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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.$valueOf(JU.CU.colorArgbs[b]))});p("JU");C(null,"JU.DF",["JU.PT",
"$.SB"],function(){var b=H(JU,"DF",null);b.setUseNumberLocalization=c(b,"setUseNumberLocalization",function(a){JU.DF.useNumberLocalization[0]=a?Boolean.TRUE:Boolean.FALSE},"~B");b.formatDecimalDbl=c(b,"formatDecimalDbl",function(a,d){return 2147483647==d||-Infinity==a||Infinity==a||Double.isNaN(a)?""+a:JU.DF.formatDecimal(a,d)},"~N,~N");b.formatDecimal=c(b,"formatDecimal",function(a,d){if(-Infinity==a||(Infinity==a||Double.isNaN(a))||2147483647==d)return""+a;var g=0>a;g&&(a=-a);var b;if(0>d){d=-d;
d>JU.DF.formattingStrings.length&&(d=JU.DF.formattingStrings.length);if(0==a)return JU.DF.formattingStrings[d-1]+"E+0";var c;1>Math.abs(a)?(b=100,c=1E-100*a):(b=-100,c=1E100*a);c=(""+c).toUpperCase();var e=c.indexOf("E");0>e?c=""+a:(b=JU.PT.parseInt(c.substring(e+(c.indexOf("E+")==e?2:1)))+b,c=JU.PT.parseFloat(c.substring(0,e)),c=JU.DF.formatDecimal(c,d-1),c.startsWith("10.")&&(c=JU.DF.formatDecimal(1,d-1),b++));return(g?"-":"")+c+"E"+(0<=b?"+":"")+b}d>=JU.DF.formattingStrings.length&&(d=JU.DF.formattingStrings.length-
1);c=(""+a).toUpperCase();b=c.indexOf(".");if(0>b)return(g?"-":"")+c+JU.DF.formattingStrings[d].substring(1);e=c.indexOf("E-");0<e&&(b=JU.PT.parseInt(c.substring(e+1)),c="0."+"0000000000000000000000000000000000000000".substring(0,-b-1)+c.substring(0,1)+c.substring(2,e),b=1);e=c.indexOf("E");0<e&&(b=JU.PT.parseInt(c.substring(e+1)),c=c.substring(0,1)+c.substring(2,e)+"0000000000000000000000000000000000000000",c=c.substring(0,b+1)+"."+c.substring(b+1),b=c.indexOf("."));var e=c.length,h=d+b+1;if(h<e&&
"5"<=c.charAt(h))return JU.DF.formatDecimal((g?-1:1)*(a+JU.DF.formatAdds[d]),d);var k=c.substring(0,0==d?b:++b),h=JU.SB.newS(k);g&&(k.equals("0.")&&d+2<=e&&c.substring(2,2+d).equals("0000000000000000000000000000000000000000".substring(0,d)))&&(g=!1);for(k=0;k<d;k++,b++)b<e?h.appendC(c.charAt(b)):h.appendC("0");c=(g?"-":"")+h;return Boolean.TRUE.equals(JU.DF.useNumberLocalization[0])?c:c.$replace(",",".")},"~N,~N");b.formatDecimalTrimmed=c(b,"formatDecimalTrimmed",function(a,d){for(var g=JU.DF.formatDecimalDbl(a,
d),b=g.length-1;0<=b&&"0"==g.charAt(b);)b--;return g.substring(0,b+1)},"~N,~N");b.formatDecimalTrimmed0=c(b,"formatDecimalTrimmed0",function(a,d){for(var g=JU.DF.formatDecimalDbl(a,d),b=g.length-1,c=g.indexOf(".")+1;b>c&&"0"==g.charAt(b);)b--;return g.substring(0,b+1)},"~N,~N");b.formattingStrings=A(-1,"0 0.0 0.00 0.000 0.0000 0.00000 0.000000 0.0000000 0.00000000 0.000000000 0.0000000000 0.00000000000 0.000000000000".split(" "));b.formatAdds=R(-1,[0.5,0.05,0.005,5E-4,5E-5,5E-6,5E-7,5E-8,5E-9,5E-10,
5E-11,5E-12,5E-13]);b.useNumberLocalization=A(-1,[Boolean.TRUE])});p("JU");C(["java.lang.Enum"],"JU.Encoding",null,function(){var b=H(JU,"Encoding",Enum);I(b,"NONE",0,[]);I(b,"UTF8",1,[]);I(b,"UTF_16BE",2,[]);I(b,"UTF_16LE",3,[]);I(b,"UTF_32BE",4,[]);I(b,"UTF_32LE",5,[])});p("JU");C(["java.util.ArrayList"],"JU.Lst",null,function(){var b=H(JU,"Lst",java.util.ArrayList);c(b,"addLast",function(a){return this.add1(a)},"~O");j(b,"add",function(a,d){return this.add2(a,d)},"~N,~O");c(b,"removeItemAt",function(a){return this._removeItemAt(a)},
"~N");c(b,"removeObj",function(a){return this._removeObject(a)},"~O")});p("JU");u=v(function(){this.m22=this.m21=this.m20=this.m12=this.m11=this.m10=this.m02=this.m01=this.m00=0;r(this,arguments)},JU,"M34",null);c(u,"setAA33",function(b){var a=b.x,d=b.y,g=b.z;b=b.angle;var l=Math.sqrt(a*a+d*d+g*g),l=1/l,a=a*l,d=d*l,g=g*l,c=Math.cos(b);b=Math.sin(b);l=1-c;this.m00=c+a*a*l;this.m11=c+d*d*l;this.m22=c+g*g*l;var c=a*d*l,e=g*b;this.m01=c-e;this.m10=c+e;c=a*g*l;e=d*b;this.m02=c+e;this.m20=c-e;c=d*g*l;e=
a*b;this.m12=c-e;this.m21=c+e},"JU.A4");c(u,"rotate",function(b){this.rotate2(b,b)},"JU.T3");c(u,"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(u,"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(u,"clear33",function(){this.m00=this.m01=this.m02=this.m10=this.m11=
this.m12=this.m20=this.m21=this.m22=0});c(u,"set33",function(b,a,d){switch(b){case 0:switch(a){case 0:this.m00=d;return;case 1:this.m01=d;return;case 2:this.m02=d;return}break;case 1:switch(a){case 0:this.m10=d;return;case 1:this.m11=d;return;case 2:this.m12=d;return}break;case 2:switch(a){case 0:this.m20=d;return;case 1:this.m21=d;return;case 2:this.m22=d;return}}this.err()},"~N,~N,~N");c(u,"get33",function(b,a){switch(b){case 0:switch(a){case 0:return this.m00;case 1:return this.m01;case 2:return this.m02}break;
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(u,"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(u,"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(u,"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(u,"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(u,"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(u,"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(u,
"mul33",function(b){this.m00*=b;this.m01*=b;this.m02*=b;this.m10*=b;this.m11*=b;this.m12*=b;this.m20*=b;this.m21*=b;this.m22*=b},"~N");c(u,"transpose33",function(){var b=this.m01;this.m01=this.m10;this.m10=b;b=this.m02;this.m02=this.m20;this.m20=b;b=this.m12;this.m12=this.m21;this.m21=b});c(u,"setXRot",function(b){var a=Math.cos(b);b=Math.sin(b);this.m00=1;this.m10=this.m02=this.m01=0;this.m11=a;this.m12=-b;this.m20=0;this.m21=b;this.m22=a},"~N");c(u,"setYRot",function(b){var a=Math.cos(b);b=Math.sin(b);
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(u,"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(u,"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(u,"err",function(){throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");
});p("JU");C(["JU.M34"],"JU.M3",["JU.T3"],function(){var b=H(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,g){this.set33(a,d,g)},"~N,~N,~N");c(b,"getElement",function(a,d){return this.get33(a,d)},"~N,~N");c(b,"setRow",function(a,d,g,b){switch(a){case 0:this.m00=d;this.m01=g;this.m02=b;break;case 1:this.m10=d;this.m11=g;this.m12=b;break;case 2:this.m20=d;this.m21=g;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");j(b,"getRow",function(a,d){this.getRow33(a,d)},"~N,~A");c(b,"setColumn3",function(a,d,g,b){switch(a){case 0:this.m00=d;this.m10=g;this.m20=b;break;case 1:this.m01=d;this.m11=g;this.m21=b;break;case 2:this.m02=d;this.m12=g;
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");j(b,"equals",
function(a){return!z(a,"JU.M3")?!1: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},"~O");j(b,"hashCode",function(){return JU.T3.floatToIntBits(this.m00)^JU.T3.floatToIntBits(this.m01)^JU.T3.floatToIntBits(this.m02)^JU.T3.floatToIntBits(this.m10)^JU.T3.floatToIntBits(this.m11)^JU.T3.floatToIntBits(this.m12)^JU.T3.floatToIntBits(this.m20)^JU.T3.floatToIntBits(this.m21)^JU.T3.floatToIntBits(this.m22)});
c(b,"setZero",function(){this.clear33()});c(b,"set9",function(a,d,g,b,c,e,h,k,m){this.m00=a;this.m01=d;this.m02=g;this.m10=b;this.m11=c;this.m12=e;this.m20=h;this.m21=k;this.m22=m},"~N,~N,~N,~N,~N,~N,~N,~N,~N");j(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,g){var b=Math.sqrt(d*
d+g*g),c=b*a;if(0==c)return this.setScale(1),!1;a=Math.cos(c);c=Math.sin(c);g=-g/b;d/=b;b=a-1;this.m00=1+b*g*g;this.m01=this.m10=b*g*d;this.m20=-(this.m02=c*g);this.m11=1+b*d*d;this.m21=-(this.m12=c*d);this.m22=a;return!0},"~N,~N,~N");c(b,"isRotation",function(){return 0.001>Math.abs(this.determinant3()-1)})});p("JU");C(["JU.M34"],"JU.M4",["JU.T3"],function(){var b=v(function(){this.m33=this.m32=this.m31=this.m30=this.m23=this.m13=this.m03=0;r(this,arguments)},JU,"M4",JU.M34);b.newA16=c(b,"newA16",
function(a){var d=new JU.M4;d.m00=a[0];d.m01=a[1];d.m02=a[2];d.m03=a[3];d.m10=a[4];d.m11=a[5];d.m12=a[6];d.m13=a[7];d.m20=a[8];d.m21=a[9];d.m22=a[10];d.m23=a[11];d.m30=a[12];d.m31=a[13];d.m32=a[14];d.m33=a[15];return d},"~A");b.newM4=c(b,"newM4",function(a){var d=new JU.M4;if(null==a)return d.setIdentity(),d;d.setToM3(a);d.m03=a.m03;d.m13=a.m13;d.m23=a.m23;d.m30=a.m30;d.m31=a.m31;d.m32=a.m32;d.m33=a.m33;return d},"JU.M4");b.newMV=c(b,"newMV",function(a,d){var g=new JU.M4;g.setMV(a,d);return g},"JU.M3,JU.T3");
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,g){if(3>a&&3>d)this.set33(a,d,g);else{(3<a||3<d)&&this.err();switch(a){case 0:this.m03=g;return;case 1:this.m13=g;return;case 2:this.m23=g;return}switch(d){case 0:this.m30=g;break;case 1:this.m31=g;break;case 2:this.m32=g;break;case 3:this.m33=g}}},"~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");j(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,g,b,c){0==a?(this.m00=d,this.m10=g,this.m20=b,this.m30=c):1==a?(this.m01=d,this.m11=g,this.m21=b,this.m31=c):2==a?(this.m02=d,this.m12=g,this.m22=b,this.m32=c):3==a?(this.m03=d,this.m13=g,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,g,b,c,e,
h,k,m,y,j,q,w,s,G,L){this.m00=a;this.m01=d;this.m02=g;this.m03=b;this.m10=c;this.m11=e;this.m12=h;this.m13=k;this.m20=m;this.m21=y;this.m22=j;this.m23=q;this.m30=w;this.m31=s;this.m32=G;this.m33=L},"~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");j(b,"equals",function(a){return!z(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");j(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)});j(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")});p("JU");C(["java.io.OutputStream","javajs.api.GenericOutputChannel"],"JU.OC",["java.io.BufferedWriter",
"$.ByteArrayOutputStream","$.OutputStreamWriter","JU.Base64","$.SB"],function(){var b=v(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.$isBase64=!1;this.bytes=this.os0=null;this.bigEndian=!0;r(this,arguments)},JU,"OC",java.io.OutputStream,javajs.api.GenericOutputChannel);x(b,function(){M(this,JU.OC,[])});x(b,function(a){M(this,JU.OC,[]);this.setParams(null,a,!1,null)},"~S");c(b,"setParams",
function(a,d,g,b){this.bytePoster=a;if(this.$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);g&&(!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");j(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(g){if(!F(g,"java.io.IOException"))throw g;}this.byteCount+=a.length;return this},"~S");j(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(F(d,Exception))System.out.println(d.toString());
else throw d;}this.byteCount=0}});j(b,"writeByteAsInt",function(a){null==this.os&&this.initOS();this.os.writeByteAsInt(a);this.byteCount++},"~N");j(b,"write",function(a,d,g){null==this.os&&this.initOS();0>g&&(g=a.length-d);try{this.os.write(a,d,g)}catch(b){if(!F(b,"java.io.IOException"))throw b;}this.byteCount+=g},"~A,~N,~N");j(b,"writeShort",function(a){this.isBigEndian()?(this.writeByteAsInt(a>>8),this.writeByteAsInt(a)):(this.writeByteAsInt(a),this.writeByteAsInt(a>>8))},"~N");j(b,"writeLong",
function(a){this.isBigEndian()?(this.writeInt(a>>32&4294967295),this.writeInt(a&4294967295)):(this.writeByteAsInt(a>>56),this.writeByteAsInt(a>>48),this.writeByteAsInt(a>>40),this.writeByteAsInt(a>>32),this.writeByteAsInt(a>>24),this.writeByteAsInt(a>>16),this.writeByteAsInt(a>>8),this.writeByteAsInt(a))},"~N");c(b,"cancel",function(){this.isCanceled=!0;this.closeChannel()});j(b,"closeChannel",function(){if(this.closed)return null;try{null!=this.bw?(this.bw.flush(),this.bw.close()):null!=this.os&&
(this.os.flush(),this.os.close()),null!=this.os0&&this.isCanceled&&(this.os0.flush(),this.os0.close())}catch(a){if(!F(a,Exception))throw a;}if(this.isCanceled)return this.closed=!0,null;if(null==this.fileName){if(this.$isBase64){var d=this.getBase64();null!=this.os0&&(this.os=this.os0,this.append(d));this.sb=new JU.SB;this.sb.append(d);this.$isBase64=!1;return this.closeChannel()}return null==this.sb?null:this.sb.toString()}this.closed=!0;if(!this.isLocalFile){d=this.postByteArray();if(null==d||d.startsWith("java.net"))this.byteCount=
-1;return d}var g=d=null,d=self.J2S||Jmol,g="function"==typeof this.fileName?this.fileName:null;if(null!=d){var b=null==this.sb?this.toByteArray():this.sb.toString();null==g?d.doAjax(this.fileName,null,b,null==this.sb):d.applyFunc(this.fileName,b)}return null});c(b,"isBase64",function(){return this.$isBase64});c(b,"getBase64",function(){return JU.Base64.getBase64(this.toByteArray()).toString()});c(b,"toByteArray",function(){return null!=this.bytes?this.bytes:z(this.os,"java.io.ByteArrayOutputStream")?
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}}return JU.Rdr.getBIS(b)},"java.io.BufferedInputStream,~B");b.getZipRoot=c(b,"getZipRoot",function(a){var g=a.indexOf("|");return 0>g?a:a.substring(0,g)},"~S");b.isTar=c(b,"isTar",function(a){a=JU.Rdr.getMagic(a,264);return-1==a[264]&&117==(a[257]&255)&&115==(a[258]&255)&&116==(a[259]&255)&&97==(a[260]&255)&&114==(a[261]&255)},"java.io.BufferedInputStream");b.streamToBytes=c(b,"streamToBytes",function(a){var g=JU.Rdr.getLimitedStreamBytes(a,-1);a.close();return g},"java.io.InputStream");b.streamToString=
c(b,"streamToString",function(a){return String.instantialize(JU.Rdr.streamToBytes(a))},"java.io.InputStream");b.isBinary=c(b,"isBinary",function(a,g){var b=JU.Rdr.getMagic(a,g);if(-1==JU.Rdr.b264[264])for(var c=0;c<g;c++)if(9>b[c])return!0;return!1},"java.io.BufferedInputStream,~N");var a=v(function(){this.stream=null;r(this,arguments)},JU.Rdr,"StreamReader",java.io.BufferedReader);x(a,function(a,g){M(this,JU.Rdr.StreamReader,[new java.io.InputStreamReader(a,null==g?"UTF-8":g)]);this.stream=a},"java.io.BufferedInputStream,~S");
c(a,"getStream",function(){try{this.stream.reset()}catch(a){if(!F(a,"java.io.IOException"))throw a;}return this.stream});b.b264=null});p("JU");u=v(function(){this.z=this.y=this.x=0;r(this,arguments)},JU,"T3d",null,java.io.Serializable);c(u,"set",function(b,a,d){this.x=b;this.y=a;this.z=d},"~N,~N,~N");c(u,"setA",function(b){this.x=b[0];this.y=b[1];this.z=b[2]},"~A");c(u,"setT",function(b){this.x=b.x;this.y=b.y;this.z=b.z},"JU.T3d");c(u,"add2",function(b,a){this.x=b.x+a.x;this.y=b.y+a.y;this.z=b.z+
a.z},"JU.T3d,JU.T3d");c(u,"add",function(b){this.x+=b.x;this.y+=b.y;this.z+=b.z},"JU.T3d");c(u,"sub2",function(b,a){this.x=b.x-a.x;this.y=b.y-a.y;this.z=b.z-a.z},"JU.T3d,JU.T3d");c(u,"sub",function(b){this.x-=b.x;this.y-=b.y;this.z-=b.z},"JU.T3d");c(u,"scale",function(b){this.x*=b;this.y*=b;this.z*=b},"~N");c(u,"scaleAdd",function(b,a,d){this.x=b*a.x+d.x;this.y=b*a.y+d.y;this.z=b*a.z+d.z},"~N,JU.T3d,JU.T3d");c(u,"scaleAdd2",function(b,a,d){this.x=b*a.x+d.x;this.y=b*a.y+d.y;this.z=b*a.z+d.z},"~N,JU.T3d,JU.T3d");
j(u,"hashCode",function(){var b=JU.T3d.doubleToLongBits0(this.x),a=JU.T3d.doubleToLongBits0(this.y),d=JU.T3d.doubleToLongBits0(this.z);return b^b>>32^a^a>>32^d^d>>32});u.doubleToLongBits0=c(u,"doubleToLongBits0",function(b){return 0==b?0:Double.doubleToLongBits(b)},"~N");j(u,"equals",function(b){return!z(b,"JU.T3d")?!1:this.x==b.x&&this.y==b.y&&this.z==b.z},"~O");j(u,"toString",function(){return"{"+this.x+", "+this.y+", "+this.z+"}"});p("JU");C(["JU.T3d"],"JU.V3d",null,function(){var b=H(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,g=this.z*a.x-this.x*a.z,b=this.x*a.y-this.y*a.x,d=Math.sqrt(d*d+g*g+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())})});p("J.adapter.readers.molxyz");C(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.MolReader","java.util.Hashtable JU.BS $.Lst $.PT J.adapter.smarter.Atom J.api.JmolAdapter JU.Logger".split(" "),function(){var b=v(function(){this.haveAtomSerials=!1;this.allow2D=!0;this.iatom0=0;this.vr=null;this.atomCount=0;this.bsDeleted=this.atomData=null;this.is3D=this.fixN=this.haveNonzeroZ=!1;this.nC=this.nH=
this.nDouble=0;r(this,arguments)},J.adapter.readers.molxyz,"MolReader",J.adapter.smarter.AtomSetCollectionReader);j(b,"initializeReader",function(){this.fixN=this.checkFilterKey("FIXN")});j(b,"checkLine",function(){var a=this.line.startsWith("$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});j(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&&this.asc.getBSAtoms(-1).andNot(this.bsDeleted);
this.isTrajectory=!1;this.finalizeReaderASCR()});c(b,"check2D3D",function(){this.haveNonzeroZ?this.is2D&&(this.is2D=this.optimize2D=!1):!this.is2D&&!this.is3D&&(0<this.nC&&0==this.nH&&0!=this.nDouble)&&(this.is2D=!0);if(this.is2D){if(!this.allow2D)throw new Exception("File is 2D, not 3D");this.set2D()}});c(b,"processMolSdHeader",function(){var a="",d=this.line.trim();this.asc.setCollectionName(d);a+=this.line+"\n";this.rd();if(null!=this.line){var a=a+(this.line+"\n"),g=22<=this.line.length?this.line.substring(20,
22):null;this.is3D="3D".equals(g);this.is2D=!this.is3D&&("2D".equals(g)||this.line.startsWith("JME "));this.rd();null!=this.line&&(this.line=this.line.trim(),a+=this.line+"\n",JU.Logger.info(a),this.checkCurrentLineForScript(),this.asc.setInfo("fileHeader",a),this.newAtomSet(d))}});c(b,"processCtab",function(a){a&&this.discardLinesUntilStartsWith("$CTAB");null!=this.rd()&&(0<=this.line.indexOf("V3000")?(this.optimize2D=this.is2D&&!this.noHydrogens,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 g=0;g<a;++g){this.rd();var b=this.line.length,c,e,h,k,m=0,y=0,j=-2147483648;e=this.parseFloatRange(this.line,0,10);h=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",y=1),39<=b&&(b=this.parseIntRange(this.line,36,39),1<=b&&7>=b&&(m=4-b),b=this.parseIntRange(this.line,34,36),0!=b&&(-3<=b&&4>=b)&&(y=J.api.JmolAdapter.getNaturalIsotope(J.api.JmolAdapter.getElementNumber(c))+b),-2147483648==j&&this.haveAtomSerials&&(j=g+1)));this.addMolAtom(j,y,c,m,e,h,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(g=0;g<d;++g){0<g&&this.rd();h=0;c=this.line.substring(0,3).trim();e=this.line.substring(3,6).trim();k=this.parseIntRange(this.line,6,9);if((this.is2D||!this.is3D)&&1==k&&12<=this.line.length)h=this.parseIntRange(this.line,9,12);0!=h&&!this.is3D&&(this.is2D=!0);k=this.fixOrder(k,h);this.haveAtomSerials?this.asc.addNewBondFromNames(c,e,k):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(c)-1,this.iatom0+this.parseIntStr(e)-1,k)}g=new java.util.Hashtable;c=new JU.Lst;for(this.rd();null!=
this.line&&0!=this.line.indexOf("$$$$");)0==this.line.indexOf(">")?this.readMolData(g,c):this.line.startsWith("M  ISO")?this.readIsotopes():this.rd();null!=this.atomData&&(e=g.get("atom_value_name"),g.put(null==e?"atom_values":e.toString(),this.atomData));g.isEmpty()||(this.asc.setCurrentModelInfo("molDataKeys",c),this.asc.setCurrentModelInfo("molData",g))},"~N,~N");c(b,"readAtomValues",function(){this.atomData=Array(this.atomCount);for(var a=this.atomData.length;0<=--a;)this.atomData[a]="";for(;0==
this.line.indexOf("V  ");){a=this.parseIntAt(this.line,3);if(1>a||a>this.atomCount){JU.Logger.error("V  nnn does not evalute to a valid atom number: "+a);break}var d=this.line.substring(6).trim();this.atomData[a-1]=d;this.rd()}});c(b,"readIsotopes",function(){var a=this.parseIntAt(this.line,6);try{for(var d=this.asc.getLastAtomSetAtomIndex(),g=0,b=9;g<a;g++){var c=this.parseIntAt(this.line,b),e=this.asc.atoms[c+d-1],h=this.parseIntAt(this.line,b+4),b=b+8,k=JU.PT.replaceAllCharacters(e.elementSymbol,
"0123456789","");17==h&&k.equals("C")?e.elementSymbol="N":5==h&&k.equals("H")?this.deleteAtom(e):e.elementSymbol=""+h+k}}catch(m){}this.rd()});c(b,"deleteAtom",function(a){null==this.bsDeleted&&(this.bsDeleted=new JU.BS);this.bsDeleted.set(a.index)},"J.adapter.smarter.Atom");c(b,"readMolData",function(a,d){for(var g=this.asc.atoms,b=JU.PT.trim(this.line,"> <").toLowerCase(),c="",e=null;null!=this.rd()&&!this.line.equals("$$$$")&&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 h=0;if(b.toUpperCase().contains("_PARTIAL_CHARGES")){try{for(var e=JU.PT.parseFloatArray(c),k=this.asc.getLastAtomSetAtomIndex(),m=this.asc.ac;k<m;k++)g[k].partialCharge=0;for(var y=0,k=D(e[y++]);0<=--k;){var j=D(e[y++])+this.iatom0-1,q=e[y++];g[j].partialCharge=q;h++}}catch(w){k=this.asc.getLastAtomSetAtomIndex();for(m=this.asc.ac;k<m;k++)g[k].partialCharge=0;JU.Logger.error("error reading "+
b+" field -- partial charges cleared")}JU.Logger.info(h+" partial charges read")}else if(b.toUpperCase().contains("ATOM_NAMES")){h=0;try{for(var s=JU.PT.getTokens(c),y=0,k=this.parseIntStr(s[y++]);0<=--k;){for(var G;-2147483648==(G=this.parseIntStr(s[y++])););var j=G+this.iatom0-1,L=s[y++];L.equals(".")||(g[j].atomName=L);h++}}catch(O){JU.Logger.error("error reading "+b+" field")}JU.Logger.info(h+" atom names read")}},"java.util.Map,JU.Lst");c(b,"addMolAtom",function(a,d,g,b,c,e,h){"H".equals(g)?
this.nH++:"C".equals(g)&&this.nC++;this.haveNonzeroZ=(new Boolean(this.haveNonzeroZ|0!=h)).valueOf();switch(d){case 0:break;case 1:g="1H";break;case 2:g="2H";break;case 3:g="3H";break;default:g=d+g}d=new J.adapter.smarter.Atom;d.elementSymbol=g;d.formalCharge=b;this.setAtomCoordXYZ(d,c,e,h);-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,"fixOrder",function(a,d){switch(a){default:case 0:case -10:return 1;
case 1:switch(d){case 1:return this.is2D=!0,1025;case 3:case 6:return this.is2D=!0,1041;case 2:case 4:return this.is2D=!0,1057}break;case 2:case 3:this.nDouble++;break;case 4:return 515;case 5:return 66;case 6:return 513;case 7:return 514;case 8:case 9:return 33;case 14:return 4;case 15:return 5;case 16:return 6}return a},"~N,~N");c(b,"addMolBond",function(a,d,g,b){g=this.fixOrder(g,b);return this.haveAtomSerials?this.asc.addNewBondFromNames(a,d,g):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(a)-
1,this.iatom0+this.parseIntStr(d)-1,g)},"~S,~S,~N,~N")});p("J.adapter.readers.molxyz");C(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["JU.Logger"],function(){var b=H(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);j(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});j(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 g=this.getTokens();if(4>g.length)JU.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var b=this.addAtomXYZSymName(g,1,null,null);this.setElementAndIsotope(b,g[0]);var c=4;switch(g.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=g[4].indexOf("."))b.partialCharge=this.parseFloatStr(g[4]);else{var e=this.parseIntStr(g[4]);-2147483648!=e&&(b.formalCharge=e)}switch(g.length){case 5:continue;case 6:b.radius=this.parseFloatStr(g[5]);
continue;case 9:b.atomSerial=this.parseIntStr(g[8])}c++;default:var e=this.parseFloatStr(g[c++]),h=this.parseFloatStr(g[c++]),g=this.parseFloatStr(g[c++]);if(Float.isNaN(e)||Float.isNaN(h)||Float.isNaN(g))continue;this.asc.addVibrationVector(b.index,e,h,g)}}}},"~N")});p("J.adapter.smarter");C(["JU.P3"],"J.adapter.smarter.Atom",["JU.AU","$.Lst","$.V3"],function(){var b=v(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;r(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);x(b,function(){M(this,J.adapter.smarter.Atom,[]);this.set(NaN,NaN,
NaN)});c(b,"addTensor",function(a,d,g){if(null==a)return null;if(g||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(F(d,"CloneNotSupportedException"))return null;throw d;}null!=this.vib&&(a.vib=z(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 g=this.tensors.size();0<=--g;)a.tensors.addLast(this.tensors.get(g).copyTensor())}return a});c(b,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=this.atomName){for(var a=this.atomName.length,d=0,g=String.fromCharCode(0);d<a&&!J.adapter.smarter.Atom.isValidSymChar1(g=this.atomName.charAt(d));)++d;switch(a-d){case 0:break;default:if(a=this.atomName.charAt(d+1),J.adapter.smarter.Atom.isValidSymNoCase(g,a)){this.elementSymbol=""+g+a;break}case 1:J.adapter.smarter.Atom.isValidSym1(g)&&
(this.elementSymbol=""+g)}}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 g=d.newCloneAtom(this);g.setT(a);return g},"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])});p("J.adapter.smarter");C(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["J.api.JmolAdapter"],function(){var b=v(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;r(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);x(b,function(a){this.ac=a.ac;this.atoms=a.atoms;this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");j(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});j(b,"getAtomSetIndex",function(){return this.atom.atomSetIndex});j(b,"getSymmetry",function(){return this.atom.bsSymmetry});j(b,"getAtomSite",function(){return this.atom.atomSite+1});j(b,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});j(b,"getElementNumber",function(){return 0<this.atom.elementNumber?
this.atom.elementNumber:J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});j(b,"getAtomName",function(){return this.atom.atomName});j(b,"getFormalCharge",function(){return-2147483648==this.atom.formalCharge?0:this.atom.formalCharge});j(b,"getPartialCharge",function(){return this.atom.partialCharge});j(b,"getTensors",function(){return this.atom.tensors});j(b,"getRadius",function(){return this.atom.radius});j(b,"getBondRadius",function(){return this.atom.bondingRadius});j(b,"getVib",
function(){return null==this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});j(b,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1094713365!=this.atom.vib.z?0:D(this.atom.vib.x)});j(b,"getBfactor",function(){return this.atom.bfactor});j(b,"getOccupancy",function(){return 100*this.atom.foccupancy});j(b,"getIsHetero",function(){return this.atom.isHetero});j(b,"getSerial",function(){return this.atom.atomSerial});j(b,"getChainID",function(){return this.atom.chainID});
j(b,"getAltLoc",function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});j(b,"getGroup3",function(){return this.atom.group3});j(b,"getSequenceNumber",function(){return this.atom.sequenceNumber});j(b,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});j(b,"getXYZ",function(){return this.atom});j(b,"getElement",function(){return this.getElementNumber()&127});j(b,"getIsotope",function(){return this.getElementNumber()>>7})});
p("J.adapter.smarter");C(["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=v(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;r(this,arguments)},J.adapter.smarter,"AtomSetCollection",null);P(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});x(b,
function(a,d,g,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!=g){d=0;this.readerList=new JU.Lst;for(b=0;b<g.length;b++)null!=
g[b]&&(0<g[b].ac||null!=g[b].reader&&g[b].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(d++,g[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 g=0;g<d;g++){var b=a.get(g);z(b,"JU.Lst")?this.appendAtomSetCollectionList(b):this.appendAtomSetCollection(g,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),g=0<a&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),a=g?Array(a):null,b=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,e=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var h=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=b&&(h=J.adapter.smarter.AtomSetCollection.fixPeriodic(h,b[c]));d[e]=h;g&&(a[e]=this.atoms[c].vib);
e++}if(g){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 g=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(g+b)}for(var b=0,c=this.atomSetCount,e=0;e<d.atomSetCount;e++){this.newAtomSet();var h=(this.atomSetAuxiliaryInfo[this.iSet]=d.atomSetAuxiliaryInfo[e]).get("PDB_CONECT_firstAtom_count_max");null!=h&&(h[0]+=g);this.setCurrentModelInfo("title",d.collectionName);this.setAtomSetName(d.getAtomSetName(e));for(h=0;h<d.atomSetAtomCounts[e];h++)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[e]}for(b=0;b<d.bondCount;b++)e=d.bonds[b],this.addNewBondWithOrder(e.atomIndex1+g,e.atomIndex2+g,e.order);for(b=JV.JC.globalBooleans.length;0<=--b;)d.getGlobalBoolean(b)&&this.setGlobalBoolean(b);for(b=0;b<d.structureCount;b++)g=d.structures[b],this.addStructure(g),g.modelStartEnd[0]+=c,g.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 g=JU.AU.createArrayOfArrayList(this.atomSetCount),a=0;a<this.atomSetCount;a++)g[a]=new JU.Lst;for(a=0;a<this.ac;a++)g[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=g[a].size();0<=--c;){var e=this.atoms[--b]=g[a].get(c);d[e.index]=b;e.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++)g=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),null!=g&&(g[0]=d[g[0]],g[1]=this.atomSetAtomCounts[a])});c(b,"reverseSets",function(a,d){for(var g=JU.AU.createArrayOfArrayList(this.atomSetCount),
b=0;b<this.atomSetCount;b++)g[b]=new JU.Lst;for(b=0;b<d;b++){if(0>a[b].atomSetIndex)return;g[a[b].atomSetIndex].addLast(a[b])}for(b=this.atomSetCount;0<=--b;)for(var c=g[b].size();0<=--c;)a[--d]=g[b].get(c)},"~A,~N");c(b,"reverseObject",function(a){for(var d=this.atomSetCount,g=B(d/2);0<=--g;)JU.AU.swap(a,g,d-1-g)},"~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,g=B(d/2);0<=--g;)JU.AU.swapInt(a,
g,d-1-g)},"~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 g=Array(this.atomSetCount);for(d=0;d<this.atomSetCount;d++)g[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>g[b=this.atoms[d].atomSetIndex].indexOf(c))g[b]+=c}a=a?"altLocs":"insertionCodes";for(d=0;d<this.atomSetCount;d++)0<g[d].length&&this.setModelInfoForSet(a,
g[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 g=0;g<d;g++){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 g=
0<a?a:this.getLastAtomSetAtomCount(),b=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<g;++c){var e=this.newCloneAtom(this.atoms[b++]);null!=d&&e.setT(d[c])}return g},"~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,g=this.atomSymbolicMap.entrySet().iterator();g.hasNext()&&((d=g.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,g){var b=null;0<=a&&(a<this.ac&&0<=d&&d<this.ac&&a!=d)&&(b=new J.adapter.smarter.Bond(a,d,g),this.addBond(b));return b},"~N,~N,~N");c(b,"addNewBondFromNames",function(a,d,g){return this.addNewBondWithOrderA(this.getAtomFromName(a),this.getAtomFromName(d),g)},"~S,~S,~N");c(b,"addNewBondWithOrderA",function(a,d,g){return null!=a&&null!=d?this.addNewBondWithOrder(a.index,
d.index,g):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 g=this.structures[d];-1==g.modelStartEnd[0]&&(g.modelStartEnd[0]=0,g.modelStartEnd[1]=this.atomSetCount-1);this.bsStructuredModels.setBits(g.modelStartEnd[0],g.modelStartEnd[1]+1);if(0!=
g.strandCount){var g=g.structureID+" "+g.modelStartEnd[0],b=a.get(g),b=(null==b?0:b.intValue())+1;a.put(g,Integer.$valueOf(b))}}for(d=0;d<this.structureCount;d++)g=this.structures[d],1==g.strandCount&&(g.strandCount=a.get(g.structureID+" "+g.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,g,b,c){if(c){c=this.atoms[a].atomSite;for(var e=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==e;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,d,g,b)}else this.addVibrationVector(a,d,g,b)},"~N,~N,~N,~N,~B");c(b,"addVibrationVector",function(a,d,g,b){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(d,g,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,g){this.haveAnisou=!0;a.anisoBorU=d;d[6]=g},"J.adapter.smarter.Atom,~A,~N");c(b,"setU",function(a,d,g){var b=a.anisoBorU;null==b&&this.setAnisoBorU(a,b=K(8,0),8);b[d]=g},"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),g=d.size(),b=this.ac;0<=
--b;)this.atoms[b].partialCharge=d.get(b%g).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),g=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&null!=d&&d.length<g||a.length<g)this.errorMessage=
"File cannot be loaded as a trajectory";else{for(var g=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?g: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,g){var b=this.getAtomSetAuxiliaryInfoValue(g,"modelProperties");null==b&&this.setModelInfoForSet("modelProperties",b=new java.util.Properties,g);b.put(a,d);a.startsWith(".")&&b.put(a.substring(1),d)},"~S,~S,~N");c(b,"setAtomProperties",function(a,d,g){"string"==typeof d&&!d.endsWith("\n")&&(d+="\n");0>g&&(g=this.iSet);var b=this.getAtomSetAuxiliaryInfoValue(g,"atomProperties");
null==b&&this.setModelInfoForSet("atomProperties",b=new java.util.Hashtable,g);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,g){0>g||(null==this.atomSetAuxiliaryInfo[g]&&(this.atomSetAuxiliaryInfo[g]=new java.util.Hashtable),null==d?this.atomSetAuxiliaryInfo[g].remove(a):this.atomSetAuxiliaryInfo[g].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,g,b,c){this.setAtomSetModelProperty("FreqValue",b);b+=" "+(null==c?"cm^-1":c);c=(null==g?"":g+" ")+b;this.setAtomSetName(c);this.setAtomSetModelProperty("Frequency",b);this.setAtomSetModelProperty("Mode",""+a);this.setModelInfoForSet("vibrationalMode",Integer.$valueOf(a),this.iSet);null!=g&&this.setAtomSetModelProperty("FrequencyLabel",g);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]=A(-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 g=this.atomSetAtomCounts[d],b=this.atomSetAtomIndexes[d];a.set(0,0,0);for(var c=b+g;--c>=b;)a.add(this.atoms[c]);a.scale(1/g);for(c=b+g;--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],
g=d+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(d,g);for(d=g;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=g=0;d<this.structureCount;d++){var b=this.structures[d];b.modelStartEnd[0]==a&&b.modelStartEnd[1]==a&&(this.structures[d]=null,g++)}if(0<g){a=Array(this.structureCount-g);for(g=d=0;d<this.structureCount;d++)null!=this.structures[d]&&(a[g++]=this.structures[d]);this.structures=a}},"~N");c(b,"removeLastUnselectedAtoms",function(){for(var a=this.ac,d=0,g=this.getLastAtomSetAtomIndex(),b=0,c=g;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(g,g+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)}})});p("J.adapter.smarter");C(["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=v(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;r(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);P(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,g){this.setupASCR(a,d,g)},"~S,java.util.Map,~O");c(b,"setupASCR",function(a,d,g){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),z(g,"java.io.BufferedReader")?this.reader=
g:z(g,"javajs.api.GenericBinaryDocument")&&(this.binaryDoc=g))},"~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(g){if(!F(g,Exception))throw g;}});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),g=d.indexOf("{ ",2);0<=g&&(d=d.substring(g+2));g=d.indexOf("_metadata");0>g&&(g=d.indexOf("metadata"));0<=g&&(d=d.substring(0,g));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 g=this.asc.atomSetCount;0<=--g;)this.asc.setModelInfoForSet("fileName",this.filePath,g),this.asc.setModelInfoForSet("fileType",d,g);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);z(a,"JU.P3")?(a=this.ptSupercell=a,1!=a.length()&&(this.strSupercell=D(a.x)+"a,"+D(a.y)+"b,"+D(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),z(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 g=a.indexOf("(");this.precision=Math.max(this.precision,(0>g?a.length:g)-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]=D(a.x);this.latticeCells[1]=D(a.y);this.latticeCells[2]=D(a.z);z(a,"JU.T4")&&(this.latticeCells[3]=D(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 g=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]);g&&0==this.desiredModelNumber&&this.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|g)).valueOf();g&&(this.doProcessLines=!0);return g},"~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=K(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 g=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 g},"~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=K(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,g,b,c,e){this.ignoreFileUnitCell||(this.clearUnitCell(),this.unitCellParams[0]=a,this.unitCellParams[1]=d,this.unitCellParams[2]=g,0!=b&&(this.unitCellParams[3]=b),0!=c&&(this.unitCellParams[4]=c),0!=e&&(this.unitCellParams[5]=e),this.iHaveUnitCell=
this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(b,"addExplicitLatticeVector",function(a,d,g){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[g++];this.unitCellParams[a++]=d[g++];this.unitCellParams[a]=d[g];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 g=this.asc.ac;0<=--g;)this.symmetry.toFractional(d[g],
!1);else for(g=this.asc.ac;0<=--g;)this.symmetry.toCartesian(d[g],!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 g=this.checkFilter(a,this.filter1,this.filter1Cased);null!=this.filter2&&(g=(new Boolean(g|this.checkFilter(a,this.filter2,this.filter2Cased))).valueOf());if(g&&this.filterEveryNth&&(!a.isHetero||!this.filterAllHetero))g=0==this.nFiltered++%
this.filterN;this.bsFilter.setBitTo(0<=d?d:this.asc.ac,g);return g},"J.adapter.smarter.Atom,~N");c(b,"checkFilter",function(a,d,g){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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b.getDimensionValue=c(b,"getDimensionValue",function(a,d){null==a&&System.out.println("bspt.Node ???");switch(d){case 0:return a.x;case 1:return a.y;default:return a.z}},"JU.T3,~N")});p("J.c");C(["java.lang.Enum"],"J.c.CBK",["JU.SB"],function(){var b=H(J.c,"CBK",Enum);b.getCallback=c(b,"getCallback",function(a){a=a.toUpperCase();var d=a.indexOf("CALLBACK");0<d&&(a=a.substring(0,d));for(var g,d=0,b=J.c.CBK.values();d<b.length&&((g=b[d])||1);d++)if(g.name().equalsIgnoreCase(a))return g;return null},
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C(["java.lang.Enum"],"J.c.STER",null,function(){var b=v(function(){this.$$name=null;this.$isBiColor=!1;r(this,arguments)},J.c,"STER",Enum);x(b,function(a,d){this.$$name=a;this.$isBiColor=d},"~S,~B");c(b,"getName",function(){return this.$$name});c(b,"isBiColor",function(){return this.$isBiColor});b.getStereoMode=c(b,"getStereoMode",function(a){for(var d,g=0,b=J.c.STER.values();g<b.length&&((d=b[g])||1);g++)if(d.$$name.equalsIgnoreCase(a))return d;return null},"~S");I(b,"NONE",0,["OFF",!1]);I(b,"DOUBLE",
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q,h-q,k-q),G=w.clipCode3(e+q,h+q,k+q),L=w.clipCode3(m-q,j-q,n-q),q=w.clipCode3(m+q,j+q,n+q),O=s|G|L|q;this.clipped=0!=O;if(!(-1==O||0!=(s&q&G&L)))if(this.dxB=m-e,this.dyB=j-h,this.dzB=n-k,1>=c)this.line3d.plotLineDeltaOld(w.getColorArgbOrGray(a),w.getColorArgbOrGray(d),e,h,k,this.dxB,this.dyB,this.dzB,this.clipped);else{m=0==g&&(this.clipped||2==b||0==b);this.diameter=c;this.xA=e;this.yA=h;this.zA=k;this.endcaps=b;this.shadesA=w.getShades(this.colixA=a);this.shadesB=w.getShades(this.colixB=d);this.calcArgbEndcap(!0,
!1);this.calcCosSin(this.dxB,this.dyB,this.dzB);this.calcPoints(3,!1);this.interpolate(0,1,this.xyzfRaster,this.xyztRaster);this.interpolate(1,2,this.xyzfRaster,this.xyztRaster);k=this.xyzfRaster;2==b&&this.renderFlatEndcap(!0,!1,k);w.setZMargin(5);a=w.width;d=w.zbuf;c=k[0];e=k[1];h=k[2];k=k[3];j=w.pixel;for(n=this.rasterCount;0<=--n;)s=k[n]>>8,G=s>>1,L=c[n],q=e[n],O=h[n],this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(w.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+L,this.yEndcap+q,this.zEndcap-
O-1,a,d,j),w.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-L,this.yEndcap-q,this.zEndcap+O-1,a,d,j)):(w.plotPixelUnclipped(this.argbEndcap,this.xEndcap+L,this.yEndcap+q,this.zEndcap-O-1,a,d,j),w.plotPixelUnclipped(this.argbEndcap,this.xEndcap-L,this.yEndcap-q,this.zEndcap+O-1,a,d,j))),this.line3d.plotLineDeltaAOld(this.shadesA,this.shadesB,g,s,this.xA+L,this.yA+q,this.zA-O,this.dxB,this.dyB,this.dzB,this.clipped),m&&this.line3d.plotLineDeltaOld(this.shadesA[G],this.shadesB[G],this.xA-L,this.yA-
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m,s+m,G+m),w=L|j|n|m;this.clipped=0!=w;if(!(-1==w||0!=(L&m&j&n))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==g&&(this.clipped||2==b||0==b);this.xA=D(this.xAf);this.yA=D(this.yAf);this.zA=D(this.zAf);this.dxB=D(this.dxBf);this.dyB=D(this.dyBf);this.dzB=D(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=d);this.endcaps=b;this.calcArgbEndcap(!0,!0);w=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);
2==b&&this.renderFlatEndcap(!0,!0,w);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;h=w[0];L=w[1];m=w[2];w=w[3];for(s=this.rasterCount;0<=--s;){var G=w[s]>>8,j=G>>1,n=h[s],q=L[s],O=m[s];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-O-1,a,d,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+O-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,
this.xEndcap+n,this.yEndcap+q,this.zEndcap-O-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+O-1,a,d,c)));this.ptA0.set(this.xA+n,this.yA+q,this.zA-O);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,G,this.ptA0,this.ptB0,g,this.clipped);e&&(this.ptA0.set(this.xA-n,this.yA-q,this.zA+O),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,j,this.ptA0,this.ptB0,g,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,g,b,c,e,h){var k=this.g3d;if(0==c||1==c)this.line3d.plotLineBits(k.getColorArgbOrGray(a),k.getColorArgbOrGray(d),e,h,0,0,!1);else{this.ptA0i.setT(e);var m=B(c/2)+1,j=e.x,n=e.y,q=e.z,w=h.x,s=h.y,G=h.z,L=k.clipCode3(j-
m,n-m,q-m),j=k.clipCode3(j+m,n+m,q+m),n=k.clipCode3(w-m,s-m,G-m),m=k.clipCode3(w+m,s+m,G+m),w=L|j|n|m;this.clipped=0!=w;if(!(-1==w||0!=(L&m&j&n))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==g&&(this.clipped||2==b||0==b);this.xA=D(this.xAf);this.yA=D(this.yAf);this.zA=D(this.zAf);this.dxB=D(this.dxBf);this.dyB=D(this.dyBf);this.dzB=D(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=
d);this.endcaps=b;this.calcArgbEndcap(!0,!0);w=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==b&&this.renderFlatEndcap(!0,!0,w);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;h=w[0];L=w[1];m=w[2];w=w[3];for(s=this.rasterCount;0<=--s;){var G=w[s]>>8,j=G>>1,n=h[s],q=L[s],O=m[s];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-O-1,a,d,c),k.plotPixelClippedArgb(this.argbEndcap,
this.xEndcap-n,this.yEndcap-q,this.zEndcap+O-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+n,this.yEndcap+q,this.zEndcap-O-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-n,this.yEndcap-q,this.zEndcap+O-1,a,d,c)));this.ptA0i.set(this.xA+n,this.yA+q,this.zA-O);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,G,this.ptA0i,this.ptB0i,g,this.clipped);e&&(this.ptA0i.set(this.xA-
n,this.yA-q,this.zA+O),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,j,this.ptA0i,this.ptB0i,g,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,g,b,c,e,h,k,m,j,n){this.dxBf=h-(this.xAf=b);this.dyBf=k-(this.yAf=c);this.dzBf=m-(this.zAf=e);this.xA=
B(Math.floor(this.xAf));this.yA=B(Math.floor(this.yAf));this.zA=B(Math.floor(this.zAf));this.dxB=B(Math.floor(this.dxBf));this.dyB=B(Math.floor(this.dyBf));this.dzB=B(Math.floor(this.dzBf));this.xTip=h;this.yTip=k;this.zTip=m;this.shadesA=this.g3d.getShades(this.colixA=a);var q=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB);a=this.g3d;b=a.pixel;c=a.width;e=a.zbuf;a.plotPixelClippedArgb(this.shadesA[q],D(h),D(k),D(m),c,e,b);this.diameter=g;if(1>=g)1==g&&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(n);!n&&2==this.endcaps&&this.renderFlatEndcap(!1,!0,this.xyzfRaster);a.setZMargin(5);d=this.xyztRaster[0];g=this.xyztRaster[1];h=this.xyztRaster[2];k=this.xyzfRaster[3];m=this.shadesA;for(var q=this.endCapHidden&&0!=this.argbEndcap,w=this.rasterCount;0<=--w;){var s=d[w],G=g[w],L=h[w],O=k[w]>>8,u=this.xAf+s,p=this.yAf+G,r=this.zAf-L,s=this.xAf-
s,G=this.yAf-G,L=this.zAf+L,v=m[0];q&&(a.plotPixelClippedArgb(this.argbEndcap,D(u),D(p),D(r),c,e,b),a.plotPixelClippedArgb(this.argbEndcap,D(s),D(G),D(L),c,e,b));0!=v&&(this.line3d.plotLineDeltaAOld(m,m,0,O,D(u),D(p),D(r),B(Math.ceil(this.xTip-u)),B(Math.ceil(this.yTip-p)),B(Math.ceil(this.zTip-r)),!0),j&&(this.line3d.plotLineDeltaAOld(m,m,0,O,D(u),D(p)+1,D(r),B(Math.ceil(this.xTip-u)),B(Math.ceil(this.yTip-p))+1,B(Math.ceil(this.zTip-r)),!0),this.line3d.plotLineDeltaAOld(m,m,0,O,D(u)+1,D(p),D(r),
B(Math.ceil(this.xTip-u))+1,B(Math.ceil(this.yTip-p)),B(Math.ceil(this.zTip-r)),!0)),!n&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDeltaOld(v,v,D(s),D(G),D(L),B(Math.ceil(this.xTip-s)),B(Math.ceil(this.yTip-G)),B(Math.ceil(this.zTip-L)),!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]=B(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,g){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+g*g);this.cosTheta=g/b;this.cosPhi=a/c;this.sinPhi=d/c}},"~N,~N,~N");c(b,"calcRotatedPoint",function(a,d,g,b,c){c[3][d]=a;a*=3.141592653589793;var e=Math.sin(a)*this.cosTheta,h=Math.cos(a);a=this.radius*(e*this.cosPhi-h*this.sinPhi);e=this.radius*(e*this.sinPhi+h*this.cosPhi);h=this.radius2-(a*a+e*e);h=0<h?Math.sqrt(h):0;g?(c[0][d]=a,c[1][d]=e,c[2][d]=h):(this.tEvenDiameter?(b[0][d]=B(a-0.5),b[1][d]=B(e-0.5)):(b[0][d]=B(a),b[1][d]=B(e)),b[2][d]=B(h+0.5));b[3][d]=this.shader.getShadeFp8(a,
e,h)},"~N,~N,~B,~A,~A");c(b,"allocRaster",function(a,d,g){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]);g[3]=JU.AU.doubleLengthF(g[3])}if(a)for(;this.rasterCount>=g[0].length;)for(b=3;0<=--b;)g[b]=JU.AU.doubleLengthF(g[b]);return this.rasterCount++},"~B,~A,~A");c(b,"interpolate",function(a,d,g,b){var c=g[0],e=g[1],c=c[d]-c[a];0>c&&(c=-c);e=e[d]-e[a];0>e&&(e=-e);if(!(1>=c+e)){for(var h=this.allocRaster(!1,g,b),c=g[0],e=g[1],
k=g[3],m=b[3][a],j=b[3][d],n=4;0<=--n;){var q=(m+j)/2;this.calcRotatedPoint(q,h,!1,g,b);if(c[h]==c[a]&&e[h]==e[a])k[a]=k[a]+k[h]>>>1,m=q;else if(c[h]==c[d]&&e[h]==e[d])k[d]=k[d]+k[h]>>>1,j=q;else{this.interpolate(a,h,g,b);this.interpolate(h,d,g,b);return}}c[h]=c[a];e[h]=e[d]}},"~N,~N,~A,~A");c(b,"interpolatePrecisely",function(a,d,g,b){var c=b[0],e=b[1],h=B(Math.floor(c[d]))-B(Math.floor(c[a]));0>h&&(h=-h);e=B(Math.floor(e[d]))-B(Math.floor(e[a]));0>e&&(e=-e);if(!(1>=h+e)){for(var e=b[3],h=e[a],k=
e[d],m=this.allocRaster(!0,g,b),c=b[0],e=b[1],j=g[3],n=4;0<=--n;){var q=(h+k)/2;this.calcRotatedPoint(q,m,!0,g,b);if(B(Math.floor(c[m]))==B(Math.floor(c[a]))&&B(Math.floor(e[m]))==B(Math.floor(e[a])))j[a]=j[a]+j[m]>>>1,h=q;else if(B(Math.floor(c[m]))==B(Math.floor(c[d]))&&B(Math.floor(e[m]))==B(Math.floor(e[d])))j[d]=j[d]+j[m]>>>1,k=q;else{this.interpolatePrecisely(a,m,g,b);this.interpolatePrecisely(m,d,g,b);return}}c[m]=c[a];e[m]=e[d]}},"~N,~N,~A,~A");c(b,"renderFlatEndcap",function(a,d,g){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=D(d);b=D(b);c=D(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 e=g[1][0];a=g[1][0];var h=0,k=0,m=g[0],j=g[1];g=g[2];for(var n=this.rasterCount;0<--n;){var q=j[n];q<e?e=q:q>a?a=q:(q=-q,q<e?e=
q:q>a&&(a=q))}for(q=e;q<=a;++q){for(var e=2147483647,w=-2147483648,n=this.rasterCount;0<=--n;){if(j[n]==q){var s=m[n];s<e&&(e=s,h=g[n]);s>w&&(w=s,k=g[n])}j[n]==-q&&(s=-m[n],s<e&&(e=s,h=-g[n]),s>w&&(w=s,k=-g[n]))}n=w-e+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(n,d+e,b+q,c-h-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 g=d?this.dzBf:this.dzB;if(!(3==this.endcaps||0==g)){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<=g||!a?(this.endcapShadeIndex=
this.shader.getShadeIndex(-b,-c,g),0==this.colixA?(this.xAend+=B(this.dxB/2),this.yAend+=B(this.dyB/2),this.zAend+=B(this.dzB/2),this.colixEndcap=this.colixB):this.colixEndcap=this.colixA):(this.endcapShadeIndex=this.shader.getShadeIndex(b,c,-g),0==this.colixB?(this.colixEndcap=this.colixA,this.xAend-=B(this.dxB/2),this.yAend-=B(this.dyB/2),this.zAend-=B(this.dzB/2)):(this.colixEndcap=this.colixB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB));g=this.colixEndcap==this.colixA?
this.shadesA:this.shadesB;56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=g[this.endcapShadeIndex];this.endCapHidden=1==this.endcaps}},"~B,~B")});p("J.g3d");N(J.g3d,"G3DRenderer");p("J.g3d");C(["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=v(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;r(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);P(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=Q(JU.GData.normixCount,0);this.shadeIndexes2Sided=Q(JU.GData.normixCount,0)});x(b,function(){M(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3});j(b,"isWebGL",function(){return!1});j(b,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});j(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");j(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");j(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");j(b,"setWindowParameters",
function(a,d,g){this.setWinParams(a,d,g);this.currentlyRendering&&this.endRendering()},"~N,~N,~B");j(b,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.isPass2==a},"~B");j(b,"beginRendering",function(a,d,g,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,g),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");j(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()});j(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");j(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,g){if(0==d||a==d)return a;0==a&&(a=g);g=a&16711935;a&=65280;var b=d&16711935,c=d&65280;switch(d>>24&15){case 0:g=b;a=c;break;case 1:g=(b<<2)+(b<<1)+b+g>>3&16711935;a=(c<<2)+ +(c<<1)+c+a>>3&65280;break;case 2:g=(b<<1)+b+g>>2&16711935;a=(c<<1)+c+a>>2&65280;break;case 3:g=(b<<2)+b+(g<<1)+g>>3&16711935;a=(c<<2)+c+(a<<1)+a>>3&65280;break;case 4:g=g+b>>1&16711935;a=a+c>>
1&65280;break;case 5:g=(b<<1)+b+(g<<2)+g>>3&16711935;a=(c<<1)+c+(a<<2)+a>>3&65280;break;case 6:g=(g<<1)+g+b>>2&16711935;a=(a<<1)+a+c>>2&65280;break;case 7:g=(g<<2)+(g<<1)+g+b>>3&16711935,a=(a<<2)+(a<<1)+a+c>>3&65280}return 4278190080|g|a},"~N,~N,~N");j(b,"getScreenImage",function(a){var d=this.platform.bufferedImage;a&&this.releaseBuffers();return d},"~B");j(b,"applyAnaglygh",function(a,d){switch(a){case J.c.STER.REDCYAN:for(var g=this.anaglyphLength;0<=--g;){var b=this.anaglyphChannelBytes[g]&255;
this.pbuf[g]=this.pbuf[g]&4294901760|b<<8|b}break;case J.c.STER.CUSTOM:for(var b=d[0],c=d[1]&16777215,g=this.anaglyphLength;0<=--g;){var e=this.anaglyphChannelBytes[g]&255,e=(e|(e|e<<8)<<8)&c;this.pbuf[g]=this.pbuf[g]&b|e}break;case J.c.STER.REDBLUE:for(g=this.anaglyphLength;0<=--g;)b=this.anaglyphChannelBytes[g]&255,this.pbuf[g]=this.pbuf[g]&4294901760|b;break;case J.c.STER.REDGREEN:for(g=this.anaglyphLength;0<=--g;)this.pbuf[g]=this.pbuf[g]&4294901760|(this.anaglyphChannelBytes[g]&255)<<8}},"J.c.STER,~A");
j(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=Q(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});j(b,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});j(b,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});
j(b,"setSlabAndZShade",function(a,d,g,b,c){this.setSlab(a);this.setDepth(d);g<b?(null==this.pixelShaded&&(this.pixelShaded=new J.g3d.PixelatorShaded(this)),this.pixel=this.pixelShaded.set(g,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,g,b){var c=d<<1;if(0!=b){b&=16777215;for(var e=a.length;0<=--e;)0==a[e]&&(a[e]=b)}for(var h=(b>>2&1061109567)<<2,h=h+((h&3233857728)>>6),k=0,m=0,e=g;0<=--e;m+=c)for(g=d;0<=--g;++k){var j=(a[m]>>2&1061109567)+(a[m++ +c]>>2&1061109567)+(a[m]>>2&1061109567)+(a[m++ +c]>>2&1061109567),j=j+((j&3233857728)>>6);j==h&&(j=b);a[k]=j&16777215|4278190080}},"~A,~N,~N,~N");b.downsample2dZ=c(b,"downsample2dZ",
function(a,d,g,b,c){for(var e=g<<1,h=0,k=0;0<=--b;k+=e)for(var m=g;0<=--m;++h,++k){var j=Math.min(d[k],d[k+e]),j=Math.min(j,d[++k]),j=Math.min(j,d[k+e]);2147483647!=j&&(j>>=1);d[h]=a[h]==c?2147483647:j}},"~A,~A,~N,~N,~N");c(b,"hasContent",function(){return this.platform.hasContent()});j(b,"setC",function(a){var d=JU.C.isColixLastAvailable(a);if(!d&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var g=a&30720;if(16384==g)return!1;this.renderLow&&(g=0);var b=0!=g,c=b&&30720==g;this.setScreened(c);
if(!this.checkTranslucent(b&&!c))return!1;this.isPass2?(this.translucencyMask=g<<13|16777215,this.translucencyLog=g>>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");j(b,"drawFilledCircle",function(a,d,g,b,c,e){if(!this.isClippedZ(e)){var h=B((g+1)/2),h=b<h||b+h>=this.width||c<h||c+h>=
this.height;if(!h||!this.isClippedXY(g,b,c))0!=a&&this.setC(a)&&(h?this.isClippedXY(g,b,c)||this.circle3d.plotCircleCenteredClipped(b,c,e,g):this.circle3d.plotCircleCenteredUnclipped(b,c,e,g)),0!=d&&this.setC(d)&&(h?this.circle3d.plotFilledCircleCenteredClipped(b,c,e,g):this.circle3d.plotFilledCircleCenteredUnclipped(b,c,e,g))}},"~N,~N,~N,~N,~N,~N");j(b,"volumeRender4",function(a,d,g,b){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,d,g,b,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(b)){var c=
B((a+1)/2),c=d<c||d+c>=this.width||g<c||g+c>=this.height;if(!c||!this.isClippedXY(a,d,g))c?this.circle3d.plotFilledCircleCenteredClipped(d,g,b,a):this.circle3d.plotFilledCircleCenteredUnclipped(d,g,b,a)}},"~N,~N,~N,~N");j(b,"fillSphereXYZ",function(a,d,g,b){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,g,b,this.width,this.zbuf,this.pixel);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,a,d,g,b,null,null,null,-1,null)},"~N,~N,~N,~N");
j(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");j(b,"fillSphereI",function(a,d){this.fillSphereXYZ(a,d.x,d.y,d.z)},"~N,JU.P3i");j(b,"fillSphereBits",function(a,d){this.fillSphereXYZ(a,Math.round(d.x),Math.round(d.y),Math.round(d.z))},"~N,JU.P3");j(b,"fillEllipsoid",
function(a,d,g,b,c,e,h,k,m,j,n){switch(e){case 1:this.plotPixelClippedArgb(this.argbCurrent,g,b,c,this.width,this.zbuf,this.pixel);return;case 0:return}e<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,e,g,b,c,h,k,m,j,n)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");j(b,"drawRect",function(a,d,g,b,c,e){if(!(0!=b&&this.isClippedZ(b))){b=c-1;e-=1;c=a+b;var h=d+e;0<=d&&d<this.height&&this.drawHLine(a,d,g,b);0<=h&&h<this.height&&this.drawHLine(a,h,g,b);0<=a&&a<this.width&&
this.drawVLine(a,d,g,e);0<=c&&c<this.width&&this.drawVLine(c,d,g,e)}},"~N,~N,~N,~N,~N,~N");c(b,"drawHLine",function(a,d,g,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,e=this.argbCurrent;a+=this.width*d;for(d=0;d<=b;d++)g<this.zbuf[a]&&c.addPixel(a,g,e),a++},"~N,~N,~N,~N");c(b,"drawVLine",function(a,d,g,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,e=0;e<=b;e++)g<this.zbuf[a]&&
d.addPixel(a,g,c),a+=this.width},"~N,~N,~N,~N");j(b,"fillTextRect",function(a,d,g,b,c,e){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){e+=d;if(0>=e)return;d=0}d+e>this.height&&(e=this.height-d);var h=this.argbCurrent;this.isAntialiased()&&(h=J.g3d.Graphics3D.fixTextImageRGB(h));for(var k=this.zbuf,m=this.pixel;0<=--e;)this.plotPixelsUnclippedCount(h,c,a,d++,g,b,k,m)}},"~N,~N,~N,~N,~N,~N");j(b,"drawString",function(a,d,g,b,c,e,h){this.currentShadeIndex=
0;null!=a&&(this.isClippedZ(e)||this.drawStringNoSlab(a,d,g,b,c,h))},"~S,JU.Font,~N,~N,~N,~N,~N");j(b,"drawStringNoSlab",function(a,d,g,b,c,e){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var h=new J.g3d.TextString;h.setText(a,null==d?this.currentFont:this.currentFont=d,this.argbCurrent,JU.C.isColixTranslucent(e)?this.getColorArgbOrGray(e)&16777215|(e&30720)<<13:0,g,b,c);this.strings[this.stringCount++]=
h}},"~S,JU.Font,~N,~N,~N,~N");j(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 g=this.strings[d];this.plotText(g.x,g.y,g.z,g.argb,g.bgargb,g.text,g.font,a)}this.strings=null;this.stringCount=0}},"~O");j(b,"plotText",function(a,d,g,b,c,e,h,k){J.g3d.TextRenderer.plot(a,d,g,b,c,e,h,this,k,this.antialiasThisFrame)},
"~N,~N,~N,~N,~N,~S,JU.Font,J.api.JmolRendererInterface");j(b,"drawImage",function(a,d,g,b,c,e,h,k){null!=a&&(0<h&&0<k&&!this.isClippedZ(c))&&this.plotImage(d,g,b,a,null,e,h,k)},"~O,~N,~N,~N,~N,~N,~N,~N");j(b,"plotImage",function(a,d,g,b,c,e,h,k){this.setC(e);this.isPass2||(this.translucencyMask=-1);0==e&&(this.argbCurrent=0);var m=-2147483648==a;e=m?this.bgcolor:this.argbCurrent;m&&(a=0,g=2147483646,h=this.width,k=this.height);if(!(0>=a+h||a>=this.width||0>=d+k||d>=this.height))if(b=this.apiPlatform.drawImageToBuffer(null,
this.platform.offscreenImage,b,h,k,m?e:0),null!=b){var m=this.zbuf,j=this.width,n=this.pixel,q=this.height,w=this.translucencyLog;if(null==c&&0<=a&&a+h<=j&&0<=d&&d+k<=q){var s=0,G=0;for(a=d*j+a;s<k;s++,a+=j-h)for(var L=0;L<h;L++,G++,a++)if(g<m[a]){var O=b[G];-16777216==(O&4278190080)&&n.addPixel(a,g,O)}}else{null==c&&(c=this);for(G=s=0;s<k;s++)for(L=0;L<h;L++)O=b[G++],-16777216==(O&4278190080)&&c.plotImagePixel(O,a+L,d+s,g,8,e,j,q,m,n,w)}}},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");j(b,
"setFont",function(a){this.currentFont=a},"JU.Font");j(b,"drawPixel",function(a,d,g){this.plotPixelClippedArgb(this.argbCurrent,a,d,g,this.width,this.zbuf,this.pixel)},"~N,~N,~N");j(b,"drawPoints",function(a,d,g){if(1<g)for(var b=0.8*g*g,c=-g;c<g;c++)for(var e=-g;e<g;e++)c*c+e*e>b||(this.plotPoints(a,d,c,e),this.plotPoints(a,d,c,e));else this.plotPoints(a,d,0,0)},"~N,~A,~N");j(b,"drawDashedLineBits",function(a,d,g,b){this.isAntialiased()&&(a+=a,d+=d);this.setScreeni(g,this.sA);this.setScreeni(b,this.sB);
this.drawLineABBits(a,d,!0)},"~N,~N,JU.P3,JU.P3");c(b,"drawLineABBits",function(a,d,g){this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,d,g);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,g)},"~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");j(b,"drawLineXYZ",
function(a,d,g,b,c,e){this.line3d.plotLineOld(this.argbCurrent,this.argbCurrent,a,d,g,b,c,e)},"~N,~N,~N,~N,~N,~N");j(b,"drawLine",function(a,d,g,b,c,e,h,k){this.setC(a)||(a=0);var m=this.argbCurrent;this.setC(d)||(d=0);(0!=a||0!=d)&&this.line3d.plotLineOld(m,this.argbCurrent,g,b,c,e,h,k)},"~N,~N,~N,~N,~N,~N,~N,~N");j(b,"drawLineBits",function(a,d,g,b){this.setC(a)||(a=0);var c=this.argbCurrent;this.setC(d)||(d=0);if(0!=a||0!=d)this.setScreeni(g,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");j(b,"drawLinePixels",function(a,d,g,b){this.sA.setT(a);this.sB.setT(d);this.sA.z=this.sB.z=g;a=this.slab;-2147483648==b&&(this.slab=0);this.drawLineABBits(0,0,!1);this.slab=a},"JU.P3i,JU.P3i,~N,~N");j(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");j(b,"fillCylinderXYZ",function(a,d,g,b,c,e,h,k,m,j){if(!(b>
this.ht3)){var n=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(n=2);this.setC(a)||(a=0);this.wasScreened&&(n+=1);0==a&&0==d||this.cylinder3d.renderOld(a,d,n,g,b,c,e,h,k,m,j)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");j(b,"fillCylinderScreen3I",function(a,d,g,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,this.colixCurrent,0,a,d,D(g.x),D(g.y),D(g.z),D(b.x),D(b.y),D(b.z))},"~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");j(b,"fillCylinder",function(a,d,g,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,
this.colixCurrent,0,a,d,g.x,g.y,g.z,b.x,b.y,b.z)},"~N,~N,JU.P3i,JU.P3i");j(b,"fillCylinderBits",function(a,d,g,b){d<=this.ht3&&(1!=g.z&&1!=b.z)&&(0==d||1==d?(this.setScreeni(g,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,g,b))},"~N,~N,JU.P3,JU.P3");j(b,"fillCylinderBits2",function(a,d,g,b,c,e){if(!(b>
this.ht3)){var h=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(h=2);this.setC(a)||(a=0);this.wasScreened&&(h+=1);0==a&&0==d||(this.setScreeni(c,this.sA),this.setScreeni(e,this.sB),this.cylinder3d.renderBits(a,d,h,g,b,this.sA,this.sB))}},"~N,~N,~N,~N,JU.P3,JU.P3");j(b,"fillConeScreen3f",function(a,d,g,b,c){d<=this.ht3&&this.cylinder3d.renderConeOld(this.colixCurrent,a,d,g.x,g.y,g.z,b.x,b.y,b.z,!0,c)},"~N,~N,JU.P3,JU.P3,~B");j(b,"drawHermite4",function(a,d,g,b,c){this.hermite3d.renderHermiteRope(!1,
a,0,0,0,d,g,b,c)},"~N,JU.P3,JU.P3,JU.P3,JU.P3");j(b,"drawHermite7",function(a,d,g,b,c,e,h,k,m,j,n,q,w){if(0==w)this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,n,q,0);else{this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,n,q,1);var s=this.colixCurrent;this.setC(w);this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,n,q,-1);this.setC(s)}},"~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");j(b,"fillHermite",function(a,d,g,b,c,e,h,k){this.hermite3d.renderHermiteRope(!0,
a,d,g,b,c,e,h,k)},"~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");j(b,"drawTriangle3C",function(a,d,g,b,c,e,h){1==(h&1)&&this.drawLine(d,b,a.x,a.y,a.z,g.x,g.y,g.z);2==(h&2)&&this.drawLine(b,e,g.x,g.y,g.z,c.x,c.y,c.z);4==(h&4)&&this.drawLine(d,e,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");j(b,"fillTriangleTwoSided",function(a,d,g,b){this.setColorNoisy(this.getShadeIndex(a));this.fillTriangleP3f(d,g,b,!1)},"~N,JU.P3,JU.P3,JU.P3");c(b,"fillTriangleP3f",function(a,d,g,b){this.setScreeni(a,this.sA);
this.setScreeni(d,this.sB);this.setScreeni(g,this.sC);this.triangle3d.fillTriangle(this.sA,this.sB,this.sC,b)},"JU.P3,JU.P3,JU.P3,~B");j(b,"fillTriangle3f",function(a,d,g,b){var c=this.getShadeIndexP3(a,d,g,b);0>c||(b?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]),this.fillTriangleP3f(a,d,g,!1))},"JU.P3,JU.P3,JU.P3,~B");j(b,"fillTriangle3i",function(a,d,g,b,c,e,h){h&&(b=this.vectorAB,b.set(d.x-a.x,d.y-a.y,d.z-a.z),null==g?b=this.shader.getShadeIndex(-b.x,-b.y,b.z):(this.vectorAC.set(g.x-
a.x,g.y-a.y,g.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,g,!1)},"JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");j(b,"fillTriangle3CN",function(a,d,b,c,f,e,h,k,m){this.triangle3d.fillTriangle(a,c,h,this.checkGouraud(d,f,k,b,e,m))},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");j(b,"fillTriangle3CNBits",function(a,d,b,c,f,e,h,k,m){this.fillTriangleP3f(a,c,h,this.checkGouraud(d,
f,k,b,e,m))},"JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");c(b,"checkGouraud",function(a,d,b,c,f,e){if(!this.isPass2&&c==f&&c==e&&a==d&&a==b){d=this.getShadeIndex(c);if(a!=this.colixCurrent||this.currentShadeIndex!=d)this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(d);return!1}this.setTriangleTranslucency(a,d,b);this.triangle3d.setGouraud(this.getShades(a)[this.getShadeIndex(c)],this.getShades(d)[this.getShadeIndex(f)],this.getShades(b)[this.getShadeIndex(e)]);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,b){this.isPass2&&(a&=14336,d&=14336,b&=14336,this.translucencyMask=(JU.GData.roundInt(B((a+d+b)/3))&30720)<<13|16777215)},"~N,~N,~N");j(b,"fillQuadrilateral",function(a,d,b,c,f){f=this.getShadeIndexP3(a,d,b,f);0>f||(this.setColorNoisy(f),this.fillTriangleP3f(a,d,b,!1),this.fillTriangleP3f(a,b,c,!1))},"JU.P3,JU.P3,JU.P3,JU.P3,~B");
j(b,"drawSurface",function(){},"JU.MeshSurface,~N");j(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,b,c,f,e,h){this.isClipped3(d,b,c)||(d=b*f+d,c<e[d]&&h.addPixel(d,c,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPixelUnclipped",function(a,d,b,c,f,e,h){d=b*f+d;c<e[d]&&h.addPixel(d,c,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotImagePixel",function(a,d,b,c,f,e,
h,k,m,j,n){0>d||(d>=h||0>b||b>=k)||j.addImagePixel(f,n,b*h+d,c,a,e)},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");c(b,"plotPixelsClippedRaster",function(a,d,b,c,f,e,h){var k,m;if(!(0>=a||0>b||b>=this.height||d>=this.width||c<(m=this.slab)&&f<m||c>(k=this.depth)&&f>k)){var j=this.zbuf,n=(d<<16)+(b<<1)^858993459,q=(c<<10)+512;c=f-c;f=B(a/2);c=JU.GData.roundInt(B(((c<<10)+(0<=c?f:-f))/a));if(0>d){d=-d;q+=c*d;a-=d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);d=b*this.width+d;b=this.pixel;if(null==e){e=
this.argbNoisyDn;f=this.argbNoisyUp;for(var w=this.argbCurrent;0<=--a;){h=q>>10;if(h>=m&&h<=k&&h<j[d]){var n=(n<<16)+(n<<1)+n&2147483647,s=n>>16&7;b.addPixel(d,h,0==s?e:1==s?f:w)}++d;q+=c}}else{n=e.r<<8;f=B((h.r-e.r<<8)/a);w=e.g;s=B((h.g-w)/a);e=e.b;for(var G=B((h.b-e)/a);0<=--a;)h=q>>10,h>=m&&(h<=k&&h<j[d])&&b.addPixel(d,h,4278190080|n&16711680|w&65280|e>>8&255),++d,q+=c,n+=f,w+=s,e+=G}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsUnclippedRaster",function(a,d,b,c,f,e,h){if(!(0>=a)){var k=
((d<<16)+(b<<1)^858993459)&2147483647,m=(c<<10)+512;c=f-c;f=B(a/2);c=JU.GData.roundInt(B(((c<<10)+(0<=c?f:-f))/a));d=b*this.width+d;b=this.zbuf;f=this.pixel;if(null==e){e=this.argbNoisyDn;for(var j=this.argbNoisyUp,n=this.argbCurrent;0<=--a;){h=m>>10;if(h<b[d]){var k=(k<<16)+(k<<1)+k&2147483647,q=k>>16&7;f.addPixel(d,h,0==q?e:1==q?j:n)}++d;m+=c}}else{k=e.r<<8;j=JU.GData.roundInt(B((h.r-e.r<<8)/a));n=e.g;q=JU.GData.roundInt(B((h.g-n)/a));e=e.b;for(var w=JU.GData.roundInt(B((h.b-e)/a));0<=--a;)h=m>>
10,h<b[d]&&f.addPixel(d,h,4278190080|k&16711680|n&65280|e>>8&255),++d,m+=c,k+=j,n+=q,e+=w}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsClippedRasterBits",function(a,d,b,c,f,e,h,k,m){var j,n;if(!(0>=a||0>b||b>=this.height||d>=this.width||c<(n=this.slab)&&f<n||c>(j=this.depth)&&f>j)){c=this.zbuf;var q=(d<<16)+(b<<1)^858993459;if(0>d){a-=-d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);b=b*this.width+d;f=this.pixel;if(null==e){e=this.argbNoisyDn;for(var w=this.argbNoisyUp,s=this.argbCurrent;0<=
--a;){h=this.line3d.getZCurrent(k,m,d++);if(h>=n&&h<=j&&h<c[b]){var q=(q<<16)+(q<<1)+q&2147483647,G=q>>16&7;f.addPixel(b,h,2>G?e:6>G?w:s)}++b}}else{q=e.r<<8;w=B((h.r-e.r<<8)/a);s=e.g;G=B((h.g-s)/a);e=e.b;for(var L=B((h.b-e)/a);0<=--a;)h=this.line3d.getZCurrent(k,m,d++),h>=n&&(h<=j&&h<c[b])&&f.addPixel(b,h,4278190080|q&16711680|s&65280|e>>8&255),++b,q+=w,s+=G,e+=L}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedRasterBits",function(a,d,b,c,f,e,h){if(!(0>=a)){var k=((d<<16)+(b<<
1)^858993459)&2147483647;b=b*this.width+d;var m=this.zbuf,j=this.pixel;if(null==c)for(var n=this.argbNoisyDn,q=this.argbNoisyUp,w=this.argbCurrent;0<=--a;)f=this.line3d.getZCurrent(e,h,d++),f<m[b]&&(k=(k<<16)+(k<<1)+k&2147483647,c=k>>16&7,j.addPixel(b,f,0==c?n:1==c?q:w)),++b;else{k=c.r<<8;n=JU.GData.roundInt(B((f.r-c.r<<8)/a));q=c.g;w=JU.GData.roundInt(B((f.g-q)/a));c=c.b;for(var s=JU.GData.roundInt(B((f.b-c)/a));0<=--a;)f=this.line3d.getZCurrent(e,h,d++),f<m[b]&&j.addPixel(b,f,4278190080|k&16711680|
q&65280|c>>8&255),++b,k+=n,q+=w,c+=s}}},"~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedCount",function(a,d,b,c,f,e,h,k){for(b=c*e+b;0<=--d;)f<h[b]&&k.addPixel(b,f,a),++b},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPoints",function(a,d,b,c){var f=this.pixel,e=this.argbCurrent,h=this.zbuf,k=this.width,m=this.antialiasThisFrame;for(a*=3;0<a;){var j=d[--a],n=d[--a]+c,q=d[--a]+b;if(!this.isClipped3(q,n,j)){var w=n*k+q++;j<h[w]&&f.addPixel(w,j,e);m&&(w=n*k+q,!this.isClipped3(q,n,j)&&
j<h[w]&&f.addPixel(w,j,e),w=++n*k+q,!this.isClipped3(q,n,j)&&j<h[w]&&f.addPixel(w,j,e),w=n*k+--q,!this.isClipped3(q,n,j)&&j<h[w]&&f.addPixel(w,j,e))}}},"~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,b,c){this.vectorAB.sub2(d,a);this.vectorAC.sub2(b,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);
return 0>a.z?this.shader.getShadeIndex(a.x,a.y,-a.z):c?-1:this.shader.getShadeIndex(-a.x,-a.y,a.z)},"JU.P3,JU.P3,JU.P3,~B");j(b,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");j(b,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom,~N");j(b,"getExportType",function(){return 0});j(b,"getExportName",function(){return null});c(b,"canDoTriangles",function(){return!0});
c(b,"isCartesianExport",function(){return!1});j(b,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");j(b,"finalizeOutput",function(){return null});j(b,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");j(b,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(b,"getPrivateKey",function(){return 0});j(b,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});c(b,"setRotationMatrix",function(a){for(var d=JU.Normix.getVertexVectors(),b=JU.GData.normixCount;0<=
--b;){var c=this.transformedVectors[b];a.rotate2(d[b],c);this.shadeIndexes[b]=this.shader.getShadeB(c.x,-c.y,c.z);this.shadeIndexes2Sided[b]=0<=c.z?this.shadeIndexes[b]:this.shader.getShadeB(-c.x,c.y,-c.z)}},"JU.M3");j(b,"renderCrossHairs",function(a,d,b,c,f){d=this.isAntialiased();this.setC(0>f?10:100<f?11:23);f=Math.max(Math.min(this.width,Math.round(c.x)),0);b=Math.max(Math.min(this.height,Math.round(c.y)),0);var e=Math.round(c.z)+1,h=d?8:4,k=d?20:10;d=d?2:1;this.drawRect(f-h,b,e,0,k,d);this.drawRect(f,
b-h,e,0,d,k);this.drawRect(f-h,b-h,e,0,k,k);h=k;k>>=1;this.setC(a[1]<c.x?21:11);this.drawRect(f-h,b,e,0,k,d);this.setC(a[0]>c.x?21:11);this.drawRect(f+k,b,e,0,k,d);this.setC(a[3]<c.y?21:11);this.drawRect(f,b-h,e,0,d,k);this.setC(a[2]>c.y?21:11);this.drawRect(f,b+k,e,0,d,k)},"~A,~N,~N,JU.P3,~N");j(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});p("J.g3d");
C(["J.g3d.PrecisionRenderer","java.util.Hashtable"],"J.g3d.LineRenderer",["JU.BS"],function(){var b=v(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;r(this,arguments)},J.g3d,"LineRenderer",J.g3d.PrecisionRenderer);P(b,function(){this.lineCache=new java.util.Hashtable});x(b,function(a){M(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 b=a;a=d;d=b}for(var b=0,c=a+a,f=d+d,e=0;e<this.nBits;e++)b+=f,b>a&&(this.lineBits.set(e),b-=c);this.lineCache.put(this.slopeKey,
this.lineBits)}},"~N,~N");c(b,"clearLineCache",function(){this.lineCache.clear()});c(b,"plotLineOld",function(a,d,b,c,f,e,h,k){this.x1t=b;this.x2t=e;this.y1t=c;this.y2t=h;this.z1t=f;this.z2t=k;var m=!0;switch(this.getTrimmedLineImpl()){case 0:m=!1;break;case 2:return}this.plotLineClippedOld(a,d,b,c,f,e-b,h-c,k-f,m,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N");c(b,"plotLineDeltaOld",function(a,d,b,c,f,e,h,k,m){this.x1t=b;this.x2t=b+e;this.y1t=c;this.y2t=c+h;this.z1t=f;this.z2t=f+k;if(m)switch(this.getTrimmedLineImpl()){case 2:return;
case 0:m=!1}this.plotLineClippedOld(a,d,b,c,f,e,h,k,m,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaAOld",function(a,d,b,c,f,e,h,k,m,j,n){this.x1t=f;this.x2t=f+k;this.y1t=e;this.y2t=e+m;this.z1t=h;this.z2t=h+j;if(n)switch(this.getTrimmedLineImpl()){case 2:return;case 0:n=!1}var q=this.g3d.zbuf,w=this.g3d.width,s=0,G=e*w+f,L=this.g3d.bufferSize,O=63>c?c+1:c,u=0<c?c-1:c,p=a[O],r=a[u],v=d[c],O=d[O];d=d[u];a=a[c];c=this.g3d.pixel;0!=b&&(c=this.g3d.setScreened(1==(b&1)),this.g3d.currentShadeIndex=
0);0!=a&&(!n&&0<=G&&G<L&&h<q[G])&&c.addPixel(G,h,a);if(!(0==k&&0==m)){n=1;u=w;f+=k;var z=e+m;0>k&&(k=-k,n=-1);0>m&&(m=-m,u=-w);w=k+k;e=m+m;h<<=10;if(m<=k){var x=k-1;0>j&&(x=-x);j=B(((j<<10)+x)/k);m=0;x=Math.abs(f-this.x2t)-1;f=Math.abs(f-this.x1t)-1;for(var z=k-1,A=B(z/2);--z>=x;){if(z==A){a=v;if(0==a)break;p=O;r=d;0!=b%3&&(c=this.g3d.setScreened(2==(b&2)),this.g3d.currentShadeIndex=0)}G+=n;h+=j;m+=e;m>k&&(G+=u,m-=w);if(0!=a&&z<f&&0<=G&&G<L&&2147483647>s){var C=h>>10;if(C<q[G]){var D=this.shader.nextRandom8Bit();
c.addPixel(G,C,85>D?r:170<D?p:a)}}s=(s+1)%1}}else{x=m-1;0>j&&(x=-x);j=B(((j<<10)+x)/m);k=0;x=Math.abs(z-this.y2t)-1;f=Math.abs(z-this.y1t)-1;z=m-1;for(A=B(z/2);--z>=x;){if(z==A){a=v;if(0==a)break;p=O;r=d;0!=b%3&&(c=this.g3d.setScreened(2==(b&2)),this.g3d.currentShadeIndex=0)}G+=u;h+=j;k+=w;k>m&&(G+=n,k-=e);0!=a&&(z<f&&0<=G&&G<L&&2147483647>s)&&(C=h>>10,C<q[G]&&(D=this.g3d.shader.nextRandom8Bit(),c.addPixel(G,C,85>D?r:170<D?p:a)));s=(s+1)%1}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaABitsFloat",
function(a,d,b,c,f,e,h){var k=Math.round(c.x),m=Math.round(c.y),j=Math.round(c.z),n=Math.round(f.x),q=Math.round(f.y),w=Math.round(f.z),s=n-k,G=q-m;this.x1t=k;this.x2t=n;this.y1t=m;this.y2t=q;this.z1t=j;this.z2t=w;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var L=this.g3d.width,n=0,w=63>b?b+1:b,q=0<b?b-1:b,O=a[b],u=a[w],p=a[q];b=d[b];a=d[w];d=d[q];var q=m*L+k,w=this.g3d.bufferSize,r,v,z,x;this.lineTypeX?(r=k,v=this.x1t,z=this.x2t,k+=B(s/2),x=m=0<=s?1:-1,s=0<=G?L:-L,this.setRastABFloat(c.x,
c.z,f.x,f.z)):(r=m,v=this.y1t,z=this.y2t,k=m+B(G/2),m=0<=G?1:-1,x=0<=G?L:-L,s=0<=s?1:-1,this.setRastABFloat(c.y,c.z,f.y,f.z));c=j;f=O;j=u;G=p;u=!1;p=this.g3d.pixel;0!=e&&(p=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(O=r;;O+=m,r+=m){O==v&&(u=!0);if(O==k){f=b;if(0==f)break;j=a;G=d;0!=e%3&&(p=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=f&&(u&&0<=q&&q<w&&2147483647>n)&&(c=this.getZCurrent(this.a,this.b,O),c<h[q]&&(L=this.shader.nextRandom8Bit(),p.addPixel(q,D(c),
85>L?G:170<L?j:f)));if(O==z)break;n=(n+1)%1;for(q+=x;0>r;)r+=this.nBits;this.lineBits.get(r%this.nBits)&&(q+=s)}}},"~A,~A,~N,JU.P3,JU.P3,~N,~B");c(b,"plotLineDeltaABitsInt",function(a,d,b,c,f,e,h){var k=c.x,m=c.y,j=c.z,n=f.x,q=f.y,w=f.z,s=n-k,G=q-m;this.x1t=k;this.x2t=n;this.y1t=m;this.y2t=q;this.z1t=j;this.z2t=w;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var L=this.g3d.width,n=0,w=63>b?b+1:b,q=0<b?b-1:b,O=a[b],u=a[w],r=a[q];b=d[b];a=d[w];d=d[q];var q=m*L+k,w=this.g3d.bufferSize,p,v,z,
x;this.lineTypeX?(p=k,v=this.x1t,z=this.x2t,k+=B(s/2),x=m=0<=s?1:-1,s=0<=G?L:-L,this.setRastAB(c.x,c.z,f.x,f.z)):(p=m,v=this.y1t,z=this.y2t,k=m+B(G/2),m=0<=G?1:-1,x=0<=G?L:-L,s=0<=s?1:-1,this.setRastAB(c.y,c.z,f.y,f.z));c=j;f=O;j=u;G=r;u=!1;r=this.g3d.pixel;0!=e&&(r=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(O=p;;O+=m,p+=m){O==v&&(u=!0);if(O==k){f=b;if(0==f)break;j=a;G=d;0!=e%3&&(r=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=f&&(u&&0<=q&&q<w&&2147483647>n)&&
(c=this.getZCurrent(this.a,this.b,O),c<h[q]&&(L=this.shader.nextRandom8Bit(),r.addPixel(q,D(c),85>L?G:170<L?j:f)));if(O==z)break;n=(n+1)%1;for(q+=x;0>p;)p+=this.nBits;this.lineBits.get(p%this.nBits)&&(q+=s)}}},"~A,~A,~N,JU.P3i,JU.P3i,~N,~B");c(b,"plotLineBits",function(a,d,b,c,f,e,h){if(!(1>=b.z||1>=c.z)){var k=!0;this.x1t=b.x;this.y1t=b.y;this.z1t=b.z;this.x2t=c.x;this.y2t=c.y;this.z2t=c.z;switch(this.getTrimmedLineImpl()){case 2:return;case 0:k=!1;break;default:h&&(b.set(this.x1t,this.y1t,this.z1t),
c.set(this.x2t,this.y2t,this.z2t))}h=this.g3d.zbuf;var m=this.g3d.width,j=0;0==f&&(e=2147483647,f=1);var n=b.x,q=b.y,w=b.z,s=c.x-n,G=n+s,L=c.y-q,u=q+L,p=q*m+n,r=this.g3d.bufferSize,v=this.g3d.pixel;0!=a&&(!k&&0<=p&&p<r&&w<h[p])&&v.addPixel(p,w,a);if(!(0==s&&0==L)){var z=k=1,w=m;0>s&&(s=-s,k=-1);0>L&&(L=-L,w=-m,z=-1);var m=s+s,x=L+L;if(L<=s){this.setRastAB(b.x,b.z,c.x,c.z);q=0;b=Math.abs(G-this.x2t)-1;G=Math.abs(G-this.x1t)-1;u=s-1;for(c=B(u/2);--u>=b&&!(u==c&&(a=d,0==a));){p+=k;n+=k;q+=x;q>s&&(p+=
w,q-=m);if(0!=a&&u<G&&0<=p&&p<r&&j<e){var A=this.getZCurrent(this.a,this.b,n);A<h[p]&&v.addPixel(p,A,a)}j=(j+1)%f}}else{this.setRastAB(b.y,b.z,c.y,c.z);n=0;b=Math.abs(u-this.y2t)-1;G=Math.abs(u-this.y1t)-1;u=L-1;for(c=B(u/2);--u>=b&&!(u==c&&(a=d,0==a));)p+=w,q+=z,n+=m,n>L&&(p+=k,n-=x),0!=a&&(u<G&&0<=p&&p<r&&j<e)&&(A=this.getZCurrent(this.a,this.b,q),A<h[p]&&v.addPixel(p,A,a)),j=(j+1)%f}}}},"~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 b=this.g3d.xLast,c=this.g3d.yLast,f=this.g3d.slab,e=this.g3d.depth;do{if(0!=(a&d))return 2;var h=this.x2t-this.x1t,k=this.y2t-this.y1t,m=this.z2t-this.z1t;0!=a?(0!=(a&8)?(this.y1t+=D(-this.x1t*k/h),this.z1t+=D(-this.x1t*m/h),this.x1t=0):0!=(a&4)?(this.y1t+=D((b-this.x1t)*k/h),this.z1t+=D((b-this.x1t)*m/h),this.x1t=b):0!=(a&2)?(this.x1t+=D(-this.y1t*h/k),this.z1t+=D(-this.y1t*m/k),this.y1t=0):
0!=(a&1)?(this.x1t+=D((c-this.y1t)*h/k),this.z1t+=D((c-this.y1t)*m/k),this.y1t=c):0!=(a&32)?(this.x1t+=D((f-this.z1t)*h/m),this.y1t+=D((f-this.z1t)*k/m),this.z1t=f):(this.x1t+=D((e-this.z1t)*h/m),this.y1t+=D((e-this.z1t)*k/m),this.z1t=e),a=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(d&8)?(this.y2t+=D(-this.x2t*k/h),this.z2t+=D(-this.x2t*m/h),this.x2t=0):0!=(d&4)?(this.y2t+=D((b-this.x2t)*k/h),this.z2t+=D((b-this.x2t)*m/h),this.x2t=b):0!=(d&2)?(this.x2t+=D(-this.y2t*h/k),this.z2t+=D(-this.y2t*
m/k),this.y2t=0):0!=(d&1)?(this.x2t+=D((c-this.y2t)*h/k),this.z2t+=D((c-this.y2t)*m/k),this.y2t=c):0!=(d&32)?(this.x2t+=D((f-this.z2t)*h/m),this.y2t+=D((f-this.z2t)*k/m),this.z2t=f):(this.x2t+=D((e-this.z2t)*h/m),this.y2t+=D((e-this.z2t)*k/m),this.z2t=e),d=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(a|d));return 1});c(b,"plotLineClippedOld",function(a,d,b,c,f,e,h,k,m,j,n){var q=this.g3d.zbuf,w=this.g3d.width,s=0;0==j&&(n=2147483647,j=1);var G=c*w+b,L=this.g3d.bufferSize,u=this.g3d.pixel;
0!=a&&(!m&&0<=G&&G<L&&f<q[G])&&u.addPixel(G,f,a);if(!(0==e&&0==h)){m=1;var p=w;b+=e;var r=c+h;0>e&&(e=-e,m=-1);0>h&&(h=-h,p=-w);w=e+e;c=h+h;f<<=10;if(h<=e){var v=e-1;0>k&&(v=-v);k=B(((k<<10)+v)/e);h=0;v=Math.abs(b-this.x2t)-1;b=Math.abs(b-this.x1t)-1;for(var r=e-1,z=B(r/2);--r>=v&&!(r==z&&(a=d,0==a));){G+=m;f+=k;h+=c;h>e&&(G+=p,h-=w);if(0!=a&&r<b&&0<=G&&G<L&&s<n){var x=f>>10;x<q[G]&&u.addPixel(G,x,a)}s=(s+1)%j}}else{v=h-1;0>k&&(v=-v);k=B(((k<<10)+v)/h);e=0;v=Math.abs(r-this.y2t)-1;b=Math.abs(r-this.y1t)-
1;r=h-1;for(z=B(r/2);--r>=v&&!(r==z&&(a=d,0==a));)G+=p,f+=k,e+=w,e>h&&(G+=m,e-=c),0!=a&&(r<b&&0<=G&&G<L&&s<n)&&(x=f>>10,x<q[G]&&u.addPixel(G,x,a)),s=(s+1)%j}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N")});p("J.g3d");C(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){var b=v(function(){this.pb=this.zb=this.p0=this.g=null;this.bgcolor=this.width=0;r(this,arguments)},J.g3d,"Pixelator",null);x(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,b){this.zb[a]=d;this.pb[a]=b},"~N,~N,~N");c(b,"addImagePixel",function(a,d,b,c,f,e){if(c<this.zb[b])switch(a){case 0:break;case 8:this.addPixel(b,c,f);break;default:a+=d,7>=a&&(d=this.pb[b],0!=e&&(d=J.g3d.Graphics3D.mergeBufferPixel(d,e,e)),d=J.g3d.Graphics3D.mergeBufferPixel(d,f&16777215|a<<24,this.bgcolor),this.addPixel(b,c,d))}},"~N,~N,~N,~N,~N,~N")});p("J.g3d");
C(["J.g3d.Pixelator"],"J.g3d.PixelatorT",["J.g3d.Graphics3D"],function(){var b=H(J.g3d,"PixelatorT",J.g3d.Pixelator);j(b,"clearPixel",function(){},"~N,~N");j(b,"addPixel",function(a,d,b){var c=this.g.zbufT[a];if(d<c){var f=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=f&&c-d>this.g.zMargin)&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],f,this.g.bgcolor));this.g.zbufT[a]=d;this.g.pbufT[a]=b&this.g.translucencyMask}else d!=c&&!this.g.translucentCoverOnly&&d-c>this.g.zMargin&&(this.pb[a]=
J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],b&this.g.translucencyMask,this.g.bgcolor))},"~N,~N,~N")});p("J.g3d");C(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){var b=v(function(){this.tmp=this.bgRGB=null;this.zShadePower=this.zDepth=this.zSlab=0;r(this,arguments)},J.g3d,"PixelatorShaded",J.g3d.Pixelator);x(b,function(a){M(this,J.g3d.PixelatorShaded,[a]);this.tmp=E(3,0)},"J.g3d.Graphics3D");c(b,"set",function(a,d,b){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=b;this.p0=this.g.pixel0;return this},"~N,~N,~N");j(b,"addPixel",function(a,d,b){if(!(d>this.zDepth)){if(d>=this.zSlab&&0<this.zShadePower){var c=this.tmp,f=this.bgRGB;c[0]=b;c[1]=b>>8;c[2]=b>>16;var e=(this.zDepth-d)/(this.zDepth-this.zSlab);if(1<this.zShadePower)for(var h=0;h<this.zShadePower;h++)e*=e;for(h=0;3>h;h++)c[h]=f[h]+D(e*((c[h]&255)-f[h]));b=c[2]<<16|c[1]<<8|c[0]|b&4278190080}this.p0.addPixel(a,d,b)}},
"~N,~N,~N");c(b,"showZBuffer",function(){for(var a=this.p0.zb.length;0<=--a;)if(0!=this.p0.pb[a]){var d=D(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}})});p("J.g3d");C(["J.g3d.Pixelator"],"J.g3d.PixelatorScreened",null,function(){var b=H(J.g3d,"PixelatorScreened",J.g3d.Pixelator);x(b,function(a,d){M(this,J.g3d.PixelatorScreened,[a]);this.width=a.width;this.p0=d},"J.g3d.Graphics3D,J.g3d.Pixelator");j(b,"addPixel",function(a,
d,b){a%this.width%2==B(a/this.width)%2&&this.p0.addPixel(a,d,b)},"~N,~N,~N")});p("J.g3d");u=v(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;r(this,arguments)},J.g3d,"Platform3D",null);x(u,function(b){this.apiPlatform=b},"J.api.GenericPlatform");
c(u,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(u,"allocateTBuffers",function(b){this.bufferSizeT=b?this.bufferSize:this.windowSize;this.zBufferT=E(this.bufferSizeT,0);this.pBufferT=E(this.bufferSizeT,0)},"~B");c(u,"allocateBuffers",function(b,a,d,g){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,g)},"~N,~N,~B,~B");c(u,"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(u,"hasContent",
function(){for(var b=this.bufferSize;0<=--b;)if(2147483647!=this.zBuffer[b])return!0;return!1});c(u,"clearScreenBuffer",function(){for(var b=this.bufferSize;0<=--b;)this.zBuffer[b]=2147483647,this.pBuffer[b]=0});c(u,"setBackgroundColor",function(b){if(null!=this.pBuffer)for(var a=this.bufferSize;0<=--a;)0==this.pBuffer[a]&&(this.pBuffer[a]=b)},"~N");c(u,"clearTBuffer",function(){for(var b=this.bufferSizeT;0<=--b;)this.zBufferT[b]=2147483647,this.pBufferT[b]=0});c(u,"clearBuffer",function(){this.clearScreenBuffer()});
c(u,"clearScreenBufferThreaded",function(){});c(u,"notifyEndOfRendering",function(){this.apiPlatform.notifyEndOfRendering()});c(u,"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(u,"allocateOffscreenImage",function(b,a){return this.apiPlatform.newOffScreenImage(b,a)},"~N,~N");c(u,"setBackgroundTransparent",function(b){J.g3d.Platform3D.backgroundTransparent=b},"~B");u.backgroundTransparent=!1;p("J.g3d");u=v(function(){this.b=this.a=0;this.isOrthographic=!1;r(this,arguments)},J.g3d,"PrecisionRenderer",
null);c(u,"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(u,"setRastABFloat",function(b,a,d,g){var c=g-a,f=d-b;0==c||0==f?(this.a=1.4E-45,this.b=a):this.isOrthographic?(this.a=c/f,this.b=a-this.a*b):(this.a=f*a*(g/c),this.b=(d*g-b*a)/c)},"~N,~N,~N,~N");c(u,"setRastAB",function(b,a,d,g){var c=g-a,f=d-b;1.4E-45==b||0==c||0==f?(this.a=1.4E-45,this.b=g):this.isOrthographic?(this.a=c/f,this.b=a-this.a*b):(this.a=f*a*(g/c),this.b=(d*g-b*a)/
c)},"~N,~N,~N,~N");p("J.g3d");C(["JU.P3"],"J.g3d.SphereRenderer",null,function(){var b=v(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;r(this,arguments)},J.g3d,"SphereRenderer",null);P(b,function(){this.zroot=R(2,0);this.ptTemp=new JU.P3;this.planeShades=E(3,0);this.dxyz=K(3,3,0)});x(b,function(a){this.g3d=
a;this.shader=a.shader},"J.g3d.Graphics3D");c(b,"render",function(a,d,b,c,f,e,h,k,m,j){if(1!=f&&(49<d&&(d&=-2),!this.g3d.isClippedXY(d,b,c))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var n=d+1>>1,q=f-n;if(!(f+n<this.slab||q>this.depth)){var w=b-n,s=b+n,G=c-n,L=c+n;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*c+b;var u=this.shader;this.mat=e;if(null!=e&&(this.coef=h,this.mDeriv=k,this.selectedOctant=
m,null==u.ellipsoidShades&&u.createEllipsoidShades(),null!=j)){this.planeShade=-1;for(h=0;3>h;h++)if(n=this.dxyz[h][0]=j[h].x-b,k=this.dxyz[h][1]=j[h].y-c,m=this.dxyz[h][2]=j[h].z-f,this.planeShades[h]=u.getShadeIndex(n,k,-m),0==n&&0==k){this.planeShade=this.planeShades[h];break}}if(null!=e||128<d)this.renderQuadrant(-1,-1,b,c,f,d,a),this.renderQuadrant(-1,1,b,c,f,d,a),this.renderQuadrant(1,-1,b,c,f,d,a),this.renderQuadrant(1,1,b,c,f,d,a),null!=e&&(this.mDeriv=this.coef=this.mat=null);else{var p=
u.sphereShapeCache[d-1];if(null==p){p=0;e=0!=(d&1);j=d/2;k=j*j;n=B((d+1)/2);m=e?0:0.5;for(h=0;h<n;++h,++m)for(var r=m*m,v=e?0:0.5,z=0;z<n;++z,++v){var x=v*v,x=k-r-x;0<=x&&++p}var p=E(p,0),A=0;m=e?0:0.5;for(h=0;h<n;++h,++m){r=m*m;v=e?0:0.5;for(z=0;z<n;++z,++v)if(x=v*v,x=k-r-x,0<=x){var C=Math.sqrt(x),x=D(C),F=u.getShadeN(v,m,C,j),H=u.getShadeN(-v,m,C,j),I=u.getShadeN(v,-m,C,j),C=u.getShadeN(-v,-m,C,j),x=x|F<<7|H<<13|I<<19|C<<25;p[A++]=x}p[A-1]|=2147483648}u.sphereShapeCache[d-1]=p}0>w||s>=this.width||
0>G||L>=this.height||q<this.slab||f>this.depth?this.renderSphereClipped(p,b,c,f,d,a):this.renderSphereUnclipped(p,f,d,a)}this.zbuf=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(b,"renderSphereUnclipped",function(a,d,b,c){var f=0,e=1-(b&1),h=this.offsetPbufBeginLine,k=h-e*this.width;b=B((b+1)/2);var m=this.zbuf,j=this.width,n=this.g3d.pixel;do{var q=h,w=h-e,s=k,G=k-e,L;do{L=a[f++];var p=d-(L&127);p<m[q]&&n.addPixel(q,p,c[L>>7&63]);p<m[w]&&n.addPixel(w,p,c[L>>13&63]);p<m[s]&&n.addPixel(s,p,c[L>>
19&63]);p<m[G]&&n.addPixel(G,p,c[L>>25&63]);++q;--w;++s;--G}while(0<=L);h+=j;k-=j}while(0<--b)},"~A,~N,~N,~A");c(b,"renderSphereClipped",function(a,d,b,c,f,e){var h=this.width,k=this.height,m=0,j=1-(f&1),n=this.offsetPbufBeginLine,q=n-j*h;f=B((f+1)/2);var w=b,s=b-j;b=(d<<16)+(b<<1)^858993459;var G=this.zbuf,L=this.g3d.pixel,p=this.slab,u=this.depth;do{var r=0<=w&&w<k,v=0<=s&&s<k,x=n,z=n-j,A=q,C=q-j,D,E=d,F=d-j;do{var H=0<=F&&F<h,I=0<=E&&E<h;D=a[m++];var M;M=D&127;var K;c<p?(K=c+M,M=K>=p):(K=c-M,M=
K<p);M&&(K=p);if(K>=p&&K<=u){if(r){if(I&&K<G[x]){var N=M?44+(b>>7&7):D>>7&63;L.addPixel(x,K,e[N])}H&&K<G[z]&&(N=M?44+(b>>13&7):D>>13&63,L.addPixel(z,K,e[N]))}v&&(I&&K<G[A]&&(N=M?44+(b>>19&7):D>>19&63,L.addPixel(A,K,e[N])),H&&K<G[C]&&(N=M?44+(b>>25&7):D>>25&63,L.addPixel(C,K,e[N])))}++x;--z;++A;--C;++E;--F;M&&(b=(b<<16)+(b<<1)+b&2147483647)}while(0<=D);n+=h;q-=h;++w;--s}while(0<--f)},"~A,~N,~N,~N,~N,~A");c(b,"renderQuadrant",function(a,d,b,c,f,e,h){e=B(e/2);var k=b+e*a,m=(0>b?-1:b<this.width?0:1)+
(0>k?-2:k<this.width?0:2);-3==m||3==m||(k=c+e*d,k=(0>c?-1:c<this.height?0:1)+(0>k?-2:k<this.height?0:2),-3==k||3==k||(null==this.mat&&0==m&&0==k&&f-e>=this.slab&&f<=this.depth?this.renderQuadrantUnclipped(e,a,d,f,h):this.renderQuadrantClipped(e,a,d,b,c,f,h)))},"~N,~N,~N,~N,~N,~N,~A");c(b,"renderQuadrantUnclipped",function(a,d,b,c,f){for(var e=a*a,h=2*a+1,k=0>b?-this.width:this.width,m=this.offsetPbufBeginLine,j=this.zbuf,n=this.g3d.pixel,q=this.shader.sphereShadeIndexes,w=0,s=0;s<=e;s+=w+ ++w,m+=
k)for(var G=m,L=e-s,p=c-a,u=B((w*b+a<<8)/h),r=0,v=0;v<=L;v+=r+ ++r,G+=d)if(!(j[G]<=p)&&(p=B(Math.sqrt(L-v)),p=c-p,!(j[G]<=p))){var x=B((r*d+a<<8)/h);n.addPixel(G,p,f[q[(u<<8)+x]])}},"~N,~N,~N,~N,~A");c(b,"renderQuadrantClipped",function(a,d,b,c,f,e,h){for(var k=null!=this.mat,m=0<=this.selectedOctant,j=a*a,n=2*a+1,q=0>b?-this.width:this.width,w=this.offsetPbufBeginLine,s=(c<<16)+(f<<1)^858993459,G=0,p=0,u=this.g3d.pixel,r=0,v=this.height,x=this.width,z=this.zbuf,A=this.dxyz,C=this.slab,D=this.depth,
E=this.ptTemp,F=this.coef,H=this.zroot,I=this.selectedOctant,K=this.shader,M=this.planeShades,N=K.sphereShadeIndexes,P=this.planeShade,Q=this.mat,U=0,V=0,R=f;V<=j;V+=U+ ++U,w+=q,R+=b)if(0>R){if(0>b)break}else if(R>=v){if(0<b)break}else{var W=j-(k?0:V);k||(G=B((U*b+a<<8)/n));for(var s=(s<<16)+(s<<1)+s&2147483647,T=c,Y=0,$=0,aa=-1,ba=1,Z=w;$<=W;$+=Y+ ++Y,Z+=d,T+=d)if(0>T){if(0>d)break}else if(T>=x){if(0<d)break}else{var S;if(k){S=(F[4]*T+F[5]*R+F[8])/F[2]/2;var X=S*S-(F[0]*T*T+F[1]*R*R+F[3]*T*R+F[6]*
T+F[7]*R-1)/F[2];if(0>X){if(0<=aa)break;continue}X=Math.sqrt(X);H[0]=-S-X;H[1]=-S+X;aa=e<C?1:0;if(0==(S=B(H[aa])))S=e;ba=2;r=S;if(m){E.set(T-c,R-f,S-e);Q.rotate(E);X=0;0>E.x&&(X|=1);0>E.y&&(X|=2);0>E.z&&(X|=4);if(X==I){if(0<=P)p=P;else{ba=3;p=3.4028235E38;for(S=0;3>S;S++)if(0!=(X=A[S][2]))X=e+(-A[S][0]*(T-c)-A[S][1]*(R-f))/X,X<p&&(p=X,ba=S);3==ba&&(ba=0,p=e);H[0]=p;p=M[ba]}S=B(H[0]);ba=3}if(X=e<C?S>=C:S<C)r=S=C,ba=0}if(S<C||S>D||z[Z]<=r)continue}else{S=B(Math.sqrt(W-$));S=e+(e<C?S:-S);if(X=e<C?S>=
C:S<C)S=C,ba=0;if(S<C||S>D||z[Z]<=S)continue}switch(ba){case 0:p=44+(s>>8&7);s=(s<<16)+(s<<1)+s&2147483647;ba=1;break;case 2:p=K.getEllipsoidShade(T,R,H[aa],a,this.mDeriv);break;case 3:u.clearPixel(Z,r);break;default:p=B((Y*d+a<<8)/n),p=N[(G<<8)+p]}u.addPixel(Z,S,h[p])}s=(s+T+R|1)&2147483647}},"~N,~N,~N,~N,~N,~N,~A")});p("J.g3d");C(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU","J.g3d.Graphics3D"],function(){var b=v(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=
null;this.isInvalid=!1;r(this,arguments)},J.g3d,"TextRenderer",null);x(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,b,c,f,e,h,k,m,j){if(0==e.length)return 0;if(0<=e.indexOf("<su")||
0<=e.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,d,b,c,f,e,h,k,m,j);var n=h.getAscent();d-=n;e=J.g3d.TextRenderer.getPlotText3D(a,d,k,e,h,j);if(e.isInvalid)return e.width;j&&(c=J.g3d.Graphics3D.fixTextImageRGB(c));j=e.height;h=e.width;var n=e.tmap,q=k.width,w=k.height,s=k.zbuf,G=k.pixel,p=k.translucencyLog;if(null!=m||(0>a||a+e.width>q||0>d||d+e.height>w)&&null!=(m=k))for(var u=k=0;u<j;u++)for(var r=0;r<h;r++){var v=n[k++];0!=v&&m.plotImagePixel(c,a+r,d+u,b,v,f,q,w,s,G,p)}else{k=
u=0;for(a=d*q+a;u<j;u++,a+=q-h)for(r=0;r<h;r++)G.addImagePixel(n[k++],p,a++,b,c,f)}return e.width},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");b.plotByCharacter=c(b,"plotByCharacter",function(a,d,b,c,f,e,h,k,m,j){for(var n=0,q=e.length,w=Math.round(0.25*h.getHeight()),s=-Math.round(0.3*h.getHeight()),G=0,p=0;p<q;p++){if("<"==e.charAt(p)){if(p+5<q&&e.substring(p,p+6).equals("<color")){var G=c,u=e.indexOf(">",p);if(0>u)continue;c=JU.CU.getArgbFromString(e.substring(p+
7,u).trim());p=u;continue}if(p+7<q&&e.substring(p,p+8).equals("</color>")){p+=7;c=G;continue}if(p+4<q&&e.substring(p,p+5).equals("<sub>")){p+=4;d+=w;continue}if(p+4<q&&e.substring(p,p+5).equals("<sup>")){p+=4;d+=s;continue}if(p+5<q&&e.substring(p,p+6).equals("</sub>")){p+=5;d-=w;continue}if(p+5<q&&e.substring(p,p+6).equals("</sup>")){p+=5;d-=s;continue}}u=J.g3d.TextRenderer.plot(a+n,d,b,c,f,e.substring(p,p+1),h,k,m,j);n+=u}return n},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");
b.getPlotText3D=c(b,"getPlotText3D",function(a,d,b,c,f,e){J.g3d.TextRenderer.working=!0;e=e?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var h=e.get(f),k=null,m=!1,j=!1;null!=h?k=h.get(c):(h=new java.util.Hashtable,m=!0);null==k&&(k=new J.g3d.TextRenderer(c,f),j=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=b.width||0>=d+k.height||d>=b.height;if(k.isInvalid)return k;m&&e.put(f,h);j&&(k.setTranslucency(c,f,b),h.put(c,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=Q(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=Q(-1,[7,6,5,4,3,2,1,8]);b.working=!1;b.htFont3d=new java.util.Hashtable;b.htFont3dAntialias=new java.util.Hashtable});p("J.g3d");
C(["JU.P3i"],"J.g3d.TextString",null,function(){var b=v(function(){this.font=this.text=null;this.bgargb=this.argb=0;r(this,arguments)},J.g3d,"TextString",JU.P3i,java.util.Comparator);c(b,"setText",function(a,d,b,c,f,e,h){this.text=a;this.font=d;this.argb=b;this.bgargb=c;this.x=f;this.y=e;this.z=h},"~S,JU.Font,~N,~N,~N,~N,~N");j(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");j(b,"toString",function(){return this.asString()+" "+this.text})});
p("J.g3d");C(["J.g3d.G3DRenderer","$.PrecisionRenderer","JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){var b=v(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;r(this,arguments)},J.g3d,"TriangleRenderer",J.g3d.PrecisionRenderer,J.g3d.G3DRenderer);P(b,function(){this.ax=E(3,0);this.ay=E(3,0);this.az=E(3,0);this.aa=K(64,0);this.bb=K(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});x(b,function(){M(this,J.g3d.TriangleRenderer,[])});j(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(!F(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 f=this.g3d.clipCode3(this.ax[2],this.ay[2],this.az[2]),e=d|b|f;a=0!=e;if(!a||!(-1==e||0!=(d&b&f))){f=0;this.ay[1]<this.ay[f]&&(f=1);this.ay[2]<this.ay[f]&&(f=2);var e=(f+1)%3,h=(f+2)%3;if(this.ay[e]>this.ay[h])var k=e,e=h,h=k;d=this.ay[f];var m=this.ay[e],j=this.ay[h];b=j-d+1;if(!(b>3*this.g3d.height)){if(b>this.axW.length){var n=b+31&-32;this.axW=E(n,0);this.azW=E(n,0);this.axE=E(n,0);this.azE=E(n,0);this.aa=K(n,0);
this.bb=K(n,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,n);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,n)}var q;c?(n=this.rgb16sW,q=this.rgb16sE):n=q=null;k=m-d;0==k?(this.ax[e]<this.ax[f]&&(k=e,e=f,f=k),this.generateRaster(b,f,h,this.axW,this.azW,0,n),this.generateRaster(b,e,h,this.axE,this.azE,0,q)):m==j?(this.ax[h]<this.ax[e]&&(k=e,e=h,h=k),this.generateRaster(b,f,e,this.axW,this.azW,0,n),this.generateRaster(b,f,h,this.axE,this.azE,0,q)):(m=this.ax[h]-this.ax[f],j=JU.GData.roundInt(B(b/2)),
0>m&&(j=-j),this.ax[f]+B((m*k+j)/b)<this.ax[e]?(this.generateRaster(b,f,h,this.axW,this.azW,0,n),this.generateRaster(k+1,f,e,this.axE,this.azE,0,q),this.generateRaster(b-k,e,h,this.axE,this.azE,k,q)):(this.generateRaster(k+1,f,e,this.axW,this.azW,0,n),this.generateRaster(b-k,e,h,this.axW,this.azW,k,n),this.generateRaster(b,f,h,this.axE,this.azE,0,q)));this.g3d.setZMargin(5);f=this.g3d.pass2Flag01;e=1-f;h=0;0>d&&(b+=d,h-=d,d=0);d+b>this.g3d.height&&(b=this.g3d.height-d);if(c)if(a)for(;--b>=f;++d,++h)a=
this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRaster(a,c,d,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else for(;--b>=f;++d,++h)a=this.axE[h]-(c=this.axW[h])+e,1==f&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRaster(a,c,d,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else if(a)for(;--b>=f;++d,++h)a=this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRasterBits(a,c,d,this.azW[h],this.azE[h],null,null,this.aa[h],this.bb[h]);else for(;--b>=f;++d,++h)a=
this.axE[h]-(c=this.axW[h])+e,1==f&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRasterBits(a,c,d,null,null,this.aa[h],this.bb[h]);this.g3d.setZMargin(0)}}}},"JU.P3i,JU.P3i,JU.P3i,~B");c(b,"generateRaster",function(a,d,b,c,f,e,h){var k=this.ax[d],m=this.ax[b]-k,j,n,q;0<=m?(j=1,n=m,q=0):(j=-1,n=-m,q=1-a);var w;n<=a?w=0:(w=JU.GData.roundInt(B(m/a)),n%=a);this.setRastAB(this.ay[d],this.az[d],this.ay[b],this.az[b]);for(var s=this.a,p=this.b,u=c===this.axE,r=0,v=this.ay[d],x=a-1,m=e;r<=x;++m,++r,++v){if(0==
m||m>e)c[m]=r==x?this.ax[b]:k,f[m]=this.getZCurrent(s,p,v),u&&(this.setRastAB(this.axW[m],this.azW[m],c[m],f[m]),this.aa[m]=this.a,this.bb[m]=this.b);k+=w;q+=n;0<q&&(k+=j,q-=a)}if(null!=h){c=this.rgb16t1;c.setRgb(this.rgb16sGouraud[d]);d=this.rgb16t2;d.diffDiv(this.rgb16sGouraud[b],c,a);m=e;for(a=e+a;m<a;++m)h[m].setAndIncrement(c,d)}},"~N,~N,~N,~A,~A,~N,~A")});p("J.i18n");C("J.api.Translator java.text.MessageFormat java.util.Hashtable JU.PT J.i18n.Language $.Resource".split(" "),"J.i18n.GT",["JU.Logger"],
function(){var b=v(function(){this.resources=null;this.resourceCount=0;this.doTranslate=!0;this.language=null;r(this,arguments)},J.i18n,"GT",null,J.api.Translator);x(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,
f=null,e=this.language.indexOf("_");if(0<=e&&(b=b.substring(0,e),c=this.language,0<=(e=c.indexOf("_",++e))))c=c.substring(0,e),f=this.language;if(null==(this.language=this.getSupported(f))&&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=f=null;switch(this.language.length){default:f=this.language;c=this.language.substring(0,5);b=this.language.substring(0,2);break;case 5:c=
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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 j=!d,n=!d&&0>this.vectorT2.x,q=null!=c&&0<c.length,w,s,p=Array(1),u=this.draw000?0:-1;k<h;){if(k>=this.tickInfo.first&&
(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,this.pointT2),this.drawLine(B(Math.floor(this.pointT2.x)),B(Math.floor(this.pointT2.y)),D(m),w=B(Math.floor(this.pointT2.x+this.vectorT2.x)),s=B(Math.floor(this.pointT2.y+this.vectorT2.y)),D(m),b),q&&(this.draw000||0!=k))){p[0]=Float.$valueOf(0==k?0:k*f);var r=JU.PT.sprintf(c[u%c.length],"f",p);this.drawString(w,s,D(m),4,n,d,j,B(Math.floor(this.pointT2.y)),r)}this.pointT.add(this.vectorT);k+=a;m+=e;u++}}}},"~N,~N,~N,~A");c(b,"drawLine",
function(a,d,b,c,f,e,h){return this.drawLine2(this.g3d,a,d,b,c,f,e,h)},"~N,~N,~N,~N,~N,~N,~N");c(b,"drawLine2",function(a,d,b,c,f,e,h,k){this.pt0.set(d,b,c);this.pt1.set(f,e,h);if(this.dotsOrDashes)null!=this.dashDots&&J.render.FontLineShapeRenderer.drawDashedCylinder(a,d,b,c,f,e,h,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 B((k+1)/2)},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~N");c(b,"drawString",function(a,d,b,c,f,e,h,k,m){if(null!=m){var j=this.font3d.stringWidth(m),n=this.font3d.getAscent();a=f?a-(B(c/2)+2+j):e?a-(B(c/2)+2+B(j/2)):a+(B(c/2)+2);f=d;f=h?f+B(n/2):0==k||k<d?f+n:f-B(c/2);d=b-c-2;1>d&&(d=1);this.g3d.drawString(m,this.font3d,a,f,d,d,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");b.drawDashedCylinder=c(b,"drawDashedCylinder",function(a,d,b,c,f,e,h,k,m,j,n,q,w,s){if(!(null==k||0>m)){var p=k[0];
f-=d;e-=b;h-=c;var u=0,r=k===J.render.FontLineShapeRenderer.ndots,v=r||k===J.render.FontLineShapeRenderer.sixdots;if(v){null==s&&(s=new JU.P3i);var x=(f*f+e*e)/(m*m);r?(p=Math.sqrt(x)/1.5,u=D(p)+2):8>x?k=J.render.FontLineShapeRenderer.twodots:32>x&&(k=J.render.FontLineShapeRenderer.fourdots)}var x=k[1],z=k[2],A=j,C=0==z?n:j;0==u&&(u=k.length);for(var E=0,F=3;F<u;F++){var E=r?E+1:k[F],H=B(Math.floor(d+f*E/p)),I=B(Math.floor(b+e*E/p)),K=B(Math.floor(c+h*E/p));if(v)s.set(H,I,K),F==x?a.setC(j):F==z&&
a.setC(n),a.fillSphereI(m,s);else{F==x&&(A=n);E=k[++F];F==z&&(C=n);var M=B(Math.floor(d+f*E/p)),N=B(Math.floor(b+e*E/p)),P=B(Math.floor(c+h*E/p));J.render.FontLineShapeRenderer.fillCylinder(a,A,C,2,H,I,K,M,N,P,q,w)}}}},"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,f,e,h,k,m,j,n,q){q?a.drawLine(d,b,f,e,h,k,m,j):a.fillCylinderXYZ(d,b,c,n,f,e,h,k,m,j)},"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])});p("J.render");C(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["JV.Viewer"],function(){var b=H(J.render,"FrankRenderer",J.render.ShapeRenderer);j(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=D(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})});p("J.render");C(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.api.Interface","JU.Logger","JV.JC","$.Viewer"],function(){var b=v(function(){this.bsTranslucent=this.renderers=this.shapeManager=
this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;r(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);P(b,function(){this.bsTranslucent=JU.BS.newN(37)});x(b,function(){});j(b,"set",function(a,d){this.vwr=a;this.shapeManager=d},"JV.Viewer,JV.ShapeManager");j(b,"isRepaintPending",function(){return this.repaintPending});j(b,"pushHoldRepaint",function(){++this.holdRepaint},"~S");j(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");j(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(F(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");j(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");j(b,"repaintDone",function(){this.repaintPending=!1});j(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");j(b,"render",function(a,d,b,c){null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();try{var f=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 e=this.vwr.getRubberBandSelection();null!=e&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(e.x,e.y,0,0,e.width,e.height);this.vwr.noFrankEcho=!0}c=null;for(e=0;37>e&&a.currentlyRendering;++e){var h=this.shapeManager.getShape(e);null!=h&&(f&&(c="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(c)),(b||this.bsTranslucent.get(e))&&
this.getRenderer(e).renderShape(a,d,h)&&this.bsTranslucent.set(e),f&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(F(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;});j(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 f=0;37>f;++f){var e=this.shapeManager.getShape(f);null!=e&&(c&&(b="rendering "+JV.JC.getShapeClassName(f,!1),JU.Logger.startTimer(b)),
this.getRenderer(f).renderShape(a,d,e),c&&JU.Logger.checkTimer(b,!1))}a.renderAllStrings(a);b=a.finalizeOutput()}catch(h){if(F(h,Exception))h.printStackTrace(),JU.Logger.error("rendering error? "+h);else throw h;}return b},"JU.GData,JM.ModelSet,java.util.Map")});p("J.render");C(null,"J.render.ShapeRenderer",["JV.JC"],function(){var b=v(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;r(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")});p("J.render");C(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["JU.A4","$.M3","J.c.PAL","JU.C","$.Edge"],function(){var b=v(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;r(this,arguments)},J.render,"SticksRenderer",
J.render.FontLineShapeRenderer);P(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)});j(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=D(this.vwr.tm.scaleToScreen(B((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=B(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=B(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=B(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 f=!this.isExport||1==this.mad?this.width:this.mad,e=1<this.bondOrder&&0<this.multipleBondSpacing,h=e&&(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&&!e){a=B(this.width/8)+3;a=this.width+a;d=this.yA-B((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,f,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,f,this.asLineOnly,this.s1):
J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,f,this.asLineOnly);else if(e)if(h||this.z.setT(JU.P3.getUnlikely()),this.x.sub2(this.b,this.a),this.y.cross(this.x,this.z),this.y.normalize(),Float.isNaN(this.y.x)&&(this.z.setT(JU.P3.getUnlikely()),this.y.cross(this.x,this.z),this.y.cross(this.y,this.x),this.y.normalize()),this.bondsPerp&&this.y.cross(this.y,this.x),this.y.scale(this.multipleBondSpacing),this.x.setT(this.y),
this.x.scale((this.bondOrder-1)/2),this.useBananas)switch(this.drawBanana(this.a,this.b,this.x,0),this.bondOrder){case 4:this.drawBanana(this.a,this.b,this.x,90),this.drawBanana(this.a,this.b,this.x,-90);default:this.drawBanana(this.a,this.b,this.x,180);break;case 3:this.drawBanana(this.a,this.b,this.x,120),this.drawBanana(this.a,this.b,this.x,-120)}else{this.p1.sub2(this.a,this.x);for(this.p2.sub2(this.b,this.x);;){this.isCartesian?this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,b,this.mad,
-2):(this.tm.transformPtScr(this.p1,this.s1),this.tm.transformPtScr(this.p2,this.s2),d?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z,this.dashDots,this.width,this.colixA,this.colixB,f,this.asLineOnly,this.s1):J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z,f,this.asLineOnly));a>>=1;d=0!=(a&1);if(0>=--this.bondOrder)break;this.p1.add(this.y);
this.p2.add(this.y);this.stepAxisCoordinates()}}else if(this.mag2d=Math.round(Math.sqrt(this.dx*this.dx+this.dy*this.dy)),this.resetAxisCoordinates(),this.isCartesian&&3==this.bondOrder)J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly),this.stepAxisCoordinates(),this.x.sub2(this.b,this.a),this.x.scale(0.05),this.p1.sub2(this.a,this.x),this.p2.add2(this.b,this.x),this.g3d.drawBond(this.p1,
this.p2,this.colixA,this.colixB,b,this.mad,-2),this.stepAxisCoordinates(),J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly);else for(;;){0!=(a&1)?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,this.dashDots,this.width,this.colixA,this.colixB,f,this.asLineOnly,this.s1):J.render.FontLineShapeRenderer.fillCylinder(this.g3d,
this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly);a>>=1;if(0>=--this.bondOrder)break;this.stepAxisCoordinates()}}}},"~N");c(b,"resetAxisCoordinates",function(){var a=this.mag2d>>3;-1!=this.multipleBondSpacing&&0>this.multipleBondSpacing&&(a*=-this.multipleBondSpacing);a=this.width+a;this.dxStep=B(a*this.dy/this.mag2d);this.dyStep=B(a*-this.dx/this.mag2d);this.xAxis1=this.xA;this.yAxis1=this.yA;this.xAxis2=this.xB;this.yAxis2=this.yB;a=this.bondOrder-
1;this.xAxis1-=B(this.dxStep*a/2);this.yAxis1-=B(this.dyStep*a/2);this.xAxis2-=B(this.dxStep*a/2);this.yAxis2-=B(this.dyStep*a/2)});c(b,"stepAxisCoordinates",function(){this.xAxis1+=this.dxStep;this.yAxis1+=this.dyStep;this.xAxis2+=this.dxStep;this.yAxis2+=this.dyStep});c(b,"getAromaticDottedBondMask",function(){var a=this.b.findAromaticNeighbor(this.a.i);return null==a?1:0>this.dx*(a.sY-this.yA)-this.dy*(a.sX-this.xA)?2:1});c(b,"drawBanana",function(a,d,b,c){this.g3d.addRenderer(553648143);this.vectorT.sub2(d,
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this.pointT3);this.g3d.setC(this.colixB);this.g3d.fillHermite(5,a,a,a,this.pointT,this.pointT2,this.pointT3,this.pointT3)},"JM.Atom,JM.Atom,JU.V3,~N")});p("JS");C(["JS.T"],"JS.ContextToken",["java.util.Hashtable","JS.SV"],function(){var b=v(function(){this.name0=this.forVars=this.contextVariables=null;r(this,arguments)},JS,"ContextToken",JS.T);b.newContext=c(b,"newContext",function(a){a=a?JS.ContextToken.newCmd(1275335685,"{"):JS.ContextToken.newCmd(1275334681,"}");a.intValue=0;return a},"~B");b.newCmd=
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h.length+")"),System.exit(1));f=a.length;for(e=0;e<f;e++)g=a[e],l=g.toLowerCase(),d=h[e],d=b=-1==d?b:JS.T.o(d,g),null!=JS.T.tokenMap.get(l)&&JU.Logger.error("duplicate token definition:"+l),JS.T.tokenMap.put(l,d);h=a=null});p("J.shape");C(["J.shape.Shape"],"J.shape.AtomShape","JU.AU $.BS J.atomdata.RadiusData J.c.PAL $.VDW JU.BSUtil $.C".split(" "),function(){var b=v(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;r(this,arguments)},J.shape,"AtomShape",J.shape.Shape);j(b,"initShape",function(){});j(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))});j(b,"getSize",function(a){return null==this.mads?0:this.mads[a]},"~N");j(b,"setSize",function(a,d){this.setSize2(a,
d)},"~N,JU.BS");c(b,"setSize2",function(a,d){0==a?this.setSizeRD(null,d):(null==this.rd?this.rd=new J.atomdata.RadiusData(null,a,J.atomdata.RadiusData.EnumType.SCREEN,null):this.rd.value=a,this.setSizeRD(this.rd,d))},"~N,JU.BS");j(b,"setSizeRD",function(a,d){if(this.isSet){this.isActive=!0;var b=null!=a&&0!=a.value,c=null==d,f=this.ms.ac,e=c?f-1:d.nextSetBit(0);null==this.bsSizeSet&&(this.bsSizeSet=JU.BS.newN(f));null==this.mads&&0<=e&&(this.mads=W(f,0));for(f=e;0<=f;f=c?f-1:d.nextSetBit(f+1))this.setSizeRD2(f,
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),f=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,f,a)}else if("params"===a){this.isActive=!0;var f=d[0],
e=d[1],h=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=W(this.ms.ac,0));d=this.checkColixLength(null==f?0:4,b.length());for(var m=0;0<=a&&a<d;a=b.nextSetBit(a+1),m++){var c=null==f?0:f[m],j=null==e?0:e[m];0.01<j&&(c=JU.C.getColixTranslucent3(c,!0,j));this.setColixAndPalette(c,J.c.PAL.UNKNOWN.id,a);null!=
h&&(c=0<(k.value=h[m]),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");j(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)}});j(b,"getShapeState",function(){return null})});p("J.shape");C(["J.shape.AtomShape"],"J.shape.Balls",
["JU.BS","J.c.PAL","JU.C"],function(){var b=H(J.shape,"Balls",J.shape.AtomShape);j(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");j(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");
j(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 f=J.c.PAL.pidOf(d);for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1)){var e=this.ms.at[a];e.colixAtom=this.getColixA(c,f,e);this.bsColixSet.setBitTo(a,2!=c||f!=J.c.PAL.NONE.id);e.paletteID=f}this.vwr.setModelkitPropertySafely("key",b)}else if("colorValues"===a){if(0!=d.length){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);var h=0,f=null;for(a=b.nextSetBit(0);0<=
a&&!(h>=d.length);a=b.nextSetBit(a+1))f=Integer.$valueOf(d[h++]),c=JU.C.getColixO(f),0==c&&(c=2),f=J.c.PAL.pidOf(f),e=this.ms.at[a],e.colixAtom=this.getColixA(c,f,e),this.bsColixSet.setBitTo(a,2!=c||f!=J.c.PAL.NONE.id),e.paletteID=f}}else if("colors"===a){h=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>=h.length||0==(c=h[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");j(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))}})});p("J.shape");C(["J.shape.Shape"],"J.shape.FontLineShape",null,function(){var b=v(function(){this.font3d=this.tickInfos=null;r(this,arguments)},J.shape,"FontLineShape",J.shape.Shape);P(b,function(){this.tickInfos=Array(4)});j(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]=
null;return}b=null}this.tickInfos["xyz".indexOf(b.type)+1]=b}else"font"===a&&(this.font3d=d)},"~S,~O");j(b,"getShapeState",function(){return null})});p("J.shape");C(["J.shape.Shape"],"J.shape.Frank",["J.i18n.GT","JV.Viewer"],function(){var b=v(function(){this.frankString="Jmol";this.baseFont3d=this.currentMetricsFont3d=null;this.scaling=this.dy=this.dx=this.y=this.x=this.frankDescent=this.frankAscent=this.frankWidth=0;this.font3d=null;r(this,arguments)},J.shape,"Frank",J.shape.Shape);j(b,"initShape",
function(){this.myType="frank";this.baseFont3d=this.font3d=this.vwr.gdata.getFont3DFSS("SansSerif","Plain",16);this.calcMetrics()});j(b,"setProperty",function(a,d){"font"===a&&10<=d.fontSize&&(this.baseFont3d=d,this.scaling=0)},"~S,~O,JU.BS");j(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");j(b,"checkObjectHovered",function(a,d){if(!this.vwr.getShowFrank()||!this.wasClicked(a,d)||!this.vwr.menuEnabled())return!1;
this.vwr.hoverOnPt(a,d,J.i18n.GT.$("Click for menu..."),null,null);return!0},"~N,~N,JU.BS");c(b,"calcMetrics",function(){JV.Viewer.isJS?this.frankString="JSmol":this.vwr.isSignedApplet&&(this.frankString="Jmol_S");this.font3d!==this.currentMetricsFont3d&&(this.currentMetricsFont3d=this.font3d,this.frankWidth=this.font3d.stringWidth(this.frankString),this.frankDescent=this.font3d.getDescent(),this.frankAscent=this.font3d.getAscent())});c(b,"getFont",function(a){a!=this.scaling&&(this.scaling=a,this.font3d=
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c(b,"checkObjectDragged",function(){return!1},"~N,~N,~N,~N,~N,JU.BS");c(b,"coordinateInRange",function(a,d,b,c,f){this.vwr.tm.transformPtScr(b,f);a=(a-f.x)*(a-f.x)+(d-f.y)*(d-f.y);return a<=c?a:-1},"~N,~N,JU.T3,~N,JU.P3i");c(b,"getColixI",function(a,d,b){return this.getColixA(a,d,this.ms.at[b])},"~N,~N,~N");c(b,"getColixA",function(a,d,b){return 2==a?this.vwr.cm.getColixAtomPalette(b,d):a},"~N,~N,JM.Atom");c(b,"getColixB",function(a,d,b){return 2==a?this.vwr.cm.getColixBondPalette(b,d):a},"~N,~N,JM.Bond");
c(b,"getShapeDetail",function(){return null});b.getColix=c(b,"getColix",function(a,d,b){return JU.C.getColixInherited(null==a||d>=a.length?0:a[d],b.colixAtom)},"~A,~N,JM.Atom");b.getFontCommand=c(b,"getFontCommand",function(a,d){return null==d?"":"font "+a+" "+d.getInfo()},"~S,JU.Font");b.getColorCommandUnk=c(b,"getColorCommandUnk",function(a,d,b){return J.shape.Shape.getColorCommand(a,J.c.PAL.UNKNOWN.id,d,b)},"~S,~N,~B");b.getColorCommand=c(b,"getColorCommand",function(a,d,b,c){if(d==J.c.PAL.UNKNOWN.id&&
0==b)return"";d=d==J.c.PAL.UNKNOWN.id&&0==b?"":(c?J.shape.Shape.getTranslucentLabel(b)+" ":"")+(d!=J.c.PAL.UNKNOWN.id&&!J.c.PAL.isPaletteVariable(d)?J.c.PAL.getPaletteName(d):J.shape.Shape.encodeColor(b));return"color "+a+" "+d},"~S,~N,~N,~B");b.encodeColor=c(b,"encodeColor",function(a){return JU.C.isColixColorInherited(a)?"none":JU.C.getHexCode(a)},"~N");b.getTranslucentLabel=c(b,"getTranslucentLabel",function(a){return JU.C.isColixTranslucent(a)?JU.C.getColixTranslucencyLabel(a):"opaque"},"~N");
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v(function(){this.myMask=0;this.reportAll=!1;this.ptXY=this.closestAtom=this.selectedBonds=this.bsOrderSet=null;r(this,arguments)},J.shape,"Sticks",J.shape.Shape);P(b,function(){this.closestAtom=E(1,0);this.ptXY=new JU.P3i});j(b,"initShape",function(){this.myMask=1023;this.reportAll=!1});j(b,"setSize",function(a,d){if(2147483647==a)this.selectedBonds=JU.BSUtil.copy(d);else if(-2147483648==a)null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS),this.bsOrderSet.or(d);else{null==this.bsSizeSet&&(this.bsSizeSet=
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");j(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=z(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 f=b.next();f.colix=c?this.getColixB(a,d.id,f):JU.C.getColix(JU.Edge.getArgbHbondType(f.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.ms.bondCount;0<=--d;){var b=a[d];0==(b.shapeVisibilityFlags&this.vf)||(this.ms.isAtomHidden(b.atom1.i)||this.ms.isAtomHidden(b.atom2.i))||(b.atom1.setClickable(this.vf),b.atom2.setClickable(this.vf))}});j(b,"getShapeState",function(){return null});j(b,"checkObjectHovered",function(a,d,b){var c=new JU.P3;b=this.findPickedBond(a,d,b,c,this.closestAtom);if(null==b)return!1;this.vwr.highlightBond(b.index,this.closestAtom[0],a,d);return!0},"~N,~N,JU.BS");j(b,"checkObjectClicked",function(a,d,b,c){b=
new JU.P3;a=this.findPickedBond(a,d,c,b,this.closestAtom);if(null==a)return null;d=a.atom1.mi;c=a.getIdentity();var f=new java.util.Hashtable;f.put("pt",b);f.put("index",Integer.$valueOf(a.index));f.put("modelIndex",Integer.$valueOf(d));f.put("model",this.vwr.getModelNumberDotted(d));f.put("type","bond");f.put("info",c);this.vwr.setStatusAtomPicked(-3,'["bond","'+a.getIdentity()+'",'+b.x+","+b.y+","+b.z+"]",f,!1);return f},"~N,~N,~N,JU.BS,~B");c(b,"findPickedBond",function(a,d,b,c,f){b=100;this.vwr.gdata.isAntialiased()&&
(a<<=1,d<<=1,b<<=1);for(var e=null,h=new JU.P3,k=this.ms.bo,m=this.ms.bondCount;0<=--m;){var j=k[m];if(0!=j.shapeVisibilityFlags){var n=j.atom1,q=j.atom2;if(n.checkVisible()&&q.checkVisible()){h.ave(n,q);var w=this.coordinateInRange(a,d,h,b,this.ptXY);if(0<=w&&40<Math.abs(n.sY-q.sY)+Math.abs(n.sX-q.sX)){var s=1*(this.ptXY.x-n.sX)/(q.sX-n.sX);0.4>s||0.6<s||(b=w,e=j,null!=f&&(f[0]=0.5>s?n.i:q.i),c.setT(h))}}}}return e},"~N,~N,JU.BS,JU.P3,~A")});p("J.thread");C(["J.thread.JmolThread"],"J.thread.HoverWatcherThread",
null,function(){var b=v(function(){this.moved=this.current=this.actionManager=null;this.hoverDelay=0;r(this,arguments)},J.thread,"HoverWatcherThread",J.thread.JmolThread);x(b,function(a,d,b,c){this.setViewer(c,"HoverWatcher");this.actionManager=a;this.current=d;this.moved=b;this.start()},"JV.ActionManager,JV.MouseState,JV.MouseState,JV.Viewer");j(b,"run1",function(a){for(;;)switch(a){case -1:this.isJS||Thread.currentThread().setPriority(1);a=0;break;case 0:this.hoverDelay=this.vwr.getHoverDelay();
if(this.stopped||0>=this.hoverDelay||!this.runSleep(this.hoverDelay,1))return;a=1;break;case 1:this.moved.is(this.current)&&(this.currentTime=System.currentTimeMillis(),this.currentTime-this.moved.time>(this.vwr.acm.zoomTrigger?100:this.hoverDelay)&&!this.stopped&&this.actionManager.checkHover()),a=0}},"~N")});p("J.thread");C(["java.lang.Thread"],"J.thread.JmolThread",["JU.Logger","JV.Viewer"],function(){var b=v(function(){this.$name="JmolThread";this.sc=this.eval=this.vwr=null;this.hoverEnabled=
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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,f){var e=d.get(b);
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b.length()?b.toString():"<no timeouts set>"},"java.util.Map,~S")});p("JM");C(["JU.Node","$.Point3fi","J.c.PAL"],"JM.Atom","JU.BS $.CU $.P3 $.PT $.SB J.atomdata.RadiusData J.c.VDW JM.Group JU.C $.Elements JV.JC".split(" "),function(){var b=v(function(){this.altloc="\x00";this.atomSite=this.atomID=0;this.group=null;this.atomNumberFlags=this.valence=this.userDefinedVanDerWaalRadius=0;this.atomSymmetry=null;this.paletteID=this.colixAtom=this.madAtom=this.formalChargeAndFlags=0;this.bonds=null;this.shapeVisibilityFlags=
this.clickabilityFlags=this.nBackbonesDisplayed=this.nBondsDisplayed=0;r(this,arguments)},JM,"Atom",JU.Point3fi,JU.Node);P(b,function(){this.paletteID=J.c.PAL.CPK.id});j(b,"setAtom",function(a,d,b,c,f,e,h,k,m){this.mi=a;this.atomSymmetry=f;this.atomSite=e;this.i=d;this.atomNumberFlags=h;m&&(this.formalChargeAndFlags=2);0!=k&&-2147483648!=k&&this.setFormalCharge(k);this.userDefinedVanDerWaalRadius=c;null!=b&&this.setT(b);return this},"~N,~N,JU.P3,~N,JU.BS,~N,~N,~N,~B");c(b,"setShapeVisibility",function(a,
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this.bonds[c];for(;c<d;++c)b[c]=this.bonds[c+1];this.bonds=b}},"~N");j(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 ca(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=
ca(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(B(this.madAtom/8))});j(b,"getEdges",function(){return null==
this.bonds?[]:this.bonds});j(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");j(b,"getElementNumber",function(){return JU.Elements.getElementNumber(this.atomNumberFlags)});j(b,"getIsotopeNumber",function(){return JU.Elements.getIsotopeNumber(this.atomNumberFlags)});j(b,"getAtomicAndIsotopeNumber",function(){return this.atomNumberFlags});c(b,"setAtomicAndIsotopeNumber",
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b<=h)return 0;h=b-(b*b+e*e-h*h)/(2*e);c-=1.0471975511965976*h*h*(3*b-h)}}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)});j(b,"getIndex",function(){return this.i});j(b,"getAtomSite",function(){return this.atomSite});j(b,"getGroupBits",function(a){this.group.setAtomBits(a)},"JU.BS");j(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]});j(b,"getAtomType",function(){var a=this.group.chain.model.ms.atomTypes,a=null==a?null:a[this.i];return null==a?this.getAtomName():a});j(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");
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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 f=B(this.sD/2);f<b&&(f=b);b=f*f;f=this.sX-a;f*=f;if(f>b)return!1;var e=this.sY-d;b-=f+e*e;if(0>b)return!1;if(null==c)return!0;var f=this.sZ,e=c.sZ,h=B(c.sD/2);if(f<e-h)return!0;a=c.sX-a;d=c.sY-d;d=h*h-(a*a+d*d);return f-Math.sqrt(b)<
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"c":" "});j(b,"isPurine",function(){return this.group.isPurine()});j(b,"isPyrimidine",function(){return this.group.isPyrimidine()});j(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");
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j(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});j(b,"getBioStructureTypeName",function(){return this.group.getProteinStructureType().getBioStructureTypeName(!0)});j(b,"equals",function(a){return this===a},"~O");j(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?B(this.sX/2):this.sX;case 1111490572:return a.getScreenHeight()-(a.antialiased?B(this.sY/2):this.sY);case 1111490573:return a.antialiased?B(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())});j(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});
j(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)});j(b,"setCIPChirality",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&-4081|a<<
4},"~N");j(b,"getCIPChiralityCode",function(){return(this.formalChargeAndFlags&496)>>4});j(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?B(this.sX/2):this.sX,a.getScreenHeight()-(a.antialiased?B(this.sY/2):this.sY),a.antialiased?B(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");j(b,"getOffsetResidueAtom",function(a,d){return this.group.getAtomIndex(a,d)},"~S,~N");j(b,"isCrossLinked",function(a){return this.group.isCrossLinked(a.group)},"JU.Node");j(b,"getCrossLinkVector",function(a,d,b){return this.group.getCrossLinkVector(a,d,b)},"JU.Lst,~B,~B");j(b,"toString",function(){return this.getInfo()});j(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");j(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(!F(b,Exception))throw b;}return d},"~S");j(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");j(b,"getExplicitHydrogenCount",
function(){return 0});b.MAD_GLOBAL=32200});p("JM");C(["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=v(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;V("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();this.atomCapacity=0;r(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=K(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,f=0;f<this.ac;f++)if(this.bsSurface.get(f)||JM.AtomCollection.isDeleted(this.at[f]))this.surfaceDistance100s[f]=0;else{for(var e=3.4028235E38,h=this.at[f],k=c.length;0<=--k;)e=Math.min(Math.abs(c[k].distance(h)-b),e);e=this.surfaceDistance100s[f]=B(Math.floor(100*e));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,e)}return c},"JU.BS,~N");c(b,"setAtomCoord2",
function(a,d,b){var c=null,f=null,e=null,h=0,k=1;if(z(b,"JU.P3"))c=b;else if(z(b,"JU.Lst")){e=b;if(0==(k=e.size()))return;h=1}else if(JU.AU.isAP(b)){f=b;if(0==(k=f.length))return;h=2}else return;b=0;if(null!=a)for(var m=a.nextSetBit(0);0<=m;m=a.nextSetBit(m+1)){switch(h){case 1:if(b>=k)return;c=e.get(b++);break;case 2:if(b>=k)return;c=f[b++]}if(null!=c)switch(d){case 1145047050:this.setAtomCoord(m,c.x,c.y,c.z);break;case 1145047051:case 1145047053:this.at[m].setFractionalCoordTo(c,!1);this.taintAtom(m,
2);break;case 1145047055:this.setAtomVibrationVector(m,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 f=this.at[a];f.set(d,b,c);this.fixTrajectory(f);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 f=
this.at[a];f.add3(d,b,c);this.fixTrajectory(f);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(b,"setAtomsCoordRelative",function(a,d,b,c){if(null!=a)for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))this.setAtomCoordRelative(f,d,b,c)},"JU.BS,~N,~N,~N");c(b,"setAPa",function(a,d,b,c,f,e,h){var k=0;if(!(null!=e&&0==e.length||null==a)){for(var m=null!=e&&e.length==this.ac||null!=h&&h.length==this.ac,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){m&&(k=j);if(null!=e){if(k>=e.length)return;c=e[k++];if(Float.isNaN(c))continue;
b=D(c)}else if(null!=h){if(k>=h.length)return;f=h[k++]}var n=this.at[j],q;switch(d){case 1086326786:this.setAtomName(j,f,!0);break;case 1086326785:this.setAtomType(j,f);break;case 1086326788:this.setChainID(j,f);break;case 1094715393:this.setAtomNumber(j,b,!0);break;case 1094713365:this.setAtomSeqID(j,b);break;case 1111492609:case 1111492629:this.setAtomCoord(j,c,n.y,n.z);break;case 1111492610:case 1111492630:this.setAtomCoord(j,n.x,c,n.z);break;case 1111492611:case 1111492631:this.setAtomCoord(j,
n.x,n.y,c);break;case 1111492626:case 1111492627:case 1111492628:this.setVibrationVector2(j,d,c);break;case 1111492612:case 1111492613:case 1111492614:case 1111492615:case 1111492616:case 1111492617:n.setFractionalCoord(d,c,!1);this.taintAtom(j,2);break;case 1094715402:case 1086326789:this.setElement(n,b,!0);break;case 1631586315:this.resetPartialCharges();n.setFormalCharge(b);this.taintAtom(j,4);break;case 1113589786:this.setHydrophobicity(j,c);break;case 1128269825:q=2>c&&0.01<=c?100*c:c;this.setOccupancy(j,
q,!0);break;case 1111492619:this.setPartialCharge(j,c,!0);break;case 1111492618:this.setBondingRadius(j,c);break;case 1111492620:this.setBFactor(j,c,!0);break;case 1094715412:this.setAtomResno(j,b);break;case 1825200146:case 1287653388:this.vwr.shm.setAtomLabel(f,j);break;case 1665140738:case 1112152075:q=c;0>q?q=0:16<q&&(q=16.1);n.madAtom=ca(2E3*q);break;case 1113589787:this.vwr.slm.setSelectedAtom(n.i,0!=c);break;case 1094715418:n.setValence(b);this.taintAtom(j,10);break;case 1648363544:n.setRadius(c)?
this.taintAtom(j,11):this.untaint(j,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 z(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);z(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=K(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=K(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=K(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=W(this.at.length,0)}this.bfactor100s[a]=va(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=K(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 f=null,e=null;switch(a){case 2:this.loadCoordinates(b,!1,!c);return;case 12:this.loadCoordinates(b,!0,!0);return;case 18:f=K(this.ac,0),e=JU.BS.newN(this.ac)}c=JU.Parser.markLines(b,";");var h=0;try{for(var k=JU.PT.parseInt(b.substring(0,c[0]-1)),m=1;m<=k;m++){var j=JU.PT.getTokens(JU.PT.parseTrimmed(b.substring(c[m],c[m+1]-1))),n=JU.PT.parseInt(j[0])-1;if(!(0>n||n>=this.ac)){var q=this.at[n];h++;var w=j.length-1,s=JU.PT.parseFloat(j[w]);
switch(a){case 18:f[n]=s;e.set(n);continue;case 0:this.setAtomName(n,j[w],!0);break;case 13:this.setAtomNumber(n,D(s),!0);break;case 15:this.setAtomResno(n,D(s));break;case 14:this.setAtomSeqID(n,D(s));break;case 1:this.setAtomType(n,j[w]);break;case 16:this.setChainID(n,j[w]);break;case 17:q.atomSite=D(s);break;case 3:q.setAtomicAndIsotopeNumber(D(s));q.paletteID=J.c.PAL.CPK.id;q.colixAtom=this.vwr.cm.getColixAtomPalette(q,J.c.PAL.CPK.id);break;case 4:q.setFormalCharge(D(s));break;case 5:this.setHydrophobicity(n,
s);break;case 6:this.setBondingRadius(n,s);break;case 8:this.setPartialCharge(n,s,!0);break;case 9:this.setBFactor(n,s,!0);break;case 10:q.setValence(D(s));break;case 11:q.setRadius(s)}this.taintAtom(n,a)}}18==a&&0<h&&this.vwr.setData(d,A(-1,[d,f,e,Integer.$valueOf(1)]),0,0,0,0,0)}catch(p){if(F(p,Exception))JU.Logger.error("loadData error: "+p);else throw p;}},"~N,~S,~S,~B");c(b,"loadCoordinates",function(a,d,b){var c=JU.Parser.markLines(a,";"),f=d?new JU.V3:null;try{for(var e=JU.PT.parseInt(a.substring(0,
c[0]-1)),h=1;h<=e;h++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[h],c[h+1]))),m=JU.PT.parseInt(k[0])-1,j=k[3].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[3]),n=k[4].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[4]),q=JU.PT.parseFloat(k[5]);d?(f.set(j,n,q),this.setAtomVibrationVector(m,f)):(this.setAtomCoord(m,j,n,q),b||this.untaint(m,2))}}catch(w){if(F(w,Exception))JU.Logger.error("Frame.loadCoordinate error: "+w);else throw w;}},"~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,f){for(var e=null,h,k=this.ac;0<=--k;)if(!(null!=c&&c.get(k)||null==(h=this.at[k])))h.isClickable()&&this.isCursorOnTopOf(h,a,d,f,e)&&(e=h);b[0]=e},"~N,~N,~A,JU.BS,~N");c(b,"isCursorOnTopOf",function(a,d,b,c,f){return 1<a.sZ&&
!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(d,b,c,f)},"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=K(this.ac,0));for(var c=0!=(d&16),f=0;f<this.ac;f++){var e=this.at[f];JM.AtomCollection.isDeleted(e)||!c&&0<=a.modelIndex&&e.mi!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(f)):(a.atomicNumber[f]=e.getElementNumber(),a.lastModelIndex=
e.mi,b&&(a.atomRadius[f]=this.getWorkingRadius(e,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 f=256==(c&256),e=512==(c&512),h=8==(c&8),k=2048==(c&2048);c=4096==(c&4096);var m=new JU.V3,j=new JU.V3,n=Array(this.ac),q=this.vwr.slm.bsDeleted,w,s=d[0]=0;if(null==a)return n;var p=this.vwr.getOperativeSymmetry();null!=p&&0==this.vwr.getObjectMad10(5)&&(p=null);for(var u=null==p?null:new JU.P3,r=a.nextSetBit(0);0<=
r;r=a.nextSetBit(r+1))if(!(null!=q&&q.get(r))){var v=this.at[r],x=v.getElementNumber();if(!(e&&6!=x)){var z=6>=x?1.1:10>=x?1:1.3;switch(x){case 7:case 8:z=1}var B=f||k||c?v.getCovalentHydrogenCount():0;if(!(f&&0<B||k&&0==B)){var A=this.getMissingHydrogenCount(v,!1);if(!(f&&0==A)){k||(B=A);var C=this.aaRet[0];w=this.aaRet[2];var D=this.aaRet[3]-(k?B:0);if(!(0==D&&v.isHetero())){n[r]=Array(B);A=0;if(0==D)switch(B){case 4:m.set(0.635,0.635,0.635),w=JU.P3.newP(m),w.add(v),A=JM.AtomCollection.addH(n[r],
A,w,v,b,p,u);case 3:m.set(-0.635,-0.635,0.635),w=JU.P3.newP(m),w.add(v),A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);case 2:m.set(-0.635,0.635,-0.635),w=JU.P3.newP(m),w.add(v),A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);case 1:m.set(0.635,-0.635,-0.635),w=JU.P3.newP(m),w.add(v),A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u)}else switch(B){case 3:this.getHybridizationAndAxes(r,x,m,j,"sp3b",!1,!0,h,null);w=new JU.P3;w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);this.getHybridizationAndAxes(r,
x,m,j,"sp3c",!1,!0,h,null);w=new JU.P3;w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);this.getHybridizationAndAxes(r,x,m,j,"sp3d",!1,!0,h,null);w=new JU.P3;w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);break;case 2:D=2==w||5==x||1==D&&4==C||7==x&&this.isAdjacentSp2(v);this.getHybridizationAndAxes(r,x,m,j,D?"sp2b":3==C?"sp3c":"lpa",!1,!0,h,null);w=JU.P3.newP(m);w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);this.getHybridizationAndAxes(r,x,m,j,D?"sp2c":
3==C?"sp3d":"lpb",!1,!0,h,null);w=JU.P3.newP(m);w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);break;case 1:switch(C-D){case 1:if(8==x&&v===v.group.getCarbonylOxygenAtom()){n[r]=null;continue}if(null!=this.getHybridizationAndAxes(r,x,m,j,2==w||5==x||6==x&&1==this.aaRet[1]||7==x&&(new Boolean((new Boolean(v.group.getNitrogenAtom()===v&0==v.getFormalCharge())).valueOf()||this.isAdjacentSp2(v))).valueOf()?"sp2c":"sp3d",!0,!1,h,null))w=JU.P3.newP(m),w.scaleAdd2(z,m,v),A=JM.AtomCollection.addH(n[r],
A,w,v,b,p,u);break;case 2:this.getHybridizationAndAxes(r,x,m,j,4==C?"sp2c":"sp2b",!1,!1,h,null);w=JU.P3.newP(m);w.scaleAdd2(z,m,v);A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u);break;case 3:this.getHybridizationAndAxes(r,x,m,j,"spb",!1,!0,h,null),w=JU.P3.newP(m),w.scaleAdd2(z,m,v),A=JM.AtomCollection.addH(n[r],A,w,v,b,p,u)}}if(A<B){v=Array(A);for(x=0;x<A;x++)v[x]=n[r][x];n[r]=v}s+=A}}}}}d[0]=s;return n},"JU.BS,~A,JU.Lst,~N");b.addH=c(b,"addH",function(a,d,b,c,f,e,h){if(null!=e&&(h.setT(b),e.toFractional(h,
!1),!e.isWithinUnitCell(h,1,1,1)))return d;a[d++]=b;null!=f&&f.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,f=0;f<c.length;f++)switch(c[f].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(),f=a.getValence(),
e=this.am[a.mi],e=e.isBioModel&&!e.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==e?0:f;null!=e&&0==c&&this.bioModelset.getAminoAcidValenceAndCharge(e,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-=f;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],f=this.getMissingHydrogenCount(c,!0);if(0!=f){var e=c.getFormalCharge(),f=e-f;c.setFormalCharge(f);this.taintAtom(b,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+e+" -> "+f);d++}}return d},"JU.BS");c(b,"getHybridizationAndAxes",function(a,d,b,c,f,e,h,k,m){var j=0<f.length&&"-"==f.charAt(0)?f.substring(1):f;if(0<=f.indexOf("d")&&!f.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,b,c,j);f=this.at[a];0==d&&(d=f.getElementNumber());var n=this.getAttached(f,4,e,
k),q=n.length,w=j.charAt(j.length-1).charCodeAt(0)-97;if(0>w||6<w)w=0;b.set(0,0,0);c.set(0,0,0);for(var s=Array(4),p=0;p<q;p++){var u=n[p];if(null==u){q=p;break}s[p]=JU.V3.newVsub(f,u);s[p].normalize();b.add(s[p])}0<q&&c.setT(s[0]);p=!1;a=new JU.V3;if(3<=q){2.9845130209103035>c.angle(s[1])?a.cross(c,s[1]):a.cross(c,s[2]);a.normalize();var r=new JU.V3;2.9845130209103035>s[1].angle(s[2])?r.cross(s[1],s[2]):r.cross(c,s[2]);r.normalize();p=0.95<=Math.abs(r.dot(a))}var v=0==j.indexOf("sp3"),u=!v&&0==j.indexOf("sp2"),
x=!v&&!u&&0==j.indexOf("sp"),A=0==j.indexOf("p"),z=0==j.indexOf("lp"),r=null;if(e){if(0==q)return null;if(v){if(3<w||4<q)return null}else if(u){if(2<w||3<q)return null}else if(x&&(1<w||2<q))return null;switch(q){case 1:if(1==d&&!v)return null;if(v){r="sp3";break}switch(n[0].getCovalentBondCount()){case 1:if(2!=n[0].getValence()){r="sp";break}case 2:r=x?"sp":"sp2";break;case 3:if(!u&&!A)return null;r="sp2"}break;case 2:if(0.1>b.length()){if(0<=j.indexOf("2")||0<=j.indexOf("3"))return null;r="sp";break}r=
v?"sp3":"sp2";if(0==j.indexOf("sp"))break;if(z){r="lp";break}r=j;break;default:if(p&&!k)r="sp2";else{p&&b.setT(a);if(z&&3==q){r="lp";break}r="sp3"}}if(null==r)return null;if(0==j.indexOf("p")){if("sp3"===r)return null}else if(0>j.indexOf(r))return null}if(w<q&&!j.startsWith("p")&&!j.startsWith("l"))return b.sub2(n[w],f),b.normalize(),r;switch(q){case 0:j.equals("sp3c")||j.equals("sp2d")||j.equals("lpa")?b.set(-0.5,-0.7,1):j.equals("sp3b")||j.equals("lpb")?b.set(0.5,-0.7,-1):j.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(p=n[0].getBondCount();0<=--p;)if(n[0].bonds[p].isCovalentNotPartial0()&&n[0].getBondedAtomIndex(p)!=f.i&&(c.sub2(n[0],n[0].bonds[p].getOtherAtom(n[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!=w&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(b.x,b.y,b.z,
2.09439507*(2==w?1:-1))).rotate(c));b.setT(c);c.cross(a,b);break}a.cross(c,b);j=n[0].getCovalentBondCount();switch(j){case 3:if(m!==n[0]){this.getHybridizationAndAxes(n[0].i,0,c,a,"pz",!1,h,k,f);a.setT(c);u?(c.cross(c,b),1==w&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,b,c)):x||(a.setT(b),b.setT(c));c.cross(a,b);break}j=2;case 1:if(1==j&&2!=n[0].getValence())break;case 2:h=n[0];c.setT(b);for(a.setT(JM.AtomCollection.vRef);null!=h&&2==h.getCovalentBondCount();){k=h.bonds;u=null;
for(p=0;p<k.length;p++)if(k[p].isCovalentNotPartial0()&&(u=k[p].getOtherAtom(h),u!==f)){a.sub2(u,h);break}a.cross(a,c);if(0.1<a.length()||2!=u.getCovalentBondCount())break;f=h;h=u}x||(0.1<a.length()?(b.cross(a,c),b.normalize(),1==w&&b.scale(-1),b.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,c,b),A&&(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(!j.equals("pz")){u=n[0];(m=3==u.getCovalentBondCount())||(m=3==(u=
n[1]).getCovalentBondCount());if(m){this.getHybridizationAndAxes(u.i,0,c,b,"pz",!1,h,k,null);j.equals("px")&&c.scale(-1);b.setT(s[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(u){c.cross(b,a);break}if(v||z){a.normalize();b.normalize();j.equals("lp")||(0==w||2==w?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(!p){c.cross(b,c);break}b.setT(a);
0>b.z&&h&&(b.scale(-1),c.scale(-1))}c.normalize();b.normalize();return r},"~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 f=c.startsWith("dsp3"),e=c.charAt(c.length-1).charCodeAt(0)-97;if(null!=d&&(!f&&(5<e||!c.startsWith("d2sp3"))||f&&4<e))return null;a=this.at[a];c=this.getAttached(a,
6,!0,!1);if(null==c)return null==d?null:"?";var h=c.length;if(3>h&&null!=d)return null;for(var k=e>=h,m=B(h*(h-1)/2),j=JU.AU.newInt2(m),n=E(3,0),m=E(3,m,0),q=0,w=0,s=0;s<h-1;s++)for(var p=s+1;p<h;p++){var r=JU.Measure.computeAngleABC(c[s],a,c[p],!0),r=105>r?0:150<=r?2:1;m[r][n[r]]=q;n[r]++;j[q++]=E(-1,[s,p]);0==s&&1==r&&w++}q=100*n[0]+10*n[1]+n[2];if(null==d)switch(q){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==w%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(q){default:return null;case 201:break;case 210:case 330:case 411:case 631:if(!f)return null;break;case 300:case 402:case 501:case 802:case 1203:if(f)return null}if(k)if(f)switch(n[1]){case 0:d.sub2(c[j[m[0][0]][0]],
a);b.sub2(c[j[m[0][0]][1]],a);d.cross(d,b);d.normalize();4==e&&d.scale(-1);n=this.findNotAttached(h,j,m[2],n[2]);s=n.nextSetBit(0);b.sub2(c[s],a);b.normalize();b.scale(0.5);d.scaleAdd2(JM.AtomCollection.sqrt3_2,d,b);e=-1;break;case 1:4==e?(b=j[m[1][0]],d.add2(c[b[0]],c[b[1]]),d.scaleAdd2(-2,a,d),e=-1):(n=this.findNotAttached(h,j,m[1],n[1]),e=n.nextSetBit(0));break;default:n=this.findNotAttached(h,j,m[1],n[1]),e=n.nextSetBit(0)}else{q=!1;if(4==h)switch(n[2]){case 1:n=this.findNotAttached(h,j,m[2],
n[2]);s=n.nextSetBit(0);e=4==e?s:n.nextSetBit(s+1);break;default:q=!0}else{n=this.findNotAttached(h,j,m[2],n[2]);s=n.nextSetBit(0);for(p=h;p<e&&0<=s;p++)s=n.nextSetBit(s+1);-1==s?q=!0:e=s}q&&(d.sub2(c[j[m[0][0]][0]],a),b.sub2(c[j[m[0][0]][1]],a),d.cross(d,b),4==e&&d.scale(-1),e=-1)}0<=e&&d.sub2(c[e],a);k&&d.scale(-1);d.normalize();return f?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(b,"getAttached",function(a,d,b,c){var f=a.getCovalentBondCount();if(f>d)return null;d=Array(f);if(0<f){for(var f=a.bonds,
e=0,h=0;h<f.length;h++)if(f[h].isCovalentNotPartial0()){var k=f[h].getOtherAtom(a);if(!c||1!=k.getAtomicAndIsotopeNumber())d[e++]=k}b&&!c&&java.util.Arrays.sort(d,U(JM.AtomCollection.AtomSorter,this,null))}return d},"JM.Atom,~N,~B,~B");c(b,"findNotAttached",function(a,d,b,c){var f=JU.BS.newN(a);f.setBits(0,a);for(var e=0;e<a;e++)for(var h=0;h<c;h++){var k=d[b[h]];(k[0]==e||k[1]==e)&&f.clear(e)}return f},"~N,~A,~A,~N");c(b,"getAtomBitsMDa",function(a,d,b){var c=z(d,Integer)?d.intValue():0;switch(a){case 1086326786:case 1086326785:var f=
1086326785==a,e=","+d+",";for(a=this.ac;0<=--a;)JM.AtomCollection.isDeleted(this.at[a])||(d=f?this.at[a].getAtomType():this.at[a].getAtomName(),0<=e.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==(f=this.at[a]).getElementNumber()&&2==f.getCovalentBondCount()){for(var c=f.bonds,h=0,k=c.length;0<=--k&&3>h;)if(c[k].isCovalentNotPartial0()&&1==(e=c[k].getOtherAtom(f)).getElementNumber())d[h++%
2]=e.i;2==h&&(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:f=d.toUpperCase();0<=f.indexOf("\\?")&&(f=JU.PT.rep(f,"\\?","\u0001"));(e=f.startsWith("?*"))&&(f=f.substring(1));for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.isAtomNameMatch(this.at[a],f,e,e)&&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}e=d.nextSetBit(0);if(0>
e)return b;switch(a){case 1094717454:f=JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))b.or(this.am[this.at[a].mi].bsAtoms),f.andNot(b);return b;case 1086326788:f=JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))this.at[a].group.chain.setAtomBits(b),f.andNot(b);return b;case 1086326789:f=new JU.BS;for(a=e;0<=a;a=d.nextSetBit(a+1))f.set(this.at[a].getElementNumber());for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&f.get(this.at[a].getElementNumber())&&b.set(a);return b;case 1086324742:f=
JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))this.at[a].group.setAtomBits(b),f.andNot(b);return b;case 1094713366:f=new JU.BS;for(a=e;0<=a;a=d.nextSetBit(a+1))f.set(this.at[a].atomSite);for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&f.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),f,e=c.nextClearBit(0);e<this.ac;e=c.nextClearBit(e+1))if(!JM.AtomCollection.isDeleted(this.at[e])){var h=this.at[e].group.chain;a==(f=h.chainID)||!d&&0<=f&&300>f&&a==this.chainToUpper(f)?(h.setAtomBits(b),c.or(b)):h.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),f=2147483647!=c,e=!0,h=JM.Group.getInsertionCodeChar(a);switch(h.charCodeAt(0)){case 63:for(var k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])){var m=this.at[k].group.seqcode;if((!f||c==JM.Group.getSeqNumberFor(m))&&0!=JM.Group.getInsertionCodeFor(m))b.set(k),e=!1}break;default:for(k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])&&(m=this.at[k].group.seqcode,
a==m||!f&&a==JM.Group.getInsertionCodeFor(m)||"*"==h&&c==JM.Group.getSeqNumberFor(m)))b.set(k),e=!1}return!e||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 f=this.ac;0<=--f;)if(!JM.AtomCollection.isDeleted(this.at[f])){var e=this.at[f].getGroup3(!0);if(null!=e&&0<e.length){if(JU.PT.isMatch(e,a,d,!0)){null==b&&(b=JU.BS.newN(f+1));for(b.set(f);0<=--f;)!JM.AtomCollection.isDeleted(this.at[f])&&this.at[f].getGroup3(!0).equals(e)&&
b.set(f);f++}}else this.isAtomNameMatch(this.at[f],a,d,c)&&(null==b&&(b=JU.BS.newN(f+1)),b.set(f))}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 f=this.at[c];if(!JM.AtomCollection.isDeleted(f)){var e=
JU.Measure.distanceToPlane(d,f);(0<a&&-0.1<=e&&e<=a||0>a&&0.1>=e&&e>=a||0==a&&0.01>Math.abs(e))&&b.set(f.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 f=this.atomTensors.get(b),e=f.size();0<=--e;){var h=f.get(e);(a.get(h.atomIndex1)||0<=h.atomIndex2&&a.get(h.atomIndex2))&&f.removeItemAt(e)}0==f.size()&&d.addLast(b)}for(e=d.size();0<=--e;)this.atomTensors.remove(d.get(e))}},"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(),f=c;0<=--f;){var e=a.get(f);e.forThermalEllipsoid?d=f:2==e.iType&&(b=!0)}var h=Array((0<=d||!b?0:1)+c);if(0<=d&&(h[0]=a.get(d),1==a.size()))return h;if(b){d=0;for(f=c;0<=--f;)e=
a.get(f),e.forThermalEllipsoid||(h[++d]=e)}else for(f=0;f<c;f++)h[f]=a.get(f);return h},"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 f=b[c];if(null!=f&&(d.equals(f.type)||d.equals(f.altType)))return f}}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 f=this.getVibration(c,!1);if(null!=f&&(-1==f.modDim||-2==f.modDim))d=Math.max(d,f.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 f=this.getVibration(c,!1),e=this.getModulation(c);if(null==e){if(0==d)return;f.scale(d)}else e.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=v(function(){Y(this,arguments);r(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);j(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});
p("JM");C(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){var b=v(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;r(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);
c(b,"initialize",function(a,d,b,c,f,e){this.bspf=a;this.bsSelected=d;this.isGreaterOnly=b;this.isZeroBased=c;this.hemisphereOnly=f;this.threadSafe=e;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");j(b,"setModel",function(a,d,b,c,f,e,h){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!=e){this.atomIndex=0>e?-1:c;if(this.isVdw=null!=h)this.radiusData=h,
this.atoms=a.at,this.vwr=a.vwr,e=h.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+h.value:5*h.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,h.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(f,e)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");j(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");j(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});j(b,"next",function(){return this.iNext-
this.zeroBase});j(b,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});j(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");j(b,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)});j(b,"getPosition",function(){return null})});p("JM");C(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){var b=v(function(){this.center=this.bsModels=null;this.distance=0;r(this,arguments)},JM,"AtomIteratorWithinModelSet",JM.AtomIteratorWithinModel);x(b,function(a){M(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=
a},"JU.BS");j(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");j(b,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});p("JM");C(["JU.Edge","JV.JC"],"JM.Bond",["JU.C"],function(){var b=v(function(){this.atom2=this.atom1=
null;this.shapeVisibilityFlags=this.colix=this.mad=0;r(this,arguments)},JM,"Bond",JU.Edge);x(b,function(a,d,b,c,f){M(this,JM.Bond,[]);this.atom1=a;this.atom2=d;this.colix=f;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)});j(b,"isCovalent",function(){return 0!=(this.order&1023)});j(b,"isHydrogen",function(){return JU.Edge.isOrderH(this.order)});c(b,"isStereo",function(){return 0!=(this.order&
1024)});j(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");j(b,"getAtomIndex1",function(){return this.atom1.i});j(b,"getAtomIndex2",function(){return this.atom2.i});j(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");j(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)});j(b,"getCIPChirality",
function(){return""},"~B");j(b,"setCIPChirality",function(){},"~N");j(b,"toString",function(){return this.atom1+" - "+this.atom2});j(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)});p("JM");C(["JM.AtomCollection","JU.V3"],"JM.BondCollection","JU.AU $.BS $.Measure JM.Bond $.BondIteratorSelected $.BondSet $.HBond JU.BSUtil $.C $.Edge".split(" "),function(){var b=
v(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;r(this,arguments)},JM,"BondCollection",JM.AtomCollection);P(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 f=this.at[a.nextSetBit(0)],e=2==c?this.at[a.nextSetBit(f.i+1)]:null;if(1==c||d){for(c=f.getBondCount();0<=--c;)b.set(f.bonds[c].index);if(null!=e)for(c=
e.getBondCount();0<=--c;)b.set(e.bonds[c].index)}else f=f.getBond(e),null!=e&&b.set(f.index);return b}for(e=0;e<this.bondCount;++e)f=this.bo[e],c=a.get(f.atom1.i),f=a.get(f.atom2.i),(d?c||f:c&&f)&&b.set(e);return b},"JU.BS,~B");c(b,"bondAtoms",function(a,d,b,c,f,e,h,k){b=this.getOrAddBond(a,d,b,c,f,e,!0);k&&(b.order|=131072,h&&(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,f,e,h){if(131071==b||65535==b)b=1;a.isBonded(d)?
(a=a.getBond(d).index,h&&(this.bo[a].setOrder(b),this.bo[a].setMad(c),z(this.bo[a],"JM.HBond")&&(this.bo[a].energy=e))):(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,e)).index);null!=f&&f.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,f){b=JU.Edge.isOrderH(b)?new JM.HBond(a,
d,b,c,0,f):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 f=c;0<=
--f;)b[f]=d[f];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?B(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(b,"deleteConnections",function(a,d,b,c,f,e,h){var k=0>a,m=0>d,j=k||m;a=this.fixD(a,k);d=this.fixD(d,m);var n=new JU.BS,q=0,w=b|=131072;!h&&JU.Edge.isOrderH(b)&&(b=30720);if(e)e=c;else{e=new JU.BS;for(var s=c.nextSetBit(0);0<=s;s=c.nextSetBit(s+1)){var p=this.at[s];if(null!=p.bonds)for(var r=p.bonds.length;0<=--r;)f.get(p.getBondedAtomIndex(r))&&
e.set(p.bonds[r].index)}}for(s=e.nextSetBit(0);s<this.bondCount&&0<=s;s=e.nextSetBit(s+1))if(c=this.bo[s],this.isInRange(c.atom1,c.atom2,a,d,k,m,j)&&(h||w==(c.order&-257|131072)||0!=(b&c.order&30720)))n.set(s),q++;0<q&&this.deleteBonds(n,!1);return E(-1,[0,q])},"~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,f,e,h){var k=a.distanceSquared(d);return h?(h=Math.sqrt(k),a=a.getBondingRadius()+d.getBondingRadius(),(f?h>=a*b:k>=b)&&(e?h<=
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,f=a.cardinality(),e=b;e<this.bondCount;++e){var h=this.bo[e];if(0<f&&a.get(e)){f--;if(!d){var k=h.atom1.mi;k!=c&&this.am[c=k].resetBoundCount()}h.deleteAtomReferences()}else this.setBond(b++,h)}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),f=c;0<=f;f=b?f-1:d.nextSetBit(f+1)){var e=this.bo[f];this.bsAromatic.get(f)&&e.setOrder(515);switch(e.order&131071){case 515:if(!this.assignAromaticMustBeSingle(e.atom1)&&
!this.assignAromaticMustBeSingle(e.atom2)){this.bsAromatic.set(f);break}e.order=513;case 513:this.bsAromaticSingle.set(f);break;case 514:this.bsAromaticDouble.set(f)}}for(var c=(b=null==d)?this.bondCount-1:d.nextSetBit(0),h=new JU.BS,f=c;0<=f;f=b?f-1:d.nextSetBit(f+1))if(e=this.bo[f],e.is(515)&&(!this.bsAromaticDouble.get(f)&&!this.bsAromaticSingle.get(f))&&(h.set(f),8==e.atom1.getElementNumber()||8==e.atom2.getElementNumber()))this.assignAromaticDouble(e)||this.assignAromaticSingle(e);for(f=h.nextSetBit(0);0<=
f;f=h.nextSetBit(f+1))this.assignAromaticDouble(e=this.bo[f])||this.assignAromaticSingle(e);h=new JU.BS;for(f=c;0<=f;f=b?f-1:d.nextSetBit(f+1))if(e=this.bo[f],this.bsAromaticDouble.get(f))e.is(514)||(this.bsAromatic.set(f),h.set(e.atom1.mi),e.setOrder(this.isLinear(e,this.v1,this.v2)?3:514));else if((this.bsAromaticSingle.get(f)||e.isAromatic())&&!e.is(513))this.bsAromatic.set(f),e.setOrder(513);b=this.am;for(f=h.nextSetBit(0);0<=f;f=h.nextSetBit(f+1))b[f].isBioModel&&(b[f].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(),f=c.length;0<=-f;)if(c[f]!==a&&c[f].isCovalent()){if(175>JU.Measure.computeAngle(c[f].getOtherNode(a.atom1),a.atom1,a.atom2,d,b,!0))return!1;break}c=a.atom2.getEdges();for(f=c.length;0<=-f;)if(c[f]!==a&&c[f].isCovalent()){if(175>JU.Measure.computeAngle(c[f].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 f=b[c],e=f.index;if(!(e==d||!f.isAromatic()||this.bsAromaticSingle.get(e)))if(this.bsAromaticDouble.get(e)||!this.assignAromaticSingle(f))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 f=a[c],e=f.index;if(f.isAromatic()&&!this.bsAromaticDouble.get(e)&&!this.bsAromaticSingle.get(e))if(!d&&this.assignAromaticDouble(f))d=!0;else if((d||c<b)&&!this.assignAromaticSingle(f))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 f,e=d.atom2,h,k=e.getElementNumber();7==k||8==k?(h=k,f=e,e=d.atom1,k=e.getElementNumber()):(f=d.atom1,h=f.getElementNumber());if(!(7!=h&&8!=h)){var m=f.getValence();if(!(0>m)){var j=f.getCovalentBondCount();f=f.getFormalCharge();switch(h){case 7:3==m&&(3==j&&1>f&&6==k&&3==e.getValence())&&
d.setOrder(514);break;case 8:1==m&&(0==f&&(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",
function(a,d){var b=new JU.BS,c=new JU.BS,f=a.bonds;if(null!=f){for(var e=0;e<f.length;e++)f[e].isCovalent()?1==f[e].getOtherAtom(a).getElementNumber()&&b.set(f[e].getOtherAtom(a).i):c.set(f[e].index);0<=c.nextSetBit(0)&&this.deleteBonds(c,!1);d&&b.set(a.i);0<=b.nextSetBit(0)&&this.vwr.deleteAtoms(b,!1)}},"JM.Atom,~B");c(b,"displayBonds",function(a,d){d||(this.haveHiddenBonds=!0);for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))b<this.bondCount&&0!=this.bo[b].mad&&this.bo[b].setShapeVisibility(d)},
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d){if(null!=a.bonds)for(var b=a.bonds.length;0<=--b;){var c=a.bonds[b].getOtherAtom(a);1==c.getElementNumber()&&d.set(c.i)}},"JM.Atom,JU.BS")});p("JM");N(JM,"BondIterator");p("JM");C(["JM.BondIterator"],"JM.BondIteratorSelected",null,function(){var b=v(function(){this.bonds=null;this.iBond=this.bondType=this.bondCount=0;this.bsSelected=null;this.bondSelectionModeOr=!1;r(this,arguments)},JM,"BondIteratorSelected",null,JM.BondIterator);x(b,function(a,d,b,c,f){this.bonds=a;this.bondCount=d;this.bondType=
b;this.bsSelected=c;this.bondSelectionModeOr=f},"~A,~N,~N,JU.BS,~B");j(b,"hasNext",function(){if(131071==this.bondType)return this.iBond=this.bsSelected.nextSetBit(this.iBond),0<=this.iBond&&this.iBond<this.bondCount;for(;this.iBond<this.bondCount;++this.iBond){var a=this.bonds[this.iBond];if(!(65535!=this.bondType&&0==(a.order&this.bondType))&&!(65535==this.bondType&&32768==a.order)){var d=this.bsSelected.get(a.atom1.i),a=this.bsSelected.get(a.atom2.i);if(!this.bondSelectionModeOr&&d&&a||this.bondSelectionModeOr&&
(d||a))return!0}}return!1});j(b,"nextIndex",function(){return this.iBond});j(b,"next",function(){return this.bonds[this.iBond++]})});p("JM");C(["JU.BS"],"JM.BondSet",["JU.BSUtil"],function(){var b=v(function(){this.associatedAtoms=null;r(this,arguments)},JM,"BondSet",JU.BS);x(b,function(){M(this,JM.BondSet,[])});b.newBS=c(b,"newBS",function(a){var d=new JM.BondSet;JU.BSUtil.copy2(a,d);return d},"JU.BS");c(b,"getAssociatedAtoms",function(a){null==this.associatedAtoms&&(this.associatedAtoms=a.getAtomIndices(a.getAtoms(1677721602,
this)));return this.associatedAtoms},"JM.ModelSet")});p("JM");C(["JM.Structure"],"JM.Chain",null,function(){var b=v(function(){this.model=null;this.chainNo=this.chainID=0;this.groups=null;this.selectedGroupCount=this.groupCount=0;r(this,arguments)},JM,"Chain",null,JM.Structure);x(b,function(a,d,b){this.model=a;this.chainID=d;this.chainNo=b;this.groups=Array(16)},"JM.Model,~N,~N");c(b,"getIDStr",function(){return 0==this.chainID?"":256>this.chainID?""+String.fromCharCode(this.chainID):this.model.ms.vwr.getChainIDStr(this.chainID)});
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d)},"JU.BS,JU.BS")});p("JM");C(["JM.Structure","java.lang.Short","JV.JC"],"JM.Group","java.util.Hashtable JU.BS $.Quat J.c.STR JU.BSUtil $.Escape $.Logger".split(" "),function(){var b=v(function(){this.chain=null;this.groupIndex=0;this.group1="\x00";this.leadAtomIndex=this.firstAtomIndex=-1;this.lastAtomIndex=0;this.bsAdded=null;this.shapeVisibilityFlags=this.selectedIndex=this.groupID=this.seqcode=0;this.dssrNT=null;r(this,arguments)},JM,"Group",null,JM.Structure);c(b,"setGroup",function(a,d,b,c,
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d)},"~N,JU.BS");c(b,"getGroupInfo",function(a,d){var b=new java.util.Hashtable;b.put("groupIndex",Integer.$valueOf(a));b.put("groupID",Short.$valueOf(this.groupID));var c=this.getSeqcodeString();null!=c&&b.put("seqCode",c);b.put("_apt1",Integer.$valueOf(this.firstAtomIndex));b.put("_apt2",Integer.$valueOf(this.lastAtomIndex));null!=this.bsAdded&&b.put("addedAtoms",this.bsAdded);b.put("atomInfo1",this.chain.model.ms.getAtomInfo(this.firstAtomIndex,null,d));b.put("atomInfo2",this.chain.model.ms.getAtomInfo(this.lastAtomIndex,
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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,f,e){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",f,e);JM.LabelToken.formatLabelAtomArray(a,d.atom2,b,"2",f,e);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,f){var e=new java.util.Hashtable;e.put("#",""+(d.index+1));e.put("VALUE",Float.$valueOf(c));e.put("UNITS",f);b=JM.LabelToken.compile(a,b,"\u0001",e);if(null==b)return"";JM.LabelToken.setValues(b,e);e=d.ms.at;d=d.countPlusIndices;
for(c=d[0];1<=c;--c)0<=d[c]&&JM.LabelToken.formatLabelAtomArray(a,e[d[c]],b,String.fromCharCode(48+c),null,null);b=JM.LabelToken.getLabel(b);return null==b?"":b},"JV.Viewer,JM.Measurement,~S,~N,~S");b.setValues=c(b,"setValues",function(a,d){for(var b=0;b<a.length;b++){var c=a[b];if(null==c)break;if(null!=c.key){var f=d.get(c.key);c.text=z(f,Float)?c.format(f.floatValue(),null,null):c.format(NaN,f,null)}}},"~A,java.util.Map");b.getLabel=c(b,"getLabel",function(a){for(var d=new JU.SB,b=0;b<a.length;b++){var c=
a[b];if(null==c)break;d.append(c.text)}return d.toString()},"~A");b.setToken=c(b,"setToken",function(a,d,b,c,f,e){var h=b.pt+1;if(h>=c)return b.text="%",h;var k;"-"==d.charAt(h)&&(b.alignLeft=!0,++h);h<c&&"0"==d.charAt(h)&&(b.zeroPad=!0,++h);for(;h<c&&JU.PT.isDigit(k=d.charAt(h));)b.width=10*b.width+(k.charCodeAt(0)-48),++h;b.precision=2147483647;var m=!1;if(h<c&&"."==d.charAt(h)){++h;if(h<c&&"-"==(k=d.charAt(h)))m=!0,++h;if(h<c&&JU.PT.isDigit(k=d.charAt(h))){++h;b.precision=k.charCodeAt(0)-48;if(h<
c&&JU.PT.isDigit(k=d.charAt(h)))++h,b.precision=10*b.precision+(k.charCodeAt(0)-48);m&&(b.precision=-1-b.precision)}}if(h<c&&null!=e){var j;for(e=e.keySet().iterator();e.hasNext()&&((j=e.next())||1);)if(d.indexOf(j,h)==h)return h+(b.key=j).length}if(h<c)switch((k=d.charAt(h++)).charCodeAt(0)){case 37:return b.text="%",h;case 91:j=d.indexOf("]",h);if(j<h){h=c;break}h=d.substring(h,j).toLowerCase();h.startsWith("property_")?(b.tok=134221834,b.data=a.getDataObj(h,null,1)):h.startsWith("validation.")?
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b.text.length-1),d);if(null==j)System.out.println("?? o is null ??");else if(1==j.size())k=j.get(0).floatValue();else{k=NaN;h="";a=0;for(var n=j.size();a<n;a++)h+=","+j.get(a);1<h.length&&(h=h.substring(1))}}break;case 1715472409:var q=a.ms.getInfo(d.mi,b.data),w=d.i-a.ms.am[d.mi].firstAtomIndex,j=null;if(0<=w)if(z(q,Array))var s=q,j=w<s.length?s[w]:null;else z(q,"JU.Lst")&&(j=w<q.size()?JS.SV.oValue(q.get(w)):null);null==j?h="":z(j,Float)?k=j.floatValue():z(j,Integer)?k=j.intValue():z(j,"JU.T3")?
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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],f=this.vwr.getDataObj(this.property,null,2),e=b.i,h=c.i;return null==f||h>=f.length||e>=f.length?NaN:f[e][h]}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=
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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 f=this.getAtomIndex(c);
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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!=
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!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")});p("JM");C(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["JU.Lst","JM.Measurement"],function(){var b=v(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;r(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,f,e,h,k,m,j,n,q,w,s,p,r){this.ms=this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(z(this.points.get(0),"JU.BS")&&z(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=f;this.units=e;this.tickInfo=h;this.mustBeConnected=k;this.mustNotBeConnected=
m;this.intramolecular=j;this.isAll=n;this.mad=q;this.colix=w;this.text=s;this.fixedValue=p;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=K(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,f=Array(4),e=E(5,0),h=(new JM.Measurement).setPoints(d,e,f,null);h.setCount(b);h.property=this.property;h.strFormat=this.strFormat;h.units=this.units;h.fixedValue=this.fixedValue;for(var k=-1,m=0;m<b;m++){var j=
this.points.get(m);if(z(j,"JU.BS")){k=j.cardinality();if(0==k)return;1<k&&(c=0);k=m;0==m&&(this.iFirstAtom=0);e[m+1]=j.nextSetBit(0)}else f[m]=j,e[m+1]=-2-m}this.nextMeasure(0,k,h,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 f=this.points.get(a),e=b.countPlusIndices,h=0==a?2147483647:e[a];if(0>h)this.nextMeasure(a+1,d,b,c);else{for(var k=!1,m=f.nextSetBit(0),j=0;0<=m;m=f.nextSetBit(m+1),j++)if(m!=h||this.allowSelf){var n=this.atoms[m].mi;if(0<=c&&this.justOneModel)if(0==a)c=n;else if(c!=n)continue;e[a+1]=m;0==a&&(this.iFirstAtom=j);k=!0;this.nextMeasure(a+1,d,b,c)}k||this.nextMeasure(a+1,d,b,c)}}},"~N,~N,JM.Measurement,~N")});p("JM");
C(["JM.Measurement"],"JM.MeasurementPending",null,function(){var b=v(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;r(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");j(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")});p("JM");C(null,"JM.Model","java.util.Hashtable JU.AU $.BS $.SB JU.BSUtil JV.FileManager".split(" "),function(){var b=v(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;r(this,arguments)},JM,"Model",null);x(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,f,e){this.ms=a;this.dataSourceFrame=this.modelIndex=d;this.trajectoryBaseIndex=(this.isTrajectory=0<=b)?b:d;null==e&&(e=new java.util.Hashtable);this.auxiliaryInfo=e;a=e.get("biosymmetryCount");null!=a&&(this.biosymmetryCount=a.intValue(),this.biosymmetry=e.get("biosymmetry"));a=e.get("fileName");null!=a&&e.put("fileName",JV.FileManager.stripTypePrefix(a));this.properties=f;null==c?this.jmolFrameType="modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,e.put("jmolData",c),e.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")});p("JM");
C(["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=v(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;r(this,arguments)},JM,"ModelLoader",null);P(b,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});x(b,function(a,d,b,c,f,e){this.vwr=a;this.ms=new JM.ModelSet(a,
d);var h=a.getModelAdapter();this.modelSet0=f;(this.merging=null!=f&&(0<f.ac||null!=f.vwr.getOperativeSymmetry()))?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);null==e?(this.initializeInfo(d,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),d=h.getAtomSetCollectionAuxiliaryInfo(c),d.put("loadScript",b),this.initializeInfo(h.getFileTypeName(c).toLowerCase().intern(),
d),this.createModelSet(h,c,e),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 f=this.vwr.getMadBond();c&&(this.ms.defaultCovalentMad=null==this.jmolData?f:0,this.iterateOverAllNewBonds(b));this.ms.defaultCovalentMad=f;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 e=this.vwr.rd;b=this.ms.ac;c=this.ms.at;for(f=this.baseAtomIndex;f<b;f++)c[f].setMadAtom(this.vwr,e);e=this.ms.am;for(f=e[this.baseModelIndex].firstAtomIndex;f<
b;f++)null!=c[f]&&e[c[f].mi].bsAtoms.set(f);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,f=this.baseModelIndex;f<b;f++)c[f].isBioModel&&c[f].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 f,b=b.entrySet().iterator();b.hasNext()&&((f=b.next())||1);){var e=f.getKey(),h=f.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(d,!0);if(this.doAddPDBHydrogens)var m=null!=c&&JU.PT.isOneOf(e,c),h=this.jbr.fixPropertyValue(k,
h,m);e="property_"+e.toLowerCase();JU.Logger.info("creating "+e+" for model "+this.ms.getModelName(d));this.vwr.setData(e,A(-1,[e,h,k,Integer.$valueOf(-1),Boolean.FALSE,f]),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,f=0;f<this.adapterModelCount;++f,++c){var e=a.getAtomSetNumber(d,f),h=a.getAtomSetName(d,f),k=a.getAtomSetAuxiliaryInfo(d,
f);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var m=k.get("modelProperties");if(!this.merging||this.appendNew){var j=k.get("fileType");this.vwr.setStringProperty("_fileType",j);this.vwr.fm.setFileType(j)}null==h&&(h=null!=this.jmolData&&2<this.jmolData.indexOf(";")?this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?""+e%1E6:"");this.setModelNameNumberProperties(c,b,h,e,m,k,this.jmolData)}b=this.ms.am[null==this.appendToModelIndex?this.baseModelIndex:
this.ms.mc-1];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));f=this.ms.msInfo.remove("loadState");e=this.ms.msInfo.remove("loadScript");if(0>e.indexOf("Viewer.AddHydrogens")||!b.isModelKit){h=JU.PT.split(f,"\n");k=new JU.SB;for(f=0;f<h.length;f++)m=b.loadState.indexOf(h[f]),(0>m||m!=b.loadState.lastIndexOf(h[f]))&&k.append(h[f]).appendC("\n");b.loadState+=b.loadScript.toString()+k.toString();b.loadScript=new JU.SB;if(0<=e.indexOf("load append ")||0<=e.indexOf('data "append '))e.insert(0,
";var anew = appendNew;"),e.append(";set appendNew anew");b.loadScript.append("  ").appendSB(e).append(";\n")}if(this.isTrajectory){f=this.ms.mc-c+1;JU.Logger.info(f+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(f));b=this.adapterModelCount;for(f=c;f<this.ms.mc;f++,b++)this.ms.am[f]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[f]=a.getAtomSetNumber(d,b),this.ms.modelNames[f]=a.getAtomSetName(d,b),this.structuresDefinedInFile.set(f)}this.finalizeModels(this.baseModelCount)},
"J.api.JmolAdapter,~O");c(b,"setModelNameNumberProperties",function(a,d,b,c,f,e,h){if(this.appendNew){var k=null!=e&&Boolean.TRUE===e.get(JV.JC.getBoolName(4));this.ms.am[a]=k?this.jbr.getBioModel(a,d,h,f,e):(new JM.Model).set(this.ms,a,d,h,f,e);this.ms.modelNumbers[a]=c;this.ms.modelNames[a]=b;k&&this.jbr.setGroupLists(a)}else d=e.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,f=-1,e=this.ms.modelNumbers,h=this.ms.modelNames;if(this.isTrajectory)for(var k=a;++k<this.ms.mc;)e[k]=e[k-1]+1;if(0<a){if(1E6>e[0])for(k=0;k<a;k++)0==h[k].length&&(h[k]=""+e[k]),e[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]="1."+(k+1);var m=e[a-1],m=m-m%1E6;1E6>e[a]&&(m+=1E6);for(k=a;k<d;k++)e[k]+=m}for(var j=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),
m=B(e[k]/1E6),m!=f&&(c=0,f=m),c++,0==m?(b=""+this.ms.getModelNumber(k),m=1):b=m+"."+c,this.ms.modelNumbersForAtomLabel[k]=b,j[k].fileIndex=m-1,this.ms.modelFileNumbers[k]=1E6*m+c,null==h[k]||0==h[k].length)h[k]=b;if(this.merging)for(k=0;k<a;k++)j[k].ms=this.ms;for(k=0;k<d;k++)this.ms.setInfo(k,"modelName",h[k]),this.ms.setInfo(k,"modelNumber",Integer.$valueOf(e[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,f=0,e=!1,h=!1,k=a.getAtomIterator(d),m=a.getAtomCount(d,-1);this.ms.setCapacity(a.getAtomCount(d,-1));d=0;var j=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 n=k.getAtomSetIndex()+this.baseModelIndex;n!=
c&&(this.iChain=0,this.iModel=n,this.model=j[n],c=this.model.bsAtoms,this.merging&&(!this.appendNew&&null!=this.vwr.getOperativeSymmetry())&&(f=this.getAtomSiteBase(c)),this.currentChainID=2147483647,this.isNewChain=!0,c.set(this.ms.ac+m),c.clearAll(),this.model.isOrderly=null==this.appendToModelIndex,e=this.model.isBioModel,c=n,h=e&&this.doAddPDBHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var n=k.getGroup3(),q=k.getChainID();this.checkNewGroup(a,q,n,k.getSequenceNumber(),k.getInsertionCode(),
h,!1);q=k.getElementNumber();h&&1==JU.Elements.getElementNumber(q)&&this.jbr.setHaveHsAlready(!0);var w=k.getAtomName(),s=h?this.getPdbCharge(n,w):k.getFormalCharge(),n=this.addAtom(e,k.getSymmetry(),k.getAtomSite()+f,q,w,s,k.getPartialCharge(),k.getTensors(),k.getOccupancy(),k.getBfactor(),k.getXYZ(),k.getIsHetero(),k.getSerial(),k.getSeqID(),n,k.getVib(),k.getAltLoc(),k.getRadius(),k.getBondRadius());b&&this.htAtomMap.put(k.getUniqueID(),n)}0<this.groupCount&&h&&this.jbr.addImplicitHydrogenAtoms(a,
this.groupCount-1,this.isNewChain?1:0);c=-1;a=null;b=this.ms.at;for(f=j[0].firstAtomIndex=0;f<this.ms.ac;f++)null!=b[f]&&b[f].mi>c&&(c=b[f].mi,k=j[c],k.firstAtomIndex=f,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(),f,e=d.entrySet().iterator();e.hasNext()&&((f=e.next())||1);){var h=f.getKey(),k=f.getValue();if(k.length!=c)break;var m=h.startsWith("property_")?1715472409:JS.T.getTokFromName(h);switch(m){default:if(JS.T.tokAttr(m,2048)){this.vwr.setAtomProperty(b,m,0,0,null,k,null);break}case 1111492629:case 1111492630:case 1111492631:h="property_"+
h;case 1715472409:this.vwr.setData(h,A(-1,[h,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,f,e,h,k,m,j,n,q,w,s,p,r,u,v,x){var z=0,A=null;if(null!=f){var B;if(0<=(B=f.indexOf("\x00")))A=f.substring(B+1),f=f.substring(0,B);a&&(0<=f.indexOf("*")&&(f=f.$replace("*","'")),z=this.vwr.getJBR().lookupSpecialAtomID(f),
2==z&&"CA".equalsIgnoreCase(p)&&(z=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,c,f,A,w,s,b,n,v,r,e,h,m,j,k,q,z,d,x);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,f,e,h){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||f!=this.currentGroupInsertionCode||d!==this.currentGroup3){0<this.groupCount&&e&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!h?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=f;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,f);++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(),f=d?1:c,e=this.bondAtoms(a.getAtomUniqueID1(),a.getAtomUniqueID2(),f);null!=e&&(1<f&&(1025!=f&&1041!=f)&&(b=!0),f=a.getRadius(),0<f&&e.setMad(ca(2E3*f)),f=a.getColix(),0<=f&&(e.colix=f),e.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 f=this.ms.getInfoM("unitCells");null!=f&&(c=f.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;f=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+
f));c+=f}d>=c&&this.ms.bsSymmetry.set(d)}}if(this.appendNew&&this.ms.someModelsHaveFractionalCoordinates){a=this.ms.at;b=-1;c=null;f=!1;for(d=this.baseAtomIndex;d<this.ms.ac;d++)if(a[d].mi!=b&&(b=a[d].mi,c=this.ms.getUnitCell(b),f=null!=c&&c.getCoordinatesAreFractional()),f){var e=null==this.ms.getModulation(d)?c:a[d].getUnitCell();e.toCartesian(e.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 f=this.vwr.getBoolean(603979794),e=this.vwr.getBoolean(603979798),h=this.vwr.getBoolean(603979847),k=null,j=!1;if(!this.noAutoBond)for(var y=this.baseModelIndex;y<a;y++){var b=d[y].bsAtoms.cardinality(),n=this.ms.getInfoI(y,"initialBondCount"),q=d[y].isBioModel;
0>n&&(n=this.ms.bondCount);if(h||e&&(0==n||q&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||n<B(b/2))||this.ms.getInfoB(y,"hasSymmetry")&&!f&&!this.ms.getInfoB(y,"hasBonds")))if(j=!0,this.merging||1<a)null==k&&(k=JU.BS.newN(this.ms.ac)),(y==this.baseModelIndex||!this.isTrajectory)&&k.or(d[y].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);j?(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,f,e){if(e<f)throw new NullPointerException;var h=null==b||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(d,b,c,f,e,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(d,b,c,f,e),null!=
this.jbr&&(h.groupID=this.jbr.getGroupID(b)),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":"o>";null!=b&&(this.countGroup(this.ms.at[f].mi,c,b),h.isNucleic()&&(b=null==this.htGroup1?null:this.htGroup1.get(b),null!=b&&(h.group1=b.charAt(0))));this.addGroup(d,h);this.groups[a]=h;h.groupIndex=a;for(a=e+1;--a>=f;)this.ms.at[a].group=h},"~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 f=(b+"   ").substring(0,3),e=this.group3Lists[c].indexOf(f);0>e&&(this.group3Lists[c]+=",["+f+"]",e=this.group3Lists[c].indexOf(f),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][B(e/6)]++;e=this.group3Lists[c].indexOf(",["+f);0<=e&&(this.group3Lists[c]=this.group3Lists[c].substring(0,e)+d+this.group3Lists[c].substring(e+
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,f=c.bonds,e=c.getBondCount();0<=--e;){var h=f[e];if(h!==b&&(h=h.getOtherAtom(c),a.sub2(h,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);f=JU.JmolMolecule.getBranchBitSet(this.ms.at,b.atom2.i,a,null,b.atom1.i,!1,!0);f.set(b.atom2.i);for(e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))this.ms.at[e].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,f=this.vwr.ms.ac,e=c;e<f;e++){var h=this.ms.at[e],k=h.getModelIndex();k!=b&&(b=k,this.ms.setInfo(k,"dimension","3D"));k=h.bonds;if(null!=k)for(var j=k.length;0<=--j;)if(null!=k[j]){var y=k[j].getOtherAtom(h);1!=y.getAtomNumber()&&y.getIndex()>e&&(a+=y.distance(h),d++)}}if(0!=d){a=1.45/(a/d);for(e=c;e<f;e++)this.ms.at[e].scale(a)}});c(b,"set2dZ",function(a){var d=this.baseAtomIndex,
b=this.vwr.ms.ac,c=JU.BS.newN(b),f=new JU.BS,e=JU.V3.new3(0,1,0),h=new JU.V3,k=new JU.BS;for(k.setBits(d,b);d<b;d++)!c.get(d)&&!f.get(d)&&(f=this.getBranch2dZ(d,-1,k,f,a,e,h,this.stereodir),c.or(f))},"JU.V3");c(b,"getBranch2dZ",function(a,d,b,c,f,e,h,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,f,e,h,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,f,e,h){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 j=a.bonds[k];j.isHydrogen()||(j=j.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,j,c,f,e,h),JM.ModelLoader.setBranch2dZ(j,d,b,c,f,e,h))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");b.setAtom2dZ=c(b,"setAtom2dZ",function(a,d,b,c,f,e){b.sub2(d,a);b.z=0;b.normalize();f.cross(c,b);b=Math.acos(b.dot(c));e=0.4*-e*Math.sin(4*b);d.z=a.z+e},"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,f){if(null==c)return null;var e=a.getModelAdapter(),h=new JU.P3,k=d.at,j=a.getFloat(570425363);if(null!=d.unitCells)for(var y=f.nextSetBit(0);0<=y;y=f.nextSetBit(y+1))if(null!=k[y].atomSymmetry){j=-j;break}for(var y=-1,n=0,q=JU.BSUtil.cardinalityOf(f)==a.ms.ac,w=e.getAtomIterator(c);w.hasNext();){var s=w.getXYZ();if(!Float.isNaN(s.x+s.y+s.z))if(1145047050==b){y=f.nextSetBit(y+1);if(0>y)break;n++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+y+": "+k[y]+" --\x3e ("+s.x+","+s.y+","+s.z);d.setAtomCoord(y,
s.x,s.y,s.z)}else{h.setT(s);s=JU.BS.newN(d.ac);d.getAtomsWithin(j,h,s,-1);s.and(f);if(q)if(n=JU.BSUtil.cardinalityOf(s),0==n){JU.Logger.warn("createAtomDataSet: no atom found at position "+h);continue}else 1<n&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+n+" atoms found at position "+h);switch(b){case 1145047055:var p=w.getVib();if(null==p)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+h+" vib: "+p);d.setAtomCoords(s,1145047055,p);break;case 1128269825:d.setAtomProperty(s,b,
0,w.getOccupancy(),null,null,null);break;case 1111492619:d.setAtomProperty(s,b,0,w.getPartialCharge(),null,null,null);break;case 1111492620:d.setAtomProperty(s,b,0,w.getBfactor(),null,null,null)}}}switch(b){case 1145047055:d=e.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+d);a.setStringProperty("_vibrationName",d);break;case 1145047050:if(JU.Logger.info(n+" atom positions read"),d.recalculateLeadMidpointsAndWingVectors(-1),n==d.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS")});
p("JM");C(["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=v(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;r(this,arguments)},JM,"ModelSet",JM.BondCollection);x(b,function(a,d){M(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 f=JU.BSUtil.copy(a),e=null,h=new JU.P3,b=0;b<this.mc;b++){c=this.am[b];if(!c.isJmolDataFrame&&!c.isTrajectory){var k=f.nextSetBit(0);c.bsAtoms.get(k)&&(null==e?e=JU.P3.newP(this.at[k]):(h.sub2(e,this.at[k]),this.translateModel(b,h)))}f.andNot(c.bsAtoms)}return null}f=Array(this.mc);for(b=this.mc;0<=--b;)f[b]=new JU.P3;for(var h=e=0,k=null,j=null!=this.trajectory&&
this.trajectory.steps.size()==this.mc,y=j?this.mc:1,c=0;c<y;c++){j&&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!=e){0<h&&(k.scale(-1/h),0!=e&&k.sub(f[0]),h=0);if(b==this.ac)break;e=this.at[b].mi;k=f[e]}a.get(b)&&(k.add(this.at[b]),h++)}}f[0].set(0,0,0);return f},"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=A(-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,f,e,h){return this.calculatePointGroupForFirstModel(a,!0,!1,d,b,c,f,e,h)},"JU.BS,~S,~N,~N,~A,JU.P3,~S");c(b,"calculatePointGroupForFirstModel",
function(a,d,b,c,f,e,h,k,j){var y=this.pointGroup,n=J.api.Interface.getSymmetry(this.vwr,"ms"),q=null,w=!1,s=!1,p=!1,r=null!=h,u=this.vwr.am.cmi;if(!r)if(h=null==a?-1:a.nextSetBit(0),0>u&&0<=h&&(u=this.at[h].mi),0>u&&(u=this.vwr.getVisibleFramesBitSet().nextSetBit(0),a=null),q=this.vwr.getModelUndeletedAtomsBitSet(u),p=null!=a&&q.cardinality()!=a.cardinality(),null!=a&&q.and(a),h=q.nextSetBit(0),0>h&&(q=this.vwr.getModelUndeletedAtomsBitSet(u),h=q.nextSetBit(0)),s=this.vwr.shm.getShapePropertyIndex(18,
"mad",h),w=null!=s&&0!=s.intValue()||this.vwr.tm.vibrationOn,s=null!=c&&0<=c.toUpperCase().indexOf(":POLY")){y=A(-1,[Integer.$valueOf(h),null]);this.vwr.shm.getShapePropertyData(21,"points",y);h=y[1];if(null==h)return null;q=null;w=!1;y=null}else h=this.at;var v;if(null!=c&&0<=(v=c.indexOf(":")))c=c.substring(0,v);if(null!=c&&0<=(v=c.indexOf(".")))f=JU.PT.parseInt(c.substring(v+1)),0>f&&(f=0),c=c.substring(0,v);y=n.setPointGroup(y,k,h,q,w,r?0:this.vwr.getFloat(570425382),this.vwr.getFloat(570425384),
null==q?h.length:q.cardinality(),p);!s&&!r&&(this.pointGroup=y);if(!d&&!b)return y.getPointGroupName();d=y.getPointGroupInfo(u,j,b,c,f,e);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,f,e,h,k,j,y){this.moleculeCount=0;var n=1073741852==c&&2048!=b?new JU.SB:null;a=this.makeConnections2(a,d,b,c,f,e,h,k,j,y,n);null!=n&&this.addStateScript(n.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 f=this.getInfo(d,"PDB_CONECT_bonds");if(null!=f){var e=f.size();this.setInfo(d,"initialBondCount",
Integer.$valueOf(e));var h=this.getInfo(d,"PDB_CONECT_firstAtom_count_max"),k=h[0]+a,j=k+h[1];j>this.atomSerials.length&&(j=this.atomSerials.length);for(var h=h[2],y=E(h+1,0),n=k;n<j;n++)if(0<(k=this.atomSerials[n]))y[k]=n+1;for(j=0;j<e;j++){var k=f.get(j),n=k[0],q=k[1],k=k[2];if(!(0>n||0>q||n>h||q>h))if(n=y[n]-1,q=y[q]-1,!(0>n||0>q)){var w=this.at[n],s=this.at[q];null!=b&&(w.isHetero()&&b.set(n),s.isHetero()&&b.set(q));if(w.altloc==s.altloc||"\x00"==w.altloc||"\x00"==s.altloc)this.getOrAddBond(w,
s,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),f=c&&a.get(d=this.am[b].trajectoryBaseIndex);if(a.get(b)){if(c&&!f){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 f;if(d==this.mc)return f=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),f;this.validateBspf(!1);f=new JU.BS;for(var e=!0,h=!1,k=new JU.BS,j=b.nextSetBit(0),c=0;c<
this.mc;c++)b=this.am[c],c<this.mc-1&&(e=(new Boolean(e&(b.isOrderly||b.bsAtoms.length()<=j))).valueOf()),a.get(c)?(0<=b.fileIndex&&k.set(b.fileIndex),f.or(this.getModelAtomBitSetIncludingDeleted(c,!1))):0<=b.fileIndex&&k.get(b.fileIndex)&&(h=!0);if(!e||h)return this.vwr.deleteAtoms(f,!1),null;d=Array(this.mc-d);e=this.am;for(h=c=0;c<this.mc;c++)a.get(c)||(b=this.am[c],b.modelIndex=h,d[h++]=b);this.am=d;b=this.mc;k=this.getBondsForSelectedAtoms(f,!0);this.deleteBonds(k,!0);for(h=c=0;c<b;c++)if(a.get(c)){var y=
e[c],j=y.act;if(0!=j){var n=y.bsAtoms,y=y.firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,n);this.deleteModel(h,n,k);this.deleteModelAtoms(y,j,n);this.vwr.deleteModelAtoms(h,y,j,n);for(var q=b;--q>c;)e[q].fixIndices(h,j,n);this.vwr.shm.deleteShapeAtoms(A(-1,[d,this.at,E(-1,[h,y,j])]),n);this.mc--}}else h++;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 f},"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"),f=this.getInfoM("group3Counts"),e=a+1;if(null!=c&&null!=c[e])for(var h=B(c[e].length/6);0<=--h;)0<f[e][h]&&(f[0][h]-=f[e][h],0==f[0][h]&&(c[0]=c[0].substring(0,6*h)+",["+c[0].substring(6*h+2)));null!=c&&(this.msInfo.put("group3Lists",
JU.AU.deleteElements(c,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(f,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(h=this.stateScripts.size();0<=--h;)this.stateScripts.get(h).deleteAtoms(a,b,d)||this.stateScripts.removeItemAt(h)}},"~N,JU.BS,JU.BS");c(b,"setAtomProperty",function(a,d,b,c,f,e,h){switch(d){case 1114249217:case 1112152066:case 1112152071:case 1112152073:case 1112152074:case 1649022989:case 1112152078:if(4<c&&(c=4),null!=e){b=
K(this.ac,0);try{var k=a.nextSetBit(0);for(f=0;0<=k;k=a.nextSetBit(k+1))b[k]=e[f++]}catch(j){if(F(j,Exception))return;throw j;}e=b}case 1112152070:case 1112152076:k=null;b=0;null==e?(16<c&&(c=16.1),0>c&&(c=0),b=B(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(e,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(d),b,k,a);return}this.setAPm(a,d,b,c,f,e,h)},"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 f=this.vwr.rd,e=this.getDefaultMadFromOrder(1);this.am[b].resetDSSR(!1);for(var h=0,k=this.am[b].act+1;h<a.size();h++,k++){var j=a.get(h),y=this.addAtom(b,j.group,1,"H"+k,null,k,j.getSeqID(),k,d[h],NaN,null,0,0,100,NaN,null,!1,
0,null,NaN);y.setMadAtom(this.vwr,f);c.set(y.i);this.bondAtoms(j,y,1,e,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 f=0;f<this.am[d].chains[c].groupCount;f++)a[b]=this.am[d].chains[c].groups[f],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 f=this.at[c];JM.AtomCollection.isDeleted(f)||(d.get(f.mi)?f.checkVisible()&&a.contains(f.sX,f.sY)&&b.set(c):c=this.am[f.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 f=this.at[c];if(!JM.AtomCollection.isDeleted(f))if(this.isJmolDataFrameForAtom(f)){for(a=f.mi;0<=c&&null!=this.at[c]&&this.at[c].mi==a;)c--;c++}else{if(f.mi!=a){a=f.mi;var e=
this.am[a].isBioModel?null:this.getUnitCell(a);if(null!=e)for(var h=e.getUnitCellVerticesNoOffset(),e=e.getCartesianOffset(),k=0;8>k;k++)this.ptTemp.setT(h[k]),this.ptTemp.add(e),b=Math.max(b,d.distance(this.ptTemp))}f=d.distance(f)+this.getRadiusVdwJmol(f);f>b&&(b=f)}}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,f=c?this.ac-1:a.nextSetBit(0);0<=f;f=c?f-1:a.nextSetBit(f+1)){b++;var e=this.at[f];null!=e&&!this.isJmolDataFrameForAtom(e)&&d.addBoundBoxPoint(e)}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(),f=0;8>f;f++)a.add2(c,b[f]),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 f=this.at[c],f=d.distance(f)+this.getRadiusVdwJmol(f);f>b&&(b=f)}return 0==b?10:b},"JU.BS");c(b,"getCenterAndPoints",function(a,d){for(var b,c,f=d?1:0,e=a.size();0<=--e;){var h=a.get(e);b=h[0];z(h[1],"JU.BS")?(c=h[1],f+=Math.min(b.cardinality(),
c.cardinality())):f+=Math.min(b.cardinality(),h[1].length)}var k=A(2,f,null);d&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(e=a.size();0<=--e;)if(h=a.get(e),b=h[0],z(h[1],"JU.BS")){c=h[1];for(var h=b.nextSetBit(0),j=c.nextSetBit(0);0<=h&&0<=j;h=b.nextSetBit(h+1),j=c.nextSetBit(j+1))k[0][--f]=this.at[h],k[1][f]=this.at[j],d&&(k[0][0].add(this.at[h]),k[1][0].add(this.at[j]))}else{c=h[1];h=b.nextSetBit(0);for(j=0;0<=h&&j<c.length;h=b.nextSetBit(h+1),j++)k[0][--f]=this.at[h],k[1][f]=c[j],d&&(k[0][0].add(this.at[h]),
k[1][0].add(c[j]))}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,f,e,h){this.setAPa(a,d,b,c,f,e,h);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,f,e,h){var k=this.vwr.am.cmi;e?(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,f,h);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 z(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,f=null==a;d=(new Boolean(d&null!=this.trajectory)).valueOf();for(var e=f?0:a.nextSetBit(0);0<=e&&e<this.ac;e=f?e+1:a.nextSetBit(e+1))JM.AtomCollection.isDeleted(this.at[e])||(b.set(c=this.at[e].mi),d&&this.trajectory.getModelBS(c,b),c=this.am[c],c.isOrderly&&(e=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 f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))a.atomMolecule[f]=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=B(Math.floor(a));for(a=B(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,f=0>=a?0:this.am[a].firstAtomIndex;--c>=f;)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 f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))z(this.vibrations[f],"J.api.JmolModulationSet")?
c.addLast(this.vibrations[f].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,f=0,e=0,h=new JU.V3,k=new JU.V3;null==d&&(d=this.getModelAtomBitSetIncludingDeleted(-1,!1));this.vwr.getOrCalcPartialCharges(this.am[a].bsAtoms,null);for(var j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(!(JM.AtomCollection.isDeleted(this.at[j])||
this.at[j].mi!=a)){var y=this.partialCharges[j];0>y?(c++,e+=y,k.scaleAdd2(y,this.at[j],k)):0<y&&(b++,f+=y,h.scaleAdd2(y,this.at[j],h))}if(0.015<Math.abs(f+e))return JU.Logger.info("Dipole calculation requires balanced charges: "+f+" "+e),null;if(0==c||0==b)return null;h.add(k);h.scale(4.8);return h},"~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,f){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,f)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(b,"getSelectedAtomIterator",function(a,d,b,c,f){this.initializeBspf();if(f){f=this.getModelBS(a,!1);for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))this.initializeBspt(e);
f=new JM.AtomIteratorWithinModelSet(f)}else f=new JM.AtomIteratorWithinModel;f.initialize(this.bspf,a,d,b,c,this.vwr.isParallel());return f},"JU.BS,~B,~B,~B,~B");j(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 f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))c.isWithin(this.at[f])||b.clear(f);return b;case 1094713350:b=JU.BSUtil.newBitSet2(0,this.ac);c=E(-1,[D(d.x)-1,D(d.y)-1,D(d.z)-1,D(d.x),D(d.y),D(d.z),0]);for(f=this.mc;0<=--f;){var e=
this.getUnitCell(f);null==e?JU.BSUtil.andNot(b,this.am[f].bsAtoms):b.andNot(e.notInCentroid(this,this.am[f].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;e=0;for(f=this.ac;0<=--f;){var h=this.at[f];if(!JM.AtomCollection.isDeleted(h)){var k=h.atomSymmetry;if(null!=k){if(h.mi!=c){c=h.mi;if(null==this.getModelCellRange(c))continue;e=this.getModelSymmetryCount(c)}for(var h=0,j=e;0<=--j;)if(k.get(j)&&
1<++h){b.set(f);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();e=-1;for(f=this.ac;0<=--f;)JM.AtomCollection.isDeleted(this.at[f])||(k=this.at[f].getModelIndex(),e!=k&&(e=k,c=this.getUnitCell(e)),null!=c&&(this.ptTemp.setT(this.at[f]),c.toFractional(this.ptTemp,!1),c.isWithinUnitCell(this.ptTemp,d.x,d.y,d.z)&&b.set(f)));return b;case 1814695966:b=new JU.BS;e=z(d,"J.api.SymmetryInterface")?
d:this.vwr.getCurrentUnitCell();if(null==e)return b;e=e.getUnitCellMultiplied();for(f=this.ac;0<=--f;)null!=this.at[f]&&(this.ptTemp1.setT(this.at[f]),e.toFractional(this.ptTemp1,!1),e.checkPeriodic(this.ptTemp1)&&b.set(f));return b}},"~N,~O");c(b,"getSelectCodeRange",function(a){var d=new JU.BS,b=a[0],c=a[1];a=a[2];var f=this.vwr.getBoolean(603979822);0<=a&&(300>a&&!f)&&(a=this.chainToUpper(a));for(var e=this.mc;0<=--e;)if(this.am[e].isBioModel)for(var h=this.am[e],k,j=h.chainCount;0<=--j;){var y=
h.chains[j];if(-1==a||a==(k=y.chainID)||!f&&0<k&&300>k&&a==this.chainToUpper(k))for(var n=y.groups,y=y.groupCount,q=0;0<=q;)q=JM.ModelSet.selectSeqcodeRange(n,y,q,b,c,d)}return d},"~A");b.selectSeqcodeRange=c(b,"selectSeqcodeRange",function(a,d,b,c,f,e){var h,k,j,y=!1;for(k=b;k<d&&a[k].seqcode!=c;k++);if(k==d){if(0<b)return-1;y=!0;j=2147483647;for(var n=d;0<=--n;)if((h=a[n].seqcode)>c&&h-c<j)k=n,j=h-c;if(2147483647==j)return-1}if(2147483647==f)c=d-1,y=!0;else{for(c=k;c<d&&a[c].seqcode!=f;c++);if(c==
d){if(0<b)return-1;y=!0;j=2147483647;for(n=k;n<d;n++)if((h=a[n].seqcode)<f&&f-h<j)c=n,j=f-h;if(2147483647==j)return-1}}for(n=k;n<=c;++n)a[n].setAtomBits(e);return y?-1:c+1},"~A,~N,~N,~N,~N,JU.BS");c(b,"getAtomsWithinRadius",function(a,d,b,c,f){var e=new JU.BS;d=JU.BSUtil.andNot(d,this.vwr.slm.bsDeleted);var h=this.getSelectedAtomIterator(f,!1,!1,!1,!1);if(b){b=!this.vwr.g.legacyJavaFloat;var k=new JU.P3;f=null==f?JU.BSUtil.newBitSet2(0,this.mc):this.getModelBS(f,!1);f.and(this.getIterativeModels(!1));
for(var j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))for(var y=f.nextSetBit(0);0<=y;y=f.nextSetBit(y+1))0>a?this.getAtomsWithin(a,this.at[j].getFractionalUnitCoordPt(b,!0,k),e,y):(this.setIteratorForAtom(h,y,j,a,c),h.addAtoms(e))}else{null==f&&e.or(d);for(j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))0>a?this.getAtomsWithin(a,this.at[j],e,this.at[j].mi):(this.setIteratorForAtom(h,-1,j,a,c),h.addAtoms(e))}h.release();return e},"~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 f=this.ac;0<=--f;){var e=this.at[f];JM.AtomCollection.isDeleted(e)||0<=c&&e.mi!=c||!b.get(f)&&e.getFractionalUnitDistance(d,this.ptTemp1,this.ptTemp2)<=a&&b.set(e.i)}return b}for(var e=this.getSelectedAtomIterator(null,!1,!1,!1,!1),h=0<=c?JU.BSUtil.newAndSetBit(c):this.getIterativeModels(!0),k=h.nextSetBit(0);0<=k;k=h.nextSetBit(k+1))f=this.am[k].bsAtoms.nextSetBit(0),0>f||(this.setIteratorForAtom(e,c,f,-1,null),e.setCenter(d,a),e.addAtoms(b));e.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,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var e=this.bo[f].atom1;this.am[e.mi].isModelKit||(b.clearAll(),c.clearAll(),b.set(e.i),c.set(this.bo[f].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,f,e,h,k,j,y,n){null==h&&(h=new JU.BS);var q=65535==b,w=131071==b,s=65537==b;w&&(b=1);var p=JU.Edge.isOrderH(b),
r=!1,u=!1,v=!1,x=!1;switch(c){case 12291:return this.deleteConnections(a,d,b,f,e,k,w);case 603979872:case 1073741852:if(515!=b){if(k){a=f;f=new JU.BS;e=new JU.BS;for(var z=a.nextSetBit(0);0<=z;z=a.nextSetBit(z+1))f.set(this.bo[z].atom1.i),e.set(this.bo[z].atom2.i)}return E(-1,[p?this.autoHbond(f,e,!1):this.autoBondBs4(f,e,null,h,this.vwr.getMadBond(),603979872==c,n),0])}u=x=!0;break;case 1086324745:r=u=!0;break;case 1073742025:u=!0;break;case 1073741904:v=!0}c=!r&&!q;this.defaultCovalentMad=this.vwr.getMadBond();
n=0>a;var w=0>d,A=n||w,B=!k||0.1!=a||1E8!=d;B&&(a=this.fixD(a,n),d=this.fixD(d,w));var C=this.getDefaultMadFromOrder(b),D=0,H=0,I=null,K=null,M=null,N="\x00",P=b|131072,Q=65535!=b&&0!=(b&512);try{for(z=f.nextSetBit(0);0<=z;z=f.nextSetBit(z+1)){if(k)I=this.bo[z],K=I.atom1,M=I.atom2;else{K=this.at[z];if(K.isDeleted())continue;N=this.isModulated(z)?"\x00":K.altloc}for(var R=k?0:e.nextSetBit(0);0<=R;R=e.nextSetBit(R+1)){if(k)R=2147483646;else{if(R==z)continue;M=this.at[R];if(null==M||K.mi!=M.mi||M.isDeleted())continue;
if("\x00"!=N&&N!=M.altloc&&"\x00"!=M.altloc)continue;I=K.getBond(M)}if(!(null==I?u:v)&&!(B&&!this.isInRange(K,M,a,d,n,w,A)||Q&&null!=I&&!this.allowAromaticBond(I)))if(null==I)h.set(this.bondAtoms(K,M,b,C,h,y,j,!0).index),D++;else if(c&&(I.setOrder(b),s&&(this.haveAtropicBonds=!0,I.setAtropisomerOptions()),this.bsAromatic.clear(I.index)),q||b==I.order||P==I.order||p&&I.isHydrogen())h.set(I.index),H++}}}catch(T){if(!F(T,Exception))throw T;}x&&this.assignAromaticBondsBs(!0,h);r||this.sm.setShapeSizeBs(1,
-2147483648,null,h);return E(-1,[D,H])},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N,JU.SB");c(b,"autoBondBs4",function(a,d,b,c,f,e,h){if(e)return this.autoBond_Pre_11_9_24(a,d,b,c,f);if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();e=this.vwr.getFloat(570425348);var k=this.vwr.getFloat(570425364),k=k*k,j=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var y=-1,n=null==a,q,w;n?(w=0,q=null):(a.equals(d)?q=a:(q=JU.BSUtil.copy(a),q.or(d)),w=q.nextSetBit(0));
for(var s=this.getSelectedAtomIterator(null,!1,!1,!0,!1),p=!1;0<=w&&w<this.ac;w=n?w+1:q.nextSetBit(w+1)){var r=n||a.get(w),u=n||d.get(w),v=this.at[w];if(!JM.AtomCollection.isDeleted(v)){var x=v.mi;if(x!=y){y=x;if(this.isJmolDataFrameForModel(x)){w=this.am[x].firstAtomIndex+this.am[x].act-1;continue}p=this.getInfoB(x,"autoBondUsingOccupation")}x=v.getBondingRadius();if(0!=x){var z=v.getFormalCharge(),A=0!=z;A&&(z=Math.signum(z));var B=null!=b&&b.get(w);for(this.setIteratorForAtom(s,-1,w,x+this.maxBondingRadius+
e,null);s.hasNext();){var C=this.at[s.next()];if(!C.isDeleted()){var D=C.i,E=n||a.get(D),F=n||d.get(D);!E&&!F||(!(r&&F||u&&E)||B&&b.get(D)||p&&null!=this.occupancies&&50>this.occupancies[w]!=50>this.occupancies[D]||A&&Math.signum(C.getFormalCharge())==z)||(E=this.isBondable(x,C.getBondingRadius(),s.foundDistance2(),k,e)?1:0,0<E&&this.autoBondCheck(v,C,E,f,c)&&(j++,null!=h&&h.append("connect ({"+w+"}) ({"+D+"});")))}}s.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return j},
"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B,JU.SB");c(b,"isBondable",function(a,d,b,c,f){if(0==a||0==d||b<c)return!1;a=a+d+f;return b<=a*a},"~N,~N,~N,~N,~N");c(b,"autoBondCheck",function(a,d,b,c,f){if(20<a.getCurrentBondCount()||20<d.getCurrentBondCount())return this.maxBondWarned||JU.Logger.warn("maximum auto bond count reached"),this.maxBondWarned=!0,!1;var e=a.getFormalCharge();if(0!=e){var h=d.getFormalCharge();if(0>e&&0>h||0<e&&0<h)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,f,0,!1);return!0},"JM.Atom,JM.Atom,~N,~N,JU.BS");c(b,"autoBond_Pre_11_9_24",function(a,d,b,c,f){if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var e=this.vwr.getFloat(570425348),h=this.vwr.getFloat(570425364),h=h*h,k=0;this.initializeBspf();for(var j=-1,y=this.ac;0<=--y;){var n=this.at[y];if(!JM.AtomCollection.isDeleted(n)){var q=null==a||a.get(y),w=null==d||d.get(y);if((q||w)&&!n.isDeleted()){var s=
n.mi;if(s!=j&&(j=s,this.isJmolDataFrameForModel(s))){for(;0<=--y&&!(JM.AtomCollection.isDeleted(this.at[y])||this.at[y].mi!=s););y++;continue}var p=n.getBondingRadius();if(0!=p){var r=p+this.maxBondingRadius+e;this.initializeBspt(s);s=this.bspf.getCubeIterator(s);for(s.initialize(n,r,!0);s.hasMoreElements();)if(r=s.nextElement(),!(r===n||r.isDeleted())){var u=r.i,v=null==a||a.get(u),x=null==d||d.get(u);if(!(!v&&!x||null!=b&&b.get(u)&&b.get(y)))if(q&&x||w&&v)u=this.isBondable(p,r.getBondingRadius(),
s.foundDistance2(),h,e)?1:0,0<u&&this.autoBondCheck(n,r,u,f,c)&&k++}s.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),f=c.nextSetBit(0);0<=f&&b;f=c.nextSetBit(f+1))b=!this.am[f].hasRasmolHBonds;if(b)return 0}b=!1;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))if(1==this.at[f].getElementNumber()){b=!0;break}c=new JU.BS;f=this.vwr.getBoolean(603979853);if(null==d||f&&!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 e=null;if(!b){e=new JU.BS;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))switch(this.at[f].atomID){case 64:case 4:case 14:case 15:case 16:case 17:e.set(f)}}var h,k;b?(h=this.vwr.getFloat(570425361),k=1):(h=this.vwr.getFloat(570425360),k=JM.ModelSet.hbondMinRasmol*JM.ModelSet.hbondMinRasmol);var j=h*h,y=3.141592653589793*this.vwr.getFloat(570425359)/
180,n=0,q=0;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var w=null,s=null;d=this.getSelectedAtomIterator(d,!1,!1,!1,!1);for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var p=this.at[f],r=p.getElementNumber(),u=1==r;if(!(u?!b:b||7!=r&&8!=r)){if(u){r=!1;w=p.bonds;if(null==w)continue;for(var v=!1,s=0;!v&&s<w.length;s++)v=w[s].getOtherAtom(p).getElementNumber(),v=7==v||8==v;if(!v)continue}else r=e.get(f);for(this.setIteratorForAtom(d,-1,p.i,h,null);d.hasNext();)if(v=this.at[d.next()],
w=v.getElementNumber(),!(v===p||(u?1==w:7!=w&&8!=w)||(q=d.foundDistance2())<k||q>j||r&&e.get(v.i)||p.isBonded(v)))if(this.v1.sub2(p,v),null!=(s=JM.ModelSet.checkMinAttachedAngle(p,y,this.v1,this.v2,b)))if(this.v1.scale(-1),null!=(w=JM.ModelSet.checkMinAttachedAngle(v,y,this.v1,this.v2,b))){var x=0,z;u&&!Float.isNaN(w.x)&&!Float.isNaN(s.x)?(z=4096,x=JM.HBond.calcEnergy(Math.sqrt(q),w.distance(p),w.distance(s),v.distance(s))/1E3):z=2048;c.set(this.addHBond(p,v,z,x));n++}}}d.release();this.sm.setShapeSizeBs(1,
-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return b?n:-n},"JU.BS,JU.BS,~B");b.checkMinAttachedAngle=c(b,"checkMinAttachedAngle",function(a,d,b,c,f){var e=a.bonds,h=!0,k=null;if(null!=e&&0<e.length)for(var j=3.4028235E38,y=e.length;0<=--y;)if(e[y].isCovalent()){var h=!1,n=e[y].getOtherAtom(a);if(f||1!=n.getElementNumber()){c.sub2(a,n);var q=c.angle(b);if(q<d)return null;q<j&&(k=n,j=q)}}return h?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,f=-1,e=0;e<this.ac;e++)if(!JM.AtomCollection.isDeleted(this.at[e])){if((c=this.at[e].mi)!=f)d=0,f=c,b=-1;if((a=this.at[e].group.getStrucNo())!=b&&0!=a)this.at[e].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=B(this.modelFileNumbers[this.mc-1]/1E6)+1,c=this.mc,f=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*b+ ++f,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=b+"."+f;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 f=JU.BSUtil.copy(a),c=0;c<this.mc;c++){var e=this.am[c];e.resetDSSR(!1);e.bsAtomsDeleted.or(a);e.bsAtomsDeleted.and(e.bsAtoms);null!=e.bsAsymmetricUnit&&e.bsAsymmetricUnit.andNot(a);d.get(e.modelIndex)&&this.updateBasisFromSite(e.modelIndex);a=JU.BSUtil.andNot(e.bsAtoms,e.bsAtomsDeleted);e.firstAtomIndex=a.nextSetBit(0);e.act=a.cardinality();e.isOrderly=e.act==e.bsAtoms.length()}this.deleteBonds(b,!1);a=this.vwr.shm.getShape(6);
null!=a&&a.setProperty("deleteAtoms",null,f);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 f=this.am[this.at[c].mi];f.firstAtomIndex==a[c]&&(f.firstAtomIndex=c);f.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(f=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=f)for(var e=f.length;0<=--e;){var h=f[e];null!=h&&(h.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,f,e,h,k,j,y,n,q,w,s,p,r,u,v,x,z){k=(new JM.Atom).setAtom(a,this.ac,j,y,x,k,b,q,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,p,!1);this.setOccupancy(this.ac,s,!1);this.setPartialCharge(this.ac,w,!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!=f&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=f),k.atomID=v,0==v&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=e&&(null==this.atomSerials&&(this.atomSerials=
E(this.at.length,0)),this.atomSerials[this.ac]=e);0!=h&&(null==this.atomSeqIDs&&(this.atomSeqIDs=E(this.at.length,0)),this.atomSeqIDs[this.ac]=h);null!=n&&this.setVibrationVector(this.ac,n);Float.isNaN(z)||this.setBondingRadius(this.ac,z);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 f=-1;c&&(f=this.at[a].mi,a=this.am[f].firstAtomIndex);null==this.atomSerials&&(this.atomSerials=E(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var e=
this.isXYZ&&this.vwr.getBoolean(603979978),h=2147483647,k=1;a<this.ac;++a){var j=this.at[a];if(!JM.AtomCollection.isDeleted(j)){if(j.mi!=h){if(c&&2147483647!=h&&j.mi!=f)continue;h=j.mi;k=e?0:1}var y=this.atomSerials[a];if(a>=-d){if(0==y||c)this.atomSerials[a]=a<d?b.atomSerials[a]:k;if(null==this.atomNames[a]||c)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}else y>k&&(k=y),c&&(this.atomNames[a]=(j.getElementSymbol()+y).intern());(!this.am[h].isModelKit||0<j.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 f=D(c[0]),e=0>f;e&&(f=-1-f);var h=D(c[1]);if(!(0>h||f>=this.ac||h>=this.ac)){var k=2<c.length?D(c[2]):1;0>k&&(k&=65535);var j=3<c.length?ca(1E3*a[b][3]):this.getDefaultMadFromOrder(k);0==
k||0==j&&32768!=k&&!JU.Edge.isOrderH(k)?(c=this.at[f].getBond(this.at[h]),null!=c&&d.set(c.index)):this.bondAtoms(this.at[f],this.at[h],k,j,null,4<c.length?c[4]:0,e,!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,f=null,e=0;e<this.mc;e++){var h=this.getInfo(e,"modelID"),k=a.startsWith("~")?"~"+this.getModelNumberDotted(e):null;if(!(null==k&&null==h&&null==(h=this.getModelTitle(e)))){d&&(f=this.getModelFileName(e),f.endsWith("#molfile")?h=f:(f+="#",h=f+h));if(a.equalsIgnoreCase(h)||a.equalsIgnoreCase(k))return b?this.vwr.getJDXBaseModelIndex(e):e;null!=f&&a.startsWith(f)&&
(c=-2)}}return null==f&&!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 f=this.getModelAuxiliaryInfo(c);f.put("modelIndex",Integer.$valueOf(c));b.addLast(f)}d.put("models",b)}return d},"JU.BS");c(b,"getDihedralMap",function(a){for(var d=new JU.Lst,b=a.length,c=null,f=null,e=null,h=null,k=b-1;0<=--k;)for(var j=b;--j>k;)if(c=this.at[a[k]],
f=this.at[a[j]],c.isBonded(f))for(var y=b;0<=--y;)if(y!=k&&y!=j&&(e=this.at[a[y]]).isBonded(c))for(var n=b;0<=--n;)if(n!=k&&n!=j&&n!=y&&(h=this.at[a[n]]).isBonded(f)){var q=E(4,0);q[0]=e.i;q[1]=c.i;q[2]=f.i;q[3]=h.i;d.addLast(q)}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 f=this.vwr.getFloat(1275072532),
e=!1,h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){var k=this.getModulation(h);null!=k&&(k.setModTQ(this.at[h],d,b,c,f),null!=this.bsModulated&&this.bsModulated.setBitTo(h,d),e=!0)}e||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(b,"getBoundBoxOrientation",function(a,d,b){var c=0,f=0,e=0,h=null,k=null,j=d.nextSetBit(0),y=0;if(0<=j){f=null==this.vOrientations?0:this.vOrientations.length;if(0==f){h=Array(3375);f=0;y=new JU.P4;for(c=-7;7>=c;c++)for(e=-7;7>=e;e++)for(var n=0;14>=n;n++,f++)1<(h[f]=JU.V3.new3(c/
7,e/7,n/14)).length()&&--f;this.vOrientations=Array(f);for(c=f;0<=--c;)n=Math.sqrt(1-h[c].lengthSquared()),Float.isNaN(n)&&(n=0),y.set4(h[c].x,h[c].y,h[c].z,n),this.vOrientations[c]=JU.Quat.newP4(y)}var n=new JU.P3,y=3.4028235E38,q=null,w=new JU.BoxInfo;w.setMargin(1312817669==a?0:0.1);for(c=0;c<f;c++){h=this.vOrientations[c];w.reset();if(null==b)for(e=j;0<=e;e=d.nextSetBit(e+1))w.addBoundBoxPoint(h.transform2(this.at[e],n));else for(e=b.length;0<=--e;)w.addBoundBoxPoint(h.transform2(b[e],n));switch(a){default:case 1312817669:case 1073741864:case 1814695966:e=
(w.bbCorner1.x-w.bbCorner0.x)*(w.bbCorner1.y-w.bbCorner0.y)*(w.bbCorner1.z-w.bbCorner0.z);break;case 1111492629:e=w.bbCorner1.x-w.bbCorner0.x;break;case 1111492630:e=w.bbCorner1.y-w.bbCorner0.y;break;case 1111492631:e=w.bbCorner1.z-w.bbCorner0.z}e<y&&(k=h,q=w,w=new JU.BoxInfo,w.setMargin(0.1),y=e)}switch(a){default:return k;case 1814695966:a=q.getBoundBoxVertices();a=A(-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:h=
JU.Quat.newQ(k),c=q.bbCorner1.x-q.bbCorner0.x,f=q.bbCorner1.y-q.bbCorner0.y,e=q.bbCorner1.z-q.bbCorner0.z,c<f&&(n.set(0,0,1),h=JU.Quat.newVA(n,90).mulQ(h),k=c,c=f,f=k),f<e&&(e>c&&(n.set(0,1,0),h=JU.Quat.newVA(n,90).mulQ(h),k=c,c=e,e=k),n.set(1,0,0),h=JU.Quat.newVA(n,90).mulQ(h),k=f,f=e,e=k)}}return 1312817669==a?y+"\t{"+c+" "+f+" "+e+"}\t"+d:1814695966==a?null:null==h||0==h.getTheta()?new JU.Quat:h},"~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=B(a.length/6),b=Array(d),c=new java.util.Hashtable,f=0,e=0;f<d;f++,e+=6)if(!(1>Math.abs(a[e+5]-a[e+4]))){var h=D(a[e+1]),k=D(a[e+2]),j=""+h+"_"+k;if(!c.containsKey(j)){c.put(j,Boolean.TRUE);for(var j=this.vwr.getBranchBitSet(k,h,!0),y=this.at[h].bonds,h=this.at[h],n=0;n<y.length;n++){var q=y[n];if(q.isCovalent()&&(q=q.getOtherAtom(h).i,q!=k&&j.get(q))){j=
null;break}}b[f]=j}}return b},"~A");c(b,"recalculatePositionDependentQuantities",function(a,d){null!=this.vwr.shm.getShape(21)&&this.vwr.shm.getShapePropertyData(21,"move",A(-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 f=this.am[c];f.isContainedIn(a)&&(null==f.mat4&&(f.mat4=JU.M4.newM4(null)),f.mat4.mul2(d,
f.mat4))}},"JU.BS,JU.M4");c(b,"moveAtoms",function(a,d,b,c,f,e,h,k){if(null!=a){for(d=f.nextSetBit(0);0<=d;d=f.nextSetBit(d+1))a.rotTrans(this.at[d]),this.taintAtom(d,2);this.mat4.setM4(a);c=null}else if(k)h||(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));h?(this.vTemp.setT(e),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=f.nextSetBit(0);0<=d;d=f.nextSetBit(d+1))h?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);h||(this.ptTemp.scale(1/f.cardinality()),null==c&&(c=new JU.V3),c.add(this.ptTemp))}if(null!=c){for(d=f.nextSetBit(0);0<=
d;d=f.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(f,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=B(a.length/6);1<b&&(b=1);for(var f=0,e=0;f<c;f++,e+=6){var h=d[f];if(!(null==h||h.isEmpty())){var k=this.at[D(a[e+1])],j=JU.V3.newVsub(this.at[D(a[e+2])],k),j=JU.A4.newVA(j,-((a[e+5]-a[e+4])*b)/57.29577951308232);
this.matTemp.setAA(j);this.ptTemp.setT(k);for(k=h.nextSetBit(0);0<=k;k=h.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 f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1)){var e=2*(a.x-this.at[f].x);b=2*(a.y-this.at[f].y);var h=2*(a.z-this.at[f].z);this.setAtomCoordRelative(f,e,b,h)}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),f=
c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))h=2*-JU.Measure.distanceToPlaneD(d,k,this.at[f]),e=a.x*h,b=a.y*h,h*=a.z,this.setAtomCoordRelative(f,e,b,h)}else if(0<=b&&(d=this.at[b],a=d.bonds,null!=a)){e=new JU.BS;h=new JU.Lst;k=this.vwr.getModelUndeletedAtomsBitSet(d.mi);for(f=0;f<a.length;f++){var j=a[f].getOtherAtom(d);c.get(j.i)?e.or(JU.JmolMolecule.getBranchBitSet(this.at,j.i,k,null,b,!0,!0)):h.addLast(j)}0!=h.size()&&(a=JU.Measure.getCenterAndPoints(h)[0],c=JU.V3.newVsub(d,a),c=JU.Quat.newVA(c,180),
this.moveAtoms(null,null,c.getMatrix(),null,e,d,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS");c(b,"getCellWeights",function(a){var d=null,b=a.nextSetBit(0),c=-1,f;if(0<=b&&null!=(f=this.getUnitCell(c=this.at[b].mi))){f=f.getUnitCellMultiplied();this.getModelAtomBitSetIncludingDeleted(c,!0).and(a);for(var d=K(a.cardinality(),0),e=new JU.P3,h=0;0<=b;b=a.nextSetBit(b+1))c=this.at[b],e.setT(c),f.toFractional(e,!1),f.unitize(e),d[h++]=f.getCellWeight(e)}return d},"JU.BS");c(b,"getAtomGroupQuaternions",function(a,
d,b){var c=0,f=new JU.Lst;a=JU.BSUtil.copy(a);for(var e=new JU.BS,h=a.nextSetBit(0);0<=h&&c<d;h=a.nextSetBit(h+1)){var k=this.at[h].group;k.setAtomBits(e);a.andNot(e);var j=k.getQuaternion(b);if(null==j&&(this.am[this.at[h].mi].isBioModel||(j=k.getQuaternionFrame(this.at)),null==j))continue;c++;f.addLast(j)}return f.toArray(Array(f.size()))},"JU.BS,~N,~S");c(b,"getConformation",function(a,d,b,c){for(var f=new JU.BS,e=this.mc;0<=--e;)if(!(0<=a&&e!=a)){var h=this.am[e],k=this.vwr.getModelUndeletedAtomsBitSet(a);
null!=c&&k.and(c);if(!(0>k.nextSetBit(0)))if(d>h.altLocCount)1==d&&f.or(k);else{if(this.am[e].isBioModel){if(-1E3>d){var h=1E3+d,j=this.getAltLocListInModel(e);-32!=h&&0>j.indexOf(String.fromCharCode(-h))&&(h=-2147483648)}else 0>d?(j=this.getAltLocListInModel(e),h=-1-d,h=h>=j.length?-2147483648:-j.charAt(h).charCodeAt(0)):h=d;if(-2147483648==h)continue;this.am[e].getConformation(h,b,k,f)}else{var y=this.getAltLocCountInModel(e),j=this.getAltLocListInModel(e),n=new JU.BS;if(-1E3>d)var q=String.fromCharCode(-1E3-
d),h=j.indexOf(q);else h=Math.abs(d)-1;if(0>h||h>=y)continue;for(q=y;0<=--q;)q!=h&&k.andNot(this.getAtomBitsMDa(1073742355,j.substring(q,q+1),n))}f.or(k)}}return f},"~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,f,e,h){this.haveBioModels&&this.bioModelset.calcAllRasmolHydrogenBonds(a,d,b,c,f,e,h,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,f,e){return this.haveBioModels?this.bioModelset.calculateAllStuctures(a,d,b,
c,f,e):""},"JU.BS,~B,~B,~B,~B,~N");c(b,"calculateStructuresAllExcept",function(a,d,b,c,f,e,h){this.freezeModels();return this.haveBioModels?this.bioModelset.calculateAllStructuresExcept(a,d,b,c,f,e,h):""},"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 f=new JU.Lst,e=null,h=null;c&&(e=new java.util.Hashtable,h=new JU.Lst,e.put("atoms",h),e.put("points",f));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 j=this.getUnitCellForAtom(k);if(null!=j){d=j.getIterator(this.vwr,this.at[k],d,a);for(null!=b&&d.setCenter(b,a);d.hasNext();)k=d.next(),b=d.getPosition(),
f.addLast(b),c&&h.addLast(Integer.$valueOf(k))}}return c?e:f},"~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=K(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),f=a.nextSetBit(0);null==d&&(d=this.getUnitCellForAtom(f));if(null!=d){null==b&&(b=this.vwr.getModelUndeletedAtomsBitSet(this.at[f].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 f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))this.at[f].getAtomSite()==a&&(c.set(f),null!=d&&(d.clear(f),b.clear(f)))},"~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 f=d.getSpaceGroupOperationCount();this.am[a].bsAsymmetricUnit=b;null==this.bsSymmetry&&(this.bsSymmetry=JU.BS.newN(this.ac));var e=this.vwr.getModelUndeletedAtomsBitSet(a);this.bsSymmetry.or(e);this.bsSymmetry.andNot(b);1<f&&this.setModelCage(a,null);var h=JU.P3.newP(d.getCartesianOffset());0==h.length()?h=null:(d.setOffsetPt(new JU.P3),this.setTaintedAtoms(e,2));if(c)this.fixP1AtomSites(d,e);else for(var k=0,j=e.nextSetBit(0);0<=j;j=e.nextSetBit(j+1)){null!=h&&this.at[j].sub(h);var y=
b.get(j);this.at[j].setSymop(y?1:0,!0);y&&this.setSite(this.at[j],++k,!0)}e.andNot(b);if(!c)for(var c=null!=this.occupancies,h=d.getSymmetryOperations(),k=new JU.P3,y=new JU.P3,n=new JU.P3,q=b.nextSetBit(0);0<=q;q=b.nextSetBit(q+1)){j=this.at[q];y.setT(j);d.toFractional(y,!0);d.unitize(y);var w=j.atomSite,s=c?this.occupancies[q]:0,j=e.nextSetBit(0);a:for(;0<=j;j=e.nextSetBit(j+1)){var p=this.at[j];if(!(p.atomNumberFlags!=p.atomNumberFlags||c&&s!=this.occupancies[j])){k.setT(p);d.toFractional(k,!0);
d.unitize(k);for(var r=0;r<f;r++)if(n.setT(y),h[r].rotTrans(n),d.unitize(n),1.96E-6>n.distanceSquared(k)){this.setSite(p,w,!0);e.clear(j);continue a}}}}e.isEmpty()||System.err.println("Model basis atoms not found for "+e);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,f=a.getPrecision(),f=f*f,e=d.nextSetBit(0);0<=e;e=d.nextSetBit(e+1)){var h=this.at[e],k=new JU.A4;k.setT(h);a.toFractional(k,!0);a.unitize(k);for(var j=!1,y=0;y<c;y++){var n=b[y];if(h.atomNumberFlags==n.angle&&n.distanceSquared(k)<f){j=!0;this.setSite(h,y+1,!0);break}}j||(k.angle=h.atomNumberFlags,b[c]=k,this.setSite(h,++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 f=this.am[b.mi].bsAsymmetricUnit;
if(null!=f)for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))if(this.at[e].atomSite==c)return this.at[e]}}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),f=0,e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))if(!JM.AtomCollection.isDeleted(this.at[e])){var h=this.at[e].atomSite;if(!b.get(h)){b.set(h);if(h>=c.length)continue;c[h]=++f;d.set(e)}this.setSite(this.at[e],
-1,!1);this.setSite(this.at[e],c[h],!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,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))for(var e=this.at[f],h=e.bonds,k=0,j=e.getBondCount();0<=--j;)if(h[j].isCovalent()&&!a.get(k=h[j].getOtherAtom(e).i))b.set(f),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});p("JM");C(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){var b=v(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;r(this,arguments)},JM,"Orientation",null);P(b,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});x(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")});p("JM");C(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){var b=v(function(){this.modelIndex=0;this.script2=
this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;r(this,arguments)},JM,"StateScript",null);x(b,function(a,d,b,c,f,e,h){this.modelIndex=a;this.script1=d;this.bsBonds=JU.BSUtil.copy(b);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(f);this.script2=e;this.inDefinedStateBlock=h},"~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))});j(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")});p("JM");N(JM,"Structure");p("JM");u=v(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=
0;this.signFactor=1;this.reference=null;r(this,arguments)},JM,"TickInfo",null);x(u,function(b){this.ticks=b},"JU.P3");p("JU");C(["JU.P3","$.V3"],"JU.BoxInfo",["java.util.Hashtable","JU.Measure","$.P4","JU.Point3fi"],function(){var b=v(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;r(this,arguments)},JU,"BoxInfo",null);P(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])});x(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,f=0;8>f;f++)b.add(a[f]);b.scale(0.125);for(f=0;8>f;f++)c.sub2(a[f],b),c.scale(d),a[f].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]),f=JU.P3.newP(a[2]),e=JU.P3.newP(a[1]);c.sub(b);f.sub(b);e.sub(b);null!=d&&b.add(d);return A(-1,[b,c,f,e])},"~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?A(-1,[this.bbCenter,
JU.P3.newP(this.bbVector),this.bbCorner0,this.bbCorner1]):A(-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,f,e){a-e<c.x&&(c.x=a-e);a+e>f.x&&(f.x=a+e);d-e<c.y&&(c.y=d-e);d+e>f.y&&(f.y=d+e);b-e<c.z&&(c.z=b-e);b+e>f.z&&(f.z=b+e)},"~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");j(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,f=new JU.P3,e=new JU.P3,h=new JU.P3;a=null==a?JU.BoxInfo.unitCubePoints:JU.BoxInfo.getVerticesFromOABC(a);for(var k=0;6>k;k++)f.setT(a[JU.BoxInfo.facePoints[k][0]]),e.setT(a[JU.BoxInfo.facePoints[k][1]]),h.setT(a[JU.BoxInfo.facePoints[k][2]]),d[k]=JU.Measure.getPlaneThroughPoints(f,
e,h,b,c,new JU.P4);return d},"~A");b.bbcageTickEdges=T(-1,"z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""));b.uccageTickEdges=T(-1,"zyx\x00\x00\x00\x00\x00\x00\x00\x00\x00".split(""));b.edges=Q(-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=A(-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=A(-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)});p("JU");C(["JU.BS"],"JU.BSUtil",null,function(){var b=H(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(),f=Math.min(c,d.length()),e;for(e=d.nextClearBit(b);e<f&&0<=e;e=d.nextClearBit(e+1))a.setBitTo(b++,a.get(e));for(e=f;e<c;e++)a.setBitTo(b++,a.get(e));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 f=d.length(),e=JU.BS.newN(f),h=!1,k=!1,j=b,y=0,n=0;y<f&&n<c;y++)d.get(y)?(k&&e.set(y),
j=b,h=!1):a.get(n++)?(e.set(y),j&&(j=!1,k=h=!0)):j&&!h&&(k=!1);a.clearAll();a.or(e)}},"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),f=a.nextSetBit(0);f>=d;f=a.nextSetBit(f+1))c.set(f+b);JU.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");b.setMapBitSet=c(b,"setMapBitSet",function(a,d,b,c){var f;a.containsKey(c)?f=a.get(c):a.put(c,f=new JU.BS);f.setBits(d,b+1)},"java.util.Map,~N,~N,~S");b.emptySet=new JU.BS});p("JU");C(["JU.Int2IntHash"],"JU.C","JU.AU $.CU $.PT $.SB J.c.PAL JU.Escape $.Logger".split(" "),
function(){var b=H(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 f=b?c+1:2*JU.C.colixMax;2048<f&&(f=2048);
JU.C.argbs=JU.AU.arrayCopyI(JU.C.argbs,f);null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale=JU.AU.arrayCopyI(JU.C.argbsGreyscale,f))}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(z(a,"J.c.PAL"))return a===J.c.PAL.NONE?0:2;if(z(a,Integer))return JU.C.getColix(a.intValue());if("string"==typeof a)return JU.C.getColixS(a);if(z(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:(B(Math.floor(1>a?256*a:15<=a?a:9>=a?B(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=W(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])});p("JU");C(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=v(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;r(this,arguments)},JU,"ColorEncoder",null);P(b,function(){this.userScale=E(-1,[-8355712]);this.thisScale=E(-1,[-8355712])});x(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=
B(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=B(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("="),f=a.indexOf("/"),e=Math.max(c,a.indexOf("[")),c=JU.ColorEncoder.fixName(a),h=JU.ColorEncoder.getSchemeIndex(c);if(-1==h&&(0>e||0<f)){b=a;f=this.schemes.get(c);if(null==f)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 j=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,j,0)}catch(y){if(F(y,"java.io.IOException")){JU.Logger.info("ColorEncoder "+y);break}else throw y;}b=j[0]}else{b=JU.PT.rep(b," ","%20");JU.Logger.info("ColorEncoder opening "+b);var n=this.vwr.fm.getFileAsBytes(b,null);if("string"==typeof n){JU.Logger.info("ColorEncoder "+n);break}c=n;JU.Logger.info("ColorEncoder read "+c.length+
" bytes");var j=0,q=c.length;if(800==q||802==q)j=32;if(768==q-j||770==q-j)for(var f=E(256,0),q=256+j,w=0;256>w;w++)f[w]=JU.CU.rgb(c[w+j]&255,c[w+j+256]&255,c[w+j+512]&255);else b=String.instantialize(c)}if(null==f)for(var p=JU.PT.split(b.trim(),"\n"),q=p.length,f=E(q,0),r=0<q&&0>p[0].indexOf("."),w=0;w<q;w++){var u=JU.PT.getTokens(p[w]);if(3>u.length){f=null;break}var v=u.length;f[w]=r?JU.CU.rgb(JU.PT.parseInt(u[v-3]),JU.PT.parseInt(u[v-2]),JU.PT.parseInt(u[v-1])):JU.CU.colorTriadToFFRGB(JU.PT.parseFloat(u[v-
3]),JU.PT.parseFloat(u[v-2]),JU.PT.parseFloat(u[v-1]))}if(null!=f&&k){w=0;q=f.length-1;for(k=q+1>>1;w<k;w++){var x=f[w];f[w]=f[q-w];f[q-w]=x}}break}}catch(z){if(F(z,Exception))JU.Logger.info("ColorEncoder "+z),f=null;else throw z;}null==f&&(f=E(-1,[-1]));this.schemes.put(a,f);this.setThisScheme(a,f);return-1}if(0<=e){a=a.toLowerCase();c=JU.PT.replaceAllCharacters(a.substring(0,e)," =","");0<c.length&&(b=!0);q=0;a.length>e+1&&!a.contains("[")&&(a="["+a.substring(e+1).trim()+"]",a=JU.PT.rep(a.$replace("\n",
" "),"  "," "),a=JU.PT.rep(a,", ",",").$replace(" ",","),a=JU.PT.rep(a,",","]["));for(e=-1;0<=(e=a.indexOf("[",e+1));)q++;if(0==q)return this.makeColorScheme(c,null,b);f=E(q,0);for(q=0;0<=(e=a.indexOf("[",e+1));){w=a.indexOf("]",e);0>w&&(w=a.length-1);x=JU.CU.getArgbFromString(a.substring(e,w+1));0==x&&(x=JU.CU.getArgbFromString(a.substring(e+1,w).trim()));if(0==x)return JU.Logger.error("error in color value: "+a.substring(e,w+1)),0;f[q++]=x}return c.equals("user")?(this.setUserScale(f),-13):this.makeColorScheme(c,
f,b)}f=this.schemes.get(c);return null!=f?(this.setThisScheme(c,f),h):-1!=h?h: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,f){c=JU.C.getColix(this.getArgbFromPalette(a,d,b,c));f&&(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 f=this.getPaletteColorCount(c);switch(c){case -1:return this.isColorIndex&&
(d=0,b=this.thisScale.length),this.thisScale[JU.ColorEncoder.quantize4(a,d,b,f)];case 10:return this.getPaletteBW()[JU.ColorEncoder.quantize4(a,d,b,f)];case 11:return this.getPaletteWB()[JU.ColorEncoder.quantize4(a,d,b,f)];case 0:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,d,b,f)];case 1:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case 8:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,d,b,f)];case 9:return this.ce.argbsRoygb[this.ce.ihalf+2*JU.ColorEncoder.quantize4(a,
d,b,f)];case 6:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(a,d,b,f)];case 7:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case -13:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(a,d,b,f)];case -14:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case 2:return this.ce.argbsCpk[JU.ColorEncoder.colorIndex(a,f)];case 3:return JU.ColorEncoder.getRasmolScale()[JU.ColorEncoder.colorIndex(a,
f)];case 4:return this.ce.getShapely()[JU.ColorEncoder.colorIndex(a,f)];case 5:return this.ce.getAmino()[JU.ColorEncoder.colorIndex(a,f)];case 17:return this.ce.getNucleic()[JU.ColorEncoder.colorIndex(a-24+2,f)];case 12:return this.getPaletteAC()[JU.ColorEncoder.colorIndexRepeat(a,f)];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=K(d+1,0),f=(this.hi-this.lo)/d,e=f*(this.isReversed?-0.5:0.5),h=0;h<d;h++)c[h]=this.isReversed?this.hi-h*f:this.lo+h*f,b.addLast(JU.CU.colorPtFromInt(this.getArgb(c[h]+e),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),f=K(3,0),e=K(3,0);JU.CU.toRGB3f(a,f);JU.CU.toRGB3f(d,e);a=(e[0]-f[0])/(b-1);d=(e[1]-f[1])/(b-1);for(var e=(e[2]-f[2])/(b-1),h=0;h<b;h++)c[h]=JU.CU.colorTriadToFFRGB(f[0]+a*h,f[1]+d*h,f[2]+e*h);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=(D(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 B(c/2);a-=d;if(0>=a)return 0;a=D(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 B(Math.floor(0>=a||a>=d?0:a))},"~N,~N");b.colorIndexRepeat=c(b,"colorIndexRepeat",function(a,d){return B(Math.floor(0>=a?0:a))%d},"~N,~N");b.colorSchemes=A(-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});p("JU");C(null,"JU.CommandHistory",["JU.Lst"],function(){var b=v(function(){this.commandList=
null;this.maxSize=100;this.cursorPos=this.nextCommand=0;this.isOn=!0;this.lstStates=null;r(this,arguments)},JU,"CommandHistory",null);x(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>
a&&(this.nextCommand=a-1);this.cursorPos=this.nextCommand;this.maxSize=a}},"~N");c(b,"getCommandUp",function(){if(0>=this.cursorPos)return null;this.cursorPos--;var a=this.getCommand();a.endsWith("#??")&&this.removeCommand(this.cursorPos--);0>this.cursorPos&&(this.cursorPos=0);return a});c(b,"getCommandDown",function(){if(this.cursorPos>=this.nextCommand)return null;this.cursorPos++;return this.getCommand()});c(b,"getCommand",function(){return this.commandList.get(this.cursorPos)});c(b,"addCommand",
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-a||b>=this.width+a||c<-a||c>=this.height+a},"~N,~N,~N");c(b,"isClippedZ",function(a){return-2147483648!=a&&(a<this.slab||a>this.depth)},"~N");c(b,"clipCode3",function(a,b,c){var l=0;0>a?l|=a<this.displayMinX2?-1:8:a>=this.width&&(l|=a>this.displayMaxX2?-1:4);0>b?l|=b<this.displayMinY2?-1:2:b>=this.height&&(l|=b>this.displayMaxY2?-1:1);c<this.slab?l|=32:c>this.depth&&(l|=16);return l},"~N,~N,~N");c(b,"clipCode",function(a){var b=0;a<this.slab?b|=32:a>this.depth&&(b|=16);return b},"~N");c(b,"getFont3D",
function(a){return JU.Font.createFont3D(0,0,a,a,this.apiPlatform,this.graphicsForMetrics)},"~N");c(b,"getFont3DFS",function(a,b){return JU.Font.createFont3D(JU.Font.getFontFaceID(a),0,b,b,this.apiPlatform,this.graphicsForMetrics)},"~S,~N");c(b,"getFontFidFS",function(a,b){return this.getFont3DFSS(a,"Bold",b).fid},"~S,~N");c(b,"getFont3DFSS",function(a,b,c){b=JU.Font.getFontStyleID(b);0>b&&(b=0);return JU.Font.createFont3D(JU.Font.getFontFaceID(a),b,c,c,this.apiPlatform,this.graphicsForMetrics)},"~S,~S,~N");
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function(a){this.textY=a},"~N");c(b,"getTextPosition",function(){return this.textY});c(b,"getTransformedVertexVectors",function(){return this.transformedVectors});j(b,"drawLinePixels",function(){},"JU.P3i,JU.P3i,~N,~N");b.normixCount=JU.Normix.getNormixCount()});p("JU");C(["javajs.api.JSInterface","J.api.JmolAppletInterface","$.JmolStatusListener"],"JU.GenericApplet","java.net.URL java.util.Hashtable JU.Lst $.PT $.SB J.awtjs2d.Platform J.c.CBK J.i18n.GT JU.Logger $.Parser JV.JC $.Viewer".split(" "),
function(){var b=v(function(){this.documentBase=this.codeBase=null;this.isSigned=!1;this.language=null;this.doTranslate=!0;this.mayScript=this.isStereoSlave=this.haveDocumentAccess=!1;this.vwrOptions=this.b$=this.viewer=this.gRight=this.statusTextarea=this.statusText=this.statusForm=this.fullName=this.htmlName=null;this.haveNotifiedError=!1;this.appletObject=null;this.loading=!1;this.htParams=this.outputBuffer=this.syncId=null;r(this,arguments)},JU,"GenericApplet",null,[javajs.api.JSInterface,J.api.JmolAppletInterface,
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48;4!=a&&System.out.println("setting logLevel="+a+' -- To change, use script "set logLevel [0-5]"');JU.Logger.setLogLevel(a);J.i18n.GT.ignoreApplicationBundle();this.initOptions();JU.GenericApplet.checkIn(this.fullName,this.appletObject);this.initApplication()},"~O");c(b,"initApplication",function(){this.vwrOptions.put("applet",Boolean.TRUE);null==this.getJmolParameter("statusListener")&&this.vwrOptions.put("statusListener",this);this.language=this.getJmolParameter("language");null!=this.language&&
this.vwrOptions.put("language",this.language);this.viewer=new JV.Viewer(this.vwrOptions);this.viewer.pushHoldRepaint();var a=this.getValueLowerCase("emulate","jmol");this.setStringProperty("defaults",a.equals("chime")?"RasMol":"Jmol");this.setStringProperty("backgroundColor",this.getValue("bgcolor",this.getValue("boxbgcolor","black")));this.viewer.setBooleanProperty("frank",!0);this.loading=!0;for(var b,a=0,c=J.c.CBK.values();a<c.length&&((b=c[a])||1);a++){var l=b.name(),f=this.getValue(l+"Callback",
null);if(null!=f)if("string"==typeof f)this.setStringProperty(l+"Callback",f);else{var e=null,e="Info."+f.name;this.setStringProperty(l+"Callback",e);this.setCallback(l,f)}}this.loading=!1;null!=this.language&&System.out.print("requested language="+this.language+"; ");this.doTranslate=!"none".equals(this.language)&&this.getBooleanValue("doTranslate",!0);this.language=J.i18n.GT.getLanguage();System.out.println("language="+this.language);if(null==this.b$.get(J.c.CBK.SCRIPT)&&null==this.b$.get(J.c.CBK.ERROR)&&
(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);b=this.getJmolParameter("menuFile");null!=b&&this.viewer.setMenu(b,!0);b=this.getValue("script","");a=this.getValue("loadInline",null);if(null==a){if(null!=(a=this.getValue("load",null)))b='load "'+a+'";'+b;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");j(b,"register",function(a,b){JU.GenericApplet.checkIn(a,b)},"~S,J.api.JmolSyncInterface");j(b,"getJSpecViewProperty",function(){return null},"~S");c(b,"syncScript",function(a){this.viewer.syncScript(a,"~",0)},"~S");j(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");j(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,b).toString()},"~S,~S");j(b,"loadInlineString",function(a,b,c){a=this.viewer.loadInlineAppend(a,c);null==a&&this.script(b);return a},"~S,~S,~B");j(b,"loadInlineArray",function(a,b,c){if(null==a||0==a.length)return null;a=this.viewer.loadInline(a,c);null==a&&this.script(b);return a},"~A,~S,~B");j(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,b){return this.loadInlineString(a,b,
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null!=c&&(this.loading||c!==J.c.CBK.EVAL)?null==b?this.b$.remove(c):this.b$.put(c,b):this.consoleMessage("Available callbacks include: "+J.c.CBK.getNameList().$replace(";"," ").trim())}},"~S,~S");c(b,"consoleMessage",function(a){this.notifyCallback(J.c.CBK.ECHO,A(-1,["",a]))},"~S");j(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,b){var c=null==a?null:this.b$.get(a),l=null==a||null!=c&&(null==b||null==b[0]),f=!1;null!=b&&(b[0]=this.htmlName);var e=null==b||null==b[1]?null:b[1].toString();if(null!=a)switch(a){case J.c.CBK.APPLETREADY:b[3]=this.appletObject;break;case J.c.CBK.CLICK:"alert".equals(c)&&(e="x="+b[1]+" y="+b[2]+" action="+b[3]+" clickCount="+b[4]);break;case J.c.CBK.ANIMFRAME:var h=b[1],k=h[0],j=h[1],y=h[2],n=h[3],h=h[4],q=-2>=k,w=0>n?-1:1,p=0>h?-1:1;l&&
(b=A(-1,[this.htmlName,Integer.$valueOf(Math.max(k,-2-k)),Integer.$valueOf(j),Integer.$valueOf(y),Integer.$valueOf(Math.abs(n)),Integer.$valueOf(Math.abs(h)),Integer.$valueOf(q?1:0),Integer.$valueOf(w),Integer.$valueOf(p),b[2],b[3]]));break;case J.c.CBK.ECHO:j=(k=2==b.length)||1==b[2].intValue();l||(j&&(f=!0),l=!k&&null!=(c=this.b$.get(a=J.c.CBK.MESSAGE)));f||this.output(e);break;case J.c.CBK.LOADSTRUCT:k=b[4];if(null!=k){k=(0<=k.indexOf("NOTE:")?"":J.i18n.GT.$("File Error:"))+k;this.doShowStatus(k);
this.notifyCallback(J.c.CBK.MESSAGE,A(-1,["",k]));return}break;case J.c.CBK.MEASURE:l||(l=null!=(c=this.b$.get(a=J.c.CBK.MESSAGE)));k=b[3];0<=k.indexOf("Picked")||0<=k.indexOf("Sequence")?(this.doShowStatus(e),f=!0):0<=k.indexOf("Completed")&&(e=k+": "+e,f=!0);break;case J.c.CBK.MESSAGE:f=!l;l=(new Boolean(l&null!=e)).valueOf();f||this.output(e);break;case J.c.CBK.PICK:this.doShowStatus(e);f=!0;break;case J.c.CBK.SCRIPT:!(0<b[3].intValue())&&!l&&(l=null!=(c=this.b$.get(a=J.c.CBK.MESSAGE)));this.output(e);
this.doShowStatus(e);break;case J.c.CBK.SYNC:this.sendScript(e,b[2],!0,l);return}f&&(f=this.viewer.getProperty("DATA_API","getAppConsole",null),null!=f&&(f.notifyCallback(a,b),this.output(e)));if(l&&this.mayScript)try{this.doSendCallback(a,c,b,e)}catch(r){if(F(r,Exception))this.haveNotifiedError||JU.Logger.debugging&&JU.Logger.debug(a.name()+"Callback call error to "+c+": "+r),this.haveNotifiedError=!0;else throw r;}},"J.c.CBK,~A");c(b,"sendScript",function(a,b,c,l){if(!JU.GenericApplet.isJS||l&&
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c(b,"getNormalFromCenter",function(a,b,c,l,f,e,h){b=JU.Measure.getNormalThroughPoints(b,c,l,e,h);a=0<JU.Measure.distanceToPlaneV(e,b,a);a==f&&e.scale(-1);return!a},"JU.P3,JU.P3,JU.P3,JU.P3,~B,JU.V3,JU.V3");b.getNormalToLine=c(b,"getNormalToLine",function(a,b,c){c.sub2(a,b);c.cross(c,JU.Measure.axisY);c.normalize();Float.isNaN(c.x)&&c.set(1,0,0)},"JU.P3,JU.P3,JU.V3");b.getBisectingPlane=c(b,"getBisectingPlane",function(a,b,c,l,f){c.scaleAdd2(0.5,b,a);l.setT(b);l.normalize();JU.Measure.getPlaneThroughPoint(c,
l,f)},"JU.P3,JU.V3,JU.T3,JU.V3,JU.P4");b.projectOntoAxis=c(b,"projectOntoAxis",function(a,b,c,l){l.sub2(a,b);var f=l.dot(c);a.scaleAdd2(f,c,b);l.sub2(a,b);return f},"JU.P3,JU.P3,JU.V3,JU.V3");b.calcBestAxisThroughPoints=c(b,"calcBestAxisThroughPoints",function(a,b,c,l,f,e){c.setT(a[0]);l.sub2(a[b-1],c);l.normalize();JU.Measure.calcAveragePointN(a,b,c);for(var h=0;h++<e&&0.001<JU.Measure.findAxis(a,b,c,l,f););a=JU.P3.newP(a[0]);JU.Measure.projectOntoAxis(a,c,l,f);c.setT(a)},"~A,~N,JU.P3,JU.V3,JU.V3,~N");
b.findAxis=c(b,"findAxis",function(a,b,c,l,f){for(var e=new JU.V3,h=new JU.V3,k=new JU.P3,j=new JU.P3,y=JU.V3.newV(l),n=0;0<=--b;)k.setT(a[b]),j.setT(k),JU.Measure.projectOntoAxis(j,c,l,f),h.sub2(k,j),h.cross(f,h),e.add(h),n+=f.lengthSquared();a=JU.V3.newV(e);a.scale(1/n);h.cross(a,l);l.add(h);l.normalize();h.sub2(l,y);return h.length()},"~A,~N,JU.P3,JU.V3,JU.V3");b.calcAveragePoint=c(b,"calcAveragePoint",function(a,b,c){c.set((a.x+b.x)/2,(a.y+b.y)/2,(a.z+b.z)/2)},"JU.P3,JU.P3,JU.P3");b.calcAveragePointN=
c(b,"calcAveragePointN",function(a,b,c){c.setT(a[0]);for(var l=1;l<b;l++)c.add(a[l]);c.scale(1/b)},"~A,~N,JU.P3");b.transformPoints=c(b,"transformPoints",function(a,b,c){for(var l=new JU.Lst,f=0;f<a.size();f++){var e=JU.P3.newP(a.get(f));e.sub(c);b.rotTrans(e);e.add(c);l.addLast(e)}return l},"JU.Lst,JU.M4,JU.P3");b.isInTetrahedron=c(b,"isInTetrahedron",function(a,b,c,l,f,e,h,k,j){var y=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(l,f,b,h,k,e),a);if(y!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(b,
f,c,h,k,e),a)||y!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(c,f,l,h,k,e),a))return!1;a=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(b,c,l,h,k,e),a);if(j)return y==0<=a;f=JU.Measure.distanceToPlane(e,f);return 0>=f*a||Math.abs(f)>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,b){var c=a.x,l=a.y,f=a.z,e=a.w,h=b.x,k=b.y,j=b.z,y=b.w,n=JU.V3.new3(c,l,f),q=JU.V3.new3(h,k,j),p=new JU.V3;p.cross(n,
q);var n=Math.abs(p.x),q=Math.abs(p.y),s=Math.abs(p.z);switch(n>q?n>s?1:3:q>s?2:3){case 1:n=0;q=l*j-k*f;if(0.01>Math.abs(q))return null;f=(f*y-j*e)/q;c=(k*e-y*l)/q;break;case 2:q=c*j-h*f;if(0.01>Math.abs(q))return null;n=(f*y-j*e)/q;f=0;c=(h*e-y*c)/q;break;default:q=c*k-h*l;if(0.01>Math.abs(q))return null;n=(l*y-k*e)/q;f=(h*e-y*c)/q;c=0}l=new JU.Lst;l.addLast(JU.P3.new3(n,f,c));p.normalize();l.addLast(p);return l},"JU.P4,JU.P4");b.getIntersection=c(b,"getIntersection",function(a,b,c,l,f,e){JU.Measure.getPlaneProjection(a,
c,l,f);f.set(c.x,c.y,c.z);f.normalize();null==b&&(b=JU.V3.newV(f));c=b.dot(f);if(0.01>Math.abs(c))return null;e.sub2(l,a);l.scaleAdd2(e.dot(f)/c,b,a);return l},"JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");b.calculateQuaternionRotation=c(b,"calculateQuaternionRotation",function(a,b){b[1]=NaN;var c=new JU.Quat,l=a[0],f=a[1],e=l.length-1;if(2>e||l.length!=f.length)return c;for(var h=0,k=0,j=0,y=0,n=0,q=0,p=0,s=0,r=0,u=new JU.P3,v=new JU.P3,x=l[0],z=f[0],e=e+1;1<=--e;)u.sub2(l[e],x),v.sub2(f[e],z),h+=u.x*v.x,
k+=u.x*v.y,j+=u.x*v.z,y+=u.y*v.x,n+=u.y*v.y,q+=u.y*v.z,p+=u.z*v.x,s+=u.z*v.y,r+=u.z*v.z;b[0]=JU.Measure.getRmsd(a,c);c=R(4,4,0);c[0][0]=h+n+r;c[0][1]=c[1][0]=q-s;c[0][2]=c[2][0]=p-j;c[0][3]=c[3][0]=k-y;c[1][1]=h-n-r;c[1][2]=c[2][1]=k+y;c[1][3]=c[3][1]=p+j;c[2][2]=-h+n-r;c[2][3]=c[3][2]=q+s;c[3][3]=-h-n+r;h=javajs.api.Interface.getInterface("JU.Eigen").setM(c).getEigenvectorsFloatTransposed()[3];c=JU.Quat.newP4(JU.P4.new4(h[1],h[2],h[3],h[0]));b[1]=JU.Measure.getRmsd(a,c);return c},"~A,~A");b.getTransformMatrix4=
c(b,"getTransformMatrix4",function(a,b,c,l){a=JU.Measure.getCenterAndPoints(a);var f=JU.Measure.getCenterAndPoints(b);b=K(2,0);var e=JU.Measure.calculateQuaternionRotation(A(-1,[a,f]),b).getMatrix();null==l?e.rotate(a[0]):l.setT(a[0]);l=JU.V3.newVsub(f[0],a[0]);c.setMV(e,l);return b[1]},"JU.Lst,JU.Lst,JU.M4,JU.P3");b.getCenterAndPoints=c(b,"getCenterAndPoints",function(a){var b=a.size(),c=Array(b+1);c[0]=new JU.P3;if(0<b){for(var l=0;l<b;l++)c[0].add(c[l+1]=a.get(l));c[0].scale(1/b)}return c},"JU.Lst");
b.getRmsd=c(b,"getRmsd",function(a,b){for(var c=0,l=a[0],f=a[1],e=l[0],h=f[0],k=l.length-1,j=new JU.P3,y=k+1;1<=--y;)j.sub2(l[y],e),b.transform2(j,j).add(h),c+=j.distanceSquared(f[y]);return Math.sqrt(c/k)},"~A,JU.Quat");b.getBestLineThroughPoints=c(b,"getBestLineThroughPoints",function(a,b){0>=b&&(b=a.length);if(2>=b)return a;var c=new JU.P3,l=new JU.V3,f=new JU.V3;JU.Measure.calcBestAxisThroughPoints(a,b,c,l,f,8);return JU.Measure.getProjectedLineSegment(a,b,c,l,f)},"~A,~N");b.getProjectedLineSegment=
c(b,"getProjectedLineSegment",function(a,b,c,l,f){null==f&&(f=new JU.V3);for(var e=b=null,h,k=3.4028235E38,j=-3.4028235E38,y=0;y<a.length;y++){JU.Measure.projectOntoAxis(h=JU.P3.newP(a[y]),c,l,f);var n=l.dot(f);n<k&&(k=n,b=h);n>j&&(j=n,e=h)}return A(-1,[b,e])},"~A,~N,JU.P3,JU.V3,JU.V3");b.isInTriangle=c(b,"isInTriangle",function(a,b,c,l,f,e,h){f.sub2(l,b);e.sub2(c,b);h.sub2(a,b);a=f.dot(f);b=f.dot(e);f=f.dot(h);c=e.dot(e);e=e.dot(h);h=1/(a*c-b*b);c=(c*f-b*e)*h;e=(a*e-b*f)*h;return 0<=c&&0<=e&&1>=
c+e},"JU.P3,JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");b.calcBestPlaneThroughPoints=c(b,"calcBestPlaneThroughPoints",function(a,b,c){0>=b&&(b=a.length);if(3==b)return JU.Measure.getPlaneThroughPoints(a[0],a[1],a[2],null,null,c),0;var l=c,f=new JU.P4,e=JU.Measure.calcPlaneForMode(a,b,c,"z");if(1E-6>e)return e;var h=JU.Measure.calcPlaneForMode(a,b,f,"y");h<e&&(e=h,l=f,f=c);1E-6<=e&&(h=JU.Measure.calcPlaneForMode(a,b,f,"x"),h<e&&(e=h,l=f));l!==c&&(c.setT(l),c.w=l.w);return e},"~A,~N,JU.P4");b.calcPlaneForMode=
c(b,"calcPlaneForMode",function(a,b,c,l){for(var f=R(b,3,0),e=R(3,b,0),h=R(3,b,0),k=R(3,3,0),j=R(b,0),y=b;0<=--y;){var n=a[y];f[y][0]=e[0][y]="x"==l?n.z:n.x;f[y][1]=e[1][y]="y"==l?n.z:n.y;f[y][2]=e[2][y]=1;j[y]=-("y"==l?n.y:"x"==l?n.x:n.z)}for(var q=new JU.M3,y=3;0<=--y;)for(n=3;0<=--n;){for(var p=0,s=b;0<=--s;)p+=e[y][s]*f[s][n];q.set33(y,n,p)}q.invert();for(y=3;0<=--y;)for(n=3;0<=--n;)k[y][n]=q.get33(y,n);for(y=3;0<=--y;)for(s=b;0<=--s;){p=0;for(n=3;0<=--n;)p+=k[y][n]*e[n][s];h[y][s]=p}switch(l.charCodeAt(0)){case 120:c.x=
1;break;case 121:c.y=1;break;case 122:c.z=1}y=1;for(n=3;0<=--n;){f=0;for(s=b;0<=--s;)f+=h[n][s]*j[s];switch(n){case 0:y+=f*f;"x"==l?c.z=f:c.x=f;break;case 1:y+=f*f;"y"==l?c.z=f:c.y=f;break;case 2:c.w=f}}l=Math.sqrt(y);c.scale4((0<1/c.w?1:-1)/l);for(y=l=0;y<b;y++)p=JU.Measure.distanceToPlane(c,a[y]),l+=p*p;return Math.sqrt(l/b)},"~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 b=new JU.P3,c=new JU.V3,l=Array(4),f=0;f<l.length;f++){l[f]=new JU.P3;var e=JU.Measure.rndPt();JU.Measure.getPlaneProjection(e,a,b,c);l[f].setT(b);e=0.1*Math.random();l[f].scaleAdd2(e,c,b);System.out.println(l[f]+" d="+e)}a=new JU.P4;l=JU.Measure.calcBestPlaneThroughPoints(l,-1,a);System.out.println("found "+a+" rmsd = "+l)});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,b){for(var c=new JU.Lst,l=a.length;0<=--l;)0.001>Math.abs(JU.Measure.distanceToPlane(b,a[l]))&&c.addLast(a[l]);return c},"~A,JU.P4");b.getLatticePoints=c(b,"getLatticePoints",function(a,b,c,l){a.addLast(new JU.P3);b=0==b?1:Math.abs(b);c=0==c?1:Math.abs(c);l=0==l?1:Math.abs(l);for(var f=a.size(),e=-b;e<=b;e++)for(var h=-c;h<=c;h++)for(var k=-l;k<=l;k++)for(var j=0;j<
f;j++){var y=JU.P3.new3(e,h,k);y.add(a.get(j));a.addLast(y)}for(j=f;0<=--j;)a.removeItemAt(0);return a},"JU.Lst,~N,~N,~N");b.computeHelicalAxis=c(b,"computeHelicalAxis",function(a,b,c){var l=new JU.V3;l.sub2(b,a);var f=c.getTheta(),e=c.getNormal(),h=l.dot(e);1E-4>Math.abs(h)&&(h=0);var k=new JU.V3;k.cross(l,e);0!=k.dot(k)&&k.normalize();var j=new JU.V3,y=JU.V3.newV(e);0==h&&(h=1.4E-45);y.scale(h);j.sub2(y,l);j.scale(0.5);k.scale(0==f?0:j.length()/Math.tan(3.141592653589793*(f/2/180)));l=JU.V3.newV(k);
0!=f&&l.add(j);j=JU.P3.newP(a);j.sub(l);1.4E-45!=h&&e.scale(h);k=JU.P3.newP(j);k.add(e);f=JU.Measure.computeTorsion(a,j,k,b,!0);if(Float.isNaN(f)||1E-4>l.length())f=c.getThetaDirectedV(e);a=Math.abs(0==f?0:360/f);h=Math.abs(1.4E-45==h?0:e.length()*(0==f?1:360/f));return A(-1,[j,e,l,JU.P3.new3(f,h,a),k])},"JU.P3,JU.P3,JU.Quat");b.axisY=JU.V3.new3(0,1,0)});p("JU");C(null,"JU.MeshSurface","JU.AU $.P3 J.api.Interface JU.BoxInfo $.C $.Geodesic $.TempArray".split(" "),function(){var b=v(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;r(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,b,c,l,f,e){var h=new JU.MeshSurface;h.pis=l;a?h.altVertices=
b:h.vs=b;h.vc=0==c?b.length:c;h.normals=f;h.normalCount=0==e&&null!=f?f.length:e;return h},"~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,b){0==this.vc?this.vs=Array(25):this.vc==this.vs.length&&(this.vs=JU.AU.doubleLength(this.vs));this.vs[this.vc]=b?JU.P3.newP(a):a;return this.vc++},
"JU.T3,~B");c(b,"addTriangle",function(a,b,c){this.addPolygon(E(-1,[a,b,c]),null)},"~N,~N,~N");c(b,"addQuad",function(a,b,c,l){this.haveQuads=!0;this.addPolygon(E(-1,[a,b,c,l]),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,b,c){0==this.vc?this.vvs=K(25,0):this.vc>=this.vvs.length&&(this.vvs=JU.AU.doubleLengthF(this.vvs));this.vvs[this.vc]=b;return this.addV(a,c)},"JU.T3,~N,~B");
c(b,"addTriangleCheck",function(a,b,c,l,f,e){return null==this.vs||null!=this.vvs&&(Float.isNaN(this.vvs[a])||Float.isNaN(this.vvs[b])||Float.isNaN(this.vvs[c]))||Float.isNaN(this.vs[a].x)||Float.isNaN(this.vs[b].x)||Float.isNaN(this.vs[c].x)?-1:this.addPolygonV3(a,b,c,l,f,e,null)},"~N,~N,~N,~N,~N,~N");c(b,"addPolygonV3",function(a,b,c,l,f,e,h){return this.dataOnly?this.addPolygon(E(-1,[a,b,c,l]),h):this.addPolygonC(E(-1,[a,b,c,l,f]),e,h,0>f)},"~N,~N,~N,~N,~N,~N,JU.BS");c(b,"addPolygonC",function(a,
b,c,l){if(0!=b){if(null==this.pcs||0==this.pc)this.lastColor=0;l?this.colorsExplicit=!0:(null==this.pcs?this.pcs=W(25,0):this.pc>=this.pcs.length&&(this.pcs=JU.AU.doubleLengthShort(this.pcs)),this.pcs[this.pc]=l?2047:b==this.lastColor?this.lastColix:this.lastColix=JU.C.getColix(this.lastColor=b))}return this.addPolygon(a,c)},"~A,~N,JU.BS,~B");c(b,"addPolygon",function(a,b){var c=this.pc;0==c?this.pis=JU.AU.newInt2(25):c==this.pis.length&&(this.pis=JU.AU.doubleLength(this.pis));null!=b&&b.set(c);this.pis[this.pc++]=
a;return c},"~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,b){this.getMeshSlicer();for(var c=
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0<this.c&&(b=!0,this.gamma=120);26<a.length&&(Float.isNaN(a[26])?a[26]=this.slop:this.slop=a[26]);var c=this.na=Math.max(1,24<a.length&&!Float.isNaN(a[22])?D(a[22]):1),l=this.nb=Math.max(1,24<a.length&&!Float.isNaN(a[23])?D(a[23]):1),f=this.nc=Math.max(1,24<a.length&&!Float.isNaN(a[24])?D(a[24]):1);if(25<a.length&&!Float.isNaN(a[25])){var e=a[25];0<e&&(c*=e,l*=e,f*=e)}else c=l=f=1;if(0>=this.a&&0>=this.c){var e=JU.V3.new3(a[6],a[7],a[8]),h=JU.V3.new3(a[9],a[10],a[11]),k=JU.V3.new3(a[12],a[13],a[14]);
this.setABC(e,h,k);0>this.c&&(a=JU.AU.arrayCopyF(a,-1),0>this.b&&(h.set(0,0,1),h.cross(h,e),0.001>h.length()&&h.set(0,1,0),h.normalize(),a[9]=h.x,a[10]=h.y,a[11]=h.z),0>this.c&&(k.cross(e,h),k.normalize(),a[12]=k.x,a[13]=k.y,a[14]=k.z))}this.a*=c;0>=this.b?this.b=this.c=1:0>=this.c?(this.c=1,this.b*=l):(this.b*=l,this.c*=f);this.setCellParams();if(21<a.length&&!Float.isNaN(a[21])){b=K(16,0);for(e=0;16>e;e++){switch(e%4){case 0:h=c;break;case 1:h=l;break;case 2:h=f;break;default:h=1}b[e]=a[6+e]*h}this.matrixCartesianToFractional=
JU.M4.newA16(b);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])?(e=this.matrixFractionalToCartesian=new JU.M4,e.setColumn4(0,a[6]*c,a[7]*c,a[8]*c,0),e.setColumn4(1,a[9]*l,a[10]*l,a[11]*l,0),e.setColumn4(2,a[12]*f,a[13]*f,a[14]*f,0),17<a.length&&!Float.isNaN(a[17])?e.setColumn4(3,a[15],a[16],a[17],1):e.setColumn4(3,
0,0,0,1)):(e=this.matrixFractionalToCartesian=new JU.M4,b?(e.setColumn4(0,-this.b*this.cosGamma,-this.b*this.sinGamma,0,0),e.setColumn4(1,-this.b*this.cosGamma,this.b*this.sinGamma,0,0)):(e.setColumn4(0,this.a,0,0,0),e.setColumn4(1,this.b*this.cosGamma,this.b*this.sinGamma,0,0)),e.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),e.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,b){for(var c=K(27,0),l=a.length,f=0;27>f;f++)c[f]=f<l?a[f]:NaN;27>l&&(c[26]=b);return c},"~A,~N");b.addVectors=c(b,"addVectors",function(a){for(var b=JU.SimpleUnitCell.newA(a).matrixFractionalToCartesian,c=0;9>c;c++)a[6+c]=b.getElement(c%3,B(c/3))},"~A");c(b,"setParamsFromMatrix",function(){var a=JU.V3.new3(1,0,0),b=JU.V3.new3(0,1,0),c=JU.V3.new3(0,
0,1);this.matrixFractionalToCartesian.rotate(a);this.matrixFractionalToCartesian.rotate(b);this.matrixFractionalToCartesian.rotate(c);this.setABC(a,b,c);this.setCellParams()});c(b,"setABC",function(a,b,c){this.a=a.length();this.b=b.length();this.c=c.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:b.angle(c)/0.017453292519943295,this.beta=0>this.c?90:a.angle(c)/0.017453292519943295,this.gamma=0>this.b?90:a.angle(b)/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,b){null!=this.matrixFractionalToCartesian&&(b?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,b){null!=this.matrixCartesianToFractional&&(b?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 b=this.matrixFractionalToCartesian;return a?K(-1,[b.m00,b.m10,b.m20,b.m01,b.m11,b.m21,b.m02,b.m12,b.m22]):K(-1,[this.a,this.b,this.c,this.alpha,this.beta,this.gamma,b.m00,b.m10,b.m20,b.m01,b.m11,b.m21,b.m02,b.m12,b.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,b,c){var l=4==a.length?1:0,f=Array(4);f[0]=1==l?JU.P3.newP(a[0]):new JU.P3;0==c&&(c=6.283185307179586);for(var e=0;3>e;e++){var h=f[e+1]=new JU.P3;h.cross(a[(e+
1)%3+l],a[(e+2)%3+l]);var k=a[e+l].dot(h);-1==c&&(c=Math.sqrt(k));h.scale(c/k)}if(null==b)return f;for(e=0;4>e;e++)b[e]=f[e];return b},"~A,~A,~N");b.setAbc=c(b,"setAbc",function(a,b,c){if(null!=a&&(null==b&&(b=K(6,0)),a=JU.PT.split(a.$replace(",","="),"="),12<=a.length))for(var l=0;6>l;l++)b[l]=JU.PT.parseFloat(a[2*l+1]);return null==c?null:JU.SimpleUnitCell.setAbcFromParams(b,c)},"~S,~A,~A");b.setAbcFromParams=c(b,"setAbcFromParams",function(a,b){var c=JU.SimpleUnitCell.newA(a).getUnitCellAsArray(!0);
b[1].set(c[0],c[1],c[2]);b[2].set(c[3],c[4],c[5]);b[3].set(c[6],c[7],c[8]);return b},"~A,~A");c(b,"unitizeDim",function(a,b){switch(a){case 3:b.z=JU.SimpleUnitCell.unitizeX(b.z,this.slop);case 2:b.y=JU.SimpleUnitCell.unitizeX(b.y,this.slop);case 1:b.x=JU.SimpleUnitCell.unitizeX(b.x,this.slop)}},"~N,JU.T3");b.unitizeDimRnd=c(b,"unitizeDimRnd",function(a,b,c){switch(a){case 3:b.z=JU.SimpleUnitCell.unitizeXRnd(b.z,c);case 2:b.y=JU.SimpleUnitCell.unitizeXRnd(b.y,c);case 1:b.x=JU.SimpleUnitCell.unitizeXRnd(b.x,
c)}},"~N,JU.T3,~N");b.unitizeX=c(b,"unitizeX",function(a,b){a-=Math.floor(a);if(a>1-b||a<b)a=0;return a},"~N,~N");b.unitizeXRnd=c(b,"unitizeXRnd",function(a,b){a-=Math.floor(a);if(a>1-b||a<b)a=0;return a},"~N,~N");c(b,"twelfthsOf",function(a){if(0==a)return 0;a=Math.abs(12*a);var b=Math.round(a);return 12>=b&&Math.abs(a-b)<12*this.slop?b:-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 b=this.twelfthsOf(a);return 0<=b?b/12:a},"~N");b.ijkToPoint3f=c(b,"ijkToPoint3f",function(a,b,c,l){var f=1E9<a?1E3:1E6<a?100:10,e=f*f;c-=0<=c?B(5*f/10):c;b.x=B(a/e)%f+c;b.y=B(a%e/f)+c;b.z=(0==l?a%f:(-500==c?B(l/f):l)%f)+c},"~N,JU.P3,~N,~N");b.ptToIJK=c(b,"ptToIJK",function(a,b){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,b,0):JU.P4.new4(1500500500,1500500500+1E6*a.x+1E3*a.y+a.z,b,1500500+a.z)},"JU.T3,~N");b.escapeMultiplier=
c(b,"escapeMultiplier",function(a){if(z(a,"JU.P4")){var b=1E3*B(Math.floor(a.x/1E3))+B(Math.floor(a.w/1E3))-1E3,c=1E3*B(Math.floor(a.y/1E3))+B(Math.floor(a.w))%1E3;return"{"+b+" "+c+" "+a.z+"}"}return JU.Escape.eP(a)},"JU.T3");b.setMinMaxLatticeParameters=c(b,"setMinMaxLatticeParameters",function(a,b,c,l){if(c.x<=c.y&&555<=c.y){var f=new JU.P3;JU.SimpleUnitCell.ijkToPoint3f(c.x,f,0,l);b.x=D(f.x);b.y=D(f.y);b.z=D(f.z);JU.SimpleUnitCell.ijkToPoint3f(c.y,f,1,l);c.x=D(f.x);c.y=D(f.y);c.z=D(f.z)}switch(a){case 1:b.y=
0,c.y=1;case 2:b.z=0,c.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");j(b,"toString",function(){return"["+this.a+" "+this.b+" "+this.c+" "+this.alpha+" "+this.beta+" "+this.gamma+"]"})});p("JU");C(null,"JU.TempArray",["JU.P3","$.P3i"],function(){var b=v(function(){this.freeEnum=this.lengthsFreeEnum=this.freeScreens=this.lengthsFreeScreens=this.freePoints=this.lengthsFreePoints=null;r(this,arguments)},JU,"TempArray",null);P(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)});x(b,function(){});c(b,"clear",function(){this.clearTempPoints();this.clearTempScreens()});b.findBestFit=c(b,"findBestFit",function(a,b){for(var c=-1,l=2147483647,f=b.length;0<=--f;){var e=b[f];e>=a&&e<l&&(l=e,c=f)}0<=c&&(b[c]=0);return c},"~N,~A");b.findShorter=c(b,"findShorter",function(a,b){for(var c=b.length;0<=--c;)if(0==b[c])return b[c]=a,c;for(var l=0,f=b[0],c=b.length;0<--c;)b[c]<f&&
(f=b[c],l=c);return f<a?(b[l]=a,l):-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 b;b=JU.TempArray.findBestFit(a,this.lengthsFreePoints);if(0<b)b=this.freePoints[b];else for(b=Array(a);0<=--a;)b[a]=new JU.P3;return b},"~N");c(b,"freeTempPoints",function(a){for(var b=0;b<this.freePoints.length;b++)if(this.freePoints[b]===a){this.lengthsFreePoints[b]=a.length;return}b=JU.TempArray.findShorter(a.length,
this.lengthsFreePoints);0<=b&&(this.freePoints[b]=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 b;b=JU.TempArray.findBestFit(a,this.lengthsFreeScreens);if(0<b)b=this.freeScreens[b];else for(b=Array(a);0<=--a;)b[a]=new JU.P3i;return b},"~N");c(b,"freeTempScreens",function(a){for(var b=0;b<this.freeScreens.length;b++)if(this.freeScreens[b]===a){this.lengthsFreeScreens[b]=a.length;return}b=
JU.TempArray.findShorter(a.length,this.lengthsFreeScreens);0<=b&&(this.freeScreens[b]=a)},"~A");c(b,"allocTempEnum",function(a){var b=JU.TempArray.findBestFit(a,this.lengthsFreeEnum);return 0<b?this.freeEnum[b]:Array(a)},"~N");c(b,"freeTempEnum",function(a){for(var b=0;b<this.freeEnum.length;b++)if(this.freeEnum[b]===a){this.lengthsFreeEnum[b]=a.length;return}b=JU.TempArray.findShorter(a.length,this.lengthsFreeEnum);0<=b&&(this.freeEnum[b]=a)},"~A");b.getSlabWithinRange=c(b,"getSlabWithinRange",function(a,
b){return A(-1,[Integer.$valueOf(1073742114),A(-1,[Float.$valueOf(a),Float.$valueOf(b)]),Boolean.FALSE,null])},"~N,~N");b.getSlabObjectType=c(b,"getSlabObjectType",function(a,b,c,l){return A(-1,[Integer.$valueOf(a),b,Boolean.$valueOf(c),l])},"~N,~O,~B,~O")});p("JU");H(JU,"Txt",null);p("JU");C(["JU.V3"],"JU.Vibration",["JU.P3"],function(){var b=v(function(){this.modDim=-1;this.modScale=NaN;this.showTrace=!1;this.trace=null;this.tracePt=0;r(this,arguments)},JU,"Vibration",JU.V3);c(b,"setCalcPoint",
function(a,b,c){switch(this.modDim){case -2:case -3:break;default:a.scaleAdd2(Math.cos(6.283185307179586*b.x)*c,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");j(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,b){(null==this.trace||0==a||a!=this.trace.length)&&this.startTrace(a);if(null!=b&&2<a){if(0>=--this.tracePt){for(var c=this.trace[this.trace.length-1],l=this.trace.length;1<=--l;)this.trace[l]=this.trace[l-1];this.trace[1]=c;this.tracePt=1}c=this.trace[this.tracePt];null==c&&(c=this.trace[this.tracePt]=
new JU.P3);c.setT(b)}return this.trace},"~N,JU.Point3fi")});p("JV");C(["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=v(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;r(this,arguments)},JV,"ActionManager",null,J.api.EventManager);P(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 b=2==this.apm&&this.bnd(JV.binding.Binding.getMouseAction(this.clickedCount,this.moved.modifiers,1),[10]);this.vwr.hoverOn(a,b)}}});c(b,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(b,"bind",
function(a,b){var c=JV.ActionManager.getActionFromName(b),l=JV.binding.Binding.getMouseActionStr(a);0!=l&&(0<=c?this.b.bindAction(l,c):this.b.bindName(l,b))},"~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,b){if(null==a&&null==b)this.clearBindings();else{var c=JV.ActionManager.getActionFromName(b),l=JV.binding.Binding.getMouseActionStr(a);0<=c?this.b.unbindAction(l,
c):0!=l&&this.b.unbindName(l,b);null==b&&this.b.unbindUserAction(a)}},"~S,~S");b.newAction=c(b,"newAction",function(a,b,c){JV.ActionManager.actionInfo[a]=c;JV.ActionManager.actionNames[a]=b},"~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})"),A(-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 b=0;b<JV.ActionManager.actionNames.length;b++)if(JV.ActionManager.actionNames[b].equalsIgnoreCase(a))return b;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,b){for(var c=b.length;0<=--c;)if(this.b.isBound(a,b[c]))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 b=JV.ActionManager.pickingModeNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingModeNames[b]))return b;
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 b=JV.ActionManager.pickingStyleNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingStyleNames[b]))return b;return-1},"~S");c(b,"getAtomPickingMode",function(){return this.apm});c(b,"setPickingMode",function(a){var b=!1;switch(a){case -1:b=
!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}b=(new Boolean(b|this.apm!=a)).valueOf();this.apm=a;b&&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,b,c,l){this.vwr.hoverOff();
this.current.set(a,b,c,l)},"~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(b){if(!F(b,Exception))throw b;}},"~B");c(b,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");j(b,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelectedXY(-2147483648,0,b);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 c=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(c)&&this.checkMotionRotateZoom(c,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,b)}this.keyProcessing=!1;return!0},"~N,~N");j(b,"keyTyped",function(){return!1},
"~N,~N");j(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 b=0!=(this.moved.modifiers&1);if(0!=a)if(0==this.moved.keybuf){if(this.moved.keybuf=a,b)return}else this.moved.keybuf+=a<<8;0<this.moved.keybuf&&(this.assignNew(this.moved.keybuf),this.moved.keybuf=0)},"~N");j(b,"mouseEnterExit",function(a,b,c,l){this.vwr.tm.stereoDoubleDTI&&(b<<=1);this.setCurrent(a,
b,c,0);l&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(b,"setMouseActions",function(a,b,c){this.pressAction=JV.binding.Binding.getMouseAction(a,b,c?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");j(b,"mouseAction",function(a,b,c,l,f,e){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&(0!=a&&this.vwr.getBoolean(603979960))&&this.vwr.showString("mouse action: "+a+" "+e+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(f,
e,a),!1),!1),this.vwr.tm.stereoDoubleDTI&&(c<<=1),a){case 0:this.hoverable||(JU.Logger.info("ActionManager: mouse move detected"),this.hoverable=!0);this.setCurrent(b,c,l,e);this.moved.setCurrent(this.current,0);this.moved.keybuf=0;if(null!=this.mp||this.hoverActive){this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,e,0);this.checkClickAction(c,l,b,0);break}if(this.isZoomArea(c)){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,c,l,e,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(b,c,l,e));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,e,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,b);this.checkPressedAction(c,l,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,
e,!1);a=c-this.dragged.x;f=l-this.dragged.y;this.setCurrent(b,c,l,e);this.dragged.setCurrent(this.current,-1);this.dragGesture.add(this.dragAction,c,l,b);this.checkDragWheelAction(this.dragAction,c,l,a,f,b,1);break;case 5:this.setMouseActions(this.pressedCount,e,!0);this.setCurrent(b,c,l,e);this.vwr.spinXYBy(0,0,0);e=!this.pressed.check(10,c,l,e,b,9223372036854775E3);this.checkReleaseAction(c,l,b,e);break;case 3:if(this.vwr.isApplet&&!this.vwr.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,
e);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,e,3),this.current.x,this.current.y,0,l,b,3);break;case 2:this.setMouseMode();this.clickedCount=1<f?f:this.clicked.check(10,0,0,e,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,c,l,e);this.setMouseActions(this.clickedCount,e,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,e,4),[31]))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,
e,2);this.checkClickAction(c,l,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(b,"checkPressedAction",function(a,b,c){var l=JV.binding.Binding.getButtonMods(this.pressAction),f=this.bnd(JV.binding.Binding.getMouseAction(1,l,4),[31]);if(0!=l){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;l=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,l,!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,b,this.dragAction)){this.checkUserAction(this.pressAction,a,b,0,0,c,4);c=!1;switch(this.apm){case 32:c=this.bnd(this.clickAction,[0]);break;case 28:c=this.bnd(this.dragAction,[7,14]);break;case 26:case 36:case 37:case 27:c=this.bnd(this.dragAction,[7,14,27]);break;case 29:c=this.bnd(this.dragAction,[11,14]);break;case 30:c=this.bnd(this.dragAction,[11,14,27]);break;default:c=34==this.bondPickingMode}if(c){this.dragAtomIndex=
this.vwr.findNearestAtomIndexMovable(a,b,!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,b):this.dragSelectedMode?(this.haveSelection=
!f||0<=this.vwr.findNearestAtomIndexMovable(a,b,!0))&&this.bnd(this.dragAction,[13,14])&&this.vwr.moveSelectedXY(-2147483648,0,l):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(b,"checkDragWheelAction",function(a,b,c,l,f,e,h){var k=JV.binding.Binding.getButtonMods(a);if(0!=k){var j=this.vwr.notifyMouseClicked(b,c,JV.binding.Binding.getMouseAction(this.pressedCount,k,h),h);if(0==j)return;0<j&&(a=j)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");
else if(!this.checkUserAction(a,b,c,l,f,e,h))if(e=34==this.bondPickingMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1,0<=e&&(0<=this.dragAtomIndex||this.mkBondPressed||this.bnd(a,[26])))0<=this.dragAtomIndex&&this.updateModelkitBranch(e,!1),this.vwr.moveSelected(l,f,-2147483648,b,c,null,null,null,!1,!1,0<=this.dragAtomIndex?0:16);else{e=null;if(0<=this.dragAtomIndex&&2!=this.apm)switch(this.apm){case 26:this.dragSelected(a,l,f,!0);return;case 36:case 37:case 27:case 30:e=this.vwr.ms.getAtoms(37==
this.apm?1094717454:1094713360,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&e.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(l,!0),this.getDegrees(f,!1),e);else{switch(this.apm){case 36:case 37:case 27:case 30:this.vwr.selectStatus(e,!1,0,!0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,l,f,this.bnd(a,
[14])?-f:-2147483648,null,e);this.vwr.checkCoordinatesChanged()}return}if(0<=this.dragAtomIndex&&1==h&&this.bnd(this.clickAction,[0])&&32==this.apm)a=this.vwr.findNearestAtomIndexMovable(b,c,!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&&(b<<=1,c<<=1),this.mp.traceX=b,this.mp.traceY=c,this.vwr.refresh(3,"assignNew"));
else if(!this.drawMode&&!this.labelMode&&this.bnd(a,[45]))this.vwr.translateXYBy(l,f);else if(this.dragSelectedMode&&this.haveSelection&&this.bnd(a,[13,27]))b=this.vwr.bsA().nextSetBit(0),0>b||(1==this.dragGesture.getPointCount()?this.vwr.undoMoveActionClear(b,2,!0):this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,null,null,!1,!1,k),this.dragSelected(a,l,f,!1));else{if(this.isDrawOrLabelAction(a)&&(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,
b,c,a)))return;if(this.checkMotionRotateZoom(a,b,l,f,!0))this.vwr.tm.slabEnabled&&this.bnd(a,[39])?this.vwr.slabDepthByPixels(f):this.vwr.zoomBy(f);else if(this.bnd(a,[25]))this.vwr.rotateXYBy(this.getDegrees(l,!0),this.getDegrees(f,!1));else if(this.bnd(a,[29]))0==l&&1<Math.abs(f)?(this.setMotion(8,!0),this.vwr.zoomBy(f+(0<f?-1:1))):0==f&&1<Math.abs(l)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-l+(0<l?1:-1),2147483647,2147483647));else{if(this.vwr.tm.slabEnabled){if(this.bnd(a,[6])){this.vwr.depthByPixels(f);
return}if(this.bnd(a,[38])){this.vwr.slabByPixels(f);return}if(this.bnd(a,[39])){this.vwr.slabDepthByPixels(f);return}}this.bnd(a,[46])?this.zoomByFactor(f,2147483647,2147483647):this.bnd(a,[28])&&(this.setMotion(13,!0),this.vwr.rotateZBy(-l,2147483647,2147483647))}}}},"~N,~N,~N,~N,~N,~N,~N");c(b,"updateModelkitBranch",function(a,b){this.vwr.setModelkitPropertySafely(b?"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,b,c,l){this.setMotion(13,!0);this.bnd(a,[27])&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(b,!0),this.getDegrees(c,!1),null):this.vwr.moveSelected(b,c,l&&this.bnd(a,[14])?-c:-2147483648,-2147483648,-2147483648,null,null,null,!0,!1,this.dragged.modifiers)},"~N,~N,~N,~B");
c(b,"checkReleaseAction",function(a,b,c,l){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,b,c);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,l&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.isDrawOrLabelAction(this.dragAction))this.vwr.checkObjectDragged(2147483647,
0,a,b,this.dragAction);else if(this.haveSelection&&(this.dragSelectedMode&&this.bnd(this.dragAction,[13]))&&this.vwr.moveSelectedXY(2147483647,0,this.dragged.modifiers),(!l||!this.checkUserAction(this.pressAction,a,b,0,0,c,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,b,c,l){if(0<l){if(this.checkUserAction(this.clickAction,a,b,0,0,c,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,b,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,b)){this.vwr.popupMenu(-a,b,"j");return}if(this.vwr.frankClickedModelKit(a,b)){this.vwr.popupMenu(10,
0,"m");return}}c=null;var f=!1,e=!1,h=null;if(!this.drawMode&&(h=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=h)){if(this.labelMode){this.pickLabel(h.get("atomIndex").intValue());return}f="bond".equals(h.get("type"));e="isosurface".equals(h.get("type"));c=this.getPoint(h);f&&this.vwr.isModelkitPickingRotateBond()&&this.vwr.highlightBond(h.get("index").intValue(),-1,a,b)}f&&(l=1);if(!(null!=c&&Float.isNaN(c.x))){var k=this.findNearestAtom(a,b,c,0<l);if(this.bnd(this.clickAction,[23]))this.doPopup(a,
b);else if(0==l&&32!=this.apm&&!this.vwr.isModelkitPickingRotateBond()){if(null!=this.mp){if(null!=c||0==this.mp.getIndexOf(k))try{this.mp.addPoint(k,c,!1)}catch(j){if(F(j,Exception)){this.exitMeasurementMode(null);return}throw j;}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*b/this.vwr.getScreenHeight()-50);else{if(f){if(this.bnd(this.clickAction,[34==this.bondPickingMode||33==this.bondPickingMode?0:5])){this.bondPicked(h.get("index").intValue());this.vwr.refresh(1,"bondpicked");return}}else{if(e)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,[20])){this.atomOrPointPicked(k,c);4==this.addToMeasurement(k,c,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,[37])){null!=this.mp?(this.addToMeasurement(k,
c,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(k),this.addToMeasurement(k,c,!0));this.atomOrPointPicked(k,c);return}}this.isSelectAction(this.clickAction)?e||this.atomOrPointPicked(k,c):this.bnd(this.clickAction,[24])&&0>k&&this.reset()}}},"~N,~N,~N,~N");c(b,"doPopup",function(a,b){this.vwr.popupMenu(a,b,this.vwr.getBoolean(603983903)?"m":"j")},"~N,~N");c(b,"pickLabel",function(a){var b=this.vwr.ms.at[a].atomPropertyString(this.vwr,
1825200146);2==this.pressedCount?(b=this.vwr.apiPlatform.prompt("Set label for atomIndex="+a,b,null,!1),null!=b&&(this.vwr.shm.setAtomLabel(b,a),this.vwr.refresh(1,"label atom"))):this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a+": "+b)},"~N");c(b,"checkUserAction",function(a,b,c,l,f,e,h){if(!this.b.isUserAction(a))return!1;for(var k=!1,j,p=this.b.getBindings(),n=a+"\t",q,w=p.keySet().iterator();w.hasNext()&&((q=w.next())||1);)if(0==q.indexOf(n)&&JU.AU.isAS(j=p.get(q))){var s=
j[1],r=null;if(0<=s.indexOf("_ATOM")){var u=this.findNearestAtom(b,c,null,!0),s=JU.PT.rep(s,"_ATOM","({"+(0<=u?""+u:"")+"})");0<=u&&(s=JU.PT.rep(s,"_POINT",JU.Escape.eP(this.vwr.ms.at[u])))}if(!this.drawMode&&(0<=s.indexOf("_POINT")||0<=s.indexOf("_OBJECT")||0<=s.indexOf("_BOND"))){u=this.vwr.checkObjectClicked(b,c,a);if(null!=u&&null!=(r=u.get("pt")))u.get("type").equals("bond")&&(s=JU.PT.rep(s,"_BOND","[{"+u.get("index")+"}]")),s=JU.PT.rep(s,"_POINT",JU.Escape.eP(r)),s=JU.PT.rep(s,"_OBJECT",JU.Escape.escapeMap(u));
s=JU.PT.rep(s,"_BOND","[{}]");s=JU.PT.rep(s,"_OBJECT","{}")}s=JU.PT.rep(s,"_POINT","{}");s=JU.PT.rep(s,"_ACTION",""+a);s=JU.PT.rep(s,"_X",""+b);s=JU.PT.rep(s,"_Y",""+(this.vwr.getScreenHeight()-c));s=JU.PT.rep(s,"_DELTAX",""+l);s=JU.PT.rep(s,"_DELTAY",""+f);s=JU.PT.rep(s,"_TIME",""+e);s=JU.PT.rep(s,"_MODE",""+h);s.startsWith("+:")&&(k=!0,s=s.substring(2));this.vwr.evalStringQuiet(s)}return!k},"~N,~N,~N,~N,~N,~N,~N");c(b,"checkMotionRotateZoom",function(a,b,c,l,f){b=this.bnd(a,[40])&&this.isZoomArea(this.pressed.x);
var e=this.bnd(a,[25]),h=this.bnd(a,[29]);if(!b&&!e&&!h)return!1;a=(c=h&&(0==c||Math.abs(l)>5*Math.abs(c)))||this.isZoomArea(this.moved.x)||this.bnd(a,[46])?8:e||h?13:this.bnd(a,[1])?12:0;this.setMotion(a,f);return c||b},"~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,b){return 180*(a/Math.min(500,b?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 b=new JU.Point3fi;b.setT(a.get("pt"));
b.mi=a.get("modelIndex").intValue();return b},"java.util.Map");c(b,"findNearestAtom",function(a,b,c,l){a=this.drawMode||null!=c?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(l||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,b,c){if(-1==a&&null==b||null==this.mp)return this.exitMeasurementMode(null),0;var l=this.mp.count;-2147483648!=this.mp.traceX&&2==l&&this.mp.setCount(l=1);return 4==l&&!c?l:this.mp.addPoint(a,b,!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),b=this.measurementQueued.getAtomIndex(2);if(!(0>a||0>b))try{var c=this.vwr.getSmilesOpt(null,a,b,1048576,null);this.vwr.setStatusMeasuring("measureSequence",
-2,c,0)}catch(l){if(F(l,Exception))JU.Logger.error(l.toString());else throw l;}});c(b,"minimize",function(a){var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1,this.mkBondPressed=!1);this.vwr.dragMinimizeAtom(b)},"~B");c(b,"queueAtom",function(a,b){var c=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+c+":"+this.vwr.getAtomInfo(a),null,!1);return c},"~N,JU.Point3fi");c(b,"setMotion",function(a,b){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}b&&
this.vwr.setInMotion(!0)},"~N,~B");c(b,"zoomByFactor",function(a,b,c){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,c),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,b){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 c=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var c=8==this.apm,l=25==this.apm;if(!this.bnd(this.clickAction,[c?5:3]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);if(2!=this.queueAtom(a,b))return;c=c||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":l?"STRUTS":"";this.runScript("connect "+
this.measurementQueued.getMeasurementScript(" ",!0)+c);this.resetMeasurement();return;case 21:c++;case 20:c++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,[20]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>c)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);l=this.measurementQueued.count;1==l&&this.vwr.setPicked(a,!0);if(l<c)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",
c,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}c=null!=this.mp&&1!=this.apm?1:this.apm;switch(c){case 3:if(!this.bnd(this.clickAction,[17]))return;null==b?this.zoomTo(a):this.runScript("zoomTo "+JU.Escape.eP(b));return;case 5:case 6:this.bnd(this.clickAction,[17])&&this.checkTwoAtomAction(b,a)}if(null==b){switch(c){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])&&(c=JU.BSUtil.newAndSetBit(a),
this.vwr.deleteAtoms(c,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(c),null,!1));return}c="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(c);break;case 10:this.selectAtoms("within(group, "+c+")");break;case 11:this.selectAtoms("within(chain, "+c+")");break;case 13:this.selectAtoms("within(polymer, "+c+")");break;case 14:this.selectAtoms("within(structure, "+c+")");break;case 12:this.selectAtoms("within(molecule, "+c+")");break;case 16:this.selectAtoms("within(model, "+
c+")");break;case 17:this.selectAtoms("visible and within(element, "+c+")");break;case 15:this.selectAtoms("visible and within(site, "+c+")")}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,b){var c=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 l=this.measurementQueued.count;if(1==l)if(null==a){if(this.measurementQueued.getAtomIndex(1)==b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(0<=b||null!=a)l=this.queueAtom(b,a);2>l?c?this.vwr.scriptStatus(1==l?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==l?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")):(l=this.measurementQueued.getMeasurementScript(" ",!1),c?this.runScript("spin"+l+" "+this.vwr.getInt(553648157)):this.runScript("draw symop "+l+";show symop "+l))}},"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 b=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!=b)try{var c=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.setAtomsPicked(c,"selected: "+JU.Escape.eBS(c));this.vwr.refresh(3,"selections set")}catch(l){if(!F(l,Exception))throw l;}this.selectionWorking=!1}},"~S");c(b,"setAtomsPicked",function(a,b){this.vwr.selectStatus(a,
!1,0,!1,!0);this.vwr.setStatusAtomPicked(-1,b,null,!1)},"JU.BS,~S");c(b,"selectRb",function(a){var b=this.vwr.ms.findAtomsInRectangle(this.rectRubber);0<b.length()&&(b=JU.Escape.eBS(b),this.bnd(a,[34])?this.runScript("selectionHalos on;select selected or "+b):this.bnd(a,[32])?this.runScript("selectionHalos on;select selected and not "+b):this.runScript("selectionHalos on;select selected tog "+b));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,b){if(!this.userActionEnabled(a))return!1;var c=JS.ScriptEval.runUserAction(JV.ActionManager.getActionName(a),
b,this.vwr);return!JS.SV.vF.equals(c)},"~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=v(function(){this.time=this.y=this.x=this.index=0;r(this,arguments)},JV,"MotionPoint",null);c(b,"set",function(a,b,c,l){this.index=a;this.x=b;this.y=c;this.time=l},"~N,~N,~N,~N");j(b,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});b=v(function(){this.action=0;this.nodes=null;this.time0=this.ptNext=0;this.vwr=null;r(this,arguments)},JV,"Gesture",null);x(b,function(a,b){this.vwr=b;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,
12);this.bindAction(33040,17);this.bindAction(33040,22);this.bindAction(33040,19);this.bindAction(33040,20);this.bindAction(33296,37);this.bindAction(33040,18);this.bindAction(33043,21);this.bindAction(33040,4);this.bindAction(33040,5);this.bindAction(33040,3);this.bindAction(33040,0);this.bindAction(33043,1)})});p("JV");C(null,"JV.ColorManager","JU.AU J.c.PAL JU.C $.ColorEncoder $.Elements $.Logger JV.JC".split(" "),function(){var b=v(function(){this.colorData=this.altArgbsCpk=this.argbsCpk=this.g3d=
this.vwr=this.ce=null;this.isDefaultColorRasmol=!1;this.colixRubberband=22;this.colixBackgroundContrast=0;r(this,arguments)},JV,"ColorManager",null);x(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,l;l=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:l=a.getAtomicAndIsotopeNumber();if(l<JU.Elements.elementNumberMax)return this.g3d.getChangeableColix(l,
this.argbsCpk[l]);c=l;l=JU.Elements.altElementIndexFromNumber(l);if(0<l)return this.g3d.getChangeableColix(JU.Elements.elementNumberMax+l,this.altArgbsCpk[l]);l=JU.Elements.getElementNumber(c);return this.g3d.getChangeableColix(l,this.argbsCpk[l]);case 2:return l=JU.ColorEncoder.quantize4(a.getPartialCharge(),-1,1,JV.JC.PARTIAL_CHARGE_RANGE_SIZE),this.g3d.getChangeableColix(JV.JC.PARTIAL_CHARGE_COLIX_RED+l,JV.JC.argbsRwbScale[l]);case 3:return l=a.getFormalCharge()- -4,this.g3d.getChangeableColix(JV.JC.FORMAL_CHARGE_COLIX_RED+
l,JV.JC.argbsFormalCharge[l]);case 68:case 5:return 68==b?(l=this.vwr.ms.getBfactor100Lo(),c=this.vwr.ms.getBfactor100Hi()):(l=0,c=1E4),this.ce.getColorIndexFromPalette(a.getBfactor100(),l,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 l=a.group.groupID,42<=l&&(l=24+"PGCATU".indexOf(Character.toUpperCase(a.group.group1))-
1),this.ce.getColorIndexFromPalette(l,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 l=this.vwr.ms.am[a.mi],this.ce.getColorIndexFromPalette(a.group.getBioPolymerIndexInModel(),0,(l.isBioModel?l.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(l.getMoleculeIndex(a.i,!0),0,l.getMoleculeCountInModel(a.mi)-1,0,!1);case 14:return c=a.mi,this.ce.getColorIndexFromPalette(l.getAltLocIndexInModel(c,a.altloc),0,l.getAltLocCountInModel(c),0,!1);case 15:return c=a.mi,this.ce.getColorIndexFromPalette(l.getInsertionCodeIndexInModel(c,a.group.getInsertionCode()),0,l.getInsertionCountInModel(c),0,!1);case 16:l=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(l,
1073741991);break;case 17:l=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(l,1073742116);break;case 7:c=a.group.getProteinStructureSubType().getColor();break;case 10:l=a.getChainID(),null==JU.ColorEncoder.argbsChainAtom&&(JU.ColorEncoder.argbsChainAtom=this.getArgbs(1153433601),JU.ColorEncoder.argbsChainHetero=this.getArgbs(1612709894)),l=((0>l?0:256<=l?l-256:l)&31)%JU.ColorEncoder.argbsChainAtom.length,c=(a.isHetero()?JU.ColorEncoder.argbsChainHetero:JU.ColorEncoder.argbsChainAtom)[l]}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?K(-1,[this.ce.hi,this.ce.lo]):K(-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,l,f=c?a.length-1:b.nextSetBit(0);0<=f;f=c?f-1:b.nextSetBit(f+1))if(!Float.isNaN(l=a[f]))this.ce.hi=Math.max(this.ce.hi,l),
this.ce.lo=Math.min(this.ce.lo,l);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 l=0==a.length;l&&(a="=");var f=this.getPropertyColorRange();this.ce.currentPalette=this.ce.createColorScheme(a,!0,c);l||this.setPropertyColorRange(f[0],f[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")});p("JV");C(["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=v(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;r(this,arguments)},JV,"FileManager",null,javajs.api.BytePoster);P(b,function(){this.cache=new java.util.Hashtable});x(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});
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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=
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b.put("dbName",l);a.endsWith("%2D%")&&(l=b.get("filter"),b.put("filter",(null==l?"":l)+"2D"),a=a.substring(0,a.length-4));l=0<=f?a.substring(f+2):a;f=0<=f?a.substring(0,f):null;JU.Logger.info("\nFileManager.getAtomSetCollectionFromFile("+l+")"+(a.equals(l)?"":" //"+a));var e=this.getClassifiedName(l,!0);if(1==e.length)return e[0];a=e[0];e=e[1];b.put("fullPathName",(null==f?"":f+"::")+JV.FileManager.fixDOSName(a));this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825)&&this.vwr.getChimeMessenger().update(a);
b=new J.io.FileReader(this.vwr,e,a,l,f,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 l=Array(a.length),f=Array(a.length),e=Array(a.length),h=0;h<a.length;h++){var k=a[h].indexOf("::"),j=0<=k?a[h].substring(k+2):a[h],k=0<=k?a[h].substring(0,k):null,p=this.getClassifiedName(j,!0);if(1==p.length)return p[0];l[h]=p[0];a[h]=JV.FileManager.fixDOSName(p[0]);e[h]=k;f[h]=j}b.put("fullPathNames",
l);b.put("fileTypes",e);a=this.newFilesReader(l,f,e,null,b,c);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(b,"createAtomSetCollectionFromString",function(a,b,c){this.setLoadState(b);var l=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!=l&&this.setFileInfo(l);!c&&"string"!=typeof b.getAtomSetCollection()&&this.setFileInfo(A(-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,l){if(!c.containsKey("isData")){var f='"'+this.vwr.getDataSeparator()+'"',e='"'+(l?"append":"model")+' inline"',h=new JU.SB;h.append('set dataSeparator "~~~next file~~~";\ndata ').append(e);for(var k=0;k<a.length;k++)0<k&&h.append("~~~next file~~~"),h.append(a[k]);h.append("end ").append(e).append(";set dataSeparator ").append(f);b.appendSB(h)}this.setLoadState(c);
JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");b=Array(a.length);f=Array(a.length);for(k=0;k<a.length;k++)b[k]="string["+k+"]",f[k]=JV.FileManager.newDataReader(this.vwr,a[k]);a=this.newFilesReader(b,b,null,f,c,l);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 l=a.size(),f=Array(l),e=Array(l),h=0;h<l;h++)f[h]="String["+
h+"]",e[h]=JV.FileManager.newDataReader(this.vwr,a.get(h));a=this.newFilesReader(f,f,null,e,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":z(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,l,f,e){var h=J.api.Interface.getOption("io.FilesReader",this.vwr,
"file");h.set(this,this.vwr,a,b,c,l,f,e);return h},"~A,~A,~A,~A,java.util.Map,~B");c(b,"createAtomSetCollectionFromReader",function(a,b,c,l){a=new J.io.FileReader(this.vwr,b,a,null,null,c,l,!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 z(a,"java.io.BufferedInputStream")?a:null},"~S");c(b,"getBufferedInputStreamOrErrorMessageFromName",function(a,b,c,l,f,e,h){var k=
null,j=null;b=(h=h||a.startsWith("cache://"))&&null==f?b=this.getPngjOrDroppedBytes(b,a):null;try{h&&(0<=a.indexOf(".png")&&null==this.pngjCache&&!this.vwr.getBoolean(603979960))&&(this.pngjCache=new java.util.Hashtable);if(null==b){var p=0<=a.indexOf("?POST?_PNGJBIN_"),n=p||0<=a.indexOf("?POST?_PNGJ_");if(0<a.indexOf("?POST?_PNG_")||n){var q=Array(1),w=this.vwr.getImageAsBytes(n?"PNGJ":"PNG",0,0,-1,q);if(null!=q[0])return q[0];p?(f=w,a=JU.PT.rep(a,"?_","=_")):a=(new JU.SB).append(a).append("=").appendSB(JU.Base64.getBase64(w)).toString()}var s=
JU.OC.urlTypeIndex(a),p=0<=s,n=null;if(p&&0<=(s=a.indexOf("?POST?")))n=a.substring(s+6),a=a.substring(0,s);var r=null!=this.appletDocumentBaseURL;if(r||p){r&&(p&&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(Z("java.net.URL"),a,null);if(l)return null;a=u.toString();c&&0>a.toLowerCase().indexOf("password")&&JU.Logger.info("FileManager opening url "+a);j=this.vwr.apiPlatform.getURLContents(u,f,n,!1);
w=null;if(z(j,"JU.SB")){a=j;if(e&&!JU.Rdr.isBase64(a))return JU.Rdr.getBR(a.toString());w=JU.Rdr.getBytesFromSB(a)}else JU.AU.isAB(j)&&(w=j);null!=w&&(j=JU.Rdr.getBIS(w))}else if(!h||null==(b=this.cacheGet(a,!0)))c&&JU.Logger.info("FileManager opening file "+a),j=this.vwr.apiPlatform.getBufferedFileInputStream(a);if("string"==typeof j)return j}k=null==b?j:JU.Rdr.getBIS(b);l&&(k.close(),k=null);return k}catch(v){if(F(v,Exception))try{null!=k&&k.close()}catch(x){if(!F(x,"java.io.IOException"))throw x;
}else throw v;}return""+v},"~S,~S,~B,~B,~A,~B,~B");b.getBufferedReaderForResource=c(b,"getBufferedReaderForResource",function(a,b,c,l){l=a.vwrOptions.get("codePath")+c+l;if(a.async){a=a.fm.cacheGet(l,!1);if(null==a)throw new JV.JmolAsyncException(l);return JU.Rdr.getBufferedReader(JU.Rdr.getBIS(a),null)}return a.fm.getBufferedReaderOrErrorMessageFromName(l,A(-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(F(b,"java.io.UnsupportedEncodingException"))return a;
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!1),e=JU.AU.isAB(f),h=e?f:null;if(a.startsWith("cache://")){if(null==f)return"cannot read "+a;if(e)h=f;else return JU.Rdr.getBR(f)}f=this.getClassifiedName(a,!0);if(null==f)return"cannot read file name: "+a;null!=b&&(b[0]=JV.FileManager.fixDOSName(f[0]));return this.getUnzippedReaderOrStreamFromName(f[0],h,!1,c,!1,l,null)},"~S,~A,~B,~B");c(b,"getUnzippedReaderOrStreamFromName",function(a,b,c,l,f,e,h){if(e&&null==b){var k=a.endsWith(".spt")?A(-1,[null,null,null]):0>a.indexOf(".spardir")?null:this.spartanUtil().getFileList(a,
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-1,!1,!0,!1,"file"),0>a.indexOf("**** Jmol Embedded Script ****")?"":JV.FileManager.getEmbeddedScript(a);for(var l=0;l<b.length;l++)if(0<=b[l].indexOf(c))return a=A(-1,[a+"|"+b[l],null]),this.getFileDataAsString(a,-1,!1,!1,!1),a[1];return""},"~S,~B,~S");b.stripTypePrefix=c(b,"stripTypePrefix",function(a){var b=a.indexOf("::");return 0>b||20<=b?a:a.substring(b+2)},"~S");b.getEmbeddedScript=c(b,"getEmbeddedScript",function(a){if(null==a)return a;var b=a.indexOf("**** Jmol Embedded Script ****");if(0>
b)return a;var c=a.lastIndexOf("/*",b),l=a.indexOf(("*"==a.charAt(c+2)?"*":"")+"*/",b);for(0<=c&&l>=b&&(a=a.substring(b+30,l)+"\n");0<=(c=a.indexOf(" #Jmol...\x00"));)a=a.substring(0,c)+a.substring(c+10+4);JU.Logger.debugging&&JU.Logger.debug(a);return a},"~S");c(b,"isZipStream",function(a){return this.vwr.getJzt().isZipStream(a)},"~O");b.SIMULATION_PROTOCOL="http://SIMULATION/";b.scriptFilePrefixes=A(-1,['/*file*/"','FILE0="','FILE1="'])});p("JV");C(["java.util.Hashtable","JU.P3","J.c.CBK"],"JV.GlobalSettings",
"JU.DF $.PT $.SB J.c.STR JS.SV JU.Escape $.Logger JV.JC $.StateManager $.Viewer".split(" "),function(){var b=v(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;r(this,arguments)},JV,"GlobalSettings",null);P(b,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;this.objColors=E(7,0);this.objStateOn=ha(7,
!1);this.objMad10=E(7,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,K(-1,[30,90,-15,95]));this.structureList.put(J.c.STR.SHEET,K(-1,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]));this.structureList.put(J.c.STR.HELIX,K(-1,[-160,0,-100,45]))});x(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 l;c=0;for(var f=J.c.CBK.values();c<f.length&&((l=f[c])||1);c++)this.resetValue(l.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",
this.wireframeRotation);this.setI("zDepth",this.zDepth);this.setB("zeroBasedXyzRasmol",this.zeroBasedXyzRasmol);this.setB("zoomHeight",this.zoomHeight);this.setB("zoomLarge",this.zoomLarge);this.setI("zShadePower",this.zShadePower);this.setI("zSlab",this.zSlab)},"JV.Viewer,JV.GlobalSettings,~B");c(b,"clear",function(){for(var a=this.htUserVariables.keySet().iterator();a.hasNext();){var b=a.next();("@"==b.charAt(0)||b.startsWith("site_"))&&a.remove()}this.vwr.setPicked(-1,!1);this.setI("_atomhovered",
-1);this.setO("_pickinfo","");this.setB("selectionhalos",!1);this.setB("hidenotselected",!1);this.setB("measurementlabels",this.measurementLabels=!0);this.setB("drawHover",this.drawHover=!1);this.vwr.stm.saveScene("DELETE",null)});c(b,"setUnits",function(a){var b=this.measureDistanceUnits,c=this.energyUnits;a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||a.equalsIgnoreCase("nm")?this.measureDistanceUnits="nanometers":a.equalsIgnoreCase("picometers")||
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this.setO("energyUnits",this.energyUnits):this.setO("measurementUnits",this.measureDistanceUnits)},"~S");c(b,"isJmolVariable",function(a){return"_"==a.charAt(0)||this.htNonbooleanParameterValues.containsKey(a=a.toLowerCase())||this.htBooleanParameterFlags.containsKey(a)||0<=JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(b,"resetValue",function(a,b){this.setO(a,null==b?"":b.getParameter(a,!0))},"~S,JV.GlobalSettings");c(b,"setB",function(a,b){a=a.toLowerCase();this.htNonbooleanParameterValues.containsKey(a)||
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c(b,"getVariableList",function(){return JV.StateManager.getVariableList(this.htUserVariables,0,!0,!1)});c(b,"setStructureList",function(a,b){this.haveSetStructureList=!0;this.structureList.put(b,a)},"~A,J.c.STR");c(b,"getStructureList",function(){return this.structureList});b.doReportProperty=c(b,"doReportProperty",function(a){return"_"!=a.charAt(0)&&0>JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(b,"getAllVariables",function(){var a=new java.util.Hashtable;a.putAll(this.htBooleanParameterFlags);
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"set defaultStructureDssp "+this.defaultStructureDSSP);var c=this.vwr.getDefaultVdwNameOrData(-2147483648,null,null);this.app(b,"set defaultVDW "+c);c.equals("User")&&this.app(b,this.vwr.getDefaultVdwNameOrData(2147483647,null,null));this.app(b,"set forceAutoBond "+this.forceAutoBond);this.app(b,"#set defaultDirectory "+JU.PT.esc(this.defaultDirectory));this.app(b,"#set loadFormat "+JU.PT.esc(this.loadFormat));this.app(b,"#set loadLigandFormat "+JU.PT.esc(this.pdbLoadLigandFormat));this.app(b,"#set smilesUrlFormat "+
JU.PT.esc(this.smilesUrlFormat));this.app(b,"#set nihResolverFormat "+JU.PT.esc(this.nihResolverFormat));this.app(b,"#set pubChemFormat "+JU.PT.esc(this.pubChemFormat));this.app(b,"set bondingVersion "+this.bondingVersion);this.app(b,"set legacyAutoBonding "+this.legacyAutoBonding);this.app(b,"set legacyAutoBonding "+this.legacyAutoBonding);this.app(b,"set legacyHAddition "+this.legacyHAddition);this.app(b,"set legacyJavaFloat "+this.legacyJavaFloat);this.app(b,"set minBondDistance "+this.minBondDistance);
this.app(b,"set minimizationCriterion  "+this.minimizationCriterion);this.app(b,"set minimizationSteps  "+this.minimizationSteps);this.app(b,"set multipleBondBananas false");this.app(b,"set pdbAddHydrogens "+(null!=a&&a.get("pdbNoHydrogens")!==Boolean.TRUE?this.pdbAddHydrogens:!1));this.app(b,"set pdbGetHeader "+this.pdbGetHeader);this.app(b,"set pdbSequential "+this.pdbSequential);this.app(b,"set percentVdwAtom "+this.percentVdwAtom);this.app(b,"set smallMoleculeMaxAtoms "+this.smallMoleculeMaxAtoms);
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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})});p("JV");C(null,"JV.ShapeManager","JU.BS $.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){var b=v(function(){this.navMinMax=this.bsSlabbedInternal=this.bsRenderableAtoms=this.scaleText=this.vwr=this.shapes=this.ms=null;r(this,arguments)},JV,"ShapeManager",null);P(b,function(){this.navMinMax=E(4,0)});x(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,l){if(null!=this.shapes)for(var f=0;f<this.shapes.length&&null==c[0];++f)null!=this.shapes[f]&&this.shapes[f].findNearestAtomIndex(a,b,c,l)},"~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 l=Integer.$valueOf(a);a=this.vwr.getModelUndeletedAtomsBitSet(a);for(var f=0;37>f;f++)null!=this.shapes[f]&&this.setShapePropertyBs(f,"refreshTrajectories",A(-1,[l,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,l){if(null!=this.shapes){if(null==l&&(1!=a||2147483647!=b))l=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,l);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,l){null==this.shapes||null==this.shapes[a]||(null==l&&(l=this.vwr.bsA()),this.vwr.setShapeErrorState(a,"set "+b),
this.shapes[a].setProperty(b.intern(),c,l),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,l,f){var e,h=null;if(2==this.vwr.getPickingMode())return null==this.shapes[5]?null:this.shapes[5].checkObjectClicked(a,b,c,l,!1);if(0!=c&&this.vwr.getBondsPickable()&&null!=(h=this.shapes[1].checkObjectClicked(a,b,c,l,!1)))return h;for(var j=0;j<JV.ShapeManager.clickableMax;j++)if(null!=
(e=this.shapes[JV.ShapeManager.hoverable[j]])&&null!=(h=e.checkObjectClicked(a,b,c,l,f)))return h;return null},"~N,~N,~N,JU.BS,~B");c(b,"checkObjectDragged",function(a,b,c,l,f,e,h){for(var j=!1,m=0<h?h+1:37;!j&&h<m;++h)null!=this.shapes[h]&&(j=this.shapes[h].checkObjectDragged(a,b,c,l,f,e));return j},"~N,~N,~N,~N,~N,JU.BS,~N");c(b,"checkObjectHovered",function(a,b,c,l){var f=this.shapes[1];if(l&&null!=f&&f.checkObjectHovered(a,b,c))return!0;for(l=0;l<JV.ShapeManager.hoverable.length;l++)if(f=this.shapes[JV.ShapeManager.hoverable[l]],
null!=f&&f.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),l=16;30>l;++l)this.getShapePropertyData(l,"getNames",
A(-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),l=this.vwr.slm.bsDeleted,f=this.ms.at;this.ms.clearVisibleSets();if(0<f.length)for(c=this.ms.ac;0<=--c;){var e=f[c];null!=e&&(e.shapeVisibilityFlags&=-64);if(!(null!=l&&l.get(c))&&b.get(e.mi)){var h=
1;if(!this.ms.isAtomHidden(c)&&(a||1!=e.getElementNumber()))h|=8,0!=e.madAtom&&(h|=16),e.setShapeVisibility(h,!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,l=c.tm;b&&c.finalizeTransformParameters();if(null!=a){var f=this.ms.getAtomSetCenter(a),e=new JU.P3;l.transformPt3f(f,e);e.add(l.ptOffset);l.unTransformPoint(e,e);e.sub(f);c.setAtomCoordsRelative(e,a);l.ptOffset.set(0,
0,0);l.bsSelectedAtoms=null}f=this.bsRenderableAtoms;this.ms.getAtomsInFrame(f);var h=this.ms.vibrations,j=null!=h&&l.vibrationOn,m=null!=this.ms.bsModulated&&null!=this.ms.occupancies,p=this.ms.at,n,q=!1,r=this.bsSlabbedInternal;r.clearAll();for(var s=f.nextSetBit(0);0<=s;s=f.nextSetBit(s+1)){var e=p[s],u=j&&e.hasVibration()?l.transformPtVib(e,h[s]):l.transformPt(e);1==u.z&&(l.internalSlab&&l.xyzIsSlabbedInternal(e))&&r.set(s);e.sX=u.x;e.sY=u.y;e.sZ=u.z;var v=Math.abs(e.madAtom);v==JM.Atom.MAD_GLOBAL&&
(v=D(2E3*c.getFloat(1153433601)));e.sD=ca(c.tm.scaleToScreen(u.z,v));if(m&&null!=h[s]&&-2147483648!=(n=h[s].getOccupancy100(j)))q=!0,e.setShapeVisibility(2,!1),0<=n&&50>n?e.setShapeVisibility(24,!1):e.setShapeVisibility(8|(0<e.madAtom?16:0),!0),this.ms.occupancies[e.i]=Math.abs(n)}q&&this.setShapeVis();n=c.gdata;if(l.slabEnabled){s=c.getBoolean(603979940);l=c.getBoolean(603979939);h=n.slab;j=n.depth;if(s){m=this.ms.getMolecules();q=this.ms.getMoleculeCountInModel(-1);for(s=0;s<q;s++)if(r=m[s],u=0,
e=r.firstAtomIndex,f.get(e)){for(;u<r.ac&&!n.isClippedZ(p[e].sZ-(p[e].sD>>1));u++,e++);if(u!=r.ac){e=r.firstAtomIndex;for(u=0;u<r.ac;u++)f.clear(e),p[e++].sZ=0}}}for(s=f.nextSetBit(0);0<=s;s=f.nextSetBit(s+1))if(e=p[s],n.isClippedZ(e.sZ-(l?p[s].sD>>1:0)))e.setClickable(0),m=B((l?-1:1)*e.sD/2),(e.sZ+m<h||e.sZ-m>j||!n.isInDisplayRange(e.sX,e.sY))&&f.clear(s)}if(0==this.ms.ac||!c.getShowNavigationPoint())return null;c=2147483647;n=-2147483648;l=2147483647;h=-2147483648;for(s=f.nextSetBit(0);0<=s;s=f.nextSetBit(s+
1))e=p[s],e.sX<c&&(c=e.sX),e.sX>n&&(n=e.sX),e.sY<l&&(l=e.sY),e.sY>h&&(h=e.sY);this.navMinMax[0]=c;this.navMinMax[1]=n;this.navMinMax[2]=l;this.navMinMax[3]=h;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 l=this.vwr.slm.bsSubset;
null!=l&&(c=this.vwr.slm.getSelectedAtomsNoSubset(),c.and(l),this.vwr.selectStatus(c,!1,0,!0,!1),JU.BSUtil.invertInPlace(c,this.vwr.ms.ac),c.and(l))}JU.BSUtil.andNot(c,this.vwr.slm.bsDeleted);l=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 f=this.vwr.bsA(),e=21;0<=
--e;)6!=e&&null!=this.getShape(e)&&this.setShapeSizeBs(e,0,null,f);null!=this.getShape(21)&&this.setShapePropertyBs(21,"off",f,null);this.setLabel(null,f);a||this.vwr.setBooleanProperty("bondModeOr",l);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});p("JV");C(["java.util.Hashtable"],["JV.Connection","$.Scene","$.StateManager","$.Connections"],"java.util.Arrays JU.BS $.Lst $.SB JM.Orientation JU.BSUtil $.Escape".split(" "),
function(){var b=v(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;r(this,arguments)},JV,"StateManager",null);P(b,function(){this.saved=new java.util.Hashtable});x(b,function(a){this.vwr=a},"JV.Viewer");b.getVariableList=c(b,"getVariableList",function(a,b,c,l){var f=new JU.SB,e=0,h=Array(a.size()),
j;for(a=a.entrySet().iterator();a.hasNext()&&((j=a.next())||1);){var m=j.getKey(),p=j.getValue();if((c||!m.startsWith("site_"))&&(!l||"@"==m.charAt(0)))h[e++]=m+("@"==m.charAt(0)?" "+p.asString():" = "+JV.StateManager.varClip(m,p.escape(),b))}java.util.Arrays.sort(h,0,e);for(b=0;b<e;b++)null!=h[b]&&f.append("  ").append(h[b]).append(";\n");0==e&&!l&&f.append("# --no global user variables defined--;\n");return f.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:B(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,l=a.entrySet().iterator();l.hasNext()&&((c=l.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=v(function(){this.scene=this.saveName=null;r(this,arguments)},JV,"Scene",null);x(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=v(function(){this.saveName=null;this.bondCount=0;this.vwr=this.connections=null;r(this,arguments)},JV,"Connections",null);x(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],l=a.ac;c.atomIndex1>=l||c.atomIndex2>=l||(l=a.bondAtoms(a.at[c.atomIndex1],a.at[c.atomIndex2],c.order,c.mad,null,c.energy,!1,
!0),l.colix=c.colix,l.shapeVisibilityFlags=c.shapeVisibilityFlags)}for(b=a.bondCount;0<=--b;)a.bo[b].index=b;this.vwr.setShapeProperty(1,"reportAll",null);return!0});b=v(function(){this.shapeVisibilityFlags=this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;r(this,arguments)},JV,"Connection",null);x(b,function(a,b,c,l,f,e,h){this.atomIndex1=a;this.atomIndex2=b;this.mad=c;this.colix=l;this.order=f;this.energy=e;this.shapeVisibilityFlags=h},"~N,~N,~N,~N,~N,~N,~N")});p("JV");
C(["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=v(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;r(this,arguments)},JV,"StatusManager",null);P(b,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});x(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,l){if(this.recordStatus(a)){var f=new JU.Lst;f.addLast(Integer.$valueOf(++this.statusPtr));
f.addLast(a);f.addLast(Integer.$valueOf(b));f.addLast(c);b=l?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(f)}},"~S,~N,~O,~B");c(b,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),c=0<a.length&&"+"==a.charAt(0),l=!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)?l=!0:(c||
(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(l)for(var f,l=this.messageQueue.entrySet().iterator();l.hasNext()&&((f=l.next())||1);)a.addLast(f.getValue());this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(b,"setCallbackFunction",function(a,b){var c=J.c.CBK.getCallback(a),l="string"==typeof b?b:null;if(null!=c)if(c=J.c.CBK.getCallback(a).name(),JU.Logger.info("StatusManager "+c+"callback set f="+
l),null!=l&&l.startsWith("SYNC:"))if(l.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 f="",e=null==l?0:(f=l.toLowerCase()).startsWith("script:")?7:f.startsWith("jmolscript:")?11:0;if(0==e)null==b&&this.jmolScriptCallbacks.remove(c);else{this.jmolScriptCallbacks.put(c,l.substring(e).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,l){var f=b.name();if(null!=c[0]){var e=Array(c.length);System.arraycopy(c,0,e,0,c.length);var h="try{\n"+e[0]+"\n}";e[0]=f;this.vwr.evalCallback(h,e,l)}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,l=this.notifyEnabled(J.c.CBK.APPLETREADY);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.APPLETREADY,A(-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,A(-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,A(-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,l,f,e){0<=a&&null==e&&(e=JU.BSUtil.newAndSetBit(a));var h=this.getJmolScriptCallback(J.c.CBK.STRUCTUREMODIFIED),j=this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED);(j||null!=h)&&this.fireJmolScriptCallback(j,J.c.CBK.STRUCTUREMODIFIED,A(-1,[h,Integer.$valueOf(c),Integer.$valueOf(a),Integer.$valueOf(b),l,Integer.$valueOf(f),e]),!0)},"~N,~N,~N,~S,~N,JU.BS");c(b,"setStatusAtomPicked",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",
a,b,!1);var f=this.notifyEnabled(J.c.CBK.PICK);(f||null!=l)&&this.fireJmolScriptCallback(f,J.c.CBK.PICK,A(-1,[l,b,Integer.$valueOf(a),c]),!0)},"~N,~S,java.util.Map");c(b,"setStatusClicked",function(a,b,c,l,f){var e=this.getJmolScriptCallback(J.c.CBK.CLICK);f=E(-1,[c,f]);var h=this.notifyEnabled(J.c.CBK.CLICK);(h||null!=e)&&this.fireJmolScriptCallback(h,J.c.CBK.CLICK,A(-1,[e,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),Integer.$valueOf(l),f]),!0);return f[0]},"~N,~N,~N,~N,~N");c(b,"setStatusResized",
function(a,b){var c=this.getJmolScriptCallback(J.c.CBK.RESIZE),l=this.notifyEnabled(J.c.CBK.RESIZE);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.RESIZE,A(-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),l=this.notifyEnabled(J.c.CBK.HOVER);(l||null!=c)&&this.fireJmolScriptCallback(l,
J.c.CBK.HOVER,A(-1,[c,b,Integer.$valueOf(a)]),!0)},"~N,~S");c(b,"setStatusObjectHovered",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.HOVER),f=this.notifyEnabled(J.c.CBK.HOVER);(f||null!=l)&&this.fireJmolScriptCallback(f,J.c.CBK.HOVER,A(-1,[l,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),l=this.notifyEnabled(J.c.CBK.IMAGE);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.IMAGE,A(-1,[c,a,b]),!0);if(Boolean.TRUE.equals(b)){if(null!=this.imageMap){for(var c=new JU.Lst,f,l=this.imageMap.keySet().iterator();l.hasNext()&&((f=l.next())||1);)c.addLast(f);for(f=c.size();0<=--f;)this.imageMap.get(c.get(f)).closeMe()}}else null==this.imageMap&&(this.imageMap=new java.util.Hashtable),f=this.imageMap.get(a),Boolean.FALSE.equals(b)?null!=
f&&f.closeMe():(null==f&&null!=b&&(f=this.vwr.apiPlatform.getImageDialog(a,this.imageMap)),null!=f&&(null==b?f.closeMe():f.setImage(b)))},"~S,~O");c(b,"setFileLoadStatus",function(a,b,c,l,f,e,h){null==a&&"resetUndo".equals(b)&&(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",f,a,!1);null!=l&&this.setStatusChanged("fileLoadError",f,l,!1);var j=this.getJmolScriptCallback(J.c.CBK.LOADSTRUCT);if((e=e&&this.notifyEnabled(J.c.CBK.LOADSTRUCT))||
null!=j){var m=this.vwr.getP("_smilesString");0!=m.length&&(b=m);this.fireJmolScriptCallback(e,J.c.CBK.LOADSTRUCT,A(-1,[j,a,b,c,l,Integer.$valueOf(f),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.ms.mc-1),h]),!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,
A(-1,[a,b]),!0)},"~N");c(b,"setStatusFrameChanged",function(a,b,c,l,f,e,h){if(null!=this.vwr.ms){var j=this.vwr.am.animationOn,m=j?-2-f:f;this.setStatusChanged("frameChanged",m,0<=f?this.vwr.getModelNumberDotted(f):"",!1);var p=this.getJmolScriptCallback(J.c.CBK.ANIMFRAME),n=this.notifyEnabled(J.c.CBK.ANIMFRAME);(n||null!=p)&&this.fireJmolScriptCallback(n,J.c.CBK.ANIMFRAME,A(-1,[p,E(-1,[m,a,b,c,l,f]),h,Float.$valueOf(e)]),!1);!j&&!this.vwr.isJSNoAWT&&this.vwr.checkMenuUpdate()}},"~N,~N,~N,~N,~N,~N,~S");
c(b,"setStatusDragDropped",function(a,b,c,l,f){this.setStatusChanged("dragDrop",0,"",!1);var e=this.getJmolScriptCallback(J.c.CBK.DRAGDROP),h=this.notifyEnabled(J.c.CBK.DRAGDROP);(h||null!=e)&&this.fireJmolScriptCallback(h,J.c.CBK.DRAGDROP,A(-1,[e,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),l,f]),!0);return h},"~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),
l=this.notifyEnabled(J.c.CBK.ECHO);if(l||null!=c)this.fireJmolScriptCallback(l,J.c.CBK.ECHO,A(-1,[c,a,Integer.$valueOf(b?1:0)]),!0);this.echoing=!1}},"~S,~B");c(b,"setStatusMeasuring",function(a,b,c,l){this.setStatusChanged(a,b,c,!1);var f=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+c),f=this.getJmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,c,!1),JU.Logger.info("measurePicked "+b+" "+c));var e=this.notifyEnabled(J.c.CBK.MEASURE);
(e||null!=f)&&this.fireJmolScriptCallback(e,J.c.CBK.MEASURE,A(-1,[f,c,Integer.$valueOf(b),a,Float.$valueOf(l)]),!0)},"~S,~N,~S,~N");c(b,"notifyError",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.ERROR),f=this.notifyEnabled(J.c.CBK.ERROR);(f||null!=l)&&this.fireJmolScriptCallback(f,J.c.CBK.ERROR,A(-1,[l,a,b,this.vwr.getShapeErrorState(),c]),!0)},"~S,~S,~S");c(b,"notifyMinimizationStatus",function(a,b,c,l,f){var e=this.getJmolScriptCallback(J.c.CBK.MINIMIZATION),h=this.notifyEnabled(J.c.CBK.MINIMIZATION);
(h||null!=e)&&this.fireJmolScriptCallback(h,J.c.CBK.MINIMIZATION,A(-1,[e,a,b,c,l,f]),!0)},"~S,Integer,Float,Float,~S");c(b,"setScriptStatus",function(a,b,c,l){if(-1>c){var f=-2-c;this.setStatusChanged("scriptStarted",f,b,!1);a="script "+f+" started"}else if(null==a)return;var f=0==c?this.getJmolScriptCallback(J.c.CBK.SCRIPT):null,e="Script completed"===a;if(this.recordStatus("script")){var h=null!=l;this.setStatusChanged(h?"scriptError":"scriptStatus",0,a,!1);if(h||e)this.setStatusChanged("scriptTerminated",
1,"Jmol script terminated"+(h?" unsuccessfully: "+a:" successfully"),!1)}e&&(this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825))&&(a=this.vwr.getChimeMessenger().scriptCompleted(this,b,l));b=A(-1,[f,a,b,Integer.$valueOf(e?-1:c),l]);((c=this.notifyEnabled(J.c.CBK.SCRIPT))||null!=f)&&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=A(-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(z(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,A(-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?K(Math.abs(b),Math.abs(c),0):this.jsl.functionXY(a,b,c)},"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,l){return null==this.jsl?K(Math.abs(b),Math.abs(c),Math.abs(c),0):this.jsl.functionXYZ(a,b,c,l)},"~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,l,f){return null==this.jsl?null:this.jsl.createImage(a,b,null==c?l:c,f)},"~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 l=a.equals("Save Image"),f=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==f)return null;f.setupUI(!1);l&&f.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);a=f.getFileNameFromDialog(this.vwr,
a,b);l&&null!=a&&(this.qualityJPG=f.getQuality("JPG"),this.qualityPNG=f.getQuality("PNG"),l=f.getType(),null!=c&&(c.put("qualityJPG",Integer.$valueOf(this.qualityJPG)),c.put("qualityPNG",Integer.$valueOf(this.qualityPNG)),null!=l&&c.put("dialogImageType",l)),null!=l&&(this.imageType=l));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 l,f=this.audios.keySet().iterator();f.hasNext()&&((l=f.next())||1);){var e=this.audios.remove(l);e.action("close")}return}e=this.audios.get(c);if(null!=e){e.action(b);return}}try{J.api.Interface.getInterface("JU.JmolAudio",
this.vwr,"script").playAudio(this.vwr,a)}catch(h){if(F(h,Exception))JU.Logger.info(h.getMessage());else throw h;}}catch(j){}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),l=this.notifyEnabled(J.c.CBK.AUDIO);(l||null!=c)&&this.fireJmolScriptCallback(l,
J.c.CBK.AUDIO,A(-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 l="~".equals(b);if(0<c||!l&&!".".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&&(l=!1),JU.Logger.debugging&&JU.Logger.debug(this.vwr.htmlName+" syncing with script: "+a),l&&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(l)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),l&&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(l){if(!F(l,Exception))throw l;}this.vwr.showString("error reading SYNC command: "+a,!1)},"~S");b.MAXIMUM_QUEUE_LENGTH=16});p("JV");C("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=v(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;r(this,arguments)},JV,"TransformManager",null);P(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});x(b,function(){});b.getTransformManager=c(b,"getTransformManager",function(a,b,c,l){l=l?J.api.Interface.getInterface("JV.TransformManager4D",
a,"tm"):new JV.TransformManager;l.vwr=a;l.setScreenParameters(b,c,!0,!1,!0,!0);return l},"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 l=JU.P3.newP(this.fixedRotationCenter),f=new JU.P3;this.transformPt3f(l,f);a=JU.P3.new3(-b,a,0);a.add(f);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,
a,l,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,l,f,e){null==c?this.matrixRotate.mul2(a,this.matrixRotate):(this.vwr.moveAtoms(e,a,this.matrixRotate,l,this.internalRotationCenter,b,c,f),null!=l&&this.internalRotationCenter.add(l))},"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,l,f,e,h){null!=b&&this.moveRotationCenter(b,!0);e&&this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(e&&3.4028235E38==f)return!1;e=!1}if(Float.isNaN(l)||0==l||0==f)return!1;null!=b&&
this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=l;if(e)return this.fixedRotationAxis.setVA(c,0.017453292519943295*l),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=h,this.setSpin(a,!0,f,null,null,h,!1),3.4028235E38!=f;a=0.017453292519943295*f;this.fixedRotationAxis.setVA(c,f);this.rotateAxisAngleRadiansFixed(a,h);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,l,f,e,h,j,m,p,n,q,r){h&&this.setSpinOff();this.setNavOn(!1);if(null==q&&(null==p||0.001>p.length())&&(h?Float.isNaN(l)||0==l:0==f))return!1;var s=null;null==q&&(s=JU.V3.newVsub(c,b),e&&s.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(s),this.internalTranslation=null==p?null:JU.V3.newV(p));b=null!=j;if(h)return null==
q?(0==f&&(f=NaN),Float.isNaN(f)?this.rotationRate=l:(r=B(Math.abs(f)/Math.abs(l)*this.spinFps+0.5),this.rotationRate=f/r*this.spinFps,null!=p&&this.internalTranslation.scale(1/r)),this.internalRotationAxis.setVA(s,0.017453292519943295*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=!0,this.isSpinFixed=!1,this.isSpinSelected=b):f=l,this.setSpin(a,!0,f,n,q,j,m),!Float.isNaN(f);a=0.017453292519943295*f;this.internalRotationAxis.setVA(s,a);this.rotateAxisAngleRadiansInternal(a,
j,r);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 B(Math.floor(b/100*this.width));case 121:return B(Math.floor(b/100*this.height));case 122:return B(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,l=this.getTranslationXPercent();JV.TransformManager.truncate2(c,b?-l:l);l=this.getTranslationYPercent();JV.TransformManager.truncate2(c,b?-l:l);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(B(this.screenWidth/2),B(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(B(this.screenWidth/2),B(this.screenHeight/2),0);this.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);
var c=JU.P3.new3(B(this.screenWidth/2),B(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);return A(-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,l,f,e){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=l)?2*a:a,this.height=l?2*b:b,this.scaleFitToScreen(!1,
c,f,e))},"~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,l){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),l&&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):B(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=D(this.pointT2.z)}catch(a){if(!F(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 B(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(F(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=B(Math.floor(a.x/100*this.screenWidth)),this.iScrPt.y=B(Math.floor((1-a.y/100)*this.screenHeight))):(this.iScrPt.x=D(a.x),this.iScrPt.y=this.screenHeight-
D(a.y));this.antialias&&(this.iScrPt.x<<=1,this.iScrPt.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.fScrPt);this.iScrPt.z=D(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(D(this.fScrPt.x),D(this.fScrPt.y),D(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,l,f,e,h){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,A(-1,[b,l,K(-1,[c,f,e,h])]));0<e&&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 l=JU.M3.newA9(c);l.invert();var f=c[9],e=-c[10],h=-c[11],j=JU.P3.new3(c[12],c[13],c[14]),m=c[15],p=c[16],n=c[17];this.setPerspectiveDepth(!(0<=n));var n=Math.abs(n)/2,q=Math.tan(3.141592653589793*n/180),n=h*q,q=0.5/q-0.5,r=50/n;0<m&&(m=50+D((h-m)*r),h=50+D((h-p)*r),this.setSlabEnabled(!0),
this.slabToPercent(m),this.depthToPercent(h),21==c.length&&(p=0!=c[18],r=0!=c[19],c=c[20],this.setZShadeEnabled(p),p&&(r?this.vwr.setIntProperty("zSlab",D(Math.min(100,m+c*(h-m)))):this.vwr.setIntProperty("zSlab",D((m+h)/2)),this.vwr.setIntProperty("zDepth",h))));this.moveTo(a,b,j,null,0,l,100,NaN,NaN,n,null,NaN,NaN,NaN,q,f,e);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(b,"moveTo",function(a,b,c,l,f,e,h,j,m,p,n,q,r,s,u,v,x){if(null==e)if(e=new JU.M3,l=JU.V3.newV(l),Float.isNaN(f))e.m00=NaN;else if(0.01>
f&&-0.01<f)e.setScale(1);else{if(0==l.x&&0==l.y&&0==l.z)return;var z=new JU.A4;z.setVA(l,f/57.29577951308232);e.setAA(z)}v==this.cameraSetting.x&&(v=NaN);x==this.cameraSetting.y&&(x=NaN);u==this.cameraDepth&&(u=NaN);Float.isNaN(v)||(j=50*v/p/this.width*this.screenPixelCount);Float.isNaN(x)||(m=50*x/p/this.height*this.screenPixelCount);f=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(p);if(0>=b)this.setAll(c,e,n,h,j,m,p,f,s,q,r,u,v,x),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();
else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm"));var B=this.movetoThread.setManager(this,this.vwr,A(-1,[c,e,n,K(-1,[b,h,j,m,p,f,s,q,r,u,v,x])]));0>=B||this.vwr.g.waitForMoveTo?(0<B&&this.movetoThread.setEval(a),this.movetoThread.run(),this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(C){if(!F(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,l,f,e,h,j,m,p,n,q,r,s){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(q)||this.setCameraDepthPercent(q,!1);!Float.isNaN(r)&&!Float.isNaN(s)&&this.setCamera(r,s);Float.isNaN(l)||this.zoomToPercent(l);Float.isNaN(h)||(this.modelRadius=h);Float.isNaN(j)||(this.scaleDefaultPixelsPerAngstrom=j);!Float.isNaN(f)&&!Float.isNaN(e)&&(this.translateToPercent("x",f),this.translateToPercent("y",
e));1==this.mode&&(!Float.isNaN(p)&&!Float.isNaN(n)&&this.navTranslatePercentOrTo(0,p,n),Float.isNaN(m)||this.setNavigationDepthPercent(m))},"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)),l;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,this.matrixRotate.m11)),l=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),l=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!=l&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,l));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 l=c.m22,f=57.29577951308232*Math.acos(l);0.999<l||-0.999>l?(l=57.29577951308232*Math.atan2(c.m10,
c.m11),c=0):(l=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=l&&(0!=f&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=l&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,l));0!=f&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,f));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,l,f,e,h){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,A(-1,[Float.$valueOf(c),l,f,e,h?Boolean.TRUE:null])),this.spinIsGesture=h,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=D(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,l){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(l,0,0);break;case 89:case 121:c.set(0,l,0);break;case 90:case 122:c.set(0,0,l)}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,l,f,e){var h=1==this.mode?JU.P3.newP(this.navigationCenter):null,j=JU.P3.newP(this.navigationOffset);j.x/=this.width;j.y/=this.height;
this.setScreenParameters0(a,b,c,l,f,e);null!=h&&(this.navigationCenter.setT(h),this.navTranslatePercentOrTo(-1,j.x*this.width,j.y*this.height),this.setNavigatePt(h))},"~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():""})});p("JV");C("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=v(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;r(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,J.api.PlatformViewer]);P(b,function(){this.ptScreen=new JU.P3;this.ptScreenNew=new JU.P3;this.ptNew=new JU.P3});x(b,function(a){M(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);$(this,JV.Viewer,"finalize",[])});c(b,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");b.getJmolVersion=j(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,f,e,h,j,m){var p=new java.util.Hashtable;p.put("display",
a);p.put("adapter",b);p.put("statusListener",j);p.put("platform",m);p.put("options",h);p.put("fullName",c);p.put("documentBase",f);p.put("codeBase",e);return new JV.Viewer(p)},"~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");j(b,"getModelAdapter",function(){return null==this.modelAdapter?this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter:this.modelAdapter});j(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(f){if(F(f,Exception))return!1;throw f;}},"~S,~S");c(b,"hasStructure",function(a,b,c){try{return 1==this.getSmilesMatcher().hasStructure(a,A(-1,[b]),(c?2:1)|8)[0]}catch(f){if(F(f,Exception))return!1;throw f;}},"~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 f=this.fullName.indexOf("__");this.htmlName=0>f?this.fullName:this.fullName.substring(0,f);this.appletName=JU.PT.split(this.htmlName+"_","_")[0];this.syncId=
0>f?"":this.fullName.substring(f+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");f="unknown";null==c&&(c=this.commandOptions.contains("platform=")?
this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if("string"==typeof c){f=c;this.isWebGL=0<=f.indexOf(".awtjs.");JV.Viewer.isJS=this.isJSNoAWT=this.isWebGL||0<=f.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||JV.Viewer.isJS&&a.containsKey("async"));var e=c=null,h="?";self.Jmol&&(e=Jmol,c=Jmol._applets[this.htmlName.split("_object")[0]],h=Jmol._version);null!=h&&(this.html5Applet=c,JV.Viewer.jmolObject=e,JV.Viewer.strJavaVersion=
h,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));c=J.api.Interface.getInterface(f,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);f=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,f);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,
f=b.indexOf("#"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("?"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("/"),0<=f&&(b=b.substring(0,f)),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();
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a)},"~S");j(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");j(b,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.tm.stereoDoubleFull&&(a=B((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,f,e){if(c||!this.creatingImage){var h=
this.antialiased;this.antialiased=e?this.g.antialiasDisplay&&this.checkMotionRendering(603979786):c&&!f?this.g.antialiasImages:!1;!f&&(!c&&(0<a||h!=this.antialiased))&&this.setShapeProperty(5,"clearBoxes",null);this.imageFontScaling=(this.antialiased?2:1)*(e||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||e?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");j(b,"getScreenWidth",function(){return this.screenWidth});j(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 B(this.screenWidth/2)});c(b,"getBoundBoxCenterY",function(){return B(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(f){if(F(f,Error))this.gdata.getScreenImage(b),this.handleError(f,!1),this.setErrorMessage("Error during rendering: "+f,null);else if(F(f,Exception))System.out.println("render error"+f);else throw f;}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,f,e){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,c,f,this.screenWidth,this.screenHeight,e);this.gdata.releaseScreenImage()},"~O,~O,~N,~N,~B");c(b,"getScreenImage",function(){return this.getScreenImageBuffer(null,!0)});j(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,f=this.tm.stereoMode.isBiColor(),
e=null==a&&c;f?(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),f=this.gdata.getScreenImage(b)):f=this.getImage(c,b);var h=null;e&&(h=this.apiPlatform.newBufferedImage(f,this.tm.stereoDoubleDTI?this.screenWidth:this.screenWidth<<1,this.screenHeight),a=this.apiPlatform.getGraphics(h));null!=a&&(c&&(this.tm.stereoMode===
J.c.STER.DTI?(this.drawImage(a,f,this.screenWidth>>1,0,!0),f=this.getImage(!1,!1),this.drawImage(a,f,0,0,!0),a=null):(this.drawImage(a,f,this.screenWidth,0,!1),f=this.getImage(!1,!1))),null!=a&&this.drawImage(a,f,0,0,!1));return e?h:f},"~O,~B");c(b,"evalStringWaitStatusQueued",function(a,b,c,f,e){return null==this.getScriptManager()?null:this.scm.evalStringWaitStatusQueued(a,b,c,f,e)},"~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(f){JU.Logger.info(f.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()});j(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,f=this.am.isMovie;a=this.am.cmi;b==c&&!f&&(a=b);var e=this.getModelFileNumber(a),h=this.am.cmi,j=e,m=e%1E6,p=f?b:this.getModelFileNumber(b),n=f?c:this.getModelFileNumber(c),q;f?q=""+(h+1):0==j?(q=this.getModelNumberDotted(b),b!=c&&(q+=" - "+this.getModelNumberDotted(c)),B(p/1E6)==B(n/1E6)&&(j=p)):q=this.getModelNumberDotted(a);
0!=j&&(j=1E6>j?1:B(j/1E6));f||(this.g.setI("_currentFileNumber",j),this.g.setI("_currentModelNumberInFile",m));b=this.am.currentMorphModel;this.g.setI("_currentFrame",h);this.g.setI("_morphCount",this.am.morphCount);this.g.setF("_currentMorphFrame",b);this.g.setI("_frameID",e);this.g.setI("_modelIndex",a);this.g.setO("_modelNumber",q);this.g.setO("_modelName",0>a?"":this.getModelName(a));e=0>a?"":this.ms.getModelTitle(a);this.g.setO("_modelTitle",null==e?"":e);this.g.setO("_modelFile",0>a?"":this.ms.getModelFileName(a));
this.g.setO("_modelType",0>a?"":this.ms.getModelFileType(a));h==this.prevFrame&&b==this.prevMorphModel||(this.prevFrame=h,this.prevMorphModel=b,e=this.getModelName(h),f?e=""+(""===e?h+1:this.am.caf+1)+": "+e:(f=""+this.getModelNumberDotted(h),e.equals(f)||(e=f+": "+e)),this.sm.setStatusFrameChanged(j,m,0>this.am.animationDirection?-p:p,0>this.am.currentDirection?-n:n,h,b,e),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,f,e,h){this.setErrorMessage(e,null);this.g.setI("_loadPoint",a.getCode());var j=a!==J.c.FIL.CREATING_MODELSET;j&&this.setStatusFrameChanged(!1,!1);this.sm.setFileLoadStatus(b,c,f,e,a.getCode(),j,h);j&&(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,f){this.sm.setStatusMeasuring(a,
b,c,f)},"~S,~N,~S,~N");c(b,"notifyMinimizationStatus",function(){var a=this.getP("_minimizationStep"),b=this.getP("_minimizationForceField"),c=this.getP("_minimizationStatus"),f="starting".equals(c),e="done".equals(c)||"failed".equals(c),h=null!=this.minimizer&&(e||f)?this.minimizer.bsAtoms:null,j=null==h?-1:h.nextSetBit(0),m=0<=j?this.getModelIndexForAtom(j):-1;f&&0<=j&&this.sm.setStatusStructureModified(j,m,3,"minimize:"+c,h.cardinality(),h);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);e&&0<=j&&this.sm.setStatusStructureModified(j,m,-3,"minimize:"+c,h.cardinality(),h)});c(b,"setStatusAtomPicked",function(a,b,c,f){f&&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&&(f=this.getPendingMeasurement(),null!=f&&(b=b.substring(0,b.length-1)+',"'+f.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");j(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:z(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,f){var e=JV.binding.Binding.getButtonMods(c),h=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",e);this.g.setI("_clickCount",h);return this.sm.setStatusClicked(a,this.screenHeight-b,c,h,f)},"~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");j(b,"getImageAsBytes",function(a,b,c,f,e){return this.getOutputManager().getImageAsBytes(a,b,c,f,e)},"~S,~N,~N,~N,~A");j(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):""});j(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(!F(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");j(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,f,e,h,j){this.tm.move(a,b,c,f,e,h,j);this.moveUpdate(h)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(b,"moveTo",function(a,b,c,f,e,h,j,m,p,n,q,r,s,u,v,x,z){this.haveDisplay||(b=0);this.setTainted(!0);
this.tm.moveTo(a,b,c,f,e,h,j,m,p,n,q,r,s,u,v,x,z)},"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");j(b,"rotateFront",function(){this.tm.resetRotation();this.refresh(1,"Viewer:rotateFront()")});c(b,"translate",function(a,b,c,f){var e="\x00"==c?
b:"%"==c?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==c?10:1));if(null!=f){if(0==b)return;this.tm.setSelectedTranslation(f,a,e,b)}else switch(a.charCodeAt(0)){case 88:case 120:"\x00"==c?this.tm.translateToPercent("x",b):this.tm.translateXYBy(D(e),0);break;case 89:case 121:"\x00"==c?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,D(e));break;case 90:case 122:"\x00"==c?this.tm.translateToPercent("z",b):this.tm.translateZBy(D(e))}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,f){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,f);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");j(b,"setVectorScale",function(a){this.g.setF("vectorScale",a);this.g.vectorScale=a},"~N");j(b,"setVibrationScale",function(a){this.tm.setVibrationScale(a);this.g.vibrationScale=a;this.g.setF("vibrationScale",a)},"~N");j(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");j(b,"setColorBackground",function(a){this.setObjectColor("background",a)},"~S");j(b,"getBackgroundArgb",function(){return this.g.objColors[0]});
c(b,"setObjectMad10",function(a,b,c){var f=JV.StateManager.getObjectIdFromName(b.equalsIgnoreCase("axes")?"axis":b);if(!(0>f)){if(-2==c||-4==c){var e=c+3;c=this.getObjectMad10(f);0==c&&(c=e)}this.g.setB("show"+b,0!=c);this.g.objStateOn[f]=0!=c;0!=c&&(this.g.objMad10[f]=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,f){b&&(a=this.getUndeletedGroupAtomBits(a));this.slm.select(a,c,f);this.shm.setShapeSizeBs(1,2147483647,null,null);this.hasSelected=!0},"JU.BS,~B,~N,~B");j(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,f,e){c&&(a=this.getUndeletedGroupAtomBits(a));b?this.slm.display(this.ms,a,f,e):this.slm.hide(this.ms,a,f,e)},"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 z(a,"JU.BS")?a:new JU.BS},"~S");j(b,"selectAll",function(){this.slm.selectAll(!1)});j(b,"clearSelection",function(){this.slm.clearSelection(!0);this.g.setB("hideNotSelected",
!1)});c(b,"bsA",function(){return this.slm.getSelectedAtoms()});j(b,"addSelectionListener",function(a){this.slm.addListener(a)},"J.api.JmolSelectionListener");j(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,f,e){return this.mouse.processEvent(a,b,c,f,e)},"~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");j(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");j(b,"openFileAsyncSpecial",function(a,b){this.getScriptManager().openFileAsync(a,b,null)},"~S,~N");j(b,"openFileAsyncSpecialType",function(a,b,c){this.getScriptManager().openFileAsync(a,b,c)},"~S,~N,~S");
j(b,"openFile",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,a,null,null)},"~S");j(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");j(b,"openDOM",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint("?","?",null,a)},"~O");c(b,"loadModelFromFileRepaint",function(a,b,c,f){a=this.loadModelFromFile(a,
b,c,f,!1,null,null,null,0," ");this.refresh(1,"loadModelFromFileRepaint");return a},"~S,~S,~A,~O");c(b,"loadModelFromFile",function(a,b,c,f,e,h,j,m,p,n){null==h&&(h=this.setLoadParameters(null,e));0!=p&&h.put("dataType",JS.T.nameOf(p));" "!==n&&h.put("concatenate",Boolean.TRUE);var q=this.fm.getFileInfo();if(null!=c){if(null==j){j=(new JU.SB).append("load files");for(a=0;a<c.length;a++)j.append(0==a||null==n?" ":n).append("/*file*/$FILENAME"+(a+1)+"$");0<m.length()&&j.append(" /*options*/ ").append(m.toString())}a=
System.currentTimeMillis();m=this.fm.createAtomSetCollectionFromFiles(c,this.setLoadParameters(h,e),e);a=System.currentTimeMillis()-a;JU.Logger.info("openFiles("+c.length+") "+a+" ms");c=h.get("fullPathNames");n=h.get("fileTypes");j=j.toString();for(a=0;a<c.length;a++)b=c[a],null!=n&&null!=n[a]&&(b=n[a]+"::"+b),j=JU.PT.rep(j,"$FILENAME"+(a+1)+"$",JU.PT.esc(JV.FileManager.fixDOSName(b)));j=(new JU.SB).append(j)}else if(null==f)null==j&&(j=(new JU.SB).append("load /*file*/$FILENAME$")),m=this.openFileFull(b,
e,h,j);else if(z(f,"java.io.Reader")||z(f,"java.io.BufferedInputStream")||JU.AU.isAB(f))m=this.fm.createAtomSetCollectionFromReader(a,b,f,this.setLoadParameters(h,e));else return"ERROR - invalid reader";if(0!=p)return this.fm.setFileInfo(q),this.loadAtomDataAndReturnError(m,p);if(h.containsKey("isData"))return m;null!=j&&"string"!=typeof m&&(b=h.get("fullPathName"),null==b&&(b=""),h.containsKey("loadScript")&&(j=h.get("loadScript")),h.put("loadScript",j=(new JU.SB).append(JU.PT.rep(j.toString(),"$FILENAME$",
JU.PT.esc(JV.FileManager.fixDOSName(b))))));return this.createModelSetAndReturnError(m,e,j,h)},"~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,f){if(null==a){if(null!=this.ligandModelSet)for(a=this.ligandModels.entrySet().iterator();a.hasNext();){var e=a.next();z(e.getValue(),Boolean)&&a.remove()}return null}a=a.$replace("\\",
"/");var h=b.equals("ligand_");a=0<=a.indexOf("/cif")?a:h?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 j=a.indexOf("|");0<=j&&(a=a.substring(a.indexOf("|")+1));var m=null==f?this.ligandModels.get(a):null,e=null;if(z(m,Boolean))return null;if(null==m&&(null==f||0<=j))m=this.ligandModels.get(a+c);var j=!1,p=null==
m;if(p){if(h){e=this.setLoadFormat(!1,"#"+a,"#",!1);if(0==e.length)return null;this.scriptEcho("fetching "+e);m=this.getFileAsString3(e,!1,null)}else this.scriptEcho("fetching "+b),m=this.getFileAsString3(b,!1,null),f=null==f?-1:m.indexOf(f),0<=f&&(m=m.substring(0,f));(j=0==m.indexOf("java."))||this.ligandModels.put(a+c,m)}if(!h)return p||this.scriptEcho(b+" loaded from cache"),m;!j&&"string"==typeof m&&(b=m,0!=b.length&&(c=new java.util.Hashtable,c.put("modelOnly",Boolean.TRUE),m=this.getModelAdapter().getAtomSetCollectionReader("ligand",
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m=0,p=0;for(e=0;e<h;e++)m=a.indexOf(b,p),0>m&&(m=a.length),j[e]=a.substring(p,m),p=m+b.length;return this.openStringsInlineParamsAppend(j,f,c)}return this.openStringInlineParamsAppend(a,f,c)},"~S,~S,~B,java.util.Map");b.fixInlineString=c(b,"fixInlineString",function(a,b){var c;0<=a.indexOf("\\/n")&&(a=JU.PT.rep(a,"\n",""),a=JU.PT.rep(a,"\\/n","\n"),b=String.fromCharCode(0));if(0!=b.charCodeAt(0)&&"\n"!=b){var f=0<=a.indexOf("\n"),e=a.length;for(c=0;c<e&&" "==a.charAt(c);++c);c<e&&a.charAt(c)==b&&
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Error))this.handleError(f,!0),c=this.getShapeErrorState(),c="ERROR adding atom data: "+f+(0==c.length?"":"|"+c),this.zapMsg(c),this.setErrorMessage(c,null),this.setParallel(!1);else throw f;}return this.getErrorMessage()},"~O,~N");c(b,"getCurrentFileAsString",function(a){var b=this.fm.getFullPathName(!1);return b.equals("string")||b.equals("Jmol Model Kit")?this.ms.getInlineData(this.am.cmi):b.equals("String[]")?b:"JSNode"===b?"<DOM NODE>":this.getFileAsString4(b,-1,!0,!1,!1,a)},"~S");c(b,"getFullPathNameOrError",
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b)},"JU.BS,~N");c(b,"getStructureList",function(){return this.g.getStructureList()});c(b,"setStructureList",function(a,b){this.g.setStructureList(a,b);this.ms.setStructureList(this.getStructureList())},"~A,J.c.STR");c(b,"calculateStructures",function(a,b,c,f){null==a&&(a=this.bsA());return this.ms.calculateStructures(a,b,!this.am.animationOn,this.g.dsspCalcHydrogen,c,f)},"JU.BS,~B,~B,~N");c(b,"getAnnotationParser",function(a){return a?null==this.dssrParser?this.dssrParser=J.api.Interface.getOption("dssx.DSSR1",
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this.am.clear(),this.tm.clear(),this.slm.clear(),this.hasSelected=!0,this.clearAllMeasurements(),this.clearMinimization(),this.gdata.clear(),this.mm.zap(),null!=this.scm&&this.scm.clear(!1),null!=this.nmrCalculation&&this.getNMRCalculation().setChemicalShiftReference(null,0),this.haveDisplay&&(this.mouse.clear(),this.clearTimeouts(),this.acm.clear()),this.stm.clear(this.g),this.tempArray.clear(),this.chainMap.clear(),this.chainList.clear(),this.chainCaseSpecified=!1,this.definedAtomSets.clear(),this.lastData=
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h.substring(1),h.equals("?")&&null==(h=this.getDBID("chemical component from RCSB")))return null}else{if(h.equals("?")&&null==(h=this.getDBID("PDB ID from RCSB")))return null;if(0<h.indexOf("/"))try{var j=h.indexOf("/"),m=h.substring(0,j),h=h.substring(j+1);m.equalsIgnoreCase("aflowlib")&&(c=1,j=h.indexOf("."),0<=j&&(c=JU.PT.parseInt(h.substring(j+1)),h=h.substring(0,j)),0>h.indexOf("_")&&(h=this.getSymTemp().getSpaceGroupJSON(this,"AFLOW",h,c)));h=JV.JC.resolveDataBase(m,h,null);null!=h&&h.startsWith("'")&&
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"smiles:"+this.getOpenSmiles(this.bsA())}catch(n){if(!F(n,Exception))throw n;}c=h.toLowerCase();j=-2147483648;try{j=Integer.parseInt(h)}catch(q){if(!F(q,Exception))throw q;}-2147483648!=j?h="cid/"+j:c.startsWith("smiles:")?(e+="?POST?smiles="+h.substring(7),h="smiles"):h.startsWith("cid:")||h.startsWith("inchikey:")||h.startsWith("cas:")?h=h.$replace(":","/"):(c.startsWith("name:")&&(h=h.substring(5)),h="name/"+JU.PT.escapeUrl(h));return JU.PT.formatStringS(e,"FILE",h);case 36:this.checkCIR(!1);if(h.equals("?")&&
null==(h=this.getDBID("structure from NCI/CADD")))return null;if(b.equals("$"))try{h=this.getOpenSmiles(this.bsA())}catch(r){if(!F(r,Exception))throw r;}else if(b.startsWith("$$")){h=h.substring(1);if(0==h.length)try{h=this.getOpenSmiles(this.bsA())}catch(s){if(!F(s,Exception))throw s;}e=JU.PT.rep(this.g.smilesUrlFormat,"get3d","get2d");return JU.PT.formatStringS(e,"FILE",JU.PT.escapeUrl(h))}case 77:case 78:case 50:case 73:case 75:case 83:case 84:case 47:h=JU.PT.escapeUrl(h);switch(c.charCodeAt(0)){case 77:case 78:e=
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b=null;j=h.indexOf(".");0<=j&&(b=h.substring(j+1),h=h.substring(0,j));(m=h.startsWith("density"))&&(h="em"+h.substring(7));if(h.equals("emdb")||h.equals("em"))h+="/";h.startsWith("em/")&&(h="emdb"+h.substring(2));if(h.startsWith("emdb/")){h=h.substring(5);0==h.length?h="=":h.startsWith("*")&&(h="="+h.substring(1));a="#-sigma=10";if(h.startsWith("=")){h=h.equals("=")?this.getPdbID():h.substring(1);if(null==h||"?"==c)break;j=JV.JC.resolveDataBase("emdbquery",h,null);f=this.fm.cacheGet(j,!1);if(null==
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"pdbemapdiff":"pdbemap")+("-"==c?"server":""),h,null);"cif".equals(b)&&(h=h.$replace("bcif","cif"))}return h},"~B,~S,~S,~B");c(b,"getDBID",function(a){return this.prompt("load a "+a,"",null,!1)},"~S");c(b,"checkCIR",function(a){if(!(this.cirChecked&&!a||null==this.g.resolverResolver)){try{this.g.removeParam("_cirStatus");var b=this.getModelSetAuxiliaryInfo();b.remove("cirInfo");var c=this.getFileAsString(this.g.resolverResolver);System.out.println(c);var f=this.parseJSONMap(c);b.put("cirInfo",f);
this.ms.msInfo=b;c=f.get("status");this.g.setO("_cirStatus",c);this.g.setCIR(f.get("rfc6570Template"),!this.isSilent);this.isSilent||JU.Logger.info("Viewer.checkCIR _.cirInfo.status = "+c)}catch(e){System.out.println("Viewer.checkCIR failed at "+this.g.resolverResolver+": "+e)}this.cirChecked=!0}},"~B");c(b,"getStandardLabelFormat",function(a){switch(a){default:case 0:return"%[identify]";case 1:return this.g.defaultLabelXYZ;case 2:return this.g.defaultLabelPDB}},"~N");c(b,"getAdditionalHydrogens",
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this.getAtomInfoXYZ(a,2));if(this.hoverEnabled&&!(null!=this.eval&&this.isScriptExecuting()||a==this.hoverAtomIndex||0==this.g.hoverDelayMs||!this.slm.isInSelectionSubset(a))){var c=b?J.i18n.GT.$("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,f,e){null!=this.eval&&this.isScriptExecuting()||(this.g.setO("_hoverLabel",
c),null!=f&&null!=e&&(this.g.setO("_objecthovered",f),this.g.setI("_atomhovered",-1),this.g.setUserVariable("hovered",JS.SV.getVariable(e)),this.sm.haveHoverCallback()&&this.sm.setStatusObjectHovered(f,c,e)),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(!F(b,Exception))throw b;}});j(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 f=null;if(null!=a){var e=a.indexOf("_");0<=e&&(f=a.substring(e+1),a=a.substring(0,e));b=JV.ActionManager.getPickingMode(a)}0>b&&(b=1);this.acm.setPickingMode(b);e=JV.ActionManager.getPickingModeName(this.acm.getAtomPickingMode());this.g.setO("picking",e);if(null!=this.modelkit)switch(this.modelkit.setProperty("atompickingmode",e),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==f||0==f.length))switch(f=Character.toUpperCase(f.charAt(0))+(1==f.length?"":f.substring(1,2)),b){case 32:this.getModelkit(!1).setProperty("atomType",f);break;case 33:this.setBooleanPropertyTok("bondPicking",603979814,!0);this.getModelkit(!1).setProperty("bondType",f);break;default:JU.Logger.error("Bad picking mode: "+a+"_"+f)}}},"~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)});j(b,"setJmolCallbackListener",function(a){this.sm.cbl=a},"J.api.JmolCallbackListener");j(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,f,e){0==a&&(this.g.setO("_fileDropped",f),this.g.setUserVariable("doDrop",JS.SV.vT),this.g.setUserVariable("dropFileType",JS.SV.newS("")),this.g.setUserVariable("dropFileName",JS.SV.newS(f)));a=this.sm.setStatusDragDropped(a,b,c,f,e);b=this.getP("dropFileType").toString();0<b.length&&null!=e&&(e[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,f){this.sm.setScriptStatus(a,b,c,f)},"~S,~S,~N,~S");j(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});j(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");j(b,"notifyStatusReady",function(a){System.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));a||this.dispose();this.sm.setStatusAppletReady(this.fullName,a)},"~B");j(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");j(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});j(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});j(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");j(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");j(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,D(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",D(c));break;case 570425378:this.setSpin("Y",D(c));break;case 570425380:this.setSpin("Z",D(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",D(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",D(c));break;case 570425400:this.setSpin("y",D(c));break;case 570425402:this.setSpin("z",D(c));break;case 570425396:this.setSpin("fps",D(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=
D(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");j(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");j(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 f=!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:f=!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:f=!1;this.g.bondModeOr=c;break;case 603979978:f=!1;this.g.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979899:f=!1;this.g.rangeSelected=c;break;case 603979877:f=!1;this.g.measureAllModels=c;break;case 603979954:f=!1;this.sm.allowStatusReporting=
c;break;case 603979822:f=!1;this.g.chainCaseSensitive=c;break;case 603979858:f=!1;this.g.hideNameInPopup=c;break;case 603979827:f=!1;this.g.disablePopupMenu=c;break;case 603979847:f=!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);f&&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)});j(b,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");j(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");j(b,"setAutoBond",function(a){this.g.setB("autobond",a);this.g.autoBond=a},"~B");c(b,"makeConnections",function(a,b,c,f,e,h,j,m,p,n){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,
b,c,f,e,h,j,m,p,n)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");j(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");j(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");j(b,"getMadBond",function(){return 2*this.g.bondRadiusMilliAngstroms});j(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",
function(a){this.setObjectMad10(33,"unitcell",a?-2:0);this.g.setB("showUnitCell",a)},"~B");c(b,"getShowUnitCell",function(){return 0!=this.getObjectMad10(5)});c(b,"setShowAxes",function(a){this.setObjectMad10(34,"axes",a?-2:0);this.g.setB("showAxes",a)},"~B");c(b,"getShowAxes",function(){return 0!=this.getObjectMad10(1)});j(b,"setFrankOn",function(a){this.isPreviewOnly&&(a=!1);this.frankOn=a;this.setObjectMad10(36,"frank",a?1:0)},"~B");c(b,"getShowFrank",function(){return this.isPreviewOnly||this.isApplet&&
this.creatingImage?!1:this.isSignedApplet&&!this.isSignedAppletLocal&&!JV.Viewer.isJS||this.frankOn});j(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");j(b,"setRasmolDefaults",function(){this.setDefaultsType("RasMol")});j(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",
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b,c,f,e){var h=0;switch(this.getPickingMode()){case 2:h=5;break;case 4:h=22}return this.shm.checkObjectDragged(a,b,c,f,e,this.getVisibleFramesBitSet(),h)?(this.refresh(1,"checkObjectDragged"),22==h&&this.scriptEcho(this.getShapeProperty(22,"command")),!0):!1},"~N,~N,~N,~N,~N");c(b,"rotateAxisAngleAtCenter",function(a,b,c,f,e,h,j){(a=this.tm.rotateAxisAngleAtCenter(a,b,c,f,e,h,j))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(b,"rotateAboutPointsInternal",function(a,
b,c,f,e,h,j,m,p,n,q){null==a&&(a=this.eval);if(this.headless){if(h&&3.4028235E38==e)return!1;h=!1}(a=this.tm.rotateAboutPointsInternal(a,b,c,f,e,!1,h,j,!1,m,p,n,q))&&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(F(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,f){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,c,f,!1)},"~O,~B,~B,~S");j(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,f){return this.getPropertyManager().getModelCml(a,b,c,f,!1)},"JU.BS,~N,~B,~B");c(b,"getPdbAtomData",function(a,b,c,f){return this.getPropertyManager().getPdbAtomData(null==
a?this.bsA():a,b,c,f,!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,f,e,h,j){1648363544==b&&this.shm.deleteVdwDependentShapes(a);
this.clearMinimization();this.ms.setAtomProperty(a,b,c,f,e,h,j);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 f=
this.ms.at[a.nextSetBit(0)],e=a.cardinality();this.sm.setStatusStructureModified(f.i,f.mi,3,"setAtomCoords",e,a);this.ms.setAtomCoords(a,b,c);this.setStatusAtomMoved(!0,a);this.sm.setStatusStructureModified(f.i,f.mi,-3,"OK",e,a)}},"JU.BS,~N,~O");c(b,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());if(!b.isEmpty()){var c=0!=a.lengthSquared(),f=this.ms.at[b.nextSetBit(0)],e=b.cardinality();c&&this.sm.setStatusStructureModified(f.i,f.mi,3,"setAtomCoords",e,b);this.ms.setAtomCoordsRelative(a,
b);this.checkMinimization();c&&(this.setStatusAtomMoved(!1,b),this.sm.setStatusStructureModified(f.i,f.mi,-3,"OK",e,b))}},"JU.T3,JU.BS");c(b,"invertAtomCoord",function(a,b,c,f,e){if(0<=f){c=JU.JmolMolecule.getBranchesForInversion(this.ms.at,f,this.ms.getMoleculeBitSetForAtom(f));var h=c.cardinality();switch(h){case 0:case 1:return;case 3:case 4:for(var j=E(h,0),m=E(h,0),p=0,n=c.nextSetBit(0);0<=n;n=c.nextSetBit(n+1),p++)j[p]=this.getBranchBitSet(n,f,!0).cardinality(),m[p]=n;for(p=0;p<h-2;p++){for(var q=
-2147483648,r=0,n=0;n<h;n++)j[n]>=q&&c.get(m[n])&&(r=m[n],q=j[n]);c.clear(r)}}e&&!c.isEmpty()&&this.undoMoveActionClear(f,2,!0)}h=c.cardinality();0!=h&&(j=this.ms.at[c.nextSetBit(0)],this.sm.setStatusStructureModified(j.i,j.mi,3,"invertAtomCoords",h,c),this.ms.invertSelected(a,b,f,c),this.setStatusAtomMoved(!0,c),this.sm.setStatusStructureModified(j.i,j.mi,-3,"OK",h,c),e&&this.setStatusAtomPicked(f,"inverted: "+JU.Escape.eBS(c),null,!1))},"JU.P3,JU.P4,JU.BS,~N,~B");c(b,"invertSelected",function(a,
b,c,f){null==f&&(f=this.bsA());f.isEmpty()||(this.ms.invertSelected(a,b,c,f),this.setStatusAtomMoved(!0,f))},"JU.P3,JU.P4,~N,JU.BS");c(b,"moveAtoms",function(a,b,c,f,e,h,j,m){if(!j.isEmpty()){var p=this.getMotionFixedAtoms(null,null);if(!j.intersects(p)){var n=this.getOperativeSymmetry(),q=null;null!=n&&(q=this.ms.saveAtomPositions());this.ms.moveAtoms(a,b,c,f,j,e,h,m);null!=n&&this.getModelkit(!1).checkMovedAtoms(p,j,q);this.setStatusAtomMoved(!0,j)}}},"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,f,e,h,j,m,p,n,q){if(0==c&&null==m||this.isJmolDataFrame())return 0;if(null==m){-2147483648==f&&null!=this.modelkit&&this.setModelkitPropertySafely("rotateBondIndex",Integer.$valueOf(-2147483648));if(-2147483648==a)return this.showSelected=!0,this.movableBitSet=this.setMovableBitSet(null,!n),this.shm.loadShape(8),this.refresh(6,"moveSelected"),
0;if(2147483647==a){if(!this.showSelected)return 0;this.showSelected=!1;this.movableBitSet=null;this.refresh(6,"moveSelected");return 0}}if(this.movingSelected)return 0;this.movingSelected=!0;this.stopMinimization();null==m&&-2147483648!=f&&null!=this.modelkit&&null!=this.modelkit.getProperty("rotateBondIndex")?this.modelkit.actionRotateBond(a,b,f,e,0!=(q&16)):(null==h&&(h=this.bsA()),f=h.nextSetBit(0),h=this.setMovableBitSet(h,!n),h.isEmpty()?(h.set(f),this.sm.setStatusStructureModified(f,this.getModelIndexForAtom(f),
-3,"FAILED",1,h)):p?(j=null==j?this.ms.getAtomSetCenter(h):j,null==m&&(this.tm.finalizeTransformParameters(),m=this.g.antialiasDisplay?2:1,this.tm.transformPt3f(j,this.ptScreen),-2147483648!=c?this.ptScreenNew.set(this.ptScreen.x,this.ptScreen.y,this.ptScreen.z+c):this.ptScreenNew.set(this.ptScreen.x+a*m,this.ptScreen.y+b*m,this.ptScreen.z),this.tm.unTransformPoint(this.ptScreenNew,this.ptNew),m=this.ptNew,null!=this.getOperativeSymmetry()&&(m.sub(j),m.add(this.ms.at[f]),this.getModelkit(!1).cmdAssignMoveAtoms(h,
f,m,null,!0,!n))),Float.isNaN(m.x)||(m.sub(j),this.setAtomCoordsRelative(m,h))):this.tm.rotateXYBy(a,b,h));this.refresh(2,"");this.movingSelected=!1;return null==h?0:h.cardinality()},"~N,~N,~N,~N,~N,JU.BS,JU.P3,JU.P3,~B,~B,~N");c(b,"highlightBond",function(a,b,c,f){if(this.hoverEnabled){b=null;if(0<=a){var e=this.ms.bo[a];b=JU.BSUtil.newAndSetBit(e.atom2.i);b.set(e.atom1.i)}this.highlight(b);this.getModelkit(!1);this.setModelkitPropertySafely("screenXY",E(-1,[c,f]));this.setModelkitPropertySafely("bondIndex",
Integer.$valueOf(a));a=this.setModelkitPropertySafely("hoverLabel",Integer.$valueOf(-2-a));null!=a&&this.hoverOnPt(c,f,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 f=null;if(0==a.indexOf("file:"))f=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==f){a=this.getDataObj(a,null,2);if(null!=a)return a;f=""}a=K(b,c,0);var e=K(b*c,0);JU.Parser.parseStringInfestedFloatArray(f,null,e);for(var h=f=0;f<b;f++)for(var j=0;j<c;j++)a[f][j]=e[h++];return a},
"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,f){var e=null;if(0==a.indexOf("file:"))e=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,c,f);b=Math.abs(b);c=Math.abs(c);f=Math.abs(f);if(null==e){a=this.getDataObj(a,null,2);if(null!=a)return a;e=""}a=K(b,c,f,0);var h=K(b*c*f,0);JU.Parser.parseStringInfestedFloatArray(e,null,h);for(var j=e=0;e<b;e++)for(var m=0;m<c;m++)for(var p=0;p<f;p++)a[e][m][p]=h[j++];return a},"~S,~N,~N,~N");j(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 f=
"/";switch(";inchi;inchikey;stdinchi;stdinchikey;name;image;drawing;names;".indexOf(";"+b+";")){case 0:f="I";break;case 6:f="K";break;case 15:f="T";break;case 24:f="S";break;case 36:f="M";break;case 41:case 47:f="2";break;case 55:f="N"}var e=this.setLoadFormat(!1,"_"+a,f,!1);if("2"==f)return this.fm.loadImage(e,"\u0001"+a,!1),e;"/"==f&&(e=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")?e+("file?format="+b):
e+JU.PT.rep(b," ","%20"));e=this.getFileAsString4(e,-1,!1,!1,!1,"file");"M"==f&&0<e.indexOf("\n")?e=e.substring(0,e.indexOf("\n")):b.equals("jme")&&(e=this.getPropertyManager().fixJMEFormalCharges(c,e));return e},"~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()});j(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");j(b,"writeTextFile",function(a,b){return this.writeFile(a,b,"txt")},"~S,~S");c(b,"writeFile",function(a,b,c){var f=new java.util.Hashtable;f.put("fileName",a);f.put("type",c);f.put("string"==typeof b?"text":"bytes",b);return this.outputToFile(f)},"~S,~O,~S");
j(b,"clipImageOrPasteText",function(a){return!this.haveAccess(JV.Viewer.ACCESS.ALL)?"no":this.getOutputManager().clipImageOrPasteText(a)},"~S");j(b,"getClipboardText",function(){if(!this.haveAccess(JV.Viewer.ACCESS.ALL))return"no";try{return this.getOutputManager().getClipboardText()}catch(a){if(F(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 f=this.getStateInfo(),e=c.get("data");null!=a&&c.put("fileName",a);c.put("type",b);c.put("text",f);z(e,Array)?c.put("scripts",e):z(e,"JU.Lst")&&c.put("imageData",e);return this.getOutputManager().outputToFile(c)},"~S,~S,java.util.Map");j(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");j(b,"syncScript",function(a,b,c){this.sm.syncScript(a,b,c)},"~S,~S,~N");j(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=K(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 f=this.ms.at[c];if(null==f)return 0;var e=f.mi;if(b)return this.deleteModels(e,a);this.sm.setStatusStructureModified(c,f.mi,4,"deleting atoms "+a,a.cardinality(),a);this.ms.deleteAtoms(a);
f=this.slm.deleteAtoms(a);this.setTainted(!0);this.sm.setStatusStructureModified(c,e,-4,"OK",f,a);return f},"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 f=b.cardinality(),e=this.am.cmi;this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var h=JU.BSUtil.copy(this.slm.bsDeleted),c=this.ms.deleteModels(c);if(null==c)return this.setCurrentModelIndexClear(e,
!1),0;this.sm.setStatusStructureModified(-1,a,5,"deleting model "+this.getModelNumberDotted(a),f,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!=h&&c.andNot(h);f=JU.BSUtil.cardinalityOf(c);
this.sm.setStatusStructureModified(-1,a,-5,"OK",f,c);return f},"~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,f){var e=f.cardinality();0!=e&&(this.sm.setStatusStructureModified(-1,a,7,"delete atoms "+JU.Escape.eBS(f),
e,f),JU.BSUtil.deleteBits(this.tm.bsFrameOffsets,f),this.getDataManager().deleteModelAtoms(b,c,f),this.sm.setStatusStructureModified(-1,a,-7,"OK",e,f))},"~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,f){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(K(-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!=f&&(f.mustResumeEval=!0,this.eval.resumeEval(f));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");j(b,"getErrorMessage",function(){return this.errorMessage});j(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(f){}}},"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(!F(a,Exception))throw a;}this.echoMessage(this.getP("_minimizationForceField")+" Energy = "+this.getP("_minimizationEnergy"))}});
c(b,"minimize",function(a,b,c,f,e,h,j,m){var p=null!=f;p&&(m|=2);var n=0!=(m&16),q=0!=(m&256),r=0!=(m&1),s=0!=(m&8),u=0!=(m&64),v=u||0!=(m&32),x=null!=e;this.isModelKitOpen()&&this.setModelkitPropertySafely("constraint",null);null==h&&(h=this.getFrameAtoms());!s&&(!n&&p&&!x&&!v)&&(x=JU.BSUtil.copy(h),e=JU.BSUtil.copy(x),e.andNot(f),f=x,x=!0);p?s||f.and(h):(f=this.getThisModelAtoms(),v&&f.and(this.bsA()));if(!f.isEmpty())if(p=q||!v?JU.BSUtil.copy(this.ms.am[this.ms.at[f.nextSetBit(0)].mi].bsAsymmetricUnit):
null,q&&null==p)this.scriptStatusMsg("MODELKIT MINIMIZE is only applicable to crystal structures.","minimization: not a crystal structure");else try{if(q)this.getModelkit(!1).cmdMinimize(a,p,b,c,j,m);else{var z=null==p?this.g.forceField:"UFF";this.getModelForAtomIndex(f.nextSetBit(0)).auxiliaryInfo.put("dimension","3D");s&&(h=f);var A=JU.BSUtil.copy(x?e:this.slm.getMotionFixedAtoms()),B=!A.isEmpty();B&&f.andNot(A);var C=null!=p&&q?this.getThisModelAtoms():v||!B?new JU.BS:this.ms.getAtomsWithinRadius(0>=
j?5:j,f,!0,null,null);C.andNot(f);B?A.and(C):A=C;A.and(h);m|=(B?4:0)|(this.getBooleanProperty("minimizationSilent")?1:0);if(!s||!this.getBoolean(603979962)){if(s)try{r||JU.Logger.info("Minimizing "+f.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,c,f,A,null,m,"UFF")}catch(D){if(F(D,Exception))JU.Logger.error("Minimization error: "+D.toString()),D.printStackTrace();else throw D;}if(n){var E=this.addHydrogens(f,m);s||f.or(E)}var H=f.cardinality();if(z.equals("MMFF")&&H>this.g.minimizationMaxAtoms)this.scriptStatusMsg("Too many atoms for minimization ("+
H+">"+this.g.minimizationMaxAtoms+"); use 'set minimizationMaxAtoms' to increase this limit","minimization: too many atoms");else if(u&&(A.or(this.ms.getConnectingAtoms(f,A)),f.andNot(A)),r||JU.Logger.info("Minimizing "+f.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,c,f,A,p,m,s?"MMFF":z),s){this.g.forceField="MMFF";this.setHydrogens(f);var I=this.getMinimizer(!1).getForceFieldUsed();null!=I&&this.showString("Minimized by Jmol using "+I,!1)}}}}catch(K){if(F(K,"JV.JmolAsyncException"))null!=
a&&a.loadFileResourceAsync(K.getFileName());else if(F(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 f=b[c];if(!(null==f||0==f.length))for(var e=this.ms.at[c],h=e.bonds,j=0,m=0,p=e.getBondCount();j<p;j++){var n=h[j].getOtherAtom(e);if(1==n.getAtomicAndIsotopeNumber()){var q=
f[m++];null!=q&&this.ms.setAtomCoord(n.i,q.x,q.y,q.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,f,e){this.getStateCreator().getAtomicPropertyStateBuffer(a,b,c,f,e)},"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,f){return this.getOutputManager().writeFileData(a,b,c,f)},"~S,~S,~N,~A");c(b,"getPdbData",function(a,b,c,f,e,h){return this.getPropertyManager().getPdbData(a,b,null==c?this.bsA():c,f,e,h)},"~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||!z(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,f,e,h){this.stopMinimization();var j=null!=e&&0==b,m=this.ms.at[a];null==h&&(h=JU.BSUtil.newAndSetBit(a),(null==this.getOperativeSymmetry()||this.isModelKitOpen()&&!this.modelkit.hasConstraint(a,!0,!1))&&!j&&this.ms.addConnectedHAtoms(m,h));return this.moveSelected(b,c,f,-2147483648,
-2147483648,h,m,e,!0,!0,0)},"~N,~N,~N,~N,JU.P3,JU.BS");c(b,"isModelPDB",function(a){return this.ms.am[a].isBioModel},"~N");j(b,"deleteMeasurement",function(a){this.setShapeProperty(6,"delete",Integer.$valueOf(a))},"~N");j(b,"getSmiles",function(a){return this.getSmilesOpt(a,-1,-1,16|(null==a&&JU.Logger.debugging?131072:0),null)},"JU.BS");j(b,"getOpenSmiles",function(a){return this.getSmilesOpt(a,-1,-1,5|(null==a&&JU.Logger.debugging?131072:0),"/open///")},"JU.BS");c(b,"getBioSmiles",function(a){return this.getSmilesOpt(a,
-1,-1,24117248|(JU.Logger.debugging?131072:0),null)},"JU.BS");c(b,"getSmilesOpt",function(a,b,c,f,e){var h=17825792==(f&17825792)?JV.Viewer.getJmolVersion()+" "+this.getModelName(this.am.cmi):e,j=this.ms.at;null==a&&(0>b||0>c?a=this.bsA():(1048576==(f&1048576)&&(b>c&&(a=b,b=c,c=a),b=j[b].group.firstAtomIndex,c=j[c].group.lastAtomIndex),a=new JU.BS,a.setBits(b,c+1)));f|=this.isModel2D(a)?134217728:0;b=this.getSmilesMatcher();return JV.JC.isSmilesCanonical(e)?(f=b.getSmiles(j,this.ms.ac,a,"/noAromatic/",
f),this.getChemicalInfo(f,"smiles",null).trim()):b.getSmiles(j,this.ms.ac,a,h,f)},"JU.BS,~N,~N,~N,~S");c(b,"isModel2D",function(a){a=this.getModelForAtomIndex(a.nextSetBit(0));return null!=a&&"2D".equals(a.auxiliaryInfo.get("dimension"))},"JU.BS");c(b,"alert",function(a){this.prompt(a,null,null,!0)},"~S");c(b,"prompt",function(a,b,c,f){return this.$isKiosk?"null":this.apiPlatform.prompt(a,b,c,f)},"~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"),f=a.get("fullPath"),c=this.getOutputChannel(c,f);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});j(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,f=null;0<=a&&(b&&this.setPicked(-1,
!1),this.g.setI("_atompicked",a),c=this.g.getParam("picked",!0),f=this.g.getParam("pickedList",!0));if(null==c||10!=c.tok)c=JS.SV.newV(10,new JU.BS),f=JS.SV.getVariableList(new JU.Lst),this.g.setUserVariable("picked",c),this.g.setUserVariable("pickedList",f);0>a||(JS.SV.getBitSet(c,!1).set(a),c=f.pushPop(null,null),10==c.tok&&f.pushPop(null,c),(10!=c.tok||!c.value.get(a))&&f.pushPop(null,JS.SV.newV(10,JU.BSUtil.newAndSetBit(a))))},"~N,~B");j(b,"runScript",function(a){return""+this.evaluateExpression(A(-1,
[A(-1,[JS.T.tokenScript,JS.T.tokenLeftParen,JS.SV.newS(a),JS.T.tokenRightParen])]))},"~S");j(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(F(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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