(function(fb,gc,hc,ic,G,jc,R,ba,S,T,I,A,kc,Y,lc,$,u,x,za,ca,ja,g,Ha,da,pa,qa,ua,D,mc,nc,Ia,oc,pc,qc,rc,Ja,gb,sc,tc,uc,vc,wc,xc,yc,zc,Ac,Bc,Cc,Dc,Ec,Fc,Gc,Hc,Ic,Jc,e,l){R("JS");S(null,"JS.ScriptExt",["JU.AU"],function(){var d=I(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;T(this,arguments)},JS,"ScriptExt",null);e(d,"init",function(a){this.e=a;this.vwr=this.e.vwr;return this},"~O");e(d,"atomExpressionAt",function(a){return this.e.atomExpressionAt(a)},"~N");e(d,"checkLength",
function(a){this.e.checkLength(a)},"~N");e(d,"error",function(a){this.e.error(a)},"~N");e(d,"invArg",function(){this.e.invArg()});e(d,"invPO",function(){this.error(23)});e(d,"getShapeProperty",function(a,b){return this.e.getShapeProperty(a,b)},"~N,~S");e(d,"paramAsStr",function(a){return this.e.paramAsStr(a)},"~N");e(d,"centerParameter",function(a){return this.e.centerParameter(a,null)},"~N");e(d,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");e(d,"getPoint3f",function(a,b){return this.e.getPoint3f(a,
b,!0)},"~N,~B");e(d,"intParameter",function(a){return this.e.intParameter(a)},"~N");e(d,"isFloatParameter",function(a){switch(this.e.tokAt(a)){case 2:case 3:return!0}return!1},"~N");e(d,"setShapeProperty",function(a,b,c){this.e.setShapeProperty(a,b,c)},"~N,~S,~O");e(d,"showString",function(a){this.e.showString(a)},"~S");e(d,"stringParameter",function(a){return this.e.stringParameter(a)},"~N");e(d,"getToken",function(a){return this.e.getToken(a)},"~N");e(d,"tokAt",function(a){return this.e.tokAt(a)},
"~N");e(d,"setShapeId",function(a,b,c){c&&this.invArg();b=this.e.setShapeNameParameter(b).toLowerCase();this.setShapeProperty(a,"thisID",b);return b},"~N,~N,~B");e(d,"getColorTrans",function(a,b,c,f){c=3.4028235E38;1765808134!=a.theTok&&--b;switch(this.tokAt(b+1)){case 603979967:b++;c=this.isFloatParameter(b+1)?a.getTranslucentLevel(++b):this.vwr.getFloat(570425353);break;case 1073742074:b++,c=0}a.isColorParam(b+1)?f[0]=a.getArgbParam(++b):1073742333==this.tokAt(b+1)?(f[0]=0,a.iToken=b+1):3.4028235E38==
c?this.invArg():f[0]=-2147483648;return c},"JS.ScriptEval,~N,~B,~A");e(d,"finalizeObject",function(a,b,c,f,z,r,d,v){z&&this.setShapeProperty(a,"set",r);-2147483648!=b&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(b),v);3.4028235E38!=c&&this.e.setShapeTranslucency(a,"","translucent",c,v);0!=f&&this.setShapeProperty(a,"scale",Integer.$valueOf(f));0<d&&(this.e.setMeshDisplayProperty(a,d,0)||this.invArg())},"~N,~N,~N,~N,~B,~O,~N,JU.BS");e(d,"getIntArray2",function(a){a=this.e.getToken(a).getList();
for(var b=JU.AU.newInt2(a.size()),c=b.length;0<=--c;){var f=a.get(c).getList();null==f&&this.invArg();b[c]=u(f.size(),0);for(var z=b[c].length;0<=--z;)b[c][z]=f.get(z).intValue}return b},"~N");e(d,"getAllPoints",function(a,b){var c=null,f=null;try{switch(this.e.tokAt(a)){case 7:c=this.e.getPointArray(a,-1,!1);break;case 12290:case 10:case 1073742325:f=this.atomExpressionAt(a)}null==c&&(null==f&&(f=this.vwr.getAllAtoms()),c=this.bsToArray(f))}catch(z){if(!$(z,Exception))throw z;}(null==c||c.length<
b)&&this.invArg();return c},"~N,~N");e(d,"bsToArray",function(a){for(var b=Array(a.cardinality()),c=a.nextSetBit(0),f=0;0<=c;c=a.nextSetBit(c+1))b[f++]=this.vwr.ms.at[c];return b},"JU.BS")});R("JS");S(["JS.ScriptExt"],"JS.IsoExt","JU.AU $.BS $.Lst $.M4 $.Measure $.P3 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.c.VDW JS.SV $.ScriptEval $.ScriptInterruption $.T JU.BSUtil $.BoxInfo $.C $.Escape $.Logger $.Parser $.TempArray $.Triangulator JV.JC".split(" "),function(){var d=za(JS,"IsoExt",
JS.ScriptExt);Y(d,function(){ja(this,JS.IsoExt,[])});l(d,"dispatch",function(a,b,c){this.chk=this.e.chk;this.slen=this.e.slen;this.st=c;switch(a){case 23:this.cgo();break;case 25:this.contact();break;case 17:this.dipole();break;case 22:this.draw();break;case 24:case 30:case 29:this.isosurface(a);break;case 26:this.lcaoCartoon();break;case 27:case 28:this.mo(b,a)}return null},"~N,~B,~A");e(d,"dipole",function(){var a=this.e,b=null,c=null,f=!1,z=!1,r=!1,d=!1,v=null;a.sm.loadShape(17);if(!(1073742001==
this.tokAt(1)&&this.listIsosurface(17)))if(this.setShapeProperty(17,"init",null),1==this.slen)this.setShapeProperty(17,"thisID",null);else{for(var e=1;e<this.slen;++e){c=b=null;switch(this.getToken(e).tok){case 1073742327:b="all";d=!0;break;case 1073742335:b="on";break;case 1073742334:b="off";break;case 12291:b="delete";break;case 2:case 3:b="value";c=Float.$valueOf(this.floatParameter(e));break;case 10:10==this.tokAt(e+1)?this.setShapeProperty(17,"startSet",this.atomExpressionAt(e++)):b="atomBitset";
case 1073742325:null==b&&(b=f||z?"endSet":"startSet");c=v=this.atomExpressionAt(e);e=a.iToken;0==this.tokAt(e+1)&&"startSet"===b&&(b="atomBitset");d=f=!0;break;case 1073742332:case 8:c=this.getPoint3f(e,!0);e=a.iToken;b=f||z?"endCoord":"startCoord";z=!0;break;case 1677721602:b="bonds";d=!0;break;case 4102:d=!0;b="calculate";a.isAtomExpression(e+1)&&(c=v=this.atomExpressionAt(++e),e=a.iToken);break;case 1073741974:this.setShapeId(17,++e,r);e=a.iToken;break;case 1275069442:b="cross";c=Boolean.TRUE;
break;case 1073742040:b="cross";c=Boolean.FALSE;break;case 1073742066:this.isFloatParameter(e+1)?(c=this.floatParameter(++e),2==a.theTok?(b="offsetPercent",c=Integer.$valueOf(A(c))):(b="offset",c=Float.$valueOf(c))):(b="offsetPt",c=this.centerParameter(++e),e=a.iToken);break;case 1073742068:b="offsetSide";c=Float.$valueOf(this.floatParameter(++e));break;case 1073742188:b="value";c=Float.$valueOf(this.floatParameter(++e));break;case 1073742196:b="width";c=Float.$valueOf(this.floatParameter(++e));break;
default:if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(17,e,r);e=a.iToken;break}this.invArg()}r=12291!=a.theTok&&4102!=a.theTok;d&&(this.chk||a.getPartialCharges(v),d=!1);null!=b&&this.setShapeProperty(17,b,c)}(z||f)&&this.setShapeProperty(17,"set",null)}});e(d,"draw",function(){var a=this.e;a.sm.loadShape(22);switch(this.tokAt(1)){case 1073742001:if(this.listIsosurface(22))return;break;case 136314895:case 134221850:case 4138:this.e.getCmdExt().dispatch(4133,!1,this.st);
return}for(var b=!1,c=!1,f=!1,z=!1,r=!1,d,e=null,j=0,n=3.4028235E38,k=u(-1,[-2147483648]),g=0,q="",N=0,w=null,na=this.initIsosurface(22),l=(d=null!=na)&&null==this.getShapeProperty(22,"ID"),x=null,Ka=0,ea=-1,P=-1,K=!1,F=0,C=null,p=a.iToken;p<this.slen;++p){var L=null,H=null,F=this.getToken(p).tok;switch(F){case 134217763:switch(F=this.getToken(p+(1073741864==this.tokAt(p+1)?2:1)).tok){case 1814695966:case 1812599299:j=F;z=!0;continue;case 1073742330:++p;L="intersect";H=a.objectNameParameter(++p);
b=z=!0;break;default:this.invArg()}break;case 1073741864:K=!0;P==p-1&&P++;switch(this.tokAt(p+1)){case 134217750:case 1073741998:case 1812599299:continue;default:this.invArg()}break;case 1073741994:case 1814695966:case 1812599299:var O=d=C=null;switch(F){case 1812599299:switch(this.tokAt(p+1)){case 1073741864:switch(this.tokAt(p+2)){case 134217750:case 1073741998:break;case 1073742330:e=D(-1,[a.objectNameParameter(p+3),null]);if(this.chk)return;this.vwr.shm.getShapePropertyData(24,"points",e);e=e[1];
null==e&&this.invArg();p+=2;default:K=!0,p++}break;case 10:case 1073742325:O=a.getAtomsStartingAt(p+1),p=a.iToken}break;case 1814695966:K&&this.invArg(),a.isArrayParameter(p+1)&&(d=this.vwr.getSymTemp().getUnitCell(a.getPointArray(p+1,-1,!1),!1,null),p=a.iToken),1073741994==this.tokAt(p+1)&&(1814695966==j&&(j=1073741994),++p,C=a.checkHKL(a.getPointOrPlane(++p,3)),p=a.iToken)}if(this.chk)break;null!=O?K&&(d=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,"array",O,null),!1,null)):
K?d=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,"array",null,e),!1,null):1814695966==F&&null==d&&(d=this.vwr.getCurrentUnitCell());if(null==C)e=this.getBoxPoints(null!=d?1814695966:F,d,O,g/100);else{O=JU.Measure.getLatticePoints(d.getLatticeCentering(),A(C.x),A(C.y),A(C.z));e=Array(O.size());for(F=0;F<O.size();F++)e[F]=O.get(F),d.toCartesian(e[F],!0)}K=!1;if(!z){null==e&&this.invArg();L="polygon";d=new JU.Lst;d.addLast(e);null==C?(this.vwr.getTriangulator(),d.addLast(JU.Triangulator.fullCubePolygon)):
d.addLast(null);H=d;b=!0;g=0;break}1073742335==this.tokAt(p+1)&&(P=++p);break;case 1073741998:case 134219777:case 134217750:C=P==p-1;if(!b&&!z&&0==j){if(134219777==a.theTok){b=!0;this.setShapeProperty(22,"plane",null);F=new JU.Lst;a.hklParameter(++p,F,!0);p=a.iToken;L="coords";H=F;break}if(!K){L=134217750==F?"plane":"line";ea=p+1;break}!this.chk&&(1073741998!=F&&null==e)&&(d=this.vwr.getCurrentUnitCell(),j=null==d?1812599299:1814695966,e=this.getBoxPoints(j,d,null,g/100),z=!0)}var O=d=null,G=!1;switch(F){case 134217750:d=
a.planeParameter(p,K);break;case 134219777:d=a.hklParameter(++p,null,!0);1073742327==this.tokAt(a.iToken+1)&&(G=!0,a.iToken++);break;case 1073741998:1073741994==j&&this.invArg(),O=K?this.bsToArray(a.getAtomsStartingAt(++p)):a.isCenterParameter(p+1)?D(-1,[this.centerParameter(++p),this.centerParameter(a.iToken+1)]):a.getPointArray(++p,2,!1),2>O.length&&this.invArg()}p=a.iToken;b=!0;if(this.chk)break;if(1073741998==F){O=JU.Measure.getBestLineThroughPoints(O,-1);if(0!=j&&(d=JU.V3.newVsub(O[1],O[0]),
d.scale(1/d.length()),O=C?JU.Measure.getProjectedLineSegment(e,-1,O[0],d,null):this.vwr.getTriangulator().intersectLine(e,-1,O[0],d),null==O||null==O[1]))return;c||(this.setShapeProperty(22,"points",Integer.$valueOf(g)),c=!0);F=new JU.Lst;F.addLast(O[0]);F.addLast(O[1]);this.setShapeProperty(22,"coords",F);break}0==j?(H=d,L="planedef"):(1073741994==j?(L="polygon",O=JU.Measure.getPointsOnPlane(e,d),e=O.toArray(Array(O.size())),d=new JU.Lst,d.addLast(e),d.addLast(null),H=d):(G&&1814695966==j&&J.api.Interface.getInterface("JU.BZone",
this.vwr,"script").drawHKL(this.vwr,na,d,e),L="polygon",H=this.vwr.getTriangulator().intersectPlane(d,e,C?-1:0)),g=0);break;case 1275068447:e=a.isArrayParameter(++p)?a.getPointArray(p,-1,!1):null;null==e&&a.isAtomExpression(p)&&(O=a.atomExpressionAt(p),e=this.vwr.ms.getAtomPointVector(O).toArray(Array(O.cardinality())));null!=e&&(p=a.iToken+1,12289==this.tokAt(p)&&(w=a.centerParameter(++p,null),p=a.iToken+1));switch(this.tokAt(p)){case 536875059:c="";break;case 1111490563:c="Cs";break;case 1073742330:e=
D(-1,[a.objectNameParameter(++p),null]);if(this.chk)return;this.vwr.shm.getShapePropertyData(21,"points",e);e=e[1];null==e&&this.invArg();c="";break;case 1275203608:c=":poly";break;case 134217764:null==w&&(w=new JU.P3);c=this.vwr.ms.generateCrystalClass(this.vwr.bsA().nextSetBit(0),JU.P3.new3(NaN,NaN,NaN));null!=e&&this.invArg();e=Array(c.size());for(F=c.size();0<=--F;)e[F]=c.get(F);p++;c="";break;default:c=a.optParameterAsString(p)}g=0==g?1:g/100;f=0;0<c.length&&this.isFloatParameter(++p)&&(f=this.intParameter(p++));
536875059==this.tokAt(p)&&(g=this.floatParameter(++p));this.chk||a.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),c,f,g,e,w,null==na?"":na));return;case 4106:x=u(4,0);Ka=4;b=a.floatParameterSet(++p,4,4);p=a.iToken;for(F=0;4>F;F++)x[F]=A(b[F]);b=!0;break;case 1677721602:case 1153433601:if(null==x||Ka>(1228931586==a.theTok?2:3))Ka=0,x=u(-1,[-1,-1,-1,-1]);x[Ka++]=this.atomExpressionAt(++p).nextSetBit(0);p=a.iToken;x[Ka++]=1677721602==a.theTok?this.atomExpressionAt(++p).nextSetBit(0):-1;p=
a.iToken;b=!0;break;case 554176565:switch(this.getToken(++p).tok){case 1073742330:L="slab";H=a.objectNameParameter(++p);p=a.iToken;b=!0;break;default:this.invArg()}break;case 1275203608:case 134217751:case 1073742106:C=134217751==F;L="polygon";b=!0;d=new JU.Lst;var Q=0,H=0,X=G=O=null;if(a.isArrayParameter(++p)){O=a.getPointArray(p,-1,!0);if(0<O.length&&null==O[0]){1275203608==F?Q=this.getIntArray2(p):(Q=JU.AU.newInt2(1),Q[0]=a.expandFloatArray(a.floatParameterSet(p,-1,2147483647),-1,!1));O=this.getAllPoints(this.e.iToken+
1,3);try{X=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulateFaces(Q,O,null)}catch(R){this.invArg()}}Q=O.length}1275203608==F&&(Q=O.length);if(null==O){Q=Math.max(0,this.intParameter(p));O=Array(Q);for(F=0;F<Q;F++)O[F]=this.centerParameter(++a.iToken)}p=a.iToken;switch(this.tokAt(p+1)){case 11:case 12:G=JS.SV.newT(this.getToken(++p)).toArray().getList();H=G.size();break;case 7:G=this.getToken(++p).getList();H=G.size();break;case 2:H=this.intParameter(++p);0>H&&(C=
!0);break;default:null==X&&(!C&&!this.chk)&&(X=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulatePolygon(O,-1))}if(null==X&&!C){X=JU.AU.newInt2(H);for(F=0;F<H;F++)C=null==G?a.floatParameterSet(++a.iToken,3,4):JS.SV.flistValue(G.get(F),0),(3>C.length||4<C.length)&&this.invArg(),X[F]=u(-1,[A(C[0]),A(C[1]),A(C[2]),3==C.length?7:A(C[3])])}0<Q?(d.addLast(O),d.addLast(X)):d=null;H=d;p=a.iToken;break;case 134217764:case 1296041985:e=null;c=2147483647;n=f=null;z=0;j=r=null;
k=1296041985==F;N=-1;l=D(-1,[null,this.vwr.getFrameAtoms()]);if(k)switch(c=0,this.tokAt(++p)){case 4:e=this.stringParameter(p);break;case 12:e=JS.SV.sValue(this.getToken(p));break;default:if(!a.isCenterParameter(p))if(a.isArrayParameter(p)){p=a.floatParameterSet(p,1,2147483647);j=u(p.length,0);for(F=j.length;0<=--F;)j[F]=A(p[F]);p=a.iToken+1}else c=this.intParameter(p++),a.isArrayParameter(p)&&(r=JU.P3.newA(a.floatParameterSet(p,3,3)),p=a.iToken+1);a.isCenterParameter(p)&&(w=a.centerParameter(p,l));
null==j&&a.isCenterParameter(a.iToken+1)&&(f=a.centerParameter(++a.iToken,l));if(this.chk)return;p=a.iToken;null==w&&p+1<this.slen&&(w=this.centerParameter(++p),n=a.isAtomExpression(p)?this.atomExpressionAt(p):null,p=a.iToken);N=(!k||null!=f)&&2==this.tokAt(p+1)?a.getToken(++p).intValue:-1;-1>N&&this.invArg();1814695966==this.tokAt(p+1)?(f=new JU.P3,z=1073742066,a.iToken=++p):1073742066==this.tokAt(p+1)&&(p++,f=this.getPoint3f(p+1,!1),z=1073742066,p=a.iToken)}else 1073742327==this.tokAt(p+1)&&(N=
-2,a.iToken=++p);null!=e&&(p++,a.isCenterParameter(p)&&(w=a.centerParameter(p,l)));a.checkLast(a.iToken);if(this.chk)return;p="";l=null!=n?n.nextSetBit(0):-1;null==n&&0<=this.vwr.am.cmi&&(n=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi));null!=n&&(p=null,0!=z&&(n=this.vwr.getSymmetryInfo(l,e,c,r,w,f,134217751,null,g/100,N,z,j),ba(n,"JU.P3")?f=n:p=""),null==na&&(na=k?"sym":"sg"),null==p&&(p=this.vwr.getSymmetryInfo(l,e,c,r,w,f,135176,na,g/100,N,z,j)),p="draw ID "+(k?"sg":"sym")+"* delete;"+
p,p="draw ID "+na+"* delete;"+p+";draw *;");a.runBufferedSafely(0<p.length?p:'draw ID "'+na+'*" delete',a.outputBuffer);return;case 4115:r=!0;continue;case 1073742332:case 9:case 8:if(9==a.theTok||!a.isPoint3f(p)){H=a.getPoint4f(p);if(r){a.checkLast(a.iToken);this.chk||a.runScript(JU.Escape.drawQuat(JU.Quat.newP4(H),null==na?"frame":na," "+q,null==w?new JU.P3:w,g/100));return}L="planedef"}else H=w=this.getPoint3f(p,!0),L="coord";p=a.iToken;b=!0;break;case 1073742E3:L="lineData";H=a.floatParameterSet(++p,
0,2147483647);p=a.iToken;b=!0;break;case 12290:case 10:case 1073742325:L="atomSet";H=this.atomExpressionAt(p);r&&(w=this.centerParameter(p));p=a.iToken;b=!0;break;case 7:b=!0;L=ea==p?"coords":"modelBasedPoints";H=a.theToken.value;break;case 1073742195:case 268436992:break;case 268437504:H=a.xypParameter(p);if(null!=H){p=a.iToken;L="coord";b=!0;break}f&&this.invArg();f=!0;break;case 268437505:f||this.invArg();f=!1;break;case 1140850693:L="reverse";break;case 1073742166:if(1765808134==this.tokAt(++p)){H=
Integer.$valueOf(this.e.getArgbParamOrNone(++p,!1));L="titlecolor";p=this.e.iToken;break}if(4114==this.tokAt(p)){--p;continue}case 4:H=this.stringParameter(p);L="title";break;case 545259562:H=this.stringParameter(++p);L="hoverlabel";break;case 4114:F=this.floatParameter(++p);H=1073741824==this.tokAt(p+1)?this.paramAsStr(++p):null;d=1073741824==this.tokAt(p+1)?this.paramAsStr(++p):null;(4!=this.tokAt(p+1)&&++p!=this.slen||0>=F||255<F)&&this.invArg();L="myfont";if(null==H||null==d)C=this.vwr.shm.getShapePropertyIndex(22,
"font",-1),null==H&&(H=C.fontFace),null==d&&(d=C.fontStyle);H=this.vwr.getFont3D(H,d,F);break;case 135198:L="vector";break;case 1140850691:H=Float.$valueOf(this.floatParameter(++p));L="length";break;case 3:H=Float.$valueOf(this.floatParameter(p));L="length";break;case 1094713359:L="modelIndex";H=Integer.$valueOf(this.intParameter(++p));break;case 2:f?(L="modelIndex",H=Integer.$valueOf(this.intParameter(p))):g=this.intParameter(p);break;case 536875059:g=Math.round(this.floatParameter(++p)*(2==this.getToken(p).tok?
1:100));continue;case 1073741974:na=this.setShapeId(22,++p,d);l=null==this.getShapeProperty(22,"ID");p=a.iToken;break;case 1073742027:L="fixed";H=Boolean.FALSE;break;case 12293:L="fixed";H=Boolean.TRUE;break;case 1073742066:F=this.getPoint3f(++p,!0);p=a.iToken;L="offset";H=F;break;case 1073741906:L="crossed";break;case 1073742196:H=Float.$valueOf(this.floatParameter(++p));L="width";q=L+" "+H;break;case 1073741908:L="curve";ea=p+1;break;case 1073741840:L="arc";ea=p+1;break;case 1073741846:L="arrow";
ea=p+1;break;case 1073742194:L="vertices";ea=p+1;break;case 1073741880:L="circle";break;case 1073741912:L="cylinder";break;case 1073742048:L="nohead";break;case 1073741860:L="isbarb";break;case 1073742130:L="rotate45";break;case 1073742092:L="perp";break;case 1665140738:case 1073741917:q=1665140738==a.theTok;C=this.floatParameter(++p);q&&(C*=2);H=Float.$valueOf(C);L=q||3==this.tokAt(p)?"width":"diameter";q=L+(3==this.tokAt(p)?" "+C:" "+A(C));break;case 1073742330:if(268437504==this.tokAt(p+2)||r){b=
w=this.centerParameter(p);p=a.iToken;L="coord";H=b;b=!0;break}H=a.objectNameParameter(++p);L="identifier";b=!0;break;case 1765808134:case 603979967:case 1073742074:d=!0;n=this.getColorTrans(a,p,!1,k);p=a.iToken;continue;default:if(!a.setMeshDisplayProperty(22,0,a.theTok)){if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){na=this.setShapeId(22,p,d);p=a.iToken;break}this.invArg()}0==N&&(N=p);p=a.iToken;continue}d=12291!=a.theTok;b&&(!c&&!r)&&(this.setShapeProperty(22,"points",Integer.$valueOf(g)),
c=!0,g=0);b&&l&&this.invArg();null!=L&&this.setShapeProperty(22,L,H)}this.finalizeObject(22,k[0],n,g,b,x,N,null)});e(d,"mo",function(a,b){var c=this.e,f=2147483647,z=!1,d=null,h=this.vwr.getVisibleFramesBitSet(),e=new JU.Lst,j=!1,n=1073877011==this.tokAt(0),k=1;if(n){var g=this.e.optParameterAsString(1).equals("view");if(1==this.e.slen||g||this.e.optParameterAsString(1).equals("options")){this.chk||(c=g?"VIEW":this.e.optParameterAsString(2),this.vwr.startNBO(c));return}}if(1094717454==this.tokAt(1)||
4115==this.tokAt(1))k=c.modelNumberParameter(2),0>k&&this.invArg(),h.clearAll(),h.set(k),k=3;c.sm.loadShape(b);for(g=h.nextSetBit(0);0<=g;g=h.nextSetBit(g+1)){var q=k;if(1073742001==this.tokAt(q)&&this.listIsosurface(b))break;this.setShapeProperty(b,"init",Integer.$valueOf(g));if(a)break;var N=null,w=this.getShapeProperty(b,"moNumber").intValue(),l=this.getShapeProperty(b,"moLinearCombination"),u=this.getShapeProperty(b,"moSquareData"),D=null==l?null:this.getShapeProperty(b,"moSquareLinear");0==w&&
(w=2147483647);var A=null,G=null,P=!1,K=null;switch(this.getToken(q).tok){case 1140850696:if(1073877010==b){this.mo(a,28);return}d=this.paramAsStr(++q).toUpperCase();4==c.tokAt(q+1)&&(K=this.paramAsStr(++c.iToken));break;case 1073741875:case 554176565:A=c.theToken.value;G=this.getCapSlabObject(q,!1);break;case 1073741914:D=Boolean.TRUE;l=x(-1,[1]);f=w=0;break;case 2:w=this.intParameter(q);1073741865==this.tokAt(q+1)&&(j=!0);l=this.moCombo(e);null==l&&0>w&&(l=x(-1,[-100,-w]));P=!0;break;case 268440576:switch(this.tokAt(++q)){case 1073741973:case 1073742008:break;
default:this.invArg()}z=!0;case 1073741973:case 1073742008:2147483647==(f=this.moOffset(q))&&this.invArg();w=0;l=this.moCombo(e);P=!0;break;case 1073742037:w=1073742037;j=!1;l=this.moCombo(e);P=!0;break;case 1073742108:w=1073742108;j=!1;l=this.moCombo(e);P=!0;break;case 1765808134:this.setColorOptions(null,q+1,b,2);break;case 134217750:A="plane";G=1073742333==this.tokAt(this.e.iToken=++q)?null:c.planeParameter(q,!1);break;case 134217751:this.addShapeProperty(e,"randomSeed",2==this.tokAt(q+2)?Integer.$valueOf(this.intParameter(q+
2)):null);A="monteCarloCount";G=Integer.$valueOf(this.intParameter(q+1));break;case 536875059:A="scale";G=Float.$valueOf(this.floatParameter(q+1));break;case 1073741910:268440577==this.tokAt(q+1)?(A="cutoffPositive",G=Float.$valueOf(this.floatParameter(q+2))):(A="cutoff",G=Float.$valueOf(this.floatParameter(q+1)));break;case 536870916:A="debug";break;case 1073742054:A="plane";break;case 1073742104:case 1073742122:A="resolution";G=Float.$valueOf(this.floatParameter(q+1));break;case 1073742156:null==
l?u=Boolean.TRUE:D=Boolean.TRUE;P=!1;break;case 1073742168:q+1<this.slen&&4==this.tokAt(q+1)&&(A="titleFormat",G=this.paramAsStr(q+1));break;case 1073741824:this.invArg();break;case 4:if(n&&1==q){K=c.stringParameter(q);break}default:n&&4==c.tokAt(q)&&(K=this.paramAsStr(q++));if(c.isArrayParameter(q)){l=c.floatParameterSet(q,1,2147483647);1073742156==this.tokAt(c.iToken+1)&&(P=!1,D=Boolean.TRUE,c.iToken++);break}f=c.iToken;c.setMeshDisplayProperty(b,0,c.theTok)||this.invArg();this.setShapeProperty(b,
"setProperties",e);c.setMeshDisplayProperty(b,f,this.tokAt(f));return}null!=A&&this.addShapeProperty(e,A,G);q=2147483647!=w||null!=l;if(this.chk)break;if(null!=d||null!=K||q){q&&4==this.tokAt(c.iToken+1)&&(N=this.paramAsStr(++c.iToken));c.setCursorWait(!0);if(null!=d||null!=K)d=d+":"+K;this.setMoData(e,w,l,f,z,g,N,d,j);q&&this.addShapeProperty(e,"finalize",null)}P||(this.setShapeProperty(b,"squareLinear",D),this.setShapeProperty(b,"squareData",u));0<e.size()&&this.setShapeProperty(b,"setProperties",
e);q&&!c.tQuiet&&(N="",n?N=this.getShapeProperty(b,"moLabel"):(w=this.getShapeProperty(b,"moNumber").intValue(),N=""+w),this.showString(JS.T.nameOf(this.tokAt(0))+" "+N+" "+(j?"beta ":"")+this.getShapeProperty(b,"message")));e.clear()}},"~B,~N");e(d,"setNBOType",function(a,b){var c=-1,f=null,z=b.indexOf(":");0<z&&(f=b.substring(z+1),b=b.substring(0,z),b.equals("null")&&(b=null),f.equals("null")&&(f=null));0>(null==b?0:JV.JC.getNBOTypeFromName(b))&&this.invArg();a.containsKey("nboLabels")||this.error(27);
if(this.chk)return-1;null!=b&&!J.api.Interface.getInterface("J.adapter.readers.quantum.GenNBOReader",this.vwr,"script").readNBOCoefficients(a,b,this.vwr)&&this.error(27);var z=a.get("auxFiles"),d=this.vwr.getCurrentModelAuxInfo().get("auxFiles");null==d?this.vwr.getCurrentModelAuxInfo().put("auxFiles",z):d.addAll(z);if(null!=f){z=f.indexOf(".");0<z&&(d=JU.PT.parseInt(f.substring(z+1)),f=f.substring(0,z),z=d);for(var d=a.get("nboLabels"),h=0,e=d.length;h<e;h++)if(f.equals(d[h])&&(0>z||0==--z)){c=h+
1;break}0>c&&this.error(27)}return c},"java.util.Map,~S");e(d,"moCombo",function(a){if(1073742156!=this.tokAt(this.e.iToken+1))return null;this.addShapeProperty(a,"squareLinear",Boolean.TRUE);this.e.iToken++;return x(0,0)},"JU.Lst");e(d,"moOffset",function(a){var b=1073741973==this.getToken(a).tok?0:1,c=this.tokAt(++a);2==c&&"-"==this.e.st[a].value.charAt(0)?b+=this.intParameter(a):268440577==c?b+=this.intParameter(++a):268440576==c&&(b-=this.intParameter(++a));return b},"~N");e(d,"setMoData",function(a,
b,c,f,z,d,h,e,j){var g=this.e;0>d&&(d=this.vwr.am.cmi,0>d&&g.errorStr(30,"MO isosurfaces"));var k=this.vwr.ms.getInfo(d,"moData");null==k&&this.error(27);this.vwr.checkMenuUpdate();if(null!=e){var t=this.setNBOType(k,e),q=k.get("nboLabels").length;g.showString(q+" orbitals of type "+e.substring(0,e.indexOf(":")+1)+" modelIndex="+this.vwr.getModelNumberDotted(d));0<t&&(b=t);if(null==c&&2147483647==b)return}e=null;t=0;d=null;if(null==c||2>c.length){null!=c&&1==c.length?f=0:j&&k.containsKey("firstBeta")&&
(f=k.get("firstBeta").intValue());e=k.containsKey("lastMoNumber")?k.get("lastMoNumber").intValue():0;t=k.containsKey("lastMoCount")?k.get("lastMoCount").intValue():1;1073742108==b?b=e-1:1073742037==b&&(b=e+t);e=k.get("mos");t=null==e?0:e.size();0==t&&this.error(25);1==t&&1<b&&this.error(29);if(2147483647!=f){if(!j)if(k.containsKey("HOMO"))b=k.get("HOMO").intValue()+f,f=0;else{b=t;for(j=0;j<t;j++)if(q=e.get(j),null!=(d=q.get("occupancy"))){if(0.5>d.floatValue()){b=j;break}}else if(null!=(d=q.get("energy"))){if(0<
d.floatValue()){b=j;break}}else break;null==d&&this.error(28)}b+=f;this.chk||JU.Logger.info("MO "+b)}(1>b||b>t)&&g.errorStr(26,""+t)}b=Math.abs(b);k.put("lastMoNumber",Integer.$valueOf(b));k.put("lastMoCount",Integer.$valueOf(1));z&&null==c&&(c=x(-1,[-100,b]));if(null!=c&&2>c.length){q=e.get(b-1);if(null==(d=q.get("energy")))c=x(-1,[100,b]);else{g=d.floatValue();f=JU.BS.newN(t);z=0;c=1==c.length&&1==c[0];for(j=0;j<t;j++)if(null!=(d=e.get(j).get("energy")))if(d=d.floatValue(),c?d<=g:d==g)f.set(j+1),
z+=2;c=x(z,0);for(g=j=0;j<z;j+=2)c[j]=1,c[j+1]=g=f.nextSetBit(g+1);k.put("lastMoNumber",Integer.$valueOf(f.nextSetBit(0)));k.put("lastMoCount",Integer.$valueOf(G(z/2)))}this.addShapeProperty(a,"squareLinear",Boolean.TRUE)}this.addShapeProperty(a,"moData",k);null!=h&&this.addShapeProperty(a,"title",h);this.addShapeProperty(a,"molecularOrbital",null!=c?c:Integer.$valueOf(Math.abs(b)));this.addShapeProperty(a,"clear",null)},"JU.Lst,~N,~A,~N,~B,~N,~S,~S,~B");e(d,"isosurface",function(a){var b=this.e;
b.sm.loadShape(a);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(a))){var c=0,f=!1,z=!1,d=24==a,h=29==a,e=30==a,j=26==a,g=j||12291==this.tokAt(1)||b.$isStateScript,k=!1,t=!1,q=!1,N=!1,w=!1,l=!1,Aa=!1,Bb=!1,R=!1,ea=!1,P=!1,K=!1,F=!1,C=!1,p=!1,L=null,H=null,O=null,T=null,Q,X,I,S,Y,da=NaN,ca=NaN,ja=0,Ba=null,pa=2147483647,W=null,Z=null,ka=null,s=new JU.SB,U,qa=null,ua=null,za=!1,fa=null,sa=0,la=null,aa=this.chk?0:-2147483648;b.setCursorWait(!0);var xa=null!=this.initIsosurface(a),hb=xa&&null==this.getShapeProperty(a,
"ID"),Ha=!1,ib=!1,La=!1,Ia=!1,Ma=null,jb=null,kb=null,ra=null,lb=null,Fa=null,Na=null,E=new JU.Lst,Ja=!1;(h||e)&&this.addShapeProperty(E,"fileType","Pmesh");for(var m=b.iToken;m<this.slen;++m){var B=null,y=null,V=this.getToken(m).tok;1073741824==V&&(la=this.paramAsStr(m),la.equalsIgnoreCase("map")&&(V=4125));switch(V){case 1073742148:g=!0;s.append(" silent");B="silent";break;case 603979868:Ba=1073742335==this.getToken(++m).tok?Boolean.TRUE:1073742334==b.theTok?Boolean.FALSE:null;null==Ba&&this.invArg();
continue;case 553648146:pa=this.intParameter(++m);continue;case 4128:B="moveIsosurface";12!=this.tokAt(++m)&&this.invArg();y=this.getToken(m++).value;break;case 1296041985:for(var Cb=this.floatArraySet(m+2,this.intParameter(m+1),16),Fa=Array(Cb.length),ga=Fa.length;0<=--ga;)Fa[ga]=JU.M4.newA16(Cb[ga]);m=b.iToken;break;case 1088421903:0>aa&&(aa=Math.min(this.vwr.am.cmi,0));var Db=null==ka;null==Z&&(Z=JU.BSUtil.copy(this.vwr.bsA()));Z.and(this.vwr.ms.getAtoms(1296041985,Integer.$valueOf(1)));Db||Z.andNot(ka);
this.addShapeProperty(E,"select",Z);Db&&(ka=JU.BSUtil.copy(Z),JU.BSUtil.invertInPlace(ka,this.vwr.ms.ac),p=!0,this.addShapeProperty(E,"ignore",ka),s.append(" ignore ").append(JU.Escape.eBS(ka)));s.append(" symmetry");0==sa&&this.addShapeProperty(E,"colorRGB",Integer.$valueOf(1296041985));Fa=this.vwr.ms.getSymMatrices(aa);break;case 1073742066:B="offset";y=this.centerParameter(++m);m=b.iToken;break;case 528432:B="rotate";y=1073742333==this.tokAt(b.iToken=++m)?null:b.getPoint4f(m);m=b.iToken;break;
case 1610612740:B="scale3d";y=Float.$valueOf(this.floatParameter(++m));break;case 1073742090:s.append(" periodic");B="periodic";break;case 1073742078:case 266298:case 134217751:B=b.theToken.value.toString();s.append(" ").appendO(b.theToken.value);y=this.centerParameter(++m);s.append(" ").append(JU.Escape.eP(y));m=b.iToken;break;case 1812599299:if(0<=b.fullCommand.indexOf("# BBOX="))var Eb=JU.PT.split(JU.PT.getQuotedAttribute(b.fullCommand,"# BBOX"),","),fa=D(-1,[JU.Escape.uP(Eb[0]),JU.Escape.uP(Eb[1])]);
else b.isCenterParameter(m+1)?(fa=D(-1,[this.getPoint3f(m+1,!0),this.getPoint3f(b.iToken+1,!0)]),m=b.iToken):fa=this.vwr.ms.getBBoxVertices();s.append(" boundBox "+JU.Escape.eP(fa[0])+" "+JU.Escape.eP(fa[fa.length-1]));B="boundingBox";y=fa;break;case 135188:h=!0;s.append(" pmesh");B="fileType";y="Pmesh";break;case 134217763:Z=this.atomExpressionAt(++m);this.chk?W=new JU.BS:1073742325==this.tokAt(b.iToken+1)||10==this.tokAt(b.iToken+1)?(W=this.atomExpressionAt(++b.iToken),W.and(this.vwr.ms.getAtomsWithinRadius(5,
Z,!1,null,null))):(W=this.vwr.ms.getAtomsWithinRadius(5,Z,!0,null,null),W.andNot(this.vwr.ms.getAtoms(1094713360,Z)));W.andNot(Z);s.append(" intersection ").append(JU.Escape.eBS(Z)).append(" ").append(JU.Escape.eBS(W));m=b.iToken;if(134320141==this.tokAt(m+1)){m++;var Oa=this.getToken(++m).value;s.append(" function ").append(JU.PT.esc(Oa));this.chk||this.addShapeProperty(E,"func",Oa.equals("a+b")||Oa.equals("a-b")?Oa:this.createFunction("__iso__","a,b",Oa))}else C=!0;B="intersection";y=D(-1,[Z,W]);
break;case 1610625028:case 134217759:if(f=1610625028==V){s.append(" display");c=m;V=this.tokAt(m+1);if(0==V)continue;m++;this.addShapeProperty(E,"token",Integer.$valueOf(1073742335));if(10==V||1073742327==V){B="bsDisplay";1073742327==V?s.append(" all"):(y=this.st[m].value,s.append(" ").append(JU.Escape.eBS(y)));b.checkLast(m);break}else 134217759!=V&&(b.iToken=m,this.invArg())}else ja=m;var Xa,Ca=null,W=null,Ya=Array(1);1073742325==this.tokAt(m+1)?(Xa=this.floatParameter(m+3),b.isPoint3f(m+4)?(Ca=
b.centerParameter(m+4,null),b.iToken+=2):b.isPoint3f(m+5)?(Ca=b.centerParameter(m+5,null),b.iToken+=2):(W=b.atomExpression(this.st,m+5,this.slen,!0,!1,Ya,!0),null==W&&this.invArg())):(Xa=this.floatParameter(++m),Ca=b.centerParameter(++m,Ya),W=ba(Ya[0],"JU.BS")?Ya[0]:null);f&&b.checkLast(b.iToken);m=b.iToken;0<=b.fullCommand.indexOf("# WITHIN=")&&(W=JU.BS.unescape(JU.PT.getQuotedAttribute(b.fullCommand,"# WITHIN")));this.chk||(null!=W&&0<=aa&&(W=this.vwr.restrictToModel(W,aa)),null==Ca&&(Ca=null==
W?new JU.P3:this.vwr.ms.getAtomSetCenter(W)),fa=this.getWithinDistanceVector(E,Xa,Ca,W,f),s.append(" within ").appendF(Xa).append(" ").append(null==W?JU.Escape.eP(Ca):JU.Escape.eBS(W)));continue;case 1073742083:var B="parameters",Fb=b.floatParameterSet(++m,1,10),m=b.iToken,y=Fb;s.append(" parameters ").append(JU.Escape.eAF(Fb));break;case 1715472409:case 1073742190:var Ma=b.theToken.value,fb=1073742190==V,Pa=this.tokAt(m+1);null==lb?(!k&&(!q&&!t)&&(this.addShapeProperty(E,"sasurface",Float.$valueOf(0)),
s.append(" vdw"),k=!0),B="property",null==Ba&&(Ba=JS.T.tokAttr(Pa,1111490560)&&1==this.vwr.getIsosurfacePropertySmoothing(!1)?Boolean.TRUE:Boolean.FALSE),this.addShapeProperty(E,"propertySmoothing",Ba),s.append(" isosurfacePropertySmoothing "+Ba),Ba===Boolean.TRUE&&(2147483647==pa&&(pa=this.vwr.getIsosurfacePropertySmoothing(!0)),this.addShapeProperty(E,"propertySmoothingPower",Integer.$valueOf(pa)),s.append(" isosurfacePropertySmoothingPower "+pa)),this.vwr.g.rangeSelected&&this.addShapeProperty(E,
"rangeSelected",Boolean.TRUE)):B=lb;la=this.paramAsStr(m);s.append(" ").append(la);if(0==la.toLowerCase().indexOf("property_")){H=x(this.vwr.ms.ac,0);if(this.chk)continue;H=this.vwr.getDataObj(la,null,1);null==H&&this.invArg();this.addShapeProperty(E,B,H);continue}var Qa=this.vwr.ms.ac,H=x(Qa,0);if(fb){var Gb=this.paramAsStr(++m);0==Gb.length?H=b.floatParameterSet(m,Qa,Qa):(H=x(Qa,0),this.chk||JU.Parser.parseStringInfestedFloatArray(""+b.getParameter(Gb,4,!0),null,H));this.chk||s.append(' "" ').append(JU.Escape.eAF(H))}else{this.getToken(++m);
if(!this.chk){s.append(" "+b.theToken.value);var gb=this.vwr.ms.at;this.vwr.autoCalculate(Pa,null);if(1765808134!=Pa){U=new JU.P3;for(var mb=Qa;0<=--mb;)H[mb]=gb[mb].atomPropertyFloat(this.vwr,Pa,U)}}1765808134==Pa&&(ra="inherit");if(134217759==this.tokAt(m+1)){var Hb=this.floatParameter(m+=2);s.append(" within "+Hb);this.addShapeProperty(E,"propertyDistanceMax",Float.$valueOf(Hb))}}y=H;break;case 1094713359:case 1094717454:k&&this.invArg();aa=1094713359==V?this.intParameter(++m):b.modelNumberParameter(++m);
s.append(" modelIndex "+aa);if(0>aa){B="fixed";y=Boolean.TRUE;break}B="modelIndex";y=Integer.$valueOf(aa);break;case 1275082241:var B="select",nb=this.atomExpressionAt(++m),y=nb,m=b.iToken;1073742072==this.tokAt(m+1)&&(m++,ka=JU.BSUtil.copy(nb),JU.BSUtil.invertInPlace(ka,this.vwr.ms.ac),this.addShapeProperty(E,"ignore",ka),s.append(" ignore ").append(JU.Escape.eBS(ka)),p=!0);k||q?s.append(" select "+JU.Escape.eBS(nb)):(Z=y,0>aa&&0<=Z.nextSetBit(0)&&(aa=this.vwr.ms.at[Z.nextSetBit(0)].mi));break;case 2109448:T=
10==b.getToken(++m).tok?b.theToken.value:b.expandFloatArray(b.floatParameterSet(m,1,2147483647),1,!0);m=b.iToken;break;case 36867:var Ib=this.intParameter(++m),T=0<Ib?JU.BSUtil.newAndSetBit(Ib-1):new JU.BS;break;case 12289:B="center";y=this.centerParameter(++m);s.append(" center "+JU.Escape.eP(y));m=b.iToken;break;case 1073742147:case 1765808134:xa=!0;if(1073742147==V)La=!0,s.append(" sign"),this.addShapeProperty(E,"sign",Boolean.TRUE);else{if(1073741914==this.tokAt(m+1)){m++;B="colorDensity";s.append(" color density");
Ia=!0;if(this.isFloatParameter(m+1)){var Jb=this.floatParameter(++m);s.append(" "+Jb);y=Float.$valueOf(Jb)}break}if(4==this.getToken(m+1).tok)ra=this.paramAsStr(++m),0<ra.indexOf(" ")&&(Na=JU.C.getColixArray(ra),null==Na&&this.error(4));else if(1073742018==b.theTok){m++;s.append(" color mesh");sa=b.getArgbParam(++m);this.addShapeProperty(E,"meshcolor",Integer.$valueOf(sa));s.append(" ").append(JU.Escape.escapeColor(sa));m=b.iToken;continue}if(603979967==(b.theTok=this.tokAt(m+1))||1073742074==b.theTok){s.append(" color");
kb=this.setColorOptions(s,m+1,24,-2);m=b.iToken;continue}switch(this.tokAt(m+1)){case 1073741826:case 1073742114:this.getToken(++m);s.append(" color range");this.addShapeProperty(E,"rangeAll",null);if(1073742327==this.tokAt(m+1)){m++;s.append(" all");continue}var Kb=this.floatParameter(++m),Lb=this.floatParameter(++m);this.addShapeProperty(E,"red",Float.$valueOf(Kb));this.addShapeProperty(E,"blue",Float.$valueOf(Lb));s.append(" ").appendF(Kb).append(" ").appendF(Lb);continue}if(b.isColorParam(m+1)&&
(sa=b.getArgbParam(m+1),1073742170==this.tokAt(m+2))){ra=b.getColorRange(m+1);m=b.iToken;break}s.append(" color")}b.isColorParam(m+1)?(sa=b.getArgbParam(++m),s.append(" ").append(JU.Escape.escapeColor(sa)),m=b.iToken,this.addShapeProperty(E,"colorRGB",Integer.$valueOf(sa)),xa=!0,b.isColorParam(m+1)?(sa=b.getArgbParam(++m),m=b.iToken,this.addShapeProperty(E,"colorRGB",Integer.$valueOf(sa)),s.append(" ").append(JU.Escape.escapeColor(sa)),N=!0):La&&this.invPO()):!La&&(null==Na&&null==ra)&&this.invPO();
continue;case 134221829:d||this.invArg();P=!this.chk;continue;case 1228935687:4!=this.tokAt(m+1)&&this.invPO();continue;case 1111492618:case 1648363544:s.append(" ").appendO(b.theToken.value);var Ra=b.encodeRadiusParameter(m,!1,!0);if(null==Ra)return;s.append(" ").appendO(Ra);Float.isNaN(Ra.value)&&(Ra.value=100);y=Ra;B="radius";ea=!0;q&&(k=!1);m=b.iToken;break;case 1073741864:z=!0;continue;case 134217750:t=!0;B="plane";y=b.planeParameter(m,z);m=b.iToken;s.append(" plane ").append(JU.Escape.eP4(y));
break;case 536875059:B="scale";y=Float.$valueOf(this.floatParameter(++m));s.append(" scale ").appendO(y);break;case 1073742327:xa&&this.invArg();B="thisID";break;case 1112150020:k=!0;++m;y=b.getPoint4f(m);B="ellipsoid";m=b.iToken;s.append(" ellipsoid ").append(JU.Escape.eP4(y));break;case 134219777:t=!0;B="plane";y=b.hklParameter(++m,null,!0);m=b.iToken;s.append(" plane ").append(JU.Escape.eP4(y));break;case 135182:var k=!0,Za=this.paramAsStr(++m);this.addShapeProperty(E,"lcaoType",Za);s.append(" lcaocartoon ").append(JU.PT.esc(Za));
switch(this.getToken(++m).tok){case 12290:case 10:case 1073742325:B="lcaoCartoon";W=this.atomExpressionAt(m);m=b.iToken;if(this.chk)continue;var Sa=W.nextSetBit(0);0>Sa&&this.error(14);s.append(" ({").appendI(Sa).append("})");aa=this.vwr.ms.at[Sa].mi;this.addShapeProperty(E,"modelIndex",Integer.$valueOf(aa));var ob=D(-1,[new JU.V3,new JU.V3,JU.V3.newV(this.vwr.ms.at[Sa]),new JU.V3]);if(!Za.equalsIgnoreCase("s")&&null==this.vwr.getHybridizationAndAxes(Sa,ob[0],ob[1],Za))return;y=ob;break;default:this.error(14)}break;
case 1073877011:L=this.paramAsStr(++m).toUpperCase(),s.append(" nbo ").append(L).append(" ");case 1073877010:null==L&&s.append(" mo ");var Ta=2147483647,Ga=2147483647,pb=268440576==this.tokAt(m+1);pb&&m++;var Ua=null;switch(this.tokAt(++m)){case 0:b.bad();break;case 1073741914:s.append("[1] squared ");this.addShapeProperty(E,"squareLinear",Boolean.TRUE);Ua=x(-1,[1]);Ga=Ta=0;m++;break;case 1073741973:case 1073742008:Ga=this.moOffset(m);Ta=0;m=b.iToken;s.append((pb?"-":"")+"HOMO ");0<Ga&&s.append("+");
0!=Ga&&s.appendI(Ga);break;case 2:Ta=this.intParameter(m);s.appendI(Ta);1073741865==this.tokAt(m+1)&&(Bb=!0,m++);break;default:b.isArrayParameter(m)&&(Ua=b.floatParameterSet(m,1,2147483647),m=b.iToken)}if(1073742156==this.tokAt(m+1))this.addShapeProperty(E,"squareLinear",Boolean.TRUE),s.append(" squared"),null==Ua&&(Ua=x(0,0));else if(134217751==this.tokAt(m+1)){++m;var Mb=this.intParameter(++m),Nb=2==this.tokAt(m+1)?this.intParameter(++m):-System.currentTimeMillis()%1E4;this.addShapeProperty(E,"monteCarloCount",
Integer.$valueOf(Mb));this.addShapeProperty(E,"randomSeed",Integer.$valueOf(Nb));s.append(" points ").appendI(Mb).appendC(" ").appendI(Nb)}this.setMoData(E,Ta,Ua,Ga,pb,aa,null,L,Bb);k=!0;continue;case 1073742036:B="nci";s.append(" "+B);var V=this.tokAt(m+1),Ob=1228935687!=V&&4!=V&&1073742032!=V,y=Boolean.$valueOf(Ob);Ob&&(k=!0);break;case 1073742016:case 1073742022:var Pb=1073742016==V,B=Pb?"mep":"mlp";s.append(" "+B);var $a=null,qb=-1,k=!0;2==this.tokAt(m+1)&&(qb=this.intParameter(++m),s.append(" "+
qb),this.addShapeProperty(E,"mepCalcType",Integer.$valueOf(qb)));if(4==this.tokAt(m+1))$a=this.stringParameter(++m),s.append(" /*file*/"+JU.PT.esc($a));else if(1715472409==this.tokAt(m+1)){lb=B;continue}if(!this.chk)try{H=null==$a&&Pb?this.vwr.getOrCalcPartialCharges(Z,ka):this.getAtomicPotentials(Z,ka,$a)}catch(Qb){if($(Qb,"JV.JmolAsyncException"))throw new JS.ScriptInterruption(this.e,"partialcharge",1);throw Qb;}!this.chk&&null==H&&this.error(32);y=H;break;case 1312817669:Aa=!this.chk;s.append(" volume");
break;case 1073741974:this.setShapeId(a,++m,xa);hb=null==this.getShapeProperty(a,"ID");m=b.iToken;break;case 1073741888:603979967==this.tokAt(m+1)&&(Ha=!0,m++);ra=this.paramAsStr(++m).toLowerCase();ra.equals("sets")?s.append(' colorScheme "sets"'):b.isColorParam(m)&&(ra=b.getColorRange(m),m=b.iToken);break;case 1073741828:B="addHydrogens";y=Boolean.TRUE;s.append(" addHydrogens");break;case 1073741836:B="angstroms";s.append(" angstroms");break;case 1073741837:B="anisotropy";y=this.getPoint3f(++m,!1);
s.append(" anisotropy").append(JU.Escape.eP(y));m=b.iToken;break;case 1073741842:l=!this.chk;s.append(" area");break;case 1073741850:case 1073742076:k=!0;N&&!w&&(s.append(' phase "_orb"'),this.addShapeProperty(E,"phase","_orb"));var ia=x(7,0);ia[0]=this.intParameter(++m);ia[1]=this.intParameter(++m);ia[2]=this.intParameter(++m);ia[3]=this.isFloatParameter(m+1)?this.floatParameter(++m):6;s.append(" atomicOrbital ").appendI(A(ia[0])).append(" ").appendI(A(ia[1])).append(" ").appendI(A(ia[2])).append(" ").appendF(ia[3]);
134217751==this.tokAt(m+1)&&(m+=2,ia[4]=this.intParameter(m),ia[5]=3==this.tokAt(m+1)?this.floatParameter(++m):0,ia[6]=2==this.tokAt(m+1)?this.intParameter(++m):-System.currentTimeMillis()%1E4,s.append(" points ").appendI(A(ia[4])).appendC(" ").appendF(ia[5]).appendC(" ").appendI(A(ia[6])));B="hydrogenOrbital";y=ia;break;case 1073741866:s.append(" binary");continue;case 1073741868:s.append(" blockData");B="blockData";y=Boolean.TRUE;break;case 1073741875:case 554176565:F=!0;B=b.theToken.value;y=this.getCapSlabObject(m,
!1);m=b.iToken;break;case 1073741876:d||this.invArg();var R=!0,Rb=this.isFloatParameter(m+1)?this.floatParameter(++m):1.2,rb=this.isFloatParameter(m+1)?this.floatParameter(++m):10;if(this.chk)continue;if(50<rb){b.integerOutOfRange(0,50);return}s.append(" cavity ").appendF(Rb).append(" ").appendF(rb);this.addShapeProperty(E,"envelopeRadius",Float.$valueOf(rb));this.addShapeProperty(E,"cavityRadius",Float.$valueOf(Rb));B="cavity";break;case 1073741896:case 1073741900:B="contour";s.append(" contour");
switch(this.tokAt(m+1)){case 1073741920:y=b.floatParameterSet(m+2,1,2147483647);s.append(" discrete ").append(JU.Escape.eAF(y));m=b.iToken;break;case 1073741981:U=this.getPoint3f(m+2,!1);(0>=U.z||U.y<U.x)&&this.invArg();U.z==A(U.z)&&U.z>U.y-U.x&&(U.z=(U.y-U.x)/U.z);y=U;m=b.iToken;s.append(" increment ").append(JU.Escape.eP(U));break;default:y=Integer.$valueOf(2==this.tokAt(m+1)?this.intParameter(++m):0),s.append(" ").appendO(y),2==this.tokAt(m+1)&&(this.addShapeProperty(E,B,y),y=Integer.$valueOf(-Math.abs(this.intParameter(++m))),
s.append(" ").appendO(y))}break;case 1073741910:s.append(" cutoff ");268440577==this.tokAt(++m)?(B="cutoffPositive",y=Float.$valueOf(ca=this.floatParameter(++m)),s.append("+").appendO(y)):this.isFloatParameter(m)?(B="cutoff",y=Float.$valueOf(ca=this.floatParameter(m)),s.appendO(y)):Ia?(B="cutoffRange",y=b.floatParameterSet(m,2,2),this.addShapeProperty(E,"cutoff",Float.$valueOf(0)),s.append(JU.Escape.eAF(y)),m=b.iToken):this.invArg();break;case 1073741928:B="downsample";y=Integer.$valueOf(this.intParameter(++m));
s.append(" downsample ").appendO(y);break;case 1073741931:B="eccentricity";y=b.getPoint4f(++m);s.append(" eccentricity ").append(JU.Escape.eP4(y));m=b.iToken;break;case 1073741932:s.append(" ed");this.setMoData(E,-1,null,0,!1,aa,null,null,!1);k=!0;continue;case 536870916:case 1073742041:s.append(" ").appendO(b.theToken.value);B="debug";y=536870916==V?Boolean.TRUE:Boolean.FALSE;break;case 12293:s.append(" fixed");B="fixed";y=Boolean.TRUE;break;case 1073741962:s.append(" fullPlane");B="fullPlane";y=
Boolean.TRUE;break;case 1073741966:case 1073741968:var bc=1073741968==V,B=""+b.theToken.value,va=new JU.Lst,y=va,K=k=!0;s.append(" ").append(B);var ma=this.paramAsStr(++m);if(ma.equals("=")){s.append(" =");ma=this.paramAsStr(++m);s.append(" ").append(JU.PT.esc(ma));va.addLast(ma);this.chk||this.addShapeProperty(E,"func",this.createFunction("__iso__","x,y,z",ma));break}var sb=JU.PT.getQuotedAttribute(b.fullCommand,"# DATA"+(K?"2":""));null==sb?sb="inline":ma=sb;var Sb=0==ma.indexOf("data2d_"),cc=0==
ma.indexOf("data3d_"),ib=ma.equals("inline");s.append(" inline");va.addLast(ma);var Tb=this.getPoint3f(++m,!1);s.append(" ").append(JU.Escape.eP(Tb));va.addLast(Tb);var wa;S=++b.iToken;va.addLast(wa=b.getPoint4f(S));s.append(" ").append(JU.Escape.eP4(wa));Q=A(wa.x);Y=++b.iToken;va.addLast(wa=b.getPoint4f(Y));s.append(" ").append(JU.Escape.eP4(wa));X=A(wa.x);va.addLast(wa=b.getPoint4f(++b.iToken));s.append(" ").append(JU.Escape.eP4(wa));I=A(wa.x);(0==Q||0==X||0==I)&&this.invArg();if(!this.chk){var oa=
null,ta=null;if(bc){ib?(Q=Math.abs(Q),X=Math.abs(X),I=Math.abs(I),ta=this.floatArraySetXYZ(++b.iToken,Q,X,I)):ta=cc?this.vwr.getDataObj(ma,null,3):this.vwr.functionXYZ(ma,Q,X,I);Q=Math.abs(Q);X=Math.abs(X);I=Math.abs(I);null==ta&&(b.iToken=S,b.errorStr(53,"xyzdata is null."));if(ta.length!=Q||ta[0].length!=X||ta[0][0].length!=I)b.iToken=S,b.errorStr(53,"xyzdata["+ta.length+"]["+ta[0].length+"]["+ta[0][0].length+"] is not of size ["+Q+"]["+X+"]["+I+"]");va.addLast(ta);s.append(" ").append(JU.Escape.e(ta))}else{ib?
(Q=Math.abs(Q),X=Math.abs(X),oa=this.floatArraySet(++b.iToken,Q,X)):Sb?(oa=this.vwr.getDataObj(ma,null,2),Q=null==oa?0:oa.length,X=3):(oa=this.vwr.functionXY(ma,Q,X),Q=Math.abs(Q),X=Math.abs(X));null==oa&&(b.iToken=S,b.errorStr(53,"fdata is null."));oa.length!=Q&&!Sb&&(b.iToken=S,b.errorStr(53,"fdata length is not correct: "+oa.length+" "+Q+"."));for(ga=0;ga<Q;ga++)null==oa[ga]&&(b.iToken=Y,b.errorStr(53,"fdata["+ga+"] is null.")),oa[ga].length!=X&&(b.iToken=Y,b.errorStr(53,"fdata["+ga+"] is not the right length: "+
oa[ga].length+" "+X+"."));va.addLast(oa);s.append(" ").append(JU.Escape.e(oa))}}m=b.iToken;break;case 1073742188:var dc=this.e.isAtomExpression(++m),Ub=this.getAllPoints(m,1);s.append(" value "+(dc?this.e.atomExpressionAt(m).toString():JU.Escape.eAP(Ub)));B="probes";y=Ub;m=this.e.iToken;break;case 1073741970:B="gridPoints";s.append(" gridPoints");break;case 1073741976:B="ignore";y=ka=this.atomExpressionAt(++m);s.append(" ignore ").append(JU.Escape.eBS(ka));m=b.iToken;break;case 1073741985:B="insideOut";
s.append(" insideout");break;case 1073741988:case 1073741986:case 1073742100:s.append(" ").appendO(b.theToken.value);B="pocket";y=1073742100==V?Boolean.TRUE:Boolean.FALSE;break;case 1073742002:B="lobe";y=b.getPoint4f(++m);m=b.iToken;s.append(" lobe ").append(JU.Escape.eP4(y));k=!0;break;case 1073742004:case 1073742006:B="lp";y=b.getPoint4f(++m);m=b.iToken;s.append(" lp ").append(JU.Escape.eP4(y));k=!0;break;case 4125:(q||this.slen==m+1)&&this.invArg();q=!0;if((R||ea||C)&&!k)k=!0,this.addShapeProperty(E,
"bsSolvent",ea||C?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(E,"sasurface",Float.$valueOf(0));0==s.length()?(qa=this.getShapeProperty(24,"plane"),null==qa?null!=this.getShapeProperty(24,"contours")&&this.addShapeProperty(E,"nocontour",null):(this.addShapeProperty(E,"plane",qa),s.append("plane ").append(JU.Escape.eP4(qa)),t=!0,qa=null)):!k&&!t&&this.invArg();s.append("; isosurface map");this.addShapeProperty(E,"map",k?Boolean.TRUE:Boolean.FALSE);break;case 1073742014:B="maxset";
y=Integer.$valueOf(this.intParameter(++m));s.append(" maxSet ").appendO(y);break;case 1073742020:B="minset";y=Integer.$valueOf(this.intParameter(++m));s.append(" minSet ").appendO(y);break;case 1073742112:k=!0;B="rad";y=b.getPoint4f(++m);m=b.iToken;s.append(" radical ").append(JU.Escape.eP4(y));break;case 1073742027:B="fixed";y=Boolean.FALSE;s.append(" modelBased");break;case 1073742028:case 1073742135:case 1612709912:var Ma=b.theToken.value,ab;1073742028==V?(B="molecular",s.append(" molecular"),
ab=this.isFloatParameter(m+1)?this.floatParameter(++m):1.4):(this.addShapeProperty(E,"bsSolvent",b.lookupIdentifierValue("solvent")),B=1073742135==V?"sasurface":"solvent",s.append(" ").appendO(b.theToken.value),ab=this.isFloatParameter(m+1)?this.floatParameter(++m):this.vwr.getFloat(570425394));s.append(" ").appendF(ab);y=Float.$valueOf(ab);1073741961==this.tokAt(m+1)&&(this.addShapeProperty(E,"doFullMolecular",null),s.append(" full"),m++);k=!0;break;case 1073742032:this.addShapeProperty(E,"fileType",
"Mrc");s.append(" mrc");continue;case 1140850696:var ha=b.stringParameter(++m);this.addShapeProperty(E,"fileType",ha);s.append(' type "'+ha+'"');continue;case 1073742064:case 1073742062:this.addShapeProperty(E,"fileType","Obj");s.append(" obj");continue;case 1073742033:this.addShapeProperty(E,"fileType","Msms");s.append(" msms");continue;case 1073742094:k&&this.invArg();B="phase";w=!0;y=4==this.tokAt(m+1)?this.stringParameter(++m):"_orb";s.append(" phase ").append(JU.PT.esc(y));break;case 1073742104:case 1073742122:B=
"resolution";y=Float.$valueOf(this.floatParameter(++m));s.append(" resolution ").appendO(y);break;case 1073742124:B="reverseColor";y=Boolean.TRUE;s.append(" reversecolor");break;case 1073742127:case 1073742146:B="sigma";y=Float.$valueOf(da=this.floatParameter(++m));s.append(" sigma ").appendO(y);break;case 1112150021:B="geodesic";y=Float.$valueOf(this.floatParameter(++m));s.append(" geosurface ").appendO(y);k=!0;break;case 1073742154:B="sphere";y=Float.$valueOf(this.floatParameter(++m));s.append(" sphere ").appendO(y);
k=!0;break;case 1073742156:B="squareData";y=Boolean.TRUE;s.append(" squared");break;case 1073741984:B=!k&&!t&&!q?"readFile":"mapColor";la=this.stringParameter(++m);null==la&&this.invArg();h&&(la=JU.PT.replaceWithCharacter(la,"{,}|"," "));b.debugHigh&&JU.Logger.debug("pmesh inline data:\n"+la);y=this.chk?null:la;this.addShapeProperty(E,"fileName","");s.append(" INLINE ").append(JU.PT.esc(la));k=!0;break;case 268437504:case 1073742195:case 7:(null!=jb||hb)&&this.invArg();var bb=b.listParameter4(m,2,
2147483647,!0),m=b.iToken,Va=G(bb.size()/2);(0==Va||2*Va!=bb.size())&&this.invArg();var tb=Array(Va),ub=x(Va,0);s.append("[");try{for(var Vb=ga=0;ga<Va;ga++)ub[ga]=bb.get(Vb++).floatValue(),tb[ga]=this.e.checkFileExists("ISOSURFACE_"+ga+"_",!1,bb.get(Vb++),m,!1),s.appendF(ub[ga]),s.append(" /*file*/").append(JU.PT.esc(tb[ga]));s.append("]")}catch(Wb){if($(Wb,Exception))this.invArg();else throw Wb;}jb=D(-1,[tb,ub]);B=!k&&!t&&!q?"readFile":"mapColor";k=!0;if(this.chk)break;this.addShapeProperty(E,"filesData",
jb);break;case 545259556:case 545259557:case 1073741914:case 4:var vb=!k&&!t,M=null,B=vb&&!q?"readFile":"mapColor";if(4==V){var M=this.paramAsStr(m),wb=M.indexOf("::");if(0<wb){var cb=M.substring(0,wb),cb=cb.substring(0,1).toUpperCase()+cb.substring(1).toLowerCase();this.addShapeProperty(E,"fileType",cb);M=M.substring(wb+2)}}else 1073741914==V&&(M="=density/");if(null==M||0==M.length||M.equals("*")||M.equals("=")){var Xb=this.vwr.getPdbID();null==Xb&&b.errorStr(22,"no PDBID available");M="*"+(545259557==
V?"*":"")+Xb}var Yb=!1;M.startsWith("http://eds.bmc.uu.se/eds/dfs/cb/")&&M.endsWith(".omap")&&(M=(0<=M.indexOf("_diff")?"*":"")+"*"+M.substring(32,36));if(M.startsWith("*")||M.startsWith("=")){var ec=!Float.isNaN(ca)||!Float.isNaN(da),xb=0<=M.indexOf("/full");xb&&(M=JU.PT.rep(M,"/full",""));0<=M.indexOf("/diff")&&(M="*"+M.substring(0,M.indexOf("/diff")));M.startsWith("**")&&(ec||this.addShapeProperty(E,"sigma",Float.$valueOf(da=3)),La||(La=!0,s.append(" sign"),this.addShapeProperty(E,"sign",Boolean.TRUE)));
var fc=M,M=this.vwr.setLoadFormat(!1,M,this.chk?"?":xb?"_":"-",!1);null==M&&b.errorStr(22,"error parsing filename: "+fc);Yb=!xb}Yb&&(null==fa&&0==ja&&(Ma=M,0>aa&&(aa=this.vwr.am.cmi),W=this.vwr.getModelUndeletedAtomsBitSet(aa),0<=W.nextSetBit(0)&&(fa=this.getWithinDistanceVector(E,2,null,W,!1),s.append(" within 2.0 ").append(JU.Escape.eBS(W)))),null!=fa&&0<=M.indexOf("/0,0,0/0,0,0?")&&(M=M.$replace("0,0,0/0,0,0",fa[0].x+","+fa[0].y+","+fa[0].z+"/"+fa[fa.length-1].x+","+fa[fa.length-1].y+","+fa[fa.length-
1].z)),vb&&(Ja=!0));var db=null==M?-1:M.indexOf("#-");if(Float.isNaN(da)&&Float.isNaN(ca))if(0<=(db=M.indexOf("#-cutoff=")))this.addShapeProperty(E,"cutoff",Float.$valueOf(ca=Float.parseFloat(M.substring(db+9)))),s.append(" cutoff "+ca);else if(0<=(db=M.indexOf("#-sigma=")))this.addShapeProperty(E,"sigma",Float.$valueOf(da=Float.parseFloat(M.substring(db+8)))),s.append(" sigma "+da);Float.isNaN(da)?Float.isNaN(ca)||this.showString("using cutoff = "+ca):this.showString("using sigma = "+da);vb&&(this.vwr.getP("_fileType").equals("Pdb")&&
Float.isNaN(da)&&Float.isNaN(ca))&&(this.addShapeProperty(E,"sigma",Float.$valueOf(-1)),s.append(" sigma -1.0"));0==M.length&&(0>aa&&(aa=this.vwr.am.cmi),M=b.getFullPathName(!1),y=this.vwr.ms.getInfo(aa,"jmolSurfaceInfo"));var yb=-1;null==y&&2==this.tokAt(m+1)&&this.addShapeProperty(E,"fileIndex",Integer.$valueOf(yb=this.intParameter(++m)));var Wa=4==this.tokAt(m+1)?this.stringParameter(++m):null,k=!0;if(this.chk)break;var Zb,ya=null;null==y&&(0<=b.fullCommand.indexOf("# FILE0=")?(M=JU.PT.getQuotedAttribute(b.fullCommand,
"# FILE0"),1073741848==this.tokAt(m+1)&&(m+=2)):1073741848==this.tokAt(m+1)&&(ya=this.vwr.fm.getFilePath(this.stringParameter(b.iToken=m+=2),!1,!1),Zb=this.vwr.getFullPathNameOrError(ya),ya=Zb[0],""!==this.vwr.fm.getPathForAllFiles()?(M=ya,ya=null):this.addShapeProperty(E,"localName",ya)));null==Wa&&(M=this.e.checkFileExists("ISOSURFACE_"+(q?"MAP_":""),!1,M,m,!1));this.showString("reading isosurface data from "+M);null!=Wa&&(y=this.vwr.fm.cacheGet(M,!1),this.addShapeProperty(E,"calculationType",Wa));
null==y&&(this.addShapeProperty(E,"fileName",M),null!=ya&&(M=ya),0<=yb&&s.append(" ").appendI(yb));s.append(" /*file*/").append(JU.PT.esc(M));null!=Wa&&s.append(" ").append(JU.PT.esc(Wa));break;case 4106:B="connections";switch(this.tokAt(++m)){case 12290:case 10:case 1073742325:y=u(-1,[this.atomExpressionAt(m).nextSetBit(0)]);break;default:y=u(-1,[A(b.floatParameterSet(m,1,1)[0])])}m=b.iToken;break;case 1094713347:B="atomIndex";y=Integer.$valueOf(this.intParameter(++m));break;case 1073741999:B="link";
s.append(" link");break;case 1814695966:24!=a&&this.invArg();268440577==this.tokAt(m+1)&&m++;B="extendGrid";y=Float.$valueOf(this.floatParameter(++m));s.append(" unitcell "+y);break;case 1073741994:24!=a&&this.invArg();U=this.getPoint3f(++m,!1);m=b.iToken;if(0>=U.x||0>=U.y||0>=U.z)break;U.x=A(U.x);U.y=A(U.y);U.z=A(U.z);s.append(" lattice ").append(JU.Escape.eP(U));q?(B="mapLattice",y=U):(ua=U,12293==this.tokAt(m+1)&&(s.append(" fixed"),za=!0,m++));break;default:1073741824==V&&(B="thisID",y=la);if(!b.setMeshDisplayProperty(a,
0,V)){if(JS.T.tokAttr(V,1073741824)&&!xa){this.setShapeId(a,m,xa);m=b.iToken;break}this.invArg()}0==c&&(c=m);m=this.slen-1}xa=12291!=V;hb&&k&&this.invArg();null!=B&&this.addShapeProperty(E,B,y)}if(!this.chk){if((R||ea)&&!k)k=!0,this.addShapeProperty(E,"bsSolvent",ea?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(E,"sasurface",Float.$valueOf(0));t&&(!k&&!q)&&(this.addShapeProperty(E,"nomap",Float.$valueOf(0)),k=!0);null!=T&&this.addShapeProperty(E,"getSurfaceSets",T);if(null!=
Na)this.addShapeProperty(E,"colorDiscrete",Na);else if("sets".equals(ra))this.addShapeProperty(E,"setColorScheme",null);else if(null!=ra){var eb=this.vwr.cm.getColorEncoder(ra);null!=eb&&(eb.isTranslucent=Ha,eb.hi=3.4028235E38,this.addShapeProperty(E,"remapColor",eb))}if(k&&!j&&0!=s.indexOf(";")){E.add(0,D(-1,["newObject",null]));var $b=null==Z;$b&&(Z=JU.BSUtil.copy(this.vwr.bsA()));0>aa&&(aa=this.vwr.am.cmi);Z.and(this.vwr.getModelUndeletedAtomsBitSet(aa));null!=Ma&&(1<this.vwr.ms.getModelBS(Z,!1).cardinality()&&
b.errorStr(30,"ISOSURFACE "+Ma),$b&&(E.add(0,D(-1,["select",Z])),0==s.indexOf("; isosurface map")&&(s=(new JU.SB).append("; isosurface map select ").append(JU.Escape.eBS(Z)).append(s.substring(16)))))}C&&!F&&(k||this.addShapeProperty(E,"sasurface",Float.$valueOf(0)),q||(this.addShapeProperty(E,"map",Boolean.TRUE),this.addShapeProperty(E,"select",W),this.addShapeProperty(E,"sasurface",Float.$valueOf(0))),this.addShapeProperty(E,"slab",this.getCapSlabObject(-100,!1)));var ac=k&&this.vwr.getBoolean(603979934);
ac&&JU.Logger.startTimer("isosurface");this.setShapeProperty(a,"setProperties",E);ac&&this.showString(JU.Logger.getTimerMsg("isosurface",0));Ja&&(this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,"token",Integer.$valueOf(1073742046)),p=!0,s.append(" mesh nofill frontOnly"))}null!=ua&&(this.setShapeProperty(a,"lattice",ua),za&&this.setShapeProperty(a,"fixLattice",Boolean.TRUE));null!=Fa&&this.setShapeProperty(a,"symops",Fa);p&&this.setShapeProperty(a,"token",Integer.$valueOf(1073741960));
0<c&&(b.setMeshDisplayProperty(a,c,0)||this.invArg());if(!this.chk){var Da=null,Ea=null;l&&(Da=this.getShapeProperty(a,"area"),ba(Da,Float)?this.vwr.setFloatProperty("isosurfaceArea",Da.floatValue()):this.vwr.g.setUserVariable("isosurfaceArea",JS.SV.getVariableAD(Da)));Aa&&(Ea=Aa?this.getShapeProperty(a,"volume"):null,ba(Ea,Float)?this.vwr.setFloatProperty("isosurfaceVolume",Ea.floatValue()):this.vwr.g.setUserVariable("isosurfaceVolume",JS.SV.getVariableAD(Ea)));if(!j){ha=null;q&&!k?this.setShapeProperty(a,
"finalize",s.toString()):k&&(O=s.toString(),this.setShapeProperty(a,"finalize",(0==O.indexOf("; isosurface map")?"":" select "+JU.Escape.eBS(Z)+" ")+O),ha=this.getShapeProperty(a,"ID"),null!=ha&&(!b.tQuiet&&!g)&&(ca=this.getShapeProperty(a,"cutoff").floatValue(),Float.isNaN(ca)&&!Float.isNaN(da)&&JU.Logger.error("sigma not supported"),ha+=" created "+this.getShapeProperty(a,"message")));var zb,Ab;if(l||Aa)zb=l?"isosurfaceArea = "+(ba(Da,Float)?""+Da:JU.Escape.eAD(Da)):null,Ab=Aa?"isosurfaceVolume = "+
(ba(Ea,Float)?""+Ea:JU.Escape.eAD(Ea)):null,null==ha?(l&&this.showString(zb),Aa&&this.showString(Ab)):(l&&(ha+="\n"+zb),Aa&&(ha+="\n"+Ab));null!=ha&&!g&&this.showString(ha);k&&(ha=this.getShapeProperty(a,"output"),null!=ha&&!g&&this.showString(ha))}null!=kb&&this.setShapeProperty(a,"translucency",kb);this.setShapeProperty(a,"clear",null);P&&this.setShapeProperty(a,"cache",null);!g&&(!f&&!F&&12291!=b.theTok)&&this.listIsosurface(a)}}},"~N");e(d,"lcaoCartoon",function(){var a=this.e;a.sm.loadShape(26);
if(!(1073742001==a.tokAt(1)&&this.listIsosurface(26)))if(this.setShapeProperty(26,"init",a.fullCommand),1==this.slen)this.setShapeProperty(26,"lcaoID",null);else{for(var b=!1,c=null,c=1;c<this.slen;c++){var f=null,z=null;switch(this.getToken(c).tok){case 1073741875:case 554176565:f=a.theToken.value;1073742334==this.tokAt(c+1)&&(a.iToken=c+1);z=this.getCapSlabObject(c,!0);c=a.iToken;break;case 12289:this.isosurface(26);return;case 528432:var d=z=0,h=0;switch(this.getToken(++c).tok){case 1111492629:z=
0.017453292519943295*this.floatParameter(++c);break;case 1111492630:d=0.017453292519943295*this.floatParameter(++c);break;case 1111492631:h=0.017453292519943295*this.floatParameter(++c);break;default:this.invArg()}f="rotationAxis";z=JU.V3.new3(z,d,h);break;case 1073742335:case 1610625028:case 2097192:f="on";break;case 1073742334:case 12294:case 2097194:f="off";break;case 12291:f="delete";break;case 12290:case 10:case 1073742325:f="select";z=this.atomExpressionAt(c);c=a.iToken;break;case 1140850693:f=
"reversecolor";z=Boolean.TRUE;1073742335==this.tokAt(c+1)?++c:1073742334==this.tokAt(c+1)&&(z=Boolean.FALSE,++c);break;case 1765808134:c=this.setColorOptions(null,c+1,26,-2);null!=c&&this.setShapeProperty(26,"settranslucency",c);c=a.iToken;b=!0;continue;case 603979967:case 1073742074:a.setMeshDisplayProperty(26,c,a.theTok);c=a.iToken;b=!0;continue;case 1112152075:case 4:z=this.paramAsStr(c).toLowerCase();z.equals("spacefill")&&(z="cpk");f="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&
(c++,f="molecular");break;case 1275082241:a.isAtomExpression(c+1)?(f="select",z=this.atomExpressionAt(c+1),c=a.iToken):(f="selectType",z=this.paramAsStr(++c),z.equals("spacefill")&&(z="cpk"));break;case 536875059:f="scale";z=Float.$valueOf(this.floatParameter(++c));break;case 1073742004:case 1073742006:f="lonePair";break;case 1073742112:case 1073742111:f="radical";break;case 1073742028:f="molecular";break;case 1073741904:z=this.paramAsStr(++c);f="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&
(c++,f="molecular");break;case 1073741974:z=a.setShapeNameParameter(++c);c=a.iToken;b&&this.invArg();f="lcaoID";break;default:if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824))268441089!=a.theTok&&(z=this.paramAsStr(c)),b&&this.invArg(),f="lcaoID"}12291!=a.theTok&&(b=!0);null==f&&this.invArg();this.setShapeProperty(26,f,z)}this.setShapeProperty(26,"clear",null)}});e(d,"contact",function(){var a=this.e;a.sm.loadShape(25);if(1073742001==this.tokAt(1)&&this.listIsosurface(25))return!1;var b=
0;a.iToken=1;for(var c=null!=this.initIsosurface(25),f=c&&null==this.getShapeProperty(25,"ID"),z=null,d=null,h=null,e=null,j=null,g=!1,k=new JU.SB,t=2147483647,q=134217750,N=0,w=NaN,l=NaN,u=!0,A=null,I=null,ea=0,P=!1,K=-2147483648,F=1<a.iToken,C=a.iToken;C<this.slen;++C){switch(h=this.getToken(C).tok){default:F=!0;if(!a.setMeshDisplayProperty(25,0,a.theTok)){268441089!=a.theTok&&!JS.T.tokAttr(a.theTok,1073741824)&&this.invArg();this.setShapeId(25,C,c);C=a.iToken;break}0==b&&(b=C);C=a.iToken;continue;
case 1073741974:F=!0;this.setShapeId(25,++C,c);f=null==this.getShapeProperty(25,"ID");C=a.iToken;break;case 1765808134:switch(this.tokAt(C+1)){case 1073741914:h=0;g=!0;k.append(" color density");C++;break;case 1140850696:h=0,P=!0,k.append(" color type"),C++}if(0==h)break;case 603979967:case 1073742074:F=!0;0==ea&&(ea=C);a.setMeshDisplayProperty(25,C,a.theTok);C=a.iToken;break;case 554176565:F=!0;I=this.getCapSlabObject(C,!1);this.setShapeProperty(25,"slab",I);C=a.iToken;break;case 1073741914:g=!0;
k.append(" density");this.isFloatParameter(C+1)&&(null==j&&(j=x(1,0)),j[0]=-Math.abs(this.floatParameter(++C)),k.append(" "+-j[0]));break;case 1073742122:c=this.floatParameter(++C);0<c&&(k.append(" resolution ").appendF(c),this.setShapeProperty(25,"resolution",Float.$valueOf(c)));break;case 1094717454:case 1094713359:K=1094713359==a.theTok?this.intParameter(++C):a.modelNumberParameter(++C);k.append(" modelIndex "+K);break;case 134217759:case 1275069443:w=this.floatParameter(++C);k.append(" within ").appendF(w);
break;case 268440577:case 2:case 3:e=a.encodeRadiusParameter(C,!1,!1);if(null==e)return!1;k.append(" ").appendO(e);C=a.iToken;break;case 1073741990:case 1073741989:A=1073741989==h?Boolean.TRUE:Boolean.FALSE;k.append(" ").appendO(a.theToken.value);break;case 1073742020:t=this.intParameter(++C);break;case 1613238294:case 1073741881:case 1648363544:N=h;k.append(" ").appendO(a.theToken.value);break;case 1073742135:this.isFloatParameter(C+1)&&(l=this.floatParameter(++C));case 1073741875:case 1073742036:case 2097180:u=
!1;case 1275068932:case 1073741961:case 134217750:case 4106:q=h;k.append(" ").appendO(a.theToken.value);1073742135==h&&k.append(" ").appendF(l);break;case 1073742083:j=a.floatParameterSet(++C,1,10);C=a.iToken;break;case 12290:case 10:case 1073742325:(f||null!=d)&&this.invArg(),h=JU.BSUtil.copy(this.atomExpressionAt(C)),C=a.iToken,null==z?z=h:d=h,k.append(" ").append(JU.Escape.eBS(h))}c=12291!=a.theTok}!F&&null==z&&this.error(13);if(this.chk)return!1;if(null!=z){1648363544==N&&null==e&&(e=new J.atomdata.RadiusData(null,
0,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO));C=null==e?new J.atomdata.RadiusData(null,0.26,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO):e;d=1073742036==q&&null==d&&null!=A&&A.booleanValue()?z:a.getMathExt().setContactBitSets(z,d,u,w,C,!0);switch(q){case 1073741875:case 1073742135:C=a.lookupIdentifierValue("solvent");z.andNot(C);d.andNot(C);d.andNot(z);break;case 2097180:d.andNot(z);break;case 1073742036:2147483647==t&&(t=100),this.setShapeProperty(25,"minset",Integer.$valueOf(t)),
k.append(" minSet ").appendI(t),null==j&&(j=x(-1,[0.5,2]))}null!=A&&(j=null==j?x(2,0):JU.AU.ensureLengthA(j,2),j[1]=A.booleanValue()?1:2);null!=j&&k.append(" parameters ").append(JU.Escape.eAF(j));this.setShapeProperty(25,"set",D(-1,[Integer.$valueOf(N),Integer.$valueOf(q),Boolean.$valueOf(g),Boolean.$valueOf(P),z,d,e,Float.$valueOf(l),j,Integer.$valueOf(K),k.toString()]));0<ea&&a.setMeshDisplayProperty(25,ea,0)}0<b&&(a.setMeshDisplayProperty(25,b,0)||this.invArg());null!=I&&null!=z&&this.setShapeProperty(25,
"slab",I);if(null!=z&&(1073742036==q||u)){z=this.getShapeProperty(25,"volume");b=1073741961==q;if(JU.AU.isAD(z))for(C=a=0;C<z.length;C++)a+=b?z[C]:Math.abs(z[C]);else a=z.floatValue();a=Math.round(1E3*a)/1E3;if(g||1275068932!=q)g=this.getShapeProperty(25,"nSets").intValue(),g="Contacts: "+(0>g?G(-g/2):g),0!=a&&(g+=", with "+(b?"approx ":"net ")+"volume "+a+" A^3"),this.showString(g)}return!0});e(d,"cgo",function(){var a=this.e;a.sm.loadShape(23);if(1073742001==this.tokAt(1)&&this.listIsosurface(23))return!1;
for(var b=0,c=null!=this.initIsosurface(23),f=c&&null==this.getShapeProperty(23,"ID"),d=!1,r=-1,h=null,e=3.4028235E38,j=u(-1,[-2147483648]),g=0,k=a.iToken;k<this.slen;++k){var t=null,r=null;switch(this.getToken(k).tok){case 268437504:case 1073742195:case 7:(null!=h||f)&&this.invArg();h=new JU.Lst;k=u(-1,[k,this.slen]);a.getShapePropertyData(23,"data",D(-1,[this.st,k,h,this.vwr]))||this.invArg();k=k[0];continue;case 536875059:++k>=this.slen&&this.error(34);switch(this.getToken(k).tok){case 2:g=this.intParameter(k);
continue;case 3:g=Math.round(100*this.floatParameter(k));continue}this.error(34);break;case 12293:t="modelIndex";r=Integer.$valueOf(-1);break;case 1094713359:case 1094717454:r=1094713359==a.theTok?this.intParameter(++k):a.modelNumberParameter(++k);t="modelIndex";r=Integer.$valueOf(r);break;case 1765808134:case 603979967:case 1073742074:e=this.getColorTrans(a,k,!1,j);k=a.iToken;c=!0;continue;case 1073741974:this.setShapeId(23,++k,c);f=null==this.getShapeProperty(23,"ID");k=a.iToken;break;default:if(!a.setMeshDisplayProperty(23,
0,a.theTok)){if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(23,k,c);k=a.iToken;break}this.invArg()}0==b&&(b=k);k=a.iToken;continue}c=12291!=a.theTok;null!=h&&!d&&(t="points",r=Integer.$valueOf(g),d=!0,g=0);null!=t&&this.setShapeProperty(23,t,r)}this.finalizeObject(23,j[0],e,g,null!=h,h,b,null);return!0});e(d,"getAtomicPotentials",function(a,b,c){var f=x(this.vwr.ms.ac,0),d=J.api.Interface.getOption("quantum.MlpCalculation",this.vwr,"script");d.set(this.vwr);c=null==c?null:
this.vwr.getFileAsString3(c,!1,null);try{d.assignPotentials(this.vwr.ms.at,f,this.vwr.getSmartsMatch("a",a),this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]",a),b,c)}catch(r){if(!$(r,Exception))throw r;}return f},"JU.BS,JU.BS,~S");e(d,"getCapSlabObject",function(a,b){if(0>a)return JU.TempArray.getSlabWithinRange(a,0);var c=this.e,f=null,d=554176565==this.tokAt(a),r=this.tokAt(a+1),h=null,e=h=null,j=null,g=null;if(603979967==r)switch(j=this.isFloatParameter(++a+1)?this.floatParameter(++a):
0.5,c.isColorParam(a+1)?(j=Short.$valueOf(JU.C.getColixTranslucent3(JU.C.getColix(c.getArgbParam(a+1)),0!=j,j)),a=c.iToken):j=Short.$valueOf(JU.C.getColixTranslucent3(1,0!=j,j)),r=this.tokAt(a+1)){case 1073742018:case 1073741938:g=Integer.$valueOf(r);r=this.tokAt(++a+1);break;default:g=Integer.$valueOf(1073741938)}switch(r){case 1073742334:return c.iToken=a+1,Integer.$valueOf(-2147483648);case 1073742333:c.iToken=a+1;break;case 1073742330:a++;f=D(-1,[Float.$valueOf(1),this.paramAsStr(++a)]);r=1073742018;
break;case 134217759:a++;if(1073742114==this.tokAt(++a))f=this.floatParameter(++a),r=this.floatParameter(++a),f=D(-1,[Float.$valueOf(f),Float.$valueOf(r)]),r=1073742114;else if(this.isFloatParameter(a)){f=this.floatParameter(a);if(c.isCenterParameter(++a)){var h=Array(1),k=c.centerParameter(a,h);if(this.chk||!ba(h[0],"JU.BS"))h=D(-1,[k]);else for(var k=this.vwr.ms.at,e=h[0],h=Array(e.cardinality()),t=0,q=e.nextSetBit(0);0<=q;q=e.nextSetBit(q+1),t++)h[t]=k[q]}else h=c.getPointArray(a,-1,!1);0==h.length&&
(c.iToken=a,this.invArg());f=D(-1,[Float.$valueOf(f),h,e])}else f=c.getPointArray(a,4,!1),r=1812599299;break;case 1812599299:c.iToken=a+1;f=JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(),null);break;case 1073741872:case 1814695966:c.iToken=a+1;c=this.vwr.getCurrentUnitCell();if(null==c)1814695966==r&&this.invArg();else{h=JU.BoxInfo.toOABC(c.getUnitCellVerticesNoOffset(),c.getCartesianOffset());c=A(c.getUnitCellInfoType(6));f=e=null;switch(c){case 1:f=JU.V3.newVsub(h[2],h[0]),f.scale(1E3);case 2:e=
JU.V3.newVsub(h[1],h[0]),e.scale(1E3),h[0].sub(e),h[1].scale(2E3),1==c&&(h[0].sub(f),h[2].scale(2E3))}f=h}break;case 12290:case 10:case 1073742325:if(f=this.atomExpressionAt(a+1),r=3,!c.isCenterParameter(++c.iToken)){d=!0;break}default:if(!b&&d&&this.isFloatParameter(a+1)){f=this.floatParameter(++a);if(!this.isFloatParameter(a+1))return Integer.$valueOf(A(f));r=this.floatParameter(++a);f=D(-1,[Float.$valueOf(f),Float.$valueOf(r)]);r=1073742114;break}h=c.planeParameter(++a,!1);r=this.isFloatParameter(c.iToken+
1)?this.floatParameter(++c.iToken):NaN;Float.isNaN(r)||(h.w-=r);f=h;r=134217750}j=null==g?null:D(-1,[g,j]);return JU.TempArray.getSlabObjectType(r,f,!d,j)},"~N,~B");e(d,"setColorOptions",function(a,b,c,f){var d=this.e;this.getToken(b);var r="opaque";if(603979967==d.theTok)if(r="translucent",0>f){var h=this.isFloatParameter(b+1)?this.floatParameter(++b):3.4028235E38;d.setShapeTranslucency(c,null,"translucent",h,null);null!=a&&(a.append(" translucent"),3.4028235E38!=h&&a.append(" ").appendF(h))}else d.setMeshDisplayProperty(c,
b,d.theTok);else 1073742074==d.theTok?0<=f&&d.setMeshDisplayProperty(c,b,d.theTok):d.iToken--;f=Math.abs(f);for(h=0;h<f;h++)if(d.isColorParam(d.iToken+1)){var e=d.getArgbParam(++d.iToken);this.setShapeProperty(c,"colorRGB",Integer.$valueOf(e));null!=a&&a.append(" ").append(JU.Escape.escapeColor(e))}else if(d.iToken<b)this.invArg();else break;return r},"JU.SB,~N,~N,~N");e(d,"createFunction",function(a,b,c){var f=(new JS.ScriptEval).setViewer(this.vwr);try{f.compileScript(null,"function "+a+"("+b+") { return "+
c+"}",!1);var d=new JU.Lst;for(a=0;a<b.length;a+=2)d.addLast(JS.SV.newF(0).setName(b.substring(a,a+1)));return D(-1,[f.aatoken[0][1].value,d])}catch(r){if($(r,Exception))return null;throw r;}},"~S,~S,~S");e(d,"getWithinDistanceVector",function(a,b,c,f,d){var r=new JU.Lst,h=Array(2);if(null==f){var e=JU.P3.new3(b,b,b),j=JU.P3.newP(c);j.sub(e);e.add(c);h[0]=j;h[1]=e;r.addLast(c)}else c=this.vwr.ms.getBoxInfo(f,-Math.abs(2*b)),h[0]=c.getBoundBoxVertices()[0],h[1]=c.getBoundBoxVertices()[7],1==f.cardinality()&&
r.addLast(this.vwr.ms.at[f.nextSetBit(0)]);1==r.size()&&!d&&(this.addShapeProperty(a,"withinDistance",Float.$valueOf(b)),this.addShapeProperty(a,"withinPoint",r.get(0)));this.addShapeProperty(a,d?"displayWithin":"withinPoints",D(-1,[Float.$valueOf(b),h,f,r]));return h},"JU.Lst,~N,JU.P3,JU.BS,~B");e(d,"addShapeProperty",function(a,b,c){this.chk||a.addLast(D(-1,[b,c]))},"JU.Lst,~S,~O");e(d,"floatArraySetXYZ",function(a,b,c,f){var d=this.e,r=this.tokAt(a++);1073742195==r&&(r=this.tokAt(a++));(268437504!=
r||0>=b)&&this.invArg();for(var h=JU.AU.newFloat3(b,-1),e=0;268437505!=r;)switch(r=this.getToken(a).tok,r){case 1073742195:case 268437505:continue;case 268436992:a++;break;case 268437504:h[e++]=this.floatArraySet(a,c,f);a=++d.iToken;r=0;e==b&&268437505!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return h},"~N,~N,~N,~N");e(d,"floatArraySet",function(a,b,c){var f=this.tokAt(a++);1073742195==f&&(f=this.tokAt(a++));268437504!=f&&this.invArg();for(var d=JU.AU.newFloat2(b),r=0;268437505!=
f;)switch(f=this.getToken(a).tok,f){case 1073742195:case 268437505:continue;case 268436992:a++;break;case 268437504:a++;f=x(c,0);d[r++]=f;for(var h=0;h<c;h++)f[h]=this.floatParameter(a++),268436992==this.tokAt(a)&&a++;268437505!=this.tokAt(a++)&&this.invArg();f=0;r==b&&268437505!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return d},"~N,~N,~N");e(d,"initIsosurface",function(a){var b=this.e;this.setShapeProperty(a,"init",b.fullCommand);b.iToken=0;var c=this.tokAt(1),f=this.tokAt(2);if(12291==
c||12291==f&&1073742327==this.tokAt(++b.iToken))return this.setShapeProperty(a,"delete",null),b.iToken+=2,this.slen>b.iToken&&(this.setShapeProperty(a,"init",b.fullCommand),this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+")),null;b.iToken=1;return!b.setMeshDisplayProperty(a,0,c)&&(this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+"),22!=a&&this.setShapeProperty(a,"title",D(-1,[b.thisCommand])),1073741974!=c&&(268441089==f||268441089==c&&b.setMeshDisplayProperty(a,0,f)))?(a=this.setShapeId(a,1,!1),
b.iToken++,a):null},"~N");e(d,"listIsosurface",function(a){var b=3<this.slen?"0":0==this.tokAt(2)?"":" "+this.getToken(2).value;this.chk||this.showString(this.getShapeProperty(a,"list"+b));return!0},"~N");e(d,"getBoxPoints",function(a,b,c,f){switch(a){case 1814695966:return null==b?null:b.getCanonicalCopy(f,!0);case 1812599299:return null==c?a=this.vwr.ms.getBoxInfo():(a=new JU.BoxInfo,this.vwr.calcAtomsMinMax(c,a)),JU.BoxInfo.getCanonicalCopy(a.getBoundBoxVertices(),f);default:return null}},"~N,J.api.SymmetryInterface,JU.BS,~N")});
R("JU");S(["JU.TriangleData"],"JU.Triangulator","JU.AU $.BS $.Lst $.Measure $.P3 $.P4 $.V3".split(" "),function(){var d=za(JU,"Triangulator",JU.TriangleData);e(d,"intersectLine",function(a,b,c,f){b=new JU.V3;for(var d=new JU.V3,r=new JU.V3,h=new JU.V3,e=null,j=null,g=new JU.P3,k=new JU.P4,t=3.4028235E38,q=-3.4028235E38,N=0;12>N;N++){var w=JU.Triangulator.fullCubePolygon[N];if(0==N%2){JU.Measure.getPlaneThroughPoints(a[w[0]],a[w[1]],a[w[2]],b,d,k);if(null==JU.Measure.getIntersection(c,f,k,g,b,r)){N++;
continue}h.sub2(g,c)}if(JU.Measure.isInTriangle(g,a[w[0]],a[w[1]],a[w[2]],b,d,r)){w=f.dot(h);w<t&&(t=w,e=g);w>q&&(q=w,j=g);0==N%2&&N++;if(0.01<q-t)break;g=new JU.P3}}return null==e||(null==j||0.001>e.distance(j))&&null==(j=e)?null:D(-1,[e,j])},"~A,~N,JU.P3,JU.V3");e(d,"getCellProjection",function(a,b){for(var c=new JU.V3,f=0,d=-3.4028235E38,r=0,h=Array(8),e=0;8>e;e++)f=b[e].dot(a),f>d&&(d=f,r=e),JU.Measure.getPlaneProjection(b[e],a,h[e]=new JU.P3,c);f=JU.Triangulator.fullCubeCorners[r][3];c=JU.AU.newInt2(6);
for(e=d=0;12>e;e++)if(0!=(f&JU.TriangleData.Pwr2[e])){var g=u(4,0),n=JU.Triangulator.fullCubePolygon[e];g[0]=n[0];g[1]=n[1];g[2]=n[2];g[3]=n[0]==r?2:n[1]==r?0:n[2]==r?1:3;c[d++]=g}r=new JU.Lst;r.addLast(h);r.addLast(c);return r},"JU.P4,~A");e(d,"intersectPlane",function(a,b,c){if(-1==c&&8==b.length)return this.getCellProjection(a,b);for(var f=new JU.Lst,d=Array(12),r=0,e=x(8,0),v=0;8>v;v++)e[v]=a.x*b[v].x+a.y*b[v].y+a.z*b[v].z+a.w,0>e[v]&&(r|=JU.TriangleData.Pwr2[v]);a=JU.TriangleData.triangleTable2[r];
if(null==a)return null;for(v=0;24>v;v+=2){var r=JU.TriangleData.edgeVertexes[v],g=JU.TriangleData.edgeVertexes[v+1],n=JU.P3.newP(b[g]);n.sub(b[r]);n.scale(e[r]/(e[r]-e[g]));n.add(b[r]);d[v>>1]=n}if(0==c){c=new JU.BS;for(v=0;v<a.length;v++)c.set(a[v]),2==v%4&&v++;v=c.cardinality();e=Array(v);f.addLast(e);b=u(12,0);for(v=r=0;v<a.length;v++)g=a[v],c.get(g)&&(c.clear(g),e[r]=d[g],b[g]=r++),2==v%4&&v++;d=JU.AU.newInt2(a.length>>2);f.addLast(d);for(v=0;v<a.length;v++)d[v>>2]=u(-1,[b[a[v++]],b[a[v++]],b[a[v++]],
a[v]]);return f}for(v=0;v<a.length;v++)b=d[a[v++]],e=d[a[v++]],r=d[a[v++]],1==(c&1)&&f.addLast(D(-1,[b,e,r])),2==(c&2)&&(g=a[v],1==(g&1)&&f.addLast(D(-1,[b,e])),2==(g&2)&&f.addLast(D(-1,[e,r])),4==(g&4)&&f.addLast(D(-1,[b,r])));return f},"JU.P4,~A,~N");d.fullCubePolygon=D(-1,[u(-1,[0,4,5,3]),u(-1,[5,1,0,3]),u(-1,[1,5,6,2]),u(-1,[6,2,1,3]),u(-1,[2,6,7,2]),u(-1,[7,3,2,3]),u(-1,[3,7,4,2]),u(-1,[4,0,3,2]),u(-1,[6,5,4,0]),u(-1,[4,7,6,0]),u(-1,[0,1,2,0]),u(-1,[2,3,0,0])]);d.fullCubeCorners=D(-1,[u(-1,[1,
4,3,3267]),u(-1,[0,2,5,3087]),u(-1,[1,3,6,3132]),u(-1,[2,0,7,3312]),u(-1,[0,5,7,963]),u(-1,[1,6,4,783]),u(-1,[2,7,5,828]),u(-1,[3,4,6,1008])])});R("JU");S(["JU.P3i"],"JU.TriangleData",null,function(){var d=za(JU,"TriangleData",null);d.Pwr2=u(-1,[1,2,4,8,16,32,64,128,256,512,1024,2048]);d.cubeVertexOffsets=D(-1,[JU.P3i.new3(0,0,0),JU.P3i.new3(1,0,0),JU.P3i.new3(1,0,1),JU.P3i.new3(0,0,1),JU.P3i.new3(0,1,0),JU.P3i.new3(1,1,0),JU.P3i.new3(1,1,1),JU.P3i.new3(0,1,1)]);d.edgeVertexes=g(-1,[0,1,1,2,2,3,3,
0,4,5,5,6,6,7,7,4,0,4,1,5,2,6,3,7]);d.triangleTable2=D(-1,[null,g(-1,[0,8,3,7]),g(-1,[0,1,9,7]),g(-1,[1,8,3,6,9,8,1,5]),g(-1,[1,2,10,7]),g(-1,[0,8,3,7,1,2,10,7]),g(-1,[9,2,10,6,0,2,9,5]),g(-1,[2,8,3,6,2,10,8,1,10,9,8,3]),g(-1,[3,11,2,7]),g(-1,[0,11,2,6,8,11,0,5]),g(-1,[1,9,0,7,2,3,11,7]),g(-1,[1,11,2,6,1,9,11,1,9,8,11,3]),g(-1,[3,10,1,6,11,10,3,5]),g(-1,[0,10,1,6,0,8,10,1,8,11,10,3]),g(-1,[3,9,0,6,3,11,9,1,11,10,9,3]),g(-1,[9,8,10,5,10,8,11,6]),g(-1,[4,7,8,7]),g(-1,[4,3,0,6,7,3,4,5]),g(-1,[0,1,9,
7,8,4,7,7]),g(-1,[4,1,9,6,4,7,1,1,7,3,1,3]),g(-1,[1,2,10,7,8,4,7,7]),g(-1,[3,4,7,6,3,0,4,3,1,2,10,7]),g(-1,[9,2,10,6,9,0,2,3,8,4,7,7]),g(-1,[2,10,9,3,2,9,7,0,2,7,3,6,7,9,4,6]),g(-1,[8,4,7,7,3,11,2,7]),g(-1,[11,4,7,6,11,2,4,1,2,0,4,3]),g(-1,[9,0,1,7,8,4,7,7,2,3,11,7]),g(-1,[4,7,11,3,9,4,11,1,9,11,2,2,9,2,1,6]),g(-1,[3,10,1,6,3,11,10,3,7,8,4,7]),g(-1,[1,11,10,6,1,4,11,0,1,0,4,3,7,11,4,5]),g(-1,[4,7,8,7,9,0,11,1,9,11,10,6,11,0,3,6]),g(-1,[4,7,11,3,4,11,9,4,9,11,10,6]),g(-1,[9,5,4,7]),g(-1,[9,5,4,7,0,
8,3,7]),g(-1,[0,5,4,6,1,5,0,5]),g(-1,[8,5,4,6,8,3,5,1,3,1,5,3]),g(-1,[1,2,10,7,9,5,4,7]),g(-1,[3,0,8,7,1,2,10,7,4,9,5,7]),g(-1,[5,2,10,6,5,4,2,1,4,0,2,3]),g(-1,[2,10,5,3,3,2,5,1,3,5,4,2,3,4,8,6]),g(-1,[9,5,4,7,2,3,11,7]),g(-1,[0,11,2,6,0,8,11,3,4,9,5,7]),g(-1,[0,5,4,6,0,1,5,3,2,3,11,7]),g(-1,[2,1,5,3,2,5,8,0,2,8,11,6,4,8,5,5]),g(-1,[10,3,11,6,10,1,3,3,9,5,4,7]),g(-1,[4,9,5,7,0,8,1,5,8,10,1,2,8,11,10,3]),g(-1,[5,4,0,3,5,0,11,0,5,11,10,6,11,0,3,6]),g(-1,[5,4,8,3,5,8,10,4,10,8,11,6]),g(-1,[9,7,8,6,5,
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1,11,0,3,6,10,5,0,1,8,0,7,5,5,7,0,1]),g(-1,[11,10,5,3,7,11,5,5]),g(-1,[10,6,5,7]),g(-1,[0,8,3,7,5,10,6,7]),g(-1,[9,0,1,7,5,10,6,7]),g(-1,[1,8,3,6,1,9,8,3,5,10,6,7]),g(-1,[1,6,5,6,2,6,1,5]),g(-1,[1,6,5,6,1,2,6,3,3,0,8,7]),g(-1,[9,6,5,6,9,0,6,1,0,2,6,3]),g(-1,[5,9,8,3,5,8,2,0,5,2,6,6,3,2,8,5]),g(-1,[2,3,11,7,10,6,5,7]),g(-1,[11,0,8,6,11,2,0,3,10,6,5,7]),g(-1,[0,1,9,7,2,3,11,7,5,10,6,7]),g(-1,[5,10,6,7,1,9,2,5,9,11,2,2,9,8,11,3]),g(-1,[6,3,11,6,6,5,3,1,5,1,3,3]),g(-1,[0,8,11,3,0,11,5,0,0,5,1,6,5,11,
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9,6,10,6,4,3,11,2,3,7]),g(-1,[0,8,2,5,2,8,11,6,4,9,10,3,4,10,6,6]),g(-1,[3,11,2,7,0,1,6,1,0,6,4,6,6,1,10,6]),g(-1,[6,4,1,1,6,1,10,6,4,8,1,1,2,1,11,5,8,11,1,1]),g(-1,[9,6,4,6,9,3,6,0,9,1,3,3,11,6,3,5]),g(-1,[8,11,1,1,8,1,0,6,11,6,1,1,9,1,4,5,6,4,1,1]),g(-1,[3,11,6,3,3,6,0,4,0,6,4,6]),g(-1,[6,4,8,3,11,6,8,5]),g(-1,[7,10,6,6,7,8,10,1,8,9,10,3]),g(-1,[0,7,3,6,0,10,7,0,0,9,10,3,6,7,10,5]),g(-1,[10,6,7,3,1,10,7,1,1,7,8,2,1,8,0,6]),g(-1,[10,6,7,3,10,7,1,4,1,7,3,6]),g(-1,[1,2,6,3,1,6,8,0,1,8,9,6,8,6,7,6]),
g(-1,[2,6,9,1,2,9,1,6,6,7,9,1,0,9,3,5,7,3,9,1]),g(-1,[7,8,0,3,7,0,6,4,6,0,2,6]),g(-1,[7,3,2,3,6,7,2,5]),g(-1,[2,3,11,7,10,6,8,1,10,8,9,6,8,6,7,6]),g(-1,[2,0,7,1,2,7,11,6,0,9,7,1,6,7,10,5,9,10,7,1]),g(-1,[1,8,0,6,1,7,8,2,1,10,7,1,6,7,10,5,2,3,11,7]),g(-1,[11,2,1,3,11,1,7,4,10,6,1,5,6,7,1,1]),g(-1,[8,9,6,1,8,6,7,6,9,1,6,1,11,6,3,5,1,3,6,1]),g(-1,[0,9,1,7,11,6,7,7]),g(-1,[7,8,0,3,7,0,6,4,3,11,0,5,11,6,0,1]),g(-1,[7,11,6,7]),g(-1,[7,6,11,7]),g(-1,[3,0,8,7,11,7,6,7]),g(-1,[0,1,9,7,11,7,6,7]),g(-1,[8,1,
9,6,8,3,1,3,11,7,6,7]),g(-1,[10,1,2,7,6,11,7,7]),g(-1,[1,2,10,7,3,0,8,7,6,11,7,7]),g(-1,[2,9,0,6,2,10,9,3,6,11,7,7]),g(-1,[6,11,7,7,2,10,3,5,10,8,3,2,10,9,8,3]),g(-1,[7,2,3,6,6,2,7,5]),g(-1,[7,0,8,6,7,6,0,1,6,2,0,3]),g(-1,[2,7,6,6,2,3,7,3,0,1,9,7]),g(-1,[1,6,2,6,1,8,6,0,1,9,8,3,8,7,6,3]),g(-1,[10,7,6,6,10,1,7,1,1,3,7,3]),g(-1,[10,7,6,6,1,7,10,4,1,8,7,2,1,0,8,3]),g(-1,[0,3,7,3,0,7,10,0,0,10,9,6,6,10,7,5]),g(-1,[7,6,10,3,7,10,8,4,8,10,9,6]),g(-1,[6,8,4,6,11,8,6,5]),g(-1,[3,6,11,6,3,0,6,1,0,4,6,3]),
g(-1,[8,6,11,6,8,4,6,3,9,0,1,7]),g(-1,[9,4,6,3,9,6,3,0,9,3,1,6,11,3,6,5]),g(-1,[6,8,4,6,6,11,8,3,2,10,1,7]),g(-1,[1,2,10,7,3,0,11,5,0,6,11,2,0,4,6,3]),g(-1,[4,11,8,6,4,6,11,3,0,2,9,5,2,10,9,3]),g(-1,[10,9,3,1,10,3,2,6,9,4,3,1,11,3,6,5,4,6,3,1]),g(-1,[8,2,3,6,8,4,2,1,4,6,2,3]),g(-1,[0,4,2,5,4,6,2,3]),g(-1,[1,9,0,7,2,3,4,1,2,4,6,6,4,3,8,6]),g(-1,[1,9,4,3,1,4,2,4,2,4,6,6]),g(-1,[8,1,3,6,8,6,1,0,8,4,6,3,6,10,1,3]),g(-1,[10,1,0,3,10,0,6,4,6,0,4,6]),g(-1,[4,6,3,1,4,3,8,6,6,10,3,1,0,3,9,5,10,9,3,1]),g(-1,
[10,9,4,3,6,10,4,5]),g(-1,[4,9,5,7,7,6,11,7]),g(-1,[0,8,3,7,4,9,5,7,11,7,6,7]),g(-1,[5,0,1,6,5,4,0,3,7,6,11,7]),g(-1,[11,7,6,7,8,3,4,5,3,5,4,2,3,1,5,3]),g(-1,[9,5,4,7,10,1,2,7,7,6,11,7]),g(-1,[6,11,7,7,1,2,10,7,0,8,3,7,4,9,5,7]),g(-1,[7,6,11,7,5,4,10,5,4,2,10,2,4,0,2,3]),g(-1,[3,4,8,6,3,5,4,2,3,2,5,1,10,5,2,5,11,7,6,7]),g(-1,[7,2,3,6,7,6,2,3,5,4,9,7]),g(-1,[9,5,4,7,0,8,6,1,0,6,2,6,6,8,7,6]),g(-1,[3,6,2,6,3,7,6,3,1,5,0,5,5,4,0,3]),g(-1,[6,2,8,1,6,8,7,6,2,1,8,1,4,8,5,5,1,5,8,1]),g(-1,[9,5,4,7,10,1,
6,5,1,7,6,2,1,3,7,3]),g(-1,[1,6,10,6,1,7,6,2,1,0,7,1,8,7,0,5,9,5,4,7]),g(-1,[4,0,10,1,4,10,5,6,0,3,10,1,6,10,7,5,3,7,10,1]),g(-1,[7,6,10,3,7,10,8,4,5,4,10,5,4,8,10,1]),g(-1,[6,9,5,6,6,11,9,1,11,8,9,3]),g(-1,[3,6,11,6,0,6,3,4,0,5,6,2,0,9,5,3]),g(-1,[0,11,8,6,0,5,11,0,0,1,5,3,5,6,11,3]),g(-1,[6,11,3,3,6,3,5,4,5,3,1,6]),g(-1,[1,2,10,7,9,5,11,1,9,11,8,6,11,5,6,6]),g(-1,[0,11,3,6,0,6,11,2,0,9,6,1,5,6,9,5,1,2,10,7]),g(-1,[11,8,5,1,11,5,6,6,8,0,5,1,10,5,2,5,0,2,5,1]),g(-1,[6,11,3,3,6,3,5,4,2,10,3,5,10,5,
3,1]),g(-1,[5,8,9,6,5,2,8,0,5,6,2,3,3,8,2,5]),g(-1,[9,5,6,3,9,6,0,4,0,6,2,6]),g(-1,[1,5,8,1,1,8,0,6,5,6,8,1,3,8,2,5,6,2,8,1]),g(-1,[1,5,6,3,2,1,6,5]),g(-1,[1,3,6,1,1,6,10,6,3,8,6,1,5,6,9,5,8,9,6,1]),g(-1,[10,1,0,3,10,0,6,4,9,5,0,5,5,6,0,1]),g(-1,[0,3,8,7,5,6,10,7]),g(-1,[10,5,6,7]),g(-1,[11,5,10,6,7,5,11,5]),g(-1,[11,5,10,6,11,7,5,3,8,3,0,7]),g(-1,[5,11,7,6,5,10,11,3,1,9,0,7]),g(-1,[10,7,5,6,10,11,7,3,9,8,1,5,8,3,1,3]),g(-1,[11,1,2,6,11,7,1,1,7,5,1,3]),g(-1,[0,8,3,7,1,2,7,1,1,7,5,6,7,2,11,6]),g(-1,
[9,7,5,6,9,2,7,0,9,0,2,3,2,11,7,3]),g(-1,[7,5,2,1,7,2,11,6,5,9,2,1,3,2,8,5,9,8,2,1]),g(-1,[2,5,10,6,2,3,5,1,3,7,5,3]),g(-1,[8,2,0,6,8,5,2,0,8,7,5,3,10,2,5,5]),g(-1,[9,0,1,7,5,10,3,1,5,3,7,6,3,10,2,6]),g(-1,[9,8,2,1,9,2,1,6,8,7,2,1,10,2,5,5,7,5,2,1]),g(-1,[1,3,5,5,3,7,5,3]),g(-1,[0,8,7,3,0,7,1,4,1,7,5,6]),g(-1,[9,0,3,3,9,3,5,4,5,3,7,6]),g(-1,[9,8,7,3,5,9,7,5]),g(-1,[5,8,4,6,5,10,8,1,10,11,8,3]),g(-1,[5,0,4,6,5,11,0,0,5,10,11,3,11,3,0,3]),g(-1,[0,1,9,7,8,4,10,1,8,10,11,6,10,4,5,6]),g(-1,[10,11,4,1,
10,4,5,6,11,3,4,1,9,4,1,5,3,1,4,1]),g(-1,[2,5,1,6,2,8,5,0,2,11,8,3,4,5,8,5]),g(-1,[0,4,11,1,0,11,3,6,4,5,11,1,2,11,1,5,5,1,11,1]),g(-1,[0,2,5,1,0,5,9,6,2,11,5,1,4,5,8,5,11,8,5,1]),g(-1,[9,4,5,7,2,11,3,7]),g(-1,[2,5,10,6,3,5,2,4,3,4,5,2,3,8,4,3]),g(-1,[5,10,2,3,5,2,4,4,4,2,0,6]),g(-1,[3,10,2,6,3,5,10,2,3,8,5,1,4,5,8,5,0,1,9,7]),g(-1,[5,10,2,3,5,2,4,4,1,9,2,5,9,4,2,1]),g(-1,[8,4,5,3,8,5,3,4,3,5,1,6]),g(-1,[0,4,5,3,1,0,5,5]),g(-1,[8,4,5,3,8,5,3,4,9,0,5,5,0,3,5,1]),g(-1,[9,4,5,7]),g(-1,[4,11,7,6,4,9,
11,1,9,10,11,3]),g(-1,[0,8,3,7,4,9,7,5,9,11,7,2,9,10,11,3]),g(-1,[1,10,11,3,1,11,4,0,1,4,0,6,7,4,11,5]),g(-1,[3,1,4,1,3,4,8,6,1,10,4,1,7,4,11,5,10,11,4,1]),g(-1,[4,11,7,6,9,11,4,4,9,2,11,2,9,1,2,3]),g(-1,[9,7,4,6,9,11,7,2,9,1,11,1,2,11,1,5,0,8,3,7]),g(-1,[11,7,4,3,11,4,2,4,2,4,0,6]),g(-1,[11,7,4,3,11,4,2,4,8,3,4,5,3,2,4,1]),g(-1,[2,9,10,6,2,7,9,0,2,3,7,3,7,4,9,3]),g(-1,[9,10,7,1,9,7,4,6,10,2,7,1,8,7,0,5,2,0,7,1]),g(-1,[3,7,10,1,3,10,2,6,7,4,10,1,1,10,0,5,4,0,10,1]),g(-1,[1,10,2,7,8,7,4,7]),g(-1,[4,
9,1,3,4,1,7,4,7,1,3,6]),g(-1,[4,9,1,3,4,1,7,4,0,8,1,5,8,7,1,1]),g(-1,[4,0,3,3,7,4,3,5]),g(-1,[4,8,7,7]),g(-1,[9,10,8,5,10,11,8,3]),g(-1,[3,0,9,3,3,9,11,4,11,9,10,6]),g(-1,[0,1,10,3,0,10,8,4,8,10,11,6]),g(-1,[3,1,10,3,11,3,10,5]),g(-1,[1,2,11,3,1,11,9,4,9,11,8,6]),g(-1,[3,0,9,3,3,9,11,4,1,2,9,5,2,11,9,1]),g(-1,[0,2,11,3,8,0,11,5]),g(-1,[3,2,11,7]),g(-1,[2,3,8,3,2,8,10,4,10,8,9,6]),g(-1,[9,10,2,3,0,9,2,5]),g(-1,[2,3,8,3,2,8,10,4,0,1,8,5,1,10,8,1]),g(-1,[1,10,2,7]),g(-1,[1,3,8,3,9,1,8,5]),g(-1,[0,9,
1,7]),g(-1,[0,3,8,7]),null])});R("J.jvxl.api");Ha(J.jvxl.api,"VertexDataServer");R("J.jvxl.api");Ha(J.jvxl.api,"MeshDataServer",J.jvxl.api.VertexDataServer);R("J.shapesurface");S(["J.jvxl.api.MeshDataServer","J.shape.MeshCollection","JU.P3i","$.P4"],"J.shapesurface.Isosurface","java.util.Hashtable JU.A4 $.AU $.BS $.CU $.Lst $.M3 $.M4 $.P3 $.PT $.Quat $.Rdr $.SB $.V3 J.jvxl.data.JvxlCoder $.JvxlData $.MeshData J.jvxl.readers.SurfaceGenerator J.shape.Mesh J.shapesurface.IsosurfaceMesh JU.C $.Escape $.Logger $.TempArray JV.JC $.Viewer".split(" "),
function(){var d=I(function(){this.actualID=this.thisMesh=this.isomeshes=null;this.explicitContours=this.iHaveBitSets=!1;this.moNumber=this.atomIndex=0;this.moLinearCombination=null;this.meshColix=this.defaultColix=this.colorType=0;this.center=null;this.scale3d=0;this.isColorExplicit=this.isPhaseColored=!1;this.scriptAppendix="";this.sg=null;this.withinDistance2=0;this.isWithinNot=!1;this.cutoffRange=this.withinPoints=null;this.allowMesh=!0;this.script=null;this.iHaveModelIndex=!1;this.nLCAO=0;this.lcaoDir=
null;this.associateNormals=!1;this.keyXy=this.ptXY=this.newFileName=this.oldFileName=null;T(this,arguments)},J.shapesurface,"Isosurface",J.shape.MeshCollection,J.jvxl.api.MeshDataServer);ca(d,function(){this.isomeshes=Array(4);this.lcaoDir=new JU.P4;this.ptXY=new JU.P3i});l(d,"allocMesh",function(a,b){var c=this.meshCount++;this.meshes=this.isomeshes=JU.AU.ensureLength(this.isomeshes,2*this.meshCount);this.currentMesh=this.thisMesh=this.isomeshes[c]=null==b?new J.shapesurface.IsosurfaceMesh(this.vwr,
a,this.colix,c):b;this.currentMesh.index=c;null!=this.sg&&this.sg.setJvxlData(this.jvxlData=this.thisMesh.jvxlData)},"~S,J.shape.Mesh");e(d,"initShape",function(){Ia(this,J.shapesurface.Isosurface,"initShape",[]);this.myType="isosurface";this.newSg()});e(d,"newSg",function(){this.sg=new J.jvxl.readers.SurfaceGenerator(this.vwr,this,null,this.jvxlData=new J.jvxl.data.JvxlData);this.sg.params.showTiming=this.vwr.getBoolean(603979934);this.sg.version="Jmol "+JV.Viewer.getJmolVersion()});e(d,"clearSg",
function(){this.sg=null});l(d,"setProperty",function(a,b,c){this.setPropI(a,b,c)},"~S,~O,JU.BS");e(d,"setPropI",function(a,b,c){if("cache"===a){if(null!=this.currentMesh){var f=this.currentMesh.thisID;c=this.currentMesh.modelIndex;this.vwr.cachePut("cache://isosurface_"+f,this.getPropI("jvxlDataXml",-1).getBytes());this.deleteMeshI(this.currentMesh.index);this.setPropI("init",null,null);this.setPropI("thisID",f,null);this.setPropI("modelIndex",Integer.$valueOf(c),null);this.setPropI("fileName","cache://isosurface_"+
f,null);this.setPropI("readFile",null,null);this.setPropI("finalize","isosurface ID "+JU.PT.esc(f)+(0<=c?" modelIndex "+c:"")+" /*file*/"+JU.PT.esc("cache://isosurface_"+f),null);this.setPropI("clear",null,null)}}else if("delete"===a)this.setPropertySuper(a,b,c),this.explicitID||(this.nLCAO=this.nUnnamed=0),this.currentMesh=this.thisMesh=null;else if("remapInherited"===a)for(f=this.meshCount;0<=--f;)null!=this.isomeshes[f]&&"#inherit;".equals(this.isomeshes[f].colorCommand)&&this.isomeshes[f].remapColors(this.vwr,
null,NaN);else if("remapColor"===a)null!=this.thisMesh&&this.thisMesh.remapColors(this.vwr,b,this.translucentLevel);else if("thisID"===a)null!=this.actualID&&(b=this.actualID),this.setPropertySuper("thisID",b,null);else if("params"===a){if(null!=this.thisMesh){this.ensureMeshSource();this.thisMesh.checkAllocColixes();a=b[0];var d=null;if(null!=a){for(f=0;f<a.length;f++)a[f]=a[f];d=u(c.length(),0);b=0;for(f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1),b++)d[f]=b}this.thisMesh.setVertexColixesForAtoms(this.vwr,
a,d,c);this.thisMesh.setVertexColorMap()}}else if("atomcolor"===a)null!=this.thisMesh&&(this.ensureMeshSource(),this.thisMesh.colorVertices(JU.C.getColixO(b),c,!0));else if("pointSize"===a)null!=this.thisMesh&&(this.thisMesh.volumeRenderPointSize=b.floatValue());else if("vertexcolor"===a)null!=this.thisMesh&&this.thisMesh.colorVertices(JU.C.getColixO(b),c,!1);else if("colorPhase"===a){f=b;c=JU.C.getColix(f[0].intValue());b=JU.C.getColix(f[1].intValue());f=null!=this.thisMesh?this.thisMesh.thisID:
JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null;d=this.getMeshList(f,!1);for(f=d.size();0<=--f;)this.setColorPhase(d.get(f),c,b)}else if("color"===a){var r=JU.C.getHexCode(JU.C.getColixO(b));if(null!=this.thisMesh)this.setIsoMeshColor(this.thisMesh,r);else{d=this.getMeshList(JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,!1);for(f=d.size();0<=--f;)this.setIsoMeshColor(d.get(f),r)}this.setPropertySuper(a,b,c)}else if("nocontour"===a)null!=this.thisMesh&&this.thisMesh.deleteContours();
else if("fixed"===a)this.isFixed=b.booleanValue(),this.setMeshI();else if("newObject"===a)null!=this.thisMesh&&this.thisMesh.clearType(this.thisMesh.meshType,!1);else if("moveIsosurface"===a)null!=this.thisMesh&&!this.thisMesh.isModelConnected&&(this.thisMesh.updateCoordinates(b,null),this.thisMesh.altVertices=null);else if("refreshTrajectories"===a){c=b[0].intValue();for(f=this.meshCount;0<=--f;)this.meshes[f].modelIndex==c&&(null!=this.meshes[f].connectedAtoms||this.meshes[f].isModelConnected)&&
this.meshes[f].updateCoordinates(b[2],b[1])}else if("modelIndex"===a)this.iHaveModelIndex||(this.modelIndex=b.intValue(),this.isFixed=0>this.modelIndex,this.sg.params.modelIndex=Math.abs(this.modelIndex));else if("lcaoCartoon"===a||"lonePair"===a||"radical"===a)f=b,this.explicitID||this.setPropertySuper("thisID",null,null),this.sg.setProp("lcaoCartoonCenter",f[2],null)||this.drawLcaoCartoon(f[0],f[1],f[3],"lonePair"===a?2:"radical"===a?1:0,null==this.thisMesh?!1:this.thisMesh.reverseColor);else if(!("select"===
a&&this.iHaveBitSets||"ignore"===a&&this.iHaveBitSets))if("reversecolor"===a)null!=this.thisMesh&&(this.thisMesh.reverseColor=b===Boolean.TRUE);else if("meshcolor"===a)f=b.intValue(),this.meshColix=JU.C.getColix(f),null!=this.thisMesh&&(this.thisMesh.meshColix=this.meshColix);else if("offset"===a)f=JU.P3.newP(b),f.equals(JV.JC.center)&&(f=null),null!=this.thisMesh&&(this.thisMesh.rotateTranslate(null,f,!0),this.thisMesh.altVertices=null);else if("rotate"===a)null!=this.thisMesh&&(this.thisMesh.rotateTranslate(JU.Quat.newP4(b),
null,!0),this.thisMesh.altVertices=null);else if("bsDisplay"===a)this.bsDisplay=b;else if("displayWithin"===a)f=b,this.displayWithinDistance2=f[0].floatValue(),this.isDisplayWithinNot=0>this.displayWithinDistance2,this.displayWithinDistance2*=this.displayWithinDistance2,this.displayWithinPoints=f[3],0==this.displayWithinPoints.size()&&(this.displayWithinPoints=this.ms.getAtomPointVector(f[2]));else if("finalize"===a)null!=this.thisMesh&&(f=b,null!=f&&!f.startsWith("; isosurface map")&&(this.thisMesh.setDiscreteColixes(this.sg.params.contoursDiscrete,
this.sg.params.contourColixes),this.setJvxlInfo()),this.setScriptInfo(f)),this.clearSg();else if("connections"===a)null!=this.currentMesh&&(this.connections=b,0<=this.connections[0]&&this.connections[0]<this.ms.ac?this.currentMesh.connectedAtoms=this.connections:this.connections=this.currentMesh.connectedAtoms=null);else if("fixLattice"===a)null!=this.thisMesh&&this.thisMesh.fixLattice();else{if("slab"===a){if(ba(b,Integer)){null!=this.thisMesh&&(this.thisMesh.jvxlData.slabValue=b.intValue());return}if(null!=
this.thisMesh){switch(b[0].intValue()){case 1073742018:f=b[1];c=this.getMesh(f[1]);if(null==c)return;f[1]=c}this.slabPolygons(b);return}}if("cap"===a&&null!=this.thisMesh&&0!=this.thisMesh.pc)this.thisMesh.getMeshSlicer().slabPolygons(b,!0),this.thisMesh.initialize(this.thisMesh.lighting,null,null);else{if("map"===a&&(null!=this.sg&&(this.sg.params.isMapped=!0),this.setProperty("squareData",Boolean.FALSE,null),null==this.thisMesh||0==this.thisMesh.vc))return;if("probes"===a)null!=this.sg&&(this.sg.params.probes=
b,this.sg.params.probeValues=x(this.sg.params.probes.length,0));else if("deleteVdw"===a){for(f=this.meshCount;0<=--f;)null!=this.isomeshes[f].bsVdw&&(null==c||c.intersects(this.isomeshes[f].bsVdw))&&this.deleteMeshI(f);this.currentMesh=this.thisMesh=null}else{if("mapColor"===a||"readFile"===a){if(null==b){if(null==this.sg.params.filesData)b=this.getFileReader(this.sg.params.fileName);else{b=this.sg.params.filesData;d=this.sg.params.filesData[0];r=Array(d.length);for(f=r.length;0<=--f&&null!=b;)if(null==
(r[f]=this.getFileReader(d[f])))b=null;null!=b&&(this.sg.params.filesData[0]=r)}if(null==b)return}}else if("atomIndex"===a)this.atomIndex=b.intValue(),null!=this.thisMesh&&(this.thisMesh.atomIndex=this.atomIndex);else if("center"===a)this.center.setT(b);else if("colorRGB"===a)f=b.intValue(),1296041985==f?this.colorType=f:(this.colorType=0,this.defaultColix=JU.C.getColix(f));else if("contour"===a)this.explicitContours=!0;else if("functionXY"===a)2==this.sg.params.state&&this.setScriptInfo(null);else if("init"===
a)this.newSg();else if("getSurfaceSets"===a){if(null!=this.thisMesh){if(ba(b,"JU.BS"))r=b,r.isEmpty()&&(r=null);else{r=new JU.BS;d=b;for(f=d.length;0<=--f;)0<d[f]&&r.set(d[f]-1)}this.thisMesh.jvxlData.thisSet=r;this.thisMesh.calculatedVolume=null;this.thisMesh.calculatedArea=null}}else if("localName"===a)b=this.vwr.getOutputChannel(b,null),a="outputChannel";else if("molecularOrbital"===a){if(this.isFixed=!1,this.setMeshI(),ba(b,Integer)?(this.moNumber=b.intValue(),this.moLinearCombination=null):(this.moLinearCombination=
b,this.moNumber=0),this.isColorExplicit||(this.isPhaseColored=!0),null==this.sg||!this.sg.params.isMapped)f=this.ms.am[this.currentMesh.modelIndex].mat4,null!=f&&(f=JU.M4.newM4(f),f.invert(),this.setPropI("modelInvRotation",f,null))}else"phase"===a?this.isPhaseColored=!0:"plane"!==a&&"pocket"!==a&&("scale3d"===a?(this.scale3d=b.floatValue(),null!=this.thisMesh&&(this.thisMesh.scale3d=this.thisMesh.jvxlData.scale3d=this.scale3d,this.thisMesh.altVertices=null)):"title"===a?("string"==typeof b&&"-".equals(b)&&
(b=null),this.setPropertySuper(a,b,c),b=this.title):"withinPoints"===a?(f=b,this.withinDistance2=f[0].floatValue(),this.isWithinNot=0>this.withinDistance2,this.withinDistance2*=this.withinDistance2,this.withinPoints=f[3],0==this.withinPoints.size()&&(this.withinPoints=this.ms.getAtomPointVector(f[2]))):("nci"===a||"orbital"===a)&&null!=this.sg?this.sg.params.testFlags=this.vwr.getBoolean(603979962)?2:0:"cutoffRange"===a&&(this.cutoffRange=b));if(null!=this.sg&&this.sg.setProp(a,b,c)){if(this.sg.isValid){"molecularOrbital"===
a&&(this.currentMesh.isModelConnected=!0,this.currentMesh.mat4=this.ms.am[this.currentMesh.modelIndex].mat4);return}a="delete"}if("init"===a)this.explicitID=!1,this.scriptAppendix="",f="string"==typeof b?b:null,b=null==f?-1:f.indexOf("# ID="),this.actualID=0<=b?JU.PT.getQuotedStringAt(f,b):null,this.setPropertySuper("thisID","+PREVIOUS_MESH+",null),null!=f&&!(this.iHaveBitSets=this.getScriptBitSets(f,null))&&this.sg.setProp("select",c,null),this.initializeIsosurface(),this.sg.params.modelIndex=this.isFixed?
-1:this.modelIndex;else if("clear"===a)this.discardTempData(!0);else if("colorDensity"===a)null!=b&&null!=this.currentMesh&&(this.currentMesh.volumeRenderPointSize=b.floatValue());else if("deleteModelAtoms"===a){a=b[2][0];d=b[2][1];b=b[2][2];for(f=this.meshCount;0<=--f;)c=this.meshes[f],null!=c&&(null!=c.connectedAtoms&&(r=c.connectedAtoms[0],r>=d+b?c.connectedAtoms[0]=r-b:r>=d&&(c.connectedAtoms=null)),c.connectedAtoms=null,c.modelIndex==a?(this.meshCount--,c===this.currentMesh&&(this.currentMesh=
this.thisMesh=null),this.meshes=this.isomeshes=JU.AU.deleteElements(this.meshes,f,1)):c.modelIndex>a&&(c.modelIndex--,c.atomIndex>=d&&(c.atomIndex-=b)))}else this.setPropertySuper(a,b,c)}}}},"~S,~O,JU.BS");e(d,"getFileReader",function(a){var b=this.vwr.fm.getBufferedReaderOrErrorMessageFromName(a,null,!0,!0);if("string"==typeof b)return JU.Logger.error("Isosurface: could not open file "+a+" -- "+b),null;if(!ba(b,"java.io.BufferedReader"))try{b=JU.Rdr.getBufferedReader(b,"ISO-8859-1")}catch(c){if(!$(c,
"java.io.IOException"))throw c;}return b},"~S");e(d,"setIsoMeshColor",function(a,b){a.jvxlData.baseColor=b;a.isColorSolid=!0;a.pcs=null;a.colorsExplicit=!1;a.colorEncoder=null;a.vertexColorMap=null},"J.shapesurface.IsosurfaceMesh,~S");e(d,"setColorPhase",function(a,b,c){a.colorPhased=!0;a.colix=a.jvxlData.minColorIndex=b;a.jvxlData.maxColorIndex=c;a.jvxlData.isBicolorMap=!0;a.jvxlData.colorDensity=!1;a.isColorSolid=!1;a.remapColors(this.vwr,null,this.translucentLevel)},"J.shapesurface.IsosurfaceMesh,~N,~N");
e(d,"ensureMeshSource",function(){var a=null!=this.thisMesh.vertexSource;if(a)for(var b=this.thisMesh.vc;0<=--b;)if(0>this.thisMesh.vertexSource[b]){a=!1;break}if(!a){var a=this.thisMesh.vertexSource,c=this.thisMesh.vcs,b=this.thisMesh.isColorSolid?this.thisMesh.colix:0;this.setProperty("init",null,null);this.setProperty("map",Boolean.FALSE,null);this.setProperty("property",x(this.ms.ac,0),null);0!=b&&(this.thisMesh.colorCommand="color isosurface "+JU.C.getHexCode(b),this.setProperty("color",Integer.$valueOf(JU.C.getArgb(b)),
null));if(null!=a){for(b=this.thisMesh.vc;0<=--b;)0>a[b]&&(a[b]=this.thisMesh.vertexSource[b]);this.thisMesh.vertexSource=a;this.thisMesh.vcs=c}}});e(d,"slabPolygons",function(a){this.thisMesh.calculatedVolume=null;this.thisMesh.calculatedArea=null;this.thisMesh.getMeshSlicer().slabPolygons(a,!1);this.thisMesh.reinitializeLightingAndColor(this.vwr)},"~A");e(d,"setPropertySuper",function(a,b,c){"thisID"===a&&null!=this.currentMesh&&null!=this.currentMesh.thisID&&this.currentMesh.thisID.equals(b)?this.checkExplicit(b):
(this.currentMesh=this.thisMesh,this.setPropMC(a,b,c),this.thisMesh=this.currentMesh,this.jvxlData=null==this.thisMesh?null:this.thisMesh.jvxlData,null!=this.sg&&this.sg.setJvxlData(this.jvxlData))},"~S,~O,JU.BS");l(d,"getPropertyData",function(a,b){var c;"keys"===a&&(c=ba(b[1],"JU.Lst")?b[1]:new JU.Lst,b[1]=c,c.addLast("info"),c.addLast("data"),c.addLast("atoms"));if("colorEncoder"===a)return c=this.getMesh(b[0]),null!=c&&null!=(b[1]=c.colorEncoder);if("intersectPlane"===a){c=this.getMesh(b[0]);
if(null==c||4>b.length)return!1;b[3]=Integer.$valueOf(c.modelIndex);c.getMeshSlicer().getIntersection(0,b[1],null,b[2],null,null,null,!1,!1,134217750,!1);return!0}if("getBoundingBox"===a){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;b[2]=c.jvxlData.boundingBox;if(null!=c.mat4){var f=Array(2);f[0]=JU.P3.newP(c.jvxlData.boundingBox[0]);f[1]=JU.P3.newP(c.jvxlData.boundingBox[1]);var d=new JU.V3;c.mat4.getTranslation(d);f[0].add(d);f[1].add(d);b[2]=f}return!0}if("unitCell"===a)return c=this.getMesh(b[0]),
null!=c&&null!=(b[1]=c.getUnitCell());if("getCenter"===a&&-2147483648==b[1].intValue()){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;f=JU.P3.newP(c.jvxlData.boundingBox[0]);f.add(c.jvxlData.boundingBox[1]);f.scale(0.5);null!=c.mat4&&(d=new JU.V3,c.mat4.getTranslation(d),f.add(d));b[2]=f;return!0}return this.getPropDataMC(a,b)},"~S,~A");l(d,"getProperty",function(a,b){return this.getPropI(a,b)},"~S,~N");e(d,"getPropI",function(a,b){var c=this.thisMesh;if(0<=b&&(b>=this.meshCount||null==
(c=this.isomeshes[b])))return null;var f=this.getPropMC(a,b);if(null!=f)return f;if("message"===a){c="";if(!this.jvxlData.isValid)return"invalid! (no atoms selected?)";Float.isNaN(this.jvxlData.integration)||(c+="integration "+this.jvxlData.integration);if(24==this.shapeID||27==this.shapeID||28==this.shapeID)c=null==this.jvxlData.cutoffRange?c+(" with cutoff="+this.jvxlData.cutoff):c+(" with cutoffRange="+JU.Escape.eAF(this.jvxlData.cutoffRange));if(27==this.shapeID||28==this.shapeID)return c;3.4028235E38!=
this.jvxlData.dataMin&&(c+=" min="+this.jvxlData.dataMin+" max="+this.jvxlData.dataMax);c+="; "+JV.JC.shapeClassBases[this.shapeID].toLowerCase()+" count: "+this.getPropMC("count",b);return c+this.getPropI("dataRangeStr",b)+this.jvxlData.msg}if("dataRange"===a)return this.getDataRange(c);if("dataRangeStr"===a)return c=this.getDataRange(c),null!=c&&3.4028235E38!=c[0]&&c[0]!=c[1]?"\nisosurface full data range "+c[0]+" to "+c[1]+" with color scheme spanning "+c[2]+" to "+c[3]:"";if("moNumber"===a)return Integer.$valueOf(this.moNumber);
if("moLinearCombination"===a)return this.moLinearCombination;if("nSets"===a)return f=null==c?-2147483648:c.nSets,0==f&&(this.calculateVolumeOrArea(c,!0),f=c.nSets),Integer.$valueOf(-2147483648==f?0:Math.abs(c.nSets));if("area"===a)return null==c?Float.$valueOf(NaN):this.calculateVolumeOrArea(c,!0);if("volume"===a)return null==c?Float.$valueOf(NaN):this.calculateVolumeOrArea(c,!1);if(null==c)return null;if("output"===a)return null==c.jvxlData.sbOut&&null==c.jvxlData.jvxlFileTitle?null:c.jvxlData.jvxlFileTitle+
"\n"+(null==c.jvxlData.sbOut?"":c.jvxlData.sbOut.toString());if("cutoff"===a)return Float.$valueOf(this.jvxlData.cutoff);if("cutoffRange"===a)return this.jvxlData.cutoffRange;if("minMaxInfo"===a)return x(-1,[this.jvxlData.dataMin,this.jvxlData.dataMax]);if("plane"===a)return this.jvxlData.jvxlPlane;if("contours"===a)return c.getContours();if("pmesh"===a||"pmeshbin"===a)return c.getPmeshData("pmeshbin"===a);if("jvxlDataXml"===a||"jvxlMeshXml"===a){var d=null;this.jvxlData.slabInfo=null;"jvxlMeshXml"===
a||this.jvxlData.vertexDataOnly||null!=c.bsSlabDisplay&&null==c.bsSlabGhost?(d=new J.jvxl.data.MeshData,this.fillMeshData(d,1,c),d.polygonColorData=J.shapesurface.Isosurface.getPolygonColorData(d.pc,d.pcs,d.colorsExplicit?d.pis:null,d.bsSlabDisplay)):null!=c.bsSlabGhost&&(this.jvxlData.slabInfo=c.slabOptions.toString());f=new JU.SB;this.getMeshCommand(f,c.index);c.setJvxlColorMap(!0);return J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,d,this.title,"",!0,1,f.toString(),null)}if("jvxlFileInfo"===
a)return J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);if("command"===a){f=new JU.SB;c=this.getMeshList(0>b?this.previousMeshID:c.thisID,!1);for(d=c.size();0<=--d;)this.getMeshCommand(f,c.get(d).index);return f.toString()}return"atoms"===a?c.surfaceAtoms:"colorEncoder"===a?c.colorEncoder:"values"===a||"value"===a?c.probeValues:null},"~S,~N");e(d,"getDataRange",function(a){return null==a?null:a.getDataRange()},"J.shapesurface.IsosurfaceMesh");e(d,"calculateVolumeOrArea",function(a,b){if(b){if(null!=
a.calculatedArea)return a.calculatedArea}else if(null!=a.calculatedVolume)return a.calculatedVolume;var c=new J.jvxl.data.MeshData;this.fillMeshData(c,1,a);c.nSets=a.nSets;c.vertexSets=a.vertexSets;if(!b&&a.jvxlData.colorDensity)return c=a.jvxlData.voxelVolume,c*=null==a.bsSlabDisplay?a.vc:a.bsSlabDisplay.cardinality(),a.calculatedVolume=Float.$valueOf(c);var f=J.jvxl.data.MeshData.calculateVolumeOrArea(c,a.jvxlData.thisSet,b,!1);0>=a.nSets&&(a.nSets=-c.nSets);b?a.calculatedArea=f:a.calculatedVolume=
f;return f},"J.shapesurface.IsosurfaceMesh,~B");d.getPolygonColorData=e(d,"getPolygonColorData",function(a,b,c,f){var d=null!=c;if(null==b&&null==c)return null;for(var r=new JU.SB,e=0,g=0,j=0,n=0,k=!1,t=0;t<a||!0==(k=!0);t++)if(k||null==f||f.get(t))if(k||(d?(n=c[t][4])!=j:b[t]!=g)){0!=e&&r.append(" ").appendI(e).append(" ").appendI(d?j:0==g?0:JU.C.getArgb(g));if(k)break;d?j=n:g=b[t];e=1}else e++;r.append("\n");return r.toString()},"~N,~A,~A,JU.BS");l(d,"getShapeState",function(){this.clean();var a=
new JU.SB;a.append("\n");for(var b=0;b<this.meshCount;b++)this.getMeshCommand(a,b);return a.toString()});e(d,"getMeshCommand",function(a,b){var c=this.meshes[b];if(!(null==c||null==c.scriptCommand)){var f=c.scriptCommand;1<this.ms.mc&&J.shape.Shape.appendCmd(a,"frame "+this.vwr.getModelNumberDotted(c.modelIndex));f=JU.PT.rep(f,";; isosurface map"," map");f=JU.PT.rep(f,"; isosurface map"," map");f.endsWith(" map")&&(f=f.substring(0,f.length-4));var f=f.$replace("\t"," "),f=JU.PT.rep(f,";#","; #"),
d=f.indexOf("; #");0<=d&&(f=f.substring(0,d));null!=c.connectedAtoms&&(f+=" connect "+JU.Escape.eAI(c.connectedAtoms));f=JU.PT.trim(f,";");null!=c.linkedMesh&&(f+=" LINK");"lcaoCartoon"===this.myType&&0<=c.atomIndex&&(f+=" ATOMINDEX "+c.atomIndex);J.shape.Shape.appendCmd(a,f);d=this.myType+" ID "+JU.PT.esc(c.thisID);null!=c.jvxlData.thisSet&&!c.jvxlData.thisSet.isEmpty()&&J.shape.Shape.appendCmd(a,d+(1==c.jvxlData.thisSet.cardinality()?" set "+(c.jvxlData.thisSet.nextSetBit(0)+1):" subset "+c.jvxlData.thisSet));
null!=c.mat4&&!c.isModelConnected&&J.shape.Shape.appendCmd(a,d+" move "+JU.Escape.matrixToScript(c.mat4));0!=c.scale3d&&J.shape.Shape.appendCmd(a,d+" scale3d "+c.scale3d);-2147483648!=c.jvxlData.slabValue&&J.shape.Shape.appendCmd(a,d+" slab "+c.jvxlData.slabValue);null!=c.slabOptions&&J.shape.Shape.appendCmd(a,c.slabOptions.toString());if("#"!=f.charAt(0)&&(this.allowMesh&&J.shape.Shape.appendCmd(a,c.getState(this.myType)),!c.isColorSolid&&(0==c.colorType&&JU.C.isColixTranslucent(c.colix))&&J.shape.Shape.appendCmd(a,
"color "+this.myType+" "+J.shape.Shape.getTranslucentLabel(c.colix)),null!=c.colorCommand&&(0==c.colorType&&!c.colorCommand.equals("#inherit;"))&&J.shape.Shape.appendCmd(a,c.colorCommand),f=c.isColorSolid&&null!=c.pcs,c.isColorSolid&&0==c.colorType&&!c.colorsExplicit&&!f?J.shape.Shape.appendCmd(a,J.shape.Shape.getColorCommandUnk(this.myType,c.colix,this.translucentAllowed)):c.jvxlData.isBicolorMap&&c.colorPhased&&J.shape.Shape.appendCmd(a,"color isosurface phase "+J.shape.Shape.encodeColor(c.jvxlData.minColorIndex)+
" "+J.shape.Shape.encodeColor(c.jvxlData.maxColorIndex)),null!=c.vertexColorMap))for(var r,c=c.vertexColorMap.entrySet().iterator();c.hasNext()&&((r=c.next())||1);)f=r.getValue(),f.isEmpty()||J.shape.Shape.appendCmd(a,"color "+this.myType+" "+JU.Escape.eBS(f)+" "+r.getKey())}},"JU.SB,~N");e(d,"getScriptBitSets",function(a,b){this.script=a;var c;this.iHaveModelIndex=!1;this.modelIndex=-1;if(null!=a&&0<=(c=a.indexOf("MODEL({"))){var f=a.indexOf("})",c);0<f&&(c=JU.BS.unescape(a.substring(c+3,f+1)),this.modelIndex=
null==c?-1:c.nextSetBit(0),this.iHaveModelIndex=0<=this.modelIndex)}if(null==a)return!1;this.getCapSlabInfo(a);c=a.indexOf("# ({");if(0>c)return!1;f=a.indexOf("})",c);if(0>f)return!1;c=JU.BS.unescape(a.substring(c+2,f+2));null==b?this.sg.setProp("select",c,null):b[0]=c;if(0>(c=a.indexOf("({",f)))return!0;f=a.indexOf("})",c);if(0>f)return!1;c=JU.BS.unescape(a.substring(c+1,f+1));null==b?this.sg.setProp("ignore",c,null):b[1]=c;if((c=a.indexOf("/({",f))==f+2){if(0>(f=a.indexOf("})",c)))return!1;c=JU.BS.unescape(a.substring(c+
3,f+1));null==b?this.ms.setTrajectoryBs(c):b[2]=c}return!0},"~S,~A");e(d,"getCapSlabInfo",function(a){var b=a.indexOf("# SLAB=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!1),null);b=a.indexOf("# CAP=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!0),null)},"~S");e(d,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var c=JU.PT.split(a.substring(6,a.length-1),",");return JU.TempArray.getSlabObjectType(1812599299,
D(-1,[JU.Escape.uP(c[0]),JU.Escape.uP(c[1]),JU.Escape.uP(c[2]),JU.Escape.uP(c[3])]),b,null)}var f=JU.Escape.uP(a);if(ba(f,"JU.P4"))return JU.TempArray.getSlabObjectType(134217750,f,b,null)}catch(d){if(!$(d,Exception))throw d;}return null},"~S,~B");e(d,"initializeIsosurface",function(){this.iHaveModelIndex||(this.modelIndex=this.vwr.am.cmi);this.atomIndex=-1;this.bsDisplay=null;this.center=JU.P3.new3(NaN,0,0);this.colix=5;this.cutoffRange=this.connections=null;this.colorType=this.defaultColix=this.meshColix=
0;this.displayWithinPoints=null;this.explicitContours=!1;this.isFixed=0>this.modelIndex;this.isPhaseColored=this.isColorExplicit=!1;this.linkedMesh=null;0>this.modelIndex&&(this.modelIndex=0);this.scale3d=0;this.title=null;this.translucentLevel=0;this.withinPoints=null;this.initState()});e(d,"initState",function(){this.associateNormals=!0;this.sg.initState()});e(d,"setMeshI",function(){this.thisMesh.visible=!0;this.thisMesh.modelIndex=0<=(this.thisMesh.atomIndex=this.atomIndex)?this.ms.at[this.atomIndex].mi:
this.isFixed?-1:0<=this.modelIndex?this.modelIndex:this.vwr.am.cmi;this.thisMesh.scriptCommand=this.script;this.thisMesh.ptCenter.setT(this.center);this.thisMesh.scale3d=null==this.thisMesh.jvxlData.jvxlPlane?0:this.scale3d});e(d,"discardTempData",function(a){a&&(this.title=null,null!=this.thisMesh&&(this.thisMesh.surfaceSet=null))},"~B");e(d,"getDefaultColix",function(){return 0!=this.defaultColix?this.defaultColix:!this.sg.jvxlData.wasCubic?this.colix:JU.C.getColix(0<=this.sg.params.cutoff?-11525984:
-6283184)});e(d,"drawLcaoCartoon",function(a,b,c,f,d){var r=this.sg.setLcao(),e=0<=r.indexOf("anti-sp");e&&(r=r.substring(5));var g=c.x+c.y+c.z;this.defaultColix=JU.C.getColix(this.sg.params.colorPos);var j=JU.C.getColix(this.sg.params.colorNeg);d&&(d=j,j=this.defaultColix,this.defaultColix=d);d=new JU.V3;var n=0<r.length&&"-"==r.charAt(0);n&&(r=r.substring(1));n=n?-1:1;d.cross(a,b);if(0!=g){var k=new JU.A4;0!=c.x?k.setVA(b,g):0!=c.y?k.setVA(d,g):k.setVA(a,g);c=(new JU.M3).setAA(k);c.rotate(b);c.rotate(d);
c.rotate(a)}null==this.thisMesh&&0==this.nLCAO&&(this.nLCAO=this.meshCount);c=null==this.thisMesh?(0<f?"lp":"lcao")+ ++this.nLCAO+"_"+r:this.thisMesh.thisID;null==this.thisMesh&&this.allocMesh(c,null);r.equals("px")?(this.thisMesh.thisID+="a",g=this.thisMesh,this.createLcaoLobe(b,n,f),0<f||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(b,-n,0),this.thisMesh.colix=j,this.linkedMesh=this.thisMesh.linkedMesh=g)):r.equals("py")?(this.thisMesh.thisID+="a",g=this.thisMesh,this.createLcaoLobe(d,
n,f),0<f||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(d,-n,0),this.thisMesh.colix=j,this.linkedMesh=this.thisMesh.linkedMesh=g)):(g=this.thisMesh,r.equals("pz")?(g.thisID+="a",this.createLcaoLobe(a,n,f),0<f||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(a,-n,0),this.thisMesh.colix=j,this.linkedMesh=this.thisMesh.linkedMesh=g)):r.equals("pza")||0==r.indexOf("sp")||0==r.indexOf("d")||0==r.indexOf("lp")?(this.createLcaoLobe(a,n,f),e&&0==f&&(g.thisID+="a",this.setProperty("thisID",
c+"b",null),this.createLcaoLobe(a,-n/2,0),this.thisMesh.colix=j,this.linkedMesh=this.thisMesh.linkedMesh=g)):r.equals("pzb")?this.createLcaoLobe(a,-n,f):r.equals("pxa")?this.createLcaoLobe(b,n,f):r.equals("pxb")?this.createLcaoLobe(b,-n,f):r.equals("pya")?this.createLcaoLobe(d,n,f):r.equals("pyb")?this.createLcaoLobe(d,-n,f):r.equals("spacefill")||r.equals("cpk")?this.createLcaoLobe(null,2*this.ms.at[this.atomIndex].getRadius(),f):this.createLcaoLobe(null,1,f))},"JU.V3,JU.V3,JU.V3,~N,~B");e(d,"createLcaoLobe",
function(a,b,c){this.initState();JU.Logger.debugging&&JU.Logger.debug("creating isosurface ID "+this.thisMesh.thisID);null==a?this.setProperty("sphere",Float.$valueOf(b/2),null):(this.lcaoDir.x=a.x*b,this.lcaoDir.y=a.y*b,this.lcaoDir.z=a.z*b,this.lcaoDir.w=0.7,this.setProperty(2==c?"lp":1==c?"rad":"lobe",this.lcaoDir,null));this.thisMesh.colix=this.defaultColix;this.setScriptInfo(null)},"JU.V3,~N,~N");l(d,"invalidateTriangles",function(){this.thisMesh.invalidatePolygons()});l(d,"setOutputChannel",
function(a,b){a.setOutputChannel(b)},"javajs.api.GenericBinaryDocument,JU.OC");l(d,"fillMeshData",function(a,b,c){if(null==a){if(null==this.thisMesh&&this.allocMesh(null,null),this.thisMesh.isMerged||this.thisMesh.clearType(this.myType,this.sg.params.iAddGridPoints),this.thisMesh.connectedAtoms=this.connections,this.thisMesh.colix=this.getDefaultColix(),this.thisMesh.colorType=this.colorType,this.thisMesh.meshColix=this.meshColix,this.isPhaseColored||this.thisMesh.jvxlData.isBicolorMap)this.thisMesh.isColorSolid=
!1}else if(null==c&&(c=this.thisMesh),null!=c)switch(b){case 1:a.mergeVertexCount0=c.mergeVertexCount0;a.vs=c.vs;a.vertexSource=c.vertexSource;a.vvs=c.vvs;a.vc=c.vc;a.vertexIncrement=c.vertexIncrement;a.pc=c.pc;a.pis=c.pis;a.pcs=c.pcs;a.bsSlabDisplay=c.bsSlabDisplay;a.bsSlabGhost=c.bsSlabGhost;a.slabColix=c.slabColix;a.slabMeshType=c.slabMeshType;a.polygonCount0=c.polygonCount0;a.vertexCount0=c.vertexCount0;a.slabOptions=c.slabOptions;a.colorsExplicit=c.colorsExplicit;break;case 2:if(null==c.vcs||
c.vc>c.vcs.length)c.vcs=da(c.vc,0);a.vcs=c.vcs;break;case 3:c.surfaceSet=a.surfaceSet;c.vertexSets=a.vertexSets;c.nSets=a.nSets;break;case 4:c.vs=a.vs,c.vvs=a.vvs,c.vc=a.vc,c.vertexIncrement=a.vertexIncrement,c.vertexSource=a.vertexSource,c.pc=a.pc,c.pis=a.pis,c.pcs=a.pcs,c.bsSlabDisplay=a.bsSlabDisplay,c.bsSlabGhost=a.bsSlabGhost,c.slabColix=a.slabColix,c.slabMeshType=a.slabMeshType,c.polygonCount0=a.polygonCount0,c.vertexCount0=a.vertexCount0,c.mergeVertexCount0=a.mergeVertexCount0,c.slabOptions=
a.slabOptions,c.colorsExplicit=a.colorsExplicit}},"J.jvxl.data.MeshData,~N,J.shapesurface.IsosurfaceMesh");l(d,"notifySurfaceGenerationCompleted",function(){this.setMeshI();this.setBsVdw();this.thisMesh.surfaceAtoms=this.sg.params.bsSelected;this.thisMesh.insideOut=this.sg.params.isInsideOut();this.thisMesh.isModelConnected=this.sg.params.isModelConnected;this.thisMesh.vertexSource=this.sg.params.vertexSource;this.thisMesh.oabc=this.sg.getOriginVaVbVc();this.thisMesh.calculatedArea=null;this.thisMesh.calculatedVolume=
null;this.thisMesh.probeValues=this.sg.params.probeValues;if(!this.thisMesh.isMerged)return this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane),null!=this.jvxlData.fixedLattice&&(this.thisMesh.lattice=this.jvxlData.fixedLattice,this.thisMesh.fixLattice()),this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);this.sg.params.allowVolumeRender||(this.thisMesh.jvxlData.allowVolumeRender=!1);this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);
null!=this.thisMesh.jvxlData.slabInfo&&this.vwr.runScriptCautiously("isosurface "+this.thisMesh.jvxlData.slabInfo);0<this.sg.params.psi_monteCarloCount&&(this.thisMesh.diameter=-1);return!1});l(d,"notifySurfaceMappingCompleted",function(){this.thisMesh.isMerged||this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane);this.setBsVdw();this.thisMesh.isColorSolid=!1;this.thisMesh.colorDensity=this.jvxlData.colorDensity;this.thisMesh.volumeRenderPointSize=
this.jvxlData.pointSize;this.thisMesh.colorEncoder=this.sg.params.colorEncoder;this.thisMesh.getContours();0!=this.thisMesh.jvxlData.nContours&&-1!=this.thisMesh.jvxlData.nContours&&(this.explicitContours=!0);this.explicitContours&&null!=this.thisMesh.jvxlData.jvxlPlane&&(this.thisMesh.havePlanarContours=!0);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073742046:1073741938),null);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073741898:1073742039),null);
this.thisMesh.isMerged||this.thisMesh.setJvxlDataRendering();null!=this.sg.params.slabInfo&&(this.thisMesh.slabPolygonsList(this.sg.params.slabInfo,!1),this.thisMesh.reinitializeLightingAndColor(this.vwr));this.thisMesh.setColorCommand()});e(d,"setBsVdw",function(){null!=this.sg.bsVdw&&(null==this.thisMesh.bsVdw&&(this.thisMesh.bsVdw=new JU.BS),this.thisMesh.bsVdw.or(this.sg.bsVdw))});l(d,"calculateGeodesicSurface",function(a,b){return this.vwr.calculateSurface(a,b)},"JU.BS,~N");l(d,"getSurfacePointIndexAndFraction",
function(){return 0},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");l(d,"addVertexCopy",function(a,b,c,f){return null!=this.cutoffRange&&(b<this.cutoffRange[0]||b>this.cutoffRange[1])?-1:null!=this.withinPoints&&!J.shape.Mesh.checkWithin(a,this.withinPoints,this.withinDistance2,this.isWithinNot)?-1:this.thisMesh.addVertexCopy(a,b,c,this.associateNormals,f)},"JU.T3,~N,~N,~B");l(d,"addTriangleCheck",function(a,b,c,f,d,r,e){return 0>a||0>b||0>c||r&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.thisMesh.vvs)?
-1:this.thisMesh.addTriangleCheck(a,b,c,f,d,e)},"~N,~N,~N,~N,~N,~B,~N");e(d,"setScriptInfo",function(a){a=null==a?this.sg.params.script:a;var b=null==a?-1:a.indexOf("; isosurface map");if(0==b)null!=this.thisMesh.scriptCommand&&(b=this.thisMesh.scriptCommand.indexOf("; isosurface map"),0<=b&&(this.thisMesh.scriptCommand=this.thisMesh.scriptCommand.substring(0,b)),this.thisMesh.scriptCommand+=a);else if(this.thisMesh.title=this.sg.params.title,this.thisMesh.dataType=this.sg.params.dataType,this.thisMesh.scale3d=
this.sg.params.scale3d,null!=a&&(null!=this.oldFileName&&(a=a.$replace(this.oldFileName,this.newFileName))," "==a.charAt(0)&&(a=this.myType+" ID "+JU.PT.esc(this.thisMesh.thisID)+a,b=a.indexOf("; isosurface map"))),this.thisMesh.scriptCommand=0<b&&0<this.scriptAppendix.length?a.substring(0,b)+this.scriptAppendix+a.substring(b):a+this.scriptAppendix,!this.explicitID&&null!=a&&0<=(b=a.indexOf("# ID=")))this.thisMesh.thisID=JU.PT.getQuotedStringAt(a,b)},"~S");l(d,"addRequiredFile",function(a){a=' # /*file*/"'+
a+'"';0>this.scriptAppendix.indexOf(a)&&(this.scriptAppendix+=a)},"~S");l(d,"setRequiredFile",function(a,b){this.oldFileName=a;this.newFileName=b},"~S,~S");e(d,"setJvxlInfo",function(){if(this.sg.jvxlData!==this.jvxlData||this.sg.jvxlData!==this.thisMesh.jvxlData)this.jvxlData=this.thisMesh.jvxlData=this.sg.jvxlData});l(d,"getShapeDetail",function(){for(var a=new JU.Lst,b=0;b<this.meshCount;b++){var c=new java.util.Hashtable,f=this.isomeshes[b];null==f||(null==f.vs||0==f.vc&&0==f.pc)||(this.addMeshInfo(f,
c),a.addLast(c))}return a});e(d,"addMeshInfo",function(a,b){b.put("ID",null==a.thisID?"<noid>":a.thisID);b.put("visible",Boolean.$valueOf(a.visible));b.put("vertexCount",Integer.$valueOf(a.vc));null!=a.calculatedVolume&&b.put("volume",a.calculatedVolume);null!=a.calculatedArea&&b.put("area",a.calculatedArea);Float.isNaN(a.ptCenter.x)||b.put("center",a.ptCenter);null!=a.mat4&&b.put("mat4",a.mat4);0!=a.scale3d&&b.put("scale3d",Float.$valueOf(a.scale3d));b.put("xyzMin",a.jvxlData.boundingBox[0]);b.put("xyzMax",
a.jvxlData.boundingBox[1]);var c=J.jvxl.data.JvxlCoder.jvxlGetInfo(a.jvxlData);null!=c&&b.put("jvxlInfo",c.$replace("\n"," "));b.put("modelIndex",Integer.$valueOf(a.modelIndex));b.put("color",JU.CU.colorPtFromInt(JU.C.getArgb(a.colix),null));null!=a.colorEncoder&&b.put("colorKey",a.colorEncoder.getColorKey());null!=a.title&&b.put("title",a.title);(null!=a.jvxlData.contourValues||null!=a.jvxlData.contourValuesUsed)&&b.put("contours",a.getContourList(this.vwr))},"J.shapesurface.IsosurfaceMesh,java.util.Map");
l(d,"getPlane",function(){return null},"~N");l(d,"getValue",function(){return 0},"~N,~N,~N,~N");l(d,"checkObjectHovered",function(a,b,c){if(null!=this.keyXy&&a>=this.keyXy[0]&&b>=this.keyXy[1]&&a<this.keyXy[2]&&b<this.keyXy[3])return this.hoverKey(a,b),!0;if(!this.vwr.getDrawHover())return!1;c=this.findValue(a,b,!1,c);if(null==c)return!1;this.vwr.hoverOnPt(a,b,c,this.pickedMesh.thisID,this.pickedPt);return!0},"~N,~N,JU.BS");e(d,"hoverKey",function(a,b){try{var c,f=1-1*(b-this.keyXy[1])/(this.keyXy[3]-
this.keyXy[1]);if(this.thisMesh.showContourLines){var d=this.thisMesh.getContours();if(null==d){if(null==this.thisMesh.jvxlData.contourValues)return;var r=G(Math.floor(f*this.thisMesh.jvxlData.contourValues.length));if(0>r||r>this.thisMesh.jvxlData.contourValues.length)return;c=""+this.thisMesh.jvxlData.contourValues[r]}else{r=G(Math.floor(f*d.length));if(0>r||r>d.length)return;c=""+d[r].get(2).floatValue()}}else{var e=this.thisMesh.colorEncoder.quantize(f,!0),f=this.thisMesh.colorEncoder.quantize(f,
!1);c=""+e+" - "+f}this.vwr.hoverOnPt(a,b,c,null,null)}catch(g){if(!$(g,Exception))throw g;}},"~N,~N");l(d,"checkObjectClicked",function(a,b,c,f,d){if(!d||!this.vwr.isBound(c,18))return null;c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var r=d=-1,e=-2147483648,g=2147483647,j=0;j<this.meshCount;j++){var n=this.isomeshes[j];if(this.isPickable(n,f)&&(n=n.vs,null!=n))for(var k=n.length;0<=--k;){var t=n[k];null!=t&&0<=this.coordinateInRange(a,b,t,c,this.ptXY)&&(this.ptXY.z<g&&(d=j,g=this.ptXY.z,
r=k),this.ptXY.z>e&&(e=this.ptXY.z))}}if(0>d)return null;this.pickedMesh=this.isomeshes[d];this.setPropertySuper("thisID",this.pickedMesh.thisID,null);this.pickedVertex=r;a=new JU.P3;a.setT(this.pickedMesh.vs[this.pickedVertex]);this.pickedModel=this.pickedMesh.modelIndex;b=this.getPickedPoint(a,this.pickedModel);this.setStatusPicked(-4,a,b);return b},"~N,~N,~N,JU.BS,~B");e(d,"isPickable",function(a,b){return 0!=a.visibilityFlags&&(0>a.modelIndex||b.get(a.modelIndex))&&!JU.C.isColixTranslucent(a.colix)},
"J.shapesurface.IsosurfaceMesh,JU.BS");e(d,"findValue",function(a,b,c,f){c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var d=-1,e=null,h=null,g=0;g<this.meshCount;g++)if(h=this.isomeshes[g],this.isPickable(h,f)){var j=h.jvxlData.vContours,n=0>h.firstRealVertex?0:h.firstRealVertex,k=0;if(null!=j&&0<j.length){for(n=0;n<j.length;n++)for(var t=j[n],q=t.size()-1,N=6;N<q;N++){var w=t.get(N),l=this.coordinateInRange(a,b,w,c,this.ptXY);0<=l&&(c=l,e=t,k=n,this.pickedMesh=h,this.pickedPt=w)}if(null!=
e)return e.get(2).toString()+(JU.Logger.debugging?" "+k:"")}else if(null!=h.jvxlData.jvxlPlane&&null!=h.vvs){j=null==h.mat4&&0==h.scale3d?h.vs:h.getOffsetVertices(h.jvxlData.jvxlPlane);for(N=h.vc;--N>=n;)w=j[N],l=this.coordinateInRange(a,b,w,c,this.ptXY),0<=l&&(c=l,d=N,this.pickedMesh=h,this.pickedPt=w);if(-1!=d)break}else if(null!=h.vvs){if(null!=h.bsSlabDisplay)for(N=h.bsSlabDisplay.nextSetBit(0);0<=N;N=h.bsSlabDisplay.nextSetBit(N+1)){if(j=h.pis[N],null!=j)for(k=0;3>k;k++)w=h.vs[j[k]],l=this.coordinateInRange(a,
b,w,c,this.ptXY),0<=l&&(c=l,d=j[k],this.pickedMesh=h,this.pickedPt=w)}else for(N=h.vc;--N>=n;)w=h.vs[N],l=this.coordinateInRange(a,b,w,c,this.ptXY),0<=l&&(c=l,d=N,this.pickedMesh=h,this.pickedPt=w);if(-1!=d)break}}return-1==d?null:(JU.Logger.debugging?"$"+h.thisID+"["+(d+1)+"] "+h.vs[d]+": ":h.thisID+": ")+h.vvs[d]},"~N,~N,~B,JU.BS");e(d,"getCmd",function(a){var b=(new JU.SB).append("\n");this.getMeshCommand(b,a);return b.toString()},"~N");l(d,"getValues",function(a){return null==a?null:a.getValidValues(null)},
"J.shape.Mesh");l(d,"getVertices",function(a){return null==a?null:a.getValidVertices(null)},"J.shape.Mesh")});R("J.jvxl.data");S(null,"J.jvxl.data.JvxlCoder","JU.BS $.Lst $.P3 $.PT $.SB J.api.Interface J.jvxl.data.VolumeData JU.BSUtil $.C $.Escape $.Logger JV.Viewer".split(" "),function(){var d=za(J.jvxl.data,"JvxlCoder",null);d.jvxlGetFile=e(d,"jvxlGetFile",function(a,b,c,f,d,e,h,g){J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var j=new JU.SB;if("TRAILERONLY".equals(f))return JU.XmlUtil.closeTag(j,"jvxlSurfaceSet"),
JU.XmlUtil.closeTag(j,"jvxl"),j.toString();var n=null!=b,k="HEADERONLY".equals(f);if(d){JU.XmlUtil.openDocument(j);JU.XmlUtil.openTagAttr(j,"jvxl",D(-1,["version","2.4","jmolVersion",a.version,"xmlns","http://jmol.org/jvxl_schema","xmlns:cml","http://www.xml-cml.org/schema"]));JU.XmlUtil.appendCdata(j,"jvxlFileTitle",null,null==a.jvxlFileTitle?"\n":"\n"+a.jvxlFileTitle);null!=a.moleculeXml&&j.append(a.moleculeXml);var t=n?null:a.jvxlVolumeDataXml;null==t&&(t=(new J.jvxl.data.VolumeData).setVolumetricXml());
j.append(t);JU.XmlUtil.openTagAttr(j,"jvxlSurfaceSet",D(-1,["count",""+(0<e?e:1)]));if(k)return j.toString()}e=n?"pmesh":null==a.jvxlPlane?"isosurface":"plane";null!=a.jvxlColorData&&0<a.jvxlColorData.length&&(e="mapped "+e);JU.XmlUtil.openTagAttr(j,"jvxlSurface",D(-1,["type",e]));j.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,n));J.jvxl.data.JvxlCoder.jvxlAppendCommandState(j,g,h);if(null!=c||null!=f&&0<f.length){h=new JU.SB;null!=f&&0<f.length&&h.append(f).append("\n");if(null!=c)for(f=0;f<c.length;f++)h.append(c[f]).appendC("\n");
JU.XmlUtil.appendCdata(j,"jvxlSurfaceTitle",null,h.toString())}h=new JU.SB;JU.XmlUtil.openTagAttr(h,"jvxlSurfaceData",n||null==a.jvxlPlane?null:null==a.mapLattice?D(-1,["plane",JU.Escape.eP4(a.jvxlPlane)]):D(-1,["plane",JU.Escape.eP4(a.jvxlPlane),"maplattice",JU.Escape.eP(a.mapLattice)]));if(n)J.jvxl.data.JvxlCoder.appendXmlVertexOnlyData(h,a,b,!0);else{if(null==a.jvxlPlane){if(null==a.jvxlEdgeData)return"";J.jvxl.data.JvxlCoder.appendXmlEdgeData(h,a)}J.jvxl.data.JvxlCoder.appendXmlColorData(h,a.jvxlColorData,
!0,a.isJvxlPrecisionColor,a.valueMappedToRed,a.valueMappedToBlue)}J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlInvalidatedVertexData",a.jvxlExcluded[1],-1,null);0<a.excludedVertexCount&&(J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlExcludedVertexData",a.jvxlExcluded[0],a.excludedVertexCount,null),J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlExcludedPlaneData",a.jvxlExcluded[2],-1,null));J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlExcludedTriangleData",a.jvxlExcluded[3],
a.excludedTriangleCount,null);JU.XmlUtil.closeTag(h,"jvxlSurfaceData");b=h.length();j.appendSB(h);null!=a.vContours&&0<a.vContours.length&&J.jvxl.data.JvxlCoder.jvxlEncodeContourData(a.vContours,j);if(null!=a.vertexColorMap){null==a.baseColor?JU.XmlUtil.openTag(j,"jvxlVertexColorData"):JU.XmlUtil.openTagAttr(j,"jvxlVertexColorData",D(-1,["baseColor",a.baseColor]));var q;for(c=a.vertexColorMap.entrySet().iterator();c.hasNext()&&((q=c.next())||1);)J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(j,"jvxlColorMap",
q.getValue(),-1,D(-1,["color",q.getKey()]));a.vertexColorMap=null;JU.XmlUtil.closeTag(j,"jvxlVertexColorData")}JU.XmlUtil.closeTag(j,"jvxlSurface");d&&(JU.XmlUtil.closeTag(j,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(j,"jvxl"));return J.jvxl.data.JvxlCoder.jvxlSetCompressionRatio(j,a,b)},"J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~A,~S,~B,~N,~S,~S");d.checkHaveXMLUtil=e(d,"checkHaveXMLUtil",function(){J.jvxl.data.JvxlCoder.haveXMLUtil||(JV.Viewer.isJS&&J.api.Interface.getInterface("JU.XmlUtil",null,"show"),
J.jvxl.data.JvxlCoder.haveXMLUtil=!0)});d.appendEncodedBitSetTag=e(d,"appendEncodedBitSetTag",function(a,b,c,f,d){0>f&&(f=JU.BSUtil.cardinalityOf(c));if(0!=f){var e=new JU.SB;e.append("\n ");J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(c,-1,e);JU.XmlUtil.appendTagObj(a,b,D(-1,[d,"bsEncoding","base90+35","count",""+f,"len",""+c.length()]),J.jvxl.data.JvxlCoder.jvxlCompressString(e.toString(),!0))}},"JU.SB,~S,JU.BS,~N,~A");d.jvxlSetCompressionRatio=e(d,"jvxlSetCompressionRatio",function(a,b,c){a=a.toString();
b=A(0<b.nBytes?b.nBytes/c:13*b.nPointsX*b.nPointsY*b.nPointsZ/c);return JU.PT.rep(a,'"not calculated"',0<b?'"'+b+':1"':'"?"')},"JU.SB,J.jvxl.data.JvxlData,~N");d.appendXmlEdgeData=e(d,"appendXmlEdgeData",function(a,b){JU.XmlUtil.appendTagObj(a,"jvxlEdgeData",D(-1,["count",""+(b.jvxlEdgeData.length-1),"encoding","base90f1","bsEncoding","base90+35c","isXLowToHigh",""+b.isXLowToHigh,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlEdgeData,!0)]),"\n"+J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlSurfaceData,
!0))},"JU.SB,J.jvxl.data.JvxlData");d.jvxlAppendCommandState=e(d,"jvxlAppendCommandState",function(a,b,c){null!=b&&JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceCommand",null,"\n"+(0>b.indexOf("#")?b:b.substring(0,b.indexOf("#")))+"\n");null!=c&&(0<=c.indexOf("** XML ** ")?(c=JU.PT.split(c,"** XML **")[1].trim(),JU.XmlUtil.appendTag(a,"jvxlIsosurfaceState","\n"+c+"\n")):JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceState",null,"\n"+c))},"JU.SB,~S,~S");d.appendXmlColorData=e(d,"appendXmlColorData",function(a,
b,c,f,d,e){var h;if(!(null==b||0>(h=b.length-1)))f&&(h/=2),JU.XmlUtil.appendTagObj(a,"jvxlColorData",D(-1,["count",""+h,"encoding",c?"base90f"+(f?"2":"1"):"none","min",""+d,"max",""+e,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b,!0)]),null)},"JU.SB,~S,~B,~B,~N,~N");d.jvxlGetInfo=e(d,"jvxlGetInfo",function(a){return J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,a.vertexDataOnly)},"J.jvxl.data.JvxlData");d.jvxlGetInfoData=e(d,"jvxlGetInfoData",function(a,b){if(null==a.jvxlSurfaceData)return"";J.jvxl.data.JvxlCoder.checkHaveXMLUtil();
var c=new JU.Lst,f=a.nSurfaceInts,d=b?0:a.jvxlEdgeData.length-1,e=null==a.jvxlColorData?-1:a.jvxlColorData.length-1;J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isModelConnected",""+a.isModelConnected);if(!b){J.jvxl.data.JvxlCoder.addAttrib(c,"\n  cutoff",null==a.cutoffRange?""+a.cutoff:a.cutoffRange[0]+" "+a.cutoffRange[1]);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isCutoffAbsolute",""+a.isCutoffAbsolute);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  pointsPerAngstrom",""+a.pointsPerAngstrom);var h=a.jvxlSurfaceData.length+
d+e+1;0<h&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesData",""+h);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isXLowToHigh",""+a.isXLowToHigh);null==a.jvxlPlane&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nSurfaceInts",""+f),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedEdgeData",""+d));0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedColorData",""+e)}a.excludedVertexCount=JU.BSUtil.cardinalityOf(a.jvxlExcluded[0]);a.excludedTriangleCount=JU.BSUtil.cardinalityOf(a.jvxlExcluded[3]);
0<a.excludedVertexCount&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nExcludedVertexes",""+a.excludedVertexCount);0<a.excludedTriangleCount&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nExcludedTriangles",""+a.excludedTriangleCount);h=JU.BSUtil.cardinalityOf(a.jvxlExcluded[1]);0<h&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nInvalidatedVertexes",""+h);null!=a.slabInfo&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  slabInfo",a.slabInfo);a.isJvxlPrecisionColor&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  precisionColor","true");
a.colorDensity&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorDensity","true");Float.isNaN(a.pointSize)?0!=a.diameter&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  diameter",""+a.diameter):J.jvxl.data.JvxlCoder.addAttrib(c,"\n  pointSize",""+a.pointSize);a.allowVolumeRender||J.jvxl.data.JvxlCoder.addAttrib(c,"\n  allowVolumeRender","false");null==a.jvxlPlane||b?(null!=a.fixedLattice&&!b&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  fixedLattice",""+a.fixedLattice),a.isContoured?(J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  contoured","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true")):a.isBicolorMap?(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  bicolorMap","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorNegative",JU.C.getHexCode(a.minColorIndex)),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorPositive",JU.C.getHexCode(a.maxColorIndex))):0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true"),null!=a.vContours&&0<a.vContours.length&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContourData",""+a.vContours.length)):
(null!=a.mapLattice&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  mapLattice",""+a.mapLattice),0!=a.scale3d&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  scale3d",""+a.scale3d),0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  plane",JU.Escape.eP4(a.jvxlPlane)));null!=a.color&&0>a.color.indexOf("null")&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  color",a.color);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  translucency",""+a.translucency);null!=a.meshColor&&J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  meshColor",a.meshColor);null!=a.colorScheme&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorScheme",a.colorScheme);null!=a.rendering&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  rendering",a.rendering);null!=a.thisSet&&(f=J.jvxl.data.JvxlCoder.subsetString(a.thisSet),f.startsWith("[")?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  subset",f):J.jvxl.data.JvxlCoder.addAttrib(c,"\n  set",f));-2147483648!=a.slabValue&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  slabValue",""+a.slabValue);a.isSlabbable&&J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  slabbable","true");0<a.nVertexColors&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nVertexColors",""+a.nVertexColors);f=3.4028235E38==a.mappedDataMin?0:a.mappedDataMin;d=a.isColorReversed?a.valueMappedToRed:a.valueMappedToBlue;e=a.isColorReversed?a.valueMappedToBlue:a.valueMappedToRed;null!=a.jvxlColorData&&(0<a.jvxlColorData.length&&!a.isBicolorMap)&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMinimum",""+f),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMaximum",""+a.mappedDataMax),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  valueMappedToRed",""+e),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToBlue",""+d));a.isContoured&&(null==a.contourValues||null==a.contourColixes?null==a.vContours&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+Math.abs(a.nContours)):(null!=a.jvxlPlane&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contoured","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+a.contourValues.length),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourValues",JU.Escape.eAF(null==a.contourValuesUsed?a.contourValues:
a.contourValuesUsed)),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourColors",a.contourColors)),0<a.thisContour&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  thisContour",""+a.thisContour));a.insideOut&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  insideOut","true");a.vertexDataOnly?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","vertex/face data only"):a.isXLowToHigh&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","progressive JVXL+ -- X values read from low(0) to high("+(a.nPointsX-1)+")");J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  xyzMin",JU.Escape.eP(a.boundingBox[0]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  xyzMax",JU.Escape.eP(a.boundingBox[1]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  approximateCompressionRatio","not calculated");J.jvxl.data.JvxlCoder.addAttrib(c,"\n  jmolVersion",a.version);f=new JU.SB;JU.XmlUtil.openTagAttr(f,"jvxlSurfaceInfo",c.toArray(Array(c.size())));JU.XmlUtil.closeTag(f,"jvxlSurfaceInfo");return f.toString()},"J.jvxl.data.JvxlData,~B");d.subsetString=e(d,"subsetString",function(a){if(1<a.cardinality()){for(var b=
"[ ",c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c))b+=++c+" ";return b+"]"}return""+(a.nextSetBit(0)+1)},"JU.BS");d.addAttrib=e(d,"addAttrib",function(a,b,c){a.addLast(D(-1,[b,c]))},"JU.Lst,~S,~S");d.jvxlEncodeContourData=e(d,"jvxlEncodeContourData",function(a,b){JU.XmlUtil.openTagAttr(b,"jvxlContourData",D(-1,["count",""+a.length]));for(var c=0;c<a.length;c++)if(!(6>a[c].size())){var f=a[c].get(0).intValue(),d=new JU.SB;d.append("\n");var e=a[c].get(1);J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(e,f,
d);JU.XmlUtil.appendTagObj(b,"jvxlContour",D(-1,["index",""+c,"value",""+a[c].get(2),"color",JU.Escape.escapeColor(a[c].get(4)[0]),"count",""+e.length(),"encoding","base90iff1","bsEncoding","base90+35c","data",J.jvxl.data.JvxlCoder.jvxlCompressString(a[c].get(5).toString(),!0)]),J.jvxl.data.JvxlCoder.jvxlCompressString(d.toString(),!0))}JU.XmlUtil.closeTag(b,"jvxlContourData")},"~A,JU.SB");d.set3dContourVector=e(d,"set3dContourVector",function(a,b,c){if(!(6>a.size()))for(var f=a.get(5),d=a.get(1),
e=0,h=f.length(),g=0,j=" ",n=" ",k=d.nextSetBit(0);0<=k;k=d.nextSetBit(k+1)){for(var t=b[k];e<h&&!JU.PT.isDigit(j=f.charAt(e++)););for(g=j.charCodeAt(0)-48;e<h&&JU.PT.isWhitespace(j=f.charAt(e++)););for(;e<h&&JU.PT.isWhitespace(n=f.charAt(e++)););var q=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(j.charCodeAt(0),35,90,0),l=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(n.charCodeAt(0),35,90,0),w,u;0==(g&1)?(w=t[1],u=g=t[2],t=t[0]):(w=t[0],u=t[1],0!=(g&2)?(g=u,t=t[2]):(g=t[2],t=w));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,
w,u,q));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,g,t,l))}},"JU.Lst,~A,~A");d.getContourPoint=e(d,"getContourPoint",function(a,b,c,f){var d=new JU.P3;d.sub2(a[c],a[b]);d.scaleAdd2(f,d,a[b]);return d},"~A,~N,~N,~N");d.appendContourTriangleIntersection=e(d,"appendContourTriangleIntersection",function(a,b,c,f){f.appendI(a);f.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(b));f.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(c))},"~N,~N,~N,JU.SB");d.jvxlCreateColorData=e(d,"jvxlCreateColorData",
function(a,b){if(null==b)a.jvxlColorData="";else{var c=a.colorFractionBase,f=a.colorFractionRange,d=0<a.saveVertexCount?a.saveVertexCount:a.vertexCount;d>b.length&&System.out.println("JVXLCODER ERROR");var e=a.isJvxlPrecisionColor,h=e?a.mappedDataMin:a.valueMappedToRed,g=e?a.mappedDataMax:a.valueMappedToBlue;b.length<d&&System.out.println("JVXLCOLOR OHOHO");a.jvxlColorData=J.jvxl.data.JvxlCoder.jvxlEncodeColorData(b,h,g,c,f,a.isTruncated,e)}},"J.jvxl.data.JvxlData,~A");d.jvxlEncodeColorData=e(d,"jvxlEncodeColorData",
function(a,b,c,f,d,e,h){for(var g=new JU.SB,j=new JU.SB,n=0,k=a.length;n<k;n++){var t=a[n];Float.isNaN(t)&&(t=b);e&&(t=0<t?0.999:-0.999);h?J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(t,b,c,f,d,g,j):g.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(t,b,c,f,d))}return g.appendSB(j).appendC("\n").toString()},"~A,~N,~N,~N,~N,~B,~B");d.appendXmlVertexOnlyData=e(d,"appendXmlVertexOnlyData",function(a,b,c,f){var d=u(c.vc,0);J.jvxl.data.JvxlCoder.appendXmlTriangleData(a,c.pis,c.pc,c.bsSlabDisplay,d,f)&&
J.jvxl.data.JvxlCoder.appendXmlVertexData(a,b,d,c.vs,c.vvs,c.vc,c.polygonColorData,c.pc,c.bsSlabDisplay,b.vertexColors,0<b.jvxlColorData.length,f)},"JU.SB,J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~B");d.appendXmlTriangleData=e(d,"appendXmlTriangleData",function(a,b,c,f,d,e){for(var h=new JU.SB,g=new JU.SB,j=1,n=0,k=0,t=!1,q=0,l=null!=f,w=0;w<c;)if(null==b[w]||l&&!f.get(w))w++;else{var u=b[w][n],u=0<d[u]?d[u]:d[u]=++k,x=u-j,j=u;0==x?(h.appendC("!"),t=!1):32<x?(t&&h.appendC("+"),h.appendI(x),t=!0):
-32>x?(h.appendI(x),t=!0):(h.appendC(String.fromCharCode(92+x)),t=!1);0==++n%3&&(g.appendI(b[w][3]),n=0,w++,q++)}if(0==h.length())return!0;JU.XmlUtil.appendTagObj(a,"jvxlTriangleData",D(-1,["count",""+q,"encoding","jvxltdiff","data",J.jvxl.data.JvxlCoder.jvxlCompressString(h.toString(),e)]),null);JU.XmlUtil.appendTagObj(a,"jvxlTriangleEdgeData",D(-1,["count",""+q,"encoding","jvxlsc","data",J.jvxl.data.JvxlCoder.jvxlCompressString(g.toString(),e)]),null);return!0},"JU.SB,~A,~N,JU.BS,~A,~B");d.appendXmlVertexData=
e(d,"appendXmlVertexData",function(a,b,c,f,d,e,h,g,j,n,k,t){var q=b.colorFractionBase,l=b.colorFractionRange,w,x=b.boundingBox[0],A=b.boundingBox[1],G=new JU.SB,I=new JU.SB,ea=null,P=null!=j;if(0<g){P&&(g=j.cardinality());for(var P=!1,ea=u(e,0),K=0;K<e;K++)0<c[K]&&(ea[c[K]-1]=K)}for(K=c=0;K<e;K++)if(!P||j.get(K))c++,w=f[0==g?K:ea[K]],J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(w.x,x.x,A.x,q,l,G,I),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(w.y,x.y,A.y,q,l,G,I),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(w.z,
x.z,A.z,q,l,G,I);G.appendSB(I);JU.XmlUtil.appendTagObj(a,"jvxlVertexData",D(-1,["count",""+c,"min",JU.Escape.eP(x),"max",JU.Escape.eP(A),"encoding","base90xyz2","data",J.jvxl.data.JvxlCoder.jvxlCompressString(G.toString(),t)]),null);null!=h&&JU.XmlUtil.appendTagObj(a,"jvxlPolygonColorData",D(-1,["encoding","jvxlnc","count",""+g]),"\n"+h);if(k){G=new JU.SB;I=new JU.SB;if(null==n)for(K=0;K<e;K++){if(!P||j.get(K))J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(d[0==g?K:ea[K]],b.mappedDataMin,b.mappedDataMax,
q,l,G,I)}else{f=0;G.appendI(c).append(" ");for(K=0;K<e;K++)if(!P||j.get(K))d=n[0==g?K:ea[K]],d==f?d=0:f=d,G.appendI(d),G.append(" ")}J.jvxl.data.JvxlCoder.appendXmlColorData(a,G.appendSB(I).append("\n").toString(),null==n,!0,b.valueMappedToRed,b.valueMappedToBlue)}},"JU.SB,J.jvxl.data.JvxlData,~A,~A,~A,~N,~S,~N,JU.BS,~A,~B,~B");d.jvxlFractionAsCharacter=e(d,"jvxlFractionAsCharacter",function(a){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,35,90)},"~N");d.jvxlFractionAsCharacterRange=
e(d,"jvxlFractionAsCharacterRange",function(a,b,c){0.9999<a?a=0.9999:Float.isNaN(a)&&(a=1.0001);a=G(Math.floor(a*c+b));return a<b?String.fromCharCode(b):92==a?"!":String.fromCharCode(a)},"~N,~N,~N");d.jvxlAppendCharacter2=e(d,"jvxlAppendCharacter2",function(a,b,c,f,d,e,h){a=b==c?a:(a-b)/(c-b);b=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,f,d);e.appendC(b);a-=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b.charCodeAt(0),f,d,0);h.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a*
d,f,d))},"~N,~N,~N,~N,~N,JU.SB,JU.SB");d.jvxlFractionFromCharacter=e(d,"jvxlFractionFromCharacter",function(a,b,c,f){if(a==b+c)return NaN;a<b&&(a=92);a=(a-b+f)/c;return 0>a?0:1<a?0.999999:a},"~N,~N,~N,~N");d.jvxlFractionFromCharacter2=e(d,"jvxlFractionFromCharacter2",function(a,b,c,f){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(a,c,f,0);b=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b,c,f,0.5);return a+b/f},"~N,~N,~N,~N");d.jvxlValueAsCharacter=e(d,"jvxlValueAsCharacter",function(a,b,c,f,
d){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(b==c?a:(a-b)/(c-b),f,d)},"~N,~N,~N,~N,~N");d.jvxlValueFromCharacter2=e(d,"jvxlValueFromCharacter2",function(a,b,c,f,d,e){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(a,b,d,e);return f==c?a:c+a*(f-c)},"~N,~N,~N,~N,~N,~N");d.jvxlEncodeBitSet0=e(d,"jvxlEncodeBitSet0",function(a,b,c){var f=0,d=-1,e=0;0>b&&(b=a.length());for(var h=0,g=!1,j=b-1,n=0;n<b;++n)g==a.get(n)?f++:(f==d&&n!=j?e++:(0<e&&(c.appendC(" ").appendI(-e),e=0,h++),c.appendC(" ").appendI(f),
h++,d=f),f=1,g=!g);c.appendC(" ").appendI(f).appendC("\n");return h},"JU.BS,~N,JU.SB");d.jvxlEncodeBitSet=e(d,"jvxlEncodeBitSet",function(a){var b=new JU.SB;J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,-1,b);return b.toString()},"JU.BS");d.jvxlEncodeBitSetBuffer=e(d,"jvxlEncodeBitSetBuffer",function(a,b,c){var f=0,d=0,e=!1;0>b&&(b=a.length());if(0==b)return 0;c.append("-");for(var h=0;h<b;++h)e==a.get(h)?f++:(J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,f,35,90),d++,f=1,e=!e);J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,
f,35,90);c.appendC("\n");return d},"JU.BS,~N,JU.SB");d.jvxlAppendEncodedNumber=e(d,"jvxlAppendEncodedNumber",function(a,b,c,f){var d=b<f;for(0==b?a.appendC(String.fromCharCode(c)):d||a.appendC(String.fromCharCode(c+f));0<b;){var e=G(b/f);b=c+b-e*f;92==b&&(b=33);a.appendC(String.fromCharCode(b));b=e}d||a.append(" ")},"JU.SB,~N,~N,~N");d.jvxlDecodeBitSetRange=e(d,"jvxlDecodeBitSetRange",function(a,b,c){for(var f=new JU.BS,d=0,e=0,h=!1,g=u(1,0);-2147483648!=(d=J.jvxl.data.JvxlCoder.jvxlParseEncodedInt(a,
b,c,g));)h&&f.setBits(e,e+d),e+=d,h=!h;return f},"~S,~N,~N");d.jvxlParseEncodedInt=e(d,"jvxlParseEncodedInt",function(a,b,c,f){var d=!1,e=0,h=f[0],g=a.length;if(0>h)return-2147483648;for(;h<g&&JU.PT.isWhitespace(a.charAt(h));)++h;if(h>=g)return-2147483648;var j=1,n=a.charAt(h).charCodeAt(0)==b+c;for(n&&h++;h<g&&!JU.PT.isWhitespace(a.charAt(h));){d=a.charAt(h).charCodeAt(0);d<b&&(d=92);e+=(d-b)*j;d=!0;++h;if(!n)break;j*=c}d||(e=-2147483648);f[0]=h;return e},"~S,~N,~N,~A");d.jvxlDecodeBitSet=e(d,"jvxlDecodeBitSet",
function(a){if(a.startsWith("-"))return J.jvxl.data.JvxlCoder.jvxlDecodeBitSetRange(J.jvxl.data.JvxlCoder.jvxlDecompressString(a.substring(1)),35,90);for(var b=new JU.BS,c=0,f=0,d=0,e=0,h=!1,g=u(1,0);;){c=0>d++?c:JU.PT.parseIntNext(a,g);if(-2147483648==c)break;0>c?(d=c,c=f):(h&&b.setBits(e,e+c),e+=c,f=c,h=!h)}return b},"~S");d.jvxlCompressString=e(d,"jvxlCompressString",function(a,b){if(0<=a.indexOf("~"))return a;for(var c=new JU.SB,f="\x00",d=!1,e=!1,h=0,g=a.length,j=0;j<=g;j++){var n=j==g?"\x00":
a.charAt(j);switch(n.charCodeAt(0)){case 10:case 13:continue;case 38:case 60:d=b;break;default:d=!1}if(n==f)++h,n="\x00";else if(0<h||e){if(4>h&&!e||" "==f||"\t"==f)for(;0<=--h;)c.appendC(f);else e?e=!1:c.appendC("~"),c.appendI(h),c.appendC(" ");h=0}"\x00"!=n&&(d?(e=!0,c.appendC("~"),f=n,n=String.fromCharCode(n.charCodeAt(0)-1)):f=n,c.appendC(n))}return c.toString()},"~S,~B");d.jvxlDecompressString=e(d,"jvxlDecompressString",function(a){if(0>a.indexOf("~"))return a;for(var b=new JU.SB,c="\x00",f=
u(1,0),d=0;d<a.length;d++){var e=a.charAt(d);if("~"==e)switch(f[0]=++d,(e=a.charAt(d)).charCodeAt(0)){case 59:case 37:f[0]++,b.appendC(c=String.fromCharCode(e.charCodeAt(0)+1));case 49:case 50:case 51:case 52:case 53:case 54:case 55:case 56:case 57:d=JU.PT.parseIntNext(a,f);for(e=0;e<d;e++)b.appendC(c);d=f[0];continue;case 126:--d;break;default:JU.Logger.error("Error uncompressing string "+a.substring(0,d)+"?")}b.appendC(e);c=e}return b.toString()},"~S");d.jvxlCreateHeaderWithoutTitleOrAtoms=e(d,
"jvxlCreateHeaderWithoutTitleOrAtoms",function(a,b){J.jvxl.data.JvxlCoder.jvxlCreateHeader(a,b)},"J.jvxl.data.VolumeData,JU.SB");d.jvxlCreateHeader=e(d,"jvxlCreateHeader",function(a,b){a.setVolumetricXml();0==b.length()&&b.append("Line 1\nLine 2\n")},"J.jvxl.data.VolumeData,JU.SB");d.haveXMLUtil=!1});R("J.jvxl.data");S(["JU.M3","$.P3","$.V3"],"J.jvxl.data.VolumeData",["java.util.Hashtable","JU.SB","JU.Escape","$.Logger"],function(){var d=I(function(){this.sr=null;this.doIterate=!0;this.voxelCounts=
this.volumetricVectors=this.origin=this.volumetricOrigin=null;this.nPoints=0;this.volumetricVectorLengths=this.voxelMap=this.voxelData=null;this.yzCount=this.minToPlaneDistance=this.maxVectorLength=0;this.thePlane=this.inverseMatrix=this.volumetricMatrix=this.unitVolumetricVectors=null;this.thePlaneNormalMag=0;this.mappingPlane=this.xmlData=this.ptXyzTemp=null;this.voxelVolume=this.maxGrid=this.minGrid=this.mappingPlaneNormalMag=0;this.oabc=null;this.isSquared=this.isPeriodic=!1;this.ptTemp=this.edgeVector=
null;T(this,arguments)},J.jvxl.data,"VolumeData",null);ca(d,function(){this.volumetricOrigin=new JU.P3;this.origin=x(3,0);this.volumetricVectors=Array(3);this.voxelCounts=u(3,0);this.volumetricVectorLengths=x(3,0);this.unitVolumetricVectors=Array(3);this.volumetricMatrix=new JU.M3;this.inverseMatrix=new JU.M3;this.ptXyzTemp=new JU.P3;this.edgeVector=new JU.V3;this.ptTemp=new JU.P3});Y(d,function(){this.volumetricVectors[0]=new JU.V3;this.volumetricVectors[1]=new JU.V3;this.volumetricVectors[2]=new JU.V3;
this.unitVolumetricVectors[0]=new JU.V3;this.unitVolumetricVectors[1]=new JU.V3;this.unitVolumetricVectors[2]=new JU.V3});e(d,"getVoxelData",function(){return this.voxelData});e(d,"setVoxelDataAsArray",function(a){this.voxelData=a;null!=a&&(this.sr=null)},"~A");e(d,"hasPlane",function(){return null!=this.thePlane});e(d,"setMappingPlane",function(a){this.mappingPlane=a;null!=a&&(this.mappingPlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z))},"JU.P4");e(d,"distanceToMappingPlane",function(a){return(this.mappingPlane.x*
a.x+this.mappingPlane.y*a.y+this.mappingPlane.z*a.z+this.mappingPlane.w)/this.mappingPlaneNormalMag},"JU.T3");e(d,"setVolumetricOrigin",function(a,b,c){this.volumetricOrigin.set(a,b,c)},"~N,~N,~N");e(d,"getOriginFloat",function(){return this.origin});e(d,"getYzCount",function(){this.minGrid=this.volumetricVectors[0].length();this.minGrid=Math.min(this.minGrid,this.volumetricVectors[1].length());this.minGrid=Math.min(this.minGrid,this.volumetricVectors[2].length());this.maxGrid=this.volumetricVectors[0].length();
this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[1].length());this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[2].length());this.nPoints=this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2];return this.yzCount=this.voxelCounts[1]*this.voxelCounts[2]});e(d,"getVolumetricVectorLengths",function(){return this.volumetricVectorLengths});e(d,"setVolumetricVector",function(a,b,c,f){this.volumetricVectors[a].x=b;this.volumetricVectors[a].y=c;this.volumetricVectors[a].z=f;this.setUnitVectors()},
"~N,~N,~N,~N");e(d,"getVoxelCounts",function(){return this.voxelCounts});e(d,"setVoxelCounts",function(a,b,c){this.voxelCounts[0]=a;this.voxelCounts[1]=b;this.voxelCounts[2]=c;return a*b*c},"~N,~N,~N");e(d,"getVoxelDataAt",function(a){var b=G(a/this.yzCount);a-=b*this.yzCount;var c=G(a/this.voxelCounts[2]);return this.voxelData[b][c][a-c*this.voxelCounts[2]]},"~N");e(d,"getPointIndex",function(a,b,c){return a*this.yzCount+b*this.voxelCounts[2]+c},"~N,~N,~N");e(d,"getPoint",function(a,b){var c=G(a/
this.yzCount);a-=c*this.yzCount;var f=G(a/this.voxelCounts[2]);this.voxelPtToXYZ(c,f,a-f*this.voxelCounts[2],b)},"~N,JU.P3");e(d,"setVoxelData",function(a,b){var c=G(a/this.yzCount);a-=c*this.yzCount;var f=G(a/this.voxelCounts[2]);this.voxelData[c][f][a-f*this.voxelCounts[2]]=b},"~N,~N");e(d,"setVoxelMap",function(){this.voxelMap=new java.util.Hashtable;this.getYzCount()});e(d,"setMatrix",function(){for(var a=0;3>a;a++)this.volumetricMatrix.setColumnV(a,this.volumetricVectors[a]);try{this.inverseMatrix.invertM(this.volumetricMatrix)}catch(b){if($(b,
Exception))return JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? "),!1;throw b;}return!0});e(d,"transform",function(a,b){this.volumetricMatrix.rotate2(a,b)},"JU.V3,JU.V3");e(d,"setPlaneParameters",function(a){this.thePlane=a;this.thePlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z)},"JU.P4");e(d,"calcVoxelPlaneDistance",function(a,b,c){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.distancePointToPlane(this.ptXyzTemp)},"~N,~N,~N");e(d,"getToPlaneParameter",function(){return Math.sqrt(this.thePlane.x*
this.thePlane.x+this.thePlane.y*this.thePlane.y+this.thePlane.z*this.thePlane.z)*this.minToPlaneDistance});e(d,"isNearPlane",function(a,b,c,f){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.thePlane.x*this.ptXyzTemp.x+this.thePlane.y*this.ptXyzTemp.y+this.thePlane.z*this.ptXyzTemp.z+this.thePlane.w<f},"~N,~N,~N,~N");e(d,"distancePointToPlane",function(a){return(this.thePlane.x*a.x+this.thePlane.y*a.y+this.thePlane.z*a.z+this.thePlane.w)/this.thePlaneNormalMag},"JU.T3");e(d,"voxelPtToXYZ",function(a,
b,c,f){f.scaleAdd2(a,this.volumetricVectors[0],this.volumetricOrigin);f.scaleAdd2(b,this.volumetricVectors[1],f);f.scaleAdd2(c,this.volumetricVectors[2],f)},"~N,~N,~N,JU.T3");e(d,"setUnitVectors",function(){this.maxVectorLength=0;this.voxelVolume=1;for(var a=0;3>a;a++){var b=this.volumetricVectorLengths[a]=this.volumetricVectors[a].length();if(0==b)return!1;b>this.maxVectorLength&&(this.maxVectorLength=b);this.voxelVolume*=b;this.unitVolumetricVectors[a].setT(this.volumetricVectors[a]);this.unitVolumetricVectors[a].normalize()}this.minToPlaneDistance=
2*this.maxVectorLength;this.origin[0]=this.volumetricOrigin.x;this.origin[1]=this.volumetricOrigin.y;this.origin[2]=this.volumetricOrigin.z;this.oabc=Array(4);this.oabc[0]=JU.V3.newV(this.volumetricOrigin);for(a=0;3>a;a++)b=this.oabc[a+1]=new JU.V3,b.scaleAdd2(this.voxelCounts[a]-1,this.volumetricVectors[a],b);return this.setMatrix()});e(d,"xyzToVoxelPt",function(a,b,c,f){this.ptXyzTemp.set(a,b,c);this.ptXyzTemp.sub(this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);f.set(Math.round(this.ptXyzTemp.x),
Math.round(this.ptXyzTemp.y),Math.round(this.ptXyzTemp.z))},"~N,~N,~N,JU.T3i");e(d,"lookupInterpolatedVoxelValue",function(a,b){if(null!=this.mappingPlane)return this.distanceToMappingPlane(a);if(null!=this.sr){var c=this.sr.getValueAtPoint(a,b);return this.isSquared?c*c:c}this.ptXyzTemp.sub2(a,this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);var f,d=this.indexLower(this.ptXyzTemp.x,f=this.voxelCounts[0]-1),e=this.indexUpper(this.ptXyzTemp.x,d,f),h=this.indexLower(this.ptXyzTemp.y,
f=this.voxelCounts[1]-1),g=this.indexUpper(this.ptXyzTemp.y,h,f),c=this.indexLower(this.ptXyzTemp.z,f=this.voxelCounts[2]-1),j=this.indexUpper(this.ptXyzTemp.z,c,f);f=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-d),this.mantissa(this.ptXyzTemp.y-h),this.getVoxelValue(d,h,c),this.getVoxelValue(e,h,c),this.getVoxelValue(d,g,c),this.getVoxelValue(e,g,c));d=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-d),this.mantissa(this.ptXyzTemp.y-h),this.getVoxelValue(d,
h,j),this.getVoxelValue(e,h,j),this.getVoxelValue(d,g,j),this.getVoxelValue(e,g,j));return f+this.mantissa(this.ptXyzTemp.z-c)*(d-f)},"JU.T3,~B");e(d,"mantissa",function(a){return this.isPeriodic?a-Math.floor(a):a},"~N");e(d,"getVoxelValue",function(a,b,c){if(null==this.voxelMap)return this.voxelData[a][b][c];a=this.voxelMap.get(Integer.$valueOf(this.getPointIndex(a,b,c)));return null==a?NaN:a.floatValue()},"~N,~N,~N");d.getFractional2DValue=e(d,"getFractional2DValue",function(a,b,c,f,d,e){c+=a*(f-
c);return c+b*(d+a*(e-d)-c)},"~N,~N,~N,~N,~N,~N");e(d,"indexLower",function(a,b){if(this.isPeriodic&&0<b){for(;0>a;)a+=b;for(;a>=b;)a-=b;return G(Math.floor(a))}if(0>a)return 0;var c=G(Math.floor(a));return c>b?b:c},"~N,~N");e(d,"indexUpper",function(a,b,c){return!this.isPeriodic&&0>a||b==c?b:b+1},"~N,~N,~N");e(d,"offsetCenter",function(a){var b=new JU.P3;b.scaleAdd2((this.voxelCounts[0]-1)/2,this.volumetricVectors[0],b);b.scaleAdd2((this.voxelCounts[1]-1)/2,this.volumetricVectors[1],b);b.scaleAdd2((this.voxelCounts[2]-
1)/2,this.volumetricVectors[2],b);this.volumetricOrigin.sub2(a,b)},"JU.P3");e(d,"setDataDistanceToPlane",function(a){this.setPlaneParameters(a);a=this.voxelCounts[0];var b=this.voxelCounts[1],c=this.voxelCounts[2];this.voxelData=x(a,b,c,0);for(var f=0;f<a;f++)for(var d=0;d<b;d++)for(var e=0;e<c;e++)this.voxelData[f][d][e]=this.calcVoxelPlaneDistance(f,d,e)},"JU.P4");e(d,"filterData",function(a,b){var c=!Float.isNaN(b);if(null!=this.sr)this.isSquared=a;else{var f=this.voxelCounts[0],d=this.voxelCounts[1],
e=this.voxelCounts[2];if(a)for(var h=0;h<f;h++)for(var g=0;g<d;g++)for(var j=0;j<e;j++)this.voxelData[h][g][j]*=this.voxelData[h][g][j];if(c)for(h=0;h<f;h++)for(g=0;g<d;g++)for(j=0;j<e;j++)this.voxelData[h][g][j]=b-this.voxelData[h][g][j]}},"~B,~N");e(d,"capData",function(a,b){if(null!=this.voxelData){var c=this.voxelCounts[0],f=this.voxelCounts[1],d=this.voxelCounts[2],e=JU.V3.new3(a.x,a.y,a.z);e.normalize();for(var h=0;h<c;h++)for(var g=0;g<f;g++)for(var j=0;j<d;j++){var n=this.voxelData[h][g][j]-
b;this.voxelPtToXYZ(h,g,j,this.ptXyzTemp);var k=(this.ptXyzTemp.x*e.x+this.ptXyzTemp.y*e.y+this.ptXyzTemp.z*e.z+a.w-b)/1;if(0<=k||k>n)this.voxelData[h][g][j]=k}}},"JU.P4,~N");e(d,"setVolumetricXml",function(){var a=new JU.SB;if(0==this.voxelCounts[0])a.append("<jvxlVolumeData>\n");else{a.append('<jvxlVolumeData origin="'+JU.Escape.eP(this.volumetricOrigin)+'">\n');for(var b=0;3>b;b++)a.append('<jvxlVolumeVector type="'+b+'" count="'+this.voxelCounts[b]+'" vector="'+JU.Escape.eP(this.volumetricVectors[b])+
'"></jvxlVolumeVector>\n')}a.append("</jvxlVolumeData>\n");return this.xmlData=a.toString()});e(d,"setVoxelMapValue",function(a,b,c,f){null!=this.voxelMap&&this.voxelMap.put(Integer.$valueOf(this.getPointIndex(a,b,c)),Float.$valueOf(f))},"~N,~N,~N,~N");e(d,"calculateFractionalPoint",function(a,b,c,f,d,e){var h=d-f,g=(a-f)/h;this.edgeVector.sub2(c,b);e.scaleAdd2(g,this.edgeVector,b);if(null==this.sr||!this.doIterate||d==f||0.01>g||0.99<g||0.01>this.edgeVector.length())return a;b=0;this.ptTemp.setT(e);
c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1);for(d=NaN;10>++b;){var j=(c-f)/h;if(0>j||1<j)break;j=(a-c)/h/2;g+=j;if(0>g||1<g)break;e.setT(this.ptTemp);d=c;if(0.005>Math.abs(j))break;this.ptTemp.scaleAdd2(j,this.edgeVector,e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1)}return d},"~N,JU.P3,JU.P3,~N,~N,JU.P3")});R("J.jvxl.data");S(null,"J.jvxl.data.JvxlData",["JU.SB","J.jvxl.data.JvxlCoder"],function(){var d=I(function(){this.msg="";this.wasCubic=this.wasJvxl=!1;this.jvxlPlane=this.jvxlExcluded=
this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData=this.jvxlFileMessage=this.jvxlFileTitle=this.jvxlFileSource=null;this.isColorReversed=this.jvxlDataIsColorDensity=this.jvxlDataIs2dContour=this.jvxlDataIsColorMapped=this.isJvxlPrecisionColor=!1;this.thisSet=null;this.edgeFractionBase=35;this.edgeFractionRange=90;this.colorFractionBase=35;this.colorFractionRange=90;this.isValid=!0;this.vertexDataOnly=this.isModelConnected=this.isCutoffAbsolute=this.isTruncated=this.isBicolorMap=
this.isContoured=this.isXLowToHigh=this.insideOut=!1;this.cutoff=this.valueMappedToBlue=this.valueMappedToRed=this.mappedDataMax=this.mappedDataMin=0;this.cutoffRange=null;this.vertexCount=this.nSurfaceInts=this.nEdges=this.nContours=this.nBytes=this.nPointsZ=this.nPointsY=this.nPointsX=this.pointsPerAngstrom=0;this.contourValuesUsed=this.contourValues=this.contourColors=this.contourColixes=this.vContours=null;this.thisContour=-1;this.scale3d=0;this.minColorIndex=-1;this.maxColorIndex=0;this.boundingBox=
this.version=this.title=null;this.excludedVertexCount=this.excludedTriangleCount=0;this.colorDensity=!1;this.pointSize=0;this.moleculeXml=null;this.saveVertexCount=this.dataMax=this.dataMin=0;this.vertexColorMap=null;this.nVertexColors=0;this.meshColor=this.color=this.vertexColors=null;this.translucency=0;this.rendering=this.colorScheme=null;this.slabValue=-2147483648;this.isSlabbable=!1;this.diameter=0;this.slabInfo=null;this.allowVolumeRender=!1;this.voxelVolume=0;this.baseColor=this.fixedLattice=
this.mapLattice=null;this.integration=NaN;this.sbOut=null;T(this,arguments)},J.jvxl.data,"JvxlData",null);ca(d,function(){this.jvxlExcluded=Array(4)});Y(d,function(){});e(d,"clear",function(){this.allowVolumeRender=!0;this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData="";this.colorScheme=this.color=null;this.colorDensity=!1;this.pointSize=NaN;this.contourColors=this.contourColixes=this.contourValuesUsed=this.contourValues=null;this.integration=NaN;this.isSlabbable=!1;
this.isValid=!0;this.meshColor=this.mapLattice=null;this.msg="";this.nVertexColors=this.nPointsX=0;this.slabInfo=this.fixedLattice=null;this.slabValue=-2147483648;this.rendering=this.thisSet=null;this.thisContour=-1;this.translucency=0;this.vertexColors=this.vertexColorMap=this.vContours=null;this.voxelVolume=0});e(d,"setSurfaceInfo",function(a,b,c,f){this.jvxlSurfaceData=f;this.jvxlPlane=a;this.mapLattice=b;this.nSurfaceInts=c},"JU.P4,JU.P3,~N,~S");e(d,"setSurfaceInfoFromBitSet",function(a,b){this.setSurfaceInfoFromBitSetPts(a,
b,null)},"JU.BS,JU.P4");e(d,"setSurfaceInfoFromBitSetPts",function(a,b,c){var f=new JU.SB;a=null!=b?0:J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,this.nPointsX*this.nPointsY*this.nPointsZ,f);this.setSurfaceInfo(b,c,a,f.toString())},"JU.BS,JU.P4,JU.P3");e(d,"jvxlUpdateInfo",function(a,b){this.title=a;this.nBytes=b},"~A,~N");d.updateSurfaceData=e(d,"updateSurfaceData",function(a,b,c,f,d){if(0==a.length)return"";a=a.toCharArray();for(var e=0,h=0;e<c;e+=f,h++)Float.isNaN(b[e])&&(a[h]=d);return String.copyValueOf(a)},
"~S,~A,~N,~N,~S")});R("J.jvxl.data");S(["JU.MeshSurface"],"J.jvxl.data.MeshData",["java.util.Arrays","JU.AU","$.BS","$.V3","JU.BSUtil"],function(){var d=I(function(){this.setsSuccessful=!1;this.vertexIncrement=1;this.polygonColorData=null;qa("J.jvxl.data.MeshData.SSet")||J.jvxl.data.MeshData.$MeshData$SSet$();qa("J.jvxl.data.MeshData.SortSet")||J.jvxl.data.MeshData.$MeshData$SortSet$();T(this,arguments)},J.jvxl.data,"MeshData",JU.MeshSurface);e(d,"addVertexCopy",function(a,b,c,f){0>c&&(this.vertexIncrement=
-c);return this.addVCVal(a,b,f)},"JU.T3,~N,~N,~B");e(d,"getSurfaceSet",function(){return null==this.surfaceSet?this.getSurfaceSetForLevel(0):this.surfaceSet});e(d,"getSurfaceSetForLevel",function(a){0==a&&(this.surfaceSet=Array(100),this.nSets=0);this.setsSuccessful=!0;for(var b=0;b<this.pc;b++)if(null!=this.pis[b]&&(null==this.bsSlabDisplay||this.bsSlabDisplay.get(b))){var c=this.pis[b],f=this.findSet(c[0]),d=this.findSet(c[1]),e=this.findSet(c[2]);0>f&&0>d&&0>e?this.createSet(c[0],c[1],c[2]):f==
d&&d==e||(0<=f?(this.surfaceSet[f].set(c[1]),this.surfaceSet[f].set(c[2]),0<=d&&d!=f&&this.mergeSets(f,d),0<=e&&(e!=f&&e!=d)&&this.mergeSets(f,e)):0<=d?(this.surfaceSet[d].set(c[0]),this.surfaceSet[d].set(c[2]),0<=e&&e!=d&&this.mergeSets(d,e)):(this.surfaceSet[e].set(c[0]),this.surfaceSet[e].set(c[1])))}for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&c++;f=Array(this.surfaceSet.length);for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&(f[c++]=this.surfaceSet[b]);this.nSets=c;this.surfaceSet=
f;!this.setsSuccessful&&2>a&&this.getSurfaceSetForLevel(a+1);if(0==a){a=Array(this.nSets);for(b=0;b<this.nSets;b++)a[b]=pa(J.jvxl.data.MeshData.SSet,this,null,this.surfaceSet[b]);java.util.Arrays.sort(a,pa(J.jvxl.data.MeshData.SortSet,this,null));for(b=0;b<this.nSets;b++)this.surfaceSet[b]=a[b].bs;this.setVertexSets(!1)}return this.surfaceSet},"~N");e(d,"setVertexSets",function(a){if(null!=this.surfaceSet){for(var b=0,c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&0>this.surfaceSet[c].nextSetBit(0)&&
(this.surfaceSet[c]=null),null==this.surfaceSet[c]&&b++;if(0<b){a=Array(this.nSets-b);for(var f=c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&(a[f++]=this.surfaceSet[c]);this.surfaceSet=a;this.nSets-=b}else if(a)return;this.vertexSets=u(this.vc,0);for(c=0;c<this.nSets;c++)for(b=this.surfaceSet[c].nextSetBit(0);0<=b;b=this.surfaceSet[c].nextSetBit(b+1))this.vertexSets[b]=c}},"~B");e(d,"findSet",function(a){for(var b=0;b<this.nSets;b++)if(null!=this.surfaceSet[b]&&this.surfaceSet[b].get(a))return b;
return-1},"~N");e(d,"createSet",function(a,b,c){var f;for(f=0;f<this.nSets&&null!=this.surfaceSet[f];f++);f==this.surfaceSet.length&&(this.surfaceSet=JU.AU.ensureLength(this.surfaceSet,this.surfaceSet.length+100));this.surfaceSet[f]=new JU.BS;this.surfaceSet[f].set(a);this.surfaceSet[f].set(b);this.surfaceSet[f].set(c);f==this.nSets&&this.nSets++},"~N,~N,~N");e(d,"mergeSets",function(a,b){this.surfaceSet[a].or(this.surfaceSet[b]);this.surfaceSet[b]=null},"~N,~N");e(d,"invalidateSurfaceSet",function(a){for(var b=
this.surfaceSet[a].nextSetBit(0);0<=b;b=this.surfaceSet[a].nextSetBit(b+1))this.vvs[b]=NaN;this.surfaceSet[a]=null},"~N");d.checkCutoff=e(d,"checkCutoff",function(a,b,c,f){if(0>a||0>b||0>c)return!1;a=f[a];b=f[b];c=f[c];return 0<=a&&0<=b&&0<=c||0>=a&&0>=b&&0>=c},"~N,~N,~N,~A");d.calculateVolumeOrArea=e(d,"calculateVolumeOrArea",function(a,b,c,f){(f||0>=a.nSets)&&a.getSurfaceSet();var d=null!=b&&1==b.cardinality(),e=d||0>=a.nSets?1:a.nSets;f=Ja(e,0);for(var h=new JU.V3,g=new JU.V3,j=new JU.V3,n=a.pc;0<=
--n;)if(null!=a.setABC(n)){var k=0>=a.nSets?0:a.vertexSets[a.iA];if(null==b||b.get(k))c?(h.sub2(a.vs[a.iB],a.vs[a.iA]),g.sub2(a.vs[a.iC],a.vs[a.iA]),j.cross(h,g),f[d?0:k]+=j.length()):(h.setT(a.vs[a.iB]),g.setT(a.vs[a.iC]),j.cross(h,g),g.setT(a.vs[a.iA]),f[d?0:k]+=g.dot(j))}a=c?2:6;for(n=0;n<e;n++)f[n]/=a;if(d)return Float.$valueOf(f[0]);if(null!=b){b.and(JU.BSUtil.newBitSet2(0,f.length));a=Ja(b.cardinality(),0);c=0;for(n=b.nextSetBit(0);0<=n;n=b.nextSetBit(n+1))a[c++]=f[n];f=a}return f},"J.jvxl.data.MeshData,JU.BS,~B,~B");
e(d,"updateInvalidatedVertices",function(a){a.clearAll();for(var b=0;b<this.vc;b+=this.vertexIncrement)Float.isNaN(this.vvs[b])&&a.set(b)},"JU.BS");e(d,"invalidateVertices",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.vvs[b]=NaN},"JU.BS");d.$MeshData$SSet$=function(){var a=I(function(){ua(this,arguments);this.bs=null;this.n=0;T(this,arguments)},J.jvxl.data.MeshData,"SSet",null);Y(a,function(a){this.bs=a;this.n=a.cardinality()},"JU.BS")};d.$MeshData$SortSet$=function(){var a=
I(function(){ua(this,arguments);T(this,arguments)},J.jvxl.data.MeshData,"SortSet",null,java.util.Comparator);l(a,"compare",function(a,c){return a.n>c.n?-1:a.n<c.n?1:0},"J.jvxl.data.MeshData.SSet,J.jvxl.data.MeshData.SSet")}});R("J.jvxl.readers");S(null,"J.jvxl.readers.XmlReader",["JU.P3","$.PT","$.SB","JU.Escape"],function(){var d=I(function(){this.line=this.br=null;T(this,arguments)},J.jvxl.readers,"XmlReader",null);Y(d,function(a){this.br=a},"java.io.BufferedReader");e(d,"getLine",function(){return this.line});
e(d,"toTag",function(a){this.skipTo("<"+a);if(null==this.line)return"";var b=this.line.indexOf("<"+a)+a.length+1;if(b==this.line.length||" "==this.line.charAt(b)||">"==this.line.charAt(b))return this.line;this.line=null;return this.toTag(a)},"~S");e(d,"skipTag",function(a){this.skipTo("</"+a+">")},"~S");e(d,"getXmlData",function(a,b,c,f){return this.getXmlDataLF(a,b,c,f,!1)},"~S,~S,~B,~B");e(d,"getXmlDataLF",function(a,b,c,f,d){var e="</"+a+">";a="<"+a;if(null==b){b=new JU.SB;try{null==this.line&&
(this.line=this.br.readLine());for(;0>this.line.indexOf(a);)this.line=this.br.readLine()}catch(h){if($(h,Exception))return null;throw h;}b.append(this.line);d&&b.append("\n");var g=!1,j=this.line.indexOf("/>"),n=this.line.indexOf(">");if(0>n||j==n-1)g=f;for(;0>this.line.indexOf(e)&&(!g||0>this.line.indexOf("/>"));)b.append(this.line=this.br.readLine()),d&&b.append("\n");b=b.toString()}return J.jvxl.readers.XmlReader.extractTag(b,a,e,c)},"~S,~S,~B,~B,~B");d.extractTagOnly=e(d,"extractTagOnly",function(a,
b){return J.jvxl.readers.XmlReader.extractTag(a,"<"+b+">","</"+b+">",!1)},"~S,~S");d.extractTag=e(d,"extractTag",function(a,b,c,f){b=a.indexOf(b);if(0>b)return"";var d=a.indexOf(c,b);0>d&&(d=a.indexOf("/>",b),c="/>");if(0>d)return"";if(f)return d+=c.length,a.substring(b,d);for(c=!1;b<d;b++)if('"'==(f=a.charAt(b)))c=!c;else if(c&&"\\"==f)b++;else if(!c&&(">"==f||"/"==f))break;if(b>=d)return"";for(;JU.PT.isWhitespace(a.charAt(++b)););return J.jvxl.readers.XmlReader.unwrapCdata(a.substring(b,d))},"~S,~S,~S,~B");
d.unwrapCdata=e(d,"unwrapCdata",function(a){return a.startsWith("<![CDATA[")&&a.endsWith("]]\x3e")?JU.PT.rep(a.substring(9,a.length-3),"]]]]\x3e<![CDATA[>","]]\x3e"):a},"~S");d.getXmlAttrib=e(d,"getXmlAttrib",function(a,b){var c=u(1,0),f=J.jvxl.readers.XmlReader.setNext(a,b,c,1);if(2>f||2>(f=J.jvxl.readers.XmlReader.setNext(a,'"',c,0)))return"";c=J.jvxl.readers.XmlReader.setNext(a,'"',c,-1);return 0>=c?"":a.substring(f,c)},"~S,~S");e(d,"getXmlPoint",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,
b).$replace("(","{").$replace(")","}"),c=JU.Escape.uP(c);return ba(c,"JU.P3")?c:new JU.P3},"~S,~S");d.setNext=e(d,"setNext",function(a,b,c,f){var d=c[0];if(0>d||0>(d=a.indexOf(b,c[0])))return-1;d+=b.length;c[0]=d+f;return 0<f&&d<a.length&&"="!=a.charAt(d)?J.jvxl.readers.XmlReader.setNext(a,b,c,f):c[0]},"~S,~S,~A,~N");e(d,"skipTo",function(a){null==this.line&&(this.line=this.br.readLine());for(;null!=this.line&&0>this.line.indexOf(a);)this.line=this.br.readLine()},"~S");e(d,"isNext",function(a){if(null==
this.line||0<=this.line.indexOf("</")&&this.line.indexOf("</")==this.line.indexOf("<"))this.line=this.br.readLine();return 0<=this.line.indexOf("<"+a)},"~S")});R("J.jvxl.readers");S(["JU.P3","$.V3"],"J.jvxl.readers.SurfaceGenerator","JU.AU $.BS $.Measure $.P4 $.PT $.Rdr $.SB J.jvxl.data.JvxlCoder $.JvxlData $.MeshData $.VolumeData J.jvxl.readers.Parameters $.SurfaceReader JU.Logger JV.FileManager".split(" "),function(){var d=I(function(){this.version=this.marchingSquares=this.atomDataServer=this.meshDataServer=
this.volumeDataTemp=this.meshData=this.jvxlData=this.params=null;this.isValid=!0;this.bsVdw=this.fileType=null;this.colorPtr=0;this.ptRef=this.vNorm=this.vAB=this.readerData=this.out=this.surfaceReader=null;T(this,arguments)},J.jvxl.readers,"SurfaceGenerator",null);ca(d,function(){this.vAB=new JU.V3;this.vNorm=new JU.V3;this.ptRef=JU.P3.new3(0,0,1E15)});Y(d,function(a,b,c,f){this.atomDataServer=a;this.meshDataServer=b;this.params=new J.jvxl.readers.Parameters;this.meshData=null==c?new J.jvxl.data.MeshData:
c;this.jvxlData=null==f?new J.jvxl.data.JvxlData:f;this.volumeDataTemp=new J.jvxl.data.VolumeData;this.initializeIsosurface()},"J.atomdata.AtomDataServer,J.jvxl.api.MeshDataServer,J.jvxl.data.MeshData,J.jvxl.data.JvxlData");e(d,"setJvxlData",function(a){this.jvxlData=a;null!=a&&(a.version=this.version)},"J.jvxl.data.JvxlData");e(d,"setProp",function(a,b){if("debug"===a){var c=b.booleanValue();this.params.logMessages=c;this.params.logCube=c;return!0}if("init"===a)return this.initializeIsosurface(),
ba(b,"J.jvxl.readers.Parameters")?this.params=b:(this.params.script=b,null!=this.params.script&&0<=this.params.script.indexOf(";#")&&(this.params.script=JU.PT.rep(this.params.script,";#","; #"))),!1;if("silent"===a)return this.params.isSilent=!0;if("map"===a)return this.params.resetForMapping(b.booleanValue()),null!=this.surfaceReader&&(this.surfaceReader.minMax=null),!0;if("finalize"===a)return this.initializeIsosurface(),!0;if("clear"===a)return null!=this.surfaceReader&&this.surfaceReader.discardTempData(!0),
!1;if("fileIndex"===a)return this.params.fileIndex=b.intValue(),0>this.params.fileIndex&&(this.params.fileIndex=0),this.params.readAllData=!1,!0;if("blockData"===a)return this.params.blockCubeData=b.booleanValue(),!0;if("withinPoints"===a)return this.params.boundingBox=b[1],!0;if("boundingBox"===a)return this.params.boundingBox=D(-1,[JU.P3.newP(b[0]),JU.P3.newP(b[b.length-1])]),!0;if("func"===a)return this.params.func=b,!0;if("intersection"===a)return this.params.intersection=b,!0;if("bsSolvent"===
a)return this.params.bsSolvent=b,!0;if("select"===a)return this.params.bsSelected=b,!0;if("ignore"===a)return this.params.bsIgnore=b,!0;if("propertySmoothing"===a)return this.params.propertySmoothing=b.booleanValue(),!0;if("propertyDistanceMax"===a)return this.params.propertyDistanceMax=b.floatValue(),!0;if("propertySmoothingPower"===a)return this.params.propertySmoothingPower=b.intValue(),!0;if("title"===a){if(null==b)this.params.title=null;else if(JU.AU.isAS(b)&&(this.params.title=b,JU.Logger.debugging))for(var f=
0;f<this.params.title.length;f++)0<this.params.title[f].length&&JU.Logger.info(this.params.title[f]);return!0}if("sigma"===a)return this.params.cutoff=this.params.sigma=b.floatValue(),this.params.cutoffRange=null,this.params.cutoffAutomatic=!1,!0;if("cutoff"===a)return this.params.cutoff=b.floatValue(),this.params.cutoffRange=null,this.params.isPositiveOnly=!1,this.params.cutoffAutomatic=!1,!0;if("cutoffPositive"===a)return this.params.cutoff=b.floatValue(),this.params.cutoffRange=null,this.params.isPositiveOnly=
!0,this.params.isCutoffAbsolute=!1,this.params.cutoffAutomatic=!1,!0;if("cutoffRange"===a)return this.params.cutoffRange=b,this.params.cutoff=this.params.cutoffRange[0],this.params.isPositiveOnly=!1,this.params.cutoffAutomatic=!1,!0;if("parameters"===a)return this.params.parameters=JU.AU.ensureLengthA(b,2),0<this.params.parameters.length&&0!=this.params.parameters[0]&&(this.params.cutoff=this.params.parameters[0]),!0;if("cap"===a||"slab"===a)return null!=b&&this.params.addSlabInfo(b),!0;if("scale"===
a)return this.params.scale=b.floatValue(),!0;if("scale3d"===a)return this.params.scale3d=b.floatValue(),!0;if("angstroms"===a)return this.params.isAngstroms=!0;if("resolution"===a)return c=b.floatValue(),this.params.resolution=0<c?c:3.4028235E38,!0;if("downsample"===a)return c=b.intValue(),this.params.downsampleFactor=0<=c?c:0,!0;if("anisotropy"===a)return 0==(this.params.dataType&32)&&this.params.setAnisotropy(b),!0;if("eccentricity"===a)return this.params.setEccentricity(b),!0;if("addHydrogens"===
a)return this.params.addHydrogens=b.booleanValue(),!0;if("squareData"===a)return this.params.isSquared=null==b?!1:b.booleanValue(),!0;if("squareLinear"===a)return this.params.isSquaredLinear=null==b?!1:b.booleanValue(),!0;if("gridPoints"===a)return this.params.iAddGridPoints=!0;if("atomIndex"===a)return this.params.atomIndex=b.intValue(),!0;if("insideOut"===a)return this.params.insideOut=!0;if("sign"===a)return this.params.isCutoffAbsolute=!this.params.isPositiveOnly,this.params.colorBySign=!0,this.colorPtr=
0,!0;if("colorRGB"===a)return c=b.intValue(),this.params.colorRgb=this.params.colorPos=this.params.colorPosLCAO=c,0==this.colorPtr++?this.params.colorNeg=this.params.colorNegLCAO=c:this.params.colorRgb=2147483647,!0;if("monteCarloCount"===a)return this.params.psi_monteCarloCount=b.intValue(),!0;if("rangeAll"===a)return this.params.rangeAll=!0;if("rangeSelected"===a)return this.params.rangeSelected=!0;if("red"===a)return this.params.valueMappedToRed=b.floatValue(),!0;if("blue"===a)return this.params.valueMappedToBlue=
b.floatValue(),this.params.valueMappedToRed>this.params.valueMappedToBlue&&(c=this.params.valueMappedToRed,this.params.valueMappedToRed=this.params.valueMappedToBlue,this.params.valueMappedToBlue=c,this.params.isColorReversed=!this.params.isColorReversed),this.params.rangeDefined=!0,this.params.rangeAll=!1,!0;if("reverseColor"===a)return this.params.isColorReversed=!0;if("setColorScheme"===a)return this.getSurfaceSets(),this.params.colorBySets=!0,this.mapSurface(),!0;if("center"===a)return this.params.center.setT(b),
!0;if("origin"===a)return this.params.origin=b,!0;if("step"===a)return this.params.steps=b,!0;if("modelInvRotation"===a)return this.params.modelInvRotation=b,!0;if("point"===a)return this.params.points=b,!0;if("withinDistance"===a)return this.params.distance=b.floatValue(),!0;if("withinPoint"===a)return this.params.point=b,!0;if("progressive"===a)return this.params.isXLowToHigh=!0;if("phase"===a)return this.params.isCutoffAbsolute=!0,this.params.colorBySign=!0,this.params.colorByPhase=!0,this.params.colorPhase=
J.jvxl.readers.SurfaceReader.getColorPhaseIndex(b),0>this.params.colorPhase&&(JU.Logger.warn(" invalid color phase: "+b),this.params.colorPhase=0),this.params.colorByPhase=0!=this.params.colorPhase,2<=this.params.state&&(this.params.dataType=this.params.surfaceType,this.params.state=3,this.params.isBicolorMap=!0,this.surfaceReader.applyColorScale()),!0;if("radius"===a)return JU.Logger.info("solvent probe radius set to "+b),this.params.atomRadiusData=b,!0;if("envelopeRadius"===a)return this.params.envelopeRadius=
b.floatValue(),!0;if("cavityRadius"===a)return this.params.cavityRadius=b.floatValue(),!0;if("cavity"===a)return this.params.isCavity=!0;if("doFullMolecular"===a)return this.params.doFullMolecular=!0;if("pocket"===a)return this.params.pocket=b,this.params.fullyLit=this.params.pocket.booleanValue(),!0;if("minset"===a)return this.params.minSet=b.intValue(),!0;if("maxset"===a)return this.params.maxSet=b.intValue(),!0;if("plane"===a)return this.params.setPlane(b),!0;if("contour"===a){this.params.isContoured=
!0;if(JU.AU.isAF(b))this.params.contoursDiscrete=b,this.params.nContours=this.params.contoursDiscrete.length;else if(ba(b,"JU.P3")){var c=this.params.contourIncrements=b,f=c.x,d=c.y,e=c.z;0>=e&&(e=1);for(var c=0,h=f;h<=d+e/10;h+=e,c++);this.params.contoursDiscrete=x(c,0);h=f;for(f=0;f<c;f++,h+=e)this.params.contoursDiscrete[f]=h;this.params.nContours=c}else c=b.intValue(),this.params.thisContour=0,0==c?this.params.nContours=9:0<c?this.params.nContours=c:this.params.thisContour=-c;return!0}if("colorDiscrete"===
a)return this.params.contourColixes=b,!0;if("colorDensity"===a)return this.params.colorDensity=!0,null!=b&&(this.params.pointSize=b.floatValue()),!1;if("fullPlane"===a)return this.params.contourFromZero=!b.booleanValue(),!0;if("mapLattice"===a)return this.params.mapLattice=b,!0;if("extendGrid"===a)return this.params.extendGrid=b.floatValue(),!0;if("property"===a)return this.params.dataType=1208,this.params.theProperty=b,this.mapSurface(),!0;if("sphere"===a)return this.params.setSphere(b.floatValue(),
!1),this.readerData=Float.$valueOf(this.params.distance),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("geodesic"===a)return this.params.setSphere(b.floatValue(),!0),this.readerData=Float.$valueOf(this.params.distance),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("ellipsoid"===a){if(ba(b,"JU.P4"))this.params.setEllipsoidP4(b);else if(JU.AU.isAF(b))this.params.setEllipsoidAF(b);else return!0;this.readerData=Float.$valueOf(this.params.distance);
this.surfaceReader=this.newReader("IsoShapeReader");this.generateSurface();return!0}if("ellipsoid3"===a)return this.params.setEllipsoidAF(b),this.readerData=Float.$valueOf(this.params.distance),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lp"===a)return this.params.setLp(b),this.readerData=x(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("rad"===a)return this.params.setRadical(b),this.readerData=x(-1,[3,2,0,15,
0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lobe"===a)return this.params.setLobe(b),this.readerData=x(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("hydrogenOrbital"===a){if(!this.params.setAtomicOrbital(b))return this.isValid=!1,!0;this.readerData=x(-1,[this.params.psi_n,this.params.psi_l,this.params.psi_m,this.params.psi_Znuc,this.params.psi_monteCarloCount]);this.surfaceReader=this.newReader("IsoShapeReader");
this.processState();return!0}if("functionXY"===a)return this.params.setFunctionXY(b),this.params.isContoured&&this.volumeDataTemp.setPlaneParameters(null==this.params.thePlane?this.params.thePlane=JU.P4.new4(0,0,1,0):this.params.thePlane),0<=this.params.functionInfo.get(0).indexOf("_xyz")&&this.getFunctionZfromXY(),this.processState(),!0;if("functionXYZ"===a)return this.params.setFunctionXYZ(b),this.processState(),!0;if("lcaoType"===a)return this.params.setLcao(b,this.colorPtr),!0;if("lcaoCartoonCenter"===
a){if(2!=++this.params.state)return!0;Float.isNaN(this.params.center.x)&&this.params.center.setT(b);return!1}if("molecular"===a||"solvent"===a||"sasurface"===a||"nomap"===a)return this.params.setSolvent(a,b.floatValue()),this.params.isSilent||JU.Logger.info(this.params.calculationType),this.processState(),!0;if("moData"===a)return this.params.moData=b,!0;if("mepCalcType"===a)return this.params.mep_calcType=b.intValue(),!0;if("mep"===a)return this.params.setMep(b,!1),this.processState(),!0;if("mlp"===
a)return this.params.setMep(b,!0),this.processState(),!0;if("nci"===a)return c=b.booleanValue(),this.params.setNci(c),c&&this.processState(),!0;if("calculationType"===a)return this.params.calculationType=b,!0;if("charges"===a)return this.params.theProperty=b,!0;if("randomSeed"===a)return this.params.randomSeed=b.intValue(),!0;if("molecularOrbital"===a)return c=0,f=null,ba(b,Integer)?c=b.intValue():f=b,this.params.setMO(c,f),JU.Logger.info(this.params.calculationType),this.processState(),!0;if("fileType"===
a)return this.fileType=b,!0;if("fileName"===a)return this.params.fileName=b,!0;if("filesData"===a)return this.params.filesData=b,!0;if("outputChannel"===a)return this.out=b,!0;if("readFile"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,b)))return JU.Logger.error("Could not set the surface data"),!0;this.surfaceReader.setOutputChannel(this.out);this.generateSurface();return!0}if("mapColor"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,b)))return JU.Logger.error("Could not set the mapping data"),
!0;this.surfaceReader.setOutputChannel(this.out);this.mapSurface();return!0}if("getSurfaceSets"===a)return this.getSurfaceSets(),!0;"periodic"===a&&(this.params.isPeriodic=!0);return!1},"~S,~O,JU.BS");e(d,"newReader",function(a){a=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=a&&a.init(this);return a},"~S");e(d,"newReaderBr",function(a,b){var c=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=c&&c.init2(this,b);return c},"~S,java.io.BufferedReader");d.getInterface=e(d,"getInterface",
function(a){try{var b=fb._4Name("J.jvxl.readers."+a);return null==b?null:b.newInstance()}catch(c){if($(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c.toString()),null;throw c;}},"~S");e(d,"getSurfaceSets",function(){null==this.meshDataServer?this.meshData.getSurfaceSet():(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.getSurfaceSet(),this.meshDataServer.fillMeshData(this.meshData,3,null))});e(d,"processState",function(){1==this.params.state&&
null!=this.params.thePlane&&this.params.state++;2<=this.params.state?this.mapSurface():this.generateSurface()});e(d,"setReader",function(){this.readerData=null;if(null!=this.surfaceReader)return!this.surfaceReader.vertexDataOnly;switch(this.params.dataType){case 1207:this.surfaceReader=this.newReader("IsoPlaneReader");break;case 1208:this.surfaceReader=this.newReader("AtomPropertyMapper");break;case 1328:case 1329:this.readerData=1328==this.params.dataType?"Mep":"Mlp";this.surfaceReader=3==this.params.state?
this.newReader("AtomPropertyMapper"):this.newReader("Iso"+this.readerData+"Reader");break;case 1334:this.surfaceReader=this.newReader("IsoIntersectFileReader");break;case 1333:this.surfaceReader=this.newReader("IsoIntersectAtomReader");break;case 1195:case 1203:case 1196:this.surfaceReader=this.newReader("IsoSolventReader");break;case 1844:case 1837:this.surfaceReader=this.newReader("IsoMOReader");break;case 8:this.surfaceReader=this.newReader("IsoFxyReader");break;case 9:this.surfaceReader=this.newReader("IsoFxyzReader")}JU.Logger.debugging&&
JU.Logger.info("Using surface reader "+this.surfaceReader);this.params.isSilent&&null!=this.surfaceReader&&(this.surfaceReader.isQuiet=!0);return!0});e(d,"generateSurface",function(){if(2==++this.params.state){this.setReader();null==this.params.sbOut&&(this.params.sbOut=new JU.SB);this.jvxlData.sbOut=this.params.sbOut;var a=null!=this.meshDataServer;this.params.colorBySign&&(this.params.isBicolorMap=!0);if(null==this.surfaceReader)JU.Logger.error("surfaceReader is null for "+this.params.dataType);
else if(this.surfaceReader.createIsosurface(!1)){if(null!=this.params.probes)for(var b=this.params.probeValues.length;0<=--b;)this.params.probeValues[b]=this.surfaceReader.getValueAtPoint(this.params.probes[b],!1);null!=this.params.pocket&&a&&this.surfaceReader.selectPocket(!this.params.pocket.booleanValue());0<this.params.minSet&&this.surfaceReader.excludeMinimumSet();0<this.params.maxSet&&this.surfaceReader.excludeMaximumSet();null!=this.params.slabInfo&&this.surfaceReader.slabIsosurface(this.params.slabInfo);
a&&this.meshDataServer.notifySurfaceGenerationCompleted()&&(this.surfaceReader.hasColorData=!1);null!=this.jvxlData.thisSet&&this.getSurfaceSets();this.jvxlData.jvxlDataIs2dContour&&(this.surfaceReader.colorIsosurface(),this.params.state=3);this.jvxlData.jvxlDataIsColorDensity&&(this.params.state=3);if(this.params.colorBySign||this.params.isBicolorMap)this.params.state=3,this.surfaceReader.applyColorScale();null!=this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=null,this.surfaceReader.hasColorData=
!1);this.surfaceReader.jvxlUpdateInfo();this.marchingSquares=this.surfaceReader.marchingSquares;this.surfaceReader.discardTempData(!1);this.params.mappedDataMin=3.4028235E38;this.surfaceReader.closeReader();if(3!=this.params.state&&(this.surfaceReader.hasColorData||this.params.colorDensity))this.params.state=3,this.colorIsosurface();this.surfaceReader=null}else JU.Logger.error("Could not create isosurface"),this.params.cutoff=NaN,this.params.cutoffRange=null,this.surfaceReader.closeReader()}});e(d,
"mapSurface",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;if(!(3>++this.params.state)&&this.setReader()){this.params.isPeriodic&&(this.surfaceReader.volumeData.isPeriodic=!0);if(null!=this.params.thePlane){var a=this.params.isSquared;this.params.isSquared=!1;this.params.cutoff=0;this.params.cutoffRange=null;this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);this.surfaceReader.createIsosurface(!this.params.isPeriodic);this.surfaceReader.volumeData.setMappingPlane(null);
null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted();if(1207==this.params.dataType){this.surfaceReader.discardTempData(!0);return}this.params.isSquared=a;this.params.mappedDataMin=3.4028235E38;this.surfaceReader.readVolumeData(!0);null!=this.params.mapLattice&&(this.surfaceReader.volumeData.isPeriodic=!0)}else!this.params.colorBySets&&!this.params.colorDensity&&(this.surfaceReader.readAndSetVolumeParameters(!0),this.params.mappedDataMin=3.4028235E38,this.surfaceReader.readVolumeData(!0));
this.colorIsosurface();this.surfaceReader.closeReader();this.surfaceReader=null}});e(d,"colorIsosurface",function(){this.surfaceReader.colorIsosurface();this.surfaceReader.jvxlUpdateInfo();this.surfaceReader.updateTriangles();this.surfaceReader.discardTempData(!0);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted()});e(d,"getProperty",function(a,b){return"jvxlFileData"===a?J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,null,this.params.title,"",!0,b,null,null):"jvxlFileInfo"===
a?J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData):null},"~S,~N");e(d,"setFileData",function(a,b){var c=this.fileType;this.fileType=null;if(ba(b,"java.util.Map")){var f=b;if(f.containsKey("__pymolSurfaceData__"))return this.readerData=f,this.newReaderBr("PyMOLMeshReader",null);b=f.get("volumeData")}if(ba(b,"J.jvxl.data.VolumeData"))return this.volumeDataTemp=b,this.newReader("VolumeDataReader");f=null;"string"==typeof b&&(f=b,b=JU.Rdr.getBR(b));if(ba(b,Array)){for(var f=b[0],d=Array(f.length),e=0;e<
f.length;e++)this.fileType=c,d[e]=this.setFileData(a,f[e]);b[0]=d;this.readerData=b;return this.newReader("IsoIntersectGridReader")}d=b;null==c&&(c=JV.FileManager.determineSurfaceFileType(d));if(null!=c&&c.startsWith("UPPSALA")){e=this.params.fileName;e=e.substring(0,e.indexOf("/",10));e+=JU.PT.getQuotedStringAt(c,c.indexOf("A HREF")+1);this.params.fileName=e;b=this.atomDataServer.getBufferedInputStream(e);if(null==b)return JU.Logger.error("Isosurface: could not open file "+e),null;try{d=JU.Rdr.getBufferedReader(b,
null)}catch(h){if(!$(h,Exception))throw h;}c=JV.FileManager.determineSurfaceFileType(d)}null==c&&(c="UNKNOWN");JU.Logger.info("data file type was determined to be "+c);if(c.equals("Jvxl+"))return this.newReaderBr("JvxlReader",d);this.readerData=D(-1,[this.params.fileName,f]);0<="MRC DELPHI DSN6".indexOf(c.toUpperCase())&&(c+="Binary");return this.newReaderBr(c+"Reader",d)},"JV.Viewer,~O");e(d,"getReaderData",function(){var a=this.readerData;this.readerData=null;return a});e(d,"initializeIsosurface",
function(){this.params.initialize();this.colorPtr=0;this.marchingSquares=this.surfaceReader=null;this.initState()});e(d,"initState",function(){this.params.state=1;this.params.dataType=this.params.surfaceType=0});e(d,"setLcao",function(){this.params.colorPos=this.params.colorPosLCAO;this.params.colorNeg=this.params.colorNegLCAO;return this.params.lcaoType});e(d,"getFunctionZfromXY",function(){for(var a=this.params.functionInfo.get(1),b=u(3,0),c=u(3,0),f=Array(3),d=0;3>d;d++){var e=this.params.functionInfo.get(d+
2);b[d]=Math.abs(A(e.x));f[d]=JU.V3.new3(e.y,e.z,e.w)}for(var e=b[0],b=b[1],h=new JU.P3,g=new JU.P3,j=new JU.P3,n=new JU.P3,k=this.params.functionInfo.get(5),t=x(e,b,0),q,d=0;d<e;d++)for(var l=0;l<b;l++){h.scaleAdd2(d,f[0],a);h.scaleAdd2(l,f[1],h);var w=J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(h.x,h.y,k,c);g.set((q=k[c[0]])[0],q[1],q[2]);1E-5>w?h.z=q[2]:(j.set((q=k[c[1]])[0],q[1],q[2]),n.set((q=k[c[2]])[0],q[1],q[2]),h.z=this.distanceVerticalToPlane(h.x,h.y,g,j,n));t[d][l]=h.z}this.params.functionInfo.set(5,
t)});e(d,"distanceVerticalToPlane",function(a,b,c,f,d){c=JU.Measure.getDirectedNormalThroughPoints(c,f,d,this.ptRef,this.vNorm,this.vAB);return(this.vNorm.x*a+this.vNorm.y*b+c)/-this.vNorm.z},"~N,~N,JU.P3,JU.P3,JU.P3");d.findNearestThreePoints=e(d,"findNearestThreePoints",function(a,b,c,f){var d,e,h,g,j,n,k;j=n=k=-1;e=h=g=3.4028235E38;for(var t=c.length;0<=--t;)d=(d=c[t][0]-a)*d+(d=c[t][1]-b)*d,d<e?(g=h,h=e,e=d,k=n,n=j,j=t):d<h?(g=h,h=d,k=n,n=t):d<g&&(g=d,k=t);f[0]=j;f[1]=n;f[2]=k;return e},"~N,~N,~A,~A");
e(d,"addRequiredFile",function(a){null!=this.meshDataServer&&this.meshDataServer.addRequiredFile(a)},"~S");e(d,"setRequiredFile",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setRequiredFile(a,b)},"~S,~S");e(d,"log",function(a){null==this.atomDataServer?System.out.println(a):this.atomDataServer.log(a)},"~S");e(d,"setOutputChannel",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setOutputChannel(a,b)},"javajs.api.GenericBinaryDocument,JU.OC");e(d,"fillAtomData",function(a,
b){0!=(b&2)&&null!=a.bsSelected&&(null==this.bsVdw&&(this.bsVdw=new JU.BS),this.bsVdw.or(a.bsSelected));this.atomDataServer.fillAtomData(a,b)},"J.atomdata.AtomData,~N");e(d,"getOriginVaVbVc",function(){return null==this.surfaceReader.volumeData?null:this.surfaceReader.volumeData.oabc})});R("J.jvxl.readers");S(null,"J.jvxl.readers.Parameters","java.util.Hashtable JU.A4 $.Lst $.M3 $.P3 $.P4 $.V3 JU.Escape $.Logger".split(" "),function(){var d=I(function(){this.testFlags=this.state=0;this.isSilent=this.logCube=
this.logCompression=this.logMessages=!1;this.assocCutoff=0.3;this.surfaceType=this.dataType=0;this.calculationType="";this.atomRadiusData=null;this.addHydrogens=!1;this.solventExtendedAtomRadius=this.solventRadius=0;this.propertySmoothing=!1;this.propertySmoothingPower=4;this.cavityRadius=this.envelopeRadius=0;this.isCavity=!1;this.pocket=null;this.minSet=0;this.slabInfo=null;this.slabPlaneOffset=NaN;this.theProperty=null;this.solvent_ptsPerAngstrom=4;this.solvent_gridMax=60;this.plane_ptsPerAngstrom=
4;this.plane_gridMax=81;this.colorBySets=this.colorByPhase=this.colorBySign=!1;this.colorPhase=this.colorNegLCAO=this.colorPosLCAO=this.colorPos=this.colorNeg=this.colorRgb=0;this.iAddGridPoints=this.colorDensity=!1;this.atomIndex=0;this.isAngstroms=!1;this.scale3d=this.scale=0;this.anisotropy=null;this.isAnisotropic=!1;this.eccentricityMatrixInverse=this.eccentricityMatrix=null;this.isEccentric=!1;this.eccentricityRatio=this.eccentricityScale=0;this.functionInfo=this.lcaoType=this.anisoB=this.aniosU=
null;this.psi_n=2;this.psi_Znuc=this.psi_m=this.psi_l=1;this.psi_ptsPerAngstrom=5;this.psi_monteCarloCount=0;this.mep_gridMax=40;this.mep_ptsPerAngstrom=3;this.mep_marginAngstroms=1;this.mep_calcType=-1;this.qmOrbitalCount=this.qmOrbitalType=0;this.moData=null;this.qm_gridMax=80;this.qm_ptsPerAngstrom=10;this.qm_marginAngstroms=1;this.qm_nAtoms=0;this.qm_moNumber=2147483647;this.point=this.center=this.qm_moLinearCombination=null;this.distance=0;this.allowVolumeRender=!1;this.title=this.func=this.bsSolvent=
this.bsIgnore=this.bsSelected=this.script=null;this.readAllData=this.blockCubeData=!1;this.fileIndex=-1;this.fileName=null;this.modelIndex=-1;this.modelInvRotation=null;this.dataXYReversed=this.insideOut=this.isXLowToHigh=!1;this.cutoff=3.4028235E38;this.cutoffRange=null;this.sigma=3.4028235E38;this.cutoffAutomatic=!0;this.rangeDefined=this.rangeSelected=this.rangeAll=this.isPositiveOnly=this.isCutoffAbsolute=!1;this.mappedDataMax=this.mappedDataMin=this.valueMappedToBlue=this.valueMappedToRed=0;
this.isSquaredLinear=this.isSquared=this.isBicolorMap=this.isColorReversed=!1;this.thePlane=null;this.isContoured=!1;this.thisContour=this.nContours=0;this.contourFromZero=!1;this.parameters=null;this.maxSet=this.downsampleFactor=this.resolution=0;this.bsExcluded=this.boundingBox=this.contourIncrements=this.contourColixes=this.contoursDiscrete=null;this.contourType=0;this.colorSchemeTranslucent=!1;this.colorEncoder=null;this.usePropertyForColorRange=!0;this.doFullMolecular=this.isPeriodic=!1;this.propertyDistanceMax=
2147483647;this.randomSeed=0;this.fullyLit=!1;this.mapLattice=this.contactPair=this.volumeData=this.points=this.steps=this.origin=this.intersection=this.vertexSource=null;this.extendGrid=0;this.showTiming=this.isMapped=!1;this.pointSize=0;this.probes=null;this.isModelConnected=!1;this.sbOut=this.probeValues=this.filesData=this.surfaceAtoms=null;T(this,arguments)},J.jvxl.readers,"Parameters",null);ca(d,function(){this.anisotropy=x(3,0)});e(d,"initialize",function(){this.addHydrogens=!1;this.allowVolumeRender=
!0;this.atomRadiusData=null;this.atomIndex=-1;this.blockCubeData=!1;this.boundingBox=null;this.bsExcluded=Array(4);this.bsSolvent=this.bsSelected=this.bsIgnore=null;this.calculationType="";this.center=new JU.P3;this.resetForMapping(!0);this.colorBySign=this.colorByPhase=this.colorBySets=!1;this.colorEncoder=null;this.colorNeg=-65536;this.colorNegLCAO=-8388480;this.colorPos=-16776961;this.colorPosLCAO=-23296;this.colorRgb=-2147483648;this.colorSchemeTranslucent=!1;this.contourColixes=this.contoursDiscrete=
this.contourIncrements=this.contactPair=null;this.contourFromZero=!0;this.cutoff=3.4028235E38;this.cutoffAutomatic=!0;this.dataXYReversed=!1;this.distance=3.4028235E38;this.doFullMolecular=!1;this.envelopeRadius=10;this.extendGrid=0;this.fileIndex=1;this.readAllData=!0;this.fileName="";this.filesData=null;this.fullyLit=!1;this.functionInfo=null;this.logCube=this.logCompression=this.isSilent=this.isPeriodic=this.isMapped=this.isEccentric=this.isContoured=this.isSquaredLinear=this.isSquared=this.isModelConnected=
this.isColorReversed=this.isCavity=this.isBicolorMap=this.isCutoffAbsolute=this.isPositiveOnly=this.isAngstroms=this.insideOut=this.iAddGridPoints=!1;this.logMessages=JU.Logger.debugging;this.mapLattice=null;this.mep_calcType=-1;this.minSet=0;this.modelIndex=-1;this.modelInvRotation=null;this.nContours=0;this.pocket=null;this.pointSize=NaN;this.probeValues=this.probes=null;this.propertyDistanceMax=2147483647;this.propertySmoothing=!1;this.propertySmoothingPower=4;this.rangeSelected=this.rangeAll=
this.rangeDefined=!1;this.resolution=3.4028235E38;this.scale=NaN;this.scale3d=0;this.sigma=NaN;this.slabInfo=null;this.solventExtendedAtomRadius=0;this.state=1;this.testFlags=0;this.theProperty=this.thePlane=null;this.thisContour=-1;this.title=null;this.usePropertyForColorRange=!0;this.vertexSource=null});e(d,"resetForMapping",function(a){a||(this.state=2);this.center.x=NaN;this.colorDensity=!1;this.intersection=this.func=null;this.isAnisotropic=!1;this.isMapped=!0;this.mappedDataMin=3.4028235E38;
this.points=this.parameters=this.origin=null;this.qmOrbitalType=0;this.volumeData=this.steps=null},"~B");e(d,"setAnisotropy",function(a){this.anisotropy[0]=a.x;this.anisotropy[1]=a.y;this.anisotropy[2]=a.z;this.isAnisotropic=!0;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P3");e(d,"setEccentricity",function(a){var b=JU.V3.new3(a.x,a.y,a.z),c=0<this.scale?this.scale:0>a.w?1:b.length();a=Math.abs(a.w);b.normalize();var f=JU.V3.new3(0,0,1);b.add(f);b.normalize();Float.isNaN(b.x)&&b.set(1,
0,0);this.eccentricityMatrixInverse=new JU.M3;this.eccentricityMatrixInverse.invertM(this.eccentricityMatrix=(new JU.M3).setAA(JU.A4.newVA(b,3.141592653589793)));this.isEccentric=this.isAnisotropic=!0;this.eccentricityScale=c;this.eccentricityRatio=a;1<a&&(this.eccentricityScale*=a);this.anisotropy[0]=a*c;this.anisotropy[1]=a*c;this.anisotropy[2]=c;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P4");e(d,"setPlane",function(a){this.thePlane=a;0==this.thePlane.x&&(0==this.thePlane.y&&0==this.thePlane.z)&&
(this.thePlane.z=1);this.isContoured=!0},"JU.P4");e(d,"setSphere",function(a,b){this.dataType=b?74:65;this.distance=a;this.setEccentricity(JU.P4.new4(0,0,1,1));this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" SPHERE "+a+";"},"~N,~B");e(d,"setEllipsoidP4",function(a){this.dataType=66;this.distance=1;this.setEccentricity(a);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages},"JU.P4");e(d,"setEllipsoidAF",function(a){this.anisoB=
a;this.dataType=67;this.distance=0.3*(Float.isNaN(this.scale)?1:this.scale);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;Float.isNaN(this.center.x)&&this.center.set(0,0,0);3.4028235E38==this.resolution&&(this.resolution=6)},"~A");e(d,"setLobe",function(a){this.dataType=68;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" LOBE {"+a.x+" "+
a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,"getScriptParams",function(){return" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)});e(d,"setLp",function(a){this.dataType=70;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" LP {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,
"setRadical",function(a){this.dataType=71;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" RAD {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,"setLcao",function(a,b){this.lcaoType=a;1==b&&(this.colorPosLCAO=this.colorNegLCAO);this.isSilent=!this.logMessages},"~S,~N");e(d,"setSolvent",function(a,b){this.isEccentric=
this.isAnisotropic=!1;this.solventRadius=Math.abs(b);this.dataType=null!=this.intersection?1333:"nomap"===a?1207:"molecular"===a?1203:"sasurface"===a||0==this.solventRadius?1196:1195;if(2>this.state&&(this.cutoffAutomatic||!this.colorDensity)&&(null==this.intersection||3.4028235E38==this.cutoff))this.cutoff=0;switch(this.dataType){case 1333:this.calculationType="VDW intersection";break;case 1207:this.calculationType="unmapped plane";break;case 1203:this.calculationType="molecular surface with radius "+
this.solventRadius;0==this.minSet&&(this.minSet=50);break;case 1195:this.calculationType="solvent-excluded surface with radius "+this.solventRadius;0==this.minSet&&(this.minSet=50);break;case 1196:this.calculationType="solvent-accessible surface with radius "+this.solventRadius,0==this.minSet&&(this.minSet=50)}switch(this.dataType){case 1207:this.solventExtendedAtomRadius=this.solventRadius;this.solventRadius=0;this.isContoured=!1;break;case 1203:this.solventExtendedAtomRadius=0;break;case 1195:this.solventExtendedAtomRadius=
0;null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent);break;case 1196:this.solventExtendedAtomRadius=this.solventRadius,this.solventRadius=0,null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent)}},"~S,~N");e(d,"setFunctionXY",function(a){this.dataType=8;this.functionInfo=a;this.cutoff=1.4E-45;this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(d,"setFunctionXYZ",function(a){this.dataType=9;this.functionInfo=
a;3.4028235E38==this.cutoff&&(this.cutoff=1.4E-45);this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(d,"setAtomicOrbital",function(a){this.dataType=1294;this.setEccentricity(JU.P4.new4(0,0,1,1));this.psi_n=A(a[0]);this.psi_l=A(a[1]);this.psi_m=A(a[2]);this.psi_Znuc=a[3];this.psi_monteCarloCount=A(a[4]);this.distance=a[5];if(0!=this.distance||null!=this.thePlane)this.allowVolumeRender=!1;this.randomSeed=A(a[6]);this.psi_ptsPerAngstrom=10;if(3.4028235E38==this.cutoff||0.14==this.cutoff)this.cutoff=
0<this.psi_monteCarloCount?0:0.04,this.isSquared&&(this.cutoff*=this.cutoff);this.isCutoffAbsolute=!0;2>this.state&&(null==this.thePlane&&this.colorBySign)&&(this.isBicolorMap=!0);return 0<this.psi_Znuc&&Math.abs(this.psi_m)<=this.psi_l&&this.psi_l<this.psi_n},"~A");e(d,"setMep",function(a,b){this.dataType=b?1329:1328;this.theProperty=a;this.isEccentric=this.isAnisotropic=this.usePropertyForColorRange=!1;3.4028235E38==this.cutoff&&(this.cutoff=0.1,this.isSquared&&(this.cutoff*=this.cutoff));this.isCutoffAbsolute=
0<this.cutoff&&!this.isPositiveOnly;this.contourFromZero=!1;2<=this.state||null!=this.thePlane?!this.rangeDefined&&!this.rangeAll&&(this.valueMappedToRed=-0.1,this.valueMappedToBlue=0.1,this.rangeDefined=!0):this.isBicolorMap=this.colorBySign=!0},"~A,~B");e(d,"setNci",function(a){this.fullyLit=!0;this.qm_gridMax=200;a&&(this.dataType=1844);this.qm_marginAngstroms=2;this.qmOrbitalType=a?3:4;if(a&&(null==this.parameters||2>this.parameters.length))this.parameters=x(-1,[this.cutoff,2]);if(3.4028235E38==
this.cutoff||0==this.cutoff)this.cutoff=0.3;this.isSquared&&(this.cutoff*=this.cutoff);null==this.title&&(this.title=[]);this.moData=new java.util.Hashtable},"~B");e(d,"setMO",function(a,b){this.isModelConnected=!0;this.qm_moLinearCombination=b;this.qm_moNumber=null==b?Math.abs(a):A(b[1]);this.qmOrbitalType=this.moData.containsKey("haveVolumeData")?5:this.moData.containsKey("gaussians")?1:this.moData.containsKey("slaters")?2:0;var c=0>=a&&null==b;0==this.qmOrbitalType?(JU.Logger.error("MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?)"),
this.title=D(-1,["no basis functions found in file"])):(this.qmOrbitalCount=this.moData.get("mos").size(),this.calculationType=this.moData.get("calculationType"),this.calculationType="Molecular orbital #"+this.qm_moNumber+"/"+this.qmOrbitalCount+" "+(null==this.calculationType?"":this.calculationType),!c&&null==this.title&&(this.title=Array(5),this.title[0]="%F",this.title[1]="Model %M  MO %I/%N %T",this.title[2]="?Energy = %E %U",this.title[3]="?Symmetry = %S",this.title[4]="?Occupancy = %O"));this.dataType=
1837;3.4028235E38==this.cutoff&&(this.cutoff=c?0.01:0.05);if(this.isSquared||this.isSquaredLinear)this.cutoff*=this.cutoff;this.isEccentric=this.isAnisotropic=!1;this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;2<=this.state||null!=this.thePlane||(this.colorBySign=!0,this.colorByPhase&&0==this.colorPhase&&(this.colorByPhase=!1),this.isBicolorMap=!0)},"~N,~A");e(d,"setMapRanges",function(a,b){if(!this.colorDensity&&(this.colorByPhase||this.colorBySign||(null!=this.thePlane||this.isBicolorMap)&&
!this.isContoured))this.mappedDataMin=-1,this.mappedDataMax=1;if(3.4028235E38==this.mappedDataMin||this.mappedDataMin==this.mappedDataMax){var c=a.getMinMaxMappedValues(b);System.out.println("parameters - setmapranges "+c[0]+" "+c[1]);this.mappedDataMin=c[0];this.mappedDataMax=c[1]}0==this.mappedDataMin&&0==this.mappedDataMax&&(this.mappedDataMin=-1,this.mappedDataMax=1);this.rangeDefined||(this.valueMappedToRed=this.mappedDataMin,this.valueMappedToBlue=this.mappedDataMax)},"J.jvxl.readers.SurfaceReader,~B");
e(d,"addSlabInfo",function(a){null==this.slabInfo&&(this.slabInfo=new JU.Lst);this.slabInfo.addLast(a)},"~A");e(d,"isInsideOut",function(){return this.insideOut!=this.dataXYReversed});e(d,"isFullyLit",function(){return null!=this.thePlane||this.fullyLit})});R("J.jvxl.readers");S(["J.jvxl.api.VertexDataServer","JU.P3"],"J.jvxl.readers.SurfaceReader","JU.AU $.BS J.jvxl.calc.MarchingCubes $.MarchingSquares J.jvxl.data.JvxlCoder $.MeshData JU.BoxInfo $.C $.ColorEncoder $.Escape $.Logger".split(" "),function(){var d=
I(function(){this.edgeData=this.volumeData=this.jvxlData=this.meshData=this.params=this.meshDataServer=this.sg=null;this.isXLowToHigh=this.isProgressive=this.allowSigma=this.haveSurfaceAtoms=!1;this.assocCutoff=0.3;this.hasColorData=this.vertexDataOnly=this.isPeriodic=this.isQuiet=!1;this.dataMin=3.4028235E38;this.dataMax=-3.4028235E38;this.dataMean=0;this.anisotropy=this.center=this.xyzMax=this.xyzMin=null;this.isAnisotropic=!1;this.eccentricityMatrixInverse=this.eccentricityMatrix=null;this.isEccentric=
!1;this.edgeCount=this.eccentricityRatio=this.eccentricityScale=0;this.voxelData=this.voxelCounts=this.volumetricVectors=this.volumetricOrigin=null;this.nPointsZ=this.nPointsY=this.nPointsX=this.nDataPoints=this.nBytes=0;this.isJvxl=!1;this.colorFractionRange=this.colorFractionBase=this.edgeFractionRange=this.edgeFractionBase=0;this.fractionData=this.jvxlFileHeaderBuffer=null;this.jvxlColorDataRead=this.jvxlEdgeDataRead="";this.jvxlVoxelBitSet=null;this.jvxlDataIsColorDensity=this.jvxlDataIs2dContour=
this.jvxlDataIsPrecisionColor=this.jvxlDataIsColorMapped=!1;this.jvxlCutoff=0;this.jvxlCutoffRange=null;this.jvxlNSurfaceInts=0;this.cJvxlEdgeNaN="\x00";this.contourVertexCount=0;this.yzPlanes=this.marchingCubes=this.marchingSquares=null;this.yzCount=0;this.minMax=this.ptTemp=this.qpc=null;this.haveSetAnisotropy=!1;T(this,arguments)},J.jvxl.readers,"SurfaceReader",null,J.jvxl.api.VertexDataServer);ca(d,function(){this.ptTemp=new JU.P3});Y(d,function(){});e(d,"initSR",function(a){this.sg=a;this.params=
a.params;this.assocCutoff=this.params.assocCutoff;this.isXLowToHigh=this.params.isXLowToHigh;this.center=this.params.center;this.anisotropy=this.params.anisotropy;this.isAnisotropic=this.params.isAnisotropic;this.eccentricityMatrix=this.params.eccentricityMatrix;this.eccentricityMatrixInverse=this.params.eccentricityMatrixInverse;this.isEccentric=this.params.isEccentric;this.eccentricityScale=this.params.eccentricityScale;this.eccentricityRatio=this.params.eccentricityRatio;this.marchingSquares=a.marchingSquares;
this.meshData=a.meshData;this.jvxlData=a.jvxlData;this.setVolumeDataV(a.volumeDataTemp);this.meshDataServer=a.meshDataServer;this.cJvxlEdgeNaN=String.fromCharCode(125)},"J.jvxl.readers.SurfaceGenerator");e(d,"setOutputChannel",function(){},"JU.OC");e(d,"newVoxelDataCube",function(){this.volumeData.setVoxelDataAsArray(this.voxelData=x(this.nPointsX,this.nPointsY,this.nPointsZ,0))});e(d,"setVolumeDataV",function(a){this.nBytes=0;this.volumetricOrigin=a.volumetricOrigin;this.volumetricVectors=a.volumetricVectors;
this.voxelCounts=a.voxelCounts;this.voxelData=a.getVoxelData();this.volumeData=a},"J.jvxl.data.VolumeData");e(d,"jvxlUpdateInfo",function(){this.jvxlData.jvxlUpdateInfo(this.params.title,this.nBytes)});e(d,"readAndSetVolumeParameters",function(a){return!this.readVolumeParameters(a)?!1:this.vertexDataOnly?!0:this.volumeData.setUnitVectors()},"~B");e(d,"createIsosurface",function(a){this.resetIsosurface();this.params.showTiming&&JU.Logger.startTimer("isosurface creation");this.jvxlData.cutoff=NaN;this.jvxlData.cutoffRange=
null;if(!this.readAndSetVolumeParameters(a))return!1;!a&&(!Float.isNaN(this.params.sigma)&&!this.allowSigma)&&(0<this.params.sigma&&JU.Logger.error("Reader does not support SIGMA option -- using cutoff 1.6"),this.params.cutoff=1.6);0>this.params.sigma&&(this.params.sigma=-this.params.sigma);this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.jvxlData.isSlabbable=0!=(this.params.dataType&1024);this.jvxlData.insideOut=this.params.isInsideOut();
this.jvxlData.isBicolorMap=this.params.isBicolorMap;this.jvxlData.nPointsX=this.nPointsX;this.jvxlData.nPointsY=this.nPointsY;this.jvxlData.nPointsZ=this.nPointsZ;this.jvxlData.jvxlVolumeDataXml=this.volumeData.xmlData;this.jvxlData.voxelVolume=this.volumeData.voxelVolume;if(a)this.volumeData.setMappingPlane(this.params.thePlane),null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null),this.params.setMapRanges(this,!1),this.generateSurfaceData(),this.volumeData.setMappingPlane(null);
else{if(!this.readVolumeData(!1))return!1;this.generateSurfaceData()}if(null==this.jvxlFileHeaderBuffer)this.jvxlData.jvxlFileTitle="",this.jvxlData.jvxlFileSource=null,this.jvxlData.jvxlFileMessage=null;else{a=this.jvxlFileHeaderBuffer.toString();var b=a.indexOf("\n",a.indexOf("\n",a.indexOf("\n")+1)+1)+1;this.jvxlData.jvxlFileTitle=a.substring(0,b);this.jvxlData.jvxlFileSource=this.params.fileName}null==this.params.contactPair&&this.setBBoxAll();this.jvxlData.isValid=3.4028235E38!=this.xyzMin.x;
this.params.isSilent||(this.jvxlData.isValid?JU.Logger.info("boundbox corners "+JU.Escape.eP(this.xyzMin)+" "+JU.Escape.eP(this.xyzMax)):JU.Logger.error("no isosurface points were found!"));this.jvxlData.boundingBox=D(-1,[this.xyzMin,this.xyzMax]);this.jvxlData.dataMin=this.dataMin;this.jvxlData.dataMax=this.dataMax;this.jvxlData.cutoffRange=this.isJvxl?this.jvxlCutoffRange:this.params.cutoffRange;this.jvxlData.cutoff=null!=this.jvxlCutoffRange?this.jvxlData.cutoffRange[0]:this.isJvxl?this.jvxlCutoff:
this.params.cutoff;this.jvxlData.isCutoffAbsolute=this.params.isCutoffAbsolute;this.jvxlData.isModelConnected=this.params.isModelConnected;this.jvxlData.pointsPerAngstrom=1/this.volumeData.volumetricVectorLengths[0];this.jvxlData.jvxlColorData="";this.jvxlData.jvxlPlane=this.params.thePlane;this.jvxlData.jvxlEdgeData=this.edgeData;this.jvxlData.isBicolorMap=this.params.isBicolorMap;this.jvxlData.isContoured=this.params.isContoured;this.jvxlData.colorDensity=this.params.colorDensity;this.jvxlData.pointSize=
this.params.pointSize;null!=this.jvxlData.vContours&&(this.params.nContours=this.jvxlData.vContours.length);this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.nEdges=this.edgeCount;this.jvxlData.edgeFractionBase=this.edgeFractionBase;this.jvxlData.edgeFractionRange=this.edgeFractionRange;this.jvxlData.colorFractionBase=this.colorFractionBase;this.jvxlData.colorFractionRange=this.colorFractionRange;
this.jvxlData.jvxlDataIs2dContour=this.jvxlDataIs2dContour;this.jvxlData.jvxlDataIsColorMapped=this.jvxlDataIsColorMapped;this.jvxlData.jvxlDataIsColorDensity=this.jvxlDataIsColorDensity;this.jvxlData.isXLowToHigh=this.isXLowToHigh;this.jvxlData.vertexDataOnly=this.vertexDataOnly;this.jvxlData.saveVertexCount=0;if(this.jvxlDataIsColorMapped||0<this.jvxlData.nVertexColors)null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshDataServer.fillMeshData(this.meshData,
2,null)),this.jvxlData.jvxlColorData=this.readColorData(),this.updateSurfaceData(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted();this.params.showTiming&&JU.Logger.checkTimer("isosurface creation",!1);return!0},"~B");e(d,"resetIsosurface",function(){this.meshData=new J.jvxl.data.MeshData;this.xyzMin=this.xyzMax=null;this.jvxlData.isBicolorMap=this.params.isBicolorMap;null!=this.meshDataServer&&this.meshDataServer.fillMeshData(null,0,null);this.contourVertexCount=0;
3.4028235E38==this.params.cutoff&&(this.params.cutoff=0.02);this.jvxlData.jvxlSurfaceData="";this.jvxlData.jvxlEdgeData="";this.jvxlData.jvxlColorData="";this.edgeCount=0;this.edgeFractionBase=35;this.edgeFractionRange=90;this.colorFractionBase=35;this.colorFractionRange=90;this.params.mappedDataMin=3.4028235E38});e(d,"discardTempData",function(a){this.discardTempDataSR(a)},"~B");e(d,"discardTempDataSR",function(a){a&&(this.voxelData=null,this.marchingCubes=this.sg.marchingSquares=this.marchingSquares=
null)},"~B");e(d,"initializeVolumetricData",function(){this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.setVolumeDataV(this.volumeData)});e(d,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0<this.nPointsX&&0<this.nPointsY&&0<this.nPointsZ)try{this.gotoData(this.params.fileIndex-1,this.nPointsX*this.nPointsY*this.nPointsZ),this.readSurfaceData(a)}catch(b){if($(b,Exception))return JU.Logger.error(b.toString()),!1;throw b;
}return!0},"~B");e(d,"gotoData",function(){},"~N,~N");e(d,"readColorData",function(){if(null==this.jvxlData.vertexColors)return"";var a=this.jvxlData.vertexCount,b=this.meshData.vcs,c=this.meshData.vvs;if(null==b||b.length<a)this.meshData.vcs=b=da(a,0);if(null==c||c.length<a)this.meshData.vvs=x(a,0);for(c=0;c<a;c++)b[c]=JU.C.getColix(this.jvxlData.vertexColors[c]);return"-"});l(d,"getPlane",function(a){return this.getPlaneSR(a)},"~N");e(d,"getPlaneSR",function(a){0==this.yzCount&&this.initPlanes();
null!=this.qpc&&this.qpc.getPlane(a,this.yzPlanes[a%2]);return this.yzPlanes[a%2]},"~N");e(d,"initPlanes",function(){this.yzCount=this.nPointsY*this.nPointsZ;this.isQuiet||JU.Logger.info("reading data progressively -- yzCount = "+this.yzCount);this.yzPlanes=JU.AU.newFloat2(2);this.yzPlanes[0]=x(this.yzCount,0);this.yzPlanes[1]=x(this.yzCount,0)});l(d,"getValue",function(a,b,c,f){return this.getValue2(a,b,c,f)},"~N,~N,~N,~N");e(d,"getValue2",function(a,b,c,f){return null==this.yzPlanes?this.voxelData[a][b][c]:
this.yzPlanes[a%2][f]},"~N,~N,~N,~N");e(d,"generateSurfaceData",function(){this.edgeData="";if(this.vertexDataOnly)try{this.readSurfaceData(!1)}catch(a){if($(a,Exception))System.out.println(a.toString()),JU.Logger.error("Exception in SurfaceReader::readSurfaceData: "+a.toString());else throw a;}else{this.contourVertexCount=0;var b=-1;this.marchingSquares=null;if(null!=this.params.thePlane||this.params.isContoured)this.marchingSquares=new J.jvxl.calc.MarchingSquares(this,this.volumeData,this.params.thePlane,
this.params.contoursDiscrete,this.params.nContours,this.params.thisContour,this.params.contourFromZero),b=this.marchingSquares.contourType,this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue);this.params.contourType=b;this.params.isXLowToHigh=this.isXLowToHigh;this.marchingCubes=new J.jvxl.calc.MarchingCubes(this,this.volumeData,this.params,this.jvxlVoxelBitSet);b=this.marchingCubes.getEdgeData();null==this.params.thePlane&&(this.edgeData=b);this.jvxlData.setSurfaceInfoFromBitSetPts(this.marchingCubes.bsVoxels,
this.params.thePlane,this.params.mapLattice);this.jvxlData.jvxlExcluded=this.params.bsExcluded;this.isJvxl&&(this.edgeData=this.jvxlEdgeDataRead);this.postProcessVertices()}});e(d,"postProcessVertices",function(){});l(d,"getSurfacePointIndexAndFraction",function(a,b,c,f,d,e,h,g,j,n,k,t,q,l){b=this.getSurfacePointAndFraction(a,b,j,n,k,t,c,f,d,h,g,l,this.ptTemp);if(null!=this.marchingSquares&&this.params.isContoured)return this.marchingSquares.addContourVertex(this.ptTemp,a);a=0<this.assocCutoff?l[0]<
this.assocCutoff?h:l[0]>1-this.assocCutoff?g:-1:-1;0<=a&&(a=this.marchingCubes.getLinearOffset(c,f,d,a));a=this.addVertexCopy(this.ptTemp,b,a,!0);0<=a&&this.params.iAddGridPoints&&(this.marchingCubes.calcVertexPoint(c,f,d,g,this.ptTemp),this.addVertexCopy(j<n?k:this.ptTemp,Math.min(j,n),-3,!0),this.addVertexCopy(j<n?this.ptTemp:k,Math.max(j,n),-3,!0));return a},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");e(d,"getSurfacePointAndFraction",function(a,b,c,f,d,e,h,g,j,n,k,t,q){return this.getSPF(a,
b,c,f,d,e,h,g,j,n,k,t,q)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getSPF",function(a,b,c,f,d,e,h,g,j,n,k,t,q){f-=c;h=(a-c)/f;if(b&&(0>h||1<h))h=(-a-c)/f;if(0>h||1<h)h=NaN;t[0]=h;q.scaleAdd2(h,e,d);return c+h*f},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"addVertexCopy",function(a,b,c,f){return this.addVC(a,b,c,f)},"JU.T3,~N,~N,~B");e(d,"addVC",function(a,b,c,f){return Float.isNaN(b)&&-3!=c?-1:null==this.meshDataServer?this.meshData.addVertexCopy(a,b,c,f):this.meshDataServer.addVertexCopy(a,
b,c,f)},"JU.T3,~N,~N,~B");e(d,"addTriangleCheck",function(a,b,c,f,d,e,h){if(null!=this.marchingSquares&&this.params.isContoured){if(0==h)return this.marchingSquares.addTriangle(a,b,c,f,d);h=0}return null!=this.meshDataServer?this.meshDataServer.addTriangleCheck(a,b,c,f,d,e,h):e&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.meshData.vvs)?-1:this.meshData.addTriangleCheck(a,b,c,f,d,h)},"~N,~N,~N,~N,~N,~B,~N");e(d,"colorIsosurface",function(){this.params.isSquared&&null!=this.volumeData&&this.volumeData.filterData(!0,
NaN);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.jvxlData.saveVertexCount=0;this.params.isContoured&&null!=this.marchingSquares&&(this.initializeMapping(),this.params.setMapRanges(this,!1),this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue),this.jvxlData.saveVertexCount=this.marchingSquares.contourVertexCount,this.contourVertexCount=this.marchingSquares.generateContourData(this.jvxlDataIs2dContour,this.params.isSquared?
1E-8:1E-4),this.jvxlData.contourValuesUsed=this.marchingSquares.contourValuesUsed,this.minMax=this.marchingSquares.getMinMax(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted(),this.finalizeMapping());this.applyColorScale();this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.jvxlFileMessage="mapped: min = "+this.params.valueMappedToRed+"; max = "+this.params.valueMappedToBlue});
e(d,"applyColorScale",function(){this.colorFractionBase=this.jvxlData.colorFractionBase=35;this.colorFractionRange=this.jvxlData.colorFractionRange=90;0==this.params.colorPhase&&(this.params.colorPhase=1);null==this.meshDataServer?this.meshData.vcs=da(this.meshData.vc,0):(this.meshDataServer.fillMeshData(this.meshData,1,null),null==this.params.contactPair&&this.meshDataServer.fillMeshData(this.meshData,2,null));var a=this.params.colorDensity||this.params.isBicolorMap||this.params.colorBySign||!this.params.colorByPhase;
null!=this.params.contactPair&&(a=!1);this.jvxlData.isJvxlPrecisionColor=!0;this.jvxlData.vertexCount=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc;this.jvxlData.minColorIndex=-1;this.jvxlData.maxColorIndex=0;this.jvxlData.contourValues=this.params.contoursDiscrete;this.jvxlData.isColorReversed=this.params.isColorReversed;if(!this.params.colorDensity&&(this.params.isBicolorMap&&!this.params.isContoured||this.params.colorBySign))this.jvxlData.minColorIndex=JU.C.getColixTranslucent3(JU.C.getColix(this.params.isColorReversed?
this.params.colorPos:this.params.colorNeg),0!=this.jvxlData.translucency,this.jvxlData.translucency),this.jvxlData.maxColorIndex=JU.C.getColixTranslucent3(JU.C.getColix(this.params.isColorReversed?this.params.colorNeg:this.params.colorPos),0!=this.jvxlData.translucency,this.jvxlData.translucency);this.jvxlData.isTruncated=0<=this.jvxlData.minColorIndex&&!this.params.isContoured;if(!this.jvxlDataIs2dContour&&!this.hasColorData&&!this.vertexDataOnly&&!(this.params.colorDensity||this.params.isBicolorMap&&
!this.params.isContoured)){this.haveSurfaceAtoms&&null==this.meshData.vertexSource&&(this.meshData.vertexSource=u(this.meshData.vc,0));var b=3.4028235E38,c=-3.4028235E38,f;this.initializeMapping();for(var d=this.meshData.vc;--d>=this.meshData.mergeVertexCount0;){if(this.params.colorBySets)f=this.meshData.vertexSets[d];else if(this.params.colorByPhase)f=this.getPhase(this.meshData.vs[d]);else{var e=this.haveSurfaceAtoms;f=this.volumeData.lookupInterpolatedVoxelValue(this.meshData.vs[d],e);e&&(this.meshData.vertexSource[d]=
this.getSurfaceAtomIndex())}f<b&&(b=f);f>c&&3.4028235E38!=f&&(c=f);this.meshData.vvs[d]=f}this.params.rangeSelected&&null==this.minMax&&(this.minMax=x(-1,[b,c]));this.finalizeMapping()}this.params.setMapRanges(this,!0);this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;null==this.params.contactPair&&null==this.jvxlData.vertexColors&&
this.colorData();J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,a?this.meshData.vvs:null);this.haveSurfaceAtoms&&null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null);null!=this.meshDataServer&&this.params.colorBySets&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"colorData",function(){var a=this.meshData.vvs,b=this.meshData.vcs;this.meshData.pcs=null;var c=this.jvxlData.valueMappedToBlue,f=this.jvxlData.valueMappedToRed,d=this.jvxlData.minColorIndex,
e=this.jvxlData.maxColorIndex;null==this.params.colorEncoder&&(this.params.colorEncoder=new JU.ColorEncoder(null,null));this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(var h=this.meshData.vc;0<=--h;){var g=a[h];0<=d?0>=g?b[h]=d:0<g&&(b[h]=e):(g<=f&&(g=f),g>=c&&(g=c),b[h]=this.params.colorEncoder.getColorIndex(g))}if((0<this.params.nContours||null!=this.jvxlData.contourValues)&&null==this.jvxlData.contourColixes){a=null==
this.jvxlData.contourValues?this.params.nContours:this.jvxlData.contourValues.length;b=this.jvxlData.contourColixes=da(a,0);d=this.jvxlData.contourValues;null==d&&(d=this.jvxlData.contourValuesUsed);null==this.jvxlData.contourValuesUsed&&(this.jvxlData.contourValuesUsed=null==d?x(a,0):d);c=(c-f)/(a+1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(h=0;h<a;h++)e=null==d?f+(h+1)*c:d[h],this.jvxlData.contourValuesUsed[h]=
e,b[h]=JU.C.getColixTranslucent(this.params.colorEncoder.getArgb(e));this.jvxlData.contourColors=JU.C.getHexCodes(b)}});d.getColorPhaseIndex=e(d,"getColorPhaseIndex",function(a){for(var b=-1,c=0;c<J.jvxl.readers.SurfaceReader.colorPhases.length;c++)if(a.equalsIgnoreCase(J.jvxl.readers.SurfaceReader.colorPhases[c])){b=c;break}return b},"~S");e(d,"getPhase",function(a){switch(this.params.colorPhase){case 0:case -1:case 1:return 0<a.x?1:-1;case 2:return 0<a.y?1:-1;case 3:return 0<a.z?1:-1;case 4:return 0<
a.x*a.y?1:-1;case 5:return 0<a.y*a.z?1:-1;case 6:return 0<a.x*a.z?1:-1;case 7:return 0<a.x*a.x-a.y*a.y?1:-1;case 8:return 0<2*a.z*a.z-a.x*a.x-a.y*a.y?1:-1}return 1},"JU.T3");e(d,"getMinMaxMappedValues",function(a){if(null!=this.minMax&&3.4028235E38!=this.minMax[0])return this.minMax;if(this.params.colorBySets)return this.minMax=x(-1,[0,Math.max(this.meshData.nSets-1,0)]);var b=3.4028235E38,c=-3.4028235E38;if(this.params.usePropertyForColorRange&&null!=this.params.theProperty){for(a=this.params.theProperty.length;0<=
--a;)if(!this.params.rangeSelected||this.params.bsSelected.get(a)){var f=this.params.theProperty[a];Float.isNaN(f)||(f<b&&(b=f),f>c&&(c=f))}return this.minMax=x(-1,[b,c])}var f=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc,d=this.meshData.vs,e=a||this.jvxlDataIs2dContour||this.vertexDataOnly||this.params.colorDensity;for(a=this.meshData.mergeVertexCount0;a<f;a++){var h;h=e?this.meshData.vvs[a]:this.volumeData.lookupInterpolatedVoxelValue(d[a],!1);h<b&&(b=h);h>c&&3.4028235E38!=
h&&(c=h)}return this.minMax=x(-1,[b,c])},"~B");e(d,"updateTriangles",function(){null==this.meshDataServer?this.meshData.invalidatePolygons():this.meshDataServer.invalidateTriangles()});e(d,"updateSurfaceData",function(){this.meshData.setVertexSets(!0);this.updateTriangles();null==this.params.bsExcluded[1]&&(this.params.bsExcluded[1]=new JU.BS);this.meshData.updateInvalidatedVertices(this.params.bsExcluded[1])});e(d,"selectPocket",function(){},"~B");e(d,"excludeMinimumSet",function(){null!=this.meshDataServer&&
this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()<this.params.minSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"excludeMaximumSet",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,
b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()>this.params.maxSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"slabIsosurface",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.slabPolygonsList(a,!0);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null)},"JU.Lst");e(d,
"setVertexAnisotropy",function(a){a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2];a.add(this.center)},"JU.T3");e(d,"setVectorAnisotropy",function(a){this.haveSetAnisotropy=!0;a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2]},"JU.T3");e(d,"setVolumetricAnisotropy",function(){this.haveSetAnisotropy||(this.setVolumetricOriginAnisotropy(),this.setVectorAnisotropy(this.volumetricVectors[0]),this.setVectorAnisotropy(this.volumetricVectors[1]),this.setVectorAnisotropy(this.volumetricVectors[2]))});
e(d,"setVolumetricOriginAnisotropy",function(){this.volumetricOrigin.setT(this.center)});e(d,"setBBoxAll",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.xyzMin=new JU.P3;this.xyzMax=new JU.P3;this.meshData.setBox(this.xyzMin,this.xyzMax)});e(d,"setBBox",function(a,b){null==this.xyzMin&&(this.xyzMin=JU.P3.new3(3.4028235E38,3.4028235E38,3.4028235E38),this.xyzMax=JU.P3.new3(-3.4028235E38,-3.4028235E38,-3.4028235E38));JU.BoxInfo.addPoint(a,this.xyzMin,
this.xyzMax,b)},"JU.T3,~N");e(d,"getValueAtPoint",function(){return 0},"JU.T3,~B");e(d,"initializeMapping",function(){});e(d,"finalizeMapping",function(){});e(d,"getSurfaceAtomIndex",function(){return-1});d.colorPhases=D(-1,"_orb x y z xy yz xz x2-y2 z2".split(" "))});R("J.jvxl.calc");S(["JU.TriangleData","JU.BS","$.P3","$.SB","$.V3"],"J.jvxl.calc.MarchingCubes",["J.jvxl.data.JvxlCoder"],function(){var d=I(function(){this.volumeData=this.surfaceReader=null;this.contourType=0;this.isContoured=!1;this.cutoff=
0;this.isXLowToHigh=this.isSquared=this.isCutoffAbsolute=!1;this.yzCount=this.nZ=this.nY=this.cubeCountZ=this.cubeCountY=this.cubeCountX=0;this.colorDensity=!1;this.integrateSquared=!0;this.edgeData=this.bsExcludedPlanes=this.bsExcludedTriangles=this.bsExcludedVertices=this.bsVoxels=null;this.excludePartialCubes=!0;this.isDensityRange=!1;this.mode=0;this.vertexValues=null;this.edgeCount=0;this.mappingPlane=this.yzPlanes=this.isoPointIndexPlanes=this.edgePointIndexes=this.edgeVectors=this.voxelVertexVectors=
null;this.$isInside=this.allInside=!1;this.voxelData=this.offset=null;this.nTriangles=0;this.linearOffsets=this.fReturn=this.edgeVertexPlanes=this.edgeVertexPointers=this.pointA=this.pt0=this.bsValues=null;T(this,arguments)},J.jvxl.calc,"MarchingCubes",JU.TriangleData);ca(d,function(){this.edgeData=new JU.SB;this.vertexValues=x(8,0);this.voxelVertexVectors=Array(8);this.edgeVectors=Array(12);for(var a=12;0<=--a;)this.edgeVectors[a]=new JU.V3;this.edgePointIndexes=u(12,0);this.bsValues=new JU.BS;this.pt0=
new JU.P3;this.pointA=new JU.P3;this.fReturn=x(1,0);this.linearOffsets=u(8,0)});Y(d,function(){ja(this,J.jvxl.calc.MarchingCubes,[])});Y(d,function(a,b,c,f){ja(this,J.jvxl.calc.MarchingCubes,[]);this.excludePartialCubes=!0;this.surfaceReader=a;this.bsVoxels=f;a=c.bsExcluded;this.bsExcludedVertices=null==a[0]?a[0]=new JU.BS:a[0];this.bsExcludedPlanes=null==a[2]?a[2]=new JU.BS:a[2];this.bsExcludedTriangles=null==a[3]?a[3]=new JU.BS:a[3];this.mode=null!=b.getVoxelData()||null!=b.mappingPlane?1:null!=
f?2:3;this.setParameters(b,c)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");e(d,"setParameters",function(a,b){this.volumeData=a;this.colorDensity=b.colorDensity;this.isContoured=null==b.thePlane&&b.isContoured&&!this.colorDensity;this.cutoff=b.cutoff;this.isCutoffAbsolute=b.isCutoffAbsolute;this.isDensityRange=null!=b.cutoffRange;this.contourType=b.contourType;this.isSquared=b.isSquared;this.isXLowToHigh=b.isXLowToHigh;this.cubeCountX=a.voxelCounts[0]-1;this.cubeCountY=
a.voxelCounts[1]-1;this.cubeCountZ=a.voxelCounts[2]-1;a.getYzCount();null!=b.mapLattice&&(this.cubeCountX*=Math.abs(b.mapLattice.x),this.cubeCountY*=Math.abs(b.mapLattice.y),this.cubeCountZ*=Math.abs(b.mapLattice.z));this.nY=this.cubeCountY+1;this.nZ=this.cubeCountZ+1;this.yzCount=this.nY*this.nZ;null==this.bsVoxels&&(this.bsVoxels=new JU.BS);this.edgeVertexPointers=this.isXLowToHigh?J.jvxl.calc.MarchingCubes.edgeVertexPointersLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPointersHighToLow;this.edgeVertexPlanes=
this.isXLowToHigh?J.jvxl.calc.MarchingCubes.edgeVertexPlanesLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPlanesHighToLow;this.isoPointIndexPlanes=u(2,this.yzCount,3,0);this.yzPlanes=3==this.mode?x(2,this.yzCount,0):null;this.setLinearOffsets();this.calcVoxelVertexVectors()},"J.jvxl.data.VolumeData,J.jvxl.readers.Parameters");e(d,"calcVoxelVertexVectors",function(){for(var a=8;0<=--a;)this.volumeData.transform(J.jvxl.calc.MarchingCubes.cubeVertexVectors[a],this.voxelVertexVectors[a]=new JU.V3);for(a=
12;0<=--a;)this.edgeVectors[a].sub2(this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a+1]],this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a]])});e(d,"resetIndexPlane",function(a){for(var b=0;b<this.yzCount;b++)for(var c=0;3>c;c++)a[b][c]=-2147483648;return a},"~A");e(d,"getEdgeData",function(){if(0>this.cubeCountX||0>this.cubeCountY||0>this.cubeCountZ)return"";this.mappingPlane=this.volumeData.mappingPlane;this.edgeCount=0;var a,b,c,f,d,e;this.isXLowToHigh?(a=0,this.colorDensity?(b=
this.cubeCountX+1,e=this.yzCount-1):(b=this.cubeCountX,e=this.yzCount-1-this.nZ-1),c=1,f=this.yzCount):(this.colorDensity?(a=this.cubeCountX,e=(this.cubeCountX+1)*this.yzCount-1):(a=this.cubeCountX-1,e=this.cubeCountX*this.yzCount-1-this.nZ-1),c=b=-1,f=-this.yzCount);d=e;this.resetIndexPlane(this.isoPointIndexPlanes[1]);this.voxelData=null;var h=this.cubeCountY+(this.colorDensity?1:0),g=this.cubeCountZ+(this.colorDensity?1:0);switch(this.mode){case 3:this.getPlane(a,!1);break;case 1:this.voxelData=
this.volumeData.getVoxelData()}this.allInside=this.colorDensity&&(0==this.cutoff||2==this.mode&&0>this.bsVoxels.nextSetBit(0));for(var j=this.colorDensity&&0==this.cutoff,n=0;a!=b;a+=c,e+=f,d=e)if(3==this.mode&&a+c<=b&&this.getPlane(a+c,!0),!this.bsExcludedPlanes.get(a)||!this.bsExcludedPlanes.get(a+c))if(this.colorDensity)for(var k=h;0<=--k;)for(var t=g;0<=--t;d--)n=this.getValue(a,k,t,d,0),(j||this.$isInside)&&this.addVertex(a,k,t,d,n);else{k=this.isoPointIndexPlanes[0];this.isoPointIndexPlanes[0]=
this.isoPointIndexPlanes[1];this.isoPointIndexPlanes[1]=this.resetIndexPlane(k);for(var q=!0,k=h;0<=--k;d--)for(t=g;0<=--t;d--){for(var l=0,w=8;0<=--w;)n=this.getValue(a,k,t,d,w),this.$isInside&&(l|=JU.TriangleData.Pwr2[w]);q&&!Float.isNaN(n)&&(q=!1);0!=l&&255!=l&&this.processOneCubical(l,a,k,t,d)&&(!this.isContoured&&!this.colorDensity)&&this.processTriangles(l)}q&&this.bsExcludedPlanes.set(a)}return this.edgeData.toString()});e(d,"getValue",function(a,b,c,f,d){this.offset=JU.TriangleData.cubeVertexOffsets[d];
f+=this.linearOffsets[d];switch(this.mode){case 3:a=this.vertexValues[d]=this.getValueArray(a+this.offset.x,b+this.offset.y,c+this.offset.z,f,this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[d]]);this.$isInside=this.allInside||this.bsVoxels.get(f);break;case 2:this.$isInside=this.allInside||this.bsVoxels.get(f);a=this.vertexValues[d]=(this.isDensityRange?!this.$isInside:this.bsExcludedVertices.get(f))?NaN:this.$isInside?1:0;break;default:case 1:null==this.mappingPlane?a=this.vertexValues[d]=this.voxelData[a+
this.offset.x][b+this.offset.y][c+this.offset.z]:(this.volumeData.voxelPtToXYZ(a+this.offset.x,b+this.offset.y,c+this.offset.z,this.pt0),a=this.vertexValues[d]=this.volumeData.distanceToMappingPlane(this.pt0)),this.isSquared&&(this.vertexValues[d]*=this.vertexValues[d]),(this.$isInside=this.allInside?!0:J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[d],this.cutoff,this.isCutoffAbsolute))&&this.bsVoxels.set(f)}return a},"~N,~N,~N,~N,~N");e(d,"getPlane",function(a,b){if(!(0>a||a>this.cubeCountX))if(this.surfaceReader.getPlane(a),
b){var c=this.yzPlanes[0];this.yzPlanes[0]=this.yzPlanes[1];this.yzPlanes[1]=c}},"~N,~B");e(d,"processTriangles",function(a){a=JU.TriangleData.triangleTable2[a];for(var b=a.length;0<=(b-=4);)this.addTriangle(a[b],a[b+1],a[b+2],a[b+3])},"~N");e(d,"addVertex",function(a,b,c,f,d){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);0>this.surfaceReader.addVertexCopy(this.pt0,d,-4,!0)&&this.bsExcludedVertices.set(f)},"~N,~N,~N,~N,~N");e(d,"addTriangle",function(a,b,c,f){!this.bsExcludedTriangles.get(this.nTriangles)&&
0>this.surfaceReader.addTriangleCheck(this.edgePointIndexes[a],this.edgePointIndexes[b],this.edgePointIndexes[c],f,0,this.isCutoffAbsolute,0)&&this.bsExcludedTriangles.set(this.nTriangles);this.nTriangles++},"~N,~N,~N,~N");e(d,"getValueArray",function(a,b,c,f,d){var e=f%this.yzCount;this.bsValues.set(f);a=this.surfaceReader.getValue(a,b,c,e);this.isSquared&&(a*=a);d[e]=a;J.jvxl.calc.MarchingCubes.isInside(a,this.cutoff,this.isCutoffAbsolute)&&this.bsVoxels.set(f);return a},"~N,~N,~N,~N,~A");d.isInside=
e(d,"isInside",function(a,b,c){return 0<b&&(c?Math.abs(a):a)>=b||0>=b&&a<=b},"~N,~N,~B");e(d,"processOneCubical",function(a,b,c,f,d){a=J.jvxl.calc.MarchingCubes.insideMaskTable[a];for(var e=!1,h=12;0<=--h;)if(0!=(a&JU.TriangleData.Pwr2[h])){var g=this.edgeVertexPlanes[h],j=(d+this.linearOffsets[this.edgeVertexPointers[h]])%this.yzCount,n=J.jvxl.calc.MarchingCubes.edgeTypeTable[h],k=this.edgePointIndexes[h]=this.isoPointIndexPlanes[g][j][n];if(-2147483648!=k)-1==k&&(e=this.excludePartialCubes);else{var k=
JU.TriangleData.edgeVertexes[h<<1],t=JU.TriangleData.edgeVertexes[(h<<1)+1],q=this.vertexValues[k],l=this.vertexValues[t];this.calcVertexPoint(b,c,f,k,this.pointA);this.edgeCount++;g=this.edgePointIndexes[h]=this.isoPointIndexPlanes[g][j][n]=this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff,this.isCutoffAbsolute,b,c,f,JU.TriangleData.cubeVertexOffsets[k],k,t,q,l,this.pointA,this.edgeVectors[h],n==this.contourType,this.fReturn);this.addEdgeData(0>g?NaN:this.fReturn[0]);if(Float.isNaN(this.fReturn[0])||
0>g)e=this.excludePartialCubes}}return!e},"~N,~N,~N,~N,~N");e(d,"addEdgeData",function(a){a=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(a);this.edgeData.appendC(a)},"~N");e(d,"calcVertexPoint",function(a,b,c,f,d){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);d.add2(this.pt0,this.voxelVertexVectors[f])},"~N,~N,~N,~N,JU.P3");e(d,"setLinearOffsets",function(){this.linearOffsets[0]=0;this.linearOffsets[1]=this.yzCount;this.linearOffsets[2]=this.yzCount+1;this.linearOffsets[3]=1;this.linearOffsets[4]=
this.nZ;this.linearOffsets[5]=this.yzCount+this.nZ;this.linearOffsets[6]=this.yzCount+this.nZ+1;this.linearOffsets[7]=this.nZ+1});e(d,"getLinearOffset",function(a,b,c,f){return a*this.yzCount+b*this.nZ+c+this.linearOffsets[f]},"~N,~N,~N,~N");d.yzPlanePts=u(-1,[0,1,1,0,0,1,1,0]);d.edgeVertexPointersLowToHigh=u(-1,[1,1,2,0,5,5,6,4,0,1,2,3]);d.edgeVertexPointersHighToLow=u(-1,[0,1,3,0,4,5,7,4,0,1,2,3]);d.edgeVertexPlanesLowToHigh=u(-1,[1,1,1,0,1,1,1,0,0,1,1,0]);d.edgeVertexPlanesHighToLow=u(-1,[1,0,
1,1,1,0,1,1,1,0,0,1]);d.cubeVertexVectors=D(-1,[JU.V3.new3(0,0,0),JU.V3.new3(1,0,0),JU.V3.new3(1,0,1),JU.V3.new3(0,0,1),JU.V3.new3(0,1,0),JU.V3.new3(1,1,0),JU.V3.new3(1,1,1),JU.V3.new3(0,1,1)]);d.edgeTypeTable=u(-1,[0,2,0,2,0,2,0,2,1,1,1,1]);d.insideMaskTable=da(-1,[0,265,515,778,1030,1295,1541,1804,2060,2309,2575,2822,3082,3331,3593,3840,400,153,915,666,1430,1183,1941,1692,2460,2197,2975,2710,3482,3219,3993,3728,560,825,51,314,1590,1855,1077,1340,2620,2869,2111,2358,3642,3891,3129,3376,928,681,419,
170,1958,1711,1445,1196,2988,2725,2479,2214,4010,3747,3497,3232,1120,1385,1635,1898,102,367,613,876,3180,3429,3695,3942,2154,2403,2665,2912,1520,1273,2035,1786,502,255,1013,764,3580,3317,4095,3830,2554,2291,3065,2800,1616,1881,1107,1370,598,863,85,348,3676,3925,3167,3414,2650,2899,2137,2384,1984,1737,1475,1226,966,719,453,204,4044,3781,3535,3270,3018,2755,2505,2240,2240,2505,2755,3018,3270,3535,3781,4044,204,453,719,966,1226,1475,1737,1984,2384,2137,2899,2650,3414,3167,3925,3676,348,85,863,598,1370,
1107,1881,1616,2800,3065,2291,2554,3830,4095,3317,3580,764,1013,255,502,1786,2035,1273,1520,2912,2665,2403,2154,3942,3695,3429,3180,876,613,367,102,1898,1635,1385,1120,3232,3497,3747,4010,2214,2479,2725,2988,1196,1445,1711,1958,170,419,681,928,3376,3129,3891,3642,2358,2111,2869,2620,1340,1077,1855,1590,314,51,825,560,3728,3993,3219,3482,2710,2975,2197,2460,1692,1941,1183,1430,666,915,153,400,3840,3593,3331,3082,2822,2575,2309,2060,1804,1541,1295,1030,778,515,265,0])});R("J.jvxl.calc");S(["JU.P3",
"java.util.Hashtable"],"J.jvxl.calc.MarchingSquares",["JU.AU","JU.Logger"],function(){var d=I(function(){this.volumeData=this.surfaceReader=null;this.valueMax=this.valueMin=this.thisContour=this.contourType=this.nContourSegments=0;this.pointB=this.pointA=null;this.contourFromZero=!0;this.contoursDiscrete=null;this.contourVertexCount=0;this.contourVertexes=null;qa("J.jvxl.calc.MarchingSquares.ContourVertex")||J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$();this.contourPlaneMaximumValue=
this.contourPlaneMinimumValue=0;this.ptTemp=this.contourValuesUsed=null;this.triangleCount=0;this.htPts=this.triangles=null;qa("J.jvxl.calc.MarchingSquares.Triangle")||J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$();T(this,arguments)},J.jvxl.calc,"MarchingSquares",null);ca(d,function(){this.pointA=new JU.P3;this.pointB=new JU.P3;this.contourVertexes=Array(1E3);this.ptTemp=new JU.P3;this.triangles=Array(1E3);this.htPts=new java.util.Hashtable});Y(d,function(a,b,c,f,d,e,h){this.surfaceReader=
a;this.volumeData=b;this.thisContour=e;this.contoursDiscrete=f;this.contourFromZero=h;null==f?(this.nContourSegments=(0==d?9:d)+0,100<this.nContourSegments&&(this.nContourSegments=100)):(this.nContourSegments=d=f.length,this.contourFromZero=!1)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,JU.P4,~A,~N,~N,~B");e(d,"setMinMax",function(a,b){this.valueMin=a;this.valueMax=b},"~N,~N");e(d,"addContourVertex",function(a,b){this.contourVertexCount==this.contourVertexes.length&&(this.contourVertexes=
JU.AU.doubleLength(this.contourVertexes));var c=this.surfaceReader.addVertexCopy(a,b,-2,!0);this.contourVertexes[this.contourVertexCount++]=pa(J.jvxl.calc.MarchingSquares.ContourVertex,this,null,a);return c},"JU.P3,~N");e(d,"setContourData",function(a,b){this.contourVertexes[a].setValue(b)},"~N,~N");e(d,"calcContourPoint",function(a,b,c,f){return this.volumeData.calculateFractionalPoint(a,this.pointA,this.pointB,b,c,f)},"~N,~N,~N,JU.P3");e(d,"addTriangle",function(a,b,c,f,d){this.triangleCount==this.triangles.length&&
(this.triangles=JU.AU.doubleLength(this.triangles));this.triangles[this.triangleCount++]=pa(J.jvxl.calc.MarchingSquares.Triangle,this,null,a,b,c,f,d);return 0},"~N,~N,~N,~N,~N");e(d,"generateContourData",function(a,b){JU.Logger.info("generateContours: "+this.nContourSegments+" segments");this.getVertexValues(a);this.createContours(this.valueMin,this.valueMax,b);this.addAllTriangles();return this.contourVertexCount},"~B,~N");e(d,"getVertexValues",function(a){this.contourPlaneMinimumValue=3.4028235E38;
this.contourPlaneMaximumValue=-3.4028235E38;for(var b=0;b<this.contourVertexCount;b++){var c=this.contourVertexes[b],f;a?f=c.value:(f=this.volumeData.lookupInterpolatedVoxelValue(c,!1),c.setValue(f));f<this.contourPlaneMinimumValue&&(this.contourPlaneMinimumValue=f);f>this.contourPlaneMaximumValue&&(this.contourPlaneMaximumValue=f)}},"~B");e(d,"createContours",function(a,b,c){b-=a;this.contourValuesUsed=x(this.nContourSegments,0);for(var f=this.triangleCount;0<=--f;)this.triangles[f].check=0;for(var d=
-3.4028235E38,f=0;f<this.nContourSegments;f++){d=null!=this.contoursDiscrete?this.contoursDiscrete[f]:this.contourFromZero?a+1*f/this.nContourSegments*b:0==f?-3.4028235E38:f==this.nContourSegments-1?3.4028235E38:a+1*(f-1)/(this.nContourSegments-1)*b;null==this.contoursDiscrete&&Math.abs(d)<c&&(d=0>d?-c:c);this.contourValuesUsed[f]=d;JU.Logger.info("#contour "+(f+1)+" "+d+" "+this.triangleCount);this.htPts.clear();for(var e=this.triangleCount;0<=--e;)this.triangles[e].isValid&&this.checkContour(this.triangles[e],
f,d)}this.valueMin=this.contourValuesUsed[0];this.valueMax=0==this.contourValuesUsed.length?this.valueMin:this.contourValuesUsed[this.contourValuesUsed.length-1];return!0},"~N,~N,~N");e(d,"intercept",function(a,b,c){var f=a.pts[b];a=a.pts[(b+1)%3];if(2147483647==f||2147483647==a)return-1;b=f<a?f+"_"+a:a+"_"+f;if(this.htPts.containsKey(b))return this.htPts.get(b).intValue();var d=this.contourVertexes[f].value,e=this.contourVertexes[a].value,h=-1;if(d!=e){var g=(c-d)/(e-d);if(0<=g&&1>=g&&(this.pointA.setT(this.contourVertexes[f]),
this.pointB.setT(this.contourVertexes[a]),c=this.calcContourPoint(c,d,e,this.ptTemp),!Float.isNaN(c))){h=this.addContourVertex(this.ptTemp,c);if(0>h)return-1;this.contourVertexes[h].setValue(c)}}this.htPts.put(b,Integer.$valueOf(h));return h},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(d,"checkContour",function(a,b,c){if(!(0<this.thisContour&&b+1!=this.thisContour)){var f=this.intercept(a,0,c),d=this.intercept(a,1,c);c=this.intercept(a,2,c);var e=a.pts,h=0;0<=f&&(h+=1);0<=d&&(h+=2);0<=c&&(h+=
4);switch(h){case 3:this.addTriangle(e[0],f,d,2|a.check&1,b);this.addTriangle(f,e[1],d,4|a.check&3,b);this.addTriangle(e[0],d,e[2],a.check&6,b);break;case 5:this.addTriangle(e[0],f,c,2|a.check&5,b);this.addTriangle(f,e[1],c,4|a.check&1,b);this.addTriangle(c,e[1],e[2],a.check&6,b);break;case 6:this.addTriangle(e[0],e[1],c,a.check&5,b);this.addTriangle(c,e[1],d,4|a.check&2,b);this.addTriangle(c,d,e[2],1|a.check&6,b);break;default:return}a.isValid=!1}},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(d,
"getMinMax",function(){return x(-1,[this.valueMin,this.valueMax])});e(d,"addAllTriangles",function(){for(var a=0;a<this.triangleCount;a++)if(this.triangles[a].isValid){var b=this.triangles[a];this.surfaceReader.addTriangleCheck(b.pts[0],b.pts[1],b.pts[2],b.check,b.contourIndex,!1,-1)}});d.$MarchingSquares$ContourVertex$=function(){var a=I(function(){ua(this,arguments);this.value=0;T(this,arguments)},J.jvxl.calc.MarchingSquares,"ContourVertex",JU.P3);Y(a,function(a){ja(this,J.jvxl.calc.MarchingSquares.ContourVertex,
[]);this.setT(a)},"JU.P3");e(a,"setValue",function(a){this.value=a},"~N");l(a,"toString",function(){return this.value+" "+this.x+" "+this.y+" "+this.z})};d.$MarchingSquares$Triangle$=function(){var a=I(function(){ua(this,arguments);this.pts=null;this.check=0;this.isValid=!0;this.contourIndex=0;T(this,arguments)},J.jvxl.calc.MarchingSquares,"Triangle",null);Y(a,function(a,c,d,e,g){this.pts=u(-1,[a,c,d]);this.check=e;this.contourIndex=g},"~N,~N,~N,~N,~N")}});R("J.shapesurface");S(["J.shape.Mesh"],"J.shapesurface.IsosurfaceMesh",
"java.util.Hashtable JU.AU $.BS $.CU $.Lst $.M4 $.P3 $.P3i $.PT $.SB $.V3 J.api.Interface J.jvxl.data.JvxlCoder $.JvxlData JS.T JU.C $.ColorEncoder $.Logger $.SimpleUnitCell JV.Viewer".split(" "),function(){var d=I(function(){this.jvxlData=null;this.vertexIncrement=1;this.firstRealVertex=-1;this.dataType=0;this.hasGridPoints=!1;this.assocGridPointNormals=this.assocGridPointMap=this.info=this.calculatedVolume=this.calculatedArea=null;this.mergeAssociatedNormalCount=0;this.bsVdw=this.colorEncoder=this.contourColixes=
this.contourValues=this.centers=null;this.colorPhased=!1;this.probeValues=null;T(this,arguments)},J.shapesurface,"IsosurfaceMesh",J.shape.Mesh);Y(d,function(a,b,c,d){ja(this,J.shapesurface.IsosurfaceMesh,[]);this.mesh1(a,b,c,d);this.jvxlData=new J.jvxl.data.JvxlData;this.checkByteCount=2;this.jvxlData.version=JV.Viewer.getJmolVersion()},"JV.Viewer,~S,~N,~N");l(d,"getResolution",function(){return 1/this.jvxlData.pointsPerAngstrom});e(d,"clearType",function(a,b){this.clear(a);this.jvxlData.clear();
this.colorEncoder=this.centers=this.calculatedArea=this.calculatedVolume=this.bsVdw=this.assocGridPointNormals=this.assocGridPointMap=null;this.colorsExplicit=this.colorPhased=!1;this.firstRealVertex=-1;this.hasGridPoints=b;this.isColorSolid=!0;this.nSets=this.mergeAssociatedNormalCount=0;this.pcs=null;this.showPoints=b;this.vertexColorMap=this.vcs=this.surfaceSet=null;this.vertexIncrement=1;this.vvs=this.vertexSets=null},"~S,~B");e(d,"allocVertexColixes",function(){if(null==this.vcs){this.vcs=da(this.vc,
0);for(var a=this.vc;0<=--a;)this.vcs[a]=this.colix}this.isColorSolid=!1});e(d,"addVertexCopy",function(a,b,c,d,e){a=this.addVCVal(a,b,e);switch(c){case -1:0>this.firstRealVertex&&(this.firstRealVertex=a);break;case -2:this.hasGridPoints=!0;break;case -3:this.vertexIncrement=3;break;default:0>this.firstRealVertex&&(this.firstRealVertex=a),d&&(null==this.assocGridPointMap&&(this.assocGridPointMap=new java.util.Hashtable),this.assocGridPointMap.put(Integer.$valueOf(a),Integer.$valueOf(c+this.mergeAssociatedNormalCount)))}return a},
"JU.T3,~N,~N,~B,~B");l(d,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b);if(null!=this.vcs)for(var c=this.vc;0<=--c;)this.vcs[c]=JU.C.getColixTranslucent3(this.vcs[c],a,b)},"~B,~N");e(d,"setMerged",function(a){this.mergePolygonCount0=(this.isMerged=a)?this.pc:0;this.mergeVertexCount0=a?this.vc:0;a&&(this.mergeAssociatedNormalCount+=this.jvxlData.nPointsX*this.jvxlData.nPointsY*this.jvxlData.nPointsZ,this.assocGridPointNormals=null)},"~B");l(d,"sumVertexNormals",
function(a,b){J.shape.Mesh.sumVertexNormals2(this,a,b);if(null!=this.assocGridPointMap&&0<b.length&&!this.isMerged){null==this.assocGridPointNormals&&(this.assocGridPointNormals=new java.util.Hashtable);for(var c,d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);){var e=c.getValue();this.assocGridPointNormals.containsKey(e)||this.assocGridPointNormals.put(e,JU.V3.new3(0,0,0));this.assocGridPointNormals.get(e).add(b[c.getKey().intValue()])}for(d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&
((c=d.next())||1);)b[c.getKey().intValue()]=this.assocGridPointNormals.get(c.getValue())}},"~A,~A");e(d,"getCenters",function(){if(null!=this.centers)return this.centers;this.centers=Array(this.pc);for(var a=0;a<this.pc;a++){var b=this.pis[a];if(null!=b){var c=this.centers[a]=JU.P3.newP(this.vs[b[0]]);c.add(this.vs[b[1]]);c.add(this.vs[b[2]]);c.scale(0.33333334)}}return this.centers});e(d,"getContours",function(){var a=this.jvxlData.nContours;if(0==a||null==this.pis||(this.havePlanarContours=null!=
this.jvxlData.jvxlPlane))return null;0>a&&(a=-1-a);var b=this.jvxlData.vContours;if(null!=b){for(var c=0;c<a&&!(6<b[c].size());c++)J.jvxl.data.JvxlCoder.set3dContourVector(b[c],this.pis,this.vs);return this.jvxlData.vContours}b=Array(a);for(c=0;c<a;c++)b[c]=new JU.Lst;if(null==this.jvxlData.contourValuesUsed){for(var d=(this.jvxlData.valueMappedToBlue-this.jvxlData.valueMappedToRed)/(a+1),c=0;c<a;c++){var e=this.jvxlData.valueMappedToRed+(c+1)*d;J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],
e,this.jvxlData.contourColixes[c])}JU.Logger.info(a+" contour lines; separation = "+d)}else for(c=0;c<a;c++)e=this.jvxlData.contourValuesUsed[c],J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c]);this.jvxlData.contourColixes=da(a,0);this.jvxlData.contourValues=x(a,0);for(c=0;c<a;c++)this.jvxlData.contourValues[c]=b[c].get(2).floatValue(),this.jvxlData.contourColixes[c]=b[c].get(3)[0];return this.jvxlData.vContours=b});e(d,"getPmeshData",function(a){return J.api.Interface.getInterface("J.shapesurface.PMeshWriter",
this.vwr,"script").write(this,a)},"~B");d.get3dContour=e(d,"get3dContour",function(a,b,c,d){var e=JU.BS.newN(a.pc),g=new JU.SB,h=JU.C.getArgb(d);J.shapesurface.IsosurfaceMesh.setContourVector(b,a.pc,e,c,d,h,g);for(d=0;d<a.pc;d++)null!=a.setABC(d)&&J.shapesurface.IsosurfaceMesh.addContourPoints(b,e,d,g,a.vs,a.vvs,a.iA,a.iB,a.iC,c)},"J.shapesurface.IsosurfaceMesh,JU.Lst,~N,~N");d.setContourVector=e(d,"setContourVector",function(a,b,c,d,e,g,h){a.add(0,Integer.$valueOf(b));a.add(1,c);a.add(2,Float.$valueOf(d));
a.add(3,da(-1,[e]));a.add(4,u(-1,[g]));a.add(5,h)},"JU.Lst,~N,JU.BS,~N,~N,~N,JU.SB");d.addContourPoints=e(d,"addContourPoints",function(a,b,c,d,e,g,h,v,j,n){var k=null,t=null,q=0,l=J.shapesurface.IsosurfaceMesh.checkPt(g,h,v,n);Float.isNaN(l)||(k=J.shapesurface.IsosurfaceMesh.getContourPoint(e,h,v,l),q|=1);var w=1==l?NaN:J.shapesurface.IsosurfaceMesh.checkPt(g,v,j,n);Float.isNaN(w)||(t=J.shapesurface.IsosurfaceMesh.getContourPoint(e,v,j,w),0==q&&(k=t,l=w),q|=2);switch(q){case 0:return;case 1:if(0==
l)return;case 2:w=1==w?NaN:J.shapesurface.IsosurfaceMesh.checkPt(g,j,h,n),Float.isNaN(w)||(t=J.shapesurface.IsosurfaceMesh.getContourPoint(e,j,h,w),q|=4)}switch(q){case 3:case 5:case 6:break;default:return}b.set(c);J.jvxl.data.JvxlCoder.appendContourTriangleIntersection(q,l,w,d);a.addLast(k);a.addLast(t)},"JU.Lst,JU.BS,~N,JU.SB,~A,~A,~N,~N,~N,~N");d.checkPt=e(d,"checkPt",function(a,b,c,d){var e,g;return d==(e=a[b])?0:d==(g=a[c])?1:e<d==d<g?(d-e)/(g-e):NaN},"~A,~N,~N,~N");d.getContourPoint=e(d,"getContourPoint",
function(a,b,c,d){var e=new JU.P3;e.sub2(a[c],a[b]);e.scaleAdd2(d,e,a[b]);return e},"~A,~N,~N,~N");e(d,"setDiscreteColixes",function(a,b){null!=a&&(this.jvxlData.contourValues=a);if(null==a||0==a.length)a=this.jvxlData.contourValues=this.jvxlData.contourValuesUsed;null==b&&null!=this.jvxlData.contourColixes?b=this.jvxlData.contourColixes:(this.jvxlData.contourColixes=b,this.jvxlData.contourColors=JU.C.getHexCodes(b));if(!(null==this.vs||null==this.vvs||null==a)){var c=a.length,d=a[c-1];this.colorCommand=
null;var e=null!=b&&0<b.length;this.isColorSolid=e&&null!=this.jvxlData.jvxlPlane;if(null!=this.jvxlData.vContours){if(e)for(var g=0;g<this.jvxlData.vContours.length;g++)c=b[g%b.length],this.jvxlData.vContours[g].get(3)[0]=c,this.jvxlData.vContours[g].get(4)[0]=JU.C.getArgb(c)}else{this.pcs=da(this.pc,0);this.colorsExplicit=!1;for(g=0;g<this.pc;g++){var h=this.pis[g];if(null!=h){this.pcs[g]=0;for(var h=(this.vvs[h[0]]+this.vvs[h[1]]+this.vvs[h[2]])/3,v=c;0<=--v;)if(h>=a[v]&&h<d){this.pcs[g]=e?b[v%
b.length]:0;break}}}}}},"~A,~A");e(d,"getContourList",function(){var a=new java.util.Hashtable;a.put("values",null==this.jvxlData.contourValuesUsed?this.jvxlData.contourValues:this.jvxlData.contourValuesUsed);var b=new JU.Lst;if(null!=this.jvxlData.contourColixes){for(var c=0;c<this.jvxlData.contourColixes.length;c++)b.addLast(JU.CU.colorPtFromInt(JU.C.getArgb(this.jvxlData.contourColixes[c]),null));a.put("colors",b)}return a},"JV.Viewer");e(d,"deleteContours",function(){this.jvxlData.contourValuesUsed=
null;this.jvxlData.contourValues=null;this.jvxlData.contourColixes=null;this.jvxlData.vContours=null});e(d,"setVertexColorMap",function(){this.vertexColorMap=new java.util.Hashtable;for(var a=-999,b=null,c=this.vc;0<=--c;){var d=this.vcs[c];d!=a&&(d=JU.C.getHexCode(a=d),b=this.vertexColorMap.get(d),null==b&&this.vertexColorMap.put(d,b=new JU.BS));b.set(c)}});e(d,"setVertexColixesForAtoms",function(a,b,c,d){this.jvxlData.vertexDataOnly=!0;this.jvxlData.vertexColors=u(this.vc,0);this.jvxlData.nVertexColors=
this.vc;var e=a.ms.at;a=a.gdata;for(var g=this.mergeVertexCount0;g<this.vc;g++){var h=this.vertexSource[g];if(!(0>h)&&d.get(h)){this.jvxlData.vertexColors[g]=a.getColorArgbOrGray(this.vcs[g]=JU.C.copyColixTranslucency(this.colix,e[h].colixAtom));var v=null==b?0:b[c[h]];0==v&&(v=e[h].colixAtom);this.vcs[g]=JU.C.copyColixTranslucency(this.colix,v)}}},"JV.Viewer,~A,~A,JU.BS");e(d,"colorVertices",function(a,b,c){if(null!=this.vertexSource){a=JU.C.copyColixTranslucency(this.colix,a);var d=c?new JU.BS:
b;this.checkAllocColixes();if(c)for(var e=0;e<this.vc;e++){var g=this.vertexSource[e];0<=g&&b.get(g)&&(this.vcs[e]=a,null!=d&&d.set(e))}else for(e=0;e<this.vc;e++)d.get(e)&&(this.vcs[e]=a);c&&(a=JU.C.getHexCode(a),null==this.vertexColorMap&&(this.vertexColorMap=new java.util.Hashtable),J.shapesurface.IsosurfaceMesh.addColorToMap(this.vertexColorMap,a,b))}},"~N,JU.BS,~B");e(d,"checkAllocColixes",function(){(null==this.vcs||null==this.vertexColorMap&&this.isColorSolid)&&this.allocVertexColixes();this.isColorSolid=
!1});d.addColorToMap=e(d,"addColorToMap",function(a,b,c){for(var d=null,e,g=a.entrySet().iterator();g.hasNext()&&((e=g.next())||1);)e.getKey()===b?(d=e.getValue(),d.or(c)):e.getValue().andNot(c);null==d&&a.put(b,c)},"java.util.Map,~S,JU.BS");e(d,"setJvxlColorMap",function(a){this.jvxlData.diameter=this.diameter;this.jvxlData.color=JU.C.getHexCode(this.colix);this.jvxlData.meshColor=0==this.meshColix?null:JU.C.getHexCode(this.meshColix);this.jvxlData.translucency=30720==(this.colix&30720)?-1:JU.C.getColixTranslucencyFractional(this.colix);
this.jvxlData.rendering=this.getRendering().substring(1);this.jvxlData.colorScheme=null==this.colorEncoder?null:this.colorEncoder.getColorScheme();null==this.jvxlData.vertexColors&&(this.jvxlData.nVertexColors=null==this.vertexColorMap?0:this.vertexColorMap.size());if(!(null==this.vertexColorMap||null==this.vertexSource||!a)){null==this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=new java.util.Hashtable);var b;for(a=this.vertexColorMap.entrySet().iterator();a.hasNext()&&((b=a.next())||
1);){var c=b.getValue();if(!c.isEmpty()){for(var d=b.getKey(),e=new JU.BS,g=0;g<this.vc;g++)c.get(this.vertexSource[g])&&e.set(g);J.shapesurface.IsosurfaceMesh.addColorToMap(this.jvxlData.vertexColorMap,d,e)}}this.jvxlData.nVertexColors=this.jvxlData.vertexColorMap.size();0==this.jvxlData.vertexColorMap.size()&&(this.jvxlData.vertexColorMap=null)}},"~B");e(d,"setColorCommand",function(){if(!(null==this.colorEncoder||null==(this.colorCommand=this.colorEncoder.getColorScheme())))this.colorCommand=this.colorCommand.equals("inherit")?
"#inherit;":"color $"+JU.PT.esc(this.thisID)+JU.PT.esc(this.colorCommand)+" range "+(this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue+" "+this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToRed+" "+this.jvxlData.valueMappedToBlue)});e(d,"setColorsFromJvxlData",function(a){this.diameter=this.jvxlData.diameter;-1!=a&&(-2147483648!=a&&2147483647!=a?this.colix=JU.C.getColix(a):null!=this.jvxlData.color&&(this.colix=JU.C.getColixS(this.jvxlData.color)));0==this.colix&&(this.colix=5);
this.colix=JU.C.getColixTranslucent3(this.colix,0!=this.jvxlData.translucency,this.jvxlData.translucency);a=0==this.jvxlData.translucency?NaN:this.jvxlData.translucency;null!=this.jvxlData.meshColor&&(this.meshColix=JU.C.getColixS(this.jvxlData.meshColor));this.setJvxlDataRendering();this.isColorSolid=!this.jvxlData.isBicolorMap&&null==this.jvxlData.vertexColors&&null==this.jvxlData.vertexColorMap;if(null==this.colorEncoder)return!1;if(null==this.jvxlData.vertexColorMap){if(null!=this.jvxlData.colorScheme){var b=
this.jvxlData.colorScheme,c=b.startsWith("translucent ");c&&(b=b.substring(12),a=NaN);this.colorEncoder.setColorScheme(b,c);this.remapColors(null,null,a)}}else{if(null!=this.jvxlData.baseColor)for(a=this.vc;0<=--a;)this.vcs[a]=this.colix;for(c=this.jvxlData.vertexColorMap.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var d=b.getValue(),e=JU.C.copyColixTranslucency(this.colix,JU.C.getColixS(b.getKey()));for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1))this.vcs[a]=e}}return!0},"~N");e(d,"setJvxlDataRendering",
function(){if(null!=this.jvxlData.rendering)for(var a=JU.PT.getTokens(this.jvxlData.rendering),b=0;b<a.length;b++)this.setTokenProperty(JS.T.getTokFromName(a[b]),!0)});e(d,"remapColors",function(a,b,c){null==b&&(b=this.colorEncoder);null==b&&(b=this.colorEncoder=new JU.ColorEncoder(null,a));this.colorEncoder=b;this.setColorCommand();Float.isNaN(c)?c=JU.C.getColixTranslucencyLevel(this.colix):this.colix=JU.C.getColixTranslucent3(this.colix,!0,c);var d=b.lo,e=b.hi,g=null!=this.vertexSource&&15==b.currentPalette;
this.pcs=this.vertexColorMap=null;this.colorsExplicit=!1;this.jvxlData.baseColor=null;this.jvxlData.vertexCount=this.vc;if(!(null==this.vvs||0==this.jvxlData.vertexCount))if((null==this.vcs||this.vcs.length!=this.vc)&&this.allocVertexColixes(),g){this.jvxlData.vertexDataOnly=!0;this.jvxlData.vertexColors=u(this.vc,0);this.jvxlData.nVertexColors=this.vc;b=a.ms.at;c=a.gdata;for(a=this.mergeVertexCount0;a<this.vc;a++)d=this.vertexSource[a],0<=d&&d<b.length&&(this.jvxlData.vertexColors[a]=c.getColorArgbOrGray(this.vcs[a]=
JU.C.copyColixTranslucency(this.colix,b[d].colixAtom)))}else if(this.jvxlData.vertexColors=null,this.jvxlData.vertexColorMap=null,this.jvxlData.isBicolorMap)for(a=this.mergeVertexCount0;a<this.vc;a++)this.vcs[a]=JU.C.copyColixTranslucency(this.colix,0>this.vvs[a]?this.jvxlData.minColorIndex:this.jvxlData.maxColorIndex);else{this.jvxlData.isColorReversed=b.isReversed;3.4028235E38!=e&&(this.jvxlData.valueMappedToRed=d,this.jvxlData.valueMappedToBlue=e);b.setRange(this.jvxlData.valueMappedToRed,this.jvxlData.valueMappedToBlue,
this.jvxlData.isColorReversed);d=JU.C.isColixTranslucent(this.colix);b.isTranslucent&&(d||(this.colix=JU.C.getColixTranslucent3(this.colix,!0,0.5)),d=!1);this.vcs=JU.AU.ensureLengthShort(this.vcs,this.vc);for(a=this.vc;--a>=this.mergeVertexCount0;)this.vcs[a]=b.getColorIndex(this.vvs[a]);this.setTranslucent(d,c);this.colorEncoder=b;c=this.getContours();if(null!=c)for(a=c.length;0<=--a;)d=c[a].get(2).floatValue(),e=c[a].get(3),e[0]=b.getColorIndex(d),c[a].get(4)[0]=JU.C.getArgb(e[0]);if(null!=this.contourValues){this.contourColixes=
da(this.contourValues.length,0);for(a=0;a<this.contourValues.length;a++)this.contourColixes[a]=b.getColorIndex(this.contourValues[a]);this.setDiscreteColixes(null,null)}this.jvxlData.isJvxlPrecisionColor=!0;J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,this.vvs);this.setColorCommand();this.isColorSolid=!1}},"JV.Viewer,JU.ColorEncoder,~N");e(d,"reinitializeLightingAndColor",function(a){this.initialize(this.lighting,null,null);if(null!=this.colorEncoder||this.jvxlData.isBicolorMap)this.vcs=
null,this.remapColors(a,null,NaN)},"JV.Viewer");l(d,"getBoundingBox",function(){return this.jvxlData.boundingBox});l(d,"setBoundingBox",function(a){this.jvxlData.boundingBox=a},"~A");e(d,"merge",function(a){var b=this.vc+(null==a?0:a.vc);null==this.pis&&(this.pis=u(0,0,0));null!=a&&null==a.pis&&(a.pis=u(0,0,0));var c=(null==this.bsSlabDisplay||0==this.pc?this.pc:this.bsSlabDisplay.cardinality())+(null==a||0==a.pc?0:null==a.bsSlabDisplay?a.pc:a.bsSlabDisplay.cardinality());null==this.vs&&(this.vs=
[]);this.vs=JU.AU.ensureLength(this.vs,b);this.vvs=JU.AU.ensureLengthA(this.vvs,b);var d=null!=this.vertexSource&&(null==a||null!=a.vertexSource);this.vertexSource=JU.AU.ensureLengthI(this.vertexSource,b);var e=JU.AU.newInt2(c),g=J.shapesurface.IsosurfaceMesh.mergePolygons(this,0,0,e);if(null!=a){J.shapesurface.IsosurfaceMesh.mergePolygons(a,g,this.vc,e);for(g=0;g<a.vc;g++,this.vc++)this.vs[this.vc]=a.vs[g],this.vvs[this.vc]=a.vvs[g],d&&(this.vertexSource[this.vc]=a.vertexSource[g])}this.pc=this.polygonCount0=
c;this.vc=this.vertexCount0=b;0<c&&this.resetSlab();this.pis=e},"J.jvxl.data.MeshData");d.mergePolygons=e(d,"mergePolygons",function(a,b,c,d){for(var e,g=0;g<a.pc;g++)if(!(null==(e=a.pis[g])||null!=a.bsSlabDisplay&&!a.bsSlabDisplay.get(g)))if(d[b++]=a.pis[g],0<c)for(var h=0;3>h;h++)e[h]+=c;return b},"JU.MeshSurface,~N,~N,~A");l(d,"getUnitCell",function(){return null!=this.unitCell||null!=(this.unitCell=this.vwr.ms.am[this.modelIndex].biosymmetry)||null!=(this.unitCell=this.vwr.ms.getUnitCell(this.modelIndex))||
null!=this.oabc&&null!=(this.unitCell=this.vwr.getSymTemp().getUnitCell(this.oabc,!0,null))?this.unitCell:null});e(d,"fixLattice",function(){if(null!=this.getUnitCell()){var a=new JU.P3i,b=JU.P3i.new3(A(this.lattice.x),A(this.lattice.y),A(this.lattice.z));this.jvxlData.fixedLattice=this.lattice;this.lattice=null;JU.SimpleUnitCell.setMinMaxLatticeParameters(A(this.unitCell.getUnitCellInfoType(6)),a,b,0);var c=(b.x-a.x)*(b.y-a.y)*(b.z-a.z),d=new JU.P3,e=this.vc,g=c*this.vc;this.vs=JU.AU.arrayCopyPt(this.vs,
g);this.vvs=null==this.vvs?null:JU.AU.ensureLengthA(this.vvs,g);var h=this.pc;this.pis=JU.AU.arrayCopyII(this.pis,c*this.pc);c=0;this.normixes=JU.AU.arrayCopyShort(this.normixes,g);for(g=a.x;g<b.x;g++)for(var v=a.y;v<b.y;v++)for(var j=a.z;j<b.z;j++)if(!(0==g&&0==v&&0==j)){d.set(g,v,j);this.unitCell.toCartesian(d,!1);for(var n=0;n<e;n++){this.normixes[this.vc]=this.normixes[n];var k=JU.P3.newP(this.vs[n]);k.add(d);this.addVCVal(k,this.vvs[n],!1)}c+=e;for(n=0;n<h;n++)k=JU.AU.arrayCopyI(this.pis[n],
-1),k[0]+=c,k[1]+=c,k[2]+=c,this.addPolygon(k,null)}a=new JU.P3;b=new JU.P3;this.setBox(a,b);this.jvxlData.boundingBox=D(-1,[a,b])}});l(d,"getMinDistance2ForVertexGrouping",function(){return null!=this.jvxlData.boundingBox&&null!=this.jvxlData.boundingBox[0]&&5>this.jvxlData.boundingBox[1].distanceSquared(this.jvxlData.boundingBox[0])?1E-10:1E-8});l(d,"getVisibleVertexBitSet",function(){var a=this.getVisibleVBS();if(null!=this.jvxlData.thisSet)for(var b=0;b<this.vc;b++)this.jvxlData.thisSet.get(this.vertexSets[b])||
a.clear(b);return a});e(d,"updateCoordinates",function(a,b){var c=null==b||this.isModelConnected;if(!c)for(var d=0;d<this.connectedAtoms.length;d++)if(0<=this.connectedAtoms[d]&&b.get(this.connectedAtoms[d])){c=!0;break}c&&(this.isModelConnected?this.mat4=this.vwr.ms.am[this.modelIndex].mat4:(null==this.mat4&&(this.mat4=JU.M4.newM4(null)),this.mat4.mul2(a,this.mat4)),this.recalcAltVertices=!0)},"JU.M4,JU.BS");e(d,"getDataMinMax",function(){for(var a=3.4028235E38,b=-3.4028235E38,c=this.vvs.length;0<=
--c;){var d=this.vvs[c];d<a&&(a=d);d>b&&(b=d)}return x(-1,[a,b])});e(d,"getDataRange",function(){return null!=this.jvxlData.jvxlPlane&&null==this.colorEncoder?null:x(-1,[this.jvxlData.mappedDataMin,this.jvxlData.mappedDataMax,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue:this.jvxlData.valueMappedToRed,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToBlue])});e(d,"getInfo",function(a){var b=Ia(this,J.shapesurface.IsosurfaceMesh,"getInfo",[a]);
if(a){a=new JU.BS;var c=this.getValidVertices(a);null!=c&&(b.put("allVertices",b.get("vertices")),b.put("vertices",c),c=b.get("vertexValues"),null!=c&&(a=this.getValidValues(a),b.put("allValues",c),b.put("vertexValues",a)))}return b},"~B");e(d,"getValidValues",function(a){null==a&&this.getInvalidBS(a=new JU.BS);for(var b=this.vc-a.cardinality(),b=x(b,0),c=0,d=a.nextClearBit(0);0<=d&&d<this.vc;d=a.nextClearBit(d+1))b[c++]=this.vvs[d];return b},"JU.BS");e(d,"getValidVertices",function(a){var b=null!=
a;null==a&&(a=new JU.BS);this.getInvalidBS(a);var c=this.vc-a.cardinality();if(c==this.vc&&b)return null;for(var b=Array(c),d=0,e=a.nextClearBit(0);0<=e&&d<c;e=a.nextClearBit(e+1))b[d++]=this.vs[e];return b},"JU.BS");e(d,"getInvalidBS",function(a){var b=this.jvxlData.jvxlExcluded[1],c=this.jvxlData.thisSet;null!=b&&a.or(b);if(null!=c)for(b=this.vc;0<=--b;)c.get(this.vertexSets[b])||a.set(b)},"JU.BS")});R("J.jvxl.readers");S(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.VolumeDataReader",["JU.AU",
"$.SB","J.jvxl.data.JvxlCoder","JU.Logger"],function(){var d=I(function(){this.dataType=0;this.allowMapData=this.precalculateVoxelData=!1;this.point=null;this.maxGrid=this.ptsPerAngstrom=0;this.useOriginStepsPoints=!1;T(this,arguments)},J.jvxl.readers,"VolumeDataReader",J.jvxl.readers.SurfaceReader);Y(d,function(){ja(this,J.jvxl.readers.VolumeDataReader,[])});l(d,"init",function(a){this.initVDR(a)},"J.jvxl.readers.SurfaceGenerator");e(d,"initVDR",function(a){this.initSR(a);this.useOriginStepsPoints=
null!=this.params.origin&&null!=this.params.points&&null!=this.params.steps;this.dataType=this.params.dataType;this.allowMapData=this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");e(d,"setup",function(){this.jvxlFileHeaderBuffer=(new JU.SB).append("volume data read from file\n\n");J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData,this.jvxlFileHeaderBuffer)},"~B");l(d,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();return!0},"~B");
l(d,"readVolumeData",function(a){try{this.readSurfaceData(a)}catch(b){if($(b,Exception))return System.out.println(b.toString()),!1;throw b;}return!0},"~B");e(d,"readVoxelDataIndividually",function(a){if(!a||this.allowMapData)if(!a||null!=this.volumeData.sr)this.volumeData.setVoxelDataAsArray(this.voxelData=null);else{this.newVoxelDataCube();for(a=0;a<this.nPointsX;++a){var b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(var c=0,d=0;d<this.nPointsY;++d)for(var e=b[d]=x(this.nPointsZ,0),g=
0;g<this.nPointsZ;++g,++c)e[g]=this.getValue(a,d,g,c)}}},"~B");e(d,"setVolumeData",function(){});e(d,"setVolumeDataParams",function(){if(null!=this.params.volumeData)return this.setVolumeDataV(this.params.volumeData),!0;if(!this.useOriginStepsPoints)return!1;this.volumetricOrigin.setT(this.params.origin);this.volumetricVectors[0].set(this.params.steps.x,0,0);this.volumetricVectors[1].set(0,this.params.steps.y,0);this.volumetricVectors[2].set(0,0,this.params.steps.z);this.voxelCounts[0]=A(this.params.points.x);
this.voxelCounts[1]=A(this.params.points.y);this.voxelCounts[2]=A(this.params.points.z);if(1>this.voxelCounts[0]||1>this.voxelCounts[1]||1>this.voxelCounts[2])return!1;this.showGridInfo();return!0});e(d,"showGridInfo",function(){JU.Logger.info("grid origin  = "+this.params.origin);JU.Logger.info("grid steps   = "+this.params.steps);JU.Logger.info("grid points  = "+this.params.points);this.ptTemp.x=this.params.steps.x*this.params.points.x;this.ptTemp.y=this.params.steps.y*this.params.points.y;this.ptTemp.z=
this.params.steps.z*this.params.points.z;JU.Logger.info("grid lengths = "+this.ptTemp);this.ptTemp.add(this.params.origin);JU.Logger.info("grid max xyz = "+this.ptTemp)});e(d,"setVoxelRange",function(a,b,c,d,e,g){-1E-4<=b-c&&(b=-10,c=10);var h=c-b,v=this.params.resolution;3.4028235E38!=v&&(d=v,g=0);c=G(Math.floor(h*d))+1;c>e&&(0<(this.dataType&256)?3.4028235E38==v?(this.isQuiet||JU.Logger.info("Maximum number of voxels for index="+a+" exceeded ("+c+") -- set to "+e),c=e):this.isQuiet||JU.Logger.info("Warning -- high number of grid points: "+
c):3.4028235E38==v&&(c=e));1==c&&(c=2);d=(c-1)/h;d<g&&(c=G(Math.floor(g*h+1)),d=(c-1)/h);e=this.volumeData.volumetricVectorLengths[a]=1/d;this.voxelCounts[a]=c;null!=this.params.sbOut&&this.params.sbOut.append("isosurface resolution for axis "+(a+1)+" set to "+d+" points/Angstrom; "+this.voxelCounts[a]+" voxels\n");switch(a){case 0:this.volumetricVectors[0].set(e,0,0);this.volumetricOrigin.x=b;break;case 1:this.volumetricVectors[1].set(0,e,0);this.volumetricOrigin.y=b;break;case 2:this.volumetricVectors[2].set(0,
0,e),this.volumetricOrigin.z=b,this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricOrigin),null!=this.center&&!Float.isNaN(this.center.x)&&this.volumetricOrigin.add(this.center),null!=this.params.sbOut&&this.params.sbOut.append(this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2]+" voxels total\n")}this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricVectors[a]);return this.voxelCounts[a]},"~N,~N,~N,~N,~N,~N");l(d,"readSurfaceData",function(a){this.readSurfaceDataVDR(a)},
"~B");e(d,"readSurfaceDataVDR",function(a){this.isProgressive&&!a?(this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null):this.precalculateVoxelData?this.generateCube():this.readVoxelDataIndividually(a)},"~B");e(d,"generateCube",function(){JU.Logger.info("data type: user volumeData");JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);for(var a=0;3>a;++a)JU.Logger.info("voxel grid vector:"+this.volumetricVectors[a]);JU.Logger.info("Read "+
this.nPointsX+" x "+this.nPointsY+" x "+this.nPointsZ+" data points")});l(d,"closeReader",function(){})});R("J.jvxl.readers");S(["J.jvxl.readers.VolumeDataReader","JU.BS","$.P3","$.P3i","J.atomdata.AtomData"],"J.jvxl.readers.AtomDataReader","java.util.Date JU.AU $.SB $.V3 J.atomdata.RadiusData J.c.VDW J.jvxl.data.JvxlCoder JU.BSUtil $.Logger".split(" "),function(){var d=I(function(){this.maxDistance=0;this.fileDotModel=this.fileName=this.contactPair=null;this.modelIndex=0;this.myIndex=this.atomIndex=
this.atomNo=this.atomProp=this.atomRadius=this.atomXyzTruncated=this.atomData=null;this.firstNearbyAtom=this.nearbyAtomCount=this.myAtomCount=this.ac=0;this.bsNearby=this.bsMyIgnored=this.bsMySelected=null;this.doUseIterator=this.havePlane=this.doAddHydrogens=!1;this.theProperty=0;this.haveOneProperty=!1;this.sr=this.minPtsPerAng=0;this.rs2=this.rs=null;this.maxRS=0;this.thisAtomSet=this.thisPlane=null;this.vl2=this.vl1=this.vl0=this.margin=this.thisX=0;this.ptV=this.pt1=this.pt0=this.ptZ0=this.ptY0=
this.voxelSource=this.noFaceSpheres=this.validSpheres=this.bsSurfaceVoxels=null;T(this,arguments)},J.jvxl.readers,"AtomDataReader",J.jvxl.readers.VolumeDataReader);ca(d,function(){this.atomData=new J.atomdata.AtomData;this.bsMySelected=new JU.BS;this.bsMyIgnored=new JU.BS;this.ptY0=new JU.P3;this.ptZ0=new JU.P3;this.pt0=new JU.P3i;this.pt1=new JU.P3i;this.ptV=new JU.P3});Y(d,function(){ja(this,J.jvxl.readers.AtomDataReader,[])});e(d,"initADR",function(a){this.initVDR(a);this.precalculateVoxelData=
!0},"J.jvxl.readers.SurfaceGenerator");l(d,"setup",function(){this.setup2()},"~B");e(d,"setup2",function(){this.contactPair=this.params.contactPair;this.doAddHydrogens=null!=this.sg.atomDataServer&&this.params.addHydrogens;this.modelIndex=this.params.modelIndex;null!=this.params.bsIgnore&&(this.bsMyIgnored=this.params.bsIgnore);if(null!=this.params.volumeData){this.setVolumeDataV(this.params.volumeData);this.setBBox(this.volumeData.volumetricOrigin,0);this.ptV.setT(this.volumeData.volumetricOrigin);
for(var a=0;3>a;a++)this.ptV.scaleAdd2(this.volumeData.voxelCounts[a]-1,this.volumeData.volumetricVectors[a],this.ptV);this.setBBox(this.ptV,0)}(this.havePlane=null!=this.params.thePlane)&&this.volumeData.setPlaneParameters(this.params.thePlane)});e(d,"markPlaneVoxels",function(a,b){for(var c=0,d=this.thisX*this.yzCount,e=d+this.yzCount;d<e;d++,c++)this.volumeData.getPoint(d,this.ptV),this.thisPlane[c]=this.ptV.distance(a)-b},"JU.P3,~N");e(d,"setVolumeForPlane",function(){this.useOriginStepsPoints?
(this.xyzMin=JU.P3.newP(this.params.origin),this.xyzMax=JU.P3.newP(this.params.origin),this.xyzMax.add3((this.params.points.x-1)*this.params.steps.x,(this.params.points.y-1)*this.params.steps.y,(this.params.points.z-1)*this.params.steps.z)):null==this.params.boundingBox?(this.getAtoms(this.params.bsSelected,!1,!0,!1,!1,!1,!1,this.params.mep_marginAngstroms,this.params.modelInvRotation),null==this.xyzMin&&(this.xyzMin=JU.P3.new3(-10,-10,-10),this.xyzMax=JU.P3.new3(10,10,10))):(this.xyzMin=JU.P3.newP(this.params.boundingBox[0]),
this.xyzMax=JU.P3.newP(this.params.boundingBox[1]));this.setRanges(this.params.plane_ptsPerAngstrom,this.params.plane_gridMax,0)});e(d,"getAtoms",function(a,b,c,d,e,g,h,v,j){g&&(c=!0);c&&(null==this.params.atomRadiusData&&(this.params.atomRadiusData=new J.atomdata.RadiusData(null,1,J.atomdata.RadiusData.EnumType.FACTOR,J.c.VDW.AUTO)),this.atomData.radiusData=this.params.atomRadiusData,this.atomData.radiusData.valueExtended=this.params.solventExtendedAtomRadius,b&&(this.atomData.radiusData.vdwType=
J.c.VDW.NOJMOL));this.atomData.modelIndex=this.modelIndex;this.atomData.bsSelected=a;this.atomData.bsIgnored=this.bsMyIgnored;this.sg.fillAtomData(this.atomData,1|(e?16:0)|(d?4:0)|(c?2:0));this.doUseIterator&&(this.atomData.bsSelected=null);this.ac=this.atomData.ac;this.modelIndex=this.atomData.firstModelIndex;null!=j&&this.atomData.transformXYZ(j,a);e=!1;for(d=0;d<this.ac;d++){if((null==a||a.get(d))&&!this.bsMyIgnored.get(d)){if(this.havePlane&&Math.abs(this.volumeData.distancePointToPlane(this.atomData.xyz[d]))>
2*(this.atomData.atomRadius[d]=this.getWorkingRadius(d,v)))continue;this.bsMySelected.set(d);e=!this.havePlane}if(c&&(g||e))this.atomData.atomRadius[d]=this.getWorkingRadius(d,v)}e=c&&b?this.getWorkingRadius(-1,v):0;this.myAtomCount=JU.BSUtil.cardinalityOf(this.bsMySelected);v=JU.BSUtil.copy(this.bsMySelected);h=0;this.atomProp=null;this.theProperty=3.4028235E38;this.haveOneProperty=!1;a=this.params.theProperty;if(0<this.myAtomCount){j=null;if(b){this.atomData.bsSelected=v;this.sg.atomDataServer.fillAtomData(this.atomData,
8);j=Array(h=this.atomData.hydrogenAtomCount);for(d=0;d<this.atomData.hAtoms.length;d++)if(null!=this.atomData.hAtoms[d])for(b=this.atomData.hAtoms[d].length;0<=--b;)j[--h]=this.atomData.hAtoms[d][b];h=j.length;JU.Logger.info(h+" attached hydrogens added")}b=h+this.myAtomCount;c&&(this.atomRadius=x(b,0));this.atomXyzTruncated=Array(b);null!=this.params.theProperty&&(this.atomProp=x(b,0));this.atomNo=u(b,0);this.atomIndex=u(b,0);this.myIndex=u(this.ac,0);for(d=0;d<h;d++)c&&(this.atomRadius[d]=e),this.atomXyzTruncated[d]=
j[d],this.atomNo[d]=-1,null!=this.atomProp&&this.addAtomProp(d,NaN);this.myAtomCount=h;for(d=v.nextSetBit(0);0<=d;d=v.nextSetBit(d+1))null!=this.atomProp&&this.addAtomProp(this.myAtomCount,null!=a&&d<a.length?a[d]:NaN),this.atomXyzTruncated[this.myAtomCount]=this.atomData.xyz[d],this.atomNo[this.myAtomCount]=this.atomData.atomicNumber[d],this.atomIndex[this.myAtomCount]=d,this.myIndex[d]=this.myAtomCount,c&&(this.atomRadius[this.myAtomCount]=this.atomData.atomRadius[d]),this.myAtomCount++}this.firstNearbyAtom=
this.myAtomCount;this.isQuiet||JU.Logger.info(this.myAtomCount+" atoms will be used in the surface calculation");0==this.myAtomCount&&(this.setBBox(JU.P3.new3(10,10,10),0),this.setBBox(JU.P3.new3(-10,-10,-10),0));for(d=0;d<this.myAtomCount;d++)this.setBBox(this.atomXyzTruncated[d],c?this.atomRadius[d]+0.5:0);Float.isNaN(this.params.scale)||(b=JU.V3.newVsub(this.xyzMax,this.xyzMin),b.scale(0.5),this.xyzMin.add(b),b.scale(this.params.scale),this.xyzMax.add2(this.xyzMin,b),this.xyzMin.sub(b));if(g&&
0!=this.myAtomCount){g=new JU.P3;this.bsNearby=new JU.BS;for(d=0;d<this.ac;d++)!v.get(d)&&!this.bsMyIgnored.get(d)&&(b=this.atomData.atomRadius[d],null!=this.params.thePlane&&Math.abs(this.volumeData.distancePointToPlane(this.atomData.xyz[d]))>2*b||(null!=this.params.theProperty&&(b+=this.maxDistance),g=this.atomData.xyz[d],g.x+b>this.xyzMin.x&&(g.x-b<this.xyzMax.x&&g.y+b>this.xyzMin.y&&g.y-b<this.xyzMax.y&&g.z+b>this.xyzMin.z&&g.z-b<this.xyzMax.z)&&(this.bsNearby.set(d),this.nearbyAtomCount++)));
g=this.myAtomCount;if(0!=this.nearbyAtomCount){g+=this.nearbyAtomCount;this.atomRadius=JU.AU.arrayCopyF(this.atomRadius,g);this.atomXyzTruncated=JU.AU.arrayCopyObject(this.atomXyzTruncated,g);null!=this.atomIndex&&(this.atomIndex=JU.AU.arrayCopyI(this.atomIndex,g));null!=a&&(this.atomProp=JU.AU.arrayCopyF(this.atomProp,g));for(d=this.bsNearby.nextSetBit(0);0<=d;d=this.bsNearby.nextSetBit(d+1))null!=a&&this.addAtomProp(this.myAtomCount,a[d]),this.myIndex[d]=this.myAtomCount,this.atomIndex[this.myAtomCount]=
d,this.atomXyzTruncated[this.myAtomCount]=this.atomData.xyz[d],this.atomRadius[this.myAtomCount++]=this.atomData.atomRadius[d]}c&&this.setRadii();this.haveOneProperty=!Float.isNaN(this.theProperty)}},"JU.BS,~B,~B,~B,~B,~B,~B,~N,JU.M4");e(d,"setRadii",function(){if(null==this.rs){this.maxRS=0;this.rs=x(this.myAtomCount,0);this.rs2=x(this.myAtomCount,0);for(var a=0;a<this.myAtomCount;a++){var b=this.rs[a]=this.atomRadius[a]+this.sr;b>this.maxRS&&(this.maxRS=b);this.rs2[a]=this.rs[a]*this.rs[a]}}});
e(d,"addAtomProp",function(a,b){this.atomProp[a]=b;!Float.isNaN(this.theProperty)&&b!=this.theProperty&&(this.theProperty=3.4028235E38==this.theProperty?b:NaN)},"~N,~N");e(d,"getWorkingRadius",function(a,b){var c=0>a?this.atomData.hAtomRadius:this.atomData.atomRadius[a];return Float.isNaN(b)?Math.max(c,0.1):c+b},"~N,~N");e(d,"setHeader",function(a,b){this.jvxlFileHeaderBuffer=new JU.SB;null!=this.atomData.programInfo&&this.jvxlFileHeaderBuffer.append("#created by ").append(this.atomData.programInfo).append(" on ").append(""+
new java.util.Date).append("\n");this.jvxlFileHeaderBuffer.append(a).append("\n").append(b).append("\n")},"~S,~S");e(d,"setRanges",function(a,b,c){null!=this.xyzMin&&(this.ptsPerAngstrom=a,this.maxGrid=b,this.minPtsPerAng=c,this.setVolumeData(),J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData,this.jvxlFileHeaderBuffer))},"~N,~N,~N");l(d,"setVolumeData",function(){this.setVolumeDataADR()});e(d,"setVolumeDataADR",function(){this.setVolumeDataParams()||(this.setVoxelRange(0,this.xyzMin.x,this.xyzMax.x,
this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(1,this.xyzMin.y,this.xyzMax.y,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(2,this.xyzMin.z,this.xyzMax.z,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng))});e(d,"setVertexSource",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);if(null!=this.params.vertexSource){this.params.vertexSource=JU.AU.arrayCopyI(this.params.vertexSource,this.meshData.vc);for(var a=
0;a<this.meshData.vc;a++)this.params.vertexSource[a]=Math.abs(this.params.vertexSource[a])-1}});e(d,"resetPlane",function(a){for(var b=0;b<this.yzCount;b++)this.thisPlane[b]=a},"~N");e(d,"resetVoxelData",function(a){for(var b=0;b<this.nPointsX;++b)for(var c=0;c<this.nPointsY;++c)for(var d=0;d<this.nPointsZ;++d)this.voxelData[b][c][d]=a},"~N");e(d,"getVoxel",function(a,b,c,d){return this.isProgressive?this.thisPlane[d%this.yzCount]:this.voxelData[a][b][c]},"~N,~N,~N,~N");e(d,"unsetVoxelData",function(){this.unsetVoxelData2()});
e(d,"unsetVoxelData2",function(){if(this.isProgressive)for(var a=0;a<this.yzCount;a++)3.4028235E38==this.thisPlane[a]&&(this.thisPlane[a]=NaN);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)3.4028235E38==this.voxelData[a][b][c]&&(this.voxelData[a][b][c]=NaN)});e(d,"setGridLimitsForAtom",function(a,b,c,d){b+=this.margin;this.volumeData.xyzToVoxelPt(a.x,a.y,a.z,c);a=G(Math.floor(b/this.volumeData.volumetricVectorLengths[0]));var e=G(Math.floor(b/this.volumeData.volumetricVectorLengths[1]));
b=G(Math.floor(b/this.volumeData.volumetricVectorLengths[2]));d.set(c.x+a,c.y+e,c.z+b);c.set(c.x-a,c.y-e,c.z-b);c.x=Math.max(c.x-1,0);c.y=Math.max(c.y-1,0);c.z=Math.max(c.z-1,0);d.x=Math.min(d.x+1,this.nPointsX);d.y=Math.min(d.y+1,this.nPointsY);d.z=Math.min(d.z+1,this.nPointsZ)},"JU.P3,~N,JU.P3i,JU.P3i");e(d,"getAtomMinMax",function(a,b){for(var c=0;c<this.nPointsX;c++)b[c]=new JU.BS;for(var d=this.myAtomCount;0<=--d;)if(null==a||a.get(d)){this.setGridLimitsForAtom(this.atomXyzTruncated[d],this.atomRadius[d],
this.pt0,this.pt1);for(c=this.pt0.x;c<this.pt1.x;c++)b[c].set(d)}},"JU.BS,~A");e(d,"markSphereVoxels",function(a,b){for(var c=3.4028235E38!=b&&null!=this.point,d=this.volumetricVectors[0],e=this.volumetricVectors[1],g=this.volumetricVectors[2],h=this.thisAtomSet.nextSetBit(0);0<=h;h=this.thisAtomSet.nextSetBit(h+1))if(this.havePlane||null==this.validSpheres||this.validSpheres.get(h)){var v=null!=this.noFaceSpheres&&this.noFaceSpheres.get(h),j=h>=this.firstNearbyAtom,n=this.atomXyzTruncated[h],k=this.atomRadius[h];
if(!(c&&n.distance(this.point)>b+k+0.5)){var t=k+a;this.setGridLimitsForAtom(n,t,this.pt0,this.pt1);this.isProgressive&&(this.pt0.x=this.thisX,this.pt1.x=this.thisX+1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(var q=this.pt0.x;q<this.pt1.x;q++,this.ptV.add2(d,this.ptY0)){this.ptY0.setT(this.ptV);for(var l=this.pt0.y;l<this.pt1.y;l++,this.ptV.add2(e,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var w=this.pt0.z;w<this.pt1.z;w++,this.ptV.add(g)){var u=this.ptV.distance(n)-
k,x=this.volumeData.getPointIndex(q,l,w);if((0==a||u<=t)&&u<this.getVoxel(q,l,w,x)){if(j||c&&this.ptV.distance(this.point)>b)u=NaN;this.setVoxel(q,l,w,x,u);Float.isNaN(u)||(null!=this.voxelSource&&(this.voxelSource[x]=h+1),0>u&&v&&this.bsSurfaceVoxels.set(x))}}}}}}},"~N,~N");e(d,"setVoxel",function(a,b,c,d,e){this.isProgressive?this.thisPlane[d%this.yzCount]=e:this.voxelData[a][b][c]=e},"~N,~N,~N,~N,~N")});R("J.jvxl.readers");S(["JU.P3","J.jvxl.readers.AtomDataReader","JU.P4","$.V3"],"J.jvxl.readers.IsoSolventReader",
"java.util.Hashtable JU.BS $.Lst $.Measure J.jvxl.data.MeshData JU.BSUtil $.Logger $.MeshSurface $.TempArray".split(" "),function(){var d=I(function(){this.envelopeRadius=this.cavityRadius=0;this.dots=null;this.isPocket=this.isCavity=this.doCalculateTroughs=!1;this.bsAtomMinMax=this.p=this.vTemp2=this.ptTemp2=this.plane=this.vTemp=this.ptS2=this.ptS1=this.vFaces=this.vEdges=this.htEdges=this.bsLocale=this.bsSurfaceDone=this.bsSurfacePoints=this.iter=null;this.isSurfacePoint=!1;this.nTest=this.iAtomSurface=
0;qa("J.jvxl.readers.IsoSolventReader.Edge")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$();qa("J.jvxl.readers.IsoSolventReader.Face")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$();this.ecosASB2=this.dAB2=this.dAB=this.rBS2=this.rAS2=this.rBS=this.rAS=0;T(this,arguments)},J.jvxl.readers,"IsoSolventReader",J.jvxl.readers.AtomDataReader);ca(d,function(){this.ptS1=new JU.P3;this.ptS2=new JU.P3;this.vTemp=new JU.V3;this.plane=new JU.P4;this.ptTemp2=new JU.P3;this.vTemp2=new JU.V3;
this.p=new JU.P3});Y(d,function(){ja(this,J.jvxl.readers.IsoSolventReader,[])});l(d,"init",function(a){this.initADR(a)},"J.jvxl.readers.SurfaceGenerator");l(d,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();this.volumeData.setUnitVectors();this.vl0=this.volumeData.volumetricVectorLengths[0];this.vl1=this.volumeData.volumetricVectorLengths[1];this.vl2=this.volumeData.volumetricVectorLengths[2];this.isProgressive&&(this.volumeData.getYzCount(),this.bsAtomMinMax=Array(this.nPointsX),
this.getAtomMinMax(null,this.bsAtomMinMax),this.voxelSource=u(this.volumeData.nPoints,0));return!0},"~B");l(d,"setup",function(a){this.setup2();if(null==this.contactPair){this.cavityRadius=this.params.cavityRadius;this.envelopeRadius=this.params.envelopeRadius;this.sr=this.params.solventRadius;this.point=this.params.point;this.isCavity=this.params.isCavity&&null!=this.meshDataServer;this.isPocket=null!=this.params.pocket&&null!=this.meshDataServer;this.doUseIterator=this.doCalculateTroughs=!a&&null!=
this.sg.atomDataServer&&!this.isCavity&&0<this.sr&&(1195==this.dataType||1203==this.dataType);this.getAtoms(this.params.bsSelected,this.doAddHydrogens,!0,!1,!1,!0,!1,NaN,null);if(this.isCavity||this.isPocket)this.dots=this.meshDataServer.calculateGeodesicSurface(this.bsMySelected,this.envelopeRadius);this.setHeader("solvent/molecular surface",this.params.calculationType);if(this.havePlane||!a){var b=Math.max(this.params.solventExtendedAtomRadius,this.params.solventRadius),b=1<=b?1.5/b:0;0<b&&System.out.println("IsoSolventReader.minPtsPerAng="+
b);this.setRanges(this.params.solvent_ptsPerAngstrom,this.params.solvent_gridMax,b);this.volumeData.getYzCount();this.margin=2*this.volumeData.maxGrid}null!=this.bsNearby&&this.bsMySelected.or(this.bsNearby)}else a||this.setVolumeData();this.doCalculateTroughs||(a?(this.precalculateVoxelData=!1,this.volumeData.sr=this):this.isCavity||(this.isProgressive=this.isXLowToHigh=!0));null==this.thisAtomSet&&(this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount))},"~B");l(d,"generateCube",function(){if(!(this.isCavity&&
null!=this.params.theProperty)){this.isCavity&&1207!=this.dataType&&1208!=this.dataType?(this.params.vertexSource=null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(this.cavityRadius,this.params.distance),this.generateSolventCavity(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(0,NaN)):(this.voxelSource=u(this.volumeData.nPoints,0),this.generateSolventCube());this.unsetVoxelData();var a=this.params.slabInfo;if(null!=a)for(var b=0;b<a.size();b++)a.get(b)[2].booleanValue()&&
ba(a.get(b)[0],"JU.P4")&&(this.volumeData.capData(a.get(b)[0],this.params.cutoff),a.removeItemAt(b--))}});l(d,"getSurfacePointAndFraction",function(a,b,c,d,e,g,h,v,j,n,k,l,q){n=this.marchingCubes.getLinearOffset(h,v,j,n);k=this.marchingCubes.getLinearOffset(h,v,j,k);this.isSurfacePoint=null!=this.bsSurfaceVoxels&&(this.bsSurfaceVoxels.get(n)||this.bsSurfaceVoxels.get(k));if(null!=this.voxelSource){var u=Math.abs(Float.isNaN(d)||c<d?this.voxelSource[n]:this.voxelSource[k]);0<u&&(this.iAtomSurface=
this.atomIndex[u-1])}if(J.jvxl.readers.IsoSolventReader.testLinear||null==this.voxelSource||0==this.voxelSource[n]||this.voxelSource[n]!=this.voxelSource[k])return this.getSPF(a,b,c,d,e,g,h,v,j,n,k,l,q);a=l[0]=JU.MeshSurface.getSphericalInterpolationFraction(0>this.voxelSource[n]?this.sr:this.atomRadius[this.voxelSource[n]-1],c,d,g.length());q.scaleAdd2(a,g,e);return c+a*(d-c)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");l(d,"addVertexCopy",function(a,b,c,d){a=this.addVC(a,b,c,d);if(0>a)return a;
this.isSurfacePoint&&this.bsSurfacePoints.set(a);null!=this.params.vertexSource&&(this.params.vertexSource[a]=this.iAtomSurface);return a},"JU.T3,~N,~N,~B");l(d,"selectPocket",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);for(var b=this.meshData.vs,c=this.meshData.vc,d=this.meshData.vvs,e=this.dots.length,g=0;g<c;g++)for(var h=0;h<e;h++)this.dots[h].distance(b[g])<this.envelopeRadius&&(d[g]=NaN);this.meshData.getSurfaceSet();b=this.meshData.nSets;c=
JU.BS.newN(b);for(g=0;g<b;g++)if(null!=(d=this.meshData.surfaceSet[g]))for(h=d.nextSetBit(0);0<=h;h=d.nextSetBit(h+1))if(Float.isNaN(this.meshData.vvs[h])){c.set(g);break}for(g=0;g<b;g++)null!=this.meshData.surfaceSet[g]&&c.get(g)==a&&this.meshData.invalidateSurfaceSet(g);this.updateSurfaceData();a||(this.meshData.surfaceSet=null);null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)},"~B");l(d,"postProcessVertices",function(){this.setVertexSource();
if(this.doCalculateTroughs&&null!=this.bsSurfacePoints){var a=new JU.BS,b=this.meshData.getSurfaceSet(),c=null,d=this.isPocket?null:J.jvxl.data.MeshData.calculateVolumeOrArea(this.meshData,null,!1,!1),e=this.isCavity?4.71238898038469*Math.pow(this.sr,3):0,g=0,h=!1;if(null!=d&&!this.isCavity)for(var v=0;v<this.meshData.nSets;v++){var j=d[v];Math.abs(j)>g&&(g=Math.abs(j),h=0>j)}g=h?-1:1;for(v=0;v<this.meshData.nSets;v++)if(h=b[v],h.intersects(this.bsSurfacePoints)&&(null==d||d[v]*g>e)&&null!=this.params.vertexSource){j=
new JU.BS;null==c&&(c=Array(b.length));for(var n=h.nextSetBit(0);0<=n;n=h.nextSetBit(n+1)){var k=this.params.vertexSource[n];if(!(0>k)){if(a.get(k)){this.meshData.invalidateSurfaceSet(v);break}j.set(k)}}a.or(j)}else this.meshData.invalidateSurfaceSet(v);this.updateSurfaceData();null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)}null!=this.params.thePlane&&null==this.params.slabInfo&&this.params.addSlabInfo(JU.TempArray.getSlabWithinRange(-100,
0))});e(d,"generateSolventCavity",function(){for(var a=JU.BS.newN(this.nPointsX*this.nPointsY*this.nPointsZ),b=0,c=this.dots.length,d=0,e,g=this.envelopeRadius,h=0;h<this.nPointsX;++h)for(var v=0;v<this.nPointsY;++v){var j=0;a:for(;j<this.nPointsZ;++j,++b)if(3.4028235E38>(e=this.voxelData[h][v][j])&&e>=this.cavityRadius){this.volumeData.voxelPtToXYZ(h,v,j,this.ptV);for(var n=0;n<c;n++)if(this.dots[n].distance(this.ptV)<g)continue a;a.set(b);d++}}JU.Logger.info("cavities include "+d+" voxel points");
this.atomRadius=x(d,0);this.atomXyzTruncated=Array(d);for(c=b=h=0;h<this.nPointsX;++h)for(v=0;v<this.nPointsY;++v)for(j=0;j<this.nPointsZ;++j)a.get(b++)&&(this.volumeData.voxelPtToXYZ(h,v,j,this.atomXyzTruncated[c]=new JU.P3),this.atomRadius[c++]=this.voxelData[h][v][j]);this.myAtomCount=this.firstNearbyAtom=d;this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount);this.rs=null;this.setRadii()});e(d,"generateSolventCube",function(){1207!=this.dataType&&(this.params.vertexSource=u(this.volumeData.nPoints,
0),this.bsSurfaceDone=new JU.BS,this.bsSurfaceVoxels=new JU.BS,this.bsSurfacePoints=new JU.BS,this.doCalculateTroughs?(this.iter=this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected,!0,!1,!1),this.vEdges=new JU.Lst,this.bsLocale=Array(this.myAtomCount),this.htEdges=new java.util.Hashtable,this.getEdges(),JU.Logger.info(this.vEdges.size()+" edges"),this.vFaces=new JU.Lst,this.getFaces(),JU.Logger.info(this.vFaces.size()+" faces"),this.htEdges=this.bsLocale=null,this.iter.release(),this.iter=
null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markFaceVoxels(!0),this.markToroidVoxels(),this.validSpheres.or(this.noFaceSpheres),this.vEdges=null,this.markFaceVoxels(!1),this.vFaces=null):(this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38)),this.markSphereVoxels(0,this.doCalculateTroughs?3.4028235E38:this.params.distance),this.validSpheres=this.noFaceSpheres=null)});e(d,"getEdges",function(){for(var a=0;a<this.myAtomCount;a++)this.bsLocale[a]=new JU.BS;for(a=0;a<this.myAtomCount;a++){var b=
this.atomXyzTruncated[a],c=this.rs[a];for(this.sg.atomDataServer.setIteratorForAtom(this.iter,this.atomIndex[a],c+this.maxRS);this.iter.hasNext();){var d=this.iter.next(),d=this.myIndex[d];if(!(a>=this.firstNearbyAtom&&d>=this.firstNearbyAtom)){var e=this.rs[d],g=b.distance(this.atomXyzTruncated[d]);g>=c+e||(e=pa(J.jvxl.readers.IsoSolventReader.Edge,this,null,this,a,d,g),this.vEdges.addLast(e),this.bsLocale[a].set(d),this.bsLocale[d].set(a),this.htEdges.put(e.toString(),e))}}}});e(d,"findEdge",function(a,
b){return this.htEdges.get(a<b?a+"_"+b:b+"_"+a)},"~N,~N");e(d,"getFaces",function(){var a=new JU.BS;this.params.surfaceAtoms=this.validSpheres=new JU.BS;this.noFaceSpheres=JU.BSUtil.setAll(this.myAtomCount);for(var b=this.vEdges.size();0<=--b;){var c=this.vEdges.get(b),d=c.ia,e=c.ib;a.clearAll();a.or(this.bsLocale[d]);a.and(this.bsLocale[e]);for(var g=a.nextSetBit(e+1);0<=g;g=a.nextSetBit(g+1))if(this.getSolventPoints(c,d,e,g)){var h,v=!1;if(null!=(h=this.validateFace(d,e,g,c,this.ptS1)))this.vFaces.addLast(h),
v=!0;if(null!=(h=this.validateFace(d,e,g,c,this.ptS2)))this.vFaces.addLast(h),v=!0;v&&(this.noFaceSpheres.clear(d),this.noFaceSpheres.clear(e),this.noFaceSpheres.clear(g))}}});e(d,"validateFace",function(a,b,c,d,e){this.sg.atomDataServer.setIteratorForPoint(this.iter,this.modelIndex,e,this.maxRS);for(var g=!0;this.iter.hasNext();){var h=this.iter.next(),v=this.myIndex[h];if(!(v==a||v==b||v==c)&&this.atomData.atoms[h].distance(e)<this.atomData.atomRadius[h]+this.sr){g=!1;break}}h=this.findEdge(b,c);
v=this.findEdge(a,c);e=g?pa(J.jvxl.readers.IsoSolventReader.Face,this,null,a,b,c,e):null;d.addFace(e);h.addFace(e);v.addFace(e);if(!g)return null;this.validSpheres.set(a);this.validSpheres.set(b);this.validSpheres.set(c);return e},"~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");e(d,"markFaceVoxels",function(a){for(var b=new JU.BS,c=this.volumetricVectors[0],d=this.volumetricVectors[1],e=this.volumetricVectors[2],g=this.vFaces.size();0<=--g;){var h=this.vFaces.get(g),v=this.atomXyzTruncated[h.ia],
j=this.atomXyzTruncated[h.ib],n=this.atomXyzTruncated[h.ic],k=h.pS;this.setGridLimitsForAtom(k,this.sr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(var l=this.pt0.x;l<this.pt1.x;l++,this.ptV.add2(c,this.ptY0)){this.ptY0.setT(this.ptV);for(var q=this.pt0.y;q<this.pt1.y;q++,this.ptV.add2(d,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var u=this.pt0.z;u<this.pt1.z;u++,this.ptV.add(e)){var w=this.sr-this.ptV.distance(k),x=this.voxelData[l][q][u],A=this.volumeData.getPointIndex(l,
q,u);a&&0<w&&this.bsSurfaceDone.set(A);if(JU.Measure.isInTetrahedron(this.ptV,v,j,n,k,this.plane,this.vTemp,this.vTemp2,!1)&&(!a?!this.bsSurfaceDone.get(A)&&0>w&&w>1.8*-this.volumeData.maxGrid&&w>x==b.get(A):0<w&&(0>x||3.4028235E38==x||w>x==b.get(A))))b.set(A),this.setVoxel(l,q,u,A,w),null!=this.voxelSource&&(this.voxelSource[A]=-1-h.ia),0<w&&this.bsSurfaceVoxels.set(A)}}}}},"~B");e(d,"markToroidVoxels",function(){for(var a=this.volumetricVectors[0],b=this.volumetricVectors[1],c=this.volumetricVectors[2],
d=this.vEdges.size();0<=--d;){var e=this.vEdges.get(d);if(e.isValid()){var g=e.ia,h=e.ib,v=this.atomXyzTruncated[g],j=this.atomXyzTruncated[h];this.rAS=this.rs[g];this.rBS=this.rs[h];this.rAS2=this.rs2[g];this.rBS2=this.rs2[h];this.dAB=e.d;this.dAB2=e.d2;this.ecosASB2=e.cosASB2;this.setGridLimitsForAtom(e,e.maxr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(e=this.pt0.x;e<this.pt1.x;e++,this.ptV.add2(a,this.ptY0)){this.ptY0.setT(this.ptV);for(h=this.pt0.y;h<
this.pt1.y;h++,this.ptV.add2(b,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var n=this.pt0.z;n<this.pt1.z;n++,this.ptV.add(c)){var k=this.checkSpecialVoxel(v,j,this.ptV);if(!Float.isNaN(k)&&(k=this.sr-k,k<this.voxelData[e][h][n])){var l=this.volumeData.getPointIndex(e,h,n);this.setVoxel(e,h,n,l,k);null!=this.voxelSource&&(this.voxelSource[l]=-1-g)}}}}}}});l(d,"unsetVoxelData",function(){if(this.havePlane)if(this.isProgressive)for(var a=0;a<this.yzCount;a++)0.001>this.thisPlane[a]||(this.thisPlane[a]=
0.001);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)0.001>this.voxelData[a][b][c]||(this.voxelData[a][b][c]=0.001);else this.unsetVoxelData2()});e(d,"getSolventPoints",function(a,b,c,d){var e=this.rs[b],g=a.v;a=(a.d2+this.rs2[b]-this.rs2[c])/(2*a.d*e);c=Math.acos(a);this.p.scaleAdd2(a*e,g,this.atomXyzTruncated[b]);JU.Measure.getPlaneThroughPoint(this.p,g,this.plane);b=Math.sin(c)*e;a=this.atomXyzTruncated[d];c=this.rs[d];e=JU.Measure.distanceToPlane(this.plane,
a);if(Math.abs(e)>=0.9*c)return!1;this.ptTemp.scaleAdd2(-e,g,a);a=this.p.distance(this.ptTemp);d=(b*b+a*a-(this.rs2[d]-e*e))/(2*b*a);if(0.99<=Math.abs(d))return!1;e=this.vTemp2;e.sub2(this.ptTemp,this.p);e.normalize();this.ptTemp.scaleAdd2(b*d,e,this.p);e.cross(g,e);e.normalize();e.scale(Math.sqrt(1-d*d)*b);this.ptS1.add2(this.ptTemp,e);this.ptS2.sub2(this.ptTemp,e);return!0},"J.jvxl.readers.IsoSolventReader.Edge,~N,~N,~N");e(d,"checkSpecialVoxel",function(a,b,c){var d=a.distance(c),e=a.distanceSquared(c),
g=this.rAS/d;if(1<g)return this.p.set(a.x+(c.x-a.x)*g,a.y+(c.y-a.y)*g,a.z+(c.z-a.z)*g),b.distanceSquared(this.p)>=this.rBS2?NaN:this.solventDistance(this.rAS,this.rAS2,this.rBS2,d,e,b.distanceSquared(c));d=b.distance(c);return 1<(g=this.rBS/d)?(this.p.set(b.x+(c.x-b.x)*g,b.y+(c.y-b.y)*g,b.z+(c.z-b.z)*g),a.distanceSquared(this.p)>=this.rAS2?NaN:this.solventDistance(this.rBS,this.rBS2,this.rAS2,d,d*d,e)):NaN},"JU.P3,JU.P3,JU.P3");e(d,"solventDistance",function(a,b,c,d,e,g){g=Math.acos((e+this.dAB2-
g)/(2*d*this.dAB));c=Math.acos((b+this.dAB2-c)/(2*a*this.dAB));e=b+e-2*a*d*Math.cos(c-g);c=Math.sqrt(e);return this.ecosASB2<(b+e-d*d)/(c*a)?c:NaN},"~N,~N,~N,~N,~N,~N");e(d,"dumpLine",function(a,b,c,d){this.sg.log('draw ID "x'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(b)+" color "+d)},"JU.P3,JU.T3,~S,~S");e(d,"dumpLine2",function(a,b,c,d,e,g){var h=new JU.V3;h.setT(b);h.sub(a);h.normalize();h.scale(d);h.add(a);this.sg.log('draw ID "'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(h)+" color "+
e);this.sg.log('draw ID "'+c+this.nTest++ +'"'+JU.P3.newP(h)+" "+JU.P3.newP(b)+" color "+g+'"'+c+'"')},"JU.P3,JU.P3,~S,~N,~S,~S");e(d,"dumpPoint",function(a,b,c){this.sg.log('draw ID "'+b+this.nTest++ +'"'+JU.P3.newP(a)+" color "+c)},"JU.P3,~S,~S");l(d,"getValueAtPoint",function(a){if(null!=this.contactPair)return a.distance(this.contactPair.myAtoms[1])-this.contactPair.radii[1];for(var b=3.4028235E38,c=0;c<this.firstNearbyAtom;c++){var d=a.distance(this.atomXyzTruncated[c])-this.rs[c];d<b&&(b=d)}return 3.4028235E38==
b?NaN:b},"JU.T3,~B");l(d,"discardTempData",function(a){this.rs2=this.rs=null;this.discardTempDataSR(a)},"~B");l(d,"getPlane",function(a){0==this.yzCount&&this.initPlanes();this.thisX=a;this.thisPlane=this.yzPlanes[a%2];null==this.contactPair?(this.resetPlane(3.4028235E38),this.thisAtomSet=this.bsAtomMinMax[a],this.markSphereVoxels(0,this.params.distance),this.unsetVoxelData()):this.markPlaneVoxels(this.contactPair.myAtoms[0],this.contactPair.radii[0]);return this.thisPlane},"~N");d.$IsoSolventReader$Edge$=
function(){var a=I(function(){ua(this,arguments);this.cosASB2=this.maxr=this.d2=this.d=this.nInvalid=this.nFaces=this.ib=this.ia=0;this.v=null;T(this,arguments)},J.jvxl.readers.IsoSolventReader,"Edge",JU.P3);gb(a,function(a,c,d,e){this.ia=Math.min(c,d);this.ib=Math.max(c,d);this.d=e;this.d2=e*e;this.maxr=Math.sqrt(this.d2/4+Math.max(a.rs2[c],a.rs2[d]));this.ave(a.atomXyzTruncated[c],a.atomXyzTruncated[d]);this.cosASB2=(a.rs2[c]+a.rs2[d]-this.d2)/(a.rs[d]*a.rs[c]);this.v=JU.V3.newVsub(a.atomXyzTruncated[d],
a.atomXyzTruncated[c]);this.v.normalize()},"J.jvxl.readers.IsoSolventReader,~N,~N,~N");e(a,"addFace",function(a){this.nFaces++;null==a&&this.nInvalid++},"J.jvxl.readers.IsoSolventReader.Face");e(a,"isValid",function(){return 0==this.nFaces||this.nInvalid!=this.nFaces});l(a,"toString",function(){return this.ia+"_"+this.ib})};d.$IsoSolventReader$Face$=function(){var a=I(function(){ua(this,arguments);this.ic=this.ib=this.ia=0;this.pS=null;T(this,arguments)},J.jvxl.readers.IsoSolventReader,"Face",null);
Y(a,function(a,c,d,e){this.ia=a;this.ib=c;this.ic=d;this.pS=JU.P3.newP(e)},"~N,~N,~N,JU.P3");l(a,"toString",function(){return this.ia+"_"+this.ib+"_"+this.ic+"_"+this.pS})};d.testLinear=!1});R("J.jvxl.readers");S(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.SurfaceFileReader",["JU.PT","$.Rdr","J.api.Interface"],function(){var d=I(function(){this.next=this.line=this.out=this.binarydoc=this.br=null;T(this,arguments)},J.jvxl.readers,"SurfaceFileReader",J.jvxl.readers.SurfaceReader);ca(d,function(){this.next=
u(1,0)});Y(d,function(){ja(this,J.jvxl.readers.SurfaceFileReader,[])});e(d,"setStream",function(a,b){if(null==a)this.binarydoc.setStream(null,b);else try{if(ba(this.br,"JU.Rdr.StreamReader")){var c=this.br.getStream();c.reset();this.binarydoc.setStream(c,!0)}}catch(d){if($(d,Exception))System.out.println("BCifDensityReader "+d),this.binarydoc.setStream(this.sg.atomDataServer.getBufferedInputStream(a),b);else throw d;}},"~S,~B");l(d,"init",function(a){this.initSR(a)},"J.jvxl.readers.SurfaceGenerator");
e(d,"init2",function(a,b){this.init2SFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2SFR",function(a,b){this.br=b;this.init(a)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"newBinaryDocument",function(){return J.api.Interface.getInterface("JU.BinaryDocument",this.sg.atomDataServer,"file")});l(d,"setOutputChannel",function(a){null==this.binarydoc?this.out=a:this.sg.setOutputChannel(this.binarydoc,a)},"JU.OC");l(d,"closeReader",function(){this.closeReaderSFR()});
e(d,"closeReaderSFR",function(){if(null!=this.br)try{this.br.close()}catch(a){if(!$(a,"java.io.IOException"))throw a;}null!=this.out&&this.out.closeChannel();null!=this.binarydoc&&this.binarydoc.close()});l(d,"discardTempData",function(a){this.closeReader();this.discardTempDataSR(a)},"~B");e(d,"getTokens",function(){return JU.PT.getTokensAt(this.line,0)});e(d,"parseFloat",function(){return JU.PT.parseFloatNext(this.line,this.next)});e(d,"parseFloatStr",function(a){this.next[0]=0;return JU.PT.parseFloatNext(a,
this.next)},"~S");e(d,"parseFloatRange",function(a,b,c){this.next[0]=b;return JU.PT.parseFloatRange(a,c,this.next)},"~S,~N,~N");e(d,"parseInt",function(){return JU.PT.parseIntNext(this.line,this.next)});e(d,"parseIntStr",function(a){this.next[0]=0;return JU.PT.parseIntNext(a,this.next)},"~S");e(d,"parseIntNext",function(a){return JU.PT.parseIntNext(a,this.next)},"~S");e(d,"parseFloatArrayStr",function(a){this.next[0]=0;return JU.PT.parseFloatArrayNext(a,this.next,null,null,null)},"~S");e(d,"parseFloatArray",
function(a,b,c){return JU.PT.parseFloatArrayNext(this.line,this.next,a,b,c)},"~A,~S,~S");e(d,"getQuotedStringNext",function(){return JU.PT.getQuotedStringNext(this.line,this.next)});e(d,"skipTo",function(a,b){if(null!=a)for(;0>this.rd().indexOf(a););null!=b&&(this.next[0]=this.line.indexOf(b)+b.length+2)},"~S,~S");e(d,"rd",function(){this.line=this.br.readLine();if(null!=this.line&&(this.nBytes+=this.line.length,null!=this.out)){var a=this.line.getBytes();this.out.write(a,0,a.length);this.out.writeByteAsInt(10)}return this.line})});
R("J.jvxl.readers");S(["J.jvxl.readers.SurfaceFileReader"],"J.jvxl.readers.VolumeFileReader","JU.AU $.PT $.SB J.api.Interface J.atomdata.AtomData JU.Logger".split(" "),function(){var d=I(function(){this.negativeAtomCount=this.endOfData=!1;this.nSurfaces=this.ac=0;this.canDownsample=this.isAngstroms=!1;this.downsampleRemainders=null;this.getNCIPlanes=!1;this.nData=0;this.readerClosed=!1;this.nSkipZ=this.nSkipY=this.nSkipX=this.downsampleFactor=0;this.yzPlanesRaw=null;this.iPlaneNCI=0;this.boundingBox=
null;this.isScaledAlready=!1;T(this,arguments)},J.jvxl.readers,"VolumeFileReader",J.jvxl.readers.SurfaceFileReader);Y(d,function(){ja(this,J.jvxl.readers.VolumeFileReader,[])});l(d,"init2",function(a,b){this.init2VFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2VFR",function(a,b){this.init2SFR(a,b);this.canDownsample=this.isProgressive=this.isXLowToHigh=!0;this.jvxlData.wasCubic=!0;this.boundingBox=this.params.boundingBox;4==this.params.qmOrbitalType&&(this.hasColorData=
null==this.params.parameters||0<=this.params.parameters[1],this.getNCIPlanes=!0,this.params.insideOut=!this.params.insideOut)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"recordData",function(a){if(Float.isNaN(a))return a;a<this.dataMin&&(this.dataMin=a);a>this.dataMax&&(this.dataMax=a);this.dataMean+=a;this.nData++;return a},"~N");l(d,"closeReader",function(){this.readerClosed||(this.readerClosed=!0,this.closeReaderSFR(),0==this.nData||-3.4028235E38==this.dataMax||(this.dataMean/=
this.nData,JU.Logger.info("VolumeFileReader closing file: "+this.nData+" points read \ndata min/max/mean = "+this.dataMin+"/"+this.dataMax+"/"+this.dataMean)))});l(d,"readVolumeParameters",function(){this.endOfData=!1;this.nSurfaces=this.readVolumetricHeader();if(0==this.nSurfaces)return!1;this.nSurfaces<this.params.fileIndex&&(JU.Logger.warn("not enough surfaces in file -- resetting params.fileIndex to "+this.nSurfaces),this.params.fileIndex=this.nSurfaces);return!0},"~B");l(d,"readVolumeData",function(a){return this.readVolumeDataVFR(a)},
"~B");e(d,"readVolumeDataVFR",function(a){if(!this.gotoAndReadVoxelData(a))return!1;this.vertexDataOnly||JU.Logger.info("JVXL read: "+this.nPointsX+" x "+this.nPointsY+" x "+this.nPointsZ+" data points");return!0},"~B");e(d,"readVolumetricHeader",function(){try{this.readParameters();if(-2147483648==this.ac)return 0;this.vertexDataOnly||JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);var a=this.params.downsampleFactor,b=this.canDownsample&&1<a;1<a&&!this.canDownsample&&(this.jvxlData.msg+=
"\ncannot downsample this file type");if(b){this.downsampleRemainders=u(3,0);JU.Logger.info("downsample factor = "+a);for(var c=0;3>c;++c){var d=this.voxelCounts[c];this.downsampleRemainders[c]=d%a;this.voxelCounts[c]/=a;this.isPeriodic&&(this.voxelCounts[c]++,this.downsampleRemainders[c]--);this.volumetricVectors[c].scale(a);JU.Logger.info("downsampling axis "+(c+1)+" from "+d+" to "+this.voxelCounts[c])}}if(!this.vertexDataOnly)for(c=0;3>c;++c)this.isAngstroms||this.volumetricVectors[c].scale(0.5291772),
this.line=this.voxelCounts[c]+" "+this.volumetricVectors[c].x+" "+this.volumetricVectors[c].y+" "+this.volumetricVectors[c].z,JU.Logger.info("voxel grid count/vector:"+this.line);this.scaleIsosurface(this.params.scale);this.volumeData.setVolumetricXml();return this.nSurfaces}catch(e){if($(e,Exception))return JU.Logger.error(e.toString()),0;throw e;}});e(d,"skipComments",function(a){for(var b=new JU.SB;null!=this.rd()&&(a&&0==this.line.length||0==this.line.indexOf("#"));)b.append(this.line).appendC("\n");
return b.toString()},"~B");e(d,"readVoxelVector",function(a){this.rd();var b=this.volumetricVectors[a];if(-2147483648==(this.voxelCounts[a]=this.parseIntStr(this.line)))this.next[0]=this.line.indexOf(" ");b.set(this.parseFloat(),this.parseFloat(),this.parseFloat());this.isAnisotropic&&this.setVectorAnisotropy(b)},"~N");e(d,"initializeSurfaceData",function(){this.downsampleFactor=this.params.downsampleFactor;this.nSkipZ=this.nSkipY=this.nSkipX=0;this.canDownsample&&0<this.downsampleFactor&&(this.nSkipX=
this.downsampleFactor-1,this.nSkipY=this.downsampleRemainders[2]+(this.downsampleFactor-1)*(this.nSkipZ=(this.nPointsZ-(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[2]),this.nSkipZ=this.downsampleRemainders[1]*this.nSkipZ+(this.downsampleFactor-1)*this.nSkipZ*((this.nPointsY-(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[1]));null!=this.params.thePlane?this.params.cutoff=0:this.isJvxl&&(this.params.cutoff=this.params.isBicolorMap||this.params.colorBySign?
0.01:this.getJVXLCutoff());this.nDataPoints=0;this.next[0]=0;this.line="";this.jvxlNSurfaceInts=0});e(d,"getJVXLCutoff",function(){return 0.5});l(d,"readSurfaceData",function(a){this.readSurfaceDataVFR(a)},"~B");e(d,"readSurfaceDataVFR",function(a){this.initializeSurfaceData();if(this.isProgressive&&!a||this.isJvxl)this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null,this.isJvxl&&(this.jvxlVoxelBitSet=this.getVoxelBitSet(this.nDataPoints));
else if(a&&this.volumeData.hasPlane()){this.volumeData.setVoxelMap();var b=this.volumeData.getToPlaneParameter();for(a=0;a<this.nPointsX;++a){for(var c=0;c<this.nPointsY;++c){for(var d=0;d<this.nPointsZ;++d){var e=this.recordData(this.getNextVoxelValue());this.volumeData.isNearPlane(a,c,d,b)&&this.volumeData.setVoxelMapValue(a,c,d,e);0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}else{this.voxelData=JU.AU.newFloat3(this.nPointsX,
-1);for(a=0;a<this.nPointsX;++a){b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(c=0;c<this.nPointsY;++c){e=x(this.nPointsZ,0);b[c]=e;for(d=0;d<this.nPointsZ;++d)e[d]=this.recordData(this.getNextVoxelValue()),0!=this.nSkipX&&this.skipVoxels(this.nSkipX);0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}this.volumeData.setVoxelDataAsArray(this.voxelData)},"~B");l(d,"getPlane",function(a){0==a&&this.initPlanes();if(this.getNCIPlanes)return this.getPlaneNCI(a);
a=this.getPlaneSR(a);null==this.qpc&&this.getPlaneVFR(a,!0);return a},"~N");e(d,"getPlaneNCI",function(a){var b;if(0==this.iPlaneNCI){this.qpc=J.api.Interface.getOption("quantum.NciCalculation",this.sg.atomDataServer,null);b=new J.atomdata.AtomData;b.modelIndex=-1;b.bsSelected=this.params.bsSelected;this.sg.fillAtomData(b,1);this.qpc.setupCalculation(this.volumeData,this.sg.params.bsSelected,null,null,b.atoms,-1,!0,null,this.params.parameters,this.params.testFlags);this.iPlaneNCI=1;this.qpc.setPlanes(this.yzPlanesRaw=
x(4,this.yzCount,0));if(this.hasColorData){this.getPlaneVFR(this.yzPlanesRaw[0],!1);this.getPlaneVFR(this.yzPlanesRaw[1],!1);b=this.yzPlanes[0];for(a=0;a<this.yzCount;a++)b[a]=NaN;return b}this.iPlaneNCI=-1}var c=this.qpc.getNoValue(),d=this.nPointsX-1;switch(this.iPlaneNCI){case -1:b=this.yzPlanes[a%2];d++;break;case 3:b=this.yzPlanesRaw[0];this.yzPlanesRaw[0]=this.yzPlanesRaw[1];this.yzPlanesRaw[1]=this.yzPlanesRaw[2];this.yzPlanesRaw[2]=this.yzPlanesRaw[3];this.yzPlanesRaw[3]=b;b=this.yzPlanesRaw[this.iPlaneNCI];
break;default:this.iPlaneNCI++,b=this.yzPlanesRaw[this.iPlaneNCI]}if(a<d){this.getPlaneVFR(b,!1);this.qpc.calcPlane(a,b=this.yzPlanes[a%2]);for(a=0;a<this.yzCount;a++)b[a]!=c&&this.recordData(b[a])}else for(a=0;a<this.yzCount;a++)b[a]=NaN;return b},"~N");e(d,"getPlaneVFR",function(a,b){try{for(var c=0,d=0;c<this.nPointsY;++c){for(var e=0;e<this.nPointsZ;++e){var g=this.getNextVoxelValue();b&&this.recordData(g);a[d++]=g;0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=
this.nSkipZ&&this.skipVoxels(this.nSkipZ)}catch(h){if(!$(h,Exception))throw h;}},"~A,~B");l(d,"getValue",function(a,b,c,d){return null!=this.boundingBox&&(this.volumeData.voxelPtToXYZ(a,b,c,this.ptTemp),this.ptTemp.x<this.boundingBox[0].x||this.ptTemp.x>this.boundingBox[1].x||this.ptTemp.y<this.boundingBox[0].y||this.ptTemp.y>this.boundingBox[1].y||this.ptTemp.z<this.boundingBox[0].z||this.ptTemp.z>this.boundingBox[1].z)?NaN:this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(d,"skipVoxels",function(a){for(;0<=
--a;)this.getNextVoxelValue()},"~N");e(d,"getVoxelBitSet",function(){return null},"~N");e(d,"getNextVoxelValue",function(){var a=0;if(1<this.nSurfaces&&!this.params.blockCubeData){for(var b=1;b<this.params.fileIndex;b++)this.nextVoxel();a=this.nextVoxel();for(b=this.params.fileIndex;b<this.nSurfaces;b++)this.nextVoxel()}else a=this.nextVoxel();return a});e(d,"nextVoxel",function(){var a=this.parseFloat();if(Float.isNaN(a)){for(;null!=this.rd()&&Float.isNaN(a=this.parseFloatStr(this.line)););null==
this.line&&(this.endOfData||JU.Logger.warn("end of file reading cube voxel data? nBytes="+this.nBytes+" nDataPoints="+this.nDataPoints+" (line):"+this.line),this.endOfData=!0,this.line="0 0 0 0 0 0 0 0 0 0")}return a});l(d,"gotoData",function(a,b){if(this.params.blockCubeData){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");for(var c=0;c<a;c++)this.skipData(b)}},"~N,~N");e(d,"skipData",function(a){this.skipDataVFR(a)},"~N");e(d,"skipDataVFR",function(a){for(var b=0;b<a;)b+=this.countData(this.rd())},
"~N");e(d,"countData",function(a){for(var b=0,c=0,d=a.length,e;c<d;){for(;c<d&&(" "==(e=a.charAt(c))||"\t"==e);)++c;for(c<d&&++b;c<d&&" "!=(e=a.charAt(c))&&"\t"!=e;)++c}return b},"~S");d.checkAtomLine=e(d,"checkAtomLine",function(a,b,c,d,e){0<=d.indexOf("ANGSTROMS")&&(b=!0);c=null==c?2147483647:JU.PT.parseInt(c);switch(c){case -2147483648:c=0;d=" "+d.substring(d.indexOf(" ")+1);break;case 2147483647:c=-2147483648;break;default:var g=""+c;d=d.substring(d.indexOf(g)+g.length)}b?0>d.indexOf("ANGSTROM")&&
(d+=" ANGSTROMS"):0>d.indexOf("BOHR")&&(d+=" BOHR");d=(-2147483648==c?"":(a?"+":"-")+Math.abs(c))+d+"\n";e.append(d);return b},"~B,~B,~S,~S,JU.SB");l(d,"getSurfacePointAndFraction",function(a,b,c,d,e,g,h,v,j,n,k,l,q){return this.getSPFv(a,b,c,d,e,g,h,v,j,n,k,l,q)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getSPFv",function(a,b,c,d,e,g,h,v,j,n,k,l,q){a=this.getSPF(a,b,c,d,e,g,h,v,j,n,k,l,q);if(null==this.qpc||Float.isNaN(a)||!this.hasColorData)return a;n=this.marchingCubes.getLinearOffset(h,
v,j,n);k=this.marchingCubes.getLinearOffset(h,v,j,k);return this.qpc.process(n,k,l[0])},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"scaleIsosurface",function(a){this.isScaledAlready||(this.isScaledAlready=!0,this.isAnisotropic&&this.setVolumetricAnisotropy(),Float.isNaN(a)||(JU.Logger.info("applying scaling factor of "+a),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[0],this.volumetricOrigin),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[1],this.volumetricOrigin),
this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[2],this.volumetricOrigin),this.volumetricVectors[0].scale(a),this.volumetricVectors[1].scale(a),this.volumetricVectors[2].scale(a)))},"~N");e(d,"swapXZ",function(){var a=this.volumetricVectors[0];this.volumetricVectors[0]=this.volumetricVectors[2];this.volumetricVectors[2]=a;a=this.voxelCounts[0];this.voxelCounts[0]=this.voxelCounts[2];this.voxelCounts[2]=a;this.params.insideOut=!this.params.insideOut})});R("J.jvxl.readers");S(["J.jvxl.readers.VolumeFileReader"],
"J.jvxl.readers.JvxlXmlReader","java.util.Hashtable JU.AU $.BS $.CU $.Lst $.P3 $.P4 $.PT $.SB J.jvxl.data.JvxlCoder $.MeshData J.jvxl.readers.XmlReader J.shapesurface.IsosurfaceMesh JU.C $.ColorEncoder $.Escape $.Logger".split(" "),function(){var d=I(function(){this.JVXL_VERSION="2.3";this.invalidatedVertexCount=this.excludedVertexCount=this.excludedTriangleCount=this.colorDataCount=this.edgeDataCount=this.surfaceDataCount=0;this.haveContourData=!1;this.xr=null;this.isXmlFile=!0;this.thisInside=!1;
this.bsVoxelBitSet=this.tempDataXml=null;this.includeValueNaN=!0;this.valueCount=0;this.valueRange=this.valueMin=NaN;this.colorPtr=this.fractionPtr=0;this.strFractionTemp="";this.haveReadColorData=!1;this.jvxlColorEncodingRead=null;T(this,arguments)},J.jvxl.readers,"JvxlXmlReader",J.jvxl.readers.VolumeFileReader);Y(d,function(){ja(this,J.jvxl.readers.JvxlXmlReader,[])});l(d,"init2",function(a,b){this.init2JXR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2JXR",function(a,
b){this.init2VFR(a,b);this.jvxlData.wasJvxl=this.isJvxl=!0;this.isXLowToHigh=this.canDownsample=!1;this.xr=new J.jvxl.readers.XmlReader(b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");l(d,"readVolumeData",function(a){if(!this.readVolumeDataVFR(a))return!1;this.strFractionTemp=this.jvxlEdgeDataRead;this.fractionPtr=0;return!0},"~B");l(d,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0>this.nPointsX||0>this.nPointsY||0>this.nPointsZ)return!0;try{this.gotoData(this.params.fileIndex-
1,this.nPointsX*this.nPointsY*this.nPointsZ);if(this.vertexDataOnly)return!0;this.volumeData.setMappingPlane(this.params.thePlane);this.readSurfaceData(a);this.volumeData.setMappingPlane(null);0<this.edgeDataCount&&(this.jvxlEdgeDataRead=this.jvxlReadFractionData("edge",this.edgeDataCount));this.params.bsExcluded=this.jvxlData.jvxlExcluded=Array(4);if(this.hasColorData=0<this.colorDataCount)this.jvxlColorDataRead=this.jvxlReadFractionData("color",this.colorDataCount);0<this.excludedVertexCount&&(this.jvxlData.jvxlExcluded[0]=
J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedVertexData",null,!1,!1)),this.xr.isNext("jvxlExcludedPlaneData")&&(this.jvxlData.jvxlExcluded[2]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedPlaneData",null,!1,!1))));0<this.excludedTriangleCount&&(this.jvxlData.jvxlExcluded[3]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedTriangleData",null,!1,!1)));0<this.invalidatedVertexCount&&(this.jvxlData.jvxlExcluded[1]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlInvalidatedVertexData",
null,!1,!1)));this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1));if(this.jvxlDataIsColorMapped&&0<this.jvxlData.nVertexColors){this.jvxlData.vertexColorMap=new java.util.Hashtable;var b=this.xr.getXmlData("jvxlVertexColorData",null,!0,!1),c=J.jvxl.readers.XmlReader.getXmlAttrib(b,"baseColor");this.jvxlData.baseColor=0<c.length?c:null;for(a=0;a<this.jvxlData.nVertexColors;a++){var d=this.xr.getXmlData("jvxlColorMap",b,!0,!1),e=J.jvxl.readers.XmlReader.getXmlAttrib(d,
"color"),g=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlColorMap",d,!1,!1));this.jvxlData.vertexColorMap.put(e,g)}}}catch(h){if($(h,Exception))return JU.Logger.error(h.toString()),!1;throw h;}return!0},"~B");l(d,"readParameters",function(){var a=this.xr.getXmlDataLF("jvxlFileTitle",null,!1,!1,!0);this.jvxlFileHeaderBuffer=JU.SB.newS(null==a?"":a);this.xr.toTag("jvxlVolumeData");a=this.tempDataXml=this.xr.getXmlData("jvxlVolumeData",null,!0,!1);this.volumetricOrigin.setT(this.xr.getXmlPoint(a,
"origin"));this.isAngstroms=!0;this.readVector(0);this.readVector(1);this.readVector(2);this.line=this.xr.toTag("jvxlSurfaceSet");this.nSurfaces=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(this.line,"count"));JU.Logger.info("jvxl file surfaces: "+this.nSurfaces);JU.Logger.info("using default edge fraction base and range");JU.Logger.info("using default color fraction base and range");this.cJvxlEdgeNaN=String.fromCharCode(this.edgeFractionBase+this.edgeFractionRange)});l(d,"getJVXLCutoff",
function(){return this.params.cutoff});e(d,"readVector",function(a){var b=this.xr.getXmlData("jvxlVolumeVector",this.tempDataXml,!0,!0);this.tempDataXml=this.tempDataXml.substring(this.tempDataXml.indexOf(b)+b.length);var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"count"));-2147483648==c&&(this.vertexDataOnly=!0);this.voxelCounts[a]=0>c?0:c;this.volumetricVectors[a].setT(this.xr.getXmlPoint(b,"vector"));this.isAnisotropic&&this.setVectorAnisotropy(this.volumetricVectors[a])},"~N");
l(d,"gotoData",function(a,b){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");this.vertexDataOnly=this.jvxlData.vertexDataOnly=0==b;for(var c=0;c<a;c++)this.jvxlSkipData(b,!0);this.xr.toTag("jvxlSurface");this.jvxlReadSurfaceInfo()},"~N,~N");e(d,"jvxlSkipData",function(){this.rd();this.xr.skipTag("jvxlSurface")},"~N,~B");e(d,"jvxlReadSurfaceInfo",function(){var a=this.xr.getXmlData("jvxlSurfaceInfo",null,!0,!0);this.isXLowToHigh=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isXLowToHigh").equals("true");
var b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"cutoff");0>b.indexOf(" ")?(this.jvxlCutoff=this.parseFloatStr(b),Double.isNaN(this.jvxlCutoff)||JU.Logger.info("JVXL read: cutoff "+this.jvxlCutoff)):(this.jvxlCutoffRange=this.parseFloatArrayStr(b),this.jvxlCutoff=this.jvxlCutoffRange[0],JU.Logger.info("JVXL read: cutoff "+JU.Escape.eAF(this.jvxlCutoffRange)));this.params.cutoff=this.jvxlCutoff;var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContourData"));this.haveContourData=0<c;this.params.isContoured=
this.jvxlData.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contoured").equals("true");this.params.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isModelConnected").equals("true");if(this.params.isContoured){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContours"));0>=d?d=0:(0>this.params.thisContour&&(this.params.thisContour=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"thisContour"))),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourValues"),
0<b.length&&(b=b.$replace("["," ").$replace("]"," "),this.jvxlData.contourValues=this.params.contoursDiscrete=this.parseFloatArrayStr(b),JU.Logger.info("JVXL read: contourValues "+JU.Escape.eAF(this.jvxlData.contourValues))),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourColors"),0<b.length&&(this.jvxlData.contourColixes=this.params.contourColixes=JU.C.getColixArray(b),this.jvxlData.contourColors=JU.C.getHexCodes(this.jvxlData.contourColixes),JU.Logger.info("JVXL read: contourColixes "+JU.C.getHexCodes(this.jvxlData.contourColixes))),
this.params.contourFromZero=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourFromZero").equals("true"));this.params.nContours=this.haveContourData?c:d}this.jvxlData.nVertexColors=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nVertexColors"));this.params.isBicolorMap=J.jvxl.readers.XmlReader.getXmlAttrib(a,"bicolorMap").equals("true");this.params.isBicolorMap&&(b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorPositive"),0<b.length&&(-2147483648==this.params.colorRgb&&-16776961==this.params.colorPos)&&
(this.params.colorPos=JU.CU.getArgbFromString(b)),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorNegative"),0<b.length&&(-2147483648==this.params.colorRgb&&-65536==this.params.colorNeg)&&(this.params.colorNeg=JU.CU.getArgbFromString(b)));if(this.params.isBicolorMap||this.params.colorBySign)this.jvxlCutoff=0;this.jvxlDataIsColorMapped=(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&(this.params.isBicolorMap||J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorMapped").equals("true"));
this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.XmlReader.getXmlAttrib(a,"precisionColor").equals("true");this.jvxlData.jvxlDataIsColorDensity=this.params.colorDensity=-2147483648==this.params.colorRgb&&J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorDensity").equals("true");this.jvxlData.jvxlDataIsColorDensity&&Float.isNaN(this.params.pointSize)&&(b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"pointSize"),0<b.length&&(this.jvxlData.pointSize=this.params.pointSize=this.parseFloatStr(b)));b=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"allowVolumeRender");this.jvxlData.allowVolumeRender=this.params.allowVolumeRender=0==b.length||b.equalsIgnoreCase("true");b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"plane");if(0<=b.indexOf("{")){this.params.thePlane=null;this.params.mapLattice=null;try{this.params.thePlane=JU.Escape.uP(b),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"maplattice"),JU.Logger.info("JVXL read: plane "+this.params.thePlane),0<=b.indexOf("{")&&(this.params.mapLattice=JU.Escape.uP(b),JU.Logger.info("JVXL read: mapLattice "+
this.params.mapLattice)),0==this.params.scale3d&&(this.params.scale3d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"scale3d"))),Float.isNaN(this.params.scale3d)&&(this.params.scale3d=0)}catch(e){if($(e,Exception))null==this.params.thePlane?(JU.Logger.error("JVXL Error reading plane definition -- setting to 0 0 1 0  (z=0)"),this.params.thePlane=JU.P4.new4(0,0,1,0)):JU.Logger.error("JVXL Error reading mapLattice definition -- ignored");else throw e;}this.edgeDataCount=this.surfaceDataCount=
0}else this.params.thePlane=null,this.surfaceDataCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nSurfaceInts")),this.edgeDataCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nBytesUncompressedEdgeData")),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"fixedLattice"),0<=b.indexOf("{")&&(this.jvxlData.fixedLattice=JU.Escape.uP(b));this.excludedVertexCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nExcludedVertexes"));this.excludedTriangleCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,
"nExcludedTriangles"));this.invalidatedVertexCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nInvalidatedVertexes"));b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"slabInfo");0<b.length&&(this.jvxlData.slabInfo=b);this.colorDataCount=Math.max(0,this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nBytesUncompressedColorData")));this.jvxlDataIs2dContour=null!=this.params.thePlane&&this.jvxlDataIsColorMapped;this.jvxlData.color=J.jvxl.readers.XmlReader.getXmlAttrib(a,"color");if(0==
this.jvxlData.color.length||0<=this.jvxlData.color.indexOf("null"))this.jvxlData.color="orange";this.jvxlData.translucency=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"translucency"));Float.isNaN(this.jvxlData.translucency)&&(this.jvxlData.translucency=0);b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"meshColor");0<b.length&&(this.jvxlData.meshColor=b);b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"rendering");0<b.length&&(this.jvxlData.rendering=b);this.jvxlData.colorScheme=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"colorScheme");0==this.jvxlData.colorScheme.length&&(this.jvxlData.colorScheme=this.jvxlDataIsColorMapped?"roygb":null);if(null==this.jvxlData.thisSet&&(b=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"set")),0<b&&(this.jvxlData.thisSet=new JU.BS,this.jvxlData.thisSet.set(b-1)),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"subset"),null!=b&&2<b.length&&(b=b.$replace("["," ").$replace("]"," ").trim().$plit(" "),0<b.length))){this.jvxlData.thisSet=new JU.BS;for(c=b.length;0<=--c;)this.jvxlData.thisSet.set(JU.PT.parseInt(b[c])-
1)}this.jvxlData.slabValue=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"slabValue"));this.jvxlData.isSlabbable=J.jvxl.readers.XmlReader.getXmlAttrib(a,"slabbable").equalsIgnoreCase("true");this.jvxlData.diameter=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"diameter"));-2147483648==this.jvxlData.diameter&&(this.jvxlData.diameter=0);this.jvxlDataIs2dContour&&(this.params.isContoured=!0);this.params.colorBySign&&(this.params.isBicolorMap=!0);var b=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"insideOut").equals("true"),g=d=c=NaN,h=NaN;this.jvxlDataIsColorMapped&&(c=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"dataMinimum")),d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"dataMaximum")),g=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"valueMappedToRed")),h=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"valueMappedToBlue")),Float.isNaN(c)&&(c=g=-1,d=h=1));this.jvxlSetColorRanges(c,d,g,h,b)});e(d,"jvxlSetColorRanges",function(a,b,c,
d,e){this.jvxlDataIsColorMapped&&(!Float.isNaN(a)&&!Float.isNaN(b)&&(0==b&&0==a&&(a=-1,b=1),this.params.mappedDataMin=a,this.params.mappedDataMax=b,JU.Logger.info("JVXL read: data_min/max "+this.params.mappedDataMin+"/"+this.params.mappedDataMax)),this.params.rangeDefined||(!Float.isNaN(c)&&!Float.isNaN(d)?(0==c&&0==d&&(c=-1,d=1),this.params.valueMappedToRed=Math.min(c,d),this.params.valueMappedToBlue=Math.max(c,d),this.params.isColorReversed=c>d):(this.params.valueMappedToRed=0,this.params.valueMappedToBlue=
1),this.params.rangeDefined=!0),JU.Logger.info("JVXL read: color red/blue: "+this.params.valueMappedToRed+"/"+this.params.valueMappedToBlue));this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.isColorReversed=this.params.isColorReversed;this.params.insideOut&&(e=!e);this.params.insideOut=this.jvxlData.insideOut=
e},"~N,~N,~N,~N,~B");l(d,"readSurfaceData",function(){this.thisInside=!this.params.isContoured;this.readSurfaceDataXML()||(this.tempDataXml=this.xr.getXmlData("jvxlEdgeData",null,!0,!1),this.bsVoxelBitSet=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlEdgeData",this.tempDataXml,!1,!1)),this.readSurfaceDataJXR())},"~B");e(d,"readSurfaceDataXML",function(){return this.vertexDataOnly?(this.getEncodedVertexData(),!0):null!=this.params.thePlane?(this.volumeData.setDataDistanceToPlane(this.params.thePlane),
this.setVolumeDataV(this.volumeData),this.params.cutoff=0,this.jvxlData.setSurfaceInfo(this.params.thePlane,this.params.mapLattice,0,""),this.jvxlData.scale3d=this.params.scale3d,!0):!1});e(d,"readSurfaceDataJXR",function(){this.readSurfaceDataVFR(!1);this.volumeData.setMappingPlane(null)});e(d,"jvxlReadFractionData",function(a){var b;try{if(a.equals("edge"))b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml,"data"));else{var c=this.xr.getXmlData("jvxlColorData",
null,!0,!1);this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.JvxlXmlReader.getEncoding(c).endsWith("2");b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(c,"data"))}}catch(d){if($(d,Exception))throw JU.Logger.error("Error reading "+a+" data "+d),new NullPointerException;throw d;}return b},"~S,~N");l(d,"getVoxelBitSet",function(a){if(null!=this.bsVoxelBitSet)return this.bsVoxelBitSet;var b=new JU.BS,c=0;if(0>=this.surfaceDataCount)return b;for(var d=0;c<a;){d=this.parseInt();
if(-2147483648==d&&(this.rd(),null==this.line||-2147483648==(d=this.parseIntStr(this.line))))this.endOfData||JU.Logger.error("end of file in JvxlReader? line="+this.line),this.endOfData=!0,d=1E4;this.thisInside=!this.thisInside;++this.jvxlNSurfaceInts;this.thisInside&&b.setBits(c,c+d);c+=d}return b},"~N");l(d,"getSurfacePointAndFraction",function(a,b,c,d,e,g,h,v,j,n,k,l,q){if(0>=this.edgeDataCount)return this.getSPFv(a,b,c,d,e,g,h,v,j,n,k,l,q);q.scaleAdd2(l[0]=this.jvxlGetNextFraction(this.edgeFractionBase,
this.edgeFractionRange,0.5),g,e);Float.isNaN(this.valueMin)&&this.setValueMinMax();return 0==this.valueCount||this.includeValueNaN&&Float.isNaN(l[0])?l[0]:this.getNextValue()},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getNextValue",function(){for(var a=NaN;this.colorPtr<this.valueCount&&Float.isNaN(a);){a=this.jvxlData.isJvxlPrecisionColor?J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(this.jvxlColorDataRead.charAt(this.colorPtr).charCodeAt(0),this.jvxlColorDataRead.charAt(this.colorPtr++ +
this.valueCount).charCodeAt(0),this.colorFractionBase,this.colorFractionRange):J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.jvxlColorDataRead.charAt(this.colorPtr++).charCodeAt(0),this.colorFractionBase,this.colorFractionRange,0.5);break}return this.valueMin+a*this.valueRange});e(d,"setValueMinMax",function(){this.valueCount=this.jvxlColorDataRead.length;this.jvxlData.isJvxlPrecisionColor&&(this.valueCount/=2);this.includeValueNaN=this.valueCount!=this.jvxlEdgeDataRead.length;this.valueMin=
!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToRed:3.4028235E38==this.params.mappedDataMin?0:this.params.mappedDataMin;this.valueRange=(!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToBlue:3.4028235E38==this.params.mappedDataMin?1:this.params.mappedDataMax)-this.valueMin;this.haveReadColorData=!0});e(d,"jvxlGetNextFraction",function(a,b,c){this.fractionPtr>=this.strFractionTemp.length&&(this.endOfData||JU.Logger.error("end of file reading compressed fraction data"),this.endOfData=
!0,this.strFractionTemp=""+String.fromCharCode(a),this.fractionPtr=0);return J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.strFractionTemp.charAt(this.fractionPtr++).charCodeAt(0),a,b,c)},"~N,~N,~N");l(d,"readColorData",function(){if(!this.jvxlDataIsColorMapped)return"";var a=this.jvxlData.vertexCount=this.meshData.vc,b=this.meshData.vcs,c=this.meshData.vvs;if("none".equals(this.jvxlColorEncodingRead)){this.jvxlData.vertexColors=u(a,0);for(var d=u(1,0),c=JU.PT.parseIntNext(this.jvxlColorDataRead,
d),c=Math.min(c,a),a=JU.PT.getTokens(this.jvxlColorDataRead.substring(d[0])),e=!1,g=this.jvxlData.translucency,h=0,d=0;d<c;d++)try{var l=J.jvxl.readers.JvxlXmlReader.getColor(a[d]);0==l?l=h:h=l;b[d]=JU.C.getColixTranslucent(this.jvxlData.vertexColors[d]=l);JU.C.isColixTranslucent(b[d])?e=!0:0!=g&&(b[d]=JU.C.getColixTranslucent3(b[d],!0,g))}catch(j){if($(j,Exception))JU.Logger.info("JvxlXmlReader: Cannot interpret color code: "+a[d]);else throw j;}e&&0==g&&(this.jvxlData.translucency=0.5);return"-"}null==
this.params.colorEncoder&&(this.params.colorEncoder=new JU.ColorEncoder(null,null));this.params.colorEncoder.setColorScheme(null,!1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);JU.Logger.info("JVXL reading color data mapped min/max: "+this.params.mappedDataMin+"/"+this.params.mappedDataMax+" for "+a+" vertices. using encoding keys "+this.colorFractionBase+" "+this.colorFractionRange);JU.Logger.info("mapping red--\x3eblue for "+
this.params.valueMappedToRed+" to "+this.params.valueMappedToBlue+" colorPrecision:"+this.jvxlData.isJvxlPrecisionColor);var n=Float.isNaN(this.valueMin);n&&this.setValueMinMax();var k=3.4028235E38,t=-3.4028235E38;if(null==b||b.length<a)this.meshData.vcs=b=da(a,0);e=l=0;this.params.colorBySign&&(e=JU.C.getColix(this.params.isColorReversed?this.params.colorNeg:this.params.colorPos),l=JU.C.getColix(this.params.isColorReversed?this.params.colorPos:this.params.colorNeg));for(var g=this.meshData.vertexIncrement,
q=3.4028235E38==this.params.mappedDataMin,d=0;d<a;d+=g)h=n?c[d]=this.getNextValue():c[d],q&&(h<k&&(k=h),h>t&&(t=h));q&&(this.params.mappedDataMin=k,this.params.mappedDataMax=t);if(null!=this.jvxlData.colorScheme){n=null!=this.marchingSquares&&this.params.isContoured;for(d=0;d<a;d+=g)h=c[d],n?this.marchingSquares.setContourData(d,h):(h=!this.params.colorBySign?this.params.colorEncoder.getColorIndex(h):(this.params.isColorReversed?0<h:0>=h)?l:e,b[d]=JU.C.getColixTranslucent3(h,!0,this.jvxlData.translucency))}return this.jvxlColorDataRead+
"\n"});d.getColor=e(d,"getColor",function(a){var b=0;try{switch(a.charAt(0).charCodeAt(0)){case 91:b=JU.CU.getArgbFromString(a);break;case 48:b=JU.PT.parseIntRadix(a.substring(2),16);break;default:b=JU.PT.parseIntRadix(a,10)}}catch(c){if(!$(c,Exception))throw c;}return b},"~S");e(d,"getEncodedVertexData",function(){var a=this.xr.getXmlData("jvxlSurfaceData",null,!0,!1);this.jvxlDecodeVertexData(this.xr.getXmlData("jvxlVertexData",a,!0,!1),!1);var b=this.xr.getXmlData("jvxlTriangleData",a,!0,!1),c=
this.xr.getXmlData("jvxlTriangleEdgeData",a,!0,!1),d=this.xr.getXmlData("jvxlPolygonColorData",a,!1,!1);this.jvxlDecodeTriangleData(b,c,d);a=this.xr.getXmlData("jvxlColorData",a,!0,!1);this.jvxlColorEncodingRead=J.jvxl.readers.JvxlXmlReader.getEncoding(a);this.jvxlData.isJvxlPrecisionColor=this.jvxlColorEncodingRead.endsWith("2");a=this.getData(a,"jvxlColorData");this.jvxlColorDataRead=this.jvxlColorEncodingRead.equals("none")?a:J.jvxl.data.JvxlCoder.jvxlDecompressString(a);this.jvxlDataIsColorMapped=
(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&0<this.jvxlColorDataRead.length;this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1))});e(d,"getData",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data");0==c.length&&(c=this.xr.getXmlData(b,a,!1,!1));return c},"~S,~S");d.getEncoding=e(d,"getEncoding",function(a){if(0<J.jvxl.readers.XmlReader.getXmlAttrib(a,"len").length)return"";a=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"encoding");return 0==a.length?"none":a},"~S");e(d,"jvxlDecodeVertexData",function(a,b){var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));b||JU.Logger.info("Reading "+c+" vertices");var d=3*c,e=b?Array(c):null,g,h=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data"),l=J.jvxl.readers.JvxlXmlReader.getEncoding(a);if("none".equals(l)){0==h.length&&(h=this.xr.getXmlData("jvxlVertexData",a,!1,!1));d=JU.PT.parseFloatArray(h);d[0]!=3*c&&JU.Logger.info("JvxlXmlReader: vertexData count="+
A(d[0])+"; expected "+3*c);h=0;for(l=1;h<c;h++){var j=JU.P3.new3(d[l++],d[l++],d[l++]);b?e[h]=j:this.addVertexCopy(j,0,h,!1)}}else{var n=this.xr.getXmlPoint(a,"min"),k=this.xr.getXmlPoint(a,"max");k.sub(n);var t=this.jvxlData.colorFractionBase,q=this.jvxlData.colorFractionRange,u=J.jvxl.data.JvxlCoder.jvxlDecompressString(h);0==u.length&&(u=this.xr.getXmlData("jvxlVertexData",a,!1,!1));h=0;for(l=-1;h<c;h++)j=new JU.P3,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charAt(++l).charCodeAt(0),
u.charAt(l+d).charCodeAt(0),t,q),j.x=n.x+g*k.x,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charAt(++l).charCodeAt(0),u.charAt(l+d).charCodeAt(0),t,q),j.y=n.y+g*k.y,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charAt(++l).charCodeAt(0),u.charAt(l+d).charCodeAt(0),t,q),j.z=n.z+g*k.z,b?e[h]=j:this.addVertexCopy(j,0,h,!1)}return e},"~S,~B");e(d,"jvxlDecodeTriangleData",function(a,b,c){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));if(!(0>d)){var e=u(1,0),g=null==
c?-1:1,h=0;JU.Logger.info("Reading "+d+" triangles");var l=J.jvxl.readers.JvxlXmlReader.getEncoding(a);a=this.getData(a,"jvxlTriangleData");b=this.getData(b,"jvxlTriangleEdgeData");var j=u(3,0),n=u(1,0),k=null,t=7,q=!"none".equals(l);if(q)a=J.jvxl.data.JvxlCoder.jvxlDecompressString(a),b=J.jvxl.data.JvxlCoder.jvxlDecompressString(b).trim(),l=b.length==d;else{var x=JU.PT.parseIntNext(a,n);(l=0<b.length)?(k=u(1,0),JU.PT.parseIntNext(b,k)):0<x&&JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count="+
x+"; expected "+d)}for(var w=x=0,A=0,G=-1;x<d;){if(q){var D=a.charAt(++G);switch(D.charCodeAt(0)){case 33:D=0;break;case 43:case 46:case 32:case 10:case 13:case 9:case 44:continue;case 45:case 48:case 49:case 50:case 51:case 52:case 53:case 54:case 55:case 56:case 57:n[0]=G;D=JU.PT.parseIntNext(a,n);G=n[0]-1;break;default:D=D.charCodeAt(0)-92}w+=D}else w=JU.PT.parseIntNext(a,n)-1;j[A]=w;if(3==++A){A=0;if(l&&(t=null==k?b.charAt(x).charCodeAt(0)-48:JU.PT.parseIntNext(b,k),0>t||7<t))t=7;0==--g&&(g=JU.PT.parseIntNext(c,
e),D=JU.PT.parseIntNext(c,e),-2147483648==D?g=0:h=D|4278190080);this.addTriangleCheck(j[0],j[1],j[2],t,h,!1,h);x++}}}},"~S,~S,~S");e(d,"jvxlDecodeContourData",function(a,b){var c=new JU.Lst,d=new JU.SB,e=new JU.SB,g=-1;a.vContours=null;if(null!=b){for(;0<=(g=b.indexOf("<jvxlContour",g+1));){var h=new JU.Lst,l=this.xr.getXmlData("jvxlContour",b.substring(g),!0,!1),j=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(l,"value"));d.append(" ").appendF(j);var n=J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(l,
"color")),k=JU.C.getColix(n);e.append(" ").append(JU.Escape.escapeColor(n));var t=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(l,"data")),q=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour",l,!1,!1)),l=q.length();J.shapesurface.IsosurfaceMesh.setContourVector(h,l,q,j,k,n,JU.SB.newS(t));c.addLast(h)}l=c.size();if(0<l){a.vContours=JU.AU.createArrayOfArrayList(l);a.contourColixes=this.params.contourColixes=da(l,0);a.contourValues=this.params.contoursDiscrete=
x(l,0);for(g=0;g<l;g++)a.vContours[g]=c.get(g),a.contourValues[g]=a.vContours[g].get(2).floatValue(),a.contourColixes[g]=a.vContours[g].get(3)[0];a.contourColors=JU.C.getHexCodes(a.contourColixes);JU.Logger.info("JVXL read: "+l+" discrete contours");JU.Logger.info("JVXL read: contour values: "+d);JU.Logger.info("JVXL read: contour colors: "+e)}}},"J.jvxl.data.JvxlData,~S");l(d,"postProcessVertices",function(){var a=this.params.bsExcluded[1];null!=a&&(null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,
1,null),this.meshData.invalidateVertices(a),null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,4,null),this.meshData=new J.jvxl.data.MeshData),this.updateTriangles())})});R("J.rendersurface");S(["J.render.MeshRenderer"],"J.rendersurface.IsosurfaceRenderer",["JU.V3","JU.C","$.Normix"],function(){var d=I(function(){this.isBicolorMap=this.iHideBackground=!1;this.nError=this.backgroundColix=0;this.isosurface=this.imesh=this.vertexValues=null;this.showNumbers=this.iShowNormals=
this.isNavigationMode=!1;this.showKey=null;this.hasColorRange=!1;this.meshScale=-1;this.globalSlabValue=this.mySlabValue=0;T(this,arguments)},J.rendersurface,"IsosurfaceRenderer",J.render.MeshRenderer);l(d,"render",function(){return this.renderIso()});e(d,"renderIso",function(){this.setGlobals();for(var a=this.isosurface.meshCount;0<=--a;)if(this.mesh=this.imesh=this.isosurface.meshes[a],null==this.imesh.connectedAtoms||this.vwr.ms.at[this.imesh.connectedAtoms[0]].checkVisible())this.hasColorRange=
!1,this.renderMeshSlab()&&(this.renderInfo(),this.isExport&&this.isGhostPass&&(this.exportPass=1,this.renderMeshSlab(),this.exportPass=2));return this.needTranslucent});e(d,"setGlobals",function(){this.needTranslucent=!1;this.antialias=this.g3d.isAntialiased();this.iShowNormals=this.vwr.getBoolean(603979965);this.showNumbers=this.vwr.getBoolean(603979964);this.isosurface=this.shape;this.exportPass=this.isExport?2:0;this.isNavigationMode=this.vwr.getBoolean(603979889);this.showKey=this.vwr.getBoolean(603979867)?
Boolean.TRUE:null;this.isosurface.keyXy=null;this.meshScale=-1;this.globalSlabValue=this.vwr.gdata.slab;this.mySlabValue=this.isNavigationMode?A(this.tm.getNavigationOffset().z):2147483647});e(d,"renderInfo",function(){if(!this.isExport&&this.hasColorRange&&!(null==this.imesh.colorEncoder||Boolean.TRUE!==this.showKey)){this.showKey=Boolean.FALSE;var a=null,b=null,c=null,d=0,e=0;if(this.imesh.showContourLines)if(c=this.imesh.getContours(),null==c){b=this.imesh.jvxlData.contourColixes;if(null==b)return;
d=b.length}else d=c.length,e=1;else a=this.imesh.colorEncoder.getColorSchemeArray(this.imesh.colorEncoder.currentPalette),d=null==a?0:a.length,e=2;if(!(2>d)){var g=this.antialias?2:1,h=this.vwr.getScreenHeight()*g,l=G(G(h/2)/(d-1)),h=3*G(h/4)-l,j=10*g,n=20*g;this.isosurface.keyXy=u(-1,[G(j/g),0,G((j+n)/g),G((h+l)/g),G(l/g)]);for(var k=0;k<d;k++,h-=l){switch(e){case 0:if(!this.g3d.setC(b[k]))return;break;case 1:if(!this.g3d.setC(c[k].get(3)[0]))return;break;case 2:this.vwr.gdata.setColor(a[k])}this.g3d.fillTextRect(j,
h,5,-2147483648,n,l)}this.isosurface.keyXy[1]=G((h+l)/g)}}});e(d,"renderMeshSlab",function(){this.volumeRender=this.imesh.jvxlData.colorDensity&&this.imesh.jvxlData.allowVolumeRender;var a=this.mySlabValue;this.frontOnly=this.mesh.frontOnly||26==this.shapeID;this.isShell=this.mesh.isShell&&26!=this.shapeID;if(!this.isNavigationMode&&(this.meshSlabValue=this.imesh.jvxlData.slabValue,-2147483648!=this.meshSlabValue&&this.imesh.jvxlData.isSlabbable)){for(var b=this.imesh.jvxlData.boundingBox,a=3.4028235E38,
c=1.4E-45,d=b.length;0<=--d;)this.pt2f.setT(b[d]),this.tm.transformPt3f(this.pt2f,this.pt2f),this.pt2f.z<a&&(a=this.pt2f.z),this.pt2f.z>c&&(c=this.pt2f.z);a=Math.round(a+(c-a)*(100-this.meshSlabValue)/100);this.frontOnly=(new Boolean(this.frontOnly&100<=this.meshSlabValue)).valueOf();this.isShell=(new Boolean(this.isShell&100<=this.meshSlabValue)).valueOf()}b=this.vwr.gdata.translucentCoverOnly;this.vwr.gdata.translucentCoverOnly=this.frontOnly||!this.vwr.getBoolean(603979967);this.thePlane=this.imesh.jvxlData.jvxlPlane;
this.vertexValues=this.mesh.vvs;2147483647!=a&&this.imesh.jvxlData.isSlabbable?(this.g3d.setSlab(a),a=this.renderMesh2(this.mesh),this.g3d.setSlab(this.globalSlabValue)):a=this.renderMesh2(this.mesh);this.vwr.gdata.translucentCoverOnly=b;return a});l(d,"render2",function(a){if(this.volumeRender)this.renderPoints();else{switch(this.imesh.dataType){case 70:this.renderLonePair(!1);return;case 71:this.renderLonePair(!0);return}this.isBicolorMap=this.imesh.jvxlData.isBicolorMap;this.render2b(a);this.g3d.setC(4)&&
this.imesh.showContourLines&&this.renderContourLines()}},"~B");e(d,"renderLonePair",function(a){this.pt2f.setT(this.vertices[1]);this.tm.transformPt3f(this.pt2f,this.pt2f);var b=A(this.vwr.tm.scaleToScreen(A(this.pt2f.z),100));1>b&&(b=1);if(!a){var c=new JU.V3;a=new JU.V3;this.pt1f.setT(this.vertices[0]);this.tm.transformPt3f(this.pt1f,this.pt1f);c.sub2(this.pt2f,this.pt1f);a.set(c.x,c.y,c.z+1);a.cross(a,c);a.normalize();c=this.vwr.tm.scaleToScreen(A(this.pt1f.z),100);a.scale(c);this.pt1f.add2(this.pt2f,
a);this.pt2f.sub(a);this.screens[0].set(Math.round(this.pt1f.x),Math.round(this.pt1f.y),Math.round(this.pt1f.z));this.g3d.fillSphereI(b,this.screens[0])}this.screens[1].set(Math.round(this.pt2f.x),Math.round(this.pt2f.y),Math.round(this.pt2f.z));this.g3d.fillSphereI(b,this.screens[1])},"~B");e(d,"renderContourLines",function(){var a=this.imesh.getContours();if(null==a)null!=this.imesh.jvxlData.contourValues&&(this.hasColorRange=!0);else{this.hasColorRange=0==this.mesh.meshColix;for(var b=a.length;0<=
--b;){var c=a[b];if(!(6>c.size())){this.colix=0==this.mesh.meshColix?c.get(3)[0]:this.mesh.meshColix;if(!this.g3d.setC(this.colix))break;for(var d=c.size()-1,e=this.getDiameter(),g=6;g<d;g++){var h=c.get(g),l=c.get(++g);if(Float.isNaN(h.x)||Float.isNaN(l.x))break;this.tm.transformPtScrT3(h,this.pt1f);this.tm.transformPtScrT3(l,this.pt2f);this.pt1f.z-=2;this.pt2f.z-=2;!this.antialias&&1==e?this.g3d.drawLineAB(this.pt1f,this.pt2f):this.g3d.fillCylinderBits(1,e,this.pt1f,this.pt2f)}}}}});l(d,"renderPoints",
function(){try{this.volumeRender&&this.g3d.volumeRender(!0);var a=(this.volumeRender||0==this.mesh.pc)&&this.selectedPolyOnly,b=this.imesh.vertexIncrement,c;0>=this.mesh.diameter?(c=this.vwr.getInt(553648140),this.frontOnly=this.isShell=!1):c=G(this.vwr.getScreenDim()/(this.volumeRender?50:100));var d=Math.round(Float.isNaN(this.mesh.volumeRenderPointSize)?150:1E3*this.mesh.volumeRenderPointSize);1>c&&(c=1);var e=this.showNumbers?G(this.vwr.getScreenWidth()/2):0,g=this.showNumbers?G(this.vwr.getScreenHeight()/
2):0;this.showNumbers&&this.vwr.gdata.setFontBold("Monospaced",24);for(var h=!this.imesh.hasGridPoints||0>this.imesh.firstRealVertex?0:this.imesh.firstRealVertex;h<this.vertexCount;h+=b)if(!(null!=this.vertexValues&&Float.isNaN(this.vertexValues[h])||this.frontOnly&&!this.isVisibleNormix(this.normixes[h])||null!=this.imesh.jvxlData.thisSet&&!this.imesh.jvxlData.thisSet.get(this.mesh.vertexSets[h])||!this.mesh.isColorSolid&&null!=this.mesh.vcs&&!this.setColix(this.mesh.vcs[h])||this.haveBsDisplay&&
!this.mesh.bsDisplay.get(h)||a&&!this.bsPolygons.get(h))){this.hasColorRange=!0;if(this.showNumbers&&10<this.screens[h].z&&150>Math.abs(this.screens[h].x-e)&&150>Math.abs(this.screens[h].y-g)){var l=h+(this.mesh.isColorSolid?"":" "+this.mesh.vvs[h]);this.g3d.setC(4);this.g3d.drawStringNoSlab(l,null,this.screens[h].x,this.screens[h].y,this.screens[h].z-30,0)}this.volumeRender?(c=A(this.vwr.tm.scaleToScreen(this.screens[h].z,d)),1>c&&(c=1),this.g3d.volumeRender4(c,this.screens[h].x,this.screens[h].y,
this.screens[h].z)):this.g3d.fillSphereI(c,this.screens[h])}if(3==b){this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(12,!0,0.5):12);for(h=1;h<this.vertexCount;h+=3)this.g3d.fillCylinder(3,G(c/4),this.screens[h],this.screens[h+1]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(21,!0,0.5):21);for(h=1;h<this.vertexCount;h+=3)this.g3d.fillSphereI(c,this.screens[h]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(7,!0,0.5):7);for(h=2;h<this.vertexCount;h+=3)this.g3d.fillSphereI(c,
this.screens[h])}}catch(j){}this.volumeRender&&this.g3d.volumeRender(!1)});l(d,"renderTriangles",function(a,b,c){this.g3d.addRenderer(1073742182);var d=this.mesh.pis;this.colix=this.isGhostPass?this.mesh.slabColix:!a&&0!=this.mesh.meshColix?this.mesh.meshColix:this.mesh.colix;var e=!a&&0!=this.mesh.meshColix?null:this.mesh.vcs;this.isTranslucentInherit&&(this.colix=JU.C.copyColixTranslucency(this.mesh.slabColix,this.mesh.colix));this.g3d.setC(this.colix);c&&(this.frontOnly&&a&&(this.frontOnly=!1),
this.bsPolygonsToExport.clearAll());1==this.exportType&&(this.frontOnly=!1);var g=this.isGhostPass&&!this.isBicolorMap||null==e||this.mesh.isColorSolid,h=this.isGhostPass&&!this.isBicolorMap||null==e||!a&&0!=this.mesh.meshColix,l=this.colix;null!=this.imesh.jvxlData.jvxlPlane&&(!g&&!a&&this.mesh.fillTriangles)&&(g=!0,l=4);var j=g&&null!=this.mesh.pcs;j&&(!a&&this.mesh.fillTriangles)&&(j=!1);var n=this.imesh.jvxlData.contourColixes;this.hasColorRange=!g&&!this.isBicolorMap;for(var k=this.getDiameter(),
t=this.mesh.pc;0<=--t;){var q=d[t];if(!(null==q||this.selectedPolyOnly&&!this.bsPolygons.get(t))){var u=q[0],w=q[1],x=q[2];if(!(null!=this.imesh.jvxlData.thisSet&&null!=this.mesh.vertexSets&&!this.imesh.jvxlData.thisSet.get(this.mesh.vertexSets[u]))&&(!this.haveBsDisplay||this.mesh.bsDisplay.get(u)&&this.mesh.bsDisplay.get(w)&&this.mesh.bsDisplay.get(x))){var A=this.normixes[u],D=this.normixes[w],G=this.normixes[x],I=this.frontOnly||this.isShell?this.checkFront(A,D,G):7;if(!(a&&0==I)){var P,K,F;if(g){if(j&&
t<this.mesh.pcs.length){P=this.mesh.pcs[t];if(0==P)continue;l=P}b&&(l=Math.round(10*Math.random())+5);P=K=F=l}else if(P=e[u],K=e[w],F=e[x],this.isBicolorMap){if(P!=K||K!=F)continue;this.isGhostPass&&(P=K=F=JU.C.copyColixTranslucency(this.mesh.slabColix,P))}if(a)c?this.bsPolygonsToExport.set(t):(w==x?(this.setColix(P),u==w?this.g3d.fillSphereI(k,this.screens[u]):this.g3d.fillCylinder(3,k,this.screens[u],this.screens[w])):this.mesh.colorsExplicit?(this.vwr.gdata.setColor(q[4]),P=JU.C.copyColixTranslucency(this.mesh.colix,
2047),this.g3d.setC(P),this.g3d.fillTriangle3CN(this.screens[u],P,A,this.screens[w],P,D,this.screens[x],P,G)):(this.isTranslucentInherit&&null!=e&&(P=JU.C.copyColixTranslucency(this.mesh.slabColix,e[u]),K=JU.C.copyColixTranslucency(this.mesh.slabColix,e[w]),F=JU.C.copyColixTranslucency(this.mesh.slabColix,e[x])),this.g3d.fillTriangle3CN(this.screens[u],P,A,this.screens[w],K,D,this.screens[x],F,G)),this.iShowNormals&&this.renderNormals());else if(I&=q[3],0!=I){b&&(I=7);this.pt1i.setT(this.screens[u]);
this.pt2i.setT(this.screens[w]);this.pt3i.setT(this.screens[x]);this.pt1i.z-=2;this.pt2i.z-=2;this.pt3i.z-=2;if(!h)if(j)this.g3d.setC(this.mesh.fillTriangles?4:n[q[4]%n.length]);else{this.drawTriangle(this.pt1i,P,this.pt2i,K,this.pt3i,F,I,k);continue}this.drawTriangle(this.pt1i,l,this.pt2i,l,this.pt3i,l,I,k)}}}}}c&&this.exportSurface(g?l:0)},"~B,~B,~B");e(d,"getDiameter",function(){var a;0>=this.mesh.diameter?(a=0>this.meshScale?this.meshScale=this.vwr.getInt(553648149):this.meshScale,this.antialias&&
(a*=2)):a=G(this.vwr.getScreenDim()/100);1>a&&(a=1);return a});e(d,"renderNormals",function(){if(this.g3d.setC(JU.C.copyColixTranslucency(this.mesh.colix,8))){this.vwr.gdata.setFontBold("Monospaced",24);for(var a=JU.Normix.getVertexVectors(),b=this.vertexCount;0<=--b;)if(!(null!=this.vertexValues&&Float.isNaN(this.vertexValues[b]))){this.pt1f.setT(this.vertices[b]);var c=this.mesh.normixes[b];0<=c&&(this.pt2f.scaleAdd2(0.3,a[c],this.pt1f),this.tm.transformPtScrT3(this.pt2f,this.pt2f),this.pt1f.set(this.screens[b].x,
this.screens[b].y,this.screens[b].z),this.g3d.drawLineAB(this.pt1f,this.pt2f))}}})})})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,
Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAB,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,
Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.cloneFinals);
