(function(eb,cc,dc,ec,D,fc,O,T,F,P,H,y,gc,W,hc,Y,u,Z,w,Aa,ha,da,g,Ha,ma,na,$,ta,va,ua,B,ic,jc,Ia,kc,lc,mc,nc,Ja,fb,oc,pc,qc,rc,sc,tc,uc,vc,wc,xc,yc,zc,Ac,Bc,Cc,Dc,Ec,Fc,e,m){O("JS");F(null,"JS.ScriptExt",["JU.AU"],function(){c$=H(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;P(this,arguments)},JS,"ScriptExt");e(c$,"init",function(a){this.e=a;this.vwr=this.e.vwr;return this},"~O");e(c$,"atomExpressionAt",function(a){return this.e.atomExpressionAt(a)},"~N");e(c$,"checkLength",
function(a){this.e.checkLength(a)},"~N");e(c$,"error",function(a){this.e.error(a)},"~N");e(c$,"invArg",function(){this.e.invArg()});e(c$,"invPO",function(){this.error(23)});e(c$,"getShapeProperty",function(a,b){return this.e.getShapeProperty(a,b)},"~N,~S");e(c$,"paramAsStr",function(a){return this.e.paramAsStr(a)},"~N");e(c$,"centerParameter",function(a){return this.e.centerParameter(a,null)},"~N");e(c$,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");e(c$,"getPoint3f",function(a,
b){return this.e.getPoint3f(a,b,!0)},"~N,~B");e(c$,"intParameter",function(a){return this.e.intParameter(a)},"~N");e(c$,"isFloatParameter",function(a){switch(this.e.tokAt(a)){case 2:case 3:return!0}return!1},"~N");e(c$,"setShapeProperty",function(a,b,c){this.e.setShapeProperty(a,b,c)},"~N,~S,~O");e(c$,"showString",function(a){this.e.showString(a)},"~S");e(c$,"stringParameter",function(a){return this.e.stringParameter(a)},"~N");e(c$,"getToken",function(a){return this.e.getToken(a)},"~N");e(c$,"tokAt",
function(a){return this.e.tokAt(a)},"~N");e(c$,"setShapeId",function(a,b,c){c&&this.invArg();b=this.e.setShapeNameParameter(b).toLowerCase();this.setShapeProperty(a,"thisID",b);return b},"~N,~N,~B");e(c$,"getColorTrans",function(a,b,c,d){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)?d[0]=a.getArgbParam(++b):1073742333==this.tokAt(b+
1)?(d[0]=0,a.iToken=b+1):3.4028235E38==c?this.invArg():d[0]=-2147483648;return c},"JS.ScriptEval,~N,~B,~A");e(c$,"finalizeObject",function(a,b,c,d,j,h,f,e){j&&this.setShapeProperty(a,"set",h);-2147483648!=b&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(b),e);3.4028235E38!=c&&this.e.setShapeTranslucency(a,"","translucent",c,e);0!=d&&this.setShapeProperty(a,"scale",Integer.$valueOf(d));0<f&&(this.e.setMeshDisplayProperty(a,f,0)||this.invArg())},"~N,~N,~N,~N,~B,~O,~N,JU.BS");e(c$,"getIntArray2",
function(a){a=this.e.getToken(a).getList();for(var b=JU.AU.newInt2(a.size()),c=b.length;0<=--c;){var d=a.get(c).getList();null==d&&this.invArg();b[c]=u(d.size(),0);for(var j=b[c].length;0<=--j;)b[c][j]=d.get(j).intValue}return b},"~N");e(c$,"getAllPoints",function(a,b){var c=null,d=null;try{switch(this.e.tokAt(a)){case 7:c=this.e.getPointArray(a,-1,!1);break;case 12290:case 10:case 1073742325:d=this.atomExpressionAt(a)}null==c&&(null==d&&(d=this.vwr.getAllAtoms()),c=this.bsToArray(d))}catch(j){if(!Y(j,
Exception))throw j;}(null==c||c.length<b)&&this.invArg();return c},"~N,~N");e(c$,"bsToArray",function(a){for(var b=Array(a.cardinality()),c=a.nextSetBit(0),d=0;0<=c;c=a.nextSetBit(c+1))b[d++]=this.vwr.ms.at[c];return b},"JU.BS")});O("JS");F(["JS.ScriptExt"],"JS.IsoExt","java.lang.Boolean $.Float $.Short 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 $.Triangulator JV.JC".split(" "),
function(){c$=Aa(JS,"IsoExt",JS.ScriptExt);W(c$,function(){da(this,JS.IsoExt,[])});m(c$,"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(c$,"dipole",function(){var a=this.e,b=null,c=null,d=!1,j=!1,h=!1,f=!1,e=null;a.sm.loadShape(17);
if(!(1073742001==this.tokAt(1)&&this.listIsosurface(17)))if(this.setShapeProperty(17,"init",null),1==this.slen)this.setShapeProperty(17,"thisID",null);else{for(var k=1;k<this.slen;++k){c=b=null;switch(this.getToken(k).tok){case 1073742327:b="all";f=!0;break;case 1073742335:b="on";break;case 1073742334:b="off";break;case 12291:b="delete";break;case 2:case 3:b="value";c=Float.$valueOf(this.floatParameter(k));break;case 10:10==this.tokAt(k+1)?this.setShapeProperty(17,"startSet",this.atomExpressionAt(k++)):
b="atomBitset";case 1073742325:null==b&&(b=d||j?"endSet":"startSet");c=e=this.atomExpressionAt(k);k=a.iToken;0==this.tokAt(k+1)&&"startSet"===b&&(b="atomBitset");f=d=!0;break;case 1073742332:case 8:c=this.getPoint3f(k,!0);k=a.iToken;b=d||j?"endCoord":"startCoord";j=!0;break;case 1677721602:b="bonds";f=!0;break;case 4102:f=!0;b="calculate";a.isAtomExpression(k+1)&&(c=e=this.atomExpressionAt(++k),k=a.iToken);break;case 1073741974:this.setShapeId(17,++k,h);k=a.iToken;break;case 1275069442:b="cross";
c=Boolean.TRUE;break;case 1073742040:b="cross";c=Boolean.FALSE;break;case 1073742066:this.isFloatParameter(k+1)?(c=this.floatParameter(++k),2==a.theTok?(b="offsetPercent",c=Integer.$valueOf(y(c))):(b="offset",c=Float.$valueOf(c))):(b="offsetPt",c=this.centerParameter(++k),k=a.iToken);break;case 1073742068:b="offsetSide";c=Float.$valueOf(this.floatParameter(++k));break;case 1073742188:b="value";c=Float.$valueOf(this.floatParameter(++k));break;case 1073742196:b="width";c=Float.$valueOf(this.floatParameter(++k));
break;default:if(268435633==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(17,k,h);k=a.iToken;break}this.invArg()}h=12291!=a.theTok&&4102!=a.theTok;f&&(this.chk||a.getPartialCharges(e),f=!1);null!=b&&this.setShapeProperty(17,b,c)}(j||d)&&this.setShapeProperty(17,"set",null)}});e(c$,"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,d=!1,j=!1,h=!1,f,e=null,k=0,t=3.4028235E38,l=u(-1,[-2147483648]),g=0,p="",N=0,v=null,qa=this.initIsosurface(22),m=(f=null!=qa)&&null==this.getShapeProperty(22,"ID"),w=null,Ka=0,oa=-1,aa=-1,I=!1,E=0,A=null,r=a.iToken;r<this.slen;++r){var K=null,G=null,E=this.getToken(r).tok;switch(E){case 134217763:switch(E=this.getToken(r+(1073741864==this.tokAt(r+1)?2:1)).tok){case 1814695966:case 1678381065:k=E;j=!0;continue;case 1073742330:++r;K="intersect";G=a.objectNameParameter(++r);
b=j=!0;break;default:this.invArg()}break;case 1073741864:I=!0;aa==r-1&&aa++;switch(this.tokAt(r+1)){case 134217750:case 1073741998:case 1678381065:continue;default:this.invArg()}break;case 1073741994:case 1814695966:case 1678381065:var M=f=A=null;switch(E){case 1678381065:switch(this.tokAt(r+1)){case 1073741864:switch(this.tokAt(r+2)){case 134217750:case 1073741998:break;default:I=!0,r++}break;case 10:case 1073742325:M=a.getAtomsStartingAt(r+1),r=a.iToken}break;case 1814695966:I&&this.invArg(),a.isArrayParameter(r+
1)&&(f=this.vwr.getSymTemp().getUnitCell(a.getPointArray(r+1,-1,!1),!1,null),r=a.iToken),1073741994==this.tokAt(r+1)&&(1814695966==k&&(k=1073741994),++r,A=a.checkHKL(a.getPointOrPlane(++r,3)),r=a.iToken)}if(this.chk)break;null!=M?I&&(f=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,"array",M),!1,null)):I?f=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,"array",null),!1,null):1814695966==E&&null==f&&(f=this.vwr.getCurrentUnitCell());if(null==A)e=this.getBoxPoints(null!=
f?1814695966:E,f,M,g/100);else{M=JU.Measure.getLatticePoints(f.getLatticeCentering(),y(A.x),y(A.y),y(A.z));e=Array(M.size());for(E=0;E<M.size();E++)e[E]=M.get(E),f.toCartesian(e[E],!0)}I=!1;if(!j){null==e&&this.invArg();K="polygon";f=new JU.Lst;f.addLast(e);null==A?(this.vwr.getTriangulator(),f.addLast(JU.Triangulator.fullCubePolygon)):f.addLast(null);G=f;b=!0;g=0;break}1073742335==this.tokAt(r+1)&&(aa=++r);break;case 1073741998:case 134219777:case 134217750:A=aa==r-1;if(!b&&!j&&0==k){if(134219777==
a.theTok){b=!0;this.setShapeProperty(22,"plane",null);E=new JU.Lst;a.hklParameter(++r,E,!0);r=a.iToken;K="coords";G=E;break}if(!I){K=134217750==E?"plane":"line";oa=r+1;break}!this.chk&&(1073741998!=E&&null==e)&&(f=this.vwr.getCurrentUnitCell(),k=null==f?1678381065:1814695966,e=this.getBoxPoints(k,f,null,g/100),j=!0)}M=f=null;switch(E){case 134217750:f=a.planeParameter(r,I);break;case 134219777:f=a.hklParameter(++r,null,!0);break;case 1073741998:1073741994==k&&this.invArg(),M=I?this.bsToArray(a.getAtomsStartingAt(++r)):
a.isCenterParameter(r+1)?B(-1,[this.centerParameter(++r),this.centerParameter(a.iToken+1)]):a.getPointArray(++r,2,!1),2>M.length&&this.invArg()}r=a.iToken;b=!0;if(this.chk)break;if(1073741998==E){M=JU.Measure.getBestLineThroughPoints(M,-1);if(0!=k&&(f=JU.V3.newVsub(M[1],M[0]),f.scale(1/f.length()),M=A?JU.Measure.getProjectedLineSegment(e,-1,M[0],f,null):this.vwr.getTriangulator().intersectLine(e,-1,M[0],f),null==M||null==M[1]))return;c||(this.setShapeProperty(22,"points",Integer.$valueOf(g)),c=!0);
E=new JU.Lst;E.addLast(M[0]);E.addLast(M[1]);this.setShapeProperty(22,"coords",E);break}0==k?(G=f,K="planedef"):(1073741994==k?(K="polygon",M=JU.Measure.getPointsOnPlane(e,f),e=M.toArray(Array(M.size())),f=new JU.Lst,f.addLast(e),f.addLast(null),G=f):(K="polygon",G=this.vwr.getTriangulator().intersectPlane(f,e,A?-1:0)),g=0);break;case 1275068447:e=a.isArrayParameter(++r)?a.getPointArray(r,-1,!1):null;null==e&&a.isAtomExpression(r)&&(M=a.atomExpressionAt(r),e=this.vwr.ms.getAtomPointVector(M).toArray(Array(M.cardinality())));
null!=e&&(r=a.iToken+1,12289==this.tokAt(r)&&(v=a.centerParameter(++r,null),r=a.iToken+1));switch(this.tokAt(r)){case 536875009:c="";break;case 1111490563:c="Cs";break;case 1073742330:e=B(-1,[a.objectNameParameter(++r),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==v&&(v=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(E=c.size();0<=--E;)e[E]=c.get(E);r++;c="";break;default:c=a.optParameterAsString(r)}g=0==g?1:g/100;d=0;0<c.length&&this.isFloatParameter(++r)&&(d=this.intParameter(r++));536875009==this.tokAt(r)&&(g=this.floatParameter(++r));this.chk||a.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),c,d,g,e,v,null==qa?"":qa));return;case 4106:w=u(4,0);Ka=4;b=a.floatParameterSet(++r,4,4);r=a.iToken;for(E=0;4>E;E++)w[E]=y(b[E]);b=!0;break;case 1677721602:case 1140850689:if(null==
w||Ka>(1228931587==a.theTok?2:3))Ka=0,w=u(-1,[-1,-1,-1,-1]);w[Ka++]=this.atomExpressionAt(++r).nextSetBit(0);r=a.iToken;w[Ka++]=1677721602==a.theTok?this.atomExpressionAt(++r).nextSetBit(0):-1;r=a.iToken;b=!0;break;case 554176565:switch(this.getToken(++r).tok){case 1073742330:K="slab";G=a.objectNameParameter(++r);r=a.iToken;b=!0;break;default:this.invArg()}break;case 1275203608:case 134217751:case 1073742106:A=134217751==E;K="polygon";b=!0;f=new JU.Lst;var D=0,G=0,U=M=null,V=null;if(a.isArrayParameter(++r)){M=
a.getPointArray(r,-1,!0);if(0<M.length&&null==M[0]){1275203608==E?D=this.getIntArray2(r):(D=JU.AU.newInt2(1),D[0]=a.expandFloatArray(a.floatParameterSet(r,-1,2147483647),-1,!1));M=this.getAllPoints(this.e.iToken+1,3);try{V=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulateFaces(D,M,null)}catch(O){this.invArg()}}D=M.length}1275203608==E&&(D=M.length);if(null==M){D=Math.max(0,this.intParameter(r));M=Array(D);for(E=0;E<D;E++)M[E]=this.centerParameter(++a.iToken)}r=
a.iToken;switch(this.tokAt(r+1)){case 11:case 12:U=JS.SV.newT(this.getToken(++r)).toArray().getList();G=U.size();break;case 7:U=this.getToken(++r).getList();G=U.size();break;case 2:G=this.intParameter(++r);0>G&&(A=!0);break;default:null==V&&(!A&&!this.chk)&&(V=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulatePolygon(M,-1))}if(null==V&&!A){V=JU.AU.newInt2(G);for(E=0;E<G;E++)A=null==U?a.floatParameterSet(++a.iToken,3,4):JS.SV.flistValue(U.get(E),0),(3>A.length||4<
A.length)&&this.invArg(),V[E]=u(-1,[y(A[0]),y(A[1]),y(A[2]),3==A.length?7:y(A[3])])}0<D?(f.addLast(M),f.addLast(V)):f=null;G=f;r=a.iToken;break;case 134217764:case 1296041986:e=null;c=2147483647;k=d=null;j=0;h=null;if(1296041986==E)switch(c=0,this.tokAt(++r)){case 4:e=this.stringParameter(r);break;case 12:e=JS.SV.sValue(this.getToken(r));break;default:a.isCenterParameter(r)||(c=this.intParameter(r++),a.isArrayParameter(r)&&(h=JU.P3.newA(a.floatParameterSet(r,3,3)),r=++a.iToken));t=B(-1,[null,this.vwr.getFrameAtoms()]);
a.isCenterParameter(r)&&(v=a.centerParameter(r,t));a.isCenterParameter(a.iToken+1)&&(d=a.centerParameter(++a.iToken,t));if(this.chk)return;r=a.iToken}null==v&&r+1<this.slen&&(v=this.centerParameter(++r),k=a.isAtomExpression(r)?this.atomExpressionAt(r):null,r=a.iToken);t=null!=d&&2==this.tokAt(r+1)?a.getToken(++r).intValue:-1;1814695966==this.tokAt(r+1)?(d=new JU.P3,j=1073742066,r++,a.iToken=r):1073742066==this.tokAt(r+1)?(r++,d=this.getPoint3f(r+1,!1),j=1073742066):1073741826==this.tokAt(r+1)&&(j=
1073741826);a.checkLast(a.iToken);this.chk||(r="",null==k&&0<=this.vwr.am.cmi&&(k=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi)),null!=k&&(r=null,k=k.nextSetBit(0),0!=j&&(l=this.vwr.getSymmetryInfo(k,e,c,h,v,d,134217751,null,g/100,t,j),T(l,JU.P3)?d=l:r=""),null==qa&&(qa="sym"),null==r&&(r=this.vwr.getSymmetryInfo(k,e,c,h,v,d,135176,qa,g/100,t,j))),a.runBufferedSafely(0<r.length?r:'draw ID "'+qa+'_*" delete',a.outputBuffer));return;case 4115:h=!0;continue;case 1073742332:case 9:case 8:if(9==
a.theTok||!a.isPoint3f(r)){G=a.getPoint4f(r);if(h){a.checkLast(a.iToken);this.chk||a.runScript(JU.Escape.drawQuat(JU.Quat.newP4(G),null==qa?"frame":qa," "+p,null==v?new JU.P3:v,g/100));return}K="planedef"}else G=v=this.getPoint3f(r,!0),K="coord";r=a.iToken;b=!0;break;case 1073742E3:K="lineData";G=a.floatParameterSet(++r,0,2147483647);r=a.iToken;b=!0;break;case 12290:case 10:case 1073742325:K="atomSet";G=this.atomExpressionAt(r);h&&(v=this.centerParameter(r));r=a.iToken;b=!0;break;case 7:b=!0;K=oa==
r?"coords":"modelBasedPoints";G=a.theToken.value;break;case 1073742195:case 268435504:break;case 268435520:G=a.xypParameter(r);if(null!=G){r=a.iToken;K="coord";b=!0;break}d&&this.invArg();d=!0;break;case 268435521:d||this.invArg();d=!1;break;case 1140850693:K="reverse";break;case 1073742166:if(1765808134==this.tokAt(++r)){G=Integer.$valueOf(this.e.getArgbParamOrNone(++r,!1));K="titlecolor";r=this.e.iToken;break}if(4114==this.tokAt(r)){--r;continue}case 4:G=this.stringParameter(r);K="title";break;
case 4114:E=this.floatParameter(++r);G=1073741824==this.tokAt(r+1)?this.paramAsStr(++r):null;f=1073741824==this.tokAt(r+1)?this.paramAsStr(++r):null;(4!=this.tokAt(r+1)&&++r!=this.slen||0>=E||255<E)&&this.invArg();K="myfont";if(null==G||null==f)A=this.vwr.shm.getShapePropertyIndex(22,"font",-1),null==G&&(G=A.fontFace),null==f&&(f=A.fontStyle);G=this.vwr.getFont3D(G,f,E);break;case 135198:K="vector";break;case 1140850691:G=Float.$valueOf(this.floatParameter(++r));K="length";break;case 3:G=Float.$valueOf(this.floatParameter(r));
K="length";break;case 1094713359:K="modelIndex";G=Integer.$valueOf(this.intParameter(++r));break;case 2:d?(K="modelIndex",G=Integer.$valueOf(this.intParameter(r))):g=this.intParameter(r);break;case 536875009:g=Math.round(this.floatParameter(++r)*(2==this.getToken(r).tok?1:100));continue;case 1073741974:qa=this.setShapeId(22,++r,f);m=null==this.getShapeProperty(22,"ID");r=a.iToken;break;case 1073742027:K="fixed";G=Boolean.FALSE;break;case 12293:K="fixed";G=Boolean.TRUE;break;case 1073742066:E=this.getPoint3f(++r,
!0);r=a.iToken;K="offset";G=E;break;case 1073741906:K="crossed";break;case 1073742196:G=Float.$valueOf(this.floatParameter(++r));K="width";p=K+" "+G;break;case 1073741908:K="curve";oa=r+1;break;case 1073741840:K="arc";oa=r+1;break;case 1073741846:K="arrow";oa=r+1;break;case 1073742194:K="vertices";oa=r+1;break;case 1073741880:K="circle";break;case 1073741912:K="cylinder";break;case 1073742048:K="nohead";break;case 1073741860:K="isbarb";break;case 1073742130:K="rotate45";break;case 1073742092:K="perp";
break;case 1665140738:case 1073741917:p=1665140738==a.theTok;A=this.floatParameter(++r);p&&(A*=2);G=Float.$valueOf(A);K=p||3==this.tokAt(r)?"width":"diameter";p=K+(3==this.tokAt(r)?" "+A:" "+y(A));break;case 1073742330:if(268435520==this.tokAt(r+2)||h){b=v=this.centerParameter(r);r=a.iToken;K="coord";G=b;b=!0;break}G=a.objectNameParameter(++r);K="identifier";b=!0;break;case 1765808134:case 603979967:case 1073742074:f=!0;t=this.getColorTrans(a,r,!1,l);r=a.iToken;continue;default:if(!a.setMeshDisplayProperty(22,
0,a.theTok)){if(268435633==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){qa=this.setShapeId(22,r,f);r=a.iToken;break}this.invArg()}0==N&&(N=r);r=a.iToken;continue}f=12291!=a.theTok;b&&(!c&&!h)&&(this.setShapeProperty(22,"points",Integer.$valueOf(g)),c=!0,g=0);b&&m&&this.invArg();null!=K&&this.setShapeProperty(22,K,G)}this.finalizeObject(22,l[0],t,g,b,w,N,null)});e(c$,"mo",function(a,b){var c=this.e,d=2147483647,j=!1,h=null,f=this.vwr.getVisibleFramesBitSet(),e=new JU.Lst,k=!1,g=1073877011==this.tokAt(0),
l=1;if(g){var q=this.e.optParameterAsString(1).equals("view");if(1==this.e.slen||q||this.e.optParameterAsString(1).equals("options")){this.chk||(c=q?"VIEW":this.e.optParameterAsString(2),this.vwr.startNBO(c));return}}if(1094717454==this.tokAt(1)||4115==this.tokAt(1))l=c.modelNumberParameter(2),0>l&&this.invArg(),f.clearAll(),f.set(l),l=3;c.sm.loadShape(b);for(q=f.nextSetBit(0);0<=q;q=f.nextSetBit(q+1)){var p=l;if(1073742001==this.tokAt(p)&&this.listIsosurface(b))break;this.setShapeProperty(b,"init",
Integer.$valueOf(q));if(a)break;var N=null,v=this.getShapeProperty(b,"moNumber").intValue(),m=this.getShapeProperty(b,"moLinearCombination"),u=this.getShapeProperty(b,"moSquareData"),B=null==m?null:this.getShapeProperty(b,"moSquareLinear");0==v&&(v=2147483647);var y=null,D=null,aa=!1,I=null;switch(this.getToken(p).tok){case 1140850696:if(1073877010==b){this.mo(a,28);return}h=this.paramAsStr(++p).toUpperCase();4==c.tokAt(p+1)&&(I=this.paramAsStr(++c.iToken));break;case 1073741875:case 554176565:y=
c.theToken.value;D=this.getCapSlabObject(p,!1);break;case 1073741914:B=Boolean.TRUE;m=w(-1,[1]);d=v=0;break;case 2:v=this.intParameter(p);1073741865==this.tokAt(p+1)&&(k=!0);m=this.moCombo(e);null==m&&0>v&&(m=w(-1,[-100,-v]));aa=!0;break;case 268435616:switch(this.tokAt(++p)){case 1073741973:case 1073742008:break;default:this.invArg()}j=!0;case 1073741973:case 1073742008:2147483647==(d=this.moOffset(p))&&this.invArg();v=0;m=this.moCombo(e);aa=!0;break;case 1073742037:v=1073742037;k=!1;m=this.moCombo(e);
aa=!0;break;case 1073742108:v=1073742108;k=!1;m=this.moCombo(e);aa=!0;break;case 1765808134:this.setColorOptions(null,p+1,b,2);break;case 134217750:y="plane";D=1073742333==this.tokAt(this.e.iToken=++p)?null:c.planeParameter(p,!1);break;case 134217751:this.addShapeProperty(e,"randomSeed",2==this.tokAt(p+2)?Integer.$valueOf(this.intParameter(p+2)):null);y="monteCarloCount";D=Integer.$valueOf(this.intParameter(p+1));break;case 536875009:y="scale";D=Float.$valueOf(this.floatParameter(p+1));break;case 1073741910:268435617==
this.tokAt(p+1)?(y="cutoffPositive",D=Float.$valueOf(this.floatParameter(p+2))):(y="cutoff",D=Float.$valueOf(this.floatParameter(p+1)));break;case 536870916:y="debug";break;case 1073742054:y="plane";break;case 1073742104:case 1073742122:y="resolution";D=Float.$valueOf(this.floatParameter(p+1));break;case 1073742156:null==m?u=Boolean.TRUE:B=Boolean.TRUE;aa=!1;break;case 1073742168:p+1<this.slen&&4==this.tokAt(p+1)&&(y="titleFormat",D=this.paramAsStr(p+1));break;case 1073741824:this.invArg();break;
case 4:if(g&&1==p){I=c.stringParameter(p);break}default:g&&4==c.tokAt(p)&&(I=this.paramAsStr(p++));if(c.isArrayParameter(p)){m=c.floatParameterSet(p,1,2147483647);1073742156==this.tokAt(c.iToken+1)&&(aa=!1,B=Boolean.TRUE,c.iToken++);break}d=c.iToken;c.setMeshDisplayProperty(b,0,c.theTok)||this.invArg();this.setShapeProperty(b,"setProperties",e);c.setMeshDisplayProperty(b,d,this.tokAt(d));return}null!=y&&this.addShapeProperty(e,y,D);p=2147483647!=v||null!=m;if(this.chk)break;if(null!=h||null!=I||p){p&&
4==this.tokAt(c.iToken+1)&&(N=this.paramAsStr(++c.iToken));c.setCursorWait(!0);if(null!=h||null!=I)h=h+":"+I;this.setMoData(e,v,m,d,j,q,N,h,k);p&&this.addShapeProperty(e,"finalize",null)}aa||(this.setShapeProperty(b,"squareLinear",B),this.setShapeProperty(b,"squareData",u));0<e.size()&&this.setShapeProperty(b,"setProperties",e);p&&!c.tQuiet&&(N="",g?N=this.getShapeProperty(b,"moLabel"):(v=this.getShapeProperty(b,"moNumber").intValue(),N=""+v),this.showString(JS.T.nameOf(this.tokAt(0))+" "+N+" "+(k?
"beta ":"")+this.getShapeProperty(b,"message")));e.clear()}},"~B,~N");e(c$,"setNBOType",function(a,b){var c=-1,d=null,j=b.indexOf(":");0<j&&(d=b.substring(j+1),b=b.substring(0,j),b.equals("null")&&(b=null),d.equals("null")&&(d=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 j=a.get("auxFiles"),h=this.vwr.getCurrentModelAuxInfo().get("auxFiles");null==h?this.vwr.getCurrentModelAuxInfo().put("auxFiles",j):h.addAll(j);if(null!=d){j=d.indexOf(".");0<j&&(h=JU.PT.parseInt(d.substring(j+1)),d=d.substring(0,j),j=h);for(var h=a.get("nboLabels"),f=0,e=h.length;f<e;f++)if(d.equals(h[f])&&(0>j||0==--j)){c=f+1;break}0>c&&this.error(27)}return c},"java.util.Map,~S");e(c$,"moCombo",function(a){if(1073742156!=this.tokAt(this.e.iToken+1))return null;this.addShapeProperty(a,"squareLinear",
Boolean.TRUE);this.e.iToken++;return w(0,0)},"JU.Lst");e(c$,"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):268435617==c?b+=this.intParameter(++a):268435616==c&&(b-=this.intParameter(++a));return b},"~N");e(c$,"setMoData",function(a,b,c,d,j,h,f,e,k){var g=this.e;0>h&&(h=this.vwr.am.cmi,0>h&&g.errorStr(30,"MO isosurfaces"));var l=this.vwr.ms.getInfo(h,"moData");null==l&&this.error(27);this.vwr.checkMenuUpdate();
if(null!=e){var q=this.setNBOType(l,e),p=l.get("nboLabels").length;g.showString(p+" orbitals of type "+e.substring(0,e.indexOf(":")+1)+" modelIndex="+this.vwr.getModelNumberDotted(h));0<q&&(b=q);if(null==c&&2147483647==b)return}e=null;q=0;h=null;if(null==c||2>c.length){null!=c&&1==c.length?d=0:k&&l.containsKey("firstBeta")&&(d=l.get("firstBeta").intValue());e=l.containsKey("lastMoNumber")?l.get("lastMoNumber").intValue():0;q=l.containsKey("lastMoCount")?l.get("lastMoCount").intValue():1;1073742108==
b?b=e-1:1073742037==b&&(b=e+q);e=l.get("mos");q=null==e?0:e.size();0==q&&this.error(25);1==q&&1<b&&this.error(29);if(2147483647!=d){if(!k)if(l.containsKey("HOMO"))b=l.get("HOMO").intValue()+d,d=0;else{b=q;for(k=0;k<q;k++)if(p=e.get(k),null!=(h=p.get("occupancy"))){if(0.5>h.floatValue()){b=k;break}}else if(null!=(h=p.get("energy"))){if(0<h.floatValue()){b=k;break}}else break;null==h&&this.error(28)}b+=d;this.chk||JU.Logger.info("MO "+b)}(1>b||b>q)&&g.errorStr(26,""+q)}b=Math.abs(b);l.put("lastMoNumber",
Integer.$valueOf(b));l.put("lastMoCount",Integer.$valueOf(1));j&&null==c&&(c=w(-1,[-100,b]));if(null!=c&&2>c.length){p=e.get(b-1);if(null==(h=p.get("energy")))c=w(-1,[100,b]);else{g=h.floatValue();d=JU.BS.newN(q);j=0;c=1==c.length&&1==c[0];for(k=0;k<q;k++)if(null!=(h=e.get(k).get("energy")))if(h=h.floatValue(),c?h<=g:h==g)d.set(k+1),j+=2;c=w(j,0);for(g=k=0;k<j;k+=2)c[k]=1,c[k+1]=g=d.nextSetBit(g+1);l.put("lastMoNumber",Integer.$valueOf(d.nextSetBit(0)));l.put("lastMoCount",Integer.$valueOf(D(j/2)))}this.addShapeProperty(a,
"squareLinear",Boolean.TRUE)}this.addShapeProperty(a,"moData",l);null!=f&&this.addShapeProperty(a,"title",f);this.addShapeProperty(a,"molecularOrbital",null!=c?c:Integer.$valueOf(Math.abs(b)));this.addShapeProperty(a,"clear",null)},"JU.Lst,~N,~A,~N,~B,~N,~S,~S,~B");e(c$,"isosurface",function(a){var b=this.e;b.sm.loadShape(a);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(a))){var c=0,d=!1,j=!1,h=24==a,f=29==a,e=30==a,k=26==a,g=k||12291==this.tokAt(1)||b.$isStateScript,l=!1,q=!1,p=!1,N=!1,v=!1,
m=!1,Ba=!1,yb=!1,O=!1,oa=!1,aa=!1,I=!1,E=!1,A=!1,r=!1,K=null,G=null,M=null,P=null,U,V,H,F,W,Z=NaN,$=NaN,ha=0,da=null,ma=2147483647,S=null,X=null,ia=null,s=new JU.SB,Q,na=null,ta=null,va=!1,ca=null,ra=0,ja=null,ba=this.chk?0:-2147483648;b.setCursorWait(!0);var ya=null!=this.initIsosurface(a),ua=ya&&null==this.getShapeProperty(a,"ID"),Aa=!1,gb=!1,La=!1,Ha=!1,Ma=null,hb=null,ib=null,pa=null,jb=null,Fa=null,Na=null,C=new JU.Lst,Ia=!1;(f||e)&&this.addShapeProperty(C,"fileType","Pmesh");for(var n=b.iToken;n<
this.slen;++n){var z=null,x=null,R=this.getToken(n).tok;1073741824==R&&(ja=this.paramAsStr(n),ja.equalsIgnoreCase("map")&&(R=4125));switch(R){case 1073742148:g=!0;s.append(" silent");z="silent";break;case 603979868:da=1073742335==this.getToken(++n).tok?Boolean.TRUE:1073742334==b.theTok?Boolean.FALSE:null;null==da&&this.invArg();continue;case 553648146:ma=this.intParameter(++n);continue;case 4128:z="moveIsosurface";12!=this.tokAt(++n)&&this.invArg();x=this.getToken(n++).value;break;case 1296041986:for(var Ja=
this.floatArraySet(n+2,this.intParameter(n+1),16),Fa=Array(Ja.length),ea=Fa.length;0<=--ea;)Fa[ea]=JU.M4.newA16(Ja[ea]);n=b.iToken;break;case 1088421903:0>ba&&(ba=Math.min(this.vwr.am.cmi,0));var zb=null==ia;null==X&&(X=JU.BSUtil.copy(this.vwr.bsA()));X.and(this.vwr.ms.getAtoms(1296041986,Integer.$valueOf(1)));zb||X.andNot(ia);this.addShapeProperty(C,"select",X);zb&&(ia=JU.BSUtil.copy(X),JU.BSUtil.invertInPlace(ia,this.vwr.ms.ac),r=!0,this.addShapeProperty(C,"ignore",ia),s.append(" ignore ").append(JU.Escape.eBS(ia)));
s.append(" symmetry");0==ra&&this.addShapeProperty(C,"colorRGB",Integer.$valueOf(1296041986));Fa=this.vwr.ms.getSymMatrices(ba);break;case 1073742066:z="offset";x=this.centerParameter(++n);n=b.iToken;break;case 528432:z="rotate";x=1073742333==this.tokAt(b.iToken=++n)?null:b.getPoint4f(n);n=b.iToken;break;case 1610612740:z="scale3d";x=Float.$valueOf(this.floatParameter(++n));break;case 1073742090:s.append(" periodic");z="periodic";break;case 1073742078:case 266298:case 134217751:z=b.theToken.value.toString();
s.append(" ").appendO(b.theToken.value);x=this.centerParameter(++n);s.append(" ").append(JU.Escape.eP(x));n=b.iToken;break;case 1678381065:if(0<=b.fullCommand.indexOf("# BBOX="))var Ab=JU.PT.split(JU.PT.getQuotedAttribute(b.fullCommand,"# BBOX"),","),ca=B(-1,[JU.Escape.uP(Ab[0]),JU.Escape.uP(Ab[1])]);else b.isCenterParameter(n+1)?(ca=B(-1,[this.getPoint3f(n+1,!0),this.getPoint3f(b.iToken+1,!0)]),n=b.iToken):ca=this.vwr.ms.getBBoxVertices();s.append(" boundBox "+JU.Escape.eP(ca[0])+" "+JU.Escape.eP(ca[ca.length-
1]));z="boundingBox";x=ca;break;case 135188:f=!0;s.append(" pmesh");z="fileType";x="Pmesh";break;case 134217763:X=this.atomExpressionAt(++n);this.chk?S=new JU.BS:1073742325==this.tokAt(b.iToken+1)||10==this.tokAt(b.iToken+1)?(S=this.atomExpressionAt(++b.iToken),S.and(this.vwr.ms.getAtomsWithinRadius(5,X,!1,null,null))):(S=this.vwr.ms.getAtomsWithinRadius(5,X,!0,null,null),S.andNot(this.vwr.ms.getAtoms(1094713360,X)));S.andNot(X);s.append(" intersection ").append(JU.Escape.eBS(X)).append(" ").append(JU.Escape.eBS(S));
n=b.iToken;if(134320141==this.tokAt(n+1)){n++;var Oa=this.getToken(++n).value;s.append(" function ").append(JU.PT.esc(Oa));this.chk||this.addShapeProperty(C,"func",Oa.equals("a+b")||Oa.equals("a-b")?Oa:this.createFunction("__iso__","a,b",Oa))}else A=!0;z="intersection";x=B(-1,[X,S]);break;case 1610625028:case 134217759:if(d=1610625028==R){s.append(" display");c=n;R=this.tokAt(n+1);if(0==R)continue;n++;this.addShapeProperty(C,"token",Integer.$valueOf(1073742335));if(10==R||1073742327==R){z="bsDisplay";
1073742327==R?s.append(" all"):(x=this.st[n].value,s.append(" ").append(JU.Escape.eBS(x)));b.checkLast(n);break}else 134217759!=R&&(b.iToken=n,this.invArg())}else ha=n;var Xa,Ca=null,S=null,Ya=Array(1);1073742325==this.tokAt(n+1)?(Xa=this.floatParameter(n+3),b.isPoint3f(n+4)?(Ca=b.centerParameter(n+4,null),b.iToken+=2):b.isPoint3f(n+5)?(Ca=b.centerParameter(n+5,null),b.iToken+=2):(S=b.atomExpression(this.st,n+5,this.slen,!0,!1,Ya,!0),null==S&&this.invArg())):(Xa=this.floatParameter(++n),Ca=b.centerParameter(++n,
Ya),S=T(Ya[0],JU.BS)?Ya[0]:null);d&&b.checkLast(b.iToken);n=b.iToken;0<=b.fullCommand.indexOf("# WITHIN=")&&(S=JU.BS.unescape(JU.PT.getQuotedAttribute(b.fullCommand,"# WITHIN")));this.chk||(null!=S&&0<=ba&&(S=this.vwr.restrictToModel(S,ba)),null==Ca&&(Ca=null==S?new JU.P3:this.vwr.ms.getAtomSetCenter(S)),ca=this.getWithinDistanceVector(C,Xa,Ca,S,d),s.append(" within ").appendF(Xa).append(" ").append(null==S?JU.Escape.eP(Ca):JU.Escape.eBS(S)));continue;case 1073742083:var z="parameters",Bb=b.floatParameterSet(++n,
1,10),n=b.iToken,x=Bb;s.append(" parameters ").append(JU.Escape.eAF(Bb));break;case 1715472409:case 1073742190:var Ma=b.theToken.value,eb=1073742190==R,Pa=this.tokAt(n+1);null==jb?(!l&&(!p&&!q)&&(this.addShapeProperty(C,"sasurface",Float.$valueOf(0)),s.append(" vdw"),l=!0),z="property",null==da&&(da=JS.T.tokAttr(Pa,1111490560)&&1==this.vwr.getIsosurfacePropertySmoothing(!1)?Boolean.TRUE:Boolean.FALSE),this.addShapeProperty(C,"propertySmoothing",da),s.append(" isosurfacePropertySmoothing "+da),da===
Boolean.TRUE&&(2147483647==ma&&(ma=this.vwr.getIsosurfacePropertySmoothing(!0)),this.addShapeProperty(C,"propertySmoothingPower",Integer.$valueOf(ma)),s.append(" isosurfacePropertySmoothingPower "+ma)),this.vwr.g.rangeSelected&&this.addShapeProperty(C,"rangeSelected",Boolean.TRUE)):z=jb;ja=this.paramAsStr(n);s.append(" ").append(ja);if(0==ja.toLowerCase().indexOf("property_")){G=w(this.vwr.ms.ac,0);if(this.chk)continue;G=this.vwr.getDataObj(ja,null,1);null==G&&this.invArg();this.addShapeProperty(C,
z,G);continue}var Qa=this.vwr.ms.ac,G=w(Qa,0);if(eb){var Cb=this.paramAsStr(++n);0==Cb.length?G=b.floatParameterSet(n,Qa,Qa):(G=w(Qa,0),this.chk||JU.Parser.parseStringInfestedFloatArray(""+b.getParameter(Cb,4,!0),null,G));this.chk||s.append(' "" ').append(JU.Escape.eAF(G))}else{this.getToken(++n);if(!this.chk){s.append(" "+b.theToken.value);var fb=this.vwr.ms.at;this.vwr.autoCalculate(Pa,null);if(1765808134!=Pa){Q=new JU.P3;for(var kb=Qa;0<=--kb;)G[kb]=fb[kb].atomPropertyFloat(this.vwr,Pa,Q)}}1765808134==
Pa&&(pa="inherit");if(134217759==this.tokAt(n+1)){var Db=this.floatParameter(n+=2);s.append(" within "+Db);this.addShapeProperty(C,"propertyDistanceMax",Float.$valueOf(Db))}}x=G;break;case 1094713359:case 1094717454:l&&this.invArg();ba=1094713359==R?this.intParameter(++n):b.modelNumberParameter(++n);s.append(" modelIndex "+ba);if(0>ba){z="fixed";x=Boolean.TRUE;break}z="modelIndex";x=Integer.$valueOf(ba);break;case 1275082245:var z="select",lb=this.atomExpressionAt(++n),x=lb,n=b.iToken;1073742072==
this.tokAt(n+1)&&(n++,ia=JU.BSUtil.copy(lb),JU.BSUtil.invertInPlace(ia,this.vwr.ms.ac),this.addShapeProperty(C,"ignore",ia),s.append(" ignore ").append(JU.Escape.eBS(ia)),r=!0);l||p?s.append(" select "+JU.Escape.eBS(lb)):(X=x,0>ba&&0<=X.nextSetBit(0)&&(ba=this.vwr.ms.at[X.nextSetBit(0)].mi));break;case 2109448:P=10==b.getToken(++n).tok?b.theToken.value:b.expandFloatArray(b.floatParameterSet(n,1,2147483647),1,!0);n=b.iToken;break;case 36867:var Eb=this.intParameter(++n),P=0<Eb?JU.BSUtil.newAndSetBit(Eb-
1):new JU.BS;break;case 12289:z="center";x=this.centerParameter(++n);s.append(" center "+JU.Escape.eP(x));n=b.iToken;break;case 1073742147:case 1765808134:ya=!0;if(1073742147==R)La=!0,s.append(" sign"),this.addShapeProperty(C,"sign",Boolean.TRUE);else{if(1073741914==this.tokAt(n+1)){n++;z="colorDensity";s.append(" color density");Ha=!0;if(this.isFloatParameter(n+1)){var Fb=this.floatParameter(++n);s.append(" "+Fb);x=Float.$valueOf(Fb)}break}if(4==this.getToken(n+1).tok)pa=this.paramAsStr(++n),0<pa.indexOf(" ")&&
(Na=JU.C.getColixArray(pa),null==Na&&this.error(4));else if(1073742018==b.theTok){n++;s.append(" color mesh");ra=b.getArgbParam(++n);this.addShapeProperty(C,"meshcolor",Integer.$valueOf(ra));s.append(" ").append(JU.Escape.escapeColor(ra));n=b.iToken;continue}if(603979967==(b.theTok=this.tokAt(n+1))||1073742074==b.theTok){s.append(" color");ib=this.setColorOptions(s,n+1,24,-2);n=b.iToken;continue}switch(this.tokAt(n+1)){case 1073741826:case 1073742114:this.getToken(++n);s.append(" color range");this.addShapeProperty(C,
"rangeAll",null);if(1073742327==this.tokAt(n+1)){n++;s.append(" all");continue}var Gb=this.floatParameter(++n),Hb=this.floatParameter(++n);this.addShapeProperty(C,"red",Float.$valueOf(Gb));this.addShapeProperty(C,"blue",Float.$valueOf(Hb));s.append(" ").appendF(Gb).append(" ").appendF(Hb);continue}if(b.isColorParam(n+1)&&(ra=b.getArgbParam(n+1),1073742170==this.tokAt(n+2))){pa=b.getColorRange(n+1);n=b.iToken;break}s.append(" color")}b.isColorParam(n+1)?(ra=b.getArgbParam(++n),s.append(" ").append(JU.Escape.escapeColor(ra)),
n=b.iToken,this.addShapeProperty(C,"colorRGB",Integer.$valueOf(ra)),ya=!0,b.isColorParam(n+1)?(ra=b.getArgbParam(++n),n=b.iToken,this.addShapeProperty(C,"colorRGB",Integer.$valueOf(ra)),s.append(" ").append(JU.Escape.escapeColor(ra)),N=!0):La&&this.invPO()):!La&&(null==Na&&null==pa)&&this.invPO();continue;case 134221829:h||this.invArg();aa=!this.chk;continue;case 1228935687:4!=this.tokAt(n+1)&&this.invPO();continue;case 1111492618:case 1648363544:s.append(" ").appendO(b.theToken.value);var Ra=b.encodeRadiusParameter(n,
!1,!0);if(null==Ra)return;s.append(" ").appendO(Ra);Float.isNaN(Ra.value)&&(Ra.value=100);x=Ra;z="radius";oa=!0;p&&(l=!1);n=b.iToken;break;case 1073741864:j=!0;continue;case 134217750:q=!0;z="plane";x=b.planeParameter(n,j);n=b.iToken;s.append(" plane ").append(JU.Escape.eP4(x));break;case 536875009:z="scale";x=Float.$valueOf(this.floatParameter(++n));s.append(" scale ").appendO(x);break;case 1073742327:ya&&this.invArg();z="thisID";break;case 1112150020:l=!0;++n;x=b.getPoint4f(n);z="ellipsoid";n=b.iToken;
s.append(" ellipsoid ").append(JU.Escape.eP4(x));break;case 134219777:q=!0;z="plane";x=b.hklParameter(++n,null,!0);n=b.iToken;s.append(" plane ").append(JU.Escape.eP4(x));break;case 135182:var l=!0,Za=this.paramAsStr(++n);this.addShapeProperty(C,"lcaoType",Za);s.append(" lcaocartoon ").append(JU.PT.esc(Za));switch(this.getToken(++n).tok){case 12290:case 10:case 1073742325:z="lcaoCartoon";S=this.atomExpressionAt(n);n=b.iToken;if(this.chk)continue;var Sa=S.nextSetBit(0);0>Sa&&this.error(14);s.append(" ({").appendI(Sa).append("})");
ba=this.vwr.ms.at[Sa].mi;this.addShapeProperty(C,"modelIndex",Integer.$valueOf(ba));var mb=B(-1,[new JU.V3,new JU.V3,JU.V3.newV(this.vwr.ms.at[Sa]),new JU.V3]);if(!Za.equalsIgnoreCase("s")&&null==this.vwr.getHybridizationAndAxes(Sa,mb[0],mb[1],Za))return;x=mb;break;default:this.error(14)}break;case 1073877011:K=this.paramAsStr(++n).toUpperCase(),s.append(" nbo ").append(K).append(" ");case 1073877010:null==K&&s.append(" mo ");var Ta=2147483647,Ga=2147483647,nb=268435616==this.tokAt(n+1);nb&&n++;var Ua=
null;switch(this.tokAt(++n)){case 0:b.bad();break;case 1073741914:s.append("[1] squared ");this.addShapeProperty(C,"squareLinear",Boolean.TRUE);Ua=w(-1,[1]);Ga=Ta=0;n++;break;case 1073741973:case 1073742008:Ga=this.moOffset(n);Ta=0;n=b.iToken;s.append((nb?"-":"")+"HOMO ");0<Ga&&s.append("+");0!=Ga&&s.appendI(Ga);break;case 2:Ta=this.intParameter(n);s.appendI(Ta);1073741865==this.tokAt(n+1)&&(yb=!0,n++);break;default:b.isArrayParameter(n)&&(Ua=b.floatParameterSet(n,1,2147483647),n=b.iToken)}if(1073742156==
this.tokAt(n+1))this.addShapeProperty(C,"squareLinear",Boolean.TRUE),s.append(" squared"),null==Ua&&(Ua=w(0,0));else if(134217751==this.tokAt(n+1)){++n;var Ib=this.intParameter(++n),Jb=2==this.tokAt(n+1)?this.intParameter(++n):-System.currentTimeMillis()%1E4;this.addShapeProperty(C,"monteCarloCount",Integer.$valueOf(Ib));this.addShapeProperty(C,"randomSeed",Integer.$valueOf(Jb));s.append(" points ").appendI(Ib).appendC(" ").appendI(Jb)}this.setMoData(C,Ta,Ua,Ga,nb,ba,null,K,yb);l=!0;continue;case 1073742036:z=
"nci";s.append(" "+z);var R=this.tokAt(n+1),Kb=1228935687!=R&&4!=R&&1073742032!=R,x=Boolean.$valueOf(Kb);Kb&&(l=!0);break;case 1073742016:case 1073742022:var Lb=1073742016==R,z=Lb?"mep":"mlp";s.append(" "+z);var $a=null,ob=-1,l=!0;2==this.tokAt(n+1)&&(ob=this.intParameter(++n),s.append(" "+ob),this.addShapeProperty(C,"mepCalcType",Integer.$valueOf(ob)));if(4==this.tokAt(n+1))$a=this.stringParameter(++n),s.append(" /*file*/"+JU.PT.esc($a));else if(1715472409==this.tokAt(n+1)){jb=z;continue}if(!this.chk)try{G=
null==$a&&Lb?this.vwr.getOrCalcPartialCharges(X,ia):this.getAtomicPotentials(X,ia,$a)}catch(Mb){if(Y(Mb,JV.JmolAsyncException))throw new JS.ScriptInterruption(this.e,"partialcharge",1);throw Mb;}!this.chk&&null==G&&this.error(32);x=G;break;case 1312817669:Ba=!this.chk;s.append(" volume");break;case 1073741974:this.setShapeId(a,++n,ya);ua=null==this.getShapeProperty(a,"ID");n=b.iToken;break;case 1073741888:603979967==this.tokAt(n+1)&&(Aa=!0,n++);pa=this.paramAsStr(++n).toLowerCase();pa.equals("sets")?
s.append(' colorScheme "sets"'):b.isColorParam(n)&&(pa=b.getColorRange(n),n=b.iToken);break;case 1073741828:z="addHydrogens";x=Boolean.TRUE;s.append(" addHydrogens");break;case 1073741836:z="angstroms";s.append(" angstroms");break;case 1073741837:z="anisotropy";x=this.getPoint3f(++n,!1);s.append(" anisotropy").append(JU.Escape.eP(x));n=b.iToken;break;case 1073741842:m=!this.chk;s.append(" area");break;case 1073741850:case 1073742076:l=!0;N&&!v&&(s.append(' phase "_orb"'),this.addShapeProperty(C,"phase",
"_orb"));var ga=w(7,0);ga[0]=this.intParameter(++n);ga[1]=this.intParameter(++n);ga[2]=this.intParameter(++n);ga[3]=this.isFloatParameter(n+1)?this.floatParameter(++n):6;s.append(" atomicOrbital ").appendI(y(ga[0])).append(" ").appendI(y(ga[1])).append(" ").appendI(y(ga[2])).append(" ").appendF(ga[3]);134217751==this.tokAt(n+1)&&(n+=2,ga[4]=this.intParameter(n),ga[5]=3==this.tokAt(n+1)?this.floatParameter(++n):0,ga[6]=2==this.tokAt(n+1)?this.intParameter(++n):-System.currentTimeMillis()%1E4,s.append(" points ").appendI(y(ga[4])).appendC(" ").appendF(ga[5]).appendC(" ").appendI(y(ga[6])));
z="hydrogenOrbital";x=ga;break;case 1073741866:s.append(" binary");continue;case 1073741868:s.append(" blockData");z="blockData";x=Boolean.TRUE;break;case 1073741875:case 554176565:E=!0;z=b.theToken.value;x=this.getCapSlabObject(n,!1);n=b.iToken;break;case 1073741876:h||this.invArg();var O=!0,Nb=this.isFloatParameter(n+1)?this.floatParameter(++n):1.2,pb=this.isFloatParameter(n+1)?this.floatParameter(++n):10;if(this.chk)continue;if(50<pb){b.integerOutOfRange(0,50);return}s.append(" cavity ").appendF(Nb).append(" ").appendF(pb);
this.addShapeProperty(C,"envelopeRadius",Float.$valueOf(pb));this.addShapeProperty(C,"cavityRadius",Float.$valueOf(Nb));z="cavity";break;case 1073741896:case 1073741900:z="contour";s.append(" contour");switch(this.tokAt(n+1)){case 1073741920:x=b.floatParameterSet(n+2,1,2147483647);s.append(" discrete ").append(JU.Escape.eAF(x));n=b.iToken;break;case 1073741981:Q=this.getPoint3f(n+2,!1);(0>=Q.z||Q.y<Q.x)&&this.invArg();Q.z==y(Q.z)&&Q.z>Q.y-Q.x&&(Q.z=(Q.y-Q.x)/Q.z);x=Q;n=b.iToken;s.append(" increment ").append(JU.Escape.eP(Q));
break;default:x=Integer.$valueOf(2==this.tokAt(n+1)?this.intParameter(++n):0),s.append(" ").appendO(x),2==this.tokAt(n+1)&&(this.addShapeProperty(C,z,x),x=Integer.$valueOf(-Math.abs(this.intParameter(++n))),s.append(" ").appendO(x))}break;case 1073741910:s.append(" cutoff ");268435617==this.tokAt(++n)?(z="cutoffPositive",x=Float.$valueOf($=this.floatParameter(++n)),s.append("+").appendO(x)):this.isFloatParameter(n)?(z="cutoff",x=Float.$valueOf($=this.floatParameter(n)),s.appendO(x)):Ha?(z="cutoffRange",
x=b.floatParameterSet(n,2,2),this.addShapeProperty(C,"cutoff",Float.$valueOf(0)),s.append(JU.Escape.eAF(x)),n=b.iToken):this.invArg();break;case 1073741928:z="downsample";x=Integer.$valueOf(this.intParameter(++n));s.append(" downsample ").appendO(x);break;case 1073741931:z="eccentricity";x=b.getPoint4f(++n);s.append(" eccentricity ").append(JU.Escape.eP4(x));n=b.iToken;break;case 1073741932:s.append(" ed");this.setMoData(C,-1,null,0,!1,ba,null,null,!1);l=!0;continue;case 536870916:case 1073742041:s.append(" ").appendO(b.theToken.value);
z="debug";x=536870916==R?Boolean.TRUE:Boolean.FALSE;break;case 12293:s.append(" fixed");z="fixed";x=Boolean.TRUE;break;case 1073741962:s.append(" fullPlane");z="fullPlane";x=Boolean.TRUE;break;case 1073741966:case 1073741968:var Yb=1073741968==R,z=""+b.theToken.value,wa=new JU.Lst,x=wa,I=l=!0;s.append(" ").append(z);var ka=this.paramAsStr(++n);if(ka.equals("=")){s.append(" =");ka=this.paramAsStr(++n);s.append(" ").append(JU.PT.esc(ka));wa.addLast(ka);this.chk||this.addShapeProperty(C,"func",this.createFunction("__iso__",
"x,y,z",ka));break}var qb=JU.PT.getQuotedAttribute(b.fullCommand,"# DATA"+(I?"2":""));null==qb?qb="inline":ka=qb;var Ob=0==ka.indexOf("data2d_"),Zb=0==ka.indexOf("data3d_"),gb=ka.equals("inline");s.append(" inline");wa.addLast(ka);var Pb=this.getPoint3f(++n,!1);s.append(" ").append(JU.Escape.eP(Pb));wa.addLast(Pb);var xa;F=++b.iToken;wa.addLast(xa=b.getPoint4f(F));s.append(" ").append(JU.Escape.eP4(xa));U=y(xa.x);W=++b.iToken;wa.addLast(xa=b.getPoint4f(W));s.append(" ").append(JU.Escape.eP4(xa));
V=y(xa.x);wa.addLast(xa=b.getPoint4f(++b.iToken));s.append(" ").append(JU.Escape.eP4(xa));H=y(xa.x);(0==U||0==V||0==H)&&this.invArg();if(!this.chk){var la=null,sa=null;if(Yb){gb?(U=Math.abs(U),V=Math.abs(V),H=Math.abs(H),sa=this.floatArraySetXYZ(++b.iToken,U,V,H)):sa=Zb?this.vwr.getDataObj(ka,null,3):this.vwr.functionXYZ(ka,U,V,H);U=Math.abs(U);V=Math.abs(V);H=Math.abs(H);null==sa&&(b.iToken=F,b.errorStr(53,"xyzdata is null."));if(sa.length!=U||sa[0].length!=V||sa[0][0].length!=H)b.iToken=F,b.errorStr(53,
"xyzdata["+sa.length+"]["+sa[0].length+"]["+sa[0][0].length+"] is not of size ["+U+"]["+V+"]["+H+"]");wa.addLast(sa);s.append(" ").append(JU.Escape.e(sa))}else{gb?(U=Math.abs(U),V=Math.abs(V),la=this.floatArraySet(++b.iToken,U,V)):Ob?(la=this.vwr.getDataObj(ka,null,2),U=null==la?0:la.length,V=3):(la=this.vwr.functionXY(ka,U,V),U=Math.abs(U),V=Math.abs(V));null==la&&(b.iToken=F,b.errorStr(53,"fdata is null."));la.length!=U&&!Ob&&(b.iToken=F,b.errorStr(53,"fdata length is not correct: "+la.length+" "+
U+"."));for(ea=0;ea<U;ea++)null==la[ea]&&(b.iToken=W,b.errorStr(53,"fdata["+ea+"] is null.")),la[ea].length!=V&&(b.iToken=W,b.errorStr(53,"fdata["+ea+"] is not the right length: "+la[ea].length+" "+V+"."));wa.addLast(la);s.append(" ").append(JU.Escape.e(la))}}n=b.iToken;break;case 1073742188:var $b=this.e.isAtomExpression(++n),Qb=this.getAllPoints(n,1);s.append(" value "+($b?this.e.atomExpressionAt(n).toString():JU.Escape.eAP(Qb)));z="probes";x=Qb;n=this.e.iToken;break;case 1073741970:z="gridPoints";
s.append(" gridPoints");break;case 1073741976:z="ignore";x=ia=this.atomExpressionAt(++n);s.append(" ignore ").append(JU.Escape.eBS(ia));n=b.iToken;break;case 1073741985:z="insideOut";s.append(" insideout");break;case 1073741988:case 1073741986:case 1073742100:s.append(" ").appendO(b.theToken.value);z="pocket";x=1073742100==R?Boolean.TRUE:Boolean.FALSE;break;case 1073742002:z="lobe";x=b.getPoint4f(++n);n=b.iToken;s.append(" lobe ").append(JU.Escape.eP4(x));l=!0;break;case 1073742004:case 1073742006:z=
"lp";x=b.getPoint4f(++n);n=b.iToken;s.append(" lp ").append(JU.Escape.eP4(x));l=!0;break;case 4125:(p||this.slen==n+1)&&this.invArg();p=!0;if((O||oa||A)&&!l)l=!0,this.addShapeProperty(C,"bsSolvent",oa||A?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(C,"sasurface",Float.$valueOf(0));0==s.length()?(na=this.getShapeProperty(24,"plane"),null==na?null!=this.getShapeProperty(24,"contours")&&this.addShapeProperty(C,"nocontour",null):(this.addShapeProperty(C,"plane",na),s.append("plane ").append(JU.Escape.eP4(na)),
q=!0,na=null)):!l&&!q&&this.invArg();s.append("; isosurface map");this.addShapeProperty(C,"map",l?Boolean.TRUE:Boolean.FALSE);break;case 1073742014:z="maxset";x=Integer.$valueOf(this.intParameter(++n));s.append(" maxSet ").appendO(x);break;case 1073742020:z="minset";x=Integer.$valueOf(this.intParameter(++n));s.append(" minSet ").appendO(x);break;case 1073742112:l=!0;z="rad";x=b.getPoint4f(++n);n=b.iToken;s.append(" radical ").append(JU.Escape.eP4(x));break;case 1073742027:z="fixed";x=Boolean.FALSE;
s.append(" modelBased");break;case 1073742028:case 1073742135:case 1612709912:var Ma=b.theToken.value,ab;1073742028==R?(z="molecular",s.append(" molecular"),ab=this.isFloatParameter(n+1)?this.floatParameter(++n):1.4):(this.addShapeProperty(C,"bsSolvent",b.lookupIdentifierValue("solvent")),z=1073742135==R?"sasurface":"solvent",s.append(" ").appendO(b.theToken.value),ab=this.isFloatParameter(n+1)?this.floatParameter(++n):this.vwr.getFloat(570425394));s.append(" ").appendF(ab);x=Float.$valueOf(ab);1073741961==
this.tokAt(n+1)&&(this.addShapeProperty(C,"doFullMolecular",null),s.append(" full"),n++);l=!0;break;case 1073742032:this.addShapeProperty(C,"fileType","Mrc");s.append(" mrc");continue;case 1140850696:var fa=b.stringParameter(++n);this.addShapeProperty(C,"fileType",fa);s.append(' type "'+fa+'"');continue;case 1073742064:case 1073742062:this.addShapeProperty(C,"fileType","Obj");s.append(" obj");continue;case 1073742033:this.addShapeProperty(C,"fileType","Msms");s.append(" msms");continue;case 1073742094:l&&
this.invArg();z="phase";v=!0;x=4==this.tokAt(n+1)?this.stringParameter(++n):"_orb";s.append(" phase ").append(JU.PT.esc(x));break;case 1073742104:case 1073742122:z="resolution";x=Float.$valueOf(this.floatParameter(++n));s.append(" resolution ").appendO(x);break;case 1073742124:z="reverseColor";x=Boolean.TRUE;s.append(" reversecolor");break;case 1073742127:case 1073742146:z="sigma";x=Float.$valueOf(Z=this.floatParameter(++n));s.append(" sigma ").appendO(x);break;case 1112150021:z="geodesic";x=Float.$valueOf(this.floatParameter(++n));
s.append(" geosurface ").appendO(x);l=!0;break;case 1073742154:z="sphere";x=Float.$valueOf(this.floatParameter(++n));s.append(" sphere ").appendO(x);l=!0;break;case 1073742156:z="squareData";x=Boolean.TRUE;s.append(" squared");break;case 1073741984:z=!l&&!q&&!p?"readFile":"mapColor";ja=this.stringParameter(++n);null==ja&&this.invArg();f&&(ja=JU.PT.replaceWithCharacter(ja,"{,}|"," "));b.debugHigh&&JU.Logger.debug("pmesh inline data:\n"+ja);x=this.chk?null:ja;this.addShapeProperty(C,"fileName","");
s.append(" INLINE ").append(JU.PT.esc(ja));l=!0;break;case 268435520:case 1073742195:case 7:(null!=hb||ua)&&this.invArg();var bb=b.listParameter4(n,2,2147483647,!0),n=b.iToken,Va=D(bb.size()/2);(0==Va||2*Va!=bb.size())&&this.invArg();var rb=Array(Va),sb=w(Va,0);s.append("[");try{for(var Rb=ea=0;ea<Va;ea++)sb[ea]=bb.get(Rb++).floatValue(),rb[ea]=this.e.checkFileExists("ISOSURFACE_"+ea+"_",!1,bb.get(Rb++),n,!1),s.appendF(sb[ea]),s.append(" /*file*/").append(JU.PT.esc(rb[ea]));s.append("]")}catch(Sb){if(Y(Sb,
Exception))this.invArg();else throw Sb;}hb=B(-1,[rb,sb]);z=!l&&!q&&!p?"readFile":"mapColor";l=!0;if(this.chk)break;this.addShapeProperty(C,"filesData",hb);break;case 545259556:case 545259557:case 1073741914:case 4:var tb=!l&&!q,L=null,z=tb&&!p?"readFile":"mapColor";4==R?L=this.paramAsStr(n):1073741914==R&&(L="=density/");if(null==L||0==L.length||L.equals("*")||L.equals("=")){var Tb=this.vwr.getPdbID();null==Tb&&b.errorStr(22,"no PDBID available");L="*"+(545259557==R?"*":"")+Tb}var Ub=!1;L.startsWith("http://eds.bmc.uu.se/eds/dfs/cb/")&&
L.endsWith(".omap")&&(L=(0<=L.indexOf("_diff")?"*":"")+"*"+L.substring(32,36));if(L.startsWith("*")||L.startsWith("=")){var ac=!Float.isNaN($)||!Float.isNaN(Z),ub=0<=L.indexOf("/full");ub&&(L=JU.PT.rep(L,"/full",""));0<=L.indexOf("/diff")&&(L="*"+L.substring(0,L.indexOf("/diff")));L.startsWith("**")&&(ac||this.addShapeProperty(C,"sigma",Float.$valueOf(Z=3)),La||(La=!0,s.append(" sign"),this.addShapeProperty(C,"sign",Boolean.TRUE)));var bc=L,L=this.vwr.setLoadFormat(L,this.chk?"?":ub?"_":"-",!1);null==
L&&b.errorStr(22,"error parsing filename: "+bc);Ub=!ub}Ub&&(null==ca&&0==ha&&(Ma=L,0>ba&&(ba=this.vwr.am.cmi),S=this.vwr.getModelUndeletedAtomsBitSet(ba),0<=S.nextSetBit(0)&&(ca=this.getWithinDistanceVector(C,2,null,S,!1),s.append(" within 2.0 ").append(JU.Escape.eBS(S)))),null!=ca&&0<=L.indexOf("/0,0,0/0,0,0?")&&(L=L.$replace("0,0,0/0,0,0",ca[0].x+","+ca[0].y+","+ca[0].z+"/"+ca[ca.length-1].x+","+ca[ca.length-1].y+","+ca[ca.length-1].z)),tb&&(Ia=!0));var cb=null==L?-1:L.indexOf("#-");if(Float.isNaN(Z)&&
Float.isNaN($))if(0<=(cb=L.indexOf("#-cutoff=")))this.addShapeProperty(C,"cutoff",Float.$valueOf($=Float.parseFloat(L.substring(cb+9)))),s.append(" cutoff "+$);else if(0<=(cb=L.indexOf("#-sigma=")))this.addShapeProperty(C,"sigma",Float.$valueOf(Z=Float.parseFloat(L.substring(cb+8)))),s.append(" sigma "+Z);Float.isNaN(Z)?Float.isNaN($)||this.showString("using cutoff = "+$):this.showString("using sigma = "+Z);tb&&(this.vwr.getP("_fileType").equals("Pdb")&&Float.isNaN(Z)&&Float.isNaN($))&&(this.addShapeProperty(C,
"sigma",Float.$valueOf(-1)),s.append(" sigma -1.0"));0==L.length&&(0>ba&&(ba=this.vwr.am.cmi),L=b.getFullPathName(!1),x=this.vwr.ms.getInfo(ba,"jmolSurfaceInfo"));var vb=-1;null==x&&2==this.tokAt(n+1)&&this.addShapeProperty(C,"fileIndex",Integer.$valueOf(vb=this.intParameter(++n)));var Wa=4==this.tokAt(n+1)?this.stringParameter(++n):null,l=!0;if(this.chk)break;var Vb,za=null;null==x&&(0<=b.fullCommand.indexOf("# FILE0=")?(L=JU.PT.getQuotedAttribute(b.fullCommand,"# FILE0"),1073741848==this.tokAt(n+
1)&&(n+=2)):1073741848==this.tokAt(n+1)&&(za=this.vwr.fm.getFilePath(this.stringParameter(b.iToken=n+=2),!1,!1),Vb=this.vwr.getFullPathNameOrError(za),za=Vb[0],""!==this.vwr.fm.getPathForAllFiles()?(L=za,za=null):this.addShapeProperty(C,"localName",za)));null==Wa&&(L=this.e.checkFileExists("ISOSURFACE_"+(p?"MAP_":""),!1,L,n,!1));this.showString("reading isosurface data from "+L);null!=Wa&&(x=this.vwr.fm.cacheGet(L,!1),this.addShapeProperty(C,"calculationType",Wa));null==x&&(this.addShapeProperty(C,
"fileName",L),null!=za&&(L=za),0<=vb&&s.append(" ").appendI(vb));s.append(" /*file*/").append(JU.PT.esc(L));null!=Wa&&s.append(" ").append(JU.PT.esc(Wa));break;case 4106:z="connections";switch(this.tokAt(++n)){case 12290:case 10:case 1073742325:x=u(-1,[this.atomExpressionAt(n).nextSetBit(0)]);break;default:x=u(-1,[y(b.floatParameterSet(n,1,1)[0])])}n=b.iToken;break;case 1094713347:z="atomIndex";x=Integer.$valueOf(this.intParameter(++n));break;case 1073741999:z="link";s.append(" link");break;case 1814695966:24!=
a&&this.invArg();268435617==this.tokAt(n+1)&&n++;z="extendGrid";x=Float.$valueOf(this.floatParameter(++n));s.append(" unitcell "+x);break;case 1073741994:24!=a&&this.invArg();Q=this.getPoint3f(++n,!1);n=b.iToken;if(0>=Q.x||0>=Q.y||0>=Q.z)break;Q.x=y(Q.x);Q.y=y(Q.y);Q.z=y(Q.z);s.append(" lattice ").append(JU.Escape.eP(Q));p?(z="mapLattice",x=Q):(ta=Q,12293==this.tokAt(n+1)&&(s.append(" fixed"),va=!0,n++));break;default:1073741824==R&&(z="thisID",x=ja);if(!b.setMeshDisplayProperty(a,0,R)){if(JS.T.tokAttr(R,
1073741824)&&!ya){this.setShapeId(a,n,ya);n=b.iToken;break}this.invArg()}0==c&&(c=n);n=this.slen-1}ya=12291!=R;ua&&l&&this.invArg();null!=z&&this.addShapeProperty(C,z,x)}if(!this.chk){if((O||oa)&&!l)l=!0,this.addShapeProperty(C,"bsSolvent",oa?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(C,"sasurface",Float.$valueOf(0));q&&(!l&&!p)&&(this.addShapeProperty(C,"nomap",Float.$valueOf(0)),l=!0);null!=P&&this.addShapeProperty(C,"getSurfaceSets",P);if(null!=Na)this.addShapeProperty(C,
"colorDiscrete",Na);else if("sets".equals(pa))this.addShapeProperty(C,"setColorScheme",null);else if(null!=pa){var db=this.vwr.cm.getColorEncoder(pa);null!=db&&(db.isTranslucent=Aa,db.hi=3.4028235E38,this.addShapeProperty(C,"remapColor",db))}if(l&&!k&&0!=s.indexOf(";")){C.add(0,B(-1,["newObject",null]));var Wb=null==X;Wb&&(X=JU.BSUtil.copy(this.vwr.bsA()));0>ba&&(ba=this.vwr.am.cmi);X.and(this.vwr.getModelUndeletedAtomsBitSet(ba));null!=Ma&&(1<this.vwr.ms.getModelBS(X,!1).cardinality()&&b.errorStr(30,
"ISOSURFACE "+Ma),Wb&&(C.add(0,B(-1,["select",X])),0==s.indexOf("; isosurface map")&&(s=(new JU.SB).append("; isosurface map select ").append(JU.Escape.eBS(X)).append(s.substring(16)))))}A&&!E&&(l||this.addShapeProperty(C,"sasurface",Float.$valueOf(0)),p||(this.addShapeProperty(C,"map",Boolean.TRUE),this.addShapeProperty(C,"select",S),this.addShapeProperty(C,"sasurface",Float.$valueOf(0))),this.addShapeProperty(C,"slab",this.getCapSlabObject(-100,!1)));var Xb=l&&this.vwr.getBoolean(603979934);Xb&&
JU.Logger.startTimer("isosurface");this.setShapeProperty(a,"setProperties",C);Xb&&this.showString(JU.Logger.getTimerMsg("isosurface",0));Ia&&(this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,"token",Integer.$valueOf(1073742046)),r=!0,s.append(" mesh nofill frontOnly"))}null!=ta&&(this.setShapeProperty(a,"lattice",ta),va&&this.setShapeProperty(a,"fixLattice",Boolean.TRUE));null!=Fa&&this.setShapeProperty(a,"symops",Fa);r&&this.setShapeProperty(a,"token",Integer.$valueOf(1073741960));
0<c&&(b.setMeshDisplayProperty(a,c,0)||this.invArg());if(!this.chk){var Da=null,Ea=null;m&&(Da=this.getShapeProperty(a,"area"),T(Da,Float)?this.vwr.setFloatProperty("isosurfaceArea",Da.floatValue()):this.vwr.g.setUserVariable("isosurfaceArea",JS.SV.getVariableAD(Da)));Ba&&(Ea=Ba?this.getShapeProperty(a,"volume"):null,T(Ea,Float)?this.vwr.setFloatProperty("isosurfaceVolume",Ea.floatValue()):this.vwr.g.setUserVariable("isosurfaceVolume",JS.SV.getVariableAD(Ea)));if(!k){fa=null;p&&!l?this.setShapeProperty(a,
"finalize",s.toString()):l&&(M=s.toString(),this.setShapeProperty(a,"finalize",(0==M.indexOf("; isosurface map")?"":" select "+JU.Escape.eBS(X)+" ")+M),fa=this.getShapeProperty(a,"ID"),null!=fa&&(!b.tQuiet&&!g)&&($=this.getShapeProperty(a,"cutoff").floatValue(),Float.isNaN($)&&!Float.isNaN(Z)&&JU.Logger.error("sigma not supported"),fa+=" created "+this.getShapeProperty(a,"message")));var wb,xb;if(m||Ba)wb=m?"isosurfaceArea = "+(T(Da,Float)?""+Da:JU.Escape.eAD(Da)):null,xb=Ba?"isosurfaceVolume = "+
(T(Ea,Float)?""+Ea:JU.Escape.eAD(Ea)):null,null==fa?(m&&this.showString(wb),Ba&&this.showString(xb)):(m&&(fa+="\n"+wb),Ba&&(fa+="\n"+xb));null!=fa&&!g&&this.showString(fa);l&&(fa=this.getShapeProperty(a,"output"),null!=fa&&!g&&this.showString(fa))}null!=ib&&this.setShapeProperty(a,"translucency",ib);this.setShapeProperty(a,"clear",null);aa&&this.setShapeProperty(a,"cache",null);!g&&(!d&&!E&&12291!=b.theTok)&&this.listIsosurface(a)}}},"~N");e(c$,"lcaoCartoon",function(){var a=this.e;a.sm.loadShape(26);
if(!(1073742001==a.tokAt(1)&&this.listIsosurface(26)))if(this.setShapeProperty(26,"init",a.fullCommand),1==this.slen)this.setShapeProperty(26,"lcaoID",null);else{for(var b=!1,c=null,c=1;c<this.slen;c++){var d=null,j=null;switch(this.getToken(c).tok){case 1073741875:case 554176565:d=a.theToken.value;1073742334==this.tokAt(c+1)&&(a.iToken=c+1);j=this.getCapSlabObject(c,!0);c=a.iToken;break;case 12289:this.isosurface(26);return;case 528432:var h=j=0,f=0;switch(this.getToken(++c).tok){case 1111492629:j=
0.017453292*this.floatParameter(++c);break;case 1111492630:h=0.017453292*this.floatParameter(++c);break;case 1111492631:f=0.017453292*this.floatParameter(++c);break;default:this.invArg()}d="rotationAxis";j=JU.V3.new3(j,h,f);break;case 1073742335:case 1610625028:case 2097192:d="on";break;case 1073742334:case 12294:case 2097194:d="off";break;case 12291:d="delete";break;case 12290:case 10:case 1073742325:d="select";j=this.atomExpressionAt(c);c=a.iToken;break;case 1765808134:c=this.setColorOptions(null,
c+1,26,-2);null!=c&&this.setShapeProperty(26,"settranslucency",c);c=a.iToken;b=!0;continue;case 603979967:case 1073742074:a.setMeshDisplayProperty(26,c,a.theTok);c=a.iToken;b=!0;continue;case 1112152075:case 4:j=this.paramAsStr(c).toLowerCase();j.equals("spacefill")&&(j="cpk");d="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,d="molecular");break;case 1275082245:a.isAtomExpression(c+1)?(d="select",j=this.atomExpressionAt(c+1),c=a.iToken):(d="selectType",j=this.paramAsStr(++c),
j.equals("spacefill")&&(j="cpk"));break;case 536875009:d="scale";j=Float.$valueOf(this.floatParameter(++c));break;case 1073742004:case 1073742006:d="lonePair";break;case 1073742112:case 1073742111:d="radical";break;case 1073742028:d="molecular";break;case 1073741904:j=this.paramAsStr(++c);d="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,d="molecular");break;case 1073741974:j=a.setShapeNameParameter(++c);c=a.iToken;b&&this.invArg();d="lcaoID";break;default:if(268435633==a.theTok||
JS.T.tokAttr(a.theTok,1073741824))268435633!=a.theTok&&(j=this.paramAsStr(c)),b&&this.invArg(),d="lcaoID"}12291!=a.theTok&&(b=!0);null==d&&this.invArg();this.setShapeProperty(26,d,j)}this.setShapeProperty(26,"clear",null)}});e(c$,"contact",function(){var a=this.e;a.sm.loadShape(25);if(1073742001==this.tokAt(1)&&this.listIsosurface(25))return!1;var b=0;a.iToken=1;for(var c=null!=this.initIsosurface(25),d=c&&null==this.getShapeProperty(25,"ID"),j=null,h=null,f=null,e=null,k=null,g=!1,l=new JU.SB,q=
2147483647,p=134217750,N=0,v=NaN,m=NaN,u=!0,y=null,H=null,F=0,aa=!1,I=-2147483648,E=1<a.iToken,A=a.iToken;A<this.slen;++A){switch(f=this.getToken(A).tok){default:E=!0;if(!a.setMeshDisplayProperty(25,0,a.theTok)){268435633!=a.theTok&&!JS.T.tokAttr(a.theTok,1073741824)&&this.invArg();this.setShapeId(25,A,c);A=a.iToken;break}0==b&&(b=A);A=a.iToken;continue;case 1073741974:E=!0;this.setShapeId(25,++A,c);d=null==this.getShapeProperty(25,"ID");A=a.iToken;break;case 1765808134:switch(this.tokAt(A+1)){case 1073741914:f=
0;g=!0;l.append(" color density");A++;break;case 1140850696:f=0,aa=!0,l.append(" color type"),A++}if(0==f)break;case 603979967:case 1073742074:E=!0;0==F&&(F=A);a.setMeshDisplayProperty(25,A,a.theTok);A=a.iToken;break;case 554176565:E=!0;H=this.getCapSlabObject(A,!1);this.setShapeProperty(25,"slab",H);A=a.iToken;break;case 1073741914:g=!0;l.append(" density");this.isFloatParameter(A+1)&&(null==k&&(k=w(1,0)),k[0]=-Math.abs(this.floatParameter(++A)),l.append(" "+-k[0]));break;case 1073742122:c=this.floatParameter(++A);
0<c&&(l.append(" resolution ").appendF(c),this.setShapeProperty(25,"resolution",Float.$valueOf(c)));break;case 1094717454:case 1094713359:I=1094713359==a.theTok?this.intParameter(++A):a.modelNumberParameter(++A);l.append(" modelIndex "+I);break;case 134217759:case 1275069443:v=this.floatParameter(++A);l.append(" within ").appendF(v);break;case 268435617:case 2:case 3:e=a.encodeRadiusParameter(A,!1,!1);if(null==e)return!1;l.append(" ").appendO(e);A=a.iToken;break;case 1073741990:case 1073741989:y=
1073741989==f?Boolean.TRUE:Boolean.FALSE;l.append(" ").appendO(a.theToken.value);break;case 1073742020:q=this.intParameter(++A);break;case 1613238294:case 1073741881:case 1648363544:N=f;l.append(" ").appendO(a.theToken.value);break;case 1073742135:this.isFloatParameter(A+1)&&(m=this.floatParameter(++A));case 1073741875:case 1073742036:case 2097180:u=!1;case 1275068932:case 1073741961:case 134217750:case 4106:p=f;l.append(" ").appendO(a.theToken.value);1073742135==f&&l.append(" ").appendF(m);break;
case 1073742083:k=a.floatParameterSet(++A,1,10);A=a.iToken;break;case 12290:case 10:case 1073742325:(d||null!=h)&&this.invArg(),f=JU.BSUtil.copy(this.atomExpressionAt(A)),A=a.iToken,null==j?j=f:h=f,l.append(" ").append(JU.Escape.eBS(f))}c=12291!=a.theTok}!E&&null==j&&this.error(13);if(this.chk)return!1;if(null!=j){1648363544==N&&null==e&&(e=new J.atomdata.RadiusData(null,0,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO));A=null==e?new J.atomdata.RadiusData(null,0.26,J.atomdata.RadiusData.EnumType.OFFSET,
J.c.VDW.AUTO):e;h=1073742036==p&&null==h&&null!=y&&y.booleanValue()?j:a.getMathExt().setContactBitSets(j,h,u,v,A,!0);switch(p){case 1073741875:case 1073742135:A=a.lookupIdentifierValue("solvent");j.andNot(A);h.andNot(A);h.andNot(j);break;case 2097180:h.andNot(j);break;case 1073742036:2147483647==q&&(q=100),this.setShapeProperty(25,"minset",Integer.$valueOf(q)),l.append(" minSet ").appendI(q),null==k&&(k=w(-1,[0.5,2]))}null!=y&&(k=null==k?w(2,0):JU.AU.ensureLengthA(k,2),k[1]=y.booleanValue()?1:2);
null!=k&&l.append(" parameters ").append(JU.Escape.eAF(k));this.setShapeProperty(25,"set",B(-1,[Integer.$valueOf(N),Integer.$valueOf(p),Boolean.$valueOf(g),Boolean.$valueOf(aa),j,h,e,Float.$valueOf(m),k,Integer.$valueOf(I),l.toString()]));0<F&&a.setMeshDisplayProperty(25,F,0)}0<b&&(a.setMeshDisplayProperty(25,b,0)||this.invArg());null!=H&&null!=j&&this.setShapeProperty(25,"slab",H);if(null!=j&&(1073742036==p||u)){j=this.getShapeProperty(25,"volume");b=1073741961==p;if(JU.AU.isAD(j))for(A=a=0;A<j.length;A++)a+=
b?j[A]:Math.abs(j[A]);else a=j.floatValue();a=Math.round(1E3*a)/1E3;if(g||1275068932!=p)g=this.getShapeProperty(25,"nSets").intValue(),g="Contacts: "+(0>g?D(-g/2):g),0!=a&&(g+=", with "+(b?"approx ":"net ")+"volume "+a+" A^3"),this.showString(g)}return!0});e(c$,"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),d=c&&null==this.getShapeProperty(23,"ID"),j=!1,h=-1,f=null,e=3.4028235E38,k=u(-1,[-2147483648]),
g=0,l=a.iToken;l<this.slen;++l){var q=null,h=null;switch(this.getToken(l).tok){case 268435520:case 1073742195:case 7:(null!=f||d)&&this.invArg();f=new JU.Lst;l=u(-1,[l,this.slen]);a.getShapePropertyData(23,"data",B(-1,[this.st,l,f,this.vwr]))||this.invArg();l=l[0];continue;case 536875009:++l>=this.slen&&this.error(34);switch(this.getToken(l).tok){case 2:g=this.intParameter(l);continue;case 3:g=Math.round(100*this.floatParameter(l));continue}this.error(34);break;case 12293:q="modelIndex";h=Integer.$valueOf(-1);
break;case 1094713359:case 1094717454:h=1094713359==a.theTok?this.intParameter(++l):a.modelNumberParameter(++l);q="modelIndex";h=Integer.$valueOf(h);break;case 1765808134:case 603979967:case 1073742074:e=this.getColorTrans(a,l,!1,k);l=a.iToken;c=!0;continue;case 1073741974:this.setShapeId(23,++l,c);d=null==this.getShapeProperty(23,"ID");l=a.iToken;break;default:if(!a.setMeshDisplayProperty(23,0,a.theTok)){if(268435633==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(23,l,c);l=a.iToken;
break}this.invArg()}0==b&&(b=l);l=a.iToken;continue}c=12291!=a.theTok;null!=f&&!j&&(q="points",h=Integer.$valueOf(g),j=!0,g=0);null!=q&&this.setShapeProperty(23,q,h)}this.finalizeObject(23,k[0],e,g,null!=f,f,b,null);return!0});e(c$,"getAtomicPotentials",function(a,b,c){var d=w(this.vwr.ms.ac,0),j=J.api.Interface.getOption("quantum.MlpCalculation",this.vwr,"script");j.set(this.vwr);c=null==c?null:this.vwr.getFileAsString3(c,!1,null);try{j.assignPotentials(this.vwr.ms.at,d,this.vwr.getSmartsMatch("a",
a),this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]",a),b,c)}catch(h){if(!Y(h,Exception))throw h;}return d},"JU.BS,JU.BS,~S");e(c$,"getCapSlabObject",function(a,b){if(0>a)return JU.TempArray.getSlabWithinRange(a,0);var c=this.e,d=null,j=554176565==this.tokAt(a),h=this.tokAt(a+1),f=null,e=f=null,k=null,g=null;if(603979967==h)switch(k=this.isFloatParameter(++a+1)?this.floatParameter(++a):0.5,c.isColorParam(a+1)?(k=Short.$valueOf(JU.C.getColixTranslucent3(JU.C.getColix(c.getArgbParam(a+1)),
0!=k,k)),a=c.iToken):k=Short.$valueOf(JU.C.getColixTranslucent3(1,0!=k,k)),h=this.tokAt(a+1)){case 1073742018:case 1073741938:g=Integer.$valueOf(h);h=this.tokAt(++a+1);break;default:g=Integer.$valueOf(1073741938)}switch(h){case 1073742334:return c.iToken=a+1,Integer.$valueOf(-2147483648);case 1073742333:c.iToken=a+1;break;case 1073742330:a++;d=B(-1,[Float.$valueOf(1),this.paramAsStr(++a)]);h=1073742018;break;case 134217759:a++;if(1073742114==this.tokAt(++a))d=this.floatParameter(++a),h=this.floatParameter(++a),
d=B(-1,[Float.$valueOf(d),Float.$valueOf(h)]),h=1073742114;else if(this.isFloatParameter(a)){d=this.floatParameter(a);if(c.isCenterParameter(++a)){var f=Array(1),l=c.centerParameter(a,f);if(this.chk||!T(f[0],JU.BS))f=B(-1,[l]);else for(var l=this.vwr.ms.at,e=f[0],f=Array(e.cardinality()),q=0,p=e.nextSetBit(0);0<=p;p=e.nextSetBit(p+1),q++)f[q]=l[p]}else f=c.getPointArray(a,-1,!1);0==f.length&&(c.iToken=a,this.invArg());d=B(-1,[Float.$valueOf(d),f,e])}else d=c.getPointArray(a,4,!1),h=1678381065;break;
case 1678381065:c.iToken=a+1;d=JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(),null);break;case 1073741872:case 1814695966:c.iToken=a+1;c=this.vwr.getCurrentUnitCell();if(null==c)1814695966==h&&this.invArg();else{f=JU.BoxInfo.toOABC(c.getUnitCellVerticesNoOffset(),c.getCartesianOffset());c=y(c.getUnitCellInfoType(6));d=e=null;switch(c){case 1:d=JU.V3.newVsub(f[2],f[0]),d.scale(1E3);case 2:e=JU.V3.newVsub(f[1],f[0]),e.scale(1E3),f[0].sub(e),f[1].scale(2E3),1==c&&(f[0].sub(d),f[2].scale(2E3))}d=f}break;
case 12290:case 10:case 1073742325:if(d=this.atomExpressionAt(a+1),h=3,!c.isCenterParameter(++c.iToken)){j=!0;break}default:if(!b&&j&&this.isFloatParameter(a+1)){d=this.floatParameter(++a);if(!this.isFloatParameter(a+1))return Integer.$valueOf(y(d));h=this.floatParameter(++a);d=B(-1,[Float.$valueOf(d),Float.$valueOf(h)]);h=1073742114;break}f=c.planeParameter(++a,!1);h=this.isFloatParameter(c.iToken+1)?this.floatParameter(++c.iToken):NaN;Float.isNaN(h)||(f.w-=h);d=f;h=134217750}k=null==g?null:B(-1,
[g,k]);return JU.TempArray.getSlabObjectType(h,d,!j,k)},"~N,~B");e(c$,"setColorOptions",function(a,b,c,d){var j=this.e;this.getToken(b);var h="opaque";if(603979967==j.theTok)if(h="translucent",0>d){var f=this.isFloatParameter(b+1)?this.floatParameter(++b):3.4028235E38;j.setShapeTranslucency(c,null,"translucent",f,null);null!=a&&(a.append(" translucent"),3.4028235E38!=f&&a.append(" ").appendF(f))}else j.setMeshDisplayProperty(c,b,j.theTok);else 1073742074==j.theTok?0<=d&&j.setMeshDisplayProperty(c,
b,j.theTok):j.iToken--;d=Math.abs(d);for(f=0;f<d;f++)if(j.isColorParam(j.iToken+1)){var e=j.getArgbParam(++j.iToken);this.setShapeProperty(c,"colorRGB",Integer.$valueOf(e));null!=a&&a.append(" ").append(JU.Escape.escapeColor(e))}else if(j.iToken<b)this.invArg();else break;return h},"JU.SB,~N,~N,~N");e(c$,"createFunction",function(a,b,c){var d=(new JS.ScriptEval).setViewer(this.vwr);try{d.compileScript(null,"function "+a+"("+b+") { return "+c+"}",!1);var j=new JU.Lst;for(a=0;a<b.length;a+=2)j.addLast(JS.SV.newF(0).setName(b.substring(a,
a+1)));return B(-1,[d.aatoken[0][1].value,j])}catch(h){if(Y(h,Exception))return null;throw h;}},"~S,~S,~S");e(c$,"getWithinDistanceVector",function(a,b,c,d,j){var h=new JU.Lst,f=Array(2);if(null==d){var e=JU.P3.new3(b,b,b),k=JU.P3.newP(c);k.sub(e);e.add(c);f[0]=k;f[1]=e;h.addLast(c)}else c=this.vwr.ms.getBoxInfo(d,-Math.abs(2*b)),f[0]=c.getBoundBoxVertices()[0],f[1]=c.getBoundBoxVertices()[7],1==d.cardinality()&&h.addLast(this.vwr.ms.at[d.nextSetBit(0)]);1==h.size()&&!j&&(this.addShapeProperty(a,
"withinDistance",Float.$valueOf(b)),this.addShapeProperty(a,"withinPoint",h.get(0)));this.addShapeProperty(a,j?"displayWithin":"withinPoints",B(-1,[Float.$valueOf(b),f,d,h]));return f},"JU.Lst,~N,JU.P3,JU.BS,~B");e(c$,"addShapeProperty",function(a,b,c){this.chk||a.addLast(B(-1,[b,c]))},"JU.Lst,~S,~O");e(c$,"floatArraySetXYZ",function(a,b,c,d){var j=this.e,h=this.tokAt(a++);1073742195==h&&(h=this.tokAt(a++));(268435520!=h||0>=b)&&this.invArg();for(var f=JU.AU.newFloat3(b,-1),e=0;268435521!=h;)switch(h=
this.getToken(a).tok,h){case 1073742195:case 268435521:continue;case 268435504:a++;break;case 268435520:f[e++]=this.floatArraySet(a,c,d);a=++j.iToken;h=0;e==b&&268435521!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return f},"~N,~N,~N,~N");e(c$,"floatArraySet",function(a,b,c){var d=this.tokAt(a++);1073742195==d&&(d=this.tokAt(a++));268435520!=d&&this.invArg();for(var j=JU.AU.newFloat2(b),h=0;268435521!=d;)switch(d=this.getToken(a).tok,d){case 1073742195:case 268435521:continue;case 268435504:a++;
break;case 268435520:a++;d=w(c,0);j[h++]=d;for(var f=0;f<c;f++)d[f]=this.floatParameter(a++),268435504==this.tokAt(a)&&a++;268435521!=this.tokAt(a++)&&this.invArg();d=0;h==b&&268435521!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return j},"~N,~N,~N");e(c$,"initIsosurface",function(a){var b=this.e;this.setShapeProperty(a,"init",b.fullCommand);b.iToken=0;var c=this.tokAt(1),d=this.tokAt(2);if(12291==c||12291==d&&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",B(-1,[b.thisCommand])),1073741974!=c&&(268435633==d||268435633==c&&b.setMeshDisplayProperty(a,0,d)))?(a=this.setShapeId(a,1,!1),b.iToken++,a):null},"~N");e(c$,"listIsosurface",function(a){var b=3<this.slen?"0":0==this.tokAt(2)?
"":" "+this.getToken(2).value;this.chk||this.showString(this.getShapeProperty(a,"list"+b));return!0},"~N");e(c$,"getBoxPoints",function(a,b,c,d){switch(a){case 1814695966:return null==b?null:b.getCanonicalCopy(d,!0);case 1678381065:return null==c?a=this.vwr.ms.getBoxInfo():(a=new JU.BoxInfo,this.vwr.calcAtomsMinMax(c,a)),JU.BoxInfo.getCanonicalCopy(a.getBoundBoxVertices(),d);default:return null}},"~N,J.api.SymmetryInterface,JU.BS,~N")});O("JU");F(["JU.TriangleData"],"JU.Triangulator","JU.AU $.BS $.Lst $.Measure $.P3 $.P4 $.V3".split(" "),
function(){c$=Aa(JU,"Triangulator",JU.TriangleData);e(c$,"intersectLine",function(a,b,c,d){b=new JU.V3;for(var j=new JU.V3,h=new JU.V3,f=new JU.V3,e=null,k=null,g=new JU.P3,l=new JU.P4,q=3.4028235E38,p=-3.4028235E38,N=0;12>N;N++){var v=JU.Triangulator.fullCubePolygon[N];if(0==N%2){JU.Measure.getPlaneThroughPoints(a[v[0]],a[v[1]],a[v[2]],b,j,l);if(null==JU.Measure.getIntersection(c,d,l,g,b,h)){N++;continue}f.sub2(g,c)}if(JU.Measure.isInTriangle(g,a[v[0]],a[v[1]],a[v[2]],b,j,h)){v=d.dot(f);v<q&&(q=
v,e=g);v>p&&(p=v,k=g);0==N%2&&N++;if(0.01<p-q)break;g=new JU.P3}}return null==e||(null==k||0.001>e.distance(k))&&null==(k=e)?null:B(-1,[e,k])},"~A,~N,JU.P3,JU.V3");e(c$,"getCellProjection",function(a,b){for(var c=new JU.V3,d=0,j=-3.4028235E38,h=0,f=Array(8),e=0;8>e;e++)d=b[e].dot(a),d>j&&(j=d,h=e),JU.Measure.getPlaneProjection(b[e],a,f[e]=new JU.P3,c);d=JU.Triangulator.fullCubeCorners[h][3];c=JU.AU.newInt2(6);for(e=j=0;12>e;e++)if(0!=(d&JU.TriangleData.Pwr2[e])){var k=u(4,0),g=JU.Triangulator.fullCubePolygon[e];
k[0]=g[0];k[1]=g[1];k[2]=g[2];k[3]=g[0]==h?2:g[1]==h?0:g[2]==h?1:3;c[j++]=k}h=new JU.Lst;h.addLast(f);h.addLast(c);return h},"JU.P4,~A");e(c$,"intersectPlane",function(a,b,c){if(-1==c&&8==b.length)return this.getCellProjection(a,b);for(var d=new JU.Lst,j=Array(12),h=0,f=w(8,0),e=0;8>e;e++)f[e]=a.x*b[e].x+a.y*b[e].y+a.z*b[e].z+a.w,0>f[e]&&(h|=JU.TriangleData.Pwr2[e]);a=JU.TriangleData.triangleTable2[h];if(null==a)return null;for(e=0;24>e;e+=2){var h=JU.TriangleData.edgeVertexes[e],k=JU.TriangleData.edgeVertexes[e+
1],g=JU.P3.newP(b[k]);g.sub(b[h]);g.scale(f[h]/(f[h]-f[k]));g.add(b[h]);j[e>>1]=g}if(0==c){c=new JU.BS;for(e=0;e<a.length;e++)c.set(a[e]),2==e%4&&e++;e=c.cardinality();f=Array(e);d.addLast(f);b=u(12,0);for(e=h=0;e<a.length;e++)k=a[e],c.get(k)&&(c.clear(k),f[h]=j[k],b[k]=h++),2==e%4&&e++;j=JU.AU.newInt2(a.length>>2);d.addLast(j);for(e=0;e<a.length;e++)j[e>>2]=u(-1,[b[a[e++]],b[a[e++]],b[a[e++]],a[e]]);return d}for(e=0;e<a.length;e++)b=j[a[e++]],f=j[a[e++]],h=j[a[e++]],1==(c&1)&&d.addLast(B(-1,[b,f,
h])),2==(c&2)&&(k=a[e],1==(k&1)&&d.addLast(B(-1,[b,f])),2==(k&2)&&d.addLast(B(-1,[f,h])),4==(k&4)&&d.addLast(B(-1,[b,h])));return d},"JU.P4,~A,~N");Z(c$,"fullCubePolygon",B(-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])]),"fullCubeCorners",B(-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])]))});O("JU");F(["JU.P3i"],"JU.TriangleData",null,function(){c$=Aa(JU,"TriangleData");Z(c$,"Pwr2",u(-1,[1,2,4,8,16,32,64,128,256,512,1024,2048]));c$.cubeVertexOffsets=c$.prototype.cubeVertexOffsets=B(-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)]);Z(c$,"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]),"triangleTable2",B(-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,
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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,
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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,
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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]))});O("J.jvxl.api");Ha(J.jvxl.api,"VertexDataServer");
O("J.jvxl.api");F(["J.jvxl.api.VertexDataServer"],"J.jvxl.api.MeshDataServer",null,function(){Ha(J.jvxl.api,"MeshDataServer",J.jvxl.api.VertexDataServer)});O("J.shapesurface");F(["J.jvxl.api.MeshDataServer","J.shape.MeshCollection","JU.P3i","$.P4"],"J.shapesurface.Isosurface","java.io.BufferedReader java.lang.Boolean $.Float 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 $.Viewer".split(" "),
function(){c$=H(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;P(this,arguments)},J.shapesurface,"Isosurface",J.shape.MeshCollection,J.jvxl.api.MeshDataServer);ha(c$,function(){this.isomeshes=Array(4);this.lcaoDir=new JU.P4;this.ptXY=new JU.P3i});m(c$,"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(c$,"initShape",function(){Ia(this,J.shapesurface.Isosurface,"initShape",[]);this.myType="isosurface";this.newSg()});e(c$,"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(c$,"clearSg",
function(){this.sg=null});m(c$,"setProperty",function(a,b,c){this.setPropI(a,b,c)},"~S,~O,JU.BS");e(c$,"setPropI",function(a,b,c){if("cache"===a){if(null!=this.currentMesh){var d=this.currentMesh.thisID;c=this.currentMesh.modelIndex;this.vwr.cachePut("cache://isosurface_"+d,this.getPropI("jvxlDataXml",-1).getBytes());this.deleteMeshI(this.currentMesh.index);this.setPropI("init",null,null);this.setPropI("thisID",d,null);this.setPropI("modelIndex",Integer.$valueOf(c),null);this.setPropI("fileName",
"cache://isosurface_"+d,null);this.setPropI("readFile",null,null);this.setPropI("finalize","isosurface ID "+JU.PT.esc(d)+(0<=c?" modelIndex "+c:"")+" /*file*/"+JU.PT.esc("cache://isosurface_"+d),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(d=this.meshCount;0<=--d;)null!=this.isomeshes[d]&&"#inherit;".equals(this.isomeshes[d].colorCommand)&&
this.isomeshes[d].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 j=null;if(null!=a){for(d=0;d<a.length;d++)a[d]=a[d];j=u(c.length(),0);b=0;for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1),b++)j[d]=b}this.thisMesh.setVertexColixesForAtoms(this.vwr,
a,j,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){d=b;c=JU.C.getColix(d[0].intValue());b=JU.C.getColix(d[1].intValue());d=null!=this.thisMesh?this.thisMesh.thisID:
JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null;j=this.getMeshList(d,!1);for(d=j.size();0<=--d;)this.setColorPhase(j.get(d),c,b)}else if("color"===a){var h=JU.C.getHexCode(JU.C.getColixO(b));if(null!=this.thisMesh)this.setIsoMeshColor(this.thisMesh,h);else{j=this.getMeshList(JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,!1);for(d=j.size();0<=--d;)this.setIsoMeshColor(j.get(d),h)}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(d=this.meshCount;0<=--d;)this.meshes[d].modelIndex==c&&(null!=this.meshes[d].connectedAtoms||this.meshes[d].isModelConnected)&&
this.meshes[d].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)d=b,this.explicitID||this.setPropertySuper("thisID",null,null),this.sg.setProp("lcaoCartoonCenter",d[2],null)||this.drawLcaoCartoon(d[0],d[1],d[3],"lonePair"===a?2:"radical"===a?1:0);else if(!("select"===a&&this.iHaveBitSets||"ignore"===a&&
this.iHaveBitSets))if("meshcolor"===a)d=b.intValue(),this.meshColix=JU.C.getColix(d),null!=this.thisMesh&&(this.thisMesh.meshColix=this.meshColix);else if("offset"===a)d=JU.P3.newP(b),d.equals(JV.JC.center)&&(d=null),null!=this.thisMesh&&(this.thisMesh.rotateTranslate(null,d,!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)d=b,this.displayWithinDistance2=d[0].floatValue(),this.isDisplayWithinNot=0>this.displayWithinDistance2,this.displayWithinDistance2*=this.displayWithinDistance2,this.displayWithinPoints=d[3],0==this.displayWithinPoints.size()&&(this.displayWithinPoints=this.ms.getAtomPointVector(d[2]));else if("finalize"===a)null!=this.thisMesh&&(d=b,null!=d&&!d.startsWith("; isosurface map")&&(this.thisMesh.setDiscreteColixes(this.sg.params.contoursDiscrete,this.sg.params.contourColixes),this.setJvxlInfo()),this.setScriptInfo(d)),
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(T(b,Integer)){null!=this.thisMesh&&(this.thisMesh.jvxlData.slabValue=b.intValue());return}if(null!=this.thisMesh){switch(b[0].intValue()){case 1073742018:d=b[1];
c=this.getMesh(d[1]);if(null==c)return;d[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=w(this.sg.params.probes.length,
0));else if("deleteVdw"===a){for(d=this.meshCount;0<=--d;)null!=this.isomeshes[d].bsVdw&&(null==c||c.intersects(this.isomeshes[d].bsVdw))&&this.deleteMeshI(d);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;j=this.sg.params.filesData[0];h=Array(j.length);for(d=h.length;0<=--d&&null!=b;)if(null==(h[d]=this.getFileReader(j[d])))b=null;null!=b&&(this.sg.params.filesData[0]=
h)}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)d=b.intValue(),1296041986==d?this.colorType=d:(this.colorType=0,this.defaultColix=JU.C.getColix(d));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(T(b,
JU.BS))h=b,0==h.cardinality()&&(h=null);else{h=new JU.BS;j=b;for(d=j.length;0<=--d;)0<j[d]&&h.set(j[d]-1)}this.thisMesh.jvxlData.thisSet=h;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(),T(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)d=this.ms.am[this.currentMesh.modelIndex].mat4,null!=d&&(d=JU.M4.newM4(d),d.invert(),this.setPropI("modelInvRotation",d,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?(T(b,String)&&"-".equals(b)&&(b=null),this.setPropertySuper(a,b,c),b=this.title):"withinPoints"===
a?(d=b,this.withinDistance2=d[0].floatValue(),this.isWithinNot=0>this.withinDistance2,this.withinDistance2*=this.withinDistance2,this.withinPoints=d[3],0==this.withinPoints.size()&&(this.withinPoints=this.ms.getAtomPointVector(d[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="",d=T(b,String)?b:null,b=null==d?-1:d.indexOf("# ID="),this.actualID=0<=b?JU.PT.getQuotedStringAt(d,b):null,this.setPropertySuper("thisID","+PREVIOUS_MESH+",null),null!=d&&!(this.iHaveBitSets=this.getScriptBitSets(d,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];j=b[2][1];b=b[2][2];for(d=this.meshCount;0<=--d;)c=this.meshes[d],null!=c&&(null!=c.connectedAtoms&&(h=c.connectedAtoms[0],h>=j+b?c.connectedAtoms[0]=h-b:h>=j&&(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,d,1)):c.modelIndex>a&&(c.modelIndex--,c.atomIndex>=j&&(c.atomIndex-=b)))}else this.setPropertySuper(a,b,c)}}}},"~S,~O,JU.BS");e(c$,"getFileReader",function(a){var b=this.vwr.fm.getBufferedReaderOrErrorMessageFromName(a,null,!0,!0);if(T(b,String))return JU.Logger.error("Isosurface: could not open file "+a+" -- "+b),null;if(!T(b,java.io.BufferedReader))try{b=JU.Rdr.getBufferedReader(b,"ISO-8859-1")}catch(c){if(!Y(c,java.io.IOException))throw c;}return b},"~S");e(c$,
"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(c$,"setColorPhase",function(a,b,c){a.colorPhased=!0;a.colix=a.jvxlData.minColorIndex=b;a.jvxlData.maxColorIndex=c;a.jvxlData.isBicolorMap=!0;a.jvxlData.colorDensity=!1;a.isColorSolid=!1;a.remapColors(this.vwr,null,this.translucentLevel)},"J.shapesurface.IsosurfaceMesh,~N,~N");e(c$,"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",w(this.ms.ac,0),null);0!=b&&(this.thisMesh.colorCommand="color isosurface "+JU.C.getHexCode(b),this.setProperty("color",Integer.$valueOf(JU.C.getArgb(b)),null));if(null!=
a){for(b=this.thisMesh.vc;0<=--b;)0>a[b]&&(a[b]=this.thisMesh.vertexSource[b]);this.thisMesh.vertexSource=a;this.thisMesh.vcs=c}}});e(c$,"slabPolygons",function(a){this.thisMesh.calculatedVolume=null;this.thisMesh.calculatedArea=null;this.thisMesh.getMeshSlicer().slabPolygons(a,!1);this.thisMesh.reinitializeLightingAndColor(this.vwr)},"~A");e(c$,"setPropertySuper",function(a,b,c){"thisID"===a&&null!=this.currentMesh&&null!=this.currentMesh.thisID&&this.currentMesh.thisID.equals(b)?this.checkExplicit(b):
(this.currentMesh=this.thisMesh,this.setPropMC(a,b,c),this.thisMesh=this.currentMesh,this.jvxlData=null==this.thisMesh?null:this.thisMesh.jvxlData,null!=this.sg&&this.sg.setJvxlData(this.jvxlData))},"~S,~O,JU.BS");m(c$,"getPropertyData",function(a,b){var c;"keys"===a&&(c=T(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.$valueOf(c.modelIndex);c.getMeshSlicer().getIntersection(0,b[1],null,b[2],null,null,null,!1,!1,134217750,!1);return!0}if("getBoundingBox"===a){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;b[2]=c.jvxlData.boundingBox;if(null!=c.mat4){var d=Array(2);d[0]=JU.P3.newP(c.jvxlData.boundingBox[0]);d[1]=JU.P3.newP(c.jvxlData.boundingBox[1]);var j=new JU.V3;c.mat4.getTranslation(j);d[0].add(j);d[1].add(j);b[2]=d}return!0}if("unitCell"===a)return c=this.getMesh(b[0]),
null!=c&&null!=(b[1]=c.getUnitCell());if("getCenter"===a&&-2147483648==b[1].intValue()){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;d=JU.P3.newP(c.jvxlData.boundingBox[0]);d.add(c.jvxlData.boundingBox[1]);d.scale(0.5);null!=c.mat4&&(j=new JU.V3,c.mat4.getTranslation(j),d.add(j));b[2]=d;return!0}return this.getPropDataMC(a,b)},"~S,~A");m(c$,"getProperty",function(a,b){return this.getPropI(a,b)},"~S,~N");e(c$,"getPropI",function(a,b){var c=this.thisMesh;if(0<=b&&(b>=this.meshCount||null==
(c=this.isomeshes[b])))return null;var d=this.getPropMC(a,b);if(null!=d)return d;if("message"===a){c="";if(!this.jvxlData.isValid)return"invalid! (no atoms selected?)";Float.isNaN(this.jvxlData.integration)||(c+="integration "+this.jvxlData.integration);if(24==this.shapeID||27==this.shapeID||28==this.shapeID)c=null==this.jvxlData.cutoffRange?c+(" with cutoff="+this.jvxlData.cutoff):c+(" with cutoffRange="+JU.Escape.eAF(this.jvxlData.cutoffRange));if(27==this.shapeID||28==this.shapeID)return c;3.4028235E38!=
this.jvxlData.dataMin&&(c+=" min="+this.jvxlData.dataMin+" max="+this.jvxlData.dataMax);c+="; "+JV.JC.shapeClassBases[this.shapeID].toLowerCase()+" count: "+this.getPropMC("count",b);return c+this.getPropI("dataRangeStr",b)+this.jvxlData.msg}if("dataRange"===a)return this.getDataRange(c);if("dataRangeStr"===a)return c=this.getDataRange(c),null!=c&&3.4028235E38!=c[0]&&c[0]!=c[1]?"\nisosurface full data range "+c[0]+" to "+c[1]+" with color scheme spanning "+c[2]+" to "+c[3]:"";if("moNumber"===a)return Integer.$valueOf(this.moNumber);
if("moLinearCombination"===a)return this.moLinearCombination;if("nSets"===a)return d=null==c?-2147483648:c.nSets,0==d&&(this.calculateVolumeOrArea(c,!0),d=c.nSets),Integer.$valueOf(-2147483648==d?0:Math.abs(c.nSets));if("area"===a)return null==c?Float.$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 w(-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 j=null;this.jvxlData.slabInfo=null;"jvxlMeshXml"===
a||this.jvxlData.vertexDataOnly||null!=c.bsSlabDisplay&&null==c.bsSlabGhost?(j=new J.jvxl.data.MeshData,this.fillMeshData(j,1,c),j.polygonColorData=J.shapesurface.Isosurface.getPolygonColorData(j.pc,j.pcs,j.colorsExplicit?j.pis:null,j.bsSlabDisplay)):null!=c.bsSlabGhost&&(this.jvxlData.slabInfo=c.slabOptions.toString());d=new JU.SB;this.getMeshCommand(d,c.index);c.setJvxlColorMap(!0);return J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,j,this.title,"",!0,1,d.toString(),null)}if("jvxlFileInfo"===
a)return J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);if("command"===a){d=new JU.SB;c=this.getMeshList(0>b?this.previousMeshID:c.thisID,!1);for(j=c.size();0<=--j;)this.getMeshCommand(d,c.get(j).index);return d.toString()}return"atoms"===a?c.surfaceAtoms:"colorEncoder"===a?c.colorEncoder:"values"===a||"value"===a?c.probeValues:null},"~S,~N");e(c$,"getDataRange",function(a){return null==a?null:a.getDataRange()},"J.shapesurface.IsosurfaceMesh");e(c$,"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.$valueOf(c);var d=J.jvxl.data.MeshData.calculateVolumeOrArea(c,a.jvxlData.thisSet,b,!1);0>=a.nSets&&(a.nSets=-c.nSets);b?a.calculatedArea=d:a.calculatedVolume=
d;return d},"J.shapesurface.IsosurfaceMesh,~B");c$.getPolygonColorData=e(c$,"getPolygonColorData",function(a,b,c,d){var j=null!=c;if(null==b&&null==c)return null;for(var h=new JU.SB,f=0,e=0,k=0,g=0,l=!1,q=0;q<a||!0==(l=!0);q++)if(l||null==d||d.get(q))if(l||(j?(g=c[q][4])!=k:b[q]!=e)){0!=f&&h.append(" ").appendI(f).append(" ").appendI(j?k:0==e?0:JU.C.getArgb(e));if(l)break;j?k=g:e=b[q];f=1}else f++;h.append("\n");return h.toString()},"~N,~A,~A,JU.BS");m(c$,"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(c$,"getMeshCommand",function(a,b){var c=this.meshes[b];if(!(null==c||null==c.scriptCommand)){var d=c.scriptCommand;1<this.ms.mc&&J.shape.Shape.appendCmd(a,"frame "+this.vwr.getModelNumberDotted(c.modelIndex));d=JU.PT.rep(d,";; isosurface map"," map");d=JU.PT.rep(d,"; isosurface map"," map");d.endsWith(" map")&&(d=d.substring(0,d.length-4));var d=d.$replace("\t"," "),d=JU.PT.rep(d,";#","; #"),
j=d.indexOf("; #");0<=j&&(d=d.substring(0,j));null!=c.connectedAtoms&&(d+=" connect "+JU.Escape.eAI(c.connectedAtoms));d=JU.PT.trim(d,";");null!=c.linkedMesh&&(d+=" LINK");"lcaoCartoon"===this.myType&&0<=c.atomIndex&&(d+=" ATOMINDEX "+c.atomIndex);J.shape.Shape.appendCmd(a,d);j=this.myType+" ID "+JU.PT.esc(c.thisID);null!=c.jvxlData.thisSet&&0<c.jvxlData.thisSet.cardinality()&&J.shape.Shape.appendCmd(a,j+(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,j+" move "+JU.Escape.matrixToScript(c.mat4));0!=c.scale3d&&J.shape.Shape.appendCmd(a,j+" scale3d "+c.scale3d);-2147483648!=c.jvxlData.slabValue&&J.shape.Shape.appendCmd(a,j+" slab "+c.jvxlData.slabValue);null!=c.slabOptions&&J.shape.Shape.appendCmd(a,c.slabOptions.toString());if("#"!=d.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),d=c.isColorSolid&&null!=c.pcs,c.isColorSolid&&0==c.colorType&&!c.colorsExplicit&&!d?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 h,c=c.vertexColorMap.entrySet().iterator();c.hasNext()&&((h=c.next())||1);)d=h.getValue(),d.isEmpty()||J.shape.Shape.appendCmd(a,"color "+this.myType+" "+JU.Escape.eBS(d)+" "+h.getKey())}},"JU.SB,~N");e(c$,"getScriptBitSets",function(a,b){this.script=a;var c;this.iHaveModelIndex=!1;this.modelIndex=-1;if(null!=a&&0<=(c=a.indexOf("MODEL({"))){var d=a.indexOf("})",c);0<d&&(c=JU.BS.unescape(a.substring(c+3,d+1)),
this.modelIndex=null==c?-1:c.nextSetBit(0),this.iHaveModelIndex=0<=this.modelIndex)}if(null==a)return!1;this.getCapSlabInfo(a);c=a.indexOf("# ({");if(0>c)return!1;d=a.indexOf("})",c);if(0>d)return!1;c=JU.BS.unescape(a.substring(c+2,d+2));null==b?this.sg.setProp("select",c,null):b[0]=c;if(0>(c=a.indexOf("({",d)))return!0;d=a.indexOf("})",c);if(0>d)return!1;c=JU.BS.unescape(a.substring(c+1,d+1));null==b?this.sg.setProp("ignore",c,null):b[1]=c;if((c=a.indexOf("/({",d))==d+2){if(0>(d=a.indexOf("})",c)))return!1;
c=JU.BS.unescape(a.substring(c+3,d+1));null==b?this.ms.setTrajectoryBs(c):b[2]=c}return!0},"~S,~A");e(c$,"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(c$,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var c=JU.PT.split(a.substring(6,a.length-1),",");return JU.TempArray.getSlabObjectType(1678381065,
B(-1,[JU.Escape.uP(c[0]),JU.Escape.uP(c[1]),JU.Escape.uP(c[2]),JU.Escape.uP(c[3])]),b,null)}var d=JU.Escape.uP(a);if(T(d,JU.P4))return JU.TempArray.getSlabObjectType(134217750,d,b,null)}catch(j){if(!Y(j,Exception))throw j;}return null},"~S,~B");e(c$,"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(c$,"initState",function(){this.associateNormals=!0;this.sg.initState()});e(c$,"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(c$,"discardTempData",function(a){a&&(this.title=null,null!=this.thisMesh&&(this.thisMesh.surfaceSet=null))},"~B");e(c$,"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(c$,"drawLcaoCartoon",function(a,b,c,d){var j=this.sg.setLcao(),h=c.x+c.y+c.z;this.defaultColix=JU.C.getColix(this.sg.params.colorPos);var f=JU.C.getColix(this.sg.params.colorNeg),e=new JU.V3,k=0<j.length&&"-"==j.charAt(0);k&&(j=j.substring(1));k=k?-1:1;e.cross(a,b);if(0!=h){var g=new JU.A4;0!=c.x?g.setVA(b,h):0!=c.y?g.setVA(e,h):g.setVA(a,h);c=(new JU.M3).setAA(g);c.rotate(b);c.rotate(e);c.rotate(a)}null==this.thisMesh&&0==this.nLCAO&&(this.nLCAO=this.meshCount);c=null==this.thisMesh?
(0<d?"lp":"lcao")+ ++this.nLCAO+"_"+j:this.thisMesh.thisID;null==this.thisMesh&&this.allocMesh(c,null);j.equals("px")?(this.thisMesh.thisID+="a",j=this.thisMesh,this.createLcaoLobe(b,k,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(b,-k,d),this.thisMesh.colix=f,this.linkedMesh=this.thisMesh.linkedMesh=j)):j.equals("py")?(this.thisMesh.thisID+="a",j=this.thisMesh,this.createLcaoLobe(e,k,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(e,-k,d),this.thisMesh.colix=
f,this.linkedMesh=this.thisMesh.linkedMesh=j)):j.equals("pz")?(this.thisMesh.thisID+="a",j=this.thisMesh,this.createLcaoLobe(a,k,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(a,-k,d),this.thisMesh.colix=f,this.linkedMesh=this.thisMesh.linkedMesh=j)):j.equals("pza")||0==j.indexOf("sp")||0==j.indexOf("d")||0==j.indexOf("lp")?this.createLcaoLobe(a,k,d):j.equals("pzb")?this.createLcaoLobe(a,-k,d):j.equals("pxa")?this.createLcaoLobe(b,k,d):j.equals("pxb")?this.createLcaoLobe(b,-k,
d):j.equals("pya")?this.createLcaoLobe(e,k,d):j.equals("pyb")?this.createLcaoLobe(e,-k,d):j.equals("spacefill")||j.equals("cpk")?this.createLcaoLobe(null,2*this.ms.at[this.atomIndex].getRadius(),d):this.createLcaoLobe(null,1,d)},"JU.V3,JU.V3,JU.V3,~N");e(c$,"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.$valueOf(b/2),null):(this.lcaoDir.x=a.x*b,this.lcaoDir.y=a.y*b,this.lcaoDir.z=
a.z*b,this.lcaoDir.w=0.7,this.setProperty(2==c?"lp":1==c?"rad":"lobe",this.lcaoDir,null));this.thisMesh.colix=this.defaultColix;this.setScriptInfo(null)},"JU.V3,~N,~N");m(c$,"invalidateTriangles",function(){this.thisMesh.invalidatePolygons()});m(c$,"setOutputChannel",function(a,b){a.setOutputChannel(b)},"javajs.api.GenericBinaryDocument,JU.OC");m(c$,"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=$(c.vc,0);a.vcs=c.vcs;break;case 3:c.surfaceSet=a.surfaceSet;c.vertexSets=a.vertexSets;c.nSets=a.nSets;break;case 4:c.vs=a.vs,c.vvs=a.vvs,c.vc=a.vc,c.vertexIncrement=a.vertexIncrement,c.vertexSource=
a.vertexSource,c.pc=a.pc,c.pis=a.pis,c.pcs=a.pcs,c.bsSlabDisplay=a.bsSlabDisplay,c.bsSlabGhost=a.bsSlabGhost,c.slabColix=a.slabColix,c.slabMeshType=a.slabMeshType,c.polygonCount0=a.polygonCount0,c.vertexCount0=a.vertexCount0,c.mergeVertexCount0=a.mergeVertexCount0,c.slabOptions=a.slabOptions,c.colorsExplicit=a.colorsExplicit}},"J.jvxl.data.MeshData,~N,J.shapesurface.IsosurfaceMesh");m(c$,"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});m(c$,"notifySurfaceMappingCompleted",
function(){this.thisMesh.isMerged||this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane);this.setBsVdw();this.thisMesh.isColorSolid=!1;this.thisMesh.colorDensity=this.jvxlData.colorDensity;this.thisMesh.volumeRenderPointSize=this.jvxlData.pointSize;this.thisMesh.colorEncoder=this.sg.params.colorEncoder;this.thisMesh.getContours();0!=this.thisMesh.jvxlData.nContours&&-1!=this.thisMesh.jvxlData.nContours&&(this.explicitContours=!0);this.explicitContours&&
null!=this.thisMesh.jvxlData.jvxlPlane&&(this.thisMesh.havePlanarContours=!0);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073742046:1073741938),null);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073741898:1073742039),null);this.thisMesh.isMerged||this.thisMesh.setJvxlDataRendering();null!=this.sg.params.slabInfo&&(this.thisMesh.slabPolygonsList(this.sg.params.slabInfo,!1),this.thisMesh.reinitializeLightingAndColor(this.vwr));this.thisMesh.setColorCommand()});
e(c$,"setBsVdw",function(){null!=this.sg.bsVdw&&(null==this.thisMesh.bsVdw&&(this.thisMesh.bsVdw=new JU.BS),this.thisMesh.bsVdw.or(this.sg.bsVdw))});m(c$,"calculateGeodesicSurface",function(a,b){return this.vwr.calculateSurface(a,b)},"JU.BS,~N");m(c$,"getSurfacePointIndexAndFraction",function(){return 0},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");m(c$,"addVertexCopy",function(a,b,c,d){return null!=this.cutoffRange&&(b<this.cutoffRange[0]||b>this.cutoffRange[1])?-1:null!=this.withinPoints&&
!J.shape.Mesh.checkWithin(a,this.withinPoints,this.withinDistance2,this.isWithinNot)?-1:this.thisMesh.addVertexCopy(a,b,c,this.associateNormals,d)},"JU.T3,~N,~N,~B");m(c$,"addTriangleCheck",function(a,b,c,d,j,h,f){return 0>a||0>b||0>c||h&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.thisMesh.vvs)?-1:this.thisMesh.addTriangleCheck(a,b,c,d,j,f)},"~N,~N,~N,~N,~N,~B,~N");e(c$,"setScriptInfo",function(a){a=null==a?this.sg.params.script:a;var b=null==a?-1:a.indexOf("; isosurface map");if(0==b)null!=this.thisMesh.scriptCommand&&
(b=this.thisMesh.scriptCommand.indexOf("; isosurface map"),0<=b&&(this.thisMesh.scriptCommand=this.thisMesh.scriptCommand.substring(0,b)),this.thisMesh.scriptCommand+=a);else if(this.thisMesh.title=this.sg.params.title,this.thisMesh.dataType=this.sg.params.dataType,this.thisMesh.scale3d=this.sg.params.scale3d,null!=a&&(null!=this.oldFileName&&(a=a.$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");m(c$,"addRequiredFile",function(a){a=' # /*file*/"'+a+'"';0>this.scriptAppendix.indexOf(a)&&(this.scriptAppendix+=a)},"~S");m(c$,"setRequiredFile",function(a,b){this.oldFileName=a;this.newFileName=b},"~S,~S");e(c$,"setJvxlInfo",function(){if(this.sg.jvxlData!==
this.jvxlData||this.sg.jvxlData!==this.thisMesh.jvxlData)this.jvxlData=this.thisMesh.jvxlData=this.sg.jvxlData});m(c$,"getShapeDetail",function(){for(var a=new JU.Lst,b=0;b<this.meshCount;b++){var c=new java.util.Hashtable,d=this.isomeshes[b];null==d||(null==d.vs||0==d.vc&&0==d.pc)||(this.addMeshInfo(d,c),a.addLast(c))}return a});e(c$,"addMeshInfo",function(a,b){b.put("ID",null==a.thisID?"<noid>":a.thisID);b.put("visible",Boolean.$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");m(c$,"getPlane",function(){return null},"~N");m(c$,"getValue",function(){return 0},"~N,~N,~N,~N");m(c$,"checkObjectHovered",function(a,b,c){if(null!=this.keyXy&&a>=this.keyXy[0]&&b>=
this.keyXy[1]&&a<this.keyXy[2]&&b<this.keyXy[3])return this.hoverKey(a,b),!0;if(!this.vwr.getDrawHover())return!1;c=this.findValue(a,b,!1,c);if(null==c)return!1;this.vwr.hoverOnPt(a,b,c,this.pickedMesh.thisID,this.pickedPt);return!0},"~N,~N,JU.BS");e(c$,"hoverKey",function(a,b){try{var c,d=1-1*(b-this.keyXy[1])/(this.keyXy[3]-this.keyXy[1]);if(this.thisMesh.showContourLines){var j=this.thisMesh.getContours();if(null==j){if(null==this.thisMesh.jvxlData.contourValues)return;var h=D(Math.floor(d*this.thisMesh.jvxlData.contourValues.length));
if(0>h||h>this.thisMesh.jvxlData.contourValues.length)return;c=""+this.thisMesh.jvxlData.contourValues[h]}else{h=D(Math.floor(d*j.length));if(0>h||h>j.length)return;c=""+j[h].get(2).floatValue()}}else{var f=this.thisMesh.colorEncoder.quantize(d,!0),d=this.thisMesh.colorEncoder.quantize(d,!1);c=""+f+" - "+d}this.vwr.hoverOnPt(a,b,c,null,null)}catch(e){if(!Y(e,Exception))throw e;}},"~N,~N");m(c$,"checkObjectClicked",function(a,b,c,d,j){if(!j||!this.vwr.isBound(c,18))return null;c=100;this.vwr.gdata.isAntialiased()&&
(a<<=1,b<<=1,c<<=1);for(var h=j=-1,f=-2147483648,e=2147483647,k=0;k<this.meshCount;k++){var g=this.isomeshes[k];if(this.isPickable(g,d)&&(g=g.vs,null!=g))for(var l=g.length;0<=--l;){var q=g[l];null!=q&&0<=this.coordinateInRange(a,b,q,c,this.ptXY)&&(this.ptXY.z<e&&(j=k,e=this.ptXY.z,h=l),this.ptXY.z>f&&(f=this.ptXY.z))}}if(0>j)return null;this.pickedMesh=this.isomeshes[j];this.setPropertySuper("thisID",this.pickedMesh.thisID,null);this.pickedVertex=h;a=new JU.P3;a.setT(this.pickedMesh.vs[this.pickedVertex]);
this.pickedModel=this.pickedMesh.modelIndex;b=this.getPickedPoint(a,this.pickedModel);this.setStatusPicked(-4,a,b);return b},"~N,~N,~N,JU.BS,~B");e(c$,"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(c$,"findValue",function(a,b,c,d){c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var j=-1,h=null,f=null,e=0;e<this.meshCount;e++)if(f=this.isomeshes[e],this.isPickable(f,
d)){var k=f.jvxlData.vContours,g=0>f.firstRealVertex?0:f.firstRealVertex,l=0;if(null!=k&&0<k.length){for(g=0;g<k.length;g++)for(var q=k[g],p=q.size()-1,N=6;N<p;N++){var v=q.get(N),m=this.coordinateInRange(a,b,v,c,this.ptXY);0<=m&&(c=m,h=q,l=g,this.pickedMesh=f,this.pickedPt=v)}if(null!=h)return h.get(2).toString()+(JU.Logger.debugging?" "+l:"")}else if(null!=f.jvxlData.jvxlPlane&&null!=f.vvs){k=null==f.mat4&&0==f.scale3d?f.vs:f.getOffsetVertices(f.jvxlData.jvxlPlane);for(N=f.vc;--N>=g;)v=k[N],m=this.coordinateInRange(a,
b,v,c,this.ptXY),0<=m&&(c=m,j=N,this.pickedMesh=f,this.pickedPt=v);if(-1!=j)break}else if(null!=f.vvs){if(null!=f.bsSlabDisplay)for(N=f.bsSlabDisplay.nextSetBit(0);0<=N;N=f.bsSlabDisplay.nextSetBit(N+1)){if(k=f.pis[N],null!=k)for(l=0;3>l;l++)v=f.vs[k[l]],m=this.coordinateInRange(a,b,v,c,this.ptXY),0<=m&&(c=m,j=k[l],this.pickedMesh=f,this.pickedPt=v)}else for(N=f.vc;--N>=g;)v=f.vs[N],m=this.coordinateInRange(a,b,v,c,this.ptXY),0<=m&&(c=m,j=N,this.pickedMesh=f,this.pickedPt=v);if(-1!=j)break}}return-1==
j?null:(JU.Logger.debugging?"$"+f.thisID+"["+(j+1)+"] "+f.vs[j]+": ":f.thisID+": ")+f.vvs[j]},"~N,~N,~B,JU.BS");e(c$,"getCmd",function(a){var b=(new JU.SB).append("\n");this.getMeshCommand(b,a);return b.toString()},"~N");m(c$,"getValues",function(a){return null==a?null:a.getValidValues(null)},"J.shape.Mesh");m(c$,"getVertices",function(a){return null==a?null:a.getValidVertices(null)},"J.shape.Mesh");Z(c$,"MAX_OBJECT_CLICK_DISTANCE_SQUARED",100)});O("J.jvxl.data");F(null,"J.jvxl.data.JvxlCoder","java.lang.Float JU.BS $.Lst $.P3 $.PT $.SB J.api.Interface J.jvxl.data.VolumeData JU.BSUtil $.C $.Escape $.Logger JV.Viewer".split(" "),
function(){c$=Aa(J.jvxl.data,"JvxlCoder");c$.jvxlGetFile=e(c$,"jvxlGetFile",function(a,b,c,d,j,h,f,e){J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var k=new JU.SB;if("TRAILERONLY".equals(d))return JU.XmlUtil.closeTag(k,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(k,"jvxl"),k.toString();var g=null!=b,l="HEADERONLY".equals(d);if(j){JU.XmlUtil.openDocument(k);JU.XmlUtil.openTagAttr(k,"jvxl",B(-1,["version","2.4","jmolVersion",a.version,"xmlns","http://jmol.org/jvxl_schema","xmlns:cml","http://www.xml-cml.org/schema"]));
JU.XmlUtil.appendCdata(k,"jvxlFileTitle",null,null==a.jvxlFileTitle?"\n":"\n"+a.jvxlFileTitle);null!=a.moleculeXml&&k.append(a.moleculeXml);var q=g?null:a.jvxlVolumeDataXml;null==q&&(q=(new J.jvxl.data.VolumeData).setVolumetricXml());k.append(q);JU.XmlUtil.openTagAttr(k,"jvxlSurfaceSet",B(-1,["count",""+(0<h?h:1)]));if(l)return k.toString()}h=g?"pmesh":null==a.jvxlPlane?"isosurface":"plane";null!=a.jvxlColorData&&0<a.jvxlColorData.length&&(h="mapped "+h);JU.XmlUtil.openTagAttr(k,"jvxlSurface",B(-1,
["type",h]));k.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,g));J.jvxl.data.JvxlCoder.jvxlAppendCommandState(k,e,f);if(null!=c||null!=d&&0<d.length){f=new JU.SB;null!=d&&0<d.length&&f.append(d).append("\n");if(null!=c)for(d=0;d<c.length;d++)f.append(c[d]).appendC("\n");JU.XmlUtil.appendCdata(k,"jvxlSurfaceTitle",null,f.toString())}f=new JU.SB;JU.XmlUtil.openTagAttr(f,"jvxlSurfaceData",g||null==a.jvxlPlane?null:null==a.mapLattice?B(-1,["plane",JU.Escape.eP4(a.jvxlPlane)]):B(-1,["plane",JU.Escape.eP4(a.jvxlPlane),
"maplattice",JU.Escape.eP(a.mapLattice)]));if(g)J.jvxl.data.JvxlCoder.appendXmlVertexOnlyData(f,a,b,!0);else{if(null==a.jvxlPlane){if(null==a.jvxlEdgeData)return"";J.jvxl.data.JvxlCoder.appendXmlEdgeData(f,a)}J.jvxl.data.JvxlCoder.appendXmlColorData(f,a.jvxlColorData,!0,a.isJvxlPrecisionColor,a.valueMappedToRed,a.valueMappedToBlue)}J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,"jvxlInvalidatedVertexData",a.jvxlExcluded[1],-1,null);0<a.excludedVertexCount&&(J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,
"jvxlExcludedVertexData",a.jvxlExcluded[0],a.excludedVertexCount,null),J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,"jvxlExcludedPlaneData",a.jvxlExcluded[2],-1,null));J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,"jvxlExcludedTriangleData",a.jvxlExcluded[3],a.excludedTriangleCount,null);JU.XmlUtil.closeTag(f,"jvxlSurfaceData");b=f.length();k.appendSB(f);null!=a.vContours&&0<a.vContours.length&&J.jvxl.data.JvxlCoder.jvxlEncodeContourData(a.vContours,k);if(null!=a.vertexColorMap){null==a.baseColor?
JU.XmlUtil.openTag(k,"jvxlVertexColorData"):JU.XmlUtil.openTagAttr(k,"jvxlVertexColorData",B(-1,["baseColor",a.baseColor]));var p;for(c=a.vertexColorMap.entrySet().iterator();c.hasNext()&&((p=c.next())||1);)J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(k,"jvxlColorMap",p.getValue(),-1,B(-1,["color",p.getKey()]));a.vertexColorMap=null;JU.XmlUtil.closeTag(k,"jvxlVertexColorData")}JU.XmlUtil.closeTag(k,"jvxlSurface");j&&(JU.XmlUtil.closeTag(k,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(k,"jvxl"));return J.jvxl.data.JvxlCoder.jvxlSetCompressionRatio(k,
a,b)},"J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~A,~S,~B,~N,~S,~S");c$.checkHaveXMLUtil=e(c$,"checkHaveXMLUtil",function(){J.jvxl.data.JvxlCoder.haveXMLUtil||(JV.Viewer.isJS&&J.api.Interface.getInterface("JU.XmlUtil",null,"show"),J.jvxl.data.JvxlCoder.haveXMLUtil=!0)});c$.appendEncodedBitSetTag=e(c$,"appendEncodedBitSetTag",function(a,b,c,d,j){0>d&&(d=JU.BSUtil.cardinalityOf(c));if(0!=d){var h=new JU.SB;h.append("\n ");J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(c,-1,h);JU.XmlUtil.appendTagObj(a,
b,B(-1,[j,"bsEncoding","base90+35","count",""+d,"len",""+c.length()]),J.jvxl.data.JvxlCoder.jvxlCompressString(h.toString(),!0))}},"JU.SB,~S,JU.BS,~N,~A");c$.jvxlSetCompressionRatio=e(c$,"jvxlSetCompressionRatio",function(a,b,c){a=a.toString();b=y(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");c$.appendXmlEdgeData=e(c$,"appendXmlEdgeData",function(a,b){JU.XmlUtil.appendTagObj(a,"jvxlEdgeData",
B(-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");c$.jvxlAppendCommandState=e(c$,"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");c$.appendXmlColorData=e(c$,"appendXmlColorData",function(a,b,c,d,j,h){var f;if(!(null==b||0>(f=b.length-1)))d&&(f/=2),JU.XmlUtil.appendTagObj(a,"jvxlColorData",B(-1,["count",""+f,"encoding",c?"base90f"+(d?"2":"1"):"none","min",""+j,"max",""+h,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b,!0)]),null)},
"JU.SB,~S,~B,~B,~N,~N");c$.jvxlGetInfo=e(c$,"jvxlGetInfo",function(a){return J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,a.vertexDataOnly)},"J.jvxl.data.JvxlData");c$.jvxlGetInfoData=e(c$,"jvxlGetInfoData",function(a,b){if(null==a.jvxlSurfaceData)return"";J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var c=new JU.Lst,d=a.nSurfaceInts,j=b?0:a.jvxlEdgeData.length-1,h=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 f=a.jvxlSurfaceData.length+j+h+1;0<f&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesData",""+f);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isXLowToHigh",""+a.isXLowToHigh);null==a.jvxlPlane&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nSurfaceInts",""+d),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  nBytesUncompressedEdgeData",""+j));0<h&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedColorData",""+h)}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);f=JU.BSUtil.cardinalityOf(a.jvxlExcluded[1]);
0<f&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nInvalidatedVertexes",""+f);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,
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"\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&&(d=J.jvxl.data.JvxlCoder.subsetString(a.thisSet),
d.startsWith("[")?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  subset",d):J.jvxl.data.JvxlCoder.addAttrib(c,"\n  set",d));-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);d=3.4028235E38==a.mappedDataMin?0:a.mappedDataMin;j=a.isColorReversed?a.valueMappedToRed:a.valueMappedToBlue;h=a.isColorReversed?
a.valueMappedToBlue:a.valueMappedToRed;null!=a.jvxlColorData&&(0<a.jvxlColorData.length&&!a.isBicolorMap)&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMinimum",""+d),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMaximum",""+a.mappedDataMax),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToRed",""+h),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToBlue",""+j));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);d=new JU.SB;JU.XmlUtil.openTagAttr(d,"jvxlSurfaceInfo",c.toArray(Array(c.size())));JU.XmlUtil.closeTag(d,"jvxlSurfaceInfo");return d.toString()},"J.jvxl.data.JvxlData,~B");c$.subsetString=e(c$,"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");c$.addAttrib=e(c$,"addAttrib",function(a,b,c){a.addLast(B(-1,[b,c]))},"JU.Lst,~S,~S");c$.jvxlEncodeContourData=
e(c$,"jvxlEncodeContourData",function(a,b){JU.XmlUtil.openTagAttr(b,"jvxlContourData",B(-1,["count",""+a.length]));for(var c=0;c<a.length;c++)if(!(6>a[c].size())){var d=a[c].get(0).intValue(),j=new JU.SB;j.append("\n");var h=a[c].get(1);J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(h,d,j);JU.XmlUtil.appendTagObj(b,"jvxlContour",B(-1,["index",""+c,"value",""+a[c].get(2),"color",JU.Escape.escapeColor(a[c].get(4)[0]),"count",""+h.length(),"encoding","base90iff1","bsEncoding","base90+35c","data",J.jvxl.data.JvxlCoder.jvxlCompressString(a[c].get(5).toString(),
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35,90,0),m=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(t.charCodeAt(0),35,90,0),v,u;0==(e&1)?(v=q[1],u=e=q[2],q=q[0]):(v=q[0],u=q[1],0!=(e&2)?(e=u,q=q[2]):(e=q[2],q=v));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,v,u,p));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,e,q,m))}},"JU.Lst,~A,~A");c$.getContourPoint=e(c$,"getContourPoint",function(a,b,c,d){var j=new JU.P3;j.sub2(a[c],a[b]);j.scaleAdd2(d,j,a[b]);return j},"~A,~N,~N,~N");c$.appendContourTriangleIntersection=e(c$,"appendContourTriangleIntersection",
function(a,b,c,d){d.appendI(a);d.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(b));d.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(c))},"~N,~N,~N,JU.SB");c$.jvxlCreateColorData=e(c$,"jvxlCreateColorData",function(a,b){if(null==b)a.jvxlColorData="";else{var c=a.isJvxlPrecisionColor,d=a.isTruncated,j=a.colorFractionBase,h=a.colorFractionRange,e=a.valueMappedToBlue,g=a.valueMappedToRed,k=0<a.saveVertexCount?a.saveVertexCount:a.vertexCount;k>b.length&&System.out.println("JVXLCODER ERROR");
var t=a.mappedDataMin,l=a.mappedDataMax,q=new JU.SB,p=new JU.SB;b.length<k&&System.out.println("JVXLCOLOR OHOHO");for(var m=0;m<k;m++){var v=b[m];Float.isNaN(v)&&(v=t);d&&(v=0<v?0.999:-0.999);c?J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v,t,l,j,h,q,p):q.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(v,g,e,j,h))}a.jvxlColorData=q.appendSB(p).appendC("\n").toString()}},"J.jvxl.data.JvxlData,~A");c$.appendXmlVertexOnlyData=e(c$,"appendXmlVertexOnlyData",function(a,b,c,d){var j=u(c.vc,0);J.jvxl.data.JvxlCoder.appendXmlTriangleData(a,
c.pis,c.pc,c.bsSlabDisplay,j,d)&&J.jvxl.data.JvxlCoder.appendXmlVertexData(a,b,j,c.vs,c.vvs,c.vc,c.polygonColorData,c.pc,c.bsSlabDisplay,b.vertexColors,0<b.jvxlColorData.length,d)},"JU.SB,J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~B");c$.appendXmlTriangleData=e(c$,"appendXmlTriangleData",function(a,b,c,d,j,h){for(var e=new JU.SB,g=new JU.SB,k=1,t=0,l=0,q=!1,p=0,m=null!=d,v=0;v<c;)if(null==b[v]||m&&!d.get(v))v++;else{var u=b[v][t],u=0<j[u]?j[u]:j[u]=++l,w=u-k,k=u;0==w?(e.appendC("!"),q=!1):32<w?(q&&
e.appendC("+"),e.appendI(w),q=!0):-32>w?(e.appendI(w),q=!0):(e.appendC(String.fromCharCode(92+w)),q=!1);0==++t%3&&(g.appendI(b[v][3]),t=0,v++,p++)}if(0==e.length())return!0;JU.XmlUtil.appendTagObj(a,"jvxlTriangleData",B(-1,["count",""+p,"encoding","jvxltdiff","data",J.jvxl.data.JvxlCoder.jvxlCompressString(e.toString(),h)]),null);JU.XmlUtil.appendTagObj(a,"jvxlTriangleEdgeData",B(-1,["count",""+p,"encoding","jvxlsc","data",J.jvxl.data.JvxlCoder.jvxlCompressString(g.toString(),h)]),null);return!0},
"JU.SB,~A,~N,JU.BS,~A,~B");c$.appendXmlVertexData=e(c$,"appendXmlVertexData",function(a,b,c,d,j,e,f,g,k,t,l,q){var p=b.colorFractionBase,m=b.colorFractionRange,v,w=b.boundingBox[0],y=b.boundingBox[1],D=new JU.SB,H=new JU.SB,F=null,aa=null!=k;if(0<g){aa&&(g=k.cardinality());for(var aa=!1,F=u(e,0),I=0;I<e;I++)0<c[I]&&(F[c[I]-1]=I)}for(I=c=0;I<e;I++)if(!aa||k.get(I))c++,v=d[0==g?I:F[I]],J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.x,w.x,y.x,p,m,D,H),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.y,w.y,
y.y,p,m,D,H),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.z,w.z,y.z,p,m,D,H);D.appendSB(H);JU.XmlUtil.appendTagObj(a,"jvxlVertexData",B(-1,["count",""+c,"min",JU.Escape.eP(w),"max",JU.Escape.eP(y),"encoding","base90xyz2","data",J.jvxl.data.JvxlCoder.jvxlCompressString(D.toString(),q)]),null);null!=f&&JU.XmlUtil.appendTagObj(a,"jvxlPolygonColorData",B(-1,["encoding","jvxlnc","count",""+g]),"\n"+f);if(l){D=new JU.SB;H=new JU.SB;if(null==t)for(I=0;I<e;I++){if(!aa||k.get(I))J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(j[0==
g?I:F[I]],b.mappedDataMin,b.mappedDataMax,p,m,D,H)}else{d=0;D.appendI(c).append(" ");for(I=0;I<e;I++)if(!aa||k.get(I))j=t[0==g?I:F[I]],j==d?j=0:d=j,D.appendI(j),D.append(" ")}J.jvxl.data.JvxlCoder.appendXmlColorData(a,D.appendSB(H).append("\n").toString(),null==t,!0,b.valueMappedToRed,b.valueMappedToBlue)}},"JU.SB,J.jvxl.data.JvxlData,~A,~A,~A,~N,~S,~N,JU.BS,~A,~B,~B");c$.jvxlFractionAsCharacter=e(c$,"jvxlFractionAsCharacter",function(a){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,
35,90)},"~N");c$.jvxlFractionAsCharacterRange=e(c$,"jvxlFractionAsCharacterRange",function(a,b,c){0.9999<a?a=0.9999:Float.isNaN(a)&&(a=1.0001);a=D(Math.floor(a*c+b));return a<b?String.fromCharCode(b):92==a?"!":String.fromCharCode(a)},"~N,~N,~N");c$.jvxlAppendCharacter2=e(c$,"jvxlAppendCharacter2",function(a,b,c,d,j,e,f){a=b==c?a:(a-b)/(c-b);b=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,d,j);e.appendC(b);a-=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b.charCodeAt(0),d,j,0);f.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a*
j,d,j))},"~N,~N,~N,~N,~N,JU.SB,JU.SB");c$.jvxlFractionFromCharacter=e(c$,"jvxlFractionFromCharacter",function(a,b,c,d){if(a==b+c)return NaN;a<b&&(a=92);a=(a-b+d)/c;return 0>a?0:1<a?0.999999:a},"~N,~N,~N,~N");c$.jvxlFractionFromCharacter2=e(c$,"jvxlFractionFromCharacter2",function(a,b,c,d){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(a,c,d,0);b=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b,c,d,0.5);return a+b/d},"~N,~N,~N,~N");c$.jvxlValueAsCharacter=e(c$,"jvxlValueAsCharacter",function(a,
b,c,d,j){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(b==c?a:(a-b)/(c-b),d,j)},"~N,~N,~N,~N,~N");c$.jvxlValueFromCharacter2=e(c$,"jvxlValueFromCharacter2",function(a,b,c,d,j,e){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(a,b,j,e);return d==c?a:c+a*(d-c)},"~N,~N,~N,~N,~N,~N");c$.jvxlEncodeBitSet0=e(c$,"jvxlEncodeBitSet0",function(a,b,c){var d=0,j=-1,e=0;0>b&&(b=a.length());for(var f=0,g=!1,k=b-1,t=0;t<b;++t)g==a.get(t)?d++:(d==j&&t!=k?e++:(0<e&&(c.appendC(" ").appendI(-e),e=0,f++),
c.appendC(" ").appendI(d),f++,j=d),d=1,g=!g);c.appendC(" ").appendI(d).appendC("\n");return f},"JU.BS,~N,JU.SB");c$.jvxlEncodeBitSet=e(c$,"jvxlEncodeBitSet",function(a){var b=new JU.SB;J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,-1,b);return b.toString()},"JU.BS");c$.jvxlEncodeBitSetBuffer=e(c$,"jvxlEncodeBitSetBuffer",function(a,b,c){var d=0,j=0,e=!1;0>b&&(b=a.length());if(0==b)return 0;c.append("-");for(var f=0;f<b;++f)e==a.get(f)?d++:(J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,d,35,90),
j++,d=1,e=!e);J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,d,35,90);c.appendC("\n");return j},"JU.BS,~N,JU.SB");c$.jvxlAppendEncodedNumber=e(c$,"jvxlAppendEncodedNumber",function(a,b,c,d){var j=b<d;for(0==b?a.appendC(String.fromCharCode(c)):j||a.appendC(String.fromCharCode(c+d));0<b;){var e=D(b/d);b=c+b-e*d;92==b&&(b=33);a.appendC(String.fromCharCode(b));b=e}j||a.append(" ")},"JU.SB,~N,~N,~N");c$.jvxlDecodeBitSetRange=e(c$,"jvxlDecodeBitSetRange",function(a,b,c){for(var d=new JU.BS,j=0,e=0,f=!1,
g=u(1,0);-2147483648!=(j=J.jvxl.data.JvxlCoder.jvxlParseEncodedInt(a,b,c,g));)f&&d.setBits(e,e+j),e+=j,f=!f;return d},"~S,~N,~N");c$.jvxlParseEncodedInt=e(c$,"jvxlParseEncodedInt",function(a,b,c,d){var j=!1,e=0,f=d[0],g=a.length;if(0>f)return-2147483648;for(;f<g&&JU.PT.isWhitespace(a.charAt(f));)++f;if(f>=g)return-2147483648;var k=1,t=a.charCodeAt(f)==b+c;for(t&&f++;f<g&&!JU.PT.isWhitespace(a.charAt(f));){j=a.charCodeAt(f);j<b&&(j=92);e+=(j-b)*k;j=!0;++f;if(!t)break;k*=c}j||(e=-2147483648);d[0]=f;
return e},"~S,~N,~N,~A");c$.jvxlDecodeBitSet=e(c$,"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,d=0,j=0,e=0,f=!1,g=u(1,0);;){c=0>j++?c:JU.PT.parseIntNext(a,g);if(-2147483648==c)break;0>c?(j=c,c=d):(f&&b.setBits(e,e+c),e+=c,d=c,f=!f)}return b},"~S");c$.jvxlCompressString=e(c$,"jvxlCompressString",function(a,b){if(0<=a.indexOf("~"))return a;for(var c=new JU.SB,
d="\x00",j=!1,e=!1,f=0,g=a.length,k=0;k<=g;k++){var t=k==g?"\x00":a.charAt(k);switch(t){case "\n":case "\r":continue;case "&":case "<":j=b;break;default:j=!1}if(t==d)++f,t="\x00";else if(0<f||e){if(4>f&&!e||" "==d||"\t"==d)for(;0<=--f;)c.appendC(d);else e?e=!1:c.appendC("~"),c.appendI(f),c.appendC(" ");f=0}"\x00"!=t&&(j?(e=!0,c.appendC("~"),d=t,t=String.fromCharCode(t.charCodeAt(0)-1)):d=t,c.appendC(t))}return c.toString()},"~S,~B");c$.jvxlDecompressString=e(c$,"jvxlDecompressString",function(a){if(0>
a.indexOf("~"))return a;for(var b=new JU.SB,c="\x00",d=u(1,0),j=0;j<a.length;j++){var e=a.charAt(j);if("~"==e)switch(d[0]=++j,e=a.charAt(j)){case ";":case "%":d[0]++,b.appendC(c=String.fromCharCode(e.charCodeAt(0)+1));case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":j=JU.PT.parseIntNext(a,d);for(e=0;e<j;e++)b.appendC(c);j=d[0];continue;case "~":--j;break;default:JU.Logger.error("Error uncompressing string "+a.substring(0,j)+"?")}b.appendC(e);c=e}return b.toString()},
"~S");c$.jvxlCreateHeaderWithoutTitleOrAtoms=e(c$,"jvxlCreateHeaderWithoutTitleOrAtoms",function(a,b){J.jvxl.data.JvxlCoder.jvxlCreateHeader(a,b)},"J.jvxl.data.VolumeData,JU.SB");c$.jvxlCreateHeader=e(c$,"jvxlCreateHeader",function(a,b){a.setVolumetricXml();0==b.length()&&b.append("Line 1\nLine 2\n")},"J.jvxl.data.VolumeData,JU.SB");Z(c$,"JVXL_VERSION1","2.0","JVXL_VERSION_XML","2.4","haveXMLUtil",!1,"CONTOUR_NPOLYGONS",0,"CONTOUR_BITSET",1,"CONTOUR_VALUE",2,"CONTOUR_COLIX",3,"CONTOUR_COLOR",4,"CONTOUR_FDATA",
5,"CONTOUR_POINTS",6,"defaultEdgeFractionBase",35,"defaultEdgeFractionRange",90,"defaultColorFractionBase",35,"defaultColorFractionRange",90)});O("J.jvxl.data");F(["JU.M3","$.P3","$.V3"],"J.jvxl.data.VolumeData",["java.lang.Float","java.util.Hashtable","JU.SB","JU.Escape","$.Logger"],function(){c$=H(function(){this.sr=null;this.doIterate=!0;this.voxelCounts=this.volumetricVectors=this.origin=this.volumetricOrigin=null;this.nPoints=0;this.volumetricVectorLengths=this.voxelMap=this.voxelData=null;this.yzCount=
this.minToPlaneDistance=this.maxVectorLength=0;this.thePlane=this.inverseMatrix=this.volumetricMatrix=this.unitVolumetricVectors=null;this.thePlaneNormalMag=0;this.mappingPlane=this.xmlData=this.ptXyzTemp=null;this.voxelVolume=this.maxGrid=this.minGrid=this.mappingPlaneNormalMag=0;this.oabc=null;this.isSquared=this.isPeriodic=!1;this.ptTemp=this.edgeVector=null;P(this,arguments)},J.jvxl.data,"VolumeData");ha(c$,function(){this.volumetricOrigin=new JU.P3;this.origin=w(3,0);this.volumetricVectors=Array(3);
this.voxelCounts=u(3,0);this.volumetricVectorLengths=w(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});e(c$,"getVoxelData",function(){return this.voxelData});e(c$,"setVoxelDataAsArray",function(a){this.voxelData=a;null!=a&&(this.sr=null)},"~A");e(c$,"hasPlane",function(){return null!=this.thePlane});W(c$,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(c$,"setMappingPlane",function(a){this.mappingPlane=a;null!=a&&(this.mappingPlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z))},"JU.P4");e(c$,"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(c$,"setVolumetricOrigin",
function(a,b,c){this.volumetricOrigin.set(a,b,c)},"~N,~N,~N");e(c$,"getOriginFloat",function(){return this.origin});e(c$,"getYzCount",function(){this.minGrid=this.volumetricVectors[0].length();this.minGrid=Math.min(this.minGrid,this.volumetricVectors[1].length());this.minGrid=Math.min(this.minGrid,this.volumetricVectors[2].length());this.maxGrid=this.volumetricVectors[0].length();this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[1].length());this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[2].length());
this.nPoints=this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2];return this.yzCount=this.voxelCounts[1]*this.voxelCounts[2]});e(c$,"getVolumetricVectorLengths",function(){return this.volumetricVectorLengths});e(c$,"setVolumetricVector",function(a,b,c,d){this.volumetricVectors[a].x=b;this.volumetricVectors[a].y=c;this.volumetricVectors[a].z=d;this.setUnitVectors()},"~N,~N,~N,~N");e(c$,"getVoxelCounts",function(){return this.voxelCounts});e(c$,"setVoxelCounts",function(a,b,c){this.voxelCounts[0]=
a;this.voxelCounts[1]=b;this.voxelCounts[2]=c;return a*b*c},"~N,~N,~N");e(c$,"getVoxelDataAt",function(a){var b=D(a/this.yzCount);a-=b*this.yzCount;var c=D(a/this.voxelCounts[2]);return this.voxelData[b][c][a-c*this.voxelCounts[2]]},"~N");e(c$,"getPointIndex",function(a,b,c){return a*this.yzCount+b*this.voxelCounts[2]+c},"~N,~N,~N");e(c$,"getPoint",function(a,b){var c=D(a/this.yzCount);a-=c*this.yzCount;var d=D(a/this.voxelCounts[2]);this.voxelPtToXYZ(c,d,a-d*this.voxelCounts[2],b)},"~N,JU.P3");e(c$,
"setVoxelData",function(a,b){var c=D(a/this.yzCount);a-=c*this.yzCount;var d=D(a/this.voxelCounts[2]);this.voxelData[c][d][a-d*this.voxelCounts[2]]=b},"~N,~N");e(c$,"setVoxelMap",function(){this.voxelMap=new java.util.Hashtable;this.getYzCount()});e(c$,"setMatrix",function(){for(var a=0;3>a;a++)this.volumetricMatrix.setColumnV(a,this.volumetricVectors[a]);try{this.inverseMatrix.invertM(this.volumetricMatrix)}catch(b){if(Y(b,Exception))return JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? "),
!1;throw b;}return!0});e(c$,"transform",function(a,b){this.volumetricMatrix.rotate2(a,b)},"JU.V3,JU.V3");e(c$,"setPlaneParameters",function(a){this.thePlane=a;this.thePlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z)},"JU.P4");e(c$,"calcVoxelPlaneDistance",function(a,b,c){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.distancePointToPlane(this.ptXyzTemp)},"~N,~N,~N");e(c$,"getToPlaneParameter",function(){return Math.sqrt(this.thePlane.x*this.thePlane.x+this.thePlane.y*this.thePlane.y+this.thePlane.z*
this.thePlane.z)*this.minToPlaneDistance});e(c$,"isNearPlane",function(a,b,c,d){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<d},"~N,~N,~N,~N");e(c$,"distancePointToPlane",function(a){return(this.thePlane.x*a.x+this.thePlane.y*a.y+this.thePlane.z*a.z+this.thePlane.w)/this.thePlaneNormalMag},"JU.T3");e(c$,"voxelPtToXYZ",function(a,b,c,d){d.scaleAdd2(a,this.volumetricVectors[0],this.volumetricOrigin);
d.scaleAdd2(b,this.volumetricVectors[1],d);d.scaleAdd2(c,this.volumetricVectors[2],d)},"~N,~N,~N,JU.T3");e(c$,"setUnitVectors",function(){this.maxVectorLength=0;this.voxelVolume=1;for(var a=0;3>a;a++){var b=this.volumetricVectorLengths[a]=this.volumetricVectors[a].length();if(0==b)return!1;b>this.maxVectorLength&&(this.maxVectorLength=b);this.voxelVolume*=b;this.unitVolumetricVectors[a].setT(this.volumetricVectors[a]);this.unitVolumetricVectors[a].normalize()}this.minToPlaneDistance=2*this.maxVectorLength;
this.origin[0]=this.volumetricOrigin.x;this.origin[1]=this.volumetricOrigin.y;this.origin[2]=this.volumetricOrigin.z;this.oabc=Array(4);this.oabc[0]=JU.V3.newV(this.volumetricOrigin);for(a=0;3>a;a++)b=this.oabc[a+1]=new JU.V3,b.scaleAdd2(this.voxelCounts[a]-1,this.volumetricVectors[a],b);return this.setMatrix()});e(c$,"xyzToVoxelPt",function(a,b,c,d){this.ptXyzTemp.set(a,b,c);this.ptXyzTemp.sub(this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);d.set(Math.round(this.ptXyzTemp.x),Math.round(this.ptXyzTemp.y),
Math.round(this.ptXyzTemp.z))},"~N,~N,~N,JU.T3i");e(c$,"lookupInterpolatedVoxelValue",function(a,b){if(null!=this.mappingPlane)return this.distanceToMappingPlane(a);if(null!=this.sr){var c=this.sr.getValueAtPoint(a,b);return this.isSquared?c*c:c}this.ptXyzTemp.sub2(a,this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);var d,j=this.indexLower(this.ptXyzTemp.x,d=this.voxelCounts[0]-1),e=this.indexUpper(this.ptXyzTemp.x,j,d),f=this.indexLower(this.ptXyzTemp.y,d=this.voxelCounts[1]-1),g=
this.indexUpper(this.ptXyzTemp.y,f,d),c=this.indexLower(this.ptXyzTemp.z,d=this.voxelCounts[2]-1),k=this.indexUpper(this.ptXyzTemp.z,c,d);d=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-j),this.mantissa(this.ptXyzTemp.y-f),this.getVoxelValue(j,f,c),this.getVoxelValue(e,f,c),this.getVoxelValue(j,g,c),this.getVoxelValue(e,g,c));j=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-j),this.mantissa(this.ptXyzTemp.y-f),this.getVoxelValue(j,f,k),this.getVoxelValue(e,
f,k),this.getVoxelValue(j,g,k),this.getVoxelValue(e,g,k));return d+this.mantissa(this.ptXyzTemp.z-c)*(j-d)},"JU.T3,~B");e(c$,"mantissa",function(a){return this.isPeriodic?a-Math.floor(a):a},"~N");e(c$,"getVoxelValue",function(a,b,c){if(null==this.voxelMap)return this.voxelData[a][b][c];a=this.voxelMap.get(Integer.$valueOf(this.getPointIndex(a,b,c)));return null==a?NaN:a.floatValue()},"~N,~N,~N");c$.getFractional2DValue=e(c$,"getFractional2DValue",function(a,b,c,d,j,e){c+=a*(d-c);return c+b*(j+a*(e-
j)-c)},"~N,~N,~N,~N,~N,~N");e(c$,"indexLower",function(a,b){if(this.isPeriodic&&0<b){for(;0>a;)a+=b;for(;a>=b;)a-=b;return D(Math.floor(a))}if(0>a)return 0;var c=D(Math.floor(a));return c>b?b:c},"~N,~N");e(c$,"indexUpper",function(a,b,c){return!this.isPeriodic&&0>a||b==c?b:b+1},"~N,~N,~N");e(c$,"offsetCenter",function(a){var b=new JU.P3;b.scaleAdd2((this.voxelCounts[0]-1)/2,this.volumetricVectors[0],b);b.scaleAdd2((this.voxelCounts[1]-1)/2,this.volumetricVectors[1],b);b.scaleAdd2((this.voxelCounts[2]-
1)/2,this.volumetricVectors[2],b);this.volumetricOrigin.sub2(a,b)},"JU.P3");e(c$,"setDataDistanceToPlane",function(a){this.setPlaneParameters(a);a=this.voxelCounts[0];var b=this.voxelCounts[1],c=this.voxelCounts[2];this.voxelData=w(a,b,c,0);for(var d=0;d<a;d++)for(var j=0;j<b;j++)for(var e=0;e<c;e++)this.voxelData[d][j][e]=this.calcVoxelPlaneDistance(d,j,e)},"JU.P4");e(c$,"filterData",function(a,b){var c=!Float.isNaN(b);if(null!=this.sr)this.isSquared=a;else{var d=this.voxelCounts[0],j=this.voxelCounts[1],
e=this.voxelCounts[2];if(a)for(var f=0;f<d;f++)for(var g=0;g<j;g++)for(var k=0;k<e;k++)this.voxelData[f][g][k]*=this.voxelData[f][g][k];if(c)for(f=0;f<d;f++)for(g=0;g<j;g++)for(k=0;k<e;k++)this.voxelData[f][g][k]=b-this.voxelData[f][g][k]}},"~B,~N");e(c$,"capData",function(a,b){if(null!=this.voxelData){var c=this.voxelCounts[0],d=this.voxelCounts[1],j=this.voxelCounts[2],e=JU.V3.new3(a.x,a.y,a.z);e.normalize();for(var f=0;f<c;f++)for(var g=0;g<d;g++)for(var k=0;k<j;k++){var t=this.voxelData[f][g][k]-
b;this.voxelPtToXYZ(f,g,k,this.ptXyzTemp);var l=(this.ptXyzTemp.x*e.x+this.ptXyzTemp.y*e.y+this.ptXyzTemp.z*e.z+a.w-b)/1;if(0<=l||l>t)this.voxelData[f][g][k]=l}}},"JU.P4,~N");e(c$,"setVolumetricXml",function(){var a=new JU.SB;if(0==this.voxelCounts[0])a.append("<jvxlVolumeData>\n");else{a.append('<jvxlVolumeData origin="'+JU.Escape.eP(this.volumetricOrigin)+'">\n');for(var b=0;3>b;b++)a.append('<jvxlVolumeVector type="'+b+'" count="'+this.voxelCounts[b]+'" vector="'+JU.Escape.eP(this.volumetricVectors[b])+
'"></jvxlVolumeVector>\n')}a.append("</jvxlVolumeData>\n");return this.xmlData=a.toString()});e(c$,"setVoxelMapValue",function(a,b,c,d){null!=this.voxelMap&&this.voxelMap.put(Integer.$valueOf(this.getPointIndex(a,b,c)),Float.$valueOf(d))},"~N,~N,~N,~N");e(c$,"calculateFractionalPoint",function(a,b,c,d,j,e){var f=j-d,g=(a-d)/f;this.edgeVector.sub2(c,b);e.scaleAdd2(g,this.edgeVector,b);if(null==this.sr||!this.doIterate||j==d||0.01>g||0.99<g||0.01>this.edgeVector.length())return a;b=0;this.ptTemp.setT(e);
c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1);for(j=NaN;10>++b;){var k=(c-d)/f;if(0>k||1<k)break;k=(a-c)/f/2;g+=k;if(0>g||1<g)break;e.setT(this.ptTemp);j=c;if(0.005>Math.abs(k))break;this.ptTemp.scaleAdd2(k,this.edgeVector,e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1)}return j},"~N,JU.P3,JU.P3,~N,~N,JU.P3")});O("J.jvxl.data");F(null,"J.jvxl.data.JvxlData",["java.lang.Float","JU.SB","J.jvxl.data.JvxlCoder"],function(){c$=H(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;P(this,arguments)},J.jvxl.data,"JvxlData");ha(c$,function(){this.jvxlExcluded=Array(4)});W(c$,function(){});e(c$,"clear",function(){this.allowVolumeRender=!0;this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData="";this.colorScheme=this.color=null;this.colorDensity=!1;this.pointSize=NaN;this.contourColors=this.contourColixes=this.contourValuesUsed=this.contourValues=null;this.integration=NaN;this.isSlabbable=
!1;this.isValid=!0;this.meshColor=this.mapLattice=null;this.msg="";this.nVertexColors=this.nPointsX=0;this.slabInfo=this.fixedLattice=null;this.slabValue=-2147483648;this.rendering=this.thisSet=null;this.thisContour=-1;this.translucency=0;this.vertexColors=this.vertexColorMap=this.vContours=null;this.voxelVolume=0});e(c$,"setSurfaceInfo",function(a,b,c,d){this.jvxlSurfaceData=d;0==this.jvxlSurfaceData.indexOf("--")&&(this.jvxlSurfaceData=this.jvxlSurfaceData.substring(2));this.jvxlPlane=a;this.mapLattice=
b;this.nSurfaceInts=c},"JU.P4,JU.P3,~N,~S");e(c$,"setSurfaceInfoFromBitSet",function(a,b){this.setSurfaceInfoFromBitSetPts(a,b,null)},"JU.BS,JU.P4");e(c$,"setSurfaceInfoFromBitSetPts",function(a,b,c){var d=new JU.SB;a=null!=b?0:J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,this.nPointsX*this.nPointsY*this.nPointsZ,d);this.setSurfaceInfo(b,c,a,d.toString())},"JU.BS,JU.P4,JU.P3");e(c$,"jvxlUpdateInfo",function(a,b){this.title=a;this.nBytes=b},"~A,~N");c$.updateSurfaceData=e(c$,"updateSurfaceData",
function(a,b,c,d,j){if(0==a.length)return"";a=a.toCharArray();for(var e=0,f=0;e<c;e+=d,f++)Float.isNaN(b[e])&&(a[f]=j);return String.copyValueOf(a)},"~S,~A,~N,~N,~S")});O("J.jvxl.data");F(["JU.MeshSurface"],"J.jvxl.data.MeshData","java.lang.Float java.util.Arrays JU.AU $.BS $.V3 JU.BSUtil".split(" "),function(){c$=H(function(){this.setsSuccessful=!1;this.vertexIncrement=1;this.polygonColorData=null;va("J.jvxl.data.MeshData.SSet")||J.jvxl.data.MeshData.$MeshData$SSet$();va("J.jvxl.data.MeshData.SortSet")||
J.jvxl.data.MeshData.$MeshData$SortSet$();P(this,arguments)},J.jvxl.data,"MeshData",JU.MeshSurface);e(c$,"addVertexCopy",function(a,b,c,d){0>c&&(this.vertexIncrement=-c);return this.addVCVal(a,b,d)},"JU.T3,~N,~N,~B");e(c$,"getSurfaceSet",function(){return null==this.surfaceSet?this.getSurfaceSetForLevel(0):this.surfaceSet});e(c$,"getSurfaceSetForLevel",function(a){0==a&&(this.surfaceSet=Array(100),this.nSets=0);this.setsSuccessful=!0;for(var b=0;b<this.pc;b++)if(null!=this.pis[b]&&(null==this.bsSlabDisplay||
this.bsSlabDisplay.get(b))){var c=this.pis[b],d=this.findSet(c[0]),j=this.findSet(c[1]),e=this.findSet(c[2]);0>d&&0>j&&0>e?this.createSet(c[0],c[1],c[2]):d==j&&j==e||(0<=d?(this.surfaceSet[d].set(c[1]),this.surfaceSet[d].set(c[2]),0<=j&&j!=d&&this.mergeSets(d,j),0<=e&&(e!=d&&e!=j)&&this.mergeSets(d,e)):0<=j?(this.surfaceSet[j].set(c[0]),this.surfaceSet[j].set(c[2]),0<=e&&e!=j&&this.mergeSets(j,e)):(this.surfaceSet[e].set(c[0]),this.surfaceSet[e].set(c[1])))}for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&
c++;d=Array(this.surfaceSet.length);for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&(d[c++]=this.surfaceSet[b]);this.nSets=c;this.surfaceSet=d;!this.setsSuccessful&&2>a&&this.getSurfaceSetForLevel(a+1);if(0==a){a=Array(this.nSets);for(b=0;b<this.nSets;b++)a[b]=ta(J.jvxl.data.MeshData.SSet,this,null,this.surfaceSet[b]);java.util.Arrays.sort(a,ta(J.jvxl.data.MeshData.SortSet,this,null));for(b=0;b<this.nSets;b++)this.surfaceSet[b]=a[b].bs;this.setVertexSets(!1)}return this.surfaceSet},"~N");e(c$,
"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 d=c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&(a[d++]=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(c$,"findSet",function(a){for(var b=0;b<this.nSets;b++)if(null!=this.surfaceSet[b]&&this.surfaceSet[b].get(a))return b;return-1},"~N");e(c$,"createSet",function(a,b,c){var d;for(d=0;d<this.nSets&&null!=this.surfaceSet[d];d++);d==this.surfaceSet.length&&(this.surfaceSet=JU.AU.ensureLength(this.surfaceSet,this.surfaceSet.length+100));this.surfaceSet[d]=new JU.BS;this.surfaceSet[d].set(a);this.surfaceSet[d].set(b);this.surfaceSet[d].set(c);d==this.nSets&&this.nSets++},
"~N,~N,~N");e(c$,"mergeSets",function(a,b){this.surfaceSet[a].or(this.surfaceSet[b]);this.surfaceSet[b]=null},"~N,~N");e(c$,"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");c$.checkCutoff=e(c$,"checkCutoff",function(a,b,c,d){if(0>a||0>b||0>c)return!1;a=d[a];b=d[b];c=d[c];return 0<=a&&0<=b&&0<=c||0>=a&&0>=b&&0>=c},"~N,~N,~N,~A");c$.calculateVolumeOrArea=e(c$,"calculateVolumeOrArea",
function(a,b,c,d){(d||0>=a.nSets)&&a.getSurfaceSet();var j=null!=b&&1==b.cardinality(),e=j||0>=a.nSets?1:a.nSets;d=Ja(e,0);for(var f=new JU.V3,g=new JU.V3,k=new JU.V3,t=a.pc;0<=--t;)if(null!=a.setABC(t)){var l=0>=a.nSets?0:a.vertexSets[a.iA];if(null==b||b.get(l))c?(f.sub2(a.vs[a.iB],a.vs[a.iA]),g.sub2(a.vs[a.iC],a.vs[a.iA]),k.cross(f,g),d[j?0:l]+=k.length()):(f.setT(a.vs[a.iB]),g.setT(a.vs[a.iC]),k.cross(f,g),g.setT(a.vs[a.iA]),d[j?0:l]+=g.dot(k))}a=c?2:6;for(t=0;t<e;t++)d[t]/=a;if(j)return Float.$valueOf(d[0]);
if(null!=b){b.and(JU.BSUtil.newBitSet2(0,d.length));a=Ja(b.cardinality(),0);c=0;for(t=b.nextSetBit(0);0<=t;t=b.nextSetBit(t+1))a[c++]=d[t];d=a}return d},"J.jvxl.data.MeshData,JU.BS,~B,~B");e(c$,"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(c$,"invalidateVertices",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.vvs[b]=NaN},"JU.BS");c$.$MeshData$SSet$=function(){na(self.c$);c$=H(function(){ua(this,
arguments);this.bs=null;this.n=0;P(this,arguments)},J.jvxl.data.MeshData,"SSet");W(c$,function(a){this.bs=a;this.n=a.cardinality()},"JU.BS");c$=ma()};c$.$MeshData$SortSet$=function(){na(self.c$);c$=H(function(){ua(this,arguments);P(this,arguments)},J.jvxl.data.MeshData,"SortSet",null,java.util.Comparator);m(c$,"compare",function(a,b){return a.n>b.n?-1:a.n<b.n?1:0},"J.jvxl.data.MeshData.SSet,J.jvxl.data.MeshData.SSet");c$=ma()};Z(c$,"MODE_GET_VERTICES",1,"MODE_GET_COLOR_INDEXES",2,"MODE_PUT_SETS",
3,"MODE_PUT_VERTICES",4)});O("J.jvxl.readers");F(null,"J.jvxl.readers.XmlReader",["JU.P3","$.PT","$.SB","JU.Escape"],function(){c$=H(function(){this.line=this.br=null;P(this,arguments)},J.jvxl.readers,"XmlReader");e(c$,"getLine",function(){return this.line});W(c$,function(a){this.br=a},"java.io.BufferedReader");e(c$,"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(c$,"skipTag",function(a){this.skipTo("</"+a+">")},"~S");e(c$,"getXmlData",function(a,b,c,d){return this.getXmlDataLF(a,b,c,d,!1)},"~S,~S,~B,~B");e(c$,"getXmlDataLF",function(a,b,c,d,j){var e="</"+a+">";a="<"+a;if(null==b){b=new JU.SB;try{null==this.line&&(this.line=this.br.readLine());for(;0>this.line.indexOf(a);)this.line=this.br.readLine()}catch(f){if(Y(f,Exception))return null;throw f;}b.append(this.line);j&&b.append("\n");var g=!1,k=this.line.indexOf("/>"),
t=this.line.indexOf(">");if(0>t||k==t-1)g=d;for(;0>this.line.indexOf(e)&&(!g||0>this.line.indexOf("/>"));)b.append(this.line=this.br.readLine()),j&&b.append("\n");b=b.toString()}return J.jvxl.readers.XmlReader.extractTag(b,a,e,c)},"~S,~S,~B,~B,~B");c$.extractTagOnly=e(c$,"extractTagOnly",function(a,b){return J.jvxl.readers.XmlReader.extractTag(a,"<"+b+">","</"+b+">",!1)},"~S,~S");c$.extractTag=e(c$,"extractTag",function(a,b,c,d){b=a.indexOf(b);if(0>b)return"";var j=a.indexOf(c,b);0>j&&(j=a.indexOf("/>",
b),c="/>");if(0>j)return"";if(d)return j+=c.length,a.substring(b,j);for(c=!1;b<j;b++)if('"'==(d=a.charAt(b)))c=!c;else if(c&&"\\"==d)b++;else if(!c&&(">"==d||"/"==d))break;if(b>=j)return"";for(;JU.PT.isWhitespace(a.charAt(++b)););return J.jvxl.readers.XmlReader.unwrapCdata(a.substring(b,j))},"~S,~S,~S,~B");c$.unwrapCdata=e(c$,"unwrapCdata",function(a){return a.startsWith("<![CDATA[")&&a.endsWith("]]\x3e")?JU.PT.rep(a.substring(9,a.length-3),"]]]]\x3e<![CDATA[>","]]\x3e"):a},"~S");c$.getXmlAttrib=
e(c$,"getXmlAttrib",function(a,b){var c=u(1,0),d=J.jvxl.readers.XmlReader.setNext(a,b,c,1);if(2>d||2>(d=J.jvxl.readers.XmlReader.setNext(a,'"',c,0)))return"";c=J.jvxl.readers.XmlReader.setNext(a,'"',c,-1);return 0>=c?"":a.substring(d,c)},"~S,~S");e(c$,"getXmlPoint",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,b).$replace("(","{").$replace(")","}"),c=JU.Escape.uP(c);return T(c,JU.P3)?c:new JU.P3},"~S,~S");c$.setNext=e(c$,"setNext",function(a,b,c,d){var j=c[0];if(0>j||0>(j=a.indexOf(b,
c[0])))return-1;j+=b.length;c[0]=j+d;return 0<d&&j<a.length&&"="!=a.charAt(j)?J.jvxl.readers.XmlReader.setNext(a,b,c,d):c[0]},"~S,~S,~A,~N");e(c$,"skipTo",function(a){null==this.line&&(this.line=this.br.readLine());for(;null!=this.line&&0>this.line.indexOf(a);)this.line=this.br.readLine()},"~S");e(c$,"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")});O("J.jvxl.readers");
F(["JU.P3","$.V3"],"J.jvxl.readers.SurfaceGenerator","java.lang.Float java.util.Map JU.AU $.BS $.Measure $.P4 $.PT $.Rdr $.SB J.jvxl.data.JvxlCoder $.JvxlData $.MeshData $.VolumeData J.jvxl.readers.Parameters $.SurfaceReader JU.Logger JV.FileManager".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"SurfaceGenerator");ha(c$,function(){this.vAB=new JU.V3;this.vNorm=new JU.V3;this.ptRef=JU.P3.new3(0,0,1E15)});W(c$,function(a,b,c,d){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==d?new J.jvxl.data.JvxlData:d;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(c$,"setJvxlData",function(a){this.jvxlData=a;null!=a&&(a.version=this.version)},"J.jvxl.data.JvxlData");e(c$,"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(),T(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=B(-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 d=0;d<this.params.title.length;d++)0<this.params.title[d].length&&JU.Logger.info(this.params.title[d]);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(T(b,JU.P3)){var c=this.params.contourIncrements=b,d=c.x,j=c.y,e=c.z;0>=e&&
(e=1);for(var c=0,f=d;f<=j+e/10;f+=e,c++);this.params.contoursDiscrete=w(c,0);f=d;for(d=0;d<c;d++,f+=e)this.params.contoursDiscrete[d]=f;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(T(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=w(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("rad"===a)return this.params.setRadical(b),this.readerData=w(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lobe"===a)return this.params.setLobe(b),this.readerData=w(-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=w(-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,d=null,T(b,Integer)?c=b.intValue():d=b,this.params.setMO(c,d),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(c$,"newReader",function(a){a=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=a&&a.init(this);return a},"~S");e(c$,"newReaderBr",function(a,b){var c=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=c&&c.init2(this,b);return c},"~S,java.io.BufferedReader");c$.getInterface=e(c$,"getInterface",function(a){try{var b=eb._4Name("J.jvxl.readers."+a);return null==b?null:b.newInstance()}catch(c){if(Y(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+
a+": \n"+c.toString()),null;throw c;}},"~S");e(c$,"getSurfaceSets",function(){null==this.meshDataServer?this.meshData.getSurfaceSet():(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.getSurfaceSet(),this.meshDataServer.fillMeshData(this.meshData,3,null))});e(c$,"processState",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;2<=this.params.state?this.mapSurface():this.generateSurface()});e(c$,"setReader",function(){this.readerData=null;if(null!=
this.surfaceReader)return!this.surfaceReader.vertexDataOnly;switch(this.params.dataType){case 1207:this.surfaceReader=this.newReader("IsoPlaneReader");break;case 1208:this.surfaceReader=this.newReader("AtomPropertyMapper");break;case 1328:case 1329:this.readerData=1328==this.params.dataType?"Mep":"Mlp";this.surfaceReader=3==this.params.state?this.newReader("AtomPropertyMapper"):this.newReader("Iso"+this.readerData+"Reader");break;case 1334:this.surfaceReader=this.newReader("IsoIntersectFileReader");
break;case 1333:this.surfaceReader=this.newReader("IsoIntersectAtomReader");break;case 1195:case 1203:case 1196:this.surfaceReader=this.newReader("IsoSolventReader");break;case 1844:case 1837:this.surfaceReader=this.newReader("IsoMOReader");break;case 8:this.surfaceReader=this.newReader("IsoFxyReader");break;case 9:this.surfaceReader=this.newReader("IsoFxyzReader")}JU.Logger.debugging&&JU.Logger.info("Using surface reader "+this.surfaceReader);this.params.isSilent&&null!=this.surfaceReader&&(this.surfaceReader.isQuiet=
!0);return!0});e(c$,"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(c$,"mapSurface",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;if(!(3>++this.params.state)&&this.setReader()){this.params.isPeriodic&&
(this.surfaceReader.volumeData.isPeriodic=!0);if(null!=this.params.thePlane){var a=this.params.isSquared;this.params.isSquared=!1;this.params.cutoff=0;this.params.cutoffRange=null;this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);this.surfaceReader.createIsosurface(!this.params.isPeriodic);this.surfaceReader.volumeData.setMappingPlane(null);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted();if(1207==this.params.dataType){this.surfaceReader.discardTempData(!0);
return}this.params.isSquared=a;this.params.mappedDataMin=3.4028235E38;this.surfaceReader.readVolumeData(!0);null!=this.params.mapLattice&&(this.surfaceReader.volumeData.isPeriodic=!0)}else!this.params.colorBySets&&!this.params.colorDensity&&(this.surfaceReader.readAndSetVolumeParameters(!0),this.params.mappedDataMin=3.4028235E38,this.surfaceReader.readVolumeData(!0));this.colorIsosurface();this.surfaceReader.closeReader();this.surfaceReader=null}});e(c$,"colorIsosurface",function(){this.surfaceReader.colorIsosurface();
this.surfaceReader.jvxlUpdateInfo();this.surfaceReader.updateTriangles();this.surfaceReader.discardTempData(!0);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted()});e(c$,"getProperty",function(a,b){return"jvxlFileData"===a?J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,null,this.params.title,"",!0,b,null,null):"jvxlFileInfo"===a?J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData):null},"~S,~N");e(c$,"setFileData",function(a,b){var c=this.fileType;this.fileType=null;if(T(b,
java.util.Map)){var d=b;if(d.containsKey("__pymolSurfaceData__"))return this.readerData=d,this.newReaderBr("PyMOLMeshReader",null);b=d.get("volumeData")}if(T(b,J.jvxl.data.VolumeData))return this.volumeDataTemp=b,this.newReader("VolumeDataReader");d=null;T(b,String)&&(d=b,b=JU.Rdr.getBR(b));if(T(b,Array)){for(var d=b[0],j=Array(d.length),e=0;e<d.length;e++)this.fileType=c,j[e]=this.setFileData(a,d[e]);b[0]=j;this.readerData=b;return this.newReader("IsoIntersectGridReader")}j=b;null==c&&(c=JV.FileManager.determineSurfaceFileType(j));
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{j=JU.Rdr.getBufferedReader(b,null)}catch(f){if(!Y(f,Exception))throw f;}c=JV.FileManager.determineSurfaceFileType(j)}null==c&&(c="UNKNOWN");JU.Logger.info("data file type was determined to be "+c);if(c.equals("Jvxl+"))return this.newReaderBr("JvxlReader",
j);this.readerData=B(-1,[this.params.fileName,d]);0<="MRC DELPHI DSN6".indexOf(c.toUpperCase())&&(c+="Binary");return this.newReaderBr(c+"Reader",j)},"JV.Viewer,~O");e(c$,"getReaderData",function(){var a=this.readerData;this.readerData=null;return a});e(c$,"initializeIsosurface",function(){this.params.initialize();this.colorPtr=0;this.marchingSquares=this.surfaceReader=null;this.initState()});e(c$,"initState",function(){this.params.state=1;this.params.dataType=this.params.surfaceType=0});e(c$,"setLcao",
function(){this.params.colorPos=this.params.colorPosLCAO;this.params.colorNeg=this.params.colorNegLCAO;return this.params.lcaoType});e(c$,"getFunctionZfromXY",function(){for(var a=this.params.functionInfo.get(1),b=u(3,0),c=u(3,0),d=Array(3),e=0;3>e;e++){var h=this.params.functionInfo.get(e+2);b[e]=Math.abs(y(h.x));d[e]=JU.V3.new3(h.y,h.z,h.w)}for(var h=b[0],b=b[1],f=new JU.P3,g=new JU.P3,k=new JU.P3,t=new JU.P3,l=this.params.functionInfo.get(5),q=w(h,b,0),p,e=0;e<h;e++)for(var m=0;m<b;m++){f.scaleAdd2(e,
d[0],a);f.scaleAdd2(m,d[1],f);var v=J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(f.x,f.y,l,c);g.set((p=l[c[0]])[0],p[1],p[2]);1E-5>v?f.z=p[2]:(k.set((p=l[c[1]])[0],p[1],p[2]),t.set((p=l[c[2]])[0],p[1],p[2]),f.z=this.distanceVerticalToPlane(f.x,f.y,g,k,t));q[e][m]=f.z}this.params.functionInfo.set(5,q)});e(c$,"distanceVerticalToPlane",function(a,b,c,d,e){c=JU.Measure.getDirectedNormalThroughPoints(c,d,e,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");c$.findNearestThreePoints=e(c$,"findNearestThreePoints",function(a,b,c,d){var e,h,f,g,k,t,l;k=t=l=-1;h=f=g=3.4028235E38;for(var q=c.length;0<=--q;)e=(e=c[q][0]-a)*e+(e=c[q][1]-b)*e,e<h?(g=f,f=h,h=e,l=t,t=k,k=q):e<f?(g=f,f=e,l=t,t=q):e<g&&(g=e,l=q);d[0]=k;d[1]=t;d[2]=l;return h},"~N,~N,~A,~A");e(c$,"addRequiredFile",function(a){null!=this.meshDataServer&&this.meshDataServer.addRequiredFile(a)},"~S");e(c$,"setRequiredFile",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setRequiredFile(a,
b)},"~S,~S");e(c$,"log",function(a){null==this.atomDataServer?System.out.println(a):this.atomDataServer.log(a)},"~S");e(c$,"setOutputChannel",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setOutputChannel(a,b)},"javajs.api.GenericBinaryDocument,JU.OC");e(c$,"fillAtomData",function(a,b){0!=(b&2)&&null!=a.bsSelected&&(null==this.bsVdw&&(this.bsVdw=new JU.BS),this.bsVdw.or(a.bsSelected));this.atomDataServer.fillAtomData(a,b)},"J.atomdata.AtomData,~N");e(c$,"getOriginVaVbVc",function(){return null==
this.surfaceReader.volumeData?null:this.surfaceReader.volumeData.oabc})});O("J.jvxl.readers");F(null,"J.jvxl.readers.Parameters","java.lang.Float java.util.Hashtable JU.A4 $.Lst $.M3 $.P3 $.P4 $.V3 JU.Escape $.Logger".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"Parameters");ha(c$,function(){this.anisotropy=w(3,0)});e(c$,"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(c$,"resetForMapping",function(a){a||(this.state=2);this.center.x=NaN;this.colorDensity=!1;this.intersection=this.func=null;this.isAnisotropic=!1;this.isMapped=!0;this.mappedDataMin=3.4028235E38;this.points=this.parameters=this.origin=null;this.qmOrbitalType=0;this.volumeData=this.steps=null},"~B");e(c$,"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(c$,"setEccentricity",function(a){var b=JU.V3.new3(a.x,a.y,a.z),c=0<this.scale?this.scale:0>a.w?1:b.length();a=Math.abs(a.w);b.normalize();var d=JU.V3.new3(0,0,1);b.add(d);b.normalize();Float.isNaN(b.x)&&b.set(1,0,0);this.eccentricityMatrixInverse=new JU.M3;this.eccentricityMatrixInverse.invertM(this.eccentricityMatrix=(new JU.M3).setAA(JU.A4.newVA(b,3.141592653589793)));this.isEccentric=this.isAnisotropic=!0;
this.eccentricityScale=c;this.eccentricityRatio=a;1<a&&(this.eccentricityScale*=a);this.anisotropy[0]=a*c;this.anisotropy[1]=a*c;this.anisotropy[2]=c;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P4");e(c$,"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(c$,"setSphere",function(a,b){this.dataType=b?74:65;this.distance=a;this.setEccentricity(JU.P4.new4(0,0,1,1));this.cutoff=1.4E-45;this.isCutoffAbsolute=
!1;this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" SPHERE "+a+";"},"~N,~B");e(c$,"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(c$,"setEllipsoidAF",function(a){this.anisoB=a;this.dataType=67;this.distance=0.3*(Float.isNaN(this.scale)?1:this.scale);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;Float.isNaN(this.center.x)&&
this.center.set(0,0,0);3.4028235E38==this.resolution&&(this.resolution=6)},"~A");e(c$,"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(c$,"getScriptParams",function(){return" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)});e(c$,"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(c$,"setRadical",function(a){this.dataType=71;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=
" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" RAD {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(c$,"setLcao",function(a,b){this.lcaoType=a;1==b&&(this.colorPosLCAO=this.colorNegLCAO);this.isSilent=!this.logMessages},"~S,~N");e(c$,"setSolvent",function(a,b){this.isEccentric=this.isAnisotropic=!1;this.solventRadius=Math.abs(b);this.dataType=null!=this.intersection?1333:"nomap"===a?1207:"molecular"===a?1203:"sasurface"===a||0==this.solventRadius?1196:1195;
if(2>this.state&&(this.cutoffAutomatic||!this.colorDensity)&&(null==this.intersection||3.4028235E38==this.cutoff))this.cutoff=0;switch(this.dataType){case 1333:this.calculationType="VDW intersection";break;case 1207:this.calculationType="unmapped plane";break;case 1203:this.calculationType="molecular surface with radius "+this.solventRadius;0==this.minSet&&(this.minSet=50);break;case 1195:this.calculationType="solvent-excluded surface with radius "+this.solventRadius;0==this.minSet&&(this.minSet=
50);break;case 1196:this.calculationType="solvent-accessible surface with radius "+this.solventRadius,0==this.minSet&&(this.minSet=50)}switch(this.dataType){case 1207:this.solventExtendedAtomRadius=this.solventRadius;this.solventRadius=0;this.isContoured=!1;break;case 1203:this.solventExtendedAtomRadius=0;break;case 1195:this.solventExtendedAtomRadius=0;null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent);break;case 1196:this.solventExtendedAtomRadius=
this.solventRadius,this.solventRadius=0,null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent)}},"~S,~N");e(c$,"setFunctionXY",function(a){this.dataType=8;this.functionInfo=a;this.cutoff=1.4E-45;this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setFunctionXYZ",function(a){this.dataType=9;this.functionInfo=a;3.4028235E38==this.cutoff&&(this.cutoff=1.4E-45);this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setAtomicOrbital",function(a){this.dataType=
1294;this.setEccentricity(JU.P4.new4(0,0,1,1));this.psi_n=y(a[0]);this.psi_l=y(a[1]);this.psi_m=y(a[2]);this.psi_Znuc=a[3];this.psi_monteCarloCount=y(a[4]);this.distance=a[5];if(0!=this.distance||null!=this.thePlane)this.allowVolumeRender=!1;this.randomSeed=y(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(c$,"setMep",function(a,b){this.dataType=b?1329:1328;this.theProperty=a;this.isEccentric=this.isAnisotropic=this.usePropertyForColorRange=!1;3.4028235E38==this.cutoff&&(this.cutoff=0.1,this.isSquared&&(this.cutoff*=this.cutoff));this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;this.contourFromZero=!1;2<=this.state||null!=this.thePlane?!this.rangeDefined&&!this.rangeAll&&(this.valueMappedToRed=
-0.1,this.valueMappedToBlue=0.1,this.rangeDefined=!0):this.isBicolorMap=this.colorBySign=!0},"~A,~B");e(c$,"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=w(-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(c$,"setMO",function(a,b){this.isModelConnected=!0;this.qm_moLinearCombination=b;this.qm_moNumber=null==b?Math.abs(a):y(b[1]);this.qmOrbitalType=this.moData.containsKey("haveVolumeData")?5:this.moData.containsKey("gaussians")?1:this.moData.containsKey("slaters")?2:0;var c=0>=a&&null==b;0==this.qmOrbitalType?(JU.Logger.error("MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?)"),this.title=B(-1,["no basis functions found in file"])):(this.qmOrbitalCount=
this.moData.get("mos").size(),this.calculationType=this.moData.get("calculationType"),this.calculationType="Molecular orbital #"+this.qm_moNumber+"/"+this.qmOrbitalCount+" "+(null==this.calculationType?"":this.calculationType),!c&&null==this.title&&(this.title=Array(5),this.title[0]="%F",this.title[1]="Model %M  MO %I/%N %T",this.title[2]="?Energy = %E %U",this.title[3]="?Symmetry = %S",this.title[4]="?Occupancy = %O"));this.dataType=1837;3.4028235E38==this.cutoff&&(this.cutoff=c?0.01:0.05);if(this.isSquared||
this.isSquaredLinear)this.cutoff*=this.cutoff;this.isEccentric=this.isAnisotropic=!1;this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;2<=this.state||null!=this.thePlane||(this.colorBySign=!0,this.colorByPhase&&0==this.colorPhase&&(this.colorByPhase=!1),this.isBicolorMap=!0)},"~N,~A");e(c$,"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(c$,"addSlabInfo",function(a){null==this.slabInfo&&(this.slabInfo=
new JU.Lst);this.slabInfo.addLast(a)},"~A");e(c$,"isInsideOut",function(){return this.insideOut!=this.dataXYReversed});e(c$,"isFullyLit",function(){return null!=this.thePlane||this.fullyLit});Z(c$,"STATE_UNINITIALIZED",0,"STATE_INITIALIZED",1,"STATE_DATA_READ",2,"STATE_DATA_COLORED",3,"NO_ANISOTROPY",32,"IS_SILENT",64,"IS_SOLVENTTYPE",128,"HAS_MAXGRID",256,"IS_POINTMAPPABLE",512,"IS_SLABBABLE",1024,"SURFACE_NONE",0,"SURFACE_SPHERE",65,"SURFACE_ELLIPSOID2",66,"SURFACE_ELLIPSOID3",67,"SURFACE_LOBE",
68,"SURFACE_LCAOCARTOON",69,"SURFACE_LONEPAIR",70,"SURFACE_RADICAL",71,"SURFACE_FUNCTIONXY",8,"SURFACE_FUNCTIONXYZ",9,"SURFACE_GEODESIC",74,"SURFACE_SOLVENT",1195,"SURFACE_SASURFACE",1196,"SURFACE_MOLECULARORBITAL",1837,"SURFACE_ATOMICORBITAL",1294,"SURFACE_MEP",1328,"SURFACE_MLP",1329,"SURFACE_MOLECULAR",1203,"SURFACE_NCI",1844,"SURFACE_INTERSECT_ATOM",1333,"SURFACE_INTERSECT_FILE",1334,"SURFACE_NOMAP",1207,"SURFACE_PROPERTY",1208,"ANGSTROMS_PER_BOHR",0.5291772,"defaultEdgeFractionBase",35,"defaultEdgeFractionRange",
90,"defaultColorFractionBase",35,"defaultColorFractionRange",90,"defaultMappedDataMin",0,"defaultMappedDataMax",1,"defaultCutoff",0.02,"defaultOrbitalCutoff",0.04,"defaultLobeCutoff",0.14,"defaultOrbitalCutoffOld",0.14,"defaultQMOrbitalCutoff",0.05,"defaultQMElectronDensityCutoff",0.01,"defaultContourCount",11,"nContourMax",100,"defaultColorNegative",4294901760,"defaultColorPositive",4278190335,"defaultColorNegativeLCAO",4286578816,"defaultColorPositiveLCAO",4294944E3,"defaultSolventRadius",1.2,"defaultMepCutoff",
0.1,"defaultMepMin",-0.1,"defaultMepMax",0.1,"MEP_MAX_GRID",40,"QM_TYPE_UNKNOWN",0,"QM_TYPE_GAUSSIAN",1,"QM_TYPE_SLATER",2,"QM_TYPE_NCI_PRO",3,"QM_TYPE_NCI_SCF",4,"QM_TYPE_VOLUME_DATA",5,"MO_MAX_GRID",80)});O("J.jvxl.readers");F(["J.jvxl.api.VertexDataServer","JU.P3"],"J.jvxl.readers.SurfaceReader","java.lang.Float JU.AU $.BS J.jvxl.calc.MarchingCubes $.MarchingSquares J.jvxl.data.JvxlCoder $.MeshData JU.BoxInfo $.C $.ColorEncoder $.Escape $.Logger".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"SurfaceReader",null,J.jvxl.api.VertexDataServer);ha(c$,function(){this.ptTemp=new JU.P3});W(c$,function(){});e(c$,"initSR",function(a){this.sg=a;this.params=a.params;this.assocCutoff=
this.params.assocCutoff;this.isXLowToHigh=this.params.isXLowToHigh;this.center=this.params.center;this.anisotropy=this.params.anisotropy;this.isAnisotropic=this.params.isAnisotropic;this.eccentricityMatrix=this.params.eccentricityMatrix;this.eccentricityMatrixInverse=this.params.eccentricityMatrixInverse;this.isEccentric=this.params.isEccentric;this.eccentricityScale=this.params.eccentricityScale;this.eccentricityRatio=this.params.eccentricityRatio;this.marchingSquares=a.marchingSquares;this.meshData=
a.meshData;this.jvxlData=a.jvxlData;this.setVolumeDataV(a.volumeDataTemp);this.meshDataServer=a.meshDataServer;this.cJvxlEdgeNaN=String.fromCharCode(125)},"J.jvxl.readers.SurfaceGenerator");e(c$,"setOutputChannel",function(){},"JU.OC");e(c$,"newVoxelDataCube",function(){this.volumeData.setVoxelDataAsArray(this.voxelData=w(this.nPointsX,this.nPointsY,this.nPointsZ,0))});e(c$,"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(c$,"jvxlUpdateInfo",function(){this.jvxlData.jvxlUpdateInfo(this.params.title,this.nBytes)});e(c$,"readAndSetVolumeParameters",function(a){return!this.readVolumeParameters(a)?!1:this.vertexDataOnly?!0:this.volumeData.setUnitVectors()},"~B");e(c$,"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=B(-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(c$,"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(c$,"discardTempData",function(a){this.discardTempDataSR(a)},"~B");e(c$,"discardTempDataSR",function(a){a&&(this.voxelData=null,this.marchingCubes=this.sg.marchingSquares=this.marchingSquares=
null)},"~B");e(c$,"initializeVolumetricData",function(){this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.setVolumeDataV(this.volumeData)});e(c$,"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(Y(b,Exception))return JU.Logger.error(b.toString()),!1;throw b;
}return!0},"~B");e(c$,"gotoData",function(){},"~N,~N");e(c$,"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=$(a,0);if(null==c||c.length<a)this.meshData.vvs=w(a,0);for(c=0;c<a;c++)b[c]=JU.C.getColix(this.jvxlData.vertexColors[c]);return"-"});m(c$,"getPlane",function(a){return this.getPlaneSR(a)},"~N");e(c$,"getPlaneSR",function(a){0==this.yzCount&&this.initPlanes();
null!=this.qpc&&this.qpc.getPlane(a,this.yzPlanes[a%2]);return this.yzPlanes[a%2]},"~N");e(c$,"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]=w(this.yzCount,0);this.yzPlanes[1]=w(this.yzCount,0)});m(c$,"getValue",function(a,b,c,d){return this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(c$,"getValue2",function(a,b,c,d){return null==this.yzPlanes?this.voxelData[a][b][c]:
this.yzPlanes[a%2][d]},"~N,~N,~N,~N");e(c$,"generateSurfaceData",function(){this.edgeData="";if(this.vertexDataOnly)try{this.readSurfaceData(!1)}catch(a){if(Y(a,Exception))System.out.println(a.toString()),JU.Logger.error("Exception in SurfaceReader::readSurfaceData: "+a.toString());else throw a;}else{this.contourVertexCount=0;var b=-1;this.marchingSquares=null;if(null!=this.params.thePlane||this.params.isContoured)this.marchingSquares=new J.jvxl.calc.MarchingSquares(this,this.volumeData,this.params.thePlane,
this.params.contoursDiscrete,this.params.nContours,this.params.thisContour,this.params.contourFromZero),b=this.marchingSquares.contourType,this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue);this.params.contourType=b;this.params.isXLowToHigh=this.isXLowToHigh;this.marchingCubes=new J.jvxl.calc.MarchingCubes(this,this.volumeData,this.params,this.jvxlVoxelBitSet);b=this.marchingCubes.getEdgeData();null==this.params.thePlane&&(this.edgeData=b);this.jvxlData.setSurfaceInfoFromBitSetPts(this.marchingCubes.bsVoxels,
this.params.thePlane,this.params.mapLattice);this.jvxlData.jvxlExcluded=this.params.bsExcluded;this.isJvxl&&(this.edgeData=this.jvxlEdgeDataRead);this.postProcessVertices()}});e(c$,"postProcessVertices",function(){});m(c$,"getSurfacePointIndexAndFraction",function(a,b,c,d,e,h,f,g,k,t,l,q,p,m){b=this.getSurfacePointAndFraction(a,b,k,t,l,q,c,d,e,f,g,m,this.ptTemp);if(null!=this.marchingSquares&&this.params.isContoured)return this.marchingSquares.addContourVertex(this.ptTemp,a);a=0<this.assocCutoff?
m[0]<this.assocCutoff?f:m[0]>1-this.assocCutoff?g:-1:-1;0<=a&&(a=this.marchingCubes.getLinearOffset(c,d,e,a));a=this.addVertexCopy(this.ptTemp,b,a,!0);0<=a&&this.params.iAddGridPoints&&(this.marchingCubes.calcVertexPoint(c,d,e,g,this.ptTemp),this.addVertexCopy(k<t?l:this.ptTemp,Math.min(k,t),-3,!0),this.addVertexCopy(k<t?this.ptTemp:l,Math.max(k,t),-3,!0));return a},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");e(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,h,f,g,k,t,l,q,p){return this.getSPF(a,
b,c,d,e,h,f,g,k,t,l,q,p)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPF",function(a,b,c,d,e,h,f,g,k,t,l,q,p){d-=c;f=(a-c)/d;if(b&&(0>f||1<f))f=(-a-c)/d;if(0>f||1<f)f=NaN;q[0]=f;p.scaleAdd2(f,h,e);return c+f*d},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"addVertexCopy",function(a,b,c,d){return this.addVC(a,b,c,d)},"JU.T3,~N,~N,~B");e(c$,"addVC",function(a,b,c,d){return Float.isNaN(b)&&-3!=c?-1:null==this.meshDataServer?this.meshData.addVertexCopy(a,b,c,d):this.meshDataServer.addVertexCopy(a,
b,c,d)},"JU.T3,~N,~N,~B");e(c$,"addTriangleCheck",function(a,b,c,d,e,h,f){if(null!=this.marchingSquares&&this.params.isContoured){if(0==f)return this.marchingSquares.addTriangle(a,b,c,d,e);f=0}return null!=this.meshDataServer?this.meshDataServer.addTriangleCheck(a,b,c,d,e,h,f):h&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.meshData.vvs)?-1:this.meshData.addTriangleCheck(a,b,c,d,e,f)},"~N,~N,~N,~N,~N,~B,~N");e(c$,"colorIsosurface",function(){this.params.isSquared&&null!=this.volumeData&&this.volumeData.filterData(!0,
NaN);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.jvxlData.saveVertexCount=0;this.params.isContoured&&null!=this.marchingSquares&&(this.initializeMapping(),this.params.setMapRanges(this,!1),this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue),this.jvxlData.saveVertexCount=this.marchingSquares.contourVertexCount,this.contourVertexCount=this.marchingSquares.generateContourData(this.jvxlDataIs2dContour,this.params.isSquared?
1E-8:1E-4),this.jvxlData.contourValuesUsed=this.marchingSquares.contourValuesUsed,this.minMax=this.marchingSquares.getMinMax(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted(),this.finalizeMapping());this.applyColorScale();this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.jvxlFileMessage="mapped: min = "+this.params.valueMappedToRed+"; max = "+this.params.valueMappedToBlue});
e(c$,"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=$(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,d;this.initializeMapping();for(var e=this.meshData.vc;--e>=this.meshData.mergeVertexCount0;){if(this.params.colorBySets)d=this.meshData.vertexSets[e];else if(this.params.colorByPhase)d=this.getPhase(this.meshData.vs[e]);else{var h=this.haveSurfaceAtoms;d=this.volumeData.lookupInterpolatedVoxelValue(this.meshData.vs[e],h);h&&(this.meshData.vertexSource[e]=
this.getSurfaceAtomIndex())}d<b&&(b=d);d>c&&3.4028235E38!=d&&(c=d);this.meshData.vvs[e]=d}this.params.rangeSelected&&null==this.minMax&&(this.minMax=w(-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(c$,"colorData",function(){var a=this.meshData.vvs,b=this.meshData.vcs;this.meshData.pcs=null;var c=this.jvxlData.valueMappedToBlue,d=this.jvxlData.valueMappedToRed,e=this.jvxlData.minColorIndex,
h=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 f=this.meshData.vc;0<=--f;){var g=a[f];0<=e?0>=g?b[f]=e:0<g&&(b[f]=h):(g<=d&&(g=d),g>=c&&(g=c),b[f]=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=$(a,0);e=this.jvxlData.contourValues;null==e&&(e=this.jvxlData.contourValuesUsed);null==this.jvxlData.contourValuesUsed&&(this.jvxlData.contourValuesUsed=null==e?w(a,0):e);c=(c-d)/(a+1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(f=0;f<a;f++)h=null==e?d+(f+1)*c:e[f],this.jvxlData.contourValuesUsed[f]=h,
b[f]=JU.C.getColixTranslucent(this.params.colorEncoder.getArgb(h));this.jvxlData.contourColors=JU.C.getHexCodes(b)}});c$.getColorPhaseIndex=e(c$,"getColorPhaseIndex",function(a){for(var b=-1,c=0;c<J.jvxl.readers.SurfaceReader.colorPhases.length;c++)if(a.equalsIgnoreCase(J.jvxl.readers.SurfaceReader.colorPhases[c])){b=c;break}return b},"~S");e(c$,"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(c$,"getMinMaxMappedValues",function(a){if(null!=this.minMax&&3.4028235E38!=this.minMax[0])return this.minMax;if(this.params.colorBySets)return this.minMax=w(-1,[0,Math.max(this.meshData.nSets-1,0)]);var b=3.4028235E38,c=-3.4028235E38;if(this.params.usePropertyForColorRange&&null!=this.params.theProperty){for(a=this.params.theProperty.length;0<=
--a;)if(!this.params.rangeSelected||this.params.bsSelected.get(a)){var d=this.params.theProperty[a];Float.isNaN(d)||(d<b&&(b=d),d>c&&(c=d))}return this.minMax=w(-1,[b,c])}var d=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc,e=this.meshData.vs,h=a||this.jvxlDataIs2dContour||this.vertexDataOnly||this.params.colorDensity;for(a=this.meshData.mergeVertexCount0;a<d;a++){var f;f=h?this.meshData.vvs[a]:this.volumeData.lookupInterpolatedVoxelValue(e[a],!1);f<b&&(b=f);f>c&&3.4028235E38!=
f&&(c=f)}return this.minMax=w(-1,[b,c])},"~B");e(c$,"updateTriangles",function(){null==this.meshDataServer?this.meshData.invalidatePolygons():this.meshDataServer.invalidateTriangles()});e(c$,"updateSurfaceData",function(){this.meshData.setVertexSets(!0);this.updateTriangles();null==this.params.bsExcluded[1]&&(this.params.bsExcluded[1]=new JU.BS);this.meshData.updateInvalidatedVertices(this.params.bsExcluded[1])});e(c$,"selectPocket",function(){},"~B");e(c$,"excludeMinimumSet",function(){null!=this.meshDataServer&&
this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()<this.params.minSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(c$,"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(c$,"slabIsosurface",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.slabPolygonsList(a,!0);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null)},"JU.Lst");e(c$,
"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(c$,"setVectorAnisotropy",function(a){this.haveSetAnisotropy=!0;a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2]},"JU.T3");e(c$,"setVolumetricAnisotropy",function(){this.haveSetAnisotropy||(this.setVolumetricOriginAnisotropy(),this.setVectorAnisotropy(this.volumetricVectors[0]),this.setVectorAnisotropy(this.volumetricVectors[1]),this.setVectorAnisotropy(this.volumetricVectors[2]))});
e(c$,"setVolumetricOriginAnisotropy",function(){this.volumetricOrigin.setT(this.center)});e(c$,"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(c$,"setBBox",function(a,b){null==this.xyzMin&&(this.xyzMin=JU.P3.new3(3.4028235E38,3.4028235E38,3.4028235E38),this.xyzMax=JU.P3.new3(-3.4028235E38,-3.4028235E38,-3.4028235E38));JU.BoxInfo.addPoint(a,this.xyzMin,
this.xyzMax,b)},"JU.T3,~N");e(c$,"getValueAtPoint",function(){return 0},"JU.T3,~B");e(c$,"initializeMapping",function(){});e(c$,"finalizeMapping",function(){});e(c$,"getSurfaceAtomIndex",function(){return-1});Z(c$,"ANGSTROMS_PER_BOHR",0.5291772,"defaultMappedDataMin",0,"defaultMappedDataMax",1,"defaultCutoff",0.02,"colorPhases",B(-1,"_orb x y z xy yz xz x2-y2 z2".split(" ")))});O("J.jvxl.calc");F(["JU.TriangleData","JU.BS","$.P3","$.SB","$.V3"],"J.jvxl.calc.MarchingCubes",["java.lang.Float","J.jvxl.data.JvxlCoder"],
function(){c$=H(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.$isInside=this.allInside=!1;this.voxelData=this.offset=null;this.nTriangles=0;this.linearOffsets=this.fReturn=this.edgeVertexPlanes=this.edgeVertexPointers=this.pointA=this.pt0=this.bsValues=null;P(this,arguments)},J.jvxl.calc,"MarchingCubes",JU.TriangleData);ha(c$,function(){this.edgeData=new JU.SB;this.vertexValues=w(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=w(1,0);this.linearOffsets=u(8,0)});W(c$,function(){da(this,J.jvxl.calc.MarchingCubes,[])});W(c$,function(a,b,c,d){da(this,J.jvxl.calc.MarchingCubes,[]);this.excludePartialCubes=!0;this.surfaceReader=a;this.bsVoxels=d;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!=d?2:3;this.setParameters(b,c)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");e(c$,"setParameters",function(a,b){this.volumeData=a;this.colorDensity=b.colorDensity;this.isContoured=null==b.thePlane&&b.isContoured&&!this.colorDensity;this.cutoff=b.cutoff;this.isCutoffAbsolute=b.isCutoffAbsolute;this.isDensityRange=null!=b.cutoffRange;this.contourType=
b.contourType;this.isSquared=b.isSquared;this.isXLowToHigh=b.isXLowToHigh;this.cubeCountX=a.voxelCounts[0]-1;this.cubeCountY=a.voxelCounts[1]-1;this.cubeCountZ=a.voxelCounts[2]-1;a.getYzCount();null!=b.mapLattice&&(this.cubeCountX*=Math.abs(b.mapLattice.x),this.cubeCountY*=Math.abs(b.mapLattice.y),this.cubeCountZ*=Math.abs(b.mapLattice.z));this.nY=this.cubeCountY+1;this.nZ=this.cubeCountZ+1;this.yzCount=this.nY*this.nZ;null==this.bsVoxels&&(this.bsVoxels=new JU.BS);this.edgeVertexPointers=this.isXLowToHigh?
J.jvxl.calc.MarchingCubes.edgeVertexPointersLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPointersHighToLow;this.edgeVertexPlanes=this.isXLowToHigh?J.jvxl.calc.MarchingCubes.edgeVertexPlanesLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPlanesHighToLow;this.isoPointIndexPlanes=u(2,this.yzCount,3,0);this.yzPlanes=3==this.mode?w(2,this.yzCount,0):null;this.setLinearOffsets();this.calcVoxelVertexVectors()},"J.jvxl.data.VolumeData,J.jvxl.readers.Parameters");e(c$,"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(c$,"resetIndexPlane",function(a){for(var b=0;b<this.yzCount;b++)for(var c=0;3>c;c++)a[b][c]=-2147483648;return a},"~A");e(c$,"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,d,e,h;this.isXLowToHigh?(a=0,this.colorDensity?(b=this.cubeCountX+1,h=this.yzCount-1):(b=this.cubeCountX,h=this.yzCount-1-this.nZ-1),c=1,d=this.yzCount):(this.colorDensity?(a=this.cubeCountX,h=(this.cubeCountX+1)*this.yzCount-1):(a=this.cubeCountX-1,h=this.cubeCountX*this.yzCount-1-this.nZ-1),c=b=-1,d=-this.yzCount);e=h;this.resetIndexPlane(this.isoPointIndexPlanes[1]);this.voxelData=null;var f=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 k=this.colorDensity&&0==this.cutoff,t=0;a!=b;a+=c,h+=d,e=h)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 l=f;0<=--l;)for(var q=g;0<=--q;e--)t=this.getValue(a,
l,q,e,0),(k||this.$isInside)&&this.addVertex(a,l,q,e,t);else{l=this.isoPointIndexPlanes[0];this.isoPointIndexPlanes[0]=this.isoPointIndexPlanes[1];this.isoPointIndexPlanes[1]=this.resetIndexPlane(l);for(var p=!0,l=f;0<=--l;e--)for(q=g;0<=--q;e--){for(var m=0,v=8;0<=--v;)t=this.getValue(a,l,q,e,v),this.$isInside&&(m|=JU.TriangleData.Pwr2[v]);p&&!Float.isNaN(t)&&(p=!1);0!=m&&255!=m&&this.processOneCubical(m,a,l,q,e)&&(!this.isContoured&&!this.colorDensity)&&this.processTriangles(m)}p&&this.bsExcludedPlanes.set(a)}return this.edgeData.toString()});
e(c$,"getValue",function(a,b,c,d,e){this.offset=JU.TriangleData.cubeVertexOffsets[e];d+=this.linearOffsets[e];switch(this.mode){case 3:a=this.vertexValues[e]=this.getValueArray(a+this.offset.x,b+this.offset.y,c+this.offset.z,d,this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[e]]);this.$isInside=this.allInside||this.bsVoxels.get(d);break;case 2:this.$isInside=this.allInside||this.bsVoxels.get(d);a=this.vertexValues[e]=(this.isDensityRange?!this.$isInside:this.bsExcludedVertices.get(d))?NaN:this.$isInside?
1:0;break;default:case 1:null==this.mappingPlane?a=this.vertexValues[e]=this.voxelData[a+this.offset.x][b+this.offset.y][c+this.offset.z]:(this.volumeData.voxelPtToXYZ(a+this.offset.x,b+this.offset.y,c+this.offset.z,this.pt0),a=this.vertexValues[e]=this.volumeData.distanceToMappingPlane(this.pt0)),this.isSquared&&(this.vertexValues[e]*=this.vertexValues[e]),(this.$isInside=this.allInside?!0:J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[e],this.cutoff,this.isCutoffAbsolute))&&this.bsVoxels.set(d)}return a},
"~N,~N,~N,~N,~N");e(c$,"getPlane",function(a,b){if(!(0>a||a>this.cubeCountX))if(this.surfaceReader.getPlane(a),b){var c=this.yzPlanes[0];this.yzPlanes[0]=this.yzPlanes[1];this.yzPlanes[1]=c}},"~N,~B");e(c$,"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(c$,"addVertex",function(a,b,c,d,e){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);0>this.surfaceReader.addVertexCopy(this.pt0,e,-4,!0)&&this.bsExcludedVertices.set(d)},
"~N,~N,~N,~N,~N");e(c$,"addTriangle",function(a,b,c,d){!this.bsExcludedTriangles.get(this.nTriangles)&&0>this.surfaceReader.addTriangleCheck(this.edgePointIndexes[a],this.edgePointIndexes[b],this.edgePointIndexes[c],d,0,this.isCutoffAbsolute,0)&&this.bsExcludedTriangles.set(this.nTriangles);this.nTriangles++},"~N,~N,~N,~N");e(c$,"getValueArray",function(a,b,c,d,e){var h=d%this.yzCount;this.bsValues.set(d);a=this.surfaceReader.getValue(a,b,c,h);this.isSquared&&(a*=a);e[h]=a;J.jvxl.calc.MarchingCubes.isInside(a,
this.cutoff,this.isCutoffAbsolute)&&this.bsVoxels.set(d);return a},"~N,~N,~N,~N,~A");c$.isInside=e(c$,"isInside",function(a,b,c){return 0<b&&(c?Math.abs(a):a)>=b||0>=b&&a<=b},"~N,~N,~B");e(c$,"processOneCubical",function(a,b,c,d,e){a=J.jvxl.calc.MarchingCubes.insideMaskTable[a];for(var h=!1,f=12;0<=--f;)if(0!=(a&JU.TriangleData.Pwr2[f])){var g=this.edgeVertexPlanes[f],k=(e+this.linearOffsets[this.edgeVertexPointers[f]])%this.yzCount,t=J.jvxl.calc.MarchingCubes.edgeTypeTable[f],l=this.edgePointIndexes[f]=
this.isoPointIndexPlanes[g][k][t];if(-2147483648!=l)-1==l&&(h=this.excludePartialCubes);else{var l=JU.TriangleData.edgeVertexes[f<<1],q=JU.TriangleData.edgeVertexes[(f<<1)+1],p=this.vertexValues[l],m=this.vertexValues[q];this.calcVertexPoint(b,c,d,l,this.pointA);this.edgeCount++;g=this.edgePointIndexes[f]=this.isoPointIndexPlanes[g][k][t]=this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff,this.isCutoffAbsolute,b,c,d,JU.TriangleData.cubeVertexOffsets[l],l,q,p,m,this.pointA,this.edgeVectors[f],
t==this.contourType,this.fReturn);this.addEdgeData(0>g?NaN:this.fReturn[0]);if(Float.isNaN(this.fReturn[0])||0>g)h=this.excludePartialCubes}}return!h},"~N,~N,~N,~N,~N");e(c$,"addEdgeData",function(a){a=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(a);this.edgeData.appendC(a)},"~N");e(c$,"calcVertexPoint",function(a,b,c,d,e){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);e.add2(this.pt0,this.voxelVertexVectors[d])},"~N,~N,~N,~N,JU.P3");e(c$,"setLinearOffsets",function(){this.linearOffsets[0]=0;this.linearOffsets[1]=
this.yzCount;this.linearOffsets[2]=this.yzCount+1;this.linearOffsets[3]=1;this.linearOffsets[4]=this.nZ;this.linearOffsets[5]=this.yzCount+this.nZ;this.linearOffsets[6]=this.yzCount+this.nZ+1;this.linearOffsets[7]=this.nZ+1});e(c$,"getLinearOffset",function(a,b,c,d){return a*this.yzCount+b*this.nZ+c+this.linearOffsets[d]},"~N,~N,~N,~N");Z(c$,"MODE_CUBE",1,"MODE_JVXL",2,"MODE_PLANES",3);Z(c$,"yzPlanePts",u(-1,[0,1,1,0,0,1,1,0]),"edgeVertexPointersLowToHigh",u(-1,[1,1,2,0,5,5,6,4,0,1,2,3]),"edgeVertexPointersHighToLow",
u(-1,[0,1,3,0,4,5,7,4,0,1,2,3]),"edgeVertexPlanesLowToHigh",u(-1,[1,1,1,0,1,1,1,0,0,1,1,0]),"edgeVertexPlanesHighToLow",u(-1,[1,0,1,1,1,0,1,1,1,0,0,1]));c$.cubeVertexVectors=c$.prototype.cubeVertexVectors=B(-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)]);Z(c$,"edgeTypeTable",u(-1,[0,2,0,2,0,2,0,2,1,1,1,1]),"insideMaskTable",$(-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]))});O("J.jvxl.calc");F(["JU.P3","java.util.Hashtable"],"J.jvxl.calc.MarchingSquares",["java.lang.Float","JU.AU","JU.Logger"],function(){c$=H(function(){this.volumeData=this.surfaceReader=null;this.valueMax=this.valueMin=this.thisContour=this.contourType=this.nContourSegments=0;this.pointB=this.pointA=null;this.contourFromZero=!0;this.contoursDiscrete=null;this.contourVertexCount=
0;this.contourVertexes=null;va("J.jvxl.calc.MarchingSquares.ContourVertex")||J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$();this.contourPlaneMaximumValue=this.contourPlaneMinimumValue=0;this.ptTemp=this.contourValuesUsed=null;this.triangleCount=0;this.htPts=this.triangles=null;va("J.jvxl.calc.MarchingSquares.Triangle")||J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$();P(this,arguments)},J.jvxl.calc,"MarchingSquares");ha(c$,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});W(c$,function(a,b,c,d,e,h,f){this.surfaceReader=a;this.volumeData=b;this.thisContour=h;this.contoursDiscrete=d;this.contourFromZero=f;null==d?(this.nContourSegments=(0==e?9:e)+0,100<this.nContourSegments&&(this.nContourSegments=100)):(this.nContourSegments=e=d.length,this.contourFromZero=!1)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,JU.P4,~A,~N,~N,~B");e(c$,"setMinMax",function(a,
b){this.valueMin=a;this.valueMax=b},"~N,~N");e(c$,"addContourVertex",function(a,b){this.contourVertexCount==this.contourVertexes.length&&(this.contourVertexes=JU.AU.doubleLength(this.contourVertexes));var c=this.surfaceReader.addVertexCopy(a,b,-2,!0);this.contourVertexes[this.contourVertexCount++]=ta(J.jvxl.calc.MarchingSquares.ContourVertex,this,null,a);return c},"JU.P3,~N");e(c$,"setContourData",function(a,b){this.contourVertexes[a].setValue(b)},"~N,~N");e(c$,"calcContourPoint",function(a,b,c,d){return this.volumeData.calculateFractionalPoint(a,
this.pointA,this.pointB,b,c,d)},"~N,~N,~N,JU.P3");e(c$,"addTriangle",function(a,b,c,d,e){this.triangleCount==this.triangles.length&&(this.triangles=JU.AU.doubleLength(this.triangles));this.triangles[this.triangleCount++]=ta(J.jvxl.calc.MarchingSquares.Triangle,this,null,a,b,c,d,e);return 0},"~N,~N,~N,~N,~N");e(c$,"generateContourData",function(a,b){JU.Logger.info("generateContours: "+this.nContourSegments+" segments");this.getVertexValues(a);this.createContours(this.valueMin,this.valueMax,b);this.addAllTriangles();
return this.contourVertexCount},"~B,~N");e(c$,"getVertexValues",function(a){this.contourPlaneMinimumValue=3.4028235E38;this.contourPlaneMaximumValue=-3.4028235E38;for(var b=0;b<this.contourVertexCount;b++){var c=this.contourVertexes[b],d;a?d=c.value:(d=this.volumeData.lookupInterpolatedVoxelValue(c,!1),c.setValue(d));d<this.contourPlaneMinimumValue&&(this.contourPlaneMinimumValue=d);d>this.contourPlaneMaximumValue&&(this.contourPlaneMaximumValue=d)}},"~B");e(c$,"createContours",function(a,b,c){b-=
a;this.contourValuesUsed=w(this.nContourSegments,0);for(var d=this.triangleCount;0<=--d;)this.triangles[d].check=0;for(var e=-3.4028235E38,d=0;d<this.nContourSegments;d++){e=null!=this.contoursDiscrete?this.contoursDiscrete[d]:this.contourFromZero?a+1*d/this.nContourSegments*b:0==d?-3.4028235E38:d==this.nContourSegments-1?3.4028235E38:a+1*(d-1)/(this.nContourSegments-1)*b;null==this.contoursDiscrete&&Math.abs(e)<c&&(e=0>e?-c:c);this.contourValuesUsed[d]=e;JU.Logger.info("#contour "+(d+1)+" "+e+" "+
this.triangleCount);this.htPts.clear();for(var h=this.triangleCount;0<=--h;)this.triangles[h].isValid&&this.checkContour(this.triangles[h],d,e)}this.valueMin=this.contourValuesUsed[0];this.valueMax=0==this.contourValuesUsed.length?this.valueMin:this.contourValuesUsed[this.contourValuesUsed.length-1];return!0},"~N,~N,~N");e(c$,"intercept",function(a,b,c){var d=a.pts[b];a=a.pts[(b+1)%3];if(2147483647==d||2147483647==a)return-1;b=d<a?d+"_"+a:a+"_"+d;if(this.htPts.containsKey(b))return this.htPts.get(b).intValue();
var e=this.contourVertexes[d].value,h=this.contourVertexes[a].value,f=-1;if(e!=h){var g=(c-e)/(h-e);if(0<=g&&1>=g&&(this.pointA.setT(this.contourVertexes[d]),this.pointB.setT(this.contourVertexes[a]),c=this.calcContourPoint(c,e,h,this.ptTemp),!Float.isNaN(c))){f=this.addContourVertex(this.ptTemp,c);if(0>f)return-1;this.contourVertexes[f].setValue(c)}}this.htPts.put(b,Integer.$valueOf(f));return f},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"checkContour",function(a,b,c){if(!(0<this.thisContour&&
b+1!=this.thisContour)){var d=this.intercept(a,0,c),e=this.intercept(a,1,c);c=this.intercept(a,2,c);var h=a.pts,f=0;0<=d&&(f+=1);0<=e&&(f+=2);0<=c&&(f+=4);switch(f){case 3:this.addTriangle(h[0],d,e,2|a.check&1,b);this.addTriangle(d,h[1],e,4|a.check&3,b);this.addTriangle(h[0],e,h[2],a.check&6,b);break;case 5:this.addTriangle(h[0],d,c,2|a.check&5,b);this.addTriangle(d,h[1],c,4|a.check&1,b);this.addTriangle(c,h[1],h[2],a.check&6,b);break;case 6:this.addTriangle(h[0],h[1],c,a.check&5,b);this.addTriangle(c,
h[1],e,4|a.check&2,b);this.addTriangle(c,e,h[2],1|a.check&6,b);break;default:return}a.isValid=!1}},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"getMinMax",function(){return w(-1,[this.valueMin,this.valueMax])});e(c$,"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)}});c$.$MarchingSquares$ContourVertex$=function(){na(self.c$);c$=H(function(){ua(this,
arguments);this.value=0;P(this,arguments)},J.jvxl.calc.MarchingSquares,"ContourVertex",JU.P3);W(c$,function(a){da(this,J.jvxl.calc.MarchingSquares.ContourVertex,[]);this.setT(a)},"JU.P3");e(c$,"setValue",function(a){this.value=a},"~N");m(c$,"toString",function(){return this.value+" "+this.x+" "+this.y+" "+this.z});c$=ma()};c$.$MarchingSquares$Triangle$=function(){na(self.c$);c$=H(function(){ua(this,arguments);this.pts=null;this.check=0;this.isValid=!0;this.contourIndex=0;P(this,arguments)},J.jvxl.calc.MarchingSquares,
"Triangle");W(c$,function(a,b,c,d,e){this.pts=u(-1,[a,b,c]);this.check=d;this.contourIndex=e},"~N,~N,~N,~N,~N");c$=ma()};Z(c$,"CONTOUR_POINT",-1,"VERTEX_POINT",-2,"EDGE_POINT",-3,"nContourMax",100,"defaultContourCount",9)});O("J.shapesurface");F(["J.shape.Mesh"],"J.shapesurface.IsosurfaceMesh","java.lang.Float 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 $.SimpleUnitCell JV.Viewer".split(" "),
function(){c$=H(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;P(this,arguments)},J.shapesurface,"IsosurfaceMesh",J.shape.Mesh);m(c$,"getResolution",function(){return 1/
this.jvxlData.pointsPerAngstrom});W(c$,function(a,b,c,d){da(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");e(c$,"clearType",function(a,b){this.clear(a);this.jvxlData.clear();this.colorEncoder=this.centers=this.calculatedArea=this.calculatedVolume=this.bsVdw=this.assocGridPointNormals=this.assocGridPointMap=null;this.colorsExplicit=this.colorPhased=!1;this.firstRealVertex=
-1;this.hasGridPoints=b;this.isColorSolid=!0;this.nSets=this.mergeAssociatedNormalCount=0;this.pcs=null;this.showPoints=b;this.vertexColorMap=this.vcs=this.surfaceSet=null;this.vertexIncrement=1;this.vvs=this.vertexSets=null},"~S,~B");e(c$,"allocVertexColixes",function(){if(null==this.vcs){this.vcs=$(this.vc,0);for(var a=this.vc;0<=--a;)this.vcs[a]=this.colix}this.isColorSolid=!1});e(c$,"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");m(c$,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b);if(null!=this.vcs)for(var c=this.vc;0<=--c;)this.vcs[c]=JU.C.getColixTranslucent3(this.vcs[c],
a,b)},"~B,~N");e(c$,"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");m(c$,"sumVertexNormals",function(a,b){J.shape.Mesh.sumVertexNormals2(this,a,b);if(null!=this.assocGridPointMap&&0<b.length&&!this.isMerged){null==this.assocGridPointNormals&&(this.assocGridPointNormals=new java.util.Hashtable);
for(var c,d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);){var e=c.getValue();this.assocGridPointNormals.containsKey(e)||this.assocGridPointNormals.put(e,JU.V3.new3(0,0,0));this.assocGridPointNormals.get(e).add(b[c.getKey().intValue()])}for(d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);)b[c.getKey().intValue()]=this.assocGridPointNormals.get(c.getValue())}},"~A,~A");e(c$,"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(c$,"getContours",function(){var a=this.jvxlData.nContours;if(0==a||null==this.pis||(this.havePlanarContours=null!=this.jvxlData.jvxlPlane))return null;0>a&&(a=-1-a);var b=this.jvxlData.vContours;if(null!=b){for(var c=0;c<a&&!(6<b[c].size());c++)J.jvxl.data.JvxlCoder.set3dContourVector(b[c],
this.pis,this.vs);return this.jvxlData.vContours}b=Array(a);for(c=0;c<a;c++)b[c]=new JU.Lst;if(null==this.jvxlData.contourValuesUsed){for(var d=(this.jvxlData.valueMappedToBlue-this.jvxlData.valueMappedToRed)/(a+1),c=0;c<a;c++){var e=this.jvxlData.valueMappedToRed+(c+1)*d;J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c])}JU.Logger.info(a+" contour lines; separation = "+d)}else for(c=0;c<a;c++)e=this.jvxlData.contourValuesUsed[c],J.shapesurface.IsosurfaceMesh.get3dContour(this,
b[c],e,this.jvxlData.contourColixes[c]);this.jvxlData.contourColixes=$(a,0);this.jvxlData.contourValues=w(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(c$,"getPmeshData",function(a){return J.api.Interface.getInterface("J.shapesurface.PMeshWriter",this.vwr,"script").write(this,a)},"~B");c$.get3dContour=e(c$,"get3dContour",function(a,b,c,d){var e=JU.BS.newN(a.pc),h=new JU.SB,f=JU.C.getArgb(d);
J.shapesurface.IsosurfaceMesh.setContourVector(b,a.pc,e,c,d,f,h);for(d=0;d<a.pc;d++)null!=a.setABC(d)&&J.shapesurface.IsosurfaceMesh.addContourPoints(b,e,d,h,a.vs,a.vvs,a.iA,a.iB,a.iC,c)},"J.shapesurface.IsosurfaceMesh,JU.Lst,~N,~N");c$.setContourVector=e(c$,"setContourVector",function(a,b,c,d,e,h,f){a.add(0,Integer.$valueOf(b));a.add(1,c);a.add(2,Float.$valueOf(d));a.add(3,$(-1,[e]));a.add(4,u(-1,[h]));a.add(5,f)},"JU.Lst,~N,JU.BS,~N,~N,~N,JU.SB");c$.addContourPoints=e(c$,"addContourPoints",function(a,
b,c,d,e,h,f,g,k,t){var l=null,q=null,p=0,m=J.shapesurface.IsosurfaceMesh.checkPt(h,f,g,t);Float.isNaN(m)||(l=J.shapesurface.IsosurfaceMesh.getContourPoint(e,f,g,m),p|=1);var v=1==m?NaN:J.shapesurface.IsosurfaceMesh.checkPt(h,g,k,t);Float.isNaN(v)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,g,k,v),0==p&&(l=q,m=v),p|=2);switch(p){case 0:return;case 1:if(0==m)return;case 2:v=1==v?NaN:J.shapesurface.IsosurfaceMesh.checkPt(h,k,f,t),Float.isNaN(v)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,
k,f,v),p|=4)}switch(p){case 3:case 5:case 6:break;default:return}b.set(c);J.jvxl.data.JvxlCoder.appendContourTriangleIntersection(p,m,v,d);a.addLast(l);a.addLast(q)},"JU.Lst,JU.BS,~N,JU.SB,~A,~A,~N,~N,~N,~N");c$.checkPt=e(c$,"checkPt",function(a,b,c,d){var e,h;return d==(e=a[b])?0:d==(h=a[c])?1:e<d==d<h?(d-e)/(h-e):NaN},"~A,~N,~N,~N");c$.getContourPoint=e(c$,"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(c$,"setDiscreteColixes",
function(a,b){null!=a&&(this.jvxlData.contourValues=a);if(null==a||0==a.length)a=this.jvxlData.contourValues=this.jvxlData.contourValuesUsed;null==b&&null!=this.jvxlData.contourColixes?b=this.jvxlData.contourColixes:(this.jvxlData.contourColixes=b,this.jvxlData.contourColors=JU.C.getHexCodes(b));if(!(null==this.vs||null==this.vvs||null==a)){var c=a.length,d=a[c-1];this.colorCommand=null;var e=null!=b&&0<b.length;this.isColorSolid=e&&null!=this.jvxlData.jvxlPlane;if(null!=this.jvxlData.vContours){if(e)for(var h=
0;h<this.jvxlData.vContours.length;h++)c=b[h%b.length],this.jvxlData.vContours[h].get(3)[0]=c,this.jvxlData.vContours[h].get(4)[0]=JU.C.getArgb(c)}else{this.pcs=$(this.pc,0);this.colorsExplicit=!1;for(h=0;h<this.pc;h++){var f=this.pis[h];if(null!=f){this.pcs[h]=0;for(var f=(this.vvs[f[0]]+this.vvs[f[1]]+this.vvs[f[2]])/3,g=c;0<=--g;)if(f>=a[g]&&f<d){this.pcs[h]=e?b[g%b.length]:0;break}}}}}},"~A,~A");e(c$,"getContourList",function(){var a=new java.util.Hashtable;a.put("values",null==this.jvxlData.contourValuesUsed?
this.jvxlData.contourValues:this.jvxlData.contourValuesUsed);var b=new JU.Lst;if(null!=this.jvxlData.contourColixes){for(var c=0;c<this.jvxlData.contourColixes.length;c++)b.addLast(JU.CU.colorPtFromInt(JU.C.getArgb(this.jvxlData.contourColixes[c]),null));a.put("colors",b)}return a},"JV.Viewer");e(c$,"deleteContours",function(){this.jvxlData.contourValuesUsed=null;this.jvxlData.contourValues=null;this.jvxlData.contourColixes=null;this.jvxlData.vContours=null});e(c$,"setVertexColorMap",function(){this.vertexColorMap=
new java.util.Hashtable;for(var a=-999,b=null,c=this.vc;0<=--c;){var d=this.vcs[c];d!=a&&(d=JU.C.getHexCode(a=d),b=this.vertexColorMap.get(d),null==b&&this.vertexColorMap.put(d,b=new JU.BS));b.set(c)}});e(c$,"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 h=this.mergeVertexCount0;h<this.vc;h++){var f=this.vertexSource[h];if(!(0>f)&&d.get(f)){this.jvxlData.vertexColors[h]=
a.getColorArgbOrGray(this.vcs[h]=JU.C.copyColixTranslucency(this.colix,e[f].colixAtom));var g=null==b?0:b[c[f]];0==g&&(g=e[f].colixAtom);this.vcs[h]=JU.C.copyColixTranslucency(this.colix,g)}}},"JV.Viewer,~A,~A,JU.BS");e(c$,"colorVertices",function(a,b,c){if(null!=this.vertexSource){a=JU.C.copyColixTranslucency(this.colix,a);var d=c?new JU.BS:b;this.checkAllocColixes();if(c)for(var e=0;e<this.vc;e++){var h=this.vertexSource[e];0<=h&&b.get(h)&&(this.vcs[e]=a,null!=d&&d.set(e))}else for(e=0;e<this.vc;e++)d.get(e)&&
(this.vcs[e]=a);c&&(a=JU.C.getHexCode(a),null==this.vertexColorMap&&(this.vertexColorMap=new java.util.Hashtable),J.shapesurface.IsosurfaceMesh.addColorToMap(this.vertexColorMap,a,b))}},"~N,JU.BS,~B");e(c$,"checkAllocColixes",function(){(null==this.vcs||null==this.vertexColorMap&&this.isColorSolid)&&this.allocVertexColixes();this.isColorSolid=!1});c$.addColorToMap=e(c$,"addColorToMap",function(a,b,c){for(var d=null,e,h=a.entrySet().iterator();h.hasNext()&&((e=h.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(c$,"setJvxlColorMap",function(a){this.jvxlData.diameter=this.diameter;this.jvxlData.color=JU.C.getHexCode(this.colix);this.jvxlData.meshColor=0==this.meshColix?null:JU.C.getHexCode(this.meshColix);this.jvxlData.translucency=30720==(this.colix&30720)?-1:JU.C.getColixTranslucencyFractional(this.colix);this.jvxlData.rendering=this.getRendering().substring(1);this.jvxlData.colorScheme=null==this.colorEncoder?null:this.colorEncoder.getColorScheme();
null==this.jvxlData.vertexColors&&(this.jvxlData.nVertexColors=null==this.vertexColorMap?0:this.vertexColorMap.size());if(!(null==this.vertexColorMap||null==this.vertexSource||!a)){null==this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=new java.util.Hashtable);var b;for(a=this.vertexColorMap.entrySet().iterator();a.hasNext()&&((b=a.next())||1);){var c=b.getValue();if(!c.isEmpty()){for(var d=b.getKey(),e=new JU.BS,h=0;h<this.vc;h++)c.get(this.vertexSource[h])&&e.set(h);J.shapesurface.IsosurfaceMesh.addColorToMap(this.jvxlData.vertexColorMap,
d,e)}}this.jvxlData.nVertexColors=this.jvxlData.vertexColorMap.size();0==this.jvxlData.vertexColorMap.size()&&(this.jvxlData.vertexColorMap=null)}},"~B");e(c$,"setColorCommand",function(){if(!(null==this.colorEncoder||null==(this.colorCommand=this.colorEncoder.getColorScheme())))this.colorCommand=this.colorCommand.equals("inherit")?"#inherit;":"color $"+JU.PT.esc(this.thisID)+JU.PT.esc(this.colorCommand)+" range "+(this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue+" "+this.jvxlData.valueMappedToRed:
this.jvxlData.valueMappedToRed+" "+this.jvxlData.valueMappedToBlue)});e(c$,"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(c$,"setJvxlDataRendering",function(){if(null!=this.jvxlData.rendering)for(var a=JU.PT.getTokens(this.jvxlData.rendering),b=0;b<a.length;b++)this.setTokenProperty(JS.T.getTokFromName(a[b]),!0)});e(c$,"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,h=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(),h){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=$(this.contourValues.length,0);for(a=0;a<this.contourValues.length;a++)this.contourColixes[a]=b.getColorIndex(this.contourValues[a]);
this.setDiscreteColixes(null,null)}this.jvxlData.isJvxlPrecisionColor=!0;J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,this.vvs);this.setColorCommand();this.isColorSolid=!1}},"JV.Viewer,JU.ColorEncoder,~N");e(c$,"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");m(c$,"getBoundingBox",function(){return this.jvxlData.boundingBox});m(c$,"setBoundingBox",
function(a){this.jvxlData.boundingBox=a},"~A");e(c$,"merge",function(a){var b=this.vc+(null==a?0:a.vc);null==this.pis&&(this.pis=u(0,0,0));null!=a&&null==a.pis&&(a.pis=u(0,0,0));var c=(null==this.bsSlabDisplay||0==this.pc?this.pc:this.bsSlabDisplay.cardinality())+(null==a||0==a.pc?0:null==a.bsSlabDisplay?a.pc:a.bsSlabDisplay.cardinality());null==this.vs&&(this.vs=[]);this.vs=JU.AU.ensureLength(this.vs,b);this.vvs=JU.AU.ensureLengthA(this.vvs,b);var d=null!=this.vertexSource&&(null==a||null!=a.vertexSource);
this.vertexSource=JU.AU.ensureLengthI(this.vertexSource,b);var e=JU.AU.newInt2(c),h=J.shapesurface.IsosurfaceMesh.mergePolygons(this,0,0,e);if(null!=a){J.shapesurface.IsosurfaceMesh.mergePolygons(a,h,this.vc,e);for(h=0;h<a.vc;h++,this.vc++)this.vs[this.vc]=a.vs[h],this.vvs[this.vc]=a.vvs[h],d&&(this.vertexSource[this.vc]=a.vertexSource[h])}this.pc=this.polygonCount0=c;this.vc=this.vertexCount0=b;0<c&&this.resetSlab();this.pis=e},"J.jvxl.data.MeshData");c$.mergePolygons=e(c$,"mergePolygons",function(a,
b,c,d){for(var e,h=0;h<a.pc;h++)if(!(null==(e=a.pis[h])||null!=a.bsSlabDisplay&&!a.bsSlabDisplay.get(h)))if(d[b++]=a.pis[h],0<c)for(var f=0;3>f;f++)e[f]+=c;return b},"JU.MeshSurface,~N,~N,~A");m(c$,"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(c$,"fixLattice",
function(){if(null!=this.getUnitCell()){var a=new JU.P3i,b=JU.P3i.new3(y(this.lattice.x),y(this.lattice.y),y(this.lattice.z));this.jvxlData.fixedLattice=this.lattice;this.lattice=null;JU.SimpleUnitCell.setMinMaxLatticeParameters(y(this.unitCell.getUnitCellInfoType(6)),a,b,0);var c=(b.x-a.x)*(b.y-a.y)*(b.z-a.z),d=new JU.P3,e=this.vc,h=c*this.vc;this.vs=JU.AU.arrayCopyPt(this.vs,h);this.vvs=null==this.vvs?null:JU.AU.ensureLengthA(this.vvs,h);var f=this.pc;this.pis=JU.AU.arrayCopyII(this.pis,c*this.pc);
c=0;this.normixes=JU.AU.arrayCopyShort(this.normixes,h);for(h=a.x;h<b.x;h++)for(var g=a.y;g<b.y;g++)for(var k=a.z;k<b.z;k++)if(!(0==h&&0==g&&0==k)){d.set(h,g,k);this.unitCell.toCartesian(d,!1);for(var t=0;t<e;t++){this.normixes[this.vc]=this.normixes[t];var l=JU.P3.newP(this.vs[t]);l.add(d);this.addVCVal(l,this.vvs[t],!1)}c+=e;for(t=0;t<f;t++)l=JU.AU.arrayCopyI(this.pis[t],-1),l[0]+=c,l[1]+=c,l[2]+=c,this.addPolygon(l,null)}a=new JU.P3;b=new JU.P3;this.setBox(a,b);this.jvxlData.boundingBox=B(-1,[a,
b])}});m(c$,"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});m(c$,"getVisibleVertexBitSet",function(){var a=this.getVisibleVBS();if(null!=this.jvxlData.thisSet)for(var b=0;b<this.vc;b++)this.jvxlData.thisSet.get(this.vertexSets[b])||a.clear(b);return a});e(c$,"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(c$,"getDataMinMax",function(){for(var a=3.4028235E38,b=-3.4028235E38,c=this.vvs.length;0<=--c;){var d=this.vvs[c];d<a&&(a=d);d>b&&(b=d)}return w(-1,[a,b])});e(c$,"getDataRange",function(){return null!=
this.jvxlData.jvxlPlane&&null==this.colorEncoder?null:w(-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(c$,"getInfo",function(a){var b=Ia(this,J.shapesurface.IsosurfaceMesh,"getInfo",[a]);if(a){a=new JU.BS;var c=this.getValidVertices(a);null!=c&&(b.put("allVertices",b.get("vertices")),b.put("vertices",
c),c=b.get("vertexValues"),null!=c&&(a=this.getValidValues(a),b.put("allValues",c),b.put("vertexValues",a)))}return b},"~B");e(c$,"getValidValues",function(a){null==a&&this.getInvalidBS(a=new JU.BS);for(var b=this.vc-a.cardinality(),b=w(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(c$,"getValidVertices",function(a){var b=null!=a;null==a&&(a=new JU.BS);this.getInvalidBS(a);var c=this.vc-a.cardinality();if(c==this.vc&&b)return null;for(var b=
Array(c),d=0,e=a.nextClearBit(0);0<=e&&d<c;e=a.nextClearBit(e+1))b[d++]=this.vs[e];return b},"JU.BS");e(c$,"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")});O("J.jvxl.readers");F(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.VolumeDataReader",["java.lang.Float","JU.AU","$.SB","J.jvxl.data.JvxlCoder","JU.Logger"],function(){c$=H(function(){this.dataType=0;this.allowMapData=
this.precalculateVoxelData=!1;this.point=null;this.maxGrid=this.ptsPerAngstrom=0;this.useOriginStepsPoints=!1;P(this,arguments)},J.jvxl.readers,"VolumeDataReader",J.jvxl.readers.SurfaceReader);W(c$,function(){da(this,J.jvxl.readers.VolumeDataReader,[])});m(c$,"init",function(a){this.initVDR(a)},"J.jvxl.readers.SurfaceGenerator");e(c$,"initVDR",function(a){this.initSR(a);this.useOriginStepsPoints=null!=this.params.origin&&null!=this.params.points&&null!=this.params.steps;this.dataType=this.params.dataType;
this.allowMapData=this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");e(c$,"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");m(c$,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();return!0},"~B");m(c$,"readVolumeData",function(a){try{this.readSurfaceData(a)}catch(b){if(Y(b,Exception))return System.out.println(b.toString()),
!1;throw b;}return!0},"~B");e(c$,"readVoxelDataIndividually",function(a){if(!a||this.allowMapData)if(!a||null!=this.volumeData.sr)this.volumeData.setVoxelDataAsArray(this.voxelData=null);else{this.newVoxelDataCube();for(a=0;a<this.nPointsX;++a){var b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(var c=0,d=0;d<this.nPointsY;++d)for(var e=b[d]=w(this.nPointsZ,0),h=0;h<this.nPointsZ;++h,++c)e[h]=this.getValue(a,d,h,c)}}},"~B");e(c$,"setVolumeData",function(){});e(c$,"setVolumeDataParams",function(){if(null!=
this.params.volumeData)return this.setVolumeDataV(this.params.volumeData),!0;if(!this.useOriginStepsPoints)return!1;this.volumetricOrigin.setT(this.params.origin);this.volumetricVectors[0].set(this.params.steps.x,0,0);this.volumetricVectors[1].set(0,this.params.steps.y,0);this.volumetricVectors[2].set(0,0,this.params.steps.z);this.voxelCounts[0]=y(this.params.points.x);this.voxelCounts[1]=y(this.params.points.y);this.voxelCounts[2]=y(this.params.points.z);if(1>this.voxelCounts[0]||1>this.voxelCounts[1]||
1>this.voxelCounts[2])return!1;this.showGridInfo();return!0});e(c$,"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(c$,"setVoxelRange",function(a,b,c,d,e,h){-1E-4<=b-c&&(b=-10,c=10);var f=c-b,g=this.params.resolution;3.4028235E38!=g&&(d=g,h=0);c=D(Math.floor(f*d))+1;c>e&&(0<(this.dataType&256)?3.4028235E38==g?(this.isQuiet||JU.Logger.info("Maximum number of voxels for index="+a+" exceeded ("+c+") -- set to "+e),c=e):this.isQuiet||JU.Logger.info("Warning -- high number of grid points: "+c):3.4028235E38==g&&(c=e));1==c&&(c=2);d=(c-1)/f;d<h&&(c=D(Math.floor(h*f+1)),d=(c-1)/f);e=this.volumeData.volumetricVectorLengths[a]=
1/d;this.voxelCounts[a]=c;null!=this.params.sbOut&&this.params.sbOut.append("isosurface resolution for axis "+(a+1)+" set to "+d+" points/Angstrom; "+this.voxelCounts[a]+" voxels\n");switch(a){case 0:this.volumetricVectors[0].set(e,0,0);this.volumetricOrigin.x=b;break;case 1:this.volumetricVectors[1].set(0,e,0);this.volumetricOrigin.y=b;break;case 2:this.volumetricVectors[2].set(0,0,e),this.volumetricOrigin.z=b,this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricOrigin),null!=this.center&&
!Float.isNaN(this.center.x)&&this.volumetricOrigin.add(this.center),null!=this.params.sbOut&&this.params.sbOut.append(this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2]+" voxels total\n")}this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricVectors[a]);return this.voxelCounts[a]},"~N,~N,~N,~N,~N,~N");m(c$,"readSurfaceData",function(a){this.readSurfaceDataVDR(a)},"~B");e(c$,"readSurfaceDataVDR",function(a){this.isProgressive&&!a?(this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,
this.nPointsY,this.nPointsZ),this.voxelData=null):this.precalculateVoxelData?this.generateCube():this.readVoxelDataIndividually(a)},"~B");e(c$,"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")});m(c$,"closeReader",function(){})});O("J.jvxl.readers");
F(["J.jvxl.readers.VolumeDataReader","JU.BS","$.P3","$.P3i","J.atomdata.AtomData"],"J.jvxl.readers.AtomDataReader","java.lang.Float java.util.Date JU.AU $.SB $.V3 J.atomdata.RadiusData J.c.VDW J.jvxl.data.JvxlCoder JU.BSUtil $.Logger".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"AtomDataReader",
J.jvxl.readers.VolumeDataReader);ha(c$,function(){this.atomData=new J.atomdata.AtomData;this.bsMySelected=new JU.BS;this.bsMyIgnored=new JU.BS;this.ptY0=new JU.P3;this.ptZ0=new JU.P3;this.pt0=new JU.P3i;this.pt1=new JU.P3i;this.ptV=new JU.P3});W(c$,function(){da(this,J.jvxl.readers.AtomDataReader,[])});e(c$,"initADR",function(a){this.initVDR(a);this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");m(c$,"setup",function(){this.setup2()},"~B");e(c$,"setup2",function(){this.contactPair=this.params.contactPair;
this.doAddHydrogens=null!=this.sg.atomDataServer&&this.params.addHydrogens;this.modelIndex=this.params.modelIndex;null!=this.params.bsIgnore&&(this.bsMyIgnored=this.params.bsIgnore);if(null!=this.params.volumeData){this.setVolumeDataV(this.params.volumeData);this.setBBox(this.volumeData.volumetricOrigin,0);this.ptV.setT(this.volumeData.volumetricOrigin);for(var a=0;3>a;a++)this.ptV.scaleAdd2(this.volumeData.voxelCounts[a]-1,this.volumeData.volumetricVectors[a],this.ptV);this.setBBox(this.ptV,0)}(this.havePlane=
null!=this.params.thePlane)&&this.volumeData.setPlaneParameters(this.params.thePlane)});e(c$,"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(c$,"setVolumeForPlane",function(){this.useOriginStepsPoints?(this.xyzMin=JU.P3.newP(this.params.origin),this.xyzMax=JU.P3.newP(this.params.origin),this.xyzMax.add3((this.params.points.x-1)*this.params.steps.x,(this.params.points.y-
1)*this.params.steps.y,(this.params.points.z-1)*this.params.steps.z)):null==this.params.boundingBox?(this.getAtoms(this.params.bsSelected,!1,!0,!1,!1,!1,!1,this.params.mep_marginAngstroms,this.params.modelInvRotation),null==this.xyzMin&&(this.xyzMin=JU.P3.new3(-10,-10,-10),this.xyzMax=JU.P3.new3(10,10,10))):(this.xyzMin=JU.P3.newP(this.params.boundingBox[0]),this.xyzMax=JU.P3.newP(this.params.boundingBox[1]));this.setRanges(this.params.plane_ptsPerAngstrom,this.params.plane_gridMax,0)});e(c$,"getAtoms",
function(a,b,c,d,e,h,f,g,k){h&&(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!=k&&this.atomData.transformXYZ(k,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,g)))continue;this.bsMySelected.set(d);e=!this.havePlane}if(c&&(h||e))this.atomData.atomRadius[d]=
this.getWorkingRadius(d,g)}e=c&&b?this.getWorkingRadius(-1,g):0;this.myAtomCount=JU.BSUtil.cardinalityOf(this.bsMySelected);g=JU.BSUtil.copy(this.bsMySelected);f=0;this.atomProp=null;this.theProperty=3.4028235E38;this.haveOneProperty=!1;a=this.params.theProperty;if(0<this.myAtomCount){k=null;if(b){this.atomData.bsSelected=g;this.sg.atomDataServer.fillAtomData(this.atomData,8);k=Array(f=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;)k[--f]=this.atomData.hAtoms[d][b];f=k.length;JU.Logger.info(f+" attached hydrogens added")}b=f+this.myAtomCount;c&&(this.atomRadius=w(b,0));this.atomXyzTruncated=Array(b);null!=this.params.theProperty&&(this.atomProp=w(b,0));this.atomNo=u(b,0);this.atomIndex=u(b,0);this.myIndex=u(this.ac,0);for(d=0;d<f;d++)c&&(this.atomRadius[d]=e),this.atomXyzTruncated[d]=k[d],this.atomNo[d]=-1,null!=this.atomProp&&this.addAtomProp(d,NaN);this.myAtomCount=f;for(d=g.nextSetBit(0);0<=
d;d=g.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(h&&0!=this.myAtomCount){h=new JU.P3;this.bsNearby=new JU.BS;for(d=0;d<this.ac;d++)!g.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),h=this.atomData.xyz[d],h.x+b>this.xyzMin.x&&(h.x-b<this.xyzMax.x&&h.y+b>this.xyzMin.y&&h.y-b<this.xyzMax.y&&h.z+b>this.xyzMin.z&&h.z-b<this.xyzMax.z)&&(this.bsNearby.set(d),this.nearbyAtomCount++)));h=this.myAtomCount;if(0!=this.nearbyAtomCount){h+=this.nearbyAtomCount;this.atomRadius=JU.AU.arrayCopyF(this.atomRadius,
h);this.atomXyzTruncated=JU.AU.arrayCopyObject(this.atomXyzTruncated,h);null!=this.atomIndex&&(this.atomIndex=JU.AU.arrayCopyI(this.atomIndex,h));null!=a&&(this.atomProp=JU.AU.arrayCopyF(this.atomProp,h));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(c$,"setRadii",function(){if(null==this.rs){this.maxRS=0;this.rs=w(this.myAtomCount,0);this.rs2=w(this.myAtomCount,0);for(var a=0;a<this.myAtomCount;a++){var b=this.rs[a]=this.atomRadius[a]+this.sr;b>this.maxRS&&(this.maxRS=b);this.rs2[a]=this.rs[a]*this.rs[a]}}});e(c$,"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(c$,"getWorkingRadius",function(a,b){var c=0>a?this.atomData.hAtomRadius:this.atomData.atomRadius[a];return Float.isNaN(b)?Math.max(c,0.1):c+b},"~N,~N");e(c$,"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(c$,"setRanges",function(a,b,c){null!=this.xyzMin&&(this.ptsPerAngstrom=a,this.maxGrid=b,this.minPtsPerAng=c,this.setVolumeData(),J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData,this.jvxlFileHeaderBuffer))},"~N,~N,~N");m(c$,"setVolumeData",function(){this.setVolumeDataADR()});e(c$,"setVolumeDataADR",function(){this.setVolumeDataParams()||(this.setVoxelRange(0,this.xyzMin.x,this.xyzMax.x,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(1,this.xyzMin.y,this.xyzMax.y,
this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(2,this.xyzMin.z,this.xyzMax.z,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng))});e(c$,"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(c$,
"resetPlane",function(a){for(var b=0;b<this.yzCount;b++)this.thisPlane[b]=a},"~N");e(c$,"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(c$,"getVoxel",function(a,b,c,d){return this.isProgressive?this.thisPlane[d%this.yzCount]:this.voxelData[a][b][c]},"~N,~N,~N,~N");e(c$,"unsetVoxelData",function(){this.unsetVoxelData2()});e(c$,"unsetVoxelData2",function(){if(this.isProgressive)for(var a=
0;a<this.yzCount;a++)3.4028235E38==this.thisPlane[a]&&(this.thisPlane[a]=NaN);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)3.4028235E38==this.voxelData[a][b][c]&&(this.voxelData[a][b][c]=NaN)});e(c$,"setGridLimitsForAtom",function(a,b,c,d){b+=this.margin;this.volumeData.xyzToVoxelPt(a.x,a.y,a.z,c);a=D(Math.floor(b/this.volumeData.volumetricVectorLengths[0]));var e=D(Math.floor(b/this.volumeData.volumetricVectorLengths[1]));b=D(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(c$,"getAtomMinMax",function(a,b){for(var c=0;c<this.nPointsX;c++)b[c]=new JU.BS;for(var d=this.myAtomCount;0<=--d;)if(null==a||a.get(d)){this.setGridLimitsForAtom(this.atomXyzTruncated[d],this.atomRadius[d],this.pt0,this.pt1);for(c=this.pt0.x;c<this.pt1.x;c++)b[c].set(d)}},
"JU.BS,~A");e(c$,"markSphereVoxels",function(a,b){for(var c=3.4028235E38!=b&&null!=this.point,d=this.volumetricVectors[0],e=this.volumetricVectors[1],h=this.volumetricVectors[2],f=this.thisAtomSet.nextSetBit(0);0<=f;f=this.thisAtomSet.nextSetBit(f+1))if(this.havePlane||null==this.validSpheres||this.validSpheres.get(f)){var g=null!=this.noFaceSpheres&&this.noFaceSpheres.get(f),k=f>=this.firstNearbyAtom,t=this.atomXyzTruncated[f],l=this.atomRadius[f];if(!(c&&t.distance(this.point)>b+l+0.5)){var q=l+
a;this.setGridLimitsForAtom(t,q,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 p=this.pt0.x;p<this.pt1.x;p++,this.ptV.add2(d,this.ptY0)){this.ptY0.setT(this.ptV);for(var m=this.pt0.y;m<this.pt1.y;m++,this.ptV.add2(e,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var v=this.pt0.z;v<this.pt1.z;v++,this.ptV.add(h)){var u=this.ptV.distance(t)-l,w=this.volumeData.getPointIndex(p,m,v);if((0==
a||u<=q)&&u<this.getVoxel(p,m,v,w)){if(k||c&&this.ptV.distance(this.point)>b)u=NaN;this.setVoxel(p,m,v,w,u);Float.isNaN(u)||(null!=this.voxelSource&&(this.voxelSource[w]=f+1),0>u&&g&&this.bsSurfaceVoxels.set(w))}}}}}}},"~N,~N");e(c$,"setVoxel",function(a,b,c,d,e){this.isProgressive?this.thisPlane[d%this.yzCount]=e:this.voxelData[a][b][c]=e},"~N,~N,~N,~N,~N")});O("J.jvxl.readers");F(["JU.P3","J.jvxl.readers.AtomDataReader","JU.P4","$.V3"],"J.jvxl.readers.IsoSolventReader","java.lang.Float java.util.Hashtable JU.BS $.Lst $.Measure J.jvxl.data.MeshData JU.BSUtil $.Logger $.MeshSurface $.TempArray".split(" "),
function(){c$=H(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;va("J.jvxl.readers.IsoSolventReader.Edge")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$();va("J.jvxl.readers.IsoSolventReader.Face")||
J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$();this.ecosASB2=this.dAB2=this.dAB=this.rBS2=this.rAS2=this.rBS=this.rAS=0;P(this,arguments)},J.jvxl.readers,"IsoSolventReader",J.jvxl.readers.AtomDataReader);ha(c$,function(){this.ptS1=new JU.P3;this.ptS2=new JU.P3;this.vTemp=new JU.V3;this.plane=new JU.P4;this.ptTemp2=new JU.P3;this.vTemp2=new JU.V3;this.p=new JU.P3});W(c$,function(){da(this,J.jvxl.readers.IsoSolventReader,[])});m(c$,"init",function(a){this.initADR(a)},"J.jvxl.readers.SurfaceGenerator");
m(c$,"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");m(c$,"setup",function(a){this.setup2();
if(null==this.contactPair){this.cavityRadius=this.params.cavityRadius;this.envelopeRadius=this.params.envelopeRadius;this.sr=this.params.solventRadius;this.point=this.params.point;this.isCavity=this.params.isCavity&&null!=this.meshDataServer;this.isPocket=null!=this.params.pocket&&null!=this.meshDataServer;this.doUseIterator=this.doCalculateTroughs=!a&&null!=this.sg.atomDataServer&&!this.isCavity&&0<this.sr&&(1195==this.dataType||1203==this.dataType);this.getAtoms(this.params.bsSelected,this.doAddHydrogens,
!0,!1,!1,!0,!1,NaN,null);if(this.isCavity||this.isPocket)this.dots=this.meshDataServer.calculateGeodesicSurface(this.bsMySelected,this.envelopeRadius);this.setHeader("solvent/molecular surface",this.params.calculationType);if(this.havePlane||!a){var b=Math.max(this.params.solventExtendedAtomRadius,this.params.solventRadius),b=1<=b?1.5/b:0;0<b&&System.out.println("IsoSolventReader.minPtsPerAng="+b);this.setRanges(this.params.solvent_ptsPerAngstrom,this.params.solvent_gridMax,b);this.volumeData.getYzCount();
this.margin=2*this.volumeData.maxGrid}null!=this.bsNearby&&this.bsMySelected.or(this.bsNearby)}else a||this.setVolumeData();this.doCalculateTroughs||(a?(this.precalculateVoxelData=!1,this.volumeData.sr=this):this.isCavity||(this.isProgressive=this.isXLowToHigh=!0));null==this.thisAtomSet&&(this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount))},"~B");m(c$,"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()&&T(a.get(b)[0],JU.P4)&&(this.volumeData.capData(a.get(b)[0],this.params.cutoff),a.removeItemAt(b--))}});
m(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,h,f,g,k,m,l,q,p){m=this.marchingCubes.getLinearOffset(f,g,k,m);l=this.marchingCubes.getLinearOffset(f,g,k,l);this.isSurfacePoint=null!=this.bsSurfaceVoxels&&(this.bsSurfaceVoxels.get(m)||this.bsSurfaceVoxels.get(l));if(null!=this.voxelSource){var u=Math.abs(Float.isNaN(d)||c<d?this.voxelSource[m]:this.voxelSource[l]);0<u&&(this.iAtomSurface=this.atomIndex[u-1])}if(J.jvxl.readers.IsoSolventReader.testLinear||null==this.voxelSource||0==this.voxelSource[m]||
this.voxelSource[m]!=this.voxelSource[l])return this.getSPF(a,b,c,d,e,h,f,g,k,m,l,q,p);a=q[0]=JU.MeshSurface.getSphericalInterpolationFraction(0>this.voxelSource[m]?this.sr:this.atomRadius[this.voxelSource[m]-1],c,d,h.length());p.scaleAdd2(a,h,e);return c+a*(d-c)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");m(c$,"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");m(c$,"selectPocket",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);for(var b=this.meshData.vs,c=this.meshData.vc,d=this.meshData.vvs,e=this.dots.length,h=0;h<c;h++)for(var f=0;f<e;f++)this.dots[f].distance(b[h])<this.envelopeRadius&&(d[h]=NaN);this.meshData.getSurfaceSet();b=this.meshData.nSets;c=JU.BS.newN(b);for(h=0;h<b;h++)if(null!=(d=this.meshData.surfaceSet[h]))for(f=d.nextSetBit(0);0<=f;f=d.nextSetBit(f+
1))if(Float.isNaN(this.meshData.vvs[f])){c.set(h);break}for(h=0;h<b;h++)null!=this.meshData.surfaceSet[h]&&c.get(h)==a&&this.meshData.invalidateSurfaceSet(h);this.updateSurfaceData();a||(this.meshData.surfaceSet=null);null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)},"~B");m(c$,"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,h=0,f=!1;if(null!=d&&!this.isCavity)for(var g=0;g<this.meshData.nSets;g++){var k=d[g];Math.abs(k)>h&&(h=Math.abs(k),f=0>k)}h=f?-1:1;for(g=0;g<this.meshData.nSets;g++)if(f=b[g],f.intersects(this.bsSurfacePoints)&&(null==d||d[g]*h>e)&&null!=this.params.vertexSource){k=new JU.BS;null==c&&(c=Array(b.length));for(var m=f.nextSetBit(0);0<=m;m=f.nextSetBit(m+
1)){var l=this.params.vertexSource[m];if(!(0>l)){if(a.get(l)){this.meshData.invalidateSurfaceSet(g);break}k.set(l)}}a.or(k)}else this.meshData.invalidateSurfaceSet(g);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(c$,"generateSolventCavity",function(){for(var a=JU.BS.newN(this.nPointsX*
this.nPointsY*this.nPointsZ),b=0,c=this.dots.length,d=0,e,h=this.envelopeRadius,f=0;f<this.nPointsX;++f)for(var g=0;g<this.nPointsY;++g){var k=0;a:for(;k<this.nPointsZ;++k,++b)if(3.4028235E38>(e=this.voxelData[f][g][k])&&e>=this.cavityRadius){this.volumeData.voxelPtToXYZ(f,g,k,this.ptV);for(var m=0;m<c;m++)if(this.dots[m].distance(this.ptV)<h)continue a;a.set(b);d++}}JU.Logger.info("cavities include "+d+" voxel points");this.atomRadius=w(d,0);this.atomXyzTruncated=Array(d);for(c=b=f=0;f<this.nPointsX;++f)for(g=
0;g<this.nPointsY;++g)for(k=0;k<this.nPointsZ;++k)a.get(b++)&&(this.volumeData.voxelPtToXYZ(f,g,k,this.atomXyzTruncated[c]=new JU.P3),this.atomRadius[c++]=this.voxelData[f][g][k]);this.myAtomCount=this.firstNearbyAtom=d;this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount);this.rs=null;this.setRadii()});e(c$,"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(c$,"getEdges",function(){for(var a=0;a<this.myAtomCount;a++)this.bsLocale[a]=new JU.BS;for(a=0;a<this.myAtomCount;a++){var b=this.atomXyzTruncated[a],c=this.rs[a];for(this.sg.atomDataServer.setIteratorForAtom(this.iter,
this.atomIndex[a],c+this.maxRS);this.iter.hasNext();){var d=this.iter.next(),d=this.myIndex[d];if(!(a>=this.firstNearbyAtom&&d>=this.firstNearbyAtom)){var e=this.rs[d],h=b.distance(this.atomXyzTruncated[d]);h>=c+e||(e=ta(J.jvxl.readers.IsoSolventReader.Edge,this,null,this,a,d,h),this.vEdges.addLast(e),this.bsLocale[a].set(d),this.bsLocale[d].set(a),this.htEdges.put(e.toString(),e))}}}});e(c$,"findEdge",function(a,b){return this.htEdges.get(a<b?a+"_"+b:b+"_"+a)},"~N,~N");e(c$,"getFaces",function(){var a=
new JU.BS;this.params.surfaceAtoms=this.validSpheres=new JU.BS;this.noFaceSpheres=JU.BSUtil.setAll(this.myAtomCount);for(var b=this.vEdges.size();0<=--b;){var c=this.vEdges.get(b),d=c.ia,e=c.ib;a.clearAll();a.or(this.bsLocale[d]);a.and(this.bsLocale[e]);for(var h=a.nextSetBit(e+1);0<=h;h=a.nextSetBit(h+1))if(this.getSolventPoints(c,d,e,h)){var f,g=!1;if(null!=(f=this.validateFace(d,e,h,c,this.ptS1)))this.vFaces.addLast(f),g=!0;if(null!=(f=this.validateFace(d,e,h,c,this.ptS2)))this.vFaces.addLast(f),
g=!0;g&&(this.noFaceSpheres.clear(d),this.noFaceSpheres.clear(e),this.noFaceSpheres.clear(h))}}});e(c$,"validateFace",function(a,b,c,d,e){this.sg.atomDataServer.setIteratorForPoint(this.iter,this.modelIndex,e,this.maxRS);for(var h=!0;this.iter.hasNext();){var f=this.iter.next(),g=this.myIndex[f];if(!(g==a||g==b||g==c)&&this.atomData.atoms[f].distance(e)<this.atomData.atomRadius[f]+this.sr){h=!1;break}}f=this.findEdge(b,c);g=this.findEdge(a,c);e=h?ta(J.jvxl.readers.IsoSolventReader.Face,this,null,
a,b,c,e):null;d.addFace(e);f.addFace(e);g.addFace(e);if(!h)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(c$,"markFaceVoxels",function(a){for(var b=new JU.BS,c=this.volumetricVectors[0],d=this.volumetricVectors[1],e=this.volumetricVectors[2],h=this.vFaces.size();0<=--h;){var f=this.vFaces.get(h),g=this.atomXyzTruncated[f.ia],k=this.atomXyzTruncated[f.ib],m=this.atomXyzTruncated[f.ic],l=f.pS;
this.setGridLimitsForAtom(l,this.sr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(var q=this.pt0.x;q<this.pt1.x;q++,this.ptV.add2(c,this.ptY0)){this.ptY0.setT(this.ptV);for(var p=this.pt0.y;p<this.pt1.y;p++,this.ptV.add2(d,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var u=this.pt0.z;u<this.pt1.z;u++,this.ptV.add(e)){var v=this.sr-this.ptV.distance(l),w=this.voxelData[q][p][u],y=this.volumeData.getPointIndex(q,p,u);a&&0<v&&this.bsSurfaceDone.set(y);if(JU.Measure.isInTetrahedron(this.ptV,
g,k,m,l,this.plane,this.vTemp,this.vTemp2,!1)&&(!a?!this.bsSurfaceDone.get(y)&&0>v&&v>1.8*-this.volumeData.maxGrid&&v>w==b.get(y):0<v&&(0>w||3.4028235E38==w||v>w==b.get(y))))b.set(y),this.setVoxel(q,p,u,y,v),null!=this.voxelSource&&(this.voxelSource[y]=-1-f.ia),0<v&&this.bsSurfaceVoxels.set(y)}}}}},"~B");e(c$,"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,f=e.ib,m=this.atomXyzTruncated[g],k=this.atomXyzTruncated[f];this.rAS=this.rs[g];this.rBS=this.rs[f];this.rAS2=this.rs2[g];this.rBS2=this.rs2[f];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(f=this.pt0.y;f<this.pt1.y;f++,this.ptV.add2(b,this.ptZ0)){this.ptZ0.setT(this.ptV);
for(var t=this.pt0.z;t<this.pt1.z;t++,this.ptV.add(c)){var l=this.checkSpecialVoxel(m,k,this.ptV);if(!Float.isNaN(l)&&(l=this.sr-l,l<this.voxelData[e][f][t])){var q=this.volumeData.getPointIndex(e,f,t);this.setVoxel(e,f,t,q,l);null!=this.voxelSource&&(this.voxelSource[q]=-1-g)}}}}}}});m(c$,"unsetVoxelData",function(){if(this.havePlane)if(this.isProgressive)for(var a=0;a<this.yzCount;a++)0.001>this.thisPlane[a]||(this.thisPlane[a]=0.001);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=
0;c<this.nPointsZ;++c)0.001>this.voxelData[a][b][c]||(this.voxelData[a][b][c]=0.001);else this.unsetVoxelData2()});e(c$,"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(c$,"checkSpecialVoxel",function(a,b,c){var d=a.distance(c),e=a.distanceSquared(c),g=this.rAS/d;if(1<g)return this.p.set(a.x+(c.x-a.x)*g,a.y+
(c.y-a.y)*g,a.z+(c.z-a.z)*g),b.distanceSquared(this.p)>=this.rBS2?NaN:this.solventDistance(this.rAS,this.rAS2,this.rBS2,d,e,b.distanceSquared(c));d=b.distance(c);return 1<(g=this.rBS/d)?(this.p.set(b.x+(c.x-b.x)*g,b.y+(c.y-b.y)*g,b.z+(c.z-b.z)*g),a.distanceSquared(this.p)>=this.rAS2?NaN:this.solventDistance(this.rBS,this.rBS2,this.rAS2,d,d*d,e)):NaN},"JU.P3,JU.P3,JU.P3");e(c$,"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(c$,"dumpLine",function(a,b,c,d){this.sg.log('draw ID "x'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(b)+" color "+d)},"JU.P3,JU.T3,~S,~S");e(c$,"dumpLine2",function(a,b,c,d,e,g){var f=new JU.V3;f.setT(b);f.sub(a);f.normalize();f.scale(d);f.add(a);this.sg.log('draw ID "'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(f)+" color "+e);this.sg.log('draw ID "'+c+this.nTest++ +'"'+JU.P3.newP(f)+
" "+JU.P3.newP(b)+" color "+g+'"'+c+'"')},"JU.P3,JU.P3,~S,~N,~S,~S");e(c$,"dumpPoint",function(a,b,c){this.sg.log('draw ID "'+b+this.nTest++ +'"'+JU.P3.newP(a)+" color "+c)},"JU.P3,~S,~S");m(c$,"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");m(c$,"discardTempData",
function(a){this.rs2=this.rs=null;this.discardTempDataSR(a)},"~B");m(c$,"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");c$.$IsoSolventReader$Edge$=function(){na(self.c$);c$=H(function(){ua(this,
arguments);this.cosASB2=this.maxr=this.d2=this.d=this.nInvalid=this.nFaces=this.ib=this.ia=0;this.v=null;P(this,arguments)},J.jvxl.readers.IsoSolventReader,"Edge",JU.P3);fb(c$,function(a,b,c,d){this.ia=Math.min(b,c);this.ib=Math.max(b,c);this.d=d;this.d2=d*d;this.maxr=Math.sqrt(this.d2/4+Math.max(a.rs2[b],a.rs2[c]));this.ave(a.atomXyzTruncated[b],a.atomXyzTruncated[c]);this.cosASB2=(a.rs2[b]+a.rs2[c]-this.d2)/(a.rs[c]*a.rs[b]);this.v=JU.V3.newVsub(a.atomXyzTruncated[c],a.atomXyzTruncated[b]);this.v.normalize()},
"J.jvxl.readers.IsoSolventReader,~N,~N,~N");e(c$,"addFace",function(a){this.nFaces++;null==a&&this.nInvalid++},"J.jvxl.readers.IsoSolventReader.Face");e(c$,"isValid",function(){return 0==this.nFaces||this.nInvalid!=this.nFaces});m(c$,"toString",function(){return this.ia+"_"+this.ib});c$=ma()};c$.$IsoSolventReader$Face$=function(){na(self.c$);c$=H(function(){ua(this,arguments);this.ic=this.ib=this.ia=0;this.pS=null;P(this,arguments)},J.jvxl.readers.IsoSolventReader,"Face");W(c$,function(a,b,c,d){this.ia=
a;this.ib=b;this.ic=c;this.pS=JU.P3.newP(d)},"~N,~N,~N,JU.P3");m(c$,"toString",function(){return this.ia+"_"+this.ib+"_"+this.ic+"_"+this.pS});c$=ma()};Z(c$,"testLinear",!1)});O("J.jvxl.readers");F(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.SurfaceFileReader",["JU.PT","J.api.Interface"],function(){c$=H(function(){this.next=this.line=this.out=this.binarydoc=this.br=null;P(this,arguments)},J.jvxl.readers,"SurfaceFileReader",J.jvxl.readers.SurfaceReader);ha(c$,function(){this.next=u(1,0)});W(c$,
function(){da(this,J.jvxl.readers.SurfaceFileReader,[])});e(c$,"setStream",function(a,b){if(null==a)this.binarydoc.setStream(null,b);else try{if(T(this.br,JU.Rdr.StreamReader)){var c=this.br.getStream();c.reset();this.binarydoc.setStream(c,!0)}}catch(d){if(Y(d,Exception))System.out.println("BCifDensityReader "+d),this.binarydoc.setStream(this.sg.atomDataServer.getBufferedInputStream(a),b);else throw d;}},"~S,~B");m(c$,"init",function(a){this.initSR(a)},"J.jvxl.readers.SurfaceGenerator");e(c$,"init2",
function(a,b){this.init2SFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2SFR",function(a,b){this.br=b;this.init(a)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"newBinaryDocument",function(){return J.api.Interface.getInterface("JU.BinaryDocument",this.sg.atomDataServer,"file")});m(c$,"setOutputChannel",function(a){null==this.binarydoc?this.out=a:this.sg.setOutputChannel(this.binarydoc,a)},"JU.OC");m(c$,"closeReader",function(){this.closeReaderSFR()});
e(c$,"closeReaderSFR",function(){if(null!=this.br)try{this.br.close()}catch(a){if(!Y(a,java.io.IOException))throw a;}null!=this.out&&this.out.closeChannel();null!=this.binarydoc&&this.binarydoc.close()});m(c$,"discardTempData",function(a){this.closeReader();this.discardTempDataSR(a)},"~B");e(c$,"getTokens",function(){return JU.PT.getTokensAt(this.line,0)});e(c$,"parseFloat",function(){return JU.PT.parseFloatNext(this.line,this.next)});e(c$,"parseFloatStr",function(a){this.next[0]=0;return JU.PT.parseFloatNext(a,
this.next)},"~S");e(c$,"parseFloatRange",function(a,b,c){this.next[0]=b;return JU.PT.parseFloatRange(a,c,this.next)},"~S,~N,~N");e(c$,"parseInt",function(){return JU.PT.parseIntNext(this.line,this.next)});e(c$,"parseIntStr",function(a){this.next[0]=0;return JU.PT.parseIntNext(a,this.next)},"~S");e(c$,"parseIntNext",function(a){return JU.PT.parseIntNext(a,this.next)},"~S");e(c$,"parseFloatArrayStr",function(a){this.next[0]=0;return JU.PT.parseFloatArrayNext(a,this.next,null,null,null)},"~S");e(c$,
"parseFloatArray",function(a,b,c){return JU.PT.parseFloatArrayNext(this.line,this.next,a,b,c)},"~A,~S,~S");e(c$,"getQuotedStringNext",function(){return JU.PT.getQuotedStringNext(this.line,this.next)});e(c$,"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(c$,"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})});O("J.jvxl.readers");F(["J.jvxl.readers.SurfaceFileReader"],"J.jvxl.readers.VolumeFileReader","java.lang.Float JU.AU $.PT $.SB J.api.Interface J.atomdata.AtomData JU.Logger".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"VolumeFileReader",J.jvxl.readers.SurfaceFileReader);W(c$,function(){da(this,J.jvxl.readers.VolumeFileReader,[])});m(c$,"init2",function(a,b){this.init2VFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2VFR",function(a,b){this.init2SFR(a,b);this.canDownsample=this.isProgressive=this.isXLowToHigh=!0;this.jvxlData.wasCubic=!0;this.boundingBox=this.params.boundingBox;
4==this.params.qmOrbitalType&&(this.hasColorData=null==this.params.parameters||0<=this.params.parameters[1],this.getNCIPlanes=!0,this.params.insideOut=!this.params.insideOut)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"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");m(c$,"closeReader",function(){this.readerClosed||(this.readerClosed=!0,this.closeReaderSFR(),0==this.nData||
-3.4028235E38==this.dataMax||(this.dataMean/=this.nData,JU.Logger.info("VolumeFileReader closing file: "+this.nData+" points read \ndata min/max/mean = "+this.dataMin+"/"+this.dataMax+"/"+this.dataMean)))});m(c$,"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");m(c$,"readVolumeData",function(a){return this.readVolumeDataVFR(a)},"~B");e(c$,"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(c$,"readVolumetricHeader",function(){try{this.readParameters();if(-2147483648==this.ac)return 0;this.vertexDataOnly||JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);var a=this.params.downsampleFactor,
b=this.canDownsample&&1<a;1<a&&!this.canDownsample&&(this.jvxlData.msg+="\ncannot downsample this file type");if(b){this.downsampleRemainders=u(3,0);JU.Logger.info("downsample factor = "+a);for(var c=0;3>c;++c){var d=this.voxelCounts[c];this.downsampleRemainders[c]=d%a;this.voxelCounts[c]/=a;this.isPeriodic&&(this.voxelCounts[c]++,this.downsampleRemainders[c]--);this.volumetricVectors[c].scale(a);JU.Logger.info("downsampling axis "+(c+1)+" from "+d+" to "+this.voxelCounts[c])}}if(!this.vertexDataOnly)for(c=
0;3>c;++c)this.isAngstroms||this.volumetricVectors[c].scale(0.5291772),this.line=this.voxelCounts[c]+" "+this.volumetricVectors[c].x+" "+this.volumetricVectors[c].y+" "+this.volumetricVectors[c].z,JU.Logger.info("voxel grid count/vector:"+this.line);this.scaleIsosurface(this.params.scale);this.volumeData.setVolumetricXml();return this.nSurfaces}catch(e){if(Y(e,Exception))return JU.Logger.error(e.toString()),0;throw e;}});e(c$,"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(c$,"readVoxelVector",function(a){this.rd();var b=this.volumetricVectors[a];if(-2147483648==(this.voxelCounts[a]=this.parseIntStr(this.line)))this.next[0]=this.line.indexOf(" ");b.set(this.parseFloat(),this.parseFloat(),this.parseFloat());this.isAnisotropic&&this.setVectorAnisotropy(b)},"~N");e(c$,"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(c$,"getJVXLCutoff",function(){return 0.5});m(c$,"readSurfaceData",function(a){this.readSurfaceDataVFR(a)},"~B");e(c$,"readSurfaceDataVFR",function(a){this.initializeSurfaceData();if(this.isProgressive&&!a||this.isJvxl)this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=
null,this.isJvxl&&(this.jvxlVoxelBitSet=this.getVoxelBitSet(this.nDataPoints));else if(a&&this.volumeData.hasPlane()){this.volumeData.setVoxelMap();var b=this.volumeData.getToPlaneParameter();for(a=0;a<this.nPointsX;++a){for(var c=0;c<this.nPointsY;++c){for(var d=0;d<this.nPointsZ;++d){var e=this.recordData(this.getNextVoxelValue());this.volumeData.isNearPlane(a,c,d,b)&&this.volumeData.setVoxelMapValue(a,c,d,e);0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=
this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}else{this.voxelData=JU.AU.newFloat3(this.nPointsX,-1);for(a=0;a<this.nPointsX;++a){b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(c=0;c<this.nPointsY;++c){e=w(this.nPointsZ,0);b[c]=e;for(d=0;d<this.nPointsZ;++d)e[d]=this.recordData(this.getNextVoxelValue()),0!=this.nSkipX&&this.skipVoxels(this.nSkipX);0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}this.volumeData.setVoxelDataAsArray(this.voxelData)},"~B");
m(c$,"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(c$,"getPlaneNCI",function(a){var b;if(0==this.iPlaneNCI){this.qpc=J.api.Interface.getOption("quantum.NciCalculation",this.sg.atomDataServer,null);b=new J.atomdata.AtomData;b.modelIndex=-1;b.bsSelected=this.params.bsSelected;this.sg.fillAtomData(b,1);this.qpc.setupCalculation(this.volumeData,this.sg.params.bsSelected,null,
null,b.atoms,-1,!0,null,this.params.parameters,this.params.testFlags);this.iPlaneNCI=1;this.qpc.setPlanes(this.yzPlanesRaw=w(4,this.yzCount,0));if(this.hasColorData){this.getPlaneVFR(this.yzPlanesRaw[0],!1);this.getPlaneVFR(this.yzPlanesRaw[1],!1);b=this.yzPlanes[0];for(a=0;a<this.yzCount;a++)b[a]=NaN;return b}this.iPlaneNCI=-1}var c=this.qpc.getNoValue(),d=this.nPointsX-1;switch(this.iPlaneNCI){case -1:b=this.yzPlanes[a%2];d++;break;case 3:b=this.yzPlanesRaw[0];this.yzPlanesRaw[0]=this.yzPlanesRaw[1];
this.yzPlanesRaw[1]=this.yzPlanesRaw[2];this.yzPlanesRaw[2]=this.yzPlanesRaw[3];this.yzPlanesRaw[3]=b;b=this.yzPlanesRaw[this.iPlaneNCI];break;default:this.iPlaneNCI++,b=this.yzPlanesRaw[this.iPlaneNCI]}if(a<d){this.getPlaneVFR(b,!1);this.qpc.calcPlane(a,b=this.yzPlanes[a%2]);for(a=0;a<this.yzCount;a++)b[a]!=c&&this.recordData(b[a])}else for(a=0;a<this.yzCount;a++)b[a]=NaN;return b},"~N");e(c$,"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(f){if(!Y(f,Exception))throw f;}},"~A,~B");m(c$,"getValue",function(a,b,c,d){return null!=this.boundingBox&&(this.volumeData.voxelPtToXYZ(a,b,c,this.ptTemp),this.ptTemp.x<this.boundingBox[0].x||this.ptTemp.x>this.boundingBox[1].x||this.ptTemp.y<this.boundingBox[0].y||this.ptTemp.y>this.boundingBox[1].y||
this.ptTemp.z<this.boundingBox[0].z||this.ptTemp.z>this.boundingBox[1].z)?NaN:this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(c$,"skipVoxels",function(a){for(;0<=--a;)this.getNextVoxelValue()},"~N");e(c$,"getVoxelBitSet",function(){return null},"~N");e(c$,"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(c$,"nextVoxel",function(){var a=this.parseFloat();if(Float.isNaN(a)){for(;null!=this.rd()&&Float.isNaN(a=this.parseFloatStr(this.line)););null==this.line&&(this.endOfData||JU.Logger.warn("end of file reading cube voxel data? nBytes="+this.nBytes+" nDataPoints="+this.nDataPoints+" (line):"+this.line),this.endOfData=!0,this.line="0 0 0 0 0 0 0 0 0 0")}return a});m(c$,"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(c$,"skipData",function(a){this.skipDataVFR(a)},"~N");e(c$,"skipDataVFR",function(a){for(var b=0;b<a;)b+=this.countData(this.rd())},"~N");e(c$,"countData",function(a){for(var b=0,c=0,d=a.length,e;c<d;){for(;c<d&&(" "==(e=a.charAt(c))||"\t"==e);)++c;for(c<d&&++b;c<d&&" "!=(e=a.charAt(c))&&"\t"!=e;)++c}return b},"~S");c$.checkAtomLine=e(c$,"checkAtomLine",function(a,b,c,d,e){0<=d.indexOf("ANGSTROMS")&&(b=!0);c=null==c?2147483647:JU.PT.parseInt(c);switch(c){case -2147483648:c=
0;d=" "+d.substring(d.indexOf(" ")+1);break;case 2147483647:c=-2147483648;break;default:var g=""+c;d=d.substring(d.indexOf(g)+g.length)}b?0>d.indexOf("ANGSTROM")&&(d+=" ANGSTROMS"):0>d.indexOf("BOHR")&&(d+=" BOHR");d=(-2147483648==c?"":(a?"+":"-")+Math.abs(c))+d+"\n";e.append(d);return b},"~B,~B,~S,~S,JU.SB");m(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,g,f,m,k,t,l,q,p){return this.getSPFv(a,b,c,d,e,g,f,m,k,t,l,q,p)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPFv",function(a,
b,c,d,e,g,f,m,k,t,l,q,p){a=this.getSPF(a,b,c,d,e,g,f,m,k,t,l,q,p);if(null==this.qpc||Float.isNaN(a)||!this.hasColorData)return a;t=this.marchingCubes.getLinearOffset(f,m,k,t);l=this.marchingCubes.getLinearOffset(f,m,k,l);return this.qpc.process(t,l,q[0])},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"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(c$,"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})});O("J.jvxl.readers");F(["J.jvxl.readers.VolumeFileReader"],"J.jvxl.readers.JvxlXmlReader","java.lang.Double $.Float $.NullPointerException 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 $.Logger".split(" "),function(){c$=H(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;P(this,arguments)},J.jvxl.readers,"JvxlXmlReader",
J.jvxl.readers.VolumeFileReader);W(c$,function(){da(this,J.jvxl.readers.JvxlXmlReader,[])});m(c$,"init2",function(a,b){this.init2JXR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2JXR",function(a,b){this.init2VFR(a,b);this.jvxlData.wasJvxl=this.isJvxl=!0;this.isXLowToHigh=this.canDownsample=!1;this.xr=new J.jvxl.readers.XmlReader(b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");m(c$,"readVolumeData",function(a){if(!this.readVolumeDataVFR(a))return!1;this.strFractionTemp=
this.jvxlEdgeDataRead;this.fractionPtr=0;return!0},"~B");m(c$,"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(f){if(Y(f,Exception))return JU.Logger.error(f.toString()),
!1;throw f;}return!0},"~B");m(c$,"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)});m(c$,"getJVXLCutoff",function(){return this.params.cutoff});e(c$,"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");m(c$,"gotoData",function(a,b){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");this.vertexDataOnly=this.jvxlData.vertexDataOnly=0==b;for(var c=0;c<a;c++)this.jvxlSkipData(b,!0);this.xr.toTag("jvxlSurface");
this.jvxlReadSurfaceInfo()},"~N,~N");e(c$,"jvxlSkipData",function(){this.rd();this.xr.skipTag("jvxlSurface")},"~N,~B");e(c$,"jvxlReadSurfaceInfo",function(){var a=this.xr.getXmlData("jvxlSurfaceInfo",null,!0,!0);this.isXLowToHigh=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isXLowToHigh").equals("true");var b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"cutoff");0>b.indexOf(" ")?(this.jvxlCutoff=this.parseFloatStr(b),Double.isNaN(this.jvxlCutoff)||JU.Logger.info("JVXL read: cutoff "+this.jvxlCutoff)):(this.jvxlCutoffRange=
this.parseFloatArrayStr(b),this.jvxlCutoff=this.jvxlCutoffRange[0],JU.Logger.info("JVXL read: cutoff "+JU.Escape.eAF(this.jvxlCutoffRange)));this.params.cutoff=this.jvxlCutoff;var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContourData"));this.haveContourData=0<c;this.params.isContoured=this.jvxlData.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contoured").equals("true");this.params.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isModelConnected").equals("true");
if(this.params.isContoured){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContours"));0>=d?d=0:(0>this.params.thisContour&&(this.params.thisContour=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"thisContour"))),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourValues"),0<b.length&&(b=b.$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(Y(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,f=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")),f=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"valueMappedToBlue")),Float.isNaN(c)&&(c=g=-1,d=f=1));this.jvxlSetColorRanges(c,d,g,f,b)});e(c$,"jvxlSetColorRanges",function(a,b,c,d,e){this.jvxlDataIsColorMapped&&(!Float.isNaN(a)&&!Float.isNaN(b)&&(0==b&&0==a&&(a=-1,b=1),this.params.mappedDataMin=a,this.params.mappedDataMax=b,JU.Logger.info("JVXL read: data_min/max "+this.params.mappedDataMin+
"/"+this.params.mappedDataMax)),this.params.rangeDefined||(!Float.isNaN(c)&&!Float.isNaN(d)?(0==c&&0==d&&(c=-1,d=1),this.params.valueMappedToRed=Math.min(c,d),this.params.valueMappedToBlue=Math.max(c,d),this.params.isColorReversed=c>d):(this.params.valueMappedToRed=0,this.params.valueMappedToBlue=1),this.params.rangeDefined=!0),JU.Logger.info("JVXL read: color red/blue: "+this.params.valueMappedToRed+"/"+this.params.valueMappedToBlue));this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=
this.params.valueMappedToBlue;this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.isColorReversed=this.params.isColorReversed;this.params.insideOut&&(e=!e);this.params.insideOut=this.jvxlData.insideOut=e},"~N,~N,~N,~N,~B");m(c$,"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(c$,"readSurfaceDataXML",function(){return this.vertexDataOnly?(this.getEncodedVertexData(),!0):null!=this.params.thePlane?(this.volumeData.setDataDistanceToPlane(this.params.thePlane),this.setVolumeDataV(this.volumeData),this.params.cutoff=0,this.jvxlData.setSurfaceInfo(this.params.thePlane,this.params.mapLattice,0,""),this.jvxlData.scale3d=this.params.scale3d,!0):!1});e(c$,"readSurfaceDataJXR",function(){this.readSurfaceDataVFR(!1);this.volumeData.setMappingPlane(null)});
e(c$,"jvxlReadFractionData",function(a){var b;try{if(a.equals("edge"))b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml,"data"));else{var c=this.xr.getXmlData("jvxlColorData",null,!0,!1);this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.JvxlXmlReader.getEncoding(c).endsWith("2");b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(c,"data"))}}catch(d){if(Y(d,Exception))throw JU.Logger.error("Error reading "+a+" data "+
d),new NullPointerException;throw d;}return b},"~S,~N");m(c$,"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");m(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,g,f,m,k,t,l,q,p){if(0>=this.edgeDataCount)return this.getSPFv(a,b,c,d,e,g,f,m,k,t,l,q,p);p.scaleAdd2(q[0]=this.jvxlGetNextFraction(this.edgeFractionBase,this.edgeFractionRange,0.5),g,e);Float.isNaN(this.valueMin)&&this.setValueMinMax();return 0==this.valueCount||this.includeValueNaN&&Float.isNaN(q[0])?q[0]:this.getNextValue()},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getNextValue",function(){for(var a=
NaN;this.colorPtr<this.valueCount&&Float.isNaN(a);){a=this.jvxlData.isJvxlPrecisionColor?J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(this.jvxlColorDataRead.charCodeAt(this.colorPtr),this.jvxlColorDataRead.charCodeAt(this.colorPtr++ +this.valueCount),this.colorFractionBase,this.colorFractionRange):J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.jvxlColorDataRead.charCodeAt(this.colorPtr++),this.colorFractionBase,this.colorFractionRange,0.5);break}return this.valueMin+a*this.valueRange});
e(c$,"setValueMinMax",function(){this.valueCount=this.jvxlColorDataRead.length;this.jvxlData.isJvxlPrecisionColor&&(this.valueCount/=2);this.includeValueNaN=this.valueCount!=this.jvxlEdgeDataRead.length;this.valueMin=!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToRed:3.4028235E38==this.params.mappedDataMin?0:this.params.mappedDataMin;this.valueRange=(!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToBlue:3.4028235E38==this.params.mappedDataMin?1:this.params.mappedDataMax)-
this.valueMin;this.haveReadColorData=!0});e(c$,"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.charCodeAt(this.fractionPtr++),a,b,c)},"~N,~N,~N");m(c$,"readColorData",function(){if(!this.jvxlDataIsColorMapped)return"";var a=
this.jvxlData.vertexCount=this.meshData.vc,b=this.meshData.vcs,c=this.meshData.vvs;if("none".equals(this.jvxlColorEncodingRead)){this.jvxlData.vertexColors=u(a,0);for(var d=u(1,0),c=JU.PT.parseIntNext(this.jvxlColorDataRead,d),c=Math.min(c,a),a=JU.PT.getTokens(this.jvxlColorDataRead.substring(d[0])),e=!1,g=this.jvxlData.translucency,f=0,d=0;d<c;d++)try{var m=J.jvxl.readers.JvxlXmlReader.getColor(a[d]);0==m?m=f:f=m;b[d]=JU.C.getColixTranslucent(this.jvxlData.vertexColors[d]=m);JU.C.isColixTranslucent(b[d])?
e=!0:0!=g&&(b[d]=JU.C.getColixTranslucent3(b[d],!0,g))}catch(k){if(Y(k,Exception))JU.Logger.info("JvxlXmlReader: Cannot interpret color code: "+a[d]);else throw k;}e&&0==g&&(this.jvxlData.translucency=0.5);return"-"}null==this.params.colorEncoder&&(this.params.colorEncoder=new JU.ColorEncoder(null,null));this.params.colorEncoder.setColorScheme(null,!1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);JU.Logger.info("JVXL reading color data mapped min/max: "+
this.params.mappedDataMin+"/"+this.params.mappedDataMax+" for "+a+" vertices. using encoding keys "+this.colorFractionBase+" "+this.colorFractionRange);JU.Logger.info("mapping red--\x3eblue for "+this.params.valueMappedToRed+" to "+this.params.valueMappedToBlue+" colorPrecision:"+this.jvxlData.isJvxlPrecisionColor);var t=Float.isNaN(this.valueMin);t&&this.setValueMinMax();var l=3.4028235E38,q=-3.4028235E38;if(null==b||b.length<a)this.meshData.vcs=b=$(a,0);e=m=0;this.params.colorBySign&&(e=JU.C.getColix(this.params.isColorReversed?
this.params.colorNeg:this.params.colorPos),m=JU.C.getColix(this.params.isColorReversed?this.params.colorPos:this.params.colorNeg));for(var g=this.meshData.vertexIncrement,p=3.4028235E38==this.params.mappedDataMin,d=0;d<a;d+=g)f=t?c[d]=this.getNextValue():c[d],p&&(f<l&&(l=f),f>q&&(q=f));p&&(this.params.mappedDataMin=l,this.params.mappedDataMax=q);if(null!=this.jvxlData.colorScheme){t=null!=this.marchingSquares&&this.params.isContoured;for(d=0;d<a;d+=g)f=c[d],t?this.marchingSquares.setContourData(d,
f):(f=!this.params.colorBySign?this.params.colorEncoder.getColorIndex(f):(this.params.isColorReversed?0<f:0>=f)?m:e,b[d]=JU.C.getColixTranslucent3(f,!0,this.jvxlData.translucency))}return this.jvxlColorDataRead+"\n"});c$.getColor=e(c$,"getColor",function(a){var b=0;try{switch(a.charAt(0)){case "[":b=JU.CU.getArgbFromString(a);break;case "0":b=JU.PT.parseIntRadix(a.substring(2),16);break;default:b=JU.PT.parseIntRadix(a,10)}}catch(c){if(!Y(c,Exception))throw c;}return b},"~S");e(c$,"getEncodedVertexData",
function(){var a=this.xr.getXmlData("jvxlSurfaceData",null,!0,!1);this.jvxlDecodeVertexData(this.xr.getXmlData("jvxlVertexData",a,!0,!1),!1);var b=this.xr.getXmlData("jvxlTriangleData",a,!0,!1),c=this.xr.getXmlData("jvxlTriangleEdgeData",a,!0,!1),d=this.xr.getXmlData("jvxlPolygonColorData",a,!1,!1);this.jvxlDecodeTriangleData(b,c,d);a=this.xr.getXmlData("jvxlColorData",a,!0,!1);this.jvxlColorEncodingRead=J.jvxl.readers.JvxlXmlReader.getEncoding(a);this.jvxlData.isJvxlPrecisionColor=this.jvxlColorEncodingRead.endsWith("2");
a=this.getData(a,"jvxlColorData");this.jvxlColorDataRead=this.jvxlColorEncodingRead.equals("none")?a:J.jvxl.data.JvxlCoder.jvxlDecompressString(a);this.jvxlDataIsColorMapped=(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&0<this.jvxlColorDataRead.length;this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1))});e(c$,"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");c$.getEncoding=e(c$,"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(c$,"jvxlDecodeVertexData",function(a,b){var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));b||JU.Logger.info("Reading "+c+" vertices");var d=3*c,e=b?Array(c):null,g,f=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data"),m=J.jvxl.readers.JvxlXmlReader.getEncoding(a);
if("none".equals(m)){0==f.length&&(f=this.xr.getXmlData("jvxlVertexData",a,!1,!1));d=JU.PT.parseFloatArray(f);d[0]!=3*c&&JU.Logger.info("JvxlXmlReader: vertexData count="+y(d[0])+"; expected "+3*c);f=0;for(m=1;f<c;f++){var k=JU.P3.new3(d[m++],d[m++],d[m++]);b?e[f]=k:this.addVertexCopy(k,0,f,!1)}}else{var t=this.xr.getXmlPoint(a,"min"),l=this.xr.getXmlPoint(a,"max");l.sub(t);var q=this.jvxlData.colorFractionBase,p=this.jvxlData.colorFractionRange,u=J.jvxl.data.JvxlCoder.jvxlDecompressString(f);0==
u.length&&(u=this.xr.getXmlData("jvxlVertexData",a,!1,!1));f=0;for(m=-1;f<c;f++)k=new JU.P3,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charCodeAt(++m),u.charCodeAt(m+d),q,p),k.x=t.x+g*l.x,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charCodeAt(++m),u.charCodeAt(m+d),q,p),k.y=t.y+g*l.y,g=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(u.charCodeAt(++m),u.charCodeAt(m+d),q,p),k.z=t.z+g*l.z,b?e[f]=k:this.addVertexCopy(k,0,f,!1)}return e},"~S,~B");e(c$,"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,f=0;JU.Logger.info("Reading "+d+" triangles");var m=J.jvxl.readers.JvxlXmlReader.getEncoding(a);a=this.getData(a,"jvxlTriangleData");b=this.getData(b,"jvxlTriangleEdgeData");var k=u(3,0),t=u(1,0),l=null,q=7,p=!"none".equals(m);if(p)a=J.jvxl.data.JvxlCoder.jvxlDecompressString(a),b=J.jvxl.data.JvxlCoder.jvxlDecompressString(b).trim(),m=b.length==d;else{var w=JU.PT.parseIntNext(a,t);
(m=0<b.length)?(l=u(1,0),JU.PT.parseIntNext(b,l)):0<w&&JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count="+w+"; expected "+d)}for(var v=w=0,y=0,D=-1;w<d;){if(p){var B=a.charAt(++D);switch(B){case "!":B=0;break;case "+":case ".":case " ":case "\n":case "\r":case "\t":case ",":continue;case "-":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":t[0]=D;B=JU.PT.parseIntNext(a,t);D=t[0]-1;break;default:B=B.charCodeAt(0)-92}v+=B}else v=JU.PT.parseIntNext(a,
t)-1;k[y]=v;if(3==++y){y=0;if(m&&(q=null==l?b.charCodeAt(w)-48:JU.PT.parseIntNext(b,l),0>q||7<q))q=7;0==--g&&(g=JU.PT.parseIntNext(c,e),B=JU.PT.parseIntNext(c,e),-2147483648==B?g=0:f=B|4278190080);this.addTriangleCheck(k[0],k[1],k[2],q,f,!1,f);w++}}}},"~S,~S,~S");e(c$,"jvxlDecodeContourData",function(a,b){var c=new JU.Lst,d=new JU.SB,e=new JU.SB,g=-1;a.vContours=null;if(null!=b){for(;0<=(g=b.indexOf("<jvxlContour",g+1));){var f=new JU.Lst,m=this.xr.getXmlData("jvxlContour",b.substring(g),!0,!1),k=
this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(m,"value"));d.append(" ").appendF(k);var t=J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(m,"color")),l=JU.C.getColix(t);e.append(" ").append(JU.Escape.escapeColor(t));var q=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(m,"data")),p=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour",m,!1,!1)),m=p.length();J.shapesurface.IsosurfaceMesh.setContourVector(f,m,p,
k,l,t,JU.SB.newS(q));c.addLast(f)}m=c.size();if(0<m){a.vContours=JU.AU.createArrayOfArrayList(m);a.contourColixes=this.params.contourColixes=$(m,0);a.contourValues=this.params.contoursDiscrete=w(m,0);for(g=0;g<m;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: "+m+" discrete contours");JU.Logger.info("JVXL read: contour values: "+d);JU.Logger.info("JVXL read: contour colors: "+
e)}}},"J.jvxl.data.JvxlData,~S");m(c$,"postProcessVertices",function(){var a=this.params.bsExcluded[1];null!=a&&(null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.invalidateVertices(a),null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,4,null),this.meshData=new J.jvxl.data.MeshData),this.updateTriangles())})});O("J.rendersurface");F(["J.render.MeshRenderer"],"J.rendersurface.IsosurfaceRenderer",["java.lang.Boolean","$.Float","JU.V3",
"JU.C","$.Normix"],function(){c$=H(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;P(this,arguments)},J.rendersurface,"IsosurfaceRenderer",J.render.MeshRenderer);m(c$,"render",function(){return this.renderIso()});e(c$,"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(c$,"setGlobals",function(){this.needTranslucent=!1;this.antialias=this.g3d.isAntialiased();this.iShowNormals=this.vwr.getBoolean(603979965);
this.showNumbers=this.vwr.getBoolean(603979964);this.isosurface=this.shape;this.exportPass=this.isExport?2:0;this.isNavigationMode=this.vwr.getBoolean(603979889);this.showKey=this.vwr.getBoolean(603979867)?Boolean.TRUE:null;this.isosurface.keyXy=null;this.meshScale=-1;this.globalSlabValue=this.vwr.gdata.slab;this.mySlabValue=this.isNavigationMode?y(this.tm.getNavigationOffset().z):2147483647});e(c$,"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,f=this.vwr.getScreenHeight()*g,m=D(D(f/2)/(d-1)),f=3*D(f/4)-m,k=10*g,t=20*g;this.isosurface.keyXy=u(-1,[D(k/g),0,D((k+
t)/g),D((f+m)/g),D(m/g)]);for(var l=0;l<d;l++,f-=m){switch(e){case 0:if(!this.g3d.setC(b[l]))return;break;case 1:if(!this.g3d.setC(c[l].get(3)[0]))return;break;case 2:this.vwr.gdata.setColor(a[l])}this.g3d.fillTextRect(k,f,5,-2147483648,t,m)}this.isosurface.keyXy[1]=D((f+m)/g)}}});e(c$,"renderMeshSlab",function(){this.volumeRender=this.imesh.jvxlData.colorDensity&&this.imesh.jvxlData.allowVolumeRender;var a=this.mySlabValue;this.frontOnly=this.mesh.frontOnly||26==this.shapeID;this.isShell=this.mesh.isShell&&
26!=this.shapeID;if(!this.isNavigationMode&&(this.meshSlabValue=this.imesh.jvxlData.slabValue,-2147483648!=this.meshSlabValue&&this.imesh.jvxlData.isSlabbable)){for(var b=this.imesh.jvxlData.boundingBox,a=3.4028235E38,c=1.4E-45,d=b.length;0<=--d;)this.pt2f.setT(b[d]),this.tm.transformPt3f(this.pt2f,this.pt2f),this.pt2f.z<a&&(a=this.pt2f.z),this.pt2f.z>c&&(c=this.pt2f.z);a=Math.round(a+(c-a)*(100-this.meshSlabValue)/100);this.frontOnly=(new Boolean(this.frontOnly&100<=this.meshSlabValue)).valueOf();
this.isShell=(new Boolean(this.isShell&100<=this.meshSlabValue)).valueOf()}b=this.vwr.gdata.translucentCoverOnly;this.vwr.gdata.translucentCoverOnly=this.frontOnly||!this.vwr.getBoolean(603979967);this.thePlane=this.imesh.jvxlData.jvxlPlane;this.vertexValues=this.mesh.vvs;2147483647!=a&&this.imesh.jvxlData.isSlabbable?(this.g3d.setSlab(a),a=this.renderMesh2(this.mesh),this.g3d.setSlab(this.globalSlabValue)):a=this.renderMesh2(this.mesh);this.vwr.gdata.translucentCoverOnly=b;return a});m(c$,"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(c$,"renderLonePair",function(a){this.pt2f.setT(this.vertices[1]);this.tm.transformPt3f(this.pt2f,this.pt2f);var b=y(this.vwr.tm.scaleToScreen(y(this.pt2f.z),100));1>b&&(b=1);if(!a){var c=
new JU.V3;a=new JU.V3;this.pt1f.setT(this.vertices[0]);this.tm.transformPt3f(this.pt1f,this.pt1f);c.sub2(this.pt2f,this.pt1f);a.set(c.x,c.y,c.z+1);a.cross(a,c);a.normalize();c=this.vwr.tm.scaleToScreen(y(this.pt1f.z),100);a.scale(c);this.pt1f.add2(this.pt2f,a);this.pt2f.sub(a);this.screens[0].set(Math.round(this.pt1f.x),Math.round(this.pt1f.y),Math.round(this.pt1f.z));this.g3d.fillSphereI(b,this.screens[0])}this.screens[1].set(Math.round(this.pt2f.x),Math.round(this.pt2f.y),Math.round(this.pt2f.z));
this.g3d.fillSphereI(b,this.screens[1])},"~B");e(c$,"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 f=c.get(g),m=c.get(++g);if(Float.isNaN(f.x)||
Float.isNaN(m.x))break;this.tm.transformPtScrT3(f,this.pt1f);this.tm.transformPtScrT3(m,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)}}}}});m(c$,"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=D(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?D(this.vwr.getScreenWidth()/2):0,g=this.showNumbers?D(this.vwr.getScreenHeight()/2):0;this.showNumbers&&this.vwr.gdata.setFontBold("Monospaced",24);for(var f=!this.imesh.hasGridPoints||0>this.imesh.firstRealVertex?0:this.imesh.firstRealVertex;f<this.vertexCount;f+=b)if(!(null!=this.vertexValues&&Float.isNaN(this.vertexValues[f])||
this.frontOnly&&!this.isVisibleNormix(this.normixes[f])||null!=this.imesh.jvxlData.thisSet&&!this.imesh.jvxlData.thisSet.get(this.mesh.vertexSets[f])||!this.mesh.isColorSolid&&null!=this.mesh.vcs&&!this.setColix(this.mesh.vcs[f])||this.haveBsDisplay&&!this.mesh.bsDisplay.get(f)||a&&!this.bsPolygons.get(f))){this.hasColorRange=!0;if(this.showNumbers&&10<this.screens[f].z&&150>Math.abs(this.screens[f].x-e)&&150>Math.abs(this.screens[f].y-g)){var m=f+(this.mesh.isColorSolid?"":" "+this.mesh.vvs[f]);
this.g3d.setC(4);this.g3d.drawStringNoSlab(m,null,this.screens[f].x,this.screens[f].y,this.screens[f].z-30,0)}this.volumeRender?(c=y(this.vwr.tm.scaleToScreen(this.screens[f].z,d)),1>c&&(c=1),this.g3d.volumeRender4(c,this.screens[f].x,this.screens[f].y,this.screens[f].z)):this.g3d.fillSphereI(c,this.screens[f])}if(3==b){this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(12,!0,0.5):12);for(f=1;f<this.vertexCount;f+=3)this.g3d.fillCylinder(3,D(c/4),this.screens[f],this.screens[f+1]);this.g3d.setC(this.isTranslucent?
JU.C.getColixTranslucent3(21,!0,0.5):21);for(f=1;f<this.vertexCount;f+=3)this.g3d.fillSphereI(c,this.screens[f]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(7,!0,0.5):7);for(f=2;f<this.vertexCount;f+=3)this.g3d.fillSphereI(c,this.screens[f])}}catch(k){}this.volumeRender&&this.g3d.volumeRender(!1)});m(c$,"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,f=this.isGhostPass&&!this.isBicolorMap||null==e||!a&&0!=this.mesh.meshColix,m=this.colix;null!=this.imesh.jvxlData.jvxlPlane&&
(!g&&!a&&this.mesh.fillTriangles)&&(g=!0,m=4);var k=g&&null!=this.mesh.pcs;k&&(!a&&this.mesh.fillTriangles)&&(k=!1);var t=this.imesh.jvxlData.contourColixes;this.hasColorRange=!g&&!this.isBicolorMap;for(var l=this.getDiameter(),q=this.mesh.pc;0<=--q;){var p=d[q];if(!(null==p||this.selectedPolyOnly&&!this.bsPolygons.get(q))){var u=p[0],v=p[1],w=p[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(v)&&this.mesh.bsDisplay.get(w))){var y=this.normixes[u],B=this.normixes[v],D=this.normixes[w],H=this.frontOnly||this.isShell?this.checkFront(y,B,D):7;if(!(a&&0==H)){var F,I,E;if(g){if(k&&q<this.mesh.pcs.length){F=this.mesh.pcs[q];if(0==F)continue;m=F}b&&(m=Math.round(10*Math.random())+5);F=I=E=m}else if(F=e[u],I=e[v],E=e[w],this.isBicolorMap){if(F!=I||I!=E)continue;this.isGhostPass&&(F=I=E=JU.C.copyColixTranslucency(this.mesh.slabColix,F))}if(a)c?
this.bsPolygonsToExport.set(q):(v==w?(this.setColix(F),u==v?this.g3d.fillSphereI(l,this.screens[u]):this.g3d.fillCylinder(3,l,this.screens[u],this.screens[v])):this.mesh.colorsExplicit?(this.vwr.gdata.setColor(p[4]),F=JU.C.copyColixTranslucency(this.mesh.colix,2047),this.g3d.setC(F),this.g3d.fillTriangle3CN(this.screens[u],F,y,this.screens[v],F,B,this.screens[w],F,D)):(this.isTranslucentInherit&&null!=e&&(F=JU.C.copyColixTranslucency(this.mesh.slabColix,e[u]),I=JU.C.copyColixTranslucency(this.mesh.slabColix,
e[v]),E=JU.C.copyColixTranslucency(this.mesh.slabColix,e[w])),this.g3d.fillTriangle3CN(this.screens[u],F,y,this.screens[v],I,B,this.screens[w],E,D)),this.iShowNormals&&this.renderNormals());else if(H&=p[3],0!=H){b&&(H=7);this.pt1i.setT(this.screens[u]);this.pt2i.setT(this.screens[v]);this.pt3i.setT(this.screens[w]);this.pt1i.z-=2;this.pt2i.z-=2;this.pt3i.z-=2;if(!f)if(k)this.g3d.setC(this.mesh.fillTriangles?4:t[p[4]%t.length]);else{this.drawTriangle(this.pt1i,F,this.pt2i,I,this.pt3i,E,H,l);continue}this.drawTriangle(this.pt1i,
m,this.pt2i,m,this.pt3i,m,H,l)}}}}}c&&this.exportSurface(g?m:0)},"~B,~B,~B");e(c$,"getDiameter",function(){var a;0>=this.mesh.diameter?(a=0>this.meshScale?this.meshScale=this.vwr.getInt(553648150):this.meshScale,this.antialias&&(a*=2)):a=D(this.vwr.getScreenDim()/100);1>a&&(a=1);return a});e(c$,"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.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,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);
