return;case 21:b++;case 20:b++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,[20]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>b)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,d,!0);this.queueAtom(a,d);c=this.measurementQueued.count;1==c&&this.vwr.setPicked(a,!0);if(c<b)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",
b,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}b=null!=this.mp&&1!=this.apm?1:this.apm;switch(b){case 3:if(!this.bnd(this.clickAction,[17]))return;null==d?this.zoomTo(a):this.runScript("zoomTo "+JU.Escape.eP(d));return;case 5:case 6:this.bnd(this.clickAction,[17])&&this.checkTwoAtomAction(d,a)}if(null==d){switch(b){case 1:!this.drawMode&&
!this.labelMode&&this.bnd(this.clickAction,[1])?this.zoomTo(a):this.bnd(this.clickAction,[17])&&this.vwr.setStatusAtomPicked(a,null,null,!1);return;case 2:this.bnd(this.clickAction,[19])&&(this.runScript("set labeltoggle {atomindex="+a+"}"),this.pickLabel(a));return;case 31:this.bnd(this.clickAction,[0])&&(this.vwr.invertAtomCoord(null,null,null,a,!0),this.vwr.setStatusAtomPicked(a,"invert stereo for atomIndex="+a,null,!1));return;case 7:this.bnd(this.clickAction,[4])&&(b=JU.BSUtil.newAndSetBit(a),
this.vwr.deleteAtoms(b,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(b),null,!1));return}b="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(b);break;case 10:this.selectAtoms("within(group, "+b+")");break;case 11:this.selectAtoms("within(chain, "+b+")");break;case 13:this.selectAtoms("within(polymer, "+b+")");break;case 14:this.selectAtoms("within(structure, "+b+")");break;case 12:this.selectAtoms("within(molecule, "+b+")");break;case 16:this.selectAtoms("within(model, "+
b+")");break;case 17:this.selectAtoms("visible and within(element, "+b+")");break;case 15:this.selectAtoms("visible and within(site, "+b+")")}this.vwr.clearClickCount();this.vwr.setStatusAtomPicked(a,null,null,!1)}},"~N,JU.Point3fi");c(b,"assignNew",function(a){0>a?this.vwr.getModelkit(!1).handleAssignNew(this.pressed,this.dragged,this.mp,this.dragAtomIndex,a)||this.exitMeasurementMode("bond dropped"):this.vwr.getModelkit(!1).handleAssignNew(this.current,this.current,null,this.dragAtomIndex,a);this.exitMeasurementMode(null)},
"~N");c(b,"bondPicked",function(a){switch(this.bondPickingMode){case 33:this.vwr.undoMoveActionClear(-1,4146,!0);this.vwr.setModelkitPropertySafely("scriptAssignBond",Integer.$valueOf(a));break;case 8:this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(a))}},"~N");c(b,"checkTwoAtomAction",function(a,d){var b=5==this.apm;if(this.vwr.tm.spinOn||this.vwr.tm.navOn||null!=this.vwr.getPendingMeasurement())this.resetMeasurement(),this.vwr.tm.spinOn&&this.runScript("spin off");else{2<=this.measurementQueued.count&&
this.resetMeasurement();var c=this.measurementQueued.count;if(1==c)if(null==a){if(this.measurementQueued.getAtomIndex(1)==d)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=d||null!=a)c=this.queueAtom(d,a);2>c?b?this.vwr.scriptStatus(1==c?J.i18n.GT.$("pick one more atom in order to spin the model around an axis"):J.i18n.GT.$("pick two atoms in order to spin the model around an axis")):this.vwr.scriptStatus(1==c?J.i18n.GT.$("pick one more atom in order to display the symmetry relationship"):
J.i18n.GT.$("pick two atoms in order to display the symmetry relationship between them")):(c=this.measurementQueued.getMeasurementScript(" ",!1),b?this.runScript("spin"+c+" "+this.vwr.getInt(553648157)):this.runScript("draw symop "+c+";show symop "+c))}},"JU.Point3fi,~N");c(b,"reset",function(){this.runScript("!reset")});c(b,"selectAtoms",function(a){if(!(null!=this.mp||this.selectionWorking)){this.selectionWorking=!0;var d=this.rubberbandSelectionMode||this.bnd(this.clickAction,[35])?"selected and not ("+
a+") or (not selected) and ":this.bnd(this.clickAction,[32])?"selected and not ":this.bnd(this.clickAction,[34])?"selected or ":0==this.clickAction||this.bnd(this.clickAction,[36])?"selected tog ":this.bnd(this.clickAction,[30])?"":null;if(null!=d)try{var b=this.vwr.getAtomBitSetEval(null,d+("("+a+")"));this.setAtomsPicked(b,"selected: "+JU.Escape.eBS(b));this.vwr.refresh(3,"selections set")}catch(c){if(!D(c,Exception))throw c;}this.selectionWorking=!1}},"~S");c(b,"setAtomsPicked",function(a,d){this.vwr.selectStatus(a,
!1,0,!1,!0);this.vwr.setStatusAtomPicked(-1,d,null,!1)},"JU.BS,~S");c(b,"selectRb",function(a){var d=this.vwr.ms.findAtomsInRectangle(this.rectRubber);0<d.length()&&(d=JU.Escape.eBS(d),this.bnd(a,[34])?this.runScript("selectionHalos on;select selected or "+d):this.bnd(a,[32])?this.runScript("selectionHalos on;select selected and not "+d):this.runScript("selectionHalos on;select selected tog "+d));this.vwr.refresh(3,"mouseReleased")},"~N");c(b,"toggleMeasurement",function(){if(null!=this.mp){var a=
this.mp.count;2<=a&&4>=a&&this.runScript("!measure "+this.mp.getMeasurementScript(" ",!0));this.exitMeasurementMode(null)}});c(b,"zoomTo",function(a){this.runScript("zoomTo (atomindex="+a+")");this.vwr.setStatusAtomPicked(a,null,null,!1)},"~N");c(b,"userActionEnabled",function(a){return this.vwr.isFunction(JV.ActionManager.getActionName(a).toLowerCase())},"~N");c(b,"userAction",function(a,d){if(!this.userActionEnabled(a))return!1;var b=JS.ScriptEval.runUserAction(JV.ActionManager.getActionName(a),
d,this.vwr);return!JS.SV.vF.equals(b)},"~N,~A");b.actionInfo=Array(47);b.actionNames=Array(47);JV.ActionManager.pickingModeNames="off identify label center draw spin symmetry deleteatom deletebond atom group chain molecule polymer structure site model element measure distance angle torsion sequence navigate connect struts dragselected dragmolecule dragatom dragminimize dragminimizemolecule invertstereo assignatom assignbond rotatebond identifybond dragligand dragmodel".$plit(" ");JV.ActionManager.pickingStyleNames=
"toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");b=r(function(){this.time=this.y=this.x=this.index=0;u(this,arguments)},JV,"MotionPoint",null);c(b,"set",function(a,d,b,c){this.index=a;this.x=d;this.y=b;this.time=c},"~N,~N,~N,~N");f(b,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});b=r(function(){this.action=0;this.nodes=null;this.time0=this.ptNext=0;this.vwr=null;u(this,arguments)},JV,"Gesture",null);y(b,function(a,d){this.vwr=d;this.nodes=
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46);this.bindAction(289,46);this.bindAction(291,46);this.bindAction(290,38);this.bindAction(289,6);this.bindAction(291,39);this.bindAction(8464,44);this.bindAction(8464,41);this.bindAction(8465,42);this.bindAction(8473,13);this.bindAction(8465,14);this.bindAction(8472,27);this.bindAction(8465,26);this.bindAction(8464,10);this.bindAction(8472,9);this.bindAction(8465,8);this.bindAction(33297,24);this.bindAction(33288,24);this.bindAction(33296,43);this.bindAction(8464,7);this.bindAction(8464,11);this.bindAction(8464,
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this.vwr=this.ce=null;this.isDefaultColorRasmol=!1;this.colixRubberband=22;this.colixBackgroundContrast=0;u(this,arguments)},JV,"ColorManager",null);y(b,function(a,b){this.vwr=a;this.ce=new JU.ColorEncoder(null,a);this.g3d=b;this.argbsCpk=J.c.PAL.argbsCpk;this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1)},"JV.Viewer,JU.GData");c(b,"setDefaultColors",function(a){a?(this.isDefaultColorRasmol=!0,this.argbsCpk=JU.AU.arrayCopyI(JU.ColorEncoder.getRasmolScale(),-1)):(this.isDefaultColorRasmol=
!1,this.argbsCpk=J.c.PAL.argbsCpk);this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1);this.ce.createColorScheme(a?"Rasmol=":"Jmol=",!0,!0);for(a=J.c.PAL.argbsCpk.length;0<=--a;)this.g3d.changeColixArgb(a,this.argbsCpk[a]);for(a=JV.JC.altArgbsCpk.length;0<=--a;)this.g3d.changeColixArgb(JU.Elements.elementNumberMax+a,this.altArgbsCpk[a])},"~B");c(b,"setRubberbandArgb",function(a){this.colixRubberband=0==a?0:JU.C.getColix(a)},"~N");c(b,"setColixBackgroundContrast",function(a){this.colixBackgroundContrast=
JU.C.getBgContrast(a)},"~N");c(b,"getColixBondPalette",function(a,b){switch(b){case 19:return this.ce.getColorIndexFromPalette(a.getEnergy(),-2.5,-0.5,7,!1)}return 10},"JM.Bond,~N");c(b,"getColixAtomPalette",function(a,b){var c=0,q;q=this.vwr.ms;switch(b){case 84:return null==this.colorData||a.i>=this.colorData.length||Float.isNaN(this.colorData[a.i])?12:this.ce.getColorIndex(this.colorData[a.i]);case 0:case 1:q=a.getAtomicAndIsotopeNumber();if(q<JU.Elements.elementNumberMax)return this.g3d.getChangeableColix(q,
this.argbsCpk[q]);c=q;q=JU.Elements.altElementIndexFromNumber(q);if(0<q)return this.g3d.getChangeableColix(JU.Elements.elementNumberMax+q,this.altArgbsCpk[q]);q=JU.Elements.getElementNumber(c);return this.g3d.getChangeableColix(q,this.argbsCpk[q]);case 2:return q=JU.ColorEncoder.quantize4(a.getPartialCharge(),-1,1,JV.JC.PARTIAL_CHARGE_RANGE_SIZE),this.g3d.getChangeableColix(JV.JC.PARTIAL_CHARGE_COLIX_RED+q,JV.JC.argbsRwbScale[q]);case 3:return q=a.getFormalCharge()- -4,this.g3d.getChangeableColix(JV.JC.FORMAL_CHARGE_COLIX_RED+
q,JV.JC.argbsFormalCharge[q]);case 68:case 5:return 68==b?(q=this.vwr.ms.getBfactor100Lo(),c=this.vwr.ms.getBfactor100Hi()):(q=0,c=1E4),this.ce.getColorIndexFromPalette(a.getBfactor100(),q,c,7,!1);case 86:return this.ce.getColorIndexFromPalette(a.group.getGroupParameter(1111490574),-1,1,7,!1);case 70:return c=this.vwr.ms.getSurfaceDistanceMax(),this.ce.getColorIndexFromPalette(a.getSurfaceDistance100(),0,c,7,!1);case 24:return q=a.group.groupID,42<=q&&(q=24+"PGCATU".indexOf(Character.toUpperCase(a.group.group1))-
1),this.ce.getColorIndexFromPalette(q,0,0,17,!1);case 8:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,5,!1);case 9:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,4,!1);case 75:return this.ce.getColorIndexFromPalette(a.group.selectedIndex,0,a.group.chain.selectedGroupCount-1,1,!1);case 87:return q=this.vwr.ms.am[a.mi],this.ce.getColorIndexFromPalette(a.group.getBioPolymerIndexInModel(),0,(q.isBioModel?q.getBioPolymerCount():0)-1,1,!1);case 76:return this.ce.getColorIndexFromPalette(a.group.getSelectedMonomerIndex(),
0,a.group.getSelectedMonomerCount()-1,1,!1);case 77:return this.ce.getColorIndexFromPalette(q.getMoleculeIndex(a.i,!0),0,q.getMoleculeCountInModel(a.mi)-1,0,!1);case 14:return c=a.mi,this.ce.getColorIndexFromPalette(q.getAltLocIndexInModel(c,a.altloc),0,q.getAltLocCountInModel(c),0,!1);case 15:return c=a.mi,this.ce.getColorIndexFromPalette(q.getInsertionCodeIndexInModel(c,a.group.getInsertionCode()),0,q.getInsertionCountInModel(c),0,!1);case 16:q=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(q,
1073741991);break;case 17:q=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(q,1073742116);break;case 7:c=a.group.getProteinStructureSubType().getColor();break;case 10:q=a.getChainID(),null==JU.ColorEncoder.argbsChainAtom&&(JU.ColorEncoder.argbsChainAtom=this.getArgbs(1153433601),JU.ColorEncoder.argbsChainHetero=this.getArgbs(1612709894)),q=((0>q?0:256<=q?q-256:q)&31)%JU.ColorEncoder.argbsChainAtom.length,c=(a.isHetero()?JU.ColorEncoder.argbsChainHetero:JU.ColorEncoder.argbsChainAtom)[q]}return 0==
c?22:JU.C.getColix(c)},"JM.Atom,~N");c(b,"getArgbs",function(a){return this.vwr.getJBR().getArgbs(a)},"~N");c(b,"getJmolOrRasmolArgb",function(a,b){switch(b){case 1073741991:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,0,0,2);case 1073742116:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,0,0,3);default:return b}return JV.JC.altArgbsCpk[JU.Elements.altElementIndexFromNumber(a)]},"~N,~N");c(b,"setElementArgb",function(a,b){if(1073741991==
b&&this.argbsCpk===J.c.PAL.argbsCpk)return 0;b=this.getJmolOrRasmolArgb(a,b);this.argbsCpk===J.c.PAL.argbsCpk&&(this.argbsCpk=JU.AU.arrayCopyRangeI(J.c.PAL.argbsCpk,0,-1),this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1));if(a<JU.Elements.elementNumberMax){if(2147483647==b)return JU.C.getColix(this.argbsCpk[a]);this.argbsCpk[a]=b;this.g3d.changeColixArgb(a,b);return 0}a=JU.Elements.altElementIndexFromNumber(a);this.altArgbsCpk[a]=b;this.g3d.changeColixArgb(JU.Elements.elementNumberMax+
a,b);return 0},"~N,~N");c(b,"getPropertyColorRange",function(){return this.ce.isReversed?L(-1,[this.ce.hi,this.ce.lo]):L(-1,[this.ce.lo,this.ce.hi])});c(b,"setPropertyColorRangeData",function(a,b){this.colorData=a;this.ce.currentPalette=this.ce.createColorScheme(this.vwr.g.propertyColorScheme,!0,!1);this.ce.hi=-3.4028235E38;this.ce.lo=3.4028235E38;if(null!=a){for(var c=null==b,q,e=c?a.length-1:b.nextSetBit(0);0<=e;e=c?e-1:b.nextSetBit(e+1))if(!Float.isNaN(q=a[e]))this.ce.hi=Math.max(this.ce.hi,q),
this.ce.lo=Math.min(this.ce.lo,q);this.setPropertyColorRange(this.ce.lo,this.ce.hi)}},"~A,JU.BS");c(b,"setPropertyColorRange",function(a,b){this.ce.setRange(a,b,a>b);JU.Logger.debugging&&JU.Logger.debug('ColorManager: color "'+this.ce.getCurrentColorSchemeName()+'" range '+a+" "+b)},"~N,~N");c(b,"setPropertyColorScheme",function(a,b,c){var q=0==a.length;q&&(a="=");var e=this.getPropertyColorRange();this.ce.currentPalette=this.ce.createColorScheme(a,!0,c);q||this.setPropertyColorRange(e[0],e[1]);this.ce.isTranslucent=
b},"~S,~B,~B");c(b,"getColorSchemeList",function(a){a=null==a||0==a.length?this.ce.currentPalette:this.ce.createColorScheme(a,!0,!1);return JU.ColorEncoder.getColorSchemeList(this.ce.getColorSchemeArray(a))},"~S");c(b,"getColorEncoder",function(a){if(null==a||0==a.length)return this.ce;var b=new JU.ColorEncoder(this.ce,this.vwr);b.currentPalette=b.createColorScheme(a,!1,!0);return 2147483647==b.currentPalette?null:b},"~S")});n("JV");z(["javajs.api.BytePoster","java.util.Hashtable"],"JV.FileManager",
"java.net.URL $.URLEncoder JU.AU $.Base64 $.LimitedLineReader $.Lst $.OC $.PT $.Rdr $.SB J.api.Interface J.io.FileReader JU.Escape $.Logger JV.JC $.JmolAsyncException $.Viewer".split(" "),function(){var b=r(function(){this.jzu=this.spartanDoc=this.vwr=null;this.pathForAllFiles="";this.nameAsGiven="zapped";this.lastFullPathName=this.fullPathName=null;this.lastNameAsGiven="zapped";this.spardirCache=this.pngjCache=this.cache=this.appletProxy=this.appletDocumentBaseURL=this.lastFileType=this.fileName=
null;u(this,arguments)},JV,"FileManager",null,javajs.api.BytePoster);N(b,function(){this.cache=new java.util.Hashtable});y(b,function(a){this.vwr=a;this.clear()},"JV.Viewer");c(b,"spartanUtil",function(){return null==this.spartanDoc?this.spartanDoc=J.api.Interface.getInterface("J.adapter.readers.spartan.SpartanUtil",this.vwr,"fm getSpartanUtil()").set(this):this.spartanDoc});c(b,"getJzu",function(){return null==this.jzu?this.jzu=J.api.Interface.getOption("io.JmolUtil",this.vwr,"file"):this.jzu});
c(b,"clear",function(){this.setFileInfo(B(-1,[this.vwr.getZapName()]));this.spardirCache=null});c(b,"setLoadState",function(a){this.vwr.getPreserveState()&&a.put("loadState",this.vwr.g.getLoadState(a))},"java.util.Map");c(b,"getPathForAllFiles",function(){return this.pathForAllFiles});c(b,"setPathForAllFiles",function(a){0<a.length&&(!a.endsWith("/")&&!a.endsWith("|"))&&(a+="/");return this.pathForAllFiles=a},"~S");c(b,"setFileInfo",function(a){null==a?(this.fullPathName=this.lastFullPathName,this.nameAsGiven=
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this.lastFullPathName?this.lastFullPathName:this.lastNameAsGiven},"~B");c(b,"getFileType",function(){return this.lastFileType});c(b,"setFileType",function(a){this.lastFileType=a},"~S");c(b,"getFileName",function(){return null!=this.fileName?this.fileName:this.nameAsGiven});c(b,"getAppletDocumentBase",function(){return null==this.appletDocumentBaseURL?"":this.appletDocumentBaseURL.toString()});c(b,"setAppletContext",function(a){try{System.out.println('setting document base to "'+a+'"'),this.appletDocumentBaseURL=
0==a.length?null:new java.net.URL(ma("java.net.URL"),a,null)}catch(b){if(D(b,"java.net.MalformedURLException"))System.out.println("error setting document base to "+a);else throw b;}},"~S");c(b,"setAppletProxy",function(a){this.appletProxy=null==a||0==a.length?null:a},"~S");c(b,"createAtomSetCollectionFromFile",function(a,b,c){null==b.get("atomDataOnly")&&this.setLoadState(b);var q=a,e=a.indexOf("::");0>e&&(a=this.vwr.resolveDatabaseFormat(a));!q.equals(a)&&(0>q.indexOf("/")&&JV.Viewer.hasDatabasePrefix(q))&&
b.put("dbName",q);a.endsWith("%2D%")&&(q=b.get("filter"),b.put("filter",(null==q?"":q)+"2D"),a=a.substring(0,a.length-4));q=0<=e?a.substring(e+2):a;e=0<=e?a.substring(0,e):null;JU.Logger.info("\nFileManager.getAtomSetCollectionFromFile("+q+")"+(a.equals(q)?"":" //"+a));var g=this.getClassifiedName(q,!0);if(1==g.length)return g[0];a=g[0];g=g[1];b.put("fullPathName",(null==e?"":e+"::")+JV.FileManager.fixDOSName(a));this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825)&&this.vwr.getChimeMessenger().update(a);
b=new J.io.FileReader(this.vwr,g,a,q,e,null,b,c);b.run();return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(b,"createAtomSetCollectionFromFiles",function(a,b,c){this.setLoadState(b);for(var q=Array(a.length),e=Array(a.length),g=Array(a.length),j=0;j<a.length;j++){var f=a[j].indexOf("::"),l=0<=f?a[j].substring(f+2):a[j],f=0<=f?a[j].substring(0,f):null,s=this.getClassifiedName(l,!0);if(1==s.length)return s[0];q[j]=s[0];a[j]=JV.FileManager.fixDOSName(s[0]);g[j]=f;e[j]=l}b.put("fullPathNames",
q);b.put("fileTypes",g);a=this.newFilesReader(q,e,g,null,b,c);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(b,"createAtomSetCollectionFromString",function(a,b,c){this.setLoadState(b);var q=0<=a.indexOf("Viewer.AddHydrogens")?this.getFileInfo():null;b=new J.io.FileReader(this.vwr,"string",null,null,null,JU.Rdr.getBR(a),b,c);b.run();null!=q&&this.setFileInfo(q);!c&&"string"!=typeof b.getAtomSetCollection()&&this.setFileInfo(B(-1,["5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63"===
a?"Jmol Model Kit":"string"]));return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(b,"createAtomSeCollectionFromStrings",function(a,b,c,q){if(!c.containsKey("isData")){var e='"'+this.vwr.getDataSeparator()+'"',g='"'+(q?"append":"model")+' inline"',j=new JU.SB;j.append('set dataSeparator "~~~next file~~~";\ndata ').append(g);for(var f=0;f<a.length;f++)0<f&&j.append("~~~next file~~~"),j.append(a[f]);j.append("end ").append(g).append(";set dataSeparator ").append(e);b.appendSB(j)}this.setLoadState(c);
JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");b=Array(a.length);e=Array(a.length);for(f=0;f<a.length;f++)b[f]="string["+f+"]",e[f]=JV.FileManager.newDataReader(this.vwr,a[f]);a=this.newFilesReader(b,b,null,e,c,q);a.run();return a.getAtomSetCollection()},"~A,JU.SB,java.util.Map,~B");c(b,"createAtomSeCollectionFromArrayData",function(a,b,c){JU.Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");for(var q=a.size(),e=Array(q),g=Array(q),j=0;j<q;j++)e[j]="String["+
j+"]",g[j]=JV.FileManager.newDataReader(this.vwr,a.get(j));a=this.newFilesReader(e,e,null,g,b,c);a.run();return a.getAtomSetCollection()},"JU.Lst,java.util.Map,~B");b.newDataReader=c(b,"newDataReader",function(a,b){var c="string"==typeof b?"String":JU.AU.isAS(b)?"Array":C(b,"JU.Lst")?"List":null;return null==c?null:J.api.Interface.getInterface("JU."+c+"DataReader",a,"file").setData(b)},"JV.Viewer,~O");c(b,"newFilesReader",function(a,b,c,q,e,g){var j=J.api.Interface.getOption("io.FilesReader",this.vwr,
"file");j.set(this,this.vwr,a,b,c,q,e,g);return j},"~A,~A,~A,~A,java.util.Map,~B");c(b,"createAtomSetCollectionFromReader",function(a,b,c,q){a=new J.io.FileReader(this.vwr,b,a,null,null,c,q,!1);a.run();return a.getAtomSetCollection()},"~S,~S,~O,java.util.Map");c(b,"getBufferedInputStream",function(a){a=this.getBufferedReaderOrErrorMessageFromName(a,Array(2),!0,!0);return C(a,"java.io.BufferedInputStream")?a:null},"~S");c(b,"getBufferedInputStreamOrErrorMessageFromName",function(a,b,c,q,e,g,j){var f=
null,l=null;b=(j=j||a.startsWith("cache://"))&&null==e?b=this.getPngjOrDroppedBytes(b,a):null;try{j&&(0<=a.indexOf(".png")&&null==this.pngjCache&&!this.vwr.getBoolean(603979960))&&(this.pngjCache=new java.util.Hashtable);if(null==b){var s=0<=a.indexOf("?POST?_PNGJBIN_"),m=s||0<=a.indexOf("?POST?_PNGJ_");if(0<a.indexOf("?POST?_PNG_")||m){var p=Array(1),x=this.vwr.getImageAsBytes(m?"PNGJ":"PNG",0,0,-1,p);if(null!=p[0])return p[0];s?(e=x,a=JU.PT.rep(a,"?_","=_")):a=(new JU.SB).append(a).append("=").appendSB(JU.Base64.getBase64(x)).toString()}var n=
JU.OC.urlTypeIndex(a),s=0<=n,m=null;if(s&&0<=(n=a.indexOf("?POST?")))m=a.substring(n+6),a=a.substring(0,n);var r=null!=this.appletDocumentBaseURL;if(r||s){r&&(s&&null!=this.appletProxy)&&(a=this.appletProxy+"?url="+this.urlEncode(a));var u=r?new java.net.URL(this.appletDocumentBaseURL,a,null):new java.net.URL(ma("java.net.URL"),a,null);if(q)return null;a=u.toString();c&&0>a.toLowerCase().indexOf("password")&&JU.Logger.info("FileManager opening url "+a);l=this.vwr.apiPlatform.getURLContents(u,e,m,
!1);x=null;if(C(l,"JU.SB")){a=l;if(g&&!JU.Rdr.isBase64(a))return JU.Rdr.getBR(a.toString());x=JU.Rdr.getBytesFromSB(a)}else JU.AU.isAB(l)&&(x=l);null!=x&&(l=JU.Rdr.getBIS(x))}else if(!j||null==(b=this.cacheGet(a,!0)))c&&JU.Logger.info("FileManager opening file "+a),l=this.vwr.apiPlatform.getBufferedFileInputStream(a);if("string"==typeof l)return l}f=null==b?l:JU.Rdr.getBIS(b);q&&(f.close(),f=null);return f}catch(v){if(D(v,Exception))try{null!=f&&f.close()}catch(w){if(!D(w,"java.io.IOException"))throw w;
}else throw v;}return""+v},"~S,~S,~B,~B,~A,~B,~B");b.getBufferedReaderForResource=c(b,"getBufferedReaderForResource",function(a,b,c,q){q=a.vwrOptions.get("codePath")+c+q;if(a.async){a=a.fm.cacheGet(q,!1);if(null==a)throw new JV.JmolAsyncException(q);return JU.Rdr.getBufferedReader(JU.Rdr.getBIS(a),null)}return a.fm.getBufferedReaderOrErrorMessageFromName(q,B(-1,[null,null]),!1,!0)},"JV.Viewer,~O,~S,~S");c(b,"urlEncode",function(a){try{return java.net.URLEncoder.encode(a,"utf-8")}catch(b){if(D(b,"java.io.UnsupportedEncodingException"))return a;
throw b;}},"~S");c(b,"getFullPathNameOrError",function(a,b,c){var q=this.getClassifiedName(JV.JC.fixProtocol(a),!0);if(null==q||null==q[0]||2>q.length)return B(-1,[null,"cannot read file name: "+a]);a=q[0];q=JV.FileManager.fixDOSName(q[0]);a=JU.Rdr.getZipRoot(a);b=this.getBufferedInputStreamOrErrorMessageFromName(a,q,!1,!b,null,!1,!b);c[0]=q;"string"==typeof b&&(c[1]=b);return b},"~S,~B,~A");c(b,"getBufferedReaderOrErrorMessageFromName",function(a,b,c,q){a=JV.JC.fixProtocol(a);var e=this.cacheGet(a,
!1),g=JU.AU.isAB(e),j=g?e:null;if(a.startsWith("cache://")){if(null==e)return"cannot read "+a;if(g)j=e;else return JU.Rdr.getBR(e)}e=this.getClassifiedName(a,!0);if(null==e)return"cannot read file name: "+a;null!=b&&(b[0]=JV.FileManager.fixDOSName(e[0]));return this.getUnzippedReaderOrStreamFromName(e[0],j,!1,c,!1,q,null)},"~S,~A,~B,~B");c(b,"getUnzippedReaderOrStreamFromName",function(a,b,c,q,e,g,j){if(g&&null==b){var f=a.endsWith(".spt")?B(-1,[null,null,null]):0>a.indexOf(".spardir")?null:this.spartanUtil().getFileList(a,
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"JU.DF $.PT $.SB J.c.STR JS.SV JU.Escape $.Logger JV.JC $.StateManager $.Viewer".split(" "),function(){var b=r(function(){this.htUserVariables=this.htPropertyFlagsRemoved=this.htBooleanParameterFlags=this.htNonbooleanParameterValues=this.vwr=null;this.zDepth=0;this.zShadePower=3;this.zSlab=50;this.slabByAtom=this.slabByMolecule=!1;this.appendNew=this.allowEmbeddedScripts=!0;this.appletProxy="";this.applySymmetryToBonds=!1;this.atomTypes="";this.autoBond=!0;this.axesOrientationRasmol=!1;this.bondRadiusMilliAngstroms=
150;this.bondTolerance=0.45;this.defaultDirectory="";this.defaultStructureDSSP=!0;this.ptDefaultLattice=null;this.defaultLoadFilter=this.defaultLoadScript="";this.defaultDropScript="zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == '' && defaultLoadScript == '' && _filetype == 'Pdb') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible && cartoons > 0}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";
this.forceAutoBond=!1;this.fractionalRelative=!0;this.inlineNewlineChar="|";this.resolverResolver=this.macroDirectory=this.pubChemFormat=this.nihResolverFormat=this.smilesUrlFormat=this.nmrPredictFormat=this.nmrUrlFormat=this.pdbLoadLigandFormat=this.pdbLoadFormat=this.loadFormat=null;this.checkCIR=!1;this.minBondDistance=0.4;this.minPixelSelRadius=6;this.pdbSequential=this.pdbGetHeader=this.pdbAddHydrogens=!1;this.percentVdwAtom=23;this.smallMoleculeMaxAtoms=4E4;this.smartAromatic=!0;this.doublePrecision=
this.legacyJavaFloat=this.legacyHAddition=this.legacyAutoBonding=this.zeroBasedXyzRasmol=!1;this.modulateOccupancy=this.jmolInJSpecView=!0;this.dotSolvent=this.allowMoveAtoms=this.allowRotateSelected=!1;this.defaultTorsionLabel=this.defaultDistanceLabel=this.defaultAngleLabel="%VALUE %UNITS";this.measureAllModels=this.justifyMeasurements=!1;this.minimizationSteps=100;this.minimizationRefresh=!0;this.minimizationSilent=!1;this.minimizationCriterion=0.001;this.minimizationMaxAtoms=200;this.minimizationReportSteps=
10;this.infoFontSize=20;this.antialiasDisplay=!1;this.displayCellParameters=this.antialiasTranslucent=this.imageState=this.antialiasImages=!0;this.dotsSelectedOnly=!1;this.dotSurface=!0;this.dotDensity=3;this.meshScale=this.dotScale=1;this.isosurfaceKey=this.greyscaleRendering=!1;this.isosurfacePropertySmoothing=!0;this.isosurfacePropertySmoothingPower=7;this.platformSpeed=10;this.repaintWaitMs=1E3;this.showHiddenSelectionHalos=!1;this.showMeasurements=this.showKeyStrokes=!0;this.showTiming=!1;this.zoomLarge=
!0;this.zoomHeight=!1;this.backgroundImageFileName=null;this.hbondsBackbone=this.bondModeOr=this.partialDots=!1;this.hbondsAngleMinimum=90;this.hbondNODistanceMaximum=3.25;this.hbondHXDistanceMaximum=2.5;this.hbondsRasmol=!0;this.hbondsSolid=!1;this.modeMultipleBond=2;this.showMultipleBonds=this.showHydrogens=!0;this.ssbondsBackbone=!1;this.multipleBondSpacing=-1;this.multipleBondRadiusFactor=0;this.multipleBondBananas=!1;this.nboCharges=!0;this.cartoonRockets=this.cartoonBaseEdges=!1;this.cartoonBlockHeight=
0.5;this.cipRule6Full=this.chainCaseSensitive=this.cartoonRibose=this.cartoonLadders=this.cartoonFancy=this.cartoonSteps=this.cartoonBlocks=!1;this.hermiteLevel=0;this.rangeSelected=this.highResolutionFlag=!1;this.rasmolHeteroSetting=this.rasmolHydrogenSetting=!0;this.ribbonAspectRatio=16;this.rocketBarrels=this.ribbonBorder=!1;this.sheetSmoothing=1;this.translucent=this.traceAlpha=!0;this.twistedSheets=!1;this.allowAudio=this.autoplayMovie=!0;this.allowGestures=!1;this.allowMultiTouch=this.allowModelkit=
!0;this.hiddenLinesDashed=this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=603979809;this.axesScale=2;this.axesOffset=0;this.starWidth=0.05;this.bondPicking=!1;this.dataSeparator="~~~";this.debugScript=!1;this.defaultDrawArrowScale=0.5;this.defaultLabelXYZ="%a";this.defaultLabelPDB="%m%r";this.defaultTranslucent=0.5;this.delayMaximumMs=0;this.dipoleScale=1;this.drawFontSize=16;this.drawPicking=this.drawHover=this.dragSelected=this.disablePopupMenu=!1;
this.dsspCalcHydrogen=!0;this.energyUnits="kJ";this.exportScale=0;this.helpPath="https://chemapps.stolaf.edu/jmol/docs/index.htm";this.fontScaling=!1;this.fontCaching=!0;this.forceField="MMFF";this.helixStep=1;this.hideNameInPopup=!1;this.hoverDelayMs=500;this.labelPointerWidth=2;this.loadAtomDataTolerance=0.01;this.logGestures=this.logCommands=!1;this.measureDistanceUnits="nanometers";this.measurementLabels=!0;this.monitorEnergy=this.messageStyleChime=!1;this.modulationScale=1;this.multiProcessor=
!0;this.particleRadius=20;this.pickingSpinRate=10;this.pickLabel="";this.pointGroupDistanceTolerance=0.2;this.pointGroupLinearTolerance=8;this.preserveState=!0;this.propertyColorScheme="roygb";this.quaternionFrame="p";this.saveProteinStructureState=!0;this.showModVecs=!1;this.showUnitCellDetails=!0;this.solventProbeRadius=1.2;this.scriptDelay=0;this.statusReporting=this.selectAllModels=!0;this.strandCountForStrands=5;this.strandCountForMeshRibbon=7;this.strutSpacing=6;this.strutLengthMaximum=7;this.strutDefaultRadius=
0.3;this.strutsMultiple=!1;this.waitForMoveTo=this.useScriptQueue=this.useNumberLocalization=this.useMinimizationThread=!0;this.noDelay=!1;this.vectorScale=1;this.vectorsCentered=this.vectorSymmetry=!1;this.vectorTrail=0;this.vibrationScale=this.vibrationPeriod=1;this.navigationPeriodic=this.navigationMode=this.hideNavigationPoint=this.wireframeRotation=!1;this.navigationSpeed=5;this.showNavigationPointAlways=!1;this.stereoState=null;this.modelKitMode=!1;this.objMad10=this.objStateOn=this.objColors=
null;this.ellipsoidFill=this.ellipsoidArrows=this.ellipsoidArcs=this.ellipsoidDots=this.ellipsoidAxes=!1;this.ellipsoidBall=!0;this.ellipsoidDotCount=200;this.ellipsoidAxisDiameter=0.02;this.testFlag4=this.testFlag3=this.testFlag2=this.testFlag1=!1;this.structureList=null;this.haveSetStructureList=!1;this.bondingVersion=0;u(this,arguments)},JV,"GlobalSettings",null);N(b,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.objColors=E(7,0);this.objStateOn=Ca(7,
!1);this.objMad10=E(7,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,L(-1,[30,90,-15,95]));this.structureList.put(J.c.STR.SHEET,L(-1,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]));this.structureList.put(J.c.STR.HELIX,L(-1,[-160,0,-100,45]))});y(b,function(a,b,c){this.vwr=a;this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;this.loadFormat=this.pdbLoadFormat=
JV.JC.databases.get("pdb");this.pdbLoadLigandFormat=JV.JC.databases.get("ligand");this.nmrUrlFormat=JV.JC.databases.get("nmr");this.nmrPredictFormat=JV.JC.databases.get("nmrdb");this.pubChemFormat=JV.JC.databases.get("pubchem");this.resolverResolver=JV.JC.databases.get("resolverresolver");this.macroDirectory="https://chemapps.stolaf.edu/jmol/macros";null==b?this.setB("undoAuto",!a.isApplet):(this.setB("undoAuto",a.getBooleanProperty("undoAuto")),c||(this.setO("_pngjFile",b.getParameter("_pngjFile",
!1)),this.htUserVariables=b.htUserVariables),this.debugScript=b.debugScript,this.disablePopupMenu=b.disablePopupMenu,this.messageStyleChime=b.messageStyleChime,this.measureDistanceUnits=b.measureDistanceUnits,this.defaultDirectory=b.defaultDirectory,this.autoplayMovie=b.autoplayMovie,this.allowAudio=b.allowAudio,this.allowGestures=b.allowGestures,this.allowModelkit=b.allowModelkit,this.allowMultiTouch=b.allowMultiTouch,this.allowKeyStrokes=b.allowKeyStrokes,this.legacyAutoBonding=b.legacyAutoBonding,
this.legacyHAddition=b.legacyHAddition,this.legacyJavaFloat=b.legacyJavaFloat,this.minimizationReportSteps=b.minimizationReportSteps,this.doublePrecision=b.doublePrecision,this.bondingVersion=b.bondingVersion,this.platformSpeed=b.platformSpeed,this.useScriptQueue=b.useScriptQueue,this.showTiming=b.showTiming,this.wireframeRotation=b.wireframeRotation,this.testFlag1=b.testFlag1,this.testFlag2=b.testFlag2,this.testFlag3=b.testFlag3,this.testFlag4=b.testFlag4,this.nihResolverFormat=b.nihResolverFormat);
null==this.nihResolverFormat&&(this.nihResolverFormat=JV.JC.databases.get("nci"));this.setCIR(this.nihResolverFormat,!1);var q;c=0;for(var e=J.c.CBK.values();c<e.length&&((q=e[c])||1);c++)this.resetValue(q.name()+"Callback",b);this.setF("cameraDepth",3);this.setI("undoMax",a.stm.getUndoMax());this.setI("contextDepthMax",100);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);this.setI("historyLevel",0);this.setO("hoverLabel","");this.setB("isKiosk",a.isKiosk());
this.setO("logFile",a.getLogFileName());this.setI("logLevel",JU.Logger.getLogLevel());this.setF("mouseWheelFactor",1.15);this.setF("mouseDragFactor",1);this.setI("navFps",10);this.setI("navigationDepth",0);this.setI("navigationSlab",0);this.setI("navX",0);this.setI("navY",0);this.setI("navZ",0);this.setO("pathForAllFiles","");this.setB("perspectiveDepth",!0);this.setI("perspectiveModel",11);this.setO("picking","identify");this.setO("pickingStyle","toggle");this.setB("refreshing",!0);this.setI("rotationRadius",
0);this.setI("scaleAngstromsPerInch",0);this.setI("scriptReportingLevel",0);this.setB("selectionHalos",!1);this.setB("showaxes",!1);this.setB("showboundbox",!1);this.setB("showfrank",!1);this.setB("showUnitcell",!1);this.setI("slab",100);this.setB("slabEnabled",!1);this.setF("slabrange",0);this.setI("spinX",0);this.setI("spinY",30);this.setI("spinZ",0);this.setI("spinFps",30);this.setF("visualRange",5);this.setI("stereoDegrees",-5);this.setB("syncScript",a.sm.syncingScripts);this.setB("syncMouse",
a.sm.syncingMouse);this.setB("syncStereo",a.sm.stereoSync);this.setB("windowCentered",!0);this.setB("zoomEnabled",!0);this.setI("_version",JV.JC.versionInt);this.setO("_versionDate",JV.Viewer.getJmolVersion());this.setB("axesWindow",!0);this.setB("axesMolecular",!1);this.setB("axesPosition",!1);this.setB("axesUnitcell",!1);this.setI("backgroundModel",0);this.setB("colorRasmol",!1);this.setO("currentLocalPath","");this.setO("defaultLattice","{0 0 0}");this.setO("defaultColorScheme","Jmol");this.setO("defaultDirectoryLocal",
"");this.setO("defaults","Jmol");this.setO("defaultVDW","Jmol");this.setO("exportDrivers","Idtf;Maya;Povray;Vrml;X3d;Stl;Tachyon;Obj");this.setI("propertyAtomNumberColumnCount",0);this.setI("propertyAtomNumberField",0);this.setI("propertyDataColumnCount",0);this.setI("propertyDataField",0);this.setI("undoMax",a.stm.getUndoMax());this.setB("allowEmbeddedScripts",this.allowEmbeddedScripts);this.setB("allowGestures",this.allowGestures);this.setB("allowKeyStrokes",this.allowKeyStrokes);this.setB("allowModelkit",
this.allowModelkit);this.setB("allowMultiTouch",this.allowMultiTouch);this.setB("allowRotateSelected",this.allowRotateSelected);this.setB("allowMoveAtoms",this.allowMoveAtoms);this.setI("animationFps",this.animationFps);this.setB("antialiasImages",this.antialiasImages);this.setB("antialiasDisplay",this.antialiasDisplay);this.setB("antialiasTranslucent",this.antialiasTranslucent);this.setB("appendNew",this.appendNew);this.setO("appletProxy",this.appletProxy);this.setB("applySymmetryToBonds",this.applySymmetryToBonds);
this.setB("atomPicking",this.atomPicking);this.setO("atomTypes",this.atomTypes);this.setB("autoBond",this.autoBond);this.setB("autoFps",this.autoFps);this.setI("axesMode",603979808==this.axesMode?2:603979804==this.axesMode?1:0);this.setF("axesScale",this.axesScale);this.setF("axesOffset",this.axesOffset);this.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setF("cartoonBlockHeight",this.cartoonBlockHeight);this.setB("cartoonBlocks",this.cartoonBlocks);this.setB("cartoonSteps",this.cartoonSteps);
this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);this.setF("bondTolerance",this.bondTolerance);this.setB("cartoonBaseEdges",this.cartoonBaseEdges);this.setB("cartoonFancy",this.cartoonFancy);this.setB("cartoonLadders",this.cartoonLadders);this.setB("cartoonLadders",this.cartoonRibose);this.setB("cartoonRockets",this.cartoonRockets);this.setB("chainCaseSensitive",this.chainCaseSensitive);this.setB("cipRule6Full",
this.cipRule6Full);this.setI("bondingVersion",this.bondingVersion);this.setO("dataSeparator",this.dataSeparator);this.setB("debugScript",this.debugScript);this.setO("defaultAngleLabel",this.defaultAngleLabel);this.setF("defaultDrawArrowScale",this.defaultDrawArrowScale);this.setO("defaultDirectory",this.defaultDirectory);this.setO("defaultDistanceLabel",this.defaultDistanceLabel);this.setO("defaultDropScript",this.defaultDropScript);this.setO("defaultLabelPDB",this.defaultLabelPDB);this.setO("defaultLabelXYZ",
this.defaultLabelXYZ);this.setO("defaultLoadFilter",this.defaultLoadFilter);this.setO("defaultLoadScript",this.defaultLoadScript);this.setB("defaultStructureDSSP",this.defaultStructureDSSP);this.setO("defaultTorsionLabel",this.defaultTorsionLabel);this.setF("defaultTranslucent",this.defaultTranslucent);this.setI("delayMaximumMs",this.delayMaximumMs);this.setF("dipoleScale",this.dipoleScale);this.setB("disablePopupMenu",this.disablePopupMenu);this.setB("displayCellParameters",this.displayCellParameters);
this.setI("dotDensity",this.dotDensity);this.setI("dotScale",this.dotScale);this.setB("dotsSelectedOnly",this.dotsSelectedOnly);this.setB("dotSurface",this.dotSurface);this.setB("dragSelected",this.dragSelected);this.setB("drawHover",this.drawHover);this.setF("drawFontSize",this.drawFontSize);this.setB("drawPicking",this.drawPicking);this.setB("dsspCalculateHydrogenAlways",this.dsspCalcHydrogen);this.setB("ellipsoidArcs",this.ellipsoidArcs);this.setB("ellipsoidArrows",this.ellipsoidArrows);this.setB("ellipsoidAxes",
this.ellipsoidAxes);this.setF("ellipsoidAxisDiameter",this.ellipsoidAxisDiameter);this.setB("ellipsoidBall",this.ellipsoidBall);this.setI("ellipsoidDotCount",this.ellipsoidDotCount);this.setB("ellipsoidDots",this.ellipsoidDots);this.setB("ellipsoidFill",this.ellipsoidFill);this.setO("energyUnits",this.energyUnits);this.setF("exportScale",this.exportScale);this.setB("doublePrecision",this.doublePrecision);this.setB("fontScaling",this.fontScaling);this.setB("fontCaching",this.fontCaching);this.setB("forceAutoBond",
this.forceAutoBond);this.setO("forceField",this.forceField);this.setB("fractionalRelative",this.fractionalRelative);this.setF("particleRadius",this.particleRadius);this.setB("greyscaleRendering",this.greyscaleRendering);this.setF("hbondsAngleMinimum",this.hbondsAngleMinimum);this.setF("hbondHXDistanceMaximum",this.hbondHXDistanceMaximum);this.setF("hbondsDistanceMaximum",this.hbondNODistanceMaximum);this.setB("hbondsBackbone",this.hbondsBackbone);this.setB("hbondsRasmol",this.hbondsRasmol);this.setB("hbondsSolid",
this.hbondsSolid);this.setI("helixStep",this.helixStep);this.setO("helpPath",this.helpPath);this.setI("hermiteLevel",this.hermiteLevel);this.setB("hideNameInPopup",this.hideNameInPopup);this.setB("hideNavigationPoint",this.hideNavigationPoint);this.setB("hiddenLinesDashed",this.hiddenLinesDashed);this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",this.hoverDelayMs/1E3);this.setB("imageState",this.imageState);this.setI("infoFontSize",this.infoFontSize);this.setB("isosurfaceKey",
this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("jmolInJSpecView",this.jmolInJSpecView);this.setI("labelPointerWidth",this.labelPointerWidth);this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",this.legacyHAddition);this.setB("legacyJavaFloat",this.legacyJavaFloat);this.setF("loadAtomDataTolerance",
this.loadAtomDataTolerance);this.setO("loadFormat",this.loadFormat);this.setO("loadLigandFormat",this.pdbLoadLigandFormat);this.setB("logCommands",this.logCommands);this.setB("logGestures",this.logGestures);this.setB("measureAllModels",this.measureAllModels);this.setB("measurementLabels",this.measurementLabels);this.setO("measurementUnits",this.measureDistanceUnits);this.setI("meshScale",this.meshScale);this.setB("messageStyleChime",this.messageStyleChime);this.setF("minBondDistance",this.minBondDistance);
this.setI("minPixelSelRadius",this.minPixelSelRadius);this.setI("minimizationReportSteps",this.minimizationReportSteps);this.setI("minimizationSteps",this.minimizationSteps);this.setB("minimizationRefresh",this.minimizationRefresh);this.setB("minimizationSilent",this.minimizationSilent);this.setF("minimizationCriterion",this.minimizationCriterion);this.setB("modelKitMode",this.modelKitMode);this.setF("modulationScale",this.modulationScale);this.setB("monitorEnergy",this.monitorEnergy);this.setF("multipleBondRadiusFactor",
this.multipleBondRadiusFactor);this.setB("multipleBondBananas",this.multipleBondBananas);this.setF("multipleBondSpacing",this.multipleBondSpacing);this.setB("multiProcessor",this.multiProcessor&&1<JV.Viewer.nProcessors);this.setB("navigationMode",this.navigationMode);this.setB("navigationPeriodic",this.navigationPeriodic);this.setF("navigationSpeed",this.navigationSpeed);this.setB("nboCharges",this.nboCharges);this.setB("noDelay",this.noDelay);this.setO("nmrPredictFormat",this.nmrPredictFormat);this.setO("nmrUrlFormat",
this.nmrUrlFormat);this.setB("partialDots",this.partialDots);this.setB("pdbAddHydrogens",this.pdbAddHydrogens);this.setB("pdbGetHeader",this.pdbGetHeader);this.setB("pdbSequential",this.pdbSequential);this.setI("percentVdwAtom",this.percentVdwAtom);this.setI("pickingSpinRate",this.pickingSpinRate);this.setO("pickLabel",this.pickLabel);this.setI("platformSpeed",this.platformSpeed);this.setF("pointGroupLinearTolerance",this.pointGroupLinearTolerance);this.setF("pointGroupDistanceTolerance",this.pointGroupDistanceTolerance);
this.setB("preserveState",this.preserveState);this.setO("propertyColorScheme",this.propertyColorScheme);this.setO("quaternionFrame",this.quaternionFrame);this.setB("rangeSelected",this.rangeSelected);this.setI("repaintWaitMs",this.repaintWaitMs);this.setI("ribbonAspectRatio",this.ribbonAspectRatio);this.setB("ribbonBorder",this.ribbonBorder);this.setB("rocketBarrels",this.rocketBarrels);this.setB("saveProteinStructureState",this.saveProteinStructureState);this.setB("scriptqueue",this.useScriptQueue);
this.setB("selectAllModels",this.selectAllModels);this.setB("selectHetero",this.rasmolHeteroSetting);this.setB("selectHydrogen",this.rasmolHydrogenSetting);this.setF("sheetSmoothing",this.sheetSmoothing);this.setB("showHiddenSelectionHalos",this.showHiddenSelectionHalos);this.setB("showHydrogens",this.showHydrogens);this.setB("showKeyStrokes",this.showKeyStrokes);this.setB("showMeasurements",this.showMeasurements);this.setB("showModulationVectors",this.showModVecs);this.setB("showMultipleBonds",this.showMultipleBonds);
this.setB("showNavigationPointAlways",this.showNavigationPointAlways);this.setI("showScript",this.scriptDelay);this.setB("showtiming",this.showTiming);this.setB("slabByMolecule",this.slabByMolecule);this.setB("slabByAtom",this.slabByAtom);this.setB("smartAromatic",this.smartAromatic);this.setI("minimizationMaxAtoms",this.minimizationMaxAtoms);this.setI("smallMoleculeMaxAtoms",this.smallMoleculeMaxAtoms);this.setO("smilesUrlFormat",this.smilesUrlFormat);this.setO("macroDirectory",this.macroDirectory);
this.setO("nihResolverFormat",this.nihResolverFormat);this.setO("pubChemFormat",this.pubChemFormat);this.setB("showUnitCellDetails",this.showUnitCellDetails);this.setB("solventProbe",this.dotSolvent);this.setF("solventProbeRadius",this.solventProbeRadius);this.setB("ssbondsBackbone",this.ssbondsBackbone);this.setF("starWidth",this.starWidth);this.setB("statusReporting",this.statusReporting);this.setI("strandCount",this.strandCountForStrands);this.setI("strandCountForStrands",this.strandCountForStrands);
this.setI("strandCountForMeshRibbon",this.strandCountForMeshRibbon);this.setF("strutDefaultRadius",this.strutDefaultRadius);this.setF("strutLengthMaximum",this.strutLengthMaximum);this.setI("strutSpacing",this.strutSpacing);this.setB("strutsMultiple",this.strutsMultiple);this.setB("testFlag1",this.testFlag1);this.setB("testFlag2",this.testFlag2);this.setB("testFlag3",this.testFlag3);this.setB("testFlag4",this.testFlag4);this.setB("traceAlpha",this.traceAlpha);this.setB("translucent",this.translucent);
this.setB("twistedSheets",this.twistedSheets);this.setB("useMinimizationThread",this.useMinimizationThread);this.setB("useNumberLocalization",this.useNumberLocalization);this.setB("vectorsCentered",this.vectorsCentered);this.setF("vectorScale",this.vectorScale);this.setB("vectorSymmetry",this.vectorSymmetry);this.setI("vectorTrail",this.vectorTrail);this.setF("vibrationPeriod",this.vibrationPeriod);this.setF("vibrationScale",this.vibrationScale);this.setB("waitForMoveTo",this.waitForMoveTo);this.setB("wireframeRotation",
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this.listeners[c]=a},"J.api.JmolSelectionListener");c(b,"selectionChanged",function(a){this.hideNotSelected&&this.hide(this.vwr.ms,JU.BSUtil.copyInvert(this.bsSelection,this.vwr.ms.ac),0,a);if(!(a||0==this.listeners.length))for(a=this.listeners.length;0<=--a;)null!=this.listeners[a]&&this.listeners[a].selectionChanged(this.bsSelection)},"~B");c(b,"deleteAtoms",function(a){var b=JU.BSUtil.copy(a);null==this.bsDeleted?this.bsDeleted=b:(b.andNot(this.bsDeleted),this.bsDeleted.or(a));this.bsHidden.andNot(this.bsDeleted);
this.bsSelection.andNot(this.bsDeleted);return b.cardinality()},"JU.BS");c(b,"getSelectedAtoms",function(){if(null==this.bsSubset)return this.bsSelection;var a=JU.BSUtil.copy(this.bsSelection);a.and(this.bsSubset);return a});c(b,"getSelectedAtomsNoSubset",function(){return JU.BSUtil.copy(this.bsSelection)});c(b,"excludeAtoms",function(a,b){null!=this.bsDeleted&&a.andNot(this.bsDeleted);!b&&null!=this.bsSubset&&(a=JU.BSUtil.copy(a)).and(this.bsSubset);return a},"JU.BS,~B");c(b,"setMotionFixedAtoms",
function(a){this.bsFixed.clearAll();null!=a&&this.bsFixed.or(a)},"JU.BS");c(b,"getMotionFixedAtoms",function(){return this.bsFixed})});n("JV");z(null,"JV.ShapeManager","JU.BS $.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){var b=r(function(){this.navMinMax=this.bsSlabbedInternal=this.bsRenderableAtoms=this.scaleText=this.vwr=this.shapes=this.ms=null;u(this,arguments)},JV,"ShapeManager",null);N(b,function(){this.navMinMax=E(4,0)});y(b,function(a){this.vwr=a;this.bsRenderableAtoms=
new JU.BS;this.bsSlabbedInternal=new JU.BS},"JV.Viewer");c(b,"findNearestShapeAtomIndex",function(a,b,c,q){if(null!=this.shapes)for(var e=0;e<this.shapes.length&&null==c[0];++e)null!=this.shapes[e]&&this.shapes[e].findNearestAtomIndex(a,b,c,q)},"~N,~N,~A,JU.BS");c(b,"getShapePropertyIndex",function(a,b,c){if(null==this.shapes||null==this.shapes[a])return null;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(b,"getShapePropertyData",
function(a,b,c){if(null==this.shapes||null==this.shapes[a])return!1;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getPropertyData(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~A");c(b,"getShapeIdFromObjectName",function(a){if(null!=this.shapes)for(var b=16;30>b;++b)if(null!=this.shapes[b]&&0<=this.shapes[b].getIndexFromName(a))return b;return null!=this.shapes[6]&&0<=this.shapes[6].getIndexFromName(a)?6:-1},"~S");c(b,"loadDefaultShapes",function(a){this.ms=a;if(null!=this.shapes)for(var b=
0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].setModelSet(a);this.loadShape(0);this.loadShape(1)},"JM.ModelSet");c(b,"loadShape",function(a){if(null==this.shapes)return null;if(null!=this.shapes[a])return this.shapes[a];if(2==a||3==a||4==a)return null;var b=JV.JC.getShapeClassName(a,!1);if(null==(b=J.api.Interface.getInterface(b,this.vwr,"shape")))return null;this.vwr.setShapeErrorState(a,"allocate");b.initializeShape(this.vwr,this.ms,a);this.vwr.setShapeErrorState(-1,null);return this.shapes[a]=
b},"~N");c(b,"notifyAtomPositionsChanged",function(a,b,c){var q=Integer.$valueOf(a);a=this.vwr.getModelUndeletedAtomsBitSet(a);for(var e=0;37>e;e++)null!=this.shapes[e]&&this.setShapePropertyBs(e,"refreshTrajectories",B(-1,[q,b,c]),a)},"~N,JU.BS,JU.M4");c(b,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");c(b,"setScale",function(){null!=this.scaleText&&(this.loadShape(31),this.setShapePropertyBs(31,"%SCALE",this.scaleText,null),this.scaleText=null)});c(b,"resetShapes",function(a){a&&
(a=Array(1),this.getShapePropertyData(31,"%SCALE",a),this.scaleText=a[0]);this.shapes=Array(37)},"~B");c(b,"setShapeSizeBs",function(a,b,c,q){if(null!=this.shapes){if(null==q&&(1!=a||2147483647!=b))q=this.vwr.bsA();null!=c&&(0!=c.value&&c.vdwType===J.c.VDW.TEMP)&&this.ms.getBfactor100Lo();this.vwr.setShapeErrorState(a,"set size");(null==c?0!=b:0!=c.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,c,q);this.vwr.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");
c(b,"setLabel",function(a,b){if(null==a){if(null==this.shapes[5])return}else this.loadShape(5),this.setShapeSizeBs(5,0,null,b);this.setShapePropertyBs(5,"label",a,b)},"~O,JU.BS");c(b,"setShapeProperties",function(a,b){this.vwr.setShapeErrorState(a,"set properties");this.loadShape(a).setProperties(b);this.vwr.setShapeErrorState(-1,null)},"~N,~A");c(b,"setShapePropertyBs",function(a,b,c,q){null==this.shapes||null==this.shapes[a]||(null==q&&(q=this.vwr.bsA()),this.vwr.setShapeErrorState(a,"set "+b),
this.shapes[a].setProperty(b.intern(),c,q),this.vwr.setShapeErrorState(-1,null))},"~N,~S,~O,JU.BS");c(b,"checkFrankclicked",function(a,b){var c=this.shapes[36];return null!=c&&c.wasClicked(a,b)},"~N,~N");c(b,"checkObjectClicked",function(a,b,c,q,e){var g,j=null;if(2==this.vwr.getPickingMode())return null==this.shapes[5]?null:this.shapes[5].checkObjectClicked(a,b,c,q,!1);if(0!=c&&this.vwr.getBondsPickable()&&null!=(j=this.shapes[1].checkObjectClicked(a,b,c,q,!1)))return j;for(var f=0;f<JV.ShapeManager.clickableMax;f++)if(null!=
(g=this.shapes[JV.ShapeManager.hoverable[f]])&&null!=(j=g.checkObjectClicked(a,b,c,q,e)))return j;return null},"~N,~N,~N,JU.BS,~B");c(b,"checkObjectDragged",function(a,b,c,q,e,g,j){for(var f=!1,l=0<j?j+1:37;!f&&j<l;++j)null!=this.shapes[j]&&(f=this.shapes[j].checkObjectDragged(a,b,c,q,e,g));return f},"~N,~N,~N,~N,~N,JU.BS,~N");c(b,"checkObjectHovered",function(a,b,c,q){var e=this.shapes[1];if(q&&null!=e&&e.checkObjectHovered(a,b,c))return!0;for(q=0;q<JV.ShapeManager.hoverable.length;q++)if(e=this.shapes[JV.ShapeManager.hoverable[q]],
null!=e&&e.checkObjectHovered(a,b,c))return!0;return!1},"~N,~N,JU.BS,~B");c(b,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var c=0;37>c;c++)null!=this.shapes[c]&&this.setShapePropertyBs(c,"deleteModelAtoms",a,b)},"~A,JU.BS");c(b,"deleteVdwDependentShapes",function(a){null==a&&(a=this.vwr.bsA());null!=this.shapes[24]&&this.shapes[24].setProperty("deleteVdw",null,a);null!=this.shapes[25]&&this.shapes[25].setProperty("deleteVdw",null,a)},"JU.BS");c(b,"getAtomShapeValue",function(a,b,c){a=
JV.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;c=this.shapes[a].getSize(c);if(0==c){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;c=this.shapes[a].getSizeG(b)}return c/2E3},"~N,JM.Group,~N");c(b,"replaceGroup",function(a,b){if(null!=this.shapes)for(var c=9;16>c;c++)null!=this.shapes[c]&&this.shapes[c].replaceGroup(a,b)},"JM.Group,JM.Group");c(b,"getObjectMap",function(a,b){if(null!=this.shapes)for(var c=Boolean.$valueOf(b),q=16;30>q;++q)this.getShapePropertyData(q,"getNames",
B(-1,[a,c]))},"java.util.Map,~B");c(b,"getProperty",function(a){return a.equals("getShapes")?this.shapes:null},"~O");c(b,"getShape",function(a){return null==this.shapes?null:this.shapes[a]},"~N");c(b,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.ms),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.c.PAL.NONE,a))},"JU.BS");c(b,"setAtomLabel",function(a,
b){null!=this.shapes&&this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null)},"~S,~N");c(b,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=this.vwr.getVisibleFramesBitSet(),c=8;33>c;c++)null!=a[c]&&a[c].setModelVisibilityFlags(b);var a=this.vwr.getBoolean(603979922),q=this.vwr.slm.bsDeleted,e=this.ms.at;this.ms.clearVisibleSets();if(0<e.length)for(c=this.ms.ac;0<=--c;){var g=e[c];null!=g&&(g.shapeVisibilityFlags&=-64);if(!(null!=q&&q.get(c))&&b.get(g.mi)){var j=
1;if(!this.ms.isAtomHidden(c)&&(a||1!=g.getElementNumber()))j|=8,0!=g.madAtom&&(j|=16),g.setShapeVisibility(j,!0)}}this.setShapeVis()}});c(b,"setShapeVis",function(){for(var a=0;37>a;++a){var b=this.shapes[a];null!=b&&b.setAtomClickability()}});c(b,"finalizeAtoms",function(a,b){var c=this.vwr,q=c.tm;b&&c.finalizeTransformParameters();if(null!=a){var e=this.ms.getAtomSetCenter(a),g=new JU.P3;q.transformPt3f(e,g);g.add(q.ptOffset);q.unTransformPoint(g,g);g.sub(e);c.setAtomCoordsRelative(g,a);q.ptOffset.set(0,
0,0);q.bsSelectedAtoms=null}e=this.bsRenderableAtoms;this.ms.getAtomsInFrame(e);var j=this.ms.vibrations,f=null!=j&&q.vibrationOn,l=null!=this.ms.bsModulated&&null!=this.ms.occupancies,s=this.ms.at,m,p=!1,x=this.bsSlabbedInternal;x.clearAll();for(var n=e.nextSetBit(0);0<=n;n=e.nextSetBit(n+1)){var g=s[n],r=f&&g.hasVibration()?q.transformPtVib(g,j[n]):q.transformPt(g);1==r.z&&(q.internalSlab&&q.xyzIsSlabbedInternal(g))&&x.set(n);g.sX=r.x;g.sY=r.y;g.sZ=r.z;var u=Math.abs(g.madAtom);u==JM.Atom.MAD_GLOBAL&&
(u=F(2E3*c.getFloat(1153433601)));g.sD=sa(c.tm.scaleToScreen(r.z,u));if(l&&null!=j[n]&&-2147483648!=(m=j[n].getOccupancy100(f)))p=!0,g.setShapeVisibility(2,!1),0<=m&&50>m?g.setShapeVisibility(24,!1):g.setShapeVisibility(8|(0<g.madAtom?16:0),!0),this.ms.occupancies[g.i]=Math.abs(m)}p&&this.setShapeVis();m=c.gdata;if(q.slabEnabled){n=c.getBoolean(603979940);q=c.getBoolean(603979939);j=m.slab;f=m.depth;if(n){l=this.ms.getMolecules();p=this.ms.getMoleculeCountInModel(-1);for(n=0;n<p;n++)if(x=l[n],r=0,
g=x.firstAtomIndex,e.get(g)){for(;r<x.ac&&!m.isClippedZ(s[g].sZ-(s[g].sD>>1));r++,g++);if(r!=x.ac){g=x.firstAtomIndex;for(r=0;r<x.ac;r++)e.clear(g),s[g++].sZ=0}}}for(n=e.nextSetBit(0);0<=n;n=e.nextSetBit(n+1))if(g=s[n],m.isClippedZ(g.sZ-(q?s[n].sD>>1:0)))g.setClickable(0),l=v((q?-1:1)*g.sD/2),(g.sZ+l<j||g.sZ-l>f||!m.isInDisplayRange(g.sX,g.sY))&&e.clear(n)}if(0==this.ms.ac||!c.getShowNavigationPoint())return null;c=2147483647;m=-2147483648;q=2147483647;j=-2147483648;for(n=e.nextSetBit(0);0<=n;n=e.nextSetBit(n+
1))g=s[n],g.sX<c&&(c=g.sX),g.sX>m&&(m=g.sX),g.sY<q&&(q=g.sY),g.sY>j&&(j=g.sY);this.navMinMax[0]=c;this.navMinMax[1]=m;this.navMinMax[2]=q;this.navMinMax[3]=j;return this.navMinMax},"JU.BS,~B");c(b,"setModelSet",function(a){this.ms=a},"JM.ModelSet");c(b,"checkInheritedShapes",function(){null!=this.shapes[24]&&this.setShapePropertyBs(24,"remapInherited",null,null)});c(b,"restrictSelected",function(a,b){var c=this.vwr.slm.getSelectedAtomsNoSubset();if(b){this.vwr.slm.invertSelection();var q=this.vwr.slm.bsSubset;
null!=q&&(c=this.vwr.slm.getSelectedAtomsNoSubset(),c.and(q),this.vwr.selectStatus(c,!1,0,!0,!1),JU.BSUtil.invertInPlace(c,this.vwr.ms.ac),c.and(q))}JU.BSUtil.andNot(c,this.vwr.slm.bsDeleted);q=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var e=this.vwr.bsA(),g=21;0<=
--g;)6!=g&&null!=this.getShape(g)&&this.setShapeSizeBs(g,0,null,e);null!=this.getShape(21)&&this.setShapePropertyBs(21,"off",e,null);this.setLabel(null,e);a||this.vwr.setBooleanProperty("bondModeOr",q);this.vwr.selectStatus(c,!1,0,!0,!1)},"~B,~B");b.hoverable=E(-1,[31,20,25,24,22,36]);b.clickableMax=JV.ShapeManager.hoverable.length-1});n("JV");z(["java.util.Hashtable"],["JV.Connection","$.Scene","$.StateManager","$.Connections"],"java.util.Arrays JU.BS $.Lst $.SB JM.Orientation JU.BSUtil $.Escape".split(" "),
function(){var b=r(function(){this.maxUndo=20;this.saved=this.vwr=null;this.lastUnitcell=this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=this.lastContext=this.lastOrientation="";this.redoStateStack=this.undoStateStack=null;u(this,arguments)},JV,"StateManager",null);N(b,function(){this.saved=new java.util.Hashtable});y(b,function(a){this.vwr=a},"JV.Viewer");b.getVariableList=c(b,"getVariableList",function(a,b,c,q){var e=new JU.SB,g=0,j=Array(a.size()),
f;for(a=a.entrySet().iterator();a.hasNext()&&((f=a.next())||1);){var l=f.getKey(),s=f.getValue();if((c||!l.startsWith("site_"))&&(!q||"@"==l.charAt(0)))j[g++]=l+("@"==l.charAt(0)?" "+s.asString():" = "+JV.StateManager.varClip(l,s.escape(),b))}java.util.Arrays.sort(j,0,g);for(b=0;b<g;b++)null!=j[b]&&e.append("  ").append(j[b]).append(";\n");0==g&&!q&&e.append("# --no global user variables defined--;\n");return e.toString()},"java.util.Map,~N,~B,~B");b.getObjectIdFromName=c(b,"getObjectIdFromName",
function(a){if(null==a)return-1;a="background axis1      axis2      axis3      boundbox   unitcell   frank      ".indexOf(a.toLowerCase());return 0>a?a:v(a/11)},"~S");b.getObjectNameFromId=c(b,"getObjectNameFromId",function(a){return 0>a||7<=a?null:"background axis1      axis2      axis3      boundbox   unitcell   frank      ".substring(11*a,11*a+11).trim()},"~N");c(b,"clear",function(a){this.vwr.setShowAxes(!1);this.vwr.setShowBbcage(!1);this.vwr.setShowUnitCell(!1);a.clear()},"JV.GlobalSettings");
c(b,"resetLighting",function(){this.vwr.setIntProperty("ambientPercent",45);this.vwr.setIntProperty("celShadingPower",10);this.vwr.setIntProperty("diffusePercent",84);this.vwr.setIntProperty("phongExponent",64);this.vwr.setIntProperty("specularExponent",6);this.vwr.setIntProperty("specularPercent",22);this.vwr.setIntProperty("specularPower",40);this.vwr.setIntProperty("zDepth",0);this.vwr.setIntProperty("zShadePower",3);this.vwr.setIntProperty("zSlab",50);this.vwr.setBooleanProperty("specular",!0);
this.vwr.setBooleanProperty("celShading",!1);this.vwr.setBooleanProperty("zshade",!1)});c(b,"setCrystallographicDefaults",function(){this.vwr.setAxesMode(603979808);this.vwr.setShowAxes(!0);this.vwr.setShowUnitCell(!0);this.vwr.setBooleanProperty("perspectiveDepth",!1)});c(b,"setCommonDefaults",function(){this.vwr.setBooleanProperty("perspectiveDepth",!0);this.vwr.setFloatProperty("bondTolerance",0.45);this.vwr.setFloatProperty("minBondDistance",0.4);this.vwr.setIntProperty("bondingVersion",0);this.vwr.setBooleanProperty("translucent",
!0)});c(b,"setJmolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","Jmol");this.vwr.setBooleanProperty("axesOrientationRasmol",!1);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",!1);this.vwr.setIntProperty("percentVdwAtom",23);this.vwr.setIntProperty("bondRadiusMilliAngstroms",150);this.vwr.setVdwStr("auto")});c(b,"setRasMolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","RasMol");this.vwr.setBooleanProperty("axesOrientationRasmol",
!0);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",!0);this.vwr.setIntProperty("percentVdwAtom",0);this.vwr.setIntProperty("bondRadiusMilliAngstroms",1);this.vwr.setVdwStr("Rasmol")});c(b,"setPyMOLDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("measurementUnits","ANGSTROMS");this.vwr.setBooleanProperty("zoomHeight",!0)});b.getNoCase=c(b,"getNoCase",function(a,b){for(var c,q=a.entrySet().iterator();q.hasNext()&&((c=q.next())||1);)if(c.getKey().equalsIgnoreCase(b))return c.getValue();
return null},"java.util.Map,~S");c(b,"listSavedStates",function(){for(var a="",b,c=this.saved.keySet().iterator();c.hasNext()&&((b=c.next())||1);)a+="\n"+b;return a});c(b,"deleteSavedType",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&b.remove()},"~S");c(b,"deleteSaved",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();){var c=b.next();(c.startsWith(a)||c.endsWith("_"+a)&&c.indexOf("_")==c.lastIndexOf("_"+a))&&b.remove()}},"~S");c(b,"saveSelection",
function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Selected_"):(a=this.lastSelected="Selected_"+a,this.saved.put(a,JU.BSUtil.copy(b)))},"~S,JU.BS");c(b,"restoreSelection",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Selected_"+a:this.lastSelected);if(null==a)return this.vwr.selectStatus(new JU.BS,!1,0,!1,!1),!1;this.vwr.selectStatus(a,!1,0,!1,!1);return!0},"~S");c(b,"saveUnitCell",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Unitcell_");else{a=
this.lastUnitcell="Unitcell_"+a;var b=this.vwr.getCurrentUnitCell();null!=b&&(b="UNITCELL "+JU.Escape.e(b.getUnitCellVectors()),this.saved.put(a,"unitcell reset;"+b))}},"~S");c(b,"getSavedUnitCell",function(a){return JV.StateManager.getNoCase(this.saved,0<a.length?"Unitcell_"+a:this.lastUnitcell)},"~S");c(b,"restoreUnitCell",function(a){a=this.getSavedUnitCell(a);if(null==a)return this.vwr.setModelCagePts(-1,null,null),!1;this.vwr.runScript(a);return!0},"~S");c(b,"saveState",function(a){a.equalsIgnoreCase("DELETE")?
(this.deleteSavedType("State_"),this.clearStateStack()):0==a.length?(this.vwr.setBooleanProperty("undoAuto",!1),this.appendState(this.getStack(603984065)),this.redoStateStack.clear()):(a=this.lastState="State_"+a,this.saved.put(a,this.vwr.getStateInfo()))},"~S");c(b,"getSavedState",function(a){if(0==a.length)return a=this.getStack(603984065),0<a.size()?a.get(a.size()-1):null;a=JV.StateManager.getNoCase(this.saved,0<a.length?"State_"+a:this.lastState);return null==a?"":a},"~S");c(b,"popStack",function(a){var b=
this.getStack(a),b=0<b.size()?b.removeItemAt(b.size()-1):null;null!=b&&this.appendState(this.getStack(603984065==a?4139:603984065));this.checkStack(this.getStack(603984065));return b},"~N");c(b,"appendState",function(a){this.checkStack(a);0<this.maxUndo&&a.addLast(this.vwr.getStateInfo())},"JU.Lst");c(b,"checkStack",function(a){for(;a.size()>this.maxUndo;)a.removeItemAt(0)},"JU.Lst");c(b,"getStack",function(a){null==this.undoStateStack&&(this.undoStateStack=new JU.Lst,this.redoStateStack=new JU.Lst);
return 603984065==a?this.undoStateStack:this.redoStateStack},"~N");c(b,"clearStateStack",function(){null!=this.undoStateStack&&(this.undoStateStack.clear(),this.redoStateStack.clear())});c(b,"saveStructure",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Shape_"):(a=this.lastShape="Shape_"+a,this.saved.put(a,this.vwr.getStructureState()))},"~S");c(b,"getSavedStructure",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Shape_"+a:this.lastShape);return null==a?"":a},"~S");
c(b,"saveCoordinates",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Coordinates_"):(a=this.lastCoordinates="Coordinates_"+a,this.saved.put(a,this.vwr.getCoordinateState(b)))},"~S,JU.BS");c(b,"getSavedCoordinates",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Coordinates_"+a:this.lastCoordinates);return null==a?"":a},"~S");c(b,"getOrientation",function(){return new JM.Orientation(this.vwr,!1,null)});c(b,"getSavedOrientationText",function(a){var b;if(null!=a)return b=
this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var c=this.saved.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(b,"saveScene",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");else{var c=new JV.Scene(b);c.saveName=this.lastScene="Scene_"+a;this.saved.put(c.saveName,c)}},"~S,java.util.Map");c(b,"restoreScene",function(a,b){var c=JV.StateManager.getNoCase(this.saved,
0<a.length?"Scene_"+a:this.lastScene);return null!=c&&c.restore(this.vwr,b)},"~S,~N");c(b,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var c=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),b);c.saveName=this.lastOrientation="Orientation_"+a;this.saved.put(c.saveName,c)}},"~S,~A");c(b,"restoreOrientation",function(a,b,c){a=this.getOrientationFor(a);return null!=a&&a.restore(b,c)},"~S,~N,~B");c(b,"getOrientationFor",function(a){return JV.StateManager.getNoCase(this.saved,
0<a.length?"Orientation_"+a:this.lastOrientation)},"~S");c(b,"saveContext",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Context_"):this.saved.put(this.lastContext="Context_"+a,b)},"~S,~O");c(b,"getContext",function(a){return this.saved.get(0==a.length?this.lastContext:"Context_"+a)},"~S");c(b,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=new JV.Connections(this.vwr);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,
b)}},"~S");c(b,"restoreBonds",function(a){this.vwr.clearModelDependentObjects();a=JV.StateManager.getNoCase(this.saved,0<a.length?"Bonds_"+a:this.lastConnections);return null!=a&&a.restore()},"~S");b.varClip=c(b,"varClip",function(a,b,c){0<c&&b.length>c&&(b=b.substring(0,c)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");c(b,"getUndoMax",function(){return this.maxUndo});c(b,"setUndoMax",function(a){this.maxUndo=Math.max(a,0);this.checkStack(this.getStack(603984065));
this.checkStack(this.getStack(4139))},"~N");c(b,"getUndoRedoState",function(a){return this.popStack(a)},"~N");c(b,"canDo",function(a){return 0<this.maxUndo&&this.vwr.getBoolean(603979898)&&!this.getStack(a).isEmpty()},"~N");c(b,"getUndoInfo",function(){var a=this.vwr.getBooleanProperty("undoAuto");return this.vwr.getBoolean(603979898)?"undoAuto="+a+(!a?"; user stack sizes: UNDO="+this.getStack(603984065).size()+", REDO="+this.getStack(4139).size():""):"SET preserveState = FALSE -- undo/redo is disabled"});
b=r(function(){this.scene=this.saveName=null;u(this,arguments)},JV,"Scene",null);y(b,function(a){this.scene=a},"java.util.Map");c(b,"restore",function(a,b){var c=this.scene.get("generator");null!=c&&c.generateScene(this.scene);c=this.scene.get("pymolView");return null!=c&&a.tm.moveToPyMOL(a.eval,b,c)},"JV.Viewer,~N");b=r(function(){this.saveName=null;this.bondCount=0;this.vwr=this.connections=null;u(this,arguments)},JV,"Connections",null);y(b,function(a){var b=a.ms;if(null!=b){this.vwr=a;this.bondCount=
b.bondCount;this.connections=Array(this.bondCount+1);a=b.bo;for(b=this.bondCount;0<=--b;){var c=a[b];this.connections[b]=new JV.Connection(c.atom1.i,c.atom2.i,c.mad,c.colix,c.order,c.getEnergy(),c.shapeVisibilityFlags)}}},"JV.Viewer");c(b,"restore",function(){var a=this.vwr.ms;if(null==a)return!1;a.deleteAllBonds();for(var b=this.bondCount;0<=--b;){var c=this.connections[b],q=a.ac;c.atomIndex1>=q||c.atomIndex2>=q||(q=a.bondAtoms(a.at[c.atomIndex1],a.at[c.atomIndex2],c.order,c.mad,null,c.energy,!1,
!0),q.colix=c.colix,q.shapeVisibilityFlags=c.shapeVisibilityFlags)}for(b=a.bondCount;0<=--b;)a.bo[b].index=b;this.vwr.setShapeProperty(1,"reportAll",null);return!0});b=r(function(){this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;u(this,arguments)},JV,"Connection",null);y(b,function(a,b,c,q,e,g,j){this.atomIndex1=a;this.atomIndex2=b;this.mad=c;this.colix=q;this.order=e;this.energy=g;this.shapeVisibilityFlags=j},"~N,~N,~N,~N,~N,~N,~N")});n("JV");
z(["java.util.Hashtable"],"JV.StatusManager","JU.Lst $.PT J.api.Interface J.c.CBK JS.SV JU.BSUtil $.Logger JV.JC".split(" "),function(){var b=r(function(){this.cbl=this.jsl=this.vwr=null;this.statusList="";this.allowStatusReporting=!1;this.messageQueue=null;this.statusPtr=0;this.imageMap=this.jmolScriptCallbacks=null;this.echoing=!1;this.minSyncRepeatMs=100;this.stereoSync=this.syncDisabled=this.isSynced=this.drivingSync=this.syncingMouse=this.syncingScripts=!1;this.qualityPNG=this.qualityJPG=-1;
this.audios=this.imageType=null;u(this,arguments)},JV,"StatusManager",null);N(b,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});y(b,function(a){this.vwr=a},"JV.Viewer");c(b,"recordStatus",function(a){return this.allowStatusReporting&&0<this.statusList.length&&(this.statusList.equals("all")||0<=this.statusList.indexOf(a))},"~S");c(b,"setStatusChanged",function(a,b,c,q){if(this.recordStatus(a)){var e=new JU.Lst;e.addLast(Integer.$valueOf(++this.statusPtr));
e.addLast(a);e.addLast(Integer.$valueOf(b));e.addLast(c);b=q?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.Lst):b.size()==JV.StatusManager.MAXIMUM_QUEUE_LENGTH&&b.removeItemAt(0);b.addLast(e)}},"~S,~N,~O,~B");c(b,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),c=0<a.length&&"+"==a.charAt(0),q=!1;b?this.statusList=JU.PT.rep(this.statusList,a.substring(1,a.length),""):(a=JU.PT.rep(a,"+",""),this.statusList.equals(a)||c&&0<=this.statusList.indexOf(a)?q=!0:(c||
(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(q)for(var e,q=this.messageQueue.entrySet().iterator();q.hasNext()&&((e=q.next())||1);)a.addLast(e.getValue());this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(b,"setCallbackFunction",function(a,b){var c=J.c.CBK.getCallback(a),q="string"==typeof b?b:null;if(null!=c)if(c=J.c.CBK.getCallback(a).name(),JU.Logger.info("StatusManager "+c+"callback set f="+
q),null!=q&&q.startsWith("SYNC:"))if(q.toLowerCase().trim().equals("sync:off"))this.jmolScriptCallbacks.remove("SYNC:"+c),JU.Logger.info("SYNC callback for "+c+" deactivated");else{this.jmolScriptCallbacks.put("SYNC:"+c,"_");JU.Logger.info("SYNC callback for "+c+" activated");return}else{var e="",g=null==q?0:(e=q.toLowerCase()).startsWith("script:")?7:e.startsWith("jmolscript:")?11:0;if(0==g)null==b&&this.jmolScriptCallbacks.remove(c);else{this.jmolScriptCallbacks.put(c,q.substring(g).trim());return}}null!=
this.cbl&&this.cbl.setCallbackFunction(a,b)},"~S,~O");c(b,"notifyEnabled",function(a){return null!=this.cbl&&this.cbl.notifyEnabled(a)},"J.c.CBK");c(b,"getJmolScriptCallback",function(a){return this.jmolScriptCallbacks.get(a.name())},"J.c.CBK");c(b,"fireJmolScriptCallback",function(a,b,c,q){var e=b.name();if(null!=c[0]){var g=Array(c.length);System.arraycopy(c,0,g,0,c.length);var j="try{\n"+g[0]+"\n}";g[0]=e;this.vwr.evalCallback(j,g,q)}this.jmolScriptCallbacks.containsKey("SYNC:"+b.name())&&(c[0]=
"SYNC");a&&this.cbl.notifyCallback(b,c)},"~B,J.c.CBK,~A,~B");c(b,"setStatusAppletReady",function(a,b){var c=b?this.getJmolScriptCallback(J.c.CBK.APPLETREADY):null,q=this.notifyEnabled(J.c.CBK.APPLETREADY);(q||null!=c)&&this.fireJmolScriptCallback(q,J.c.CBK.APPLETREADY,B(-1,[c,a,Boolean.$valueOf(b),null]),!0)},"~S,~B");c(b,"setStatusAtomMoved",function(a){var b=this.getJmolScriptCallback(J.c.CBK.ATOMMOVED);this.setStatusChanged("atomMoved",-1,a,!1);var c=this.notifyEnabled(J.c.CBK.ATOMMOVED);(c||null!=
b)&&this.fireJmolScriptCallback(c,J.c.CBK.ATOMMOVED,B(-1,[b,a,Integer.$valueOf(a.cardinality())]),!0)},"JU.BS");c(b,"setStatusSelect",function(a){var b=this.getJmolScriptCallback(J.c.CBK.SELECT);this.setStatusChanged("select",-1,a,!1);var c=this.notifyEnabled(J.c.CBK.SELECT);(c||null!=b)&&this.fireJmolScriptCallback(c,J.c.CBK.SELECT,B(-1,[b,a,Integer.$valueOf(a.cardinality()),Integer.$valueOf(a.nextSetBit(0)),Integer.$valueOf(a.length())]),!0)},"JU.BS");c(b,"setStatusStructureModified",function(a,
b,c,q,e,g){0<=a&&null==g&&(g=JU.BSUtil.newAndSetBit(a));var j=this.getJmolScriptCallback(J.c.CBK.STRUCTUREMODIFIED),f=this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED);(f||null!=j)&&this.fireJmolScriptCallback(f,J.c.CBK.STRUCTUREMODIFIED,B(-1,[j,Integer.$valueOf(c),Integer.$valueOf(a),Integer.$valueOf(b),q,Integer.$valueOf(e),g]),!0)},"~N,~N,~N,~S,~N,JU.BS");c(b,"setStatusAtomPicked",function(a,b,c){var q=this.getJmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",
a,b,!1);var e=this.notifyEnabled(J.c.CBK.PICK);(e||null!=q)&&this.fireJmolScriptCallback(e,J.c.CBK.PICK,B(-1,[q,b,Integer.$valueOf(a),c]),!0)},"~N,~S,java.util.Map");c(b,"setStatusClicked",function(a,b,c,q,e){var g=this.getJmolScriptCallback(J.c.CBK.CLICK);e=E(-1,[c,e]);var j=this.notifyEnabled(J.c.CBK.CLICK);(j||null!=g)&&this.fireJmolScriptCallback(j,J.c.CBK.CLICK,B(-1,[g,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),Integer.$valueOf(q),e]),!0);return e[0]},"~N,~N,~N,~N,~N");c(b,"setStatusResized",
function(a,b){var c=this.getJmolScriptCallback(J.c.CBK.RESIZE),q=this.notifyEnabled(J.c.CBK.RESIZE);(q||null!=c)&&this.fireJmolScriptCallback(q,J.c.CBK.RESIZE,B(-1,[c,Integer.$valueOf(a),Integer.$valueOf(b)]),!0)},"~N,~N");c(b,"haveHoverCallback",function(){return this.jmolScriptCallbacks.containsKey(J.c.CBK.HOVER.name())||this.notifyEnabled(J.c.CBK.HOVER)});c(b,"setStatusAtomHovered",function(a,b){var c=this.getJmolScriptCallback(J.c.CBK.HOVER),q=this.notifyEnabled(J.c.CBK.HOVER);(q||null!=c)&&this.fireJmolScriptCallback(q,
J.c.CBK.HOVER,B(-1,[c,b,Integer.$valueOf(a)]),!0)},"~N,~S");c(b,"setStatusObjectHovered",function(a,b,c){var q=this.getJmolScriptCallback(J.c.CBK.HOVER),e=this.notifyEnabled(J.c.CBK.HOVER);(e||null!=q)&&this.fireJmolScriptCallback(e,J.c.CBK.HOVER,B(-1,[q,b,Integer.$valueOf(-1),a,Float.$valueOf(c.x),Float.$valueOf(c.y),Float.$valueOf(c.z)]),!0)},"~S,~S,JU.T3");c(b,"showImage",function(a,b){var c=JU.PT.split(a,"\u0001");a=2>c.length?"Jmol":3>c.length||c[2].equals("null")?c[1].substring(c[1].lastIndexOf("/")+
1):c[2];var c=this.getJmolScriptCallback(J.c.CBK.IMAGE),q=this.notifyEnabled(J.c.CBK.IMAGE);(q||null!=c)&&this.fireJmolScriptCallback(q,J.c.CBK.IMAGE,B(-1,[c,a,b]),!0);if(Boolean.TRUE.equals(b)){if(null!=this.imageMap){for(var c=new JU.Lst,e,q=this.imageMap.keySet().iterator();q.hasNext()&&((e=q.next())||1);)c.addLast(e);for(e=c.size();0<=--e;)this.imageMap.get(c.get(e)).closeMe()}}else null==this.imageMap&&(this.imageMap=new java.util.Hashtable),e=this.imageMap.get(a),Boolean.FALSE.equals(b)?null!=
e&&e.closeMe():(null==e&&null!=b&&(e=this.vwr.apiPlatform.getImageDialog(a,this.imageMap)),null!=e&&(null==b?e.closeMe():e.setImage(b)))},"~S,~O");c(b,"setFileLoadStatus",function(a,b,c,q,e,g,j){null==a&&"resetUndo".equals(b)&&(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",e,a,!1);null!=q&&this.setStatusChanged("fileLoadError",e,q,!1);var f=this.getJmolScriptCallback(J.c.CBK.LOADSTRUCT);if((g=g&&this.notifyEnabled(J.c.CBK.LOADSTRUCT))||
null!=f){var l=this.vwr.getP("_smilesString");0!=l.length&&(b=l);this.fireJmolScriptCallback(g,J.c.CBK.LOADSTRUCT,B(-1,[f,a,b,c,q,Integer.$valueOf(e),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.ms.mc-1),j]),!0)}},"~S,~S,~S,~S,~N,~B,Boolean");c(b,"setStatusModelKit",function(a){var b=1==a?"ON":"OFF";this.setStatusChanged("modelkit",a,b,!1);a=this.getJmolScriptCallback(J.c.CBK.MODELKIT);var c=this.notifyEnabled(J.c.CBK.MODELKIT);(c||null!=a)&&this.fireJmolScriptCallback(c,J.c.CBK.MODELKIT,
B(-1,[a,b]),!0)},"~N");c(b,"setStatusFrameChanged",function(a,b,c,q,e,g,j){if(null!=this.vwr.ms){var f=this.vwr.am.animationOn,l=f?-2-e:e;this.setStatusChanged("frameChanged",l,0<=e?this.vwr.getModelNumberDotted(e):"",!1);var s=this.getJmolScriptCallback(J.c.CBK.ANIMFRAME),m=this.notifyEnabled(J.c.CBK.ANIMFRAME);(m||null!=s)&&this.fireJmolScriptCallback(m,J.c.CBK.ANIMFRAME,B(-1,[s,E(-1,[l,a,b,c,q,e]),j,Float.$valueOf(g)]),!1);!f&&!this.vwr.isJSNoAWT&&this.vwr.checkMenuUpdate()}},"~N,~N,~N,~N,~N,~N,~S");
c(b,"setStatusDragDropped",function(a,b,c,q,e){this.setStatusChanged("dragDrop",0,"",!1);var g=this.getJmolScriptCallback(J.c.CBK.DRAGDROP),j=this.notifyEnabled(J.c.CBK.DRAGDROP);(j||null!=g)&&this.fireJmolScriptCallback(j,J.c.CBK.DRAGDROP,B(-1,[g,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),q,e]),!0);return j},"~N,~N,~N,~S,~A");c(b,"setScriptEcho",function(a,b){if(!(null==a||this.echoing)){this.echoing=!0;this.setStatusChanged("scriptEcho",0,a,!1);var c=this.getJmolScriptCallback(J.c.CBK.ECHO),
q=this.notifyEnabled(J.c.CBK.ECHO);if(q||null!=c)this.fireJmolScriptCallback(q,J.c.CBK.ECHO,B(-1,[c,a,Integer.$valueOf(b?1:0)]),!0);this.echoing=!1}},"~S,~B");c(b,"setStatusMeasuring",function(a,b,c,q){this.setStatusChanged(a,b,c,!1);var e=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+c),e=this.getJmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,c,!1),JU.Logger.info("measurePicked "+b+" "+c));var g=this.notifyEnabled(J.c.CBK.MEASURE);
(g||null!=e)&&this.fireJmolScriptCallback(g,J.c.CBK.MEASURE,B(-1,[e,c,Integer.$valueOf(b),a,Float.$valueOf(q)]),!0)},"~S,~N,~S,~N");c(b,"notifyError",function(a,b,c){var q=this.getJmolScriptCallback(J.c.CBK.ERROR),e=this.notifyEnabled(J.c.CBK.ERROR);(e||null!=q)&&this.fireJmolScriptCallback(e,J.c.CBK.ERROR,B(-1,[q,a,b,this.vwr.getShapeErrorState(),c]),!0)},"~S,~S,~S");c(b,"notifyMinimizationStatus",function(a,b,c,q,e){var g=this.getJmolScriptCallback(J.c.CBK.MINIMIZATION),j=this.notifyEnabled(J.c.CBK.MINIMIZATION);
(j||null!=g)&&this.fireJmolScriptCallback(j,J.c.CBK.MINIMIZATION,B(-1,[g,a,b,c,q,e]),!0)},"~S,Integer,Float,Float,~S");c(b,"setScriptStatus",function(a,b,c,q){if(-1>c){var e=-2-c;this.setStatusChanged("scriptStarted",e,b,!1);a="script "+e+" started"}else if(null==a)return;var e=0==c?this.getJmolScriptCallback(J.c.CBK.SCRIPT):null,g="Script completed"===a;if(this.recordStatus("script")){var j=null!=q;this.setStatusChanged(j?"scriptError":"scriptStatus",0,a,!1);if(j||g)this.setStatusChanged("scriptTerminated",
1,"Jmol script terminated"+(j?" unsuccessfully: "+a:" successfully"),!1)}g&&(this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825))&&(a=this.vwr.getChimeMessenger().scriptCompleted(this,b,q));b=B(-1,[e,a,b,Integer.$valueOf(g?-1:c),q]);((c=this.notifyEnabled(J.c.CBK.SCRIPT))||null!=e)&&this.fireJmolScriptCallback(c,J.c.CBK.SCRIPT,b,!0);this.processScript(b)},"~S,~S,~N,~S");c(b,"processScript",function(a){var b=a[3].intValue();this.vwr.notifyScriptEditor(b,a);0==b&&this.vwr.sendConsoleMessage(null==
a[1]?null:a[1].toString())},"~A");c(b,"doSync",function(){return this.isSynced&&this.drivingSync&&!this.syncDisabled});c(b,"setSync",function(a){this.syncingMouse?null!=a&&this.syncSend(a,"*",0):this.syncingScripts||this.syncSend("!"+this.vwr.tm.getMoveToText(this.minSyncRepeatMs/1E3,!1),"*",0)},"~S");c(b,"setSyncDriver",function(a){this.stereoSync&&4!=a&&(this.syncSend("SET_GRAPHICS_OFF","*",0),this.stereoSync=!1);switch(a){case 4:if(!this.syncDisabled)return;this.syncDisabled=!1;break;case 3:this.syncDisabled=
!0;break;case 5:this.stereoSync=this.isSynced=this.drivingSync=!0;break;case 1:this.isSynced=this.drivingSync=!0;break;case 2:this.drivingSync=!1;this.isSynced=!0;break;default:this.isSynced=this.drivingSync=!1}JU.Logger.debugging&&JU.Logger.debug(this.vwr.appletName+" sync mode="+a+"; synced? "+this.isSynced+"; driving? "+this.drivingSync+"; disabled? "+this.syncDisabled)},"~N");c(b,"syncSend",function(a,b,c){return 0!=c||this.notifyEnabled(J.c.CBK.SYNC)?(a=B(-1,[null,a,b,Integer.$valueOf(c)]),null!=
this.cbl&&this.cbl.notifyCallback(J.c.CBK.SYNC,a),a[0]):null},"~S,~O,~N");c(b,"processService",function(a){var b=a.get("service");if(null==b)return null;if(C(b,"JS.SV")){var b=new java.util.Hashtable,c;for(a=a.entrySet().iterator();a.hasNext()&&((c=a.next())||1);)b.put(c.getKey(),JS.SV.oValue(c.getValue()));a=b}this.notifyEnabled(J.c.CBK.SERVICE)&&this.cbl.notifyCallback(J.c.CBK.SERVICE,B(-1,[null,a]));return a},"java.util.Map");c(b,"getSyncMode",function(){return!this.isSynced?0:this.drivingSync?
1:2});c(b,"showUrl",function(a){null!=this.jsl&&this.jsl.showUrl(a)},"~S");c(b,"clearConsole",function(){this.vwr.sendConsoleMessage(null);null!=this.jsl&&this.cbl.notifyCallback(J.c.CBK.MESSAGE,null)});c(b,"functionXY",function(a,b,c){return null==this.jsl?L(Math.abs(b),Math.abs(c),0):this.jsl.functionXY(a,b,c)},"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,q){return null==this.jsl?L(Math.abs(b),Math.abs(c),Math.abs(c),0):this.jsl.functionXYZ(a,b,c,q)},"~S,~N,~N,~N");c(b,"jsEval",function(a){return null==
this.jsl?"":this.jsl.eval(a)},"~S");c(b,"createImage",function(a,b,c,q,e){return null==this.jsl?null:this.jsl.createImage(a,b,null==c?q:c,e)},"~S,~S,~S,~A,~N");c(b,"getRegistryInfo",function(){return null==this.jsl?null:this.jsl.getRegistryInfo()});c(b,"dialogAsk",function(a,b,c){var q=a.equals("Save Image"),e=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==e)return null;e.setupUI(!1);q&&e.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);a=e.getFileNameFromDialog(this.vwr,
a,b);q&&null!=a&&(this.qualityJPG=e.getQuality("JPG"),this.qualityPNG=e.getQuality("PNG"),q=e.getType(),null!=c&&(c.put("qualityJPG",Integer.$valueOf(this.qualityJPG)),c.put("qualityPNG",Integer.$valueOf(this.qualityPNG)),null!=q&&c.put("dialogImageType",q)),null!=q&&(this.imageType=q));return a},"~S,~S,java.util.Map");c(b,"getJspecViewProperties",function(a){return null==this.jsl?null:this.jsl.getJSpecViewProperty(null==a||0==a.length?"":":"+a)},"~S");c(b,"resizeInnerPanel",function(a,b){return null==
this.jsl||a==this.vwr.getScreenWidth()&&b==this.vwr.getScreenHeight()?E(-1,[a,b]):this.jsl.resizeInnerPanel("preferredWidthHeight "+a+" "+b+";")},"~N,~N");c(b,"resizeInnerPanelString",function(a){null!=this.jsl&&this.jsl.resizeInnerPanel(a)},"~S");c(b,"registerAudio",function(a,b){this.stopAudio(a);null==this.audios&&(this.audios=new java.util.Hashtable);null==b?this.audios.remove(a):this.audios.put(a,b.get("audioPlayer"))},"~S,java.util.Map");c(b,"stopAudio",function(a){null!=this.audios&&(a=this.audios.get(a),
null!=a&&a.action("kill"))},"~S");c(b,"playAudio",function(a){if(this.vwr.getBoolean(603979797))try{var b=null==a?"close":a.get("action"),c=null==a?null:a.get("id");if(null!=b&&0<b.length){if(null==c||0==c.length){if(null==this.audios||this.audios.isEmpty())return;if(b.equals("close"))for(var q,e=this.audios.keySet().iterator();e.hasNext()&&((q=e.next())||1);){var g=this.audios.remove(q);g.action("close")}return}g=this.audios.get(c);if(null!=g){g.action(b);return}}try{J.api.Interface.getInterface("JU.JmolAudio",
this.vwr,"script").playAudio(this.vwr,a)}catch(j){if(D(j,Exception))JU.Logger.info(j.getMessage());else throw j;}}catch(f){}else null!=a&&(a.put("status","close"),JU.Logger.info("allowAudio is set false"),this.notifyAudioStatus(a))},"java.util.Map");c(b,"notifyAudioStatus",function(a){var b=a.get("status"),c=a.get(b);null!=c&&this.vwr.script(c);"ended"===b&&this.registerAudio(a.get("id"),null);var c=this.getJmolScriptCallback(J.c.CBK.AUDIO),q=this.notifyEnabled(J.c.CBK.AUDIO);(q||null!=c)&&this.fireJmolScriptCallback(q,
J.c.CBK.AUDIO,B(-1,[c,a,b]),!0)},"java.util.Map");c(b,"syncScript",function(a,b,c){if("GET_GRAPHICS".equalsIgnoreCase(a))this.setSyncDriver(5),this.syncSend(a,b,0),this.vwr.setBooleanProperty("_syncMouse",!1),this.vwr.setBooleanProperty("_syncScript",!1);else{"=".equals(b)&&(b="~",this.setSyncDriver(2));var q="~".equals(b);if(0<c||!q&&!".".equals(b))if(this.syncSend(a,b,c),!"*".equals(b)||a.startsWith("{"))return;if(a.equalsIgnoreCase("on")||a.equalsIgnoreCase("true"))this.setSyncDriver(1);else if(a.equalsIgnoreCase("off")||
a.equalsIgnoreCase("false"))this.setSyncDriver(0);else if(a.equalsIgnoreCase("slave"))this.setSyncDriver(2);else if(b=this.getSyncMode(),0!=b)if(1!=b&&(q=!1),JU.Logger.debugging&&JU.Logger.debug(this.vwr.htmlName+" syncing with script: "+a),q&&this.setSyncDriver(3),0!=a.indexOf("Mouse: ")){b=JV.JC.getServiceCommand(a);switch(b){case 70:case 42:case 49:case 56:case 63:this.syncSend(a,".",c);return;case 0:case 77:case 28:case 35:if(q)return;case 21:case 7:case 14:if(null==(a=this.vwr.getJSV().processSync(a,
b)))return}this.vwr.evalStringQuietSync(a,!0,!1)}else this.mouseScript(a),q&&this.vwr.setSyncDriver(4)}},"~S,~S,~N");c(b,"mouseScript",function(a){var b=JU.PT.getTokens(a),c=b[1];try{switch(c=(c.toLowerCase()+"...............").substring(0,15),"zoombyfactor...zoomby.........rotatezby......rotatexyby.....translatexyby..rotatemolecule.spinxyby.......rotatearcball..".indexOf(c)){case 0:switch(b.length){case 3:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),2147483647,2147483647);return;case 5:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),
JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]));return}break;case 15:switch(b.length){case 3:this.vwr.zoomBy(JU.PT.parseInt(b[2]));return}break;case 30:switch(b.length){case 3:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),2147483647,2147483647);return;case 5:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]))}break;case 45:this.vwr.rotateXYBy(JU.PT.parseFloat(b[2]),JU.PT.parseFloat(b[3]));return;case 60:this.vwr.translateXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]));return;case 75:this.vwr.rotateSelected(JU.PT.parseFloat(b[2]),
JU.PT.parseFloat(b[3]),null);return;case 90:this.vwr.spinXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseFloat(b[4]));return;case 105:this.vwr.rotateXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]));return}}catch(q){if(!D(q,Exception))throw q;}this.vwr.showString("error reading SYNC command: "+a,!1)},"~S");b.MAXIMUM_QUEUE_LENGTH=16});n("JV");z("JU.A4 $.M3 $.M4 $.P3 $.P3i $.V3 J.c.STER JU.Point3fi".split(" "),"JV.TransformManager","java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),
function(){var b=r(function(){this.spinThread=this.vibrationThread=this.movetoThread=this.vwr=null;this.perspectiveModel=11;this.modelRadiusPixels=this.modelRadius=this.modelCenterOffset=this.cameraDistanceFromCenter=this.aperatureAngle=this.referencePlaneOffset=this.cameraScaleFactor=0;this.navigationShiftXY=this.navigationOffset=this.navigationCenter=null;this.navigationDepthPercent=0;this.vectorTemp=this.matrixTemp=null;this.haveNotifiedNaN=!1;this.spinX=0;this.spinY=30;this.spinZ=0;this.spinFps=
30;this.navZ=this.navY=this.navX=0;this.navFps=NaN;this.doTransform4D=this.isSpinSelected=this.isSpinFixed=this.isSpinInternal=!1;this.rotationCenterDefault=this.perspectiveShiftXY=this.perspectiveOffset=this.fixedRotationCenter=this.fixedRotationOffset=null;this.rotationRadiusDefault=0;this.internalRotationCenter=this.internalTranslation=this.internalRotationAxis=this.fixedRotationAxis=null;this.internalRotationAngle=0;this.rotationAxis=this.pointT2=this.vectorT2=this.vectorT=this.axisangleT=this.matrixTemp4=
this.matrixTemp3=this.matrixRotate=null;this.rotationRate=0;this.cameraSetting=this.camera=this.fixedTranslation=null;this.yTranslationFraction=this.xTranslationFraction=0.5;this.previousY=this.previousX=this.prevZoomSetting=0;this.zoomEnabled=!0;this.zmPctSet=this.zmPct=100;this.zoomRatio=0;this.internalSlab=this.zShadeEnabled=this.slabEnabled=!1;this.depthValue=this.slabValue=this.depthPercentSetting=this.slabPercentSetting=0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=
null;this.slabRange=this.zDepthValue=this.zSlabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRangeAngstroms=0;this.cameraDistance=1E3;this.scale3DAngstromsPerInch=this.scaleDefaultPixelsPerAngstrom=this.scalePixelsPerAngstrom=this.screenPixelCount=this.height=this.width=0;this.zoomHeight=this.useZoomLarge=this.antialias=!1;this.screenHeight=this.screenWidth=0;this.ptVibTemp=this.iScrPt=this.fScrPt=this.matrixTransformInv=
this.matrixTransform=null;this.navigating=!1;this.defaultMode=this.mode=0;this.matrixTest=this.aaTest1=this.ptTest3=this.ptTest2=this.ptTest1=this.untransformedPoint=null;this.vibrationOn=this.spinIsGesture=this.navOn=this.spinOn=!1;this.vibrationScale=this.vibrationPeriodMs=this.vibrationPeriod=0;this.stereoColors=this.stereoMode=this.vibrationT=null;this.stereoDoubleFull=this.stereoDoubleDTI=!1;this.stereoDegrees=NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=
!1;this.ptOffset=this.bsSelectedAtoms=this.bsFrameOffsets=this.frameOffsets=this.frameOffset=null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;u(this,arguments)},JV,"TransformManager",null);N(b,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=
new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=
new JU.M4;this.fScrPt=new JU.P3;this.iScrPt=new JU.P3i;this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});y(b,function(){});b.getTransformManager=c(b,"getTransformManager",function(a,b,c,q){q=q?J.api.Interface.getInterface("JV.TransformManager4D",
a,"tm"):new JV.TransformManager;q.vwr=a;q.setScreenParameters(b,c,!0,!1,!0,!0);return q},"JV.Viewer,~N,~N,~B");c(b,"setDefaultPerspective",function(){this.setCameraDepthPercent(3,!0);this.setPerspectiveDepth(!0);this.setStereoDegrees(-5);this.visualRangeAngstroms=5;this.setSpinOff();this.setVibrationPeriod(0)});c(b,"homePosition",function(a){a&&this.setSpinOff();this.setNavOn(!1);this.navFps=10;this.navX=this.navY=this.navZ=0;this.rotationCenterDefault.setT(this.vwr.getBoundBoxCenter());this.setFixedRotationCenter(this.rotationCenterDefault);
this.rotationRadiusDefault=this.setRotationRadius(0,!0);this.windowCentered=!0;this.setRotationCenterAndRadiusXYZ(null,!0);this.resetRotation();a=this.vwr.ms.getInfoM("defaultOrientationMatrix");null!=a&&this.setRotation(a);this.setZoomEnabled(!0);this.zoomToPercent(this.vwr.g.modelKitMode?50:100);this.zmPct=this.zmPctSet;this.slabReset();this.resetFitToScreen(!0);this.vwr.isJmolDataFrame()?this.fixedRotationCenter.set(0,0,0):this.vwr.g.axesOrientationRasmol&&this.matrixRotate.setAsXRotation(3.141592653589793);
this.vwr.stm.saveOrientation("default",null);1==this.mode&&this.setNavigationMode(!0)},"~B");c(b,"setRotation",function(a){a.isRotation()?this.matrixRotate.setM3(a):this.resetRotation()},"JU.M3");c(b,"resetRotation",function(){this.matrixRotate.setScale(1)});c(b,"clearThreads",function(){this.clearVibration();this.clearSpin();this.setNavOn(!1);this.stopMotion()});c(b,"clear",function(){this.fixedRotationCenter.set(0,0,0);this.navigating=!1;this.zSlabPoint=this.depthPlane=this.slabPlane=null;this.resetNavigationPoint(!0)});
c(b,"setFixedRotationCenter",function(a){null!=a&&this.fixedRotationCenter.setT(a)},"JU.T3");c(b,"setRotationPointXY",function(a){a=this.transformPt(a);this.fixedTranslation.set(a.x,a.y,0)},"JU.P3");c(b,"spinXYBy",function(a,b,c){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var q=JU.P3.newP(this.fixedRotationCenter),e=new JU.P3;this.transformPt3f(q,e);a=JU.P3.new3(-b,a,0);a.add(e);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,
a,q,10*c,NaN,!1,!0,null,!0,null,null,null,null)}},"~N,~N,~N");c(b,"rotateXYBy",function(a,b,c){this.rotate3DBall(a,b,c)},"~N,~N,JU.BS");c(b,"rotateZBy",function(a,b,c){2147483647!=b&&2147483647!=c&&this.resetXYCenter(b,c);this.rotateZRadians(a/57.29577951308232)},"~N,~N,~N");c(b,"applyRotation",function(a,b,c,q,e,g){null==c?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(g,a,this.matrixRotate,q,this.internalRotationCenter,b,c,e),null!=q&&this.internalRotationCenter.add(q))},"JU.M3,~B,JU.BS,JU.V3,~B,JU.M4");
c(b,"rotate3DBall",function(a,b,c){this.matrixTemp3.setAsBallRotation(0.017453292519943295,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,c,null,!1,null)},"~N,~N,JU.BS");c(b,"rotateXRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsXRotation(a),!1,b,null,!1,null)},"~N,JU.BS");c(b,"rotateYRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsYRotation(a),!1,b,null,!1,null)},"~N,JU.BS");c(b,"rotateZRadians",function(a){this.applyRotation(this.matrixTemp3.setAsZRotation(a),!1,
null,null,!1,null)},"~N");c(b,"rotateAxisAngle",function(a,b){this.axisangleT.setVA(a,b);this.rotateAxisAngle2(this.axisangleT,null)},"JU.V3,~N");c(b,"rotateAxisAngle2",function(a,b){this.applyRotation(this.matrixTemp3.setAA(a),!1,b,null,!1,null)},"JU.A4,JU.BS");c(b,"rotateAxisAngleAtCenter",function(a,b,c,q,e,g,j){null!=b&&this.moveRotationCenter(b,!0);g&&this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(g&&3.4028235E38==e)return!1;g=!1}if(Float.isNaN(q)||0==q||0==e)return!1;null!=b&&
this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=q;if(g)return this.fixedRotationAxis.setVA(c,0.017453292519943295*q),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=j,this.setSpin(a,!0,e,null,null,j,!1),3.4028235E38!=e;a=0.017453292519943295*e;this.fixedRotationAxis.setVA(c,e);this.rotateAxisAngleRadiansFixed(a,j);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(b,"rotateAxisAngleRadiansFixed",function(a,
b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(b,"rotateAboutPointsInternal",function(a,b,c,q,e,g,j,f,l,s,m,p,n){j&&this.setSpinOff();this.setNavOn(!1);if(null==p&&(null==s||0.001>s.length())&&(j?Float.isNaN(q)||0==q:0==e))return!1;var r=null;null==p&&(r=JU.V3.newVsub(c,b),g&&r.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(r),this.internalTranslation=null==s?null:JU.V3.newV(s));b=null!=f;if(j)return null==
p?(0==e&&(e=NaN),Float.isNaN(e)?this.rotationRate=q:(n=v(Math.abs(e)/Math.abs(q)*this.spinFps+0.5),this.rotationRate=e/n*this.spinFps,null!=s&&this.internalTranslation.scale(1/n)),this.internalRotationAxis.setVA(r,0.017453292519943295*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):e=q,this.setSpin(a,!0,e,m,p,f,l),!Float.isNaN(e);a=0.017453292519943295*e;this.internalRotationAxis.setVA(r,a);this.rotateAxisAngleRadiansInternal(a,
f,n);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A,JU.M4");c(b,"rotateAxisAngleRadiansInternal",function(a,b,c){this.internalRotationAngle=a;this.vectorT.set(this.internalRotationAxis.x,this.internalRotationAxis.y,this.internalRotationAxis.z);this.matrixRotate.rotate2(this.vectorT,this.vectorT2);this.axisangleT.setVA(this.vectorT2,a);this.applyRotation(this.matrixTemp3.setAA(this.axisangleT),!0,b,this.internalTranslation,1E6<a,c);null==b&&this.getNewFixedRotationCenter()},
"~N,JU.BS,JU.M4");c(b,"getNewFixedRotationCenter",function(){this.axisangleT.setAA(this.internalRotationAxis);this.axisangleT.angle=-this.internalRotationAngle;this.matrixTemp4.setToAA(this.axisangleT);this.vectorT.setT(this.internalRotationCenter);this.pointT2.sub2(this.fixedRotationCenter,this.vectorT);var a=this.matrixTemp4.rotTrans2(this.pointT2,new JU.P3);a.add(this.vectorT);this.setRotationCenterAndRadiusXYZ(a,!1)});c(b,"setTranslationFractions",function(){this.xTranslationFraction=this.fixedTranslation.x/
this.width;this.yTranslationFraction=this.fixedTranslation.y/this.height});c(b,"centerAt",function(a,b,c){null==c?this.translateXYBy(a,b):(this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(c))},"~N,~N,JU.P3");c(b,"percentToPixels",function(a,b){switch(a.charCodeAt(0)){case 120:return v(Math.floor(b/100*this.width));case 121:return v(Math.floor(b/100*this.height));case 122:return v(Math.floor(b/100*
this.screenPixelCount))}return 0},"~S,~N");c(b,"angstromsToPixels",function(a){return this.scalePixelsPerAngstrom*a},"~N");c(b,"translateXYBy",function(a,b){this.fixedTranslation.x+=a;this.fixedTranslation.y+=b;this.setTranslationFractions()},"~N,~N");c(b,"setCamera",function(a,b){this.cameraSetting.set(a,b,0==a&&0==b?0:1)},"~N,~N");c(b,"translateToPercent",function(a,b){switch(a.charCodeAt(0)){case 120:this.xTranslationFraction=0.5+b/100;this.fixedTranslation.x=this.width*this.xTranslationFraction;
break;case 121:this.yTranslationFraction=0.5+b/100;this.fixedTranslation.y=this.height*this.yTranslationFraction;break;case 122:1==this.mode&&this.setNavigationDepthPercent(b)}},"~S,~N");c(b,"getTranslationXPercent",function(){return 0==this.width?0:100*(this.fixedTranslation.x-this.width/2)/this.width});c(b,"getTranslationYPercent",function(){return 0==this.height?0:100*(this.fixedTranslation.y-this.height/2)/this.height});c(b,"getTranslationScript",function(){var a="",b=this.getTranslationXPercent();
0!=b&&(a+="translate x "+b+";");b=this.getTranslationYPercent();0!=b&&(a+="translate y "+b+";");return a});c(b,"getOrientationText",function(a,b){switch(a){case 4129:return this.getMoveToText(1,!1);case 1073742132:var c=this.getRotationQ();b&&(c=c.inv());return c.toString();case 1073742178:var c=new JU.SB,q=this.getTranslationXPercent();JV.TransformManager.truncate2(c,b?-q:q);q=this.getTranslationYPercent();JV.TransformManager.truncate2(c,b?-q:q);return c.toString();default:return this.getMoveToText(1,
!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N,~B");c(b,"getRotationQ",function(){return JU.Quat.newM(this.matrixRotate)});c(b,"getOrientationInfo",function(){var a=new java.util.Hashtable;a.put("moveTo",this.getMoveToText(1,!1));a.put("center","center "+this.getCenterText());a.put("centerPt",this.fixedRotationCenter);var b=new JU.A4;b.setM(this.matrixRotate);a.put("axisAngle",b);a.put("quaternion",this.getRotationQ().toPoint4f());a.put("rotationMatrix",this.matrixRotate);a.put("rotateZYZ",this.getRotateZyzText(!1));
a.put("rotateXYZ",this.getRotateXyzText());a.put("transXPercent",Float.$valueOf(this.getTranslationXPercent()));a.put("transYPercent",Float.$valueOf(this.getTranslationYPercent()));a.put("zoom",Float.$valueOf(this.zmPct));a.put("modelRadius",Float.$valueOf(this.modelRadius));1==this.mode&&(a.put("navigationCenter","navigate center "+JU.Escape.eP(this.navigationCenter)),a.put("navigationOffsetXPercent",Float.$valueOf(this.getNavigationOffsetPercent("X"))),a.put("navigationOffsetYPercent",Float.$valueOf(this.getNavigationOffsetPercent("Y"))),
a.put("navigationDepthPercent",Float.$valueOf(this.navigationDepthPercent)));return a});c(b,"getRotation",function(a){a.setM3(this.matrixRotate)},"JU.M3");c(b,"setZoomHeight",function(a,b){this.zoomHeight=a;this.scaleFitToScreen(!1,b,!1,!0)},"~B,~B");c(b,"zoomBy",function(a){20<a?a=20:-20>a&&(a=-20);var b=a*this.zmPctSet/50;0==b&&(b=0<a?1:0>b?-1:0);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(b,"zoomByFactor",function(a,b,c){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=
a,this.zmPctSet*=a,this.resetXYCenter(b,c)):this.getNav()&&this.nav.zoomByFactor(a,b,c))},"~N,~N,~N");c(b,"zoomToPercent",function(a){this.zmPctSet=a;this.zoomRatio=0},"~N");c(b,"translateZBy",function(a){a>=this.screenPixelCount||(a=this.scalePixelsPerAngstrom/(1-1*a/this.screenPixelCount),a>=this.screenPixelCount||(a=100*(a/this.scaleDefaultPixelsPerAngstrom),this.zoomRatio=a/this.zmPctSet,this.zmPctSet=a))},"~N");c(b,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&
this.vwr.setBooleanProperty("windowCentered",!1);var c=new JU.P3;this.transformPt3f(this.fixedRotationCenter,c);c.set(a,b,c.z);this.unTransformPoint(c,c);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(c)}},"~N,~N");c(b,"zoomByPercent",function(a){var b=a*this.zmPctSet/100;0==b&&(b=0>a?-1:1);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(b,"setScaleAngstromsPerInch",function(a){if(this.scale3D=0<a)this.scale3DAngstromsPerInch=a;this.perspectiveDepth=!this.scale3D},
"~N");c(b,"setSlabRange",function(a){this.slabRange=a},"~N");c(b,"setSlabEnabled",function(a){this.vwr.g.setB("slabEnabled",this.slabEnabled=a)},"~B");c(b,"setZShadeEnabled",function(a){this.zShadeEnabled=a;this.vwr.g.setB("zShade",a)},"~B");c(b,"setZoomEnabled",function(a){this.zoomEnabled=a;this.vwr.g.setB("zoomEnabled",a)},"~B");c(b,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1);this.slabDepthChanged()});
c(b,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(b,"slabDepthChanged",function(){this.vwr.g.setI("slab",this.slabPercentSetting);this.vwr.g.setI("depth",this.depthPercentSetting);this.finalizeTransformParameters()});c(b,"slabByPercentagePoints",function(a){this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=Math.max(0,this.depthPercentSetting):100<=this.slabPercentSetting))this.slabPercentSetting+=a,this.slabDepthChanged(),this.depthPercentSetting>=this.slabPercentSetting&&
(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(b,"depthByPercentagePoints",function(a){this.depthPlane=null;if(!(0>a?0>=this.depthPercentSetting:this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.depthPercentSetting+=a,this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1),this.slabDepthChanged()},"~N");c(b,"slabDepthByPercentagePoints",function(a){this.depthPlane=this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=
Math.max(0,this.depthPercentSetting):this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.slabPercentSetting+=a,this.depthPercentSetting+=a,this.slabDepthChanged()},"~N");c(b,"slabToPercent",function(a){this.slabPlane=null;this.vwr.setFloatProperty("slabRange",0);this.slabPercentSetting=a;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(b,"depthToPercent",function(a){this.depthPlane=null;this.vwr.g.setI("depth",
a);this.depthPercentSetting=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(b,"zSlabToPercent",function(a){this.zSlabPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zDepthPercentSetting=a)},"~N");c(b,"zDepthToPercent",function(a){this.zDepthPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zSlabPercentSetting=a)},"~N");c(b,"slabInternal",function(a,b){b?(this.depthPlane=
a,this.depthPercentSetting=0):(this.slabPlane=a,this.slabPercentSetting=100);this.slabDepthChanged()},"JU.P4,~B");c(b,"setSlabDepthInternal",function(a){a?this.depthPlane=null:this.slabPlane=null;this.finalizeTransformParameters();this.slabInternal(this.getSlabDepthPlane(a),a)},"~B");c(b,"getSlabDepthPlane",function(a){if(a){if(null!=this.depthPlane)return this.depthPlane}else if(null!=this.slabPlane)return this.slabPlane;var b=this.matrixTransform;return JU.P4.new4(-b.m20,-b.m21,-b.m22,-b.m23+(a?
this.depthValue:this.slabValue))},"~B");c(b,"getCameraFactors",function(){this.aperatureAngle=360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(v(this.screenWidth/2),v(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(v(this.screenWidth/2),v(this.screenHeight/2),0);this.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);
var c=JU.P3.new3(v(this.screenWidth/2),v(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);return B(-1,[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)])});c(b,"setPerspectiveDepth",function(a){this.perspectiveDepth!=a&&(this.perspectiveDepth=a,this.vwr.g.setB("perspectiveDepth",a),this.resetFitToScreen(!1))},"~B");c(b,"getPerspectiveDepth",
function(){return this.perspectiveDepth});c(b,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);var c=0>a?-a/100:a;0!=c&&(this.cameraDepthSetting=c,this.vwr.g.setF("cameraDepth",this.cameraDepthSetting),this.cameraDepth=NaN)},"~N,~B");c(b,"getCameraDepth",function(){return this.cameraDepthSetting});c(b,"setScreenParameters0",function(a,b,c,q,e,g){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=q)?2*a:a,this.height=q?2*b:b,this.scaleFitToScreen(!1,
c,e,g))},"~N,~N,~B,~B,~B,~B");c(b,"setAntialias",function(a){var b=this.antialias!=a;this.width=(this.antialias=a)?2*this.screenWidth:this.screenWidth;this.height=this.antialias?2*this.screenHeight:this.screenHeight;b&&this.scaleFitToScreen(!1,this.useZoomLarge,!1,!1)},"~B");c(b,"defaultScaleToScreen",function(a){return this.screenPixelCount/2/a},"~N");c(b,"resetFitToScreen",function(a){this.scaleFitToScreen(a,this.vwr.g.zoomLarge,!0,!0)},"~B");c(b,"scaleFitToScreen",function(a,b,c,q){0==this.width||
0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),q&&this.resetNavigationPoint(c),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");
c(b,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var c=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/1E3);return 0<c?c:1},"~N,~N");c(b,"unscaleToScreen",function(a,b){var c=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?c/this.getPerspectiveFactor(a):c},"~N,~N");c(b,"scaleToPerspective",function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(b,"setNavigationMode",function(a){this.mode=a?1:this.defaultMode;this.resetNavigationPoint(!0)},
"~B");c(b,"isNavigating",function(){return this.navigating||this.navOn});c(b,"finalizeTransformParameters",function(){this.haveNotifiedNaN=!1;this.fixedRotationOffset.setT(this.fixedTranslation);this.camera.setT(this.cameraSetting);this.internalSlab=this.slabEnabled&&(null!=this.slabPlane||null!=this.depthPlane);var a=this.getZoomSetting();this.zmPct!=a&&(this.zmPct=a,this.vwr.g.fontCaching||this.vwr.gdata.clearFontCache());this.calcCameraFactors();this.calcTransformMatrix();1==this.mode?this.calcNavigationPoint():
this.calcSlabAndDepthValues()});c(b,"getZoomSetting",function(){5>this.zmPctSet&&(this.zmPctSet=5);2E5<this.zmPctSet&&(this.zmPctSet=2E5);return this.zoomEnabled||1==this.mode?this.zmPctSet:100});c(b,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):v(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==
this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=F(this.pointT2.z)}catch(a){if(!D(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));
this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(b,"zValueFromPercent",function(a){return v(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},"~N");c(b,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.frameOffset,this.fixedRotationCenter);this.matrixTransform.setTranslation(this.vectorTemp);this.matrixTemp.setToM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);
this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=this.matrixTemp.m22=-this.scalePixelsPerAngstrom;this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.setM4(this.matrixTransform).invert()}catch(a){if(D(a,Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(b,"rotatePoint",function(a,b){this.matrixRotate.rotate2(a,
b);b.y=-b.y},"JU.T3,JU.T3");c(b,"getScreenTemp",function(a){this.matrixTransform.rotTrans2(a,this.fScrPt)},"JU.T3");c(b,"transformPtScr",function(a,b){b.setT(this.transformPt(a))},"JU.T3,JU.P3i");c(b,"transformPtScrT3",function(a,b){this.transformPt(a);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(b,"transformPt3f",function(a,b){this.applyPerspective(a,a);b.setT(this.fScrPt)},"JU.T3,JU.P3");c(b,"transformPtNoClip",function(a,b){this.applyPerspective(a,null);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(b,"transformPt",
function(a){return this.applyPerspective(a,this.internalSlab?a:null)},"JU.T3");c(b,"transformPtVib",function(a,b){this.ptVibTemp.setT(a);return this.applyPerspective(this.getVibrationPoint(b,this.ptVibTemp,NaN),a)},"JU.P3,JU.Vibration");c(b,"getVibrationPoint",function(a,b,c){return a.setCalcPoint(b,this.vibrationT,Float.isNaN(c)?this.vibrationScale:c,this.vwr.g.modulationScale)},"JU.Vibration,JU.T3,~N");c(b,"transformPt2Df",function(a,b){-3.4028235E38==a.z||3.4028235E38==a.z?(this.transformPt2D(a),
b.set(this.iScrPt.x,this.iScrPt.y,this.iScrPt.z)):this.transformPt3f(a,b)},"JU.T3,JU.P3");c(b,"transformPtScrT32D",function(a,b){-3.4028235E38==a.z||3.4028235E38==a.z?(this.transformPt2D(a),b.set(this.iScrPt.x,this.iScrPt.y,this.iScrPt.z)):this.transformPtScrT3(a,b)},"JU.T3,JU.P3");c(b,"transformPt2D",function(a){-3.4028235E38==a.z?(this.iScrPt.x=v(Math.floor(a.x/100*this.screenWidth)),this.iScrPt.y=v(Math.floor((1-a.y/100)*this.screenHeight))):(this.iScrPt.x=F(a.x),this.iScrPt.y=this.screenHeight-
F(a.y));this.antialias&&(this.iScrPt.x<<=1,this.iScrPt.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.fScrPt);this.iScrPt.z=F(this.fScrPt.z);return this.iScrPt},"JU.T3");c(b,"applyPerspective",function(a,b){this.getScreenTemp(a);var c=this.fScrPt.z;Float.isNaN(c)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=!0,c=this.fScrPt.z=1):0>=c&&(c=this.fScrPt.z=1);switch(this.mode){case 1:this.fScrPt.x-=this.navigationShiftXY.x;
this.fScrPt.y-=this.navigationShiftXY.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(c=this.getPerspectiveFactor(c),this.fScrPt.x*=c,this.fScrPt.y*=c);switch(this.mode){case 1:this.fScrPt.x+=this.navigationOffset.x;this.fScrPt.y+=this.navigationOffset.y;break;case 2:this.fScrPt.x-=this.perspectiveShiftXY.x,this.fScrPt.y-=this.perspectiveShiftXY.y;case 0:this.fScrPt.x+=this.fixedRotationOffset.x,this.fScrPt.y+=this.fixedRotationOffset.y}Float.isNaN(this.fScrPt.x)&&
!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.iScrPt.set(F(this.fScrPt.x),F(this.fScrPt.y),F(this.fScrPt.z));null!=b&&this.xyzIsSlabbedInternal(b)&&(this.fScrPt.z=this.iScrPt.z=1);return this.iScrPt},"JU.T3,JU.T3");c(b,"xyzIsSlabbedInternal",function(a){return null!=this.slabPlane&&0<a.x*this.slabPlane.x+a.y*this.slabPlane.y+a.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>a.x*this.depthPlane.x+a.y*this.depthPlane.y+
a.z*this.depthPlane.z+this.depthPlane.w},"JU.T3");c(b,"move",function(a,b,c,q,e,g,j){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,B(-1,[b,q,L(-1,[c,e,g,j])]));0<g&&this.movetoThread.setEval(a);this.movetoThread.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(b,"isInPosition",function(a,b){if(Float.isNaN(b))return!0;this.aaTest1.setVA(a,b/57.29577951308232);this.ptTest1.set(4.321,1.23456,3.14159);this.getRotation(this.matrixTest);
this.matrixTest.rotate2(this.ptTest1,this.ptTest2);this.matrixTest.setAA(this.aaTest1).rotate2(this.ptTest1,this.ptTest3);return 0.1>this.ptTest3.distance(this.ptTest2)},"JU.V3,~N");c(b,"moveToPyMOL",function(a,b,c){var q=JU.M3.newA9(c);q.invert();var e=c[9],g=-c[10],j=-c[11],f=JU.P3.new3(c[12],c[13],c[14]),l=c[15],s=c[16],m=c[17];this.setPerspectiveDepth(!(0<=m));var m=Math.abs(m)/2,p=Math.tan(3.141592653589793*m/180),m=j*p,p=0.5/p-0.5,n=50/m;0<l&&(l=50+F((j-l)*n),j=50+F((j-s)*n),this.setSlabEnabled(!0),
this.slabToPercent(l),this.depthToPercent(j),21==c.length&&(s=0!=c[18],n=0!=c[19],c=c[20],this.setZShadeEnabled(s),s&&(n?this.vwr.setIntProperty("zSlab",F(Math.min(100,l+c*(j-l)))):this.vwr.setIntProperty("zSlab",F((l+j)/2)),this.vwr.setIntProperty("zDepth",j))));this.moveTo(a,b,f,null,0,q,100,NaN,NaN,m,null,NaN,NaN,NaN,p,e,g);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(b,"moveTo",function(a,b,c,q,e,g,j,f,l,s,m,p,n,r,u,v,w){if(null==g)if(g=new JU.M3,q=JU.V3.newV(q),Float.isNaN(e))g.m00=NaN;else if(0.01>
e&&-0.01<e)g.setScale(1);else{if(0==q.x&&0==q.y&&0==q.z)return;var y=new JU.A4;y.setVA(q,e/57.29577951308232);g.setAA(y)}v==this.cameraSetting.x&&(v=NaN);w==this.cameraSetting.y&&(w=NaN);u==this.cameraDepth&&(u=NaN);Float.isNaN(v)||(f=50*v/s/this.width*this.screenPixelCount);Float.isNaN(w)||(l=50*w/s/this.height*this.screenPixelCount);e=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(s);if(0>=b)this.setAll(c,g,m,j,f,l,s,e,r,p,n,u,v,w),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();
else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm"));var z=this.movetoThread.setManager(this,this.vwr,B(-1,[c,g,m,L(-1,[b,j,f,l,s,e,r,p,n,u,v,w])]));0>=z||this.vwr.g.waitForMoveTo?(0<z&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(C){if(!D(C,Exception))throw C;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");
c(b,"setAll",function(a,b,c,q,e,g,j,f,l,s,m,p,n,r){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=c&&1==this.mode&&this.navigationCenter.setT(c);Float.isNaN(p)||this.setCameraDepthPercent(p,!1);!Float.isNaN(n)&&!Float.isNaN(r)&&this.setCamera(n,r);Float.isNaN(q)||this.zoomToPercent(q);Float.isNaN(j)||(this.modelRadius=j);Float.isNaN(f)||(this.scaleDefaultPixelsPerAngstrom=f);!Float.isNaN(e)&&!Float.isNaN(g)&&(this.translateToPercent("x",e),this.translateToPercent("y",
g));1==this.mode&&(!Float.isNaN(s)&&!Float.isNaN(m)&&this.navTranslatePercentOrTo(0,s,m),Float.isNaN(l)||this.setNavigationDepthPercent(l))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(b,"stopMotion",function(){this.movetoThread=null});c(b,"getRotationText",function(){this.axisangleT.setM(this.matrixRotate);var a=57.29577951308232*this.axisangleT.angle,b=new JU.SB;this.vectorT.set(this.axisangleT.x,this.axisangleT.y,this.axisangleT.z);if(0.01>a)return"{0 0 1 0}";this.vectorT.normalize();
this.vectorT.scale(1E3);b.append("{");JV.TransformManager.truncate0(b,this.vectorT.x);JV.TransformManager.truncate0(b,this.vectorT.y);JV.TransformManager.truncate0(b,this.vectorT.z);JV.TransformManager.truncate2(b,a);b.append("}");return b.toString()});c(b,"getMoveToText",function(a,b){this.finalizeTransformParameters();var c=new JU.SB;c.append("moveto ");b&&c.append("/* time, axisAngle */ ");c.appendF(a);c.append(" ").append(this.getRotationText());b&&c.append(" /* zoom, translation */ ");JV.TransformManager.truncate2(c,
this.zmPctSet);JV.TransformManager.truncate2(c,this.getTranslationXPercent());JV.TransformManager.truncate2(c,this.getTranslationYPercent());c.append(" ");b&&c.append(" /* center, rotationRadius */ ");c.append(this.getCenterText());c.append(" ").appendF(this.modelRadius);c.append(this.getNavigationText(b));b&&c.append(" /* cameraDepth, cameraX, cameraY */ ");JV.TransformManager.truncate2(c,this.cameraDepth);JV.TransformManager.truncate2(c,this.cameraSetting.x);JV.TransformManager.truncate2(c,this.cameraSetting.y);
c.append(";");return c.toString()},"~N,~B");c(b,"getCenterText",function(){return JU.Escape.eP(this.fixedRotationCenter)});c(b,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,c=-(57.29577951308232*Math.asin(b)),q;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,this.matrixRotate.m11)),q=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),q=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");
a.append(";center ").append(this.getCenterText());0!=b&&(a.append("; rotate x"),JV.TransformManager.truncate2(a,b));0!=c&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,c));0!=q&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,q));a.append(";");this.addZoomTranslationNavigationText(a);return a.toString()});c(b,"addZoomTranslationNavigationText",function(a){100!=this.zmPct&&(a.append(" zoom"),JV.TransformManager.truncate2(a,this.zmPct),a.append(";"));var b=this.getTranslationXPercent();
0!=b&&(a.append(" translate x"),JV.TransformManager.truncate2(a,b),a.append(";"));b=this.getTranslationYPercent();0!=b&&(a.append(" translate y"),JV.TransformManager.truncate2(a,b),a.append(";"));if(this.modelRadius!=this.rotationRadiusDefault||10==this.modelRadius)a.append(" set rotationRadius"),JV.TransformManager.truncate2(a,this.modelRadius),a.append(";");1==this.mode&&(a.append("navigate 0 center ").append(JU.Escape.eP(this.navigationCenter)),a.append(";navigate 0 translate"),JV.TransformManager.truncate2(a,
this.getNavigationOffsetPercent("X")),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("Y")),a.append(";navigate 0 depth "),JV.TransformManager.truncate2(a,this.navigationDepthPercent),a.append(";"))},"JU.SB");c(b,"getRotateZyzText",function(a){var b=new JU.SB,c=this.vwr.ms.getInfoM("defaultOrientationMatrix");null==c?c=this.matrixRotate:(c=JU.M3.newM3(c),c.invert(),c.mul2(this.matrixRotate,c));var q=c.m22,e=57.29577951308232*Math.acos(q);0.999<q||-0.999>q?(q=57.29577951308232*Math.atan2(c.m10,
c.m11),c=0):(q=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=q&&(0!=e&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=q&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,q));0!=e&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,e));0!=c&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,c));b.append(";");this.addZoomTranslationNavigationText(b);
return b.toString()},"~B");b.truncate0=c(b,"truncate0",function(a,b){a.appendC(" ");a.appendI(Math.round(b))},"JU.SB,~N");b.truncate2=c(b,"truncate2",function(a,b){a.appendC(" ");a.appendF(Math.round(100*b)/100)},"JU.SB,~N");c(b,"setSpinXYZ",function(a,b,c){Float.isNaN(a)||(this.spinX=a);Float.isNaN(b)||(this.spinY=b);Float.isNaN(c)||(this.spinZ=c);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(b,"setSpinFps",function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(b,"setNavXYZ",
function(a,b,c){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(c)||(this.navZ=c)},"~N,~N,~N");c(b,"clearSpin",function(){this.setSpinOff();this.setNavOn(!1);this.isSpinFixed=this.isSpinInternal=!1});c(b,"setSpinOn",function(){this.setSpin(null,!0,3.4028235E38,null,null,null,!1)});c(b,"setSpinOff",function(){this.setSpin(null,!1,3.4028235E38,null,null,null,!1)});c(b,"setSpin",function(a,b,c,q,e,g,j){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",
b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,B(-1,[Float.$valueOf(c),q,e,g,j?Boolean.TRUE:null])),this.spinIsGesture=j,Float.isNaN(c)||3.4028235E38==c||!this.vwr.g.waitForMoveTo?this.spinThread.start():(this.spinThread.setEval(a),this.spinThread.run())):null!=this.spinThread&&(this.spinThread.reset(),this.spinThread=null))},"J.api.JmolScriptEvaluator,~B,~N,JU.Lst,~A,JU.BS,~B");c(b,"setNavOn",function(a){if(!Float.isNaN(this.navFps)){var b=
this.navOn;a&&this.spinOn&&this.setSpin(null,!1,0,null,null,null,!1);this.navOn=a;this.vwr.g.setB("_navigating",a);a||this.navInterrupt();a?(0==this.navX&&(0==this.navY&&0==this.navZ)&&(this.navZ=1),0==this.navFps&&(this.navFps=10),null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,null),this.spinThread.start())):b&&null!=this.spinThread&&(this.spinThread.interrupt(),this.spinThread=null)}},"~B");c(b,"setVibrationScale",
function(a){this.vibrationScale=a},"~N");c(b,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=F(1E3*this.vibrationPeriod);if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.ms.getLastVibrationVector(this.vwr.am.cmi,0))},"~N");c(b,"setVibrationT",function(a){this.vibrationT.x=this.vibrationT.y=this.vibrationT.z=a;0==this.vibrationScale&&(this.vibrationScale=
this.vwr.g.vibrationScale)},"~N");c(b,"isVibrationOn",function(){return this.vibrationOn});c(b,"setVibrationOn",function(a){a?1>this.vwr.ms.mc?(this.vibrationOn=!1,this.vibrationT.x=0):(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOption("thread.VibrationThread",this.vwr,"tm"),this.vibrationThread.setManager(this,this.vwr,null),this.vibrationThread.start()),this.vibrationOn=!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=
!1,this.vibrationT.x=0)},"~B");c(b,"clearVibration",function(){this.setVibrationOn(!1);this.vibrationScale=0});c(b,"setStereoMode2",function(a){this.stereoMode=J.c.STER.CUSTOM;this.stereoColors=a},"~A");c(b,"setStereoMode",function(a){this.stereoColors=null;this.stereoMode=a;this.stereoDoubleDTI=a===J.c.STER.DTI;this.stereoDoubleFull=a===J.c.STER.DOUBLE},"J.c.STER");c(b,"setStereoDegrees",function(a){this.stereoDegrees=a;this.stereoRadians=0.017453292519943295*a},"~N");c(b,"getStereoRotationMatrix",
function(a){this.stereoFrame=a;if(!a)return this.matrixRotate;this.matrixTemp3.setAsYRotation(-this.stereoRadians);this.matrixStereo.mul2(this.matrixTemp3,this.matrixRotate);return this.matrixStereo},"~B");c(b,"isWindowCentered",function(){return this.windowCentered});c(b,"setWindowCentered",function(a){this.windowCentered=a;this.resetNavigationPoint(!0)},"~B");c(b,"setRotationRadius",function(a,b){a=this.modelRadius=0>=a?this.vwr.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0):
a;b&&this.vwr.setRotationRadius(a,!1);return a},"~N,~B");c(b,"setRotationCenterAndRadiusXYZ",function(a,b){this.resetNavigationPoint(!1);null==a?(this.setFixedRotationCenter(this.rotationCenterDefault),this.modelRadius=this.rotationRadiusDefault):(this.setFixedRotationCenter(a),b&&this.windowCentered&&(this.modelRadius=this.vwr.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0)))},"JU.T3,~B");c(b,"setNewRotationCenter",function(a,b){null==a&&(a=this.rotationCenterDefault);this.windowCentered?
(this.translateToPercent("x",0),this.translateToPercent("y",0),this.setRotationCenterAndRadiusXYZ(a,!0),b&&this.resetFitToScreen(!0)):this.moveRotationCenter(a,!0)},"JU.P3,~B");c(b,"moveRotationCenter",function(a,b){this.setRotationCenterAndRadiusXYZ(a,!1);b&&this.setRotationPointXY(this.fixedRotationCenter)},"JU.P3,~B");c(b,"setCenter",function(){this.setRotationCenterAndRadiusXYZ(this.fixedRotationCenter,!0)});c(b,"setCenterAt",function(a,b){var c=JU.P3.newP(b);switch(a){case 1073741826:break;case 96:c.add(this.vwr.ms.getAverageAtomPoint());
break;case 1812599299:c.add(this.vwr.getBoundBoxCenter());break;default:c.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(c,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(b,"setFrameOffset",function(a){null==this.frameOffsets||0>a||a>=this.frameOffsets.length?this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(b,"setSelectedTranslation",function(a,b,c,q){if(this.perspectiveDepth)switch(this.bsSelectedAtoms=a,b.charCodeAt(0)){case 88:case 120:this.ptOffset.x+=
c;break;case 89:case 121:this.ptOffset.y+=c;break;case 90:case 122:this.ptOffset.z+=c}else{c=new JU.V3;switch(b.charCodeAt(0)){case 88:case 120:c.set(q,0,0);break;case 89:case 121:c.set(0,q,0);break;case 90:case 122:c.set(0,0,q)}this.vwr.moveAtoms(null,null,this.matrixRotate,c,this.internalRotationCenter,!1,a,!0)}},"JU.BS,~S,~N,~N");c(b,"setNavFps",function(a){this.navFps=a},"~N");c(b,"calcCameraFactors",function(){Float.isNaN(this.cameraDepth)&&(this.cameraDepth=this.cameraDepthSetting,this.zoomFactor=
3.4028235E38);this.cameraDistance=this.cameraDepth*this.screenPixelCount;this.referencePlaneOffset=this.cameraDistance+this.screenPixelCount/2;this.scalePixelsPerAngstrom=this.scale3D&&!this.perspectiveDepth&&1!=this.mode?72/this.scale3DAngstromsPerInch*(this.antialias?2:1):this.screenPixelCount/this.visualRangeAngstroms;1!=this.mode&&(this.mode=0==this.camera.z?0:2);this.perspectiveShiftXY.set(0==this.camera.z?0:100*(this.camera.x*this.scalePixelsPerAngstrom/this.screenWidth),0==this.camera.z?0:
100*(this.camera.y*this.scalePixelsPerAngstrom/this.screenHeight),0);this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom;var a=2*this.modelRadius/this.visualRangeAngstroms*this.referencePlaneOffset;if(1==this.mode)this.calcNavCameraFactors(a);else{this.zoomFactor=3.4028235E38;this.modelCenterOffset=this.referencePlaneOffset;if(!this.scale3D||this.perspectiveDepth)this.scalePixelsPerAngstrom*=this.modelCenterOffset/a*this.zmPct/100;this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom}});
c(b,"calcNavCameraFactors",function(a){3.4028235E38==this.zoomFactor?(1E4<this.zmPct&&(this.zmPct=1E4),this.modelCenterOffset=100*a/this.zmPct):this.prevZoomSetting!=this.zmPctSet&&(this.modelCenterOffset=0==this.zoomRatio?100*a/this.zmPctSet:this.modelCenterOffset+(1-this.zoomRatio)*this.referencePlaneOffset,this.navMode=-1);this.prevZoomSetting=this.zmPctSet;this.zoomFactor=this.modelCenterOffset/this.referencePlaneOffset;this.zmPct=0==this.zoomFactor?1E4:100*(a/this.modelCenterOffset)},"~N");c(b,
"getPerspectiveFactor",function(a){return 0>=a?this.referencePlaneOffset:this.referencePlaneOffset/a},"~N");c(b,"unTransformPoint",function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=this.navigationOffset.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var c=
this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=c;this.untransformedPoint.y/=c}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,b)},"JU.T3,JU.T3");c(b,"resetNavigationPoint",function(a){5>this.zmPct&&1!=this.mode?
(this.perspectiveDepth=!0,this.mode=1):(1==this.mode?(this.navMode=1,this.slabPercentSetting=0,this.perspectiveDepth=!0):a&&(this.slabPercentSetting=100),this.vwr.setFloatProperty("slabRange",0),a&&this.setSlabEnabled(1==this.mode),this.zoomFactor=3.4028235E38,this.zmPctSet=this.zmPct)},"~B");c(b,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();this.navigating=!1},"JU.P3");c(b,"setNavigationSlabOffsetPercent",function(a){this.vwr.g.setF("navigationSlab",
a);this.calcCameraFactors();this.navigationSlabOffset=a/50*this.modelRadiusPixels},"~N");c(b,"getNavigationOffset",function(){this.transformPt3f(this.navigationCenter,this.navigationOffset);return this.navigationOffset});c(b,"getNavPtHeight",function(){return this.height/2});c(b,"getNavigationOffsetPercent",function(a){this.getNavigationOffset();return 0==this.width||0==this.height?0:"X"==a?100*(this.navigationOffset.x-this.width/2)/this.width:100*(this.navigationOffset.y-this.getNavPtHeight())/this.height},
"~S");c(b,"getNavigationText",function(a){a=a?" /* navigation center, translation, depth */ ":" ";if(1!=this.mode)return a+"{0 0 0} 0 0 0";this.getNavigationOffset();return a+JU.Escape.eP(this.navigationCenter)+" "+this.getNavigationOffsetPercent("X")+" "+this.getNavigationOffsetPercent("Y")+" "+this.navigationDepthPercent},"~B");c(b,"setScreenParameters",function(a,b,c,q,e,g){var j=1==this.mode?JU.P3.newP(this.navigationCenter):null,f=JU.P3.newP(this.navigationOffset);f.x/=this.width;f.y/=this.height;
this.setScreenParameters0(a,b,c,q,e,g);null!=j&&(this.navigationCenter.setT(j),this.navTranslatePercentOrTo(-1,f.x*this.width,f.y*this.height),this.setNavigatePt(j))},"~N,~N,~B,~B,~B,~B");c(b,"navInterrupt",function(){null!=this.nav&&this.nav.interrupt()});c(b,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator",this.vwr,"tm");if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(b,"navigateList",function(a,b){this.getNav()&&this.nav.navigateList(a,
b)},"J.api.JmolScriptEvaluator,JU.Lst");c(b,"navigateAxis",function(a,b){this.getNav()&&this.nav.navigateAxis(a,b)},"JU.V3,~N");c(b,"setNavigationOffsetRelative",function(){this.getNav()&&this.nav.setNavigationOffsetRelative()});c(b,"navigateKey",function(a,b){this.getNav()&&this.nav.navigateKey(a,b)},"~N,~N");c(b,"setNavigationDepthPercent",function(a){this.getNav()&&this.nav.setNavigationDepthPercent(a)},"~N");c(b,"navTranslatePercentOrTo",function(a,b,c){this.getNav()&&this.nav.navTranslatePercentOrTo(a,
b,c)},"~N,~N,~N");c(b,"calcNavigationPoint",function(){this.getNav()&&this.nav.calcNavigationPoint()});c(b,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""})});n("JV");z("java.lang.Enum J.api.JmolViewer $.PlatformViewer J.atomdata.AtomDataServer java.util.Hashtable JU.P3".split(" "),"JV.Viewer","java.util.Arrays JU.AU $.BS $.CU $.DF $.Lst $.P3i $.PT $.Quat $.Rdr $.SB J.adapter.smarter.SmarterJmolAdapter J.api.Interface J.atomdata.RadiusData J.c.FIL $.STER $.VDW J.i18n.GT JM.Measurement $.ModelSet JS.SV $.T J.thread.TimeoutThread JU.BSUtil $.C $.CommandHistory $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Parser $.TempArray JV.ActionManager $.AnimationManager $.ColorManager $.FileManager $.GlobalSettings $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager JV.binding.Binding".split(" "),
function(){var b=r(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJSNoAWT=this.haveDisplay=this.autoExit=this.testAsync=!1;this.fullName="";this.fm=this.ms=this.definedAtomSets=this.compiler=null;this.mustRender=this.listCommands=this.isSyntaxCheck=this.isSyntaxAndFileCheck=this.isJNLP=this.isApplet=!1;this.appletName=this.htmlName="";this.tryPt=0;this.insertedCommand="";this.tm=this.sm=this.g=this.rm=this.slm=this.shm=this.dm=this.cm=this.am=this.acm=this.html5Applet=this.gdata=
null;this.logFilePath=this.syncId="";this.useCommandThread=this.noGraphicsAllowed=this.multiTouch=this.isSilent=this.isSignedAppletLocal=this.isSignedApplet=this.isPrintOnly=this.allowScripting=!1;this.tempArray=this.eval=this.scm=this.stm=this.mm=this.commandHistory=this.access=this.modelAdapter=this.display=this.vwrOptions=this.commandOptions=null;this.async=this.allowArrayDotNotation=!1;this.executor=null;this.screenHeight=this.screenWidth=0;this.errorMessageUntranslated=this.errorMessage=this.chainList=
this.chainMap=this.rd=this.defaultVdw=null;this.privateKey=0;this.dataOnly=!1;this.maximumSize=2147483647;this.gRight=null;this.isStereoSlave=!1;this.imageFontScaling=1;this.antialiased=!1;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.jzt=this.outputManager=this.jsv=null;this.headless=this.isPreviewOnly=!1;this.movableBitSet=null;this.hasSelected=!1;this.lastData=this.jsc=this.smilesMatcher=this.minimizer=this.dssrParser=this.annotationParser=this.ligandModelSet=this.ligandModels=
this.mouse=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.jsParams=this.captureParams=null;this.cirChecked=!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverLabel="%U";this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.selectionHalosEnabled=!1;this.noFrankEcho=this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkit=this.jmolpopup=this.scriptEditor=this.appConsole=null;this.isTainted=!0;this.showSelected=
this.movingSelected=!1;this.ptNew=this.ptScreenNew=this.ptScreen=null;this.atomHighlighted=-1;this.creatingImage=!1;this.userVdwMars=this.userVdws=this.bsUserVdws=null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.$isKiosk=!1;this.displayLoadErrors=!0;this.$isParallel=!1;this.stateScriptVersionInt=2147483647;this.timeouts=this.jsExporter3D=null;this.chainCaseSpecified=!1;this.macros=this.nboParser=this.triangulator=this.jsonParser=this.jcm=this.jbr=this.logFileName=this.nmrCalculation=
null;this.consoleFontScale=1;u(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,J.api.PlatformViewer]);N(b,function(){this.ptScreen=new JU.P3;this.ptScreenNew=new JU.P3;this.ptNew=new JU.P3});y(b,function(a){I(this,JV.Viewer,[]);this.commandHistory=new JU.CommandHistory;this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();this.chainMap=new java.util.Hashtable;this.chainList=
new JU.Lst;this.setOptions(a)},"java.util.Map");c(b,"finalize",function(){JU.Logger.debugging&&JU.Logger.debug("vwr finalize "+this);ha(this,JV.Viewer,"finalize",[])});c(b,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");b.getJmolVersion=f(b,"getJmolVersion",function(){return null==JV.Viewer.version_date?JV.Viewer.version_date=JV.JC.version+"  "+JV.JC.date:JV.Viewer.version_date});b.allocateViewer=c(b,"allocateViewer",function(a,b,c,e,g,j,f,l){var s=new java.util.Hashtable;s.put("display",
a);s.put("adapter",b);s.put("statusListener",f);s.put("platform",l);s.put("options",j);s.put("fullName",c);s.put("documentBase",e);s.put("codeBase",g);return new JV.Viewer(s)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,J.api.GenericPlatform");c(b,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");f(b,"getModelAdapter",function(){return null==this.modelAdapter?this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter:this.modelAdapter});f(b,"getSmartsMatch",
function(a,b){null==b&&(b=this.bsA());return this.getSmilesMatcher().getSubstructureSet(a,this.ms.at,this.ms.ac,b,2)},"~S,JU.BS");c(b,"isSubstructure",function(a,b){try{var c=this.getSmilesMatcher().find(a,b,10);return null!=c&&0<c.length}catch(e){if(D(e,Exception))return!1;throw e;}},"~S,~S");c(b,"hasStructure",function(a,b,c){try{return 1==this.getSmilesMatcher().hasStructure(a,B(-1,[b]),(c?2:1)|8)[0]}catch(e){if(D(e,Exception))return!1;throw e;}},"~S,~S,~B");c(b,"getSmartsMatchForNodes",function(a,
b){return this.getSmilesMatcher().getSubstructureSet(a,b,b.length,null,2)},"~S,~A");c(b,"getSmartsMap",function(a,b,c){null==b&&(b=this.bsA());0==c&&(c=2);return this.getSmilesMatcher().getCorrelationMaps(a,this.ms.at,this.ms.ac,b,c)},"~S,JU.BS,~N");c(b,"setOptions",function(a){this.vwrOptions=a;JU.Logger.debugging&&JU.Logger.debug("Viewer constructor "+this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==this.fullName&&(this.fullName="");var c=
a.get("codePath");null==c&&(c="../java/");JV.Viewer.appletCodeBase=c.toString();JV.Viewer.appletIdiomaBase=JV.Viewer.appletCodeBase.substring(0,JV.Viewer.appletCodeBase.lastIndexOf("/",JV.Viewer.appletCodeBase.length-2)+1)+"idioma";c=a.get("documentBase");JV.Viewer.appletDocumentBase=null==c?"":c.toString();c=a.get("options");this.commandOptions=null==c?"":c.toString();(a.containsKey("debug")||0<=this.commandOptions.indexOf("-debug"))&&JU.Logger.setLogLevel(5);this.isApplet&&a.containsKey("maximumSize")&&
this.setMaximumSize(a.get("maximumSize").intValue());(this.isJNLP=this.checkOption2("isJNLP","-jnlp"))&&JU.Logger.info("setting JNLP mode TRUE");this.isApplet=(this.isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet","-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");var e=this.fullName.indexOf("__");this.htmlName=0>e?this.fullName:this.fullName.substring(0,e);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=
0>e?"":this.fullName.substring(e+2,this.fullName.length-2);this.access=this.checkOption2("access:READSPT","-r")?JV.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?JV.Viewer.ACCESS.NONE:JV.Viewer.ACCESS.ALL;(this.isPreviewOnly=a.containsKey("previewOnly"))&&a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly","-p");this.dataOnly=this.checkOption2("isDataOnly","\x00");this.autoExit=this.checkOption2("exit","-x");c=a.get("platform");e="unknown";null==c&&(c=this.commandOptions.contains("platform=")?
this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if("string"==typeof c){e=c;this.isWebGL=0<=e.indexOf(".awtjs.");JV.Viewer.isJS=this.isJSNoAWT=this.isWebGL||0<=e.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||JV.Viewer.isJS&&a.containsKey("async"));var g=c=null,j="?";self.Jmol&&(g=Jmol,c=Jmol._applets[this.htmlName.split("_object")[0]],j=Jmol._version);null!=j&&(this.html5Applet=c,JV.Viewer.jmolObject=g,JV.Viewer.strJavaVersion=
j,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));c=J.api.Interface.getInterface(e,this,"setOptions")}this.apiPlatform=c;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.noGraphicsAllowed=this.checkOption2("noDisplay","-n");this.headless=this.apiPlatform.isHeadless();this.haveDisplay=this.isWebGL||null!=this.display&&!this.noGraphicsAllowed&&!this.headless&&!this.dataOnly;this.noGraphicsAllowed=(new Boolean(this.noGraphicsAllowed&
null==this.display)).valueOf();this.headless=(new Boolean(this.headless|this.noGraphicsAllowed)).valueOf();this.haveDisplay?(this.mustRender=!0,this.multiTouch=this.checkOption2("multiTouch","-multitouch"),this.isWebGL||(this.display=document.getElementById(this.display))):this.display=null;this.apiPlatform.setViewer(this,this.display);c=a.get("graphicsAdapter");null==c&&!this.isWebGL&&(c=J.api.Interface.getOption("g3d.Graphics3D",this,"setOptions"));this.gdata=null==c&&(this.isWebGL||!JV.Viewer.isJS)?
new JU.GData:c;this.gdata.initialize(this,this.apiPlatform);this.stm=new JV.StateManager(this);this.cm=new JV.ColorManager(this,this.gdata);this.sm=new JV.StatusManager(this);e=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,e);this.slm=new JV.SelectionManager(this);this.haveDisplay&&(this.acm=this.multiTouch?J.api.Interface.getOption("multitouch.ActionManagerMT",null,null):new JV.ActionManager,this.acm.setViewer(this,this.commandOptions+"-multitouch-"+a.get("multiTouch")),
this.mouse=this.apiPlatform.getMouseManager(this.privateKey,this.display),this.multiTouch&&!this.checkOption2("-simulated","-simulated")&&this.apiPlatform.setTransparentCursor(this.display));this.mm=new JV.ModelManager(this);this.shm=new JV.ShapeManager(this);this.tempArray=new JU.TempArray;this.am=new JV.AnimationManager(this);c=a.get("repaintManager");null==c&&(c=J.api.Interface.getOption("render.RepaintManager",this,"setOptions"));if(JV.Viewer.isJS||null!=c&&!c.equals(""))(this.rm=c).set(this,
this.shm);this.ms=new JM.ModelSet(this,null);this.initialize(!0,!1);this.fm=new JV.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.isApplet?(JU.Logger.info("vwrOptions: \n"+JU.Escape.escapeMap(this.vwrOptions)),b=this.vwrOptions.get("documentLocation"),!JV.Viewer.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),JU.Logger.info("setting current directory to "+b),this.cd(b)),b=JV.Viewer.appletDocumentBase,
e=b.indexOf("#"),0<=e&&(b=b.substring(0,e)),e=b.lastIndexOf("?"),0<=e&&(b=b.substring(0,e)),e=b.lastIndexOf("/"),0<=e&&(b=b.substring(0,e)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),b=a.get("appletProxy"),null!=b&&this.setStringProperty("appletProxy",b),this.isSignedApplet?(this.logFilePath=JU.PT.rep(JV.Viewer.appletCodeBase,"file://",""),this.logFilePath=JU.PT.rep(this.logFilePath,"file:/",""),0<=this.logFilePath.indexOf("//")?this.logFilePath=null:this.isSignedAppletLocal=
!0):JV.Viewer.isJS||(this.logFilePath=null),new J.i18n.GT(this,a.get("language")),JV.Viewer.isJS&&this.acm.createActions()):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&JU.Logger.setLogLevel(3),this.headless&&!this.isSilent&&JU.Logger.info("Operating headless display="+this.display+" nographicsallowed="+this.noGraphicsAllowed),this.isSyntaxCheck=(this.isSyntaxAndFileCheck=this.checkOption2("checkLoad","-C"))||
this.checkOption2("check","-c"),this.listCommands=this.checkOption2("listCommands","-l"),this.cd("."),this.headless&&(this.headlessImageParams=a.get("headlessImage"),c=a.get("headlistMaxTimeMs"),null==c&&(c=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),c.intValue(),"exitJmol")));this.useCommandThread=!this.headless&&this.checkOption2("useCommandThread","-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",JV.Viewer.nProcessors);this.isSilent||JU.Logger.info("(C) 2015 Jmol Development\nJmol Version: "+
JV.Viewer.getJmolVersion()+"\njava.vendor: "+JV.Viewer.strJavaVendor+"\njava.version: "+JV.Viewer.strJavaVersion+"\nos.name: "+JV.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getP("_memory")+"\nprocessors available: "+JV.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.isApplet?"":"\nappletId:"+this.htmlName+(this.isSignedApplet?" (signed)":"")));this.zap(!1,!0,!1);this.g.setO("language",J.i18n.GT.getLanguage());this.g.setO("_hoverLabel",this.hoverLabel);this.stm.setJmolDefaults();
JU.Elements.covalentVersion=1;this.allowArrayDotNotation=!0;this.allowScripting&&this.getScriptManager()},"java.util.Map");c(b,"setMaximumSize",function(a){this.maximumSize=Math.max(a,100)},"~N");c(b,"setStereo",function(a,b){this.isStereoSlave=a;this.gRight=b},"~B,~O");c(b,"getMenu",function(a){this.getPopupMenu();return a.equals("\x00")?(this.popupMenu(this.screenWidth-120,0,"j"),"OK"):null==this.jmolpopup?"":this.jmolpopup.jpiGetMenuAsString("Jmol version "+JV.Viewer.getJmolVersion()+"|_GET_MENU|"+
a)},"~S");f(b,"resizeInnerPanel",function(a,b){if(!this.autoExit&&this.haveDisplay)return this.sm.resizeInnerPanel(a,b);this.setScreenDimension(a,b);return E(-1,[this.screenWidth,this.screenHeight])},"~N,~N");f(b,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.tm.stereoDoubleFull&&(a=v((a+1)/2));this.screenWidth==a&&this.screenHeight==b||this.resizeImage(a,b,!1,!1,!0)},"~N,~N");c(b,"resizeImage",function(a,b,c,e,g){if(c||!this.creatingImage){var j=
this.antialiased;this.antialiased=g?this.g.antialiasDisplay&&this.checkMotionRendering(603979786):c&&!e?this.g.antialiasImages:!1;!e&&(!c&&(0<a||j!=this.antialiased))&&this.setShapeProperty(5,"clearBoxes",null);this.imageFontScaling=(this.antialiased?2:1)*(g||this.tm.scale3D||0>=a?1:1*(this.g.zoomLarge==b>a?b:a)/this.getScreenDim());0<a?(this.screenWidth=a,this.screenHeight=b,c||(this.g.setI("_width",a),this.g.setI("_height",b))):(a=0==this.screenWidth?this.screenWidth=500:this.screenWidth,b=0==this.screenHeight?
this.screenHeight=500:this.screenHeight);this.tm.setScreenParameters(a,b,c||g?this.g.zoomLarge:!1,this.antialiased,!1,!1);this.setModelkitPropertySafely("modelkeys",JU.BSUtil.newBitSet2(0,this.ms.mc));this.gdata.setWindowParameters(a,b,this.antialiased);0<a&&!c&&this.setStatusResized(a,b)}},"~N,~N,~B,~B,~B");f(b,"getScreenWidth",function(){return this.screenWidth});f(b,"getScreenHeight",function(){return this.screenHeight});c(b,"getScreenDim",function(){return this.g.zoomLarge==this.screenHeight>
this.screenWidth?this.screenHeight:this.screenWidth});c(b,"setWidthHeightVar",function(){this.g.setI("_width",this.screenWidth);this.g.setI("_height",this.screenHeight)});c(b,"getBoundBoxCenterX",function(){return v(this.screenWidth/2)});c(b,"getBoundBoxCenterY",function(){return v(this.screenHeight/2)});c(b,"updateWindow",function(a,b){if(!this.refreshing||this.creatingImage)return this.refreshing?!1:!JV.Viewer.isJS;(this.isTainted||this.tm.slabEnabled)&&this.setModelVisibility();this.isTainted=
!1;null!=this.rm&&0!=a&&this.setScreenDimension(a,b);return!0},"~N,~N");c(b,"getImage",function(a,b){var c=null;try{this.beginRendering(a,b),this.render(),this.gdata.endRendering(),c=this.gdata.getScreenImage(b)}catch(e){if(D(e,Error))this.gdata.getScreenImage(b),this.handleError(e,!1),this.setErrorMessage("Error during rendering: "+e,null);else if(D(e,Exception))System.out.println("render error"+e);else throw e;}return c},"~B,~B");c(b,"beginRendering",function(a,b){this.gdata.beginRendering(this.tm.getStereoRotationMatrix(a),
this.g.translucent,b,!this.checkMotionRendering(603979967))},"~B,~B");c(b,"render",function(){if(!(null==this.mm.modelSet||!this.mustRender||!this.refreshing&&!this.creatingImage||null==this.rm)){var a=this.antialiased&&this.g.antialiasTranslucent,b=this.shm.finalizeAtoms(this.tm.bsSelectedAtoms,!0);this.isWebGL?(this.rm.renderExport(this.gdata,this.ms,this.jsParams),this.notifyViewerRepaintDone()):(this.rm.render(this.gdata,this.ms,!0,b),this.gdata.setPass2(a)&&(this.tm.setAntialias(a),this.rm.render(this.gdata,
this.ms,!1,null),this.tm.setAntialias(this.antialiased)))}});c(b,"drawImage",function(a,b,c,e,g){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,c,e,this.screenWidth,this.screenHeight,g);this.gdata.releaseScreenImage()},"~O,~O,~N,~N,~B");c(b,"getScreenImage",function(){return this.getScreenImageBuffer(null,!0)});f(b,"getScreenImageBuffer",function(a,b){if(this.isWebGL)return b?this.apiPlatform.allocateRgbImage(0,0,null,0,!1,!0):null;var c=this.tm.stereoDoubleFull||this.tm.stereoDoubleDTI,e=this.tm.stereoMode.isBiColor(),
g=null==a&&c;e?(this.beginRendering(!0,b),this.render(),this.gdata.endRendering(),this.gdata.snapshotAnaglyphChannelBytes(),this.beginRendering(!1,b),this.render(),this.gdata.endRendering(),this.gdata.applyAnaglygh(this.tm.stereoMode,this.tm.stereoColors),e=this.gdata.getScreenImage(b)):e=this.getImage(c,b);var j=null;g&&(j=this.apiPlatform.newBufferedImage(e,this.tm.stereoDoubleDTI?this.screenWidth:this.screenWidth<<1,this.screenHeight),a=this.apiPlatform.getGraphics(j));null!=a&&(c&&(this.tm.stereoMode===
J.c.STER.DTI?(this.drawImage(a,e,this.screenWidth>>1,0,!0),e=this.getImage(!1,!1),this.drawImage(a,e,0,0,!0),a=null):(this.drawImage(a,e,this.screenWidth,0,!1),e=this.getImage(!1,!1))),null!=a&&this.drawImage(a,e,0,0,!1));return g?j:e},"~O,~B");c(b,"evalStringWaitStatusQueued",function(a,b,c,e,g){return null==this.getScriptManager()?null:this.scm.evalStringWaitStatusQueued(a,b,c,e,g)},"~S,~S,~S,~B,~B");c(b,"popupMenu",function(a,b,c){if(this.haveDisplay&&this.refreshing&&!this.isPreviewOnly&&!this.g.disablePopupMenu)switch(c.charCodeAt(0)){case 106:try{this.getPopupMenu(),
this.jmolpopup.jpiShow(a,b)}catch(e){JU.Logger.info(e.toString()),this.g.disablePopupMenu=!0}break;case 97:case 98:case 109:if(null==this.getModelkit(!0))break;this.modelkit.showMenu(a,b)}},"~N,~N,~S");c(b,"getModelkit",function(a){null==this.modelkit?(this.modelkit=J.api.Interface.getInterface("J.modelkit.ModelKit",this,"script")).setMenu(this.apiPlatform.getMenuPopup(null,"m")):a&&this.modelkit.updateMenu();return this.modelkit},"~B");c(b,"getPopupMenu",function(){if(this.g.disablePopupMenu)return null;
if(null==this.jmolpopup&&(this.jmolpopup=this.allowScripting?this.apiPlatform.getMenuPopup(this.menuStructure,"j"):null,null==this.jmolpopup))return this.async||(this.g.disablePopupMenu=!0),null;this.isJSNoAWT&&this.checkMenuUpdate();return this.jmolpopup.jpiGetMenuAsObject()});f(b,"setMenu",function(a,b){b&&JU.Logger.info("Setting menu "+(0==a.length?"to Jmol defaults":"from file "+a));0==a.length?a=null:b&&(a=this.getFileAsString3(a,!1,null));this.getProperty("DATA_API","setMenu",a);this.sm.setCallbackFunction("menu",
a)},"~S,~B");c(b,"setStatusFrameChanged",function(a){a&&(this.prevFrame=-2147483648);this.tm.setVibrationPeriod(NaN);var b=this.am.firstFrameIndex,c=this.am.lastFrameIndex,e=this.am.isMovie;a=this.am.cmi;b==c&&!e&&(a=b);var g=this.getModelFileNumber(a),j=this.am.cmi,f=g,l=g%1E6,s=e?b:this.getModelFileNumber(b),m=e?c:this.getModelFileNumber(c),p;e?p=""+(j+1):0==f?(p=this.getModelNumberDotted(b),b!=c&&(p+=" - "+this.getModelNumberDotted(c)),v(s/1E6)==v(m/1E6)&&(f=s)):p=this.getModelNumberDotted(a);
0!=f&&(f=1E6>f?1:v(f/1E6));e||(this.g.setI("_currentFileNumber",f),this.g.setI("_currentModelNumberInFile",l));b=this.am.currentMorphModel;this.g.setI("_currentFrame",j);this.g.setI("_morphCount",this.am.morphCount);this.g.setF("_currentMorphFrame",b);this.g.setI("_frameID",g);this.g.setI("_modelIndex",a);this.g.setO("_modelNumber",p);this.g.setO("_modelName",0>a?"":this.getModelName(a));g=0>a?"":this.ms.getModelTitle(a);this.g.setO("_modelTitle",null==g?"":g);this.g.setO("_modelFile",0>a?"":this.ms.getModelFileName(a));
this.g.setO("_modelType",0>a?"":this.ms.getModelFileType(a));j==this.prevFrame&&b==this.prevMorphModel||(this.prevFrame=j,this.prevMorphModel=b,g=this.getModelName(j),e?g=""+(""===g?j+1:this.am.caf+1)+": "+g:(e=""+this.getModelNumberDotted(j),g.equals(e)||(g=e+": "+g)),this.sm.setStatusFrameChanged(f,l,0>this.am.animationDirection?-s:s,0>this.am.currentDirection?-m:m,j,b,g),this.doHaveJDX()&&this.getJSV().setModel(a),JV.Viewer.isJS&&this.updateJSView(a,-1))},"~B,~B");c(b,"doHaveJDX",function(){return this.haveJDX||
(this.haveJDX=this.getBooleanProperty("_jspecview"))});c(b,"getJSV",function(){null==this.jsv&&(this.jsv=J.api.Interface.getOption("jsv.JSpecView",this,"script"),this.jsv.setViewer(this));return this.jsv});c(b,"getJDXBaseModelIndex",function(a){return!this.doHaveJDX()?a:this.getJSV().getBaseModelIndex(a)},"~N");c(b,"getJspecViewProperties",function(a){a=this.sm.getJspecViewProperties(""+a);null!=a&&(this.haveJDX=!0);return a},"~O");c(b,"scriptEcho",function(a){JU.Logger.isActiveLevel(4)&&(JV.Viewer.isJS&&
System.out.println(a),this.sm.setScriptEcho(a,this.isScriptQueued()),this.listCommands&&(null!=a&&0==a.indexOf("$["))&&JU.Logger.info(a))},"~S");c(b,"isScriptQueued",function(){return null!=this.scm&&this.scm.isScriptQueued()});c(b,"notifyError",function(a,b,c){this.g.setO("_errormessage",c);this.sm.notifyError(a,b,c)},"~S,~S,~S");c(b,"jsEval",function(a){return""+this.sm.jsEval(a)},"~S");c(b,"jsEvalSV",function(a){return JS.SV.getVariable(JV.Viewer.isJS?this.sm.jsEval(a):this.jsEval(a))},"~S");c(b,
"setFileLoadStatus",function(a,b,c,e,g,j){this.setErrorMessage(g,null);this.g.setI("_loadPoint",a.getCode());var f=a!==J.c.FIL.CREATING_MODELSET;f&&this.setStatusFrameChanged(!1,!1);this.sm.setFileLoadStatus(b,c,e,g,a.getCode(),f,j);f&&(this.doHaveJDX()&&this.getJSV().setModel(this.am.cmi),JV.Viewer.isJS&&this.updateJSView(this.am.cmi,-2))},"J.c.FIL,~S,~S,~S,~S,Boolean");c(b,"getZapName",function(){return this.g.modelKitMode?"Jmol Model Kit":"zapped"});c(b,"setStatusMeasuring",function(a,b,c,e){this.sm.setStatusMeasuring(a,
b,c,e)},"~S,~N,~S,~N");c(b,"notifyMinimizationStatus",function(){var a=this.getP("_minimizationStep"),b=this.getP("_minimizationForceField"),c=this.getP("_minimizationStatus"),e="starting".equals(c),g="done".equals(c)||"failed".equals(c),j=null!=this.minimizer&&(g||e)?this.minimizer.bsAtoms:null,f=null==j?-1:j.nextSetBit(0),l=0<=f?this.getModelIndexForAtom(f):-1;e&&0<=f&&this.sm.setStatusStructureModified(f,l,3,"minimize:"+c,j.cardinality(),j);this.sm.notifyMinimizationStatus(c,"string"==typeof a?
Integer.$valueOf(0):a,this.getP("_minimizationEnergy"),a.toString().equals("0")?Float.$valueOf(0):this.getP("_minimizationEnergyDiff"),b);g&&0<=f&&this.sm.setStatusStructureModified(f,l,-3,"minimize:"+c,j.cardinality(),j)});c(b,"setStatusAtomPicked",function(a,b,c,e){e&&this.setSelectionSet(JU.BSUtil.newAndSetBit(a));null==b&&(b=this.g.pickLabel,b=0==b.length?this.getAtomInfoXYZ(a,this.g.messageStyleChime?4:2)+(null==this.getOperativeSymmetry()?"":" ("+this.getAtomInfoXYZ(a,3)+")"):this.ms.getAtomInfo(a,
b,this.ptTemp));this.setPicked(a,!1);0>a&&(e=this.getPendingMeasurement(),null!=e&&(b=b.substring(0,b.length-1)+',"'+e.getString()+'"]'));this.g.setO("_pickinfo",b);this.sm.setStatusAtomPicked(a,b,c);0>a||(1==this.sm.getSyncMode()&&this.doHaveJDX()&&this.getJSV().atomPicked(a),JV.Viewer.isJS&&this.updateJSView(this.ms.at[a].mi,a))},"~N,~S,java.util.Map,~B");f(b,"getProperty",function(a,b,c){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,c);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........getPreference.......".indexOf(b)){case 0:return this.scriptCheckRet(c,
!0);case 20:return null==this.appConsole?"":this.appConsole.getText();case 40:return this.showEditor(c),null;case 60:return this.scriptEditorVisible=c.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:C(c,"J.api.JmolAppConsoleInterface")?this.appConsole=c:null!=c&&!c.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=c&&c.booleanValue())&&(JV.Viewer.isJS&&(this.appConsole=J.api.Interface.getOption("consolejs.AppletConsole",this,"script")),null!=this.appConsole&&
this.appConsole.start(this)),this.scriptEditor=JV.Viewer.isJS||null==this.appConsole?null:this.appConsole.getScriptEditor(),this.appConsole;case 100:return null==this.appConsole&&(null!=c&&c.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=c;case 140:return this.getSymTemp().getSpaceGroupInfo(this.ms,
null,-1,!1,null);case 160:return this.g.disablePopupMenu=!0,null;case 180:return this.g.defaultDirectory;case 200:return"string"==typeof c?this.getMenu(c):this.getPopupMenu();case 220:return this.shm.getProperty(c);case 240:return this.sm.syncSend("getPreference",c,1)}JU.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(b,"notifyMouseClicked",function(a,b,c,e){var g=JV.binding.Binding.getButtonMods(c),j=JV.binding.Binding.getClickCount(c);this.g.setI("_mouseX",a);this.g.setI("_mouseY",
this.screenHeight-b);this.g.setI("_mouseAction",c);this.g.setI("_mouseModifiers",g);this.g.setI("_clickCount",j);return this.sm.setStatusClicked(a,this.screenHeight-b,c,j,e)},"~N,~N,~N,~N");c(b,"getOutputManager",function(){return null!=this.outputManager?this.outputManager:(this.outputManager=J.api.Interface.getInterface("JV.OutputManager"+(JV.Viewer.isJS?"JS":"Awt"),this,"file")).setViewer(this,this.privateKey)});c(b,"getJzt",function(){return null==this.jzt?this.jzt=J.api.Interface.getInterface("JU.ZipTools",
this,"zip"):this.jzt});c(b,"readFileAsMap",function(a,b,c){this.getJzt().readFileAsMap(a,b,c)},"java.io.BufferedInputStream,java.util.Map,~S");c(b,"getZipDirectoryAsString",function(a){a=this.fm.getBufferedInputStreamOrErrorMessageFromName(a,a,!1,!1,null,!1,!0);return this.getJzt().getZipDirectoryAsStringAndClose(a)},"~S");f(b,"getImageAsBytes",function(a,b,c,e,g){return this.getOutputManager().getImageAsBytes(a,b,c,e,g)},"~S,~N,~N,~N,~A");f(b,"releaseScreenImage",function(){this.gdata.releaseScreenImage()});
c(b,"setDisplay",function(a){this.display=a;this.apiPlatform.setViewer(this,a)},"~O");c(b,"newMeasurementData",function(a,b){return J.api.Interface.getInterface("JM.MeasurementData",this,"script").init(a,this,b)},"~S,JU.Lst");c(b,"getDataManager",function(){return null==this.dm?this.dm=J.api.Interface.getInterface("JV.DataManager",this,"script").set(this):this.dm});c(b,"getScriptManager",function(){if(this.allowScripting&&null==this.scm){this.scm=J.api.Interface.getInterface("JS.ScriptManager",this,
"setOptions");if(JV.Viewer.isJS&&null==this.scm)throw new NullPointerException;if(null==this.scm)return this.allowScripting=!1,null;this.eval=this.scm.setViewer(this);this.useCommandThread&&this.scm.startCommandWatcher(!0)}return this.scm});c(b,"checkOption2",function(a,b){return this.vwrOptions.containsKey(a)&&!this.vwrOptions.get(a).toString().equals("false")||0<=this.commandOptions.indexOf(b)},"~S,~S");c(b,"setStartupBooleans",function(){this.setBooleanProperty("_applet",this.isApplet);this.setBooleanProperty("_jspecview",
!1);this.setBooleanProperty("_signedApplet",this.isSignedApplet);this.setBooleanProperty("_headless",this.headless);this.setStringProperty("_restrict",'"'+this.access+'"');this.setBooleanProperty("_useCommandThread",this.useCommandThread);this.setBooleanPropertyTok("doubleprecision",603979831,!0)});c(b,"getExportDriverList",function(){return this.haveAccess(JV.Viewer.ACCESS.ALL)?this.g.getParameter("exportDrivers",!0):""});f(b,"dispose",function(){this.gRight=null;null!=this.mouse&&(this.acm.dispose(),
this.mouse.dispose(),this.mouse=null);this.clearScriptQueue();this.clearThreads();this.haltScriptExecution();null!=this.scm&&this.scm.clear(!0);this.gdata.destroy();null!=this.jmolpopup&&this.jmolpopup.jpiDispose();null!=this.modelkit&&this.modelkit.dispose();try{null!=this.appConsole&&(this.appConsole.dispose(),this.appConsole=null),null!=this.scriptEditor&&(this.scriptEditor.dispose(),this.scriptEditor=null)}catch(a){if(!D(a,Exception))throw a;}});c(b,"reset",function(a){this.ms.setBoundBox(null,
null,!0,0);this.axesAreTainted=!0;this.tm.homePosition(a);this.ms.setCrystallographicDefaults()?this.stm.setCrystallographicDefaults():this.setAxesMode(603979809);this.prevFrame=-2147483648;this.tm.spinOn||this.setSync()},"~B");f(b,"homePosition",function(){this.evalString("reset spin")});c(b,"initialize",function(a,b){this.g=new JV.GlobalSettings(this,this.g,a);this.setStartupBooleans();this.setWidthHeightVar();this.haveDisplay&&(this.g.setB("_is2D",JV.Viewer.isJS&&!this.isWebGL),this.g.setB("_multiTouchClient",
this.acm.isMTClient()),this.g.setB("_multiTouchServer",this.acm.isMTServer()));this.cm.setDefaultColors(!1);this.setObjectColor("background","black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.am.setAnimationOn(!1);this.am.setAnimationFps(this.g.animationFps);this.sm.playAudio(null);this.sm.allowStatusReporting=this.g.statusReporting;this.setBooleanPropertyTok("antialiasDisplay",603979786,b?!0:this.g.antialiasDisplay);this.stm.resetLighting();
this.tm.setDefaultPerspective()},"~B,~B");c(b,"saveModelOrientation",function(){this.ms.saveModelOrientation(this.am.cmi,this.stm.getOrientation())});c(b,"restoreModelOrientation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!0)},"~N");c(b,"restoreModelRotation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!1)},"~N");c(b,"getGLmolView",function(){var a=this.tm,b=a.fixedRotationCenter,c=a.getRotationQ();return{center:b,quaternion:c,xtrans:a.xTranslationFraction,
ytrans:a.yTranslationFraction,scale:a.scalePixelsPerAngstrom,zoom:a.zmPctSet,cameraDistance:a.cameraDistance,pixelCount:a.screenPixelCount,perspective:a.perspectiveDepth,width:a.width,height:a.height}});c(b,"setRotationRadius",function(a,b){b&&(a=this.tm.setRotationRadius(a,!1));this.ms.setRotationRadius(this.am.cmi,a)&&this.g.setF("rotationRadius",a)},"~N,~B");c(b,"setCenterBitSet",function(a,b){this.isJmolDataFrame()||this.tm.setNewRotationCenter(0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):
null,b)},"JU.BS,~B");c(b,"setNewRotationCenter",function(a){this.isJmolDataFrame()||this.tm.setNewRotationCenter(a,!0)},"JU.P3");c(b,"navigate",function(a,b){this.isJmolDataFrame()||(this.tm.navigateKey(a,b),!this.tm.vibrationOn&&0!=a&&this.refresh(1,"Viewer:navigate()"))},"~N,~N");c(b,"move",function(a,b,c,e,g,j,f){this.tm.move(a,b,c,e,g,j,f);this.moveUpdate(j)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(b,"moveTo",function(a,b,c,e,g,j,f,l,s,m,p,n,r,u,v,w,y){this.haveDisplay||(b=0);this.setTainted(!0);
this.tm.moveTo(a,b,c,e,g,j,f,l,s,m,p,n,r,u,v,w,y)},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(b,"moveUpdate",function(a){0<a?this.requestRepaintAndWait("moveUpdate"):0==a&&this.setSync()},"~N");c(b,"navigatePt",function(a){this.tm.setNavigatePt(a);this.setSync()},"JU.P3");c(b,"navigateAxis",function(a,b){this.tm.navigateAxis(a,b);this.setSync()},"JU.V3,~N");c(b,"navTranslatePercent",function(a,b){this.isJmolDataFrame()||(this.tm.navTranslatePercentOrTo(0,
a,b),this.setSync())},"~N,~N");c(b,"zoomBy",function(a){this.tm.zoomBy(a);this.refresh(2,this.sm.syncingMouse?"Mouse: zoomBy "+a:"")},"~N");c(b,"zoomByFactor",function(a,b,c){this.tm.zoomByFactor(a,b,c);this.refresh(2,!this.sm.syncingMouse?"":"Mouse: zoomByFactor "+a+(2147483647==b?"":" "+b+" "+c))},"~N,~N,~N");c(b,"rotateXYBy",function(a,b){this.tm.rotateXYBy(a,b,null);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateXYBy "+a+" "+b:"")},"~N,~N");c(b,"spinXYBy",function(a,b,c){this.tm.spinXYBy(a,
b,c);0==a&&0==b||this.refresh(2,this.sm.syncingMouse?"Mouse: spinXYBy "+a+" "+b+" "+c:"")},"~N,~N,~N");c(b,"rotateZBy",function(a,b,c){this.tm.rotateZBy(a,b,c);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateZBy "+a+(2147483647==b?"":" "+b+" "+c):"")},"~N,~N,~N");c(b,"rotateSelected",function(a,b,c){this.isJmolDataFrame()||(this.tm.rotateXYBy(a,b,this.setMovableBitSet(c,!0)),this.refreshMeasures(!0),this.refresh(2,this.sm.syncingMouse?"Mouse: rotateMolecule "+a+" "+b:""))},"~N,~N,JU.BS");c(b,"setMovableBitSet",
function(a,b){null==a&&(a=this.bsA());a=JU.BSUtil.copy(a);JU.BSUtil.andNot(a,this.getMotionFixedAtoms(null,null));b&&!this.g.allowMoveAtoms&&(a=this.ms.getMoleculeBitSet(a));return this.movableBitSet=a},"JU.BS,~B");c(b,"translateXYBy",function(a,b){this.tm.translateXYBy(a,b);this.refresh(2,this.sm.syncingMouse?"Mouse: translateXYBy "+a+" "+b:"")},"~N,~N");f(b,"rotateFront",function(){this.tm.resetRotation();this.refresh(1,"Viewer:rotateFront()")});c(b,"translate",function(a,b,c,e){var g="\x00"==c?
b:"%"==c?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==c?10:1));if(null!=e){if(0==b)return;this.tm.setSelectedTranslation(e,a,g,b)}else switch(a.charCodeAt(0)){case 88:case 120:"\x00"==c?this.tm.translateToPercent("x",b):this.tm.translateXYBy(F(g),0);break;case 89:case 121:"\x00"==c?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,F(g));break;case 90:case 122:"\x00"==c?this.tm.translateToPercent("z",b):this.tm.translateZBy(F(g))}this.refresh(1,"Viewer:translate()")},"~S,~N,~S,JU.BS");
c(b,"slabByPixels",function(a){this.tm.slabByPercentagePoints(a);this.refresh(3,"slabByPixels")},"~N");c(b,"depthByPixels",function(a){this.tm.depthByPercentagePoints(a);this.refresh(3,"depthByPixels")},"~N");c(b,"slabDepthByPixels",function(a){this.tm.slabDepthByPercentagePoints(a);this.refresh(3,"slabDepthByPixels")},"~N");c(b,"finalizeTransformParameters",function(){this.tm.finalizeTransformParameters();this.gdata.setSlabAndZShade(this.tm.slabValue,this.tm.depthValue,this.tm.zShadeEnabled?this.tm.zSlabValue:
2147483647,this.tm.zDepthValue,this.g.zShadePower)});c(b,"getScalePixelsPerAngstrom",function(a){return this.tm.scalePixelsPerAngstrom*(a||!this.antialiased?1:0.5)},"~B");c(b,"setSpin",function(a,b){if(JU.PT.isOneOf(a,";x;y;z;fps;X;Y;Z;FPS;")){var c="x;y;z;fps;X;Y;Z;FPS".indexOf(a);switch(c){case 0:this.tm.setSpinXYZ(b,NaN,NaN);break;case 2:this.tm.setSpinXYZ(NaN,b,NaN);break;case 4:this.tm.setSpinXYZ(NaN,NaN,b);break;default:this.tm.setSpinFps(b);break;case 10:this.tm.setNavXYZ(b,NaN,NaN);break;
case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>c?"spin":"nav")+a,b)}},"~S,~N");c(b,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});c(b,"getOrientation",function(a,b,c,e){switch(a){case 1312817669:case 1814695966:case 1073741864:case 1111492629:case 1111492630:case 1111492631:case 134221850:null==c&&(c=this.bsA());if(c.isEmpty())return 1312817669==a?"0":1814695966==a||1073741864==a?null:new JU.Quat;
c=this.ms.getBoundBoxOrientation(a,c,e);return"best"===b&&1312817669!=a?c.div(this.tm.getRotationQ()):c;case 1073742034:return this.stm.getSavedOrientationText(b);default:return this.tm.getOrientationText(a,"best"===b)}},"~N,~S,JU.BS,~A");c(b,"getCurrentColorRange",function(){return this.cm.getPropertyColorRange()});c(b,"setDefaultColors",function(a){this.cm.setDefaultColors(a);this.g.setB("colorRasmol",a);this.g.setO("defaultColorScheme",a?"rasmol":"jmol")},"~B");c(b,"setElementArgb",function(a,
b){this.g.setO("=color "+JU.Elements.elementNameFromNumber(a),JU.Escape.escapeColor(b));this.cm.setElementArgb(a,b)},"~N,~N");f(b,"setVectorScale",function(a){this.g.setF("vectorScale",a);this.g.vectorScale=a},"~N");f(b,"setVibrationScale",function(a){this.tm.setVibrationScale(a);this.g.vibrationScale=a;this.g.setF("vibrationScale",a)},"~N");f(b,"setVibrationPeriod",function(a){Double.isNaN(a)&&(a=this.g.vibrationPeriod);this.tm.setVibrationPeriod(a);a=Math.abs(a);this.g.vibrationPeriod=a;this.g.setF("vibrationPeriod",
a)},"~N");c(b,"setObjectColor",function(a,b){null==b||0==b.length||this.setObjectArgb(a,JU.CU.getArgbFromString(b))},"~S,~S");c(b,"setObjectVisibility",function(a,b){var c=JV.StateManager.getObjectIdFromName(a);0<=c&&this.setShapeProperty(c,"display",b?Boolean.TRUE:Boolean.FALSE)},"~S,~B");c(b,"setObjectArgb",function(a,b){var c=JV.StateManager.getObjectIdFromName(a);if(0>c)a.equalsIgnoreCase("axes")&&(this.setObjectArgb("axis1",b),this.setObjectArgb("axis2",b),this.setObjectArgb("axis3",b));else{this.g.objColors[c]=
b;switch(c){case 0:this.gdata.setBackgroundArgb(b),this.cm.setColixBackgroundContrast(b)}this.g.setO(a+"Color",JU.Escape.escapeColor(b))}},"~S,~N");c(b,"setBackgroundImage",function(a,b){this.g.backgroundImageFileName=a;this.gdata.setBackgroundImage(b)},"~S,~O");c(b,"getObjectColix",function(a){a=this.g.objColors[a];return 0==a?this.cm.colixBackgroundContrast:JU.C.getColix(a)},"~N");f(b,"setColorBackground",function(a){this.setObjectColor("background",a)},"~S");f(b,"getBackgroundArgb",function(){return this.g.objColors[0]});
c(b,"setObjectMad10",function(a,b,c){var e=JV.StateManager.getObjectIdFromName(b.equalsIgnoreCase("axes")?"axis":b);if(!(0>e)){if(-2==c||-4==c){var g=c+3;c=this.getObjectMad10(e);0==c&&(c=g)}this.g.setB("show"+b,0!=c);this.g.objStateOn[e]=0!=c;0!=c&&(this.g.objMad10[e]=c,this.setShapeSize(a,c,null))}},"~N,~S,~N");c(b,"getObjectMad10",function(a){return this.g.objStateOn[a]?this.g.objMad10[a]:0},"~N");c(b,"setPropertyColorScheme",function(a,b,c){this.g.propertyColorScheme=a;a.startsWith("translucent ")&&
(b=!0,a=a.substring(12).trim());this.cm.setPropertyColorScheme(a,b,c)},"~S,~B,~B");c(b,"getLightingState",function(){return this.getStateCreator().getLightingState(!0)});c(b,"getColorPointForPropertyValue",function(a){return JU.CU.colorPtFromInt(this.gdata.getColorArgbOrGray(this.cm.ce.getColorIndex(a)),null)},"~N");c(b,"select",function(a,b,c,e){b&&(a=this.getUndeletedGroupAtomBits(a));this.slm.select(a,c,e);this.shm.setShapeSizeBs(1,2147483647,null,null);this.hasSelected=!0},"JU.BS,~B,~N,~B");f(b,
"setSelectionSet",function(a){this.selectStatus(a,!1,0,!0,!0)},"JU.BS");c(b,"selectBonds",function(a){this.shm.setShapeSizeBs(1,2147483647,null,a)},"JU.BS");c(b,"displayAtoms",function(a,b,c,e,g){c&&(a=this.getUndeletedGroupAtomBits(a));b?this.slm.display(this.ms,a,e,g):this.slm.hide(this.ms,a,e,g)},"JU.BS,~B,~B,~N,~B");c(b,"getUndeletedGroupAtomBits",function(a){a=this.ms.getAtoms(1086324742,a);JU.BSUtil.andNot(a,this.slm.bsDeleted);return a},"JU.BS");c(b,"reportSelection",function(a){this.selectionHalosEnabled&&
this.setTainted(!0);(this.isScriptQueued()||this.g.debugScript)&&this.scriptStatus(a)},"~S");c(b,"clearAtomSets",function(){this.slm.setSelectionSubset(null);this.definedAtomSets.clear();this.haveDisplay&&this.acm.exitMeasurementMode("clearAtomSets")});c(b,"getDefinedAtomSet",function(a){a=this.definedAtomSets.get(a.toLowerCase());return C(a,"JU.BS")?a:new JU.BS},"~S");f(b,"selectAll",function(){this.slm.selectAll(!1)});f(b,"clearSelection",function(){this.slm.clearSelection(!0);this.g.setB("hideNotSelected",
!1)});c(b,"bsA",function(){return this.slm.getSelectedAtoms()});f(b,"addSelectionListener",function(a){this.slm.addListener(a)},"J.api.JmolSelectionListener");f(b,"removeSelectionListener",function(a){this.slm.addListener(a)},"J.api.JmolSelectionListener");c(b,"getAtomBitSetEval",function(a,b){return this.allowScripting?this.getScriptManager().getAtomBitSetEval(a,b):new JU.BS},"J.api.JmolScriptEvaluator,~O");c(b,"processTwoPointGesture",function(a){this.mouse.processTwoPointGesture(a)},"~A");c(b,
"processMouseEvent",function(a,b,c,e,g){return this.mouse.processEvent(a,b,c,e,g)},"~N,~N,~N,~N,~N");c(b,"processKeyEvent",function(a){this.mouse.processKeyEvent(a)},"~O");c(b,"getRubberBandSelection",function(){return this.haveDisplay?this.acm.getRubberBand():null});c(b,"isBound",function(a,b){return this.haveDisplay&&this.acm.bnd(a,[b])},"~N,~N");c(b,"getCursorX",function(){return this.haveDisplay?this.acm.getCurrentX():0});c(b,"getCursorY",function(){return this.haveDisplay?this.acm.getCurrentY():
0});c(b,"getDefaultDirectory",function(){return this.g.defaultDirectory});c(b,"getLocalUrl",function(a){return this.apiPlatform.getLocalUrl(a)},"~S");c(b,"getFileAsString",function(a){return this.getAsciiFileOrNull(a)},"~S");f(b,"getBufferedInputStream",function(a){return this.fm.getBufferedInputStream(a)},"~S");c(b,"setLoadParameters",function(a,b){null==a&&(a=new java.util.Hashtable);a.put("vwr",this);0<this.g.atomTypes.length&&a.put("atomTypes",this.g.atomTypes);a.containsKey("lattice")||a.put("lattice",
this.g.ptDefaultLattice);this.g.applySymmetryToBonds&&a.put("applySymmetryToBonds",Boolean.TRUE);this.g.pdbGetHeader&&a.put("getHeader",Boolean.TRUE);this.g.pdbSequential&&a.put("isSequential",Boolean.TRUE);(this.g.legacyJavaFloat||this.g.doublePrecision)&&a.put("highPrecision",Boolean.TRUE);this.g.doublePrecision||a.put("lowPrecision",Boolean.TRUE);a.put("stateScriptVersionInt",Integer.$valueOf(this.stateScriptVersionInt));if(!a.containsKey("filter")){var c=this.g.defaultLoadFilter;0<c.length&&a.put("filter",
c)}c=b&&!this.g.appendNew&&0<this.ms.ac;a.put("baseAtomIndex",Integer.$valueOf(b?this.ms.ac:0));a.put("baseBondIndex",Integer.$valueOf(b?this.ms.bondCount:0));a.put("baseModelIndex",Integer.$valueOf(0==this.ms.ac?0:this.ms.mc+(c?-1:0)));c&&a.put("merging",Boolean.TRUE);return a},"java.util.Map,~B");f(b,"openFileAsyncSpecial",function(a,b){this.getScriptManager().openFileAsync(a,b,null)},"~S,~N");f(b,"openFileAsyncSpecialType",function(a,b,c){this.getScriptManager().openFileAsync(a,b,c)},"~S,~N,~S");
f(b,"openFile",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,a,null,null)},"~S");f(b,"openFiles",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,null,a,null)},"~A");c(b,"openReader",function(a,b,c){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(a,b,null,c)},"~S,~S,~O");f(b,"openDOM",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint("?","?",null,a)},"~O");c(b,"loadModelFromFileRepaint",function(a,b,c,e){a=this.loadModelFromFile(a,
b,c,e,!1,null,null,null,0," ");this.refresh(1,"loadModelFromFileRepaint");return a},"~S,~S,~A,~O");c(b,"loadModelFromFile",function(a,b,c,e,g,j,f,l,s,m){null==j&&(j=this.setLoadParameters(null,g));0!=s&&j.put("dataType",JS.T.nameOf(s));" "!==m&&j.put("concatenate",Boolean.TRUE);var p=this.fm.getFileInfo();if(null!=c){if(null==f){f=(new JU.SB).append("load files");for(a=0;a<c.length;a++)f.append(0==a||null==m?" ":m).append("/*file*/$FILENAME"+(a+1)+"$");0<l.length()&&f.append(" /*options*/ ").append(l.toString())}a=
System.currentTimeMillis();l=this.fm.createAtomSetCollectionFromFiles(c,this.setLoadParameters(j,g),g);a=System.currentTimeMillis()-a;JU.Logger.info("openFiles("+c.length+") "+a+" ms");c=j.get("fullPathNames");m=j.get("fileTypes");f=f.toString();for(a=0;a<c.length;a++)b=c[a],null!=m&&null!=m[a]&&(b=m[a]+"::"+b),f=JU.PT.rep(f,"$FILENAME"+(a+1)+"$",JU.PT.esc(JV.FileManager.fixDOSName(b)));f=(new JU.SB).append(f)}else if(null==e)null==f&&(f=(new JU.SB).append("load /*file*/$FILENAME$")),l=this.openFileFull(b,
g,j,f);else if(C(e,"java.io.Reader")||C(e,"java.io.BufferedInputStream")||JU.AU.isAB(e))l=this.fm.createAtomSetCollectionFromReader(a,b,e,this.setLoadParameters(j,g));else return"ERROR - invalid reader";if(0!=s)return this.fm.setFileInfo(p),this.loadAtomDataAndReturnError(l,s);if(j.containsKey("isData"))return l;null!=f&&"string"!=typeof l&&(b=j.get("fullPathName"),null==b&&(b=""),j.containsKey("loadScript")&&(f=j.get("loadScript")),j.put("loadScript",f=(new JU.SB).append(JU.PT.rep(f.toString(),"$FILENAME$",
JU.PT.esc(JV.FileManager.fixDOSName(b))))));return this.createModelSetAndReturnError(l,g,f,j)},"~S,~S,~A,~O,~B,java.util.Map,JU.SB,JU.SB,~N,~S");c(b,"setLigandModel",function(a,b){null==this.ligandModels&&(this.ligandModels=new java.util.Hashtable);this.ligandModels.put(a,b)},"~S,~S");c(b,"getLigandModel",function(a,b,c,e){if(null==a){if(null!=this.ligandModelSet)for(a=this.ligandModels.entrySet().iterator();a.hasNext();){var g=a.next();C(g.getValue(),Boolean)&&a.remove()}return null}a=a.$replace("\\",
"/");var j=b.equals("ligand_");a=0<=a.indexOf("/cif")?a:j?a.toUpperCase():a.substring(a.lastIndexOf("/")+1);null==this.ligandModelSet&&(this.ligandModelSet=new java.util.Hashtable);this.ligandModelSet.put(a,Boolean.TRUE);null==this.ligandModels&&(this.ligandModels=new java.util.Hashtable);var f=a.indexOf("|");0<=f&&(a=a.substring(a.indexOf("|")+1));var l=null==e?this.ligandModels.get(a):null,g=null;if(C(l,Boolean))return null;if(null==l&&(null==e||0<=f))l=this.ligandModels.get(a+c);var f=!1,s=null==
l;if(s){if(j){g=this.setLoadFormat(!1,"#"+a,"#",!1);if(0==g.length)return null;this.scriptEcho("fetching "+g);l=this.getFileAsString3(g,!1,null)}else this.scriptEcho("fetching "+b),l=this.getFileAsString3(b,!1,null),e=null==e?-1:l.indexOf(e),0<=e&&(l=l.substring(0,e));(f=0==l.indexOf("java."))||this.ligandModels.put(a+c,l)}if(!j)return s||this.scriptEcho(b+" loaded from cache"),l;!f&&"string"==typeof l&&(b=l,0!=b.length&&(c=new java.util.Hashtable,c.put("modelOnly",Boolean.TRUE),l=this.getModelAdapter().getAtomSetCollectionReader("ligand",
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null==(j=this.getDBID("structure from NCI/CADD")))return null;if(b.equals("$"))try{j=this.getOpenSmiles(this.bsA())}catch(n){if(!D(n,Exception))throw n;}else if(b.startsWith("$$")){j=j.substring(1);if(0==j.length)try{j=this.getOpenSmiles(this.bsA())}catch(r){if(!D(r,Exception))throw r;}g=JU.PT.rep(this.g.smilesUrlFormat,"get3d","get2d");return JU.PT.formatStringS(g,"FILE",JU.PT.escapeUrl(j))}case 77:case 78:case 50:case 73:case 75:case 83:case 84:case 47:j=JU.PT.escapeUrl(j);switch(c.charCodeAt(0)){case 77:case 78:g=
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this.getAtomInfoXYZ(a,2));if(this.hoverEnabled&&!(null!=this.eval&&this.isScriptExecuting()||a==this.hoverAtomIndex||0==this.g.hoverDelayMs||!this.slm.isInSelectionSubset(a))){var c=b?J.i18n.GT.$("Drag to move label"):this.isModelKitOpen()||this.isModelkitPickingActive()?this.getModelkit(!1).setProperty("hoverLabel",Integer.$valueOf(a)):null;this.shm.loadShape(35);null!=c&&(!b||this.ms.at[a].isVisible(512))&&this.setShapeProperty(35,"specialLabel",c);this.setShapeProperty(35,"text",this.hoverText=
null);this.setShapeProperty(35,"target",Integer.$valueOf(this.hoverAtomIndex=a));this.refresh(3,"hover on atom")}},"~N,~B");c(b,"isModelkitPickingActive",function(){if(32==this.acm.getAtomPickingMode())return!0;switch(this.acm.getBondPickingMode()){case 34:case 33:case 8:case 35:return this.g.bondPicking}return!1});c(b,"isModelkitPickingRotateBond",function(){return 34==this.acm.getBondPickingMode()});c(b,"hoverOnPt",function(a,b,c,e,g){null!=this.eval&&this.isScriptExecuting()||(this.g.setO("_hoverLabel",
c),null!=e&&null!=g&&(this.g.setO("_objecthovered",e),this.g.setI("_atomhovered",-1),this.g.setUserVariable("hovered",JS.SV.getVariable(g)),this.sm.haveHoverCallback()&&this.sm.setStatusObjectHovered(e,c,g)),this.hoverEnabled&&(this.shm.loadShape(35),this.gdata.antialiasEnabled&&(a<<=1,b<<=1),this.setShapeProperty(35,"xy",JU.P3i.new3(a,b,0)),this.setShapeProperty(35,"target",null),this.setShapeProperty(35,"specialLabel",null),this.setShapeProperty(35,"text",c),this.hoverAtomIndex=-1,this.hoverText=
c,this.refresh(3,"hover on point")))},"~N,~N,~S,~S,JU.T3");c(b,"hoverOff",function(){try{if((this.isModelKitOpen()||null!=this.modelkit&&this.modelkit.wasRotating())&&!this.isModelkitPickingRotateBond()&&this.highlight(null),this.hoverEnabled){var a=null!=this.hoverText||0<=this.hoverAtomIndex;0<=this.hoverAtomIndex&&(this.setShapeProperty(35,"target",null),this.hoverAtomIndex=-1);null!=this.hoverText&&(this.setShapeProperty(35,"text",null),this.hoverText=null);this.setShapeProperty(35,"specialLabel",
null);a&&this.refresh(3,"hover off")}}catch(b){if(!D(b,Exception))throw b;}});f(b,"setDebugScript",function(a){this.g.debugScript=a;this.g.setB("debugScript",a);null!=this.eval&&this.eval.setDebugging()},"~B");c(b,"clearClickCount",function(){this.setTainted(!0)});c(b,"setCursor",function(a){if(!this.$isKiosk&&!(this.currentCursor==a||this.multiTouch||!this.haveDisplay))this.apiPlatform.setCursor(this.currentCursor=a,this.display)},"~N");c(b,"setPickingMode",function(a,b){if(this.haveDisplay){var c=
this.acm.getAtomPickingMode();this.showSelected=!1;var e=null;if(null!=a){var g=a.indexOf("_");0<=g&&(e=a.substring(g+1),a=a.substring(0,g));b=JV.ActionManager.getPickingMode(a)}0>b&&(b=1);this.acm.setPickingMode(b);g=JV.ActionManager.getPickingModeName(this.acm.getAtomPickingMode());this.g.setO("picking",g);if(null!=this.modelkit)switch(this.modelkit.setProperty("atompickingmode",g),this.acm.setPickingMode(b),b){case 1:b!=c&&this.setModelKitMode(!1);break;case 8:case 35:this.modelkit.setProperty("bondpickingmode",
a.toLowerCase())}if(!(null==e||0==e.length))switch(e=Character.toUpperCase(e.charAt(0))+(1==e.length?"":e.substring(1,2)),b){case 32:this.getModelkit(!1).setProperty("atomType",e);break;case 33:this.setBooleanPropertyTok("bondPicking",603979814,!0);this.getModelkit(!1).setProperty("bondType",e);break;default:JU.Logger.error("Bad picking mode: "+a+"_"+e)}}},"~S,~N");c(b,"getPickingMode",function(){return this.haveDisplay?this.acm.getAtomPickingMode():0});c(b,"setPickingStyle",function(a,b){this.haveDisplay&&
(null!=a&&(b=JV.ActionManager.getPickingStyleIndex(a)),0>b&&(b=0),this.acm.setPickingStyle(b),this.g.setO("pickingStyle",JV.ActionManager.getPickingStyleName(this.acm.getPickingStyle())))},"~S,~N");c(b,"getDrawHover",function(){return this.haveDisplay&&this.g.drawHover});c(b,"getAtomInfo",function(a){null==this.ptTemp&&(this.ptTemp=new JU.P3);return 0<=a?this.ms.getAtomInfo(a,null,this.ptTemp):this.shm.getShapePropertyIndex(6,"pointInfo",-a)},"~N");c(b,"getAtomInfoXYZ",function(a,b){var c=this.ms.at[a];
if(4==b)return this.getChimeMessenger().getInfoXYZ(c);null==this.ptTemp&&(this.ptTemp=new JU.P3);return c.getIdentityXYZ(this.ptTemp,b)},"~N,~N");c(b,"setSync",function(){this.sm.doSync()&&this.sm.setSync(null)});f(b,"setJmolCallbackListener",function(a){this.sm.cbl=a},"J.api.JmolCallbackListener");f(b,"setJmolStatusListener",function(a){this.sm.cbl=this.sm.jsl=a},"J.api.JmolStatusListener");c(b,"getStatusChanged",function(a){return null==a?null:this.sm.getStatusChanged(a)},"~S");c(b,"menuEnabled",
function(){return!this.g.disablePopupMenu&&null!=this.getPopupMenu()});c(b,"setStatusDragDropped",function(a,b,c,e,g){0==a&&(this.g.setO("_fileDropped",e),this.g.setUserVariable("doDrop",JS.SV.vT),this.g.setUserVariable("dropFileType",JS.SV.newS("")),this.g.setUserVariable("dropFileName",JS.SV.newS(e)));a=this.sm.setStatusDragDropped(a,b,c,e,g);b=this.getP("dropFileType").toString();0<b.length&&null!=g&&(g[0]=b);return!a||this.getP("doDrop").toString().equals("true")},"~N,~N,~N,~S,~A");c(b,"setStatusResized",
function(a,b){this.sm.setStatusResized(a,b)},"~N,~N");c(b,"scriptStatus",function(a){this.setScriptStatus(a,"",0,null)},"~S");c(b,"scriptStatusMsg",function(a,b){this.setScriptStatus(a,b,0,null)},"~S,~S");c(b,"setScriptStatus",function(a,b,c,e){this.sm.setScriptStatus(a,b,c,e)},"~S,~S,~N,~S");f(b,"showUrl",function(a){if(null!=a){if(0>a.indexOf(":")){var b=this.fm.getAppletDocumentBase();""===b&&(b=this.fm.getFullPathName(!1));0<=b.indexOf("/")?b=b.substring(0,b.lastIndexOf("/")+1):0<=b.indexOf("\\")&&
(b=b.substring(0,b.lastIndexOf("\\")+1));a=b+a}JU.Logger.info("showUrl:"+a);this.sm.showUrl(a)}},"~S");c(b,"setMeshCreator",function(a){this.shm.loadShape(24);this.setShapeProperty(24,"meshCreator",a)},"~O");c(b,"showConsole",function(a){if(this.haveDisplay)try{null==this.appConsole&&a&&this.getConsole(),this.appConsole.setVisible(!0)}catch(b){}},"~B");c(b,"getConsole",function(){this.getProperty("DATA_API","getAppConsole",Boolean.TRUE);return this.appConsole});f(b,"getParameter",function(a){return this.getP(a)},
"~S");c(b,"getP",function(a){return this.g.getParameter(a,!0)},"~S");c(b,"getPOrNull",function(a){return this.g.getParameter(a,!1)},"~S");c(b,"unsetProperty",function(a){a=a.toLowerCase();(a.equals("all")||a.equals("variables"))&&this.fm.setPathForAllFiles("");this.g.unsetUserVariable(a)},"~S");f(b,"notifyStatusReady",function(a){System.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));a||this.dispose();this.sm.setStatusAppletReady(this.fullName,a)},"~B");f(b,"getBooleanProperty",
function(a){a=a.toLowerCase();if(this.g.htBooleanParameterFlags.containsKey(a))return this.g.htBooleanParameterFlags.get(a).booleanValue();if(a.endsWith("p!")){if(null==this.acm)return!1;var b=this.acm.getPickingState().toLowerCase();a=a.substring(0,a.length-2)+";";return 0<=b.indexOf(a)}if(a.equalsIgnoreCase("executionPaused"))return null!=this.eval&&this.eval.isPaused();if(a.equalsIgnoreCase("executionStepping"))return null!=this.eval&&this.eval.isStepping();if(a.equalsIgnoreCase("haveBFactors"))return null!=
this.ms.getBFactors();if(a.equalsIgnoreCase("colorRasmol"))return this.cm.isDefaultColorRasmol;if(a.equalsIgnoreCase("frank"))return this.getShowFrank();if(a.equalsIgnoreCase("spinOn"))return this.tm.spinOn;if(a.equalsIgnoreCase("isNavigating"))return this.tm.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.selectionHalosEnabled;if(this.g.htUserVariables.containsKey(a)){b=this.g.getUserVariable(a);if(1073742335==b.tok)return!0;if(1073742334==b.tok)return!1}JU.Logger.error("vwr.getBooleanProperty("+
a+") - unrecognized");return!1},"~S");f(b,"getInt",function(a){switch(a){case 553648132:return this.am.animationFps;case 553648139:return this.g.dotDensity;case 553648140:return this.g.dotScale;case 553648142:return this.g.helixStep;case 553648145:return this.g.infoFontSize;case 553648147:return this.g.labelPointerWidth;case 553648149:return this.g.meshScale;case 553648150:return this.g.minimizationReportSteps;case 553648153:return this.g.minPixelSelRadius;case 553648154:return this.g.percentVdwAtom;
case 553648157:return this.g.pickingSpinRate;case 553648166:return this.g.ribbonAspectRatio;case 536870922:return this.g.scriptDelay;case 553648152:return this.g.minimizationMaxAtoms;case 553648170:return this.g.smallMoleculeMaxAtoms;case 553648183:return this.g.strutSpacing;case 553648184:return this.stm.getUndoMax();case 553648185:return this.g.vectorTrail}JU.Logger.error("viewer.getInt("+JS.T.nameOf(a)+") - not listed");return 0},"~N");c(b,"getDelayMaximumMs",function(){return this.haveDisplay?
this.g.delayMaximumMs:1});c(b,"getHermiteLevel",function(){return this.tm.spinOn&&0<this.g.hermiteLevel?0:this.g.hermiteLevel});c(b,"getHoverDelay",function(){return this.isModelKitOpen()||this.isModelkitPickingActive()||this.getDrawHover()?20:this.g.hoverDelayMs});f(b,"getBoolean",function(a){switch(a){case 603979970:return this.g.useMinimizationThread;case 603979891:return this.g.nboCharges;case 603979856:return this.g.hiddenLinesDashed;case 1073742086:return this.ms.getMSInfoB(JV.JC.getBoolName(4));
case 603979802:return this.g.autoplayMovie;case 603979797:return!this.headless&&this.g.allowAudio;case 603979780:return this.g.allowGestures;case 603979784:return this.g.allowMultiTouch;case 603979785:return this.g.allowRotateSelected;case 603979792:return this.g.appendNew;case 603979794:return this.g.applySymmetryToBonds;case 603979796:return this.g.atomPicking;case 603979798:return this.g.autoBond;case 603979800:return this.g.autoFps;case 603979806:return this.g.axesOrientationRasmol;case 603979811:return this.g.cartoonSteps;
case 603979810:return this.g.cartoonBlocks;case 603979821:return this.g.checkCIR;case 603979812:return this.g.bondModeOr;case 603979815:return this.g.cartoonBaseEdges;case 603979816:return this.g.cartoonFancy;case 603979817:return this.g.cartoonLadders;case 603979818:return this.g.cartoonRibose;case 603979819:return this.g.cartoonRockets;case 603979822:return this.g.chainCaseSensitive||this.chainCaseSpecified;case 603979823:return this.g.cipRule6Full;case 603979825:return this.g.debugScript;case 603979826:return this.g.defaultStructureDSSP;
case 603979827:return this.g.disablePopupMenu;case 603979828:return this.g.displayCellParameters;case 603979830:return this.g.dotSurface;case 603979829:return this.g.dotsSelectedOnly;case 603979831:return this.g.doublePrecision;case 603979834:return this.g.drawPicking;case 603979844:return this.g.fontCaching;case 603979845:return this.g.fontScaling;case 603979847:return this.g.forceAutoBond;case 603979848:return!1;case 603979850:return this.g.greyscaleRendering;case 603979852:return this.g.hbondsBackbone;
case 603979853:return this.g.hbondsRasmol;case 603979854:return this.g.hbondsSolid;case 1612709894:return this.g.rasmolHeteroSetting;case 603979858:return this.g.hideNameInPopup;case 603979864:return this.g.highResolutionFlag;case 1612709900:return this.g.rasmolHydrogenSetting;case 603979867:return this.g.isosurfaceKey;case 603979869:return this.g.jmolInJSpecView;case 603979870:return this.g.justifyMeasurements;case 603979872:return this.g.legacyAutoBonding;case 603979873:return this.g.legacyHAddition;
case 603979874:return this.g.legacyJavaFloat;case 603979876:return this.g.logGestures;case 603979877:return this.g.measureAllModels;case 603979878:return this.g.measurementLabels;case 603979879:return this.g.messageStyleChime;case 603983903:return this.g.modelKitMode;case 603979886:return this.g.multipleBondBananas;case 603979889:return this.g.navigationMode;case 603979890:return this.g.navigationPeriodic;case 603979893:return this.g.partialDots;case 603979894:return this.g.pdbAddHydrogens;case 603979896:return this.g.pdbSequential;
case 603979898:return this.g.preserveState;case 603979900:return this.refreshing;case 603979901:return this.g.ribbonBorder;case 603979902:return this.g.rocketBarrels;case 603979892:return this.g.noDelay;case 603979906:return this.g.selectAllModels;case 603979920:return this.g.showHiddenSelectionHalos;case 603979922:return this.g.showHydrogens;case 603979926:return this.g.showMeasurements;case 603979927:return this.g.showModVecs;case 603979928:return this.g.showMultipleBonds;case 603979934:return this.g.showTiming;
case 603979937:return this.g.showUnitCellDetails;case 603979939:return this.g.slabByAtom;case 603979940:return this.g.slabByMolecule;case 603979944:return this.g.smartAromatic;case 603979948:return this.g.dotSolvent;case 603979952:return this.g.ssbondsBackbone;case 603979955:return this.g.strutsMultiple;case 603979960:return this.g.testFlag1;case 603979962:return this.g.testFlag2;case 603979964:return this.g.testFlag3;case 603979965:return this.g.testFlag4;case 603979966:return this.g.traceAlpha;
case 603979967:return this.g.translucent;case 603979968:return this.g.twistedSheets;case 603979972:return this.g.vectorsCentered;case 603979973:return this.g.vectorSymmetry;case 603979975:return this.g.waitForMoveTo;case 603979978:return this.g.zeroBasedXyzRasmol}JU.Logger.error("viewer.getBoolean("+JS.T.nameOf(a)+") - not listed");return!1},"~N");c(b,"allowEmbeddedScripts",function(){return this.g.allowEmbeddedScripts&&!this.isPreviewOnly});c(b,"getDragSelected",function(){return this.g.dragSelected&&
!this.g.modelKitMode});c(b,"getBondsPickable",function(){return this.g.bondPicking||this.isModelKitOpen()&&this.getModelkitPropertySafely("isMolecular")===Boolean.TRUE||this.isModelkitPickingActive()});c(b,"isModelKitOpen",function(){return this.g.modelKitMode&&null!=this.modelkit&&!this.modelkit.isHidden()});c(b,"useMinimizationThread",function(){return this.g.useMinimizationThread&&!this.autoExit});f(b,"getFloat",function(a){switch(a){case 1153433601:return this.g.particleRadius;case 570425345:return this.g.axesOffset;
case 570425346:return this.g.axesScale;case 570425348:return this.g.bondTolerance;case 570425353:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425354:return this.g.dipoleScale;case 570425355:return this.g.drawFontSize;case 570425357:return this.g.exportScale;case 570425359:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondHXDistanceMaximum;case 570425360:return this.g.hbondNODistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;
case 570425364:return this.g.minBondDistance;case 1275072532:return this.g.modulationScale;case 570425370:return this.g.multipleBondSpacing;case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.modelRadius;case 570425392:return this.g.sheetSmoothing;case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;
case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;case 1648361473:return this.g.vectorScale;case 570425412:return this.g.vibrationPeriod;case 570425347:return this.g.cartoonBlockHeight}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");f(b,"setStringProperty",function(a,b){if(!(null==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setO(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 603979776:this.setBooleanPropertyTok(a,
c,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,c,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,c,JU.PT.parseFloat(b));break;default:this.setStringPropertyTok(a,c,b)}}},"~S,~S");c(b,"setStringPropertyTok",function(a,b,c){switch(b){case 545259567:this.g.macroDirectory=c=null==c||0==c.length?"https://chemapps.stolaf.edu/jmol/macros":c;this.macros=null;break;case 545259570:this.g.nihResolverFormat=c;break;case 545259521:this.setAnimationMode(c);
return;case 545259569:this.g.nmrPredictFormat=c;break;case 545259548:this.g.defaultDropScript=c;break;case 545259572:c=this.fm.setPathForAllFiles(c);break;case 545259558:this.setUnits(c,!1);return;case 545259560:this.g.forceField.equals(c)||(this.g.forceField=c="UFF".equalsIgnoreCase(c)?"UFF":"UFF2D".equalsIgnoreCase(c)?"UFF2D":"MMFF2D".equalsIgnoreCase(c)?"MMFF2D":"MMFF",this.minimizer=null);break;case 545259571:this.g.nmrUrlFormat=c;break;case 545259568:this.setUnits(c,!0);return;case 545259565:this.g.pdbLoadLigandFormat=
c;break;case 545259543:this.g.defaultLabelPDB=c;break;case 545259544:this.g.defaultLabelXYZ=c;break;case 545259549:this.g.defaultLoadFilter=c;break;case 545259566:c=this.getOutputManager().setLogFile(c);if(null==c)return;break;case 545259559:break;case 545259524:this.g.atomTypes=c;break;case 545259538:break;case 545259576:this.g.pickLabel=c;break;case 545259580:this.g.quaternionFrame=2==c.length&&c.startsWith("R")?c.substring(0,2):""+(c.toLowerCase()+"p").charAt(0);JU.PT.isOneOf(this.g.quaternionFrame,
"RC;RP;a;b;c;n;p;q;x;")||(this.g.quaternionFrame="p");this.ms.haveStraightness=!1;break;case 545259555:this.setVdwStr(c);return;case 545259563:new J.i18n.GT(this,c);b=J.i18n.GT.getLanguage();this.modelkit=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);c=J.i18n.GT.getLanguage();break;case 545259564:this.g.loadFormat=c;break;case 545259534:this.setObjectColor("background",c);return;case 545259528:this.setObjectColor("axis1",
c);return;case 545259530:this.setObjectColor("axis2",c);return;case 545259532:this.setObjectColor("axis3",c);return;case 545259536:this.setObjectColor("boundbox",c);return;case 545259586:this.setObjectColor("unitcell",c);return;case 545259578:this.setPropertyColorScheme(c,!1,!1);break;case 545259562:this.shm.loadShape(35);this.setShapeProperty(35,"atomLabel",c);break;case 545259547:this.g.defaultDistanceLabel=c;break;case 545259542:this.g.defaultAngleLabel=c;break;case 545259554:this.g.defaultTorsionLabel=
c;break;case 545259550:this.g.defaultLoadScript=c;break;case 545259522:this.fm.setAppletProxy(c);break;case 545259546:null==c&&(c="");c=c.$replace("\\","/");this.g.defaultDirectory=c;break;case 545259561:this.g.helpPath=c;break;case 545259552:!c.equalsIgnoreCase("RasMol")&&!c.equalsIgnoreCase("PyMOL")&&(c="Jmol");this.setDefaultsType(c);break;case 545259545:this.setDefaultColors(c.equalsIgnoreCase("rasmol"));return;case 545259573:this.setPickingMode(c,0);return;case 545259574:this.setPickingStyle(c,
0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==c.length||c.equalsIgnoreCase("none")?null:c);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,c));return}}this.g.setO(a,c)},"~S,~N,~S");f(b,"setFloatProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setF(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,
c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 553648128:this.setIntPropertyTok(a,c,F(b));break;case 570425344:if(Float.isNaN(b))break;default:this.setFloatPropertyTok(a,c,b)}}},"~S,~N");c(b,"setFloatPropertyTok",function(a,b,c){switch(b){case 570425347:this.g.cartoonBlockHeight=c;break;case 570425366:this.ms.setModulation(null,!1,null,!1);this.g.modulationScale=c=Math.max(0.1,c);this.ms.setModulation(null,!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(c);
break;case 570425355:this.g.drawFontSize=c;this.shm.setShapePropertyBs(22,"font",null,null);break;case 570425357:this.g.exportScale=c;break;case 570425403:this.g.starWidth=c;break;case 570425369:this.g.multipleBondRadiusFactor=c;break;case 570425370:this.g.multipleBondSpacing=c;break;case 570425393:this.tm.setSlabRange(c);break;case 570425365:this.g.minimizationCriterion=c;break;case 570425358:this.haveDisplay&&this.acm.setGestureSwipeFactor(c);break;case 570425367:this.haveDisplay&&this.acm.setMouseDragFactor(c);
break;case 570425368:this.haveDisplay&&this.acm.setMouseWheelFactor(c);break;case 570425408:this.g.strutLengthMaximum=c;break;case 570425406:this.g.strutDefaultRadius=c;break;case 570425376:this.setSpin("X",F(c));break;case 570425378:this.setSpin("Y",F(c));break;case 570425380:this.setSpin("Z",F(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",F(c));break;case 570425363:this.g.loadAtomDataTolerance=c;break;case 570425359:this.g.hbondsAngleMinimum=c;break;case 570425361:this.g.hbondHXDistanceMaximum=
c;break;case 570425360:this.g.hbondNODistanceMaximum=c;break;case 570425382:this.g.pointGroupDistanceTolerance=c;break;case 570425384:this.g.pointGroupLinearTolerance=c;break;case 570425356:this.g.ellipsoidAxisDiameter=c;break;case 570425398:this.setSpin("x",F(c));break;case 570425400:this.setSpin("y",F(c));break;case 570425402:this.setSpin("z",F(c));break;case 570425396:this.setSpin("fps",F(c));break;case 570425352:this.g.defaultDrawArrowScale=c;break;case 570425353:this.g.defaultTranslucent=c;break;
case 570425345:this.setAxesScale(b,c);break;case 570425346:this.setAxesScale(b,c);break;case 570425416:this.tm.visualRangeAngstroms=c;this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(c);break;case 570425374:this.g.navigationSpeed=c;break;case 570425373:this.tm.setNavigationSlabOffsetPercent(c);break;case 570425350:this.tm.setCameraDepthPercent(c,!1);this.refresh(1,"set cameraDepth");return;case 570425388:this.setRotationRadius(c,!0);return;case 570425362:this.g.hoverDelayMs=
F(1E3*c);break;case 570425392:this.g.sheetSmoothing=c;break;case 570425354:c=JV.Viewer.checkFloatRange(c,-10,10);this.g.dipoleScale=c;break;case 570425404:this.tm.setStereoDegrees(c);break;case 1648361473:this.setVectorScale(c);return;case 570425412:this.setVibrationPeriod(c);return;case 570425414:this.setVibrationScale(c);return;case 570425348:this.setBondTolerance(c);return;case 570425364:this.setMinBondDistance(c);return;case 570425390:this.tm.setScaleAngstromsPerInch(c);break;case 570425394:c=
JV.Viewer.checkFloatRange(c,0,10);this.g.solventProbeRadius=c;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newF(c));return}}this.g.setF(a,c)},"~S,~N,~N");f(b,"setIntProperty",function(a,b){if(!(-2147483648==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setI(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,
c,0!=b);break;case 570425344:this.setFloatPropertyTok(a,c,b);break;default:this.setIntPropertyTok(a,c,b)}}},"~S,~N");c(b,"setIntPropertyTok",function(a,b,c){switch(b){case 553648150:this.g.minimizationReportSteps=Math.min(Math.max(c,1),20);break;case 553648184:this.stm.setUndoMax(c);break;case 553648147:this.g.labelPointerWidth=c;break;case 553648152:this.g.minimizationMaxAtoms=c;break;case 553648145:this.g.infoFontSize=Math.max(0,c);break;case 553648167:case 553648144:case 553648168:c=this.eval.setStatic(b,
c);break;case 553648185:this.g.vectorTrail=c;break;case 553648136:c=0==c?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=c;break;case 553648135:this.gdata.setCelPower(c);break;case 553648129:this.gdata.setAmbientOcclusion(c);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(c,0),10);break;case 553648149:this.g.meshScale=c;break;case 553648153:this.g.minPixelSelRadius=c;break;case 553648146:this.g.isosurfacePropertySmoothingPower=c;break;case 553648165:this.g.repaintWaitMs=c;break;case 553648170:this.g.smallMoleculeMaxAtoms=
c;break;case 553648151:this.g.minimizationSteps=c;break;case 553648183:this.g.strutSpacing=c;break;case 553648156:c=JV.Viewer.checkIntRange(c,0,1E3);this.gdata.setPhongExponent(c);break;case 553648142:this.g.helixStep=c;this.ms.haveStraightness=!1;break;case 553648140:this.g.dotScale=c;break;case 553648139:this.g.dotDensity=c;break;case 553648137:this.g.delayMaximumMs=c;break;case 553648148:JU.Logger.setLogLevel(c);JU.Logger.info("logging level set to "+c);this.g.setI("logLevel",c);null!=this.eval&&
this.eval.setDebugging();return;case 553648133:this.setAxesMode(2==c?603979808:1==c?603979804:603979809);return;case 553648178:this.setStrandCount(0,c);return;case 553648182:this.setStrandCount(12,c);return;case 553648180:this.setStrandCount(13,c);return;case 553648155:return;case 536870922:this.g.scriptDelay=c;break;case 553648176:c=0>c?JV.Viewer.checkIntRange(c,-10,-1):JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPower(c);break;case 553648172:c=JV.Viewer.checkIntRange(-c,-10,-1);this.gdata.setSpecularPower(c);
break;case 553648134:this.setMarBond(c);return;case 536870924:this.setBooleanPropertyTok(a,b,1==c);return;case 553648174:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPercent(c);break;case 553648138:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setDiffusePercent(c);break;case 553648130:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setAmbientPercent(c);break;case 553648186:this.tm.zDepthToPercent(c);break;case 553648188:this.tm.zSlabToPercent(c);break;case 554176526:this.tm.depthToPercent(c);
break;case 554176565:this.tm.slabToPercent(c);break;case 553648190:this.g.zShadePower=c=Math.max(c,0);break;case 553648166:this.g.ribbonAspectRatio=c;break;case 553648157:this.g.pickingSpinRate=1>c?1:c;break;case 553648132:this.setAnimationFps(c);return;case 553648154:this.setPercentVdwAtom(c);break;case 553648143:this.g.hermiteLevel=c;break;case 553648141:case 553648161:case 553648160:case 553648162:case 553648164:break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a)){this.g.setUserVariable(a,
JS.SV.newI(c));return}}this.g.setI(a,c)},"~S,~N,~N");b.checkIntRange=c(b,"checkIntRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");b.checkFloatRange=c(b,"checkFloatRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");f(b,"setBooleanProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setB(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,"");break;case 553648128:this.setIntPropertyTok(a,c,b?1:0);break;
case 570425344:this.setFloatPropertyTok(a,c,b?1:0);break;default:this.setBooleanPropertyTok(a,c,b)}}},"~S,~B");c(b,"setBooleanPropertyTok",function(a,b,c){var e=!0;switch(b){case 603979831:c=(new Boolean(c&JV.Viewer.isJS)).valueOf();this.g.doublePrecision=c;JV.Viewer.isHighPrecision=this.g.doublePrecision;this.setBooleanPropertyTok("legacyJavaFloat",603979874,c);break;case 603979821:(this.g.checkCIR=c)&&this.checkCIR(!0);break;case 603979823:this.g.cipRule6Full=c;break;case 603979802:this.g.autoplayMovie=
c;break;case 603979797:c=!1;this.g.allowAudio=c;break;case 603979892:this.g.noDelay=c;break;case 603979891:this.g.nboCharges=c;break;case 603979856:this.g.hiddenLinesDashed=c;break;case 603979886:this.g.multipleBondBananas=c;break;case 603979884:this.g.modulateOccupancy=c;break;case 603979874:if(c||!this.g.doublePrecision)this.g.legacyJavaFloat=c;c=this.g.legacyJavaFloat;break;case 603979927:this.g.showModVecs=c;break;case 603979937:this.g.showUnitCellDetails=c;break;case 603979848:e=!1;break;case 603979972:this.g.vectorsCentered=
c;break;case 603979810:this.g.cartoonBlocks=c;break;case 603979811:this.g.cartoonSteps=c;break;case 603979818:this.g.cartoonRibose=c;break;case 603979838:this.g.ellipsoidArrows=c;break;case 603979967:this.g.translucent=c;break;case 603979817:this.g.cartoonLadders=c;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=c;b!=c&&this.checkCoordinatesChanged();break;case 603979820:this.gdata.setCel(c);break;case 603979816:this.g.cartoonFancy=c;break;case 603979934:this.g.showTiming=c;break;
case 603979973:this.g.vectorSymmetry=c;break;case 603979867:this.g.isosurfaceKey=c;break;case 603979893:this.g.partialDots=c;break;case 603979872:this.g.legacyAutoBonding=c;break;case 603979826:this.g.defaultStructureDSSP=c;break;case 603979835:this.g.dsspCalcHydrogen=c;break;case 603979782:(this.g.allowModelkit=c)||this.setModelKitMode(!1);break;case 603983903:this.setModelKitMode(c);break;case 603979887:this.g.multiProcessor=c&&1<JV.Viewer.nProcessors;break;case 603979885:this.g.monitorEnergy=c;
break;case 603979853:this.g.hbondsRasmol=c;break;case 603979880:this.g.minimizationRefresh=c;break;case 603979881:this.g.minimizationSilent=c;break;case 603979866:c&&(this.$isKiosk=!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));break;case 603979975:this.g.waitForMoveTo=c;break;case 603979875:this.g.logCommands=!0;break;case 603979876:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=c;break;case 603979898:this.g.preserveState=
c;this.ms.setPreserveState(c);this.undoMoveAction(4165,-2);break;case 603979955:this.g.strutsMultiple=c;break;case 603979843:break;case 603979939:this.g.slabByAtom=c;break;case 603979940:this.g.slabByMolecule=c;break;case 603979903:this.g.saveProteinStructureState=c;break;case 603979780:this.g.allowGestures=c;break;case 603979865:this.g.imageState=c;break;case 603979970:this.g.useMinimizationThread=c;break;case 603979781:this.g.allowKeyStrokes=c;break;case 603979832:this.g.dragSelected=c;this.showSelected=
!1;break;case 603979924:this.g.showKeyStrokes=c;break;case 603979844:this.g.fontCaching=c;break;case 603979796:this.g.atomPicking=c;break;case 603979814:this.highlight(null);this.g.bondPicking=c;break;case 603979906:(this.g.selectAllModels=c)?this.slm.setSelectionSubset(null):this.am.setSelectAllSubset(!1);break;case 603979879:this.g.messageStyleChime=c;break;case 603979896:this.g.pdbSequential=c;break;case 603979894:this.g.pdbAddHydrogens=c;break;case 603979895:this.g.pdbGetHeader=c;break;case 603979839:this.g.ellipsoidAxes=
c;break;case 603979837:this.g.ellipsoidArcs=c;break;case 603979840:this.g.ellipsoidBall=c;break;case 603979841:this.g.ellipsoidDots=c;break;case 603979842:this.g.ellipsoidFill=c;break;case 603979845:this.g.fontScaling=c;break;case 603979956:this.setSyncTarget(0,c);break;case 603979958:this.setSyncTarget(1,c);break;case 603979977:this.g.wireframeRotation=c;break;case 603979868:this.g.isosurfacePropertySmoothing=c;break;case 603979834:this.g.drawPicking=c;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,
c);break;case 603979944:this.g.smartAromatic=c;break;case 603979794:this.setApplySymmetryToBonds(c);break;case 603979792:this.g.appendNew=c;break;case 603979800:this.g.autoFps=c;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=c);break;case 603979918:case 1611272202:a="showFrank";this.setFrankOn(c);break;case 1612709912:a="solventProbe";this.g.dotSolvent=c;break;case 603979948:this.g.dotSolvent=c;break;case 603979785:this.g.allowRotateSelected=c;break;case 603979783:this.g.allowMoveAtoms=
c;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,c?1:0);return;case 603979778:this.g.allowEmbeddedScripts=c;break;case 603979890:this.g.navigationPeriodic=c;break;case 603979984:this.tm.setZShadeEnabled(c);return;case 603979833:this.haveDisplay&&(this.g.drawHover=c);break;case 603979889:this.setNavigationMode(c);break;case 603979888:return;case 603979860:this.g.hideNavigationPoint=c;break;case 603979930:this.g.showNavigationPointAlways=c;break;case 603979900:this.setRefreshing(c);
break;case 603979869:this.g.jmolInJSpecView=c;break;case 603979870:this.g.justifyMeasurements=c;break;case 603979952:this.g.ssbondsBackbone=c;break;case 603979852:this.g.hbondsBackbone=c;break;case 603979854:this.g.hbondsSolid=c;break;case 536870924:this.gdata.setSpecular(c);break;case 603979942:this.tm.setSlabEnabled(c);return;case 603979980:this.tm.setZoomEnabled(c);return;case 603979864:this.g.highResolutionFlag=c;break;case 603979966:this.g.traceAlpha=c;break;case 603979983:this.g.zoomLarge=c;
this.tm.setZoomHeight(this.g.zoomHeight,c);break;case 603979982:this.g.zoomHeight=c;this.tm.setZoomHeight(c,this.g.zoomLarge);break;case 603979871:J.i18n.GT.setDoTranslate(c);break;case 603979862:this.slm.setHideNotSelected(c);break;case 603979904:this.setScriptQueue(c);break;case 603979830:this.g.dotSurface=c;break;case 603979829:this.g.dotsSelectedOnly=c;break;case 1611141172:this.setSelectionHalosEnabled(c);break;case 603979910:this.g.rasmolHydrogenSetting=c;break;case 603979908:this.g.rasmolHeteroSetting=
c;break;case 603979928:this.g.showMultipleBonds=c;break;case 603979920:this.g.showHiddenSelectionHalos=c;break;case 603979976:this.tm.setWindowCentered(c);break;case 603979828:this.g.displayCellParameters=c;break;case 603979960:this.g.testFlag1=c;break;case 603979962:this.g.testFlag2=c;break;case 603979964:this.g.testFlag3=c;break;case 603979965:this.jmolTest();this.g.testFlag4=c;break;case 603979901:this.g.ribbonBorder=c;break;case 603979815:this.g.cartoonBaseEdges=c;break;case 603979819:this.g.cartoonRockets=
c;break;case 603979902:this.g.rocketBarrels=c;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=c);break;case 603979878:this.g.measurementLabels=c;break;case 603979809:case 603979804:case 603979808:this.setAxesMode(b);return;case 603979806:this.setAxesOrientationRasmol(c);return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,c?"rasmol":"jmol");return;case 603979825:this.setDebugScript(c);return;case 603979897:this.setPerspectiveDepth(c);return;case 603979798:this.setAutoBond(c);
return;case 603979914:this.setShowAxes(c);return;case 603979916:this.setShowBbcage(c);return;case 603979922:this.setShowHydrogens(c);return;case 603979926:this.setShowMeasurements(c);return;case 603979936:this.setShowUnitCell(c);return;case 603979812:e=!1;this.g.bondModeOr=c;break;case 603979978:e=!1;this.g.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979899:e=!1;this.g.rangeSelected=c;break;case 603979877:e=!1;this.g.measureAllModels=c;break;case 603979954:e=!1;this.sm.allowStatusReporting=
c;break;case 603979822:e=!1;this.g.chainCaseSensitive=c;break;case 603979858:e=!1;this.g.hideNameInPopup=c;break;case 603979827:e=!1;this.g.disablePopupMenu=c;break;case 603979847:e=!1;this.g.forceAutoBond=c;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.getBoolean(c));return}}this.g.setB(a,c);e&&this.setTainted(!0)},"~S,~N,~B");c(b,"setModelKitMode",function(a){if(null!=this.acm&&this.allowScripting){if(a||this.g.modelKitMode)this.setPickingMode(null,
a?33:1),this.setPickingMode(null,a?32:1);var b=this.g.modelKitMode!=a;this.g.modelKitMode=a;this.g.setB("modelkitmode",a);this.highlight(null);b&&this.setModelkitPropertySafely("constraint",null);a?(this.setNavigationMode(!1),this.selectAll(),this.setStringProperty("picking","assignAtom_C"),this.setStringProperty("picking","assignBond_p"),this.isApplet||this.popupMenu(10,0,"m"),b&&this.sm.setStatusModelKit(1),this.g.modelKitMode=!0,null==this.getOperativeSymmetry()&&(0==this.ms.ac?this.zap(!1,!0,
!0):0<=this.am.cmi&&this.getModelUndeletedAtomsBitSet(this.am.cmi).isEmpty()&&(a=new java.util.Hashtable,a.put("appendToModelIndex",Integer.$valueOf(this.am.cmi)),this.loadDefaultModelKitModel(a)))):(this.acm.setPickingMode(-1),b?this.sm.setStatusModelKit(0):a||this.getModelkit(!1).setProperty("hideMenu",null))}},"~B");c(b,"setSmilesString",function(a){null==a?this.g.removeParam("_smilesString"):this.g.setO("_smilesString",a)},"~S");c(b,"removeUserVariable",function(a){this.g.removeUserVariable(a);
a.endsWith("callback")&&this.sm.setCallbackFunction(a,null)},"~S");c(b,"jmolTest",function(){});c(b,"showParameter",function(a,b,c){c=""+this.g.getParameterEscaped(a,c);(b||0>c.indexOf("<not defined>"))&&this.showString(a+" = "+c,!1)},"~S,~B,~N");c(b,"showString",function(a,b){!JV.Viewer.isJS&&(this.isScriptQueued()&&(!this.isSilent||b)&&!"\x00".equals(a))&&JU.Logger.warn(a);this.scriptEcho(a)},"~S,~B");c(b,"getAllSettings",function(a){return this.getStateCreator().getAllSettings(a)},"~S");c(b,"getBindingInfo",
function(a){return this.haveDisplay?this.acm.getBindingInfo(a):""},"~S");c(b,"getIsosurfacePropertySmoothing",function(a){return a?this.g.isosurfacePropertySmoothingPower:this.g.isosurfacePropertySmoothing?1:0},"~B");c(b,"setNavigationDepthPercent",function(a){this.tm.setNavigationDepthPercent(a);this.refresh(1,"set navigationDepth")},"~N");c(b,"getShowNavigationPoint",function(){return!this.g.navigationMode?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||
this.getInMotion(!0)});f(b,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");f(b,"setAxesOrientationRasmol",function(a){this.g.setB("axesOrientationRasmol",a);this.g.axesOrientationRasmol=a;this.reset(!0)},"~B");c(b,"setAxesScale",function(a,b){b=JV.Viewer.checkFloatRange(b,-100,100);570425345==a?this.g.axesOffset=b:this.g.axesScale=b;this.axesAreTainted=!0},"~N,~N");c(b,"setAxesMode",function(a){this.g.axesMode=a;this.axesAreTainted=!0;switch(a){case 603979808:this.g.removeParam("axesmolecular");
this.g.removeParam("axeswindow");this.g.setB("axesUnitcell",!0);a=2;break;case 603979804:this.g.removeParam("axesunitcell");this.g.removeParam("axeswindow");this.g.setB("axesMolecular",!0);a=1;break;case 603979809:this.g.removeParam("axesunitcell"),this.g.removeParam("axesmolecular"),this.g.setB("axesWindow",!0),a=0}this.g.setI("axesMode",a)},"~N");c(b,"getSelectionHalosEnabled",function(){return this.selectionHalosEnabled});c(b,"setSelectionHalosEnabled",function(a){this.selectionHalosEnabled!=a&&
(this.g.setB("selectionHalos",a),this.shm.loadShape(8),this.selectionHalosEnabled=a)},"~B");c(b,"getShowSelectedOnce",function(){var a=this.showSelected;this.showSelected=!1;return a});c(b,"setStrandCount",function(a,b){b=JV.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.g.strandCountForStrands=b;break;case 13:this.g.strandCountForMeshRibbon=b;break;default:this.g.strandCountForStrands=b,this.g.strandCountForMeshRibbon=b}this.g.setI("strandCount",b);this.g.setI("strandCountForStrands",this.g.strandCountForStrands);
this.g.setI("strandCountForMeshRibbon",this.g.strandCountForMeshRibbon)},"~N,~N");c(b,"getStrandCount",function(a){return 12==a?this.g.strandCountForStrands:this.g.strandCountForMeshRibbon},"~N");c(b,"setNavigationMode",function(a){this.g.navigationMode=a;this.tm.setNavigationMode(a)},"~B");f(b,"setAutoBond",function(a){this.g.setB("autobond",a);this.g.autoBond=a},"~B");c(b,"makeConnections",function(a,b,c,e,g,j,f,l,s,m){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,
b,c,e,g,j,f,l,s,m)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");f(b,"rebond",function(){this.rebondState(!1)});c(b,"rebondState",function(a){this.clearModelDependentObjects();this.ms.deleteAllBonds();a=a&&this.g.legacyAutoBonding;this.ms.autoBondBs4(null,null,null,null,this.getMadBond(),a,null);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":"connect;",!1,!0)},"~B");f(b,"setPercentVdwAtom",function(a){this.g.setI("percentVdwAtom",a);this.g.percentVdwAtom=a;this.rd.value=
a/100;this.rd.factorType=J.atomdata.RadiusData.EnumType.FACTOR;this.rd.vdwType=J.c.VDW.AUTO;this.shm.setShapeSizeBs(0,0,this.rd,null)},"~N");f(b,"getMadBond",function(){return 2*this.g.bondRadiusMilliAngstroms});f(b,"setShowHydrogens",function(a){this.g.setB("showHydrogens",a);this.g.showHydrogens=a},"~B");c(b,"setShowBbcage",function(a){this.setObjectMad10(32,"boundbox",a?-4:0);this.g.setB("showBoundBox",a)},"~B");c(b,"getShowBbcage",function(){return 0!=this.getObjectMad10(4)});c(b,"setShowUnitCell",
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this.creatingImage?!1:this.isSignedApplet&&!this.isSignedAppletLocal&&!JV.Viewer.isJS||this.frankOn});f(b,"setShowMeasurements",function(a){this.g.setB("showMeasurements",a);this.g.showMeasurements=a},"~B");c(b,"setUnits",function(a,b){var c="default".equals(a);(!b||!c)&&this.g.setUnits(a);b&&this.setShapeProperty(6,"reformatDistances",a)},"~S,~B");f(b,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});f(b,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(b,"setDefaultsType",
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b;return}c&&(this.resizeImage(0,0,!1,!1,!0),this.refresh(3,"Viewer:setAntialias()"))},"~N,~B");c(b,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(b,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(b,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},"~N");c(b,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},"~A");c(b,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(b,"freeTempEnum",
function(a){this.tempArray.freeTempEnum(a)},"~A");c(b,"getFont3D",function(a,b,c){return this.gdata.getFont3DFSS(a,b,c)},"~S,~S,~N");c(b,"getAtomGroupQuaternions",function(a,b){return this.ms.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(b,"setStereoMode",function(a,b,c){this.setFloatProperty("stereoDegrees",c);this.setBooleanPropertyTok("greyscaleRendering",603979850,b.isBiColor());null!=a?this.tm.setStereoMode2(a):this.tm.setStereoMode(b)},"~A,J.c.STER,~N");c(b,"getChimeInfo",
function(a){return this.getPropertyManager().getChimeInfo(a,this.bsA())},"~N");c(b,"getModelFileInfo",function(){return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet())});c(b,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});c(b,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},"~A");c(b,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getInterface("JV.PropertyManager",
this,"prop")).setViewer(this);return this.pm});c(b,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(b,"checkObjectClicked",function(a,b,c){return this.shm.checkObjectClicked(a,b,c,this.getVisibleFramesBitSet(),this.g.drawPicking)},"~N,~N,~N");c(b,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shm&&this.shm.checkObjectHovered(a,b,this.getVisibleFramesBitSet(),this.getBondsPickable())},"~N,~N");c(b,"checkObjectDragged",function(a,
b,c,e,g){var j=0;switch(this.getPickingMode()){case 2:j=5;break;case 4:j=22}return this.shm.checkObjectDragged(a,b,c,e,g,this.getVisibleFramesBitSet(),j)?(this.refresh(1,"checkObjectDragged"),22==j&&this.scriptEcho(this.getShapeProperty(22,"command")),!0):!1},"~N,~N,~N,~N,~N");c(b,"rotateAxisAngleAtCenter",function(a,b,c,e,g,j,f){(a=this.tm.rotateAxisAngleAtCenter(a,b,c,e,g,j,f))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(b,"rotateAboutPointsInternal",function(a,
b,c,e,g,j,f,l,s,m,p){null==a&&(a=this.eval);if(this.headless){if(j&&3.4028235E38==g)return!1;j=!1}(a=this.tm.rotateAboutPointsInternal(a,b,c,e,g,!1,j,f,!1,l,s,m,p))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A,JU.M4");c(b,"startSpinningAxis",function(a,b,c){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,a,b,this.g.pickingSpinRate,3.4028235E38,c,!0,null,!1,null,null,null,null)},"JU.T3,JU.T3,~B");
c(b,"getModelDipole",function(){return this.ms.getModelDipole(this.am.cmi)});c(b,"calculateMolecularDipole",function(a){try{return this.ms.calculateMolecularDipole(this.am.cmi,a)}catch(b){if(D(b,"JV.JmolAsyncException"))return null!=this.eval&&this.eval.loadFileResourceAsync(b.getFileName()),null;throw b;}},"JU.BS");c(b,"setDefaultLattice",function(a){Float.isNaN(a.x+a.y+a.z)||this.g.ptDefaultLattice.setT(a);this.g.setO("defaultLattice",JU.Escape.eP(a))},"JU.P3");c(b,"getDefaultLattice",function(){return this.g.ptDefaultLattice});
c(b,"getModelExtract",function(a,b,c,e){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,c,e,!1)},"~O,~B,~B,~S");f(b,"getData",function(a,b){return this.getModelFileData(a,b,!0)},"~S,~S");c(b,"getModelFileData",function(a,b,c){return this.getPropertyManager().getAtomData(a,b,c)},"~S,~S,~B");c(b,"getModelCml",function(a,b,c,e){return this.getPropertyManager().getModelCml(a,b,c,e,!1)},"JU.BS,~N,~B,~B");c(b,"getPdbAtomData",function(a,b,c,e){return this.getPropertyManager().getPdbAtomData(null==
a?this.bsA():a,b,c,e,!1)},"JU.BS,JU.OC,~B,~B");c(b,"isJmolDataFrame",function(){return this.ms.isJmolDataFrameForModel(this.am.cmi)});c(b,"setFrameTitle",function(a,b){this.ms.setFrameTitle(JU.BSUtil.newAndSetBit(a),b)},"~N,~S");c(b,"setFrameTitleObj",function(a){this.shm.loadShape(31);this.ms.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(b,"getFrameTitle",function(){return this.ms.getFrameTitle(this.am.cmi)});c(b,"setAtomProperty",function(a,b,c,e,g,j,f){1648363544==b&&this.shm.deleteVdwDependentShapes(a);
this.clearMinimization();this.ms.setAtomProperty(a,b,c,e,g,j,f);switch(b){case 1086326789:this.setModelkitPropertySafely("key",a);case 1111492609:case 1111492610:case 1111492611:case 1111492612:case 1111492613:case 1111492614:case 1111490577:case 1111490578:case 1111490579:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"checkCoordinatesChanged",function(){this.ms.recalculatePositionDependentQuantities(null,null);this.refreshMeasures(!0)});c(b,"setAtomCoords",function(a,b,c){if(!a.isEmpty()){var e=
this.ms.at[a.nextSetBit(0)],g=a.cardinality();this.sm.setStatusStructureModified(e.i,e.mi,3,"setAtomCoords",g,a);this.ms.setAtomCoords(a,b,c);this.setStatusAtomMoved(!0,a);this.sm.setStatusStructureModified(e.i,e.mi,-3,"OK",g,a)}},"JU.BS,~N,~O");c(b,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());if(!b.isEmpty()){var c=0!=a.lengthSquared(),e=this.ms.at[b.nextSetBit(0)],g=b.cardinality();c&&this.sm.setStatusStructureModified(e.i,e.mi,3,"setAtomCoords",g,b);this.ms.setAtomCoordsRelative(a,
b);this.checkMinimization();c&&(this.setStatusAtomMoved(!1,b),this.sm.setStatusStructureModified(e.i,e.mi,-3,"OK",g,b))}},"JU.T3,JU.BS");c(b,"invertAtomCoord",function(a,b,c,e,g){if(0<=e){c=JU.JmolMolecule.getBranchesForInversion(this.ms.at,e,this.ms.getMoleculeBitSetForAtom(e));var j=c.cardinality();switch(j){case 0:case 1:return;case 3:case 4:for(var f=E(j,0),l=E(j,0),s=0,m=c.nextSetBit(0);0<=m;m=c.nextSetBit(m+1),s++)f[s]=this.getBranchBitSet(m,e,!0).cardinality(),l[s]=m;for(s=0;s<j-2;s++){for(var p=
-2147483648,n=0,m=0;m<j;m++)f[m]>=p&&c.get(l[m])&&(n=l[m],p=f[m]);c.clear(n)}}g&&!c.isEmpty()&&this.undoMoveActionClear(e,2,!0)}j=c.cardinality();0!=j&&(f=this.ms.at[c.nextSetBit(0)],this.sm.setStatusStructureModified(f.i,f.mi,3,"invertAtomCoords",j,c),this.ms.invertSelected(a,b,e,c),this.setStatusAtomMoved(!0,c),this.sm.setStatusStructureModified(f.i,f.mi,-3,"OK",j,c),g&&this.setStatusAtomPicked(e,"inverted: "+JU.Escape.eBS(c),null,!1))},"JU.P3,JU.P4,JU.BS,~N,~B");c(b,"invertSelected",function(a,
b,c,e){null==e&&(e=this.bsA());e.isEmpty()||(this.ms.invertSelected(a,b,c,e),this.setStatusAtomMoved(!0,e))},"JU.P3,JU.P4,~N,JU.BS");c(b,"moveAtoms",function(a,b,c,e,g,j,f,l){if(!f.isEmpty()){var s=this.getMotionFixedAtoms(null,null);if(!f.intersects(s)){var m=this.getOperativeSymmetry(),p=null;null!=m&&(p=this.ms.saveAtomPositions());this.ms.moveAtoms(a,b,c,e,f,g,j,l);null!=m&&this.getModelkit(!1).checkMovedAtoms(s,f,p);this.setStatusAtomMoved(!0,f)}}},"JU.M4,JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B");
c(b,"moveSelectedXY",function(a,b,c){this.moveSelected(a,b,-2147483648,-2147483648,-2147483648,null,null,null,!1,!1,c)},"~N,~N,~N");c(b,"moveSelected",function(a,b,c,e,g,j,f,l,s,m,p){if(0==c&&null==l||this.isJmolDataFrame())return 0;if(null==l){-2147483648==e&&null!=this.modelkit&&this.setModelkitPropertySafely("rotateBondIndex",Integer.$valueOf(-2147483648));if(-2147483648==a)return this.showSelected=!0,this.movableBitSet=this.setMovableBitSet(null,!m),this.shm.loadShape(8),this.refresh(6,"moveSelected"),
0;if(2147483647==a){if(!this.showSelected)return 0;this.showSelected=!1;this.movableBitSet=null;this.refresh(6,"moveSelected");return 0}}if(this.movingSelected)return 0;this.movingSelected=!0;this.stopMinimization();null==l&&-2147483648!=e&&null!=this.modelkit&&null!=this.modelkit.getProperty("rotateBondIndex")?this.modelkit.actionRotateBond(a,b,e,g,0!=(p&16)):(null==j&&(j=this.bsA()),e=j.nextSetBit(0),j=this.setMovableBitSet(j,!m),j.isEmpty()?(j.set(e),this.sm.setStatusStructureModified(e,this.getModelIndexForAtom(e),
-3,"FAILED",1,j)):s?(f=null==f?this.ms.getAtomSetCenter(j):f,null==l&&(this.tm.finalizeTransformParameters(),l=this.g.antialiasDisplay?2:1,this.tm.transformPt3f(f,this.ptScreen),-2147483648!=c?this.ptScreenNew.set(this.ptScreen.x,this.ptScreen.y,this.ptScreen.z+c):this.ptScreenNew.set(this.ptScreen.x+a*l,this.ptScreen.y+b*l,this.ptScreen.z),this.tm.unTransformPoint(this.ptScreenNew,this.ptNew),l=this.ptNew,null!=this.getOperativeSymmetry()&&(l.sub(f),l.add(this.ms.at[e]),this.getModelkit(!1).cmdAssignMoveAtoms(j,
e,l,null,!0,!m))),Float.isNaN(l.x)||(l.sub(f),this.setAtomCoordsRelative(l,j))):this.tm.rotateXYBy(a,b,j));this.refresh(2,"");this.movingSelected=!1;return null==j?0:j.cardinality()},"~N,~N,~N,~N,~N,JU.BS,JU.P3,JU.P3,~B,~B,~N");c(b,"highlightBond",function(a,b,c,e){if(this.hoverEnabled){b=null;if(0<=a){var g=this.ms.bo[a];b=JU.BSUtil.newAndSetBit(g.atom2.i);b.set(g.atom1.i)}this.highlight(b);this.getModelkit(!1);this.setModelkitPropertySafely("screenXY",E(-1,[c,e]));this.setModelkitPropertySafely("bondIndex",
Integer.$valueOf(a));a=this.setModelkitPropertySafely("hoverLabel",Integer.$valueOf(-2-a));null!=a&&this.hoverOnPt(c,e,a,null,null);this.refresh(3,"highlightBond")}},"~N,~N,~N,~N");c(b,"highlight",function(a){this.atomHighlighted=null!=a&&1==a.cardinality()?a.nextSetBit(0):-1;null==a?this.setCursor(0):(this.shm.loadShape(8),this.setCursor(12));this.setModelkitPropertySafely("highlight",a);this.setShapeProperty(8,"highlight",a)},"JU.BS");c(b,"refreshMeasures",function(a){this.setShapeProperty(6,"refresh",
null);this.setStatusMeasuring("refreshed",-3,"",0);a&&this.stopMinimization()},"~B");c(b,"functionXY",function(a,b,c){var e=null;if(0==a.indexOf("file:"))e=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data2d_"))return this.sm.functionXY(a,b,c);b=Math.abs(b);c=Math.abs(c);if(null==e){a=this.getDataObj(a,null,2);if(null!=a)return a;e=""}a=L(b,c,0);var g=L(b*c,0);JU.Parser.parseStringInfestedFloatArray(e,null,g);for(var j=e=0;e<b;e++)for(var f=0;f<c;f++)a[e][f]=g[j++];return a},
"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,e){var g=null;if(0==a.indexOf("file:"))g=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,c,e);b=Math.abs(b);c=Math.abs(c);e=Math.abs(e);if(null==g){a=this.getDataObj(a,null,2);if(null!=a)return a;g=""}a=L(b,c,e,0);var j=L(b*c*e,0);JU.Parser.parseStringInfestedFloatArray(g,null,j);for(var f=g=0;g<b;g++)for(var l=0;l<c;l++)for(var s=0;s<e;s++)a[g][l][s]=j[f++];return a},"~S,~N,~N,~N");f(b,"extractMolData",
function(a){if(null==a){a=this.am.cmi;if(0>a||0==this.ms.ac)return null;a=this.getModelNumberDotted(a)}return this.getModelExtract(a,!0,!1,"V2000")},"~S");c(b,"getNMRPredict",function(a){a=a.toUpperCase();if(a.equals("H")||a.equals("1H")||a.equals(""))a="H1";else if(a.equals("C")||a.equals("13C"))a="C13";if(!a.equals("NONE")){if(!a.equals("C13")&&!a.equals("H1"))return"Type must be H1 or C13";var b=this.getModelExtract("selected",!0,!1,"V2000"),c=b.indexOf("\n");if(0>c)return null;b="Jmol "+JV.Viewer.version_date+
b.substring(c);if(this.isApplet)return this.showUrl(this.g.nmrUrlFormat+b),"opening "+this.g.nmrUrlFormat}this.syncScript("true","*",0);this.syncScript(a+"Simulate:",".",0);return"sending request to JSpecView"},"~S");c(b,"getHelp",function(a){0>this.g.helpPath.indexOf("?")?(0<a.length&&0!=a.indexOf("?")&&(a="?search="+JU.PT.rep(a," ","%20")),a+=(0==a.length?"?ver=":"&ver=")+JV.JC.majorVersion):a="&"+a;this.showUrl(this.g.helpPath+a)},"~S");c(b,"getChemicalInfo",function(a,b,c){b=b.toLowerCase();var e=
"/";switch(";inchi;inchikey;stdinchi;stdinchikey;name;image;drawing;names;".indexOf(";"+b+";")){case 0:e="I";break;case 6:e="K";break;case 15:e="T";break;case 24:e="S";break;case 36:e="M";break;case 41:case 47:e="2";break;case 55:e="N"}var g=this.setLoadFormat(!1,"_"+a,e,!1);if("2"==e)return this.fm.loadImage(g,"\u0001"+a,!1),g;"/"==e&&(g=JU.PT.isOneOf(b,";alc;cdxml;cerius;charmm;cif;cml;ctx;gjf;gromacs;hyperchem;jme;maestro;mol;mol2;sybyl2;mrv;pdb;sdf;sdf3000;sln;smiles;xyz")?g+("file?format="+b):
g+JU.PT.rep(b," ","%20"));g=this.getFileAsString4(g,-1,!1,!1,!1,"file");"M"==e&&0<g.indexOf("\n")?g=g.substring(0,g.indexOf("\n")):b.equals("jme")&&(g=this.getPropertyManager().fixJMEFormalCharges(c,g));return g},"~S,~S,JU.BS");c(b,"addCommand",function(a){if(!this.autoExit&&this.haveDisplay&&this.getPreserveState()){if(a.startsWith("pause ")||a.equals("pause"))a="resume"+a.substring(5);this.commandHistory.addCommand(JU.PT.replaceAllCharacters(a,"\r\n\t"," "))}},"~S");c(b,"pushState",function(){!this.autoExit&&
(this.haveDisplay&&this.getPreserveState())&&this.commandHistory.pushState(this.getStateInfo())});c(b,"popState",function(){if(!this.autoExit&&this.haveDisplay&&this.getPreserveState()){var a=this.commandHistory.popState();null!=a&&this.evalStringQuiet(a)}});c(b,"removeCommand",function(){return this.commandHistory.removeCommand()});f(b,"getSetHistory",function(a){return this.commandHistory.getSetHistory(a)},"~N");c(b,"historyFind",function(a,b){return this.commandHistory.find(a,b)},"~S,~N");c(b,
"setHistory",function(a){this.commandHistory.getSetHistory(-2147483648);this.commandHistory.addCommand(this.getFileAsString4(a,-1,!1,!1,!0,null))},"~S");c(b,"getOutputChannel",function(a,b){return this.getOutputManager().getOutputChannel(a,b)},"~S,~A");f(b,"writeTextFile",function(a,b){return this.writeFile(a,b,"txt")},"~S,~S");c(b,"writeFile",function(a,b,c){var e=new java.util.Hashtable;e.put("fileName",a);e.put("type",c);e.put("string"==typeof b?"text":"bytes",b);return this.outputToFile(e)},"~S,~O,~S");
f(b,"clipImageOrPasteText",function(a){return!this.haveAccess(JV.Viewer.ACCESS.ALL)?"no":this.getOutputManager().clipImageOrPasteText(a)},"~S");f(b,"getClipboardText",function(){if(!this.haveAccess(JV.Viewer.ACCESS.ALL))return"no";try{return this.getOutputManager().getClipboardText()}catch(a){if(D(a,Error))return J.i18n.GT.$("clipboard is not accessible -- use signed applet");throw a;}});c(b,"processWriteOrCapture",function(a){return this.getOutputManager().processWriteOrCapture(a)},"java.util.Map");
c(b,"createZip",function(a,b,c){var e=this.getStateInfo(),g=c.get("data");null!=a&&c.put("fileName",a);c.put("type",b);c.put("text",e);C(g,Array)?c.put("scripts",g):C(g,"JU.Lst")&&c.put("imageData",g);return this.getOutputManager().outputToFile(c)},"~S,~S,java.util.Map");f(b,"outputToFile",function(a){return this.getOutputManager().outputToFile(a)},"java.util.Map");c(b,"setSyncTarget",function(a,b){switch(a){case 0:this.sm.syncingMouse=b;break;case 1:this.sm.syncingScripts=b;break;case 2:this.sm.syncSend(b?
"GET_GRAPHICS":"SET_GRAPHICS_OFF","*",0);Float.isNaN(this.tm.stereoDegrees)&&this.setFloatProperty("stereoDegrees",-5);b&&(this.setBooleanProperty("_syncMouse",!1),this.setBooleanProperty("_syncScript",!1));return}!this.sm.syncingScripts&&!this.sm.syncingMouse&&this.setSync()},"~N,~B");f(b,"syncScript",function(a,b,c){this.sm.syncScript(a,b,c)},"~S,~S,~N");f(b,"getModelIndexFromId",function(a){return this.ms.getModelIndexFromId(a)},"~S");c(b,"setSyncDriver",function(a){this.sm.setSyncDriver(a)},"~N");
c(b,"setProteinType",function(a,b){this.ms.setProteinType(null==b?this.bsA():b,a)},"J.c.STR,JU.BS");c(b,"getVanderwaalsMar",function(a){return this.defaultVdw===J.c.VDW.USER?this.userVdwMars[a]:JU.Elements.getVanderwaalsMar(a,this.defaultVdw)},"~N");c(b,"getVanderwaalsMarType",function(a,b){if(null==b)b=this.defaultVdw;else switch(b){case J.c.VDW.AUTO:case J.c.VDW.AUTO_BABEL:case J.c.VDW.AUTO_JMOL:case J.c.VDW.AUTO_RASMOL:this.defaultVdw!==J.c.VDW.AUTO&&(b=this.defaultVdw)}b===J.c.VDW.USER&&null==
this.bsUserVdws&&(b=J.c.VDW.JMOL);return b===J.c.VDW.USER?this.userVdwMars[a&127]:JU.Elements.getVanderwaalsMar(a,b)},"~N,J.c.VDW");c(b,"setVdwStr",function(a){a=J.c.VDW.getVdwType(a);null==a&&(a=J.c.VDW.AUTO);switch(a){case J.c.VDW.JMOL:case J.c.VDW.BABEL:case J.c.VDW.RASMOL:case J.c.VDW.AUTO:case J.c.VDW.USER:break;default:a=J.c.VDW.JMOL}a!==this.defaultVdw&&(a===J.c.VDW.USER&&null==this.bsUserVdws)&&this.setUserVdw(this.defaultVdw);this.defaultVdw=a;this.g.setO("defaultVDW",a.getVdwLabel())},"~S");
c(b,"setUserVdw",function(a){this.userVdwMars=E(JU.Elements.elementNumberMax,0);this.userVdws=L(JU.Elements.elementNumberMax,0);this.bsUserVdws=new JU.BS;a===J.c.VDW.USER&&(a=J.c.VDW.JMOL);for(var b=1;b<JU.Elements.elementNumberMax;b++)this.userVdwMars[b]=JU.Elements.getVanderwaalsMar(b,a),this.userVdws[b]=this.userVdwMars[b]/1E3},"J.c.VDW");c(b,"getDefaultVdwNameOrData",function(a,b,c){switch(a){case -2147483648:return this.defaultVdw.getVdwLabel();case 2147483647:if(null==(c=this.bsUserVdws))return"";
b=J.c.VDW.USER}if(null==b||b===J.c.VDW.AUTO)b=this.defaultVdw;b===J.c.VDW.USER&&null==this.bsUserVdws&&this.setUserVdw(this.defaultVdw);return this.getDataManager().getDefaultVdwNameOrData(b,c)},"~N,J.c.VDW,JU.BS");c(b,"deleteAtoms",function(a,b){var c=null==a?-1:a.nextSetBit(0);if(0>c)return 0;this.clearModelDependentObjects();var e=this.ms.at[c];if(null==e)return 0;var g=e.mi;if(b)return this.deleteModels(g,a);this.sm.setStatusStructureModified(c,e.mi,4,"deleting atoms "+a,a.cardinality(),a);this.ms.deleteAtoms(a);
e=this.slm.deleteAtoms(a);this.setTainted(!0);this.sm.setStatusStructureModified(c,g,-4,"OK",e,a);return e},"JU.BS,~B");c(b,"deleteModels",function(a,b){var c=null==b?JU.BSUtil.newAndSetBit(a):this.ms.getModelBS(b,!1);this.clearModelDependentObjects();b=this.getModelUndeletedAtomsBitSetBs(c);var e=b.cardinality(),g=this.am.cmi;this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var j=JU.BSUtil.copy(this.slm.bsDeleted),c=this.ms.deleteModels(c);if(null==c)return this.setCurrentModelIndexClear(g,
!1),0;this.sm.setStatusStructureModified(-1,a,5,"deleting model "+this.getModelNumberDotted(a),e,b);this.slm.processDeletedModelAtoms(c);null!=this.eval&&this.eval.deleteAtomsInVariables(c);this.setAnimationRange(0,0);this.clearRepaintManager(-1);this.am.clear();this.am.initializePointers(1);this.setCurrentModelIndexClear(1<this.ms.mc?-1:0,1<this.ms.mc);this.hoverAtomIndex=-1;this.setFileLoadStatus(J.c.FIL.DELETED,null,null,null,null,null);this.refreshMeasures(!0);null!=j&&c.andNot(j);e=JU.BSUtil.cardinalityOf(c);
this.sm.setStatusStructureModified(-1,a,-5,"OK",e,c);return e},"~N,JU.BS");c(b,"deleteBonds",function(a){var b=this.ms.bo[a.nextSetBit(0)].atom1.mi;0!=a.cardinality()&&(this.sm.setStatusStructureModified(-1,b,2,"delete bonds "+JU.Escape.eBond(a),a.cardinality(),a),this.ms.deleteBonds(a,!1),this.sm.setStatusStructureModified(-1,b,-2,"OK",a.cardinality(),a))},"JU.BS");c(b,"deleteModelAtoms",function(a,b,c,e){var g=e.cardinality();0!=g&&(this.sm.setStatusStructureModified(-1,a,7,"delete atoms "+JU.Escape.eBS(e),
g,e),JU.BSUtil.deleteBits(this.tm.bsFrameOffsets,e),this.getDataManager().deleteModelAtoms(b,c,e),this.sm.setStatusStructureModified(-1,a,-7,"OK",g,e))},"~N,~N,~N,JU.BS");c(b,"getQuaternionFrame",function(){return this.g.quaternionFrame.charAt(2==this.g.quaternionFrame.length?1:0)});c(b,"loadImageData",function(a,b,c,e){null==a&&null!=b&&this.scriptEcho(b);null==c?this.setBackgroundImage(null==a?null:b,a):c.startsWith("\u0001")?this.sm.showImage(c,a):c.startsWith("\x00")?null!=a&&this.setWindowDimensions(L(-1,
[this.apiPlatform.getImageWidth(a),this.apiPlatform.getImageHeight(a)])):(this.shm.loadShape(31),this.setShapeProperty(31,"text",b),null!=a&&this.setShapeProperty(31,"image",a));JV.Viewer.isJS&&null!=e&&(e.mustResumeEval=!0,this.eval.resumeEval(e));return!1},"~O,~S,~S,~O");c(b,"cd",function(a){null==a?a=".":0==a.length&&(this.setStringProperty("defaultDirectory",""),a=".");a=this.fm.getDefaultDirectory(a+(a.equals("=")?"":a.endsWith("/")?"X.spt":"/X.spt"));0<a.length&&this.setStringProperty("defaultDirectory",
a);this.fm.getFilePath(a+"/",!0,!1).startsWith("file:/")&&JV.FileManager.setLocalPath(this,a,!1);return a},"~S");c(b,"setErrorMessage",function(a,b){this.errorMessageUntranslated=b;null!=a&&this.eval.stopScriptThreads();return this.errorMessage=a},"~S,~S");f(b,"getErrorMessage",function(){return this.errorMessage});f(b,"getErrorMessageUn",function(){return null==this.errorMessageUntranslated?this.errorMessage:this.errorMessageUntranslated});c(b,"setShapeErrorState",function(a,b){this.currentShapeID=
a;this.currentShapeState=b},"~N,~S");c(b,"getShapeErrorState",function(){if(0>this.currentShapeID)return"";this.shm.releaseShape(this.currentShapeID);this.clearRepaintManager(this.currentShapeID);return JV.JC.getShapeClassName(this.currentShapeID,!1)+" "+this.currentShapeState});c(b,"handleError",function(a,b){try{b&&this.zapMsg(""+a),this.undoMoveAction(4165,-2),0==JU.Logger.getLogLevel()&&JU.Logger.setLogLevel(4),this.setCursor(0),this.setBooleanPropertyTok("refreshing",603979900,!0),this.fm.setPathForAllFiles(""),
JU.Logger.error("vwr handling error condition: "+a+"  "),this.notifyError("Error","doClear="+b+"; "+a,""+a)}catch(c){try{JU.Logger.error("Could not notify error "+a+": due to "+c)}catch(e){}}},"Throwable,~B");c(b,"getFunctions",function(a){return a?JV.Viewer.staticFunctions:this.localFunctions},"~B");c(b,"removeFunction",function(a){a=a.toLowerCase();null!=this.getFunction(a)&&(JV.Viewer.staticFunctions.remove(a),this.localFunctions.remove(a))},"~S");c(b,"getFunction",function(a){if(null==a)return null;
a=(JV.Viewer.isStaticFunction(a)?JV.Viewer.staticFunctions:this.localFunctions).get(a);return null==a||null==a.geTokens()?null:a},"~S");b.isStaticFunction=c(b,"isStaticFunction",function(a){return a.startsWith("static_")},"~S");c(b,"isFunction",function(a){return(JV.Viewer.isStaticFunction(a)?JV.Viewer.staticFunctions:this.localFunctions).containsKey(a)},"~S");c(b,"clearFunctions",function(){JV.Viewer.staticFunctions.clear();this.localFunctions.clear()});c(b,"addFunction",function(a){var b=a.getName();
(JV.Viewer.isStaticFunction(b)?JV.Viewer.staticFunctions:this.localFunctions).put(b,a)},"J.api.JmolScriptFunction");c(b,"getFunctionCalls",function(a){return this.getStateCreator().getFunctionCalls(a)},"~S");c(b,"checkPrivateKey",function(a){return a==this.privateKey},"~N");c(b,"bindAction",function(a,b){this.haveDisplay&&this.acm.bind(a,b)},"~S,~S");c(b,"unBindAction",function(a,b){this.haveDisplay&&this.acm.unbindAction(a,b)},"~S,~S");c(b,"calculateStruts",function(a,b){return this.ms.calculateStruts(null==
a?this.bsA():a,null==b?this.bsA():b)},"JU.BS,JU.BS");c(b,"getPreserveState",function(){return this.g.preserveState&&null!=this.scm});c(b,"isKiosk",function(){return this.$isKiosk});c(b,"hasFocus",function(){return this.haveDisplay&&(this.$isKiosk||this.apiPlatform.hasFocus(this.display))});c(b,"setFocus",function(){this.haveDisplay&&!this.apiPlatform.hasFocus(this.display)&&this.apiPlatform.requestFocusInWindow(this.display)});c(b,"stopMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("stop",
null)});c(b,"clearMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("clear",null)});c(b,"getMinimizationInfo",function(){return null==this.minimizer?"":this.minimizer.getProperty("log",0)});c(b,"checkMinimization",function(){this.refreshMeasures(!0);if(this.g.monitorEnergy){try{this.minimize(null,0,0,this.getFrameAtoms(),null,null,0,1)}catch(a){if(!D(a,Exception))throw a;}this.echoMessage(this.getP("_minimizationForceField")+" Energy = "+this.getP("_minimizationEnergy"))}});
c(b,"minimize",function(a,b,c,e,g,j,f,l){var s=null!=e;s&&(l|=2);var m=0!=(l&16),p=0!=(l&256),n=0!=(l&1),r=0!=(l&8),u=0!=(l&64),v=u||0!=(l&32),w=null!=g;this.isModelKitOpen()&&this.setModelkitPropertySafely("constraint",null);null==j&&(j=this.getFrameAtoms());!r&&(!m&&s&&!w&&!v)&&(w=JU.BSUtil.copy(j),g=JU.BSUtil.copy(w),g.andNot(e),e=w,w=!0);s?r||e.and(j):(e=this.getThisModelAtoms(),v&&e.and(this.bsA()));if(!e.isEmpty())if(s=p||!v?JU.BSUtil.copy(this.ms.am[this.ms.at[e.nextSetBit(0)].mi].bsAsymmetricUnit):
null,p&&null==s)this.scriptStatusMsg("MODELKIT MINIMIZE is only applicable to crystal structures.","minimization: not a crystal structure");else try{if(p)this.getModelkit(!1).cmdMinimize(a,s,b,c,f,l);else{var y=null==s?this.g.forceField:"UFF";this.getModelForAtomIndex(e.nextSetBit(0)).auxiliaryInfo.put("dimension","3D");r&&(j=e);var z=JU.BSUtil.copy(w?g:this.slm.getMotionFixedAtoms()),B=!z.isEmpty();B&&e.andNot(z);var C=null!=s&&p?this.getThisModelAtoms():v||!B?new JU.BS:this.ms.getAtomsWithinRadius(0>=
f?5:f,e,!0,null,null);C.andNot(e);B?z.and(C):z=C;z.and(j);l|=(B?4:0)|(this.getBooleanProperty("minimizationSilent")?1:0);if(!r||!this.getBoolean(603979962)){if(r)try{n||JU.Logger.info("Minimizing "+e.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,c,e,z,null,l,"UFF")}catch(E){if(D(E,Exception))JU.Logger.error("Minimization error: "+E.toString()),E.printStackTrace();else throw E;}if(m){var F=this.addHydrogens(e,l);r||e.or(F)}var G=e.cardinality();if(y.equals("MMFF")&&G>this.g.minimizationMaxAtoms)this.scriptStatusMsg("Too many atoms for minimization ("+
G+">"+this.g.minimizationMaxAtoms+"); use 'set minimizationMaxAtoms' to increase this limit","minimization: too many atoms");else if(u&&(z.or(this.ms.getConnectingAtoms(e,z)),e.andNot(z)),n||JU.Logger.info("Minimizing "+e.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,c,e,z,s,l,r?"MMFF":y),r){this.g.forceField="MMFF";this.setHydrogens(e);var I=this.getMinimizer(!1).getForceFieldUsed();null!=I&&this.showString("Minimized by Jmol using "+I,!1)}}}}catch(K){if(D(K,"JV.JmolAsyncException"))null!=
a&&a.loadFileResourceAsync(K.getFileName());else if(D(K,Exception))a=K,JU.Logger.error("Minimization error: "+a.toString()),a.printStackTrace();else throw K;}},"J.api.JmolScriptEvaluator,~N,~N,JU.BS,JU.BS,JU.BS,~N,~N");c(b,"setHydrogens",function(a){for(var b=E(1,0),b=this.ms.calculateHydrogens(a,b,null,2056),c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var e=b[c];if(!(null==e||0==e.length))for(var g=this.ms.at[c],j=g.bonds,f=0,l=0,s=g.getBondCount();f<s;f++){var m=j[f].getOtherAtom(g);if(1==m.getAtomicAndIsotopeNumber()){var p=
e[l++];null!=p&&this.ms.setAtomCoord(m.i,p.x,p.y,p.z)}}}this.ms.resetMolecules()},"JU.BS");c(b,"setMotionFixedAtoms",function(a){this.slm.setMotionFixedAtoms(a)},"JU.BS");c(b,"setMotionFixed",function(a){this.slm.setMotionFixedAtoms(a)},"JU.BS");c(b,"getMotionFixedAtoms",function(a,b){if(0>this.am.cmi)return new JU.BS;null==b&&(b=new JU.BS);b.or(this.slm.getMotionFixedAtoms());b.and(this.getThisModelAtoms());null==a&&(a=this.getOperativeSymmetry());null!=a&&null!=this.getModelkit(!1)&&this.modelkit.addLockedAtoms(a,
b);return b},"J.api.SymmetryInterface,JU.BS");c(b,"getAtomicPropertyState",function(a,b,c,e,g){this.getStateCreator().getAtomicPropertyStateBuffer(a,b,c,e,g)},"JU.SB,~N,JU.BS,~S,~A");c(b,"getCenterAndPoints",function(a,b){return this.ms.getCenterAndPoints(a,b)},"JU.Lst,~B");c(b,"writeFileData",function(a,b,c,e){return this.getOutputManager().writeFileData(a,b,c,e)},"~S,~S,~N,~A");c(b,"getPdbData",function(a,b,c,e,g,j){return this.getPropertyManager().getPdbData(a,b,null==c?this.bsA():c,e,g,j)},"~N,~S,JU.BS,~A,JU.OC,~B");
c(b,"getGroupsWithin",function(a,b){return this.ms.getGroupsWithin(a,b)},"~N,JU.BS");c(b,"setShapeSize",function(a,b,c){null==c&&(c=this.bsA());this.shm.setShapeSizeBs(a,b,null,c)},"~N,~N,JU.BS");c(b,"setShapeProperty",function(a,b,c){0<=a&&this.shm.setShapePropertyBs(a,b,c,null)},"~N,~S,~O");c(b,"getShapeProperty",function(a,b){return this.shm.getShapePropertyIndex(a,b,-2147483648)},"~N,~S");c(b,"getShapePropertyAsInt",function(a,b){var c=this.getShapeProperty(a,b);return null==c||!C(c,Integer)?
-2147483648:c.intValue()},"~N,~S");c(b,"setModelVisibility",function(){null!=this.shm&&this.shm.setModelVisibility()});c(b,"resetShapes",function(a){this.shm.resetShapes(!a);a&&(this.shm.loadDefaultShapes(this.ms),this.clearRepaintManager(-1))},"~B");c(b,"setParallel",function(a){return this.$isParallel=this.g.multiProcessor&&a},"~B");c(b,"isParallel",function(){return this.g.multiProcessor&&this.$isParallel});c(b,"undoMoveAction",function(a,b){return this.g.preserveState?this.getStateCreator().undoMoveAction(a,
b):0},"~N,~N");c(b,"undoMoveActionClear",function(a,b,c){this.g.preserveState&&null==this.getOperativeSymmetry()&&this.getStateCreator().undoMoveActionClear(a,b,c)},"~N,~N,~B");c(b,"moveAtomWithHydrogens",function(a,b,c,e,g,j){this.stopMinimization();var f=null!=g&&0==b,l=this.ms.at[a];null==j&&(j=JU.BSUtil.newAndSetBit(a),(null==this.getOperativeSymmetry()||this.isModelKitOpen()&&!this.modelkit.hasConstraint(a,!0,!1))&&!f&&this.ms.addConnectedHAtoms(l,j));return this.moveSelected(b,c,e,-2147483648,
-2147483648,j,l,g,!0,!0,0)},"~N,~N,~N,~N,JU.P3,JU.BS");c(b,"isModelPDB",function(a){return this.ms.am[a].isBioModel},"~N");f(b,"deleteMeasurement",function(a){this.setShapeProperty(6,"delete",Integer.$valueOf(a))},"~N");f(b,"getSmiles",function(a){return this.getSmilesOpt(a,-1,-1,16|(null==a&&JU.Logger.debugging?131072:0),null)},"JU.BS");f(b,"getOpenSmiles",function(a){return this.getSmilesOpt(a,-1,-1,5|(null==a&&JU.Logger.debugging?131072:0),"/open///")},"JU.BS");c(b,"getBioSmiles",function(a){return this.getSmilesOpt(a,
-1,-1,24117248|(JU.Logger.debugging?131072:0),null)},"JU.BS");c(b,"getSmilesOpt",function(a,b,c,e,g){var j=17825792==(e&17825792)?JV.Viewer.getJmolVersion()+" "+this.getModelName(this.am.cmi):g,f=this.ms.at;null==a&&(0>b||0>c?a=this.bsA():(1048576==(e&1048576)&&(b>c&&(a=b,b=c,c=a),b=f[b].group.firstAtomIndex,c=f[c].group.lastAtomIndex),a=new JU.BS,a.setBits(b,c+1)));e|=this.isModel2D(a)?134217728:0;b=this.getSmilesMatcher();return JV.JC.isSmilesCanonical(g)?(e=b.getSmiles(f,this.ms.ac,a,"/noAromatic/",
e),this.getChemicalInfo(e,"smiles",null).trim()):b.getSmiles(f,this.ms.ac,a,j,e)},"JU.BS,~N,~N,~N,~S");c(b,"isModel2D",function(a){a=this.getModelForAtomIndex(a.nextSetBit(0));return null!=a&&"2D".equals(a.auxiliaryInfo.get("dimension"))},"JU.BS");c(b,"alert",function(a){this.prompt(a,null,null,!0)},"~S");c(b,"prompt",function(a,b,c,e){return this.$isKiosk?"null":this.apiPlatform.prompt(a,b,c,e)},"~S,~S,~A,~B");c(b,"dialogAsk",function(a,b){return prompt(a,b)},"~S,~S,java.util.Map");c(b,"initializeExporter",
function(a){var b=a.get("type").equals("JS");if(b){if(null!=this.jsExporter3D)return this.jsExporter3D.initializeOutput(this,this.privateKey,a),this.jsExporter3D}else{var c=a.get("fileName"),e=a.get("fullPath"),c=this.getOutputChannel(c,e);if(null==c)return null;a.put("outputChannel",c)}c=J.api.Interface.getOption("export.Export3D",this,"export");if(null==c)return null;a=c.initializeExporter(this,this.privateKey,this.gdata,a);b&&null!=a&&(this.jsExporter3D=c);return null==a?null:c},"java.util.Map");
c(b,"getMouseEnabled",function(){return this.refreshing&&!this.creatingImage});f(b,"calcAtomsMinMax",function(a,b){this.ms.calcAtomsMinMax(a,b)},"JU.BS,JU.BoxInfo");c(b,"getObjectMap",function(a,b){switch(b.charCodeAt(0)){case 123:null!=this.getScriptManager()&&(null!=this.definedAtomSets&&a.putAll(this.definedAtomSets),JS.T.getTokensType(a,2097152));break;case 36:case 48:this.shm.getObjectMap(a,"$"==b)}},"java.util.Map,~S");c(b,"setPicked",function(a,b){var c=null,e=null;0<=a&&(b&&this.setPicked(-1,
!1),this.g.setI("_atompicked",a),c=this.g.getParam("picked",!0),e=this.g.getParam("pickedList",!0));if(null==c||10!=c.tok)c=JS.SV.newV(10,new JU.BS),e=JS.SV.getVariableList(new JU.Lst),this.g.setUserVariable("picked",c),this.g.setUserVariable("pickedList",e);0>a||(JS.SV.getBitSet(c,!1).set(a),c=e.pushPop(null,null),10==c.tok&&e.pushPop(null,c),(10!=c.tok||!c.value.get(a))&&e.pushPop(null,JS.SV.newV(10,JU.BSUtil.newAndSetBit(a))))},"~N,~B");f(b,"runScript",function(a){return""+this.evaluateExpression(B(-1,
[B(-1,[JS.T.tokenScript,JS.T.tokenLeftParen,JS.SV.newS(a),JS.T.tokenRightParen])]))},"~S");f(b,"runScriptCautiously",function(a){var b=new JU.SB;try{if(null==this.getScriptManager())return null;this.eval.runScriptBuffer(a,b,!1)}catch(c){if(D(c,Exception))return this.eval.getErrorMessage();throw c;}return b.toString()},"~S");c(b,"setFrameDelayMs",function(a){this.ms.setFrameDelayMs(a,this.getVisibleFramesBitSet())},"~N");c(b,"getBaseModelBitSet",function(){return this.ms.getModelAtomBitSetIncludingDeleted(this.getJDXBaseModelIndex(this.am.cmi),
!0)});c(b,"clearTimeouts",function(){null!=this.timeouts&&J.thread.TimeoutThread.clear(this.timeouts)});c(b,"setTimeout",function(a,b,c){this.haveDisplay&&(!this.headless&&!this.autoExit)&&(null==a?this.clearTimeouts():(null==this.timeouts&&(this.timeouts=new java.util.Hashtable),J.thread.TimeoutThread.setTimeout(this,this.timeouts,a,b,c)))},"~S,~N,~S");c(b,"triggerTimeout",function(a){this.haveDisplay&&null!=this.timeouts&&J.thread.TimeoutThread.trigger(this.timeouts,a)},"~S");c(b,"clearTimeout",
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f(b,"siLoaded",function(a){null!=this.loadFileCallbackFunctionName&&this.appletFrame.callToJavaScript(this.loadFileCallbackFunctionName,B(-1,[this.vwr.appletName,a]));this.updateJSView(null);return null},"~S");f(b,"siExecHidden",function(){},"~B");f(b,"siExecScriptComplete",function(a,b){b||this.vwr.showMessage(a);this.siValidateAndRepaint(!1)},"~S,~B");f(b,"siUpdateBoolean",function(){},"JSV.common.ScriptToken,~B");f(b,"siCheckCallbacks",function(){this.checkCallbacks()},"~S");f(b,"siNodeSet",function(){this.appletFrame.validateContent(2);
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a,b,c,0,f&-29))},"~N,~N,~N,~N");c(b,"wheeled",function(a,b,c){null!=this.pd&&this.pd.mouseAction(3,a,0,b,0,c)},"~N,~N,~N");c(b,"pressed",function(a,b,c,f){null==this.pd?this.disposed||this.jsvp.showMenu(b,c):(this.isMouseDown=!0,this.pd.mouseAction(4,a,b,c,0,f))},"~N,~N,~N,~N,~B");c(b,"released",function(a,b,c,f){null!=this.pd&&(this.isMouseDown=!1,this.pd.mouseAction(5,a,b,c,0,f))},"~N,~N,~N,~N");c(b,"dragged",function(a,b,c,f){null!=this.pd&&(20==(f&20)&&(f=f&-5|2),this.pd.mouseAction(1,a,b,c,0,
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null!=this.app.appletReadyCallbackFunctionName&&null!=this.viewer.fullName&&this.callToJavaScript(this.app.appletReadyCallbackFunctionName,B(-1,[this.viewer.appletName,this.viewer.fullName,Boolean.TRUE,this]))});c(b,"initViewer",function(){this.viewer=this.app.vwr;this.setLogging();this.viewerOptions.remove("debug");var a=this.viewerOptions.get("display"),a=document.getElementById(a);this.viewer.setDisplay(a);JU.Logger.info(this.getAppletInfo())});c(b,"setLogging",function(){var a=this.getValue("logLevel",
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this.getParameter(a);System.out.println("getValue "+a+" = "+c);return null!=c?c:b},"~S,~S");f(b,"isPro",function(){return this.app.isPro()});f(b,"isSigned",function(){return this.app.isSigned()});f(b,"destroy",function(){this.app.dispose();this.app=null});c(b,"getParameter",function(a,b){return this.isStandalone?System.getProperty(a,b):null!=this.getParameter(a)?this.getParameter(a):b},"~S,~S");f(b,"getAppletInfo",function(){return JSV.app.JSVApp.getAppletInfo()});f(b,"getSolnColour",function(){return this.app.getSolnColour()});
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throw u;}},"J.api.GenericGraphics,JSV.common.Spectrum,JU.Lst,JSV.common.Annotation");b=G(JSV.common.Annotation,"AType",Enum);w(b,"Integration",0,[]);w(b,"PeakList",1,[]);w(b,"Measurements",2,[]);w(b,"OverlayLegend",3,[]);w(b,"Views",4,[]);w(b,"NONE",5,[])});n("JSV.common");z(["JSV.common.Annotation"],"JSV.common.ColoredAnnotation",null,function(){var b=r(function(){this.color=null;u(this,arguments)},JSV.common,"ColoredAnnotation",JSV.common.Annotation);y(b,function(){I(this,JSV.common.ColoredAnnotation,
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this.setColor(JSV.common.ScriptToken.TITLECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.UNITSCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.SCALECOLOR,JSV.common.ColorParameters.BLACK);this.setColor(JSV.common.ScriptToken.COORDINATESCOLOR,JSV.common.ColorParameters.RED);this.setColor(JSV.common.ScriptToken.GRIDCOLOR,JSV.common.ColorParameters.LIGHT_GRAY);this.setColor(JSV.common.ScriptToken.PLOTCOLOR,JSV.common.ColorParameters.BLUE);this.setColor(JSV.common.ScriptToken.PLOTAREACOLOR,
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this.displayFontName=b:this.displayFontName}return null},"JSV.common.ScriptToken,~S");b.BLACK=null;b.RED=null;b.LIGHT_GRAY=null;b.DARK_GRAY=null;b.BLUE=null;b.WHITE=null;b.defaultPlotColors=Array(8);b.defaultPlotColorNames=B(-1,"black darkGreen darkred orange magenta cyan maroon darkGray".split(" "))});n("JSV.common");var rb=G(JSV.common,"CoordComparator",null,java.util.Comparator);f(rb,"compare",function(b,a){return b.getXVal()>a.getXVal()?1:b.getXVal()<a.getXVal()?-1:0},"JSV.common.Coordinate,JSV.common.Coordinate");
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e)/(c-b);for(var g=0;g<a.length;g++)f[g]=(new JSV.common.Coordinate).set(a[g].getXVal(),(a[g].getYVal()-e)/c-b);return f},"~A,~N,~N");b.reverse=c(b,"reverse",function(a){for(var b=a.length,c=0;c<b;c++){var f=a[c];a[c]=a[--b];a[b]=f}return a},"~A");b.parseDSV=c(b,"parseDSV",function(a,b,c){var f,e=f=0,g=new JU.Lst;for(a=new java.util.StringTokenizer(a," \t\n\r\f,;");a.hasMoreTokens();)f=a.nextToken().trim(),e=a.nextToken().trim(),f=Double.parseDouble(f),e=Double.parseDouble(e),f=(new JSV.common.Coordinate).set(f*
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f=0;f<a.size();f++){var e=a.get(f).getXYCoords(),e=JSV.common.Coordinate.getMaxX(e,b.getStartingPointIndex(f),b.getEndingPointIndex(f));e>c&&(c=e)}return c},"JU.Lst,JSV.common.ViewData");b.getMinY=c(b,"getMinY",function(a,b,c){for(var f=1.7976931348623157E308;b<=c;b++){var e=a[b].getYVal();e<f&&(f=e)}return f},"~A,~N,~N");b.getMinYUser=c(b,"getMinYUser",function(a,b){for(var c=1.7976931348623157E308,f=0;f<a.size();f++){var e=a.get(f).getUserYFactor(),g=a.get(f).getYRef(),j=a.get(f).getXYCoords(),
e=(JSV.common.Coordinate.getMinY(j,b.getStartingPointIndex(f),b.getEndingPointIndex(f))-g)*e+g;e<c&&(c=e)}return c},"JU.Lst,JSV.common.ViewData");b.getMaxY=c(b,"getMaxY",function(a,b,c){for(var f=-1.7976931348623157E308;b<=c;b++){var e=a[b].getYVal();e>f&&(f=e)}return f},"~A,~N,~N");b.getMaxYUser=c(b,"getMaxYUser",function(a,b){for(var c=-1.7976931348623157E308,f=0;f<a.size();f++){var e=a.get(f).getUserYFactor(),g=a.get(f).getYRef(),j=a.get(f).getXYCoords(),e=(JSV.common.Coordinate.getMaxY(j,b.getStartingPointIndex(f),
b.getEndingPointIndex(f))-g)*e+g;e>c&&(c=e)}return c},"JU.Lst,JSV.common.ViewData");b.getYValueAt=c(b,"getYValueAt",function(a,b){var c=JSV.common.Coordinate.getNearestIndexForX(a,b);if(0==c||c==a.length)return NaN;var f=a[c].getXVal(),e=a[c-1].getXVal(),g=a[c].getYVal(),c=a[c-1].getYVal();return f==e?g:c+(g-c)/(f-e)*(b-e)},"~A,~N");b.intoRange=c(b,"intoRange",function(a,b,c){return Math.max(Math.min(a,c),b)},"~N,~N,~N");b.getNearestIndexForX=c(b,"getNearestIndexForX",function(a,b){var c=(new JSV.common.Coordinate).set(b,
0),c=java.util.Arrays.binarySearch(a,c,JSV.common.Coordinate.c);0>c&&(c=-1-c);return 0>c?0:c>a.length-1?a.length-1:c},"~A,~N");b.findXForPeakNearest=c(b,"findXForPeakNearest",function(a,b,c){b=JSV.common.Coordinate.getNearestIndexForX(a,b);for(c=c?-1:1;b<a.length-1&&0<c*(a[b+1].yVal-a[b].yVal);)b++;for(;1<=b&&0<c*(a[b-1].yVal-a[b].yVal);)b--;return 0==b||b==a.length-1?a[b].xVal:JSV.common.Coordinate.parabolicInterpolation(a,b)},"~A,~N,~B");b.parabolicInterpolation=c(b,"parabolicInterpolation",function(a,
b){var c=a[b-1].yVal,f=a[b+1].yVal;return a[b].xVal+(c-f)/2/(c-2*a[b].yVal+f)*(a[b+1].xVal-a[b].xVal)},"~A,~N");b.getPickedCoordinates=c(b,"getPickedCoordinates",function(a,b,c,f){if(null==b)return!1;var e=b.getXVal();c.setXVal(e);c.setYVal(b.getYVal());if(null==f)return!0;b=JSV.common.Coordinate.getNearestIndexForX(a,e);f.setXVal(a[b].getXVal());f.setYVal(a[b].getYVal());return!0},"~A,JSV.common.Coordinate,JSV.common.Coordinate,JSV.common.Coordinate");b.shiftX=c(b,"shiftX",function(a,b){for(var c=
a.length;0<=--c;)a[c].xVal+=b},"~A,~N");b.getNearestXWithYAbove=c(b,"getNearestXWithYAbove",function(a,b,c,f,e){b=JSV.common.Coordinate.getNearestIndexForX(a,b);var g=f?-1:1;if(e)for(;b<a.length&&0>g*(a[b].yVal-c);)b++;else for(;0<=b&&0>g*(a[b].yVal-c);)b--;return-1==b||b==a.length?NaN:JSV.common.Coordinate.findXForPeakNearest(a,a[b].getXVal(),f)},"~A,~N,~N,~B,~B");b.c=new JSV.common.CoordComparator});n("JSV.common");z(["java.lang.Enum"],"JSV.common.ExportType",null,function(){var b=G(JSV.common,
"ExportType",Enum);b.getType=c(b,"getType",function(a){a=a.toUpperCase();if(a.equalsIgnoreCase("Original..."))return JSV.common.ExportType.SOURCE;if(a.startsWith("XML"))return JSV.common.ExportType.AML;for(var b,c=0,f=JSV.common.ExportType.values();c<f.length&&((b=f[c])||1);c++)if(b.name().equals(a))return b;return JSV.common.ExportType.UNK},"~S");b.isExportMode=c(b,"isExportMode",function(a){return JSV.common.ExportType.getType(a)!==JSV.common.ExportType.UNK},"~S");w(b,"UNK",0,[]);w(b,"SOURCE",1,
[]);w(b,"DIF",2,[]);w(b,"FIX",3,[]);w(b,"SQZ",4,[]);w(b,"PAC",5,[]);w(b,"XY",6,[]);w(b,"DIFDUP",7,[]);w(b,"PNG",8,[]);w(b,"JPG",9,[]);w(b,"SVG",10,[]);w(b,"SVGI",11,[]);w(b,"CML",12,[]);w(b,"AML",13,[]);w(b,"PDF",14,[])});n("JSV.common");z(["JSV.common.XYScaleConverter","java.util.Hashtable","JU.BS","$.Lst","JSV.common.Coordinate"],"JSV.common.GraphSet","JU.DF $.PT JSV.common.Annotation $.ColorParameters $.ColoredAnnotation $.ImageView $.IntegralData $.Measurement $.MeasurementData $.PanelData $.Parameters $.PeakData $.PeakPickEvent $.PlotWidget $.ScaleData $.ScriptToken $.Spectrum $.ViewData JU.Logger".split(" "),
function(){var b=r(function(){this.gs2dLinkedY=this.gs2dLinkedX=null;this.cur1D2Locked=!1;this.spectra=this.highlights=null;this.allowStacking=this.isSplittable=!0;this.widgets=this.graphsTemp=this.pendingIntegral=this.pendingMeasurement=this.lastAnnotation=this.selectedSpectrumIntegrals=this.selectedSpectrumMeasurements=this.annotations=null;this.haveSingleYScale=this.isLinked=!1;this.iSpectrumClicked=this.iSpectrumMovedTo=0;this.iSpectrumSelected=-1;this.stackSelected=!1;this.viewData=this.bsSelected=
null;this.reversePlot=!1;this.nSplit=1;this.yStackOffsetPercent=0;this.showAllStacked=!0;this.pd=this.imageView=this.viewList=null;this.sticky2Dcursor=!1;this.nSpectra=0;this.fracY=this.fracX=1;this.fY0=this.fX0=0;this.cur2Dy=this.cur1D2x2=this.cur1D2x1=this.cur2Dx1=this.cur2Dx0=this.pin2Dy01=this.pin2Dx01=this.pin2Dy1=this.pin2Dy0=this.pin2Dx1=this.pin2Dx0=this.pin1Dy01=this.pin1Dx01=this.pin1Dy1=this.pin1Dy0=this.pin1Dx1=this.pin1Dx0=this.zoomBox2D=this.zoomBox1D=null;this.xPixels0=this.xPixel10=
this.yPixels=this.xPixels=this.yPixel000=this.yPixel11=this.xPixel11=this.yPixel00=this.xPixel00=this.yHArrows=this.xHArrows=this.xVArrows=this.yPixel1=this.xPixel1=this.yPixel0=this.xPixel0=0;this.allowStackedYScale=!0;this.drawXAxisLeftToRight=!1;this.xAxisLeftToRight=!0;this.iPreviousSpectrumClicked=-1;this.zoomEnabled=this.$haveSelectedSpectrum=!1;this.currentZoomIndex=0;this.lastClickX=NaN;this.lastPixelX=2147483647;this.bottom=this.left=this.top=this.right=this.width=this.height=0;this.coordTemp=
this.piMouseOver=null;this.FONT_PLAIN=0;this.FONT_BOLD=1;this.FONT_ITALIC=2;this.is2DSpectrum=!1;this.selectedIntegral=this.selectedMeasurement=null;this.lastXMax=NaN;this.lastSpecClicked=-1;this.inPlotMove=!1;this.xPixelMovedTo2=this.xPixelMovedTo=-1;this.xValueMovedTo=this.yValueMovedTo=0;this.haveLeftRightArrows=!1;this.yPixelPlot1=this.yPixelPlot0=this.xPixelPlot0=this.xPixelPlot1=0;this.nextClickForSetPeak=null;this.splitterY=this.splitterX=this.closerY=this.closerX=0;this.mapX=null;W("JSV.common.GraphSet.Highlight")||
JSV.common.GraphSet.$GraphSet$Highlight$();this.widgetsAreSet=!0;this.nextClickMode=this.lastIntDragX=0;this.gMain=this.g2d=this.plotColors=this.image2D=this.jsvp=this.aIntegrationRatios=this.dialogs=null;this.COLOR_GREY=-3;this.COLOR_BLACK=-2;this.COLOR_INTEGRAL=-1;u(this,arguments)},JSV.common,"GraphSet",null,JSV.common.XYScaleConverter);N(b,function(){this.highlights=new JU.Lst;this.spectra=new JU.Lst;this.graphsTemp=new JU.Lst;this.bsSelected=new JU.BS;this.coordTemp=new JSV.common.Coordinate;
this.mapX=new java.util.Hashtable});y(b,function(a){this.pd=a;this.jsvp=a.jsvp;this.g2d=a.g2d},"JSV.common.PanelData");c(b,"setSpectrumMovedTo",function(a){return this.iSpectrumMovedTo=a},"~N");c(b,"setSpectrumClicked",function(a){this.stackSelected=this.showAllStacked;if(0>a||this.iSpectrumClicked!=a)this.lastClickX=NaN,this.lastPixelX=2147483647;this.iSpectrumClicked=this.setSpectrumSelected(this.setSpectrumMovedTo(a))},"~N");c(b,"setSpectrumSelected",function(a){var b=a!=this.iSpectrumSelected;
this.iSpectrumSelected=a;b&&this.getCurrentView();return this.iSpectrumSelected},"~N");c(b,"closeDialogsExcept",function(a){if(null!=this.dialogs)for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var f=b.getValue();f.isDialog()&&(a===JSV.common.Annotation.AType.NONE||f.getAType()!==a)&&f.setVisible(!1)}},"JSV.common.Annotation.AType");c(b,"dispose",function(){this.widgets=this.graphsTemp=this.imageView=this.pendingMeasurement=this.lastAnnotation=this.annotations=this.viewList=
this.viewData=this.spectra=null;this.disposeImage();if(null!=this.dialogs)for(var a,b=this.dialogs.entrySet().iterator();b.hasNext()&&((a=b.next())||1);){var c=a.getValue();c.isDialog()&&c.dispose()}this.dialogs=null});c(b,"isDrawNoSpectra",function(){return-2147483648==this.iSpectrumSelected});c(b,"getFixedSelectedSpectrumIndex",function(){return Math.max(this.iSpectrumSelected,0)});c(b,"getSpectrum",function(){return this.getSpectrumAt(this.getFixedSelectedSpectrumIndex()).getCurrentSubSpectrum()});
c(b,"getSpectrumAt",function(a){return this.spectra.get(a)},"~N");c(b,"getSpectrumIndex",function(a){for(var b=this.spectra.size();0<=--b;)if(this.spectra.get(b)===a)return b;return-1},"JSV.common.Spectrum");c(b,"addSpec",function(a){this.spectra.addLast(a);this.nSpectra++},"JSV.common.Spectrum");c(b,"splitStack",function(a){a&&this.isSplittable?(this.nSplit=this.nSpectra,this.showAllStacked=!1,this.setSpectrumClicked(this.iSpectrumSelected),this.pd.currentSplitPoint=this.iSpectrumSelected):(this.nSplit=
1,this.showAllStacked=this.allowStacking&&!a,this.setSpectrumClicked(this.iSpectrumSelected));this.stackSelected=!1;JSV.common.GraphSet.setFractionalPositions(this.pd,this.pd.graphSets,JSV.common.PanelData.LinkMode.NONE);this.pd.setTaintedAll()},"~B");c(b,"setPositionForFrame",function(a){0>a&&(a=0);var b=this.height-50;this.xPixel00=v(this.width*this.fX0);this.xPixel11=v(this.xPixel00+this.width*this.fracX-1);this.xHArrows=this.xPixel00+25;this.xVArrows=this.xPixel11-v(this.right/2);this.xPixel0=
this.xPixel00+v(this.left*(1-this.fX0));this.xPixel10=this.xPixel1=this.xPixel11-this.right;this.xPixels0=this.xPixels=this.xPixel1-this.xPixel0+1;this.yPixel000=(0==this.fY0?25:0)+v(this.height*this.fY0);this.yPixel00=this.yPixel000+v(b*this.fracY*a);this.yPixel11=this.yPixel00+v(b*this.fracY)-1;this.yHArrows=this.yPixel11-12;this.yPixel0=this.yPixel00+v(this.top/2);this.yPixel1=this.yPixel11-v(this.bottom/2);this.yPixels=this.yPixel1-this.yPixel0+1;null!=this.imageView&&this.is2DSpectrum&&(this.setImageWindow(),
this.pd.display1D?(this.xPixels=v(Math.floor(0.8*(this.pd.display1D?1*(this.xPixels0-this.imageView.xPixels)/this.xPixels0:1)*this.xPixels0)),this.xPixel1=this.xPixel0+this.xPixels-1):(this.xPixels=0,this.xPixel1=this.imageView.xPixel0-30))},"~N");c(b,"hasPoint",function(a,b){return a>=this.xPixel00&&a<=this.xPixel11&&b>=this.yPixel000&&b<=this.yPixel11*this.nSplit},"~N,~N");c(b,"isInPlotRegion",function(a,b){return a>=this.xPixel0&&a<=this.xPixel1&&b>=this.yPixel0&&b<=this.yPixel1},"~N,~N");c(b,
"getSplitPoint",function(a){return Math.max(0,Math.min(v((a-this.yPixel000)/(this.yPixel11-this.yPixel00)),this.nSplit-1))},"~N");c(b,"isSplitWidget",function(a,b){return this.isFrameBox(a,b,this.splitterX,this.splitterY)},"~N,~N");c(b,"isCloserWidget",function(a,b){return this.isFrameBox(a,b,this.closerX,this.closerY)},"~N,~N");c(b,"initGraphSet",function(a,b){null==JSV.common.GraphSet.veryLightGrey&&(JSV.common.GraphSet.veryLightGrey=this.g2d.getColor3(200,200,200));this.setPlotColors(JSV.common.ColorParameters.defaultPlotColors);
this.xAxisLeftToRight=this.getSpectrumAt(0).shouldDisplayXAxisIncreasing();this.setDrawXAxis();var c=E(this.nSpectra,0),f=E(this.nSpectra,0);this.bsSelected.setBits(0,this.nSpectra);this.allowStackedYScale=!0;0>=b&&(b=2147483647);this.isSplittable=1<this.nSpectra;this.showAllStacked=(this.allowStacking=this.spectra.get(0).isStackable())&&1<this.nSpectra;for(var e=0;e<this.nSpectra;e++){var g=this.spectra.get(e).getXYCoords().length-1;c[e]=JSV.common.Coordinate.intoRange(a,0,g);f[e]=JSV.common.Coordinate.intoRange(b,
0,g);this.allowStackedYScale=(new Boolean(this.allowStackedYScale&(this.spectra.get(e).getYUnits().equals(this.spectra.get(0).getYUnits())&&this.spectra.get(e).getUserYFactor()==this.spectra.get(0).getUserYFactor()))).valueOf()}this.getView(0,0,0,0,c,f,null,null);this.viewList=new JU.Lst;this.viewList.addLast(this.viewData)},"~N,~N");c(b,"getView",function(a,b,c,f,e,g,j,k){var l=0==this.graphsTemp.size()?this.spectra:this.graphsTemp,s=this.getSpectrumAt(0).getSubSpectra(),m=null==s||2==s.size()&&
s.get(1).isImaginary(),p=!this.getSpectrumAt(0).is1D();m&&c==f?l=this.spectra:c==f&&(this.viewData=new JSV.common.ViewData(s,c,f,this.getSpectrum().isContinuous()),l=null);null!=l&&(this.viewData=new JSV.common.ViewData(l,c,f,e,g,this.getSpectrumAt(0).isContinuous(),p),a!=b&&this.getScale().setXRange(a,b));null!=j&&(JSV.common.ScaleData.copyScaleFactors(j,this.viewData.getScaleData()),null!=k&&JSV.common.ScaleData.copyYScales(k,this.viewData.getScaleData()),this.getCurrentView())},"~N,~N,~N,~N,~A,~A,~A,~A");
c(b,"isNearby",function(a,b,c,f){var e=a.getXVal(),g=c.toPixelX(e);a=this.toPixelY(a.getYVal());e=b.getXVal();c=c.toPixelX(e);b=this.toPixelY(b.getYVal());return Math.abs(g-c)+Math.abs(a-b)<f},"JSV.common.Coordinate,JSV.common.Coordinate,JSV.common.XYScaleConverter,~N");c(b,"setReversePlot",function(a){(this.reversePlot=a)&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);this.setDrawXAxis()},"~B");c(b,"setDrawXAxis",function(){this.drawXAxisLeftToRight=(new Boolean(this.xAxisLeftToRight^
this.reversePlot)).valueOf();for(var a=0;a<this.spectra.size();a++)this.spectra.get(a).setExportXAxisDirection(this.drawXAxisLeftToRight)});c(b,"isInTopBar",function(a,b){return a==this.fixX(a)&&b>this.pin1Dx0.yPixel0-2&&b<this.pin1Dx0.yPixel1},"~N,~N");c(b,"isInTopBar2D",function(a,b){return null!=this.imageView&&a==this.imageView.fixX(a)&&b>this.pin2Dx0.yPixel0-2&&b<this.pin2Dx0.yPixel1},"~N,~N");c(b,"isInRightBar",function(a,b){return b==this.fixY(b)&&a>this.pin1Dy0.xPixel1&&a<this.pin1Dy0.xPixel0+
2},"~N,~N");c(b,"isInRightBar2D",function(a,b){return null!=this.imageView&&b==this.fixY(b)&&a>this.pin2Dy0.xPixel1&&a<this.pin2Dy0.xPixel0+2},"~N,~N");c(b,"toX0",function(a){return this.viewList.get(0).getScale().toX0(this.fixX(a),this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(b,"toY0",function(a){return this.viewList.get(0).getScale().toY0(this.fixY(a),this.yPixel0,this.yPixel1)},"~N");f(b,"toX",function(a){return null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toX(a):
this.getScale().toX(this.fixX(a),this.xPixel1,this.drawXAxisLeftToRight)},"~N");f(b,"toY",function(a){return this.getScale().toY(a,this.yPixel0)},"~N");c(b,"toPixelX",function(a){return this.getScale().toPixelX(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(b,"toPixelY",function(a){return this.getScale().toPixelY(a,this.yPixel1)},"~N");c(b,"toPixelX0",function(a){return this.viewList.get(0).getScale().toPixelX0(a,this.xPixel0,this.xPixel1,this.drawXAxisLeftToRight)},"~N");c(b,"toPixelY0",
function(a){return this.fixY(this.viewList.get(0).getScale().toPixelY0(a,this.yPixel0,this.yPixel1))},"~N");c(b,"fixX",function(a){return JSV.common.Coordinate.intoRange(a,this.xPixel0,this.xPixel1)},"~N");c(b,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,this.yPixel0,this.yPixel1)},"~N");c(b,"getXPixel0",function(){return this.xPixel0});c(b,"getXPixels",function(){return this.xPixels});f(b,"getYPixels",function(){return this.yPixels});c(b,"getScale",function(){return this.viewData.getScale()});
c(b,"toPixelYint",function(a){return this.yPixel1-v(Double.isNaN(a)?-2147483648:this.yPixels*a)},"~N");c(b,"findAnnotation2D",function(a){for(var b=this.annotations.size();0<=--b;){var c=this.annotations.get(b);if(this.isNearby(c,a,this.imageView,10))return c}return null},"JSV.common.Coordinate");c(b,"addAnnotation",function(a,b){null==this.annotations&&(this.annotations=new JU.Lst);for(var c=!1,f=this.annotations.size();0<=--f;)if(a.is2D?this.isNearby(this.annotations.get(f),a,this.imageView,10):
a.equals(this.annotations.get(f)))c=!0,this.annotations.removeItemAt(f);0<a.text.length&&(!c||!b)&&this.annotations.addLast(a)},"JSV.common.Annotation,~B");c(b,"setImageWindow",function(){this.imageView.setPixelWidthHeight(v((this.pd.display1D?0.6:1)*this.xPixels0),this.yPixels);this.imageView.setXY0(this.getSpectrumAt(0),v(Math.floor(this.xPixel10-this.imageView.xPixels)),this.yPixel0)});c(b,"findNearestMaxMin",function(){if(1<this.nSpectra&&0>this.iSpectrumClicked)return!1;this.xValueMovedTo=this.getSpectrum().findXForPeakNearest(this.xValueMovedTo);
this.setXPixelMovedTo(this.xValueMovedTo,1.7976931348623157E308,0,0);return!Double.isNaN(this.xValueMovedTo)});c(b,"setXPixelMovedTo",function(a,b,c,f){1.7976931348623157E308==a&&1.7976931348623157E308==b?(this.xPixelMovedTo=c,this.xPixelMovedTo2=f,this.isLinked&&this.sticky2Dcursor&&this.pd.setlinkedXMove(this,this.toX(this.xPixelMovedTo),!1)):(1.7976931348623157E308!=a&&(this.xPixelMovedTo=this.toPixelX(a),this.fixX(this.xPixelMovedTo)!=this.xPixelMovedTo&&(this.xPixelMovedTo=-1),this.xPixelMovedTo2=
-1,1E10!=a&&this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex())),1.7976931348623157E308!=b&&(this.xPixelMovedTo2=this.toPixelX(b)))},"~N,~N,~N,~N");c(b,"processPendingMeasurement",function(a,b,c){if(!this.isInPlotRegion(a,b)||this.is2dClick(a,b))this.pendingMeasurement=null;else{var f=this.toX(a),e=this.toY(b),g=f;switch(c){case 0:this.pendingMeasurement.setPt2(this.toX(a),this.toY(b));break;case 3:case 2:if(0>this.iSpectrumClicked)break;var j=this.spectra.get(this.iSpectrumClicked);this.setScale(this.iSpectrumClicked);
3!=c&&(c=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,1),null!=c?(f=c.getXVal(),e=c.getYVal()):null!=(c=this.findMeasurement(this.selectedSpectrumMeasurements,a,b,2))?(f=c.getXVal2(),e=c.getYVal2()):f=this.getNearestPeak(j,f,e));this.pendingMeasurement=(new JSV.common.Measurement).setM1(f,e,j);this.pendingMeasurement.setPt2(g,e);this.pd.setTaintedAll();this.pd.repaint();break;case 1:case -2:case -3:for(g=null!=this.pendingMeasurement&&this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,
-1));g;){this.setScale(this.getSpectrumIndex(this.pendingMeasurement.spec));if(3!=c){if(!this.findNearestMaxMin()){g=!1;break}a=this.xPixelMovedTo}f=this.toX(a);e=this.toY(b);this.pendingMeasurement.setPt2(f,e);if(0==this.pendingMeasurement.text.length){g=!1;break}this.setMeasurement(this.pendingMeasurement);if(1!=c){g=!1;break}this.setSpectrumClicked(this.getSpectrumIndex(this.pendingMeasurement.spec));this.pendingMeasurement=(new JSV.common.Measurement).setM1(f,e,this.pendingMeasurement.spec);break}g||
(this.pendingMeasurement=null);this.pd.setTaintedAll();this.pd.repaint();break;case 5:this.findNearestMaxMin()?(a=this.getFixedSelectedSpectrumIndex(),Double.isNaN(this.lastXMax)||this.lastSpecClicked!=a||null==this.pendingMeasurement?(this.lastXMax=this.xValueMovedTo,this.lastSpecClicked=a,this.pendingMeasurement=(new JSV.common.Measurement).setM1(this.xValueMovedTo,this.yValueMovedTo,this.spectra.get(a))):(this.pendingMeasurement.setPt2(this.xValueMovedTo,this.yValueMovedTo),0<this.pendingMeasurement.text.length&&
this.setMeasurement(this.pendingMeasurement),this.pendingMeasurement=null,this.lastXMax=NaN)):this.lastXMax=NaN}}},"~N,~N,~N");c(b,"checkIntegralNormalizationClick",function(a,b){if(null==this.selectedSpectrumIntegrals)return!1;var c=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5);if(null==c)return!1;this.selectedIntegral=c;this.pd.normalizeIntegral();this.updateDialog(JSV.common.Annotation.AType.Integration,-1);this.setSpectrumClicked(this.getSpectrumIndex(c.spec));return!0},"~N,~N");
c(b,"getNearestPeak",function(a,b,c){var f=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!1);a=JSV.common.Coordinate.getNearestXWithYAbove(a.getXYCoords(),b,c,a.isInverted(),!0);return Double.isNaN(f)?a:Double.isNaN(a)?f:Math.abs(f-b)<Math.abs(a-b)?f:a},"JSV.common.Spectrum,~N,~N");c(b,"findMeasurement",function(a,b,c,f){if(null==a||0==a.size())return null;if(0==f){var e=this.findMeasurement(a,b,c,-1);return null!=e||C(a.get(0),"JSV.common.Integral")?e:this.findMeasurement(a,
b,c,-2)}for(var g=a.size();0<=--g;){var e=a.get(g),j,k,l,s;C(e,"JSV.common.Integral")?(j=k=this.toPixelX(e.getXVal2()),l=this.toPixelYint(e.getYVal()),s=this.toPixelYint(e.getYVal2())):(j=this.toPixelX(e.getXVal()),k=this.toPixelX(e.getXVal2()),l=s=-2==f?this.yPixel1-2:this.toPixelY(e.getYVal()));switch(f){case 1:if(4>Math.abs(b-j)+Math.abs(c-l))return e;break;case 2:if(4>Math.abs(b-k)+Math.abs(c-s))return e;break;case -5:l=s=v((l+s)/2),k=j+20;default:case -1:case -2:if(JSV.common.GraphSet.isOnLine(b,
c,j,l,k,s))return e}}return null},"JSV.common.MeasurementData,~N,~N,~N");c(b,"setMeasurement",function(a){var b=this.getSpectrumIndex(a.spec),c=this.getDialog(JSV.common.Annotation.AType.Measurements,b);null==c&&this.addDialog(b,JSV.common.Annotation.AType.Measurements,c=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,a.spec));c.getData().addLast(a.copyM());this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)},"JSV.common.Measurement");c(b,"checkArrowUpDownClick",
function(a,b){var c=!1,f=this.isArrowClick(a,b,3)?JSV.common.GraphSet.RT2:this.isArrowClick(a,b,4)?1/JSV.common.GraphSet.RT2:0;if(0!=f){1<this.nSplit&&this.setSpectrumSelected(this.iSpectrumMovedTo);if((1==this.nSpectra||0<=this.iSpectrumSelected)&&this.spectra.get(this.getFixedSelectedSpectrumIndex()).isTransmittance())f=1/f;this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,f);c=!0}else this.isArrowClick(a,b,-1)&&(this.resetViewCompletely(),c=!0);c&&(null!=this.imageView&&
(this.update2dImage(!1),this.resetPinsFromView()),this.pd.setTaintedAll());return c},"~N,~N");c(b,"resetViewCompletely",function(){this.clearViews();this.showAllStacked&&!this.stackSelected&&this.closeDialogsExcept(JSV.common.Annotation.AType.NONE);this.viewData.resetScaleFactors();this.updateDialogs()});c(b,"checkArrowLeftRightClick",function(a,b){if(this.haveLeftRightArrows){var c=this.isArrowClick(a,b,1)?-1:this.isArrowClick(a,b,2)?1:0;if(0!=c)return c=this.iSpectrumSelected+c,0>c&&(c=this.nSpectra-
1),this.setSpectrumClicked(c%this.nSpectra),!0;if(this.isArrowClick(a,b,0)){if(this.showAllStacked)return this.showAllStacked=!1,this.setSpectrumClicked(this.getFixedSelectedSpectrumIndex()),!0;this.showAllStacked=this.allowStacking;this.setSpectrumSelected(-1);this.stackSelected=!1}}return!1},"~N,~N");c(b,"isArrowClick",function(a,b,c){switch(c){case 3:case 4:case -1:return c=v((this.yPixel00+this.yPixel11)/2)+15*(3==c?-1:4==c?1:0),10>Math.abs(this.xVArrows-a)&&10>Math.abs(c-b);case 1:case 2:case 0:return c=
this.xHArrows+15*(1==c?-1:2==c?1:0),10>Math.abs(c-a)&&10>Math.abs(this.yHArrows-b)}return!1},"~N,~N,~N");c(b,"setWidgetValueByUser",function(a){var b;b=a===this.cur2Dy?""+this.imageView.toSubspectrumIndex(a.yPixel0):a===this.pin1Dx01?""+Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal())+" - "+Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()):a===this.pin1Dy01?""+Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal())+" - "+Math.max(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()):a===this.pin2Dx01?
""+Math.min(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal())+" - "+Math.max(this.pin2Dx0.getXVal(),this.pin2Dx1.getXVal()):a===this.pin2Dy01?""+v(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+v(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):""+a.getValue();b=this.pd.getInput("New value?","Set Slider",b);if(null!=b){b=b.trim();try{if(a===this.pin1Dx01||a===this.pin1Dy01||a===this.pin2Dx01||a===this.pin2Dy01){var c=b.indexOf("-",1);if(!(0>c)){var f=Double.$valueOf(b.substring(0,
c)).doubleValue(),e=Double.$valueOf(b.substring(c+1)).doubleValue();a===this.pin1Dx01?this.doZoom(f,this.pin1Dy0.getYVal(),e,this.pin1Dy1.getYVal(),!0,!1,!1,!0,!0):a===this.pin1Dy01?this.doZoom(this.pin1Dx0.getXVal(),f,this.pin1Dx1.getXVal(),e,null==this.imageView,null==this.imageView,!1,!1,!0):a===this.pin2Dx01?(this.imageView.setView0(this.imageView.toPixelX0(f),this.pin2Dy0.yPixel0,this.imageView.toPixelX0(e),this.pin2Dy1.yPixel0),this.doZoom(f,this.pin1Dy0.getYVal(),e,this.pin1Dy1.getYVal(),!1,
!1,!1,!0,!0)):a===this.pin2Dy01&&(this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.toPixelY0(f),this.pin2Dx1.xPixel0,this.imageView.toPixelY0(e)),this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!1,!0))}}else{var g=Double.$valueOf(b).doubleValue();a.isXtype?(e=a===this.pin1Dx0||a===this.cur2Dx0||a===this.pin2Dx0?this.pin1Dx1.getXVal():this.pin1Dx0.getXVal(),this.doZoom(g,
0,e,0,!a.is2D,!1,!1,!0,!0)):a===this.cur2Dy?this.setCurrentSubSpectrum(v(g)):a===this.pin2Dy0||a===this.pin2Dy1?(e=a===this.pin2Dy0?this.pin2Dy1.yPixel0:this.pin2Dy0.yPixel0,this.imageView.setView0(this.pin2Dx0.xPixel0,this.imageView.subIndexToPixelY(v(g)),this.pin2Dx1.xPixel0,e)):(e=a===this.pin1Dy0?this.pin1Dy1.getYVal():this.pin1Dy0.getYVal(),this.doZoom(this.pin1Dx0.getXVal(),g,this.pin1Dx1.getXVal(),e,null==this.imageView,null==this.imageView,!1,!1,!0))}}catch(j){if(!D(j,Exception))throw j;}}},
"JSV.common.PlotWidget");c(b,"removeAllHighlights",function(a){if(null==a)this.highlights.clear();else for(var b=this.highlights.size();0<=--b;)this.highlights.get(b).spectrum===a&&this.highlights.removeItemAt(b)},"JSV.common.Spectrum");c(b,"setCoordClicked",function(a,b,c){0==c&&(this.nextClickForSetPeak=null);if(Double.isNaN(b))return this.pd.coordClicked=null,this.pd.coordsClicked=null;this.pd.coordClicked=(new JSV.common.Coordinate).set(this.lastClickX=b,c);this.pd.coordsClicked=this.getSpectrum().getXYCoords();
this.pd.xPixelClicked=this.lastPixelX=a;return this.pd.coordClicked},"~N,~N,~N");c(b,"setWidgets",function(a,b,c){if(a||null==this.pin1Dx0)null==this.zoomBox1D?this.newPins():this.resetPinPositions();this.setDerivedPins(b);this.setPinSliderPositions(c)},"~B,~N,~B");c(b,"newPins",function(){this.zoomBox1D=new JSV.common.PlotWidget("zoomBox1D");this.pin1Dx0=new JSV.common.PlotWidget("pin1Dx0");this.pin1Dx1=new JSV.common.PlotWidget("pin1Dx1");this.pin1Dy0=new JSV.common.PlotWidget("pin1Dy0");this.pin1Dy1=
new JSV.common.PlotWidget("pin1Dy1");this.pin1Dx01=new JSV.common.PlotWidget("pin1Dx01");this.pin1Dy01=new JSV.common.PlotWidget("pin1Dy01");this.cur1D2x1=new JSV.common.PlotWidget("cur1D2x1");this.cur1D2x1.color=JSV.common.ScriptToken.PEAKTABCOLOR;this.cur1D2x2=new JSV.common.PlotWidget("cur1D2x2");this.cur1D2x2.color=JSV.common.ScriptToken.PEAKTABCOLOR;if(null!=this.imageView){this.zoomBox2D=new JSV.common.PlotWidget("zoomBox2D");this.pin2Dx0=new JSV.common.PlotWidget("pin2Dx0");this.pin2Dx1=new JSV.common.PlotWidget("pin2Dx1");
this.pin2Dy0=new JSV.common.PlotWidget("pin2Dy0");this.pin2Dy1=new JSV.common.PlotWidget("pin2Dy1");this.pin2Dx01=new JSV.common.PlotWidget("pin2Dx01");this.pin2Dy01=new JSV.common.PlotWidget("pin2Dy01");this.cur2Dx0=new JSV.common.PlotWidget("cur2Dx0");this.cur2Dx1=new JSV.common.PlotWidget("cur2Dx1");this.cur2Dy=new JSV.common.PlotWidget("cur2Dy");this.pin2Dy0.setY(0,this.imageView.toPixelY0(0));var a=this.getSpectrumAt(0).getSubSpectra().size();this.pin2Dy1.setY(a,this.imageView.toPixelY0(a))}this.setWidgetX(this.pin1Dx0,
this.getScale().minX);this.setWidgetX(this.pin1Dx1,this.getScale().maxX);this.setWidgetY(this.pin1Dy0,this.getScale().minY);this.setWidgetY(this.pin1Dy1,this.getScale().maxY);this.widgets=B(-1,[this.zoomBox1D,this.zoomBox2D,this.pin1Dx0,this.pin1Dx01,this.pin1Dx1,this.pin1Dy0,this.pin1Dy01,this.pin1Dy1,this.pin2Dx0,this.pin2Dx01,this.pin2Dx1,this.pin2Dy0,this.pin2Dy01,this.pin2Dy1,this.cur2Dx0,this.cur2Dx1,this.cur2Dy,this.cur1D2x1,this.cur1D2x2])});c(b,"setWidgetX",function(a,b){a.setX(b,this.toPixelX0(b))},
"JSV.common.PlotWidget,~N");c(b,"setWidgetY",function(a,b){a.setY(b,this.toPixelY0(b))},"JSV.common.PlotWidget,~N");c(b,"resetPinsFromView",function(){null!=this.pin1Dx0&&(this.setWidgetX(this.pin1Dx0,this.getScale().minXOnScale),this.setWidgetX(this.pin1Dx1,this.getScale().maxXOnScale),this.setWidgetY(this.pin1Dy0,this.getScale().minYOnScale),this.setWidgetY(this.pin1Dy1,this.getScale().maxYOnScale))});c(b,"resetPinPositions",function(){this.resetX(this.pin1Dx0);this.resetY(this.pin1Dy0);this.resetY(this.pin1Dy1);
null==this.imageView?(null!=this.gs2dLinkedX&&this.resetX(this.cur1D2x1),null!=this.gs2dLinkedY&&this.resetX(this.cur1D2x2)):(this.pin2Dy0.setY(this.pin2Dy0.getYVal(),this.imageView.toPixelY0(this.pin2Dy0.getYVal())),this.pin2Dy1.setY(this.pin2Dy1.getYVal(),this.imageView.toPixelY0(this.pin2Dy1.getYVal())))});c(b,"resetX",function(a){this.setWidgetX(a,a.getXVal())},"JSV.common.PlotWidget");c(b,"resetY",function(a){this.setWidgetY(a,a.getYVal())},"JSV.common.PlotWidget");c(b,"setPinSliderPositions",
function(a){this.pin1Dx0.yPixel0=this.pin1Dx1.yPixel0=this.pin1Dx01.yPixel0=this.yPixel0-5;this.pin1Dx0.yPixel1=this.pin1Dx1.yPixel1=this.pin1Dx01.yPixel1=this.yPixel0;this.cur1D2x1.yPixel1=this.cur1D2x2.yPixel1=this.yPixel0-5;this.cur1D2x1.yPixel0=this.cur1D2x2.yPixel0=this.yPixel1+6;null==this.imageView?(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=this.pin1Dy01.xPixel0=this.xPixel1+5,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.xPixel1):(this.pin1Dy0.xPixel0=this.pin1Dy1.xPixel0=
this.pin1Dy01.xPixel0=this.imageView.xPixel1+15,this.pin1Dy0.xPixel1=this.pin1Dy1.xPixel1=this.pin1Dy01.xPixel1=this.imageView.xPixel1+10,this.pin2Dx0.yPixel0=this.pin2Dx1.yPixel0=this.pin2Dx01.yPixel0=this.yPixel0-5,this.pin2Dx0.yPixel1=this.pin2Dx1.yPixel1=this.pin2Dx01.yPixel1=this.yPixel0,this.pin2Dy0.xPixel0=this.pin2Dy1.xPixel0=this.pin2Dy01.xPixel0=this.imageView.xPixel1+5,this.pin2Dy0.xPixel1=this.pin2Dy1.xPixel1=this.pin2Dy01.xPixel1=this.imageView.xPixel1,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=
this.yPixel1+6,this.cur2Dx0.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dx0.yPixel0=this.cur2Dx1.yPixel0=this.yPixel1+6,this.cur2Dx1.yPixel1=this.cur2Dx1.yPixel1=this.yPixel0-5,this.cur2Dy.xPixel0=a?v((this.xPixel1+this.imageView.xPixel0)/2):this.imageView.xPixel0-6,this.cur2Dy.xPixel1=this.imageView.xPixel1+5)},"~B");c(b,"setDerivedPins",function(a){this.widgetsAreSet=!0;null!=this.gs2dLinkedX&&this.cur1D2x1.setX(this.cur1D2x1.getXVal(),this.toPixelX(this.cur1D2x1.getXVal()));null!=this.gs2dLinkedY&&
this.cur1D2x2.setX(this.cur1D2x2.getXVal(),this.toPixelX(this.cur1D2x2.getXVal()));this.pin1Dx01.setX(0,v((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2));this.pin1Dy01.setY(0,v((this.pin1Dy0.yPixel0+this.pin1Dy1.yPixel0)/2));this.pin1Dx01.setEnabled(Math.min(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)>this.xPixel0||Math.max(this.pin1Dx0.xPixel0,this.pin1Dx1.xPixel0)<this.xPixel1);this.pin1Dy01.setEnabled(Math.min(this.pin1Dy0.yPixel0,this.pin1Dy1.yPixel0)>Math.min(this.toPixelY(this.getScale().minY),
this.toPixelY(this.getScale().maxY))||Math.max(this.pin1Dy0.yPixel0,this.pin1Dy1.yPixel0)<Math.max(this.toPixelY(this.getScale().minY),this.toPixelY(this.getScale().maxY)));if(null!=this.imageView){var b=this.pin1Dx0.getXVal();this.cur2Dx0.setX(b,this.imageView.toPixelX(b));b=this.pin1Dx1.getXVal();this.cur2Dx1.setX(b,this.imageView.toPixelX(b));b=this.imageView.toX(this.imageView.xPixel0);this.pin2Dx0.setX(b,this.imageView.toPixelX0(b));b=this.imageView.toX(this.imageView.xPixel1);this.pin2Dx1.setX(b,
this.imageView.toPixelX0(b));this.pin2Dx01.setX(0,v((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2));b=this.imageView.imageHeight-1-this.imageView.yView1;this.pin2Dy0.setY(b,this.imageView.toPixelY0(b));b=this.imageView.imageHeight-1-this.imageView.yView2;this.pin2Dy1.setY(b,this.imageView.toPixelY0(b));this.pin2Dy01.setY(0,v((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2));this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=this.imageView.subIndexToPixelY(a);this.pin2Dx01.setEnabled(Math.min(this.pin2Dx0.xPixel0,
this.pin2Dx1.xPixel0)!=this.imageView.xPixel0||Math.max(this.pin2Dx0.xPixel0,this.pin2Dx1.xPixel1)!=this.imageView.xPixel1);this.pin2Dy01.setEnabled(Math.min(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel0)!=this.yPixel0||Math.max(this.pin2Dy0.yPixel0,this.pin2Dy1.yPixel1)!=this.yPixel1)}},"~N");c(b,"doZoom",function(a,b,c,f,e,g,j,k,l){a==c?(a=this.getScale().minXOnScale,c=this.getScale().maxXOnScale):this.isLinked&&k&&this.pd.doZoomLinked(this,a,c,l,j,e);a>c&&(k=a,a=c,c=k);b>f&&(k=b,b=f,f=k);k=!e&&null!=
this.imageView&&(this.imageView.minZ!=b||this.imageView.maxZ!=f);if(this.zoomEnabled||k){if(j){if(!this.getScale().isInRangeX(a)&&!this.getScale().isInRangeX(c))return;this.getScale().isInRangeX(a)?this.getScale().isInRangeX(c)||(c=this.getScale().maxX):a=this.getScale().minX}this.pd.setTaintedAll();j=this.viewData.getScaleData();var s=E(this.nSpectra,0),m=E(this.nSpectra,0);this.graphsTemp.clear();var p=this.getSpectrumAt(0).getSubSpectra(),p=null==p||2==p.size();if(this.getSpectrumAt(0).is1D()&&
!p){if(this.graphsTemp.addLast(this.getSpectrum()),!JSV.common.ScaleData.setDataPointIndices(this.graphsTemp,a,c,3,s,m))return}else if(!JSV.common.ScaleData.setDataPointIndices(this.spectra,a,c,3,s,m))return;if(p=b==f)e=!k&&e?e=this.getScale().spectrumScaleFactor:1,1E-4>Math.abs(e-1)&&(b=this.getScale().minYOnScale,f=this.getScale().maxYOnScale);e=null;if(p||g)this.getCurrentView(),e=this.viewData.getNewScales(this.iSpectrumSelected,p,b,f);this.getView(a,c,b,f,s,m,j,e);this.setXPixelMovedTo(1E10,
1.7976931348623157E308,0,0);this.setWidgetX(this.pin1Dx0,a);this.setWidgetX(this.pin1Dx1,c);this.setWidgetY(this.pin1Dy0,b);this.setWidgetY(this.pin1Dy1,f);null==this.imageView?this.updateDialogs():(a=this.getSpectrumAt(0).getSubIndex(),c=this.imageView.fixSubIndex(a),c!=a&&this.setCurrentSubSpectrum(c),k&&this.update2dImage(!1));l&&this.addCurrentZoom()}},"~N,~N,~N,~N,~B,~B,~B,~B,~B");c(b,"updateDialogs",function(){this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);this.updateDialog(JSV.common.Annotation.AType.Measurements,
-1)});c(b,"setCurrentSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.setCurrentSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(b,"addCurrentZoom",function(){if(this.viewList.size()>this.currentZoomIndex+1)for(var a=this.viewList.size()-1;a>this.currentZoomIndex;a--)this.viewList.removeItemAt(a);this.viewList.addLast(this.viewData);this.currentZoomIndex++});c(b,"setZoomTo",
function(a){this.currentZoomIndex=a;this.viewData=this.viewList.get(a);this.resetPinsFromView()},"~N");c(b,"clearViews",function(){this.isLinked&&this.pd.clearLinkViews(this);this.setZoom(0,0,0,0);for(var a=this.viewList.size();1<=--a;)this.viewList.removeItemAt(a)});c(b,"drawAll",function(a,b,c,f,e,g,j){this.g2d=this.pd.g2d;this.gMain=a;var k=this.getSpectrumAt(0),l=k.getSubIndex();this.is2DSpectrum=!k.is1D()&&(this.isLinked||this.pd.getBoolean(JSV.common.ScriptToken.DISPLAY2D))&&(null!=this.imageView||
this.get2DImage(k));null!=this.imageView&&g&&(this.pd.isPrinting&&this.g2d!==this.pd.g2d0&&this.g2d.newGrayScaleImage(a,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,this.imageView.getBuffer()),this.is2DSpectrum&&this.setPositionForFrame(f),this.draw2DImage());var s=this.stackSelected||!this.showAllStacked?this.iSpectrumSelected:-1,m=!this.showAllStacked||1==this.nSpectra||0<=s,k=null==this.imageView||this.pd.display1D,p=0<=s?1:0,n=this.getFixedSelectedSpectrumIndex();if(k&&g&&
(this.fillBox(a,this.xPixel0,this.yPixel0,this.xPixel1,this.yPixel1,JSV.common.ScriptToken.PLOTAREACOLOR),0>s)){m=!0;for(s=0;s<this.nSpectra;s++)this.doPlot(s,f)&&0!=p++&&(m=(new Boolean(m&this.viewData.areYScalesSame(s-1,s))).valueOf())}var r=1==this.nSpectra?0:!this.showAllStacked?this.iSpectrumMovedTo:this.iSpectrumSelected;c=c===a?b:c;if(g){var s=this.pd.getCurrentGraphSet()===this&&!this.isLinked&&(!this.isSplittable||1==this.nSplit||this.pd.currentSplitPoint==f),u=this.zoomEnabled&&!this.isDrawNoSpectra()&&
this.pd.isCurrentGraphSet(this)&&this.spectra.get(0).isScalable()&&(s||1==this.nSpectra)&&(1==this.nSplit||this.pd.currentSplitPoint==this.iSpectrumMovedTo);this.drawFrame(a,r,s,this.isSplittable,u)}if(this.pd.isCurrentGraphSet(this)&&f==this.pd.currentSplitPoint&&(2>p||0<=this.iSpectrumSelected))this.$haveSelectedSpectrum=!0;this.haveSingleYScale=this.showAllStacked&&1<this.nSpectra?this.allowStackedYScale&&m:!0;if(k){m=F(this.yPixels*(this.yStackOffsetPercent/100));this.haveLeftRightArrows=!1;for(u=
s=0;s<this.nSpectra;s++)if(this.doPlot(s,f)){var r=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=s,v=!this.reversePlot&&this.getShowAnnotation(JSV.common.Annotation.AType.Integration,s)&&(!this.showAllStacked||this.iSpectrumSelected==s)?this.getDialog(JSV.common.Annotation.AType.Integration,s).getData():null;this.setScale(s);var w=this.spectra.get(s);1<this.nSplit&&(n=s);var y=!r&&(1==this.nSplit||this.showAllStacked||this.iSpectrumSelected==f),z=y&&this.$haveSelectedSpectrum&&
s==n;y&&(this.resetPinsFromView(),this.drawWidgets(b,c,l,e,k,z,!1));this.haveSingleYScale&&(s==n&&g)&&(this.drawGrid(a),this.pd.isPrinting&&1<this.nSplit&&this.drawSpectrumSource(a,s));y&&this.drawWidgets(b,c,l,!1,k,z,!0);!this.isDrawNoSpectra()&&((1==this.nSpectra||0<=this.iSpectrumSelected)&&(this.haveSingleYScale&&s==n||this.showAllStacked&&this.stackSelected&&s==this.iSpectrumSelected))&&this.drawHighlightsAndPeakTabs(b,c,s);if(g){if((1==p&&0>this.iSpectrumSelected||this.iSpectrumSelected==s&&
this.pd.isCurrentGraphSet(this))&&this.pd.titleOn&&!this.pd.titleDrawn)this.pd.drawTitle(a,this.height,this.width,this.pd.getDrawTitle(this.pd.isPrinting)),this.pd.titleDrawn=!0;this.haveSingleYScale&&s==n&&(this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.YUNITSON)&&this.drawYUnits(a))}var y=w.isContinuous(),z=(1<this.nSplit?s==this.iSpectrumMovedTo:this.isLinked||s==n)&&!this.pd.isPrinting&&y,B=!r&&null!=this.pendingIntegral&&
w===this.pendingIntegral.spec;if(g||B)this.drawPlot(B&&!g?b:a,s,w,y,u,r,null,z,B,j);this.drawIntegration(b,s,u,r,v,y,z);this.drawMeasurements(b,s);null!=this.pendingMeasurement&&this.pendingMeasurement.spec===w&&this.drawMeasurement(b,this.pendingMeasurement);z&&0<=this.xPixelMovedTo&&this.drawSpectrumPointer(b,w,u,v);1<this.nSpectra&&(1==this.nSplit&&this.pd.isCurrentGraphSet(this)&&g)&&(this.haveLeftRightArrows=!0,this.pd.isPrinting||(this.setScale(0),r=this.iSpectrumSelected,2!=this.nSpectra&&
(this.setPlotColor(a,(r+this.nSpectra-1)%this.nSpectra),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,1,this.yHArrows,this.xHArrows-9,!1)),0<=r&&(this.setPlotColor(a,r),this.fillCircle(a,this.xHArrows,this.yHArrows,!0)),this.setCurrentBoxColor(a),this.fillCircle(a,this.xHArrows,this.yHArrows,!1),this.setPlotColor(a,(r+1)%this.nSpectra),this.fillArrow(a,2,this.yHArrows,this.xHArrows+9,!0),this.setCurrentBoxColor(a),this.fillArrow(a,2,this.yHArrows,
this.xHArrows+9,!1)));u-=m}g&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&this.drawXScale(a,this),this.pd.getBoolean(JSV.common.ScriptToken.XUNITSON)&&this.drawXUnits(a))}else g&&(this.pd.getBoolean(JSV.common.ScriptToken.XSCALEON)&&this.drawXScale(a,this.imageView),this.pd.getBoolean(JSV.common.ScriptToken.YSCALEON)&&this.drawYScale(a,this.imageView),0<=l&&this.draw2DUnits(a)),this.drawWidgets(b,c,l,e,k,!0,!1),this.drawWidgets(b,c,l,e,k,!0,!0),this.widgetsAreSet=!0;null!=this.annotations&&
this.drawAnnotations(b,this.annotations,null)},"~O,~O,~O,~N,~B,~B,~B");c(b,"drawSpectrumSource",function(a,b){this.pd.printFilePath(a,this.pd.thisWidth-this.pd.right,this.yPixel0,this.spectra.get(b).getFilePath())},"~O,~N");c(b,"doPlot",function(a,b){var c=this.stackSelected&&0<=this.iSpectrumSelected&&this.iSpectrumSelected!=a,f=this.showAllStacked||-1==this.iSpectrumSelected||this.iSpectrumSelected==a;return 1<this.nSplit?a==b:f&&(!this.pd.isPrinting||!c)},"~N,~N");c(b,"drawSpectrumPointer",function(a,
b,c,f){this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);var e=this.pd.integralShiftMode;null!=f&&((!this.pd.ctrlPressed||this.pd.isIntegralDrag)&&!this.isOnSpectrum(this.pd.mouseX,this.pd.mouseY,-1)?f=null:0==e&&(e=this.getShiftMode(this.pd.mouseX,this.pd.mouseY),0==e&&(e=2147483647)));var g=this.yValueMovedTo;this.yValueMovedTo=null==f?b.getYValueAt(this.xValueMovedTo):f.getPercentYValueAt(this.xValueMovedTo);this.setCoordStr(this.xValueMovedTo,this.yValueMovedTo);if(0!=e&&(this.setPlotColor(a,
2147483647==e?-1:0),(0>e||2147483647==e)&&this.drawHandle(a,this.xPixelPlot1,this.yPixelPlot0,3,!1),0<e&&this.drawHandle(a,this.xPixelPlot0,this.yPixelPlot1,3,!1),2147483647!=e))return;null!=f&&this.g2d.setStrokeBold(a,!0);Double.isNaN(g)||null!=this.pendingMeasurement?(this.g2d.drawLine(a,this.xPixelMovedTo,this.yPixel0,this.xPixelMovedTo,this.yPixel1),0<=this.xPixelMovedTo2&&this.g2d.drawLine(a,this.xPixelMovedTo2,this.yPixel0,this.xPixelMovedTo2,this.yPixel1),this.yValueMovedTo=NaN):(b=null==f?
c+this.toPixelY(this.yValueMovedTo):this.toPixelYint(this.yValueMovedTo/100),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixelMovedTo,b-10,this.xPixelMovedTo,b+10));null!=f&&this.g2d.setStrokeBold(a,!1)},"~O,JSV.common.Spectrum,~N,JSV.common.IntegralData");c(b,"setScale",function(a){this.viewData.setScale(a,this.xPixels,this.yPixels,this.spectra.get(a).isInverted())},"~N");c(b,"draw2DUnits",function(a){var b=this.getSpectrumAt(0).nucleusX,c=this.getSpectrumAt(0).nucleusY;this.setColorFromToken(a,JSV.common.ScriptToken.PLOTCOLOR);
this.drawUnits(a,b,this.imageView.xPixel1+5*this.pd.scalingFactor,this.yPixel1,1,1);this.drawUnits(a,c,this.imageView.xPixel0-5*this.pd.scalingFactor,this.yPixel0,1,0)},"~O");c(b,"drawPeakTabs",function(a,b,c){var f=1==this.nSpectra||0<=this.iSpectrumSelected?c.getPeakList():null;if(null!=f&&0<f.size()){null!=this.piMouseOver&&this.piMouseOver.spectrum===c&&this.pd.isMouseUp()?(this.g2d.setGraphicsColor(b,this.g2d.getColor4(240,240,240,140)),this.drawPeak(b,this.piMouseOver,0),c.setHighlightedPeak(this.piMouseOver)):
c.setHighlightedPeak(null);this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(b=f.size();0<=--b;){var e=f.get(b);this.drawPeak(a,e,e===c.getSelectedPeak()?14:7)}}},"~O,~O,JSV.common.Spectrum");c(b,"drawPeak",function(a,b,c){if(!this.pd.isPrinting){var f=b.getXMin(),e=b.getXMax();f!=e&&this.drawBar(a,b,f,e,null,c)}},"~O,JSV.common.PeakInfo,~N");c(b,"drawWidgets",function(a,b,c,f,e,g,j){this.setWidgets(f,c,e);if(!this.pd.isPrinting||!(null==this.imageView?!this.cur1D2Locked:this.sticky2Dcursor)){!this.pd.isPrinting&&
!j&&(e?(this.fillBox(a,this.xPixel0,this.pin1Dx0.yPixel1,this.xPixel1,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin1Dx0.xPixel0,this.pin1Dx0.yPixel1,this.pin1Dx1.xPixel0,this.pin1Dx1.yPixel1+2,JSV.common.ScriptToken.PLOTCOLOR)):(this.fillBox(a,this.imageView.xPixel0,this.pin2Dx0.yPixel1,this.imageView.xPixel1,this.pin2Dx0.yPixel1+2,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dx0.xPixel0,this.pin2Dx0.yPixel1,this.pin2Dx1.xPixel0,this.pin2Dx1.yPixel1+
2,JSV.common.ScriptToken.PLOTCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.yPixel1,this.pin2Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),this.fillBox(a,this.pin2Dy0.xPixel1,this.pin2Dy0.yPixel1,this.pin2Dy1.xPixel1+2,this.pin2Dy1.yPixel0,JSV.common.ScriptToken.PLOTCOLOR)),this.fillBox(a,this.pin1Dy0.xPixel1,this.yPixel1,this.pin1Dy1.xPixel1+2,this.yPixel0,JSV.common.ScriptToken.GRIDCOLOR),g&&this.fillBox(a,this.pin1Dy0.xPixel1,this.pin1Dy0.yPixel1,this.pin1Dy1.xPixel1+2,this.pin1Dy1.yPixel0,
JSV.common.ScriptToken.PLOTCOLOR));for(c=0;c<this.widgets.length;c++)if(f=this.widgets[c],!(null==f||!f.isPinOrCursor&&!this.zoomEnabled)){var k=f===this.cur1D2x1||f===this.cur1D2x2||f===this.cur2Dx0||f===this.cur2Dx1||f===this.cur2Dy;if((f.isPin||!f.isPinOrCursor)!=j){if(f.is2D){if(f===this.cur2Dx0&&!e)continue}else{var l=f===this.pin1Dy0||f===this.pin1Dy1||f===this.pin1Dy01;if(null!=this.imageView&&e==l||l&&!g||f===this.cur1D2x1&&null==this.gs2dLinkedX||f===this.cur1D2x2&&null==this.gs2dLinkedY||
f===this.zoomBox1D&&(this.pd.isIntegralDrag||0!=this.pd.integralShiftMode))if(!this.isLinked||null!=this.imageView)continue}if(!this.pd.isPrinting||k)f.isPinOrCursor?(this.setColorFromToken(a,f.color),this.g2d.drawLine(a,f.xPixel0,f.yPixel0,f.xPixel1,f.yPixel1),f.isVisible=!0,f.isPin&&this.drawHandle(a,f.xPixel0,f.yPixel0,2,!f.isEnabled)):f.xPixel1!=f.xPixel0&&this.fillBox(b,f.xPixel0,f.yPixel0,f.xPixel1,f.yPixel1,f===this.zoomBox1D&&this.pd.shiftPressed?JSV.common.ScriptToken.ZOOMBOXCOLOR2:JSV.common.ScriptToken.ZOOMBOXCOLOR)}}}},
"~O,~O,~N,~B,~B,~B,~B");c(b,"drawBar",function(a,b,c,f,e,g){Math.abs(f-c);Math.abs(this.toX(this.xPixel1)-this.toX(this.xPixel0));c=this.toPixelX(c);f=this.toPixelX(f);if(c>f){var j=c;c=f;f=j}c=this.fixX(c);f=this.fixX(f);3>f-c&&(c-=2,f+=2);null!=b&&b.setPixelRange(c,f);0==g?this.fillBox(a,c,this.yPixel0,f,this.yPixel0+this.yPixels,e):(this.fillBox(a,c,this.yPixel0+2,f,this.yPixel0+5,e),null!=b&&(c=v((c+f)/2),this.fillBox(a,c-1,this.yPixel0+2,c+1,this.yPixel0+2+g,e)))},"~O,JSV.common.PeakInfo,~N,~N,JSV.common.ScriptToken,~N");
c(b,"drawIntegration",function(a,b,c,f,e){null!=e&&(this.haveIntegralDisplayed(b)&&this.drawPlot(a,b,this.spectra.get(b),!0,c,!1,e,!0,!1,!1),this.drawIntegralValues(a,b,c));b=this.getIntegrationRatios(b);null!=b&&this.drawAnnotations(a,b,JSV.common.ScriptToken.INTEGRALPLOTCOLOR)},"~O,~N,~N,~B,JSV.common.IntegralData,~B,~B");c(b,"getMeasurements",function(a,b){var c=this.getDialog(a,b);return null==c||0==c.getData().size()||!c.getState()?null:c.getData()},"JSV.common.Annotation.AType,~N");c(b,"drawPlot",
function(a,b,c,f,e,g,j,k,l,s){var m=null==j?c.getXYCoords():this.getIntegrationGraph(b).getXYCoords(),p=null!=j;j=p?j.getBitSet():null;k=l||null!=c.fillColor&&k;g=g?-2:p?-1:!this.allowStacking?0:b;this.setPlotColor(a,g);var n=!0,r=this.toPixelY(0);p?k=(new Boolean(k&r==this.fixY(r))).valueOf():r=this.fixY(r);var u=p||k?this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR):null;c=null==u||null==c.fillColor?u:c.fillColor;u=this.viewData.getStartingPointIndex(b);b=this.viewData.getEndingPointIndex(b);
if(f&&!s){b--;(s=(p||null!=this.pendingIntegral)&&this.g2d.canDoLineTo())&&this.g2d.doStroke(a,!0);var v=!1;for(f=u;f<=b;f++){var w=m[f],y=m[f+1],z=p?this.toPixelYint(w.getYVal()):this.toPixelY(w.getYVal());if(-2147483648!=z){var B=p?this.toPixelYint(y.getYVal()):this.toPixelY(y.getYVal());if(-2147483648!=B){var w=w.getXVal(),C=y.getXVal(),y=this.toPixelX(w),D=this.toPixelX(C),z=this.fixY(e+z),B=this.fixY(e+B);p&&(f==u&&(this.xPixelPlot1=y,this.yPixelPlot0=z),this.xPixelPlot0=D,this.yPixelPlot1=B);
if(!(D==y&&z==B))if(k&&l&&this.pendingIntegral.overlaps(w,C))null!=c&&(this.g2d.doStroke(a,!1),this.g2d.setGraphicsColor(a,c)),this.g2d.fillRect(a,Math.min(y,D),Math.min(r,z),Math.max(1,Math.abs(D-y)),Math.abs(r-z)),null!=c&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),v=!1,this.setPlotColor(a,g));else if(!(z==B&&z==this.yPixel0)&&(null!=j&&j.get(f)!=n&&(n=j.get(f),s&&v&&(this.g2d.doStroke(a,!1),this.g2d.doStroke(a,!0),v=!1),!this.pd.isPrinting&&0!=this.pd.integralShiftMode?this.setPlotColor(a,
0):n?this.setColorFromToken(a,JSV.common.ScriptToken.INTEGRALPLOTCOLOR):this.setPlotColor(a,-3)),!this.pd.isPrinting||n))v?this.g2d.lineTo(a,D,B):(this.g2d.drawLine(a,y,z,D,B),v=s)}}}s&&this.g2d.doStroke(a,!1)}else{for(f=u;f<=b;f++)l=m[f],B=this.toPixelY(l.getYVal()),-2147483648!=B&&(y=this.toPixelX(l.getXVal()),z=this.toPixelY(Math.max(this.getScale().minYOnScale,0)),z=this.fixY(e+z),B=this.fixY(e+B),z==B&&(z==this.yPixel0||z==this.yPixel1)||(s?this.g2d.fillRect(a,y-1,B-1,3,3):this.g2d.drawLine(a,
y,z,y,B)));!s&&this.getScale().isYZeroOnScale()&&(e+=this.toPixelY(this.getScale().spectrumYRef),e==this.fixY(e)&&this.g2d.drawLine(a,this.xPixel1,e,this.xPixel0,e))}},"~O,~N,JSV.common.Spectrum,~B,~N,~B,JSV.common.IntegralData,~B,~B,~B");c(b,"drawFrame",function(a,b,c,f,e){if(!this.pd.gridOn||this.pd.isPrinting)if(this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR),this.g2d.drawRect(a,this.xPixel0,this.yPixel0,this.xPixels,this.yPixels),this.pd.isPrinting)return;this.setCurrentBoxColor(a);
e&&(0<=b&&(this.setPlotColor(a,b),this.fillArrow(a,3,this.xVArrows,v((this.yPixel00+this.yPixel11)/2)-9,!0),this.fillArrow(a,4,this.xVArrows,v((this.yPixel00+this.yPixel11)/2)+9,!0),this.setCurrentBoxColor(a)),this.fillArrow(a,3,this.xVArrows,v((this.yPixel00+this.yPixel11)/2)-9,!1),this.fillCircle(a,this.xVArrows,v((this.yPixel00+this.yPixel11)/2),!1),this.fillArrow(a,4,this.xVArrows,v((this.yPixel00+this.yPixel11)/2)+9,!1));if(null==this.imageView&&c){b=this.xPixel00+10;c=this.xPixel11-10;e=this.yPixel00+
1;var g=this.yPixel11-2;this.g2d.drawLine(a,b,e,c,e);this.g2d.drawLine(a,c,e,c,g);this.g2d.drawLine(a,b,g,c,g);this.splitterX=this.closerX=-2147483648;this.drawBox(a,c-10,e,c,e+10,null);this.g2d.drawLine(a,c-10,e+10,c,e);this.g2d.drawLine(a,c,e+10,c-10,e);this.closerX=c-10;this.closerY=e;f&&(c-=10,this.fillBox(a,c-10,e,c,e+10,null),this.splitterX=c-10,this.splitterY=e)}},"~O,~N,~B,~B,~B");c(b,"drawGrid",function(a){if(this.pd.gridOn&&null==this.imageView){this.setColorFromToken(a,JSV.common.ScriptToken.GRIDCOLOR);
var b;if(Double.isNaN(this.getScale().firstX)){b=this.getScale().maxXOnScale+this.getScale().steps[0]/2;for(var c=this.getScale().minXOnScale;c<b;c+=this.getScale().steps[0]){var f=this.toPixelX(c);this.g2d.drawLine(a,f,this.yPixel0,f,this.yPixel1)}}else{b=1.0001*this.getScale().maxXOnScale;for(c=this.getScale().firstX;c<=b;c+=this.getScale().steps[0])f=this.toPixelX(c),this.g2d.drawLine(a,f,this.yPixel0,f,this.yPixel1)}for(c=this.getScale().firstY;c<this.getScale().maxYOnScale+this.getScale().steps[1]/
2;c+=this.getScale().steps[1])b=this.toPixelY(c),b==this.fixY(b)&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b)}},"~O");c(b,"drawXScale",function(a,b){this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);this.pd.isPrinting&&this.g2d.drawLine(a,b.getXPixel0(),this.yPixel1,b.getXPixel0()+b.getXPixels()-1,this.yPixel1);for(var c=this.getScale().precision[0],f=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1),e=this.yPixel1,g=this.yPixel1+4*this.pd.scalingFactor,j=this.yPixel1+
2*this.pd.scalingFactor,f=f.getHeight(),k=b.toPixelX(this.getScale().steps[0])-b.toPixelX(0),l=Math.abs(0.95*k),s=this.getScale().firstX-this.getScale().steps[0],m=1.0001*(this.getScale().maxXOnScale+this.getScale().steps[0]),p=0;2>p;p++){1==p&&JSV.common.ScaleData.fixScale(this.mapX);for(var n=1E10,r=s;r<=m;r+=this.getScale().steps[0]){var k=b.toPixelX(r),u=Double.$valueOf(r),w;switch(p){case 0:w=JU.DF.formatDecimalDbl(r,c);this.mapX.put(u,w);this.drawTick(a,k,e,g,b);k=Math.abs(n-r);n=this.getScale().minorTickCounts[0];
if(0!=n){k/=n;for(w=1;w<n;w++)this.drawTick(a,b.toPixelX(r-w*k),e,j,b)}n=r;continue;case 1:w=this.mapX.get(u);if(null==w||k!=b.fixX(k))continue;var u=this.pd.getStringWidth(w),y=k+v(u/2)==b.fixX(k+v(u/2))?2:0;0<y&&this.g2d.drawString(a,w,k-v(u/y),g+f);r+=Math.floor(u/l)*this.getScale().steps[0]}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(b,"drawTick",function(a,b,c,f,e){b==e.fixX(b)&&this.g2d.drawLine(a,b,c,b,f)},"~O,~N,~N,~N,JSV.common.XYScaleConverter");c(b,"drawYScale",function(a,
b){var c=b.getScale(),f=c.precision[1],e=this.pd.setFont(a,b.getXPixels(),0,this.pd.isPrinting?10:12,!1).getHeight(),g=c.maxYOnScale+c.steps[1]/2,j=-2147483648;this.setColorFromToken(a,JSV.common.ScriptToken.SCALECOLOR);for(var k=0;2>k;k++){1==k&&JSV.common.ScaleData.fixScale(this.mapX);for(var l=c.firstY;l<g;l+=c.steps[1]){var s=Double.$valueOf(l),m=b.getXPixel0(),p=b.toPixelY(l);if(p==b.fixY(p)){var n;0==k&&this.g2d.drawLine(a,m,p,m-3*this.pd.scalingFactor,p);if(!(Math.abs(p-j)<=e))switch(j=p,k){case 0:n=
JU.DF.formatDecimalDbl(l,f);this.mapX.put(s,n);break;case 1:n=this.mapX.get(s);if(null==n)continue;n.startsWith("0")&&n.contains("E")&&(n="0");this.g2d.drawString(a,n,m-4*this.pd.scalingFactor-this.pd.getStringWidth(n),p+v(e/3))}}}}this.mapX.clear()},"~O,JSV.common.XYScaleConverter");c(b,"drawXUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!0);null!=b&&this.drawUnits(a,b,this.xPixel1+25*this.pd.scalingFactor,this.yPixel1+5*this.pd.scalingFactor,1,1)},"~O");c(b,"drawUnits",function(a,b,
c,f,e,g){this.setColorFromToken(a,JSV.common.ScriptToken.UNITSCOLOR);this.pd.setFont(a,(null==this.imageView?this:this.imageView).getXPixels(),3,10,!1);this.g2d.drawString(a,b,v(c-this.pd.getStringWidth(b)*e),v(f+this.pd.getFontHeight()*g))},"~O,~S,~N,~N,~N,~N");c(b,"drawYUnits",function(a){var b=this.spectra.get(0).getAxisLabel(!1);null!=b&&this.drawUnits(a,b,(this.pd.isPrinting?30:5)*this.pd.scalingFactor,this.yPixel0+(this.pd.isPrinting?0:5)*this.pd.scalingFactor,0,-1)},"~O");c(b,"drawHighlightsAndPeakTabs",
function(a,b,c){var f=this.getMeasurements(JSV.common.Annotation.AType.PeakList,c),e=this.spectra.get(c);if(this.pd.isPrinting)null!=f&&(this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR),this.printPeakList(a,e,f));else{if(null==f){for(var g=0;g<this.highlights.size();g++){var j=this.highlights.get(g);j.spectrum===e&&(this.pd.setHighlightColor(j.color),this.drawBar(b,null,j.x1,j.x2,JSV.common.ScriptToken.HIGHLIGHTCOLOR,0))}this.pd.peakTabsOn&&this.drawPeakTabs(a,b,e)}if(null!=f){b=e.isInverted()?
this.yPixel1-10*this.pd.scalingFactor:this.yPixel0;this.setColorFromToken(a,JSV.common.ScriptToken.PEAKTABCOLOR);for(g=f.size();0<=--g;)e=f.get(g),e=this.toPixelX(e.getXVal()),this.g2d.drawLine(a,e,b,e,b+10*this.pd.scalingFactor);this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,c))&&(b=this.toPixelY(f.getThresh()),b==this.fixY(b)&&!this.pd.isPrinting&&this.g2d.drawLine(a,this.xPixel0,b,this.xPixel1,b))}}},"~O,~O,~N");c(b,"printPeakList",function(a,b,c){var f=c.getMeasurementListArray(null);
if(0!=f.length){this.pd.setFont(a,this.xPixels,0,8,!1);for(var e=this.pd.getFontHeight(),g=E(c.size(),0),j=E(c.size(),0),k=0,l=5*this.pd.scalingFactor,s=10*this.pd.scalingFactor,m=15*this.pd.scalingFactor,p=25*this.pd.scalingFactor,n=0;n<f.length;n++)j[n]=this.toPixelX(Double.parseDouble(f[n][1])),0==n?g[n]=j[n]:(g[n]=Math.max(g[n-1]+e,j[n]+e),k+=g[n]-j[n]);k/=2*f.length;g[0]-k<this.xPixel0+p&&(k=g[0]-(this.xPixel0+p));for(n=0;n<f.length;n++)g[n]-=k;n=b.isInverted();b=this.pd.getStringWidth("99.9999");
for(var k=6<=f[0].length?this.pd.getStringWidth("99.99"):0,p=n?-1:1,r=(n?this.yPixel1:this.yPixel0)+p*(k+b+m),n=0;n<f.length;n++)this.g2d.drawLine(a,g[n],r,g[n],r+l*p),this.g2d.drawLine(a,g[n],r+l*p,j[n],r+s*p),this.g2d.drawLine(a,j[n],r+s*p,j[n],r+m*p),0<k&&0<f[n][4].length&&this.g2d.drawLine(a,v((g[n]+g[n-1])/2),r-b+l,v((g[n]+g[n-1])/2),r-b-l);r-=2*p*this.pd.scalingFactor;0<k&&(this.drawStringRotated(a,-90,g[0]-m,r,"  ppm"),this.drawStringRotated(a,-90,g[0]-m,r-b-l," Hz"));for(n=c.size();0<=--n;)this.drawStringRotated(a,
-90*p,g[n]+v(p*e/3),r,f[n][1]),0<k&&0<f[n][4].length&&(c=v((g[n]+g[n-1])/2)+v(e/3),this.drawStringRotated(a,-90,c,r-b-l,f[n][4]))}},"~O,JSV.common.Spectrum,JSV.common.PeakData");c(b,"drawStringRotated",function(a,b,c,f,e){this.g2d.drawStringRotated(a,e,c,f,b)},"~O,~N,~N,~N,~S");c(b,"drawAnnotations",function(a,b,c){this.pd.setFont(a,this.xPixels,1,18,!1);for(var f=b.size();0<=--f;){var e=b.get(f);this.setAnnotationColor(a,e,c);var g=(e.is2D?this.imageView:this).toPixelX(e.getXVal()),j=e.isPixels()?
v(this.yPixel0+10+10*this.pd.scalingFactor-e.getYVal()):e.is2D?this.imageView.subIndexToPixelY(v(e.getYVal())):this.toPixelY(e.getYVal());this.g2d.drawString(a,e.text,g+e.offsetX*this.pd.scalingFactor,j-e.offsetY*this.pd.scalingFactor)}},"~O,JU.Lst,JSV.common.ScriptToken");c(b,"drawIntegralValues",function(a,b,c){var f=this.getMeasurements(JSV.common.Annotation.AType.Integration,b);if(null!=f){this.pd.isPrinting?this.pd.setFont(a,this.xPixels,0,8,!1):this.pd.setFont(a,this.xPixels,1,12,!1);this.setColorFromToken(a,
JSV.common.ScriptToken.INTEGRALPLOTCOLOR);var e=this.pd.getFontHeight();this.g2d.setStrokeBold(a,!0);for(var g=f.size();0<=--g;){var j=f.get(g);if(0!=j.getValue()){var k=this.toPixelX(j.getXVal2()),l=c*this.pd.scalingFactor+this.toPixelYint(j.getYVal()),n=c*this.pd.scalingFactor+this.toPixelYint(j.getYVal2());k!=this.fixX(k)||(l!=this.fixY(l)||n!=this.fixY(n))||(this.pd.isPrinting||this.g2d.drawLine(a,k,l,k,n),this.g2d.drawString(a,"  "+j.text,k,v((l+n)/2)+v(e/3)))}}this.g2d.setStrokeBold(a,!1)}b==
this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumIntegrals=f)},"~O,~N,~N");c(b,"drawMeasurements",function(a,b){var c=this.getMeasurements(JSV.common.Annotation.AType.Measurements,b);if(null!=c)for(var f=c.size();0<=--f;)this.drawMeasurement(a,c.get(f));b==this.getFixedSelectedSpectrumIndex()&&(this.selectedSpectrumMeasurements=c)},"~O,~N");c(b,"drawMeasurement",function(a,b){if(!(0==b.text.length&&b!==this.pendingMeasurement)){this.pd.setFont(a,this.xPixels,1,12,!1);this.g2d.setGraphicsColor(a,
b===this.pendingMeasurement?this.pd.getColor(JSV.common.ScriptToken.PEAKTABCOLOR):this.pd.BLACK);var c=this.toPixelX(b.getXVal()),f=this.toPixelY(b.getYVal()),e=this.toPixelX(b.getXVal2());if(!Double.isNaN(b.getXVal())&&!(c!=this.fixX(c)||e!=this.fixX(e))){var g=2<=Math.abs(c-e),j=this.getScale().isYZeroOnScale()&&b.spec.isHNMR(),k=v((c+e)/2);this.g2d.setStrokeBold(a,!0);g&&this.g2d.drawLine(a,c,f,e,f);j&&this.g2d.drawLine(a,c+1,this.yPixel1-1,e,this.yPixel1-1);this.g2d.setStrokeBold(a,!1);g&&this.g2d.drawString(a,
b.text,k+b.offsetX,f-b.offsetY);j&&(this.g2d.drawLine(a,c,this.yPixel1,c,this.yPixel1-6*this.pd.scalingFactor),this.g2d.drawLine(a,e,this.yPixel1,e,this.yPixel1-6*this.pd.scalingFactor))}}},"~O,JSV.common.Measurement");c(b,"getPinSelected",function(a,b){if(null!=this.widgets)for(var c=0;c<this.widgets.length;c++)if(null!=this.widgets[c]&&this.widgets[c].isPinOrCursor&&this.widgets[c].selected(a,b))return this.widgets[c];return null},"~N,~N");c(b,"set2DCrossHairs",function(a,b){var c;if(a==this.imageView.fixX(a)&&
b==this.fixY(b)&&(this.pin1Dx1.setX(c=this.imageView.toX(a),this.toPixelX(c)),this.cur2Dx1.setX(c,a),this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),this.isLinked)){var f=this.imageView.toY(b);this.pd.set2DCrossHairsLinked(this,c,f,!this.sticky2Dcursor)}},"~N,~N");c(b,"reset2D",function(a){a?(this.imageView.setView0(this.imageView.xPixel0,this.pin2Dy0.yPixel0,this.imageView.xPixel1,this.pin2Dy1.yPixel0),this.doZoom(0,this.getScale().minY,0,this.getScale().maxY,!0,!1,!1,!1,!0)):this.imageView.setView0(this.pin2Dx0.xPixel0,
this.imageView.yPixel0,this.pin2Dx1.xPixel0,this.imageView.yPixel1)},"~B");c(b,"setAnnotationText",function(a){var b=this.pd.getInput("New text?","Set Label",a.text);if(null==b)return!1;0==b.length?this.annotations.removeObj(a):a.text=b;return!0},"JSV.common.Annotation");c(b,"checkIntegral",function(a,b,c){var f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==f)return!1;a=f.getData().addIntegralRegion(a,b);c&&f.isDialog()&&f.update(null,0,0);if(Double.isNaN(b))return!1;this.pendingIntegral=
c?null:a;this.pd.isIntegralDrag=!c;this.selectedSpectrumIntegrals=null;return!0},"~N,~N,~B");c(b,"setToolTipForPixels",function(a,b){if(this.iSpectrumMovedTo!=this.iSpectrumClicked||this.pd.getCurrentGraphSet()!==this)this.pd.setToolTipText("click spectrum to activate");else if(this.isSplitWidget(a,b))this.pd.setToolTipText("click to "+(1<this.nSplit?"combine":"split"));else if(this.isCloserWidget(a,b))this.pd.setToolTipText("click to close");else{var c=this.getPinSelected(a,b),f=this.getScale().precision[0],
e=this.getScale().precision[1];if(null!=c)this.setStartupPinTip()||(c===this.pin1Dx01||c===this.pin2Dx01?f=JU.DF.formatDecimalDbl(Math.min(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),f)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dx0.getXVal(),this.pin1Dx1.getXVal()),f):c===this.pin1Dy01?f=JU.DF.formatDecimalDbl(Math.min(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),e)+" - "+JU.DF.formatDecimalDbl(Math.max(this.pin1Dy0.getYVal(),this.pin1Dy1.getYVal()),e):c===this.cur2Dy?(c=this.imageView.toSubspectrumIndex(c.yPixel0),
f=this.get2DYLabel(c,f)):f=c===this.pin2Dy01?""+v(Math.min(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal()))+" - "+v(Math.max(this.pin2Dy0.getYVal(),this.pin2Dy1.getYVal())):c.isXtype?JU.DF.formatDecimalDbl(c.getXVal(),f):c.is2D?""+v(c.getYVal()):JU.DF.formatDecimalDbl(c.getYVal(),e),this.pd.setToolTipText(f));else{if(null!=this.imageView){if(this.imageView.fixX(a)==a&&this.fixY(b)==b){c=this.imageView.toSubspectrumIndex(b);f="y="+this.get2DYLabel(c,f)+" / x="+JU.DF.formatDecimalDbl(this.imageView.toX(a),
f)+" "+this.getSpectrum().getAxisLabel(!0);this.pd.setToolTipText(f);this.pd.coordStr=f;return}if(!this.pd.display1D){this.pd.setToolTipText("");this.pd.coordStr="";return}}var c=this.toX(this.fixX(a)),f=null!=this.imageView&&this.imageView.isXWithinRange(a)?this.imageView.toSubspectrumIndex(this.fixY(b)):this.toY(this.fixY(b)),e=this.setCoordStr(c,f),g=this.getFixedSelectedSpectrumIndex();this.isInPlotRegion(a,b)?1!=this.nSpectra&&this.haveIntegralDisplayed(g)&&(f=this.getIntegrationGraph(g).getPercentYValueAt(c),
e+=", "+JU.DF.formatDecimalDbl(f,1)):f=NaN;this.pd.setToolTipText(null!=this.selectedIntegral?"click to set value":null!=this.pendingMeasurement||null!=this.selectedMeasurement?this.pd.hasFocus()?"Press ESC to delete "+(null!=this.selectedIntegral?"integral, DEL to delete all visible, or N to normalize":null==this.pendingMeasurement?'"'+this.selectedMeasurement.text+'" or DEL to delete all visible':"measurement"):"":Double.isNaN(f)?null:e)}}},"~N,~N");c(b,"isFrameBox",function(a,b,c,f){return 5>Math.abs(a-
(c+5))&&5>Math.abs(b-(f+5))},"~N,~N,~N,~N");c(b,"setCoordStr",function(a,b){var c=JU.DF.formatDecimalDbl(a,this.getScale().precision[0]);this.pd.coordStr="("+c+(this.haveSingleYScale||0<=this.iSpectrumSelected?", "+JU.DF.formatDecimalDbl(b,this.getScale().precision[1]):"")+")";return c},"~N,~N");c(b,"setStartupPinTip",function(){if(null==this.pd.startupPinTip)return!1;this.pd.setToolTipText(this.pd.startupPinTip);this.pd.startupPinTip=null;return!0});c(b,"get2DYLabel",function(a,b){var c=this.getSpectrumAt(0).getSubSpectra().get(a);
return JU.DF.formatDecimalDbl(c.getY2DPPM(),b)+" PPM"+(c.y2DUnits.equals("HZ")?" ("+JU.DF.formatDecimalDbl(c.getY2D(),b)+" HZ) ":"")},"~N,~N");c(b,"isOnSpectrum",function(a,b,c){var f=null,e=!0,g=0>c;if(g){f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==f)return!1;f=f.getData().getXYCoords();c=this.getFixedSelectedSpectrumIndex()}else{this.setScale(c);var j=this.spectra.get(c),f=j.xyCoords,e=j.isContinuous()}var j=c*F(this.yPixels*(this.yStackOffsetPercent/100)),k=this.viewData.getStartingPointIndex(c);
c=this.viewData.getEndingPointIndex(c);if(e)for(e=k;e<c;e++){var l=f[e],n=f[e+1],k=this.toPixelX(l.getXVal()),m=this.toPixelX(n.getXVal()),l=g?this.toPixelYint(l.getYVal()):this.toPixelY(l.getYVal()),n=g?this.toPixelYint(n.getYVal()):this.toPixelY(n.getYVal());if(!(-2147483648==l||-2147483648==n))if(l=this.fixY(l)-j,n=this.fixY(n)-j,JSV.common.GraphSet.isOnLine(a,b,k,l,m,n))return!0}else for(e=k;e<=c;e++)if(g=f[e],n=this.toPixelY(g.getYVal()),-2147483648!=n&&(k=this.toPixelX(g.getXVal()),l=this.toPixelY(Math.max(this.getScale().minYOnScale,
0)),l=this.fixY(l),n=this.fixY(n),!(l==n&&(l==this.yPixel0||l==this.yPixel1))&&JSV.common.GraphSet.isOnLine(a,b,k,l,k,n)))return!0;return!1},"~N,~N,~N");b.distance=c(b,"distance",function(a,b){return Math.sqrt(a*a+b*b)},"~N,~N");b.findCompatibleGraphSet=c(b,"findCompatibleGraphSet",function(a,b){for(var c=0;c<a.size();c++)if(JSV.common.Spectrum.areXScalesCompatible(b,a.get(c).getSpectrum(),!1,!1))return a.get(c);return null},"JU.Lst,JSV.common.Spectrum");b.isGoodEvent=c(b,"isGoodEvent",function(a,
b,c){return null==b?5<Math.abs(a.xPixel1-a.xPixel0)&&5<Math.abs(a.yPixel1-a.yPixel0):c?5<Math.abs(a.xPixel0-b.xPixel0):5<Math.abs(a.yPixel0-b.yPixel0)},"JSV.common.PlotWidget,JSV.common.PlotWidget,~B");b.isOnLine=c(b,"isOnLine",function(a,b,c,f,e,g){var j=Math.abs(c-a);if(2>j&&2>Math.abs(f-b))return!0;var k=e-a;if(2>Math.abs(k)&&2>Math.abs(g-b))return!0;var l=f-g;if(2<Math.abs(l)&&f<b==g<b)return!1;var n=c-e;return 2<Math.abs(n)&&c<a==e<a?!1:JSV.common.GraphSet.distance(j,f-b)+JSV.common.GraphSet.distance(k,
b-g)<JSV.common.GraphSet.distance(n,l)+2},"~N,~N,~N,~N,~N,~N");b.setFractionalPositions=c(b,"setFractionalPositions",function(a,b,c){var f=b.size(),e=0,g=0;a.isLinked=c!==JSV.common.PanelData.LinkMode.NONE;if(c===JSV.common.PanelData.LinkMode.NONE){for(var j=0;j<f;j++)c=b.get(j),e+=(c.getSpectrumAt(0).is1D(),1)*c.nSplit;e=1/e;for(j=0;j<f;j++)c=b.get(j),c.isLinked=!1,a=c.getSpectrumAt(0).is1D()?e:1*e,c.fX0=0,c.fY0=g,c.fracX=1,c.fracY=a,g+=a*c.nSplit}else{var e=null,k=-1;if(2==f||3==f)for(j=0;j<f;j++)if(c=
b.get(j),!c.getSpectrum().is1D()){e=c;0<=k&&(j=-2);k=j;break}if(-2==k||-1==k&&2!=f)JSV.common.GraphSet.setFractionalPositions(a,b,JSV.common.PanelData.LinkMode.NONE);else for(j=0;j<f;j++)c=b.get(j),c.isLinked=!0,a=c.getSpectrumAt(0),a.is1D()?(null!=e&&(k=e.getSpectrumAt(0),JSV.common.Spectrum.areLinkableX(a,k)&&(c.gs2dLinkedX=e),JSV.common.Spectrum.areLinkableY(a,k)&&(c.gs2dLinkedY=e)),c.fX0=0,c.fY0=g,c.fracX=null==e?1:0.5,c.fracY=3==f||null==e?0.5:1,g+=0.5):(c.fX0=0.5,c.fY0=0,c.fracX=0.5,c.fracY=
1)}},"JSV.common.PanelData,JU.Lst,JSV.common.PanelData.LinkMode");c(b,"addAnnotation",function(a,b){if(0==a.size()||1==a.size()&&a.get(0).equalsIgnoreCase("none"))return this.lastAnnotation=this.annotations=null;4>a.size()&&null==this.lastAnnotation&&(this.lastAnnotation=this.getAnnotation((this.getScale().maxXOnScale+this.getScale().minXOnScale)/2,(this.getScale().maxYOnScale+this.getScale().minYOnScale)/2,b,!1,!1,0,0));var c=this.getAnnotation(a,this.lastAnnotation);if(null==c)return null;if(null==
this.annotations&&1==a.size()&&'"'==a.get(0).charAt(0))return c=c.text,this.getSpectrum().setTitle(c),c;this.lastAnnotation=c;this.addAnnotation(c,!1);return null},"JU.Lst,~S");c(b,"addHighlight",function(a,b,c,f){null==c&&(c=this.getSpectrumAt(0));a=Y(JSV.common.GraphSet.Highlight,this,null,a,b,c,null==f?this.pd.getColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR):f);this.highlights.contains(a)||this.highlights.addLast(a)},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");c(b,"addPeakHighlight",function(a){for(var b=
this.spectra.size();0<=--b;){var c=this.spectra.get(b);this.removeAllHighlights(c);if(!(null==a||a.isClearAll()||c!==a.spectrum)){var f=a.toString();if(null!=f){var e=JU.PT.getQuotedAttribute(f,"xMin"),f=JU.PT.getQuotedAttribute(f,"xMax");if(null==e||null==f)break;e=JU.PT.parseFloat(e);f=JU.PT.parseFloat(f);if(Float.isNaN(e)||Float.isNaN(f))break;this.pd.addHighlight(this,e,f,c,200,140,140,100);c.setSelectedPeak(a);!this.getScale().isInRangeX(e)&&!(this.getScale().isInRangeX(f)||e<this.getScale().minX&&
this.getScale().maxX<f)&&this.setZoomTo(0)}}}},"JSV.common.PeakInfo");c(b,"advanceSubSpectrum",function(a){var b=this.getSpectrumAt(0);a=b.advanceSubSpectrum(a);b.isForcedSubset()&&this.viewData.setXRangeForSubSpectrum(this.getSpectrum().getXYCoords());this.pd.notifySubSpectrumChange(a,this.getSpectrum())},"~N");c(b,"checkSpectrumClickedEvent",function(a,b,c){if(null!=this.nextClickForSetPeak||(1<c||null!=this.pendingMeasurement||!this.isInPlotRegion(a,b))||0==c&&(c=this.isOnSpectrum(a,b,-1),this.pd.integralShiftMode=
c?this.getShiftMode(a,b):0,this.pd.isIntegralDrag=0==this.pd.integralShiftMode&&(c||this.haveIntegralDisplayed(-1)&&null!=this.findMeasurement(this.getIntegrationGraph(-1),a,b,0)),0!=this.pd.integralShiftMode)||!this.showAllStacked)return!1;this.stackSelected=!1;for(c=0;c<this.nSpectra;c++)if(this.isOnSpectrum(a,b,c))return this.setSpectrumClicked(this.iPreviousSpectrumClicked=c),!1;if(this.isDialogOpen())return!1;this.setSpectrumClicked(-1);return this.stackSelected=!1},"~N,~N,~N");c(b,"getShiftMode",
function(a,b){return this.isStartEndIntegral(a,!1)?b:this.isStartEndIntegral(a,!0)?-b:0},"~N,~N");c(b,"isDialogOpen",function(){return this.isVisible(this.getDialog(JSV.common.Annotation.AType.Integration,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.Measurements,-1))||this.isVisible(this.getDialog(JSV.common.Annotation.AType.PeakList,-1))});c(b,"isStartEndIntegral",function(a,b){return b?20>this.xPixelPlot1-a:20>a-this.xPixelPlot0},"~N,~B");c(b,"checkWidgetEvent",function(a,b,c){if(!this.widgetsAreSet)return!1;
this.widgetsAreSet=!1;if(c){if(2==this.pd.clickCount&&this.lastIntDragX!=a&&!this.is2dClick(a,b)){if(null==this.pendingMeasurement)return-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),this.processPendingMeasurement(a,b,2),!0}else if(!this.is2dClick(a,b)&&(this.isOnSpectrum(a,b,-1)&&this.checkIntegral(this.toX(a),NaN,!1),this.lastIntDragX==a&&(this.pd.isIntegralDrag=!0,!this.checkIntegral(this.toX(a),this.toX(a),!1))))return!1;if(null!=
this.pendingMeasurement)return!0;c=this.getPinSelected(a,b);null==c&&(b=this.fixY(b),a<this.xPixel1?(this.pd.shiftPressed&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),a=this.fixX(a),null==this.zoomBox1D&&this.newPins(),this.zoomBox1D.setX(this.toX(a),a),this.zoomBox1D.yPixel0=b,c=this.zoomBox1D):null!=this.imageView&&a<this.imageView.xPixel1&&(this.zoomBox2D.setX(this.imageView.toX(a),this.imageView.fixX(a)),this.zoomBox2D.yPixel0=b,c=this.zoomBox2D));this.pd.thisWidget=c;return!1}this.nextClickForSetPeak=
null;c=this.pd.thisWidget;if(null==c)return!1;if(c===this.zoomBox1D)return this.zoomBox1D.xPixel1=this.fixX(a),this.zoomBox1D.yPixel1=this.fixY(b),this.pd.isIntegralDrag&&this.zoomBox1D.xPixel0!=this.zoomBox1D.xPixel1&&(this.lastIntDragX<=a!=this.zoomBox1D.xPixel0<=a&&(this.zoomBox1D.xPixel0=this.lastIntDragX,this.zoomBox1D.xPixel1=a,this.zoomBox1D.setXVal(this.toX(this.zoomBox1D.xPixel0))),this.lastIntDragX=a,this.checkIntegral(this.zoomBox1D.getXVal(),this.toX(this.zoomBox1D.xPixel1),!1)),!1;if(!this.zoomEnabled)return!1;
if(c===this.zoomBox2D)return this.zoomBox2D.xPixel1=this.imageView.fixX(a),this.zoomBox2D.yPixel1=this.fixY(b),!0;if(c===this.cur2Dy)return b=this.fixY(b),this.cur2Dy.yPixel0=this.cur2Dy.yPixel1=b,this.setCurrentSubSpectrum(this.imageView.toSubspectrumIndex(b)),!0;if(c===this.cur2Dx0||c===this.cur2Dx1)return!1;if(c===this.pin1Dx0||c===this.pin1Dx1||c===this.pin1Dx01){a=this.fixX(a);c.setX(this.toX0(a),a);if(c===this.pin1Dx01){c=a-v((this.pin1Dx0.xPixel0+this.pin1Dx1.xPixel0)/2);a=this.pin1Dx0.xPixel0+
c;b=this.pin1Dx1.xPixel0+c;if(0==c||this.fixX(a)!=a||this.fixX(b)!=b)return!0;this.pin1Dx0.setX(this.toX0(a),a);this.pin1Dx1.setX(this.toX0(b),b)}this.doZoom(this.pin1Dx0.getXVal(),0,this.pin1Dx1.getXVal(),0,!0,!1,!1,!0,!1);return!0}if(c===this.pin1Dy0||c===this.pin1Dy1||c===this.pin1Dy01){b=this.fixY(b);c.setY(this.toY0(b),b);if(c===this.pin1Dy01){c=b-v((this.pin1Dy0.yPixel0+this.pin1Dy1.yPixel0)/2)+1;b=this.pin1Dy0.yPixel0+c;a=this.pin1Dy1.yPixel0+c;c=this.toY0(b);var f=this.toY0(a);if(Math.min(c,
f)==this.getScale().minY||Math.max(c,f)==this.getScale().maxY)return!0;this.pin1Dy0.setY(c,b);this.pin1Dy1.setY(f,a)}this.doZoom(0,this.pin1Dy0.getYVal(),0,this.pin1Dy1.getYVal(),null==this.imageView,null==this.imageView,!1,!1,!1);return!0}if(c===this.pin2Dx0||c===this.pin2Dx1||c===this.pin2Dx01){a=this.imageView.fixX(a);c.setX(this.imageView.toX0(a),a);if(c===this.pin2Dx01){c=a-v((this.pin2Dx0.xPixel0+this.pin2Dx1.xPixel0)/2)+1;a=this.pin2Dx0.xPixel0+c;b=this.pin2Dx1.xPixel0+c;if(this.imageView.fixX(a)!=
a||this.imageView.fixX(b)!=b)return!0;this.pin2Dx0.setX(this.imageView.toX0(a),a);this.pin2Dx1.setX(this.imageView.toX0(b),b)}if(!JSV.common.GraphSet.isGoodEvent(this.pin2Dx0,this.pin2Dx1,!0))return this.reset2D(!0),!0;this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,this.pin2Dx1.xPixel0,this.pin2Dy1.yPixel0);this.doZoom(this.pin2Dx0.getXVal(),this.getScale().minY,this.pin2Dx1.getXVal(),this.getScale().maxY,!1,!1,!1,!0,!1);return!0}if(c===this.pin2Dy0||c===this.pin2Dy1||c===this.pin2Dy01){b=
this.fixY(b);c.setY(this.imageView.toSubspectrumIndex(b),b);if(c===this.pin2Dy01){c=b-v((this.pin2Dy0.yPixel0+this.pin2Dy1.yPixel0)/2)+1;b=this.pin2Dy0.yPixel0+c;a=this.pin2Dy1.yPixel0+c;if(b!=this.fixY(b)||a!=this.fixY(a))return!0;this.pin2Dy0.setY(this.imageView.toSubspectrumIndex(b),b);this.pin2Dy1.setY(this.imageView.toSubspectrumIndex(a),a)}if(!JSV.common.GraphSet.isGoodEvent(this.pin2Dy0,this.pin2Dy1,!1))return this.reset2D(!1),!0;this.imageView.setView0(this.pin2Dx0.xPixel0,this.pin2Dy0.yPixel0,
this.pin2Dx1.xPixel1,this.pin2Dy1.yPixel1);return!0}return!1},"~N,~N,~B");c(b,"clearIntegrals",function(){this.checkIntegral(NaN,0,!1)});c(b,"clearMeasurements",function(){this.removeDialog(this.getFixedSelectedSpectrumIndex(),JSV.common.Annotation.AType.Measurements)});b.createGraphSetsAndSetLinkMode=c(b,"createGraphSetsAndSetLinkMode",function(a,b,c,f,e,g){for(var j=new JU.Lst,k=0;k<c.size();k++){var l=c.get(k),n=g===JSV.common.PanelData.LinkMode.NONE?JSV.common.GraphSet.findCompatibleGraphSet(j,
l):null;null==n&&j.addLast(n=new JSV.common.GraphSet(b.getPanelData()));n.addSpec(l)}JSV.common.GraphSet.setFractionalPositions(a,j,g);for(k=j.size();0<=--k;)j.get(k).initGraphSet(f,e),JU.Logger.info("JSVGraphSet "+(k+1)+" nSpectra = "+j.get(k).nSpectra);return j},"JSV.common.PanelData,JSV.api.JSVPanel,JU.Lst,~N,~N,JSV.common.PanelData.LinkMode");c(b,"drawGraphSet",function(a,b,c,f,e,g,j,k,l,n,m,p){this.zoomEnabled=this.pd.getBoolean(JSV.common.ScriptToken.ENABLEZOOM);this.height=e*this.pd.scalingFactor;
this.width=f*this.pd.scalingFactor;this.left=g*this.pd.scalingFactor;this.right=j*this.pd.scalingFactor;this.top=k*this.pd.scalingFactor;this.bottom=l*this.pd.scalingFactor;this.$haveSelectedSpectrum=!1;this.selectedSpectrumMeasurements=this.selectedSpectrumIntegrals=null;if(!this.pd.isPrinting&&null!=this.widgets)for(f=0;f<this.widgets.length;f++)null!=this.widgets[f]&&(this.widgets[f].isVisible=!1);for(f=0;f<this.nSplit;f++)this.setPositionForFrame(f),this.drawAll(a,b,c,f,n||1<this.nSplit,m,p);
this.setPositionForFrame(1<this.nSplit?this.pd.currentSplitPoint:0)},"~O,~O,~O,~N,~N,~N,~N,~N,~N,~B,~B,~B");c(b,"escapeKeyPressed",function(a){null!=this.zoomBox1D&&(this.zoomBox1D.xPixel0=this.zoomBox1D.xPixel1=0);null!=this.zoomBox2D&&(this.zoomBox2D.xPixel0=this.zoomBox2D.xPixel1=0);this.inPlotMove&&(null!=this.pendingMeasurement?this.pendingMeasurement=null:(this.pendingMeasurement=this.pd.thisWidget=null,null!=this.selectedSpectrumMeasurements&&null!=this.selectedMeasurement&&(a?this.selectedSpectrumMeasurements.clear(this.getScale().minXOnScale,
this.getScale().maxXOnScale):this.selectedSpectrumMeasurements.removeObj(this.selectedMeasurement),this.selectedMeasurement=null,this.updateDialog(JSV.common.Annotation.AType.Measurements,-1)),null!=this.selectedSpectrumIntegrals&&null!=this.selectedIntegral&&(a?this.selectedSpectrumIntegrals.clear(this.getScale().minXOnScale,this.getScale().maxXOnScale):this.selectedSpectrumIntegrals.removeObj(this.selectedIntegral),this.selectedIntegral=null,this.updateDialog(JSV.common.Annotation.AType.Integration,
-1))))},"~B");b.findGraphSet=c(b,"findGraphSet",function(a,b,c){for(var f=a.size();0<=--f;)if(a.get(f).hasPoint(b,c))return a.get(f);return null},"JU.Lst,~N,~N");c(b,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.spectra.size()&&null==(b=this.spectra.get(c).findMatchingPeakInfo(a));c++);return b},"JSV.common.PeakInfo");c(b,"getCurrentSpectrumIndex",function(){return 1==this.nSpectra?0:this.iSpectrumSelected});c(b,"getSelectedIntegral",function(){return this.selectedIntegral});c(b,"getShowAnnotation",
function(a,b){var c=this.getDialog(a,b);return null!=c&&c.getState()},"JSV.common.Annotation.AType,~N");c(b,"hasFileLoaded",function(a){for(var b=this.spectra.size();0<=--b;)if(this.spectra.get(b).getFilePathForwardSlash().equals(a))return!0;return!1},"~S");c(b,"haveSelectedSpectrum",function(){return this.$haveSelectedSpectrum});c(b,"mouseClickedEvent",function(a,b,c,f){this.selectedIntegral=this.selectedMeasurement=null;var e=this.nextClickForSetPeak;this.nextClickForSetPeak=null;if(!this.checkArrowUpDownClick(a,
b)&&!this.checkArrowLeftRightClick(a,b))if(this.lastClickX=NaN,this.lastPixelX=2147483647,this.isSplitWidget(a,b))this.splitStack(1==this.nSplit);else if(this.isCloserWidget(a,b))this.pd.closeSpectrum();else{var g=this.getPinSelected(a,b);if(null!=g)this.setWidgetValueByUser(g);else if(g=this.is2dClick(a,b),2==c&&(-1==this.iSpectrumClicked&&0<=this.iPreviousSpectrumClicked)&&this.setSpectrumClicked(this.iPreviousSpectrumClicked),!g&&f)this.setSpectrumClicked(this.iPreviousSpectrumClicked),null!=this.pendingMeasurement?
this.processPendingMeasurement(a,b,-3):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,3);else if(this.lastXMax=NaN,2==c)g?(this.sticky2Dcursor&&this.addAnnotation(this.getAnnotation(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b),this.pd.coordStr,!1,!0,5,5),!0),this.sticky2Dcursor=!0,this.set2DCrossHairs(a,b)):this.isInTopBar(a,b)?this.doZoom(this.toX0(this.xPixel0),0,this.toX0(this.xPixel1),0,!0,!1,!1,!0,!0):this.isInRightBar(a,b)?this.doZoom(this.getScale().minXOnScale,
this.viewList.get(0).getScale().minYOnScale,this.getScale().maxXOnScale,this.viewList.get(0).getScale().maxYOnScale,!0,!0,!1,!1,!1):this.isInTopBar2D(a,b)?this.reset2D(!0):this.isInRightBar2D(a,b)?this.reset2D(!1):null!=this.pendingMeasurement?this.processPendingMeasurement(a,b,-2):0<=this.iSpectrumClicked&&this.processPendingMeasurement(a,b,2);else if(g){if(null!=this.annotations&&(f=(new JSV.common.Coordinate).set(this.imageView.toX(a),this.imageView.toSubspectrumIndex(b)),f=this.findAnnotation2D(f),
null!=f&&this.setAnnotationText(f)))return;1==c&&(this.sticky2Dcursor=!1);this.set2DCrossHairs(a,b)}else{if(this.isInPlotRegion(a,b)){if(null!=this.selectedSpectrumIntegrals&&this.checkIntegralNormalizationClick(a,b))return;if(null!=this.pendingMeasurement){this.processPendingMeasurement(a,b,1);return}this.setCoordClicked(a,this.toX(a),this.toY(b));this.updateDialog(JSV.common.Annotation.AType.PeakList,-1);if(null!=e){this.nextClickForSetPeak=e;this.shiftSpectrum(4,NaN,NaN);this.nextClickForSetPeak=
null;return}}else this.setCoordClicked(0,NaN,0);this.pd.notifyPeakPickedListeners(null)}}},"~N,~N,~N,~B");c(b,"is2dClick",function(a,b){return null!=this.imageView&&a==this.imageView.fixX(a)&&b==this.fixY(b)},"~N,~N");c(b,"updateDialog",function(a,b){var c=this.getDialog(a,b);if(null!=c&&this.isVisible(c)){var f=this.toX(this.xPixel1)-this.toX(this.xPixel0),e=this.getSpectrum().isInverted()?this.yPixel1-this.pd.mouseY:this.pd.mouseY-this.yPixel0;c.update(this.pd.coordClicked,f,e)}},"JSV.common.Annotation.AType,~N");
c(b,"isVisible",function(a){return null!=a&&a.isDialog()&&a.isVisible()},"JSV.api.AnnotationData");c(b,"mousePressedEvent",function(a,b){this.checkWidgetEvent(a,b,!0)},"~N,~N,~N");c(b,"mouseReleasedEvent",function(a,b){if(null!=this.pendingMeasurement)2>Math.abs(this.toPixelX(this.pendingMeasurement.getXVal())-a)&&(this.pendingMeasurement=null),this.processPendingMeasurement(a,b,-2),this.setToolTipForPixels(a,b);else if(0!=this.pd.integralShiftMode)this.pd.integralShiftMode=0,this.zoomBox1D.xPixel1=
this.zoomBox1D.xPixel0;else{0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo);var c=this.pd.thisWidget;if(this.pd.isIntegralDrag)JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)&&this.checkIntegral(this.toX(this.zoomBox1D.xPixel0),this.toX(this.zoomBox1D.xPixel1),!0),this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0=0,this.pendingIntegral=null,this.pd.isIntegralDrag=!1;else if(c===this.zoomBox2D)JSV.common.GraphSet.isGoodEvent(this.zoomBox2D,null,!0)&&(this.imageView.setZoom(this.zoomBox2D.xPixel0,
this.zoomBox2D.yPixel0,this.zoomBox2D.xPixel1,this.zoomBox2D.yPixel1),this.zoomBox2D.xPixel1=this.zoomBox2D.xPixel0,this.doZoom(this.imageView.toX(this.imageView.xPixel0),this.getScale().minY,this.imageView.toX(this.imageView.xPixel0+this.imageView.xPixels-1),this.getScale().maxY,!1,!1,!1,!0,!0));else if(c===this.zoomBox1D){if(JSV.common.GraphSet.isGoodEvent(this.zoomBox1D,null,!0)){var c=this.zoomBox1D.xPixel1,f=this.pd.shiftPressed;this.doZoom(this.toX(this.zoomBox1D.xPixel0),f?this.toY(this.zoomBox1D.yPixel0):
0,this.toX(c),f?this.toY(this.zoomBox1D.yPixel1):0,!0,f,!0,!0,!0);this.zoomBox1D.xPixel1=this.zoomBox1D.xPixel0}}else(c===this.pin1Dx0||c===this.pin1Dx1||c===this.cur2Dx0||c===this.cur2Dx1)&&this.addCurrentZoom()}},"~N,~N");c(b,"mouseMovedEvent",function(a,b){if(1<this.nSpectra){var c=this.getSplitPoint(b);this.setPositionForFrame(c);this.setSpectrumMovedTo(1<this.nSplit?c:this.iSpectrumSelected);0<=this.iSpectrumMovedTo&&this.setScale(this.iSpectrumMovedTo)}this.inPlotMove=this.isInPlotRegion(a,
b);this.setXPixelMovedTo(1.7976931348623157E308,1.7976931348623157E308,this.inPlotMove?a:-1,-1);this.inPlotMove&&(this.xValueMovedTo=this.toX(this.xPixelMovedTo),this.yValueMovedTo=this.getSpectrum().getYValueAt(this.xValueMovedTo));if(0!=this.pd.integralShiftMode){var c=this.getDialog(JSV.common.Annotation.AType.Integration,-1),f=c.getData().getXYCoords(),f=f[0<this.pd.integralShiftMode?f.length-1:0].getYVal();c.getData().shiftY(this.pd.integralShiftMode,this.toPixelYint(f)+b-(0<this.pd.integralShiftMode?
this.yPixelPlot1:this.yPixelPlot0),this.yPixel0,this.yPixels)}else this.pd.isIntegralDrag||(null!=this.pendingMeasurement?(this.processPendingMeasurement(a,b,0),this.setToolTipForPixels(a,b)):(this.selectedMeasurement=this.inPlotMove&&null!=this.selectedSpectrumMeasurements?this.findMeasurement(this.selectedSpectrumMeasurements,a,b,0):null,this.selectedIntegral=null,this.inPlotMove&&(null!=this.selectedSpectrumIntegrals&&null==this.selectedMeasurement)&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,
a,b,0),null==this.selectedIntegral&&(this.selectedIntegral=this.findMeasurement(this.selectedSpectrumIntegrals,a,b,-5))),this.setToolTipForPixels(a,b),null==this.imageView?(this.piMouseOver=null,c=1<this.nSplit?this.iSpectrumMovedTo:this.iSpectrumClicked,!this.isDrawNoSpectra()&&0<=c&&(c=this.spectra.get(c),null!=c.getPeakList()&&(this.coordTemp.setXVal(this.toX(a)),this.coordTemp.setYVal(this.toY(b)),this.piMouseOver=c.findPeakByCoord(a,this.coordTemp)))):!this.pd.display1D&&this.sticky2Dcursor&&
this.set2DCrossHairs(a,b)))},"~N,~N");c(b,"nextView",function(){this.currentZoomIndex+1<this.viewList.size()&&this.setZoomTo(this.currentZoomIndex+1)});c(b,"previousView",function(){0<this.currentZoomIndex&&this.setZoomTo(this.currentZoomIndex-1)});c(b,"resetView",function(){this.setZoomTo(0)});c(b,"removeAllHighlights",function(){this.removeAllHighlights(null)});c(b,"removeHighlight",function(a){this.highlights.removeItemAt(a)},"~N");c(b,"removeHighlight",function(a,b){for(var c=this.highlights.size();0<=
--c;){var f=this.highlights.get(c);f.x1==a&&f.x2==b&&this.highlights.removeItemAt(c)}},"~N,~N");c(b,"scaleYBy",function(a){if(null!=this.imageView||this.zoomEnabled)this.viewData.scaleSpectrum(null==this.imageView?this.iSpectrumSelected:-2,a),null!=this.imageView&&(this.update2dImage(!1),this.resetPinsFromView()),this.pd.refresh()},"~N");c(b,"selectSpectrum",function(a,b,c){for(var f=!1,e=this.spectra.size();0<=--e;)if((null==a||this.getSpectrumAt(e).getFilePathForwardSlash().equals(a))&&this.getSpectrumAt(e).matchesPeakTypeModel(b,
c))this.setSpectrumSelected(e),1<this.nSplit&&this.splitStack(!0),f=!0;1<this.nSpectra&&(!f&&0<=this.iSpectrumSelected&&!this.pd.isCurrentGraphSet(this))&&this.setSpectrumSelected(-2147483648);return f},"~S,~S,~S");c(b,"selectPeakByFileIndex",function(a,b,c){for(var f,e=this.spectra.size();0<=--e;)if(null!=(f=this.getSpectrumAt(e).selectPeakByFileIndex(a,b,c)))return f;return null},"~S,~S,~S");c(b,"setSelected",function(a){0>a?(this.bsSelected.clearAll(),this.setSpectrumClicked(-1)):(this.bsSelected.set(a),
this.setSpectrumClicked(1==this.bsSelected.cardinality()?a:-1),1<this.nSplit&&0<=a&&(this.pd.currentSplitPoint=a))},"~N");c(b,"setSelectedIntegral",function(a){var b=this.selectedIntegral.getSpectrum();this.getIntegrationGraph(this.getSpectrumIndex(b)).setSelectedIntegral(this.selectedIntegral,a)},"~N");c(b,"setShowAnnotation",function(a,b){var c=this.getDialog(a,-1);if(null==c)null!=b&&b!==Boolean.TRUE||(a===JSV.common.Annotation.AType.PeakList||a===JSV.common.Annotation.AType.Integration||a===JSV.common.Annotation.AType.Measurements)&&
this.pd.showDialog(a);else if(null==b)c.isDialog()?c.setVisible(!c.isVisible()):this.pd.showDialog(a);else{var f=b.booleanValue();f&&c.setState(f);(f||c.isDialog())&&this.pd.showDialog(a);!f&&c.isDialog()&&c.setVisible(!1)}},"JSV.common.Annotation.AType,Boolean");c(b,"checkIntegralParams",function(a,b){if(!this.getSpectrum().canIntegrate()||this.reversePlot)return!1;var c=this.getFixedSelectedSpectrumIndex(),f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==b)return!0;switch(JSV.common.IntegralData.IntMode.getMode(b.toUpperCase())){case JSV.common.IntegralData.IntMode.NA:return!1;
case JSV.common.IntegralData.IntMode.CLEAR:this.integrate(c,null);this.integrate(c,a);break;case JSV.common.IntegralData.IntMode.ON:null==f?this.integrate(c,a):f.setState(!0);break;case JSV.common.IntegralData.IntMode.OFF:null!=f&&f.setState(!1);break;case JSV.common.IntegralData.IntMode.TOGGLE:null==f?this.integrate(c,a):f.setState(!f.getState());break;case JSV.common.IntegralData.IntMode.AUTO:null==f&&(this.checkIntegralParams(a,"ON"),f=this.getDialog(JSV.common.Annotation.AType.Integration,-1));
null!=f&&f.getData().autoIntegrate();break;case JSV.common.IntegralData.IntMode.LIST:this.pd.showDialog(JSV.common.Annotation.AType.Integration);break;case JSV.common.IntegralData.IntMode.MARK:null==f&&(this.checkIntegralParams(a,"ON"),f=this.getDialog(JSV.common.Annotation.AType.Integration,-1));null!=f&&f.getData().addMarks(b.substring(4).trim());break;case JSV.common.IntegralData.IntMode.MIN:if(null!=f)try{var e=Double.parseDouble(JSV.common.ScriptToken.getTokens(b).get(1));f.getData().setMinimumIntegral(e)}catch(g){if(!D(g,
Exception))throw g;}break;case JSV.common.IntegralData.IntMode.UPDATE:null!=f&&f.getData().update(a)}this.updateDialog(JSV.common.Annotation.AType.Integration,-1);return!0},"JSV.common.Parameters,~S");c(b,"setSpectrum",function(a,b){b&&1<this.nSplit?1<this.nSplit&&this.setSpectrumClicked(a):(this.setSpectrumClicked(a),this.showAllStacked=this.stackSelected=!1);0<=a&&this.dialogsToFront(this.getSpectrum())},"~N,~B");c(b,"setSpectrumJDX",function(a){var b=this.getFixedSelectedSpectrumIndex();this.spectra.removeItemAt(b);
this.spectra.add(b,a);this.pendingMeasurement=null;this.clearViews();this.viewData.newSpectrum(this.spectra)},"JSV.common.Spectrum");c(b,"setZoom",function(a,b,c,f){this.setZoomTo(0);0==a&&0==c&&0==b&&0==f?(this.newPins(),this.imageView=null,this.getScale(),this.getScale()):this.doZoom(a,b,c,f,!0,b!=f,!1,!0,!0)},"~N,~N,~N,~N");c(b,"shiftSpectrum",function(a,b,c){var f=this.getSpectrum();if(!f.isNMR()||!f.is1D())return!1;var e=null,e=0;if(1.7976931348623157E308==c)e=-f.addSpecShift(0);else switch(a){case 3:e=
c;break;case 1:case 2:this.nextClickMode=a;if(Double.isNaN(b))return e=this.pd.getInput("Click on "+(1==a?"or beside a peak to set its chemical shift":"the spectrum set the chemical shift at that point")+(-2147483648==c?"":" to "+c)+".","Set Reference "+(1==a?"for Peak":"at Point"),"OK"),this.nextClickForSetPeak="OK".equals(e)?Double.$valueOf(c):null,!1;this.nextClickForSetPeak=null;case 4:null!=this.nextClickForSetPeak&&(c=this.nextClickForSetPeak.doubleValue(),this.nextClickForSetPeak=null);Double.isNaN(b)&&
(b=this.lastClickX);1==this.nextClickMode&&(b=this.getNearestPeak(f,b,this.toY(this.pd.mouseY)));if(Double.isNaN(c))try{var g=this.pd.getInput("New chemical shift (set blank to reset)","Set Reference",JU.DF.formatDecimalDbl(b,this.getScale().precision[0])).trim();c=0==g.length?b-f.addSpecShift(0):Double.parseDouble(g)}catch(j){if(D(j,Exception))return!1;throw j;}e=c-b}if(0==e)return!1;f.addSpecShift(e);if(null!=this.annotations)for(a=this.annotations.size();0<=--a;)this.annotations.get(a).spec===
f&&this.annotations.get(a).addSpecShift(e);if(null!=this.dialogs){var k;for(a=this.dialogs.entrySet().iterator();a.hasNext()&&((k=a.next())||1);)k.getValue().getSpectrum()===f&&k.getValue().setSpecShift(e)}this.getScale().addSpecShift(e);Double.isNaN(this.lastClickX)||(this.lastClickX+=e);this.updateDialogs();this.doZoom(0,this.getScale().minYOnScale,0,this.getScale().maxYOnScale,!0,!0,!1,!0,!1);this.pd.setTaintedAll();this.pd.repaint();return!0},"~N,~N,~N");c(b,"toPeak",function(a){a*=this.drawXAxisLeftToRight?
1:-1;Double.isNaN(this.lastClickX)&&(this.lastClickX=this.lastPixelX=0);var b=this.getSpectrum(),c=this.setCoordClicked(this.lastPixelX,this.lastClickX,0);a=b.setNextPeak(c,a);0>a||(a=b.getPeakList().get(a),b.setSelectedPeak(a),this.setCoordClicked(a.getXPixel(),a.getX(),0),this.pd.notifyPeakPickedListeners(new JSV.common.PeakPickEvent(this.jsvp,this.pd.coordClicked,a)))},"~N");c(b,"scaleSelectedBy",function(a){for(var b=this.bsSelected.nextSetBit(0);0<=b;b=this.bsSelected.nextSetBit(b+1))this.viewData.scaleSpectrum(b,
a)},"~N");f(b,"toString",function(){return"gs: "+this.nSpectra+" "+this.spectra+" "+this.spectra.get(0).getFilePath()});c(b,"setXPointer",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.xValueMovedTo=this.lastClickX=b;this.lastPixelX=this.toPixelX(b);this.setXPixelMovedTo(b,1.7976931348623157E308,0,0);this.yValueMovedTo=NaN},"JSV.common.Spectrum,~N");c(b,"setXPointer2",function(a,b){null!=a&&this.setSpectrumClicked(this.getSpectrumIndex(a));this.setXPixelMovedTo(1.7976931348623157E308,
b,0,0)},"JSV.common.Spectrum,~N");c(b,"hasCurrentMeasurement",function(a){return null!=(a===JSV.common.Annotation.AType.Integration?this.selectedSpectrumIntegrals:this.selectedSpectrumMeasurements)},"JSV.common.Annotation.AType");c(b,"getDialog",function(a,b){-1==b&&(b=this.getCurrentSpectrumIndex());return null==this.dialogs||0>b?null:this.dialogs.get(a+"_"+b)},"JSV.common.Annotation.AType,~N");c(b,"removeDialog",function(a,b){null!=this.dialogs&&0<=a&&this.dialogs.remove(b+"_"+a)},"~N,JSV.common.Annotation.AType");
c(b,"addDialog",function(a,b,c){null==this.dialogs&&(this.dialogs=new java.util.Hashtable);a=b+"_"+a;c.setGraphSetKey(a);this.dialogs.put(a,c);return c},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(b,"removeDialog",function(a){var b=a.getGraphSetKey();this.dialogs.remove(b);a=a.getData();null!=a&&this.dialogs.put(b,a)},"JSV.dialog.JSVDialog");c(b,"getPeakListing",function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var f=this.getDialog(JSV.common.Annotation.AType.PeakList,
-1);if(null==f){if(!c)return null;this.addDialog(a,JSV.common.Annotation.AType.PeakList,f=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.getSpectrum()))}f.getData().setPeakList(b,-2147483648,this.viewData.getScale());f.isDialog()&&f.setFields();return f.getData()},"~N,JSV.common.Parameters,~B");c(b,"setPeakListing",function(a){var b=this.getDialog(JSV.common.Annotation.AType.PeakList,-1),c=null!=b&&b.isDialog()?b:null;(null==a?null==c||!c.isVisible():a.booleanValue())?this.pd.showDialog(JSV.common.Annotation.AType.PeakList):
b.isDialog()&&b.setVisible(!1)},"Boolean");c(b,"haveIntegralDisplayed",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null!=a&&a.getState()},"~N");c(b,"getIntegrationGraph",function(a){a=this.getDialog(JSV.common.Annotation.AType.Integration,a);return null==a?null:a.getData()},"~N");c(b,"setIntegrationRatios",function(a){var b=this.getFixedSelectedSpectrumIndex();null==this.aIntegrationRatios&&(this.aIntegrationRatios=Array(this.nSpectra));this.aIntegrationRatios[b]=
JSV.common.IntegralData.getIntegrationRatiosFromString(this.getSpectrum(),a)},"~S");c(b,"getIntegrationRatios",function(a){return null==this.aIntegrationRatios?null:this.aIntegrationRatios[a]},"~N");c(b,"integrate",function(a,b){var c=this.getSpectrumAt(a);if(null==b||!c.canIntegrate())return this.removeDialog(a,JSV.common.Annotation.AType.Integration),!1;this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(c,b));return!0},"~N,JSV.common.Parameters");c(b,"getIntegration",
function(a,b,c){0>a&&(a=this.getCurrentSpectrumIndex());if(0>a)return null;var f=this.getDialog(JSV.common.Annotation.AType.Integration,-1);if(null==f){if(!c)return null;f=this.addDialog(a,JSV.common.Annotation.AType.Integration,new JSV.common.IntegralData(this.getSpectrum(),b))}return f.getData()},"~N,JSV.common.Parameters,~B");c(b,"getMeasurementInfo",function(a,b){var c;switch(a){case JSV.common.Annotation.AType.PeakList:c=this.getPeakListing(b,null,!1);break;case JSV.common.Annotation.AType.Integration:c=
this.getIntegration(b,null,!1);break;default:return null}if(null==c)return null;var f=new java.util.Hashtable;c.getInfo(f);return f},"JSV.common.Annotation.AType,~N");c(b,"getInfo",function(a,b){var c=new java.util.Hashtable;if("".equals(a))c.put("KEYS","viewInfo spectra");else if("viewInfo".equalsIgnoreCase(a))return this.getScale().getInfo(c);var f=new JU.Lst;c.put("spectra",f);for(var e=0;e<this.nSpectra;e++)if(!(0<=b&&e!=b)){var g=this.spectra.get(e),j=g.getInfo(a);if(0<=b&&null!=a&&(2==j.size()||
a.equalsIgnoreCase("id")))return 2==j.size()&&j.remove("id"),j;JSV.common.Parameters.putInfo(a,j,"type",g.getDataType());JSV.common.Parameters.putInfo(a,j,"titleLabel",g.getTitleLabel());JSV.common.Parameters.putInfo(a,j,"filePath",g.getFilePath().$replace("\\","/"));JSV.common.Parameters.putInfo(a,j,"PeakList",JSV.common.Parameters.isMatch(a,"PeakList")?this.getMeasurementInfo(JSV.common.Annotation.AType.PeakList,e):null);JSV.common.Parameters.putInfo(a,j,"Integration",JSV.common.Parameters.isMatch(a,
"Integration")?this.getMeasurementInfo(JSV.common.Annotation.AType.Integration,e):null);if(0<=b)return j;f.addLast(j)}return c},"~S,~N");c(b,"getTitle",function(a){return 1==this.nSpectra||0<=this.iSpectrumSelected&&(!a||1==this.nSplit)?this.getSpectrum().getTitle():null},"~B");c(b,"getCurrentView",function(){this.setScale(this.getFixedSelectedSpectrumIndex());return this.viewData.getScale()});c(b,"set2DXY",function(a,b,c){var f;null!=this.gs2dLinkedX&&(f=this.toPixelX(a),f!=this.fixX(f)&&(f=-2147483648,
a=1.7976931348623157E308),this.cur1D2x1.setX(a,f));null!=this.gs2dLinkedY&&(f=this.toPixelX(b),f!=this.fixX(f)&&(f=-2147483648,b=1.7976931348623157E308),this.cur1D2x2.setX(b,f));this.cur1D2Locked=c},"~N,~N,~B");c(b,"dialogsToFront",function(a){if(null!=this.dialogs){null==a&&(a=this.getSpectrum());for(var b,c=this.dialogs.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var f=b.getValue();this.isVisible(f)&&(null==a?f.setVisible(!0):f.setFocus(f.getSpectrum()===a))}}},"JSV.common.Spectrum");
c(b,"setPlotColors",function(a){var b=a;if(b.length>this.nSpectra)a=Array(this.nSpectra),System.arraycopy(b,0,a,0,this.nSpectra),b=a;else if(this.nSpectra>b.length){a=Array(this.nSpectra);var c=this.nSpectra-b.length;System.arraycopy(b,0,a,0,b.length);for(var f=0,b=b.length;f<c;f++,b++)a[b]=this.generateRandomColor();b=a}this.plotColors=b},"~O");c(b,"disposeImage",function(){null!=this.image2D&&this.image2D.parentNode.removeChild(this.image2D);this.plotColors=this.highlights=this.pd=this.jsvp=this.image2D=
null});c(b,"generateRandomColor",function(){for(;;){var a=v(255*Math.random()),b=v(255*Math.random()),c=v(255*Math.random()),a=this.g2d.getColor3(a,b,c);if(0!=a.getRGB())return a}});c(b,"setPlotColor0",function(a){this.plotColors[0]=a},"~O");c(b,"getPlotColor",function(a){return a>=this.plotColors.length?null:this.plotColors[a]},"~N");c(b,"setColorFromToken",function(a,b){null!=b&&this.g2d.setGraphicsColor(a,b===JSV.common.ScriptToken.PLOTCOLOR?this.plotColors[0]:this.pd.getColor(b))},"~O,JSV.common.ScriptToken");
c(b,"setPlotColor",function(a,b){var c;switch(b){case -3:c=JSV.common.GraphSet.veryLightGrey;break;case -2:c=this.pd.BLACK;break;case -1:c=this.pd.getColor(JSV.common.ScriptToken.INTEGRALPLOTCOLOR);break;default:c=this.plotColors[b]}this.g2d.setGraphicsColor(a,c)},"~O,~N");c(b,"draw2DImage",function(){null!=this.imageView&&this.g2d.drawGrayScaleImage(this.gMain,this.image2D,this.imageView.xPixel0,this.imageView.yPixel0,this.imageView.xPixel0+this.imageView.xPixels-1,this.imageView.yPixel0+this.imageView.yPixels-
1,this.imageView.xView1,this.imageView.yView1,this.imageView.xView2,this.imageView.yView2)});c(b,"get2DImage",function(){this.imageView=new JSV.common.ImageView;this.imageView.set(this.viewList.get(0).getScale());if(!this.update2dImage(!0))return!1;this.imageView.resetZoom();return this.sticky2Dcursor=!0},"JSV.common.Spectrum");c(b,"update2dImage",function(a){this.imageView.set(this.viewData.getScale());var b=this.getSpectrumAt(0),c=this.imageView.get2dBuffer(b,!a);if(null==c)return this.imageView=
this.image2D=null,!1;a&&(c=this.imageView.adjustView(b,this.viewData),this.imageView.resetView());this.image2D=this.g2d.newGrayScaleImage(this.gMain,this.image2D,this.imageView.imageWidth,this.imageView.imageHeight,c);this.setImageWindow();return!0},"~B");c(b,"getAnnotation",function(a,b,c,f,e,g,j){return(new JSV.common.ColoredAnnotation).setCA(a,b,this.getSpectrum(),c,this.pd.BLACK,f,e,g,j)},"~N,~N,~S,~B,~B,~N,~N");c(b,"getAnnotation",function(a,b){return JSV.common.Annotation.getColoredAnnotation(this.g2d,
this.getSpectrum(),a,b)},"JU.Lst,JSV.common.Annotation");c(b,"fillBox",function(a,b,c,f,e,g){this.setColorFromToken(a,g);this.g2d.fillRect(a,Math.min(b,f),Math.min(c,e),Math.abs(b-f),Math.abs(c-e))},"~O,~N,~N,~N,~N,JSV.common.ScriptToken");c(b,"drawBox",function(a,b,c,f,e,g){this.setColorFromToken(a,g);this.g2d.drawRect(a,Math.min(b,f),Math.min(c,e),Math.abs(b-f)-1,Math.abs(c-e)-1)},"~O,~N,~N,~N,~N,JSV.common.ScriptToken");c(b,"drawHandle",function(a,b,c,f,e){e?this.g2d.drawRect(a,b-f,c-f,2*f,2*f):
this.g2d.fillRect(a,b-f,c-f,2*f+1,2*f+1)},"~O,~N,~N,~N,~B");c(b,"setCurrentBoxColor",function(a){this.g2d.setGraphicsColor(a,this.pd.BLACK)},"~O");c(b,"fillArrow",function(a,b,c,f,e){var g=1;switch(b){case 1:case 3:g=-1}c=E(-1,[c-5,c-5,c+5,c+5,c+8,c,c-8]);f=E(-1,[f+5*g,f-g,f-g,f+5*g,f+5*g,f+10*g,f+5*g]);switch(b){case 1:case 2:e?this.g2d.fillPolygon(a,f,c,7):this.g2d.drawPolygon(a,f,c,7);break;case 3:case 4:e?this.g2d.fillPolygon(a,c,f,7):this.g2d.drawPolygon(a,c,f,7)}},"~O,~N,~N,~N,~B");c(b,"fillCircle",
function(a,b,c,f){f?this.g2d.fillCircle(a,b-4,c-4,8):this.g2d.drawCircle(a,b-4,c-4,8)},"~O,~N,~N,~B");c(b,"setAnnotationColor",function(a,b,c){null!=c?this.setColorFromToken(a,c):(c=null,C(b,"JSV.common.ColoredAnnotation")&&(c=b.getColor()),null==c&&(c=this.pd.BLACK),this.g2d.setGraphicsColor(a,c))},"~O,JSV.common.Annotation,JSV.common.ScriptToken");c(b,"setSolutionColor",function(a,b,c){for(var f=0;f<this.nSpectra;f++){var e=this.spectra.get(f),g=b||!e.canShowSolutionColor()?-1:a.getColour(e,c);
e.setFillColor(-1==g?null:this.pd.vwr.parameters.getColor1(g))}},"JSV.api.VisibleInterface,~B,~B");c(b,"setIRMode",function(a,b){for(var c=0;c<this.nSpectra;c++){var f=this.spectra.get(c);if(f.dataType.equals(b)){var e=JSV.common.Spectrum.taConvert(f,a);e!==f&&this.pd.setSpecForIRMode(e)}}},"JSV.common.Spectrum.IRMode,~S");c(b,"getSpectrumCount",function(){return 0});c(b,"invertYAxis",function(){this.viewList.get(0).init(null,0,0,this.getSpectrum().invertYAxis().isContinuous());this.resetViewCompletely()});
b.$GraphSet$Highlight$=function(){var a=r(function(){fa(this,arguments);this.x2=this.x1=0;this.spectrum=this.color=null;u(this,arguments)},JSV.common.GraphSet,"Highlight",null);y(a,function(a,b,c,e){this.x1=a;this.x2=b;this.color=e;this.spectrum=c},"~N,~N,JSV.common.Spectrum,javajs.api.GenericColor");f(a,"toString",function(){return"highlight "+this.x1+" "+this.x2+" "+this.spectrum});f(a,"equals",function(a){return!C(a,"JSV.common.GraphSet.Highlight")?!1:a.x1==this.x1&&a.x2==this.x2},"~O")};b.RT2=
Math.sqrt(2);b.veryLightGrey=null});n("JSV.common");z(["JSV.common.XYScaleConverter"],"JSV.common.ImageView",["JSV.common.Coordinate","$.ScaleData"],function(){var b=r(function(){this.buf2d=null;this.yView2=this.xView2=this.yView1=this.xView1=this.yPixelZoom2=this.xPixelZoom2=this.yPixelZoom1=this.xPixelZoom1=this.yPixels=this.xPixels=this.imageHeight=this.imageWidth=this.yPixel1=this.xPixel1=this.yPixel0=this.xPixel0=this.averageGray=this.grayFactorLast=0;this.minX=NaN;this.maxZ=this.minZ=this.maxY=
this.minY=this.maxX=0;this.scaleData=null;u(this,arguments)},JSV.common,"ImageView",null,JSV.common.XYScaleConverter);c(b,"set",function(a){Double.isNaN(this.minX)&&(this.minX=a.minX,this.maxX=a.maxX);this.minZ=a.minY;this.maxZ=a.maxY;this.scaleData=new JSV.common.ScaleData},"JSV.common.ScaleData");c(b,"setZoom",function(a,b,c,f){this.xPixelZoom1=Math.min(a,c);this.yPixelZoom1=Math.min(b,f);this.xPixelZoom2=Math.max(a,c);this.yPixelZoom2=Math.max(b,f);this.setView()},"~N,~N,~N,~N");c(b,"setXY0",function(a,
b,c){this.xPixel0=b;this.yPixel0=c;this.xPixel1=this.xPixel0+this.xPixels-1;this.yPixel1=this.yPixel0+this.yPixels-1;this.setMinMaxY(a)},"JSV.common.Spectrum,~N,~N");c(b,"setPixelWidthHeight",function(a,b){this.xPixels=a;this.yPixels=b},"~N,~N");c(b,"resetView",function(){this.yView1=this.xView1=0;this.xView2=this.imageWidth-1;this.yView2=this.imageHeight-1});c(b,"setView",function(){0==this.xPixelZoom1&&this.resetZoom();var a=this.toImageX(this.xPixelZoom1),b=this.toImageY(this.yPixelZoom1),c=this.toImageX(this.xPixelZoom2),
f=this.toImageY(this.yPixelZoom2);this.xView1=Math.min(a,c);this.yView1=Math.min(b,f);this.xView2=Math.max(a,c);this.yView2=Math.max(b,f);this.setScaleData();this.resetZoom()});c(b,"resetZoom",function(){this.xPixelZoom1=this.xPixel0;this.yPixelZoom1=this.yPixel0;this.xPixelZoom2=this.xPixel1;this.yPixelZoom2=this.yPixel1});c(b,"toImageX",function(a){return this.xView1+v(Math.floor((a-this.xPixel0)/(this.xPixels-1)*(this.xView2-this.xView1)))},"~N");c(b,"toImageY",function(a){return this.yView1+v(Math.floor((a-
this.yPixel0)/(this.yPixels-1)*(this.yView2-this.yView1)))},"~N");c(b,"toImageX0",function(a){return JSV.common.Coordinate.intoRange(v((1*a-this.xPixel0)/(this.xPixels-1)*(this.imageWidth-1)),0,this.imageWidth-1)},"~N");c(b,"toImageY0",function(a){return JSV.common.Coordinate.intoRange(v((1*a-this.yPixel0)/(this.yPixels-1)*(this.imageHeight-1)),0,this.imageHeight-1)},"~N");c(b,"isXWithinRange",function(a){return a>=this.xPixel0-5&&a<this.xPixel0+this.xPixels+5},"~N");c(b,"toSubspectrumIndex",function(a){return JSV.common.Coordinate.intoRange(this.imageHeight-
1-this.toImageY(a),0,this.imageHeight-1)},"~N");c(b,"toX0",function(a){return this.maxX+(this.minX-this.maxX)*(this.fixX(a)-this.xPixel0)/(this.xPixels-1)},"~N");c(b,"toPixelX0",function(a){return this.xPixel1-v((a-this.minX)/(this.maxX-this.minX)*(this.xPixels-1))},"~N");c(b,"toPixelY0",function(a){return this.yPixel1-v(a/(this.imageHeight-1)*(this.yPixels-1))},"~N");c(b,"subIndexToPixelY",function(a){return this.yPixel0+v(1*(this.imageHeight-1-a-this.yView1)/(this.yView2-this.yView1)*(this.yPixels-
1))},"~N");c(b,"fixSubIndex",function(a){return JSV.common.Coordinate.intoRange(a,this.imageHeight-1-this.yView2,this.imageHeight-1-this.yView1)},"~N");c(b,"setView0",function(a,b,c,f){a=this.toImageX0(a);b=this.toImageY0(b);c=this.toImageX0(c);f=this.toImageY0(f);this.xView1=Math.min(a,c);this.yView1=Math.min(b,f);this.xView2=Math.max(a,c);this.yView2=Math.max(b,f);this.resetZoom()},"~N,~N,~N,~N");c(b,"get2dBuffer",function(a,b){var c=a.getSubSpectra();if(null==c||!c.get(0).isContinuous())return null;
var f=a.getXYCoords(),e=c.size();this.imageWidth=f.length;this.imageHeight=e;var g=255/(this.maxZ-this.minZ);if(!b&&null!=this.buf2d&&g==this.grayFactorLast)return this.buf2d;this.grayFactorLast=g;for(var j=this.imageWidth*this.imageHeight,k=null==this.buf2d||this.buf2d.length!=j?E(j,0):this.buf2d,l=0,n=0;n<e;n++){var m=c.get(n).xyCoords;if(m.length!=f.length)return null;for(var p=0;p<f.length;p++){var r=m[p].getYVal(),r=255-JSV.common.Coordinate.intoRange(v((r-this.minZ)*g),0,255);k[--j]=r;l+=r}}this.averageGray=
1-l/(this.imageWidth*this.imageHeight)/255;System.out.println("Average gray = "+this.averageGray);return this.buf2d=k},"JSV.common.Spectrum,~B");c(b,"adjustView",function(a,b){for(var c=0,f=!1;((f=0.05>this.averageGray)||0.3<this.averageGray)&&10>c++;)b.scaleSpectrum(-2,f?2:0.5),this.set(b.getScale()),this.get2dBuffer(a,!1);return this.buf2d},"JSV.common.Spectrum,JSV.common.ViewData");c(b,"getBuffer",function(){return this.buf2d});c(b,"setMinMaxY",function(a){a=a.getSubSpectra();var b=a.get(0);this.maxY=
b.getY2D();this.minY=a.get(a.size()-1).getY2D();b.y2DUnits.equalsIgnoreCase("Hz")&&(this.maxY/=b.freq2dY,this.minY/=b.freq2dY);this.setScaleData()},"JSV.common.Spectrum");c(b,"setScaleData",function(){this.scaleData.minY=this.minY;this.scaleData.maxY=this.maxY;this.scaleData.setYScale(this.toY(this.yPixel0),this.toY(this.yPixel1),!1,!1)});f(b,"fixX",function(a){return a<this.xPixel0?this.xPixel0:a>this.xPixel1?this.xPixel1:a},"~N");f(b,"fixY",function(a){return JSV.common.Coordinate.intoRange(a,this.yPixel0,
this.yPixel1)},"~N");f(b,"getScale",function(){return this.scaleData});f(b,"toX",function(a){return this.maxX+(this.minX-this.maxX)*this.toImageX(this.fixX(a))/(this.imageWidth-1)},"~N");f(b,"toY",function(a){a=this.toSubspectrumIndex(a);return this.maxY+(this.minY-this.maxY)*a/(this.imageHeight-1)},"~N");f(b,"toPixelX",function(a){var b=this.toX(this.xPixel0),c=this.toX(this.xPixel1);return this.xPixel0+v((a-b)/(c-b)*(this.xPixels-1))},"~N");f(b,"toPixelY",function(a){return v(this.yPixel0+(a-this.scaleData.minYOnScale)/
(this.scaleData.maxYOnScale-this.scaleData.minYOnScale)*this.yPixels)},"~N");f(b,"getXPixels",function(){return this.xPixels});f(b,"getYPixels",function(){return this.yPixels});f(b,"getXPixel0",function(){return this.xPixel0})});n("JSV.common");z(["JSV.common.Measurement"],"JSV.common.Integral",null,function(){var b=G(JSV.common,"Integral",JSV.common.Measurement);c(b,"setInt",function(a,b,c,f,e,g){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(e,g);this.setValue(f);return this},"~N,~N,JSV.common.Spectrum,~N,~N,~N")});
n("JSV.common");var sb=G(JSV.common,"IntegralComparator",null,java.util.Comparator);f(sb,"compare",function(b,a){return b.getXVal()<a.getXVal()?-1:b.getXVal()>a.getXVal()?1:0},"JSV.common.Measurement,JSV.common.Measurement");n("JSV.common");z(["java.lang.Enum","JSV.common.MeasurementData","$.IntegralComparator"],"JSV.common.IntegralData","java.util.Collections $.StringTokenizer JU.AU $.BS $.DF $.Lst $.PT JSV.common.Annotation $.Coordinate $.Integral $.ScriptToken".split(" "),function(){var b=r(function(){this.intRange=
this.percentOffset=this.percentMinY=0;this.normalizationFactor=1;this.integralTotal=this.offset=this.percentRange=0;this.haveRegions=!1;this.xyCoords=null;u(this,arguments)},JSV.common,"IntegralData",JSV.common.MeasurementData);y(b,function(a,b,c,e){I(this,JSV.common.IntegralData,[JSV.common.Annotation.AType.Integration,e]);this.percentMinY=a;this.percentOffset=b;this.percentRange=c;this.calculateIntegral()},"~N,~N,~N,JSV.common.Spectrum");y(b,function(a,b){I(this,JSV.common.IntegralData,[JSV.common.Annotation.AType.Integration,
a]);null==b?this.autoIntegrate():(this.percentOffset=b.integralOffset,this.percentRange=b.integralRange,this.calculateIntegral())},"JSV.common.Spectrum,JSV.common.Parameters");c(b,"getPercentMinimumY",function(){return this.percentMinY});c(b,"getPercentOffset",function(){return this.percentOffset});c(b,"getIntegralFactor",function(){return this.intRange});c(b,"update",function(a){this.update(a.integralMinY,a.integralOffset,a.integralRange)},"JSV.common.Parameters");c(b,"update",function(a,b,c){var e=
this.percentRange;if(!(0>=c||c==this.percentRange&&b==this.percentOffset)){this.percentOffset=b;this.percentRange=c;this.checkRange();a=c/100/this.integralTotal;b/=100;for(var g=0;g<this.xyCoords.length;g++){var f=this.xyCoords[g].getYVal(),f=(f-this.offset)/this.intRange;this.xyCoords[g].setYVal(f*a+b)}1!=this.normalizationFactor&&(this.normalizationFactor*=e/c);if(this.haveRegions)for(g=this.size();0<=--g;)c=this.get(g),e=this.getYValueAt(c.getXVal()),f=this.getYValueAt(c.getXVal2()),c.setYVal(e),
c.setYVal2(f),c.setValue(100*Math.abs(f-e)*this.normalizationFactor);this.intRange=a;this.offset=b}},"~N,~N,~N");c(b,"getYValueAt",function(a){return JSV.common.Coordinate.getYValueAt(this.xyCoords,a)},"~N");c(b,"addIntegralRegion",function(a,b){if(Double.isNaN(a))return this.haveRegions=!1,this.clear(),null;if(Double.isNaN(b))return this.splitIntegral(a);if(a==b)return null;if(a<b)return this.clear(a,b),null;var c=this.getYValueAt(a),e=this.getYValueAt(b);this.haveRegions=!0;c=(new JSV.common.Integral).setInt(a,
c,this.spec,100*Math.abs(e-c)*this.normalizationFactor,b,e);this.clear(a,b);this.addLast(c);java.util.Collections.sort(this,JSV.common.IntegralData.c);return c},"~N,~N");c(b,"splitIntegral",function(a){var b=this.find(a);if(0>b)return null;var c=this.removeItemAt(b),b=c.getXVal(),c=c.getXVal2();this.addIntegralRegion(b,a);return this.addIntegralRegion(a,c)},"~N");f(b,"setSpecShift",function(a){JSV.common.Coordinate.shiftX(this.xyCoords,a);for(var b=this.size();1<=--b;)this.get(b).addSpecShift(a)},
"~N");c(b,"addMarks",function(a){a=JU.PT.rep(" "+a,","," ");a=JU.PT.rep(a," -"," #");a=JU.PT.rep(a,"--","-#");a=a.$replace("-","^");a=a.$replace("#","-");a=JSV.common.ScriptToken.getTokens(a);for(var b=0;b<a.size();b++)try{var c=a.get(b),e=0,g=c.indexOf("^");if(!(0>g)){var f=c.indexOf(":");f>g&&(e=Double.$valueOf(c.substring(f+1).trim()).doubleValue(),c=c.substring(0,f).trim());var k=Double.$valueOf(c.substring(0,g).trim()).doubleValue(),l=Double.$valueOf(c.substring(g+1).trim()).doubleValue();0==
l&&0==k&&this.clear();if(l!=k){var n=this.addIntegralRegion(Math.max(l,k),Math.min(l,k));null!=n&&0<e&&this.setSelectedIntegral(n,e)}}}catch(m){if(!D(m,Exception))throw m;}},"~S");c(b,"calculateIntegral",function(){var a=this.spec.getXYCoords();this.xyCoords=Array(a.length);this.integralTotal=0;this.checkRange();for(var b=1E100,c=0;c<a.length;c++){var e=a[c].getYVal();e<b&&0<=e&&(b=e)}for(var g=1E100,f=-1E100,c=0;c<a.length;c++)e=a[c].getYVal(),this.integralTotal+=e-b,this.integralTotal<g&&(g=this.integralTotal),
this.integralTotal>f&&(f=this.integralTotal);this.integralTotal=f-g;this.intRange=this.percentRange/100/this.integralTotal;this.offset=this.percentOffset/100;g=0;for(c=a.length;0<=--c;)e=a[c].getYVal(),g+=e-b,this.xyCoords[c]=(new JSV.common.Coordinate).set(a[c].getXVal(),g*this.intRange+this.offset);return this.xyCoords});c(b,"checkRange",function(){this.percentOffset=Math.max(5,this.percentOffset);this.percentRange=Math.max(10,this.percentRange)});b.getIntegrationRatiosFromString=c(b,"getIntegrationRatiosFromString",
function(a,b){for(var c=new JU.Lst,e=new java.util.StringTokenizer(b,",");e.hasMoreTokens();){var g=e.nextToken(),g=new java.util.StringTokenizer(g,":"),g=(new JSV.common.Annotation).setA(Double.parseDouble(g.nextToken()),0,a,g.nextToken(),!0,!1,0,0);c.addLast(g)}return c},"JSV.common.Spectrum,~S");c(b,"getXYCoords",function(){return this.xyCoords});c(b,"getPercentYValueAt",function(a){return 100*this.getYValueAt(a)},"~N");c(b,"dispose",function(){this.xyCoords=this.spec=null});c(b,"setSelectedIntegral",
function(a,b){var c=a.getValue();this.factorAllIntegrals(0>=b?1/this.normalizationFactor:b/c,0>=b)},"JSV.common.Measurement,~N");c(b,"factorAllIntegrals",function(a,b){for(var c=0;c<this.size();c++){var e=this.get(c);e.setValue(a*e.getValue())}this.normalizationFactor=b?1:this.normalizationFactor*a},"~N,~B");c(b,"remove",function(a){return this.removeItemAt(a)},"~N");c(b,"getBitSet",function(){var a=JU.BS.newN(this.xyCoords.length);if(0==this.size())return a.setBits(0,this.xyCoords.length),a;for(var b=
this.size();0<=--b;){var c=this.get(b),e=JSV.common.Coordinate.getNearestIndexForX(this.xyCoords,c.getXVal()),c=JSV.common.Coordinate.getNearestIndexForX(this.xyCoords,c.getXVal2());a.setBits(Math.min(e,c),Math.max(e,c))}return a});f(b,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=0,c=this.size();0<=--c;)a[b++]=B(-1,[""+b,JU.DF.formatDecimalDbl(this.get(c).getXVal(),2),JU.DF.formatDecimalDbl(this.get(c).getXVal2(),2),this.get(c).text]);return a},"~S");f(b,"getMeasurementListArrayReal",
function(){for(var a=JU.AU.newDouble2(this.size()),b=0,c=this.size();0<=--c;b++)a[b]=R(-1,[this.get(c).getXVal(),this.get(c).getXVal2(),this.get(c).getValue()]);return a},"~S");f(b,"getDataHeader",function(){return JSV.common.IntegralData.$HEADER});c(b,"shiftY",function(a,b,c,e){b=v(100*(c+e-b)/e);0>a&&(b-=this.percentOffset);0>a?this.update(0,this.percentOffset,b):this.update(0,b,this.percentRange)},"~N,~N,~N,~N");c(b,"autoIntegrate",function(){null==this.xyCoords&&this.calculateIntegral();if(0!=
this.xyCoords.length){this.clear();for(var a=-1,b=0,c=this.xyCoords[this.xyCoords.length-1].getYVal(),e=this.xyCoords.length-1;0<=--e;){var g=this.xyCoords[e].getYVal();b++;1E-4>g-c&&0>a?g<c&&(c=g,b=0):0>a?(a=e+Math.min(b,20),c=g,b=0):1E-4>g-c?(1==b&&(c=g),20<=b&&(this.addIntegralRegion(this.xyCoords[a].getXVal(),this.xyCoords[e].getXVal()),a=-1,c=g,b=0)):(b=0,c=g)}a=this.spec.getHydrogenCount();0<a&&this.factorAllIntegrals(a/this.percentRange,!1)}});c(b,"getInfo",function(a){a.put("offset",Double.$valueOf(this.myParams.integralOffset));
a.put("range",Double.$valueOf(this.myParams.integralRange));a.put("normalizationFactor",Double.$valueOf(this.normalizationFactor));a.put("integralTotal",Double.$valueOf(this.integralTotal));ha(this,JSV.common.IntegralData,"getInfo",[a])},"java.util.Map");c(b,"setMinimumIntegral",function(a){for(var b=this.size();0<=--b;)this.get(b).getValue()<a&&this.removeItemAt(b)},"~N");var a=G(JSV.common.IntegralData,"IntMode",Enum);a.getMode=c(a,"getMode",function(a){for(var b,c=0,e=JSV.common.IntegralData.IntMode.values();c<
e.length&&((b=e[c])||1);c++)if(a.startsWith(b.name()))return b;return JSV.common.IntegralData.IntMode.NA},"~S");w(a,"OFF",0,[]);w(a,"ON",1,[]);w(a,"TOGGLE",2,[]);w(a,"AUTO",3,[]);w(a,"LIST",4,[]);w(a,"MARK",5,[]);w(a,"MIN",6,[]);w(a,"UPDATE",7,[]);w(a,"CLEAR",8,[]);w(a,"NA",9,[]);b.c=new JSV.common.IntegralComparator;b.$HEADER=B(-1,["peak","start/ppm","end/ppm","value"])});n("JSV.common");z(["java.lang.Enum","JSV.source.JDXDataObject","JU.Lst"],"JSV.common.Spectrum","java.util.Hashtable JU.PT JSV.common.Coordinate $.Parameters $.PeakInfo JSV.source.JDXSourceStreamTokenizer JU.Logger".split(" "),
function(){var b=r(function(){this.id="";this.convertedSpectrum=this.highlightedPeak=this.selectedPeak=this.peakYLabel=this.peakXLabel=this.peakList=this.subSpectra=this.fillColor=null;this.specShift=0;this.userYFactor=1;this.currentSubSpectrumIndex=0;this.exportXAxisLeftToRight=this.$isForcedSubset=!1;this.titleLabel=null;u(this,arguments)},JSV.common,"Spectrum",JSV.source.JDXDataObject);N(b,function(){this.peakList=new JU.Lst});y(b,function(){I(this,JSV.common.Spectrum,[]);this.headerTable=new JU.Lst;
this.xyCoords=[];this.parent=this});c(b,"dispose",function(){});c(b,"isForcedSubset",function(){return this.$isForcedSubset});c(b,"setId",function(a){this.id=a},"~S");c(b,"copy",function(){var a=new JSV.common.Spectrum;this.copyTo(a);a.setPeakList(this.peakList,this.peakXLabel,null);a.fillColor=this.fillColor;return a});c(b,"getXYCoords",function(){return this.getCurrentSubSpectrum().xyCoords});c(b,"getPeakList",function(){return this.peakList});c(b,"setPeakList",function(a,b,c){this.peakList=a;this.peakXLabel=
b;this.peakYLabel=c;for(b=a.size();0<=--b;)this.peakList.get(b).spectrum=this;JU.Logger.debugging&&JU.Logger.info("Spectrum "+this.getTitle()+" peaks: "+a.size());return a.size()},"JU.Lst,~S,~S");c(b,"selectPeakByFileIndex",function(a,b,c){if(null!=this.peakList&&0<this.peakList.size()&&(null==c||this.sourceID.equals(b)))for(var f=0;f<this.peakList.size();f++)if(this.peakList.get(f).checkFileIndex(a,b,c))return System.out.println("selecting peak by FileIndex "+this+" "+this.peakList.get(f)),this.selectedPeak=
this.peakList.get(f);return null},"~S,~S,~S");c(b,"selectPeakByFilePathTypeModel",function(a,b,c){if(null!=this.peakList&&0<this.peakList.size())for(var f=0;f<this.peakList.size();f++)if(this.peakList.get(f).checkFileTypeModel(a,b,c))return System.out.println("selecting peak byFilePathTypeModel "+this+" "+this.peakList.get(f)),this.selectedPeak=this.peakList.get(f);return null},"~S,~S,~S");c(b,"matchesPeakTypeModel",function(a,b){if(a.equals("ID"))return this.sourceID.equalsIgnoreCase(b);if(null!=
this.peakList&&0<this.peakList.size())for(var c=0;c<this.peakList.size();c++)if(this.peakList.get(c).checkTypeModel(a,b))return!0;return!1},"~S,~S");c(b,"setSelectedPeak",function(a){this.selectedPeak=a},"JSV.common.PeakInfo");c(b,"setHighlightedPeak",function(a){this.highlightedPeak=a},"JSV.common.PeakInfo");c(b,"getSelectedPeak",function(){return this.selectedPeak});c(b,"getModelPeakInfoForAutoSelectOnLoad",function(){if(null!=this.peakList)for(var a=0;a<this.peakList.size();a++)if(this.peakList.get(a).autoSelectOnLoad())return this.peakList.get(a);
return null});c(b,"getAssociatedPeakInfo",function(a,b){this.selectedPeak=this.findPeakByCoord(a,b);return null==this.selectedPeak?this.getBasePeakInfo():this.selectedPeak},"~N,JSV.common.Coordinate");c(b,"findPeakByCoord",function(a,b){if(null!=b&&null!=this.peakList&&0<this.peakList.size()){for(var c=b.getXVal(),f=-1,e=1E100,g=0;g<this.peakList.size();g++){var j=this.peakList.get(g).checkRange(a,c);j<e&&(e=j,f=g)}if(0<=f)return this.peakList.get(f)}return null},"~N,JSV.common.Coordinate");c(b,"getPeakTitle",
function(){return null!=this.selectedPeak?this.selectedPeak.getTitle():null!=this.highlightedPeak?this.highlightedPeak.getTitle():this.getTitleLabel()});c(b,"getTitleLabel",function(){if(null!=this.titleLabel)return this.titleLabel;var a=null==this.peakList||0==this.peakList.size()?this.getQualifiedDataType():this.peakList.get(0).getType();null!=a&&a.startsWith("NMR")&&(a=null!=this.nucleusY&&!this.nucleusY.equals("?")?"2D"+a:JSV.source.JDXDataObject.getNominalSpecFreq(this.nucleusX,this.getObservedFreq())+
" MHz "+this.nucleusX+" "+a);return this.titleLabel=(null!=a&&0<a.length?a+" ":"")+this.getTitle()});c(b,"setNextPeak",function(a,b){if(null==this.peakList||0==this.peakList.size())return-1;for(var c=a.getXVal()+1E-6*b,f=-1,e=-1,g=1.7976931348623157E308*b,j=0,k=this.peakList.size();0<=--k;){var l=this.peakList.get(k).getX();0<b?l>c&&l<g?(f=k,g=l):l<c&&l-c<j&&(e=k,j=l-c):l<c&&l>g?(f=k,g=l):l>c&&l-c>j&&(e=k,j=l-c)}if(0>f){if(0>e)return-1;f=e}return f},"JSV.common.Coordinate,~N");c(b,"getPercentYValueAt",
function(a){return!this.isContinuous()?NaN:this.getYValueAt(a)},"~N");c(b,"getYValueAt",function(a){return JSV.common.Coordinate.getYValueAt(this.xyCoords,a)},"~N");c(b,"setUserYFactor",function(a){this.userYFactor=a},"~N");c(b,"getUserYFactor",function(){return this.userYFactor});c(b,"getConvertedSpectrum",function(){return this.convertedSpectrum});c(b,"setConvertedSpectrum",function(a){this.convertedSpectrum=a},"JSV.common.Spectrum");b.taConvert=c(b,"taConvert",function(a,b){if(!a.isContinuous())return a;
switch(b){case JSV.common.Spectrum.IRMode.NO_CONVERT:return a;case JSV.common.Spectrum.IRMode.TO_ABS:if(!a.isTransmittance())return a;break;case JSV.common.Spectrum.IRMode.TO_TRANS:if(!a.isAbsorbance())return a}var c=a.getConvertedSpectrum();return null!=c?c:a.isAbsorbance()?JSV.common.Spectrum.toT(a):JSV.common.Spectrum.toA(a)},"JSV.common.Spectrum,JSV.common.Spectrum.IRMode");b.toT=c(b,"toT",function(a){if(!a.isAbsorbance())return null;var b=a.getXYCoords(),c=Array(b.length);JSV.common.Coordinate.isYInRange(b,
0,4)||(b=JSV.common.Coordinate.normalise(b,0,4));for(var f=0;f<b.length;f++)c[f]=(new JSV.common.Coordinate).set(b[f].getXVal(),JSV.common.Spectrum.toTransmittance(b[f].getYVal()));return JSV.common.Spectrum.newSpectrum(a,c,"TRANSMITTANCE")},"JSV.common.Spectrum");b.toA=c(b,"toA",function(a){if(!a.isTransmittance())return null;for(var b=a.getXYCoords(),c=Array(b.length),f=JSV.common.Coordinate.isYInRange(b,-2,2),e=0;e<b.length;e++)c[e]=(new JSV.common.Coordinate).set(b[e].getXVal(),JSV.common.Spectrum.toAbsorbance(b[e].getYVal(),
f));return JSV.common.Spectrum.newSpectrum(a,c,"ABSORBANCE")},"JSV.common.Spectrum");b.newSpectrum=c(b,"newSpectrum",function(a,b,c){var f=a.copy();f.setOrigin("JSpecView Converted");f.setOwner("JSpecView Generated");f.setXYCoords(b);f.setYUnits(c);a.setConvertedSpectrum(f);f.setConvertedSpectrum(a);return f},"JSV.common.Spectrum,~A,~S");b.toAbsorbance=c(b,"toAbsorbance",function(a,b){return Math.min(4,b?2-JSV.common.Spectrum.log10(a):-JSV.common.Spectrum.log10(a))},"~N,~B");b.toTransmittance=c(b,
"toTransmittance",function(a){return 0>=a?1:Math.pow(10,-a)},"~N");b.log10=c(b,"log10",function(a){return Math.log(a)/Math.log(10)},"~N");b.process=c(b,"process",function(a,b){if(b===JSV.common.Spectrum.IRMode.TO_ABS||b===JSV.common.Spectrum.IRMode.TO_TRANS)for(var c=0;c<a.size();c++)a.set(c,JSV.common.Spectrum.taConvert(a.get(c),b));return!0},"JU.Lst,JSV.common.Spectrum.IRMode");c(b,"getSubSpectra",function(){return this.subSpectra});c(b,"getCurrentSubSpectrum",function(){return null==this.subSpectra?
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function(a,b,c){var f=null;try{if(null==(f=a.getClass().getResource(b)))c[0]="Couldn't find file: "+b}catch(e){if(D(e,Exception))c[0]="Exception "+e+" in getResource "+b;else throw e;}return f},"~O,~S,~A");b.getResourceString=c(b,"getResourceString",function(a,b,c){a=JSV.common.JSVFileManager.getResource(a,b,c);if(null==a)return c[0]="Error loading resource "+b,null;if("string"==typeof a)return JSV.common.JSVFileManager.getFileAsString(a);b=new JU.SB;try{for(var f=new java.io.BufferedReader(new java.io.InputStreamReader(a.getContent(),
"UTF-8")),e;null!=(e=f.readLine());)b.append(e).append("\n");f.close()}catch(g){if(D(g,Exception))c[0]=g.toString();else throw g;}return b.toString()},"~O,~S,~A");b.getJmolFilePath=c(b,"getJmolFilePath",function(a){try{a=JSV.common.JSVFileManager.getFullPathName(a)}catch(b){if(D(b,"JSV.exception.JSVException"))return null;throw b;}return null==JSV.common.JSVFileManager.appletDocumentBase?a.$replace("\\","/"):a},"~S");b.getTagName=c(b,"getTagName",function(a){if(null==a)return"String"+ ++JSV.common.JSVFileManager.stringCount;
if(JSV.common.JSVFileManager.isURL(a))try{if(a.startsWith("http://SIMULATION/"))return JSV.common.JSVFileManager.getAbbrSimulationFileName(a);var b=(new java.net.URL(ma("java.net.URL"),a,null)).getFile();return b.substring(b.lastIndexOf("/")+1)}catch(c){if(D(c,"java.io.IOException"))return null;throw c;}return JSV.common.JSVFileManager.viewer.apiPlatform.newFile(a).getName()},"~S");b.setDocumentBase=c(b,"setDocumentBase",function(a,b){JSV.common.JSVFileManager.viewer=a;JSV.common.JSVFileManager.appletDocumentBase=
b},"JSV.common.JSViewer,java.net.URL");b.getSimulationType=c(b,"getSimulationType",function(a){return 0<=a.indexOf("C13/")?"C13":"H1"},"~S");b.appletDocumentBase=null;b.viewer=null;b.jsDocumentBase="";b.urlPrefixes=B(-1,["http:","https:","ftp:","http://SIMULATION/","file:"]);b.htCorrelationCache=new java.util.Hashtable;b.nciResolver="https://cactus.nci.nih.gov/chemical/structure/%FILE/file?format=sdf&get3d=True";b.nmrdbServerH1="https://www.nmrdb.org/tools/jmol/predict.php?POST?molfile=";b.nmrdbServerC13=
"https://www.nmrdb.org/service/jsmol13c?POST?molfile=";b.stringCount=0});n("JSV.common");z(["javajs.api.BytePoster","J.api.PlatformViewer","JSV.common.Spectrum"],"JSV.common.JSViewer","java.io.File java.net.URL java.util.Arrays $.Hashtable JU.CU $.Lst $.OC $.PT $.SB JSV.common.Annotation $.ExportType $.JSVFileManager $.PanelData $.PanelNode $.Parameters $.PeakInfo $.PrintLayout $.RepaintManager $.ScriptToken $.ScriptTokenizer JSV.source.JDXReader $.JDXSource JSV.tree.SimpleTree JU.Logger".split(" "),
function(){var b=r(function(){this.irMode=this.overlayLegendDialog=this.viewDialog=this.dialogManager=this.jsvpPopupMenu=this.fileHelper=this.scriptQueue=this.properties=this.mainPanel=this.selectedPanel=this.repaintManager=this.parameters=this.panelNodes=this.currentSource=this.spectraTree=this.g2d=this.si=null;this.autoShowLegend=this.autoIntegrate=this.interfaceOverlaid=this.loadImaginary=!1;this.obscureTitleFromUser=null;this.allowMenu=!0;this.initialEndIndex=this.initialStartIndex=-1;this.isSigned=
this.isApplet=this.isSingleThreaded=!1;this.recentScript="";this.display=this.html5Applet=this.syncID=this.fullName=this.appletName=null;this.maximumSize=2147483647;this.scriptLevelCount=this.nViews=this.fileCount=this.screenWidth=this.screenHeight=0;this.apiPlatform=this.integrationRatios=this.returnFromJmolModel=null;this.popupZoomEnabled=this.popupAllowMenu=!0;this.defaultLoadScript=null;this.nmrMaxY=NaN;this.overlayLegendVisible=!1;this.recentStackPercent=5;this.offWindowFrame=this.lastPrintLayout=
null;this.recentOpenURL="http://";this.recentURL=null;this.recentSimulation="tylenol";u(this,arguments)},JSV.common,"JSViewer",null,[J.api.PlatformViewer,javajs.api.BytePoster]);N(b,function(){this.irMode=JSV.common.Spectrum.IRMode.NO_CONVERT});y(b,function(a,b,c){this.si=a;this.isApplet=b;JSV.common.JSViewer.isJS=b&&c;c=null;self.Jmol&&(c=Jmol);JSV.common.JSViewer.jmolObject=c;this.isSigned=a.isSigned();this.apiPlatform=this.getPlatformInterface("Platform");this.apiPlatform.setViewer(this,this.display);
this.g2d=this.getPlatformInterface("G2D");this.spectraTree=new JSV.tree.SimpleTree(this);this.parameters=this.getPlatformInterface("Parameters");this.parameters.setName("applet");this.fileHelper=this.getPlatformInterface("FileHelper").set(this);this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.panelNodes=new JU.Lst;this.repaintManager=new JSV.common.RepaintManager(this);b||this.setPopupMenu(!0,!0)},"JSV.api.ScriptInterface,~B,~B");c(b,"setProperty",function(a,b){null!=this.properties&&
this.properties.setProperty(a,b)},"~S,~S");c(b,"setNode",function(a){a.jsvp!==this.selectedPanel&&this.si.siSetSelectedPanel(a.jsvp);this.si.siSendPanelChange();this.si.siNodeSet(a)},"JSV.common.PanelNode");c(b,"setPopupMenu",function(a,b){this.popupAllowMenu=a;this.popupZoomEnabled=b},"~B,~B");c(b,"showMenu",function(a,b){if(this.popupAllowMenu){if(null==this.jsvpPopupMenu)try{this.jsvpPopupMenu=this.getPlatformInterface("Popup"),this.jsvpPopupMenu.jpiInitialize(this,this.isApplet?"appletMenu":"appMenu"),
this.jsvpPopupMenu.setEnabled(this.popupAllowMenu,this.popupZoomEnabled)}catch(c){if(D(c,Exception)){JU.Logger.error(c+" initializing popup menu");return}throw c;}this.jsvpPopupMenu.jpiShow(a,b)}},"~N,~N");c(b,"runScriptNow",function(a){System.out.println(this.checkScript(a));this.scriptLevelCount++;null==a&&(a="");a=a.trim();if(a.startsWith("!"))a=a.substring(1).trim();else if(a.startsWith(">"))return JU.Logger.error(a),!0;if(0<=a.indexOf("<PeakData"))return this.syncScript(a),!0;JU.Logger.info("RUNSCRIPT "+
a);var b=!0,c=10;a=new JSV.common.ScriptTokenizer(a,!0);for(var f=null;null!=a&&a.hasMoreTokens()&&0<c&&b;){var e=a.nextToken(),g=new JSV.common.ScriptTokenizer(e,!1),j=JSV.common.ScriptToken.getKey(g);if(null!=j){var k=JSV.common.ScriptToken.getScriptToken(j),g=JSV.common.ScriptToken.getValue(k,g,e);try{switch(k){case JSV.common.ScriptToken.UNKNOWN:JU.Logger.info("Unrecognized parameter: "+j);--c;break;default:if(null==this.selectedPanel)break;this.parameters.set(this.pd(),k,g);this.si.siUpdateBoolean(k,
JSV.common.Parameters.isTrue(g));break;case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:this.si.siExecSetCallback(k,g);break;case JSV.common.ScriptToken.DEFAULTLOADSCRIPT:g=JU.PT.rep(g,"''",'"');this.defaultLoadScript=0<g.length?g:null;break;case JSV.common.ScriptToken.DEFAULTNMRNORMALIZATION:this.nmrMaxY=JU.PT.parseFloat(g);break;
case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(g);break;case JSV.common.ScriptToken.CLOSE:this.execClose(g);break;case JSV.common.ScriptToken.DEBUG:JU.Logger.setLogLevel(g.toLowerCase().equals("high")?6:JSV.common.Parameters.isTrue(g)?5:4);break;case JSV.common.ScriptToken.GETPROPERTY:var l=null==this.selectedPanel?null:this.getPropertyAsJavaObject(g);null!=l&&this.selectedPanel.showMessage(JU.PT.toJSON(null,l),g);break;case JSV.common.ScriptToken.HELP:this.execHelp(g);
break;case JSV.common.ScriptToken.HIDDEN:this.si.siExecHidden(JSV.common.Parameters.isTrue(g));break;case JSV.common.ScriptToken.INTEGRATIONRATIOS:this.integrationRatios=g;this.execIntegrate(null);break;case JSV.common.ScriptToken.INTERFACE:this.interfaceOverlaid=this.checkOvelayInterface(g);break;case JSV.common.ScriptToken.INTEGRALOFFSET:case JSV.common.ScriptToken.INTEGRALRANGE:this.execSetIntegralParameter(k,Double.parseDouble(g));break;case JSV.common.ScriptToken.INVERTY:this.execZoom("invertY");
break;case JSV.common.ScriptToken.JMOL:this.si.syncToJmol(g);break;case JSV.common.ScriptToken.JSV:this.syncScript(JU.PT.trimQuotes(g));break;case JSV.common.ScriptToken.LOAD:if(0==g.length){null!=this.defaultLoadScript&&this.runScriptNow(this.defaultLoadScript);break}this.execLoad(g,(null==this.defaultLoadScript?"":this.defaultLoadScript+";")+a.getRemainingScript());f=null==this.selectedPanel?null:this.si.siLoaded(g);a=null;break;case JSV.common.ScriptToken.LOADIMAGINARY:this.loadImaginary=JSV.common.Parameters.isTrue(g);
break;case JSV.common.ScriptToken.PEAK:this.execPeak(g);break;case JSV.common.ScriptToken.PEAKLIST:this.execPeakList(g);break;case JSV.common.ScriptToken.SCALEBY:this.scaleSelectedBy(this.panelNodes,g);break;case JSV.common.ScriptToken.SCRIPT:if(g.equals("")||g.toLowerCase().startsWith("inline"))this.execScriptInline(g);else{var n=JSV.common.JSVFileManager.getFileAsString(g);null!=n&&100>this.scriptLevelCount&&this.runScriptNow(n)}break;case JSV.common.ScriptToken.SELECT:this.execSelect(g);break;
case JSV.common.ScriptToken.SPECTRUM:case JSV.common.ScriptToken.SPECTRUMNUMBER:this.setSpectrum(g)||(b=!1);break;case JSV.common.ScriptToken.STACKOFFSETY:this.execOverlayOffsetY(JU.PT.parseInt(""+JU.PT.parseFloat(g)));break;case JSV.common.ScriptToken.TEST:this.si.siExecTest(g);break;case JSV.common.ScriptToken.OVERLAY:case JSV.common.ScriptToken.VIEW:this.execView(g,!0);break;case JSV.common.ScriptToken.HIGHLIGHT:b=this.highlight(e);break;case JSV.common.ScriptToken.FINDX:case JSV.common.ScriptToken.GETSOLUTIONCOLOR:case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:case JSV.common.ScriptToken.IRMODE:case JSV.common.ScriptToken.LABEL:case JSV.common.ScriptToken.LINK:case JSV.common.ScriptToken.OVERLAYSTACKED:case JSV.common.ScriptToken.PRINT:case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:case JSV.common.ScriptToken.SHOWERRORS:case JSV.common.ScriptToken.SHOWMEASUREMENTS:case JSV.common.ScriptToken.SHOWMENU:case JSV.common.ScriptToken.SHOWKEY:case JSV.common.ScriptToken.SHOWPEAKLIST:case JSV.common.ScriptToken.SHOWINTEGRATION:case JSV.common.ScriptToken.SHOWPROPERTIES:case JSV.common.ScriptToken.SHOWSOURCE:case JSV.common.ScriptToken.YSCALE:case JSV.common.ScriptToken.WRITE:case JSV.common.ScriptToken.ZOOM:if(this.isClosed()){b=
!1;break}switch(k){case JSV.common.ScriptToken.FINDX:this.pd().findX(null,Double.parseDouble(g));break;case JSV.common.ScriptToken.GETSOLUTIONCOLOR:this.show("solutioncolor"+g.toLowerCase());break;case JSV.common.ScriptToken.INTEGRATION:case JSV.common.ScriptToken.INTEGRATE:this.execIntegrate(g);break;case JSV.common.ScriptToken.IRMODE:this.execIRMode(g);break;case JSV.common.ScriptToken.LABEL:this.pd().addAnnotation(JSV.common.ScriptToken.getTokens(g));break;case JSV.common.ScriptToken.LINK:this.pd().linkSpectra(JSV.common.PanelData.LinkMode.getMode(g));
break;case JSV.common.ScriptToken.OVERLAYSTACKED:this.pd().splitStack(!JSV.common.Parameters.isTrue(g));break;case JSV.common.ScriptToken.PRINT:f=this.execWrite(null);break;case JSV.common.ScriptToken.SETPEAK:case JSV.common.ScriptToken.SETX:case JSV.common.ScriptToken.SHIFTX:this.execShiftSpectrum(k,e);break;case JSV.common.ScriptToken.SHOWERRORS:this.show("errors");break;case JSV.common.ScriptToken.SHOWINTEGRATION:this.pd().showAnnotation(JSV.common.Annotation.AType.Integration,JSV.common.Parameters.getTFToggle(g));
break;case JSV.common.ScriptToken.SHOWKEY:this.setOverlayLegendVisibility(JSV.common.Parameters.getTFToggle(g),!0);break;case JSV.common.ScriptToken.SHOWMEASUREMENTS:this.pd().showAnnotation(JSV.common.Annotation.AType.Measurements,JSV.common.Parameters.getTFToggle(g));break;case JSV.common.ScriptToken.SHOWMENU:this.showMenu(-2147483648,0);break;case JSV.common.ScriptToken.SHOWPEAKLIST:this.pd().showAnnotation(JSV.common.Annotation.AType.PeakList,JSV.common.Parameters.getTFToggle(g));break;case JSV.common.ScriptToken.SHOWPROPERTIES:this.show("properties");
break;case JSV.common.ScriptToken.SHOWSOURCE:this.show("source");break;case JSV.common.ScriptToken.YSCALE:this.setYScale(g);break;case JSV.common.ScriptToken.WINDOW:this.si.siNewWindow(JSV.common.Parameters.isTrue(g),!1);break;case JSV.common.ScriptToken.WRITE:f=this.execWrite(g);break;case JSV.common.ScriptToken.ZOOM:b=this.execZoom(g)}}}catch(m){if(D(m,Exception))f=m.toString(),JU.Logger.error(m.toString()),b=!1,--c;else throw m;}}}this.scriptLevelCount--;this.si.siExecScriptComplete(f,!0);return b},
"~S");c(b,"execShiftSpectrum",function(a,b){var c=JSV.common.ScriptToken.getTokens(b),f=NaN,e=NaN;switch(c.size()){case 2:e=c.get(1);e.equals("")&&(e="?");e=e.equalsIgnoreCase("NONE")?1.7976931348623157E308:e.equalsIgnoreCase("?")?NaN:Double.parseDouble(e);break;case 3:f=Double.parseDouble(c.get(1));e=Double.parseDouble(c.get(2));break;default:Double.parseDouble("")}c=0;switch(a){case JSV.common.ScriptToken.SETPEAK:c=1;break;case JSV.common.ScriptToken.SETX:c=2;break;case JSV.common.ScriptToken.SHIFTX:c=
3;Double.isNaN(e)&&Double.parseDouble("");break;default:return}this.pd().shiftSpectrum(c,f,e)},"JSV.common.ScriptToken,~S");c(b,"execClose",function(a){var b=!a.startsWith("!");b||(a=a.substring(1));this.close(JU.PT.trimQuotes(a));(!b||0==this.panelNodes.size())&&this.si.siValidateAndRepaint(!0)},"~S");c(b,"checkOvelayInterface",function(a){return a.equalsIgnoreCase("single")||a.equalsIgnoreCase("overlay")},"~S");c(b,"execPeak",function(a){try{var b=JSV.common.ScriptToken.getTokens(JU.PT.rep(a,"#",
"INDEX="));a=' type="'+b.get(0).toUpperCase()+'" _match="'+JU.PT.trimQuotes(b.get(1).toUpperCase())+'"';2<b.size()&&b.get(2).equalsIgnoreCase("all")&&(a+=' title="ALL"');this.processPeakPickEvent(new JSV.common.PeakInfo(a),!1)}catch(c){if(!D(c,Exception))throw c;}},"~S");c(b,"execPeakList",function(a){var b=this.parameters,c=JSV.common.Parameters.getTFToggle(a);if(0>a.indexOf("="))this.isClosed()||this.pd().getPeakListing(null,c);else{var c=JSV.common.ScriptToken.getTokens(a),f=b.peakListThreshold,
e=b.peakListInterpolation;try{for(var g=c.size();0<=--g;){var j=c.get(g),k=j.indexOf("=");if(!(0>=k)){var l=j.substring(0,k);a=j.substring(k+1);l.startsWith("thr")?f=Double.$valueOf(a).doubleValue():l.startsWith("int")&&(e=a.equalsIgnoreCase("none")?"NONE":"parabolic")}}b.peakListThreshold=f;b.peakListInterpolation=e;this.isClosed()||this.pd().getPeakListing(b,Boolean.TRUE)}catch(n){if(!D(n,Exception))throw n;}}},"~S");c(b,"highlight",function(a){var b=JSV.common.ScriptToken.getTokens(a),c=b.size();
switch(c){case 3:case 5:case 6:case 7:break;case 2:case 4:if(b.get(c-1).equalsIgnoreCase("OFF"))break;default:return!1}if(!this.isClosed()){a=JU.PT.parseFloat(1<c?b.get(1):"");var f=JU.PT.parseFloat(2<c?b.get(2):""),e=this.getRGB(3<c?b.get(3):"100"),g=this.getRGB(4<c?b.get(4):"100"),j=this.getRGB(5<c?b.get(5):"100"),b=this.getRGB(6<c?b.get(6):"100");Float.isNaN(a)||Float.isNaN(f)?this.pd().removeAllHighlights():(this.pd().removeHighlight(a,f),0>b&&(b=150),0<=e&&(0<=g&&0<=j)&&this.pd().addHighlight(null,
a,f,null,e,g,j,b));this.repaint(!0)}return!0},"~S");c(b,"getRGB",function(a){a=JU.PT.parseFloat(a);return F(Float.isNaN(a)?-1:1<a?a:255*a)},"~S");c(b,"execZoom",function(a){var b=0,c=0,f=0,e=0;a=JU.PT.rep(a," - "," ").$replace(","," ");a=JSV.common.ScriptToken.getTokens(a);switch(a.size()){default:return!1;case 0:return b=this.pd().getCurrentGraphSet().getCurrentView(),a=Math.round(100*b.minXOnScale)/100+","+Math.round(100*b.maxXOnScale)/100,a=this.selectedPanel.getInput("Enter zoom range x1 x2",
"Zoom",a),null==a||this.execZoom(a);case 1:return a=a.get(0),a.equalsIgnoreCase("next")?this.pd().nextView():a.toLowerCase().startsWith("prev")?this.pd().previousView():a.equalsIgnoreCase("out")?this.pd().resetView():a.equalsIgnoreCase("clear")?this.pd().clearAllView():a.equalsIgnoreCase("invertY")&&this.pd().getCurrentGraphSet().invertYAxis(),!0;case 2:b=Double.parseDouble(a.get(0));c=Double.parseDouble(a.get(1));break;case 3:var g=a.get(0);g.equalsIgnoreCase("X")?(b=Double.parseDouble(a.get(1)),
c=Double.parseDouble(a.get(2))):g.equalsIgnoreCase("Y")&&(f=Double.parseDouble(a.get(1)),e=Double.parseDouble(a.get(2)));break;case 4:b=Double.parseDouble(a.get(0)),f=Double.parseDouble(a.get(1)),c=Double.parseDouble(a.get(2)),e=Double.parseDouble(a.get(3))}this.pd().setZoom(b,f,c,e);return!0},"~S");c(b,"scaleSelectedBy",function(a,b){try{for(var c=Double.parseDouble(b),f=a.size();0<=--f;)a.get(f).pd().scaleSelectedBy(c)}catch(e){if(!D(e,Exception))throw e;}},"JU.Lst,~S");c(b,"pd",function(){return null==
this.selectedPanel?null:this.selectedPanel.getPanelData()});c(b,"isClosed",function(){return null==this.pd()});c(b,"execSelect",function(a){if(a.startsWith("ID ")){if(!this.isClosed())try{this.pd().selectSpectrum(null,"ID",JU.PT.trimQuotes(a.substring(3)),!0)}catch(b){if(!D(b,Exception))throw b;}}else{for(var c=this.panelNodes,f=c.size();0<=--f;)c.get(f).pd().selectFromEntireSet(-2147483648);c=new JU.Lst;this.fillSpecList(a,c,!1)}},"~S");c(b,"execView",function(a,b){if(a.equals(""))this.checkOverlay();
else{var c=new JU.Lst,f=this.fillSpecList(a,c,!0);0<c.size()&&this.si.siOpenDataOrFile(null,f,c,f,-1,-1,!1,null,null);b||this.si.siValidateAndRepaint(!1)}},"~S,~B");c(b,"execIRMode",function(a){for(var b=JSV.common.Spectrum.IRMode.getMode(a),c=this.pd().getSpectrum().dataType,f=this.panelNodes.size();0<=--f;)this.panelNodes.get(f).pd().setIRMode(b,c);this.setIRmode(a)},"~S");c(b,"execIntegrate",function(a){this.isClosed()||(this.pd().checkIntegral(this.parameters,a),null!=this.integrationRatios&&
this.pd().setIntegrationRatios(this.integrationRatios),this.integrationRatios=null,this.repaint(!0))},"~S");c(b,"repaint",function(a){this.selectedPanel.doRepaint(a)},"~B");c(b,"execSetIntegralParameter",function(a,b){var c=this.parameters;switch(a){case JSV.common.ScriptToken.INTEGRALRANGE:c.integralRange=b;break;case JSV.common.ScriptToken.INTEGRALOFFSET:c.integralOffset=b}this.isClosed()||this.pd().checkIntegral(this.parameters,"update")},"JSV.common.ScriptToken,~N");c(b,"setYScale",function(a){var b=
JSV.common.ScriptToken.getTokens(a),c=0,f=!1;1<b.size()&&b.get(0).equalsIgnoreCase("ALL")&&(f=!0,c++);a=Double.parseDouble(b.get(c++));b=Double.parseDouble(b.get(c));if(f){f=this.pd().getSpectrum();for(c=this.panelNodes.size();0<=--c;){var e=this.panelNodes.get(c);e.source===this.currentSource&&JSV.common.Spectrum.areXScalesCompatible(f,e.getSpectrum(),!1,!1)&&e.pd().setZoom(0,a,0,b)}}else this.pd().setZoom(0,a,0,b)},"~S");c(b,"setOverlayLegendVisibility",function(a,b){b&&(this.overlayLegendVisible=
null==a?!this.overlayLegendVisible:a===Boolean.TRUE);for(var c=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes),f=this.panelNodes.size();0<=--f;)this.showOverlayLegend(this.panelNodes.get(f),this.panelNodes.get(f)===c&&this.overlayLegendVisible)},"Boolean,~B");c(b,"showOverlayLegend",function(a,b){var c=a.legend;null==c&&b&&(c=a.setLegend(1<a.pd().getNumberOfSpectraInCurrentSet()&&1==a.pd().getNumberOfGraphSets()?this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null):null));
null!=c&&c.setVisible(b)},"JSV.common.PanelNode,~B");c(b,"syncScript",function(a){a.equals("TEST")&&(a=JSV.common.JSViewer.testScript);JU.Logger.info("JSViewer.syncScript Jmol>JSV "+a);if(0>a.indexOf("<PeakData"))a.startsWith("JSVSTR:")?this.si.syncToJmol(a):(this.runScriptNow(a),0<=a.indexOf("#SYNC_PEAKS")&&this.syncPeaksAfterSyncScript());else{JU.Logger.info(">>toJSV>> "+a);var b=JU.PT.getQuotedAttribute(a,"sourceID"),c,f,e,g;if(null==b){f=JU.PT.getQuotedAttribute(a,"file");e=JU.PT.getQuotedAttribute(a,
"index");if(null==f||null==e)return;f=JU.PT.rep(f,"#molfile","");c=JU.PT.getQuotedAttribute(a,"model");b=JU.PT.getQuotedAttribute(a,"src");g=null!=b&&b.startsWith("Jmol")?null:this.returnFromJmolModel;if(null!=c&&null!=g&&!c.equals(g)){JU.Logger.info("JSV ignoring model "+c+"; should be "+g);return}this.returnFromJmolModel=null;if(0==this.panelNodes.size()||!this.checkFileAlreadyLoaded(f))JU.Logger.info("file "+f+" not found -- JSViewer closing all and reopening"),this.si.siSyncLoad(f);a=JU.PT.getQuotedAttribute(a,
"type");g=null}else f=null,e=c=b,g=","+JU.PT.getQuotedAttribute(a,"atom")+",",a="ID";e=this.selectPanelByPeak(f,e,g);g=this.pd();g.selectSpectrum(f,a,c,!0);this.si.siSendPanelChange();g.addPeakHighlight(e);this.repaint(!0);(null==b||null!=e&&null!=e.getAtoms())&&this.si.syncToJmol(this.jmolSelect(e))}},"~S");c(b,"syncPeaksAfterSyncScript",function(){var a=this.currentSource;if(null!=a)try{var b="file="+JU.PT.esc(a.getFilePath()),c=a.getSpectra().get(0).getPeakList(),f=new JU.SB;f.append("[");for(var e=
c.size(),a=0;a<e;a++){var g=c.get(a).toString(),g=g+" "+b;f.append(JU.PT.esc(g));0<a&&f.append(",")}f.append("]");this.si.syncToJmol("Peaks: "+f)}catch(j){if(!D(j,Exception))throw j;}});c(b,"checkFileAlreadyLoaded",function(a){if(this.isClosed())return!1;if(this.pd().hasFileLoaded(a))return!0;for(var b=this.panelNodes.size();0<=--b;)if(this.panelNodes.get(b).pd().hasFileLoaded(a))return this.si.siSetSelectedPanel(this.panelNodes.get(b).jsvp),!0;return!1},"~S");c(b,"selectPanelByPeak",function(a,b,
c){if(null==this.panelNodes)return null;for(var f=null,e=this.panelNodes.size();0<=--e;)this.panelNodes.get(e).pd().addPeakHighlight(null);f=this.pd().selectPeakByFileIndex(a,b,c);if(null!=f)this.setNode(JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes));else for(e=this.panelNodes.size();0<=--e;){var g=this.panelNodes.get(e);if(null!=(f=g.pd().selectPeakByFileIndex(a,b,c))){this.setNode(g);break}}return f},"~S,~S,~S");c(b,"processPeakPickEvent",function(a){if(C(a,"JSV.common.PeakInfo")){var b=
this.pd().findMatchingPeakInfo(a);if(null==b){if(!"ALL".equals(a.getTitle()))return;for(var c=null,f=0;f<this.panelNodes.size();f++)if(null!=(b=this.panelNodes.get(f).pd().findMatchingPeakInfo(a))){c=this.panelNodes.get(f);break}if(null==c)return;this.setNode(c)}a=b}else this.si.siSetSelectedPanel(a.getSource()),a=a.getPeakInfo();this.pd().addPeakHighlight(a);this.syncToJmol(a);a.isClearAll()?this.repaint(!1):this.pd().selectSpectrum(a.getFilePath(),a.getType(),a.getModel(),!0);this.si.siCheckCallbacks(a.getTitle())},
"~O,~B");c(b,"newStructToJmol",function(a){JU.Logger.info("sending new structure to Jmol:\n"+a);this.si.syncToJmol("struct:"+a)},"~S");c(b,"syncToJmol",function(a){this.repaint(!0);this.returnFromJmolModel=a.getModel();this.si.syncToJmol(this.jmolSelect(a))},"JSV.common.PeakInfo");c(b,"sendPanelChange",function(){var a=this.pd(),b=a.getSpectrum(),c=b.getSelectedPeak();null==c&&(c=b.getModelPeakInfoForAutoSelectOnLoad());null==c&&(c=b.getBasePeakInfo());a.addPeakHighlight(c);JU.Logger.info(Thread.currentThread()+
"JSViewer sendFrameChange "+this.selectedPanel);this.syncToJmol(c)});c(b,"jmolSelect",function(a){var b="IR".equals(a.getType())||"RAMAN".equals(a.getType())?"vibration ON; selectionHalos OFF;":"vibration OFF; selectionhalos "+(null==a.getAtoms()?"OFF":"ON");return"Select: "+a+' script="'+b+' " sourceID="'+this.pd().getSpectrum().sourceID+'"'},"JSV.common.PeakInfo");c(b,"getPropertyAsJavaObject",function(a){var b=new java.util.Hashtable;if("SOURCEID".equalsIgnoreCase(a))return b.put(a,null==this.pd()?
"":this.pd().getSpectrum().sourceID),b;if(null!=a&&a.startsWith("DATA_"))return b.put(a,""+JSV.common.JSVFileManager.cacheGet(a.substring(5))),b;var c=!1;if(null!=a&&a.toUpperCase().startsWith("ALL ")||"all".equalsIgnoreCase(a))a=a.substring(3).trim(),c=!0;"".equals(a)&&(a=null);if("NAMES".equalsIgnoreCase(a)||"KEYS".equalsIgnoreCase(a))a="";var f=this.pd().getInfo(!0,a);if(!c&&null!=f)return f;null!=f&&b.put("current",f);c=new JU.Lst;for(f=0;f<this.panelNodes.size();f++)null!=this.panelNodes.get(f).jsvp&&
c.addLast(this.panelNodes.get(f).getInfo(a));b.put("items",c);return b},"~S");c(b,"getCoordinate",function(){if(!this.isClosed()){var a=this.pd().getClickedCoordinate();if(null!=a)return a.getXVal()+" "+a.getYVal()}return""});c(b,"fillSpecList",function(a,b,c){var f,e=null,g=a.equalsIgnoreCase("NONE");if(g||a.equalsIgnoreCase("all"))a="*";if(0>a.indexOf("*")){f=a.$plit(" ");a=new JU.SB;for(var j=0;j<f.length;j++){var k=f[j].indexOf(".");k!=f[j].lastIndexOf(".")&&(f[j]=f[j].substring(0,k+1)+f[j].substring(k+
1).$replace(".","_"));a.append(f[j]).append(" ")}a=a.toString().trim()}if(a.equals("*"))f=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes));else if(a.startsWith('"')||a.startsWith("'"))f=JSV.common.ScriptToken.getTokens(a);else if(a=JU.PT.rep(a,"_"," _ "),a=JU.PT.rep(a,"-"," - "),f=JSV.common.ScriptToken.getTokens(a),e=JSV.common.ScriptToken.getTokens(JSV.common.PanelNode.getSpectrumListAsString(this.panelNodes)),0==e.size())return null;var l=this.isClosed()?
"1.":JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes).id,l=l.substring(0,l.indexOf(".")+1);a=new JU.SB;for(var n=f.size(),m=null,j=0;j<n;j++){var p=f.get(j),k=NaN,r=-1;j+1<n&&f.get(j+1).equals("*")?(j+=2,k=Double.parseDouble(f.get(j))):j+1<n&&f.get(j+1).equals("_")&&(j+=2,r=Integer.parseInt(f.get(j)));if(p.equals("-")){null==m&&(m=e.get(0));p=j+1==n?e.get(e.size()-1):f.get(++j);p.contains(".")||(p=l+p);for(k=0;k<e.size()&&!e.get(k).equals(m);)k++;for(k++;k<e.size()&&!m.equals(p);){var u=
JSV.common.PanelNode.findNodeById(m=e.get(k++),this.panelNodes);b.addLast(u.pd().getSpectrumAt(0));a.append(",").append(m)}}else if(p.startsWith("'")&&p.endsWith("'")&&(p='"'+JU.PT.trim(p,"'")+'"'),p.startsWith('"'))for(var p=JU.PT.trim(p,'"'),r=this.panelNodes.size(),v=0;v<r;v++){if(u=this.panelNodes.get(v),null!=u.fileName&&u.fileName.startsWith(p)||null!=u.frameTitle&&u.frameTitle.startsWith(p))this.addSpecToList(u.pd(),k,-1,b,c),a.append(",").append(u.id)}else p.contains(".")||(p=l+p),u=JSV.common.PanelNode.findNodeById(p,
this.panelNodes),null!=u&&(m=p,this.addSpecToList(u.pd(),k,r,b,c),a.append(",").append(p),0<r&&a.append(".").appendI(r))}c&&0<b.size()&&(u=JSV.common.PanelNode.findNodeById(a.substring(1),this.panelNodes),null!=u&&(this.setNode(u),b.clear()));return g?"NONE":0<a.length()?a.toString().substring(1):null},"~S,JU.Lst,~B");c(b,"addSpecToList",function(a,b,c,f,e){e?(a.getSpectrumAt(0).setUserYFactor(Double.isNaN(b)?1:b),a.addToList(c-1,f)):a.selectFromEntireSet(c-1)},"JSV.common.PanelData,~N,~N,JU.Lst,~B");
c(b,"getSolutionColor",function(a){var b=this.pd().getSpectrum(),c=b.canShowSolutionColor()?JSV.common.JSViewer.getInterface("JSV.common.Visible"):null;return null==c?-1:c.getColour(b,a)},"~B");c(b,"openDataOrFile",function(a,b,c,f,e,g,j,k){if("NONE".equals(b))return this.close("View*"),0;this.si.writeStatus("");var l=null,n=null,m=null,p=!1;null!=f&&f.startsWith("cache://")&&(a=Jmol.Cache.get(b=f));var r=null;if(null!=a)try{m=b,n=l=JSV.common.JSVFileManager.getFullPathName(b)}catch(u){if(!D(u,"JSV.exception.JSVException"))throw u;
}else if(null!=c)p=!0,n=m=l="View"+ ++this.nViews;else if(null!=f)try{r=this.apiPlatform.newFile(f),this.recentURL=l=(new java.net.URL(JSV.common.JSVFileManager.appletDocumentBase,f,null)).toString(),m=JSV.common.JSVFileManager.getTagName(l)}catch(v){if(D(v,"java.net.MalformedURLException"))m=r.getName(),n=l=r.getFullPath(),this.recentURL=null;else throw v;}b=-1;if(0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,l))||0<=(b=JSV.common.PanelNode.isOpen(this.panelNodes,f)))return p?(--this.nViews,
this.setNode(this.panelNodes.get(b))):this.si.writeStatus(l+" is already open"),-1;!j&&!p&&this.close("all");this.si.setCursor(3);try{this.si.siSetCurrentSource(p?JSV.source.JDXSource.createView(c):JSV.source.JDXReader.createJDXSource(r,a,l,this.obscureTitleFromUser===Boolean.TRUE,this.loadImaginary,e,g,this.nmrMaxY))}catch(w){if(D(w,Exception))return alert(w.toString()),this.si.setCursor(0),this.isApplet&&this.selectedPanel.showMessage(w.toString(),"Error Opening File"),-3;throw w;}this.si.setCursor(0);
System.gc();null==n?(n=this.currentSource.getFilePath(),null!=n&&(m=n.substring(n.lastIndexOf("/")+1))):this.currentSource.setFilePath(n);null==k&&!p&&(k=n);null!=k&&this.currentSource.setID(k);this.si.siSetLoaded(m,n);a=this.currentSource.getJDXSpectrum(0);if(null==a)return-4;c=this.currentSource.getSpectra();JSV.common.Spectrum.process(c,this.irMode);c=this.interfaceOverlaid||a.isAutoOverlayFromJmolClick();p||c&&this.currentSource.isCompoundSource?this.combineSpectra(p?f:null):this.splitSpectra();
this.pd().setTaintedAll();p||this.si.siUpdateRecentMenus(l);return 0},"~O,~S,JU.Lst,~S,~N,~N,~B,~S");c(b,"close",function(a){var b=0,c=null==a?-2:a.indexOf(">");0<c&&(b=JU.PT.parseInt(a.substring(c+1).trim()),a=a.substring(0,c).trim());"*".equals(a)&&(a="all");var f="all"===a;if(null==a||0==b&&a.equalsIgnoreCase("all"))this.closeSource(null);else{var e=a.equalsIgnoreCase("views"),c=new JU.Lst;a=a.$replace("\\","/");var g=this.panelNodes.size(),b=g-b;if(a.endsWith("*"))for(a=a.substring(0,a.length-
1);0<=--g;)this.panelNodes.get(g).fileName.startsWith(a)&&c.addLast(this.panelNodes.get(g).source);else if(a.equalsIgnoreCase("selected"))for(a=null;0<=--g;)f=this.panelNodes.get(g).source,this.panelNodes.get(g).isSelected&&(null==a||a!==f)&&c.addLast(f),a=f;else if(f||e||a.equalsIgnoreCase("simulations"))for(a=0;0<=--g&&a<b;){if(f||(e?this.panelNodes.get(g).isView:this.panelNodes.get(g).isSimulation))c.addLast(this.panelNodes.get(g).source),a++}else f=0==a.length?this.currentSource:JSV.common.PanelNode.findSourceByNameOrId(a,
this.panelNodes),null!=f&&c.addLast(f);for(g=c.size();0<=--g;)this.closeSource(c.get(g));null==this.selectedPanel&&0<this.panelNodes.size()&&this.si.siSetSelectedPanel(JSV.common.PanelNode.getLastFileFirstNode(this.panelNodes))}},"~S");c(b,"execLoad",function(a,b){var c=JSV.common.ScriptToken.getTokens(a),f=c.get(0),e=null,g=0;f.equalsIgnoreCase("ID")&&(e=JU.PT.trimQuotes(c.get(1)),f=c.get(2),g=2);var j=f.equalsIgnoreCase("APPEND"),k=f.equalsIgnoreCase("CHECK");(j||k)&&g++;0<g&&(f=c.get(g));null==
b&&(b=this.defaultLoadScript);if(f.equals("?"))this.openFileFromDialog(j,!1,null,b);else if(f.equals("http://?"))this.openFileFromDialog(j,!0,null,null);else if(f.equals("$?")||f.equals("$H1?"))this.openFileFromDialog(j,!0,"H1",null);else if(f.equals("$C13?"))this.openFileFromDialog(j,!0,"C13",null);else{var l=f.equalsIgnoreCase("MOL")||f.equalsIgnoreCase("H1"),n=f.equalsIgnoreCase("C13");if(l||n)f="http://SIMULATION/"+(l?"H1/":"C13/")+"MOL="+JU.PT.trimQuotes(c.get(++g));!k&&!j&&(f.equals('""')&&
null!=this.currentSource&&(f=this.currentSource.getFilePath()),this.close("all"));f=JU.PT.trimQuotes(f);if(k=f.startsWith("$"))!f.startsWith("$H1")&&!f.startsWith("$C13")&&(f="$H1/"+f.substring(1)),f="http://SIMULATION/"+f.substring(1);l=g+1<c.size()?Integer.$valueOf(c.get(++g)).intValue():-1;c=g+1<c.size()?Integer.$valueOf(c.get(++g)).intValue():l;this.si.siOpenDataOrFile(null,null,null,f,l,c,j,b,e);k&&(this.close("views"),this.execView("*",!0))}},"~S,~S");c(b,"combineSpectra",function(a){for(var b=
this.currentSource,c=b.getSpectra(),f=!1,e=c.size();0<=--e;)if(c.get(e).isSimulation){f=!0;break}c=this.si.siGetNewJSVPanel2(c);c.setTitle(b.getTitle());c.getTitle().equals("")&&(c.getPanelData().setViewTitle(b.getFilePath()),c.setTitle(a));this.si.siSetPropertiesFromPreferences(c,!0);this.spectraTree.createTree(++this.fileCount,b,B(-1,[c])).getPanelNode().isView=!0;b=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);b.setFrameTitle(a);b.isView=!0;this.autoShowLegend&&1==this.pd().getNumberOfGraphSets()&&
b.setLegend(this.getDialog(JSV.common.Annotation.AType.OverlayLegend,null));this.si.siSetMenuEnables(b,!1);f&&this.pd().splitStack(!0)},"~S");c(b,"closeSource",function(a){for(var b=this.spectraTree.getRootNode(),c=null==a?null:a.getFilePath(),f=new JU.Lst,b=b.children();b.hasMoreElements();){var e=b.nextElement();if(null==c||e.getPanelNode().source.matchesFilePath(c)){JU.Logger.info("Closing "+e.getPanelNode().source.getFilePath());for(var g=e.children();g.hasMoreElements();){var j=g.nextElement();
f.addLast(j);this.panelNodes.removeObj(j.getPanelNode())}f.addLast(e);if(null!=c)break}}this.spectraTree.deleteNodes(f);null==a&&(null!=this.currentSource&&this.currentSource.dispose(),this.currentSource=null,null!=this.selectedPanel&&this.selectedPanel.dispose());this.currentSource===a&&(this.si.siSetSelectedPanel(null),this.si.siSetCurrentSource(null));for(f=c=0;f<this.panelNodes.size();f++)b=JU.PT.parseFloat(this.panelNodes.get(f).id),b>=c+1&&(c=v(Math.floor(b)));this.fileCount=c;System.gc();JU.Logger.debugging&&
JU.Logger.checkMemory();this.si.siSourceClosed(a)},"JSV.source.JDXSource");c(b,"setFrameAndTreeNode",function(a){null==this.panelNodes||(0>a||a>=this.panelNodes.size())||this.setNode(this.panelNodes.get(a))},"~N");c(b,"selectFrameNode",function(a){a=JSV.common.PanelNode.findNode(a,this.panelNodes);if(null==a)return null;this.spectraTree.setPath(this.spectraTree.newTreePath(a.treeNode.getPath()));this.setOverlayLegendVisibility(null,!1);return a},"JSV.api.JSVPanel");c(b,"setSpectrum",function(a){if(0<=
a.indexOf(".")){a=JSV.common.PanelNode.findNodeById(a,this.panelNodes);if(null==a)return!1;this.setNode(a)}else{a=JU.PT.parseInt(a);if(0>=a)return this.checkOverlay(),!1;this.setFrameAndTreeNode(a-1)}return!0},"~S");c(b,"splitSpectra",function(){for(var a=this.currentSource,b=a.getSpectra(),c=Array(b.size()),f=null,e=0;e<b.size();e++)f=b.get(e),f=this.si.siGetNewJSVPanel(f),this.si.siSetPropertiesFromPreferences(f,!0),c[e]=f;this.spectraTree.createTree(++this.fileCount,a,c);this.si.siGetNewJSVPanel(null);
a=JSV.common.PanelNode.findNode(this.selectedPanel,this.panelNodes);this.si.siSetMenuEnables(a,!0)});c(b,"selectedTreeNode",function(a){null!=a&&(a.isLeaf()?this.setNode(a.getPanelNode()):System.out.println("not a leaf"),this.si.siSetCurrentSource(a.getPanelNode().source))},"JSV.api.JSVTreeNode");c(b,"dispose",function(){this.fileHelper=null;null!=this.viewDialog&&this.viewDialog.dispose();this.viewDialog=null;null!=this.overlayLegendDialog&&this.overlayLegendDialog.dispose();this.overlayLegendDialog=
null;null!=this.jsvpPopupMenu&&(this.jsvpPopupMenu.jpiDispose(),this.jsvpPopupMenu=null);if(null!=this.panelNodes)for(var a=this.panelNodes.size();0<=--a;)this.panelNodes.get(a).dispose(),this.panelNodes.removeItemAt(a)});c(b,"runScript",function(a){null==this.scriptQueue?this.si.siProcessCommand(a):this.scriptQueue.addLast(a)},"~S");c(b,"requestRepaint",function(){null!=this.selectedPanel&&this.repaintManager.refresh()});c(b,"repaintDone",function(){this.repaintManager.repaintDone()});c(b,"checkOverlay",
function(){null!=this.mainPanel&&this.markSelectedPanels(this.panelNodes,this.mainPanel.getCurrentPanelIndex());this.viewDialog=this.getDialog(JSV.common.Annotation.AType.Views,null)});c(b,"markSelectedPanels",function(a,b){for(var c=a.size();0<=--c;)a.get(c).isSelected=b==c},"JU.Lst,~N");c(b,"execOverlayOffsetY",function(a){if(-2147483648==a){if(null==this.selectedPanel)return;a=this.selectedPanel.getInput("Enter a vertical offset in percent for stacked plots","Overlay",""+this.recentStackPercent);
a=JU.PT.parseFloat(a);if(Float.isNaN(a))return;a=F(a)}this.recentStackPercent=a;this.parameters.viewOffset=a;this.isClosed()&&this.pd().setYStackOffsetPercent(a)},"~N");c(b,"execScriptInline",function(a){0<a.length&&(a=a.substring(6).trim());0==a.length&&(a=this.selectedPanel.getInput("Enter a JSpecView script","Script",this.recentScript));null!=a&&(this.recentScript=a,this.runScriptNow(a))},"~S");c(b,"setDisplay",function(a){this.apiPlatform.setViewer(this,this.display=a);var b=E(2,0);this.apiPlatform.getFullScreenDimensions(a,
b);this.setScreenDimension(b[0],b[1])},"~O");c(b,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.screenWidth==a&&this.screenHeight==b||this.resizeImage(a,b)},"~N,~N");c(b,"resizeImage",function(a,b){0<a?(this.screenWidth=a,this.screenHeight=b):(a=0==this.screenWidth?this.screenWidth=500:this.screenWidth,b=0==this.screenHeight?this.screenHeight=500:this.screenHeight);this.g2d.setWindowParameters(a,b)},"~N,~N");c(b,"updateJS",function(){null!=this.selectedPanel&&
this.selectedPanel.paintComponent(this.apiPlatform.getGraphics(null))});c(b,"processMouseEvent",function(a,b,c,f,e){return null!=this.selectedPanel&&this.selectedPanel.processMouseEvent(a,b,c,f,e)},"~N,~N,~N,~N,~N");c(b,"processTwoPointGesture",function(a){this.isClosed()||this.selectedPanel.processTwoPointGesture(a)},"~A");c(b,"getApplet",function(){return this.html5Applet});c(b,"openFileAsyncSpecial",function(a){var b=null==this.currentSource?"NO":this.getDialogManager().getDialogInput(this,"Do you want to append this file? (Answer NO to replace.)",
"Drag/Drop Action",3,null,null,"YES");null!=b&&(b=b.toLowerCase().startsWith("y")?"append":"",this.runScript("load "+b+' "'+a+'"'+(""===b?"":"; view *")))},"~S,~N");c(b,"getHeight",function(){return this.screenHeight});c(b,"getWidth",function(){return this.screenWidth});c(b,"getPlatformInterface",function(a){return JSV.common.JSViewer.getInterface("JSV."+(JSV.common.JSViewer.isJS?"js2d.Js":"java.Awt")+a)},"~S");c(b,"getDialogManager",function(){if(null!=this.dialogManager)return this.dialogManager;
this.dialogManager=this.getPlatformInterface("DialogManager");return this.dialogManager.set(this)});c(b,"getDialog",function(a,b){switch(a){case JSV.common.Annotation.AType.Integration:return JSV.common.JSViewer.getInterface("JSV.dialog.IntegrationDialog").setParams("Integration for "+b,this,b);case JSV.common.Annotation.AType.Measurements:return JSV.common.JSViewer.getInterface("JSV.dialog.MeasurementsDialog").setParams("Measurements for "+b,this,b);case JSV.common.Annotation.AType.PeakList:return JSV.common.JSViewer.getInterface("JSV.dialog.PeakListDialog").setParams("Peak List for "+
b,this,b);case JSV.common.Annotation.AType.OverlayLegend:return this.overlayLegendDialog=JSV.common.JSViewer.getInterface("JSV.dialog.OverlayLegendDialog").setParams(this.pd().getViewTitle(),this,null);case JSV.common.Annotation.AType.Views:return this.viewDialog=JSV.common.JSViewer.getInterface("JSV.dialog.ViewsDialog").setParams("View/Combine/Close Spectra",this,null);default:return null}},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(b,"show",function(a){this.getDialogManager();if(a.equals("properties"))this.dialogManager.showProperties(null,
this.pd().getSpectrum());else if(a.equals("errors"))this.dialogManager.showSourceErrors(null,this.currentSource);else if(a.equals("source"))null==this.currentSource?0<this.panelNodes.size()&&this.dialogManager.showMessageDialog(null,"Please Select a Spectrum","Select Spectrum",0):this.dialogManager.showSource(this,this.pd().getSpectrum());else if(a.startsWith("solutioncolorfill"))if(0<=a.indexOf("all"))for(var b=this.panelNodes.size();0<=--b;)this.panelNodes.get(b).pd().setSolutionColor(a);else this.pd().setSolutionColor(a);
else a.startsWith("solutioncolor")&&(a=this.getSolutionColorStr(0>a.indexOf("false")),a="background-color:rgb("+a+")'><br />Predicted Solution Colour- RGB("+a+")<br /><br />",JSV.common.JSViewer.isJS?this.dialogManager.showMessage(this,"<div style='width:100%;height:100%;"+a+"</div>","Predicted Colour"):this.selectedPanel.showMessage("<html><body style='"+a+"</body></html>","Predicted Colour"))},"~S");c(b,"getDialogPrint",function(a){if(!JSV.common.JSViewer.isJS)try{var b=this.getPlatformInterface("PrintDialog").set(this.offWindowFrame,
this.lastPrintLayout,a).getPrintLayout();null!=b&&(this.lastPrintLayout=b);return b}catch(c){if(!D(c,Exception))throw c;}return new JSV.common.PrintLayout(this.pd())},"~B");c(b,"setIRmode",function(a){this.irMode=a.equals("AtoT")?JSV.common.Spectrum.IRMode.TO_TRANS:a.equals("TtoA")?JSV.common.Spectrum.IRMode.TO_ABS:JSV.common.Spectrum.IRMode.getMode(a)},"~S");c(b,"getOptionFromDialog",function(a,b,c){return this.getDialogManager().getOptionFromDialog(null,a,this.selectedPanel,b,c)},"~A,~S,~S");c(b,
"print",function(a){return this.execWrite('PDF "'+a+'"')},"~S");c(b,"execWrite",function(a){JSV.common.JSViewer.isJS&&null==a&&(a="PDF");a=JSV.common.JSViewer.getInterface("JSV.export.Exporter").write(this,null==a?null:JSV.common.ScriptToken.getTokens(a),!1);this.si.writeStatus(a);return a},"~S");c(b,"$export",function(a,b){null==a&&(a="XY");var c=this.pd(),f=c.getNumberOfSpectraInCurrentSet();if(-1>b||b>=f)return"Maximum spectrum index (0-based) is "+(f-1)+".";c=0>b?c.getSpectrum():c.getSpectrumAt(b);
try{return JSV.common.JSViewer.getInterface("JSV.export.Exporter").exportTheSpectrum(this,JSV.common.ExportType.getType(a),null,c,0,c.getXYCoords().length-1,null,a.equalsIgnoreCase("PDF"))}catch(e){if(D(e,Exception))return JU.Logger.error(e.toString()),null;throw e;}},"~S,~N");f(b,"postByteArray",function(a,b){return JSV.common.JSVFileManager.postByteArray(a,b)},"~S,~A");c(b,"getOutputChannel",function(a,b){for(;a.startsWith("/");)a=a.substring(1);return(new JU.OC).setParams(this,a,!b,null)},"~S,~B");
b.getInterface=c(b,"getInterface",function(a){try{var b=ra._4Name(a);return null==b?null:b.newInstance()}catch(c){if(D(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c),null;throw c;}},"~S");c(b,"showMessage",function(a){null!=this.selectedPanel&&null!=a&&this.selectedPanel.showMessage(a,null)},"~S");c(b,"openFileFromDialog",function(a,b,c,f){var e=null;if(null!=c){e=this.fileHelper.getUrlFromDialog("Enter the name or identifier of a compound",this.recentSimulation);
if(null==e)return;this.recentSimulation=e;e="$"+c+"/"+e}else if(b){e=this.fileHelper.getUrlFromDialog("Enter the URL of a JCAMP-DX File",null==this.recentURL?this.recentOpenURL:this.recentURL);if(null==e)return;this.recentOpenURL=e}else b=B(-1,[Boolean.$valueOf(a),f]),b=this.fileHelper.showFileOpenDialog(this.mainPanel,b),null!=b&&(e=b.getFullPath());null!=e&&this.runScriptNow("load "+(a?"APPEND ":"")+'"'+e+'"'+(null==f?"":";"+f))},"~B,~B,~S,~S");c(b,"openFile",function(a,b){if(b&&null!=this.panelNodes){var c=
JSV.common.PanelNode.findSourceByNameOrId((new java.io.File(a)).getAbsolutePath(),this.panelNodes);null!=c&&this.closeSource(c)}this.si.siOpenDataOrFile(null,null,null,a,-1,-1,!0,this.defaultLoadScript,null)},"~S,~B");c(b,"selectPanel",function(a,b){var c=-1;if(null!=b){for(var f=b.size();0<=--f;){var e=b.get(f).jsvp;e===a?c=f:(e.setEnabled(!1),e.setFocusable(!1),e.getPanelData().closeAllDialogsExcept(JSV.common.Annotation.AType.NONE))}this.markSelectedPanels(b,c)}return c},"JSV.api.JSVPanel,JU.Lst");
c(b,"checkAutoIntegrate",function(){this.autoIntegrate&&this.pd().integrateAll(this.parameters)});c(b,"parseInitScript",function(a){null==a&&(a="");a=new JSV.common.ScriptTokenizer(a,!0);for(JU.Logger.debugging&&JU.Logger.info("Running in DEBUG mode");a.hasMoreTokens();){var b=a.nextToken(),c=new JSV.common.ScriptTokenizer(b,!1),f=c.nextToken();f.equalsIgnoreCase("SET")&&(f=c.nextToken());var f=f.toUpperCase(),e=JSV.common.ScriptToken.getScriptToken(f),b=JSV.common.ScriptToken.getValue(e,c,b);JU.Logger.info("KEY-> "+
f+" VALUE-> "+b+" : "+e);try{switch(e){default:this.parameters.set(null,e,b);break;case JSV.common.ScriptToken.UNKNOWN:break;case JSV.common.ScriptToken.APPLETID:this.fullName=this.appletName+"__"+(this.appletName=b)+"__";f=null;self.Jmol&&(f=Jmol._applets[b]);this.html5Applet=f;break;case JSV.common.ScriptToken.AUTOINTEGRATE:this.autoIntegrate=JSV.common.Parameters.isTrue(b);break;case JSV.common.ScriptToken.COMPOUNDMENUON:break;case JSV.common.ScriptToken.APPLETREADYCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.COORDCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.LOADFILECALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.PEAKCALLBACKFUNCTIONNAME:case JSV.common.ScriptToken.SYNCCALLBACKFUNCTIONNAME:this.si.siExecSetCallback(e,
b);break;case JSV.common.ScriptToken.ENDINDEX:this.initialEndIndex=Integer.parseInt(b);break;case JSV.common.ScriptToken.INTERFACE:this.checkOvelayInterface(b);break;case JSV.common.ScriptToken.IRMODE:this.setIRmode(b);break;case JSV.common.ScriptToken.MENUON:this.allowMenu=Boolean.parseBoolean(b);break;case JSV.common.ScriptToken.OBSCURE:null==this.obscureTitleFromUser&&(this.obscureTitleFromUser=Boolean.$valueOf(b));break;case JSV.common.ScriptToken.STARTINDEX:this.initialStartIndex=Integer.parseInt(b);
break;case JSV.common.ScriptToken.SYNCID:this.fullName=this.appletName+"__"+(this.syncID=b)+"__"}}catch(g){if(!D(g,Exception))throw g;}}},"~S");c(b,"getSolutionColorStr",function(a){a=JU.CU.colorPtFromInt(this.getSolutionColor(a),null);return F(a.x)+","+F(a.y)+","+F(a.z)},"~B");c(b,"checkCommandLineForTip",function(a,b,c){var f="\u0001"==a;if(!f&&"\x00"!=a){if("\t"!=a&&("\n"==a||32>a.charCodeAt(0)||126<a.charCodeAt(0)))return null;b+=Character.isISOControl(a)?"":""+a}var e;0<=b.indexOf(";")&&(b=b.substring(b.lastIndexOf(";")+
1));for(var g=null;b.startsWith(" ");)b=b.substring(1);if(0==b.length&&!f)e="";else{e=JSV.common.ScriptToken.getTokens(b);if(0==e.size()&&!f)return"";b=b.endsWith(" ")||1<e.size()&&c;e=JSV.common.ScriptToken.getScriptTokenList(0==e.size()?null:e.get(0),b);switch(e.size()){case 0:e="?";break;case 1:f=e.get(0);e=f.getTip();try{e=0<=e.indexOf("TRUE")?" ("+this.parameters.getBoolean(f)+")":0<=f.name().indexOf("COLOR")?" ("+JU.CU.toRGBHexString(this.parameters.getElementColor(f))+")":""}catch(j){if(D(j,
Exception))return null;throw j;}if("\t"==a||b||!c){e=f.name()+" "+f.getTip()+e+" "+f.getDescription();"\t"==a&&(g=f.name()+" ");break}e=f.name()+" "+e;break;default:e=JSV.common.ScriptToken.getNameList(e)}}c?this.si.writeStatus(e):g=e;return g},"~S,~S,~B");c(b,"checkScript",function(a){return this.checkCommandLineForTip("\x00",a,!1)},"~S");c(b,"execHelp",function(a){var b=this.checkCommandLineForTip("\u0001",a,!1);if(0>b.indexOf(" ")&&0<b.indexOf(",")){var c=JU.PT.split(b,",");java.util.Arrays.sort(c);
for(var b="",f=0;f<c.length;f++)var e=JSV.common.ScriptToken.getScriptToken(c[f]),b=b+(c[f]+" "+e.getTip()+"\n  "+e.getDescription()+"\n\n");this.getDialogManager().showMessage(null,b,"HELP "+a)}else this.selectedPanel.showMessage(b,"Help "+a);System.out.println(b)},"~S");b.testScript='<PeakData  index="1" title="" model="~1.1" type="1HNMR" xMin="3.2915" xMax="3.2965" atoms="15,16,17,18,19,20" multiplicity="" integral="1"> src="JPECVIEW" file="http://SIMULATION/$caffeine"';b.isJS=!1;b.isSwingJS=!1;
b.jmolObject=null});n("JSV.common");z(["JSV.common.Annotation","$.Coordinate"],"JSV.common.Measurement",null,function(){var b=r(function(){this.pt2=null;this.value=0;u(this,arguments)},JSV.common,"Measurement",JSV.common.Annotation);N(b,function(){this.pt2=new JSV.common.Coordinate});c(b,"setM1",function(a,b,c){this.setA(a,b,c,"",!1,!1,0,6);this.setPt2(this.getXVal(),this.getYVal());return this},"~N,~N,JSV.common.Spectrum");c(b,"copyM",function(){var a=new JSV.common.Measurement;a.setA(this.getXVal(),
this.getYVal(),this.spec,this.text,!1,!1,this.offsetX,this.offsetY);a.setPt2(this.pt2.getXVal(),this.pt2.getYVal());return a});c(b,"setPt2",function(a,b){this.spec=a;b&&this.setPt2(this.getXVal(),this.getYVal());return this},"JSV.common.Spectrum,~B");c(b,"setPt2",function(a,b){this.pt2.setXVal(a);this.pt2.setYVal(b);this.value=Math.abs(a-this.getXVal());this.text=this.spec.setMeasurementText(this)},"~N,~N");c(b,"getSpectrum",function(){return this.spec});c(b,"setValue",function(a){this.value=a;this.text=
this.spec.setMeasurementText(this)},"~N");c(b,"getValue",function(){return this.value});c(b,"getXVal2",function(){return this.pt2.getXVal()});c(b,"getYVal2",function(){return this.pt2.getYVal()});f(b,"addSpecShift",function(a){this.setXVal(this.getXVal()+a);this.pt2.setXVal(this.pt2.getXVal()+a)},"~N");c(b,"setYVal2",function(a){this.pt2.setYVal(a)},"~N");c(b,"overlaps",function(a,b){return Math.min(this.getXVal(),this.getXVal2())<Math.max(a,b)&&Math.max(this.getXVal(),this.getXVal2())>Math.min(a,
b)},"~N,~N");f(b,"toString",function(){return"["+this.getXVal()+","+this.pt2.getXVal()+"]"})});n("JSV.common");z(["JU.Lst","JSV.api.AnnotationData"],"JSV.common.MeasurementData",["JU.AU","$.DF","JSV.common.Annotation","$.Parameters"],function(){var b=r(function(){this.units=this.spec=this.type=null;this.precision=0;this.myParams=null;this.isON=!0;this.key=null;u(this,arguments)},JSV.common,"MeasurementData",JU.Lst,JSV.api.AnnotationData);y(b,function(a,b){I(this,JSV.common.MeasurementData,[]);this.type=
a;this.spec=b;this.myParams=(new JSV.common.Parameters).setName("MeasurementData")},"JSV.common.Annotation.AType,JSV.common.Spectrum");c(b,"getMeasurements",function(){return this});f(b,"getAType",function(){return this.type});f(b,"getState",function(){return this.isON});f(b,"setState",function(a){this.isON=a},"~B");c(b,"setMeasurements",function(){},"JU.Lst");f(b,"getParameters",function(){return this.myParams});c(b,"getDataHeader",function(){return JSV.common.MeasurementData.HEADER});c(b,"getMeasurementListArray",
function(a){this.units=a;var b=this.getMeasurementListArrayReal(a),c=this.spec.isNMR()?4:2;a=this.spec.isHNMR()&&a.equals("ppm")?4:2;for(var f=Array(this.size()),e=this.size();0<=--e;)f[e]=B(-1,[""+(e+1),JU.DF.formatDecimalDbl(b[e][0],c),JU.DF.formatDecimalDbl(b[e][1],c),JU.DF.formatDecimalDbl(b[e][2],a)]);return f},"~S");c(b,"getMeasurementListArrayReal",function(a){a=this.spec.isNMR()&&a.equalsIgnoreCase("HZ");for(var b=JU.AU.newDouble2(this.size()),c=0,f=this.size();0<=--f;){var e=this.get(f).getValue();
a&&(e*=this.spec.getObservedFreq());b[c++]=R(-1,[this.get(f).getXVal(),this.get(f).getXVal2(),e])}return b},"~S");b.checkParameters=c(b,"checkParameters",function(a,b){if(0==a.size())return!1;var c=a.getParameters();switch(a.getAType()){case JSV.common.Annotation.AType.PeakList:return b.peakListInterpolation.equals(c.peakListInterpolation)&&b.peakListThreshold==c.peakListThreshold}return!1},"JSV.common.MeasurementData,JSV.common.ColorParameters");f(b,"getSpectrum",function(){return this.spec});f(b,
"getData",function(){return this});c(b,"clear",function(a,b){for(var c=this.size();0<=--c;){var f=this.get(c);(0==f.text.length||f.overlaps(a,b))&&this.removeItemAt(c)}},"~N,~N");c(b,"find",function(a){for(var b=this.size();0<=--b;)if(this.get(b).overlaps(a,a))return b;return-1},"~N");f(b,"setSpecShift",function(a){for(var b=this.size();0<=--b;){var c=this.get(b),f=c.getXVal()+a;c.setXVal(f);c.setValue(f);c.text=JU.DF.formatDecimalDbl(f,this.precision)}},"~N");f(b,"getGraphSetKey",function(){return this.key});
f(b,"setGraphSetKey",function(a){this.key=a},"~S");f(b,"isVisible",function(){return!0});c(b,"getInfo",function(a){a.put("header",this.getDataHeader());a.put("table",this.getMeasurementListArrayReal("ppm"));null!=this.units&&a.put("units",this.units)},"java.util.Map");f(b,"isDialog",function(){return!1});b.HEADER=B(-1,["","start","end","value"])});n("JSV.common");z(["java.lang.Enum","J.api.EventManager","java.util.Hashtable","JU.Lst"],"JSV.common.PanelData","JU.CU JSV.common.Annotation $.Coordinate $.GraphSet $.JSVFileManager $.JSVersion $.JSViewer $.MeasurementData $.Parameters $.PeakPickEvent $.ScriptToken $.Spectrum $.SubSpecChangeEvent $.ZoomEvent JU.Font $.Logger".split(" "),
function(){var b=r(function(){this.graphSets=this.jsvp=this.options=this.currentGraphSet=this.listeners=this.vwr=this.g2d0=this.g2d=null;this.currentSplitPoint=0;this.coordsClicked=this.coordClicked=this.thisWidget=null;this.isIntegralDrag=this.drawXAxisLeftToRight=this.shiftPressed=this.ctrlPressed=!1;this.xAxisLeftToRight=!0;this.scalingFactor=1;this.integralShiftMode=0;this.left=60;this.right=50;this.coordStr="";this.startupPinTip="Click to set.";this.title=null;this.endIndex=this.startIndex=this.thisHeight=
this.thisWidth=this.nSpectra=this.clickCount=0;this.titleFontName=this.displayFontName=this.viewTitle=this.commonFilePath=null;this.isPrinting=!1;this.doReset=!0;this.printingFontName=null;this.printGraphPosition="default";this.isLinked=this.display1D=this.titleDrawn=!1;this.spectra=this.printJobTitle=null;this.taintedAll=!0;this.testingJavaScript=!1;this.mouseState=this.currentFont=null;this.peakTabsOn=this.titleOn=this.gridOn=!1;this.mouseY=this.mouseX=0;this.linking=!1;this.xPixelClicked=0;this.gMain=
this.optionsSaved=this.bgcolor=this.BLACK=this.zoomBoxColor2=this.zoomBoxColor=this.highlightColor=this.unitsColor=this.titleColor=this.scaleColor=this.plotAreaColor=this.peakTabColor=this.integralPlotColor=this.gridColor=this.coordinatesColor=null;u(this,arguments)},JSV.common,"PanelData",null,J.api.EventManager);N(b,function(){this.listeners=new JU.Lst;this.options=new java.util.Hashtable});y(b,function(a,b){this.vwr=b;this.jsvp=a;this.g2d=this.g2d0=b.g2d;this.BLACK=this.g2d.getColor1(0);this.highlightColor=
this.g2d.getColor4(255,0,0,200);this.zoomBoxColor=this.g2d.getColor4(150,150,100,130);this.zoomBoxColor2=this.g2d.getColor4(150,100,100,130)},"JSV.api.JSVPanel,JSV.common.JSViewer");c(b,"addListener",function(a){this.listeners.contains(a)||this.listeners.addLast(a)},"JSV.api.PanelListener");c(b,"getCurrentGraphSet",function(){return this.currentGraphSet});c(b,"dispose",function(){this.jsvp=null;for(var a=0;a<this.graphSets.size();a++)this.graphSets.get(a).dispose();this.listeners=this.options=this.thisWidget=
this.coordsClicked=this.coordClicked=this.currentGraphSet=this.currentFont=this.graphSets=null});c(b,"setViewTitle",function(a){this.viewTitle=a},"~S");c(b,"getViewTitle",function(){return null==this.viewTitle?this.getTitle():this.viewTitle});c(b,"getInfo",function(a,b){var c=new java.util.Hashtable,f=null;if(a)return this.currentGraphSet.getInfo(b,this.getCurrentSpectrumIndex());var e=this.options.entrySet();if("".equals(b)){for(var f="type title nSets ",g,e=e.iterator();e.hasNext()&&((g=e.next())||
1);)f+=g.getKey().name()+" ";c.put("KEYS",f)}else{for(e=e.iterator();e.hasNext()&&((g=e.next())||1);)JSV.common.Parameters.putInfo(b,c,g.getKey().name(),g.getValue());JSV.common.Parameters.putInfo(b,c,"type",this.getSpectrumAt(0).getDataType());JSV.common.Parameters.putInfo(b,c,"title",this.title);JSV.common.Parameters.putInfo(b,c,"nSets",Integer.$valueOf(this.graphSets.size()))}f=new JU.Lst;for(g=this.graphSets.size();0<=--g;)f.addLast(this.graphSets.get(g).getInfo(b,-1));c.put("sets",f);return c},
"~B,~S");c(b,"setBooleans",function(a,b){if(null==b)for(var c,f=a.getBooleans().entrySet().iterator();f.hasNext()&&((c=f.next())||1);)this.setBooleans(a,c.getKey());else this.setBoolean(b,a.getBoolean(b))},"JSV.common.Parameters,JSV.common.ScriptToken");c(b,"setBoolean",function(a,b){this.setTaintedAll();if(a===JSV.common.ScriptToken.REVERSEPLOT)this.currentGraphSet.setReversePlot(b);else switch(this.options.put(a,Boolean.$valueOf(b)),a){case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:this.doReset=
!0}},"JSV.common.ScriptToken,~B");c(b,"getBoolean",function(a){if(a===JSV.common.ScriptToken.REVERSEPLOT)return this.currentGraphSet.reversePlot;if(null==this.options)return!1;a=this.options.get(a);return null!=a&&C(a,Boolean)&&a===Boolean.TRUE},"JSV.common.ScriptToken");c(b,"setFontName",function(a,b){switch(a){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.displayFontName=b;break;case JSV.common.ScriptToken.TITLEFONTNAME:this.titleFontName=b}null!=b&&this.options.put(a,b)},"JSV.common.ScriptToken,~S");
c(b,"getDisplay1D",function(){return this.display1D});c(b,"setTaintedAll",function(){this.taintedAll=!0});c(b,"initOne",function(a){this.spectra=new JU.Lst;this.spectra.addLast(a);this.initMany(this.spectra,0,0)},"JSV.common.Spectrum");c(b,"initMany",function(a,b,c){this.startIndex=b;this.endIndex=c;this.nSpectra=a.size();this.spectra=a;this.commonFilePath=a.get(0).getFilePath();for(b=0;b<this.nSpectra;b++)if(!this.commonFilePath.equalsIgnoreCase(a.get(b).getFilePath())){this.commonFilePath=null;
break}this.setGraphSets(JSV.common.PanelData.LinkMode.NONE)},"JU.Lst,~N,~N");c(b,"setGraphSets",function(a){this.graphSets=JSV.common.GraphSet.createGraphSetsAndSetLinkMode(this,this.jsvp,this.spectra,this.startIndex,this.endIndex,a);this.currentGraphSet=this.graphSets.get(0);this.title=this.getSpectrum().getTitleLabel()},"JSV.common.PanelData.LinkMode");c(b,"findMatchingPeakInfo",function(a){for(var b=null,c=0;c<this.graphSets.size()&&null==(b=this.graphSets.get(c).findMatchingPeakInfo(a));c++);
return b},"JSV.common.PeakInfo");c(b,"integrateAll",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).integrate(-1,a)},"JSV.common.ColorParameters");c(b,"getNumberOfGraphSets",function(){return this.graphSets.size()});c(b,"getTitle",function(){return this.title});c(b,"refresh",function(){this.doReset=!0});c(b,"addAnnotation",function(a){a=this.currentGraphSet.addAnnotation(a,this.getTitle());null!=a&&(this.title=a)},"JU.Lst");c(b,"addPeakHighlight",function(a){for(var b=0;b<
this.graphSets.size();b++)this.graphSets.get(b).addPeakHighlight(a)},"JSV.common.PeakInfo");c(b,"selectPeakByFileIndex",function(a,b,c){var f=this.currentGraphSet.selectPeakByFileIndex(a,b,c);if(null==f)for(var e=this.graphSets.size();0<=--e&&!(this.graphSets.get(e)!==this.currentGraphSet&&null!=(f=this.graphSets.get(e).selectPeakByFileIndex(a,b,c))););return f},"~S,~S,~S");c(b,"setPlotColors",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).setPlotColors(a)},"~A");c(b,"selectSpectrum",
function(a,b,c,f){f&&this.currentGraphSet.selectSpectrum(a,b,c);if("ID".equals(b))this.jumpToSpectrumIndex(this.getCurrentSpectrumIndex(),!0);else for(f=0;f<this.graphSets.size();f++)this.graphSets.get(f)!==this.currentGraphSet&&this.graphSets.get(f).selectSpectrum(a,b,c)},"~S,~S,~S,~B");c(b,"hasFileLoaded",function(a){for(var b=this.graphSets.size();0<=--b;)if(this.graphSets.get(b).hasFileLoaded(a))return!0;return!1},"~S");c(b,"clearAllView",function(){for(var a=this.graphSets.size();0<=--a;)this.graphSets.get(a).resetViewCompletely()});
c(b,"drawGraph",function(a,b,c,f,e,g){var j;this.gMain=a;this.display1D=!this.isLinked&&this.getBoolean(JSV.common.ScriptToken.DISPLAY1D);var k=40,l=50,n=this.isPrinting||this.doReset||this.thisWidth!=f||this.thisHeight!=e;n&&this.setTaintedAll();this.taintedAll&&this.g2d.fillBackground(c,this.bgcolor);b!==a&&(this.g2d.fillBackground(b,null),a!==c&&this.g2d.fillBackground(a,null),this.g2d.setStrokeBold(a,!1));this.isPrinting?(k*=3,l*=3,this.scalingFactor=10,j=!1):(this.scalingFactor=1,j=this.getBoolean(JSV.common.ScriptToken.COORDINATESON),
this.titleOn=this.getBoolean(JSV.common.ScriptToken.TITLEON),this.gridOn=this.getBoolean(JSV.common.ScriptToken.GRIDON),this.peakTabsOn=this.getBoolean(JSV.common.ScriptToken.PEAKTABSON));var m=this.getBoolean(JSV.common.ScriptToken.POINTSONLY);this.titleDrawn=this.doReset=!1;this.thisWidth=f;this.thisHeight=e;for(var p=this.graphSets.size();0<=--p;)this.graphSets.get(p).drawGraphSet(a,b,c,f,e,this.left,this.right,k,l,n,this.taintedAll,m);this.titleOn&&(!this.titleDrawn&&this.taintedAll)&&this.drawTitle(a,
e*this.scalingFactor,f*this.scalingFactor,this.getDrawTitle(this.isPrinting));j&&null!=this.coordStr&&this.drawCoordinates(b,k,this.thisWidth-this.right,k-20);g&&this.taintedAll&&this.printFilePath(a,this.left,e,null!=this.commonFilePath?this.commonFilePath:1==this.graphSets.size()&&null!=this.currentGraphSet.getTitle(!0)?this.getSpectrum().getFilePath():null);this.isPrinting&&this.printVersion(a,e);!this.testingJavaScript&&(this.isPrinting||a===b)?this.setTaintedAll():this.taintedAll=!1},"~O,~O,~O,~N,~N,~B");
c(b,"drawCoordinates",function(a,b,c,f){this.g2d.setGraphicsColor(a,this.coordinatesColor);b=this.setFont(a,this.jsvp.getWidth(),1,14,!0);this.g2d.drawString(a,this.coordStr,c-b.stringWidth(this.coordStr),f)},"~O,~N,~N,~N");c(b,"setFont",function(a,b,c,f,e){return this.g2d.setFont(a,this.getFont(a,b,c,f,e))},"~O,~N,~N,~N,~B");c(b,"printFilePath",function(a,b,c,f){if(null!=f){b*=this.scalingFactor;c*=this.scalingFactor;0<f.indexOf("?")&&(f=f.substring(f.indexOf("?")+1));f=f.substring(f.lastIndexOf("/")+
1);f=f.substring(f.lastIndexOf("\\")+1);this.g2d.setGraphicsColor(a,this.BLACK);var e=this.setFont(a,1E3,0,9,!0);b!=this.left*this.scalingFactor&&(b-=e.stringWidth(f));this.g2d.drawString(a,f,b,c-e.getHeight())}},"~O,~N,~N,~S");c(b,"printVersion",function(a,b){this.g2d.setGraphicsColor(a,this.BLACK);var c=this.setFont(a,100,0,12,!0),f=this.jsvp.getApiPlatform().getDateFormat(null)+" JSpecView "+JSV.common.JSVersion.VERSION_SHORT,e=c.stringWidth(f);this.g2d.drawString(a,f,(this.thisWidth-this.right)*
this.scalingFactor-e,b*this.scalingFactor-3*c.getHeight())},"~O,~N");c(b,"drawTitle",function(a,b,c,f){f=f.$replace("\n"," ");var e=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?1:0,14,!0),g=e.stringWidth(f);g>c&&(e=v(14*c/g),10>e&&(e=10),e=this.getFont(a,c,this.isPrinting||this.getBoolean(JSV.common.ScriptToken.TITLEBOLDON)?1:0,e,!0));this.g2d.setGraphicsColor(a,this.titleColor);this.setCurrentFont(this.g2d.setFont(a,e));this.g2d.drawString(a,f,this.isPrinting?
this.left*this.scalingFactor:5,b-v(e.getHeight()*(this.isPrinting?2:0.5)))},"~O,~N,~N,~S");c(b,"setCurrentFont",function(a){this.currentFont=a},"JU.Font");c(b,"getFontHeight",function(){return this.currentFont.getAscent()});c(b,"getStringWidth",function(a){return this.currentFont.stringWidth(a)},"~S");c(b,"selectFromEntireSet",function(a){for(var b=0,c=0;b<this.graphSets.size();b++)if(-2147483648==a)this.graphSets.get(b).setSelected(-1);else for(var f=this.graphSets.get(b).spectra,e=0;e<f.size();e++,
c++)(0>a||a==c)&&this.graphSets.get(b).setSelected(e)},"~N");c(b,"addToList",function(a,b){for(var c=0;c<this.spectra.size();c++)(0>a||c==a)&&b.addLast(this.spectra.get(c))},"~N,JU.Lst");c(b,"scaleSelectedBy",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).scaleSelectedBy(a)},"~N");c(b,"setCurrentGraphSet",function(a,b){var c=1<a.nSplit?a.getSplitPoint(b):a.getCurrentSpectrumIndex(),f=this.currentGraphSet!==a,e=f||this.currentSplitPoint!=c;this.currentGraphSet=a;this.currentSplitPoint=
c;(f||1<a.nSplit&&e)&&this.setSpectrum(c,!0);if(!f){f=a.checkSpectrumClickedEvent(this.mouseX,this.mouseY,this.clickCount);if(!f)return!1;this.currentSplitPoint=c=a.getCurrentSpectrumIndex();this.setSpectrum(c,!0)}this.jumpToSpectrumIndex(c,f||1<a.nSplit&&e);return f},"JSV.common.GraphSet,~N");c(b,"jumpToSpectrum",function(a){a=this.currentGraphSet.getSpectrumIndex(a);this.jumpToSpectrumIndex(a,!0)},"JSV.common.Spectrum");c(b,"jumpToSpectrumIndex",function(a,b){if(!(0>a||a>=this.currentGraphSet.nSpectra)){this.currentSplitPoint=
a;b&&this.setSpectrum(this.currentSplitPoint,1<this.currentGraphSet.nSplit);var c=this.getSpectrum();this.notifySubSpectrumChange(c.getSubIndex(),c)}},"~N,~B");c(b,"splitStack",function(a){this.currentGraphSet.splitStack(a)},"~B");c(b,"getNumberOfSpectraInCurrentSet",function(){return this.currentGraphSet.nSpectra});c(b,"getSourceID",function(){var a=this.getSpectrum().sourceID;return null==a?this.getSpectrumAt(0).sourceID:a});c(b,"getStartingPointIndex",function(a){return this.currentGraphSet.viewData.getStartingPointIndex(a)},
"~N");c(b,"getEndingPointIndex",function(a){return this.currentGraphSet.viewData.getEndingPointIndex(a)},"~N");c(b,"haveSelectedSpectrum",function(){return this.currentGraphSet.haveSelectedSpectrum()});c(b,"getShowAnnotation",function(a){return this.currentGraphSet.getShowAnnotation(a,-1)},"JSV.common.Annotation.AType");c(b,"showAnnotation",function(a,b){this.currentGraphSet.setShowAnnotation(a,b)},"JSV.common.Annotation.AType,Boolean");c(b,"setYStackOffsetPercent",function(a){this.currentGraphSet.yStackOffsetPercent=
a},"~N");c(b,"setSpectrum",function(a,b){this.currentGraphSet.setSpectrum(a,b)},"~N,~B");c(b,"getSpectrum",function(){return this.currentGraphSet.getSpectrum()});c(b,"setSpecForIRMode",function(a){this.setTaintedAll();var b=this.currentGraphSet.getSpectrum();this.currentGraphSet.setSpectrumJDX(a);for(var c=0;c<this.spectra.size();c++)this.spectra.get(c)===b&&this.spectra.set(c,a)},"JSV.common.Spectrum");c(b,"isShowAllStacked",function(){return this.currentGraphSet.showAllStacked});c(b,"getCurrentSpectrumIndex",
function(){return this.currentGraphSet.getCurrentSpectrumIndex()});c(b,"getSpectrumAt",function(a){return null==this.currentGraphSet?null:this.currentGraphSet.getSpectrumAt(a)},"~N");c(b,"addHighlight",function(a,b,c,f,e,g,j,k){(null==a?this.currentGraphSet:a).addHighlight(b,c,f,this.g2d.getColor4(e,g,j,k))},"JSV.common.GraphSet,~N,~N,JSV.common.Spectrum,~N,~N,~N,~N");c(b,"removeHighlight",function(a,b){this.currentGraphSet.removeHighlight(a,b)},"~N,~N");c(b,"removeAllHighlights",function(){this.currentGraphSet.removeAllHighlights()});
c(b,"setZoom",function(a,b,c,f){this.currentGraphSet.setZoom(a,b,c,f);this.doReset=!0;this.setTaintedAll();this.notifyListeners(new JSV.common.ZoomEvent)},"~N,~N,~N,~N");c(b,"resetView",function(){this.currentGraphSet.resetView()});c(b,"previousView",function(){this.currentGraphSet.previousView()});c(b,"nextView",function(){this.currentGraphSet.nextView()});c(b,"getSelectedIntegral",function(){return this.currentGraphSet.getSelectedIntegral()});c(b,"advanceSubSpectrum",function(a){this.currentGraphSet.advanceSubSpectrum(a)},
"~N");c(b,"setSelectedIntegral",function(a){this.currentGraphSet.setSelectedIntegral(a)},"~N");c(b,"scaleYBy",function(a){this.currentGraphSet.scaleYBy(a)},"~N");c(b,"toPeak",function(a){this.currentGraphSet.toPeak(a)},"~N");c(b,"getClickedCoordinate",function(){return this.coordClicked});c(b,"getPickedCoordinates",function(a,b){return JSV.common.Coordinate.getPickedCoordinates(this.coordsClicked,this.coordClicked,a,b)},"JSV.common.Coordinate,JSV.common.Coordinate");c(b,"shiftSpectrum",function(a,
b,c){return this.currentGraphSet.shiftSpectrum(a,b,c)},"~N,~N,~N");c(b,"findX",function(a,b){this.currentGraphSet.setXPointer(a,b)},"JSV.common.Spectrum,~N");c(b,"setXPointers",function(a,b,c,f){this.currentGraphSet.setXPointer(a,b);this.currentGraphSet.setXPointer2(c,f)},"JSV.common.Spectrum,~N,JSV.common.Spectrum,~N");c(b,"isCurrentGraphSet",function(a){return a===this.currentGraphSet},"JSV.common.GraphSet");c(b,"repaint",function(){this.jsvp.doRepaint(!1)});c(b,"setToolTipText",function(a){this.jsvp.setToolTipText(a)},
"~S");c(b,"setHighlightColor",function(a){this.setColor(JSV.common.ScriptToken.HIGHLIGHTCOLOR,a)},"javajs.api.GenericColor");c(b,"getInput",function(a,b,c){return this.jsvp.getInput(a,b,c)},"~S,~S,~S");c(b,"getFont",function(a,b,c,f,e){f*=this.scalingFactor;e?400>b&&(f=b*f/400):250>b&&(f=b*f/250);b=this.jsvp.getFontFaceID(this.isPrinting?this.printingFontName:this.displayFontName);return this.currentFont=JU.Font.createFont3D(b,c,f,f,this.jsvp.getApiPlatform(),a)},"~O,~N,~N,~N,~B");c(b,"notifySubSpectrumChange",
function(a,b){this.notifyListeners(new JSV.common.SubSpecChangeEvent(a,null==b?null:b.getTitleLabel()))},"~N,JSV.common.Spectrum");c(b,"notifyPeakPickedListeners",function(a){null==a&&(a=new JSV.common.PeakPickEvent(this.jsvp,this.coordClicked,this.getSpectrum().getAssociatedPeakInfo(this.xPixelClicked,this.coordClicked)));this.notifyListeners(a)},"JSV.common.PeakPickEvent");c(b,"notifyListeners",function(a){for(var b=0;b<this.listeners.size();b++)null!=this.listeners.get(b)&&this.listeners.get(b).panelEvent(a)},
"~O");c(b,"escapeKeyPressed",function(a){this.currentGraphSet.escapeKeyPressed(a)},"~B");c(b,"hasFocus",function(){return this.jsvp.hasFocus()});c(b,"isMouseUp",function(){return this.mouseState===JSV.common.PanelData.Mouse.UP});c(b,"doMouseMoved",function(a,b){this.mouseX=a;this.mouseY=b;this.mouseState=JSV.common.PanelData.Mouse.UP;this.clickCount=0;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&c.mouseMovedEvent(a,b)},"~N,~N");c(b,"doMousePressed",function(a,b){this.mouseState=
JSV.common.PanelData.Mouse.DOWN;var c=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=c&&(this.setCurrentGraphSet(c,b),this.clickCount=++this.clickCount%3,this.currentGraphSet.mousePressedEvent(a,b,this.clickCount))},"~N,~N");c(b,"doMouseDragged",function(a,b){this.isIntegralDrag=(new Boolean(this.isIntegralDrag|this.ctrlPressed)).valueOf();this.mouseState=JSV.common.PanelData.Mouse.DOWN;JSV.common.GraphSet.findGraphSet(this.graphSets,a,b)===this.currentGraphSet&&(this.currentGraphSet.checkWidgetEvent(a,
b,!1)&&this.setTaintedAll(),this.currentGraphSet.mouseMovedEvent(a,b))},"~N,~N");c(b,"doMouseReleased",function(a,b,c){this.mouseState=JSV.common.PanelData.Mouse.UP;!(null==this.thisWidget&&null==this.currentGraphSet.pendingMeasurement)&&c&&(this.currentGraphSet.mouseReleasedEvent(a,b),this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0)},"~N,~N,~B");c(b,"doMouseClicked",function(a,b,c){var f=JSV.common.GraphSet.findGraphSet(this.graphSets,a,b);null!=f&&(this.setCurrentGraphSet(f,
b),f.mouseClickedEvent(a,b,this.clickCount,c),this.setTaintedAll(),this.repaint())},"~N,~N,~B");c(b,"hasCurrentMeasurements",function(a){return this.currentGraphSet.hasCurrentMeasurement(a)},"JSV.common.Annotation.AType");c(b,"getDialog",function(a){return this.currentGraphSet.getDialog(a,-1)},"JSV.common.Annotation.AType");c(b,"addDialog",function(a,b,c){this.currentGraphSet.addDialog(a,b,c)},"~N,JSV.common.Annotation.AType,JSV.api.AnnotationData");c(b,"getPeakListing",function(a,b){null!=a&&this.currentGraphSet.getPeakListing(-1,
a,!0);this.currentGraphSet.setPeakListing(b)},"JSV.common.Parameters,Boolean");c(b,"checkIntegral",function(a,b){this.currentGraphSet.checkIntegralParams(a,b)},"JSV.common.Parameters,~S");c(b,"setIntegrationRatios",function(a){this.currentGraphSet.setIntegrationRatios(a)},"~S");c(b,"getView",function(){return this.currentGraphSet.getCurrentView()});c(b,"closeAllDialogsExcept",function(a){for(var b=this.graphSets.size();0<=--b;)this.graphSets.get(b).closeDialogsExcept(a)},"JSV.common.Annotation.AType");
c(b,"removeDialog",function(a){this.currentGraphSet.removeDialog(a)},"JSV.dialog.JSVDialog");c(b,"normalizeIntegral",function(){var a=this.getSelectedIntegral();if(null!=a){var b=a.text;0==b.length&&(b=""+a.getValue());a=this.getInput("Enter a new value for this integral","Normalize Integral",b);try{this.setSelectedIntegral(Double.parseDouble(a))}catch(c){if(!D(c,Exception))throw c;}}});c(b,"getDrawTitle",function(a){var b=null;a?b=this.printJobTitle:1==this.nSpectra?b=this.getSpectrum().getPeakTitle():
null!=this.viewTitle?(null!=this.currentGraphSet.getTitle(!1)&&(b=this.getSpectrum().getPeakTitle()),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")&&(b=b.substring(0,b.indexOf("\n")).trim());return b},"~B");c(b,"getPrintJobTitle",function(a){var b=null;1==this.nSpectra?b=this.getSpectrum().getTitle():null!=this.viewTitle?(1==this.graphSets.size()&&(b=this.currentGraphSet.getTitle(a)),null==b&&(b=this.viewTitle)):b=this.jsvp.getTitle().trim();0<=b.indexOf("\n")?b=b.substring(0,
b.indexOf("\n")).trim():b.startsWith("$")&&(b=b.substring(1));return b},"~B");c(b,"linkSpectra",function(a){a===JSV.common.PanelData.LinkMode.ALL&&(a=2==this.nSpectra?JSV.common.PanelData.LinkMode.AB:3==this.nSpectra?JSV.common.PanelData.LinkMode.ABC:JSV.common.PanelData.LinkMode.NONE);a!==JSV.common.PanelData.LinkMode.NONE&&a.toString().length!=this.nSpectra||this.setGraphSets(a)},"JSV.common.PanelData.LinkMode");c(b,"doZoomLinked",function(a,b,c,f,e,g){if(!this.linking){this.linking=!0;for(var j=
a.getSpectrumAt(0),k=this.graphSets.size();0<=--k;){var l=this.graphSets.get(k);l!==a&&JSV.common.Spectrum.areXScalesCompatible(j,this.graphSets.get(k).getSpectrumAt(0),!1,!0)&&l.doZoom(b,0,c,0,g,!1,e,!1,f)}this.linking=!1}},"JSV.common.GraphSet,~N,~N,~B,~B,~B");c(b,"clearLinkViews",function(a){if(!this.linking){this.linking=!0;for(var b=a.getSpectrum(),c=this.graphSets.size();0<=--c;){var f=this.graphSets.get(c);f!==a&&JSV.common.Spectrum.areXScalesCompatible(b,this.graphSets.get(c).getSpectrum(),
!1,!0)&&f.clearViews()}this.linking=!1}},"JSV.common.GraphSet");c(b,"setlinkedXMove",function(a,b,c){if(!this.linking){this.linking=!0;for(var f=a.getSpectrum(),e=this.graphSets.size();0<=--e;){var g=this.graphSets.get(e);g!==a&&JSV.common.Spectrum.areXScalesCompatible(f,this.graphSets.get(e).getSpectrum(),!1,!0)&&null==g.imageView&&(c?g.setXPixelMovedTo(1.7976931348623157E308,b,0,0):g.setXPixelMovedTo(b,1.7976931348623157E308,0,0))}this.linking=!1}},"JSV.common.GraphSet,~N,~B");c(b,"set2DCrossHairsLinked",
function(a,b,c,f){for(var e=this.graphSets.size();0<=--e;){var g=this.graphSets.get(e);g!==a&&g.set2DXY(b,c,f)}},"JSV.common.GraphSet,~N,~N,~B");c(b,"dialogsToFront",function(a){this.currentGraphSet.dialogsToFront(a)},"JSV.common.Spectrum");c(b,"setColor",function(a,b){null!=b&&this.options.put(a,JU.CU.toRGBHexString(b));switch(a){case JSV.common.ScriptToken.COORDINATESCOLOR:this.coordinatesColor=b;return;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:this.highlightColor=b;255==this.highlightColor.getOpacity255()&&
this.highlightColor.setOpacity255(150);return;case JSV.common.ScriptToken.ZOOMBOXCOLOR:this.zoomBoxColor=b;return;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:this.zoomBoxColor2=b;return;case JSV.common.ScriptToken.BACKGROUNDCOLOR:this.jsvp.setBackgroundColor(this.bgcolor=b);break;case JSV.common.ScriptToken.GRIDCOLOR:this.gridColor=b;break;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:this.integralPlotColor=b;break;case JSV.common.ScriptToken.PEAKTABCOLOR:this.peakTabColor=b;break;case JSV.common.ScriptToken.PLOTCOLOR:for(var c=
this.graphSets.size();0<=--c;)this.graphSets.get(c).setPlotColor0(b);break;case JSV.common.ScriptToken.PLOTAREACOLOR:this.plotAreaColor=b;break;case JSV.common.ScriptToken.SCALECOLOR:this.scaleColor=b;break;case JSV.common.ScriptToken.TITLECOLOR:this.titleColor=b;break;case JSV.common.ScriptToken.UNITSCOLOR:this.unitsColor=b;break;default:JU.Logger.warn("AwtPanel --- unrecognized color: "+a);return}this.taintedAll=!0},"JSV.common.ScriptToken,javajs.api.GenericColor");c(b,"getColor",function(a){switch(a){default:return JU.Logger.error("awtgraphset missing color "+
a),this.BLACK;case JSV.common.ScriptToken.ZOOMBOXCOLOR2:return this.zoomBoxColor2;case JSV.common.ScriptToken.ZOOMBOXCOLOR:return this.zoomBoxColor;case JSV.common.ScriptToken.HIGHLIGHTCOLOR:return this.highlightColor;case JSV.common.ScriptToken.INTEGRALPLOTCOLOR:return this.integralPlotColor;case JSV.common.ScriptToken.GRIDCOLOR:return this.gridColor;case JSV.common.ScriptToken.PEAKTABCOLOR:return this.peakTabColor;case JSV.common.ScriptToken.PLOTAREACOLOR:return this.plotAreaColor;case JSV.common.ScriptToken.SCALECOLOR:return this.scaleColor;
case JSV.common.ScriptToken.TITLECOLOR:return this.titleColor;case JSV.common.ScriptToken.UNITSCOLOR:return this.unitsColor}},"JSV.common.ScriptToken");c(b,"getOverlayLegendData",function(){for(var a=this.currentGraphSet.nSpectra,b=Array(a),c=this.getSpectrumAt(0).getFilePath(),f=this.getSpectrumAt(a-1).getFilePath(),c=null!=c&&null!=f&&!c.equals(f),f=0;f<a;f++){var e=Array(3),g=this.getSpectrumAt(f);this.title=g.getTitle();c&&(this.title=JSV.common.JSVFileManager.getTagName(g.getFilePath())+" - "+
this.title);g=this.getCurrentPlotColor(f);e[0]=new Integer(f+1);e[1]=g;e[2]=" "+this.title;b[f]=e}return b});c(b,"setColorOrFont",function(a,b){if(null==b){for(var c,f=a.elementColors.entrySet().iterator();f.hasNext()&&((c=f.next())||1);)this.setColorOrFont(a,c.getKey());this.setColorOrFont(a,JSV.common.ScriptToken.DISPLAYFONTNAME);this.setColorOrFont(a,JSV.common.ScriptToken.TITLEFONTNAME)}else{switch(b){case JSV.common.ScriptToken.DISPLAYFONTNAME:this.setFontName(b,a.displayFontName);return;case JSV.common.ScriptToken.TITLEFONTNAME:this.setFontName(b,
a.titleFontName);return}this.setColor(b,a.getElementColor(b))}},"JSV.common.ColorParameters,JSV.common.ScriptToken");c(b,"getCurrentPlotColor",function(a){return this.currentGraphSet.getPlotColor(a)},"~N");c(b,"setPrint",function(a,b){null==a?(this.options.putAll(this.optionsSaved),this.optionsSaved=null):(this.printJobTitle=a.title,this.printingFontName=b,this.printGraphPosition=a.position,this.optionsSaved=new java.util.Hashtable,this.optionsSaved.putAll(this.options),this.gridOn=a.showGrid,this.titleOn=
a.showTitle,this.setBoolean(JSV.common.ScriptToken.XSCALEON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.XUNITSON,a.showXScale),this.setBoolean(JSV.common.ScriptToken.YSCALEON,a.showYScale),this.setBoolean(JSV.common.ScriptToken.YUNITSON,a.showYScale))},"JSV.common.PrintLayout,~S");c(b,"setDefaultPrintOptions",function(a){a.showGrid=this.gridOn;a.showXScale=this.getBoolean(JSV.common.ScriptToken.XSCALEON);a.showYScale=this.getBoolean(JSV.common.ScriptToken.YSCALEON);a.showTitle=this.titleOn},
"JSV.common.PrintLayout");c(b,"showDialog",function(a){var b=this.getDialog(a);this.closeAllDialogsExcept(a);if(null!=b&&C(b,"JSV.dialog.JSVDialog"))return b.reEnable();var c=this.getCurrentSpectrumIndex();if(0>c)return this.jsvp.showMessage("To enable "+a+" first select a spectrum by clicking on it.",""+a),null;var f=this.getSpectrum(),e=this.vwr.getDialog(a,f);null==b&&a===JSV.common.Annotation.AType.Measurements&&(b=new JSV.common.MeasurementData(JSV.common.Annotation.AType.Measurements,f));null!=
b&&e.setData(b);this.addDialog(c,a,e);e.reEnable();return e},"JSV.common.Annotation.AType");c(b,"printPdf",function(a,b){var c=!b.layout.equals("landscape");this.print(a,c?b.imageableHeight:b.imageableWidth,c?b.imageableWidth:b.imageableHeight,b.imageableX,b.imageableY,b.paperHeight,b.paperWidth,c,0)},"J.api.GenericGraphics,JSV.common.PrintLayout");c(b,"print",function(a,b,c,f,e,g,j,k,l){this.g2d=this.g2d0;if(0==l)return this.isPrinting=!0,l=!1,C(a,"J.api.GenericGraphics")&&(this.g2d=a,a=this.gMain),
this.printGraphPosition.equals("default")?k?(b=450,c=280):(b=280,c=450):this.printGraphPosition.equals("fit to page")?l=!0:k?(b=450,c=280,f=v(v(j-c)/2),e=v(v(g-b)/2)):(b=280,c=450,e=v(v(j-280)/2),f=v(v(g-450)/2)),this.g2d.translateScale(a,f,e,0.1),this.setTaintedAll(),this.drawGraph(a,a,a,v(c),v(b),l),this.isPrinting=!1,0;this.isPrinting=!1;return 1},"~O,~N,~N,~N,~N,~N,~N,~B,~N");f(b,"keyPressed",function(a,b){if(this.isPrinting)return!1;this.checkKeyControl(a,!0);switch(a){case 27:case 127:case 8:return this.escapeKeyPressed(27!=
a),this.isIntegralDrag=!1,this.setTaintedAll(),this.repaint(),!0}var c=0,f=!1;if(0==b)switch(a){case 37:case 39:this.doMouseMoved(39==a?++this.mouseX:--this.mouseX,this.mouseY);this.repaint();f=!0;break;case 33:case 34:c=33==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;f=!0;break;case 40:case 38:f=40==a?-1:1,null==this.getSpectrumAt(0).getSubSpectra()?this.notifySubSpectrumChange(f,null):(this.advanceSubSpectrum(f),this.setTaintedAll(),this.repaint()),f=!0}else if(this.checkMod(a,2))switch(a){case 40:case 38:case 45:case 61:c=
61==a||38==a?JSV.common.GraphSet.RT2:1/JSV.common.GraphSet.RT2;f=!0;break;case 37:case 39:this.toPeak(39==a?1:-1),f=!0}0!=c&&(this.scaleYBy(c),this.setTaintedAll(),this.repaint());return f},"~N,~N");f(b,"keyReleased",function(a){this.isPrinting||this.checkKeyControl(a,!1)},"~N");f(b,"keyTyped",function(a,b){if(this.isPrinting)return!1;switch(a){case 110:if(0!=b)break;this.normalizeIntegral();return!0;case 26:if(2!=b)break;this.previousView();this.setTaintedAll();this.repaint();return!0;case 25:if(2!=
b)break;this.nextView();this.setTaintedAll();this.repaint();return!0}return!1},"~N,~N");f(b,"mouseAction",function(a,b,c,f,e,g){if(!this.isPrinting)switch(a){case 4:if(!this.checkMod(g,16))break;this.doMousePressed(c,f);break;case 5:this.doMouseReleased(c,f,this.checkMod(g,16));this.setTaintedAll();this.repaint();break;case 1:this.doMouseDragged(c,f);this.repaint();break;case 0:this.jsvp.getFocusNow(!1);if(0!=(g&28)){this.doMouseDragged(c,f);this.repaint();break}this.doMouseMoved(c,f);null!=this.coordStr&&
this.repaint();break;case 2:if(this.checkMod(g,4)){this.jsvp.showMenu(c,f);break}this.ctrlPressed=!1;this.doMouseClicked(c,f,this.updateControlPressed(g))}},"~N,~N,~N,~N,~N,~N");c(b,"checkMod",function(a,b){return(a&b)==b},"~N,~N");c(b,"checkKeyControl",function(a,b){switch(a){case 17:case 157:this.ctrlPressed=b;break;case 16:this.shiftPressed=b}},"~N,~B");c(b,"updateControlPressed",function(a){return this.ctrlPressed=(new Boolean(this.ctrlPressed|(this.checkMod(a,2)||this.checkMod(a,20)))).valueOf()},
"~N");f(b,"mouseEnterExit",function(a,b,c,f){if(f)this.thisWidget=null,this.isIntegralDrag=!1,this.integralShiftMode=0;else try{this.jsvp.getFocusNow(!1)}catch(e){if(D(e,Exception))System.out.println("pd "+this+" cannot focus");else throw e;}},"~N,~N,~N,~B");c(b,"setSolutionColor",function(a){var b=0<=a.indexOf("none"),c=0>a.indexOf("false");if(0>a.indexOf("all"))b=b?-1:this.vwr.getSolutionColor(c),this.getSpectrum().setFillColor(-1==b?null:this.vwr.parameters.getColor1(b));else{a=JSV.common.JSViewer.getInterface("JSV.common.Visible");
for(var f=this.graphSets.size();0<=--f;)this.graphSets.get(f).setSolutionColor(a,b,c)}},"~S");c(b,"setIRMode",function(a,b){for(var c=this.graphSets.size();0<=--c;)this.graphSets.get(c).setIRMode(a,b)},"JSV.common.Spectrum.IRMode,~S");c(b,"closeSpectrum",function(){this.vwr.close("views");this.vwr.close(this.getSourceID());this.vwr.execView("*",!0)});b=G(JSV.common.PanelData,"LinkMode",Enum);b.getMode=c(b,"getMode",function(a){if(a.equals("*"))return JSV.common.PanelData.LinkMode.ALL;for(var b,c=
0,f=JSV.common.PanelData.LinkMode.values();c<f.length&&((b=f[c])||1);c++)if(b.name().equalsIgnoreCase(a))return b;return JSV.common.PanelData.LinkMode.NONE},"~S");w(b,"ALL",0,[]);w(b,"NONE",1,[]);w(b,"AB",2,[]);w(b,"ABC",3,[]);b=G(JSV.common.PanelData,"Mouse",Enum);w(b,"UP",0,[]);w(b,"DOWN",1,[])});n("JSV.common");z(null,"JSV.common.PanelNode",["JU.SB","JSV.common.Parameters"],function(){var b=r(function(){this.legend=this.id=this.jsvp=this.fileName=this.source=this.treeNode=null;this.isSimulation=
this.isView=this.isSelected=!1;this.frameTitle=null;u(this,arguments)},JSV.common,"PanelNode",null);y(b,function(a,b,c,f){this.id=a;this.source=c;this.fileName=b;this.isSimulation=0<=c.getFilePath().indexOf("http://SIMULATION/");this.jsvp=f;null!=f&&(this.pd().getSpectrumAt(0).setId(a),this.frameTitle=f.getTitle())},"~S,~S,JSV.source.JDXSource,JSV.api.JSVPanel");c(b,"setTreeNode",function(a){this.treeNode=a},"JSV.api.JSVTreeNode");c(b,"getTreeNode",function(){return this.treeNode});c(b,"dispose",
function(){this.source.dispose();null!=this.jsvp&&this.jsvp.dispose();this.legend=this.jsvp=this.source=null});c(b,"pd",function(){return this.jsvp.getPanelData()});c(b,"getSpectrum",function(){return this.pd().getSpectrum()});c(b,"setLegend",function(a){null!=this.legend&&this.legend.dispose();return this.legend=a},"JSV.dialog.JSVDialog");f(b,"toString",function(){return(null==this.id?"":this.id+": ")+(null==this.frameTitle?this.fileName:this.frameTitle)});b.findSourceByNameOrId=c(b,"findSourceByNameOrId",
function(a,b){for(var c=b.size();0<=--c;){var f=b.get(c);if(a.equals(f.id)||a.equals(f.source.getSpectra().get(0).sourceID)||f.source.matchesFilePath(a))return f.source}for(c=b.size();0<=--c;)if(f=b.get(c),a.equals(f.fileName))return f.source;return null},"~S,JU.Lst");b.findNodeById=c(b,"findNodeById",function(a,b){if(null!=a)for(var c=b.size();0<=--c;)if(a.equals(b.get(c).id)||a.equals(b.get(c).frameTitle))return b.get(c);return null},"~S,JU.Lst");b.findNode=c(b,"findNode",function(a,b){for(var c=
b.size();0<=--c;)if(b.get(c).jsvp===a)return b.get(c);return null},"JSV.api.JSVPanel,JU.Lst");b.getSpectrumListAsString=c(b,"getSpectrumListAsString",function(a){for(var b=new JU.SB,c=0;c<a.size();c++){var f=a.get(c);f.isView||b.append(" ").append(f.id)}return b.toString().trim()},"JU.Lst");b.isOpen=c(b,"isOpen",function(a,b){if(null!=b)for(var c=a.size();0<=--c&&!a.get(c).source.matchesFilePath(b)&&!b.equals(a.get(c).frameTitle););return-1},"JU.Lst,~S");c(b,"setFrameTitle",function(a){this.frameTitle=
a},"~S");b.getLastFileFirstNode=c(b,"getLastFileFirstNode",function(a){for(var b=a.size(),c=0==b?null:a.get(b-1),b=b-1;0<=--b&&a.get(b).source===c.source;)c=a.get(b);return null==c?null:c.jsvp},"JU.Lst");c(b,"getInfo",function(a){var b=this.pd().getInfo(!1,a);JSV.common.Parameters.putInfo(a,b,"panelId",this.id);JSV.common.Parameters.putInfo(a,b,"panelFileName",this.fileName);JSV.common.Parameters.putInfo(a,b,"panelSource",this.source.getFilePath());return b},"~S")});n("JSV.common");z(null,"JSV.common.Parameters",
["java.util.Hashtable","JSV.common.ScriptToken"],function(){var b=r(function(){this.name=null;this.integralMinY=0.1;this.integralRange=50;this.integralOffset=30;this.integralDrawAll=!1;this.viewOffset=0;this.peakListThreshold=NaN;this.peakListInterpolation="parabolic";this.precision=2;this.htBooleans=null;u(this,arguments)},JSV.common,"Parameters",null);y(b,function(){this.htBooleans=new java.util.Hashtable;this.setBoolean(JSV.common.ScriptToken.TITLEON,!0);this.setBoolean(JSV.common.ScriptToken.ENABLEZOOM,
!0);this.setBoolean(JSV.common.ScriptToken.DISPLAY2D,!0);this.setBoolean(JSV.common.ScriptToken.COORDINATESON,!0);this.setBoolean(JSV.common.ScriptToken.PEAKTABSON,!0);this.setBoolean(JSV.common.ScriptToken.POINTSONLY,!1);this.setBoolean(JSV.common.ScriptToken.GRIDON,!0);this.setBoolean(JSV.common.ScriptToken.XSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.YSCALEON,!0);this.setBoolean(JSV.common.ScriptToken.XUNITSON,!0);this.setBoolean(JSV.common.ScriptToken.YUNITSON,!0)});c(b,"setName",function(a){this.name=
a;return this},"~S");c(b,"getBooleans",function(){return this.htBooleans});c(b,"setBoolean",function(a,b){this.htBooleans.put(a,Boolean.$valueOf(b));return b},"JSV.common.ScriptToken,~B");c(b,"getBoolean",function(a){return Boolean.TRUE===this.htBooleans.get(a)},"JSV.common.ScriptToken");b.isTrue=c(b,"isTrue",function(a){return 0==a.length||Boolean.parseBoolean(a)},"~S");b.getTFToggle=c(b,"getTFToggle",function(a){return a.equalsIgnoreCase("TOGGLE")?null:JSV.common.Parameters.isTrue(a)?Boolean.TRUE:
Boolean.FALSE},"~S");c(b,"setP",function(a,b,c){switch(b){default:return;case JSV.common.ScriptToken.COORDINATESON:case JSV.common.ScriptToken.DISPLAY1D:case JSV.common.ScriptToken.DISPLAY2D:case JSV.common.ScriptToken.ENABLEZOOM:case JSV.common.ScriptToken.GRIDON:case JSV.common.ScriptToken.POINTSONLY:case JSV.common.ScriptToken.PEAKTABSON:case JSV.common.ScriptToken.REVERSEPLOT:case JSV.common.ScriptToken.TITLEON:case JSV.common.ScriptToken.TITLEBOLDON:case JSV.common.ScriptToken.XSCALEON:case JSV.common.ScriptToken.XUNITSON:case JSV.common.ScriptToken.YSCALEON:case JSV.common.ScriptToken.YUNITSON:c=
JSV.common.Parameters.getTFToggle(c);if(null!=c){this.setBoolean(b,c.booleanValue());break}if(null==a)return;c=!a.getBoolean(b);switch(b){case JSV.common.ScriptToken.XSCALEON:this.setBoolean(JSV.common.ScriptToken.XUNITSON,c);a.setBoolean(JSV.common.ScriptToken.XUNITSON,c);break;case JSV.common.ScriptToken.YSCALEON:this.setBoolean(JSV.common.ScriptToken.YUNITSON,c),a.setBoolean(JSV.common.ScriptToken.YUNITSON,c)}this.setBoolean(b,c)}null!=a&&a.setBooleans(this,b)},"JSV.common.PanelData,JSV.common.ScriptToken,~S");
b.isMatch=c(b,"isMatch",function(a,b){return null==a||b.equalsIgnoreCase(a)},"~S,~S");b.putInfo=c(b,"putInfo",function(a,b,c,f){null!=f&&JSV.common.Parameters.isMatch(a,c)&&b.put(null==a?c:a,f)},"~S,java.util.Map,~S,~O")});n("JSV.common");z(["JSV.common.MeasurementData"],"JSV.common.PeakData",["JU.DF","JSV.common.Coordinate","$.PeakPick"],function(){var b=r(function(){this.maxY=this.minY=this.thresh=0;u(this,arguments)},JSV.common,"PeakData",JSV.common.MeasurementData);c(b,"getThresh",function(){return this.thresh});
f(b,"getDataHeader",function(){return this.spec.isHNMR()?JSV.common.PeakData.HNMR_HEADER:B(-1,["peak",this.spec.getXUnits(),this.spec.getYUnits()])});f(b,"getMeasurementListArray",function(){for(var a=Array(this.size()),b=R(-1,[-1E100,1E100,1E100]),c,f=0,e=this.size();0<=--e;f++)c=this.spec.getPeakListArray(this.get(e),b,this.maxY),a[f]=2==c.length?B(-1,[""+(f+1),JU.DF.formatDecimalDbl(c[0],2),JU.DF.formatDecimalDbl(c[1],4)]):B(-1,[""+(f+1),JU.DF.formatDecimalDbl(c[0],4),JU.DF.formatDecimalDbl(c[1],
4),JU.DF.formatDecimalDbl(c[2],2),0==c[3]?"":JU.DF.formatDecimalDbl(c[3],2),0==c[4]?"":JU.DF.formatDecimalDbl(c[4],2),0==c[5]?"":JU.DF.formatDecimalDbl(c[5],2)]);return a},"~S");f(b,"getMeasurementListArrayReal",function(){for(var a=R(this.size(),0),b=R(-1,[-1E100,1E100,1E100]),c=0,f=this.size();0<=--f;c++)a[c]=this.spec.getPeakListArray(this.get(f),b,this.maxY);return a},"~S");c(b,"getInfo",function(a){a.put("interpolation",this.myParams.peakListInterpolation);a.put("threshold",Double.$valueOf(this.myParams.peakListThreshold));
ha(this,JSV.common.PeakData,"getInfo",[a])},"java.util.Map");c(b,"setPeakList",function(a,b,c){this.precision=-2147483648==b?this.spec.getDefaultUnitPrecision():b;var f=this.spec.getXYCoords();if(!(3>f.length)){this.clear();null!=a&&(this.myParams.peakListInterpolation=a.peakListInterpolation,this.myParams.peakListThreshold=a.peakListThreshold);a=this.myParams.peakListInterpolation.equals("parabolic");var e=this.spec.isInverted();this.minY=c.minYOnScale;this.maxY=c.maxYOnScale;var g=c.minXOnScale;
c=c.maxXOnScale;this.thresh=this.myParams.peakListThreshold;Double.isNaN(this.thresh)&&(this.thresh=this.myParams.peakListThreshold=(this.minY+this.maxY)/2);var j=0,k=R(-1,[f[0].getYVal(),j=f[1].getYVal(),0]),l=0;if(e)for(e=2;e<f.length;e++){var n=k[e%3]=f[e].getYVal();if(j<this.thresh&&(k[(e-2)%3]>j&&j<n)&&(j=a?JSV.common.Coordinate.parabolicInterpolation(f,e-1):f[e-1].getXVal(),j>=g||j<=c))if(j=(new JSV.common.PeakPick).setValue(j,n,this.spec,null,0),this.addLast(j),100==++l)break;j=n}else for(e=
2;e<f.length;e++){n=k[e%3]=f[e].getYVal();if(j>this.thresh&&(k[(e-2)%3]<j&&j>n)&&(j=a?JSV.common.Coordinate.parabolicInterpolation(f,e-1):f[e-1].getXVal(),j>=g&&j<=c&&(j=(new JSV.common.PeakPick).setValue(j,n,this.spec,JU.DF.formatDecimalDbl(j,b),j),this.addLast(j),100==++l)))break;j=n}}},"JSV.common.Parameters,~N,JSV.common.ScaleData");b.HNMR_HEADER=B(-1,"peak shift/ppm intens shift/hz diff/hz 2-diff 3-diff".split(" "))});n("JSV.common");z(null,"JSV.common.PeakInfo",["JU.PT"],function(){var b=r(function(){this.px1=
this.px0=this.yMax=this.yMin=this.xMax=this.xMin=0;this.atomKey=this._match=this.spectrum=this.id=this.atoms=this.model=this.title=this.filePathForwardSlash=this.file=this.index=this.type2=this.type=this.stringInfo=null;u(this,arguments)},JSV.common,"PeakInfo",null);y(b,function(a){this.stringInfo=a;this.type=JU.PT.getQuotedAttribute(a,"type");null==this.type&&(this.type="");this.type=this.type.toUpperCase();var b=this.type.indexOf("/");this.type2=0>b?"":JSV.common.PeakInfo.fixType(this.type.substring(this.type.indexOf("/")+
1));this.type=0<=b?JSV.common.PeakInfo.fixType(this.type.substring(0,b))+"/"+this.type2:JSV.common.PeakInfo.fixType(this.type);this.id=JU.PT.getQuotedAttribute(a,"id");this.index=JU.PT.getQuotedAttribute(a,"index");this.file=JU.PT.getQuotedAttribute(a,"file");System.out.println("pi file="+this.file);this.filePathForwardSlash=null==this.file?null:this.file.$replace("\\","/");this.model=JU.PT.getQuotedAttribute(a,"model");a.contains('baseModel=""')||(this.atoms=JU.PT.getQuotedAttribute(a,"atoms"));
this.atomKey=","+this.atoms+",";this.title=JU.PT.getQuotedAttribute(a,"title");this._match=JU.PT.getQuotedAttribute(a,"_match");this.xMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMax"));this.xMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"xMin"));this.yMax=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMax"));this.yMin=JU.PT.parseFloat(JU.PT.getQuotedAttribute(a,"yMin"))},"~S");c(b,"isClearAll",function(){return null==this.spectrum});c(b,"getType",function(){return this.type});c(b,"getAtoms",
function(){return this.atoms});c(b,"getXMax",function(){return this.xMax});c(b,"getXMin",function(){return this.xMin});c(b,"getYMin",function(){return this.yMin});c(b,"getYMax",function(){return this.yMax});c(b,"getX",function(){return(this.xMax+this.xMin)/2});c(b,"getMatch",function(){return this._match});b.fixType=c(b,"fixType",function(a){return a.equals("HNMR")?"1HNMR":a.equals("CNMR")?"13CNMR":a},"~S");f(b,"toString",function(){return this.stringInfo});c(b,"getIndex",function(){return this.index});
c(b,"getTitle",function(){return this.title});c(b,"checkFileIndex",function(a,b,c){return null!=c?0<=this.atomKey.indexOf(c):b.equals(this.index)&&(a.equals(this.file)||a.equals(this.filePathForwardSlash))},"~S,~S,~S");c(b,"checkFileTypeModel",function(a,b,c){return a.equals(this.file)&&this.checkModel(c)&&this.type.endsWith(b)},"~S,~S,~S");c(b,"checkTypeModel",function(a,b){return this.checkType(a)&&this.checkModel(b)},"~S,~S");c(b,"checkModel",function(a){return null!=a&&a.equals(this.model)},"~S");
c(b,"checkType",function(a){return a.endsWith(this.type)},"~S");c(b,"checkTypeMatch",function(a){return this.checkType(a.type)&&(this.checkId(a._match)||this.checkModel(a._match)||0<=this.title.toUpperCase().indexOf(a._match))},"JSV.common.PeakInfo");c(b,"checkId",function(a){return null==a?!1:null!=this.id&&a.toUpperCase().startsWith("ID=")&&a.substring(3).equals(this.id)||(a=a.toUpperCase()).startsWith("INDEX=")&&a.equals("INDEX="+this.index)||a.startsWith("#=")&&a.equals("#="+this.index)},"~S");
c(b,"getModel",function(){return this.model});c(b,"getFilePath",function(){return this.file});c(b,"autoSelectOnLoad",function(){return this.type.startsWith("GC")});c(b,"setPixelRange",function(a,b){this.px0=a;this.px1=b},"~N,~N");c(b,"checkRange",function(a,b){return(2147483647!=a?this.px0<=a&&this.px1>=a:b>=this.xMin&&b<=this.xMax)?Math.abs(b-this.getX()):1E100},"~N,~N");c(b,"getXPixel",function(){return v((this.px0+this.px1)/2)});b.nullPeakInfo=new JSV.common.PeakInfo});n("JSV.common");z(["JSV.common.Measurement"],
"JSV.common.PeakPick",null,function(){var b=G(JSV.common,"PeakPick",JSV.common.Measurement);c(b,"setValue",function(a,b,c,f,e){null==f?(this.set(a,b),this.setPt2(c,!1)):(this.setA(a,b,c,f,!1,!1,0,6),this.value=e,this.setPt2(this.getXVal(),this.getYVal()));return this},"~N,~N,JSV.common.Spectrum,~S,~N")});n("JSV.common");z(["java.util.EventObject"],"JSV.common.PeakPickEvent",null,function(){var b=r(function(){this.peakInfo=this.coord=null;u(this,arguments)},JSV.common,"PeakPickEvent",java.util.EventObject);
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["xNew, xOld xNew, ?, or NONE","sets nearest peak to xOld ppm to a new value; NONE resets (1D NMR only)"]);w(b,"SETX",63,["xNew, xOld xNew, ?, or NONE","sets an old ppm position in the spectrum to a new value; NONE resets (1D NMR only)"]);w(b,"SHIFTX",64,["dx or NONE","shifts the x-axis of a 1D NMR spectrum by the given ppm; NONE resets (1D NMR only)"]);w(b,"SHOWERRORS",65,["shows recent errors"]);w(b,"SHOWINTEGRATION",66,["T","shows an integration listing"]);w(b,"SHOWKEY",67,["T","shows a color key when multiple spectra are displayed"]);
w(b,"SHOWMEASUREMENTS",68,["T","shows a listing of measurements"]);w(b,"SHOWMENU",69,["displays the popup menu"]);w(b,"SHOWPEAKLIST",70,["T","shows a listing for peak picking"]);w(b,"SHOWPROPERTIES",71,["displays the header information of a JDX file"]);w(b,"SHOWSOURCE",72,["displays the source JDX file associated with the selected data"]);w(b,"SPECTRUM",73,["id","displays a specific spectrum, where id is a number 1, 2, 3... or a file.spectrum number such as 2.1"]);w(b,"SPECTRUMNUMBER",74,["n","displays the nth spectrum loaded"]);
w(b,"STACKOFFSETY",75,["percent","sets the y-axis offset of stacked spectra"]);w(b,"STARTINDEX",76,[]);w(b,"SYNCCALLBACKFUNCTIONNAME",77,[]);w(b,"SYNCID",78,[]);w(b,"TEST",79,[]);w(b,"TITLEON",80,["T","turns the title in the bottom left corner on or off"]);w(b,"TITLEBOLDON",81,["T","makes the title bold"]);w(b,"TITLECOLOR",82,["C","sets the color of the title"]);w(b,"TITLEFONTNAME",83,["fontName","sets the title font"]);w(b,"UNITSCOLOR",84,["C","sets the color of the x-axis and y-axis units"]);w(b,
"VERSION",85,[]);w(b,"VIEW",86,['spectrumID, spectrumID, ... Example: VIEW 3.1, 3.2  or  VIEW "acetophenone"',"creates a view of one or more spectra"]);w(b,"XSCALEON",87,["T","set FALSE to turn off the x-axis scale"]);w(b,"XUNITSON",88,["T","set FALSE to turn off the x-axis units"]);w(b,"YSCALE",89,["[ALL] lowValue highValue"]);w(b,"YSCALEON",90,["T","set FALSE to turn off the y-axis scale"]);w(b,"YUNITSON",91,["T","set FALSE to turn off the y-axis units"]);w(b,"WINDOW",92,[]);w(b,"WRITE",93,['[XY,DIF,DIFDUP,PAC,FIX,SQZ,AML,CML,JPG,PDF,PNG,SVG] "filename"',
"writes a file in the specified format"]);w(b,"ZOOM",94,["OUT or PREVIOUS or NEXT or x1,x2 or x1,y1 x2,y2","sets the zoom"]);w(b,"ZOOMBOXCOLOR",95,[]);w(b,"ZOOMBOXCOLOR2",96,[])});n("JSV.common");z(null,"JSV.common.ScriptTokenizer",["JU.PT"],function(){var b=r(function(){this.str=null;this.pt=-1;this.len=0;this.isCmd=!1;this.doCheck=!0;u(this,arguments)},JSV.common,"ScriptTokenizer",null);y(b,function(a,b){this.str=a;this.len=a.length;this.isCmd=b},"~S,~B");b.nextStringToken=c(b,"nextStringToken",
function(a,b){var c=a.nextToken();return b&&'"'==c.charAt(0)&&c.endsWith('"')&&1<c.length?JU.PT.trimQuotes(c):c},"JSV.common.ScriptTokenizer,~B");c(b,"nextToken",function(){this.doCheck&&this.hasMoreTokens();for(var a=this.pt,b='"'==this.str.charAt(this.pt);++this.pt<this.len;){switch(this.str.charAt(this.pt).charCodeAt(0)){case 34:if(b){if(this.isCmd){b=!1;continue}this.pt++;break}this.isCmd&&(b=!0);continue;case 32:if(!this.isCmd&&!b)break;continue;case 59:case 10:if(this.isCmd&&!b)break;continue;
default:continue}break}this.doCheck=!0;return this.str.substring(a,this.pt)});c(b,"hasMoreTokens",function(){for(;++this.pt<this.len;){switch(this.str.charAt(this.pt).charCodeAt(0)){case 32:case 59:case 10:continue}break}this.doCheck=!1;return this.pt<this.len});c(b,"getRemainingScript",function(){return this.str.substring(this.pt)})});n("JSV.common");var Ha=r(function(){this.isub=0;this.title=null;u(this,arguments)},JSV.common,"SubSpecChangeEvent",null);y(Ha,function(b,a){this.isub=b;this.title=
a},"~N,~S");c(Ha,"isValid",function(){return null!=this.title});c(Ha,"getSubIndex",function(){return this.isub});f(Ha,"toString",function(){return this.title});n("JSV.common");z(null,"JSV.common.ViewData",["JSV.common.Coordinate","$.ScaleData"],function(){var b=r(function(){this.thisScale=this.scaleData=null;this.iThisScale=this.nSpectra=0;this.spectra=null;u(this,arguments)},JSV.common,"ViewData",null);y(b,function(a,b,c,f,e,g,j){this.nSpectra=j?1:a.size();this.scaleData=Array(this.nSpectra);for(j=
0;j<this.nSpectra;j++)this.scaleData[j]=new JSV.common.ScaleData(f[j],e[j]);this.init(a,b,c,g)},"JU.Lst,~N,~N,~A,~A,~B,~B");y(b,function(a,b,c,f){this.nSpectra=a.size();var e=a.get(0).getXYCoords().length;this.scaleData=Array(1);this.scaleData[0]=new JSV.common.ScaleData(0,e-1);this.init(a,b,c,f)},"JU.Lst,~N,~N,~B");c(b,"getScaleData",function(){return this.scaleData});c(b,"getScale",function(){return this.thisScale});c(b,"init",function(a,b,c,f){null==a?a=this.spectra:this.spectra=a;this.thisScale=
this.scaleData[this.iThisScale=0];for(var e=0;e<this.scaleData.length;e++)this.scaleData[e].userYFactor=a.get(e).getUserYFactor(),this.scaleData[e].spectrumYRef=a.get(e).getYRef();this.resetScaleFactors();var g=JSV.common.Coordinate.getMinX(a,this),j=JSV.common.Coordinate.getMaxX(a,this),k=JSV.common.Coordinate.getMinYUser(a,this),l=JSV.common.Coordinate.getMaxYUser(a,this);b!=c&&(k=b,l=c,k>l&&(e=k,k=l,l=e));a=a.get(0).isInverted();for(e=0;e<this.scaleData.length;e++)this.scaleData[e].setMinMax(g,
j,k,l),this.scaleData[e].setScale(f,a)},"JU.Lst,~N,~N,~B");c(b,"newSpectrum",function(a){this.init(a,0,0,!1)},"JU.Lst");c(b,"setXRangeForSubSpectrum",function(a){this.setXRange(0,a,this.scaleData[0].minX,this.scaleData[0].maxX,0,a.length-1)},"~A");c(b,"setXRange",function(a,b,c,f,e,g){for(var j=0,k=0,j=e;j<=g;j++)if(e=b[j].getXVal(),e>=c){this.scaleData[a%this.scaleData.length].startDataPointIndex=j;break}for(;j<=g&&!(e=b[j].getXVal(),k++,e>=f);j++);this.scaleData[a%this.scaleData.length].endDataPointIndex=
j;return k},"~N,~A,~N,~N,~N,~N");c(b,"getStartingPointIndex",function(a){return this.scaleData[a%this.scaleData.length].startDataPointIndex},"~N");c(b,"getEndingPointIndex",function(a){return this.scaleData[a%this.scaleData.length].endDataPointIndex},"~N");c(b,"areYScalesSame",function(a,b){a%=this.scaleData.length;b%=this.scaleData.length;return this.scaleData[a].minYOnScale==this.scaleData[b].minYOnScale&&this.scaleData[a].maxYOnScale==this.scaleData[b].maxYOnScale},"~N,~N");c(b,"setScale",function(a,
b,c,f){this.iThisScale=a%this.scaleData.length;this.thisScale=this.scaleData[this.iThisScale];this.thisScale.setXYScale(b,c,f)},"~N,~N,~N,~B");c(b,"resetScaleFactors",function(){for(var a=0;a<this.scaleData.length;a++)this.scaleData[a].spectrumScaleFactor=1});c(b,"scaleSpectrum",function(a,b){if(!(0>=b||a>=this.nSpectra))if(-2==a)this.thisScale.scale2D(b);else if(0>a)for(a=0;a<this.scaleData.length;a++)this.scaleData[a].scaleBy(b);else this.scaleData[a%this.scaleData.length].scaleBy(b)},"~N,~N");
c(b,"getNewScales",function(a,b,c,f){if(b)return this.scaleData;a%=this.scaleData.length;b=(c-this.thisScale.minYOnScale)/(this.thisScale.maxYOnScale-this.thisScale.minYOnScale);f=(f-this.thisScale.minYOnScale)/(this.thisScale.maxYOnScale-this.thisScale.minYOnScale);c=Array(this.scaleData.length);for(var e=0;e<this.scaleData.length;e++)c[e]=0<=a&&e!=a?this.scaleData[e]:new JSV.common.ScaleData;JSV.common.ScaleData.copyScaleFactors(this.scaleData,c);JSV.common.ScaleData.copyYScales(this.scaleData,
c);for(e=0;e<this.scaleData.length;e++)0<=a&&e!=a||(c[e].isShiftZoomedY=!0,c[e].minYOnScale=this.scaleData[e].minYOnScale*(1-b)+b*this.scaleData[e].maxYOnScale,c[e].maxYOnScale=this.scaleData[e].minYOnScale*(1-f)+f*this.scaleData[e].maxYOnScale);return c},"~N,~B,~N,~N")});n("JSV.common");K(JSV.common,"XYScaleConverter");n("JSV.common");G(JSV.common,"ZoomEvent",null);n("JSV.dialog");z(["JSV.api.AnnotationData","JSV.common.Annotation"],"JSV.dialog.JSVDialog",["JU.DF","$.PT","JSV.common.IntegralData",
"$.PeakData","JSV.dialog.DialogManager"],function(){var b=r(function(){this.myParams=this.xyData=this.combo1=this.txt3=this.txt2=this.txt1=this.jsvp=this.dialog=this.manager=this.$spec=this.vwr=this.title=this.type=this.options=this.optionKey=null;this.precision=1;this.showHideButton=this.loc=null;this.defaultVisible=this.isNumeric=this.addApplyBtn=this.addCombo1=this.addClearBtn=!1;this.tableData=this.graphSetKey=this.subType=null;this.addUnits=!1;this.unitPtr=this.formatOptions=this.unitOptions=
null;this.isON=!0;this.lastNorm=1;this.iSelected=this.iRowColSelected=-1;this.skipCreate=!1;this.iColSelected=this.iRowSelected=-1;u(this,arguments)},JSV.dialog,"JSVDialog",JSV.common.Annotation,JSV.api.AnnotationData);f(b,"isDialog",function(){return!0});c(b,"setParams",function(a,b,c){this.title=a=JSV.dialog.DialogManager.fixTitle(a);this.vwr=b;this.$spec=c;this.manager=b.getDialogManager();this.jsvp=b.selectedPanel;this.myParams=b.getPlatformInterface("Parameters").setName("dialogParams");this.subType=
null==c?"!":c.getTypeLabel();this.optionKey=this.type+"_"+this.subType;this.options=this.manager.getDialogOptions();null!=c&&(a=c.getDefaultAnnotationInfo(this.type),this.options.put(this.optionKey,a),this.unitOptions=a[0],this.formatOptions=a[1],this.unitPtr=this.options.get(this.optionKey+"_unitPtr"),null==this.unitPtr&&(this.unitPtr=a[2]));switch(this.type){case JSV.common.Annotation.AType.Integration:this.addApplyBtn=this.defaultVisible=this.addClearBtn=this.isNumeric=!0;break;case JSV.common.Annotation.AType.Measurements:this.defaultVisible=
this.addCombo1=this.addClearBtn=this.isNumeric=!0;break;case JSV.common.Annotation.AType.PeakList:this.defaultVisible=this.addApplyBtn=this.isNumeric=!0;break;case JSV.common.Annotation.AType.Views:this.defaultVisible=!0}this.initDialog();return this},"~S,JSV.common.JSViewer,JSV.common.Spectrum");c(b,"initDialog",function(){this.dialog=this.manager.getDialog(this);this.restoreDialogPosition(this.jsvp,this.getPosXY());this.dialog.setTitle(this.title);this.layoutDialog()});c(b,"layoutDialog",function(){this.dialog.startLayout();
this.addUniqueControls();this.isNumeric&&(this.getUnitOptions(),this.addCombo1&&(this.combo1=this.dialog.addSelectOption("cmbUnits","Units",this.unitOptions,this.unitPtr.intValue(),this.addUnits)),this.addApplyBtn&&this.dialog.addButton("btnApply","Apply"),this.showHideButton=this.dialog.addButton("btnShow","Show"),this.addClearBtn&&this.dialog.addButton("btnClear","Clear"));this.dialog.endLayout();this.checkEnables();this.dialog.setVisible(this.defaultVisible)});c(b,"callbackAD",function(a,b){if(a.equals("FOCUS"))this.eventFocus();
else if(a.equals("tableSelect"))this.tableSelect(b);else if(a.equals("btnClear"))this.clear();else if(a.equals("btnApply"))this.eventApply();else if(a.equals("btnShow")){var c=this.dialog.getText(this.showHideButton);this.eventShowHide(c.equals("Show"))}else if(a.equals("cmbUnits"))this.setPrecision(this.dialog.getSelectedIndex(this.combo1));else if(a.startsWith("txt"))this.eventApply();else if(a.equals("windowClosing"))return this.done(),!0;null!=this.jsvp&&this.jsvp.doRepaint(!0);return!0},"~S,~S");
c(b,"addUniqueControls",function(){},"JSV.dialog.DialogManager");f(b,"getAType",function(){return this.type});f(b,"getGraphSetKey",function(){return this.graphSetKey});f(b,"setGraphSetKey",function(a){this.graphSetKey=a},"~S");f(b,"getSpectrum",function(){return this.$spec});f(b,"getState",function(){return this.isON});f(b,"setState",function(a){this.isON=a},"~B");c(b,"checkEnables",function(){var a=this.checkVisible();this.dialog.setText(this.showHideButton,a?"Hide":"Show")});c(b,"createTable",function(a,
b,c){this.tableData=a;this.dialog.createTable(a,b,c)},"~A,~A,~A");c(b,"setTableSelectionEnabled",function(a){this.dialog.setCellSelectionEnabled(a)},"~B");c(b,"getParameters",function(){return this.myParams});c(b,"showMessage",function(a,b,c){this.manager.showMessageDialog(this.dialog,a,b,c)},"~S,~S,~N");c(b,"setThreshold",function(a){this.dialog.setText(this.txt1,this.getThreasholdText(a))},"~N");c(b,"setComboSelected",function(a){this.dialog.setSelectedIndex(this.combo1,a)},"~N");c(b,"applyFromFields",
function(){this.apply(null)});c(b,"reEnable",function(){this.paramsReEnable();return this});c(b,"dispose",function(){this.dialog.dispose()});c(b,"setVisible",function(a){this.dialog.setVisible(a)},"~B");f(b,"isVisible",function(){return this.dialog.isVisible()});c(b,"selectTableRow",function(a){this.dialog.selectTableRow(a)},"~N");c(b,"repaint",function(){this.dialog.repaint()});c(b,"setFields",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.myParams=this.xyData.getParameters(),
this.setThreshold(this.myParams.peakListThreshold),this.setComboSelected(this.myParams.peakListInterpolation.equals("none")?1:0),this.createData()}});c(b,"setFocus",function(a){this.dialog.setFocus(a)},"~B");c(b,"update",function(a,b,c){this.selectTableRow(-1);switch(this.type){case JSV.common.Annotation.AType.Integration:this.loadData();this.checkEnables();break;case JSV.common.Annotation.AType.Measurements:this.loadData();this.checkEnables();break;case JSV.common.Annotation.AType.PeakList:20<c&&
this.applyFromFields();if(null==this.xyData||null==a||20<c)break;c=0;var f=1E100;a=a.getXVal();var e=this.xyData;b=Math.abs(b/20);for(var g=e.size();0<=--g;){var j=Math.abs(a-e.get(g).getXVal());j<f&&(f=j,c=g)}f<b&&(this.selectTableRow(e.size()-2-c),this.repaint())}},"JSV.common.Coordinate,~N,~N");c(b,"getPeakData",function(){var a=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,this.$spec);a.setPeakList(this.myParams,this.precision,this.jsvp.getPanelData().getView());this.xyData=a;return null});
f(b,"getData",function(){null==this.xyData&&this.createData();return this.xyData});c(b,"setData",function(a){this.myParams=a.getParameters();this.xyData=a},"JSV.api.AnnotationData");f(b,"setSpecShift",function(a){null!=this.xyData&&this.xyData.setSpecShift(a)},"~N");c(b,"setType",function(a){this.type=a;switch(a){case JSV.common.Annotation.AType.Measurements:this.addUnits=!0}},"JSV.common.Annotation.AType");c(b,"apply",function(a){try{switch(this.type){case JSV.common.Annotation.AType.Integration:var b=
Double.parseDouble(a[0]),c=Double.parseDouble(a[1]);this.myParams.integralOffset=b;this.myParams.integralRange=c;this.myParams.integralDrawAll=!1;this.getData().update(this.myParams);break;case JSV.common.Annotation.AType.NONE:return;case JSV.common.Annotation.AType.PeakList:this.skipCreate||(this.setThreshold(NaN),this.createData());this.skipCreate=!1;break;case JSV.common.Annotation.AType.Views:this.vwr.parameters.viewOffset=Double.parseDouble(a[0])}this.loadData();this.checkEnables();this.jsvp.doRepaint(!0)}catch(f){if(!D(f,
Exception))throw f;}},"~A");c(b,"done",function(){null!=this.jsvp&&null!=this.$spec&&this.jsvp.getPanelData().removeDialog(this);null!=this.xyData&&this.xyData.setState(this.isON);this.saveDialogPosition(this.getPosXY());this.dispose();this.jsvp.doRepaint(!0)});c(b,"restoreDialogPosition",function(a,b){if(null!=a){-2147483648==b[0]&&(b[0]=0,b[1]=-20);var c=this.manager.getLocationOnScreen(a),f=a.getHeight();this.loc=E(-1,[Math.max(0,c[0]+b[0]),Math.max(0,c[1]+f+b[1])]);this.dialog.setIntLocation(this.loc)}},
"JSV.api.JSVPanel,~A");c(b,"saveDialogPosition",function(a){try{var b=this.manager.getLocationOnScreen(this.dialog);a[0]+=b[0]-this.loc[0];a[1]+=b[1]-this.loc[1]}catch(c){if(!D(c,Exception))throw c;}},"~A");c(b,"getThreasholdText",function(a){if(Double.isNaN(a)){a=this.jsvp.getPanelData();var b=a.getSpectrum().isInverted()?0.1:0.9,c=a.getClickedCoordinate();a=null==c?(a.getView().minYOnScale*b+a.getView().maxYOnScale)*(1-b):c.getYVal()}return" "+JU.DF.formatDecimalDbl(a,1E3>a?2:-2)},"~N");c(b,"checkVisible",
function(){return this.vwr.pd().getShowAnnotation(this.type)});c(b,"getUnitOptions",function(){var a=this.optionKey+"_format";null==this.options.get(a)&&this.options.put(a,Integer.$valueOf(this.formatOptions[null==this.unitPtr?0:this.unitPtr.intValue()]))});c(b,"eventFocus",function(){null!=this.$spec&&this.jsvp.getPanelData().jumpToSpectrum(this.$spec);switch(this.type){case JSV.common.Annotation.AType.Integration:0<=this.iRowSelected&&(this.iRowSelected++,this.tableCellSelect(-1,-1));break;case JSV.common.Annotation.AType.PeakList:this.createData(),
this.skipCreate=!0}});c(b,"eventApply",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.createData(),this.skipCreate=!0}this.applyFromFields()});c(b,"eventShowHide",function(a){(this.isON=a)&&this.eventApply();this.jsvp.doRepaint(!0);this.checkEnables()},"~B");c(b,"clear",function(){this.setState(!0);null!=this.xyData&&(this.xyData.clear(),this.applyFromFields())});c(b,"paramsReEnable",function(){switch(this.type){case JSV.common.Annotation.AType.PeakList:this.skipCreate=
!0}this.setVisible(!0);this.isON=!0;this.applyFromFields()});c(b,"tableCellSelect",function(a,b){System.out.println(a+" jSVDial "+b);0>a&&(a=v(this.iRowColSelected/1E3),b=this.iRowColSelected%1E3,this.iRowColSelected=-1);var c=this.tableData[a][1],f=1E3*a+b;if(f!=this.iRowColSelected){this.iRowColSelected=f;System.out.println("Setting rc = "+this.iRowColSelected+" "+this.$spec);this.selectTableRow(this.iRowSelected);try{switch(this.type){case JSV.common.Annotation.AType.Integration:this.callback("SHOWSELECTION",
c.toString());this.checkEnables();break;case JSV.common.Annotation.AType.PeakList:try{switch(b){case 6:case 5:case 4:var e=Double.parseDouble(c),g=Double.parseDouble(this.tableData[a+3-b][1]);this.jsvp.getPanelData().setXPointers(this.$spec,e,this.$spec,g);break;default:this.jsvp.getPanelData().findX(this.$spec,Double.parseDouble(c))}}catch(j){if(D(j,Exception))this.jsvp.getPanelData().findX(this.$spec,1E100);else throw j;}this.jsvp.doRepaint(!1);break;case JSV.common.Annotation.AType.OverlayLegend:this.jsvp.getPanelData().setSpectrum(a,
!1)}}catch(k){if(!D(k,Exception))throw k;}}},"~N,~N");c(b,"loadData",function(){var a,b,c;switch(this.type){case JSV.common.Annotation.AType.Integration:null==this.xyData&&this.createData();this.iSelected=-1;a=this.xyData.getMeasurementListArray(null);b=this.xyData.getDataHeader();c=E(-1,[40,65,65,50]);this.createTable(a,b,c);break;case JSV.common.Annotation.AType.Measurements:if(null==this.xyData)break;a=this.xyData.getMeasurementListArray(this.dialog.getSelectedItem(this.combo1).toString());b=this.xyData.getDataHeader();
c=E(-1,[40,65,65,50]);this.createTable(a,b,c);break;case JSV.common.Annotation.AType.PeakList:null==this.xyData&&this.createData();a=this.xyData.getMeasurementListArray(null);b=this.xyData.getDataHeader();c=E(-1,[40,65,50,50,50,50,50]);this.createTable(a,b,c);this.setTableSelectionEnabled(!0);break;case JSV.common.Annotation.AType.OverlayLegend:b=B(-1,["No.","Plot Color","Title"]),a=this.vwr.selectedPanel.getPanelData().getOverlayLegendData(),c=E(-1,[30,60,250]),this.createTable(a,b,c),this.setTableSelectionEnabled(!0)}});
c(b,"createData",function(){switch(this.type){case JSV.common.Annotation.AType.Integration:this.xyData=new JSV.common.IntegralData(this.$spec,this.myParams);this.iSelected=-1;break;case JSV.common.Annotation.AType.PeakList:try{var a=Double.parseDouble(this.dialog.getText(this.txt1));this.myParams.peakListThreshold=a;this.myParams.peakListInterpolation=this.dialog.getSelectedItem(this.combo1).toString();this.myParams.precision=this.precision;var b=new JSV.common.PeakData(JSV.common.Annotation.AType.PeakList,
this.$spec);b.setPeakList(this.myParams,this.precision,this.jsvp.getPanelData().getView());this.xyData=b;this.loadData()}catch(c){if(!D(c,Exception))throw c;}}});c(b,"setPrecision",function(a){this.precision=this.formatOptions[a]},"~N");c(b,"tableSelect",function(a){if("true".equals(this.getField(a,"adjusting")))this.iColSelected=this.iRowSelected=-1,System.out.println("adjusting"+a);else{var b=JU.PT.parseInt(this.getField(a,"index"));switch("ROW COL ROWCOL".indexOf(this.getField(a,"selector"))){case 8:this.iColSelected=
JU.PT.parseInt(this.getField(a,"index2"));case 0:this.iRowSelected=b;System.out.println("r set to "+b);break;case 4:this.iColSelected=b,System.out.println("c set to "+b)}0<=this.iColSelected&&0<=this.iRowSelected&&this.tableCellSelect(this.iRowSelected,this.iColSelected)}},"~S");c(b,"getField",function(a,b){a+="&";var c="&"+b+"=",f=a.indexOf(c);return 0>f?null:a.substring(f+c.length,a.indexOf("&",f+1))},"~S,~S")});n("JSV.exception");z(["java.lang.Exception"],"JSV.exception.JSVException",null,function(){G(JSV.exception,
"JSVException",Exception)});n("JSV.js2d");var $=G(JSV.js2d,"Display",null);$.getFullScreenDimensions=c($,"getFullScreenDimensions",function(b,a){a[0]=b.width;a[1]=b.height},"~O,~A");$.hasFocus=c($,"hasFocus",function(){return!0},"~O");$.requestFocusInWindow=c($,"requestFocusInWindow",function(){},"~O");$.repaint=c($,"repaint",function(){},"~O");$.renderScreenImage=c($,"renderScreenImage",function(){},"J.api.PlatformViewer,~O,~O");$.setTransparentCursor=c($,"setTransparentCursor",function(){},"~O");
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c);0<=a&&(this.currentPanelIndex=a);this.visible=!0},"JSV.common.JSViewer,JSV.api.JSVPanel,JU.Lst");c(b,"getHeight",function(){return null==this.selectedPanel?0:this.selectedPanel.getHeight()});c(b,"getWidth",function(){return null==this.selectedPanel?0:this.selectedPanel.getWidth()});f(b,"isEnabled",function(){return this.enabled});f(b,"isFocusable",function(){return this.focusable});f(b,"isVisible",function(){return this.visible});f(b,"setEnabled",function(a){this.enabled=a},"~B");f(b,"setFocusable",
function(a){this.focusable=a},"~B")});n("JSV.source");z(["JSV.source.JDXHeader","java.util.Hashtable"],"JSV.source.JDXDataObject","JU.DF $.PT JSV.common.Annotation $.Coordinate JSV.exception.JSVException JU.Logger".split(" "),function(){var b=r(function(){this.sourceID="";this.isSimulation=!1;this.blockID=0;this.inlineData=this.filePathForwardSlash=this.filePath=null;this.fileShiftRef=1.7976931348623157E308;this.fileShiftRefDataPt=this.fileShiftRefType=-1;this.deltaX=this.maxY=this.maxX=this.minY=
this.minX=NaN;this.xyCoords=null;this.$isHZtoPPM=this.continuous=!1;this.xIncreases=!0;this.fileLastX=this.fileFirstX=1.7976931348623157E308;this.fileNPoints=-1;this.yFactor=this.xFactor=1.7976931348623157E308;this.nucleusX=null;this.nucleusY="?";this.freq2dY=this.freq2dX=NaN;this.y2DUnits="";this.parent=null;this.yUnits=this.xUnits="";this.yLabel=this.xLabel=null;this.observedNucl=this.varName="";this.observedFreq=1.7976931348623157E308;this.numDim=1;this.nH=0;this.y2D=NaN;u(this,arguments)},JSV.source,
"JDXDataObject",JSV.source.JDXHeader);c(b,"setInlineData",function(a){this.inlineData=a},"~S");c(b,"getInlineData",function(){return this.inlineData});c(b,"setFilePath",function(a){null!=a&&(this.filePathForwardSlash=(this.filePath=a.trim()).$replace("\\","/"))},"~S");c(b,"getFilePath",function(){return this.filePath});c(b,"getFilePathForwardSlash",function(){return this.filePathForwardSlash});c(b,"setBlockID",function(a){this.blockID=a},"~N");c(b,"checkJDXRequiredTokens",function(){var a=1.7976931348623157E308==
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c(b,"setVarName",function(a){this.varName=a},"~S");c(b,"isImaginary",function(){return this.varName.contains("IMAG")});c(b,"setXUnits",function(a){this.xUnits=a},"~S");c(b,"getXUnits",function(){return this.xUnits});c(b,"setYUnits",function(a){a.equals("PPM")&&(a="ARBITRARY UNITS");this.yUnits=a},"~S");c(b,"getYUnits",function(){return this.yUnits});c(b,"setXLabel",function(a){this.xLabel=a},"~S");c(b,"setYLabel",function(a){this.yLabel=a},"~S");c(b,"setObservedNucleus",function(a){this.observedNucl=
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function(a){var b=null;try{b=JSV.source.JDXDataObject.gyroMap.get(a);if(null!=b)return b.doubleValue();for(var c=0;c<a.length&&Character.isDigit(a.charAt(c));)c++;b=JSV.source.JDXDataObject.gyroMap.get(a.substring(0,c));null!=b&&JSV.source.JDXDataObject.gyroMap.put(a,b)}catch(e){if(!D(e,Exception))throw e;}return null==b?NaN:b.doubleValue()},"~S");c(b,"isTransmittance",function(){var a=this.yUnits.toLowerCase();return a.equals("transmittance")||a.contains("trans")||a.equals("t")});c(b,"isAbsorbance",
function(){var a=this.yUnits.toLowerCase();return a.equals("absorbance")||a.contains("abs")||a.equals("a")});c(b,"canSaveAsJDX",function(){return this.getDataClass().equals("XYDATA")});c(b,"canIntegrate",function(){return this.continuous&&(this.isHNMR()||this.isGC())&&this.is1D()});c(b,"isAutoOverlayFromJmolClick",function(){return this.isGC()});c(b,"isGC",function(){return this.dataType.startsWith("GC")||this.dataType.startsWith("GAS")});c(b,"isMS",function(){return this.dataType.startsWith("MASS")||
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this.canConvertTransAbs()&&(this.xUnits.toLowerCase().contains("nanometer")||this.xUnits.equalsIgnoreCase("nm"))&&401>this.getFirstX()&&699<this.getLastX()&&30<=this.xyCoords.length});c(b,"isHZtoPPM",function(){return this.$isHZtoPPM});c(b,"setHZtoPPM",function(a){this.$isHZtoPPM=a},"~B");c(b,"setIncreasing",function(a){this.xIncreases=a},"~B");c(b,"isXIncreasing",function(){return this.xIncreases});c(b,"shouldDisplayXAxisIncreasing",function(){var a=this.dataType.toUpperCase(),b=this.xUnits.toUpperCase();
return a.contains("NMR")&&!a.contains("FID")||a.contains("LINK")&&b.contains("CM")||a.startsWith("IR")||a.contains("INFRA")&&b.contains("CM")||a.contains("RAMAN")&&b.contains("CM")?!1:a.contains("VIS")&&b.contains("NANOMETERS")?!0:this.xIncreases});c(b,"setContinuous",function(a){this.continuous=a},"~B");c(b,"isContinuous",function(){return this.continuous});c(b,"getHeaderRowDataAsArray",function(){var a=8;1.7976931348623157E308!=this.observedFreq&&a++;""!==this.observedNucl&&a++;var b=this.getHeaderRowDataAsArray(!0,
a),a=b.length-a;1.7976931348623157E308!=this.observedFreq&&(b[a++]=B(-1,["##.OBSERVE FREQUENCY",""+this.observedFreq]));""!==this.observedNucl&&(b[a++]=B(-1,["##.OBSERVE NUCLEUS",this.observedNucl]));b[a++]=B(-1,["##XUNITS",this.$isHZtoPPM?"HZ":this.xUnits]);b[a++]=B(-1,["##YUNITS",this.yUnits]);var c=this.xIncreases?this.getFirstX():this.getLastX();b[a++]=B(-1,["##FIRSTX",String.valueOf(this.isHZtoPPM()?c*this.observedFreq:c)]);c=this.xIncreases?this.getLastX():this.getFirstX();b[a++]=B(-1,["##FIRSTY",
String.valueOf(this.xIncreases?this.getFirstY():this.getLastY())]);b[a++]=B(-1,["##LASTX",String.valueOf(this.isHZtoPPM()?c*this.observedFreq:c)]);b[a++]=B(-1,["##XFACTOR",String.valueOf(this.getXFactor())]);b[a++]=B(-1,["##YFACTOR",String.valueOf(this.getYFactor())]);b[a++]=B(-1,["##NPOINTS",String.valueOf(this.xyCoords.length)]);return b});c(b,"getDefaultUnitPrecision",function(){return 2});c(b,"setMeasurementText",function(a){var b=a.getValue();if(Double.isNaN(b))return"";var c=1,e="";if(this.isNMR())if(this.is1D())a=
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a=this.minY;this.minY=-this.maxY;this.maxY=-a;return this});c(b,"getFirstX",function(){return this.xyCoords[0].getXVal()});c(b,"getFirstY",function(){return this.xyCoords[0].getYVal()});c(b,"getLastX",function(){return this.xyCoords[this.xyCoords.length-1].getXVal()});c(b,"getLastY",function(){return this.xyCoords[this.xyCoords.length-1].getYVal()});c(b,"getMinX",function(){return Double.isNaN(this.minX)?this.minX=JSV.common.Coordinate.getMinX(this.xyCoords,0,this.xyCoords.length-1):this.minX});c(b,
"getMinY",function(){return Double.isNaN(this.minY)?this.minY=JSV.common.Coordinate.getMinY(this.xyCoords,0,this.xyCoords.length-1):this.minY});c(b,"getMaxX",function(){return Double.isNaN(this.maxX)?this.maxX=JSV.common.Coordinate.getMaxX(this.xyCoords,0,this.xyCoords.length-1):this.maxX});c(b,"getMaxY",function(){return Double.isNaN(this.maxY)?this.maxY=JSV.common.Coordinate.getMaxY(this.xyCoords,0,this.xyCoords.length-1):this.maxY});c(b,"normalizeSimulation",function(a){this.isNMR()&&this.is1D()&&
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a.setHeaderTable(this.headerTable);a.setXFactor(this.xFactor);a.setYFactor(this.yFactor);a.setXUnits(this.xUnits);a.setYUnits(this.yUnits);a.setXLabel(this.xLabel);a.setYLabel(this.yLabel);a.setXYCoords(this.xyCoords);a.setContinuous(this.continuous);a.setIncreasing(this.xIncreases);a.observedFreq=this.observedFreq;a.observedNucl=this.observedNucl;a.fileShiftRef=this.fileShiftRef;a.fileShiftRefDataPt=this.fileShiftRefDataPt;a.fileShiftRefType=this.fileShiftRefType;a.$isHZtoPPM=this.$isHZtoPPM;a.numDim=
this.numDim;a.nucleusX=this.nucleusX;a.nucleusY=this.nucleusY;a.freq2dX=this.freq2dX;a.freq2dY=this.freq2dY;a.setFilePath(this.filePath);a.nH=this.nH},"JSV.source.JDXDataObject");c(b,"getTypeLabel",function(){return this.isNMR()?this.nucleusX+"NMR":this.dataType});c(b,"getDefaultAnnotationInfo",function(a){var b,c=this.isNMR();switch(a){case JSV.common.Annotation.AType.Integration:return B(-1,[null,E(-1,[1]),null]);case JSV.common.Annotation.AType.Measurements:return a=c?B(-1,["Hz","ppm"]):B(-1,[""]),
b=this.isHNMR()?E(-1,[1,4]):E(-1,[1,3]),B(-1,[a,b,Integer.$valueOf(0)]);case JSV.common.Annotation.AType.PeakList:return a=c?B(-1,["Hz","ppm"]):B(-1,[""]),b=this.isHNMR()?E(-1,[1,2]):E(-1,[1,1]),B(-1,[a,b,Integer.$valueOf(c?1:0)])}return null},"JSV.common.Annotation.AType");c(b,"getPeakListArray",function(a,b,c){var e=a.getXVal();a=a.getYVal();this.isNMR()&&(a/=c);c=Math.abs(e-b[0]);b[0]=e;var g=c+b[1];b[1]=c;var f=g+b[2];b[2]=g;return this.isNMR()?R(-1,[e,a,e*this.observedFreq,20<c*this.observedFreq?
0:c*this.observedFreq,20<g*this.observedFreq?0:g*this.observedFreq,20<f*this.observedFreq?0:f*this.observedFreq]):R(-1,[e,a])},"JSV.common.Measurement,~A,~N");c(b,"finalizeCoordinates",function(){var a=Double.isNaN(this.freq2dX)?this.observedFreq:this.freq2dX,b=1.7976931348623157E308!=a&&this.getXUnits().toUpperCase().equals("HZ");1.7976931348623157E308!=this.fileShiftRef&&(1.7976931348623157E308!=a&&this.dataType.toUpperCase().contains("SPECTRUM")&&0>this.jcampdx.indexOf("JEOL"))&&this.applyShiftReference(b?
a:1,this.fileShiftRef);this.fileFirstX>this.fileLastX&&JSV.common.Coordinate.reverse(this.xyCoords);b&&(JSV.common.Coordinate.applyScale(this.xyCoords,1/a,1),this.setXUnits("PPM"),this.setHZtoPPM(!0))});c(b,"setShiftReference",function(a,b,c){this.fileShiftRef=a;this.fileShiftRefDataPt=0<b?b:1;this.fileShiftRefType=c},"~N,~N,~N");c(b,"isShiftTypeSpecified",function(){return-1!=this.fileShiftRefType});c(b,"applyShiftReference",function(a,b){if(!(this.fileShiftRefDataPt>this.xyCoords.length||0>this.fileShiftRefDataPt)){var c;
switch(this.fileShiftRefType){case 0:b=this.xyCoords[this.fileShiftRefDataPt-1].getXVal()-b*a;break;case 1:b=this.fileFirstX-b*a;break;case 2:b=this.fileLastX+b}for(var e=0;e<this.xyCoords.length;e++)c=this.xyCoords[e],c.setXVal(c.getXVal()-b),this.xyCoords[e]=c}},"~N,~N");b.gyroData=R(-1,[1,42.5774806,2,6.53590131,3,45.4148,3,32.436,6,6.2661,7,16.5483,9,5.9842,10,4.5752,11,13.663,13,10.70839657,14,3.07770646,15,4.3172657,17,5.7742,19,40.07757016,21,3.3631,23,11.26952167,25,2.6083,27,11.1031,29,8.4655,
31,17.2514409,33,3.2717,35,4.1765,37,3.4765,37,5.819,39,3.46,39,1.9893,40,2.4737,41,1.0919,43,2.8688,45,10.3591,47,2.4041,49,2.4048,50,4.2505,51,11.2133,53,2.4115,55,10.5763,57,1.3816,59,10.077,61,3.8114,63,11.2982,65,12.103,67,2.6694,69,10.2478,71,13.0208,73,1.4897,75,7.315,77,8.1571,79,10.7042,81,11.5384,83,1.6442,85,4.1254,87,13.9811,87,1.8525,89,2.0949,91,3.9748,93,10.4523,95,2.7874,97,2.8463,99,9.6294,99,1.9553,101,2.1916,103,1.3477,105,1.957,107,1.7331,109,1.9924,111,9.0692,113,9.4871,113,9.3655,
115,9.3856,115,14.0077,117,15.261,119,15.966,121,10.2551,123,5.5532,123,11.2349,125,13.5454,127,8.5778,129,11.8604,131,3.5159,133,5.6234,135,4.2582,137,4.7634,138,5.6615,139,6.0612,137,4.88,139,5.39,141,2.37,141,13.0359,143,2.319,145,1.429,143,11.59,147,5.62,147,1.7748,149,14631,151,10.5856,153,4.6745,155,1.312,157,1.72,159,10.23,161,1.4654,163,2.0508,165,9.0883,167,1.2281,169,3.531,171,7.5261,173,2.073,175,4.8626,176,3.451,177,1.7282,179,1.0856,180,4.087,181,5.1627,183,1.7957,185,9.7176,187,9.817,
187,0.9856,189,3.3536,191,0.7658,191,0.8319,195,9.2922,197,0.7406,199,7.7123,201,2.8469,203,24.7316,205,24.9749,207,9.034,209,6.963,209,11.7,211,9.16,223,5.95,223,1.3746,225,11.187,227,5.6,229,1.4,231,10.2,235,0.83,237,9.57,239,3.09,243,4.6,1E100]);b.gyroMap=new java.util.Hashtable;for(var b=0,a=JSV.source.JDXDataObject.gyroData.length-1;b<a;b+=2)JSV.source.JDXDataObject.gyroMap.put(""+v(JSV.source.JDXDataObject.gyroData[b]),Double.$valueOf(JSV.source.JDXDataObject.gyroData[b+1]))});n("JSV.source");
z(["java.util.Iterator"],"JSV.source.JDXDecompressor",["JSV.common.Coordinate","JU.Logger"],function(){var b=r(function(){this.ich=this.nPoints=this.yFactor=this.xFactor=0;this.t=null;this.lastX=this.firstX=0;this.maxY=4.9E-324;this.minY=1.7976931348623157E308;this.debugging=!1;this.line=this.xyCoords=null;this.lineLen=0;this.errorLog=null;this.lastDif=-2147483648;this.lastY=this.nptsFound=this.dupCount=0;this.isDIF=!0;u(this,arguments)},JSV.source,"JDXDecompressor",null,java.util.Iterator);y(b,function(a,
b,c,f,e,g){this.t=a;this.firstX=b;this.lastX=c;this.xFactor=f;this.yFactor=e;this.nPoints=g;this.debugging=JU.Logger.isActiveLevel(6)},"JSV.source.JDXSourceStreamTokenizer,~N,~N,~N,~N,~N");y(b,function(a,b){this.line=a.trim();this.lineLen=a.length;this.lastY=b},"~S,~N");c(b,"getMinY",function(){return this.minY});c(b,"getMaxY",function(){return this.maxY});c(b,"decompressData",function(a){this.errorLog=a;a=JSV.common.Coordinate.deltaX(this.lastX,this.firstX,this.nPoints);this.debugging&&this.logError("firstX="+
this.firstX+" lastX="+this.lastX+" xFactor="+this.xFactor+" yFactor="+this.yFactor+" deltaX="+a+" nPoints="+this.nPoints);this.xyCoords=Array(this.nPoints);var b=0,c=0,f=this.lastX,e=this.lastX=this.firstX,g=null,j=0,k=0,l=!1,n=this.t.labelLineNo;try{for(;null!=(this.line=this.t.readLineTrimmed())&&0>this.line.indexOf("##");)if(n++,0!=(this.lineLen=this.line.length)){this.ich=0;var m=this.isDIF,p=this.readSignedFloat()*this.xFactor,k=this.nextValue(k);!m&&0<j&&(e+=a);this.debugging&&this.logError("Line: "+
n+" isCP="+m+"\t>>"+this.line+"<<\n x, xcheck "+e+" "+e/this.xFactor+" "+p/this.xFactor+" "+a/this.xFactor);var r=k*this.yFactor,u=(new JSV.common.Coordinate).set(e,r);if(0==j||!m)this.addPoint(u,j++);else if(j<this.nPoints){var v=this.xyCoords[j-1].getYVal();r!=v&&(this.xyCoords[j-1]=u,this.logError(g+"\n"+this.line+"\nY-value Checkpoint Error! Line "+n+" for y="+r+" yLast="+v));(p==b||p<b!=0>a)&&this.logError(g+"\n"+this.line+"\nX-sequence Checkpoint Error! Line "+n+" order for xCheck="+p+" after prevXCheck="+
b);var w=Math.abs(p-b),y=Math.abs((j-c)*a),z=Math.abs(w-y)/w;this.debugging&&System.err.println("JDXD fracDif = "+p+"\t"+b+"\txcheckDif="+w+"\txiptDif="+y+"\tf="+z);0.5<z&&this.logError(g+"\n"+this.line+"\nX-value Checkpoint Error! Line "+n+" expected "+y+" but X-Sequence Check difference reads "+w)}for(var c=1==j?0:j,b=p,B=0;this.hasNext();){var C=this.ich;this.debugging&&this.logError("line "+n+" char "+C+":"+this.line.substring(0,C)+">>>>"+this.line.substring(this.ich));Double.isNaN(k=this.nextValue(k))?
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case 63:JSV.source.JDXDecompressor.actions[b]=-1;break;case 64:case 65:case 66:case 67:case 68:case 69:case 70:case 71:case 72:case 73:case 97:case 98:case 99:case 100:case 101:case 102:case 103:case 104:case 105:JSV.source.JDXDecompressor.actions[b]=3;break;case 83:case 84:case 85:case 86:case 87:case 88:case 89:case 90:case 115:JSV.source.JDXDecompressor.actions[b]=2}});n("JSV.source");z(["JU.Lst"],"JSV.source.JDXHeader",null,function(){var b=r(function(){this.title="";this.jcampdx="5.01";this.origin=
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function(){var b=r(function(){this.nmrMaxY=NaN;this.errorLog=this.t=this.source=null;this.isZipFile=this.done=this.obscure=!1;this.filePath=null;this.loadImaginary=!0;this.ignorePeakTables=this.ignoreShiftReference=this.isSimulation=!1;this.lastErrPath=null;this.isTabularData=!1;this.blockID=this.nSpec=this.lastSpec=this.firstSpec=0;this.peakData=this.acdMolFile=this.acdAssignments=this.modelSpectrum=this.reader=this.mpr=null;u(this,arguments)},JSV.source,"JDXReader",null,J.api.JmolJDXMOLReader);
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b){if(null!=a&&a.isDirectory())return JSV.source.JDXReader.readBrukerFileDir(a.getFullPath());b=JSV.common.JSVFileManager.getBufferedReaderFromName(c,"##TITLE")}if(!l){b.mark(400);var r=ba(400,"\x00");b.read(r,0,400);b.reset();m=String.instantialize(r);if(m.startsWith("PK"))return b.close(),JSV.source.JDXReader.readBrukerFileZip(null,a.getFullPath());if(0<=m.indexOf("\x00")||0==m.indexOf("##TITLE= Parameter file")||0==m.indexOf("##TITLE= Audit trail"))return b.close(),JSV.source.JDXReader.readBrukerFileDir(a.getParentAsFile().getFullPath());
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c,f)},"JSV.common.Spectrum,JU.Lst,~S,~S,~B");c(b,"logError",function(a){this.errorLog.append(null==this.filePath||this.filePath.equals(this.lastErrPath)?"":this.filePath).append("\n").append(a).append("\n");this.lastErrPath=this.filePath},"~S");c(b,"setVenderSpecificValues",function(a){0<=a.indexOf("JEOL")&&(System.out.println("Skipping ##SHIFTREFERENCE for JEOL "+a),this.ignoreShiftReference=!0);0<=a.indexOf("MestReNova")&&(this.ignorePeakTables=!0)},"~S");c(b,"getValue",function(a){var b=this.isTabularDataLabel(a)?
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a),!0;if(0<this.acdAssignments.size())try{this.mpr.setACDAssignments(a.title,a.getTypeLabel(),this.source.peakCount,this.acdAssignments,this.acdMolFile)}catch(c){if(D(c,Exception))JU.Logger.info("Failed to create peak data: "+c);else throw c;}null!=this.acdMolFile&&JSV.common.JSVFileManager.cachePut("mol",this.acdMolFile)}Float.isNaN(this.nmrMaxY)?1E4<=a.getMaxY()&&a.normalizeSimulation(1E3):a.normalizeSimulation(this.nmrMaxY);this.isSimulation&&a.setSimulated(this.filePath);this.nSpec++;if(0<this.firstSpec&&
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m),k.substring(m+1).trim()));var p=k.substring(0,m).trim(),r=e.indexOf(p);0<=r&&l.setY2DUnits(g.get("##UNITS").get(r))}catch(u){if(!D(u,Exception))throw u;}}m=new JU.Lst;for(l.setHeaderTable(m);!c.equals("##DATATABLE");)JSV.source.JDXReader.addHeader(m,this.t.rawLabel,this.t.getValue()),c=this.t.getLabel();c=!0;r=this.t.flushLine();0<r.trim().indexOf("PEAKS")&&(c=!1);var v=r.indexOf("("),w=r.lastIndexOf(")");if(-1==v||-1==w)throw new JSV.exception.JSVException("Variable List not Found");v=r.substring(v,
w+1);for(r=w=0;r<e.size();r++){var y=e.get(r).trim();-1!=v.indexOf(y)&&(j[w++]=y);if(2==w)break}this.setTabularDataType(l,"##"+(c?"XYDATA":"PEAKTABLE"));if(!this.readNTUPLECoords(l,g,j,f))throw new JSV.exception.JSVException("Unable to read Ntuple Source");l.nucleusX.equals("?")||(b.nucleusX=l.nucleusX);b.nucleusY=l.nucleusY;b.freq2dX=l.freq2dX;b.freq2dY=l.freq2dY;b.y2DUnits=l.y2DUnits;for(r=0;r<a.size();r++)c=a.get(r),v=JSV.source.JDXSourceStreamTokenizer.cleanLabel(c[0]),!v.equals("##TITLE")&&(!v.equals("##DATACLASS")&&
!v.equals("##NTUPLES"))&&m.addLast(c);this.addSpectrum(l,!n);n=!1;l=null}}this.addErrorLogSeparator();this.source.setErrorLog(this.errorLog.toString());JU.Logger.info("NTUPLE MIN/MAX Y = "+f[0]+" "+f[1]);return this.source},"JU.Lst,JSV.source.JDXDataObject,~S");c(b,"readDataLabel",function(a,b,c,f,e){if(!JSV.source.JDXReader.readHeaderLabel(a,b,c,f,e))return!1;b+=" ";if(0<="##MINX ##MINY ##MAXX ##MAXY ##FIRSTY ##DELTAX ##DATACLASS ".indexOf(b))return!1;switch("##FIRSTX  ##LASTX   ##NPOINTS ##XFACTOR ##YFACTOR ##XUNITS  ##YUNITS  ##XLABEL  ##YLABEL  ##NUMDIM  ##OFFSET  ".indexOf(b)){case 0:return a.fileFirstX=
this.parseAFFN(b,c),!1;case 10:return a.fileLastX=this.parseAFFN(b,c),!1;case 20:return a.fileNPoints=Integer.parseInt(c),!1;case 30:return a.setXFactor(this.parseAFFN(b,c)),!1;case 40:return a.yFactor=this.parseAFFN(b,c),!1;case 50:return a.setXUnits(c),!1;case 60:return a.setYUnits(c),!1;case 70:return a.setXLabel(c),!0;case 80:return a.setYLabel(c),!0;case 90:return a.setNumDim(Integer.parseInt(c)),!1;case 100:return a.isShiftTypeSpecified()||a.setShiftReference(this.parseAFFN(b,c),1,1),!1;default:if(17>
b.length)return!0;if(b.equals("##.OBSERVEFREQUENCY "))return a.setObservedFreq(this.parseAFFN(b,c)),!1;if(b.equals("##.OBSERVENUCLEUS "))return a.setObservedNucleus(c),!1;if(b.equals("##$REFERENCEPOINT ")&&!a.isShiftTypeSpecified()){var g=c.indexOf(" ");0<g&&(c=c.substring(0,g));a.setShiftReference(this.parseAFFN(b,c),1,2);return!1}if(b.equals("##.SHIFTREFERENCE ")){if(this.ignoreShiftReference||!a.dataType.toUpperCase().contains("SPECTRUM"))return!1;c=JU.PT.replaceAllCharacters(c,")(","");c=new java.util.StringTokenizer(c,
",");if(4!=c.countTokens())return!1;try{c.nextToken();c.nextToken();var g=Integer.parseInt(c.nextToken().trim()),j=this.parseAFFN(b,c.nextToken().trim());a.setShiftReference(j,g,0)}catch(k){if(!D(k,Exception))throw k;}return!1}return!0}},"JSV.source.JDXDataObject,~S,~S,JU.SB,~B,~B");b.readHeaderLabel=c(b,"readHeaderLabel",function(a,b,c,f,e){switch("##TITLE#####JCAMPDX###ORIGIN####OWNER#####DATATYPE##LONGDATE##DATE######TIME####".indexOf(b+"#")){case 0:return a.setTitle(e||null==c||c.equals("")?"Unknown":
c),!1;case 10:return a.jcampdx=c,a=JU.PT.parseFloat(c),(6<=a||Float.isNaN(a))&&null!=f&&f.append("Warning: JCAMP-DX version may not be fully supported: "+c),!1;case 20:return a.origin=null!=c&&!c.equals("")?c:"Unknown",!1;case 30:return a.owner=null!=c&&!c.equals("")?c:"Unknown",!1;case 40:return a.dataType=c,!1;case 50:return a.longDate=c,!1;case 60:return a.date=c,!1;case 70:return a.time=c,!1}return!0},"JSV.source.JDXHeader,~S,~S,JU.SB,~B");c(b,"setTabularDataType",function(a,b){b.equals("##PEAKASSIGNMENTS")?
a.setDataClass("PEAKASSIGNMENTS"):b.equals("##PEAKTABLE")?a.setDataClass("PEAKTABLE"):b.equals("##XYDATA")?a.setDataClass("XYDATA"):b.equals("##XYPOINTS")&&a.setDataClass("XYPOINTS")},"JSV.source.JDXDataObject,~S");c(b,"processTabularData",function(a,b,c,f){this.setTabularDataType(a,c);a.setHeaderTable(b);if(a.dataClass.equals("XYDATA"))a.checkJDXRequiredTokens(),f||this.decompressData(a,null);else if(a.dataClass.equals("PEAKTABLE")||a.dataClass.equals("XYPOINTS")){a.setContinuous(a.dataClass.equals("XYPOINTS"));
try{this.t.readLineTrimmed()}catch(e){if(!D(e,"java.io.IOException"))throw e;}1.7976931348623157E308!=a.xFactor&&1.7976931348623157E308!=a.yFactor?(b=this.t.getValue(),b=JSV.common.Coordinate.parseDSV(b,a.xFactor,a.yFactor)):b=JSV.common.Coordinate.parseDSV(this.t.getValue(),1,1);a.setXYCoords(b);b=JSV.common.Coordinate.deltaX(b[b.length-1].getXVal(),b[0].getXVal(),b.length);a.setIncreasing(0<b)}else throw new JSV.exception.JSVException("Unable to read JDX file tabular data for line "+this.t.labelLineNo);
},"JSV.source.JDXDataObject,JU.Lst,~S,~B");c(b,"readNTUPLECoords",function(a,b,c,f){var e;if(a.dataClass.equals("XYDATA")){e=b.get("##SYMBOL");var g=e.indexOf(c[0]),j=e.indexOf(c[1]);e=b.get("##VARNAME");a.setVarName(e.get(j).toUpperCase());e=b.get(c="##FACTOR");a.setXFactor(this.parseAFFN(c,e.get(g)));a.setYFactor(this.parseAFFN(c,e.get(j)));e=b.get(c="##LAST");a.fileLastX=this.parseAFFN(c,e.get(g));e=b.get(c="##FIRST");a.fileFirstX=this.parseAFFN(c,e.get(g));e=b.get("##VARDIM");a.fileNPoints=Integer.parseInt(e.get(g));
e=b.get("##UNITS");a.setXUnits(e.get(g));a.setYUnits(e.get(j));null==a.nucleusX&&null!=(e=b.get("##.NUCLEUS"))?(a.setNucleusAndFreq(e.get(0),!1),a.setNucleusAndFreq(e.get(g),!0)):null==a.nucleusX&&(a.nucleusX="?");this.decompressData(a,f);return!0}return a.dataClass.equals("PEAKTABLE")||a.dataClass.equals("XYPOINTS")?(a.setContinuous(a.dataClass.equals("XYPOINTS")),e=b.get("##SYMBOL"),g=e.indexOf(c[0]),j=e.indexOf(c[1]),e=b.get("##UNITS"),a.setXUnits(e.get(g)),a.setYUnits(e.get(j)),a.setXYCoords(JSV.common.Coordinate.parseDSV(this.t.getValue(),
a.xFactor,a.yFactor)),!0):!1},"JSV.source.JDXDataObject,java.util.Map,~A,~A");c(b,"parseAFFN",function(a,b){var c=b.indexOf("E");if(0<c){var f;switch(b.length-c){case 2:case 3:this.logError("Warning - "+a+" value "+b+" is not of the format xxxE[+/-]nn or xxxE[+/-]nnn (spec. 4.5.3) -- warning only; accepted");break;case 4:case 5:if("+"==(f=b.charAt(c+1))||"-"==f)break;default:this.logError("Error - "+a+" value "+b+" is not of the format xxxE[+/-]nn or xxxE[+/-]nnn (spec. 4.5.3) -- "+b.substring(c)+
" ignored!"),b=b.substring(0,c)}}return Double.parseDouble(b)},"~S,~S");c(b,"decompressData",function(a,b){var c=this.errorLog.length();a.setIncreasing(a.fileLastX>a.fileFirstX);a.setContinuous(!0);var f=new JSV.source.JDXDecompressor(this.t,a.fileFirstX,a.fileLastX,a.xFactor,a.yFactor,a.fileNPoints),e=System.currentTimeMillis(),g=f.decompressData(this.errorLog);JU.Logger.debugging&&JU.Logger.debug("decompression time = "+(System.currentTimeMillis()-e)+" ms");a.setXYCoords(g);e=f.getMinY();null!=
b&&(e<b[0]&&(b[0]=e),e=f.getMaxY(),e>b[1]&&(b[1]=e));a.finalizeCoordinates();this.errorLog.length()!=c&&(c=JSV.common.Coordinate.deltaX(a.fileLastX,a.fileFirstX,a.fileNPoints),this.logError(a.getTitle()),this.logError("firstX from Header "+a.fileFirstX),this.logError("lastX from Header "+a.fileLastX+" Found "+f.lastX),this.logError("deltaX from Header "+c),this.logError("Number of points in Header "+a.fileNPoints+" Found "+f.getNPointsFound()));JU.Logger.debugging&&System.err.println(this.errorLog.toString())},
"JSV.source.JDXDataObject,~A");b.addHeader=c(b,"addHeader",function(a,b,c){for(var f=null,e=0;e<a.size();e++)if((f=a.get(e))[0].equals(b)){f[1]=c;return}a.addLast(B(-1,[b,c,JSV.source.JDXSourceStreamTokenizer.cleanLabel(b)]))},"JU.Lst,~S,~S");c(b,"checkCustomTags",function(a,b,c){10<b.length&&(b=b.substring(0,10));null==a?System.out.println(b):this.modelSpectrum=a;b="##$MODELS ##$PEAKS  ##$SIGNALS##$MOLFILE##PEAKASSI##$UVIRASS##$MSFRAGM".indexOf(b);if(0>b)return!1;this.getMpr().set(this,this.filePath,
null);try{switch(this.reader=new java.io.BufferedReader(new java.io.StringReader(c)),b){case 0:this.mpr.readModels();break;case 10:case 20:this.peakData=new JU.Lst;this.source.peakCount+=this.mpr.readPeaks(20==b,this.source.peakCount);break;case 30:this.acdAssignments=new JU.Lst;this.acdMolFile=JU.PT.rep(c,"$$ Empty String","");break;case 40:case 50:case 60:this.acdAssignments=this.mpr.readACDAssignments(a.fileNPoints,40==b);break}}catch(f){if(D(f,Exception))throw new JSV.exception.JSVException(f.getMessage());
throw f;}finally{this.reader=null}return!0},"JSV.common.Spectrum,~S,~S");c(b,"getMpr",function(){return null==this.mpr?this.mpr=JSV.common.JSViewer.getInterface("J.jsv.JDXMOLParser"):this.mpr});f(b,"rd",function(){return this.reader.readLine()});f(b,"setSpectrumPeaks",function(a,b,c){this.modelSpectrum.setPeakList(this.peakData,b,c);this.modelSpectrum.isNMR()&&this.modelSpectrum.setHydrogenCount(a)},"~N,~S,~S");f(b,"addPeakData",function(a){null==this.peakData&&(this.peakData=new JU.Lst);this.peakData.addLast(new JSV.common.PeakInfo(a))},
"~S");f(b,"processModelData",function(){},"~S,~S,~S,~S,~S,~N,~N,~B");f(b,"discardLinesUntilContains",function(a){for(var b;null!=(b=this.rd())&&0>b.indexOf(a););return b},"~S");f(b,"discardLinesUntilContains2",function(a,b){for(var c;null!=(c=this.rd())&&0>c.indexOf(a)&&0>c.indexOf(b););return c},"~S,~S");f(b,"discardLinesUntilNonBlank",function(){for(var a;null!=(a=this.rd())&&0==a.trim().length;);return a});b.VAR_LIST_TABLE=B(-1,["PEAKTABLE   XYDATA      XYPOINTS"," (XY..XY)    (X++(Y..Y)) (XY..XY)    "])});
n("JSV.source");z(["JSV.source.JDXHeader"],"JSV.source.JDXSource",["JU.Lst"],function(){var b=r(function(){this.type=0;this.isCompoundSource=!1;this.jdxSpectra=null;this.errors="";this.filePath=null;this.peakCount=0;this.isView=!1;this.inlineData=null;u(this,arguments)},JSV.source,"JDXSource",JSV.source.JDXHeader);y(b,function(a,b){I(this,JSV.source.JDXSource,[]);this.type=a;this.setFilePath(b);this.headerTable=new JU.Lst;this.jdxSpectra=new JU.Lst;this.isCompoundSource=0!=a},"~N,~S");c(b,"dispose",
function(){this.jdxSpectra=this.headerTable=null});c(b,"getJDXSpectrum",function(a){return this.jdxSpectra.size()<=a?null:this.jdxSpectra.get(a)},"~N");c(b,"addJDXSpectrum",function(a,b,c){null==a&&(a=this.filePath);b.setFilePath(a);null!=this.inlineData&&b.setInlineData(this.inlineData);a=this.jdxSpectra.size();(0==a||!this.jdxSpectra.get(a-1).addSubSpectrum(b,c))&&this.jdxSpectra.addLast(b)},"~S,JSV.common.Spectrum,~B");c(b,"getNumberOfSpectra",function(){return this.jdxSpectra.size()});c(b,"getSpectra",
function(){return this.jdxSpectra});c(b,"getSpectraAsArray",function(){return null==this.jdxSpectra?null:this.jdxSpectra.toArray()});c(b,"getErrorLog",function(){return this.errors});c(b,"setErrorLog",function(a){this.errors=a},"~S");c(b,"setFilePath",function(a){this.filePath=a},"~S");c(b,"getFilePath",function(){return this.filePath});b.createView=c(b,"createView",function(a){var b=new JSV.source.JDXSource(-2,"view");b.isView=!0;for(var c=0;c<a.size();c++)b.addJDXSpectrum(a.get(c).getFilePath(),
a.get(c),!1);return b},"JU.Lst");c(b,"getHeaderRowDataAsArray",function(a,b){null==b&&(b=B(0,0,null));for(var c=this.getHeaderRowDataAsArray(a,b.length),f=b.length;0<=--f;)c[c.length-b.length+f]=b[f];return c},"~B,~A");c(b,"setID",function(a){this.jdxSpectra.get(0).sourceID=a},"~S");c(b,"matchesFilePath",function(a){return this.filePath.equals(a)||this.filePath.$replace("\\","/").equals(a)},"~S");c(b,"setInlineData",function(a){this.inlineData=a;if(null!=this.jdxSpectra)for(var b=this.jdxSpectra.size();0<=
--b;)this.jdxSpectra.get(b).setInlineData(a)},"~S")});n("JSV.source");z(null,"JSV.source.JDXSourceStreamTokenizer",["JU.SB","JU.Logger"],function(){var b=r(function(){this.value=this.rawLabel=this.br=null;this.labelLineNo=0;this.line=null;this.lineNo=0;this.rawLine=null;u(this,arguments)},JSV.source,"JDXSourceStreamTokenizer",null);y(b,function(a){this.br=a},"java.io.BufferedReader");c(b,"peakLabel",function(){return this.nextLabel(!1)});c(b,"getLabel",function(){return this.nextLabel(!0)});c(b,"nextLabel",
function(a){for(this.value=this.rawLabel=null;null==this.line||0==this.line.length;){try{this.readLine();if(null==this.line)return this.line="",null;this.line=this.line.trim()}catch(b){if(D(b,"java.io.IOException"))return this.line="",null;throw b;}if(this.line.startsWith("##"))break;this.line=null}this.rawLine=this.line;var c=this.line.indexOf("=");0>c?(a&&JU.Logger.info("BAD JDX LINE -- no '=' (line "+this.lineNo+"): "+this.line),this.rawLabel=this.line,a||(this.line="")):(this.rawLabel=this.line.substring(0,
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var a=(new JU.SB).append(this.line);0<a.length()&&a.appendC("\n");try{for(;null!=this.readLine()&&!(0<=this.line.indexOf("##")&&this.line.trim().startsWith("##"));)a.append(this.line).appendC("\n")}catch(b){if(D(b,"java.io.IOException"))JU.Logger.info(b.toString());else throw b;}this.value=this.rawLabel.startsWith("##$")?a.toString().trim():JSV.source.JDXSourceStreamTokenizer.trimLines(a);JU.Logger.debugging&&JU.Logger.info(this.value);return this.value});c(b,"readLineTrimmed",function(){this.readLine();
if(null==this.line)return null;if(0>this.line.indexOf("$$"))return this.line.trim();var a=(new JU.SB).append(this.line);return JSV.source.JDXSourceStreamTokenizer.trimLines(a)});c(b,"flushLine",function(){var a=(new JU.SB).append(this.line);this.line=null;return JSV.source.JDXSourceStreamTokenizer.trimLines(a)});c(b,"readLine",function(){this.line=this.br.readLine();this.lineNo++;return this.line});b.trimLines=c(b,"trimLines",function(a){var b=a.length(),c=b-1,f=JSV.source.JDXSourceStreamTokenizer.ptNonWhite(a,
0,b);if(f>=b)return"";for(var e=ba(b-f,"\x00"),g=0;f<b;f++){var j;switch((j=a.charAt(f)).charCodeAt(0)){case 13:if(f<c&&"\n"==a.charAt(f+1))continue;j="\n";break;case 10:0<g&&"\n"!=e[g-1]&&(g-=f-JSV.source.JDXSourceStreamTokenizer.ptNonSpaceRev(a,f)-1);f=JSV.source.JDXSourceStreamTokenizer.ptNonSpace(a,++f,b)-1;break;case 36:if(f<c&&"$"==a.charAt(f+1)){for(f++;++f<b&&0>"\n\r".indexOf(a.charAt(f)););continue}}"\n"==j&&0<g&&"\n"==e[g-1]||(e[g++]=j)}0<g&&"\n"==e[g-1]&&--g;return String.instantialize(e).substring(0,
g).trim()},"JU.SB");b.ptNonWhite=c(b,"ptNonWhite",function(a,b,c){for(;b<c&&Character.isWhitespace(a.charAt(b));)b++;return b},"JU.SB,~N,~N");b.ptNonSpace=c(b,"ptNonSpace",function(a,b,c){for(;b<c&&(" "==a.charAt(b)||"\t"==a.charAt(b));)b++;return b},"JU.SB,~N,~N");b.ptNonSpaceRev=c(b,"ptNonSpaceRev",function(a,b){for(;0<=--b&&(" "==a.charAt(b)||"\t"==a.charAt(b)););return b},"JU.SB,~N")});n("JSV.tree");z(["JSV.api.JSVTree"],"JSV.tree.SimpleTree",["JSV.common.JSVFileManager","$.PanelNode","JSV.tree.SimpleTreeModel",
"$.SimpleTreeNode","$.SimpleTreePath"],function(){var b=r(function(){this.selectedPath=this.vwr=this.spectraTreeModel=this.rootNode=this.si=null;u(this,arguments)},JSV.tree,"SimpleTree",null,JSV.api.JSVTree);y(b,function(a){this.vwr=a;this.rootNode=new JSV.tree.SimpleTreeNode("Spectra",null);this.spectraTreeModel=new JSV.tree.SimpleTreeModel(this.rootNode)},"JSV.common.JSViewer");f(b,"getRootNode",function(){return this.rootNode});c(b,"valueChanged",function(){this.vwr.selectedTreeNode(this.getLastSelectedPathComponent())});
c(b,"getLastSelectedPathComponent",function(){return null==this.selectedPath?null:this.selectedPath.getLastPathComponent()});f(b,"setSelectedPanel",function(a,b){if(null!=b){var c=JSV.common.PanelNode.findNode(b,this.vwr.panelNodes).treeNode;this.setSelectionPath(this.vwr.spectraTree.newTreePath(c.getPath()))}},"JSV.api.ScriptInterface,JSV.api.JSVPanel");c(b,"setSelectionPath",function(a){this.selectedPath=a;this.valueChanged()},"JSV.api.JSVTreePath");f(b,"createTree",function(a,b,c){var f=this.vwr.spectraTree,
e=f.getRootNode(),g=this.vwr.panelNodes,j=JSV.common.JSVFileManager.getTagName(b.getFilePath()),k=new JSV.common.PanelNode(null,j,b,null),l=new JSV.tree.SimpleTreeNode(j,k);k.setTreeNode(l);f.spectraTreeModel.insertNodeInto(l,e,e.getChildCount());for(e=0;e<c.length;e++){var k=new JSV.common.PanelNode(a+"."+(e+1),j,b,c[e]),n=new JSV.tree.SimpleTreeNode(k.toString(),k);k.setTreeNode(n);g.addLast(k);f.spectraTreeModel.insertNodeInto(n,l,l.getChildCount())}this.vwr.selectFrameNode(c[0]);return l},"~N,JSV.source.JDXSource,~A");
f(b,"setPath",function(a){this.setSelectionPath(a)},"JSV.api.JSVTreePath");c(b,"newTreePath",function(a){return new JSV.tree.SimpleTreePath(a)},"~A");f(b,"deleteNodes",function(a){for(var b=0;b<a.size();b++)this.spectraTreeModel.removeNodeFromParent(a.get(b))},"JU.Lst")});n("JSV.tree");z(["java.util.Enumeration"],"JSV.tree.SimpleTreeEnumeration",null,function(){var b=r(function(){this.node=null;this.pt=0;u(this,arguments)},JSV.tree,"SimpleTreeEnumeration",null,java.util.Enumeration);y(b,function(a){this.node=
a},"JSV.tree.SimpleTreeNode");f(b,"hasMoreElements",function(){return this.pt<this.node.$children.size()});f(b,"nextElement",function(){return this.node.$children.get(this.pt++)})});n("JSV.tree");var Na=r(function(){this.rootNode=null;u(this,arguments)},JSV.tree,"SimpleTreeModel",null);y(Na,function(b){this.rootNode=b},"JSV.api.JSVTreeNode");c(Na,"insertNodeInto",function(b,a,c){a.$children.add(c,b);b.prevNode=a},"JSV.api.JSVTreeNode,JSV.api.JSVTreeNode,~N");c(Na,"removeNodeFromParent",function(b){b.prevNode.$children.removeObj(b)},
"JSV.api.JSVTreeNode");n("JSV.tree");z(["JSV.api.JSVTreeNode"],"JSV.tree.SimpleTreeNode",["JU.Lst","JSV.tree.SimpleTreeEnumeration"],function(){var b=r(function(){this.panelNode=null;this.index=0;this.text=this.$children=this.prevNode=null;u(this,arguments)},JSV.tree,"SimpleTreeNode",null,JSV.api.JSVTreeNode);y(b,function(a,b){this.text=a;this.panelNode=b;this.$children=new JU.Lst},"~S,JSV.common.PanelNode");f(b,"getPanelNode",function(){return this.panelNode});f(b,"getIndex",function(){return this.index});
f(b,"setIndex",function(a){this.index=a},"~N");f(b,"children",function(){return new JSV.tree.SimpleTreeEnumeration(this)});f(b,"getChildCount",function(){return this.$children.size()});f(b,"getPath",function(){var a=new JU.Lst,b=this;for(a.addLast(b);null!=(b=b.prevNode);)a.add(0,b);return a.toArray()});f(b,"isLeaf",function(){return null!=this.prevNode&&null!=this.prevNode.prevNode});f(b,"toString",function(){return this.text})});n("JSV.tree");z(["JSV.api.JSVTreePath"],"JSV.tree.SimpleTreePath",
null,function(){var b=r(function(){this.path=null;u(this,arguments)},JSV.tree,"SimpleTreePath",null,JSV.api.JSVTreePath);y(b,function(a){this.path=a},"~A");f(b,"getLastPathComponent",function(){return null==this.path||0==this.path.length?null:this.path[this.path.length-1]})})}ra._coreLoaded=!0})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,
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