(function(jb,hc,ic,jc,D,kc,L,$,R,C,N,w,lc,da,mc,ea,r,t,Ca,ia,ja,f,Ka,fa,va,xa,wa,y,nc,oc,La,pc,qc,rc,sc,Ma,kb,tc,uc,vc,wc,xc,yc,zc,Ac,Bc,Cc,Dc,Ec,Fc,Gc,Hc,Ic,Jc,Kc,e,j){L("JS");R(null,"JS.ScriptExt",["JU.AU"],function(){var d=N(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;C(this,arguments)},JS,"ScriptExt",null);e(d,"init",function(a){this.e=a;this.vwr=this.e.vwr;return this},"~O");e(d,"atomExpressionAt",function(a){return this.e.atomExpressionAt(a)},"~N");e(d,"checkLength",
function(a){this.e.checkLength(a)},"~N");e(d,"error",function(a){this.e.error(a)},"~N");e(d,"invArg",function(){this.e.invArg()});e(d,"invPO",function(){this.error(23)});e(d,"getShapeProperty",function(a,b){return this.e.getShapeProperty(a,b)},"~N,~S");e(d,"paramAsStr",function(a){return this.e.paramAsStr(a)},"~N");e(d,"centerParameter",function(a){return this.e.centerParameter(a,null)},"~N");e(d,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");e(d,"getPoint3f",function(a,b){return this.e.getPoint3f(a,
b,!0)},"~N,~B");e(d,"intParameter",function(a){return this.e.intParameter(a)},"~N");e(d,"isFloatParameter",function(a){switch(this.e.tokAt(a)){case 2:case 3:return!0}return!1},"~N");e(d,"setShapeProperty",function(a,b,c){this.e.setShapeProperty(a,b,c)},"~N,~S,~O");e(d,"showString",function(a){this.e.showString(a)},"~S");e(d,"stringParameter",function(a){return this.e.stringParameter(a)},"~N");e(d,"getToken",function(a){return this.e.getToken(a)},"~N");e(d,"tokAt",function(a){return this.e.tokAt(a)},
"~N");e(d,"setShapeId",function(a,b,c){c&&this.invArg();b=this.e.setShapeNameParameter(b).toLowerCase();this.setShapeProperty(a,"thisID",b);return b},"~N,~N,~B");e(d,"getColorTrans",function(a,b,c,g){c=3.4028235E38;1765808134!=a.theTok&&--b;switch(this.tokAt(b+1)){case 1111490588:b++;c=this.isFloatParameter(b+1)?a.getTranslucentLevel(++b):this.vwr.getFloat(570425353);break;case 1073742074:b++,c=0}a.isColorParam(b+1)?g[0]=a.getArgbParam(++b):1073742333==this.tokAt(b+1)?(g[0]=0,a.iToken=b+1):3.4028235E38==
c?this.invArg():g[0]=-2147483648;return c},"JS.ScriptEval,~N,~B,~A");e(d,"finalizeObject",function(a,b,c,g,u,aa,d,ba){u&&this.setShapeProperty(a,"set",aa);-2147483648!=b&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(b),ba);3.4028235E38!=c&&this.e.setShapeTranslucency(a,"","translucent",c,ba);0!=g&&this.setShapeProperty(a,"scale",Integer.$valueOf(g));0>d&&(d=-1-d,this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,"token",Integer.$valueOf(1073742046)));0<d&&
(this.e.setMeshDisplayProperty(a,d,0)||this.invArg())},"~N,~N,~N,~N,~B,~O,~N,JU.BS");e(d,"getIntArray2",function(a){a=this.e.getToken(a).getList();for(var b=JU.AU.newInt2(a.size()),c=b.length;0<=--c;){var g=a.get(c).getList();null==g&&this.invArg();b[c]=r(g.size(),0);for(var u=b[c].length;0<=--u;)b[c][u]=g.get(u).intValue}return b},"~N");e(d,"getAllPoints",function(a,b){var c=null,g=null;try{switch(this.e.tokAt(a)){case 7:c=this.e.getPointArray(a,-1,!1,!0);break;case 12290:case 10:case 1073742325:g=
this.atomExpressionAt(a)}null==c&&(null==g&&(g=this.vwr.getAllAtoms()),c=this.bsToArray(g))}catch(u){if(!ea(u,Exception))throw u;}(null==c||c.length<b)&&this.invArg();return c},"~N,~N");e(d,"bsToArray",function(a){for(var b=Array(a.cardinality()),c=a.nextSetBit(0),g=0;0<=c;c=a.nextSetBit(c+1))b[g++]=this.vwr.ms.at[c];return b},"JU.BS")});L("JS");R(["JS.ScriptExt"],"JS.IsoExt","JU.AU $.BS $.Lst $.M4 $.Measure $.P3 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.c.VDW JS.SV $.ScriptEval $.ScriptInterruption $.T JU.BSUtil $.BoxInfo $.C $.Escape $.GData $.Logger $.Parser $.Triangulator JV.JC".split(" "),
function(){var d=Ca(JS,"IsoExt",JS.ScriptExt);da(d,function(){ja(this,JS.IsoExt,[])});j(d,"dispatch",function(a,b,c){this.chk=this.e.chk;this.slen=this.e.slen;this.st=c;switch(a){case 23:this.cgo();break;case 25:this.contact();break;case 17:this.dipole();break;case 22:this.draw();break;case 24:case 30:case 29:this.isosurface(a);break;case 26:this.lcaoCartoon();break;case 27:case 28:this.mo(b,a)}return null},"~N,~B,~A");e(d,"dipole",function(){var a=this.e,b=null,c=null,g=!1,u=!1,aa=!1,d=!1,ba=null;
a.sm.loadShape(17);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(17)))if(this.setShapeProperty(17,"init",null),1==this.slen)this.setShapeProperty(17,"thisID",null);else{for(var e=1;e<this.slen;++e){c=b=null;switch(this.getToken(e).tok){case 1073742327:b="all";d=!0;break;case 1073742335:b="on";break;case 1073742334:b="off";break;case 12291:b="delete";break;case 2:case 3:b="value";c=Float.$valueOf(this.floatParameter(e));break;case 10:10==this.tokAt(e+1)?this.setShapeProperty(17,"startSet",this.atomExpressionAt(e++)):
b="atomBitset";case 1073742325:null==b&&(b=g||u?"endSet":"startSet");c=ba=this.atomExpressionAt(e);e=a.iToken;0==this.tokAt(e+1)&&"startSet"===b&&(b="atomBitset");d=g=!0;break;case 1073742332:case 8:c=this.getPoint3f(e,!0);e=a.iToken;b=g||u?"endCoord":"startCoord";u=!0;break;case 1677721602:b="bonds";d=!0;break;case 4102:d=!0;b="calculate";a.isAtomExpression(e+1)&&(c=ba=this.atomExpressionAt(++e),e=a.iToken);break;case 1073741974:this.setShapeId(17,++e,aa);e=a.iToken;break;case 1275069442:b="cross";
c=Boolean.TRUE;break;case 1073742040:b="cross";c=Boolean.FALSE;break;case 1073742066:this.isFloatParameter(e+1)?(c=this.floatParameter(++e),2==a.theTok?(b="offsetPercent",c=Integer.$valueOf(w(c))):(b="offset",c=Float.$valueOf(c))):(b="offsetPt",c=this.centerParameter(++e),e=a.iToken);break;case 1073742068:b="offsetSide";c=Float.$valueOf(this.floatParameter(++e));break;case 1073742188:b="value";c=Float.$valueOf(this.floatParameter(++e));break;case 1073742196:b="width";c=Float.$valueOf(this.floatParameter(++e));
break;default:if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(17,e,aa);e=a.iToken;break}this.invArg()}aa=12291!=a.theTok&&4102!=a.theTok;d&&(this.chk||a.getPartialCharges(ba),d=!1);null!=b&&this.setShapeProperty(17,b,c)}(u||g)&&this.setShapeProperty(17,"set",null)}});e(d,"draw",function(){var a=this.e;a.sm.loadShape(22);switch(this.tokAt(1)){case 1073742001:if(this.listIsosurface(22))return;break;case 136314895:case 134221850:case 4138:this.e.getCmdExt().dispatch(4133,!1,
this.st);return}for(var b=!1,c=!1,g=!1,u=!1,aa=!1,d=0,e,k=null,l=0,n=3.4028235E38,f=r(-1,[-2147483648]),q=0,S="",v=0,ka=null,j=this.initIsosurface(22),t=(e=null!=j)&&null==this.getShapeProperty(22,"ID"),sa=null,Q=0,Ha=-1,E=-1,M=!1,G=!1,D=!1,L=!1,A=0,K=null,P=null,p=a.iToken;p<this.slen;++p){var F=null,H=null,A=this.getToken(p).tok;switch(A){case 134217763:switch(A=this.getToken(p+(1073741864==this.tokAt(p+1)?2:1)).tok){case 1814695966:case 1812599299:l=A;u=!0;continue;case 1073742330:++p;F="intersect";
H=a.objectNameParameter(++p);b=u=!0;break;default:this.invArg()}break;case 1073741864:M=!0;E==p-1&&E++;switch(this.tokAt(p+1)){case 134217750:case 1073741998:case 1812599299:continue;default:this.invArg()}break;case 1611272194:this.chk||this.vwr.getModelkit(!1).drawAxes(null,j,S);return;case 1073741994:case 1814695966:case 1812599299:var Y=K=null;e=null;switch(A){case 1812599299:switch(this.tokAt(p+1)){case 1073741864:switch(this.tokAt(p+2)){case 134217750:case 1073741998:break;case 1073742330:M=
y(-1,[a.objectNameParameter(p+3),null]);if(this.chk)return;this.vwr.shm.getShapePropertyData(24,"points",M);k=M[1];null==k&&this.invArg();p+=2;default:M=!0,p++}break;case 10:case 1073742325:e=a.getAtomsStartingAt(p+1),p=a.iToken}break;case 1814695966:M&&this.invArg();L=!0;if(a.isArrayParameter(p+1)){var W=a.getPointArray(p+1,-1,!1,!0),p=a.iToken;this.chk||(P=this.vwr.getSymTemp().getUnitCell(W,!1,null))}else switch(this.tokAt(p+1)){case 4:W=this.stringParameter(p+1).toLowerCase();p=a.iToken;W.startsWith("unitcell_")&&
(W=this.vwr.getCurrentModelAuxInfo().get(W));if(!this.chk&&0<W.length&&null!=(P=this.vwr.getCurrentUnitCell()))P=this.vwr.getSymTemp().getUnitCell(P.getV0abc(W,null),!1,"draw");break;case 8:case 1073742332:Y=a.getFractionalPoint(p+1),p=a.iToken}1073741994==this.tokAt(p+1)&&(1814695966==l&&(l=1073741994),++p,K=a.checkHKL(a.getPointOrPlane(++p,3)),p=a.iToken);1611272194==this.tokAt(p+1)&&(D=!0,null==P&&null==Y&&(Y=JU.P3.new3(555,555,1)),p++)}if(this.chk)break;if(null!=e)M&&(P=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,
"array",e,null),!1,null));else if(M)P=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientation(1814695966,"array",null,k),!1,null);else if(1814695966==A&&null==P){if(null!=Y){this.vwr.getModelkit(!1).drawUnitCell(j,Y,S);return}P=this.vwr.getCurrentUnitCell()}if(null==K){k=null;if(null==P&&1073742330==this.tokAt(p+1)&&(++p,k=this.e.objectNameParameter(++p),p=this.e.iToken,null==k||this.chk))return;k=this.getBoxPoints(null!=P?1814695966:A,P,e,k,q/100);if(null==k)return}else{e=JU.Measure.getLatticePoints(P.getLatticeCentering(),
w(K.x),w(K.y),w(K.z));k=Array(e.size());for(A=0;A<e.size();A++)k[A]=e.get(A),P.toCartesian(k[A],!0)}M=!1;if(!u){F="polygon";e=new JU.Lst;e.addLast(k);if(null==K){this.vwr.getTriangulator();var V;switch(null==P?7:P.getPeriodicity()){case 1:V=JU.Triangulator.edgeA;break;case 2:V=JU.Triangulator.edgeB;break;case 4:V=JU.Triangulator.edgeC;break;case 3:V=JU.Triangulator.abFace;break;default:case 7:V=JU.Triangulator.fullCubePolygon}e.addLast(V)}else e.addLast(null);H=e;b=!0;q=0;G=!0;break}1073742335==this.tokAt(p+
1)&&(E=++p);break;case 1073741998:case 134219777:case 134217750:Y=E==p-1;if(!b&&!u&&0==l){if(134219777==a.theTok){b=!0;this.setShapeProperty(22,"plane",null);A=new JU.Lst;a.hklParameter(++p,A,!0);p=a.iToken;F="coords";H=A;break}if(!M){F=134217750==A?"plane":"line";Ha=p+1;break}!this.chk&&(1073741998!=A&&null==k)&&(P=this.vwr.getCurrentUnitCell(),l=null==P?1812599299:1814695966,k=this.getBoxPoints(l,P,null,null,q/100),u=!0)}K=e=null;W=!1;switch(A){case 134217750:e=a.planeParameter(p,M);break;case 134219777:e=
a.hklParameter(++p,null,!0);1073742327==this.tokAt(a.iToken+1)&&(W=!0,a.iToken++);break;case 1073741998:1073741994==l&&this.invArg(),K=M?this.bsToArray(a.getAtomsStartingAt(++p)):a.isCenterParameter(p+1)?y(-1,[this.centerParameter(++p),this.centerParameter(a.iToken+1)]):a.getPointArray(++p,2,!1,!0),2>K.length&&this.invArg()}p=a.iToken;b=!0;if(this.chk)break;if(1073741998==A){K=JU.Measure.getBestLineThroughPoints(K,-1);if(0!=l&&(e=JU.V3.newVsub(K[1],K[0]),e.scale(1/e.length()),K=Y?JU.Measure.getProjectedLineSegment(k,
-1,K[0],e,null):this.vwr.getTriangulator().intersectLine(k,-1,K[0],e),null==K||null==K[1]))return;c||(this.setShapeProperty(22,"points",Integer.$valueOf(q)),c=!0);A=new JU.Lst;A.addLast(K[0]);A.addLast(K[1]);this.setShapeProperty(22,"coords",A);break}0==l?(H=e,F="planedef"):(1073741994==l?(F="polygon",e=JU.Measure.getPointsOnPlane(k,e),k=e.toArray(Array(e.size())),e=new JU.Lst,e.addLast(k),e.addLast(null),H=e):(W&&1814695966==l&&J.api.Interface.getInterface("JU.BZone",this.vwr,"script").drawHKL(this.vwr,
j,e,k),F="polygon",H=this.vwr.getTriangulator().intersectPlane(e,k,Y?-1:0)),q=0);break;case 1275068447:k=a.isArrayParameter(++p)?a.getPointArray(p,-1,!1,!0):null;null==k&&a.isAtomExpression(p)&&(e=a.atomExpressionAt(p),k=this.vwr.ms.getAtomPointVector(e).toArray(Array(e.cardinality())));null!=k&&(p=a.iToken+1,12289==this.tokAt(p)&&(ka=a.centerParameter(++p,null),p=a.iToken+1));switch(this.tokAt(p)){case 536875059:c="";break;case 1111490563:c="Cs";break;case 1073742330:M=y(-1,[a.objectNameParameter(++p),
null]);if(this.chk)return;this.vwr.shm.getShapePropertyData(21,"points",M);k=M[1];null==k&&this.invArg();c="";break;case 1275203608:c=":poly";break;case 134217764:null==ka&&(ka=new JU.P3);c=this.vwr.ms.generateCrystalClass(this.vwr.bsA().nextSetBit(0),JU.P3.new3(NaN,NaN,NaN));null!=k&&this.invArg();k=Array(c.size());for(A=c.size();0<=--A;)k[A]=c.get(A);p++;c="";break;default:c=a.optParameterAsString(p)}q=0==q?1:q/100;g=0;0<c.length&&this.isFloatParameter(++p)&&(g=this.intParameter(p++));536875059==
this.tokAt(p)&&(q=this.floatParameter(++p));this.chk||a.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),0<c.length?c:null,g,q,k,ka,null==j?"":j));return;case 4106:sa=r(4,0);Q=4;b=a.floatParameterSet(++p,4,4);p=a.iToken;for(A=0;4>A;A++)sa[A]=w(b[A]);b=!0;break;case 1677721602:case 1153433601:if(null==sa||Q>(1228931586==a.theTok?2:3))Q=0,sa=r(-1,[-1,-1,-1,-1]);sa[Q++]=this.atomExpressionAt(++p).nextSetBit(0);p=a.iToken;sa[Q++]=1677721602==a.theTok?this.atomExpressionAt(++p).nextSetBit(0):
-1;p=a.iToken;b=!0;break;case 554176565:switch(this.getToken(++p).tok){case 1073742330:F="slab";H=a.objectNameParameter(++p);p=a.iToken;b=!0;break;default:this.invArg()}break;case 1275203608:case 134217751:case 1073742106:K=134217751==A;F="polygon";b=!0;e=new JU.Lst;var H=V=0,C=W=Y=null;if(a.isArrayParameter(++p)){Y=a.getPointArray(p,-1,!0,!0);if(0<Y.length&&null==Y[0]){1275203608==A?V=this.getIntArray2(p):(V=JU.AU.newInt2(1),V[0]=a.expandFloatArray(a.floatParameterSet(p,-1,2147483647),-1,!1));Y=
this.getAllPoints(this.e.iToken+1,3);try{C=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulateFaces(V,Y,null)}catch(N){this.invArg()}}V=Y.length}1275203608==A&&(V=Y.length);if(null==Y){V=Math.max(0,this.intParameter(p));Y=Array(V);for(A=0;A<V;A++)Y[A]=this.centerParameter(++a.iToken)}p=a.iToken;switch(this.tokAt(p+1)){case 11:case 12:W=JS.SV.newT(this.getToken(++p)).toArray().getList();H=W.size();break;case 7:W=this.getToken(++p).getList();H=W.size();break;case 2:H=
this.intParameter(++p);0>H&&(K=!0);break;default:null==C&&(!K&&!this.chk)&&(C=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulatePolygon(Y,-1))}if(null==C&&!K){C=JU.AU.newInt2(H);for(A=0;A<H;A++)K=null==W?a.floatParameterSet(++a.iToken,3,4):JS.SV.flistValue(W.get(A),0),(3>K.length||4<K.length)&&this.invArg(),C[A]=r(-1,[w(K[0]),w(K[1]),w(K[2]),3==K.length?7:w(K[3])])}0<V?(e.addLast(Y),e.addLast(C)):e=null;H=e;p=a.iToken;break;case 134217764:case 1296041986:case 1296041985:k=
null;c=2147483647;u=g=null;aa=0;l=d=null;n=1296041986==A;f=1296041985==A;v=-1;t=y(-1,[null,this.vwr.getVisibleFrameAtomsNoSplitData()]);sa=!1;if(n||f)switch(c=0,this.tokAt(++p)){case 4:k=this.stringParameter(p);break;case 12:k=this.vwr.getSymStatic().convertTransform("xyz",this.getToken(p).value);break;default:if(!a.isCenterParameter(p))if(a.isArrayParameter(p)){p=a.floatParameterSet(p,1,2147483647);l=r(p.length,0);for(A=l.length;0<=--A;)l[A]=w(p[A]);p=a.iToken+1}else c=this.intParameter(p++),a.isArrayParameter(p)&&
(d=JU.P3.newA(a.floatParameterSet(p,3,3)),p=a.iToken+1);a.isCenterParameter(p)&&(ka=a.centerParameter(p,t));null==l&&a.isCenterParameter(a.iToken+1)&&(g=a.centerParameter(++a.iToken,t));if(this.chk)return;p=a.iToken;sa=!0}else 1073742327==this.tokAt(p+1)?(v=-2,a.iToken=++p):sa=!0;sa&&(null==ka&&a.isCenterParameter(p+1)&&(ka=this.centerParameter(++p),u=a.isAtomExpression(p)?this.atomExpressionAt(p):null,p=a.iToken),v=(!n&&!f&&null!=ka||null!=g)&&2==this.tokAt(p+1)?a.getToken(++p).intValue:-1,-1>v&&
this.invArg(),n?1814695966==this.tokAt(p+1)?(g=new JU.P3,aa=1073742066,a.iToken=++p):1073742066==this.tokAt(p+1)&&(p++,g=this.getPoint3f(p+1,!1),aa=1073742066,p=a.iToken):f&&(aa=1296041985));if((n||f)&&null!=k)p++,a.isCenterParameter(p)&&(ka=a.centerParameter(p,t));a.checkLast(a.iToken);if(this.chk)return;p="";t=null!=u?u.nextSetBit(0):-1;null==u&&0<=this.vwr.am.cmi&&(u=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi));if(null!=u){p=this.vwr.getModelkit(!1).drawSymmetry(j,n,t,k,c,d,ka,g,q,v,
aa,l,!1);if(null==p)return;if((n||f)&&$(g,"JM.Atom")&&$(ka,"JM.Atom"))0<=a.fullCommand.indexOf("#quiet")&&(p=JU.PT.rep(p,"print","#print")),p+="\nmodelkit set atomset "+JU.PT.esc(j+"|"+ka.i+"|"+g.i+"|"+a.fullCommand)+";"}a.runBufferedSafely(0<p.length?p:'draw ID "'+j+'*" delete',a.outputBuffer);return;case 4115:aa=!0;continue;case 1073742332:case 9:case 8:if(9==a.theTok||!a.isPoint3f(p)){H=a.getPoint4f(p);if(aa){a.checkLast(a.iToken);this.chk||a.runScript(JU.Escape.drawQuat(JU.Quat.newP4(H),null==
j?"frame":j," "+S,null==ka?new JU.P3:ka,q/100));return}F="planedef"}else H=ka=this.getPoint3f(p,!0),F="coord";p=a.iToken;b=!0;break;case 1073742E3:F="lineData";H=a.floatParameterSet(++p,0,2147483647);p=a.iToken;b=!0;break;case 12290:case 10:case 1073742325:F="atomSet";H=this.atomExpressionAt(p);aa&&(ka=this.centerParameter(p));p=a.iToken;b=!0;break;case 7:b=!0;F=Ha==p?"coords":"modelBasedPoints";H=a.theToken.value;break;case 1073742195:case 268436992:break;case 268437504:H=a.xypParameter(p);if(null!=
H){p=a.iToken;F="coord";b=!0;break}g&&this.invArg();g=!0;break;case 268437505:g||this.invArg();g=!1;break;case 1140850693:F="reverse";break;case 1073742166:if(1765808134==this.tokAt(++p)){H=Integer.$valueOf(this.e.getArgbParamOrNone(++p,!1));F="titlecolor";p=this.e.iToken;break}if(4114==this.tokAt(p)){--p;continue}case 4:H=this.stringParameter(p);F="title";break;case 545259562:H=this.stringParameter(++p);F="hoverlabel";break;case 4114:A=this.floatParameter(++p);H=1073741824==this.tokAt(p+1)?this.paramAsStr(++p):
null;e=1073741824==this.tokAt(p+1)?this.paramAsStr(++p):null;(4!=this.tokAt(p+1)&&++p!=this.slen||0>=A||255<A)&&this.invArg();F="myfont";if(null==H||null==e)K=this.vwr.shm.getShapePropertyIndex(22,"font",-1),null==H&&(H=K.fontFace),null==e&&(e=K.fontStyle);H=this.vwr.getFont3D(H,e,A);break;case 135198:F="vector";break;case 1275068435:H=Float.$valueOf(this.floatParameter(++p));F="length";break;case 3:H=Float.$valueOf(this.floatParameter(p));F="length";break;case 1094717454:F="imodel";H=Integer.$valueOf(this.intParameter(++p));
d=p;break;case 1094713359:F="modelIndex";H=Integer.$valueOf(this.intParameter(++p));break;case 2:g?(F="modelIndex",H=Integer.$valueOf(this.intParameter(p))):q=this.intParameter(p);break;case 536875059:q=Math.round(this.floatParameter(++p)*(2==this.getToken(p).tok?1:100));continue;case 1073741974:j=this.setShapeId(22,++p,e);t=null==this.getShapeProperty(22,"ID");p=a.iToken;break;case 1073742027:F="fixed";H=Boolean.FALSE;break;case 12293:F="fixed";H=Boolean.TRUE;break;case 1073742066:A=this.getPoint3f(++p,
!0);p=a.iToken;F="offset";H=A;break;case 1073741906:F="crossed";break;case 1073742196:H=Float.$valueOf(this.floatParameter(++p));F="width";S=F+" "+H;break;case 1073741908:F="curve";Ha=p+1;break;case 1073741840:F="arc";Ha=p+1;break;case 1073741846:F="arrow";Ha=p+1;break;case 1073742194:F="vertices";Ha=p+1;break;case 1073741880:F="circle";break;case 1073741912:F="cylinder";break;case 1073742048:F="nohead";break;case 1073741860:F="isbarb";break;case 1073742130:F="rotate45";break;case 1073742092:F="perp";
break;case 1665140738:case 1073741917:S=1665140738==a.theTok;K=this.floatParameter(++p);S&&(K*=2);H=Float.$valueOf(K);F=S||3==this.tokAt(p)?"width":"diameter";S=F+(3==this.tokAt(p)?" "+K:" "+w(K));break;case 1073742330:if(268437504==this.tokAt(p+2)||aa){b=ka=this.centerParameter(p);p=a.iToken;F="coord";H=b;b=!0;break}H=a.objectNameParameter(++p);F="identifier";b=!0;break;case 1765808134:case 1111490588:case 1073742074:e=!0;n=this.getColorTrans(a,p,!1,f);p=a.iToken;continue;default:if(!a.setMeshDisplayProperty(22,
0,a.theTok)){if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){j=this.setShapeId(22,p,e);p=a.iToken;break}this.invArg()}0==v&&(v=p);p=a.iToken;continue}e=12291!=a.theTok&&(2<p||p>d);b&&(!c&&!aa)&&(this.setShapeProperty(22,"points",Integer.$valueOf(q)),c=!0,q=0);b&&t&&this.invArg();if(null!=F){if(""===S){A=0;switch(F){case "vector":A=0.1;break;case "line":A=0.05}0!=A&&(S="width "+A,this.setShapeProperty(22,"width",Float.$valueOf(A)))}this.setShapeProperty(22,F,H)}}G&&(v=-1-v);this.chk||(this.finalizeObject(22,
f[0],n,q,b,sa,v,null),L&&(null==j&&(M=Array(1),this.vwr.shm.getShapePropertyData(22,"id",M),j=M[0],A=j.indexOf("_"),0<=A&&(j=j.substring(0,A))),this.vwr.getModelkit(!1).drawAxes(k,j,D?S:"delete")))});e(d,"mo",function(a,b){var c=this.e,g=2147483647,u=!1,d=null,h=this.vwr.getVisibleFramesBitSet(),e=new JU.Lst,k=!1,l=1073877011==this.tokAt(0),n=1;if(l){var f=this.e.optParameterAsString(1).equals("view");if(1==this.e.slen||f||this.e.optParameterAsString(1).equals("options")){this.chk||(c=f?"VIEW":this.e.optParameterAsString(2),
this.vwr.plugin("NBO","start",c));return}}if(1094717454==this.tokAt(1)||4115==this.tokAt(1))n=c.modelNumberParameter(2),0>n&&this.invArg(),h.clearAll(),h.set(n),n=3;c.sm.loadShape(b);for(f=h.nextSetBit(0);0<=f;f=h.nextSetBit(f+1)){var q=n;if(1073742001==this.tokAt(q)&&this.listIsosurface(b))break;this.setShapeProperty(b,"init",Integer.$valueOf(f));if(a)break;var S=null,v=this.getShapeProperty(b,"moNumber").intValue(),j=this.getShapeProperty(b,"moLinearCombination"),r=this.getShapeProperty(b,"moSquareData"),
y=null==j?null:this.getShapeProperty(b,"moSquareLinear");0==v&&(v=2147483647);var w=null,Q=null,D=!1,E=null,M=null;switch(this.getToken(q).tok){case 1275082241:w="select";M=this.atomExpressionAt(++q);JU.BSUtil.andNot(M,this.vwr.slm.bsDeleted);Q=M;break;case 1140850696:if(1073877010==b){this.mo(a,28);return}d=this.paramAsStr(++q).toUpperCase();4==c.tokAt(q+1)&&(E=this.paramAsStr(++c.iToken));break;case 1073741875:case 554176565:w=c.theToken.value;Q=this.getCapSlabObject(q,!1);break;case 1073741914:y=
Boolean.TRUE;j=t(-1,[1]);g=v=0;break;case 2:v=this.intParameter(q);1073741865==this.tokAt(q+1)&&(k=!0);j=this.moCombo(e);null==j&&0>v&&(j=t(-1,[-100,-v]));D=!0;break;case 268440576:switch(this.tokAt(++q)){case 1073741973:case 1073742008:break;default:this.invArg()}u=!0;case 1073741973:case 1073742008:2147483647==(g=this.moOffset(q))&&this.invArg();v=0;j=this.moCombo(e);D=!0;break;case 1073742037:v=1073742037;k=!1;j=this.moCombo(e);D=!0;break;case 1073742108:v=1073742108;k=!1;j=this.moCombo(e);D=!0;
break;case 1765808134:this.setColorOptions(null,q+1,b,2);break;case 134217750:w="plane";Q=1073742333==this.tokAt(this.e.iToken=++q)?null:c.planeParameter(q,!1);break;case 134217751:this.addShapeProperty(e,"randomSeed",2==this.tokAt(q+2)?Integer.$valueOf(this.intParameter(q+2)):null);w="monteCarloCount";Q=Integer.$valueOf(this.intParameter(q+1));break;case 536875059:w="scale";Q=Float.$valueOf(this.floatParameter(q+1));break;case 1073741910:268440577==this.tokAt(q+1)?(w="cutoffPositive",Q=Float.$valueOf(this.floatParameter(q+
2))):(w="cutoff",Q=Float.$valueOf(this.floatParameter(q+1)));break;case 536870916:w="debug";break;case 1073742054:w="plane";break;case 1073742104:case 1073742122:w="resolution";Q=Float.$valueOf(this.floatParameter(q+1));break;case 1073742156:null==j?r=Boolean.TRUE:y=Boolean.TRUE;D=!1;break;case 1073742168:q+1<this.slen&&4==this.tokAt(q+1)&&(w="titleFormat",Q=this.paramAsStr(q+1));break;case 1073741824:this.invArg();break;case 4:if(l&&1==q){E=c.stringParameter(q);break}default:l&&4==c.tokAt(q)&&(E=
this.paramAsStr(q++));if(c.isArrayParameter(q)){j=c.floatParameterSet(q,1,2147483647);1073742156==this.tokAt(c.iToken+1)&&(D=!1,y=Boolean.TRUE,c.iToken++);break}g=c.iToken;c.setMeshDisplayProperty(b,0,c.theTok)||this.invArg();this.setShapeProperty(b,"setProperties",e);c.setMeshDisplayProperty(b,g,this.tokAt(g));return}null!=w&&this.addShapeProperty(e,w,Q);q=2147483647!=v||null!=j;if(this.chk)break;if(null!=d||null!=E||q){q&&4==this.tokAt(c.iToken+1)&&(S=this.paramAsStr(++c.iToken));c.setCursorWait(!0);
if(null!=d||null!=E)d=d+":"+E;this.setMoData(e,v,j,g,u,f,S,d,k);q&&this.addShapeProperty(e,"finalize",null)}null==M&&null!=this.vwr.slm.bsDeleted&&(M=this.vwr.bsA(),this.addShapeProperty(e,"select",M));D||(this.setShapeProperty(b,"squareLinear",y),this.setShapeProperty(b,"squareData",r));0<e.size()&&this.setShapeProperty(b,"setProperties",e);q&&!c.tQuiet&&(S="",l?S=this.getShapeProperty(b,"moLabel"):(v=this.getShapeProperty(b,"moNumber").intValue(),S=""+v),this.showString(JS.T.nameOf(this.tokAt(0))+
" "+S+" "+(k?"beta ":"")+this.getShapeProperty(b,"message")));e.clear()}},"~B,~N");e(d,"setNBOType",function(a,b){var c=-1,g=null,u=b.indexOf(":");0<u&&(g=b.substring(u+1),b=b.substring(0,u),b.equals("null")&&(b=null),g.equals("null")&&(g=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 u=a.get("auxFiles"),d=this.vwr.getCurrentModelAuxInfo().get("auxFiles");null==d?this.vwr.getCurrentModelAuxInfo().put("auxFiles",u):d.addAll(u);if(null!=g){u=g.indexOf(".");0<u&&(d=JU.PT.parseInt(g.substring(u+1)),g=g.substring(0,u),u=d);for(var d=a.get("nboLabels"),h=0,e=d.length;h<e;h++)if(g.equals(d[h])&&(0>u||0==--u)){c=h+1;break}0>c&&this.error(27)}return c},"java.util.Map,~S");e(d,"moCombo",function(a){if(1073742156!=this.tokAt(this.e.iToken+1))return null;this.addShapeProperty(a,
"squareLinear",Boolean.TRUE);this.e.iToken++;return t(0,0)},"JU.Lst");e(d,"moOffset",function(a){var b=1073741973==this.getToken(a).tok?0:1,c=this.tokAt(++a);2==c&&"-"==this.e.st[a].value.charAt(0)?b+=this.intParameter(a):268440577==c?b+=this.intParameter(++a):268440576==c&&(b-=this.intParameter(++a));return b},"~N");e(d,"setMoData",function(a,b,c,g,u,d,h,e,k){var l=this.e;0>d&&(d=this.vwr.am.cmi,0>d&&l.errorStr(30,"MO isosurfaces"));var n=this.vwr.ms.getInfo(d,"moData");null==n&&this.error(27);this.vwr.checkMenuUpdate();
if(null!=e){var f=this.setNBOType(n,e),q=n.get("nboLabels").length;l.showString(q+" orbitals of type "+e.substring(0,e.indexOf(":")+1)+" modelIndex="+this.vwr.getModelNumberDotted(d));0<f&&(b=f);if(null==c&&2147483647==b)return}e=null;f=0;d=null;if(null==c||2>c.length){null!=c&&1==c.length?g=0:k&&n.containsKey("firstBeta")&&(g=n.get("firstBeta").intValue());e=n.containsKey("lastMoNumber")?n.get("lastMoNumber").intValue():0;f=n.containsKey("lastMoCount")?n.get("lastMoCount").intValue():1;1073742108==
b?b=e-1:1073742037==b&&(b=e+f);e=n.get("mos");f=null==e?0:e.size();0==f&&this.error(25);1==f&&1<b&&this.error(29);if(2147483647!=g){if(!k)if(n.containsKey("HOMO"))b=n.get("HOMO").intValue()+g,g=0;else{b=f;for(k=0;k<f;k++)if(q=e.get(k),null!=(d=q.get("occupancy"))){if(0.5>d.floatValue()){b=k;break}}else if(null!=(d=q.get("energy"))){if(0<d.floatValue()){b=k;break}}else break;null==d&&this.error(28)}b+=g;this.chk||JU.Logger.info("MO "+b)}(1>b||b>f)&&l.errorStr(26,""+f)}b=Math.abs(b);n.put("lastMoNumber",
Integer.$valueOf(b));n.put("lastMoCount",Integer.$valueOf(1));u&&null==c&&(c=t(-1,[-100,b]));if(null!=c&&2>c.length){q=e.get(b-1);if(null==(d=q.get("energy")))c=t(-1,[100,b]);else{l=d.floatValue();g=JU.BS.newN(f);u=0;c=1==c.length&&1==c[0];for(k=0;k<f;k++)if(null!=(d=e.get(k).get("energy")))if(d=d.floatValue(),c?d<=l:d==l)g.set(k+1),u+=2;c=t(u,0);for(l=k=0;k<u;k+=2)c[k]=1,c[k+1]=l=g.nextSetBit(l+1);n.put("lastMoNumber",Integer.$valueOf(g.nextSetBit(0)));n.put("lastMoCount",Integer.$valueOf(D(u/2)))}this.addShapeProperty(a,
"squareLinear",Boolean.TRUE)}this.addShapeProperty(a,"moData",n);null!=h&&this.addShapeProperty(a,"title",h);this.addShapeProperty(a,"molecularOrbital",null!=c?c:Integer.$valueOf(Math.abs(b)));this.addShapeProperty(a,"clear",null)},"JU.Lst,~N,~A,~N,~B,~N,~S,~S,~B");e(d,"isosurface",function(a){var b=this.e;b.sm.loadShape(a);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(a))){var c=0,g=!1,u=!1,d=24==a,h=29==a,e=30==a,k=26==a,l=k||12291==this.tokAt(1)||b.$isStateScript,f=!1,O=!1,q=!1,S=!1,v=!1,
j=!1,Da=!1,Db=!1,C=!1,Q=!1,L=!1,E=!1,M=!1,G=!1,N=!1,R=null,A=null,K=null,P,p,F,H,Y,W=NaN,V=NaN,da=0,fa=null,ia=2147483647,X=null,Z=null,la=null,s=new JU.SB,T,ja=null,va=null,xa=!1,ga=null,ta=0,oa=null,ca=this.chk?0:-2147483648;b.setCursorWait(!0);var Aa=null!=this.initIsosurface(a),wa=Aa&&null==this.getShapeProperty(a,"ID"),Ca=!1,lb=!1,Na=!1,Ka=!1,Oa=null,mb=null,nb=null,ra=null,ob=null,Ia=null,Pa=null,B=new JU.Lst,La=!1;(h||e)&&this.addShapeProperty(B,"fileType","Pmesh");for(var m=b.iToken;m<this.slen;++m){var z=
null,x=null,U=this.getToken(m).tok;1073741824==U&&(oa=this.paramAsStr(m),oa.equalsIgnoreCase("map")&&(U=4125));switch(U){case 1073742148:l=!0;s.append(" silent");z="silent";break;case 603979867:fa=1073742335==this.getToken(++m).tok?Boolean.TRUE:1073742334==b.theTok?Boolean.FALSE:null;null==fa&&this.invArg();continue;case 553648146:ia=this.intParameter(++m);continue;case 4128:z="moveIsosurface";12!=this.tokAt(++m)&&this.invArg();x=this.getToken(m++).value;break;case 1296041986:for(var Ma=this.floatArraySet(m+
2,this.intParameter(m+1),16),Ia=Array(Ma.length),ha=Ia.length;0<=--ha;)Ia[ha]=JU.M4.newA16(Ma[ha]);m=b.iToken;break;case 1088421903:0>ca&&(ca=Math.min(this.vwr.am.cmi,0));var Eb=null==la;null==Z&&(Z=JU.BSUtil.andNot(JU.BSUtil.copy(this.vwr.bsA()),this.vwr.slm.bsDeleted));Z.and(this.vwr.ms.getAtoms(1296041986,Integer.$valueOf(1)));Eb||Z.andNot(la);this.addShapeProperty(B,"select",Z);Eb&&(la=JU.BSUtil.copy(Z),JU.BSUtil.invertInPlace(la,this.vwr.ms.ac),N=!0,this.addShapeProperty(B,"ignore",la),s.append(" ignore ").append(JU.Escape.eBS(la)));
s.append(" symmetry");0==ta&&this.addShapeProperty(B,"colorRGB",Integer.$valueOf(1296041986));Ia=this.vwr.ms.getSymMatrices(ca);break;case 1073742066:z="offset";x=this.centerParameter(++m);m=b.iToken;break;case 528432:z="rotate";x=1073742333==this.tokAt(b.iToken=++m)?null:b.getPoint4f(m);m=b.iToken;break;case 1610612740:z="scale3d";x=Float.$valueOf(this.floatParameter(++m));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(++m);s.append(" ").append(JU.Escape.eP(x));m=b.iToken;break;case 1812599299:if(0<=b.fullCommand.indexOf("# BBOX="))var Fb=JU.PT.split(JU.PT.getQuotedAttribute(b.fullCommand,"# BBOX"),","),ga=y(-1,[JU.Escape.uP(Fb[0]),JU.Escape.uP(Fb[1])]);else b.isCenterParameter(m+1)?(ga=y(-1,[this.getPoint3f(m+1,!0),this.getPoint3f(b.iToken+1,!0)]),m=b.iToken):ga=this.vwr.ms.getBBoxVertices();s.append(" boundBox "+JU.Escape.eP(ga[0])+" "+JU.Escape.eP(ga[ga.length-
1]));z="boundingBox";x=ga;break;case 135188:h=!0;s.append(" pmesh");z="fileType";x="Pmesh";break;case 134217763:Z=JU.BSUtil.andNot(this.atomExpressionAt(++m),this.vwr.slm.bsDeleted);this.chk?X=new JU.BS:1073742325==this.tokAt(b.iToken+1)||10==this.tokAt(b.iToken+1)?(X=JU.BSUtil.andNot(this.atomExpressionAt(++b.iToken),this.vwr.slm.bsDeleted),X.and(this.vwr.ms.getAtomsWithinRadius(5,Z,!1,null,null))):(X=this.vwr.ms.getAtomsWithinRadius(5,Z,!0,null,null),X.andNot(this.vwr.ms.getAtoms(1094713360,Z)));
X.andNot(Z);s.append(" intersection ").append(JU.Escape.eBS(Z)).append(" ").append(JU.Escape.eBS(X));m=b.iToken;if(134320141==this.tokAt(m+1)){m++;var Qa=this.getToken(++m).value;s.append(" function ").append(JU.PT.esc(Qa));this.chk||this.addShapeProperty(B,"func",Qa.equals("a+b")||Qa.equals("a-b")?Qa:this.createFunction("__iso__","a,b",Qa))}else G=!0;z="intersection";x=y(-1,[Z,X]);break;case 1610625028:case 134217759:if(g=1610625028==U){s.append(" display");c=m;U=this.tokAt(m+1);if(0==U)continue;
m++;this.addShapeProperty(B,"token",Integer.$valueOf(1073742335));if(10==U||1073742327==U){z="bsDisplay";1073742327==U?s.append(" all"):(x=this.st[m].value,s.append(" ").append(JU.Escape.eBS(x)));b.checkLast(m);break}else 134217759!=U&&(b.iToken=m,this.invArg())}else da=m;var Za,Ea=null,X=null,$a=Array(1);1073742325==this.tokAt(m+1)?(Za=this.floatParameter(m+3),b.isPoint3f(m+4)?(Ea=b.centerParameter(m+4,null),b.iToken+=2):b.isPoint3f(m+5)?(Ea=b.centerParameter(m+5,null),b.iToken+=2):(X=b.atomExpression(this.st,
m+5,this.slen,!0,!1,$a,!0),null==X&&this.invArg())):(Za=this.floatParameter(++m),Ea=b.centerParameter(++m,$a),X=$($a[0],"JU.BS")?$a[0]:null);g&&b.checkLast(b.iToken);m=b.iToken;0<=b.fullCommand.indexOf("# WITHIN=")&&(X=JU.BS.unescape(JU.PT.getQuotedAttribute(b.fullCommand,"# WITHIN")));this.chk||(null!=X&&0<=ca&&(X=this.vwr.restrictToModel(X,ca)),null==Ea&&(Ea=null==X?new JU.P3:this.vwr.ms.getAtomSetCenter(X)),ga=this.getWithinDistanceVector(B,Za,Ea,X,g),s.append(" within ").appendF(Za).append(" ").append(null==
X?JU.Escape.eP(Ea):JU.Escape.eBS(X)));continue;case 1073742083:var z="parameters",Gb=b.floatParameterSet(++m,1,10),m=b.iToken,x=Gb;s.append(" parameters ").append(JU.Escape.eAF(Gb));break;case 1715472409:case 1073742190:var Oa=b.theToken.value,jb=1073742190==U,Ra=this.tokAt(m+1);null==ob?(!f&&(!q&&!O)&&(this.addShapeProperty(B,"sasurface",Float.$valueOf(0)),s.append(" vdw"),f=!0),z="property",null==fa&&(fa=JS.T.tokAttr(Ra,1111490560)&&1==this.vwr.getIsosurfacePropertySmoothing(!1)?Boolean.TRUE:Boolean.FALSE),
this.addShapeProperty(B,"propertySmoothing",fa),s.append(" isosurfacePropertySmoothing "+fa),fa===Boolean.TRUE&&(2147483647==ia&&(ia=this.vwr.getIsosurfacePropertySmoothing(!0)),this.addShapeProperty(B,"propertySmoothingPower",Integer.$valueOf(ia)),s.append(" isosurfacePropertySmoothingPower "+ia)),this.vwr.g.rangeSelected&&this.addShapeProperty(B,"rangeSelected",Boolean.TRUE)):z=ob;oa=this.paramAsStr(m);s.append(" ").append(oa);if(0==oa.toLowerCase().indexOf("property_")){A=t(this.vwr.ms.ac,0);if(this.chk)continue;
A=this.vwr.getDataObj(oa,null,1);null==A&&this.invArg();this.addShapeProperty(B,z,A);continue}var Sa=this.vwr.ms.ac,A=t(Sa,0);if(jb){var Hb=this.paramAsStr(++m);0==Hb.length?A=b.floatParameterSet(m,Sa,Sa):(A=t(Sa,0),this.chk||JU.Parser.parseStringInfestedFloatArray(""+b.getParameter(Hb,4,!0),null,A));this.chk||s.append(' "" ').append(JU.Escape.eAF(A))}else{this.getToken(++m);if(!this.chk){s.append(" "+b.theToken.value);var kb=this.vwr.ms.at;this.vwr.autoCalculate(Ra,null);if(1765808134!=Ra){T=new JU.P3;
for(var pb=Sa;0<=--pb;)A[pb]=kb[pb].atomPropertyFloat(this.vwr,Ra,T)}}1765808134==Ra&&(ra="inherit");if(134217759==this.tokAt(m+1)){var Ib=this.floatParameter(m+=2);s.append(" within "+Ib);this.addShapeProperty(B,"propertyDistanceMax",Float.$valueOf(Ib))}}x=A;break;case 1094713359:case 1094717454:f&&this.invArg();ca=1094713359==U?this.intParameter(++m):b.modelNumberParameter(++m);s.append(" modelIndex "+ca);if(0>ca){z="fixed";x=Boolean.TRUE;break}z="modelIndex";x=Integer.$valueOf(ca);break;case 1275082241:var z=
"select",ab=this.atomExpressionAt(++m);JU.BSUtil.andNot(ab,this.vwr.slm.bsDeleted);x=ab;m=b.iToken;1073742072==this.tokAt(m+1)&&(m++,la=JU.BSUtil.copy(ab),JU.BSUtil.invertInPlace(la,this.vwr.ms.ac),this.addShapeProperty(B,"ignore",la),s.append(" ignore ").append(JU.Escape.eBS(la)),N=!0);f||q?s.append(" select "+JU.Escape.eBS(ab)):(Z=JU.BSUtil.andNot(x,this.vwr.slm.bsDeleted),0>ca&&0<=Z.nextSetBit(0)&&(ca=this.vwr.ms.at[Z.nextSetBit(0)].mi));break;case 2109448:K=10==b.getToken(++m).tok?b.theToken.value:
b.expandFloatArray(b.floatParameterSet(m,1,2147483647),1,!0);m=b.iToken;break;case 36867:var Jb=this.intParameter(++m),K=0<Jb?JU.BSUtil.newAndSetBit(Jb-1):new JU.BS;break;case 12289:z="center";x=this.centerParameter(++m);s.append(" center "+JU.Escape.eP(x));m=b.iToken;break;case 1073742147:case 1765808134:Aa=!0;if(1073742147==U)Na=!0,s.append(" sign"),this.addShapeProperty(B,"sign",Boolean.TRUE);else{if(1073741914==this.tokAt(m+1)){m++;z="colorDensity";s.append(" color density");Ka=!0;if(this.isFloatParameter(m+
1)){var Kb=this.floatParameter(++m);s.append(" "+Kb);x=Float.$valueOf(Kb)}break}if(4==this.getToken(m+1).tok)ra=this.paramAsStr(++m),0<ra.indexOf(" ")&&(Pa=JU.C.getColixArray(ra),null==Pa&&this.error(4));else if(1073742018==b.theTok){m++;s.append(" color mesh");ta=b.getArgbParam(++m);this.addShapeProperty(B,"meshcolor",Integer.$valueOf(ta));s.append(" ").append(JU.Escape.escapeColor(ta));m=b.iToken;continue}if(1111490588==(b.theTok=this.tokAt(m+1))||1073742074==b.theTok){s.append(" color");nb=this.setColorOptions(s,
m+1,24,-2);m=b.iToken;continue}switch(this.tokAt(m+1)){case 1073741826:case 1073742114:this.getToken(++m);s.append(" color range");this.addShapeProperty(B,"rangeAll",null);if(1073742327==this.tokAt(m+1)){m++;s.append(" all");continue}var Lb=this.floatParameter(++m),Mb=this.floatParameter(++m);this.addShapeProperty(B,"red",Float.$valueOf(Lb));this.addShapeProperty(B,"blue",Float.$valueOf(Mb));s.append(" ").appendF(Lb).append(" ").appendF(Mb);continue}if(b.isColorParam(m+1)&&(ta=b.getArgbParam(m+1),
1073742170==this.tokAt(m+2))){ra=b.getColorRange(m+1);m=b.iToken;break}s.append(" color")}b.isColorParam(m+1)?(ta=b.getArgbParam(++m),s.append(" ").append(JU.Escape.escapeColor(ta)),m=b.iToken,this.addShapeProperty(B,"colorRGB",Integer.$valueOf(ta)),Aa=!0,b.isColorParam(m+1)?(ta=b.getArgbParam(++m),m=b.iToken,this.addShapeProperty(B,"colorRGB",Integer.$valueOf(ta)),s.append(" ").append(JU.Escape.escapeColor(ta)),S=!0):Na&&this.invPO()):!Na&&(null==Pa&&null==ra)&&this.invPO();continue;case 134221829:d||
this.invArg();L=!this.chk;continue;case 1228935687:4!=this.tokAt(m+1)&&this.invPO();continue;case 1111492618:case 1648363544:s.append(" ").appendO(b.theToken.value);var Ta=b.encodeRadiusParameter(m,!1,!0);if(null==Ta)return;s.append(" ").appendO(Ta);Float.isNaN(Ta.value)&&(Ta.value=100);x=Ta;z="radius";Q=!0;q&&(f=!1);m=b.iToken;break;case 1073741864:u=!0;continue;case 134217750:O=!0;z="plane";x=b.planeParameter(m,u);m=b.iToken;s.append(" plane ").append(JU.Escape.eP4(x));break;case 536875059:z="scale";
x=Float.$valueOf(this.floatParameter(++m));s.append(" scale ").appendO(x);break;case 1073742327:Aa&&this.invArg();z="thisID";break;case 1112150020:f=!0;++m;x=b.getPoint4f(m);z="ellipsoid";m=b.iToken;s.append(" ellipsoid ").append(JU.Escape.eP4(x));break;case 134219777:O=!0;z="plane";x=b.hklParameter(++m,null,!0);m=b.iToken;s.append(" plane ").append(JU.Escape.eP4(x));break;case 135182:var f=!0,bb=this.paramAsStr(++m);this.addShapeProperty(B,"lcaoType",bb);s.append(" lcaocartoon ").append(JU.PT.esc(bb));
switch(this.getToken(++m).tok){case 12290:case 10:case 1073742325:z="lcaoCartoon";X=this.atomExpressionAt(m);m=b.iToken;if(this.chk)continue;var Ua=X.nextSetBit(0);0>Ua&&this.error(14);s.append(" ({").appendI(Ua).append("})");ca=this.vwr.ms.at[Ua].mi;this.addShapeProperty(B,"modelIndex",Integer.$valueOf(ca));var qb=y(-1,[new JU.V3,new JU.V3,JU.V3.newV(this.vwr.ms.at[Ua]),new JU.V3]);if(!bb.equalsIgnoreCase("s")&&null==this.vwr.getHybridizationAndAxes(Ua,qb[0],qb[1],bb))return;x=qb;break;default:this.error(14)}break;
case 1073877011:R=this.paramAsStr(++m).toUpperCase(),s.append(" nbo ").append(R).append(" ");case 1073877010:null==R&&s.append(" mo ");var Va=2147483647,Ja=2147483647,rb=268440576==this.tokAt(m+1);rb&&m++;var Wa=null;switch(this.tokAt(++m)){case 0:b.bad();break;case 1073741914:s.append("[1] squared ");this.addShapeProperty(B,"squareLinear",Boolean.TRUE);Wa=t(-1,[1]);Ja=Va=0;m++;break;case 1073741973:case 1073742008:Ja=this.moOffset(m);Va=0;m=b.iToken;s.append((rb?"-":"")+"HOMO ");0<Ja&&s.append("+");
0!=Ja&&s.appendI(Ja);break;case 2:Va=this.intParameter(m);s.appendI(Va);1073741865==this.tokAt(m+1)&&(Db=!0,m++);break;default:b.isArrayParameter(m)&&(Wa=b.floatParameterSet(m,1,2147483647),m=b.iToken)}if(1073742156==this.tokAt(m+1))this.addShapeProperty(B,"squareLinear",Boolean.TRUE),s.append(" squared"),null==Wa&&(Wa=t(0,0));else if(134217751==this.tokAt(m+1)){++m;var Nb=this.intParameter(++m),Ob=2==this.tokAt(m+1)?this.intParameter(++m):-System.currentTimeMillis()%1E4;this.addShapeProperty(B,"monteCarloCount",
Integer.$valueOf(Nb));this.addShapeProperty(B,"randomSeed",Integer.$valueOf(Ob));s.append(" points ").appendI(Nb).appendC(" ").appendI(Ob)}this.setMoData(B,Va,Wa,Ja,rb,ca,null,R,Db);f=!0;continue;case 1073742036:z="nci";s.append(" "+z);var U=this.tokAt(m+1),Pb=1228935687!=U&&4!=U&&1073742032!=U,x=Boolean.$valueOf(Pb);Pb&&(f=!0);break;case 1073742016:case 1073742022:var Qb=1073742016==U,z=Qb?"mep":"mlp";s.append(" "+z);var cb=null,sb=-1,f=!0;2==this.tokAt(m+1)&&(sb=this.intParameter(++m),s.append(" "+
sb),this.addShapeProperty(B,"mepCalcType",Integer.$valueOf(sb)));if(4==this.tokAt(m+1))cb=this.stringParameter(++m),s.append(" /*file*/"+JU.PT.esc(cb));else if(1715472409==this.tokAt(m+1)){ob=z;continue}if(!this.chk)try{A=null==cb&&Qb?this.vwr.getOrCalcPartialCharges(Z,la):this.getAtomicPotentials(Z,la,cb)}catch(Rb){if(ea(Rb,"JV.JmolAsyncException"))throw new JS.ScriptInterruption(this.e,"partialcharge",1);throw Rb;}!this.chk&&null==A&&this.error(32);x=A;break;case 1312817669:Da=!this.chk;s.append(" volume");
break;case 1073741974:this.setShapeId(a,++m,Aa);wa=null==this.getShapeProperty(a,"ID");m=b.iToken;break;case 1073741888:1111490588==this.tokAt(m+1)&&(Ca=!0,m++);ra=this.paramAsStr(++m).toLowerCase();ra.equals("sets")?s.append(' colorScheme "sets"'):b.isColorParam(m)&&(ra=b.getColorRange(m),m=b.iToken);break;case 1073741828:z="addHydrogens";x=Boolean.TRUE;s.append(" addHydrogens");break;case 1073741836:z="angstroms";s.append(" angstroms");break;case 1073741837:z="anisotropy";x=this.getPoint3f(++m,
!1);s.append(" anisotropy").append(JU.Escape.eP(x));m=b.iToken;break;case 1073741842:j=!this.chk;s.append(" area");break;case 1073741850:case 1073742076:f=!0;S&&!v&&(s.append(' phase "_orb"'),this.addShapeProperty(B,"phase","_orb"));var na=t(7,0);na[0]=this.intParameter(++m);na[1]=this.intParameter(++m);na[2]=this.intParameter(++m);na[3]=this.isFloatParameter(m+1)?this.floatParameter(++m):6;s.append(" atomicOrbital ").appendI(w(na[0])).append(" ").appendI(w(na[1])).append(" ").appendI(w(na[2])).append(" ").appendF(na[3]);
134217751==this.tokAt(m+1)&&(m+=2,na[4]=this.intParameter(m),na[5]=3==this.tokAt(m+1)?this.floatParameter(++m):0,na[6]=2==this.tokAt(m+1)?this.intParameter(++m):-System.currentTimeMillis()%1E4,s.append(" points ").appendI(w(na[4])).appendC(" ").appendF(na[5]).appendC(" ").appendI(w(na[6])));z="hydrogenOrbital";x=na;break;case 1073741866:s.append(" binary");continue;case 1073741868:s.append(" blockData");z="blockData";x=Boolean.TRUE;break;case 1073741875:case 554176565:M=!0;z=b.theToken.value;x=this.getCapSlabObject(m,
!1);m=b.iToken;break;case 1073741876:d||this.invArg();var C=!0,Sb=this.isFloatParameter(m+1)?this.floatParameter(++m):1.2,tb=this.isFloatParameter(m+1)?this.floatParameter(++m):10;if(this.chk)continue;if(50<tb){b.integerOutOfRange(0,50);return}s.append(" cavity ").appendF(Sb).append(" ").appendF(tb);this.addShapeProperty(B,"envelopeRadius",Float.$valueOf(tb));this.addShapeProperty(B,"cavityRadius",Float.$valueOf(Sb));z="cavity";break;case 1073741896:case 1073741900:z="contour";s.append(" contour");
switch(this.tokAt(m+1)){case 1073741920:x=b.floatParameterSet(m+2,1,2147483647);s.append(" discrete ").append(JU.Escape.eAF(x));m=b.iToken;break;case 1073741981:T=this.getPoint3f(m+2,!1);(0>=T.z||T.y<T.x)&&this.invArg();T.z==w(T.z)&&T.z>T.y-T.x&&(T.z=(T.y-T.x)/T.z);x=T;m=b.iToken;s.append(" increment ").append(JU.Escape.eP(T));break;default:x=Integer.$valueOf(2==this.tokAt(m+1)?this.intParameter(++m):0),s.append(" ").appendO(x),2==this.tokAt(m+1)&&(this.addShapeProperty(B,z,x),x=Integer.$valueOf(-Math.abs(this.intParameter(++m))),
s.append(" ").appendO(x))}break;case 1073741910:s.append(" cutoff ");268440577==this.tokAt(++m)?(z="cutoffPositive",x=Float.$valueOf(V=this.floatParameter(++m)),s.append("+").appendO(x)):this.isFloatParameter(m)?(z="cutoff",x=Float.$valueOf(V=this.floatParameter(m)),s.appendO(x)):Ka?(z="cutoffRange",x=b.floatParameterSet(m,2,2),this.addShapeProperty(B,"cutoff",Float.$valueOf(0)),s.append(JU.Escape.eAF(x)),m=b.iToken):this.invArg();break;case 1073741928:z="downsample";x=Integer.$valueOf(this.intParameter(++m));
s.append(" downsample ").appendO(x);break;case 1073741931:z="eccentricity";x=b.getPoint4f(++m);s.append(" eccentricity ").append(JU.Escape.eP4(x));m=b.iToken;break;case 1073741932:s.append(" ed");this.setMoData(B,-1,null,0,!1,ca,null,null,!1);f=!0;continue;case 536870916:case 1073742041:s.append(" ").appendO(b.theToken.value);z="debug";x=536870916==U?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 cc=1073741968==U,z=""+b.theToken.value,ya=new JU.Lst,x=ya,E=f=!0;s.append(" ").append(z);var pa=this.paramAsStr(++m);if(pa.equals("=")){s.append(" =");pa=this.paramAsStr(++m);s.append(" ").append(JU.PT.esc(pa));ya.addLast(pa);this.chk||this.addShapeProperty(B,"func",this.createFunction("__iso__","x,y,z",pa));break}var ub=JU.PT.getQuotedAttribute(b.fullCommand,"# DATA"+(E?"2":""));null==ub?ub="inline":pa=ub;var Tb=0==pa.indexOf("data2d_"),dc=0==
pa.indexOf("data3d_"),lb=pa.equals("inline");s.append(" inline");ya.addLast(pa);var Ub=this.getPoint3f(++m,!1);s.append(" ").append(JU.Escape.eP(Ub));ya.addLast(Ub);var za;H=++b.iToken;ya.addLast(za=b.getPoint4f(H));s.append(" ").append(JU.Escape.eP4(za));P=w(za.x);Y=++b.iToken;ya.addLast(za=b.getPoint4f(Y));s.append(" ").append(JU.Escape.eP4(za));p=w(za.x);ya.addLast(za=b.getPoint4f(++b.iToken));s.append(" ").append(JU.Escape.eP4(za));F=w(za.x);(0==P||0==p||0==F)&&this.invArg();if(!this.chk){var qa=
null,ua=null;if(cc){lb?(P=Math.abs(P),p=Math.abs(p),F=Math.abs(F),ua=this.floatArraySetXYZ(++b.iToken,P,p,F)):ua=dc?this.vwr.getDataObj(pa,null,3):this.vwr.functionXYZ(pa,P,p,F);P=Math.abs(P);p=Math.abs(p);F=Math.abs(F);null==ua&&(b.iToken=H,b.errorStr(53,"xyzdata is null."));if(ua.length!=P||ua[0].length!=p||ua[0][0].length!=F)b.iToken=H,b.errorStr(53,"xyzdata["+ua.length+"]["+ua[0].length+"]["+ua[0][0].length+"] is not of size ["+P+"]["+p+"]["+F+"]");ya.addLast(ua);s.append(" ").append(JU.Escape.e(ua))}else{lb?
(P=Math.abs(P),p=Math.abs(p),qa=this.floatArraySet(++b.iToken,P,p)):Tb?(qa=this.vwr.getDataObj(pa,null,2),P=null==qa?0:qa.length,p=3):(qa=this.vwr.functionXY(pa,P,p),P=Math.abs(P),p=Math.abs(p));null==qa&&(b.iToken=H,b.errorStr(53,"fdata is null."));qa.length!=P&&!Tb&&(b.iToken=H,b.errorStr(53,"fdata length is not correct: "+qa.length+" "+P+"."));for(ha=0;ha<P;ha++)null==qa[ha]&&(b.iToken=Y,b.errorStr(53,"fdata["+ha+"] is null.")),qa[ha].length!=p&&(b.iToken=Y,b.errorStr(53,"fdata["+ha+"] is not the right length: "+
qa[ha].length+" "+p+"."));ya.addLast(qa);s.append(" ").append(JU.Escape.e(qa))}}m=b.iToken;break;case 1073742188:var ec=this.e.isAtomExpression(++m),Vb=this.getAllPoints(m,1);s.append(" value "+(ec?this.e.atomExpressionAt(m).toString():JU.Escape.eAP(Vb)));z="probes";x=Vb;m=this.e.iToken;break;case 1073741970:z="gridPoints";s.append(" gridPoints");break;case 1073741976:la=this.atomExpressionAt(++m);null!=this.vwr.slm.bsDeleted&&la.or(this.vwr.slm.bsDeleted);z="ignore";x=la;s.append(" ignore ").append(JU.Escape.eBS(la));
m=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==U?Boolean.TRUE:Boolean.FALSE;break;case 1073742002:z="lobe";x=b.getPoint4f(++m);m=b.iToken;s.append(" lobe ").append(JU.Escape.eP4(x));f=!0;break;case 1073742004:case 1073742006:z="lp";x=b.getPoint4f(++m);m=b.iToken;s.append(" lp ").append(JU.Escape.eP4(x));f=!0;break;case 4125:(q||this.slen==m+1)&&this.invArg();
q=!0;if((C||Q||G)&&!f)f=!0,this.addShapeProperty(B,"bsSolvent",Q||G?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(B,"sasurface",Float.$valueOf(0));0==s.length()?(ja=this.getShapeProperty(24,"plane"),null==ja?null!=this.getShapeProperty(24,"contours")&&this.addShapeProperty(B,"nocontour",null):(this.addShapeProperty(B,"plane",ja),s.append("plane ").append(JU.Escape.eP4(ja)),O=!0,ja=null)):!f&&!O&&this.invArg();s.append("; isosurface map");this.addShapeProperty(B,"map",f?Boolean.TRUE:
Boolean.FALSE);break;case 1073742014:z="maxset";x=Integer.$valueOf(this.intParameter(++m));s.append(" maxSet ").appendO(x);break;case 1073742020:z="minset";x=Integer.$valueOf(this.intParameter(++m));s.append(" minSet ").appendO(x);break;case 1073742112:f=!0;z="rad";x=b.getPoint4f(++m);m=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 Oa=b.theToken.value,db;1073742028==
U?(z="molecular",s.append(" molecular"),db=this.isFloatParameter(m+1)?this.floatParameter(++m):1.4):(this.addShapeProperty(B,"bsSolvent",b.lookupIdentifierValue("solvent")),z=1073742135==U?"sasurface":"solvent",s.append(" ").appendO(b.theToken.value),db=this.isFloatParameter(m+1)?this.floatParameter(++m):this.vwr.getFloat(570425394));s.append(" ").appendF(db);x=Float.$valueOf(db);1073741961==this.tokAt(m+1)&&(this.addShapeProperty(B,"doFullMolecular",null),s.append(" full"),m++);f=!0;break;case 1073742032:this.addShapeProperty(B,
"fileType","Mrc");s.append(" mrc");continue;case 1140850696:var ma=b.stringParameter(++m);this.addShapeProperty(B,"fileType",ma);s.append(' type "'+ma+'"');continue;case 1073742064:case 1073742062:this.addShapeProperty(B,"fileType","Obj");s.append(" obj");continue;case 1073742033:this.addShapeProperty(B,"fileType","Msms");s.append(" msms");continue;case 1073742094:f&&this.invArg();z="phase";v=!0;x=4==this.tokAt(m+1)?this.stringParameter(++m):"_orb";s.append(" phase ").append(JU.PT.esc(x));break;case 1073742104:case 1073742122:z=
"resolution";x=Float.$valueOf(this.floatParameter(++m));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.$valueOf(W=this.floatParameter(++m));s.append(" sigma ").appendO(x);break;case 1112150021:z="geodesic";x=Float.$valueOf(this.floatParameter(++m));s.append(" geosurface ").appendO(x);f=!0;break;case 1073742154:z="sphere";x=Float.$valueOf(this.floatParameter(++m));s.append(" sphere ").appendO(x);
f=!0;break;case 1073742156:z="squareData";x=Boolean.TRUE;s.append(" squared");break;case 1073741984:z=!f&&!O&&!q?"readFile":"mapColor";oa=this.stringParameter(++m);null==oa&&this.invArg();h&&(oa=JU.PT.replaceWithCharacter(oa,"{,}|"," "));b.debugHigh&&JU.Logger.debug("pmesh inline data:\n"+oa);x=this.chk?null:oa;this.addShapeProperty(B,"fileName","");s.append(" INLINE ").append(JU.PT.esc(oa));f=!0;break;case 268437504:case 1073742195:case 7:(null!=mb||wa)&&this.invArg();var eb=b.listParameter4(m,2,
2147483647,!0),m=b.iToken,Xa=D(eb.size()/2);(0==Xa||2*Xa!=eb.size())&&this.invArg();var vb=Array(Xa),wb=t(Xa,0);s.append("[");try{for(var Wb=ha=0;ha<Xa;ha++)wb[ha]=eb.get(Wb++).floatValue(),vb[ha]=this.e.checkFileExists("ISOSURFACE_"+ha+"_",!1,eb.get(Wb++),m,!1),s.appendF(wb[ha]),s.append(" /*file*/").append(JU.PT.esc(vb[ha]));s.append("]")}catch(Xb){if(ea(Xb,Exception))this.invArg();else throw Xb;}mb=y(-1,[vb,wb]);z=!f&&!O&&!q?"readFile":"mapColor";f=!0;if(this.chk)break;this.addShapeProperty(B,
"filesData",mb);break;case 545259556:case 545259557:case 1073741914:case 4:var xb=!f&&!O,I=null,z=xb&&!q?"readFile":"mapColor";if(4==U){var I=this.paramAsStr(m),yb=I.indexOf("::");if(0<yb){var fb=I.substring(0,yb),fb=fb.substring(0,1).toUpperCase()+fb.substring(1).toLowerCase();this.addShapeProperty(B,"fileType",fb);I=I.substring(yb+2)}}else 1073741914==U&&(I="=density/");if(null==I||0==I.length||I.equals("*")||I.equals("=")){var Yb=this.vwr.getPdbID(),I=null==Yb?this.vwr.ms.getModelFileName(this.vwr.am.cmi):
"*"+(545259557==U?"*":"")+Yb;null==I&&b.errorStr(22,"no PDBID available")}var Zb=!1;I.startsWith("http://eds.bmc.uu.se/eds/dfs/cb/")&&I.endsWith(".omap")&&(I=(0<=I.indexOf("_diff")?"*":"")+"*"+I.substring(32,36));if(I.startsWith("*")||I.startsWith("=")){var fc=!Float.isNaN(V)||!Float.isNaN(W),zb=0<=I.indexOf("/full");zb&&(I=JU.PT.rep(I,"/full",""));0<=I.indexOf("/diff")&&(I="*"+I.substring(0,I.indexOf("/diff")));I.startsWith("**")&&(fc||this.addShapeProperty(B,"sigma",Float.$valueOf(W=3)),Na||(Na=
!0,s.append(" sign"),this.addShapeProperty(B,"sign",Boolean.TRUE)));var gc=I,I=this.vwr.setLoadFormat(!1,I,this.chk?"?":zb?"_":"-",!1);null==I&&b.errorStr(22,"error parsing filename: "+gc);Zb=!zb}Zb&&(null==ga&&0==da&&(Oa=I,0>ca&&(ca=this.vwr.am.cmi),X=this.vwr.getModelUndeletedAtomsBitSet(ca),0<=X.nextSetBit(0)&&(ga=this.getWithinDistanceVector(B,2,null,X,!1),s.append(" within 2.0 ").append(JU.Escape.eBS(X)))),null!=ga&&0<=I.indexOf("/0,0,0/0,0,0?")&&(I=I.$replace("0,0,0/0,0,0",ga[0].x+","+ga[0].y+
","+ga[0].z+"/"+ga[ga.length-1].x+","+ga[ga.length-1].y+","+ga[ga.length-1].z)),xb&&(La=!0));var gb=null==I?-1:I.indexOf("#-");if(Float.isNaN(W)&&Float.isNaN(V))if(0<=(gb=I.indexOf("#-cutoff=")))this.addShapeProperty(B,"cutoff",Float.$valueOf(V=Float.parseFloat(I.substring(gb+9)))),s.append(" cutoff "+V);else if(0<=(gb=I.indexOf("#-sigma=")))this.addShapeProperty(B,"sigma",Float.$valueOf(W=Float.parseFloat(I.substring(gb+8)))),s.append(" sigma "+W);Float.isNaN(W)?Float.isNaN(V)||this.showString("using cutoff = "+
V):this.showString("using sigma = "+W);xb&&(this.vwr.getP("_fileType").equals("Pdb")&&Float.isNaN(W)&&Float.isNaN(V))&&(this.addShapeProperty(B,"sigma",Float.$valueOf(-1)),s.append(" sigma -1.0"));0==I.length&&(0>ca&&(ca=this.vwr.am.cmi),I=b.getFullPathName(!1),x=this.vwr.ms.getInfo(ca,"jmolSurfaceInfo"));var Ab=-1;null==x&&2==this.tokAt(m+1)&&this.addShapeProperty(B,"fileIndex",Integer.$valueOf(Ab=this.intParameter(++m)));var Ya=4==this.tokAt(m+1)?this.stringParameter(++m):null,f=!0;if(this.chk)break;
var $b,Ba=null;null==x&&(0<=b.fullCommand.indexOf("# FILE0=")?(I=JU.PT.getQuotedAttribute(b.fullCommand,"# FILE0"),1073741848==this.tokAt(m+1)&&(m+=2)):1073741848==this.tokAt(m+1)&&(Ba=this.vwr.fm.getFilePath(this.stringParameter(b.iToken=m+=2),!1,!1),$b=this.vwr.getFullPathNameOrError(Ba),Ba=$b[0],""!==this.vwr.fm.getPathForAllFiles()?(I=Ba,Ba=null):this.addShapeProperty(B,"localName",Ba)));null==Ya&&(I=this.e.checkFileExists("ISOSURFACE_"+(q?"MAP_":""),!1,I,m,!1));this.showString("reading isosurface data from "+
I);null!=Ya&&(x=this.vwr.fm.cacheGet(I,!1),this.addShapeProperty(B,"calculationType",Ya));null==x&&(this.addShapeProperty(B,"fileName",I),null!=Ba&&(I=Ba),0<=Ab&&s.append(" ").appendI(Ab));s.append(" /*file*/").append(JU.PT.esc(I));null!=Ya&&s.append(" ").append(JU.PT.esc(Ya));break;case 4106:z="connections";switch(this.tokAt(++m)){case 12290:case 10:case 1073742325:x=r(-1,[this.atomExpressionAt(m).nextSetBit(0)]);break;default:x=r(-1,[w(b.floatParameterSet(m,1,1)[0])])}m=b.iToken;break;case 1094713347:z=
"atomIndex";x=Integer.$valueOf(this.intParameter(++m));break;case 1073741999:z="link";s.append(" link");break;case 1814695966:24!=a&&this.invArg();268440577==this.tokAt(m+1)&&m++;z="extendGrid";x=Float.$valueOf(this.floatParameter(++m));s.append(" unitcell "+x);break;case 1073741994:24!=a&&this.invArg();T=this.getPoint3f(++m,!1);m=b.iToken;if(0>=T.x||0>=T.y||0>=T.z)break;T.x=w(T.x);T.y=w(T.y);T.z=w(T.z);s.append(" lattice ").append(JU.Escape.eP(T));q?(z="mapLattice",x=T):(va=T,12293==this.tokAt(m+
1)&&(s.append(" fixed"),xa=!0,m++));break;default:1073741824==U&&(z="thisID",x=oa);if(!b.setMeshDisplayProperty(a,0,U)){if(JS.T.tokAttr(U,1073741824)&&!Aa){this.setShapeId(a,m,Aa);m=b.iToken;break}this.invArg()}0==c&&(c=m);m=this.slen-1}Aa=12291!=U;wa&&f&&this.invArg();null!=z&&this.addShapeProperty(B,z,x)}if(!this.chk){if((C||Q)&&!f)f=!0,this.addShapeProperty(B,"bsSolvent",Q?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(B,"sasurface",Float.$valueOf(0));O&&(!f&&!q)&&(this.addShapeProperty(B,
"nomap",Float.$valueOf(0)),f=!0);null!=K&&this.addShapeProperty(B,"getSurfaceSets",K);if(null!=Pa)this.addShapeProperty(B,"colorDiscrete",Pa);else if("sets".equals(ra))this.addShapeProperty(B,"setColorScheme",null);else if(null!=ra){var hb=this.vwr.cm.getColorEncoder(ra);null!=hb&&(hb.isTranslucent=Ca,hb.hi=3.4028235E38,this.addShapeProperty(B,"remapColor",hb))}if(f&&!k&&0!=s.indexOf(";")){B.add(0,y(-1,["newObject",null]));var ac=null==Z;ac&&(Z=JU.BSUtil.andNot(JU.BSUtil.copy(this.vwr.bsA()),this.vwr.slm.bsDeleted));
0>ca&&(ca=this.vwr.am.cmi);Z.and(this.vwr.getModelUndeletedAtomsBitSet(ca));null!=this.vwr.slm.bsDeleted&&null==la&&(B.add(1,y(-1,["ignore",JU.BS.copy(this.vwr.slm.bsDeleted)])),s.insert(0," ignore "+this.vwr.slm.bsDeleted));null!=Oa&&(1<this.vwr.ms.getModelBS(Z,!1).cardinality()&&b.errorStr(30,"ISOSURFACE "+Oa),ac&&(B.add(0,y(-1,["select",Z])),0==s.indexOf("; isosurface map")&&(s=(new JU.SB).append("; isosurface map select ").append(JU.Escape.eBS(Z)).append(s.substring(16)))))}G&&!M&&(f||this.addShapeProperty(B,
"sasurface",Float.$valueOf(0)),q||(this.addShapeProperty(B,"map",Boolean.TRUE),this.addShapeProperty(B,"select",X),this.addShapeProperty(B,"sasurface",Float.$valueOf(0))),this.addShapeProperty(B,"slab",this.getCapSlabObject(-100,!1)));var bc=f&&this.vwr.getBoolean(603979934);bc&&JU.Logger.startTimer("isosurface");this.setShapeProperty(a,"setProperties",B);bc&&this.showString(JU.Logger.getTimerMsg("isosurface",0));La&&(this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,
"token",Integer.$valueOf(1073742046)),N=!0,s.append(" mesh nofill frontOnly"))}null!=va&&(this.setShapeProperty(a,"lattice",va),xa&&this.setShapeProperty(a,"fixLattice",Boolean.TRUE));null!=Ia&&this.setShapeProperty(a,"symops",Ia);N&&this.setShapeProperty(a,"token",Integer.$valueOf(1073741960));0<c&&(b.setMeshDisplayProperty(a,c,0)||this.invArg());if(!this.chk){var Fa=null,Ga=null;j&&(Fa=this.getShapeProperty(a,"area"),$(Fa,Float)?this.vwr.setFloatProperty("isosurfaceArea",Fa.floatValue()):this.vwr.g.setUserVariable("isosurfaceArea",
JS.SV.getVariableAD(Fa)));Da&&(Ga=Da?this.getShapeProperty(a,"volume"):null,$(Ga,Float)?this.vwr.setFloatProperty("isosurfaceVolume",Ga.floatValue()):this.vwr.g.setUserVariable("isosurfaceVolume",JS.SV.getVariableAD(Ga)));if(!k){ma=null;if(q&&!f)this.setShapeProperty(a,"finalize",s.toString());else if(f){var ib=s.toString(),ib=(0==ib.indexOf("; isosurface map")?"":" select "+JU.Escape.eBS(Z)+" ")+ib;this.setShapeProperty(a,"finalize",ib);ma=this.getShapeProperty(a,"ID");null!=ma&&(!b.tQuiet&&!l)&&
(V=this.getShapeProperty(a,"cutoff").floatValue(),Float.isNaN(V)&&!Float.isNaN(W)&&JU.Logger.error("sigma not supported"),ma+=" created "+this.getShapeProperty(a,"message"))}var Bb,Cb;if(j||Da)Bb=j?"isosurfaceArea = "+($(Fa,Float)?""+Fa:JU.Escape.eAD(Fa)):null,Cb=Da?"isosurfaceVolume = "+($(Ga,Float)?""+Ga:JU.Escape.eAD(Ga)):null,null==ma?(j&&this.showString(Bb),Da&&this.showString(Cb)):(j&&(ma+="\n"+Bb),Da&&(ma+="\n"+Cb));null!=ma&&!l&&this.showString(ma);f&&(ma=this.getShapeProperty(a,"output"),
null!=ma&&!l&&this.showString(ma))}null!=nb&&this.setShapeProperty(a,"translucency",nb);this.setShapeProperty(a,"clear",null);L&&this.setShapeProperty(a,"cache",null);!l&&(!g&&!M&&12291!=b.theTok)&&this.listIsosurface(a)}}},"~N");e(d,"lcaoCartoon",function(){var a=this.e;a.sm.loadShape(26);if(!(1073742001==a.tokAt(1)&&this.listIsosurface(26)))if(this.setShapeProperty(26,"init",a.fullCommand),1==this.slen)this.setShapeProperty(26,"lcaoID",null);else{for(var b=!1,c=null,c=1;c<this.slen;c++){var g=null,
u=null;switch(this.getToken(c).tok){case 1073741875:case 554176565:g=a.theToken.value;1073742334==this.tokAt(c+1)&&(a.iToken=c+1);u=this.getCapSlabObject(c,!0);c=a.iToken;break;case 12289:this.isosurface(26);return;case 528432:var d=u=0,h=0;switch(this.getToken(++c).tok){case 1111492629:u=0.017453292519943295*this.floatParameter(++c);break;case 1111492630:d=0.017453292519943295*this.floatParameter(++c);break;case 1111492631:h=0.017453292519943295*this.floatParameter(++c);break;default:this.invArg()}g=
"rotationAxis";u=JU.V3.new3(u,d,h);break;case 1073742335:case 1610625028:case 2097192:g="on";break;case 1073742334:case 12294:case 2097194:g="off";break;case 12291:g="delete";break;case 12290:case 10:case 1073742325:g="select";u=this.atomExpressionAt(c);c=a.iToken;break;case 1140850693:g="reversecolor";u=Boolean.TRUE;1073742335==this.tokAt(c+1)?++c:1073742334==this.tokAt(c+1)&&(u=Boolean.FALSE,++c);break;case 1765808134:c=this.setColorOptions(null,c+1,26,-2);null!=c&&this.setShapeProperty(26,"settranslucency",
c);c=a.iToken;b=!0;continue;case 1111490588:case 1073742074:a.setMeshDisplayProperty(26,c,a.theTok);c=a.iToken;b=!0;continue;case 1112152075:case 4:u=this.paramAsStr(c).toLowerCase();u.equals("spacefill")&&(u="cpk");g="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,g="molecular");break;case 1275082241:a.isAtomExpression(c+1)?(g="select",u=this.atomExpressionAt(c+1),c=a.iToken):(g="selectType",u=this.paramAsStr(++c),u.equals("spacefill")&&(u="cpk"));break;case 536875059:g=
"scale";u=Float.$valueOf(this.floatParameter(++c));break;case 1073742004:case 1073742006:g="lonePair";break;case 1073742112:case 1073742111:g="radical";break;case 1073742028:g="molecular";break;case 1073741904:u=this.paramAsStr(++c);g="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,g="molecular");break;case 1073741974:u=a.setShapeNameParameter(++c);c=a.iToken;b&&this.invArg();g="lcaoID";break;default:if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824))268441089!=a.theTok&&
(u=this.paramAsStr(c)),b&&this.invArg(),g="lcaoID"}12291!=a.theTok&&(b=!0);null==g&&this.invArg();this.setShapeProperty(26,g,u)}this.setShapeProperty(26,"clear",null)}});e(d,"contact",function(){var a=this.e;a.sm.loadShape(25);if(1073742001==this.tokAt(1)&&this.listIsosurface(25))return!1;var b=0;a.iToken=1;for(var c=null!=this.initIsosurface(25),g=c&&null==this.getShapeProperty(25,"ID"),u=null,d=null,h=null,e=null,k=null,f=!1,n=new JU.SB,O=2147483647,q=134217750,j=0,v=NaN,r=NaN,w=!0,C=null,L=null,
Q=0,N=!1,E=-2147483648,M=1<a.iToken,G=a.iToken;G<this.slen;++G){switch(h=this.getToken(G).tok){default:M=!0;if(!a.setMeshDisplayProperty(25,0,a.theTok)){268441089!=a.theTok&&!JS.T.tokAttr(a.theTok,1073741824)&&this.invArg();this.setShapeId(25,G,c);G=a.iToken;break}0==b&&(b=G);G=a.iToken;continue;case 1073741974:M=!0;this.setShapeId(25,++G,c);g=null==this.getShapeProperty(25,"ID");G=a.iToken;break;case 1765808134:switch(this.tokAt(G+1)){case 1073741914:h=0;f=!0;n.append(" color density");G++;break;
case 1140850696:h=0,N=!0,n.append(" color type"),G++}if(0==h)break;case 1111490588:case 1073742074:M=!0;0==Q&&(Q=G);a.setMeshDisplayProperty(25,G,a.theTok);G=a.iToken;break;case 554176565:M=!0;L=this.getCapSlabObject(G,!1);this.setShapeProperty(25,"slab",L);G=a.iToken;break;case 1073741914:f=!0;n.append(" density");this.isFloatParameter(G+1)&&(null==k&&(k=t(1,0)),k[0]=-Math.abs(this.floatParameter(++G)),n.append(" "+-k[0]));break;case 1073742122:c=this.floatParameter(++G);0<c&&(n.append(" resolution ").appendF(c),
this.setShapeProperty(25,"resolution",Float.$valueOf(c)));break;case 1094717454:case 1094713359:E=1094713359==a.theTok?this.intParameter(++G):a.modelNumberParameter(++G);n.append(" modelIndex "+E);break;case 134217759:case 1275069443:v=this.floatParameter(++G);n.append(" within ").appendF(v);break;case 268440577:case 2:case 3:e=a.encodeRadiusParameter(G,!1,!1);if(null==e)return!1;n.append(" ").appendO(e);G=a.iToken;break;case 1073741990:case 1073741989:C=1073741989==h?Boolean.TRUE:Boolean.FALSE;n.append(" ").appendO(a.theToken.value);
break;case 1073742020:O=this.intParameter(++G);break;case 1613238294:case 1073741881:case 1648363544:j=h;n.append(" ").appendO(a.theToken.value);break;case 1073742135:this.isFloatParameter(G+1)&&(r=this.floatParameter(++G));case 1073741875:case 1073742036:case 2097180:w=!1;case 1275068932:case 1073741961:case 134217750:case 4106:q=h;n.append(" ").appendO(a.theToken.value);1073742135==h&&n.append(" ").appendF(r);break;case 1073742083:k=a.floatParameterSet(++G,1,10);G=a.iToken;break;case 12290:case 10:case 1073742325:(g||
null!=d)&&this.invArg(),h=JU.BSUtil.copy(this.atomExpressionAt(G)),G=a.iToken,null==u?u=h:d=h,n.append(" ").append(JU.Escape.eBS(h))}c=12291!=a.theTok}!M&&null==u&&this.error(13);if(this.chk)return!1;if(null!=u){1648363544==j&&null==e&&(e=new J.atomdata.RadiusData(null,0,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO));G=null==e?new J.atomdata.RadiusData(null,0.26,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO):e;d=1073742036==q&&null==d&&null!=C&&C.booleanValue()?u:a.getMathExt().setContactBitSets(u,
d,w,v,G,!0);switch(q){case 1073741875:case 1073742135:G=a.lookupIdentifierValue("solvent");u.andNot(G);d.andNot(G);d.andNot(u);break;case 2097180:d.andNot(u);break;case 1073742036:2147483647==O&&(O=100),this.setShapeProperty(25,"minset",Integer.$valueOf(O)),n.append(" minSet ").appendI(O),null==k&&(k=t(-1,[0.5,2]))}null!=C&&(k=null==k?t(2,0):JU.AU.ensureLengthA(k,2),k[1]=C.booleanValue()?1:2);null!=k&&n.append(" parameters ").append(JU.Escape.eAF(k));this.setShapeProperty(25,"set",y(-1,[Integer.$valueOf(j),
Integer.$valueOf(q),Boolean.$valueOf(f),Boolean.$valueOf(N),u,d,e,Float.$valueOf(r),k,Integer.$valueOf(E),n.toString()]));0<Q&&a.setMeshDisplayProperty(25,Q,0)}0<b&&(a.setMeshDisplayProperty(25,b,0)||this.invArg());null!=L&&null!=u&&this.setShapeProperty(25,"slab",L);if(null!=u&&(1073742036==q||w)){u=this.getShapeProperty(25,"volume");b=1073741961==q;if(JU.AU.isAD(u))for(G=a=0;G<u.length;G++)a+=b?u[G]:Math.abs(u[G]);else a=u.floatValue();a=Math.round(1E3*a)/1E3;if(f||1275068932!=q)f=this.getShapeProperty(25,
"nSets").intValue(),f="Contacts: "+(0>f?D(-f/2):f),0!=a&&(f+=", with "+(b?"approx ":"net ")+"volume "+a+" A^3"),this.showString(f)}return!0});e(d,"cgo",function(){var a=this.e;a.sm.loadShape(23);if(1073742001==this.tokAt(1)&&this.listIsosurface(23))return!1;for(var b=0,c=null!=this.initIsosurface(23),g=c&&null==this.getShapeProperty(23,"ID"),u=!1,d=-1,h=null,e=3.4028235E38,k=r(-1,[-2147483648]),f=0,n=a.iToken;n<this.slen;++n){var O=null,d=null;switch(this.getToken(n).tok){case 268437504:case 1073742195:case 7:(null!=
h||g)&&this.invArg();h=new JU.Lst;n=r(-1,[n,this.slen]);a.getShapePropertyData(23,"data",y(-1,[this.st,n,h,this.vwr]))||this.invArg();n=n[0];continue;case 536875059:++n>=this.slen&&this.error(34);switch(this.getToken(n).tok){case 2:f=this.intParameter(n);continue;case 3:f=Math.round(100*this.floatParameter(n));continue}this.error(34);break;case 12293:O="modelIndex";d=Integer.$valueOf(-1);break;case 1094713359:case 1094717454:d=1094713359==a.theTok?this.intParameter(++n):a.modelNumberParameter(++n);
O="modelIndex";d=Integer.$valueOf(d);break;case 1765808134:case 1111490588:case 1073742074:e=this.getColorTrans(a,n,!1,k);n=a.iToken;c=!0;continue;case 1073741974:this.setShapeId(23,++n,c);g=null==this.getShapeProperty(23,"ID");n=a.iToken;break;default:if(!a.setMeshDisplayProperty(23,0,a.theTok)){if(268441089==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(23,n,c);n=a.iToken;break}this.invArg()}0==b&&(b=n);n=a.iToken;continue}c=12291!=a.theTok;null!=h&&!u&&(O="points",d=Integer.$valueOf(f),
u=!0,f=0);null!=O&&this.setShapeProperty(23,O,d)}this.finalizeObject(23,k[0],e,f,null!=h,h,b,null);return!0});e(d,"getAtomicPotentials",function(a,b,c){var g=t(this.vwr.ms.ac,0),u=J.api.Interface.getOption("quantum.MlpCalculation",this.vwr,"script");u.set(this.vwr);c=null==c?null:this.vwr.getFileAsString3(c,!1,null);try{u.assignPotentials(this.vwr.ms.at,g,this.vwr.getSmartsMatch("a",a),this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]",a),b,c)}catch(d){if(!ea(d,Exception))throw d;}return g},
"JU.BS,JU.BS,~S");e(d,"getCapSlabObject",function(a,b){if(0>a)return JU.GData.getSlabWithinRange(a,0);var c=this.e,g=null,u=554176565==this.tokAt(a),d=this.tokAt(a+1),h=null,e=h=null,k=null,f=null;if(1111490588==d)switch(k=this.isFloatParameter(++a+1)?this.floatParameter(++a):0.5,c.isColorParam(a+1)?(k=Short.$valueOf(JU.C.getColixTranslucent3(JU.C.getColix(c.getArgbParam(a+1)),0!=k,k)),a=c.iToken):k=Short.$valueOf(JU.C.getColixTranslucent3(1,0!=k,k)),d=this.tokAt(a+1)){case 1073742018:case 1073741938:f=
Integer.$valueOf(d);d=this.tokAt(++a+1);break;default:f=Integer.$valueOf(1073741938)}switch(d){case 1073742334:return c.iToken=a+1,Integer.$valueOf(-2147483648);case 1073742333:c.iToken=a+1;break;case 1073742330:a++;g=y(-1,[Float.$valueOf(1),this.paramAsStr(++a)]);d=1073742018;break;case 134217759:a++;if(1073742114==this.tokAt(++a))g=this.floatParameter(++a),d=this.floatParameter(++a),g=y(-1,[Float.$valueOf(g),Float.$valueOf(d)]),d=1073742114;else if(this.isFloatParameter(a)){g=this.floatParameter(a);
if(c.isCenterParameter(++a)){var h=Array(1),n=c.centerParameter(a,h);if(this.chk||!$(h[0],"JU.BS"))h=y(-1,[n]);else for(var n=this.vwr.ms.at,e=h[0],h=Array(e.cardinality()),O=0,q=e.nextSetBit(0);0<=q;q=e.nextSetBit(q+1),O++)h[O]=n[q]}else h=c.getPointArray(a,-1,!1,!0);0==h.length&&(c.iToken=a,this.invArg());g=y(-1,[Float.$valueOf(g),h,e])}else g=c.getPointArray(a,4,!1,!0),d=1812599299;break;case 1812599299:c.iToken=a+1;g=JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(),null);break;case 1073741872:case 1814695966:c.iToken=
a+1;c=this.vwr.getCurrentUnitCell();if(null==c)1814695966==d&&this.invArg();else{h=JU.BoxInfo.toOABC(c.getUnitCellVerticesNoOffset(),c.getCartesianOffset());c=w(c.getUnitCellInfoType(6));g=e=null;switch(c){case 1:g=JU.V3.newVsub(h[2],h[0]),g.scale(1E3);case 2:e=JU.V3.newVsub(h[1],h[0]),e.scale(1E3),h[0].sub(e),h[1].scale(2E3),1==c&&(h[0].sub(g),h[2].scale(2E3))}g=h}break;case 12290:case 10:case 1073742325:if(g=this.atomExpressionAt(a+1),d=3,!c.isCenterParameter(++c.iToken)){u=!0;break}default:if(!b&&
u&&this.isFloatParameter(a+1)){g=this.floatParameter(++a);if(!this.isFloatParameter(a+1))return Integer.$valueOf(w(g));d=this.floatParameter(++a);g=y(-1,[Float.$valueOf(g),Float.$valueOf(d)]);d=1073742114;break}h=c.planeParameter(++a,!1);d=this.isFloatParameter(c.iToken+1)?this.floatParameter(++c.iToken):NaN;Float.isNaN(d)||(h.w-=d);g=h;d=134217750}k=null==f?null:y(-1,[f,k]);return JU.GData.getSlabObjectType(d,g,!u,k)},"~N,~B");e(d,"setColorOptions",function(a,b,c,g){var u=this.e;this.getToken(b);
var d="opaque";if(1111490588==u.theTok)if(d="translucent",0>g){var h=this.isFloatParameter(b+1)?this.floatParameter(++b):3.4028235E38;u.setShapeTranslucency(c,null,"translucent",h,null);null!=a&&(a.append(" translucent"),3.4028235E38!=h&&a.append(" ").appendF(h))}else u.setMeshDisplayProperty(c,b,u.theTok);else 1073742074==u.theTok?0<=g&&u.setMeshDisplayProperty(c,b,u.theTok):u.iToken--;g=Math.abs(g);for(h=0;h<g;h++)if(u.isColorParam(u.iToken+1)){var e=u.getArgbParam(++u.iToken);this.setShapeProperty(c,
"colorRGB",Integer.$valueOf(e));null!=a&&a.append(" ").append(JU.Escape.escapeColor(e))}else if(u.iToken<b)this.invArg();else break;return d},"JU.SB,~N,~N,~N");e(d,"createFunction",function(a,b,c){var g=(new JS.ScriptEval).setViewer(this.vwr);try{g.compileScript(null,"function "+a+"("+b+") { return "+c+"}",!1);var u=new JU.Lst;for(a=0;a<b.length;a+=2)u.addLast(JS.SV.newF(0).setName(b.substring(a,a+1)));return y(-1,[g.aatoken[0][1].value,u])}catch(d){if(ea(d,Exception))return null;throw d;}},"~S,~S,~S");
e(d,"getWithinDistanceVector",function(a,b,c,g,u){var d=new JU.Lst,h=Array(2);if(null==g){var e=JU.P3.new3(b,b,b),f=JU.P3.newP(c);f.sub(e);e.add(c);h[0]=f;h[1]=e;d.addLast(c)}else c=this.vwr.ms.getBoxInfo(g,-Math.abs(2*b)),h[0]=c.getBoundBoxVertices()[0],h[1]=c.getBoundBoxVertices()[7],1==g.cardinality()&&d.addLast(this.vwr.ms.at[g.nextSetBit(0)]);1==d.size()&&!u&&(this.addShapeProperty(a,"withinDistance",Float.$valueOf(b)),this.addShapeProperty(a,"withinPoint",d.get(0)));this.addShapeProperty(a,
u?"displayWithin":"withinPoints",y(-1,[Float.$valueOf(b),h,g,d]));return h},"JU.Lst,~N,JU.P3,JU.BS,~B");e(d,"addShapeProperty",function(a,b,c){this.chk||a.addLast(y(-1,[b,c]))},"JU.Lst,~S,~O");e(d,"floatArraySetXYZ",function(a,b,c,g){var d=this.e,aa=this.tokAt(a++);1073742195==aa&&(aa=this.tokAt(a++));(268437504!=aa||0>=b)&&this.invArg();for(var h=JU.AU.newFloat3(b,-1),e=0;268437505!=aa;)switch(aa=this.getToken(a).tok,aa){case 1073742195:case 268437505:continue;case 268436992:a++;break;case 268437504:h[e++]=
this.floatArraySet(a,c,g);a=++d.iToken;aa=0;e==b&&268437505!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return h},"~N,~N,~N,~N");e(d,"floatArraySet",function(a,b,c){var g=this.tokAt(a++);1073742195==g&&(g=this.tokAt(a++));268437504!=g&&this.invArg();for(var d=JU.AU.newFloat2(b),e=0;268437505!=g;)switch(g=this.getToken(a).tok,g){case 1073742195:case 268437505:continue;case 268436992:a++;break;case 268437504:a++;g=t(c,0);d[e++]=g;for(var h=0;h<c;h++)g[h]=this.floatParameter(a++),268436992==
this.tokAt(a)&&a++;268437505!=this.tokAt(a++)&&this.invArg();g=0;e==b&&268437505!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return d},"~N,~N,~N");e(d,"initIsosurface",function(a){var b=this.e;this.setShapeProperty(a,"init",b.fullCommand);b.iToken=0;var c=this.tokAt(1),g=this.tokAt(2);if(12291==c||12291==g&&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",y(-1,[b.thisCommand])),1073741974!=c&&(268441089==g||268441089==c&&b.setMeshDisplayProperty(a,0,g)))?(a=this.setShapeId(a,1,!1),b.iToken++,a):null},"~N");e(d,"listIsosurface",function(a){var b=3<this.slen?"0":0==this.tokAt(2)?"":" "+this.getToken(2).value;this.chk||this.showString(this.getShapeProperty(a,"list"+b));return!0},
"~N");e(d,"getBoxPoints",function(a,b,c,g,d){switch(a){case 1814695966:return null==b?null:b.getCanonicalCopy(d,!0);case 1812599299:if(null==c)if(null==g)a=this.vwr.ms.getBoxInfo();else{c=this.e.getObjectBoundingBox(g);if(null==c)return null;a=new JU.BoxInfo;a.addBoundBoxPoint(c[0]);a.addBoundBoxPoint(c[1])}else a=new JU.BoxInfo,this.vwr.calcAtomsMinMax(c,a);return JU.BoxInfo.getCanonicalCopy(a.getBoundBoxVertices(),d);default:return null}},"~N,J.api.SymmetryInterface,JU.BS,~S,~N")});L("JU");R(["JU.TriangleData"],
"JU.Triangulator","JU.AU $.BS $.Lst $.Measure $.P3 $.P4 $.V3".split(" "),function(){var d=Ca(JU,"Triangulator",JU.TriangleData);e(d,"intersectLine",function(a,b,c,g){b=new JU.V3;for(var d=new JU.V3,e=new JU.V3,h=new JU.V3,ba=null,f=null,l=new JU.P3,n=new JU.P4,O=3.4028235E38,q=-3.4028235E38,j=0;12>j;j++){var v=JU.Triangulator.fullCubePolygon[j];if(0==j%2){JU.Measure.getPlaneThroughPoints(a[v[0]],a[v[1]],a[v[2]],b,d,n);if(null==JU.Measure.getIntersection(c,g,n,l,b,e)){j++;continue}h.sub2(l,c)}if(JU.Measure.isInTriangle(l,
a[v[0]],a[v[1]],a[v[2]],b,d,e)){v=g.dot(h);v<O&&(O=v,ba=l);v>q&&(q=v,f=l);0==j%2&&j++;if(0.01<q-O)break;l=new JU.P3}}return null==ba||(null==f||0.001>ba.distance(f))&&null==(f=ba)?null:y(-1,[ba,f])},"~A,~N,JU.P3,JU.V3");e(d,"getCellProjection",function(a,b){for(var c=new JU.V3,g=0,d=-3.4028235E38,e=0,h=Array(8),ba=0;8>ba;ba++)g=b[ba].dot(a),g>d&&(d=g,e=ba),JU.Measure.getPlaneProjection(b[ba],a,h[ba]=new JU.P3,c);g=JU.Triangulator.fullCubeCorners[e][3];c=JU.AU.newInt2(6);for(ba=d=0;12>ba;ba++)if(0!=
(g&JU.TriangleData.Pwr2[ba])){var f=r(4,0),l=JU.Triangulator.fullCubePolygon[ba];f[0]=l[0];f[1]=l[1];f[2]=l[2];f[3]=l[0]==e?2:l[1]==e?0:l[2]==e?1:3;c[d++]=f}e=new JU.Lst;e.addLast(h);e.addLast(c);return e},"JU.P4,~A");e(d,"intersectPlane",function(a,b,c){if(-1==c&&8==b.length)return this.getCellProjection(a,b);for(var g=new JU.Lst,d=Array(12),e=0,h=t(8,0),f=0;8>f;f++)h[f]=a.x*b[f].x+a.y*b[f].y+a.z*b[f].z+a.w,0>h[f]&&(e|=JU.TriangleData.Pwr2[f]);a=JU.TriangleData.triangleTable2[e];if(null==a)return null;
for(f=0;24>f;f+=2){var e=JU.TriangleData.edgeVertexes[f],k=JU.TriangleData.edgeVertexes[f+1],l=JU.P3.newP(b[k]);l.sub(b[e]);l.scale(h[e]/(h[e]-h[k]));l.add(b[e]);d[f>>1]=l}if(0==c){c=new JU.BS;for(f=0;f<a.length;f++)c.set(a[f]),2==f%4&&f++;f=c.cardinality();h=Array(f);g.addLast(h);b=r(12,0);for(f=e=0;f<a.length;f++)k=a[f],c.get(k)&&(c.clear(k),h[e]=d[k],b[k]=e++),2==f%4&&f++;d=JU.AU.newInt2(a.length>>2);g.addLast(d);for(f=0;f<a.length;f++)d[f>>2]=r(-1,[b[a[f++]],b[a[f++]],b[a[f++]],a[f]]);return g}for(f=
0;f<a.length;f++)b=d[a[f++]],h=d[a[f++]],e=d[a[f++]],1==(c&1)&&g.addLast(y(-1,[b,h,e])),2==(c&2)&&(k=a[f],1==(k&1)&&g.addLast(y(-1,[b,h])),2==(k&2)&&g.addLast(y(-1,[h,e])),4==(k&4)&&g.addLast(y(-1,[b,e])));return g},"JU.P4,~A,~N");d.edgeC=y(-1,[r(-1,[0,3,0,1])]);d.edgeB=y(-1,[r(-1,[0,4,0,1])]);d.edgeA=y(-1,[r(-1,[0,1,0,1])]);d.abFace=y(-1,[r(-1,[0,4,5,3]),r(-1,[5,1,0,3])]);d.fullCubePolygon=y(-1,[r(-1,[0,4,5,3]),r(-1,[5,1,0,3]),r(-1,[1,5,6,2]),r(-1,[6,2,1,3]),r(-1,[2,6,7,2]),r(-1,[7,3,2,3]),r(-1,
[3,7,4,2]),r(-1,[4,0,3,2]),r(-1,[6,5,4,0]),r(-1,[4,7,6,0]),r(-1,[0,1,2,0]),r(-1,[2,3,0,0])]);d.fullCubeCorners=y(-1,[r(-1,[1,4,3,3267]),r(-1,[0,2,5,3087]),r(-1,[1,3,6,3132]),r(-1,[2,0,7,3312]),r(-1,[0,5,7,963]),r(-1,[1,6,4,783]),r(-1,[2,7,5,828]),r(-1,[3,4,6,1008])])});L("JU");R(["JU.P3i"],"JU.TriangleData",null,function(){var d=Ca(JU,"TriangleData",null);d.Pwr2=r(-1,[1,2,4,8,16,32,64,128,256,512,1024,2048]);d.cubeVertexOffsets=y(-1,[JU.P3i.new3(0,0,0),JU.P3i.new3(1,0,0),JU.P3i.new3(1,0,1),JU.P3i.new3(0,
0,1),JU.P3i.new3(0,1,0),JU.P3i.new3(1,1,0),JU.P3i.new3(1,1,1),JU.P3i.new3(0,1,1)]);d.edgeVertexes=f(-1,[0,1,1,2,2,3,3,0,4,5,5,6,6,7,7,4,0,4,1,5,2,6,3,7]);d.triangleTable2=y(-1,[null,f(-1,[0,8,3,7]),f(-1,[0,1,9,7]),f(-1,[1,8,3,6,9,8,1,5]),f(-1,[1,2,10,7]),f(-1,[0,8,3,7,1,2,10,7]),f(-1,[9,2,10,6,0,2,9,5]),f(-1,[2,8,3,6,2,10,8,1,10,9,8,3]),f(-1,[3,11,2,7]),f(-1,[0,11,2,6,8,11,0,5]),f(-1,[1,9,0,7,2,3,11,7]),f(-1,[1,11,2,6,1,9,11,1,9,8,11,3]),f(-1,[3,10,1,6,11,10,3,5]),f(-1,[0,10,1,6,0,8,10,1,8,11,10,
3]),f(-1,[3,9,0,6,3,11,9,1,11,10,9,3]),f(-1,[9,8,10,5,10,8,11,6]),f(-1,[4,7,8,7]),f(-1,[4,3,0,6,7,3,4,5]),f(-1,[0,1,9,7,8,4,7,7]),f(-1,[4,1,9,6,4,7,1,1,7,3,1,3]),f(-1,[1,2,10,7,8,4,7,7]),f(-1,[3,4,7,6,3,0,4,3,1,2,10,7]),f(-1,[9,2,10,6,9,0,2,3,8,4,7,7]),f(-1,[2,10,9,3,2,9,7,0,2,7,3,6,7,9,4,6]),f(-1,[8,4,7,7,3,11,2,7]),f(-1,[11,4,7,6,11,2,4,1,2,0,4,3]),f(-1,[9,0,1,7,8,4,7,7,2,3,11,7]),f(-1,[4,7,11,3,9,4,11,1,9,11,2,2,9,2,1,6]),f(-1,[3,10,1,6,3,11,10,3,7,8,4,7]),f(-1,[1,11,10,6,1,4,11,0,1,0,4,3,7,11,
4,5]),f(-1,[4,7,8,7,9,0,11,1,9,11,10,6,11,0,3,6]),f(-1,[4,7,11,3,4,11,9,4,9,11,10,6]),f(-1,[9,5,4,7]),f(-1,[9,5,4,7,0,8,3,7]),f(-1,[0,5,4,6,1,5,0,5]),f(-1,[8,5,4,6,8,3,5,1,3,1,5,3]),f(-1,[1,2,10,7,9,5,4,7]),f(-1,[3,0,8,7,1,2,10,7,4,9,5,7]),f(-1,[5,2,10,6,5,4,2,1,4,0,2,3]),f(-1,[2,10,5,3,3,2,5,1,3,5,4,2,3,4,8,6]),f(-1,[9,5,4,7,2,3,11,7]),f(-1,[0,11,2,6,0,8,11,3,4,9,5,7]),f(-1,[0,5,4,6,0,1,5,3,2,3,11,7]),f(-1,[2,1,5,3,2,5,8,0,2,8,11,6,4,8,5,5]),f(-1,[10,3,11,6,10,1,3,3,9,5,4,7]),f(-1,[4,9,5,7,0,8,1,
5,8,10,1,2,8,11,10,3]),f(-1,[5,4,0,3,5,0,11,0,5,11,10,6,11,0,3,6]),f(-1,[5,4,8,3,5,8,10,4,10,8,11,6]),f(-1,[9,7,8,6,5,7,9,5]),f(-1,[9,3,0,6,9,5,3,1,5,7,3,3]),f(-1,[0,7,8,6,0,1,7,1,1,5,7,3]),f(-1,[1,5,3,5,3,5,7,6]),f(-1,[9,7,8,6,9,5,7,3,10,1,2,7]),f(-1,[10,1,2,7,9,5,0,5,5,3,0,2,5,7,3,3]),f(-1,[8,0,2,3,8,2,5,0,8,5,7,6,10,5,2,5]),f(-1,[2,10,5,3,2,5,3,4,3,5,7,6]),f(-1,[7,9,5,6,7,8,9,3,3,11,2,7]),f(-1,[9,5,7,3,9,7,2,0,9,2,0,6,2,7,11,6]),f(-1,[2,3,11,7,0,1,8,5,1,7,8,2,1,5,7,3]),f(-1,[11,2,1,3,11,1,7,4,
7,1,5,6]),f(-1,[9,5,8,5,8,5,7,6,10,1,3,3,10,3,11,6]),f(-1,[5,7,0,1,5,0,9,6,7,11,0,1,1,0,10,5,11,10,0,1]),f(-1,[11,10,0,1,11,0,3,6,10,5,0,1,8,0,7,5,5,7,0,1]),f(-1,[11,10,5,3,7,11,5,5]),f(-1,[10,6,5,7]),f(-1,[0,8,3,7,5,10,6,7]),f(-1,[9,0,1,7,5,10,6,7]),f(-1,[1,8,3,6,1,9,8,3,5,10,6,7]),f(-1,[1,6,5,6,2,6,1,5]),f(-1,[1,6,5,6,1,2,6,3,3,0,8,7]),f(-1,[9,6,5,6,9,0,6,1,0,2,6,3]),f(-1,[5,9,8,3,5,8,2,0,5,2,6,6,3,2,8,5]),f(-1,[2,3,11,7,10,6,5,7]),f(-1,[11,0,8,6,11,2,0,3,10,6,5,7]),f(-1,[0,1,9,7,2,3,11,7,5,10,
6,7]),f(-1,[5,10,6,7,1,9,2,5,9,11,2,2,9,8,11,3]),f(-1,[6,3,11,6,6,5,3,1,5,1,3,3]),f(-1,[0,8,11,3,0,11,5,0,0,5,1,6,5,11,6,6]),f(-1,[3,11,6,3,0,3,6,1,0,6,5,2,0,5,9,6]),f(-1,[6,5,9,3,6,9,11,4,11,9,8,6]),f(-1,[5,10,6,7,4,7,8,7]),f(-1,[4,3,0,6,4,7,3,3,6,5,10,7]),f(-1,[1,9,0,7,5,10,6,7,8,4,7,7]),f(-1,[10,6,5,7,1,9,7,1,1,7,3,6,7,9,4,6]),f(-1,[6,1,2,6,6,5,1,3,4,7,8,7]),f(-1,[1,2,5,5,5,2,6,6,3,0,4,3,3,4,7,6]),f(-1,[8,4,7,7,9,0,5,5,0,6,5,2,0,2,6,3]),f(-1,[7,3,9,1,7,9,4,6,3,2,9,1,5,9,6,5,2,6,9,1]),f(-1,[3,11,
2,7,7,8,4,7,10,6,5,7]),f(-1,[5,10,6,7,4,7,2,1,4,2,0,6,2,7,11,6]),f(-1,[0,1,9,7,4,7,8,7,2,3,11,7,5,10,6,7]),f(-1,[9,2,1,6,9,11,2,2,9,4,11,1,7,11,4,5,5,10,6,7]),f(-1,[8,4,7,7,3,11,5,1,3,5,1,6,5,11,6,6]),f(-1,[5,1,11,1,5,11,6,6,1,0,11,1,7,11,4,5,0,4,11,1]),f(-1,[0,5,9,6,0,6,5,2,0,3,6,1,11,6,3,5,8,4,7,7]),f(-1,[6,5,9,3,6,9,11,4,4,7,9,5,7,11,9,1]),f(-1,[10,4,9,6,6,4,10,5]),f(-1,[4,10,6,6,4,9,10,3,0,8,3,7]),f(-1,[10,0,1,6,10,6,0,1,6,4,0,3]),f(-1,[8,3,1,3,8,1,6,0,8,6,4,6,6,1,10,6]),f(-1,[1,4,9,6,1,2,4,1,
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8,7,6]),f(-1,[3,6,2,6,3,7,6,3,1,5,0,5,5,4,0,3]),f(-1,[6,2,8,1,6,8,7,6,2,1,8,1,4,8,5,5,1,5,8,1]),f(-1,[9,5,4,7,10,1,6,5,1,7,6,2,1,3,7,3]),f(-1,[1,6,10,6,1,7,6,2,1,0,7,1,8,7,0,5,9,5,4,7]),f(-1,[4,0,10,1,4,10,5,6,0,3,10,1,6,10,7,5,3,7,10,1]),f(-1,[7,6,10,3,7,10,8,4,5,4,10,5,4,8,10,1]),f(-1,[6,9,5,6,6,11,9,1,11,8,9,3]),f(-1,[3,6,11,6,0,6,3,4,0,5,6,2,0,9,5,3]),f(-1,[0,11,8,6,0,5,11,0,0,1,5,3,5,6,11,3]),f(-1,[6,11,3,3,6,3,5,4,5,3,1,6]),f(-1,[1,2,10,7,9,5,11,1,9,11,8,6,11,5,6,6]),f(-1,[0,11,3,6,0,6,11,2,
0,9,6,1,5,6,9,5,1,2,10,7]),f(-1,[11,8,5,1,11,5,6,6,8,0,5,1,10,5,2,5,0,2,5,1]),f(-1,[6,11,3,3,6,3,5,4,2,10,3,5,10,5,3,1]),f(-1,[5,8,9,6,5,2,8,0,5,6,2,3,3,8,2,5]),f(-1,[9,5,6,3,9,6,0,4,0,6,2,6]),f(-1,[1,5,8,1,1,8,0,6,5,6,8,1,3,8,2,5,6,2,8,1]),f(-1,[1,5,6,3,2,1,6,5]),f(-1,[1,3,6,1,1,6,10,6,3,8,6,1,5,6,9,5,8,9,6,1]),f(-1,[10,1,0,3,10,0,6,4,9,5,0,5,5,6,0,1]),f(-1,[0,3,8,7,5,6,10,7]),f(-1,[10,5,6,7]),f(-1,[11,5,10,6,7,5,11,5]),f(-1,[11,5,10,6,11,7,5,3,8,3,0,7]),f(-1,[5,11,7,6,5,10,11,3,1,9,0,7]),f(-1,[10,
7,5,6,10,11,7,3,9,8,1,5,8,3,1,3]),f(-1,[11,1,2,6,11,7,1,1,7,5,1,3]),f(-1,[0,8,3,7,1,2,7,1,1,7,5,6,7,2,11,6]),f(-1,[9,7,5,6,9,2,7,0,9,0,2,3,2,11,7,3]),f(-1,[7,5,2,1,7,2,11,6,5,9,2,1,3,2,8,5,9,8,2,1]),f(-1,[2,5,10,6,2,3,5,1,3,7,5,3]),f(-1,[8,2,0,6,8,5,2,0,8,7,5,3,10,2,5,5]),f(-1,[9,0,1,7,5,10,3,1,5,3,7,6,3,10,2,6]),f(-1,[9,8,2,1,9,2,1,6,8,7,2,1,10,2,5,5,7,5,2,1]),f(-1,[1,3,5,5,3,7,5,3]),f(-1,[0,8,7,3,0,7,1,4,1,7,5,6]),f(-1,[9,0,3,3,9,3,5,4,5,3,7,6]),f(-1,[9,8,7,3,5,9,7,5]),f(-1,[5,8,4,6,5,10,8,1,10,
11,8,3]),f(-1,[5,0,4,6,5,11,0,0,5,10,11,3,11,3,0,3]),f(-1,[0,1,9,7,8,4,10,1,8,10,11,6,10,4,5,6]),f(-1,[10,11,4,1,10,4,5,6,11,3,4,1,9,4,1,5,3,1,4,1]),f(-1,[2,5,1,6,2,8,5,0,2,11,8,3,4,5,8,5]),f(-1,[0,4,11,1,0,11,3,6,4,5,11,1,2,11,1,5,5,1,11,1]),f(-1,[0,2,5,1,0,5,9,6,2,11,5,1,4,5,8,5,11,8,5,1]),f(-1,[9,4,5,7,2,11,3,7]),f(-1,[2,5,10,6,3,5,2,4,3,4,5,2,3,8,4,3]),f(-1,[5,10,2,3,5,2,4,4,4,2,0,6]),f(-1,[3,10,2,6,3,5,10,2,3,8,5,1,4,5,8,5,0,1,9,7]),f(-1,[5,10,2,3,5,2,4,4,1,9,2,5,9,4,2,1]),f(-1,[8,4,5,3,8,5,
3,4,3,5,1,6]),f(-1,[0,4,5,3,1,0,5,5]),f(-1,[8,4,5,3,8,5,3,4,9,0,5,5,0,3,5,1]),f(-1,[9,4,5,7]),f(-1,[4,11,7,6,4,9,11,1,9,10,11,3]),f(-1,[0,8,3,7,4,9,7,5,9,11,7,2,9,10,11,3]),f(-1,[1,10,11,3,1,11,4,0,1,4,0,6,7,4,11,5]),f(-1,[3,1,4,1,3,4,8,6,1,10,4,1,7,4,11,5,10,11,4,1]),f(-1,[4,11,7,6,9,11,4,4,9,2,11,2,9,1,2,3]),f(-1,[9,7,4,6,9,11,7,2,9,1,11,1,2,11,1,5,0,8,3,7]),f(-1,[11,7,4,3,11,4,2,4,2,4,0,6]),f(-1,[11,7,4,3,11,4,2,4,8,3,4,5,3,2,4,1]),f(-1,[2,9,10,6,2,7,9,0,2,3,7,3,7,4,9,3]),f(-1,[9,10,7,1,9,7,4,
6,10,2,7,1,8,7,0,5,2,0,7,1]),f(-1,[3,7,10,1,3,10,2,6,7,4,10,1,1,10,0,5,4,0,10,1]),f(-1,[1,10,2,7,8,7,4,7]),f(-1,[4,9,1,3,4,1,7,4,7,1,3,6]),f(-1,[4,9,1,3,4,1,7,4,0,8,1,5,8,7,1,1]),f(-1,[4,0,3,3,7,4,3,5]),f(-1,[4,8,7,7]),f(-1,[9,10,8,5,10,11,8,3]),f(-1,[3,0,9,3,3,9,11,4,11,9,10,6]),f(-1,[0,1,10,3,0,10,8,4,8,10,11,6]),f(-1,[3,1,10,3,11,3,10,5]),f(-1,[1,2,11,3,1,11,9,4,9,11,8,6]),f(-1,[3,0,9,3,3,9,11,4,1,2,9,5,2,11,9,1]),f(-1,[0,2,11,3,8,0,11,5]),f(-1,[3,2,11,7]),f(-1,[2,3,8,3,2,8,10,4,10,8,9,6]),f(-1,
[9,10,2,3,0,9,2,5]),f(-1,[2,3,8,3,2,8,10,4,0,1,8,5,1,10,8,1]),f(-1,[1,10,2,7]),f(-1,[1,3,8,3,9,1,8,5]),f(-1,[0,9,1,7]),f(-1,[0,3,8,7]),null])});L("J.jvxl.api");Ka(J.jvxl.api,"VertexDataServer");L("J.jvxl.api");Ka(J.jvxl.api,"MeshDataServer",J.jvxl.api.VertexDataServer);L("J.shapesurface");R(["J.jvxl.api.MeshDataServer","J.shape.MeshCollection","JU.P3i","$.P4"],"J.shapesurface.Isosurface","java.util.Hashtable JU.A4 $.AU $.BS $.CU $.Lst $.M3 $.M4 $.P3 $.PT $.Quat $.Rdr $.SB $.V3 J.jvxl.data.JvxlCoder $.JvxlData $.MeshData J.jvxl.readers.SurfaceGenerator J.shape.Mesh J.shapesurface.IsosurfaceMesh JU.C $.Escape $.GData $.Logger JV.JC $.Viewer".split(" "),
function(){var d=N(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;C(this,arguments)},J.shapesurface,"Isosurface",J.shape.MeshCollection,J.jvxl.api.MeshDataServer);ia(d,function(){this.isomeshes=Array(4);this.lcaoDir=new JU.P4;this.ptXY=new JU.P3i});j(d,"allocMesh",function(a,b){var c=this.meshCount++;this.meshes=this.isomeshes=JU.AU.ensureLength(this.isomeshes,2*this.meshCount);this.currentMesh=this.thisMesh=this.isomeshes[c]=null==b?new J.shapesurface.IsosurfaceMesh(this.vwr,
a,this.colix,c):b;this.currentMesh.index=c;null!=this.sg&&this.sg.setJvxlData(this.jvxlData=this.thisMesh.jvxlData)},"~S,J.shape.Mesh");e(d,"initShape",function(){La(this,J.shapesurface.Isosurface,"initShape",[]);this.myType="isosurface";this.newSg()});e(d,"newSg",function(){this.sg=new J.jvxl.readers.SurfaceGenerator(this.vwr,this,null,this.jvxlData=new J.jvxl.data.JvxlData);this.sg.params.showTiming=this.vwr.getBoolean(603979934);this.sg.version="Jmol "+JV.Viewer.getJmolVersion()});e(d,"clearSg",
function(){this.sg=null});j(d,"setProperty",function(a,b,c){this.setPropI(a,b,c)},"~S,~O,JU.BS");e(d,"setPropI",function(a,b,c){if("cache"===a){if(null!=this.currentMesh){var g=this.currentMesh.thisID;b=this.currentMesh.modelIndex;this.vwr.cachePut("cache://isosurface_"+g,this.getPropI("jvxlDataXml",-1).getBytes());this.deleteMeshI(this.currentMesh.index);this.setPropI("init",null,null);this.setPropI("thisID",g,null);this.setPropI("modelIndex",Integer.$valueOf(b),null);this.setPropI("fileName","cache://isosurface_"+
g,null);this.setPropI("readFile",null,null);this.setPropI("finalize","isosurface ID "+JU.PT.esc(g)+(0<=b?" modelIndex "+b:"")+" /*file*/"+JU.PT.esc("cache://isosurface_"+g),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(g=this.meshCount;0<=--g;)null!=this.isomeshes[g]&&"#inherit;".equals(this.isomeshes[g].colorCommand)&&this.isomeshes[g].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("pymolparams"===a)null!=this.thisMesh&&(this.ensureMeshSource(),this.thisMesh.setPymolVertexColixesForAtoms(this.vwr,b,c));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&&(g=JU.C.getColixO(b[0]),b=b[1].floatValue(),1.7976931348623157E308!=b&&0!=b&&(g=JU.C.getColixTranslucent3(g,!0,b)),this.thisMesh.colorVertices(g,c,!1));else if("colorPhase"===a){c=b;b=JU.C.getColix(c[0].intValue());c=JU.C.getColix(c[1].intValue());for(var g=null!=this.thisMesh?this.thisMesh.thisID:JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,d=this.getMeshList(g,!1),g=d.size();0<=--g;)d.get(g).setPropertyColorPhase(b,
c,this.translucentLevel)}else if("color"===a){var e=JU.C.getHexCode(JU.C.getColixO(b));if(null!=this.thisMesh)this.thisMesh.setPropertyColor(e);else{d=this.getMeshList(JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,!1);for(g=d.size();0<=--g;)d.get(g).setPropertyColor(e)}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(g=this.meshCount;0<=--g;)this.meshes[g].modelIndex==c&&(null!=this.meshes[g].connectedAtoms||this.meshes[g].isModelConnected)&&this.meshes[g].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)this.explicitID||this.setPropertySuper("thisID",null,null),this.sg.setProp("lcaoCartoonCenter",b[2],null)||this.drawLcaoCartoon(b[0],b[1],b[3],"lonePair"===a?2:"radical"===a?1:0,null==this.thisMesh?!1:this.thisMesh.reverseColor);else if(!("select"===a&&this.iHaveBitSets||"ignore"===a&&this.iHaveBitSets))if("reversecolor"===a)null!=this.thisMesh&&(this.thisMesh.reverseColor=b===Boolean.TRUE);else if("meshcolor"===a)g=
b.intValue(),this.meshColix=JU.C.getColix(g),null!=this.thisMesh&&(this.thisMesh.meshColix=this.meshColix);else if("offset"===a)b=JU.P3.newP(b),0==b.lengthSquared()&&(b=null),null!=this.thisMesh&&(this.thisMesh.rotateTranslate(null,b,!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)g=b,this.displayWithinDistance2=
g[0].floatValue(),this.isDisplayWithinNot=0>this.displayWithinDistance2,this.displayWithinDistance2*=this.displayWithinDistance2,this.displayWithinPoints=g[3],0==this.displayWithinPoints.size()&&(this.displayWithinPoints=this.ms.getAtomPointVector(g[2]));else if("finalize"===a)null!=this.thisMesh&&(null!=b&&!b.startsWith("; isosurface map")&&(this.thisMesh.setDiscreteColixes(this.sg.params.contoursDiscrete,this.sg.params.contourColixes),this.setJvxlInfo()),this.setScriptInfo(b)),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($(b,Integer)){null!=this.thisMesh&&(this.thisMesh.jvxlData.slabValue=b.intValue());return}if(null!=this.thisMesh){switch(b[0].intValue()){case 1073742018:g=b[1];c=this.getMesh(g[1]);if(null==c)return;
g[1]=c}this.slabPolygons(b);return}}if("cap"===a&&null!=this.thisMesh&&0!=this.thisMesh.pc)this.thisMesh.getMeshSlicer().slabPolygons(b,!0),this.thisMesh.initialize(this.thisMesh.lighting,null,null);else{if("map"===a&&(null!=this.sg&&(this.sg.params.isMapped=!0),this.setProperty("squareData",Boolean.FALSE,null),null==this.thisMesh||0==this.thisMesh.vc))return;if("probes"===a)null!=this.sg&&(this.sg.params.probes=b,this.sg.params.probeValues=t(this.sg.params.probes.length,0));else if("deleteVdw"===
a){for(g=this.meshCount;0<=--g;)null!=this.isomeshes[g].bsVdw&&(null==c||c.intersects(this.isomeshes[g].bsVdw))&&this.deleteMeshI(g);this.currentMesh=this.thisMesh=null}else{if("mapColor"===a||"readFile"===a){if(null==b){if(null==this.sg.params.filesData)b=this.getFileReader(this.sg.params.fileName);else{b=this.sg.params.filesData;d=this.sg.params.filesData[0];e=Array(d.length);for(g=e.length;0<=--g&&null!=b;)if(null==(e[g]=this.getFileReader(d[g])))b=null;null!=b&&(this.sg.params.filesData[0]=e)}if(null==
b)return}}else if("atomIndex"===a)this.atomIndex=b.intValue(),null!=this.thisMesh&&(this.thisMesh.atomIndex=this.atomIndex);else if("center"===a)this.center.setT(b);else if("colorRGB"===a)g=b.intValue(),1296041986==g?this.colorType=g:(this.colorType=0,this.defaultColix=JU.C.getColix(g));else if("contour"===a)this.explicitContours=!0;else if("functionXY"===a)2==this.sg.params.state&&this.setScriptInfo(null);else if("init"===a)this.newSg();else if("getSurfaceSets"===a){if(null!=this.thisMesh){if($(b,
"JU.BS"))e=b,e.isEmpty()&&(e=null);else{e=new JU.BS;d=b;for(g=d.length;0<=--g;)0<d[g]&&e.set(d[g]-1)}this.thisMesh.jvxlData.thisSet=e;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(),$(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)g=this.ms.am[this.currentMesh.modelIndex].mat4,null!=g&&(g=JU.M4.newM4(g),g.invert(),this.setPropI("modelInvRotation",g,null))}else"phase"===a?this.isPhaseColored=!0:"plane"!==a&&"pocket"!==a&&("scale3d"===a?(this.scale3d=b.floatValue(),null!=this.thisMesh&&(this.thisMesh.scale3d=this.thisMesh.jvxlData.scale3d=this.scale3d,this.thisMesh.altVertices=null)):"title"===a?("string"==typeof b&&"-".equals(b)&&(b=null),this.setPropertySuper(a,b,c),b=this.title):
"withinPoints"===a?(g=b,this.withinDistance2=g[0].floatValue(),this.isWithinNot=0>this.withinDistance2,this.withinDistance2*=this.withinDistance2,this.withinPoints=g[3],0==this.withinPoints.size()&&(this.withinPoints=this.ms.getAtomPointVector(g[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="",b="string"==typeof b?b:null,g=null==b?-1:b.indexOf("# ID="),this.actualID=0<=g?JU.PT.getQuotedStringAt(b,g):null,this.setPropertySuper("thisID","+PREVIOUS_MESH+",null),null!=b&&!(this.iHaveBitSets=this.getScriptBitSets(b,null))&&this.sg.setProp("select",c,null),this.initializeIsosurface(),this.sg.params.modelIndex=this.isFixed?-1:this.modelIndex;else if("clear"===
a)this.discardTempData(!0);else if("colorDensity"===a)null!=b&&null!=this.currentMesh&&(this.currentMesh.volumeRenderPointSize=b.floatValue());else if("deleteModelAtoms"===a){a=b[2][0];d=b[2][1];b=b[2][2];for(g=this.meshCount;0<=--g;)c=this.meshes[g],null!=c&&(null!=c.connectedAtoms&&(e=c.connectedAtoms[0],e>=d+b?c.connectedAtoms[0]=e-b:e>=d&&(c.connectedAtoms=null)),c.connectedAtoms=null,c.modelIndex==a?(this.meshCount--,c===this.currentMesh&&(this.currentMesh=this.thisMesh=null),this.meshes=this.isomeshes=
JU.AU.deleteElements(this.meshes,g,1)):c.modelIndex>a&&(c.modelIndex--,c.atomIndex>=d&&(c.atomIndex-=b)))}else this.setPropertySuper(a,b,c)}}}},"~S,~O,JU.BS");e(d,"getFileReader",function(a){var b=this.vwr.fm.getBufferedReaderOrErrorMessageFromName(a,null,!0,!0);if("string"==typeof b)return JU.Logger.error("Isosurface: could not open file "+a+" -- "+b),null;if(!$(b,"java.io.BufferedReader"))try{b=JU.Rdr.getBufferedReader(b,"ISO-8859-1")}catch(c){if(!ea(c,"java.io.IOException"))throw c;}return b},
"~S");e(d,"ensureMeshSource",function(){var a=null!=this.thisMesh.vertexSource;if(a)for(var b=this.thisMesh.vc;0<=--b;)if(0>this.thisMesh.vertexSource[b]){a=!1;break}if(!a){var a=this.thisMesh.vertexSource,c=this.thisMesh.vcs,b=this.thisMesh.isColorSolid?this.thisMesh.colix:0;this.setProperty("init",null,null);this.setProperty("map",Boolean.FALSE,null);this.setProperty("property",t(this.ms.ac,0),null);0!=b&&(this.thisMesh.colorCommand="color isosurface "+JU.C.getHexCode(b),this.setProperty("color",
Integer.$valueOf(JU.C.getArgb(b)),null));if(null!=a){for(b=this.thisMesh.vc;0<=--b;)0>a[b]&&(a[b]=this.thisMesh.vertexSource[b]);this.thisMesh.vertexSource=a;this.thisMesh.vcs=c}}});e(d,"slabPolygons",function(a){this.thisMesh.calculatedVolume=null;this.thisMesh.calculatedArea=null;this.thisMesh.getMeshSlicer().slabPolygons(a,!1);this.thisMesh.reinitializeLightingAndColor(this.vwr)},"~A");e(d,"setPropertySuper",function(a,b,c){"thisID"===a&&null!=this.currentMesh&&null!=this.currentMesh.thisID&&this.currentMesh.thisID.equals(b)?
this.checkExplicit(b):(this.currentMesh=this.thisMesh,this.setPropMC(a,b,c),this.thisMesh=this.currentMesh,this.jvxlData=null==this.thisMesh?null:this.thisMesh.jvxlData,null!=this.sg&&this.sg.setJvxlData(this.jvxlData))},"~S,~O,JU.BS");j(d,"getPropertyData",function(a,b){var c;"keys"===a&&(c=$(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 g=Array(2);g[0]=JU.P3.newP(c.jvxlData.boundingBox[0]);g[1]=JU.P3.newP(c.jvxlData.boundingBox[1]);var d=new JU.V3;c.mat4.getTranslation(d);g[0].add(d);g[1].add(d);b[2]=g}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;g=JU.P3.newP(c.jvxlData.boundingBox[0]);g.add(c.jvxlData.boundingBox[1]);g.scale(0.5);null!=c.mat4&&(d=new JU.V3,c.mat4.getTranslation(d),g.add(d));b[2]=g;return!0}return this.getPropDataMC(a,b)},"~S,~A");j(d,"getProperty",function(a,b){return this.getPropI(a,b)},"~S,~N");e(d,"getPropI",function(a,b){var c=this.thisMesh;if(0<=
b&&(b>=this.meshCount||null==(c=this.isomeshes[b])))return null;var g=this.getPropMC(a,b);if(null!=g)return g;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 g=null==c?-2147483648:c.nSets,0==g&&(this.calculateVolumeOrArea(c,!0),g=c.nSets),Integer.$valueOf(-2147483648==g?0:Math.abs(c.nSets));if("area"===a)return null==c?Float.$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 t(-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("ply"===a||
"plybin"===a)return c.getPLYData("plybin"===a);if("jvxlDataXml"===a||"jvxlMeshXml"===a){var d=null;this.jvxlData.slabInfo=null;"jvxlMeshXml"===a||this.jvxlData.vertexDataOnly||null!=c.bsSlabDisplay&&null==c.bsSlabGhost?(d=new J.jvxl.data.MeshData,this.fillMeshData(d,1,c),d.polygonColorData=J.shapesurface.Isosurface.getPolygonColorData(d.pc,d.pcs,d.colorsExplicit?d.pis:null,d.bsSlabDisplay)):null!=c.bsSlabGhost&&(this.jvxlData.slabInfo=c.slabOptions.toString());g=new JU.SB;this.getMeshCommand(g,c.index);
c.setJvxlColorMap(!0);null!=c.vertexColorMap&&(this.jvxlData.vertexColorMap=c.copyVertexColorMap());null!=this.jvxlData.vertexColorMap&&(this.jvxlData.nVertexColors=this.jvxlData.vertexColorMap.size());return J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,d,this.title,"",!0,1,g.toString(),null)}if("jvxlFileInfo"===a)return J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);if("command"===a){g=new JU.SB;c=this.getMeshList(0>b?this.previousMeshID:c.thisID,!1);for(d=c.size();0<=--d;)this.getMeshCommand(g,
c.get(d).index);return g.toString()}return"atoms"===a?c.surfaceAtoms:"colorEncoder"===a?c.colorEncoder:"values"===a||"value"===a?c.probeValues:null},"~S,~N");e(d,"getDataRange",function(a){return null==a?null:a.getDataRange()},"J.shapesurface.IsosurfaceMesh");e(d,"calculateVolumeOrArea",function(a,b){if(b){if(null!=a.calculatedArea)return a.calculatedArea}else if(null!=a.calculatedVolume)return a.calculatedVolume;var c=new J.jvxl.data.MeshData;this.fillMeshData(c,1,a);c.nSets=a.nSets;c.vertexSets=
a.vertexSets;if(!b&&a.jvxlData.colorDensity)return c=a.jvxlData.voxelVolume,c*=null==a.bsSlabDisplay?a.vc:a.bsSlabDisplay.cardinality(),a.calculatedVolume=Float.$valueOf(c);var g=J.jvxl.data.MeshData.calculateVolumeOrArea(c,a.jvxlData.thisSet,b,!1);0>=a.nSets&&(a.nSets=-c.nSets);b?a.calculatedArea=g:a.calculatedVolume=g;return g},"J.shapesurface.IsosurfaceMesh,~B");d.getPolygonColorData=e(d,"getPolygonColorData",function(a,b,c,g){var d=null!=c;if(null==b&&null==c)return null;for(var e=new JU.SB,h=
0,f=0,k=0,l=0,n=!1,O=0;O<a||!0==(n=!0);O++)if(n||null==g||g.get(O))if(n||(d?(l=c[O][4])!=k:b[O]!=f)){0!=h&&e.append(" ").appendI(h).append(" ").appendI(d?k:0==f?0:JU.C.getArgb(f));if(n)break;d?k=l:f=b[O];h=1}else h++;e.append("\n");return e.toString()},"~N,~A,~A,JU.BS");j(d,"getShapeState",function(){this.clean();var a=new JU.SB;a.append("\n");for(var b=0;b<this.meshCount;b++)this.getMeshCommand(a,b);return a.toString()});e(d,"getMeshCommand",function(a,b){var c=this.meshes[b];if(!(null==c||null==
c.scriptCommand)){var g=c.scriptCommand;1<this.ms.mc&&J.shape.Shape.appendCmd(a,"frame "+this.vwr.getModelNumberDotted(c.modelIndex));g=JU.PT.rep(g,";; isosurface map"," map");g=JU.PT.rep(g,"; isosurface map"," map");g.endsWith(" map")&&(g=g.substring(0,g.length-4));var g=g.$replace("\t"," "),g=JU.PT.rep(g,";#","; #"),d=g.indexOf("; #");0<=d&&(g=g.substring(0,d));null!=c.connectedAtoms&&(g+=" connect "+JU.Escape.eAI(c.connectedAtoms));g=JU.PT.trim(g,";");null!=c.linkedMesh&&(g+=" LINK");"lcaoCartoon"===
this.myType&&0<=c.atomIndex&&(g+=" ATOMINDEX "+c.atomIndex);J.shape.Shape.appendCmd(a,g);d=this.myType+" ID "+JU.PT.esc(c.thisID);null!=c.jvxlData.thisSet&&!c.jvxlData.thisSet.isEmpty()&&J.shape.Shape.appendCmd(a,d+(1==c.jvxlData.thisSet.cardinality()?" set "+(c.jvxlData.thisSet.nextSetBit(0)+1):" subset "+c.jvxlData.thisSet));null!=c.mat4&&!c.isModelConnected&&J.shape.Shape.appendCmd(a,d+" move "+JU.Escape.matrixToScript(c.mat4));0!=c.scale3d&&J.shape.Shape.appendCmd(a,d+" scale3d "+c.scale3d);-2147483648!=
c.jvxlData.slabValue&&J.shape.Shape.appendCmd(a,d+" slab "+c.jvxlData.slabValue);null!=c.slabOptions&&J.shape.Shape.appendCmd(a,c.slabOptions.toString());if("#"!=g.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),g=c.isColorSolid&&null!=c.pcs,c.isColorSolid&&0==c.colorType&&!c.colorsExplicit&&!g?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&&c.vertexColorMap!==c.pymolVertexColorMap))for(var e,c=c.vertexColorMap.entrySet().iterator();c.hasNext()&&
((e=c.next())||1);)g=e.getValue(),g.isEmpty()||J.shape.Shape.appendCmd(a,"color "+this.myType+" "+JU.Escape.eBond(g)+" "+e.getKey())}},"JU.SB,~N");e(d,"getScriptBitSets",function(a,b){this.script=a;var c;this.iHaveModelIndex=!1;this.modelIndex=-1;if(null!=a&&0<=(c=a.indexOf("MODEL({"))){var g=a.indexOf("})",c);0<g&&(c=JU.BS.unescape(a.substring(c+3,g+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;g=a.indexOf("})",c);if(0>g)return!1;c=JU.BS.unescape(a.substring(c+2,g+2));null==b?this.sg.setProp("select",c,null):b[0]=c;if(0>(c=a.indexOf("({",g)))return!0;g=a.indexOf("})",c);if(0>g)return!1;c=JU.BS.unescape(a.substring(c+1,g+1));null==b?this.sg.setProp("ignore",c,null):b[1]=c;if((c=a.indexOf("/({",g))==g+2){if(0>(g=a.indexOf("})",c)))return!1;c=JU.BS.unescape(a.substring(c+3,g+1));null==b?this.ms.setTrajectoryBs(c):b[2]=c}return!0},"~S,~A");e(d,"getCapSlabInfo",function(a){var b=
a.indexOf("# SLAB=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!1),null);b=a.indexOf("# CAP=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!0),null)},"~S");e(d,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var c=JU.PT.split(a.substring(6,a.length-1),",");return JU.GData.getSlabObjectType(1812599299,y(-1,[JU.Escape.uP(c[0]),JU.Escape.uP(c[1]),JU.Escape.uP(c[2]),JU.Escape.uP(c[3])]),b,null)}var g=JU.Escape.uP(a);
if($(g,"JU.P4"))return JU.GData.getSlabObjectType(134217750,g,b,null)}catch(d){if(!ea(d,Exception))throw d;}return null},"~S,~B");e(d,"initializeIsosurface",function(){this.iHaveModelIndex||(this.modelIndex=this.vwr.am.cmi);this.atomIndex=-1;this.bsDisplay=null;this.center=JU.P3.new3(NaN,0,0);this.colix=5;this.cutoffRange=this.connections=null;this.colorType=this.defaultColix=this.meshColix=0;this.displayWithinPoints=null;this.explicitContours=!1;this.isFixed=0>this.modelIndex;this.isPhaseColored=
this.isColorExplicit=!1;this.linkedMesh=null;0>this.modelIndex&&(this.modelIndex=0);this.scale3d=0;this.title=null;this.translucentLevel=0;this.withinPoints=null;this.initState()});e(d,"initState",function(){this.associateNormals=!0;this.sg.initState()});e(d,"setMeshI",function(){this.thisMesh.visible=!0;this.thisMesh.modelIndex=0<=(this.thisMesh.atomIndex=this.atomIndex)?this.ms.at[this.atomIndex].mi:this.isFixed?-1:0<=this.modelIndex?this.modelIndex:this.vwr.am.cmi;this.thisMesh.scriptCommand=this.script;
this.thisMesh.ptCenter.setT(this.center);this.thisMesh.scale3d=null==this.thisMesh.jvxlData.jvxlPlane?0:this.scale3d});e(d,"discardTempData",function(a){a&&(this.title=null,null!=this.thisMesh&&(this.thisMesh.surfaceSet=null))},"~B");e(d,"getDefaultColix",function(){return 0!=this.defaultColix?this.defaultColix:!this.sg.jvxlData.wasCubic?this.colix:JU.C.getColix(0<=this.sg.params.cutoff?-11525984:-6283184)});e(d,"drawLcaoCartoon",function(a,b,c,g,d){var e=this.sg.setLcao(),h=0<=e.indexOf("anti-sp");
h&&(e=e.substring(5));var f=c.x+c.y+c.z;this.defaultColix=JU.C.getColix(this.sg.params.colorPos);var k=JU.C.getColix(this.sg.params.colorNeg);d&&(d=k,k=this.defaultColix,this.defaultColix=d);d=new JU.V3;var l=0<e.length&&"-"==e.charAt(0);l&&(e=e.substring(1));l=l?-1:1;d.cross(a,b);if(0!=f){var n=new JU.A4;0!=c.x?n.setVA(b,f):0!=c.y?n.setVA(d,f):n.setVA(a,f);c=(new JU.M3).setAA(n);c.rotate(b);c.rotate(d);c.rotate(a)}null==this.thisMesh&&0==this.nLCAO&&(this.nLCAO=this.meshCount);c=null==this.thisMesh?
(0<g?"lp":"lcao")+ ++this.nLCAO+"_"+e:this.thisMesh.thisID;null==this.thisMesh&&this.allocMesh(c,null);e.equals("px")?(this.thisMesh.thisID+="a",f=this.thisMesh,this.createLcaoLobe(b,l,g),0<g||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(b,-l,0),this.thisMesh.colix=k,this.linkedMesh=this.thisMesh.linkedMesh=f)):e.equals("py")?(this.thisMesh.thisID+="a",f=this.thisMesh,this.createLcaoLobe(d,l,g),0<g||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(d,-l,0),this.thisMesh.colix=
k,this.linkedMesh=this.thisMesh.linkedMesh=f)):(f=this.thisMesh,e.equals("pz")?(f.thisID+="a",this.createLcaoLobe(a,l,g),0<g||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(a,-l,0),this.thisMesh.colix=k,this.linkedMesh=this.thisMesh.linkedMesh=f)):e.equals("pza")||0==e.indexOf("sp")||0==e.indexOf("d")||0==e.indexOf("lp")?(this.createLcaoLobe(a,l,g),h&&0==g&&(f.thisID+="a",this.setProperty("thisID",c+"b",null),this.createLcaoLobe(a,-l/2,0),this.thisMesh.colix=k,this.linkedMesh=this.thisMesh.linkedMesh=
f)):e.equals("pzb")?this.createLcaoLobe(a,-l,g):e.equals("pxa")?this.createLcaoLobe(b,l,g):e.equals("pxb")?this.createLcaoLobe(b,-l,g):e.equals("pya")?this.createLcaoLobe(d,l,g):e.equals("pyb")?this.createLcaoLobe(d,-l,g):e.equals("spacefill")||e.equals("cpk")?this.createLcaoLobe(null,2*this.ms.at[this.atomIndex].getRadius(),g):this.createLcaoLobe(null,1,g))},"JU.V3,JU.V3,JU.V3,~N,~B");e(d,"createLcaoLobe",function(a,b,c){this.initState();JU.Logger.debugging&&JU.Logger.debug("creating isosurface ID "+
this.thisMesh.thisID);null==a?this.setProperty("sphere",Float.$valueOf(b/2),null):(this.lcaoDir.x=a.x*b,this.lcaoDir.y=a.y*b,this.lcaoDir.z=a.z*b,this.lcaoDir.w=0.7,this.setProperty(2==c?"lp":1==c?"rad":"lobe",this.lcaoDir,null));this.thisMesh.colix=this.defaultColix;this.setScriptInfo(null)},"JU.V3,~N,~N");j(d,"invalidateTriangles",function(){this.thisMesh.invalidatePolygons()});j(d,"setOutputChannel",function(a,b){a.setOutputChannel(b)},"javajs.api.GenericBinaryDocument,JU.OC");j(d,"fillMeshData",
function(a,b,c){if(null==a){if(null==this.thisMesh&&this.allocMesh(null,null),this.thisMesh.isMerged||this.thisMesh.clearType(this.myType,this.sg.params.iAddGridPoints),this.thisMesh.connectedAtoms=this.connections,this.thisMesh.colix=this.getDefaultColix(),this.thisMesh.colorType=this.colorType,this.thisMesh.meshColix=this.meshColix,this.isPhaseColored||this.thisMesh.jvxlData.isBicolorMap)this.thisMesh.isColorSolid=!1}else if(null==c&&(c=this.thisMesh),null!=c)switch(b){case 1:a.mergeVertexCount0=
c.mergeVertexCount0;a.vs=c.vs;a.vertexSource=c.vertexSource;a.vvs=c.vvs;a.vc=c.vc;a.vertexIncrement=c.vertexIncrement;a.pc=c.pc;a.pis=c.pis;a.pcs=c.pcs;a.bsSlabDisplay=c.bsSlabDisplay;a.bsSlabGhost=c.bsSlabGhost;a.slabColix=c.slabColix;a.slabMeshType=c.slabMeshType;a.polygonCount0=c.polygonCount0;a.vertexCount0=c.vertexCount0;a.slabOptions=c.slabOptions;a.colorsExplicit=c.colorsExplicit;break;case 2:if(null==c.vcs||c.vc>c.vcs.length)c.vcs=fa(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");
j(d,"notifySurfaceGenerationCompleted",function(){this.setMeshI();this.setBsVdw();this.thisMesh.surfaceAtoms=this.sg.params.bsSelected;this.thisMesh.insideOut=this.sg.params.isInsideOut();this.thisMesh.isModelConnected=this.sg.params.isModelConnected;this.thisMesh.vertexSource=this.sg.params.vertexSource;this.thisMesh.oabc=this.sg.getOriginVaVbVc();this.thisMesh.calculatedArea=null;this.thisMesh.calculatedVolume=null;this.thisMesh.probeValues=this.sg.params.probeValues;if(!this.thisMesh.isMerged)return this.thisMesh.initialize(this.sg.params.isFullyLit()?
1073741964:1073741958,null,this.sg.params.thePlane),null!=this.jvxlData.fixedLattice&&(this.thisMesh.lattice=this.jvxlData.fixedLattice,this.thisMesh.fixLattice()),this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);this.sg.params.allowVolumeRender||(this.thisMesh.jvxlData.allowVolumeRender=!1);this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);null!=this.thisMesh.jvxlData.slabInfo&&this.vwr.runScriptCautiously("isosurface "+this.thisMesh.jvxlData.slabInfo);0<this.sg.params.psi_monteCarloCount&&
(this.thisMesh.diameter=-1);return!1});j(d,"notifySurfaceMappingCompleted",function(){this.thisMesh.isMerged||this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane);this.setBsVdw();this.thisMesh.isColorSolid=!1;this.thisMesh.colorDensity=this.jvxlData.colorDensity;this.thisMesh.volumeRenderPointSize=this.jvxlData.pointSize;this.thisMesh.colorEncoder=this.sg.params.colorEncoder;this.thisMesh.getContours();0!=this.thisMesh.jvxlData.nContours&&-1!=this.thisMesh.jvxlData.nContours&&
(this.explicitContours=!0);this.explicitContours&&null!=this.thisMesh.jvxlData.jvxlPlane&&(this.thisMesh.havePlanarContours=!0);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073742046:1073741938),null);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073741898:1073742039),null);this.thisMesh.isMerged||this.thisMesh.setJvxlDataRendering();null!=this.sg.params.slabInfo&&(this.thisMesh.slabPolygonsList(this.sg.params.slabInfo,!1),this.thisMesh.reinitializeLightingAndColor(this.vwr));
this.thisMesh.setColorCommand()});e(d,"setBsVdw",function(){null!=this.sg.bsVdw&&(null==this.thisMesh.bsVdw&&(this.thisMesh.bsVdw=new JU.BS),this.thisMesh.bsVdw.or(this.sg.bsVdw))});j(d,"calculateGeodesicSurface",function(a,b){return this.vwr.calculateSurface(a,b)},"JU.BS,~N");j(d,"getSurfacePointIndexAndFraction",function(){return 0},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");j(d,"addVertexCopy",function(a,b,c,g){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,g)},"JU.T3,~N,~N,~B");j(d,"addTriangleCheck",function(a,b,c,g,d,e,h){return 0>a||0>b||0>c||e&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.thisMesh.vvs)?-1:this.thisMesh.addTriangleCheck(a,b,c,g,d,h)},"~N,~N,~N,~N,~N,~B,~N");e(d,"setScriptInfo",function(a){a=null==a?this.sg.params.script:a;var b=null==a?-1:a.indexOf("; isosurface map");
if(0==b)null!=this.thisMesh.scriptCommand&&(b=this.thisMesh.scriptCommand.indexOf("; isosurface map"),0<=b&&(this.thisMesh.scriptCommand=this.thisMesh.scriptCommand.substring(0,b)),this.thisMesh.scriptCommand+=a);else if(this.thisMesh.title=this.sg.params.title,this.thisMesh.dataType=this.sg.params.dataType,this.thisMesh.scale3d=this.sg.params.scale3d,null!=a&&(null!=this.oldFileName&&(a=a.$replace(this.oldFileName,this.newFileName))," "==a.charAt(0)&&(a=this.myType+" ID "+JU.PT.esc(this.thisMesh.thisID)+
a,b=a.indexOf("; isosurface map"))),this.thisMesh.scriptCommand=0<b&&0<this.scriptAppendix.length?a.substring(0,b)+this.scriptAppendix+a.substring(b):a+this.scriptAppendix,!this.explicitID&&null!=a&&0<=(b=a.indexOf("# ID=")))this.thisMesh.thisID=JU.PT.getQuotedStringAt(a,b)},"~S");j(d,"addRequiredFile",function(a){a=' # /*file*/"'+a+'"';0>this.scriptAppendix.indexOf(a)&&(this.scriptAppendix+=a)},"~S");j(d,"setRequiredFile",function(a,b){this.oldFileName=a;this.newFileName=b},"~S,~S");e(d,"setJvxlInfo",
function(){if(this.sg.jvxlData!==this.jvxlData||this.sg.jvxlData!==this.thisMesh.jvxlData)this.jvxlData=this.thisMesh.jvxlData=this.sg.jvxlData});j(d,"getShapeDetail",function(){for(var a=new JU.Lst,b=0;b<this.meshCount;b++){var c=new java.util.Hashtable,g=this.isomeshes[b];null==g||(null==g.vs||0==g.vc&&0==g.pc)||(this.addMeshInfo(g,c),a.addLast(c))}return a});e(d,"addMeshInfo",function(a,b){b.put("ID",null==a.thisID?"<noid>":a.thisID);b.put("visible",Boolean.$valueOf(a.visible));b.put("vertexCount",
Integer.$valueOf(a.vc));null!=a.calculatedVolume&&b.put("volume",a.calculatedVolume);null!=a.calculatedArea&&b.put("area",a.calculatedArea);Float.isNaN(a.ptCenter.x)||b.put("center",a.ptCenter);null!=a.mat4&&b.put("mat4",a.mat4);0!=a.scale3d&&b.put("scale3d",Float.$valueOf(a.scale3d));b.put("xyzMin",a.jvxlData.boundingBox[0]);b.put("xyzMax",a.jvxlData.boundingBox[1]);var c=J.jvxl.data.JvxlCoder.jvxlGetInfo(a.jvxlData);null!=c&&b.put("jvxlInfo",c.$replace("\n"," "));b.put("modelIndex",Integer.$valueOf(a.modelIndex));
b.put("color",JU.CU.colorPtFromInt(JU.C.getArgb(a.colix),null));null!=a.colorEncoder&&b.put("colorKey",a.colorEncoder.getColorKey());null!=a.title&&b.put("title",a.title);(null!=a.jvxlData.contourValues||null!=a.jvxlData.contourValuesUsed)&&b.put("contours",a.getContourList(this.vwr))},"J.shapesurface.IsosurfaceMesh,java.util.Map");j(d,"getPlane",function(){return null},"~N");j(d,"getValue",function(){return 0},"~N,~N,~N,~N");j(d,"checkObjectHovered",function(a,b,c){if(null!=this.keyXy&&a>=this.keyXy[0]&&
b>=this.keyXy[1]&&a<this.keyXy[2]&&b<this.keyXy[3])return this.hoverKey(a,b),!0;if(!this.vwr.getDrawHover())return!1;c=this.findValue(a,b,!1,c);if(null==c)return!1;this.vwr.hoverOnPt(a,b,c,this.pickedMesh.thisID,this.pickedPt);return!0},"~N,~N,JU.BS");e(d,"hoverKey",function(a,b){try{var c,g=1-1*(b-this.keyXy[1])/(this.keyXy[3]-this.keyXy[1]);if(this.thisMesh.showContourLines){var d=this.thisMesh.getContours();if(null==d){if(null==this.thisMesh.jvxlData.contourValues)return;var e=D(Math.floor(g*this.thisMesh.jvxlData.contourValues.length));
if(0>e||e>this.thisMesh.jvxlData.contourValues.length)return;c=""+this.thisMesh.jvxlData.contourValues[e]}else{e=D(Math.floor(g*d.length));if(0>e||e>d.length)return;c=""+d[e].get(2).floatValue()}}else{var h=this.thisMesh.colorEncoder.quantize(g,!0),g=this.thisMesh.colorEncoder.quantize(g,!1);c=""+h+" - "+g}this.vwr.hoverOnPt(a,b,c,null,null)}catch(f){if(!ea(f,Exception))throw f;}},"~N,~N");j(d,"checkObjectClicked",function(a,b,c,g,d){if(!d||!this.vwr.isBound(c,18))return null;c=100;this.vwr.gdata.isAntialiased()&&
(a<<=1,b<<=1,c<<=1);for(var e=d=-1,h=-2147483648,f=2147483647,k=0;k<this.meshCount;k++){var l=this.isomeshes[k];if(this.isPickable(l,g)&&(l=l.vs,null!=l))for(var n=l.length;0<=--n;){var O=l[n];null!=O&&0<=this.coordinateInRange(a,b,O,c,this.ptXY)&&(this.ptXY.z<f&&(d=k,f=this.ptXY.z,e=n),this.ptXY.z>h&&(h=this.ptXY.z))}}if(0>d)return null;this.pickedMesh=this.isomeshes[d];this.setPropertySuper("thisID",this.pickedMesh.thisID,null);this.pickedVertex=e;a=new JU.P3;a.setT(this.pickedMesh.vs[this.pickedVertex]);
this.pickedModel=this.pickedMesh.modelIndex;b=this.getPickedPoint(a,this.pickedModel);this.setStatusPicked(-4,a,b);return b},"~N,~N,~N,JU.BS,~B");e(d,"isPickable",function(a,b){return 0!=a.visibilityFlags&&(0>a.modelIndex||b.get(a.modelIndex))&&!JU.C.isColixTranslucent(a.colix)},"J.shapesurface.IsosurfaceMesh,JU.BS");e(d,"findValue",function(a,b,c,g){c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var d=-1,e=null,h=null,f=0;f<this.meshCount;f++)if(h=this.isomeshes[f],this.isPickable(h,
g)){var k=h.jvxlData.vContours,l=0>h.firstRealVertex?0:h.firstRealVertex,n=0;if(null!=k&&0<k.length){for(l=0;l<k.length;l++)for(var O=k[l],q=O.size()-1,j=6;j<q;j++){var v=O.get(j),r=this.coordinateInRange(a,b,v,c,this.ptXY);0<=r&&(c=r,e=O,n=l,this.pickedMesh=h,this.pickedPt=v)}if(null!=e)return e.get(2).toString()+(JU.Logger.debugging?" "+n:"")}else if(null!=h.jvxlData.jvxlPlane&&null!=h.vvs){k=null==h.mat4&&0==h.scale3d?h.vs:h.getOffsetVertices(h.jvxlData.jvxlPlane);for(j=h.vc;--j>=l;)v=k[j],r=this.coordinateInRange(a,
b,v,c,this.ptXY),0<=r&&(c=r,d=j,this.pickedMesh=h,this.pickedPt=v);if(-1!=d)break}else if(null!=h.vvs){if(null!=h.bsSlabDisplay)for(j=h.bsSlabDisplay.nextSetBit(0);0<=j;j=h.bsSlabDisplay.nextSetBit(j+1)){if(k=h.pis[j],null!=k)for(n=0;3>n;n++)v=h.vs[k[n]],r=this.coordinateInRange(a,b,v,c,this.ptXY),0<=r&&(c=r,d=k[n],this.pickedMesh=h,this.pickedPt=v)}else for(j=h.vc;--j>=l;)v=h.vs[j],r=this.coordinateInRange(a,b,v,c,this.ptXY),0<=r&&(c=r,d=j,this.pickedMesh=h,this.pickedPt=v);if(-1!=d)break}}return-1==
d?null:(JU.Logger.debugging?"$"+h.thisID+"["+(d+1)+"] "+h.vs[d]+": ":h.thisID+": ")+h.vvs[d]},"~N,~N,~B,JU.BS");e(d,"getCmd",function(a){var b=(new JU.SB).append("\n");this.getMeshCommand(b,a);return b.toString()},"~N");j(d,"getValues",function(a){return null==a?null:a.getValidValues(null)},"J.shape.Mesh");j(d,"getVertices",function(a){return null==a?null:a.getValidVertices(null)},"J.shape.Mesh")});L("J.jvxl.data");R(null,"J.jvxl.data.JvxlCoder","JU.BS $.Lst $.P3 $.PT $.SB J.api.Interface J.jvxl.data.VolumeData JU.BSUtil $.C $.Escape $.Logger JV.Viewer".split(" "),
function(){var d=Ca(J.jvxl.data,"JvxlCoder",null);d.jvxlGetFile=e(d,"jvxlGetFile",function(a,b,c,g,d,e,h,f){J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var k=new JU.SB;if("TRAILERONLY".equals(g))return JU.XmlUtil.closeTag(k,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(k,"jvxl"),k.toString();var l=null!=b,n="HEADERONLY".equals(g);if(d){JU.XmlUtil.openDocument(k);JU.XmlUtil.openTagAttr(k,"jvxl",y(-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 j=l?null:a.jvxlVolumeDataXml;null==j&&(j=(new J.jvxl.data.VolumeData).setVolumetricXml());k.append(j);JU.XmlUtil.openTagAttr(k,"jvxlSurfaceSet",y(-1,["count",""+(0<e?e:1)]));if(n)return k.toString()}e=l?"pmesh":null==a.jvxlPlane?"isosurface":"plane";null!=a.jvxlColorData&&0<a.jvxlColorData.length&&(e="mapped "+e);JU.XmlUtil.openTagAttr(k,"jvxlSurface",y(-1,
["type",e]));k.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,l));J.jvxl.data.JvxlCoder.jvxlAppendCommandState(k,f,h);if(null!=c||null!=g&&0<g.length){h=new JU.SB;null!=g&&0<g.length&&h.append(g).append("\n");if(null!=c)for(g=0;g<c.length;g++)h.append(c[g]).appendC("\n");JU.XmlUtil.appendCdata(k,"jvxlSurfaceTitle",null,h.toString())}h=new JU.SB;JU.XmlUtil.openTagAttr(h,"jvxlSurfaceData",l||null==a.jvxlPlane?null:null==a.mapLattice?y(-1,["plane",JU.Escape.eP4(a.jvxlPlane)]):y(-1,["plane",JU.Escape.eP4(a.jvxlPlane),
"maplattice",JU.Escape.eP(a.mapLattice)]));if(l)J.jvxl.data.JvxlCoder.appendXmlVertexOnlyData(h,a,b,!0);else{if(null==a.jvxlPlane){if(null==a.jvxlEdgeData)return"";J.jvxl.data.JvxlCoder.appendXmlEdgeData(h,a)}J.jvxl.data.JvxlCoder.appendXmlColorData(h,a.jvxlColorData,!0,a.isJvxlPrecisionColor,a.valueMappedToRed,a.valueMappedToBlue)}l||(J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlInvalidatedVertexData",a.jvxlExcluded[1],-1,null),0<a.excludedVertexCount&&(J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,
"jvxlExcludedVertexData",a.jvxlExcluded[0],a.excludedVertexCount,null),J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlExcludedPlaneData",a.jvxlExcluded[2],-1,null)));J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(h,"jvxlExcludedTriangleData",a.jvxlExcluded[3],a.excludedTriangleCount,null);JU.XmlUtil.closeTag(h,"jvxlSurfaceData");b=h.length();k.appendSB(h);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",y(-1,["baseColor",a.baseColor]));var q;for(c=a.vertexColorMap.entrySet().iterator();c.hasNext()&&((q=c.next())||1);)J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(k,"jvxlColorMap",q.getValue(),-1,y(-1,["color",q.getKey()]));a.vertexColorMap=null;JU.XmlUtil.closeTag(k,"jvxlVertexColorData")}JU.XmlUtil.closeTag(k,"jvxlSurface");d&&(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");d.checkHaveXMLUtil=e(d,"checkHaveXMLUtil",function(){J.jvxl.data.JvxlCoder.haveXMLUtil||(JV.Viewer.isJS&&J.api.Interface.getInterface("JU.XmlUtil",null,"show"),J.jvxl.data.JvxlCoder.haveXMLUtil=!0)});d.appendEncodedBitSetTag=e(d,"appendEncodedBitSetTag",function(a,b,c,g,d){0>g&&(g=JU.BSUtil.cardinalityOf(c));if(0!=g){var e=new JU.SB;e.append("\n ");J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(c,-1,e);JU.XmlUtil.appendTagObj(a,b,
y(-1,[d,"bsEncoding","base90+35","count",""+g,"len",""+c.length()]),J.jvxl.data.JvxlCoder.jvxlCompressString(e.toString(),!0))}},"JU.SB,~S,JU.BS,~N,~A");d.jvxlSetCompressionRatio=e(d,"jvxlSetCompressionRatio",function(a,b,c){a=a.toString();b=w(0<b.nBytes?b.nBytes/c:13*b.nPointsX*b.nPointsY*b.nPointsZ/c);return JU.PT.rep(a,'"not calculated"',0<b?'"'+b+':1"':'"?"')},"JU.SB,J.jvxl.data.JvxlData,~N");d.appendXmlEdgeData=e(d,"appendXmlEdgeData",function(a,b){JU.XmlUtil.appendTagObj(a,"jvxlEdgeData",y(-1,
["count",""+(b.jvxlEdgeData.length-1),"encoding","base90f1","bsEncoding","base90+35c","isXLowToHigh",""+b.isXLowToHigh,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlEdgeData,!0)]),"\n"+J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlSurfaceData,!0))},"JU.SB,J.jvxl.data.JvxlData");d.jvxlAppendCommandState=e(d,"jvxlAppendCommandState",function(a,b,c){null!=b&&JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceCommand",null,"\n"+(0>b.indexOf("#")?b:b.substring(0,b.indexOf("#")))+"\n");null!=c&&(0<=c.indexOf("** XML ** ")?
(c=JU.PT.split(c,"** XML **")[1].trim(),JU.XmlUtil.appendTag(a,"jvxlIsosurfaceState","\n"+c+"\n")):(b=c.indexOf("color isosurface [{"),0<=b&&(c=c.substring(0,b)),JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceState",null,"\n"+c)))},"JU.SB,~S,~S");d.appendXmlColorData=e(d,"appendXmlColorData",function(a,b,c,g,d,e){var h;if(!(null==b||0>(h=b.length-1)))g&&(h/=2),JU.XmlUtil.appendTagObj(a,"jvxlColorData",y(-1,["count",""+h,"encoding",c?"base90f"+(g?"2":"1"):"none","min",""+d,"max",""+e,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b,
!0)]),null)},"JU.SB,~S,~B,~B,~N,~N");d.jvxlGetInfo=e(d,"jvxlGetInfo",function(a){return J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,a.vertexDataOnly)},"J.jvxl.data.JvxlData");d.jvxlGetInfoData=e(d,"jvxlGetInfoData",function(a,b){if(null==a.jvxlSurfaceData)return"";J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var c=new JU.Lst,g=a.nSurfaceInts,d=b?0:a.jvxlEdgeData.length-1,e=null==a.jvxlColorData?-1:a.jvxlColorData.length-1;J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isModelConnected",""+a.isModelConnected);if(!b){J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  cutoff",null==a.cutoffRange?""+a.cutoff:a.cutoffRange[0]+" "+a.cutoffRange[1]);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isCutoffAbsolute",""+a.isCutoffAbsolute);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  pointsPerAngstrom",""+a.pointsPerAngstrom);var h=a.jvxlSurfaceData.length+d+e+1;0<h&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesData",""+h);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isXLowToHigh",""+a.isXLowToHigh);null==a.jvxlPlane&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nSurfaceInts",""+g),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  nBytesUncompressedEdgeData",""+d));0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedColorData",""+e)}a.excludedVertexCount=JU.BSUtil.cardinalityOf(a.jvxlExcluded[0]);a.excludedTriangleCount=JU.BSUtil.cardinalityOf(a.jvxlExcluded[3]);0<a.excludedVertexCount&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nExcludedVertexes",""+a.excludedVertexCount);0<a.excludedTriangleCount&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nExcludedTriangles",""+a.excludedTriangleCount);h=JU.BSUtil.cardinalityOf(a.jvxlExcluded[1]);
0<h&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nInvalidatedVertexes",""+h);null!=a.slabInfo&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  slabInfo",a.slabInfo);a.isJvxlPrecisionColor&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  precisionColor","true");a.colorDensity&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorDensity","true");Float.isNaN(a.pointSize)?0!=a.diameter&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  diameter",""+a.diameter):J.jvxl.data.JvxlCoder.addAttrib(c,"\n  pointSize",""+a.pointSize);a.allowVolumeRender||
J.jvxl.data.JvxlCoder.addAttrib(c,"\n  allowVolumeRender","false");null==a.jvxlPlane||b?(null!=a.fixedLattice&&!b&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  fixedLattice",""+a.fixedLattice),a.isContoured?(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contoured","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true")):a.isBicolorMap?(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  bicolorMap","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorNegative",JU.C.getHexCode(a.minColorIndex)),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  colorPositive",JU.C.getHexCode(a.maxColorIndex))):0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true"),null!=a.vContours&&0<a.vContours.length&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContourData",""+a.vContours.length)):(null!=a.mapLattice&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  mapLattice",""+a.mapLattice),0!=a.scale3d&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  scale3d",""+a.scale3d),0<e&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorMapped","true"),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  plane",JU.Escape.eP4(a.jvxlPlane)));null!=a.color&&0>a.color.indexOf("null")&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  color",a.color);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  translucency",""+a.translucency);null!=a.meshColor&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  meshColor",a.meshColor);null!=a.colorScheme&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  colorScheme",a.colorScheme);null!=a.rendering&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  rendering",a.rendering);null!=a.thisSet&&(g=J.jvxl.data.JvxlCoder.subsetString(a.thisSet),
g.startsWith("[")?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  subset",g):J.jvxl.data.JvxlCoder.addAttrib(c,"\n  set",g));-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);g=3.4028235E38==a.mappedDataMin?0:a.mappedDataMin;d=a.isColorReversed?a.valueMappedToRed:a.valueMappedToBlue;e=a.isColorReversed?
a.valueMappedToBlue:a.valueMappedToRed;null!=a.jvxlColorData&&(0<a.jvxlColorData.length&&!a.isBicolorMap)&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMinimum",""+g),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMaximum",""+a.mappedDataMax),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToRed",""+e),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToBlue",""+d));a.isContoured&&(null==a.contourValues||null==a.contourColixes?null==a.vContours&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+Math.abs(a.nContours)):
(null!=a.jvxlPlane&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contoured","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+a.contourValues.length),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourValues",JU.Escape.eAF(null==a.contourValuesUsed?a.contourValues:a.contourValuesUsed)),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourColors",a.contourColors)),0<a.thisContour&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  thisContour",""+a.thisContour));a.insideOut&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  insideOut",
"true");a.vertexDataOnly?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","vertex/face data only"):a.isXLowToHigh&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","progressive JVXL+ -- X values read from low(0) to high("+(a.nPointsX-1)+")");J.jvxl.data.JvxlCoder.addAttrib(c,"\n  xyzMin",JU.Escape.eP(a.boundingBox[0]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  xyzMax",JU.Escape.eP(a.boundingBox[1]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  jmolVersion",a.version);g=new JU.SB;JU.XmlUtil.openTagAttr(g,"jvxlSurfaceInfo",
c.toArray(Array(c.size())));JU.XmlUtil.closeTag(g,"jvxlSurfaceInfo");return g.toString()},"J.jvxl.data.JvxlData,~B");d.subsetString=e(d,"subsetString",function(a){if(1<a.cardinality()){for(var b="[ ",c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c))b+=++c+" ";return b+"]"}return""+(a.nextSetBit(0)+1)},"JU.BS");d.addAttrib=e(d,"addAttrib",function(a,b,c){a.addLast(y(-1,[b,c]))},"JU.Lst,~S,~S");d.jvxlEncodeContourData=e(d,"jvxlEncodeContourData",function(a,b){JU.XmlUtil.openTagAttr(b,"jvxlContourData",y(-1,
["count",""+a.length]));for(var c=0;c<a.length;c++)if(!(6>a[c].size())){var g=a[c].get(0).intValue(),d=new JU.SB;d.append("\n");var e=a[c].get(1);J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(e,g,d);JU.XmlUtil.appendTagObj(b,"jvxlContour",y(-1,["index",""+c,"value",""+a[c].get(2),"color",JU.Escape.escapeColor(a[c].get(4)[0]),"count",""+e.length(),"encoding","base90iff1","bsEncoding","base90+35c","data",J.jvxl.data.JvxlCoder.jvxlCompressString(a[c].get(5).toString(),!0)]),J.jvxl.data.JvxlCoder.jvxlCompressString(d.toString(),
!0))}JU.XmlUtil.closeTag(b,"jvxlContourData")},"~A,JU.SB");d.set3dContourVector=e(d,"set3dContourVector",function(a,b,c){if(!(6>a.size()))for(var g=a.get(5),d=a.get(1),e=0,h=g.length(),f=0,k=" ",l=" ",n=d.nextSetBit(0);0<=n;n=d.nextSetBit(n+1)){for(var j=b[n];e<h&&!JU.PT.isDigit(k=g.charAt(e++)););for(f=k.charCodeAt(0)-48;e<h&&JU.PT.isWhitespace(k=g.charAt(e++)););for(;e<h&&JU.PT.isWhitespace(l=g.charAt(e++)););var q=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(k.charCodeAt(0),35,90,0),r=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(l.charCodeAt(0),
35,90,0),v,t;0==(f&1)?(v=j[1],t=f=j[2],j=j[0]):(v=j[0],t=j[1],0!=(f&2)?(f=t,j=j[2]):(f=j[2],j=v));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,v,t,q));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,f,j,r))}},"JU.Lst,~A,~A");d.getContourPoint=e(d,"getContourPoint",function(a,b,c,g){var d=new JU.P3;d.sub2(a[c],a[b]);d.scaleAdd2(g,d,a[b]);return d},"~A,~N,~N,~N");d.appendContourTriangleIntersection=e(d,"appendContourTriangleIntersection",function(a,b,c,g){g.appendI(a);g.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(b));
g.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(c))},"~N,~N,~N,JU.SB");d.jvxlCreateColorData=e(d,"jvxlCreateColorData",function(a,b){if(null==b)a.jvxlColorData="";else{var c=a.colorFractionBase,g=a.colorFractionRange;(0<a.saveVertexCount?a.saveVertexCount:a.vertexCount)>b.length&&System.out.println("JVXLCODER ERROR");var d=a.isJvxlPrecisionColor;a.jvxlColorData=J.jvxl.data.JvxlCoder.jvxlEncodeColorData(b,d?a.mappedDataMin:a.valueMappedToRed,d?a.mappedDataMax:a.valueMappedToBlue,c,g,a.isTruncated,
d)}},"J.jvxl.data.JvxlData,~A");d.jvxlEncodeColorData=e(d,"jvxlEncodeColorData",function(a,b,c,g,d,e,h){for(var f=new JU.SB,k=new JU.SB,l=0,n=a.length;l<n;l++){var j=a[l];Float.isNaN(j)&&(j=b);e&&(j=0<j?0.999:-0.999);h?J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(j,b,c,g,d,f,k):f.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(j,b,c,g,d))}return f.appendSB(k).appendC("\n").toString()},"~A,~N,~N,~N,~N,~B,~B");d.appendXmlVertexOnlyData=e(d,"appendXmlVertexOnlyData",function(a,b,c,g){var d=r(c.vc,0);
J.jvxl.data.JvxlCoder.appendXmlTriangleData(a,c.pis,c.pc,c.bsSlabDisplay,d,g)&&J.jvxl.data.JvxlCoder.appendXmlVertexData(a,b,d,c.vs,c.vvs,c.vc,c.polygonColorData,c.pc,c.bsSlabDisplay,b.vertexColors,0<b.jvxlColorData.length,g)},"JU.SB,J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~B");d.appendXmlTriangleData=e(d,"appendXmlTriangleData",function(a,b,c,g,d,e){for(var h=new JU.SB,f=new JU.SB,k=1,l=0,n=0,j=!1,q=0,r=null!=g,v=0;v<c;)if(null==b[v]||r&&!g.get(v))v++;else{var t=b[v][l],t=0<d[t]?d[t]:d[t]=++n,
w=t-k,k=t;0==w?(h.appendC("!"),j=!1):32<w?(j&&h.appendC("+"),h.appendI(w),j=!0):-32>w?(h.appendI(w),j=!0):(h.appendC(String.fromCharCode(92+w)),j=!1);0==++l%3&&(f.appendI(b[v][3]),l=0,v++,q++)}if(0==h.length())return!0;JU.XmlUtil.appendTagObj(a,"jvxlTriangleData",y(-1,["count",""+q,"encoding","jvxltdiff","data",J.jvxl.data.JvxlCoder.jvxlCompressString(h.toString(),e)]),null);JU.XmlUtil.appendTagObj(a,"jvxlTriangleEdgeData",y(-1,["count",""+q,"encoding","jvxlsc","data",J.jvxl.data.JvxlCoder.jvxlCompressString(f.toString(),
e)]),null);return!0},"JU.SB,~A,~N,JU.BS,~A,~B");d.appendXmlVertexData=e(d,"appendXmlVertexData",function(a,b,c,g,d,e,h,f,k,l,n,j){var q=b.colorFractionBase,S=b.colorFractionRange,v,t=b.boundingBox[0],w=b.boundingBox[1],D=new JU.SB,C=new JU.SB,Q=null,L=null!=k;if(0<f){L&&(f=k.cardinality());for(var L=!1,Q=r(e,0),E=0;E<e;E++)0<c[E]&&(Q[c[E]-1]=E)}for(E=c=0;E<e;E++)if(!L||k.get(E))c++,v=g[0==f?E:Q[E]],J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.x,t.x,w.x,q,S,D,C),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.y,
t.y,w.y,q,S,D,C),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(v.z,t.z,w.z,q,S,D,C);D.appendSB(C);JU.XmlUtil.appendTagObj(a,"jvxlVertexData",y(-1,["count",""+c,"min",JU.Escape.eP(t),"max",JU.Escape.eP(w),"encoding","base90xyz2","data",J.jvxl.data.JvxlCoder.jvxlCompressString(D.toString(),j)]),null);null!=h&&JU.XmlUtil.appendTagObj(a,"jvxlPolygonColorData",y(-1,["encoding","jvxlnc","count",""+f]),"\n"+h);if(n){D=new JU.SB;C=new JU.SB;if(null==l)for(E=0;E<e;E++){if(!L||k.get(E))J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(d[0==
f?E:Q[E]],b.mappedDataMin,b.mappedDataMax,q,S,D,C)}else{g=0;D.appendI(c).append(" ");for(E=0;E<e;E++)if(!L||k.get(E))d=l[0==f?E:Q[E]],d==g?d=0:g=d,D.appendI(d),D.append(" ")}J.jvxl.data.JvxlCoder.appendXmlColorData(a,D.appendSB(C).append("\n").toString(),null==l,!0,b.valueMappedToRed,b.valueMappedToBlue)}},"JU.SB,J.jvxl.data.JvxlData,~A,~A,~A,~N,~S,~N,JU.BS,~A,~B,~B");d.jvxlFractionAsCharacter=e(d,"jvxlFractionAsCharacter",function(a){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,35,
90)},"~N");d.jvxlFractionAsCharacterRange=e(d,"jvxlFractionAsCharacterRange",function(a,b,c){0.9999<a?a=0.9999:Float.isNaN(a)&&(a=1.0001);a=D(Math.floor(a*c+b));return a<b?String.fromCharCode(b):92==a?"!":String.fromCharCode(a)},"~N,~N,~N");d.jvxlAppendCharacter2=e(d,"jvxlAppendCharacter2",function(a,b,c,g,d,e,h){a=b==c?a:(a-b)/(c-b);b=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,g,d);e.appendC(b);a-=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b.charCodeAt(0),g,d,0);h.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a*
d,g,d))},"~N,~N,~N,~N,~N,JU.SB,JU.SB");d.jvxlFractionFromCharacter=e(d,"jvxlFractionFromCharacter",function(a,b,c,g){if(a==b+c)return NaN;a<b&&(a=92);a=(a-b+g)/c;return 0>a?0:1<a?0.999999:a},"~N,~N,~N,~N");d.jvxlFractionFromCharacter2=e(d,"jvxlFractionFromCharacter2",function(a,b,c,g){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(a,c,g,0);b=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b,c,g,0.5);return a+b/g},"~N,~N,~N,~N");d.jvxlValueAsCharacter=e(d,"jvxlValueAsCharacter",function(a,b,c,g,
d){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(b==c?a:(a-b)/(c-b),g,d)},"~N,~N,~N,~N,~N");d.jvxlValueFromCharacter2=e(d,"jvxlValueFromCharacter2",function(a,b,c,g,d,e){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(a,b,d,e);return g==c?a:c+a*(g-c)},"~N,~N,~N,~N,~N,~N");d.jvxlEncodeBitSet0=e(d,"jvxlEncodeBitSet0",function(a,b,c){var g=0,d=-1,e=0;0>b&&(b=a.length());for(var h=0,f=!1,k=b-1,l=0;l<b;++l)f==a.get(l)?g++:(g==d&&l!=k?e++:(0<e&&(c.appendC(" ").appendI(-e),e=0,h++),c.appendC(" ").appendI(g),
h++,d=g),g=1,f=!f);c.appendC(" ").appendI(g).appendC("\n");return h},"JU.BS,~N,JU.SB");d.jvxlEncodeBitSet=e(d,"jvxlEncodeBitSet",function(a){var b=new JU.SB;J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,-1,b);return b.toString()},"JU.BS");d.jvxlEncodeBitSetBuffer=e(d,"jvxlEncodeBitSetBuffer",function(a,b,c){var g=0,d=0,e=!1;0>b&&(b=a.length());if(0==b)return 0;c.append("-");for(var h=0;h<b;++h)e==a.get(h)?g++:(J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,g,35,90),d++,g=1,e=!e);J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,
g,35,90);c.appendC("\n");return d},"JU.BS,~N,JU.SB");d.jvxlAppendEncodedNumber=e(d,"jvxlAppendEncodedNumber",function(a,b,c,g){var d=b<g;for(0==b?a.appendC(String.fromCharCode(c)):d||a.appendC(String.fromCharCode(c+g));0<b;){var e=D(b/g);b=c+b-e*g;92==b&&(b=33);a.appendC(String.fromCharCode(b));b=e}d||a.append(" ")},"JU.SB,~N,~N,~N");d.jvxlDecodeBitSetRange=e(d,"jvxlDecodeBitSetRange",function(a,b,c){for(var g=new JU.BS,d=0,e=0,h=!1,f=r(1,0);-2147483648!=(d=J.jvxl.data.JvxlCoder.jvxlParseEncodedInt(a,
b,c,f));)h&&g.setBits(e,e+d),e+=d,h=!h;return g},"~S,~N,~N");d.jvxlParseEncodedInt=e(d,"jvxlParseEncodedInt",function(a,b,c,g){var d=!1,e=0,h=g[0],f=a.length;if(0>h)return-2147483648;for(;h<f&&JU.PT.isWhitespace(a.charAt(h));)++h;if(h>=f)return-2147483648;var k=1,l=a.charAt(h).charCodeAt(0)==b+c;for(l&&h++;h<f&&!JU.PT.isWhitespace(a.charAt(h));){d=a.charAt(h).charCodeAt(0);d<b&&(d=92);e+=(d-b)*k;d=!0;++h;if(!l)break;k*=c}d||(e=-2147483648);g[0]=h;return e},"~S,~N,~N,~A");d.jvxlDecodeBitSet=e(d,"jvxlDecodeBitSet",
function(a){if(a.startsWith("-"))return J.jvxl.data.JvxlCoder.jvxlDecodeBitSetRange(J.jvxl.data.JvxlCoder.jvxlDecompressString(a.substring(1)),35,90);for(var b=new JU.BS,c=0,g=0,d=0,e=0,h=!1,f=r(1,0);;){c=0>d++?c:JU.PT.parseIntNext(a,f);if(-2147483648==c)break;0>c?(d=c,c=g):(h&&b.setBits(e,e+c),e+=c,g=c,h=!h)}return b},"~S");d.jvxlCompressString=e(d,"jvxlCompressString",function(a,b){if(0<=a.indexOf("~"))return a;for(var c=new JU.SB,g="\x00",d=!1,e=!1,h=0,f=a.length,k=0;k<=f;k++){var l=k==f?"\x00":
a.charAt(k);switch(l.charCodeAt(0)){case 10:case 13:continue;case 38:case 60:d=b;break;default:d=!1}if(l==g)++h,l="\x00";else if(0<h||e){if(4>h&&!e||" "==g||"\t"==g)for(;0<=--h;)c.appendC(g);else e?e=!1:c.appendC("~"),c.appendI(h),c.appendC(" ");h=0}"\x00"!=l&&(d?(e=!0,c.appendC("~"),g=l,l=String.fromCharCode(l.charCodeAt(0)-1)):g=l,c.appendC(l))}return c.toString()},"~S,~B");d.jvxlDecompressString=e(d,"jvxlDecompressString",function(a){if(0>a.indexOf("~"))return a;for(var b=new JU.SB,c="\x00",g=
r(1,0),d=0;d<a.length;d++){var e=a.charAt(d);if("~"==e)switch(g[0]=++d,(e=a.charAt(d)).charCodeAt(0)){case 59:case 37:g[0]++,b.appendC(c=String.fromCharCode(e.charCodeAt(0)+1));case 49:case 50:case 51:case 52:case 53:case 54:case 55:case 56:case 57:d=JU.PT.parseIntNext(a,g);for(e=0;e<d;e++)b.appendC(c);d=g[0];continue;case 126:--d;break;default:JU.Logger.error("Error uncompressing string "+a.substring(0,d)+"?")}b.appendC(e);c=e}return b.toString()},"~S");d.jvxlCreateHeaderWithoutTitleOrAtoms=e(d,
"jvxlCreateHeaderWithoutTitleOrAtoms",function(a,b){J.jvxl.data.JvxlCoder.jvxlCreateHeader(a,b)},"J.jvxl.data.VolumeData,JU.SB");d.jvxlCreateHeader=e(d,"jvxlCreateHeader",function(a,b){a.setVolumetricXml();0==b.length()&&b.append("Line 1\nLine 2\n")},"J.jvxl.data.VolumeData,JU.SB");d.haveXMLUtil=!1});L("J.jvxl.data");R(["JU.M3","$.P3","$.V3"],"J.jvxl.data.VolumeData",["java.util.Hashtable","JU.SB","JU.Escape","$.Logger"],function(){var d=N(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;C(this,arguments)},J.jvxl.data,"VolumeData",null);ia(d,function(){this.volumetricOrigin=new JU.P3;this.origin=t(3,0);this.volumetricVectors=Array(3);this.voxelCounts=r(3,0);this.volumetricVectorLengths=t(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});da(d,function(){this.volumetricVectors[0]=new JU.V3;this.volumetricVectors[1]=new JU.V3;this.volumetricVectors[2]=new JU.V3;
this.unitVolumetricVectors[0]=new JU.V3;this.unitVolumetricVectors[1]=new JU.V3;this.unitVolumetricVectors[2]=new JU.V3});e(d,"getVoxelData",function(){return this.voxelData});e(d,"setVoxelDataAsArray",function(a){this.voxelData=a;null!=a&&(this.sr=null)},"~A");e(d,"hasPlane",function(){return null!=this.thePlane});e(d,"setMappingPlane",function(a){this.mappingPlane=a;null!=a&&(this.mappingPlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z))},"JU.P4");e(d,"distanceToMappingPlane",function(a){return(this.mappingPlane.x*
a.x+this.mappingPlane.y*a.y+this.mappingPlane.z*a.z+this.mappingPlane.w)/this.mappingPlaneNormalMag},"JU.T3");e(d,"setVolumetricOrigin",function(a,b,c){this.volumetricOrigin.set(a,b,c)},"~N,~N,~N");e(d,"getOriginFloat",function(){return this.origin});e(d,"getYzCount",function(){this.minGrid=this.volumetricVectors[0].length();this.minGrid=Math.min(this.minGrid,this.volumetricVectors[1].length());this.minGrid=Math.min(this.minGrid,this.volumetricVectors[2].length());this.maxGrid=this.volumetricVectors[0].length();
this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[1].length());this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[2].length());this.nPoints=this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2];return this.yzCount=this.voxelCounts[1]*this.voxelCounts[2]});e(d,"getVolumetricVectorLengths",function(){return this.volumetricVectorLengths});e(d,"setVolumetricVector",function(a,b,c,g){this.volumetricVectors[a].x=b;this.volumetricVectors[a].y=c;this.volumetricVectors[a].z=g;this.setUnitVectors()},
"~N,~N,~N,~N");e(d,"getVoxelCounts",function(){return this.voxelCounts});e(d,"setVoxelCounts",function(a,b,c){this.voxelCounts[0]=a;this.voxelCounts[1]=b;this.voxelCounts[2]=c;return a*b*c},"~N,~N,~N");e(d,"getVoxelDataAt",function(a){var b=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(d,"getPointIndex",function(a,b,c){return a*this.yzCount+b*this.voxelCounts[2]+c},"~N,~N,~N");e(d,"getPoint",function(a,b){var c=D(a/
this.yzCount);a-=c*this.yzCount;var g=D(a/this.voxelCounts[2]);this.voxelPtToXYZ(c,g,a-g*this.voxelCounts[2],b)},"~N,JU.P3");e(d,"setVoxelData",function(a,b){var c=D(a/this.yzCount);a-=c*this.yzCount;var g=D(a/this.voxelCounts[2]);this.voxelData[c][g][a-g*this.voxelCounts[2]]=b},"~N,~N");e(d,"setVoxelMap",function(){this.voxelMap=new java.util.Hashtable;this.getYzCount()});e(d,"setMatrix",function(){for(var a=0;3>a;a++)this.volumetricMatrix.setColumnV(a,this.volumetricVectors[a]);try{this.inverseMatrix.invertM(this.volumetricMatrix)}catch(b){if(ea(b,
Exception))return JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? "),!1;throw b;}return!0});e(d,"transform",function(a,b){this.volumetricMatrix.rotate2(a,b)},"JU.V3,JU.V3");e(d,"setPlaneParameters",function(a){this.thePlane=a;this.thePlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z)},"JU.P4");e(d,"calcVoxelPlaneDistance",function(a,b,c){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.distancePointToPlane(this.ptXyzTemp)},"~N,~N,~N");e(d,"getToPlaneParameter",function(){return Math.sqrt(this.thePlane.x*
this.thePlane.x+this.thePlane.y*this.thePlane.y+this.thePlane.z*this.thePlane.z)*this.minToPlaneDistance});e(d,"isNearPlane",function(a,b,c,g){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<g},"~N,~N,~N,~N");e(d,"distancePointToPlane",function(a){return(this.thePlane.x*a.x+this.thePlane.y*a.y+this.thePlane.z*a.z+this.thePlane.w)/this.thePlaneNormalMag},"JU.T3");e(d,"voxelPtToXYZ",function(a,
b,c,g){g.scaleAdd2(a,this.volumetricVectors[0],this.volumetricOrigin);g.scaleAdd2(b,this.volumetricVectors[1],g);g.scaleAdd2(c,this.volumetricVectors[2],g)},"~N,~N,~N,JU.T3");e(d,"setUnitVectors",function(){this.maxVectorLength=0;this.voxelVolume=1;for(var a=0;3>a;a++){var b=this.volumetricVectorLengths[a]=this.volumetricVectors[a].length();if(0==b)return!1;b>this.maxVectorLength&&(this.maxVectorLength=b);this.voxelVolume*=b;this.unitVolumetricVectors[a].setT(this.volumetricVectors[a]);this.unitVolumetricVectors[a].normalize()}this.minToPlaneDistance=
2*this.maxVectorLength;this.origin[0]=this.volumetricOrigin.x;this.origin[1]=this.volumetricOrigin.y;this.origin[2]=this.volumetricOrigin.z;this.oabc=Array(4);this.oabc[0]=JU.V3.newV(this.volumetricOrigin);for(a=0;3>a;a++)b=this.oabc[a+1]=new JU.V3,b.scaleAdd2(this.voxelCounts[a]-1,this.volumetricVectors[a],b);return this.setMatrix()});e(d,"xyzToVoxelPt",function(a,b,c,g){this.ptXyzTemp.set(a,b,c);this.ptXyzTemp.sub(this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);g.set(Math.round(this.ptXyzTemp.x),
Math.round(this.ptXyzTemp.y),Math.round(this.ptXyzTemp.z))},"~N,~N,~N,JU.T3i");e(d,"lookupInterpolatedVoxelValue",function(a,b){if(null!=this.mappingPlane)return this.distanceToMappingPlane(a);if(null!=this.sr){var c=this.sr.getValueAtPoint(a,b);return this.isSquared?c*c:c}this.ptXyzTemp.sub2(a,this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);var g,d=this.indexLower(this.ptXyzTemp.x,g=this.voxelCounts[0]-1),e=this.indexUpper(this.ptXyzTemp.x,d,g),h=this.indexLower(this.ptXyzTemp.y,
g=this.voxelCounts[1]-1),f=this.indexUpper(this.ptXyzTemp.y,h,g),c=this.indexLower(this.ptXyzTemp.z,g=this.voxelCounts[2]-1),k=this.indexUpper(this.ptXyzTemp.z,c,g);g=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-d),this.mantissa(this.ptXyzTemp.y-h),this.getVoxelValue(d,h,c),this.getVoxelValue(e,h,c),this.getVoxelValue(d,f,c),this.getVoxelValue(e,f,c));d=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-d),this.mantissa(this.ptXyzTemp.y-h),this.getVoxelValue(d,
h,k),this.getVoxelValue(e,h,k),this.getVoxelValue(d,f,k),this.getVoxelValue(e,f,k));return g+this.mantissa(this.ptXyzTemp.z-c)*(d-g)},"JU.T3,~B");e(d,"mantissa",function(a){return this.isPeriodic?a-Math.floor(a):a},"~N");e(d,"getVoxelValue",function(a,b,c){if(null==this.voxelMap)return this.voxelData[a][b][c];a=this.voxelMap.get(Integer.$valueOf(this.getPointIndex(a,b,c)));return null==a?NaN:a.floatValue()},"~N,~N,~N");d.getFractional2DValue=e(d,"getFractional2DValue",function(a,b,c,g,d,e){c+=a*(g-
c);return c+b*(d+a*(e-d)-c)},"~N,~N,~N,~N,~N,~N");e(d,"indexLower",function(a,b){if(this.isPeriodic&&0<b){for(;0>a;)a+=b;for(;a>=b;)a-=b;return D(Math.floor(a))}if(0>a)return 0;var c=D(Math.floor(a));return c>b?b:c},"~N,~N");e(d,"indexUpper",function(a,b,c){return!this.isPeriodic&&0>a||b==c?b:b+1},"~N,~N,~N");e(d,"offsetCenter",function(a){var b=new JU.P3;b.scaleAdd2((this.voxelCounts[0]-1)/2,this.volumetricVectors[0],b);b.scaleAdd2((this.voxelCounts[1]-1)/2,this.volumetricVectors[1],b);b.scaleAdd2((this.voxelCounts[2]-
1)/2,this.volumetricVectors[2],b);this.volumetricOrigin.sub2(a,b)},"JU.P3");e(d,"setDataDistanceToPlane",function(a){this.setPlaneParameters(a);a=this.voxelCounts[0];var b=this.voxelCounts[1],c=this.voxelCounts[2];this.voxelData=t(a,b,c,0);for(var g=0;g<a;g++)for(var d=0;d<b;d++)for(var e=0;e<c;e++)this.voxelData[g][d][e]=this.calcVoxelPlaneDistance(g,d,e)},"JU.P4");e(d,"filterData",function(a,b){var c=!Float.isNaN(b);if(null!=this.sr)this.isSquared=a;else{var g=this.voxelCounts[0],d=this.voxelCounts[1],
e=this.voxelCounts[2];if(a)for(var h=0;h<g;h++)for(var f=0;f<d;f++)for(var k=0;k<e;k++)this.voxelData[h][f][k]*=this.voxelData[h][f][k];if(c)for(h=0;h<g;h++)for(f=0;f<d;f++)for(k=0;k<e;k++)this.voxelData[h][f][k]=b-this.voxelData[h][f][k]}},"~B,~N");e(d,"capData",function(a,b){if(null!=this.voxelData){var c=this.voxelCounts[0],g=this.voxelCounts[1],d=this.voxelCounts[2],e=JU.V3.new3(a.x,a.y,a.z);e.normalize();for(var h=0;h<c;h++)for(var f=0;f<g;f++)for(var k=0;k<d;k++){var l=this.voxelData[h][f][k]-
b;this.voxelPtToXYZ(h,f,k,this.ptXyzTemp);var n=(this.ptXyzTemp.x*e.x+this.ptXyzTemp.y*e.y+this.ptXyzTemp.z*e.z+a.w-b)/1;if(0<=n||n>l)this.voxelData[h][f][k]=n}}},"JU.P4,~N");e(d,"setVolumetricXml",function(){var a=new JU.SB;if(0==this.voxelCounts[0])a.append("<jvxlVolumeData>\n");else{a.append('<jvxlVolumeData origin="'+JU.Escape.eP(this.volumetricOrigin)+'">\n');for(var b=0;3>b;b++)a.append('<jvxlVolumeVector type="'+b+'" count="'+this.voxelCounts[b]+'" vector="'+JU.Escape.eP(this.volumetricVectors[b])+
'"></jvxlVolumeVector>\n')}a.append("</jvxlVolumeData>\n");return this.xmlData=a.toString()});e(d,"setVoxelMapValue",function(a,b,c,g){null!=this.voxelMap&&this.voxelMap.put(Integer.$valueOf(this.getPointIndex(a,b,c)),Float.$valueOf(g))},"~N,~N,~N,~N");e(d,"calculateFractionalPoint",function(a,b,c,g,d,e){var h=d-g,f=(a-g)/h;this.edgeVector.sub2(c,b);e.scaleAdd2(f,this.edgeVector,b);if(null==this.sr||!this.doIterate||d==g||0.01>f||0.99<f||0.01>this.edgeVector.length())return a;b=0;this.ptTemp.setT(e);
c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1);for(d=NaN;10>++b;){var k=(c-g)/h;if(0>k||1<k)break;k=(a-c)/h/2;f+=k;if(0>f||1<f)break;e.setT(this.ptTemp);d=c;if(0.005>Math.abs(k))break;this.ptTemp.scaleAdd2(k,this.edgeVector,e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1)}return d},"~N,JU.P3,JU.P3,~N,~N,JU.P3")});L("J.jvxl.data");R(null,"J.jvxl.data.JvxlData",["JU.SB","J.jvxl.data.JvxlCoder"],function(){var d=N(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;C(this,arguments)},J.jvxl.data,"JvxlData",null);ia(d,function(){this.jvxlExcluded=Array(4)});da(d,function(){});e(d,"clear",function(){this.allowVolumeRender=!0;this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData="";this.colorScheme=this.color=null;this.colorDensity=!1;this.pointSize=NaN;this.contourColors=this.contourColixes=this.contourValuesUsed=this.contourValues=null;this.integration=NaN;this.isSlabbable=!1;
this.isValid=!0;this.meshColor=this.mapLattice=null;this.msg="";this.nVertexColors=this.nPointsX=0;this.slabInfo=this.fixedLattice=null;this.slabValue=-2147483648;this.rendering=this.thisSet=null;this.thisContour=-1;this.translucency=0;this.vertexColors=this.vertexColorMap=this.vContours=null;this.voxelVolume=0});e(d,"setSurfaceInfo",function(a,b,c,g){this.jvxlSurfaceData=g;this.jvxlPlane=a;this.mapLattice=b;this.nSurfaceInts=c},"JU.P4,JU.P3,~N,~S");e(d,"setSurfaceInfoFromBitSet",function(a,b){this.setSurfaceInfoFromBitSetPts(a,
b,null)},"JU.BS,JU.P4");e(d,"setSurfaceInfoFromBitSetPts",function(a,b,c){var g=new JU.SB;a=null!=b?0:J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,this.nPointsX*this.nPointsY*this.nPointsZ,g);this.setSurfaceInfo(b,c,a,g.toString())},"JU.BS,JU.P4,JU.P3");e(d,"jvxlUpdateInfo",function(a,b){this.title=a;this.nBytes=b},"~A,~N");d.updateSurfaceData=e(d,"updateSurfaceData",function(a,b,c,g,d){if(0==a.length)return"";a=a.toCharArray();for(var e=0,h=0;e<c;e+=g,h++)Float.isNaN(b[e])&&(a[h]=d);return String.copyValueOf(a)},
"~S,~A,~N,~N,~S")});L("J.jvxl.data");R(["JU.MeshSurface"],"J.jvxl.data.MeshData",["java.util.Arrays","JU.AU","$.BS","$.V3","JU.BSUtil"],function(){var d=N(function(){this.setsSuccessful=!1;this.vertexIncrement=1;this.polygonColorData=null;xa("J.jvxl.data.MeshData.SSet")||J.jvxl.data.MeshData.$MeshData$SSet$();xa("J.jvxl.data.MeshData.SortSet")||J.jvxl.data.MeshData.$MeshData$SortSet$();C(this,arguments)},J.jvxl.data,"MeshData",JU.MeshSurface);e(d,"addVertexCopy",function(a,b,c,g){0>c&&(this.vertexIncrement=
-c);return this.addVCVal(a,b,g)},"JU.T3,~N,~N,~B");e(d,"getSurfaceSet",function(){return null==this.surfaceSet?this.getSurfaceSetForLevel(0):this.surfaceSet});e(d,"getSurfaceSetForLevel",function(a){0==a&&(this.surfaceSet=Array(100),this.nSets=0);this.setsSuccessful=!0;for(var b=0;b<this.pc;b++)if(null!=this.pis[b]&&(null==this.bsSlabDisplay||this.bsSlabDisplay.get(b))){var c=this.pis[b],g=this.findSet(c[0]),d=this.findSet(c[1]),e=this.findSet(c[2]);0>g&&0>d&&0>e?this.createSet(c[0],c[1],c[2]):g==
d&&d==e||(0<=g?(this.surfaceSet[g].set(c[1]),this.surfaceSet[g].set(c[2]),0<=d&&d!=g&&this.mergeSets(g,d),0<=e&&(e!=g&&e!=d)&&this.mergeSets(g,e)):0<=d?(this.surfaceSet[d].set(c[0]),this.surfaceSet[d].set(c[2]),0<=e&&e!=d&&this.mergeSets(d,e)):(this.surfaceSet[e].set(c[0]),this.surfaceSet[e].set(c[1])))}for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&c++;g=Array(this.surfaceSet.length);for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&(g[c++]=this.surfaceSet[b]);this.nSets=c;this.surfaceSet=
g;!this.setsSuccessful&&2>a&&this.getSurfaceSetForLevel(a+1);if(0==a){a=Array(this.nSets);for(b=0;b<this.nSets;b++)a[b]=va(J.jvxl.data.MeshData.SSet,this,null,this.surfaceSet[b]);java.util.Arrays.sort(a,va(J.jvxl.data.MeshData.SortSet,this,null));for(b=0;b<this.nSets;b++)this.surfaceSet[b]=a[b].bs;this.setVertexSets(!1)}return this.surfaceSet},"~N");e(d,"setVertexSets",function(a){if(null!=this.surfaceSet){for(var b=0,c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&0>this.surfaceSet[c].nextSetBit(0)&&
(this.surfaceSet[c]=null),null==this.surfaceSet[c]&&b++;if(0<b){a=Array(this.nSets-b);for(var g=c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&(a[g++]=this.surfaceSet[c]);this.surfaceSet=a;this.nSets-=b}else if(a)return;this.vertexSets=r(this.vc,0);for(c=0;c<this.nSets;c++)for(b=this.surfaceSet[c].nextSetBit(0);0<=b;b=this.surfaceSet[c].nextSetBit(b+1))this.vertexSets[b]=c}},"~B");e(d,"findSet",function(a){for(var b=0;b<this.nSets;b++)if(null!=this.surfaceSet[b]&&this.surfaceSet[b].get(a))return b;
return-1},"~N");e(d,"createSet",function(a,b,c){var g;for(g=0;g<this.nSets&&null!=this.surfaceSet[g];g++);g==this.surfaceSet.length&&(this.surfaceSet=JU.AU.ensureLength(this.surfaceSet,this.surfaceSet.length+100));this.surfaceSet[g]=new JU.BS;this.surfaceSet[g].set(a);this.surfaceSet[g].set(b);this.surfaceSet[g].set(c);g==this.nSets&&this.nSets++},"~N,~N,~N");e(d,"mergeSets",function(a,b){this.surfaceSet[a].or(this.surfaceSet[b]);this.surfaceSet[b]=null},"~N,~N");e(d,"invalidateSurfaceSet",function(a){for(var b=
this.surfaceSet[a].nextSetBit(0);0<=b;b=this.surfaceSet[a].nextSetBit(b+1))this.vvs[b]=NaN;this.surfaceSet[a]=null},"~N");d.checkCutoff=e(d,"checkCutoff",function(a,b,c,g){if(0>a||0>b||0>c)return!1;a=g[a];b=g[b];c=g[c];return 0<=a&&0<=b&&0<=c||0>=a&&0>=b&&0>=c},"~N,~N,~N,~A");d.calculateVolumeOrArea=e(d,"calculateVolumeOrArea",function(a,b,c,g){(g||0>=a.nSets)&&a.getSurfaceSet();var d=null!=b&&1==b.cardinality(),e=d||0>=a.nSets?1:a.nSets;g=Ma(e,0);for(var h=new JU.V3,f=new JU.V3,k=new JU.V3,l=a.pc;0<=
--l;)if(null!=a.setABC(l)){var n=0>=a.nSets?0:a.vertexSets[a.iA];if(null==b||b.get(n))c?(h.sub2(a.vs[a.iB],a.vs[a.iA]),f.sub2(a.vs[a.iC],a.vs[a.iA]),k.cross(h,f),g[d?0:n]+=k.length()):(h.setT(a.vs[a.iB]),f.setT(a.vs[a.iC]),k.cross(h,f),f.setT(a.vs[a.iA]),g[d?0:n]+=f.dot(k))}a=c?2:6;for(l=0;l<e;l++)g[l]/=a;if(d)return Float.$valueOf(g[0]);if(null!=b){b.and(JU.BSUtil.newBitSet2(0,g.length));a=Ma(b.cardinality(),0);c=0;for(l=b.nextSetBit(0);0<=l;l=b.nextSetBit(l+1))a[c++]=g[l];g=a}return g},"J.jvxl.data.MeshData,JU.BS,~B,~B");
e(d,"updateInvalidatedVertices",function(a){a.clearAll();for(var b=0;b<this.vc;b+=this.vertexIncrement)Float.isNaN(this.vvs[b])&&a.set(b)},"JU.BS");e(d,"invalidateVertices",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.vvs[b]=NaN},"JU.BS");d.$MeshData$SSet$=function(){var a=N(function(){wa(this,arguments);this.bs=null;this.n=0;C(this,arguments)},J.jvxl.data.MeshData,"SSet",null);da(a,function(a){this.bs=a;this.n=a.cardinality()},"JU.BS")};d.$MeshData$SortSet$=function(){var a=
N(function(){wa(this,arguments);C(this,arguments)},J.jvxl.data.MeshData,"SortSet",null,java.util.Comparator);j(a,"compare",function(a,c){return a.n>c.n?-1:a.n<c.n?1:0},"J.jvxl.data.MeshData.SSet,J.jvxl.data.MeshData.SSet")}});L("J.jvxl.readers");R(null,"J.jvxl.readers.XmlReader",["JU.P3","$.PT","$.SB","JU.Escape"],function(){var d=N(function(){this.line=this.br=null;C(this,arguments)},J.jvxl.readers,"XmlReader",null);da(d,function(a){this.br=a},"java.io.BufferedReader");e(d,"getLine",function(){return this.line});
e(d,"toTag",function(a){this.skipTo("<"+a);if(null==this.line)return"";var b=this.line.indexOf("<"+a)+a.length+1;if(b==this.line.length||" "==this.line.charAt(b)||">"==this.line.charAt(b))return this.line;this.line=null;return this.toTag(a)},"~S");e(d,"skipTag",function(a){this.skipTo("</"+a+">")},"~S");e(d,"getXmlData",function(a,b,c,g){return this.getXmlDataLF(a,b,c,g,!1,null)},"~S,~S,~B,~B");e(d,"getXmlDataLF",function(a,b,c,g,d,e){var h="</"+a+">";a="<"+a;if(null==b){b=new JU.SB;null==this.line&&
(this.line=this.br.readLine());for(;null!=this.line&&0>this.line.indexOf(a);)this.line=this.br.readLine();if(null==this.line)return null;b.append(this.line);d&&b.append("\n");var f=!1,k=this.line.indexOf("/>"),l=this.line.indexOf(">");if(0>l||k==l-1)f=g;for(;0>this.line.indexOf(h)&&(!f||0>this.line.indexOf("/>"));)b.append(this.line=this.br.readLine()),d&&b.append("\n");b=b.toString()}return J.jvxl.readers.XmlReader.extractTag(b,a,h,c,e)},"~S,~S,~B,~B,~B,~A");d.extractTagOnly=e(d,"extractTagOnly",
function(a,b){return J.jvxl.readers.XmlReader.extractTag(a,"<"+b+">","</"+b+">",!1,null)},"~S,~S");d.extractTag=e(d,"extractTag",function(a,b,c,g,d){b=a.indexOf(b,null==d?0:d[0]);null!=d&&(d[0]=a.length);if(0>b)return"";var e=a.indexOf(c,b);0>e&&(e=a.indexOf("/>",b),c="/>");if(0>e)return"";if(g)return e+=c.length,null!=d&&(d[0]=e),a.substring(b,e);for(c=!1;b<e;b++)if('"'==(g=a.charAt(b)))c=!c;else if(c&&"\\"==g)b++;else if(!c&&(">"==g||"/"==g))break;if(b>=e)return"";for(;JU.PT.isWhitespace(a.charAt(++b)););
null!=d&&(d[0]=e);return J.jvxl.readers.XmlReader.unwrapCdata(a.substring(b,e))},"~S,~S,~S,~B,~A");d.unwrapCdata=e(d,"unwrapCdata",function(a){return a.startsWith("<![CDATA[")&&a.endsWith("]]\x3e")?JU.PT.rep(a.substring(9,a.length-3),"]]]]\x3e<![CDATA[>","]]\x3e"):a},"~S");d.getXmlAttrib=e(d,"getXmlAttrib",function(a,b){var c=r(1,0),g=J.jvxl.readers.XmlReader.setNext(a,b,c,1);if(2>g||2>(g=J.jvxl.readers.XmlReader.setNext(a,'"',c,0)))return"";c=J.jvxl.readers.XmlReader.setNext(a,'"',c,-1);return 0>=
c?"":a.substring(g,c)},"~S,~S");e(d,"getXmlPoint",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,b).$replace("(","{").$replace(")","}"),c=JU.Escape.uP(c);return $(c,"JU.P3")?c:new JU.P3},"~S,~S");d.setNext=e(d,"setNext",function(a,b,c,g){var d=c[0];if(0>d||0>(d=a.indexOf(b,c[0])))return-1;d+=b.length;c[0]=d+g;return 0<g&&d<a.length&&"="!=a.charAt(d)?J.jvxl.readers.XmlReader.setNext(a,b,c,g):c[0]},"~S,~S,~A,~N");e(d,"skipTo",function(a){null==this.line&&(this.line=this.br.readLine());
for(;null!=this.line&&0>this.line.indexOf(a);)this.line=this.br.readLine()},"~S");e(d,"isNext",function(a){if(null==this.line||0<=this.line.indexOf("</")&&this.line.indexOf("</")==this.line.indexOf("<"))this.line=this.br.readLine();return 0<=this.line.indexOf("<"+a)},"~S")});L("J.jvxl.readers");R(["JU.P3","$.V3"],"J.jvxl.readers.SurfaceGenerator","JU.AU $.BS $.Measure $.P4 $.PT $.Rdr $.SB J.jvxl.data.JvxlCoder $.JvxlData $.MeshData $.VolumeData J.jvxl.readers.Parameters $.SurfaceReader JU.Logger JV.FileManager".split(" "),
function(){var d=N(function(){this.version=this.marchingSquares=this.atomDataServer=this.meshDataServer=this.volumeDataTemp=this.meshData=this.jvxlData=this.params=null;this.isValid=!0;this.bsVdw=this.fileType=null;this.colorPtr=0;this.ptRef=this.vNorm=this.vAB=this.readerData=this.out=this.surfaceReader=null;C(this,arguments)},J.jvxl.readers,"SurfaceGenerator",null);ia(d,function(){this.vAB=new JU.V3;this.vNorm=new JU.V3;this.ptRef=JU.P3.new3(0,0,1E15)});da(d,function(a,b,c,g){this.atomDataServer=
a;this.meshDataServer=b;this.params=new J.jvxl.readers.Parameters;this.meshData=null==c?new J.jvxl.data.MeshData:c;this.jvxlData=null==g?new J.jvxl.data.JvxlData:g;this.volumeDataTemp=new J.jvxl.data.VolumeData;this.initializeIsosurface()},"J.atomdata.AtomDataServer,J.jvxl.api.MeshDataServer,J.jvxl.data.MeshData,J.jvxl.data.JvxlData");e(d,"setJvxlData",function(a){this.jvxlData=a;null!=a&&(a.version=this.version)},"J.jvxl.data.JvxlData");e(d,"setProp",function(a,b){if("debug"===a){var c=b.booleanValue();
this.params.logMessages=c;this.params.logCube=c;return!0}if("init"===a)return this.initializeIsosurface(),$(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=y(-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 g=0;g<this.params.title.length;g++)0<this.params.title[g].length&&JU.Logger.info(this.params.title[g]);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($(b,"JU.P3")){var c=this.params.contourIncrements=b,g=c.x,d=c.y,e=c.z;0>=e&&(e=1);for(var c=0,h=g;h<=d+e/10;h+=e,c++);this.params.contoursDiscrete=t(c,0);h=g;for(g=0;g<c;g++,h+=e)this.params.contoursDiscrete[g]=h;this.params.nContours=c}else c=b.intValue(),this.params.thisContour=0,0==c?this.params.nContours=
9:0<c?this.params.nContours=c:this.params.thisContour=-c;return!0}if("colorDiscrete"===a)return this.params.contourColixes=b,!0;if("colorDensity"===a)return this.params.colorDensity=!0,null!=b&&(this.params.pointSize=b.floatValue()),!1;if("fullPlane"===a)return this.params.contourFromZero=!b.booleanValue(),!0;if("mapLattice"===a)return this.params.mapLattice=b,!0;if("extendGrid"===a)return this.params.extendGrid=b.floatValue(),!0;if("property"===a)return this.params.dataType=1208,this.params.theProperty=
b,this.mapSurface(),!0;if("sphere"===a)return this.params.setSphere(b.floatValue(),!1),this.readerData=Float.$valueOf(this.params.distance),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("geodesic"===a)return this.params.setSphere(b.floatValue(),!0),this.readerData=Float.$valueOf(this.params.distance),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("ellipsoid"===a){if($(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=t(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("rad"===
a)return this.params.setRadical(b),this.readerData=t(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lobe"===a)return this.params.setLobe(b),this.readerData=t(-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=t(-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,g=null,$(b,Integer)?c=b.intValue():g=b,this.params.setMO(c,g),JU.Logger.info(this.params.calculationType),
this.processState(),!0;if("fileType"===a)return this.fileType=b,!0;if("fileName"===a)return this.params.fileName=b,!0;if("filesData"===a)return this.params.filesData=b,!0;if("outputChannel"===a)return this.out=b,!0;if("readFile"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,b)))return JU.Logger.error("Could not set the surface data"),!0;this.surfaceReader.setOutputChannel(this.out);this.generateSurface();return!0}if("mapColor"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,
b)))return JU.Logger.error("Could not set the mapping data"),!0;this.surfaceReader.setOutputChannel(this.out);this.mapSurface();return!0}if("getSurfaceSets"===a)return this.getSurfaceSets(),!0;"periodic"===a&&(this.params.isPeriodic=!0);return!1},"~S,~O,JU.BS");e(d,"newReader",function(a){a=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=a&&a.init(this);return a},"~S");e(d,"newReaderBr",function(a,b){var c=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=c&&c.init2(this,b);return c},"~S,java.io.BufferedReader");
d.getInterface=e(d,"getInterface",function(a){try{var b=jb._4Name("J.jvxl.readers."+a);return null==b?null:b.newInstance()}catch(c){if(ea(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c.toString()),null;throw c;}},"~S");e(d,"getSurfaceSets",function(){null==this.meshDataServer?this.meshData.getSurfaceSet():(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.getSurfaceSet(),this.meshDataServer.fillMeshData(this.meshData,3,null))});e(d,
"processState",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;2<=this.params.state?this.mapSurface():this.generateSurface()});e(d,"setReader",function(){this.readerData=null;if(null!=this.surfaceReader)return!this.surfaceReader.vertexDataOnly;switch(this.params.dataType){case 1207:this.surfaceReader=this.newReader("IsoPlaneReader");break;case 1208:this.surfaceReader=this.newReader("AtomPropertyMapper");break;case 1328:case 1329:this.readerData=1328==this.params.dataType?
"Mep":"Mlp";this.surfaceReader=3==this.params.state?this.newReader("AtomPropertyMapper"):this.newReader("Iso"+this.readerData+"Reader");break;case 1334:this.surfaceReader=this.newReader("IsoIntersectFileReader");break;case 1333:this.surfaceReader=this.newReader("IsoIntersectAtomReader");break;case 1195:case 1203:case 1196:this.surfaceReader=this.newReader("IsoSolventReader");break;case 1844:case 1837:this.surfaceReader=this.newReader("IsoMOReader");break;case 8:this.surfaceReader=this.newReader("IsoFxyReader");
break;case 9:this.surfaceReader=this.newReader("IsoFxyzReader")}JU.Logger.debugging&&JU.Logger.info("Using surface reader "+this.surfaceReader);this.params.isSilent&&null!=this.surfaceReader&&(this.surfaceReader.isQuiet=!0);return!0});e(d,"generateSurface",function(){if(2==++this.params.state){this.setReader();null==this.params.sbOut&&(this.params.sbOut=new JU.SB);this.jvxlData.sbOut=this.params.sbOut;var a=null!=this.meshDataServer;this.params.colorBySign&&(this.params.isBicolorMap=!0);if(null==
this.surfaceReader)JU.Logger.error("surfaceReader is null for "+this.params.dataType);else if(this.surfaceReader.createIsosurface(!1)){if(null!=this.params.probes)for(var b=this.params.probeValues.length;0<=--b;)this.params.probeValues[b]=this.surfaceReader.getValueAtPoint(this.params.probes[b],!1);null!=this.params.pocket&&a&&this.surfaceReader.selectPocket(!this.params.pocket.booleanValue());0<this.params.minSet&&this.surfaceReader.excludeMinimumSet();0<this.params.maxSet&&this.surfaceReader.excludeMaximumSet();
null!=this.params.slabInfo&&this.surfaceReader.slabIsosurface(this.params.slabInfo);a&&this.meshDataServer.notifySurfaceGenerationCompleted()&&(this.surfaceReader.hasColorData=!1);null!=this.jvxlData.thisSet&&this.getSurfaceSets();this.jvxlData.jvxlDataIs2dContour&&(this.surfaceReader.colorIsosurface(),this.params.state=3);this.jvxlData.jvxlDataIsColorDensity&&(this.params.state=3);if(this.params.colorBySign||this.params.isBicolorMap)this.params.state=3,this.surfaceReader.applyColorScale();null!=
this.jvxlData.vertexColorMap&&(this.surfaceReader.hasColorData=!1);this.surfaceReader.jvxlUpdateInfo();this.marchingSquares=this.surfaceReader.marchingSquares;this.surfaceReader.discardTempData(!1);this.params.mappedDataMin=3.4028235E38;this.surfaceReader.closeReader();if(3!=this.params.state&&(this.surfaceReader.hasColorData||this.params.colorDensity))this.params.state=3,this.colorIsosurface();this.surfaceReader=null}else JU.Logger.error("Could not create isosurface"),this.params.cutoff=NaN,this.params.cutoffRange=
null,this.surfaceReader.closeReader()}});e(d,"mapSurface",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;if(!(3>++this.params.state)&&this.setReader()){this.params.isPeriodic&&(this.surfaceReader.volumeData.isPeriodic=!0);if(null!=this.params.thePlane){var a=this.params.isSquared;this.params.isSquared=!1;this.params.cutoff=0;this.params.cutoffRange=null;this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);this.surfaceReader.createIsosurface(!this.params.isPeriodic);
this.surfaceReader.volumeData.setMappingPlane(null);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted();if(1207==this.params.dataType){this.surfaceReader.discardTempData(!0);return}this.params.isSquared=a;this.params.mappedDataMin=3.4028235E38;this.surfaceReader.readVolumeData(!0);null!=this.params.mapLattice&&(this.surfaceReader.volumeData.isPeriodic=!0)}else!this.params.colorBySets&&!this.params.colorDensity&&(this.surfaceReader.readAndSetVolumeParameters(!0),this.params.mappedDataMin=
3.4028235E38,this.surfaceReader.readVolumeData(!0));this.colorIsosurface();this.surfaceReader.closeReader();this.surfaceReader=null}});e(d,"colorIsosurface",function(){this.surfaceReader.colorIsosurface();this.surfaceReader.jvxlUpdateInfo();this.surfaceReader.updateTriangles();this.surfaceReader.discardTempData(!0);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted()});e(d,"getProperty",function(a,b){return"jvxlFileData"===a?J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,
null,this.params.title,"",!0,b,null,null):"jvxlFileInfo"===a?J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData):null},"~S,~N");e(d,"setFileData",function(a,b){var c=this.fileType;this.fileType=null;if($(b,"java.util.Map")){var g=b;if(g.containsKey("__pymolSurfaceData__"))return this.readerData=g,this.newReaderBr("PyMOLMeshReader",null);b=g.get("volumeData")}if($(b,"J.jvxl.data.VolumeData"))return this.volumeDataTemp=b,this.newReader("VolumeDataReader");g=null;"string"==typeof b&&(g=b,b=JU.Rdr.getBR(b));
if($(b,Array)){for(var g=b[0],d=Array(g.length),e=0;e<g.length;e++)this.fileType=c,d[e]=this.setFileData(a,g[e]);b[0]=d;this.readerData=b;return this.newReader("IsoIntersectGridReader")}d=b;null==c&&(c=JV.FileManager.determineSurfaceFileType(d));if(null!=c&&c.startsWith("UPPSALA")){e=this.params.fileName;e=e.substring(0,e.indexOf("/",10));e+=JU.PT.getQuotedStringAt(c,c.indexOf("A HREF")+1);this.params.fileName=e;b=this.atomDataServer.getBufferedInputStream(e);if(null==b)return JU.Logger.error("Isosurface: could not open file "+
e),null;try{d=JU.Rdr.getBufferedReader(b,null)}catch(h){if(!ea(h,Exception))throw h;}c=JV.FileManager.determineSurfaceFileType(d)}null==c&&(c="UNKNOWN");JU.Logger.info("data file type was determined to be "+c);if(c.equals("Jvxl+"))return this.newReaderBr("JvxlReader",d);this.readerData=y(-1,[this.params.fileName,g]);0<="MRC DELPHI DSN6".indexOf(c.toUpperCase())&&(c+="Binary");return this.newReaderBr(c+"Reader",d)},"JV.Viewer,~O");e(d,"getReaderData",function(){var a=this.readerData;this.readerData=
null;return a});e(d,"initializeIsosurface",function(){this.params.initialize();this.colorPtr=0;this.marchingSquares=this.surfaceReader=null;this.initState()});e(d,"initState",function(){this.params.state=1;this.params.dataType=this.params.surfaceType=0});e(d,"setLcao",function(){this.params.colorPos=this.params.colorPosLCAO;this.params.colorNeg=this.params.colorNegLCAO;return this.params.lcaoType});e(d,"getFunctionZfromXY",function(){for(var a=this.params.functionInfo.get(1),b=r(3,0),c=r(3,0),g=Array(3),
d=0;3>d;d++){var e=this.params.functionInfo.get(d+2);b[d]=Math.abs(w(e.x));g[d]=JU.V3.new3(e.y,e.z,e.w)}for(var e=b[0],b=b[1],h=new JU.P3,f=new JU.P3,k=new JU.P3,l=new JU.P3,n=this.params.functionInfo.get(5),j=t(e,b,0),q,d=0;d<e;d++)for(var S=0;S<b;S++){h.scaleAdd2(d,g[0],a);h.scaleAdd2(S,g[1],h);var v=J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(h.x,h.y,n,c);f.set((q=n[c[0]])[0],q[1],q[2]);1E-5>v?h.z=q[2]:(k.set((q=n[c[1]])[0],q[1],q[2]),l.set((q=n[c[2]])[0],q[1],q[2]),h.z=this.distanceVerticalToPlane(h.x,
h.y,f,k,l));j[d][S]=h.z}this.params.functionInfo.set(5,j)});e(d,"distanceVerticalToPlane",function(a,b,c,g,d){c=JU.Measure.getDirectedNormalThroughPoints(c,g,d,this.ptRef,this.vNorm,this.vAB);return(this.vNorm.x*a+this.vNorm.y*b+c)/-this.vNorm.z},"~N,~N,JU.P3,JU.P3,JU.P3");d.findNearestThreePoints=e(d,"findNearestThreePoints",function(a,b,c,g){var d,e,h,f,k,l,n;k=l=n=-1;e=h=f=3.4028235E38;for(var j=c.length;0<=--j;)d=(d=c[j][0]-a)*d+(d=c[j][1]-b)*d,d<e?(f=h,h=e,e=d,n=l,l=k,k=j):d<h?(f=h,h=d,n=l,l=
j):d<f&&(f=d,n=j);g[0]=k;g[1]=l;g[2]=n;return e},"~N,~N,~A,~A");e(d,"addRequiredFile",function(a){null!=this.meshDataServer&&this.meshDataServer.addRequiredFile(a)},"~S");e(d,"setRequiredFile",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setRequiredFile(a,b)},"~S,~S");e(d,"log",function(a){null==this.atomDataServer?System.out.println(a):this.atomDataServer.log(a)},"~S");e(d,"setOutputChannel",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setOutputChannel(a,b)},"javajs.api.GenericBinaryDocument,JU.OC");
e(d,"fillAtomData",function(a,b){0!=(b&2)&&null!=a.bsSelected&&(null==this.bsVdw&&(this.bsVdw=new JU.BS),this.bsVdw.or(a.bsSelected));this.atomDataServer.fillAtomData(a,b)},"J.atomdata.AtomData,~N");e(d,"getOriginVaVbVc",function(){return null==this.surfaceReader.volumeData?null:this.surfaceReader.volumeData.oabc})});L("J.jvxl.readers");R(null,"J.jvxl.readers.Parameters","java.util.Hashtable JU.A4 $.Lst $.M3 $.P3 $.P4 $.V3 JU.Escape $.Logger".split(" "),function(){var d=N(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;C(this,arguments)},J.jvxl.readers,"Parameters",null);ia(d,function(){this.anisotropy=t(3,0)});e(d,"initialize",
function(){this.addHydrogens=!1;this.allowVolumeRender=!0;this.atomRadiusData=null;this.atomIndex=-1;this.blockCubeData=!1;this.boundingBox=null;this.bsExcluded=Array(4);this.bsSolvent=this.bsSelected=this.bsIgnore=null;this.calculationType="";this.center=new JU.P3;this.resetForMapping(!0);this.colorBySign=this.colorByPhase=this.colorBySets=!1;this.colorEncoder=null;this.colorNeg=-65536;this.colorNegLCAO=-8388480;this.colorPos=-16776961;this.colorPosLCAO=-23296;this.colorRgb=-2147483648;this.colorSchemeTranslucent=
!1;this.contourColixes=this.contoursDiscrete=this.contourIncrements=this.contactPair=null;this.contourFromZero=!0;this.cutoff=3.4028235E38;this.cutoffAutomatic=!0;this.dataXYReversed=!1;this.distance=3.4028235E38;this.doFullMolecular=!1;this.envelopeRadius=10;this.extendGrid=0;this.fileIndex=1;this.readAllData=!0;this.fileName="";this.filesData=null;this.fullyLit=!1;this.functionInfo=null;this.logCube=this.logCompression=this.isSilent=this.isPeriodic=this.isMapped=this.isEccentric=this.isContoured=
this.isSquaredLinear=this.isSquared=this.isModelConnected=this.isColorReversed=this.isCavity=this.isBicolorMap=this.isCutoffAbsolute=this.isPositiveOnly=this.isAngstroms=this.insideOut=this.iAddGridPoints=!1;this.logMessages=JU.Logger.debugging;this.mapLattice=null;this.mep_calcType=-1;this.minSet=0;this.modelIndex=-1;this.modelInvRotation=null;this.nContours=0;this.pocket=null;this.pointSize=NaN;this.probeValues=this.probes=null;this.propertyDistanceMax=2147483647;this.propertySmoothing=!1;this.propertySmoothingPower=
4;this.rangeSelected=this.rangeAll=this.rangeDefined=!1;this.resolution=3.4028235E38;this.scale=NaN;this.scale3d=0;this.sigma=NaN;this.slabInfo=null;this.solventExtendedAtomRadius=0;this.state=1;this.testFlags=0;this.theProperty=this.thePlane=null;this.thisContour=-1;this.title=null;this.usePropertyForColorRange=!0;this.vertexSource=null});e(d,"resetForMapping",function(a){a||(this.state=2);this.center.x=NaN;this.colorDensity=!1;this.intersection=this.func=null;this.isAnisotropic=!1;this.isMapped=
!0;this.mappedDataMin=3.4028235E38;this.points=this.parameters=this.origin=null;this.qmOrbitalType=0;this.volumeData=this.steps=null},"~B");e(d,"setAnisotropy",function(a){this.anisotropy[0]=a.x;this.anisotropy[1]=a.y;this.anisotropy[2]=a.z;this.isAnisotropic=!0;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P3");e(d,"setEccentricity",function(a){var b=JU.V3.new3(a.x,a.y,a.z),c=0<this.scale?this.scale:0>a.w?1:b.length();a=Math.abs(a.w);b.normalize();var g=JU.V3.new3(0,0,1);b.add(g);b.normalize();
Float.isNaN(b.x)&&b.set(1,0,0);this.eccentricityMatrixInverse=new JU.M3;this.eccentricityMatrixInverse.invertM(this.eccentricityMatrix=(new JU.M3).setAA(JU.A4.newVA(b,3.141592653589793)));this.isEccentric=this.isAnisotropic=!0;this.eccentricityScale=c;this.eccentricityRatio=a;1<a&&(this.eccentricityScale*=a);this.anisotropy[0]=a*c;this.anisotropy[1]=a*c;this.anisotropy[2]=c;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P4");e(d,"setPlane",function(a){this.thePlane=a;0==this.thePlane.x&&
(0==this.thePlane.y&&0==this.thePlane.z)&&(this.thePlane.z=1);this.isContoured=!0},"JU.P4");e(d,"setSphere",function(a,b){this.dataType=b?74:65;this.distance=a;this.setEccentricity(JU.P4.new4(0,0,1,1));this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" SPHERE "+a+";"},"~N,~B");e(d,"setEllipsoidP4",function(a){this.dataType=66;this.distance=1;this.setEccentricity(a);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages},
"JU.P4");e(d,"setEllipsoidAF",function(a){this.anisoB=a;this.dataType=67;this.distance=0.3*(Float.isNaN(this.scale)?1:this.scale);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;Float.isNaN(this.center.x)&&this.center.set(0,0,0);3.4028235E38==this.resolution&&(this.resolution=6)},"~A");e(d,"setLobe",function(a){this.dataType=68;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;
this.script=this.getScriptParams()+" LOBE {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,"getScriptParams",function(){return" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)});e(d,"setLp",function(a){this.dataType=70;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+
" LP {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,"setRadical",function(a){this.dataType=71;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" RAD {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(d,"setLcao",function(a,b){this.lcaoType=a;1==b&&(this.colorPosLCAO=this.colorNegLCAO);this.isSilent=!this.logMessages},
"~S,~N");e(d,"setSolvent",function(a,b){this.isEccentric=this.isAnisotropic=!1;this.solventRadius=Math.abs(b);this.dataType=null!=this.intersection?1333:"nomap"===a?1207:"molecular"===a?1203:"sasurface"===a||0==this.solventRadius?1196:1195;if(2>this.state&&(this.cutoffAutomatic||!this.colorDensity)&&(null==this.intersection||3.4028235E38==this.cutoff))this.cutoff=0;switch(this.dataType){case 1333:this.calculationType="VDW intersection";break;case 1207:this.calculationType="unmapped plane";break;case 1203:this.calculationType=
"molecular surface with radius "+this.solventRadius;0==this.minSet&&(this.minSet=50);break;case 1195:this.calculationType="solvent-excluded surface with radius "+this.solventRadius;0==this.minSet&&(this.minSet=50);break;case 1196:this.calculationType="solvent-accessible surface with radius "+this.solventRadius,0==this.minSet&&(this.minSet=50)}switch(this.dataType){case 1207:this.solventExtendedAtomRadius=this.solventRadius;this.solventRadius=0;this.isContoured=!1;break;case 1203:this.solventExtendedAtomRadius=
0;break;case 1195:this.solventExtendedAtomRadius=0;null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent);break;case 1196:this.solventExtendedAtomRadius=this.solventRadius,this.solventRadius=0,null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent)}},"~S,~N");e(d,"setFunctionXY",function(a){this.dataType=8;this.functionInfo=a;this.cutoff=1.4E-45;this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(d,"setFunctionXYZ",
function(a){this.dataType=9;this.functionInfo=a;3.4028235E38==this.cutoff&&(this.cutoff=1.4E-45);this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(d,"setAtomicOrbital",function(a){this.dataType=1294;this.setEccentricity(JU.P4.new4(0,0,1,1));this.psi_n=w(a[0]);this.psi_l=w(a[1]);this.psi_m=w(a[2]);this.psi_Znuc=a[3];this.psi_monteCarloCount=w(a[4]);this.distance=a[5];if(0!=this.distance||null!=this.thePlane)this.allowVolumeRender=!1;this.randomSeed=w(a[6]);this.psi_ptsPerAngstrom=10;if(3.4028235E38==
this.cutoff||0.14==this.cutoff)this.cutoff=0<this.psi_monteCarloCount?0:0.04,this.isSquared&&(this.cutoff*=this.cutoff);this.isCutoffAbsolute=!0;2>this.state&&(null==this.thePlane&&this.colorBySign)&&(this.isBicolorMap=!0);return 0<this.psi_Znuc&&Math.abs(this.psi_m)<=this.psi_l&&this.psi_l<this.psi_n},"~A");e(d,"setMep",function(a,b){this.dataType=b?1329:1328;this.theProperty=a;this.isEccentric=this.isAnisotropic=this.usePropertyForColorRange=!1;3.4028235E38==this.cutoff&&(this.cutoff=0.1,this.isSquared&&
(this.cutoff*=this.cutoff));this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;this.contourFromZero=!1;2<=this.state||null!=this.thePlane?!this.rangeDefined&&!this.rangeAll&&(this.valueMappedToRed=-0.1,this.valueMappedToBlue=0.1,this.rangeDefined=!0):this.isBicolorMap=this.colorBySign=!0},"~A,~B");e(d,"setNci",function(a){this.fullyLit=!0;this.qm_gridMax=200;a&&(this.dataType=1844);this.qm_marginAngstroms=2;this.qmOrbitalType=a?3:4;if(a&&(null==this.parameters||2>this.parameters.length))this.parameters=
t(-1,[this.cutoff,2]);if(3.4028235E38==this.cutoff||0==this.cutoff)this.cutoff=0.3;this.isSquared&&(this.cutoff*=this.cutoff);null==this.title&&(this.title=[]);this.moData=new java.util.Hashtable},"~B");e(d,"setMO",function(a,b){this.isModelConnected=!0;this.qm_moLinearCombination=b;this.qm_moNumber=null==b?Math.abs(a):w(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=y(-1,["no basis functions found in file"])):(this.qmOrbitalCount=this.moData.get("mos").size(),this.calculationType=this.moData.get("calculationType"),this.calculationType="Molecular orbital #"+this.qm_moNumber+"/"+this.qmOrbitalCount+" "+(null==this.calculationType?"":this.calculationType),!c&&null==this.title&&(this.title=Array(5),this.title[0]="%F",this.title[1]=
"Model %M  MO %I/%N %T",this.title[2]="?Energy = %E %U",this.title[3]="?Symmetry = %S",this.title[4]="?Occupancy = %O"));this.dataType=1837;3.4028235E38==this.cutoff&&(this.cutoff=c?0.01:0.05);if(this.isSquared||this.isSquaredLinear)this.cutoff*=this.cutoff;this.isEccentric=this.isAnisotropic=!1;this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;2<=this.state||null!=this.thePlane||(this.colorBySign=!0,this.colorByPhase&&0==this.colorPhase&&(this.colorByPhase=!1),this.isBicolorMap=!0)},"~N,~A");
e(d,"setMapRanges",function(a,b){if(!this.colorDensity&&(this.colorByPhase||this.colorBySign||(null!=this.thePlane||this.isBicolorMap)&&!this.isContoured))this.mappedDataMin=-1,this.mappedDataMax=1;if(3.4028235E38==this.mappedDataMin||this.mappedDataMin==this.mappedDataMax){var c=a.getMinMaxMappedValues(b);System.out.println("parameters - setmapranges "+c[0]+" "+c[1]);this.mappedDataMin=c[0];this.mappedDataMax=c[1]}0==this.mappedDataMin&&0==this.mappedDataMax&&(this.mappedDataMin=-1,this.mappedDataMax=
1);this.rangeDefined||(this.valueMappedToRed=this.mappedDataMin,this.valueMappedToBlue=this.mappedDataMax)},"J.jvxl.readers.SurfaceReader,~B");e(d,"addSlabInfo",function(a){null==this.slabInfo&&(this.slabInfo=new JU.Lst);this.slabInfo.addLast(a)},"~A");e(d,"isInsideOut",function(){return this.insideOut!=this.dataXYReversed});e(d,"isFullyLit",function(){return null!=this.thePlane||this.fullyLit})});L("J.jvxl.readers");R(["J.jvxl.api.VertexDataServer","JU.P3"],"J.jvxl.readers.SurfaceReader","JU.AU $.BS J.jvxl.calc.MarchingCubes $.MarchingSquares J.jvxl.data.JvxlCoder $.MeshData JU.BoxInfo $.C $.ColorEncoder $.Escape $.Logger".split(" "),
function(){var d=N(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;C(this,arguments)},J.jvxl.readers,"SurfaceReader",null,J.jvxl.api.VertexDataServer);ia(d,function(){this.ptTemp=new JU.P3});da(d,function(){});e(d,"initSR",function(a){this.sg=
a;this.params=a.params;this.assocCutoff=this.params.assocCutoff;this.isXLowToHigh=this.params.isXLowToHigh;this.center=this.params.center;this.anisotropy=this.params.anisotropy;this.isAnisotropic=this.params.isAnisotropic;this.eccentricityMatrix=this.params.eccentricityMatrix;this.eccentricityMatrixInverse=this.params.eccentricityMatrixInverse;this.isEccentric=this.params.isEccentric;this.eccentricityScale=this.params.eccentricityScale;this.eccentricityRatio=this.params.eccentricityRatio;this.marchingSquares=
a.marchingSquares;this.meshData=a.meshData;this.jvxlData=a.jvxlData;this.setVolumeDataV(a.volumeDataTemp);this.meshDataServer=a.meshDataServer;this.cJvxlEdgeNaN=String.fromCharCode(125)},"J.jvxl.readers.SurfaceGenerator");e(d,"setOutputChannel",function(){},"JU.OC");e(d,"newVoxelDataCube",function(){this.volumeData.setVoxelDataAsArray(this.voxelData=t(this.nPointsX,this.nPointsY,this.nPointsZ,0))});e(d,"setVolumeDataV",function(a){this.nBytes=0;this.volumetricOrigin=a.volumetricOrigin;this.volumetricVectors=
a.volumetricVectors;this.voxelCounts=a.voxelCounts;this.voxelData=a.getVoxelData();this.volumeData=a},"J.jvxl.data.VolumeData");e(d,"jvxlUpdateInfo",function(){this.jvxlData.jvxlUpdateInfo(this.params.title,this.nBytes)});e(d,"readAndSetVolumeParameters",function(a){return!this.readVolumeParameters(a)?!1:this.vertexDataOnly?!0:this.volumeData.setUnitVectors()},"~B");e(d,"createIsosurface",function(a){this.resetIsosurface();this.params.showTiming&&JU.Logger.startTimer("isosurface creation");this.jvxlData.cutoff=
NaN;this.jvxlData.cutoffRange=null;if(!this.readAndSetVolumeParameters(a))return!1;!a&&(!Float.isNaN(this.params.sigma)&&!this.allowSigma)&&(0<this.params.sigma&&JU.Logger.error("Reader does not support SIGMA option -- using cutoff 1.6"),this.params.cutoff=1.6);0>this.params.sigma&&(this.params.sigma=-this.params.sigma);this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.jvxlData.isSlabbable=0!=(this.params.dataType&1024);this.jvxlData.insideOut=
this.params.isInsideOut();this.jvxlData.isBicolorMap=this.params.isBicolorMap;this.jvxlData.nPointsX=this.nPointsX;this.jvxlData.nPointsY=this.nPointsY;this.jvxlData.nPointsZ=this.nPointsZ;this.jvxlData.jvxlVolumeDataXml=this.volumeData.xmlData;this.jvxlData.voxelVolume=this.volumeData.voxelVolume;if(a)this.volumeData.setMappingPlane(this.params.thePlane),null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null),this.params.setMapRanges(this,!1),this.generateSurfaceData(),
this.volumeData.setMappingPlane(null);else{if(!this.readVolumeData(!1))return!1;this.generateSurfaceData()}if(null==this.jvxlFileHeaderBuffer)this.jvxlData.jvxlFileTitle="",this.jvxlData.jvxlFileSource=null,this.jvxlData.jvxlFileMessage=null;else{a=this.jvxlFileHeaderBuffer.toString();var b=a.indexOf("\n",a.indexOf("\n",a.indexOf("\n")+1)+1)+1;this.jvxlData.jvxlFileTitle=a.substring(0,b);this.jvxlData.jvxlFileSource=this.params.fileName}null==this.params.contactPair&&this.setBBoxAll();this.jvxlData.isValid=
3.4028235E38!=this.xyzMin.x;this.params.isSilent||(this.jvxlData.isValid?JU.Logger.info("boundbox corners "+JU.Escape.eP(this.xyzMin)+" "+JU.Escape.eP(this.xyzMax)):JU.Logger.error("no isosurface points were found!"));this.jvxlData.boundingBox=y(-1,[this.xyzMin,this.xyzMax]);this.jvxlData.dataMin=this.dataMin;this.jvxlData.dataMax=this.dataMax;this.jvxlData.cutoffRange=this.isJvxl?this.jvxlCutoffRange:this.params.cutoffRange;this.jvxlData.cutoff=null!=this.jvxlCutoffRange?this.jvxlData.cutoffRange[0]:
this.isJvxl?this.jvxlCutoff:this.params.cutoff;this.jvxlData.isCutoffAbsolute=this.params.isCutoffAbsolute;this.jvxlData.isModelConnected=this.params.isModelConnected;this.jvxlData.pointsPerAngstrom=1/this.volumeData.volumetricVectorLengths[0];this.jvxlData.jvxlColorData="";this.jvxlData.jvxlPlane=this.params.thePlane;this.jvxlData.jvxlEdgeData=this.edgeData;this.jvxlData.isBicolorMap=this.params.isBicolorMap;this.jvxlData.isContoured=this.params.isContoured;this.jvxlData.colorDensity=this.params.colorDensity;
this.jvxlData.pointSize=this.params.pointSize;null!=this.jvxlData.vContours&&(this.params.nContours=this.jvxlData.vContours.length);this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.nEdges=this.edgeCount;this.jvxlData.edgeFractionBase=this.edgeFractionBase;this.jvxlData.edgeFractionRange=this.edgeFractionRange;this.jvxlData.colorFractionBase=this.colorFractionBase;this.jvxlData.colorFractionRange=
this.colorFractionRange;this.jvxlData.jvxlDataIs2dContour=this.jvxlDataIs2dContour;this.jvxlData.jvxlDataIsColorMapped=this.jvxlDataIsColorMapped;this.jvxlData.jvxlDataIsColorDensity=this.jvxlDataIsColorDensity;this.jvxlData.isXLowToHigh=this.isXLowToHigh;this.jvxlData.vertexDataOnly=this.vertexDataOnly;this.jvxlData.saveVertexCount=0;if(this.jvxlDataIsColorMapped||0<this.jvxlData.nVertexColors)null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshDataServer.fillMeshData(this.meshData,
2,null)),this.jvxlData.jvxlColorData=this.readColorData(),this.updateSurfaceData(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted();this.params.showTiming&&JU.Logger.checkTimer("isosurface creation",!1);return!0},"~B");e(d,"resetIsosurface",function(){this.meshData=new J.jvxl.data.MeshData;this.xyzMin=this.xyzMax=null;this.jvxlData.isBicolorMap=this.params.isBicolorMap;null!=this.meshDataServer&&this.meshDataServer.fillMeshData(null,0,null);this.contourVertexCount=0;
3.4028235E38==this.params.cutoff&&(this.params.cutoff=0.02);this.jvxlData.jvxlSurfaceData="";this.jvxlData.jvxlEdgeData="";this.jvxlData.jvxlColorData="";this.edgeCount=0;this.edgeFractionBase=35;this.edgeFractionRange=90;this.colorFractionBase=35;this.colorFractionRange=90;this.params.mappedDataMin=3.4028235E38});e(d,"discardTempData",function(a){this.discardTempDataSR(a)},"~B");e(d,"discardTempDataSR",function(a){a&&(this.voxelData=null,this.marchingCubes=this.sg.marchingSquares=this.marchingSquares=
null)},"~B");e(d,"initializeVolumetricData",function(){this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.setVolumeDataV(this.volumeData)});e(d,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0<this.nPointsX&&0<this.nPointsY&&0<this.nPointsZ)try{this.gotoData(this.params.fileIndex-1,this.nPointsX*this.nPointsY*this.nPointsZ),this.readSurfaceData(a)}catch(b){if(ea(b,Exception))return JU.Logger.error(b.toString()),!1;throw b;
}return!0},"~B");e(d,"gotoData",function(){},"~N,~N");e(d,"readColorData",function(){if(null==this.jvxlData.vertexColors)return"";var a=this.jvxlData.vertexCount,b=this.meshData.vcs,c=this.meshData.vvs;if(null==b||b.length<a)this.meshData.vcs=b=fa(a,0);if(null==c||c.length<a)this.meshData.vvs=t(a,0);for(c=0;c<a;c++)b[c]=JU.C.getColix(this.jvxlData.vertexColors[c]);return"-"});j(d,"getPlane",function(a){return this.getPlaneSR(a)},"~N");e(d,"getPlaneSR",function(a){0==this.yzCount&&this.initPlanes();
null!=this.qpc&&this.qpc.getPlane(a,this.yzPlanes[a%2]);return this.yzPlanes[a%2]},"~N");e(d,"initPlanes",function(){this.yzCount=this.nPointsY*this.nPointsZ;this.isQuiet||JU.Logger.info("reading data progressively -- yzCount = "+this.yzCount);this.yzPlanes=JU.AU.newFloat2(2);this.yzPlanes[0]=t(this.yzCount,0);this.yzPlanes[1]=t(this.yzCount,0)});j(d,"getValue",function(a,b,c,g){return this.getValue2(a,b,c,g)},"~N,~N,~N,~N");e(d,"getValue2",function(a,b,c,g){return null==this.yzPlanes?this.voxelData[a][b][c]:
this.yzPlanes[a%2][g]},"~N,~N,~N,~N");e(d,"generateSurfaceData",function(){this.edgeData="";if(this.vertexDataOnly)try{this.readSurfaceData(!1)}catch(a){if(ea(a,Exception))System.out.println(a.toString()),JU.Logger.error("Exception in SurfaceReader::readSurfaceData: "+a.toString());else throw a;}else{this.contourVertexCount=0;var b=-1;this.marchingSquares=null;if(null!=this.params.thePlane||this.params.isContoured)this.marchingSquares=new J.jvxl.calc.MarchingSquares(this,this.volumeData,this.params.thePlane,
this.params.contoursDiscrete,this.params.nContours,this.params.thisContour,this.params.contourFromZero),b=this.marchingSquares.contourType,this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue);this.params.contourType=b;this.params.isXLowToHigh=this.isXLowToHigh;this.marchingCubes=new J.jvxl.calc.MarchingCubes(this,this.volumeData,this.params,this.jvxlVoxelBitSet);b=this.marchingCubes.getEdgeData();null==this.params.thePlane&&(this.edgeData=b);this.jvxlData.setSurfaceInfoFromBitSetPts(this.marchingCubes.bsVoxels,
this.params.thePlane,this.params.mapLattice);this.jvxlData.jvxlExcluded=this.params.bsExcluded;this.isJvxl&&(this.edgeData=this.jvxlEdgeDataRead);this.postProcessVertices()}});e(d,"postProcessVertices",function(){});j(d,"getSurfacePointIndexAndFraction",function(a,b,c,g,d,e,h,f,k,l,n,j,q,r){b=this.getSurfacePointAndFraction(a,b,k,l,n,j,c,g,d,h,f,r,this.ptTemp);if(null!=this.marchingSquares&&this.params.isContoured)return this.marchingSquares.addContourVertex(this.ptTemp,a);a=0<this.assocCutoff?r[0]<
this.assocCutoff?h:r[0]>1-this.assocCutoff?f:-1:-1;0<=a&&(a=this.marchingCubes.getLinearOffset(c,g,d,a));a=this.addVertexCopy(this.ptTemp,b,a,!0);0<=a&&this.params.iAddGridPoints&&(this.marchingCubes.calcVertexPoint(c,g,d,f,this.ptTemp),this.addVertexCopy(k<l?n:this.ptTemp,Math.min(k,l),-3,!0),this.addVertexCopy(k<l?this.ptTemp:n,Math.max(k,l),-3,!0));return a},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");e(d,"getSurfacePointAndFraction",function(a,b,c,g,d,e,h,f,k,l,n,j,q){return this.getSPF(a,
b,c,g,d,e,h,f,k,l,n,j,q)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getSPF",function(a,b,c,g,d,e,h,f,k,l,n,j,q){g-=c;h=(a-c)/g;if(b&&(0>h||1<h))h=(-a-c)/g;if(0>h||1<h)h=NaN;j[0]=h;q.scaleAdd2(h,e,d);return c+h*g},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"addVertexCopy",function(a,b,c,g){return this.addVC(a,b,c,g)},"JU.T3,~N,~N,~B");e(d,"addVC",function(a,b,c,g){return Float.isNaN(b)&&-3!=c?-1:null==this.meshDataServer?this.meshData.addVertexCopy(a,b,c,g):this.meshDataServer.addVertexCopy(a,
b,c,g)},"JU.T3,~N,~N,~B");e(d,"addTriangleCheck",function(a,b,c,g,d,e,h){if(null!=this.marchingSquares&&this.params.isContoured){if(0==h)return this.marchingSquares.addTriangle(a,b,c,g,d);h=0}return null!=this.meshDataServer?this.meshDataServer.addTriangleCheck(a,b,c,g,d,e,h):e&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.meshData.vvs)?-1:this.meshData.addTriangleCheck(a,b,c,g,d,h)},"~N,~N,~N,~N,~N,~B,~N");e(d,"colorIsosurface",function(){this.params.isSquared&&null!=this.volumeData&&this.volumeData.filterData(!0,
NaN);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.jvxlData.saveVertexCount=0;this.params.isContoured&&null!=this.marchingSquares&&(this.initializeMapping(),this.params.setMapRanges(this,!1),this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue),this.jvxlData.saveVertexCount=this.marchingSquares.contourVertexCount,this.contourVertexCount=this.marchingSquares.generateContourData(this.jvxlDataIs2dContour,this.params.isSquared?
1E-8:1E-4),this.jvxlData.contourValuesUsed=this.marchingSquares.contourValuesUsed,this.minMax=this.marchingSquares.getMinMax(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted(),this.finalizeMapping());this.applyColorScale();this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.jvxlFileMessage="mapped: min = "+this.params.valueMappedToRed+"; max = "+this.params.valueMappedToBlue});
e(d,"applyColorScale",function(){this.colorFractionBase=this.jvxlData.colorFractionBase=35;this.colorFractionRange=this.jvxlData.colorFractionRange=90;0==this.params.colorPhase&&(this.params.colorPhase=1);null==this.meshDataServer?this.meshData.vcs=fa(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=r(this.meshData.vc,0));var b=3.4028235E38,c=-3.4028235E38,g;this.initializeMapping();for(var d=this.meshData.vc;--d>=this.meshData.mergeVertexCount0;){if(this.params.colorBySets)g=this.meshData.vertexSets[d];else if(this.params.colorByPhase)g=this.getPhase(this.meshData.vs[d]);else{var e=this.haveSurfaceAtoms;g=this.volumeData.lookupInterpolatedVoxelValue(this.meshData.vs[d],e);e&&(this.meshData.vertexSource[d]=
this.getSurfaceAtomIndex())}g<b&&(b=g);g>c&&3.4028235E38!=g&&(c=g);this.meshData.vvs[d]=g}this.params.rangeSelected&&null==this.minMax&&(this.minMax=t(-1,[b,c]));this.finalizeMapping()}this.params.setMapRanges(this,!0);this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;null==this.params.contactPair&&null==this.jvxlData.vertexColors&&
this.colorData();J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,a?this.meshData.vvs:null);this.haveSurfaceAtoms&&null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null);null!=this.meshDataServer&&this.params.colorBySets&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"colorData",function(){var a=this.meshData.vvs,b=this.meshData.vcs;this.meshData.pcs=null;var c=this.jvxlData.valueMappedToBlue,g=this.jvxlData.valueMappedToRed,d=this.jvxlData.minColorIndex,
e=this.jvxlData.maxColorIndex;null==this.params.colorEncoder&&(this.params.colorEncoder=new JU.ColorEncoder(null,null));this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(var h=this.meshData.vc;0<=--h;){var f=a[h];0<=d?0>=f?b[h]=d:0<f&&(b[h]=e):(f<=g&&(f=g),f>=c&&(f=c),b[h]=this.params.colorEncoder.getColorIndex(f))}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=fa(a,0);d=this.jvxlData.contourValues;null==d&&(d=this.jvxlData.contourValuesUsed);null==this.jvxlData.contourValuesUsed&&(this.jvxlData.contourValuesUsed=null==d?t(a,0):d);c=(c-g)/(a+1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(h=0;h<a;h++)e=null==d?g+(h+1)*c:d[h],this.jvxlData.contourValuesUsed[h]=
e,b[h]=JU.C.getColixTranslucent(this.params.colorEncoder.getArgb(e));this.jvxlData.contourColors=JU.C.getHexCodes(b)}});d.getColorPhaseIndex=e(d,"getColorPhaseIndex",function(a){for(var b=-1,c=0;c<J.jvxl.readers.SurfaceReader.colorPhases.length;c++)if(a.equalsIgnoreCase(J.jvxl.readers.SurfaceReader.colorPhases[c])){b=c;break}return b},"~S");e(d,"getPhase",function(a){switch(this.params.colorPhase){case 0:case -1:case 1:return 0<a.x?1:-1;case 2:return 0<a.y?1:-1;case 3:return 0<a.z?1:-1;case 4:return 0<
a.x*a.y?1:-1;case 5:return 0<a.y*a.z?1:-1;case 6:return 0<a.x*a.z?1:-1;case 7:return 0<a.x*a.x-a.y*a.y?1:-1;case 8:return 0<2*a.z*a.z-a.x*a.x-a.y*a.y?1:-1}return 1},"JU.T3");e(d,"getMinMaxMappedValues",function(a){if(null!=this.minMax&&3.4028235E38!=this.minMax[0])return this.minMax;if(this.params.colorBySets)return this.minMax=t(-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 g=this.params.theProperty[a];Float.isNaN(g)||(g<b&&(b=g),g>c&&(c=g))}return this.minMax=t(-1,[b,c])}var g=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc,d=this.meshData.vs,e=a||this.jvxlDataIs2dContour||this.vertexDataOnly||this.params.colorDensity;for(a=this.meshData.mergeVertexCount0;a<g;a++){var h;h=e?this.meshData.vvs[a]:this.volumeData.lookupInterpolatedVoxelValue(d[a],!1);h<b&&(b=h);h>c&&3.4028235E38!=
h&&(c=h)}return this.minMax=t(-1,[b,c])},"~B");e(d,"updateTriangles",function(){null==this.meshDataServer?this.meshData.invalidatePolygons():this.meshDataServer.invalidateTriangles()});e(d,"updateSurfaceData",function(){this.meshData.setVertexSets(!0);this.updateTriangles();null==this.params.bsExcluded[1]&&(this.params.bsExcluded[1]=new JU.BS);this.meshData.updateInvalidatedVertices(this.params.bsExcluded[1])});e(d,"selectPocket",function(){},"~B");e(d,"excludeMinimumSet",function(){null!=this.meshDataServer&&
this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()<this.params.minSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"excludeMaximumSet",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,
b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()>this.params.maxSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(d,"slabIsosurface",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.slabPolygonsList(a,!0);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null)},"JU.Lst");e(d,
"setVertexAnisotropy",function(a){a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2];a.add(this.center)},"JU.T3");e(d,"setVectorAnisotropy",function(a){this.haveSetAnisotropy=!0;a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2]},"JU.T3");e(d,"setVolumetricAnisotropy",function(){this.haveSetAnisotropy||(this.setVolumetricOriginAnisotropy(),this.setVectorAnisotropy(this.volumetricVectors[0]),this.setVectorAnisotropy(this.volumetricVectors[1]),this.setVectorAnisotropy(this.volumetricVectors[2]))});
e(d,"setVolumetricOriginAnisotropy",function(){this.volumetricOrigin.setT(this.center)});e(d,"setBBoxAll",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.xyzMin=new JU.P3;this.xyzMax=new JU.P3;this.meshData.setBox(this.xyzMin,this.xyzMax)});e(d,"setBBox",function(a,b){null==this.xyzMin&&(this.xyzMin=JU.P3.new3(3.4028235E38,3.4028235E38,3.4028235E38),this.xyzMax=JU.P3.new3(-3.4028235E38,-3.4028235E38,-3.4028235E38));JU.BoxInfo.addPoint(a,this.xyzMin,
this.xyzMax,b)},"JU.T3,~N");e(d,"getValueAtPoint",function(){return 0},"JU.T3,~B");e(d,"initializeMapping",function(){});e(d,"finalizeMapping",function(){});e(d,"getSurfaceAtomIndex",function(){return-1});d.colorPhases=y(-1,"_orb x y z xy yz xz x2-y2 z2".split(" "))});L("J.jvxl.calc");R(["JU.TriangleData","JU.BS","$.P3","$.SB","$.V3"],"J.jvxl.calc.MarchingCubes",["J.jvxl.data.JvxlCoder"],function(){var d=N(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;C(this,arguments)},J.jvxl.calc,"MarchingCubes",JU.TriangleData);ia(d,function(){this.edgeData=new JU.SB;this.vertexValues=t(8,0);this.voxelVertexVectors=Array(8);this.edgeVectors=Array(12);for(var a=12;0<=--a;)this.edgeVectors[a]=new JU.V3;this.edgePointIndexes=r(12,0);this.bsValues=new JU.BS;this.pt0=
new JU.P3;this.pointA=new JU.P3;this.fReturn=t(1,0);this.linearOffsets=r(8,0)});da(d,function(){ja(this,J.jvxl.calc.MarchingCubes,[])});da(d,function(a,b,c,g){ja(this,J.jvxl.calc.MarchingCubes,[]);this.excludePartialCubes=!0;this.surfaceReader=a;this.bsVoxels=g;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!=
g?2:3;this.setParameters(b,c)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");e(d,"setParameters",function(a,b){this.volumeData=a;this.colorDensity=b.colorDensity;this.isContoured=null==b.thePlane&&b.isContoured&&!this.colorDensity;this.cutoff=b.cutoff;this.isCutoffAbsolute=b.isCutoffAbsolute;this.isDensityRange=null!=b.cutoffRange;this.contourType=b.contourType;this.isSquared=b.isSquared;this.isXLowToHigh=b.isXLowToHigh;this.cubeCountX=a.voxelCounts[0]-1;this.cubeCountY=
a.voxelCounts[1]-1;this.cubeCountZ=a.voxelCounts[2]-1;a.getYzCount();null!=b.mapLattice&&(this.cubeCountX*=Math.abs(b.mapLattice.x),this.cubeCountY*=Math.abs(b.mapLattice.y),this.cubeCountZ*=Math.abs(b.mapLattice.z));this.nY=this.cubeCountY+1;this.nZ=this.cubeCountZ+1;this.yzCount=this.nY*this.nZ;null==this.bsVoxels&&(this.bsVoxels=new JU.BS);this.edgeVertexPointers=this.isXLowToHigh?J.jvxl.calc.MarchingCubes.edgeVertexPointersLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPointersHighToLow;this.edgeVertexPlanes=
this.isXLowToHigh?J.jvxl.calc.MarchingCubes.edgeVertexPlanesLowToHigh:J.jvxl.calc.MarchingCubes.edgeVertexPlanesHighToLow;this.isoPointIndexPlanes=r(2,this.yzCount,3,0);this.yzPlanes=3==this.mode?t(2,this.yzCount,0):null;this.setLinearOffsets();this.calcVoxelVertexVectors()},"J.jvxl.data.VolumeData,J.jvxl.readers.Parameters");e(d,"calcVoxelVertexVectors",function(){for(var a=8;0<=--a;)this.volumeData.transform(J.jvxl.calc.MarchingCubes.cubeVertexVectors[a],this.voxelVertexVectors[a]=new JU.V3);for(a=
12;0<=--a;)this.edgeVectors[a].sub2(this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a+1]],this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a]])});e(d,"resetIndexPlane",function(a){for(var b=0;b<this.yzCount;b++)for(var c=0;3>c;c++)a[b][c]=-2147483648;return a},"~A");e(d,"getEdgeData",function(){if(0>this.cubeCountX||0>this.cubeCountY||0>this.cubeCountZ)return"";this.mappingPlane=this.volumeData.mappingPlane;this.edgeCount=0;var a,b,c,g,d,e;this.isXLowToHigh?(a=0,this.colorDensity?(b=
this.cubeCountX+1,e=this.yzCount-1):(b=this.cubeCountX,e=this.yzCount-1-this.nZ-1),c=1,g=this.yzCount):(this.colorDensity?(a=this.cubeCountX,e=(this.cubeCountX+1)*this.yzCount-1):(a=this.cubeCountX-1,e=this.cubeCountX*this.yzCount-1-this.nZ-1),c=b=-1,g=-this.yzCount);d=e;this.resetIndexPlane(this.isoPointIndexPlanes[1]);this.voxelData=null;var h=this.cubeCountY+(this.colorDensity?1:0),f=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,l=0;a!=b;a+=c,e+=g,d=e)if(3==this.mode&&a+c<=b&&this.getPlane(a+c,!0),!this.bsExcludedPlanes.get(a)||!this.bsExcludedPlanes.get(a+c))if(this.colorDensity)for(var n=h;0<=--n;)for(var j=f;0<=--j;d--)l=this.getValue(a,n,j,d,0),(k||this.$isInside)&&this.addVertex(a,n,j,d,l);else{n=this.isoPointIndexPlanes[0];this.isoPointIndexPlanes[0]=
this.isoPointIndexPlanes[1];this.isoPointIndexPlanes[1]=this.resetIndexPlane(n);for(var q=!0,n=h;0<=--n;d--)for(j=f;0<=--j;d--){for(var r=0,v=8;0<=--v;)l=this.getValue(a,n,j,d,v),this.$isInside&&(r|=JU.TriangleData.Pwr2[v]);q&&!Float.isNaN(l)&&(q=!1);0!=r&&255!=r&&this.processOneCubical(r,a,n,j,d)&&(!this.isContoured&&!this.colorDensity)&&this.processTriangles(r)}q&&this.bsExcludedPlanes.set(a)}return this.edgeData.toString()});e(d,"getValue",function(a,b,c,g,d){this.offset=JU.TriangleData.cubeVertexOffsets[d];
g+=this.linearOffsets[d];switch(this.mode){case 3:a=this.vertexValues[d]=this.getValueArray(a+this.offset.x,b+this.offset.y,c+this.offset.z,g,this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[d]]);this.$isInside=this.allInside||this.bsVoxels.get(g);break;case 2:this.$isInside=this.allInside||this.bsVoxels.get(g);a=this.vertexValues[d]=(this.isDensityRange?!this.$isInside:this.bsExcludedVertices.get(g))?NaN:this.$isInside?1:0;break;default:case 1:null==this.mappingPlane?a=this.vertexValues[d]=this.voxelData[a+
this.offset.x][b+this.offset.y][c+this.offset.z]:(this.volumeData.voxelPtToXYZ(a+this.offset.x,b+this.offset.y,c+this.offset.z,this.pt0),a=this.vertexValues[d]=this.volumeData.distanceToMappingPlane(this.pt0)),this.isSquared&&(this.vertexValues[d]*=this.vertexValues[d]),(this.$isInside=this.allInside?!0:J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[d],this.cutoff,this.isCutoffAbsolute))&&this.bsVoxels.set(g)}return a},"~N,~N,~N,~N,~N");e(d,"getPlane",function(a,b){if(!(0>a||a>this.cubeCountX))if(this.surfaceReader.getPlane(a),
b){var c=this.yzPlanes[0];this.yzPlanes[0]=this.yzPlanes[1];this.yzPlanes[1]=c}},"~N,~B");e(d,"processTriangles",function(a){a=JU.TriangleData.triangleTable2[a];for(var b=a.length;0<=(b-=4);)this.addTriangle(a[b],a[b+1],a[b+2],a[b+3])},"~N");e(d,"addVertex",function(a,b,c,g,d){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);0>this.surfaceReader.addVertexCopy(this.pt0,d,-4,!0)&&this.bsExcludedVertices.set(g)},"~N,~N,~N,~N,~N");e(d,"addTriangle",function(a,b,c,g){!this.bsExcludedTriangles.get(this.nTriangles)&&
0>this.surfaceReader.addTriangleCheck(this.edgePointIndexes[a],this.edgePointIndexes[b],this.edgePointIndexes[c],g,0,this.isCutoffAbsolute,0)&&this.bsExcludedTriangles.set(this.nTriangles);this.nTriangles++},"~N,~N,~N,~N");e(d,"getValueArray",function(a,b,c,g,d){var e=g%this.yzCount;this.bsValues.set(g);a=this.surfaceReader.getValue(a,b,c,e);this.isSquared&&(a*=a);d[e]=a;J.jvxl.calc.MarchingCubes.isInside(a,this.cutoff,this.isCutoffAbsolute)&&this.bsVoxels.set(g);return a},"~N,~N,~N,~N,~A");d.isInside=
e(d,"isInside",function(a,b,c){return 0<b&&(c?Math.abs(a):a)>=b||0>=b&&a<=b},"~N,~N,~B");e(d,"processOneCubical",function(a,b,c,g,d){a=J.jvxl.calc.MarchingCubes.insideMaskTable[a];for(var e=!1,h=12;0<=--h;)if(0!=(a&JU.TriangleData.Pwr2[h])){var f=this.edgeVertexPlanes[h],k=(d+this.linearOffsets[this.edgeVertexPointers[h]])%this.yzCount,l=J.jvxl.calc.MarchingCubes.edgeTypeTable[h],n=this.edgePointIndexes[h]=this.isoPointIndexPlanes[f][k][l];if(-2147483648!=n)-1==n&&(e=this.excludePartialCubes);else{var n=
JU.TriangleData.edgeVertexes[h<<1],j=JU.TriangleData.edgeVertexes[(h<<1)+1],q=this.vertexValues[n],r=this.vertexValues[j];this.calcVertexPoint(b,c,g,n,this.pointA);this.edgeCount++;f=this.edgePointIndexes[h]=this.isoPointIndexPlanes[f][k][l]=this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff,this.isCutoffAbsolute,b,c,g,JU.TriangleData.cubeVertexOffsets[n],n,j,q,r,this.pointA,this.edgeVectors[h],l==this.contourType,this.fReturn);this.addEdgeData(0>f?NaN:this.fReturn[0]);if(Float.isNaN(this.fReturn[0])||
0>f)e=this.excludePartialCubes}}return!e},"~N,~N,~N,~N,~N");e(d,"addEdgeData",function(a){a=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(a);this.edgeData.appendC(a)},"~N");e(d,"calcVertexPoint",function(a,b,c,g,d){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);d.add2(this.pt0,this.voxelVertexVectors[g])},"~N,~N,~N,~N,JU.P3");e(d,"setLinearOffsets",function(){this.linearOffsets[0]=0;this.linearOffsets[1]=this.yzCount;this.linearOffsets[2]=this.yzCount+1;this.linearOffsets[3]=1;this.linearOffsets[4]=
this.nZ;this.linearOffsets[5]=this.yzCount+this.nZ;this.linearOffsets[6]=this.yzCount+this.nZ+1;this.linearOffsets[7]=this.nZ+1});e(d,"getLinearOffset",function(a,b,c,g){return a*this.yzCount+b*this.nZ+c+this.linearOffsets[g]},"~N,~N,~N,~N");d.yzPlanePts=r(-1,[0,1,1,0,0,1,1,0]);d.edgeVertexPointersLowToHigh=r(-1,[1,1,2,0,5,5,6,4,0,1,2,3]);d.edgeVertexPointersHighToLow=r(-1,[0,1,3,0,4,5,7,4,0,1,2,3]);d.edgeVertexPlanesLowToHigh=r(-1,[1,1,1,0,1,1,1,0,0,1,1,0]);d.edgeVertexPlanesHighToLow=r(-1,[1,0,
1,1,1,0,1,1,1,0,0,1]);d.cubeVertexVectors=y(-1,[JU.V3.new3(0,0,0),JU.V3.new3(1,0,0),JU.V3.new3(1,0,1),JU.V3.new3(0,0,1),JU.V3.new3(0,1,0),JU.V3.new3(1,1,0),JU.V3.new3(1,1,1),JU.V3.new3(0,1,1)]);d.edgeTypeTable=r(-1,[0,2,0,2,0,2,0,2,1,1,1,1]);d.insideMaskTable=fa(-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])});L("J.jvxl.calc");R(["JU.P3",
"java.util.Hashtable"],"J.jvxl.calc.MarchingSquares",["JU.AU","JU.Logger"],function(){var d=N(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;xa("J.jvxl.calc.MarchingSquares.ContourVertex")||J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$();this.contourPlaneMaximumValue=
this.contourPlaneMinimumValue=0;this.ptTemp=this.contourValuesUsed=null;this.triangleCount=0;this.htPts=this.triangles=null;xa("J.jvxl.calc.MarchingSquares.Triangle")||J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$();C(this,arguments)},J.jvxl.calc,"MarchingSquares",null);ia(d,function(){this.pointA=new JU.P3;this.pointB=new JU.P3;this.contourVertexes=Array(1E3);this.ptTemp=new JU.P3;this.triangles=Array(1E3);this.htPts=new java.util.Hashtable});da(d,function(a,b,c,g,d,e,h){this.surfaceReader=
a;this.volumeData=b;this.thisContour=e;this.contoursDiscrete=g;this.contourFromZero=h;null==g?(this.nContourSegments=(0==d?9:d)+0,100<this.nContourSegments&&(this.nContourSegments=100)):(this.nContourSegments=d=g.length,this.contourFromZero=!1)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,JU.P4,~A,~N,~N,~B");e(d,"setMinMax",function(a,b){this.valueMin=a;this.valueMax=b},"~N,~N");e(d,"addContourVertex",function(a,b){this.contourVertexCount==this.contourVertexes.length&&(this.contourVertexes=
JU.AU.doubleLength(this.contourVertexes));var c=this.surfaceReader.addVertexCopy(a,b,-2,!0);this.contourVertexes[this.contourVertexCount++]=va(J.jvxl.calc.MarchingSquares.ContourVertex,this,null,a);return c},"JU.P3,~N");e(d,"setContourData",function(a,b){this.contourVertexes[a].setValue(b)},"~N,~N");e(d,"calcContourPoint",function(a,b,c,g){return this.volumeData.calculateFractionalPoint(a,this.pointA,this.pointB,b,c,g)},"~N,~N,~N,JU.P3");e(d,"addTriangle",function(a,b,c,g,d){this.triangleCount==this.triangles.length&&
(this.triangles=JU.AU.doubleLength(this.triangles));this.triangles[this.triangleCount++]=va(J.jvxl.calc.MarchingSquares.Triangle,this,null,a,b,c,g,d);return 0},"~N,~N,~N,~N,~N");e(d,"generateContourData",function(a,b){JU.Logger.info("generateContours: "+this.nContourSegments+" segments");this.getVertexValues(a);this.createContours(this.valueMin,this.valueMax,b);this.addAllTriangles();return this.contourVertexCount},"~B,~N");e(d,"getVertexValues",function(a){this.contourPlaneMinimumValue=3.4028235E38;
this.contourPlaneMaximumValue=-3.4028235E38;for(var b=0;b<this.contourVertexCount;b++){var c=this.contourVertexes[b],g;a?g=c.value:(g=this.volumeData.lookupInterpolatedVoxelValue(c,!1),c.setValue(g));g<this.contourPlaneMinimumValue&&(this.contourPlaneMinimumValue=g);g>this.contourPlaneMaximumValue&&(this.contourPlaneMaximumValue=g)}},"~B");e(d,"createContours",function(a,b,c){b-=a;this.contourValuesUsed=t(this.nContourSegments,0);for(var g=this.triangleCount;0<=--g;)this.triangles[g].check=0;for(var d=
-3.4028235E38,g=0;g<this.nContourSegments;g++){d=null!=this.contoursDiscrete?this.contoursDiscrete[g]:this.contourFromZero?a+1*g/this.nContourSegments*b:0==g?-3.4028235E38:g==this.nContourSegments-1?3.4028235E38:a+1*(g-1)/(this.nContourSegments-1)*b;null==this.contoursDiscrete&&Math.abs(d)<c&&(d=0>d?-c:c);this.contourValuesUsed[g]=d;JU.Logger.info("#contour "+(g+1)+" "+d+" "+this.triangleCount);this.htPts.clear();for(var e=this.triangleCount;0<=--e;)this.triangles[e].isValid&&this.checkContour(this.triangles[e],
g,d)}this.valueMin=this.contourValuesUsed[0];this.valueMax=0==this.contourValuesUsed.length?this.valueMin:this.contourValuesUsed[this.contourValuesUsed.length-1];return!0},"~N,~N,~N");e(d,"intercept",function(a,b,c){var g=a.pts[b];a=a.pts[(b+1)%3];if(2147483647==g||2147483647==a)return-1;b=g<a?g+"_"+a:a+"_"+g;if(this.htPts.containsKey(b))return this.htPts.get(b).intValue();var d=this.contourVertexes[g].value,e=this.contourVertexes[a].value,h=-1;if(d!=e){var f=(c-d)/(e-d);if(0<=f&&1>=f&&(this.pointA.setT(this.contourVertexes[g]),
this.pointB.setT(this.contourVertexes[a]),c=this.calcContourPoint(c,d,e,this.ptTemp),!Float.isNaN(c))){h=this.addContourVertex(this.ptTemp,c);if(0>h)return-1;this.contourVertexes[h].setValue(c)}}this.htPts.put(b,Integer.$valueOf(h));return h},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(d,"checkContour",function(a,b,c){if(!(0<this.thisContour&&b+1!=this.thisContour)){var g=this.intercept(a,0,c),d=this.intercept(a,1,c);c=this.intercept(a,2,c);var e=a.pts,h=0;0<=g&&(h+=1);0<=d&&(h+=2);0<=c&&(h+=
4);switch(h){case 3:this.addTriangle(e[0],g,d,2|a.check&1,b);this.addTriangle(g,e[1],d,4|a.check&3,b);this.addTriangle(e[0],d,e[2],a.check&6,b);break;case 5:this.addTriangle(e[0],g,c,2|a.check&5,b);this.addTriangle(g,e[1],c,4|a.check&1,b);this.addTriangle(c,e[1],e[2],a.check&6,b);break;case 6:this.addTriangle(e[0],e[1],c,a.check&5,b);this.addTriangle(c,e[1],d,4|a.check&2,b);this.addTriangle(c,d,e[2],1|a.check&6,b);break;default:return}a.isValid=!1}},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(d,
"getMinMax",function(){return t(-1,[this.valueMin,this.valueMax])});e(d,"addAllTriangles",function(){for(var a=0;a<this.triangleCount;a++)if(this.triangles[a].isValid){var b=this.triangles[a];this.surfaceReader.addTriangleCheck(b.pts[0],b.pts[1],b.pts[2],b.check,b.contourIndex,!1,-1)}});d.$MarchingSquares$ContourVertex$=function(){var a=N(function(){wa(this,arguments);this.value=0;C(this,arguments)},J.jvxl.calc.MarchingSquares,"ContourVertex",JU.P3);da(a,function(a){ja(this,J.jvxl.calc.MarchingSquares.ContourVertex,
[]);this.setT(a)},"JU.P3");e(a,"setValue",function(a){this.value=a},"~N");j(a,"toString",function(){return this.value+" "+this.x+" "+this.y+" "+this.z})};d.$MarchingSquares$Triangle$=function(){var a=N(function(){wa(this,arguments);this.pts=null;this.check=0;this.isValid=!0;this.contourIndex=0;C(this,arguments)},J.jvxl.calc.MarchingSquares,"Triangle",null);da(a,function(a,c,d,e,f){this.pts=r(-1,[a,c,d]);this.check=e;this.contourIndex=f},"~N,~N,~N,~N,~N")}});L("J.shapesurface");R(["J.shape.Mesh"],
"J.shapesurface.IsosurfaceMesh","java.util.Hashtable JU.AU $.BS $.CU $.Lst $.M4 $.P3 $.P3i $.PT $.SB $.V3 J.api.Interface J.jvxl.data.JvxlCoder $.JvxlData JS.T JU.BSUtil $.C $.ColorEncoder $.Logger $.SimpleUnitCell JV.Viewer".split(" "),function(){var d=N(function(){this.jvxlData=null;this.vertexIncrement=1;this.firstRealVertex=-1;this.dataType=0;this.hasGridPoints=!1;this.colorEncoder=this.contourColixes=this.contourValues=this.info=this.calculatedVolume=this.calculatedArea=this.vertexColorMap=null;
this.colorPhased=!1;this.assocGridPointNormals=this.assocGridPointMap=this.bsVdw=this.pymolVertexColorMap=this.probeValues=null;this.mergeAssociatedNormalCount=0;this.centers=null;C(this,arguments)},J.shapesurface,"IsosurfaceMesh",J.shape.Mesh);da(d,function(a,b,c,d){ja(this,J.shapesurface.IsosurfaceMesh,[]);this.mesh1(a,b,c,d);this.jvxlData=new J.jvxl.data.JvxlData;this.checkByteCount=2;this.jvxlData.version=JV.Viewer.getJmolVersion()},"JV.Viewer,~S,~N,~N");j(d,"getResolution",function(){return 1/
this.jvxlData.pointsPerAngstrom});e(d,"clearType",function(a,b){this.clear(a);this.jvxlData.clear();this.colorEncoder=this.centers=this.calculatedArea=this.calculatedVolume=this.bsVdw=this.assocGridPointNormals=this.assocGridPointMap=null;this.colorsExplicit=this.colorPhased=!1;this.firstRealVertex=-1;this.hasGridPoints=b;this.isColorSolid=!0;this.nSets=this.mergeAssociatedNormalCount=0;this.pcs=null;this.showPoints=b;this.vertexColorMap=this.vcs=this.surfaceSet=null;this.vertexIncrement=1;this.vvs=
this.vertexSets=null},"~S,~B");e(d,"allocVertexColixes",function(){if(null==this.vcs){this.vcs=fa(this.vc,0);for(var a=this.vc;0<=--a;)this.vcs[a]=this.colix}this.isColorSolid=!1});e(d,"addVertexCopy",function(a,b,c,d,e){a=this.addVCVal(a,b,e);switch(c){case -1:0>this.firstRealVertex&&(this.firstRealVertex=a);break;case -2:this.hasGridPoints=!0;break;case -3:this.vertexIncrement=3;break;default:0>this.firstRealVertex&&(this.firstRealVertex=a),d&&(null==this.assocGridPointMap&&(this.assocGridPointMap=
new java.util.Hashtable),this.assocGridPointMap.put(Integer.$valueOf(a),Integer.$valueOf(c+this.mergeAssociatedNormalCount)))}return a},"JU.T3,~N,~N,~B,~B");j(d,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b);if(null!=this.vcs)for(var c=this.vc;0<=--c;)this.vcs[c]=JU.C.getColixTranslucent3(this.vcs[c],a,b)},"~B,~N");e(d,"setMerged",function(a){this.mergePolygonCount0=(this.isMerged=a)?this.pc:0;this.mergeVertexCount0=a?this.vc:0;a&&(this.mergeAssociatedNormalCount+=
this.jvxlData.nPointsX*this.jvxlData.nPointsY*this.jvxlData.nPointsZ,this.assocGridPointNormals=null)},"~B");j(d,"sumVertexNormals",function(a,b){J.shape.Mesh.sumVertexNormals2(this,a,b);if(null!=this.assocGridPointMap&&0<b.length&&!this.isMerged){null==this.assocGridPointNormals&&(this.assocGridPointNormals=new java.util.Hashtable);for(var c,d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);){var e=c.getValue();this.assocGridPointNormals.containsKey(e)||this.assocGridPointNormals.put(e,
JU.V3.new3(0,0,0));this.assocGridPointNormals.get(e).add(b[c.getKey().intValue()])}for(d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);)b[c.getKey().intValue()]=this.assocGridPointNormals.get(c.getValue())}},"~A,~A");e(d,"getCenters",function(){if(null!=this.centers)return this.centers;this.centers=Array(this.pc);for(var a=0;a<this.pc;a++){var b=this.pis[a];if(null!=b){var c=this.centers[a]=JU.P3.newP(this.vs[b[0]]);c.add(this.vs[b[1]]);c.add(this.vs[b[2]]);c.scale(0.33333334)}}return this.centers});
e(d,"getContours",function(){var a=this.jvxlData.nContours;if(0==a||null==this.pis||(this.havePlanarContours=null!=this.jvxlData.jvxlPlane))return null;0>a&&(a=-1-a);var b=this.jvxlData.vContours;if(null!=b){for(var c=0;c<a&&!(6<b[c].size());c++)J.jvxl.data.JvxlCoder.set3dContourVector(b[c],this.pis,this.vs);return this.jvxlData.vContours}b=Array(a);for(c=0;c<a;c++)b[c]=new JU.Lst;if(null==this.jvxlData.contourValuesUsed){for(var d=(this.jvxlData.valueMappedToBlue-this.jvxlData.valueMappedToRed)/
(a+1),c=0;c<a;c++){var e=this.jvxlData.valueMappedToRed+(c+1)*d;J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c])}JU.Logger.info(a+" contour lines; separation = "+d)}else for(c=0;c<a;c++)e=this.jvxlData.contourValuesUsed[c],J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c]);this.jvxlData.contourColixes=fa(a,0);this.jvxlData.contourValues=t(a,0);for(c=0;c<a;c++)this.jvxlData.contourValues[c]=b[c].get(2).floatValue(),this.jvxlData.contourColixes[c]=
b[c].get(3)[0];return this.jvxlData.vContours=b});e(d,"getPmeshData",function(a){return J.api.Interface.getInterface("J.shapesurface.PMeshWriter",this.vwr,"script").write(this,a)},"~B");e(d,"getPLYData",function(a){return J.api.Interface.getInterface("J.shapesurface.PLYWriter",this.vwr,"script").write(this,a)},"~B");d.get3dContour=e(d,"get3dContour",function(a,b,c,d){var e=JU.BS.newN(a.pc),f=new JU.SB,h=JU.C.getArgb(d);J.shapesurface.IsosurfaceMesh.setContourVector(b,a.pc,e,c,d,h,f);for(d=0;d<a.pc;d++)null!=
a.setABC(d)&&J.shapesurface.IsosurfaceMesh.addContourPoints(b,e,d,f,a.vs,a.vvs,a.iA,a.iB,a.iC,c)},"J.shapesurface.IsosurfaceMesh,JU.Lst,~N,~N");d.setContourVector=e(d,"setContourVector",function(a,b,c,d,e,f,h){a.add(0,Integer.$valueOf(b));a.add(1,c);a.add(2,Float.$valueOf(d));a.add(3,fa(-1,[e]));a.add(4,r(-1,[f]));a.add(5,h)},"JU.Lst,~N,JU.BS,~N,~N,~N,JU.SB");d.addContourPoints=e(d,"addContourPoints",function(a,b,c,d,e,f,h,j,k,l){var n=null,r=null,q=0,t=J.shapesurface.IsosurfaceMesh.checkPt(f,h,j,
l);Float.isNaN(t)||(n=J.shapesurface.IsosurfaceMesh.getContourPoint(e,h,j,t),q|=1);var v=1==t?NaN:J.shapesurface.IsosurfaceMesh.checkPt(f,j,k,l);Float.isNaN(v)||(r=J.shapesurface.IsosurfaceMesh.getContourPoint(e,j,k,v),0==q&&(n=r,t=v),q|=2);switch(q){case 0:return;case 1:if(0==t)return;case 2:v=1==v?NaN:J.shapesurface.IsosurfaceMesh.checkPt(f,k,h,l),Float.isNaN(v)||(r=J.shapesurface.IsosurfaceMesh.getContourPoint(e,k,h,v),q|=4)}switch(q){case 3:case 5:case 6:break;default:return}b.set(c);J.jvxl.data.JvxlCoder.appendContourTriangleIntersection(q,
t,v,d);a.addLast(n);a.addLast(r)},"JU.Lst,JU.BS,~N,JU.SB,~A,~A,~N,~N,~N,~N");d.checkPt=e(d,"checkPt",function(a,b,c,d){var e,f;return d==(e=a[b])?0:d==(f=a[c])?1:e<d==d<f?(d-e)/(f-e):NaN},"~A,~N,~N,~N");d.getContourPoint=e(d,"getContourPoint",function(a,b,c,d){var e=new JU.P3;e.sub2(a[c],a[b]);e.scaleAdd2(d,e,a[b]);return e},"~A,~N,~N,~N");e(d,"setDiscreteColixes",function(a,b){null!=a&&(this.jvxlData.contourValues=a);if(null==a||0==a.length)a=this.jvxlData.contourValues=this.jvxlData.contourValuesUsed;
null==b&&null!=this.jvxlData.contourColixes?b=this.jvxlData.contourColixes:(this.jvxlData.contourColixes=b,this.jvxlData.contourColors=JU.C.getHexCodes(b));if(!(null==this.vs||null==this.vvs||null==a)){var c=a.length,d=a[c-1];this.colorCommand=null;var e=null!=b&&0<b.length;this.isColorSolid=e&&null!=this.jvxlData.jvxlPlane;if(null!=this.jvxlData.vContours){if(e)for(var f=0;f<this.jvxlData.vContours.length;f++)c=b[f%b.length],this.jvxlData.vContours[f].get(3)[0]=c,this.jvxlData.vContours[f].get(4)[0]=
JU.C.getArgb(c)}else{this.pcs=fa(this.pc,0);this.colorsExplicit=!1;for(f=0;f<this.pc;f++){var h=this.pis[f];if(null!=h){this.pcs[f]=0;for(var h=(this.vvs[h[0]]+this.vvs[h[1]]+this.vvs[h[2]])/3,j=c;0<=--j;)if(h>=a[j]&&h<d){this.pcs[f]=e?b[j%b.length]:0;break}}}}}},"~A,~A");e(d,"getContourList",function(){var a=new java.util.Hashtable;a.put("values",null==this.jvxlData.contourValuesUsed?this.jvxlData.contourValues:this.jvxlData.contourValuesUsed);var b=new JU.Lst;if(null!=this.jvxlData.contourColixes){for(var c=
0;c<this.jvxlData.contourColixes.length;c++)b.addLast(JU.CU.colorPtFromInt(JU.C.getArgb(this.jvxlData.contourColixes[c]),null));a.put("colors",b)}return a},"JV.Viewer");e(d,"deleteContours",function(){this.jvxlData.contourValuesUsed=null;this.jvxlData.contourValues=null;this.jvxlData.contourColixes=null;this.jvxlData.vContours=null});e(d,"setPymolVertexColixesForAtoms",function(a,b,c){this.checkAllocColixes();var d=b[0],e=null,f=b[1];b=null==f?null:fa(f.length,0);if(null!=d){for(var h=0;h<d.length;h++){var j=
d[h];d[h]=j;e=null==f?0:f[h];0.01<e&&(b[h]=JU.C.getColixTranslucent3(j,!0,e))}e=r(c.length(),0);j=0;for(h=c.nextSetBit(0);0<=h;h=c.nextSetBit(h+1),j++)e[h]=j}this.jvxlData.vertexColors=r(this.vc,0);this.jvxlData.nVertexColors=this.vc;f=a.ms.at;a=a.gdata;for(var k=JU.C.isTransparent(this.colix),h=this.mergeVertexCount0;h<this.vc;h++){var l=this.vertexSource[h];if(!(0>l)&&c.get(l)){this.jvxlData.vertexColors[h]=a.getColorArgbOrGray(this.vcs[h]=JU.C.copyColixTranslucency(this.colix,f[l].colixAtom));
var j=null==d?0:d[e[l]],n=null==b?-1:b[e[l]];0==j&&(j=f[l].colixAtom);this.vcs[h]=k?JU.C.copyColixTranslucency(this.colix,j):0==n?j:JU.C.copyColixTranslucency(n,j)}}this.setPymolColors()},"JV.Viewer,~A,JU.BS");e(d,"setPymolColors",function(){this.pymolVertexColorMap=this.vertexColorMap=new java.util.Hashtable;for(var a=-999,b=null,c=this.vc;0<=--c;){var d=this.vcs[c];if(d!=a){var e=J.shapesurface.IsosurfaceMesh.getVertexColorString(a=d);JU.C.isColixTranslucent(d)&&(this.hasTranslucentVertices=!0);
b=this.vertexColorMap.get(e);null==b&&this.vertexColorMap.put(e,b=new JU.BS)}b.set(c)}System.out.println("IsosurfaceMesh pymol colors "+this.vertexColorMap.keySet());for(var f,a=this.vertexColorMap.keySet().iterator();a.hasNext()&&((f=a.next())||1);)System.out.println(f+" "+this.vertexColorMap.get(f).cardinality())});d.getVertexColorString=e(d,"getVertexColorString",function(a){var b=JU.C.getHexCode(a);JU.C.isColixTranslucent(a)&&(b+=" translucent "+JU.C.getColixTranslucencyFractional(a));return b},
"~N");e(d,"colorVertices",function(a,b,c){if(null!=this.vertexSource){JU.C.isColixTranslucent(a)?this.hasTranslucentVertices=!0:a=JU.C.copyColixTranslucency(this.colix,a);var d=c?new JU.BS:b;this.checkAllocColixes();if(c)for(c=0;c<this.vc;c++){var e=this.vertexSource[c];0<=e&&b.get(e)&&(this.vcs[c]=a,null!=d&&d.set(c))}else for(c=0;c<this.vc;c++)d.get(c)&&(this.vcs[c]=a);a=J.shapesurface.IsosurfaceMesh.getVertexColorString(a);null==this.vertexColorMap&&(this.vertexColorMap=new java.util.Hashtable);
J.shapesurface.IsosurfaceMesh.addColorToMap(this.vertexColorMap,a,b)}},"~N,JU.BS,~B");e(d,"checkAllocColixes",function(){(null==this.vcs||null==this.vertexColorMap&&this.isColorSolid)&&this.allocVertexColixes();this.isColorSolid=!1});d.addColorToMap=e(d,"addColorToMap",function(a,b,c){for(var d=null,e=new JU.Lst,f,h=a.entrySet().iterator();h.hasNext()&&((f=h.next())||1);){var j=f.getKey();if(j===b)d=f.getValue(),d.or(c);else{var k=f.getValue();k.andNot(c);k.isEmpty()&&e.addLast(j)}}for(;!e.isEmpty();)a.remove(e.removeItemAt(0));
null==d&&a.put(b,c)},"java.util.Map,~S,JU.BS");e(d,"setJvxlColorMap",function(a){this.jvxlData.diameter=this.diameter;this.jvxlData.color=JU.C.getHexCode(this.colix);this.jvxlData.meshColor=0==this.meshColix?null:JU.C.getHexCode(this.meshColix);this.jvxlData.translucency=30720==(this.colix&30720)?-1:JU.C.getColixTranslucencyFractional(this.colix);this.jvxlData.rendering=this.getRendering().substring(1);this.jvxlData.colorScheme=null==this.colorEncoder?null:this.colorEncoder.getColorScheme();null==
this.jvxlData.vertexColors&&(this.jvxlData.nVertexColors=null==this.vertexColorMap?0:this.vertexColorMap.size());if(!(null==this.vertexColorMap||null==this.vertexSource||!a)){null==this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=new java.util.Hashtable);var b;for(a=this.vertexColorMap.entrySet().iterator();a.hasNext()&&((b=a.next())||1);){var c=b.getValue();if(!c.isEmpty()){for(var d=b.getKey(),e=new JU.BS,f=0;f<this.vc;f++)c.get(this.vertexSource[f])&&e.set(f);J.shapesurface.IsosurfaceMesh.addColorToMap(this.jvxlData.vertexColorMap,
d,e)}}this.jvxlData.nVertexColors=this.jvxlData.vertexColorMap.size();0==this.jvxlData.vertexColorMap.size()&&(this.jvxlData.vertexColorMap=null)}},"~B");e(d,"setColorCommand",function(){if(!(null==this.colorEncoder||null==(this.colorCommand=this.colorEncoder.getColorScheme())))this.colorCommand=this.colorCommand.equals("inherit")?"#inherit;":"color $"+JU.PT.esc(this.thisID)+JU.PT.esc(this.colorCommand)+" range "+(this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue+" "+this.jvxlData.valueMappedToRed:
this.jvxlData.valueMappedToRed+" "+this.jvxlData.valueMappedToBlue)});e(d,"setColorsFromJvxlData",function(a){this.diameter=this.jvxlData.diameter;-1!=a&&(-2147483648!=a&&2147483647!=a?this.colix=JU.C.getColix(a):null!=this.jvxlData.color&&(this.colix=JU.C.getColixS(this.jvxlData.color)));0==this.colix&&(this.colix=5);this.colix=JU.C.getColixTranslucent3(this.colix,0!=this.jvxlData.translucency,this.jvxlData.translucency);var b=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&&null==this.jvxlData.vertexColorMap)return!1;if(null==this.jvxlData.vertexColorMap){if(null!=this.jvxlData.colorScheme){var c=this.jvxlData.colorScheme;if(a=c.startsWith("translucent "))c=c.substring(12),b=NaN;this.colorEncoder.setColorScheme(c,a);this.remapColors(null,null,
b)}}else{if(null!=this.jvxlData.baseColor)for(a=this.vc;0<=--a;)this.vcs[a]=this.colix;for(b=this.jvxlData.vertexColorMap.entrySet().iterator();b.hasNext()&&((c=b.next())||1);){var d=c.getValue(),e=c.getKey(),f=e.indexOf(" translucent"),h=(a=0<=f)?JU.PT.parseFloat(e.substring(f+12)):-1;Float.isNaN(h)?(System.out.println("Isourface error reading JVXL file translucent vertex color:"+e),a=!1):a&&(e=e.substring(0,f),this.hasTranslucentVertices=!0);e=JU.C.getColixS(e);e=a?JU.C.getColixTranslucent3(e,!0,
h):JU.C.copyColixTranslucency(this.colix,e);for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1))this.vcs[a]=e}}return!0},"~N");e(d,"setJvxlDataRendering",function(){if(null!=this.jvxlData.rendering)for(var a=JU.PT.getTokens(this.jvxlData.rendering),b=0;b<a.length;b++)this.setTokenProperty(JS.T.getTokFromName(a[b]),!0)});e(d,"remapColors",function(a,b,c){null==b&&(b=this.colorEncoder);null==b&&(b=this.colorEncoder=new JU.ColorEncoder(null,a));this.colorEncoder=b;this.setColorCommand();Float.isNaN(c)?c=
JU.C.getColixTranslucencyLevel(this.colix):this.colix=JU.C.getColixTranslucent3(this.colix,!0,c);var d=b.lo,e=b.hi,f=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(),f){this.jvxlData.vertexColors=r(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=fa(this.contourValues.length,0);for(a=0;a<this.contourValues.length;a++)this.contourColixes[a]=b.getColorIndex(this.contourValues[a]);this.setDiscreteColixes(null,null)}this.jvxlData.isJvxlPrecisionColor=!0;J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,this.vvs);this.setColorCommand();
this.isColorSolid=!1}},"JV.Viewer,JU.ColorEncoder,~N");e(d,"reinitializeLightingAndColor",function(a){this.initialize(this.lighting,null,null);if(null!=this.colorEncoder||this.jvxlData.isBicolorMap)this.vcs=null,this.remapColors(a,null,NaN)},"JV.Viewer");j(d,"getBoundingBox",function(){return this.jvxlData.boundingBox});j(d,"setBoundingBox",function(a){this.jvxlData.boundingBox=a},"~A");e(d,"merge",function(a){var b=this.vc+(null==a?0:a.vc);null==this.pis&&(this.pis=r(0,0,0));null!=a&&null==a.pis&&
(a.pis=r(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),f=J.shapesurface.IsosurfaceMesh.mergePolygons(this,0,0,e);if(null!=a){J.shapesurface.IsosurfaceMesh.mergePolygons(a,
f,this.vc,e);for(f=0;f<a.vc;f++,this.vc++)this.vs[this.vc]=a.vs[f],this.vvs[this.vc]=a.vvs[f],d&&(this.vertexSource[this.vc]=a.vertexSource[f])}this.pc=this.polygonCount0=c;this.vc=this.vertexCount0=b;0<c&&this.resetSlab();this.pis=e},"J.jvxl.data.MeshData");d.mergePolygons=e(d,"mergePolygons",function(a,b,c,d){for(var e,f=0;f<a.pc;f++)if(!(null==(e=a.pis[f])||null!=a.bsSlabDisplay&&!a.bsSlabDisplay.get(f)))if(d[b++]=a.pis[f],0<c)for(var h=0;3>h;h++)e[h]+=c;return b},"JU.MeshSurface,~N,~N,~A");j(d,
"getUnitCell",function(){return null!=this.unitCell||null!=(this.unitCell=this.vwr.ms.am[this.modelIndex].biosymmetry)||null!=(this.unitCell=this.vwr.ms.getUnitCell(this.modelIndex))||null!=this.oabc&&null!=(this.unitCell=this.vwr.getSymTemp().getUnitCell(this.oabc,!0,null))?this.unitCell:null});e(d,"fixLattice",function(){if(null!=this.getUnitCell()){var a=new JU.P3i,b=JU.P3i.new3(w(this.lattice.x),w(this.lattice.y),w(this.lattice.z));this.jvxlData.fixedLattice=this.lattice;this.lattice=null;JU.SimpleUnitCell.setMinMaxLatticeParameters(w(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,f=c*this.vc;this.vs=JU.AU.arrayCopyPt(this.vs,f);this.vvs=null==this.vvs?null:JU.AU.ensureLengthA(this.vvs,f);var h=this.pc;this.pis=JU.AU.arrayCopyII(this.pis,c*this.pc);c=0;this.normixes=JU.AU.arrayCopyShort(this.normixes,f);for(f=a.x;f<b.x;f++)for(var j=a.y;j<b.y;j++)for(var k=a.z;k<b.z;k++)if(!(0==f&&0==j&&0==k)){d.set(f,j,k);this.unitCell.toCartesian(d,!1);for(var l=0;l<e;l++){this.normixes[this.vc]=this.normixes[l];var n=JU.P3.newP(this.vs[l]);
n.add(d);this.addVCVal(n,this.vvs[l],!1)}c+=e;for(l=0;l<h;l++)n=JU.AU.arrayCopyI(this.pis[l],-1),n[0]+=c,n[1]+=c,n[2]+=c,this.addPolygon(n,null)}a=new JU.P3;b=new JU.P3;this.setBox(a,b);this.jvxlData.boundingBox=y(-1,[a,b])}});j(d,"getMinDistance2ForVertexGrouping",function(){return null!=this.jvxlData.boundingBox&&null!=this.jvxlData.boundingBox[0]&&5>this.jvxlData.boundingBox[1].distanceSquared(this.jvxlData.boundingBox[0])?1E-10:1E-8});j(d,"getVisibleVertexBitSet",function(){var a=this.getVisibleVBS();
if(null!=this.jvxlData.thisSet)for(var b=0;b<this.vc;b++)this.jvxlData.thisSet.get(this.vertexSets[b])||a.clear(b);return a});e(d,"updateCoordinates",function(a,b){var c=null==b||this.isModelConnected;if(!c)for(var d=0;d<this.connectedAtoms.length;d++)if(0<=this.connectedAtoms[d]&&b.get(this.connectedAtoms[d])){c=!0;break}c&&(this.isModelConnected?this.mat4=this.vwr.ms.am[this.modelIndex].mat4:(null==this.mat4&&(this.mat4=JU.M4.newM4(null)),this.mat4.mul2(a,this.mat4)),this.recalcAltVertices=!0)},
"JU.M4,JU.BS");e(d,"getDataMinMax",function(){for(var a=3.4028235E38,b=-3.4028235E38,c=this.vvs.length;0<=--c;){var d=this.vvs[c];d<a&&(a=d);d>b&&(b=d)}return t(-1,[a,b])});e(d,"getDataRange",function(){return null!=this.jvxlData.jvxlPlane&&null==this.colorEncoder?null:t(-1,[this.jvxlData.mappedDataMin,this.jvxlData.mappedDataMax,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue:this.jvxlData.valueMappedToRed,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToBlue])});
e(d,"getInfo",function(a){var b=La(this,J.shapesurface.IsosurfaceMesh,"getInfo",[a]);null!=this.vertexColorMap&&b.put("vertexColorMap",this.vertexColorMap);if(a){a=new JU.BS;var c=this.getValidVertices(a);null!=c&&(b.put("allVertices",b.get("vertices")),b.put("vertices",c),c=b.get("vertexValues"),null!=c&&(a=this.getValidValues(a),b.put("allValues",c),b.put("vertexValues",a)))}return b},"~B");e(d,"getValidValues",function(a){null==a&&this.getInvalidBS(a=new JU.BS);for(var b=this.vc-a.cardinality(),
b=t(b,0),c=0,d=a.nextClearBit(0);0<=d&&d<this.vc;d=a.nextClearBit(d+1))b[c++]=this.vvs[d];return b},"JU.BS");e(d,"getValidVertices",function(a){var b=null!=a;null==a&&(a=new JU.BS);this.getInvalidBS(a);var c=this.vc-a.cardinality();if(c==this.vc&&b)return null;for(var b=Array(c),d=0,e=a.nextClearBit(0);0<=e&&d<c;e=a.nextClearBit(e+1))b[d++]=this.vs[e];return b},"JU.BS");e(d,"getInvalidBS",function(a){var b=this.jvxlData.jvxlExcluded[1],c=this.jvxlData.thisSet;null!=b&&a.or(b);if(null!=c)for(b=this.vc;0<=
--b;)c.get(this.vertexSets[b])||a.set(b)},"JU.BS");e(d,"copyVertexColorMap",function(){if(null==this.vertexColorMap)return null;for(var a=new java.util.Hashtable,b,c=this.vertexColorMap.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)a.put(b.getKey(),JU.BSUtil.copy(b.getValue()));return a});e(d,"setPropertyColor",function(a){this.colorsExplicit=!1;this.vertexSource=this.colorEncoder=null;this.jvxlData.baseColor=a;this.jvxlData.nVertexColors=0;this.jvxlData.jvxlColorData=null;this.jvxlData.vertexColorMap=
this.pymolVertexColorMap=this.vertexColorMap=null;this.hasTranslucentVertices=!1;this.pcs=this.vcs=null;this.isColorSolid=!0},"~S");e(d,"setPropertyColorPhase",function(a,b,c){this.colorPhased=!0;this.colix=this.jvxlData.minColorIndex=a;this.jvxlData.maxColorIndex=b;this.jvxlData.isBicolorMap=!0;this.isColorSolid=this.jvxlData.colorDensity=!1;this.remapColors(this.vwr,null,c)},"~N,~N,~N")});L("J.jvxl.readers");R(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.VolumeDataReader",["JU.AU","$.SB","J.jvxl.data.JvxlCoder",
"JU.Logger"],function(){var d=N(function(){this.dataType=0;this.allowMapData=this.precalculateVoxelData=!1;this.point=null;this.maxGrid=this.ptsPerAngstrom=0;this.useOriginStepsPoints=!1;C(this,arguments)},J.jvxl.readers,"VolumeDataReader",J.jvxl.readers.SurfaceReader);da(d,function(){ja(this,J.jvxl.readers.VolumeDataReader,[])});j(d,"init",function(a){this.initVDR(a)},"J.jvxl.readers.SurfaceGenerator");e(d,"initVDR",function(a){this.initSR(a);this.useOriginStepsPoints=null!=this.params.origin&&null!=
this.params.points&&null!=this.params.steps;this.dataType=this.params.dataType;this.allowMapData=this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");e(d,"setup",function(){this.jvxlFileHeaderBuffer=(new JU.SB).append("volume data read from file\n\n");J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData,this.jvxlFileHeaderBuffer)},"~B");j(d,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();return!0},"~B");j(d,"readVolumeData",function(a){try{this.readSurfaceData(a)}catch(b){if(ea(b,
Exception))return System.out.println(b.toString()),!1;throw b;}return!0},"~B");e(d,"readVoxelDataIndividually",function(a){if(!a||this.allowMapData)if(!a||null!=this.volumeData.sr)this.volumeData.setVoxelDataAsArray(this.voxelData=null);else{this.newVoxelDataCube();for(a=0;a<this.nPointsX;++a){var b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(var c=0,d=0;d<this.nPointsY;++d)for(var e=b[d]=t(this.nPointsZ,0),f=0;f<this.nPointsZ;++f,++c)e[f]=this.getValue(a,d,f,c)}}},"~B");e(d,"setVolumeData",
function(){});e(d,"setVolumeDataParams",function(){if(null!=this.params.volumeData)return this.setVolumeDataV(this.params.volumeData),!0;if(!this.useOriginStepsPoints)return!1;this.volumetricOrigin.setT(this.params.origin);this.volumetricVectors[0].set(this.params.steps.x,0,0);this.volumetricVectors[1].set(0,this.params.steps.y,0);this.volumetricVectors[2].set(0,0,this.params.steps.z);this.voxelCounts[0]=w(this.params.points.x);this.voxelCounts[1]=w(this.params.points.y);this.voxelCounts[2]=w(this.params.points.z);
if(1>this.voxelCounts[0]||1>this.voxelCounts[1]||1>this.voxelCounts[2])return!1;this.showGridInfo();return!0});e(d,"showGridInfo",function(){JU.Logger.info("grid origin  = "+this.params.origin);JU.Logger.info("grid steps   = "+this.params.steps);JU.Logger.info("grid points  = "+this.params.points);this.ptTemp.x=this.params.steps.x*this.params.points.x;this.ptTemp.y=this.params.steps.y*this.params.points.y;this.ptTemp.z=this.params.steps.z*this.params.points.z;JU.Logger.info("grid lengths = "+this.ptTemp);
this.ptTemp.add(this.params.origin);JU.Logger.info("grid max xyz = "+this.ptTemp)});e(d,"setVoxelRange",function(a,b,c,d,e,f){-1E-4<=b-c&&(b=-10,c=10);var h=c-b,j=this.params.resolution;3.4028235E38!=j&&(d=j,f=0);c=D(Math.floor(h*d))+1;c>e&&(0<(this.dataType&256)?3.4028235E38==j?(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==j&&(c=e));1==c&&(c=2);d=
(c-1)/h;d<f&&(c=D(Math.floor(f*h+1)),d=(c-1)/h);e=this.volumeData.volumetricVectorLengths[a]=1/d;this.voxelCounts[a]=c;null!=this.params.sbOut&&this.params.sbOut.append("isosurface resolution for axis "+(a+1)+" set to "+d+" points/Angstrom; "+this.voxelCounts[a]+" voxels\n");switch(a){case 0:this.volumetricVectors[0].set(e,0,0);this.volumetricOrigin.x=b;break;case 1:this.volumetricVectors[1].set(0,e,0);this.volumetricOrigin.y=b;break;case 2:this.volumetricVectors[2].set(0,0,e),this.volumetricOrigin.z=
b,this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricOrigin),null!=this.center&&!Float.isNaN(this.center.x)&&this.volumetricOrigin.add(this.center),null!=this.params.sbOut&&this.params.sbOut.append(this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2]+" voxels total\n")}this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricVectors[a]);return this.voxelCounts[a]},"~N,~N,~N,~N,~N,~N");j(d,"readSurfaceData",function(a){this.readSurfaceDataVDR(a)},"~B");e(d,"readSurfaceDataVDR",
function(a){this.isProgressive&&!a?(this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null):this.precalculateVoxelData?this.generateCube():this.readVoxelDataIndividually(a)},"~B");e(d,"generateCube",function(){JU.Logger.info("data type: user volumeData");JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);for(var a=0;3>a;++a)JU.Logger.info("voxel grid vector:"+this.volumetricVectors[a]);JU.Logger.info("Read "+this.nPointsX+" x "+this.nPointsY+
" x "+this.nPointsZ+" data points")});j(d,"closeReader",function(){})});L("J.jvxl.readers");R(["J.jvxl.readers.VolumeDataReader","JU.BS","$.P3","$.P3i","J.atomdata.AtomData"],"J.jvxl.readers.AtomDataReader","java.util.Date JU.AU $.SB $.V3 J.atomdata.RadiusData J.c.VDW J.jvxl.data.JvxlCoder JU.BSUtil $.Logger".split(" "),function(){var d=N(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;C(this,arguments)},J.jvxl.readers,"AtomDataReader",J.jvxl.readers.VolumeDataReader);ia(d,function(){this.atomData=new J.atomdata.AtomData;this.bsMySelected=new JU.BS;this.bsMyIgnored=new JU.BS;this.ptY0=new JU.P3;this.ptZ0=new JU.P3;this.pt0=new JU.P3i;this.pt1=new JU.P3i;this.ptV=new JU.P3});da(d,function(){ja(this,J.jvxl.readers.AtomDataReader,[])});e(d,"initADR",function(a){this.initVDR(a);this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");j(d,"setup",function(){this.setup2()},
"~B");e(d,"setup2",function(){this.contactPair=this.params.contactPair;this.doAddHydrogens=null!=this.sg.atomDataServer&&this.params.addHydrogens;this.modelIndex=this.params.modelIndex;null!=this.params.bsIgnore&&(this.bsMyIgnored=this.params.bsIgnore);if(null!=this.params.volumeData){this.setVolumeDataV(this.params.volumeData);this.setBBox(this.volumeData.volumetricOrigin,0);this.ptV.setT(this.volumeData.volumetricOrigin);for(var a=0;3>a;a++)this.ptV.scaleAdd2(this.volumeData.voxelCounts[a]-1,this.volumeData.volumetricVectors[a],
this.ptV);this.setBBox(this.ptV,0)}(this.havePlane=null!=this.params.thePlane)&&this.volumeData.setPlaneParameters(this.params.thePlane)});e(d,"markPlaneVoxels",function(a,b){for(var c=0,d=this.thisX*this.yzCount,e=d+this.yzCount;d<e;d++,c++)this.volumeData.getPoint(d,this.ptV),this.thisPlane[c]=this.ptV.distance(a)-b},"JU.P3,~N");e(d,"setVolumeForPlane",function(){this.useOriginStepsPoints?(this.xyzMin=JU.P3.newP(this.params.origin),this.xyzMax=JU.P3.newP(this.params.origin),this.xyzMax.add3((this.params.points.x-
1)*this.params.steps.x,(this.params.points.y-1)*this.params.steps.y,(this.params.points.z-1)*this.params.steps.z)):null==this.params.boundingBox?(this.getAtoms(this.params.bsSelected,!1,!0,!1,!1,!1,!1,this.params.mep_marginAngstroms,this.params.modelInvRotation),null==this.xyzMin&&(this.xyzMin=JU.P3.new3(-10,-10,-10),this.xyzMax=JU.P3.new3(10,10,10))):(this.xyzMin=JU.P3.newP(this.params.boundingBox[0]),this.xyzMax=JU.P3.newP(this.params.boundingBox[1]));this.setRanges(this.params.plane_ptsPerAngstrom,
this.params.plane_gridMax,0)});e(d,"getAtoms",function(a,b,c,d,e,f,h,j,k){f&&(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,j)))continue;this.bsMySelected.set(d);
e=!this.havePlane}if(c&&(f||e))this.atomData.atomRadius[d]=this.getWorkingRadius(d,j)}e=c&&b?this.getWorkingRadius(-1,j):0;this.myAtomCount=JU.BSUtil.cardinalityOf(this.bsMySelected);j=JU.BSUtil.copy(this.bsMySelected);h=0;this.atomProp=null;this.theProperty=3.4028235E38;this.haveOneProperty=!1;a=this.params.theProperty;if(0<this.myAtomCount){k=null;if(b){this.atomData.bsSelected=j;this.sg.atomDataServer.fillAtomData(this.atomData,8);k=Array(h=this.atomData.hydrogenAtomCount);for(d=0;d<this.atomData.hAtoms.length;d++)if(null!=
this.atomData.hAtoms[d])for(b=this.atomData.hAtoms[d].length;0<=--b;)k[--h]=this.atomData.hAtoms[d][b];h=k.length;JU.Logger.info(h+" attached hydrogens added")}b=h+this.myAtomCount;c&&(this.atomRadius=t(b,0));this.atomXyzTruncated=Array(b);null!=this.params.theProperty&&(this.atomProp=t(b,0));this.atomNo=r(b,0);this.atomIndex=r(b,0);this.myIndex=r(this.ac,0);for(d=0;d<h;d++)c&&(this.atomRadius[d]=e),this.atomXyzTruncated[d]=k[d],this.atomNo[d]=-1,null!=this.atomProp&&this.addAtomProp(d,NaN);this.myAtomCount=
h;for(d=j.nextSetBit(0);0<=d;d=j.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(f&&0!=this.myAtomCount){f=new JU.P3;this.bsNearby=new JU.BS;for(d=0;d<this.ac;d++)!j.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),f=this.atomData.xyz[d],f.x+b>this.xyzMin.x&&(f.x-b<this.xyzMax.x&&f.y+b>this.xyzMin.y&&f.y-b<this.xyzMax.y&&f.z+b>this.xyzMin.z&&f.z-b<this.xyzMax.z)&&(this.bsNearby.set(d),this.nearbyAtomCount++)));f=this.myAtomCount;if(0!=this.nearbyAtomCount){f+=this.nearbyAtomCount;this.atomRadius=JU.AU.arrayCopyF(this.atomRadius,
f);this.atomXyzTruncated=JU.AU.arrayCopyObject(this.atomXyzTruncated,f);null!=this.atomIndex&&(this.atomIndex=JU.AU.arrayCopyI(this.atomIndex,f));null!=a&&(this.atomProp=JU.AU.arrayCopyF(this.atomProp,f));for(d=this.bsNearby.nextSetBit(0);0<=d;d=this.bsNearby.nextSetBit(d+1))null!=a&&this.addAtomProp(this.myAtomCount,a[d]),this.myIndex[d]=this.myAtomCount,this.atomIndex[this.myAtomCount]=d,this.atomXyzTruncated[this.myAtomCount]=this.atomData.xyz[d],this.atomRadius[this.myAtomCount++]=this.atomData.atomRadius[d]}c&&
this.setRadii();this.haveOneProperty=!Float.isNaN(this.theProperty)}},"JU.BS,~B,~B,~B,~B,~B,~B,~N,JU.M4");e(d,"setRadii",function(){if(null==this.rs){this.maxRS=0;this.rs=t(this.myAtomCount,0);this.rs2=t(this.myAtomCount,0);for(var a=0;a<this.myAtomCount;a++){var b=this.rs[a]=this.atomRadius[a]+this.sr;b>this.maxRS&&(this.maxRS=b);this.rs2[a]=this.rs[a]*this.rs[a]}}});e(d,"addAtomProp",function(a,b){this.atomProp[a]=b;!Float.isNaN(this.theProperty)&&b!=this.theProperty&&(this.theProperty=3.4028235E38==
this.theProperty?b:NaN)},"~N,~N");e(d,"getWorkingRadius",function(a,b){var c=0>a?this.atomData.hAtomRadius:this.atomData.atomRadius[a];return Float.isNaN(b)?Math.max(c,0.1):c+b},"~N,~N");e(d,"setHeader",function(a,b){this.jvxlFileHeaderBuffer=new JU.SB;null!=this.atomData.programInfo&&this.jvxlFileHeaderBuffer.append("#created by ").append(this.atomData.programInfo).append(" on ").append(""+new java.util.Date).append("\n");this.jvxlFileHeaderBuffer.append(a).append("\n").append(b).append("\n")},"~S,~S");
e(d,"setRanges",function(a,b,c){null!=this.xyzMin&&(this.ptsPerAngstrom=a,this.maxGrid=b,this.minPtsPerAng=c,this.setVolumeData(),J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData,this.jvxlFileHeaderBuffer))},"~N,~N,~N");j(d,"setVolumeData",function(){this.setVolumeDataADR()});e(d,"setVolumeDataADR",function(){this.setVolumeDataParams()||(this.setVoxelRange(0,this.xyzMin.x,this.xyzMax.x,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(1,this.xyzMin.y,this.xyzMax.y,this.ptsPerAngstrom,
this.maxGrid,this.minPtsPerAng),this.setVoxelRange(2,this.xyzMin.z,this.xyzMax.z,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng))});e(d,"setVertexSource",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);if(null!=this.params.vertexSource){this.params.vertexSource=JU.AU.arrayCopyI(this.params.vertexSource,this.meshData.vc);for(var a=0;a<this.meshData.vc;a++)this.params.vertexSource[a]=Math.abs(this.params.vertexSource[a])-1}});e(d,"resetPlane",function(a){for(var b=
0;b<this.yzCount;b++)this.thisPlane[b]=a},"~N");e(d,"resetVoxelData",function(a){for(var b=0;b<this.nPointsX;++b)for(var c=0;c<this.nPointsY;++c)for(var d=0;d<this.nPointsZ;++d)this.voxelData[b][c][d]=a},"~N");e(d,"getVoxel",function(a,b,c,d){return this.isProgressive?this.thisPlane[d%this.yzCount]:this.voxelData[a][b][c]},"~N,~N,~N,~N");e(d,"unsetVoxelData",function(){this.unsetVoxelData2()});e(d,"unsetVoxelData2",function(){if(this.isProgressive)for(var a=0;a<this.yzCount;a++)3.4028235E38==this.thisPlane[a]&&
(this.thisPlane[a]=NaN);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)3.4028235E38==this.voxelData[a][b][c]&&(this.voxelData[a][b][c]=NaN)});e(d,"setGridLimitsForAtom",function(a,b,c,d){b+=this.margin;this.volumeData.xyzToVoxelPt(a.x,a.y,a.z,c);a=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(d,"getAtomMinMax",function(a,b){for(var c=0;c<this.nPointsX;c++)b[c]=new JU.BS;for(var d=this.myAtomCount;0<=--d;)if(null==a||a.get(d)){this.setGridLimitsForAtom(this.atomXyzTruncated[d],this.atomRadius[d],this.pt0,this.pt1);for(c=this.pt0.x;c<this.pt1.x;c++)b[c].set(d)}},
"JU.BS,~A");e(d,"markSphereVoxels",function(a,b){for(var c=3.4028235E38!=b&&null!=this.point,d=this.volumetricVectors[0],e=this.volumetricVectors[1],f=this.volumetricVectors[2],h=this.thisAtomSet.nextSetBit(0);0<=h;h=this.thisAtomSet.nextSetBit(h+1))if(this.havePlane||null==this.validSpheres||this.validSpheres.get(h)){var j=null!=this.noFaceSpheres&&this.noFaceSpheres.get(h),k=h>=this.firstNearbyAtom,l=this.atomXyzTruncated[h],n=this.atomRadius[h];if(!(c&&l.distance(this.point)>b+n+0.5)){var r=n+
a;this.setGridLimitsForAtom(l,r,this.pt0,this.pt1);this.isProgressive&&(this.pt0.x=this.thisX,this.pt1.x=this.thisX+1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(var q=this.pt0.x;q<this.pt1.x;q++,this.ptV.add2(d,this.ptY0)){this.ptY0.setT(this.ptV);for(var t=this.pt0.y;t<this.pt1.y;t++,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(f)){var w=this.ptV.distance(l)-n,y=this.volumeData.getPointIndex(q,t,v);if((0==
a||w<=r)&&w<this.getVoxel(q,t,v,y)){if(k||c&&this.ptV.distance(this.point)>b)w=NaN;this.setVoxel(q,t,v,y,w);Float.isNaN(w)||(null!=this.voxelSource&&(this.voxelSource[y]=h+1),0>w&&j&&this.bsSurfaceVoxels.set(y))}}}}}}},"~N,~N");e(d,"setVoxel",function(a,b,c,d,e){this.isProgressive?this.thisPlane[d%this.yzCount]=e:this.voxelData[a][b][c]=e},"~N,~N,~N,~N,~N")});L("J.jvxl.readers");R(["JU.P3","J.jvxl.readers.AtomDataReader","JU.P4","$.V3"],"J.jvxl.readers.IsoSolventReader","java.util.Hashtable JU.BS $.Lst $.Measure J.jvxl.data.MeshData JU.BSUtil $.GData $.Logger $.MeshSurface".split(" "),
function(){var d=N(function(){this.envelopeRadius=this.cavityRadius=0;this.dots=null;this.isPocket=this.isCavity=this.doCalculateTroughs=!1;this.bsAtomMinMax=this.p=this.vTemp2=this.ptTemp2=this.plane=this.vTemp=this.ptS2=this.ptS1=this.vFaces=this.vEdges=this.htEdges=this.bsLocale=this.bsSurfaceDone=this.bsSurfacePoints=this.iter=null;this.isSurfacePoint=!1;this.nTest=this.iAtomSurface=0;xa("J.jvxl.readers.IsoSolventReader.Edge")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$();xa("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;C(this,arguments)},J.jvxl.readers,"IsoSolventReader",J.jvxl.readers.AtomDataReader);ia(d,function(){this.ptS1=new JU.P3;this.ptS2=new JU.P3;this.vTemp=new JU.V3;this.plane=new JU.P4;this.ptTemp2=new JU.P3;this.vTemp2=new JU.V3;this.p=new JU.P3});da(d,function(){ja(this,J.jvxl.readers.IsoSolventReader,[])});j(d,"init",function(a){this.initADR(a)},"J.jvxl.readers.SurfaceGenerator");
j(d,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();this.volumeData.setUnitVectors();this.vl0=this.volumeData.volumetricVectorLengths[0];this.vl1=this.volumeData.volumetricVectorLengths[1];this.vl2=this.volumeData.volumetricVectorLengths[2];this.isProgressive&&(this.volumeData.getYzCount(),this.bsAtomMinMax=Array(this.nPointsX),this.getAtomMinMax(null,this.bsAtomMinMax),this.voxelSource=r(this.volumeData.nPoints,0));return!0},"~B");j(d,"setup",function(a){this.setup2();
if(null==this.contactPair){this.cavityRadius=this.params.cavityRadius;this.envelopeRadius=this.params.envelopeRadius;this.sr=this.params.solventRadius;this.point=this.params.point;this.isCavity=this.params.isCavity&&null!=this.meshDataServer;this.isPocket=null!=this.params.pocket&&null!=this.meshDataServer;this.doUseIterator=this.doCalculateTroughs=!a&&null!=this.sg.atomDataServer&&!this.isCavity&&0<this.sr&&(1195==this.dataType||1203==this.dataType);this.getAtoms(this.params.bsSelected,this.doAddHydrogens,
!0,!1,!1,!0,!1,NaN,null);if(this.isCavity||this.isPocket)this.dots=this.meshDataServer.calculateGeodesicSurface(this.bsMySelected,this.envelopeRadius);this.setHeader("solvent/molecular surface",this.params.calculationType);if(this.havePlane||!a){var b=Math.max(this.params.solventExtendedAtomRadius,this.params.solventRadius),b=1<=b?1.5/b:0;0<b&&System.out.println("IsoSolventReader.minPtsPerAng="+b);this.setRanges(this.params.solvent_ptsPerAngstrom,this.params.solvent_gridMax,b);this.volumeData.getYzCount();
this.margin=2*this.volumeData.maxGrid}null!=this.bsNearby&&this.bsMySelected.or(this.bsNearby)}else a||this.setVolumeData();this.doCalculateTroughs||(a?(this.precalculateVoxelData=!1,this.volumeData.sr=this):this.isCavity||(this.isProgressive=this.isXLowToHigh=!0));null==this.thisAtomSet&&(this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount))},"~B");j(d,"generateCube",function(){if(!(this.isCavity&&null!=this.params.theProperty)){this.isCavity&&1207!=this.dataType&&1208!=this.dataType?(this.params.vertexSource=
null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(this.cavityRadius,this.params.distance),this.generateSolventCavity(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(0,NaN)):(this.voxelSource=r(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()&&$(a.get(b)[0],"JU.P4")&&(this.volumeData.capData(a.get(b)[0],this.params.cutoff),a.removeItemAt(b--))}});
j(d,"getSurfacePointAndFraction",function(a,b,c,d,e,f,h,j,k,l,n,r,q){l=this.marchingCubes.getLinearOffset(h,j,k,l);n=this.marchingCubes.getLinearOffset(h,j,k,n);this.isSurfacePoint=null!=this.bsSurfaceVoxels&&(this.bsSurfaceVoxels.get(l)||this.bsSurfaceVoxels.get(n));if(null!=this.voxelSource){var t=Math.abs(Float.isNaN(d)||c<d?this.voxelSource[l]:this.voxelSource[n]);0<t&&(this.iAtomSurface=this.atomIndex[t-1])}if(J.jvxl.readers.IsoSolventReader.testLinear||null==this.voxelSource||0==this.voxelSource[l]||
this.voxelSource[l]!=this.voxelSource[n])return this.getSPF(a,b,c,d,e,f,h,j,k,l,n,r,q);a=r[0]=JU.MeshSurface.getSphericalInterpolationFraction(0>this.voxelSource[l]?this.sr:this.atomRadius[this.voxelSource[l]-1],c,d,f.length());q.scaleAdd2(a,f,e);return c+a*(d-c)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");j(d,"addVertexCopy",function(a,b,c,d){a=this.addVC(a,b,c,d);if(0>a)return a;this.isSurfacePoint&&this.bsSurfacePoints.set(a);null!=this.params.vertexSource&&(this.params.vertexSource[a]=
this.iAtomSurface);return a},"JU.T3,~N,~N,~B");j(d,"selectPocket",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);for(var b=this.meshData.vs,c=this.meshData.vc,d=this.meshData.vvs,e=this.dots.length,f=0;f<c;f++)for(var h=0;h<e;h++)this.dots[h].distance(b[f])<this.envelopeRadius&&(d[f]=NaN);this.meshData.getSurfaceSet();b=this.meshData.nSets;c=JU.BS.newN(b);for(f=0;f<b;f++)if(null!=(d=this.meshData.surfaceSet[f]))for(h=d.nextSetBit(0);0<=h;h=d.nextSetBit(h+
1))if(Float.isNaN(this.meshData.vvs[h])){c.set(f);break}for(f=0;f<b;f++)null!=this.meshData.surfaceSet[f]&&c.get(f)==a&&this.meshData.invalidateSurfaceSet(f);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");j(d,"postProcessVertices",function(){this.setVertexSource();if(this.doCalculateTroughs&&null!=this.bsSurfacePoints){var a=new JU.BS,b=this.meshData.getSurfaceSet(),
c=null,d=this.isPocket?null:J.jvxl.data.MeshData.calculateVolumeOrArea(this.meshData,null,!1,!1),e=this.isCavity?4.71238898038469*Math.pow(this.sr,3):0,f=0,h=!1;if(null!=d&&!this.isCavity)for(var j=0;j<this.meshData.nSets;j++){var k=d[j];Math.abs(k)>f&&(f=Math.abs(k),h=0>k)}f=h?-1:1;for(j=0;j<this.meshData.nSets;j++)if(h=b[j],h.intersects(this.bsSurfacePoints)&&(null==d||d[j]*f>e)&&null!=this.params.vertexSource){k=new JU.BS;null==c&&(c=Array(b.length));for(var l=h.nextSetBit(0);0<=l;l=h.nextSetBit(l+
1)){var n=this.params.vertexSource[l];if(!(0>n)){if(a.get(n)){this.meshData.invalidateSurfaceSet(j);break}k.set(n)}}a.or(k)}else this.meshData.invalidateSurfaceSet(j);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.GData.getSlabWithinRange(-100,0))});e(d,"generateSolventCavity",function(){for(var a=JU.BS.newN(this.nPointsX*
this.nPointsY*this.nPointsZ),b=0,c=this.dots.length,d=0,e,f=this.envelopeRadius,h=0;h<this.nPointsX;++h)for(var j=0;j<this.nPointsY;++j){var k=0;a:for(;k<this.nPointsZ;++k,++b)if(3.4028235E38>(e=this.voxelData[h][j][k])&&e>=this.cavityRadius){this.volumeData.voxelPtToXYZ(h,j,k,this.ptV);for(var l=0;l<c;l++)if(this.dots[l].distance(this.ptV)<f)continue a;a.set(b);d++}}JU.Logger.info("cavities include "+d+" voxel points");this.atomRadius=t(d,0);this.atomXyzTruncated=Array(d);for(c=b=h=0;h<this.nPointsX;++h)for(j=
0;j<this.nPointsY;++j)for(k=0;k<this.nPointsZ;++k)a.get(b++)&&(this.volumeData.voxelPtToXYZ(h,j,k,this.atomXyzTruncated[c]=new JU.P3),this.atomRadius[c++]=this.voxelData[h][j][k]);this.myAtomCount=this.firstNearbyAtom=d;this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount);this.rs=null;this.setRadii()});e(d,"generateSolventCube",function(){1207!=this.dataType&&(this.params.vertexSource=r(this.volumeData.nPoints,0),this.bsSurfaceDone=new JU.BS,this.bsSurfaceVoxels=new JU.BS,this.bsSurfacePoints=new JU.BS,
this.doCalculateTroughs?(this.iter=this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected,!0,!1,!1),this.vEdges=new JU.Lst,this.bsLocale=Array(this.myAtomCount),this.htEdges=new java.util.Hashtable,this.getEdges(),JU.Logger.info(this.vEdges.size()+" edges"),this.vFaces=new JU.Lst,this.getFaces(),JU.Logger.info(this.vFaces.size()+" faces"),this.htEdges=this.bsLocale=null,this.iter.release(),this.iter=null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markFaceVoxels(!0),this.markToroidVoxels(),
this.validSpheres.or(this.noFaceSpheres),this.vEdges=null,this.markFaceVoxels(!1),this.vFaces=null):(this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38)),this.markSphereVoxels(0,this.doCalculateTroughs?3.4028235E38:this.params.distance),this.validSpheres=this.noFaceSpheres=null)});e(d,"getEdges",function(){for(var a=0;a<this.myAtomCount;a++)this.bsLocale[a]=new JU.BS;for(a=0;a<this.myAtomCount;a++){var b=this.atomXyzTruncated[a],c=this.rs[a];for(this.sg.atomDataServer.setIteratorForAtom(this.iter,
this.atomIndex[a],c+this.maxRS);this.iter.hasNext();){var d=this.iter.next(),d=this.myIndex[d];if(!(a>=this.firstNearbyAtom&&d>=this.firstNearbyAtom)){var e=this.rs[d],f=b.distance(this.atomXyzTruncated[d]);f>=c+e||(e=va(J.jvxl.readers.IsoSolventReader.Edge,this,null,this,a,d,f),this.vEdges.addLast(e),this.bsLocale[a].set(d),this.bsLocale[d].set(a),this.htEdges.put(e.toString(),e))}}}});e(d,"findEdge",function(a,b){return this.htEdges.get(a<b?a+"_"+b:b+"_"+a)},"~N,~N");e(d,"getFaces",function(){var a=
new JU.BS;this.params.surfaceAtoms=this.validSpheres=new JU.BS;this.noFaceSpheres=JU.BSUtil.setAll(this.myAtomCount);for(var b=this.vEdges.size();0<=--b;){var c=this.vEdges.get(b),d=c.ia,e=c.ib;a.clearAll();a.or(this.bsLocale[d]);a.and(this.bsLocale[e]);for(var f=a.nextSetBit(e+1);0<=f;f=a.nextSetBit(f+1))if(this.getSolventPoints(c,d,e,f)){var h,j=!1;if(null!=(h=this.validateFace(d,e,f,c,this.ptS1)))this.vFaces.addLast(h),j=!0;if(null!=(h=this.validateFace(d,e,f,c,this.ptS2)))this.vFaces.addLast(h),
j=!0;j&&(this.noFaceSpheres.clear(d),this.noFaceSpheres.clear(e),this.noFaceSpheres.clear(f))}}});e(d,"validateFace",function(a,b,c,d,e){this.sg.atomDataServer.setIteratorForPoint(this.iter,this.modelIndex,e,this.maxRS);for(var f=!0;this.iter.hasNext();){var h=this.iter.next(),j=this.myIndex[h];if(!(j==a||j==b||j==c)&&this.atomData.atoms[h].distance(e)<this.atomData.atomRadius[h]+this.sr){f=!1;break}}h=this.findEdge(b,c);j=this.findEdge(a,c);e=f?va(J.jvxl.readers.IsoSolventReader.Face,this,null,a,
b,c,e):null;d.addFace(e);h.addFace(e);j.addFace(e);if(!f)return null;this.validSpheres.set(a);this.validSpheres.set(b);this.validSpheres.set(c);return e},"~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");e(d,"markFaceVoxels",function(a){for(var b=new JU.BS,c=this.volumetricVectors[0],d=this.volumetricVectors[1],e=this.volumetricVectors[2],f=this.vFaces.size();0<=--f;){var h=this.vFaces.get(f),j=this.atomXyzTruncated[h.ia],k=this.atomXyzTruncated[h.ib],l=this.atomXyzTruncated[h.ic],n=h.pS;this.setGridLimitsForAtom(n,
this.sr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(var r=this.pt0.x;r<this.pt1.x;r++,this.ptV.add2(c,this.ptY0)){this.ptY0.setT(this.ptV);for(var q=this.pt0.y;q<this.pt1.y;q++,this.ptV.add2(d,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var t=this.pt0.z;t<this.pt1.z;t++,this.ptV.add(e)){var v=this.sr-this.ptV.distance(n),w=this.voxelData[r][q][t],y=this.volumeData.getPointIndex(r,q,t);a&&0<v&&this.bsSurfaceDone.set(y);if(JU.Measure.isInTetrahedron(this.ptV,
j,k,l,n,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(r,q,t,y,v),null!=this.voxelSource&&(this.voxelSource[y]=-1-h.ia),0<v&&this.bsSurfaceVoxels.set(y)}}}}},"~B");e(d,"markToroidVoxels",function(){for(var a=this.volumetricVectors[0],b=this.volumetricVectors[1],c=this.volumetricVectors[2],d=this.vEdges.size();0<=--d;){var e=this.vEdges.get(d);if(e.isValid()){var f=
e.ia,h=e.ib,j=this.atomXyzTruncated[f],k=this.atomXyzTruncated[h];this.rAS=this.rs[f];this.rBS=this.rs[h];this.rAS2=this.rs2[f];this.rBS2=this.rs2[h];this.dAB=e.d;this.dAB2=e.d2;this.ecosASB2=e.cosASB2;this.setGridLimitsForAtom(e,e.maxr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(e=this.pt0.x;e<this.pt1.x;e++,this.ptV.add2(a,this.ptY0)){this.ptY0.setT(this.ptV);for(h=this.pt0.y;h<this.pt1.y;h++,this.ptV.add2(b,this.ptZ0)){this.ptZ0.setT(this.ptV);
for(var l=this.pt0.z;l<this.pt1.z;l++,this.ptV.add(c)){var n=this.checkSpecialVoxel(j,k,this.ptV);if(!Float.isNaN(n)&&(n=this.sr-n,n<this.voxelData[e][h][l])){var r=this.volumeData.getPointIndex(e,h,l);this.setVoxel(e,h,l,r,n);null!=this.voxelSource&&(this.voxelSource[r]=-1-f)}}}}}}});j(d,"unsetVoxelData",function(){if(this.havePlane)if(this.isProgressive)for(var a=0;a<this.yzCount;a++)0.001>this.thisPlane[a]||(this.thisPlane[a]=0.001);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=
0;c<this.nPointsZ;++c)0.001>this.voxelData[a][b][c]||(this.voxelData[a][b][c]=0.001);else this.unsetVoxelData2()});e(d,"getSolventPoints",function(a,b,c,d){var e=this.rs[b],f=a.v;a=(a.d2+this.rs2[b]-this.rs2[c])/(2*a.d*e);c=Math.acos(a);this.p.scaleAdd2(a*e,f,this.atomXyzTruncated[b]);JU.Measure.getPlaneThroughPoint(this.p,f,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,f,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(f,e);e.normalize();e.scale(Math.sqrt(1-d*d)*b);this.ptS1.add2(this.ptTemp,e);this.ptS2.sub2(this.ptTemp,e);return!0},"J.jvxl.readers.IsoSolventReader.Edge,~N,~N,~N");e(d,"checkSpecialVoxel",function(a,b,c){var d=a.distance(c),e=a.distanceSquared(c),f=this.rAS/d;if(1<f)return this.p.set(a.x+(c.x-a.x)*f,a.y+
(c.y-a.y)*f,a.z+(c.z-a.z)*f),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<(f=this.rBS/d)?(this.p.set(b.x+(c.x-b.x)*f,b.y+(c.y-b.y)*f,b.z+(c.z-b.z)*f),a.distanceSquared(this.p)>=this.rAS2?NaN:this.solventDistance(this.rBS,this.rBS2,this.rAS2,d,d*d,e)):NaN},"JU.P3,JU.P3,JU.P3");e(d,"solventDistance",function(a,b,c,d,e,f){f=Math.acos((e+this.dAB2-f)/(2*d*this.dAB));c=Math.acos((b+this.dAB2-c)/(2*a*this.dAB));
e=b+e-2*a*d*Math.cos(c-f);c=Math.sqrt(e);return this.ecosASB2<(b+e-d*d)/(c*a)?c:NaN},"~N,~N,~N,~N,~N,~N");e(d,"dumpLine",function(a,b,c,d){this.sg.log('draw ID "x'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(b)+" color "+d)},"JU.P3,JU.T3,~S,~S");e(d,"dumpLine2",function(a,b,c,d,e,f){var h=new JU.V3;h.setT(b);h.sub(a);h.normalize();h.scale(d);h.add(a);this.sg.log('draw ID "'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(h)+" color "+e);this.sg.log('draw ID "'+c+this.nTest++ +'"'+JU.P3.newP(h)+
" "+JU.P3.newP(b)+" color "+f+'"'+c+'"')},"JU.P3,JU.P3,~S,~N,~S,~S");e(d,"dumpPoint",function(a,b,c){this.sg.log('draw ID "'+b+this.nTest++ +'"'+JU.P3.newP(a)+" color "+c)},"JU.P3,~S,~S");j(d,"getValueAtPoint",function(a){if(null!=this.contactPair)return a.distance(this.contactPair.myAtoms[1])-this.contactPair.radii[1];for(var b=3.4028235E38,c=0;c<this.firstNearbyAtom;c++){var d=a.distance(this.atomXyzTruncated[c])-this.rs[c];d<b&&(b=d)}return 3.4028235E38==b?NaN:b},"JU.T3,~B");j(d,"discardTempData",
function(a){this.rs2=this.rs=null;this.discardTempDataSR(a)},"~B");j(d,"getPlane",function(a){0==this.yzCount&&this.initPlanes();this.thisX=a;this.thisPlane=this.yzPlanes[a%2];null==this.contactPair?(this.resetPlane(3.4028235E38),this.thisAtomSet=this.bsAtomMinMax[a],this.markSphereVoxels(0,this.params.distance),this.unsetVoxelData()):this.markPlaneVoxels(this.contactPair.myAtoms[0],this.contactPair.radii[0]);return this.thisPlane},"~N");d.$IsoSolventReader$Edge$=function(){var a=N(function(){wa(this,
arguments);this.cosASB2=this.maxr=this.d2=this.d=this.nInvalid=this.nFaces=this.ib=this.ia=0;this.v=null;C(this,arguments)},J.jvxl.readers.IsoSolventReader,"Edge",JU.P3);kb(a,function(a,c,d,e){this.ia=Math.min(c,d);this.ib=Math.max(c,d);this.d=e;this.d2=e*e;this.maxr=Math.sqrt(this.d2/4+Math.max(a.rs2[c],a.rs2[d]));this.ave(a.atomXyzTruncated[c],a.atomXyzTruncated[d]);this.cosASB2=(a.rs2[c]+a.rs2[d]-this.d2)/(a.rs[d]*a.rs[c]);this.v=JU.V3.newVsub(a.atomXyzTruncated[d],a.atomXyzTruncated[c]);this.v.normalize()},
"J.jvxl.readers.IsoSolventReader,~N,~N,~N");e(a,"addFace",function(a){this.nFaces++;null==a&&this.nInvalid++},"J.jvxl.readers.IsoSolventReader.Face");e(a,"isValid",function(){return 0==this.nFaces||this.nInvalid!=this.nFaces});j(a,"toString",function(){return this.ia+"_"+this.ib})};d.$IsoSolventReader$Face$=function(){var a=N(function(){wa(this,arguments);this.ic=this.ib=this.ia=0;this.pS=null;C(this,arguments)},J.jvxl.readers.IsoSolventReader,"Face",null);da(a,function(a,c,d,e){this.ia=a;this.ib=
c;this.ic=d;this.pS=JU.P3.newP(e)},"~N,~N,~N,JU.P3");j(a,"toString",function(){return this.ia+"_"+this.ib+"_"+this.ic+"_"+this.pS})};d.testLinear=!1});L("J.jvxl.readers");R(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.SurfaceFileReader",["JU.PT","$.Rdr","J.api.Interface"],function(){var d=N(function(){this.next=this.line=this.out=this.binarydoc=this.br=null;C(this,arguments)},J.jvxl.readers,"SurfaceFileReader",J.jvxl.readers.SurfaceReader);ia(d,function(){this.next=r(1,0)});da(d,function(){ja(this,
J.jvxl.readers.SurfaceFileReader,[])});e(d,"setStream",function(a,b){if(null==a)this.binarydoc.setStream(null,b);else try{if($(this.br,"JU.Rdr.StreamReader")){var c=this.br.getStream();c.reset();this.binarydoc.setStream(c,!0)}}catch(d){if(ea(d,Exception))System.out.println("BCifDensityReader "+d),this.binarydoc.setStream(this.sg.atomDataServer.getBufferedInputStream(a),b);else throw d;}},"~S,~B");j(d,"init",function(a){this.initSR(a)},"J.jvxl.readers.SurfaceGenerator");e(d,"init2",function(a,b){this.init2SFR(a,
b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2SFR",function(a,b){this.br=b;this.init(a)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"newBinaryDocument",function(){return J.api.Interface.getInterface("JU.BinaryDocument",this.sg.atomDataServer,"file")});j(d,"setOutputChannel",function(a){null==this.binarydoc?this.out=a:this.sg.setOutputChannel(this.binarydoc,a)},"JU.OC");j(d,"closeReader",function(){this.closeReaderSFR()});e(d,"closeReaderSFR",function(){if(null!=
this.br)try{this.br.close()}catch(a){if(!ea(a,"java.io.IOException"))throw a;}null!=this.out&&this.out.closeChannel();null!=this.binarydoc&&this.binarydoc.close()});j(d,"discardTempData",function(a){this.closeReader();this.discardTempDataSR(a)},"~B");e(d,"getTokens",function(){return JU.PT.getTokensAt(this.line,0)});e(d,"parseFloat",function(){return JU.PT.parseFloatNext(this.line,this.next)});e(d,"parseFloatStr",function(a){this.next[0]=0;return JU.PT.parseFloatNext(a,this.next)},"~S");e(d,"parseFloatRange",
function(a,b,c){this.next[0]=b;return JU.PT.parseFloatRange(a,c,this.next)},"~S,~N,~N");e(d,"parseInt",function(){return JU.PT.parseIntNext(this.line,this.next)});e(d,"parseIntStr",function(a){this.next[0]=0;return JU.PT.parseIntNext(a,this.next)},"~S");e(d,"parseIntNext",function(a){return JU.PT.parseIntNext(a,this.next)},"~S");e(d,"parseFloatArrayStr",function(a){this.next[0]=0;return JU.PT.parseFloatArrayNext(a,this.next,null,null,null)},"~S");e(d,"parseFloatArray",function(a,b,c){return JU.PT.parseFloatArrayNext(this.line,
this.next,a,b,c)},"~A,~S,~S");e(d,"getQuotedStringNext",function(){return JU.PT.getQuotedStringNext(this.line,this.next)});e(d,"skipTo",function(a,b){if(null!=a)for(;0>this.rd().indexOf(a););null!=b&&(this.next[0]=this.line.indexOf(b)+b.length+2)},"~S,~S");e(d,"rd",function(){this.line=this.br.readLine();if(null!=this.line&&(this.nBytes+=this.line.length,null!=this.out)){var a=this.line.getBytes();this.out.write(a,0,a.length);this.out.writeByteAsInt(10)}return this.line})});L("J.jvxl.readers");R(["J.jvxl.readers.SurfaceFileReader"],
"J.jvxl.readers.VolumeFileReader","JU.AU $.PT $.SB J.api.Interface J.atomdata.AtomData JU.Logger".split(" "),function(){var d=N(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;C(this,arguments)},J.jvxl.readers,
"VolumeFileReader",J.jvxl.readers.SurfaceFileReader);da(d,function(){ja(this,J.jvxl.readers.VolumeFileReader,[])});j(d,"init2",function(a,b){this.init2VFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2VFR",function(a,b){this.init2SFR(a,b);this.canDownsample=this.isProgressive=this.isXLowToHigh=!0;this.jvxlData.wasCubic=!0;this.boundingBox=this.params.boundingBox;4==this.params.qmOrbitalType&&(this.hasColorData=null==this.params.parameters||0<=this.params.parameters[1],
this.getNCIPlanes=!0,this.params.insideOut=!this.params.insideOut)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"recordData",function(a){if(Float.isNaN(a))return a;a<this.dataMin&&(this.dataMin=a);a>this.dataMax&&(this.dataMax=a);this.dataMean+=a;this.nData++;return a},"~N");j(d,"closeReader",function(){this.readerClosed||(this.readerClosed=!0,this.closeReaderSFR(),0==this.nData||-3.4028235E38==this.dataMax||(this.dataMean/=this.nData,JU.Logger.info("VolumeFileReader closing file: "+
this.nData+" points read \ndata min/max/mean = "+this.dataMin+"/"+this.dataMax+"/"+this.dataMean)))});j(d,"readVolumeParameters",function(){this.endOfData=!1;this.nSurfaces=this.readVolumetricHeader();if(0==this.nSurfaces)return!1;this.nSurfaces<this.params.fileIndex&&(JU.Logger.warn("not enough surfaces in file -- resetting params.fileIndex to "+this.nSurfaces),this.params.fileIndex=this.nSurfaces);return!0},"~B");j(d,"readVolumeData",function(a){return this.readVolumeDataVFR(a)},"~B");e(d,"readVolumeDataVFR",
function(a){if(!this.gotoAndReadVoxelData(a))return!1;this.vertexDataOnly||JU.Logger.info("JVXL read: "+this.nPointsX+" x "+this.nPointsY+" x "+this.nPointsZ+" data points");return!0},"~B");e(d,"readVolumetricHeader",function(){try{this.readParameters();if(-2147483648==this.ac)return 0;this.vertexDataOnly||JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);var a=this.params.downsampleFactor,b=this.canDownsample&&1<a;1<a&&!this.canDownsample&&(this.jvxlData.msg+="\ncannot downsample this file type");
if(b){this.downsampleRemainders=r(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(ea(e,Exception))return JU.Logger.error(e.toString()),0;throw e;}});e(d,"skipComments",function(a){for(var b=new JU.SB;null!=this.rd()&&(a&&0==this.line.length||0==this.line.indexOf("#"));)b.append(this.line).appendC("\n");return b.toString()},
"~B");e(d,"readVoxelVector",function(a){this.rd();var b=this.volumetricVectors[a];if(-2147483648==(this.voxelCounts[a]=this.parseIntStr(this.line)))this.next[0]=this.line.indexOf(" ");b.set(this.parseFloat(),this.parseFloat(),this.parseFloat());this.isAnisotropic&&this.setVectorAnisotropy(b)},"~N");e(d,"initializeSurfaceData",function(){this.downsampleFactor=this.params.downsampleFactor;this.nSkipZ=this.nSkipY=this.nSkipX=0;this.canDownsample&&0<this.downsampleFactor&&(this.nSkipX=this.downsampleFactor-
1,this.nSkipY=this.downsampleRemainders[2]+(this.downsampleFactor-1)*(this.nSkipZ=(this.nPointsZ-(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[2]),this.nSkipZ=this.downsampleRemainders[1]*this.nSkipZ+(this.downsampleFactor-1)*this.nSkipZ*((this.nPointsY-(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[1]));null!=this.params.thePlane?this.params.cutoff=0:this.isJvxl&&(this.params.cutoff=this.params.isBicolorMap||this.params.colorBySign?0.01:this.getJVXLCutoff());
this.nDataPoints=0;this.next[0]=0;this.line="";this.jvxlNSurfaceInts=0});e(d,"getJVXLCutoff",function(){return 0.5});j(d,"readSurfaceData",function(a){this.readSurfaceDataVFR(a)},"~B");e(d,"readSurfaceDataVFR",function(a){this.initializeSurfaceData();if(this.isProgressive&&!a||this.isJvxl)this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null,this.isJvxl&&(this.jvxlVoxelBitSet=this.getVoxelBitSet(this.nDataPoints));else if(a&&this.volumeData.hasPlane()){this.volumeData.setVoxelMap();
var b=this.volumeData.getToPlaneParameter();for(a=0;a<this.nPointsX;++a){for(var c=0;c<this.nPointsY;++c){for(var d=0;d<this.nPointsZ;++d){var e=this.recordData(this.getNextVoxelValue());this.volumeData.isNearPlane(a,c,d,b)&&this.volumeData.setVoxelMapValue(a,c,d,e);0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}else{this.voxelData=JU.AU.newFloat3(this.nPointsX,-1);for(a=0;a<this.nPointsX;++a){b=JU.AU.newFloat2(this.nPointsY);
this.voxelData[a]=b;for(c=0;c<this.nPointsY;++c){e=t(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");j(d,"getPlane",function(a){0==a&&this.initPlanes();if(this.getNCIPlanes)return this.getPlaneNCI(a);a=this.getPlaneSR(a);null==this.qpc&&this.getPlaneVFR(a,
!0);return a},"~N");e(d,"getPlaneNCI",function(a){var b;if(0==this.iPlaneNCI){this.qpc=J.api.Interface.getOption("quantum.NciCalculation",this.sg.atomDataServer,null);b=new J.atomdata.AtomData;b.modelIndex=-1;b.bsSelected=this.params.bsSelected;this.sg.fillAtomData(b,1);this.qpc.setupCalculation(this.volumeData,this.sg.params.bsSelected,null,null,b.atoms,-1,!0,null,this.params.parameters,this.params.testFlags);this.iPlaneNCI=1;this.qpc.setPlanes(this.yzPlanesRaw=t(4,this.yzCount,0));if(this.hasColorData){this.getPlaneVFR(this.yzPlanesRaw[0],
!1);this.getPlaneVFR(this.yzPlanesRaw[1],!1);b=this.yzPlanes[0];for(a=0;a<this.yzCount;a++)b[a]=NaN;return b}this.iPlaneNCI=-1}var c=this.qpc.getNoValue(),d=this.nPointsX-1;switch(this.iPlaneNCI){case -1:b=this.yzPlanes[a%2];d++;break;case 3:b=this.yzPlanesRaw[0];this.yzPlanesRaw[0]=this.yzPlanesRaw[1];this.yzPlanesRaw[1]=this.yzPlanesRaw[2];this.yzPlanesRaw[2]=this.yzPlanesRaw[3];this.yzPlanesRaw[3]=b;b=this.yzPlanesRaw[this.iPlaneNCI];break;default:this.iPlaneNCI++,b=this.yzPlanesRaw[this.iPlaneNCI]}if(a<
d){this.getPlaneVFR(b,!1);this.qpc.calcPlane(a,b=this.yzPlanes[a%2]);for(a=0;a<this.yzCount;a++)b[a]!=c&&this.recordData(b[a])}else for(a=0;a<this.yzCount;a++)b[a]=NaN;return b},"~N");e(d,"getPlaneVFR",function(a,b){try{for(var c=0,d=0;c<this.nPointsY;++c){for(var e=0;e<this.nPointsZ;++e){var f=this.getNextVoxelValue();b&&this.recordData(f);a[d++]=f;0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}catch(h){if(!ea(h,
Exception))throw h;}},"~A,~B");j(d,"getValue",function(a,b,c,d){return null!=this.boundingBox&&(this.volumeData.voxelPtToXYZ(a,b,c,this.ptTemp),this.ptTemp.x<this.boundingBox[0].x||this.ptTemp.x>this.boundingBox[1].x||this.ptTemp.y<this.boundingBox[0].y||this.ptTemp.y>this.boundingBox[1].y||this.ptTemp.z<this.boundingBox[0].z||this.ptTemp.z>this.boundingBox[1].z)?NaN:this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(d,"skipVoxels",function(a){for(;0<=--a;)this.getNextVoxelValue()},"~N");e(d,"getVoxelBitSet",
function(){return null},"~N");e(d,"getNextVoxelValue",function(){var a=0;if(1<this.nSurfaces&&!this.params.blockCubeData){for(var b=1;b<this.params.fileIndex;b++)this.nextVoxel();a=this.nextVoxel();for(b=this.params.fileIndex;b<this.nSurfaces;b++)this.nextVoxel()}else a=this.nextVoxel();return a});e(d,"nextVoxel",function(){var a=this.parseFloat();if(Float.isNaN(a)){for(;null!=this.rd()&&Float.isNaN(a=this.parseFloatStr(this.line)););null==this.line&&(this.endOfData||JU.Logger.warn("end of file reading cube voxel data? nBytes="+
this.nBytes+" nDataPoints="+this.nDataPoints+" (line):"+this.line),this.endOfData=!0,this.line="0 0 0 0 0 0 0 0 0 0")}return a});j(d,"gotoData",function(a,b){if(this.params.blockCubeData){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");for(var c=0;c<a;c++)this.skipData(b)}},"~N,~N");e(d,"skipData",function(a){this.skipDataVFR(a)},"~N");e(d,"skipDataVFR",function(a){for(var b=0;b<a;)b+=this.countData(this.rd())},"~N");e(d,"countData",function(a){for(var b=0,c=0,d=a.length,e;c<d;){for(;c<
d&&(" "==(e=a.charAt(c))||"\t"==e);)++c;for(c<d&&++b;c<d&&" "!=(e=a.charAt(c))&&"\t"!=e;)++c}return b},"~S");d.checkAtomLine=e(d,"checkAtomLine",function(a,b,c,d,e){0<=d.indexOf("ANGSTROMS")&&(b=!0);c=null==c?2147483647:JU.PT.parseInt(c);switch(c){case -2147483648:c=0;d=" "+d.substring(d.indexOf(" ")+1);break;case 2147483647:c=-2147483648;break;default:var f=""+c;d=d.substring(d.indexOf(f)+f.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");j(d,"getSurfacePointAndFraction",function(a,b,c,d,e,f,h,j,k,l,n,r,q){return this.getSPFv(a,b,c,d,e,f,h,j,k,l,n,r,q)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getSPFv",function(a,b,c,d,e,f,h,j,k,l,n,r,q){a=this.getSPF(a,b,c,d,e,f,h,j,k,l,n,r,q);if(null==this.qpc||Float.isNaN(a)||!this.hasColorData)return a;l=this.marchingCubes.getLinearOffset(h,j,k,l);n=this.marchingCubes.getLinearOffset(h,j,k,n);return this.qpc.process(l,
n,r[0])},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"scaleIsosurface",function(a){this.isScaledAlready||(this.isScaledAlready=!0,this.isAnisotropic&&this.setVolumetricAnisotropy(),Float.isNaN(a)||(JU.Logger.info("applying scaling factor of "+a),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[0],this.volumetricOrigin),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[1],this.volumetricOrigin),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[2],
this.volumetricOrigin),this.volumetricVectors[0].scale(a),this.volumetricVectors[1].scale(a),this.volumetricVectors[2].scale(a)))},"~N");e(d,"swapXZ",function(){var a=this.volumetricVectors[0];this.volumetricVectors[0]=this.volumetricVectors[2];this.volumetricVectors[2]=a;a=this.voxelCounts[0];this.voxelCounts[0]=this.voxelCounts[2];this.voxelCounts[2]=a;this.params.insideOut=!this.params.insideOut})});L("J.jvxl.readers");R(["J.jvxl.readers.VolumeFileReader"],"J.jvxl.readers.JvxlXmlReader","java.util.Hashtable JU.AU $.BS $.CU $.Lst $.P3 $.P4 $.PT $.SB J.jvxl.data.JvxlCoder $.MeshData J.jvxl.readers.XmlReader J.shapesurface.IsosurfaceMesh JU.C $.ColorEncoder $.Escape $.Logger".split(" "),
function(){var d=N(function(){this.JVXL_VERSION="2.4";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;
C(this,arguments)},J.jvxl.readers,"JvxlXmlReader",J.jvxl.readers.VolumeFileReader);da(d,function(){ja(this,J.jvxl.readers.JvxlXmlReader,[])});j(d,"init2",function(a,b){this.init2JXR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(d,"init2JXR",function(a,b){this.init2VFR(a,b);this.jvxlData.wasJvxl=this.isJvxl=!0;this.isXLowToHigh=this.canDownsample=!1;this.xr=new J.jvxl.readers.XmlReader(b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");j(d,"readVolumeData",function(a){if(!this.readVolumeDataVFR(a))return!1;
this.strFractionTemp=this.jvxlEdgeDataRead;this.fractionPtr=0;return!0},"~B");j(d,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0>this.nPointsX||0>this.nPointsY||0>this.nPointsZ)return!0;try{this.gotoData(this.params.fileIndex-1,this.nPointsX*this.nPointsY*this.nPointsZ);if(this.vertexDataOnly)return!0;this.volumeData.setMappingPlane(this.params.thePlane);this.readSurfaceData(a);this.volumeData.setMappingPlane(null);0<this.edgeDataCount&&(this.jvxlEdgeDataRead=this.jvxlReadFractionData("edge",
this.edgeDataCount));this.params.bsExcluded=this.jvxlData.jvxlExcluded=Array(4);if(this.hasColorData=0<this.colorDataCount)this.jvxlColorDataRead=this.jvxlReadFractionData("color",this.colorDataCount);0<this.excludedVertexCount&&(this.jvxlData.jvxlExcluded[0]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedVertexData",null,!1,!1)),this.xr.isNext("jvxlExcludedPlaneData")&&(this.jvxlData.jvxlExcluded[2]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedPlaneData",
null,!1,!1))));0<this.excludedTriangleCount&&(this.jvxlData.jvxlExcluded[3]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedTriangleData",null,!1,!1)));0<this.invalidatedVertexCount&&(this.jvxlData.jvxlExcluded[1]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlInvalidatedVertexData",null,!1,!1)));this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1));this.getVertexColorData()}catch(b){if(ea(b,Exception))return JU.Logger.error(b.toString()),
!1;throw b;}return!0},"~B");e(d,"getVertexColorData",function(){if(this.jvxlDataIsColorMapped&&0<this.jvxlData.nVertexColors){var a=this.xr.getXmlData("jvxlVertexColorData",null,!0,!1);if(null==a)this.jvxlData.nVertexColors=0,this.jvxlDataIsColorMapped=!1;else{this.jvxlData.vertexColorMap=new java.util.Hashtable;var b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"baseColor");this.jvxlData.baseColor=0<b.length?b:null;for(var b=r(1,0),c=0;c<this.jvxlData.nVertexColors;c++){var d=this.xr.getXmlDataLF("jvxlColorMap",
a,!0,!1,!1,b),e=J.jvxl.readers.XmlReader.getXmlAttrib(d,"color"),d=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlColorMap",d,!1,!1));this.jvxlData.vertexColorMap.put(e,d)}}}});j(d,"readParameters",function(){var a=this.xr.getXmlDataLF("jvxlFileTitle",null,!1,!1,!0,null);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)});j(d,"getJVXLCutoff",function(){return this.params.cutoff});
e(d,"readVector",function(a){var b=this.xr.getXmlData("jvxlVolumeVector",this.tempDataXml,!0,!0);this.tempDataXml=this.tempDataXml.substring(this.tempDataXml.indexOf(b)+b.length);var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"count"));-2147483648==c&&(this.vertexDataOnly=!0);this.voxelCounts[a]=0>c?0:c;this.volumetricVectors[a].setT(this.xr.getXmlPoint(b,"vector"));this.isAnisotropic&&this.setVectorAnisotropy(this.volumetricVectors[a])},"~N");j(d,"gotoData",function(a,b){0<a&&JU.Logger.info("skipping "+
a+" data sets, "+b+" points each");this.vertexDataOnly=this.jvxlData.vertexDataOnly=0==b;for(var c=0;c<a;c++)this.jvxlSkipData(b,!0);this.xr.toTag("jvxlSurface");this.jvxlReadSurfaceInfo()},"~N,~N");e(d,"jvxlSkipData",function(){this.rd();this.xr.skipTag("jvxlSurface")},"~N,~B");e(d,"jvxlReadSurfaceInfo",function(){var a=this.xr.getXmlData("jvxlSurfaceInfo",null,!0,!0);this.isXLowToHigh=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isXLowToHigh").equals("true");var b=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"cutoff");0>b.indexOf(" ")?(this.jvxlCutoff=this.parseFloatStr(b),Double.isNaN(this.jvxlCutoff)||JU.Logger.info("JVXL read: cutoff "+this.jvxlCutoff)):(this.jvxlCutoffRange=this.parseFloatArrayStr(b),this.jvxlCutoff=this.jvxlCutoffRange[0],JU.Logger.info("JVXL read: cutoff "+JU.Escape.eAF(this.jvxlCutoffRange)));this.params.cutoff=this.jvxlCutoff;var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContourData"));this.haveContourData=0<c;this.params.isContoured=this.jvxlData.isModelConnected=
J.jvxl.readers.XmlReader.getXmlAttrib(a,"contoured").equals("true");this.params.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(a,"isModelConnected").equals("true");if(this.params.isContoured){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nContours"));0>=d?d=0:(0>this.params.thisContour&&(this.params.thisContour=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"thisContour"))),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourValues"),0<b.length&&(b=b.$replace("[",
" ").$replace("]"," "),this.jvxlData.contourValues=this.params.contoursDiscrete=this.parseFloatArrayStr(b),JU.Logger.info("JVXL read: contourValues "+JU.Escape.eAF(this.jvxlData.contourValues))),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourColors"),0<b.length&&(this.jvxlData.contourColixes=this.params.contourColixes=JU.C.getColixArray(b),this.jvxlData.contourColors=JU.C.getHexCodes(this.jvxlData.contourColixes),JU.Logger.info("JVXL read: contourColixes "+JU.C.getHexCodes(this.jvxlData.contourColixes))),
this.params.contourFromZero=J.jvxl.readers.XmlReader.getXmlAttrib(a,"contourFromZero").equals("true"));this.params.nContours=this.haveContourData?c:d}this.jvxlData.nVertexColors=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"nVertexColors"));this.params.isBicolorMap=J.jvxl.readers.XmlReader.getXmlAttrib(a,"bicolorMap").equals("true");this.params.isBicolorMap&&(b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorPositive"),0<b.length&&(-2147483648==this.params.colorRgb&&-16776961==this.params.colorPos)&&
(this.params.colorPos=JU.CU.getArgbFromString(b)),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorNegative"),0<b.length&&(-2147483648==this.params.colorRgb&&-65536==this.params.colorNeg)&&(this.params.colorNeg=JU.CU.getArgbFromString(b)));if(this.params.isBicolorMap||this.params.colorBySign)this.jvxlCutoff=0;this.jvxlDataIsColorMapped=(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&(this.params.isBicolorMap||J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorMapped").equals("true"));
this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.XmlReader.getXmlAttrib(a,"precisionColor").equals("true");this.jvxlData.jvxlDataIsColorDensity=this.params.colorDensity=-2147483648==this.params.colorRgb&&J.jvxl.readers.XmlReader.getXmlAttrib(a,"colorDensity").equals("true");this.jvxlData.jvxlDataIsColorDensity&&Float.isNaN(this.params.pointSize)&&(b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"pointSize"),0<b.length&&(this.jvxlData.pointSize=this.params.pointSize=this.parseFloatStr(b)));b=J.jvxl.readers.XmlReader.getXmlAttrib(a,
"allowVolumeRender");this.jvxlData.allowVolumeRender=this.params.allowVolumeRender=0==b.length||b.equalsIgnoreCase("true");b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"plane");if(0<=b.indexOf("{")){this.params.thePlane=null;this.params.mapLattice=null;try{this.params.thePlane=JU.Escape.uP(b),b=J.jvxl.readers.XmlReader.getXmlAttrib(a,"maplattice"),JU.Logger.info("JVXL read: plane "+this.params.thePlane),0<=b.indexOf("{")&&(this.params.mapLattice=JU.Escape.uP(b),JU.Logger.info("JVXL read: mapLattice "+
this.params.mapLattice)),0==this.params.scale3d&&(this.params.scale3d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"scale3d"))),Float.isNaN(this.params.scale3d)&&(this.params.scale3d=0)}catch(e){if(ea(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"),f=d=c=NaN,h=NaN;this.jvxlDataIsColorMapped&&(c=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"dataMinimum")),d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"dataMaximum")),f=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"valueMappedToRed")),h=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"valueMappedToBlue")),Float.isNaN(c)&&(c=f=-1,d=h=1));this.jvxlSetColorRanges(c,d,f,h,b)});e(d,"jvxlSetColorRanges",function(a,b,c,
d,e){this.jvxlDataIsColorMapped&&(!Float.isNaN(a)&&!Float.isNaN(b)&&(0==b&&0==a&&(a=-1,b=1),this.params.mappedDataMin=a,this.params.mappedDataMax=b,JU.Logger.info("JVXL read: data_min/max "+this.params.mappedDataMin+"/"+this.params.mappedDataMax)),this.params.rangeDefined||(!Float.isNaN(c)&&!Float.isNaN(d)?(0==c&&0==d&&(c=-1,d=1),this.params.valueMappedToRed=Math.min(c,d),this.params.valueMappedToBlue=Math.max(c,d),this.params.isColorReversed=c>d):(this.params.valueMappedToRed=0,this.params.valueMappedToBlue=
1),this.params.rangeDefined=!0),JU.Logger.info("JVXL read: color red/blue: "+this.params.valueMappedToRed+"/"+this.params.valueMappedToBlue));this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.isColorReversed=this.params.isColorReversed;this.params.insideOut&&(e=!e);this.params.insideOut=this.jvxlData.insideOut=
e},"~N,~N,~N,~N,~B");j(d,"readSurfaceData",function(){this.thisInside=!this.params.isContoured;this.readSurfaceDataXML()||(this.tempDataXml=this.xr.getXmlData("jvxlEdgeData",null,!0,!1),this.bsVoxelBitSet=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlEdgeData",this.tempDataXml,!1,!1)),this.readSurfaceDataJXR())},"~B");e(d,"readSurfaceDataXML",function(){return this.vertexDataOnly?(this.getEncodedVertexData(),!0):null!=this.params.thePlane?(this.volumeData.setDataDistanceToPlane(this.params.thePlane),
this.setVolumeDataV(this.volumeData),this.params.cutoff=0,this.jvxlData.setSurfaceInfo(this.params.thePlane,this.params.mapLattice,0,""),this.jvxlData.scale3d=this.params.scale3d,!0):!1});e(d,"readSurfaceDataJXR",function(){this.readSurfaceDataVFR(!1);this.volumeData.setMappingPlane(null)});e(d,"jvxlReadFractionData",function(a){var b;try{if(a.equals("edge"))b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml,"data"));else{var c=this.xr.getXmlData("jvxlColorData",
null,!0,!1);this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.JvxlXmlReader.getEncoding(c).endsWith("2");b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(c,"data"))}}catch(d){if(ea(d,Exception))throw JU.Logger.error("Error reading "+a+" data "+d),new NullPointerException;throw d;}return b},"~S,~N");j(d,"getVoxelBitSet",function(a){if(null!=this.bsVoxelBitSet)return this.bsVoxelBitSet;var b=new JU.BS,c=0;if(0>=this.surfaceDataCount)return b;for(var d=0;c<a;){d=this.parseInt();
if(-2147483648==d&&(this.rd(),null==this.line||-2147483648==(d=this.parseIntStr(this.line))))this.endOfData||JU.Logger.error("end of file in JvxlReader? line="+this.line),this.endOfData=!0,d=1E4;this.thisInside=!this.thisInside;++this.jvxlNSurfaceInts;this.thisInside&&b.setBits(c,c+d);c+=d}return b},"~N");j(d,"getSurfacePointAndFraction",function(a,b,c,d,e,f,h,j,k,l,n,r,q){if(0>=this.edgeDataCount)return this.getSPFv(a,b,c,d,e,f,h,j,k,l,n,r,q);q.scaleAdd2(r[0]=this.jvxlGetNextFraction(this.edgeFractionBase,
this.edgeFractionRange,0.5),f,e);Float.isNaN(this.valueMin)&&this.setValueMinMax();return 0==this.valueCount||this.includeValueNaN&&Float.isNaN(r[0])?r[0]:this.getNextValue()},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(d,"getNextValue",function(){for(var a=NaN;this.colorPtr<this.valueCount&&Float.isNaN(a);){a=this.jvxlData.isJvxlPrecisionColor?J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(this.jvxlColorDataRead.charAt(this.colorPtr).charCodeAt(0),this.jvxlColorDataRead.charAt(this.colorPtr++ +
this.valueCount).charCodeAt(0),this.colorFractionBase,this.colorFractionRange):J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.jvxlColorDataRead.charAt(this.colorPtr++).charCodeAt(0),this.colorFractionBase,this.colorFractionRange,0.5);break}return this.valueMin+a*this.valueRange});e(d,"setValueMinMax",function(){this.valueCount=this.jvxlColorDataRead.length;this.jvxlData.isJvxlPrecisionColor&&(this.valueCount/=2);this.includeValueNaN=this.valueCount!=this.jvxlEdgeDataRead.length;this.valueMin=
!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToRed:3.4028235E38==this.params.mappedDataMin?0:this.params.mappedDataMin;this.valueRange=(!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToBlue:3.4028235E38==this.params.mappedDataMin?1:this.params.mappedDataMax)-this.valueMin;this.haveReadColorData=!0});e(d,"jvxlGetNextFraction",function(a,b,c){this.fractionPtr>=this.strFractionTemp.length&&(this.endOfData||JU.Logger.error("end of file reading compressed fraction data"),this.endOfData=
!0,this.strFractionTemp=""+String.fromCharCode(a),this.fractionPtr=0);return J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.strFractionTemp.charAt(this.fractionPtr++).charCodeAt(0),a,b,c)},"~N,~N,~N");j(d,"readColorData",function(){if(!this.jvxlDataIsColorMapped)return"";var a=this.jvxlData.vertexCount=this.meshData.vc,b=this.meshData.vcs,c=this.meshData.vvs;if("none".equals(this.jvxlColorEncodingRead)){this.jvxlData.vertexColors=r(a,0);for(var d=r(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,f=this.jvxlData.translucency,h=0,d=0;d<c;d++)try{var j=J.jvxl.readers.JvxlXmlReader.getColor(a[d]);0==j?j=h:h=j;b[d]=JU.C.getColixTranslucent(this.jvxlData.vertexColors[d]=j);JU.C.isColixTranslucent(b[d])?e=!0:0!=f&&(b[d]=JU.C.getColixTranslucent3(b[d],!0,f))}catch(k){if(ea(k,Exception))JU.Logger.info("JvxlXmlReader: Cannot interpret color code: "+a[d]);else throw k;}e&&0==f&&(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 l=Float.isNaN(this.valueMin);l&&this.setValueMinMax();var n=3.4028235E38,t=-3.4028235E38;if(null==b||b.length<a)this.meshData.vcs=b=fa(a,0);e=j=0;this.params.colorBySign&&(e=JU.C.getColix(this.params.isColorReversed?this.params.colorNeg:this.params.colorPos),j=JU.C.getColix(this.params.isColorReversed?this.params.colorPos:this.params.colorNeg));for(var f=this.meshData.vertexIncrement,
q=3.4028235E38==this.params.mappedDataMin,d=0;d<a;d+=f)h=l?c[d]=this.getNextValue():c[d],q&&(h<n&&(n=h),h>t&&(t=h));q&&(this.params.mappedDataMin=n,this.params.mappedDataMax=t);if(null!=this.jvxlData.colorScheme){l=null!=this.marchingSquares&&this.params.isContoured;for(d=0;d<a;d+=f)h=c[d],l?this.marchingSquares.setContourData(d,h):(h=!this.params.colorBySign?this.params.colorEncoder.getColorIndex(h):(this.params.isColorReversed?0<h:0>=h)?j:e,b[d]=JU.C.getColixTranslucent3(h,!0,this.jvxlData.translucency))}return this.jvxlColorDataRead+
"\n"});d.getColor=e(d,"getColor",function(a){var b=0;try{switch(a.charAt(0).charCodeAt(0)){case 91:b=JU.CU.getArgbFromString(a);break;case 48:if(1==a.length)break;b=JU.PT.parseIntRadix(a.substring(2),16);break;default:b=JU.PT.parseIntRadix(a,10)}}catch(c){if(!ea(c,Exception))throw c;}return b},"~S");e(d,"getEncodedVertexData",function(){var a=this.xr.getXmlData("jvxlSurfaceData",null,!0,!1);this.jvxlDecodeVertexData(this.xr.getXmlData("jvxlVertexData",a,!0,!1),!1);var b=this.xr.getXmlData("jvxlTriangleData",
a,!0,!1),c=this.xr.getXmlData("jvxlTriangleEdgeData",a,!0,!1),d=this.xr.getXmlData("jvxlPolygonColorData",a,!1,!1);this.jvxlDecodeTriangleData(b,c,d);a=this.xr.getXmlData("jvxlColorData",a,!0,!1);this.jvxlColorEncodingRead=J.jvxl.readers.JvxlXmlReader.getEncoding(a);this.jvxlData.isJvxlPrecisionColor=this.jvxlColorEncodingRead.endsWith("2");a=this.getData(a,"jvxlColorData");this.jvxlColorDataRead=this.jvxlColorEncodingRead.equals("none")?a:J.jvxl.data.JvxlCoder.jvxlDecompressString(a);this.jvxlDataIsColorMapped=
(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&0<this.jvxlColorDataRead.length;this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1));this.getVertexColorData()});e(d,"getData",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data");0==c.length&&(c=this.xr.getXmlData(b,a,!1,!1));return c},"~S,~S");d.getEncoding=e(d,"getEncoding",function(a){if(0<J.jvxl.readers.XmlReader.getXmlAttrib(a,"len").length)return"";
a=J.jvxl.readers.XmlReader.getXmlAttrib(a,"encoding");return 0==a.length?"none":a},"~S");e(d,"jvxlDecodeVertexData",function(a,b){var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));b||JU.Logger.info("Reading "+c+" vertices");var d=3*c,e=b?Array(c):null,f,h=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data"),j=J.jvxl.readers.JvxlXmlReader.getEncoding(a);if("none".equals(j)){0==h.length&&(h=this.xr.getXmlData("jvxlVertexData",a,!1,!1));d=JU.PT.parseFloatArray(h);d[0]!=3*c&&JU.Logger.info("JvxlXmlReader: vertexData count="+
w(d[0])+"; expected "+3*c);h=0;for(j=1;h<c;h++){var k=JU.P3.new3(d[j++],d[j++],d[j++]);b?e[h]=k:this.addVertexCopy(k,0,h,!1)}}else{var l=this.xr.getXmlPoint(a,"min"),n=this.xr.getXmlPoint(a,"max");n.sub(l);var r=this.jvxlData.colorFractionBase,q=this.jvxlData.colorFractionRange,t=J.jvxl.data.JvxlCoder.jvxlDecompressString(h);0==t.length&&(t=this.xr.getXmlData("jvxlVertexData",a,!1,!1));h=0;for(j=-1;h<c;h++)k=new JU.P3,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(t.charAt(++j).charCodeAt(0),
t.charAt(j+d).charCodeAt(0),r,q),k.x=l.x+f*n.x,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(t.charAt(++j).charCodeAt(0),t.charAt(j+d).charCodeAt(0),r,q),k.y=l.y+f*n.y,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(t.charAt(++j).charCodeAt(0),t.charAt(j+d).charCodeAt(0),r,q),k.z=l.z+f*n.z,b?e[h]=k:this.addVertexCopy(k,0,h,!1)}return e},"~S,~B");e(d,"jvxlDecodeTriangleData",function(a,b,c){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));if(!(0>d)){var e=r(1,0),f=null==
c?-1:1,h=0;JU.Logger.info("Reading "+d+" triangles");var j=J.jvxl.readers.JvxlXmlReader.getEncoding(a);a=this.getData(a,"jvxlTriangleData");b=this.getData(b,"jvxlTriangleEdgeData");var k=r(3,0),l=r(1,0),n=null,t=7,q=!"none".equals(j);if(q)a=J.jvxl.data.JvxlCoder.jvxlDecompressString(a),b=J.jvxl.data.JvxlCoder.jvxlDecompressString(b).trim(),j=b.length==d;else{var w=JU.PT.parseIntNext(a,l);(j=0<b.length)?(n=r(1,0),JU.PT.parseIntNext(b,n)):0<w&&JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count="+
w+"; expected "+d)}for(var v=w=0,y=0,D=-1;w<d;){if(q){var C=a.charAt(++D);switch(C.charCodeAt(0)){case 33:C=0;break;case 43:case 46:case 32:case 10:case 13:case 9:case 44:continue;case 45:case 48:case 49:case 50:case 51:case 52:case 53:case 54:case 55:case 56:case 57:l[0]=D;C=JU.PT.parseIntNext(a,l);D=l[0]-1;break;default:C=C.charCodeAt(0)-92}v+=C}else v=JU.PT.parseIntNext(a,l)-1;k[y]=v;if(3==++y){y=0;if(j&&(t=null==n?b.charAt(w).charCodeAt(0)-48:JU.PT.parseIntNext(b,n),0>t||7<t))t=7;0==--f&&(f=JU.PT.parseIntNext(c,
e),C=JU.PT.parseIntNext(c,e),-2147483648==C?f=0:h=C|4278190080);this.addTriangleCheck(k[0],k[1],k[2],t,h,!1,h);w++}}}},"~S,~S,~S");e(d,"jvxlDecodeContourData",function(a,b){var c=new JU.Lst,d=new JU.SB,e=new JU.SB,f=-1;a.vContours=null;if(null!=b){for(;0<=(f=b.indexOf("<jvxlContour",f+1));){var h=new JU.Lst,j=this.xr.getXmlData("jvxlContour",b.substring(f),!0,!1),k=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(j,"value"));d.append(" ").appendF(k);var l=J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(j,
"color")),n=JU.C.getColix(l);e.append(" ").append(JU.Escape.escapeColor(l));var r=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(j,"data")),q=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour",j,!1,!1)),j=q.length();J.shapesurface.IsosurfaceMesh.setContourVector(h,j,q,k,n,l,JU.SB.newS(r));c.addLast(h)}j=c.size();if(0<j){a.vContours=JU.AU.createArrayOfArrayList(j);a.contourColixes=this.params.contourColixes=fa(j,0);a.contourValues=this.params.contoursDiscrete=
t(j,0);for(f=0;f<j;f++)a.vContours[f]=c.get(f),a.contourValues[f]=a.vContours[f].get(2).floatValue(),a.contourColixes[f]=a.vContours[f].get(3)[0];a.contourColors=JU.C.getHexCodes(a.contourColixes);JU.Logger.info("JVXL read: "+j+" discrete contours");JU.Logger.info("JVXL read: contour values: "+d);JU.Logger.info("JVXL read: contour colors: "+e)}}},"J.jvxl.data.JvxlData,~S");j(d,"postProcessVertices",function(){var a=this.params.bsExcluded[1];null!=a&&(null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,
1,null),this.meshData.invalidateVertices(a),null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,4,null),this.meshData=new J.jvxl.data.MeshData),this.updateTriangles())})});L("J.rendersurface");R(["J.render.MeshRenderer"],"J.rendersurface.IsosurfaceRenderer",["JU.V3","JU.C","$.Normix"],function(){var d=N(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;C(this,arguments)},J.rendersurface,"IsosurfaceRenderer",J.render.MeshRenderer);j(d,"render",function(){return this.renderIso()});e(d,"renderIso",function(){this.setGlobals();for(var a=this.isosurface.meshCount;0<=--a;)if(this.mesh=this.imesh=this.isosurface.meshes[a],null==this.imesh.connectedAtoms||this.vwr.ms.at[this.imesh.connectedAtoms[0]].checkVisible())this.hasColorRange=
!1,this.renderMeshSlab()&&(this.renderInfo(),this.isExport&&this.isGhostPass&&(this.exportPass=1,this.renderMeshSlab(),this.exportPass=2));return this.needTranslucent});e(d,"setGlobals",function(){this.needTranslucent=!1;this.antialias=this.g3d.isAntialiased();this.iShowNormals=this.vwr.getBoolean(603979965);this.showNumbers=this.vwr.getBoolean(603979964);this.isosurface=this.shape;this.exportPass=this.isExport?2:0;this.isNavigationMode=this.vwr.getBoolean(603979889);this.showKey=this.vwr.getBoolean(603979866)?
Boolean.TRUE:null;this.isosurface.keyXy=null;this.meshScale=-1;this.globalSlabValue=this.vwr.gdata.slab;this.mySlabValue=this.isNavigationMode?w(this.tm.getNavigationOffset().z):2147483647});e(d,"renderInfo",function(){if(!this.isExport&&this.hasColorRange&&!(null==this.imesh.colorEncoder||Boolean.TRUE!==this.showKey)){this.showKey=Boolean.FALSE;var a=null,b=null,c=null,d=0,e=0;if(this.imesh.showContourLines)if(c=this.imesh.getContours(),null==c){b=this.imesh.jvxlData.contourColixes;if(null==b)return;
d=b.length}else d=c.length,e=1;else a=this.imesh.colorEncoder.getColorSchemeArray(this.imesh.colorEncoder.currentPalette),d=null==a?0:a.length,e=2;if(!(2>d)){var f=this.antialias?2:1,h=this.vwr.getScreenHeight()*f,j=D(D(h/2)/(d-1)),h=3*D(h/4)-j,k=10*f,l=20*f;this.isosurface.keyXy=r(-1,[D(k/f),0,D((k+l)/f),D((h+j)/f),D(j/f)]);for(var n=0;n<d;n++,h-=j){switch(e){case 0:if(!this.g3d.setC(b[n]))return;break;case 1:if(!this.g3d.setC(c[n].get(3)[0]))return;break;case 2:this.vwr.gdata.setColor(a[n])}this.g3d.fillTextRect(k,
h,5,-2147483648,l,j)}this.isosurface.keyXy[1]=D((h+j)/f)}}});e(d,"renderMeshSlab",function(){this.volumeRender=this.imesh.jvxlData.colorDensity&&this.imesh.jvxlData.allowVolumeRender;var a=this.mySlabValue;this.frontOnly=this.mesh.frontOnly||26==this.shapeID;this.isShell=this.mesh.isShell&&26!=this.shapeID;if(!this.isNavigationMode&&(this.meshSlabValue=this.imesh.jvxlData.slabValue,-2147483648!=this.meshSlabValue&&this.imesh.jvxlData.isSlabbable)){for(var b=this.imesh.jvxlData.boundingBox,a=3.4028235E38,
c=1.4E-45,d=b.length;0<=--d;)this.pt2f.setT(b[d]),this.tm.transformPt3f(this.pt2f,this.pt2f),this.pt2f.z<a&&(a=this.pt2f.z),this.pt2f.z>c&&(c=this.pt2f.z);a=Math.round(a+(c-a)*(100-this.meshSlabValue)/100);this.frontOnly=(new Boolean(this.frontOnly&100<=this.meshSlabValue)).valueOf();this.isShell=(new Boolean(this.isShell&100<=this.meshSlabValue)).valueOf()}b=this.vwr.gdata.translucentCoverOnly;this.vwr.gdata.translucentCoverOnly=this.frontOnly||!this.vwr.getBoolean(1111490588);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});j(d,"render2",function(a){if(this.volumeRender)this.renderPoints();else{switch(this.imesh.dataType){case 70:this.renderLonePair(!1);return;case 71:this.renderLonePair(!0);return}this.isBicolorMap=this.imesh.jvxlData.isBicolorMap;this.render2b(a);this.g3d.setC(4)&&
this.imesh.showContourLines&&this.renderContourLines()}},"~B");e(d,"renderLonePair",function(a){this.pt2f.setT(this.vertices[1]);this.tm.transformPt3f(this.pt2f,this.pt2f);var b=w(this.vwr.tm.scaleToScreen(w(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);if(this.pt2f.z>this.pt1f.z&&0>this.pt1f.z-this.pt2f.z+Math.sqrt((this.pt1f.x-this.pt2f.x)*(this.pt1f.x-this.pt2f.x)+(this.pt1f.y-this.pt2f.y)*(this.pt1f.y-
this.pt2f.y)))return;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(w(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)-110);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)-110);this.g3d.fillSphereI(b,this.screens[1])},"~B");e(d,"renderContourLines",
function(){var a=this.imesh.getContours();if(null==a)null!=this.imesh.jvxlData.contourValues&&(this.hasColorRange=!0);else{this.hasColorRange=0==this.mesh.meshColix;for(var b=a.length;0<=--b;){var c=a[b];if(!(6>c.size())){this.colix=0==this.mesh.meshColix?c.get(3)[0]:this.mesh.meshColix;if(!this.g3d.setC(this.colix))break;for(var d=c.size()-1,e=this.getDiameter(),f=6;f<d;f++){var h=c.get(f),j=c.get(++f);if(Float.isNaN(h.x)||Float.isNaN(j.x))break;this.tm.transformPtScrT3(h,this.pt1f);this.tm.transformPtScrT3(j,
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)}}}}});j(d,"renderPoints",function(){try{this.volumeRender&&this.g3d.volumeRender(!0);var a=(this.volumeRender||0==this.mesh.pc)&&this.selectedPolyOnly,b=this.imesh.vertexIncrement,c;0>=this.mesh.diameter?(c=this.vwr.getInt(553648140),this.frontOnly=this.isShell=!1):c=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,f=this.showNumbers?D(this.vwr.getScreenHeight()/2):0;this.showNumbers&&this.vwr.gdata.setFontBold("Monospaced",24);for(var h=!this.imesh.hasGridPoints||0>this.imesh.firstRealVertex?0:this.imesh.firstRealVertex;h<this.vertexCount;h+=b)if(!(null!=this.vertexValues&&Float.isNaN(this.vertexValues[h])||this.frontOnly&&!this.isVisibleNormix(this.normixes[h])||null!=this.imesh.jvxlData.thisSet&&!this.imesh.jvxlData.thisSet.get(this.mesh.vertexSets[h])||
!this.mesh.isColorSolid&&null!=this.mesh.vcs&&!this.setColix(this.mesh.vcs[h])||this.haveBsDisplay&&!this.mesh.bsDisplay.get(h)||a&&!this.bsPolygons.get(h))){this.hasColorRange=!0;if(this.showNumbers&&10<this.screens[h].z&&150>Math.abs(this.screens[h].x-e)&&150>Math.abs(this.screens[h].y-f)){var j=h+(this.mesh.isColorSolid?"":" "+this.mesh.vvs[h]);this.g3d.setC(4);this.g3d.drawStringNoSlab(j,null,this.screens[h].x,this.screens[h].y,this.screens[h].z-30,0)}this.volumeRender?(c=w(this.vwr.tm.scaleToScreen(this.screens[h].z,
d)),1>c&&(c=1),this.g3d.volumeRender4(c,this.screens[h].x,this.screens[h].y,this.screens[h].z)):this.g3d.fillSphereI(c,this.screens[h])}if(3==b){this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(12,!0,0.5):12);for(h=1;h<this.vertexCount;h+=3)this.g3d.fillCylinder(3,D(c/4),this.screens[h],this.screens[h+1]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(21,!0,0.5):21);for(h=1;h<this.vertexCount;h+=3)this.g3d.fillSphereI(c,this.screens[h]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(7,
!0,0.5):7);for(h=2;h<this.vertexCount;h+=3)this.g3d.fillSphereI(c,this.screens[h])}}catch(k){}this.volumeRender&&this.g3d.volumeRender(!1)});j(d,"renderTriangles",function(a,b,c){this.g3d.addRenderer(1073742182);var d=this.mesh.pis;this.colix=this.isGhostPass?this.mesh.slabColix:!a&&0!=this.mesh.meshColix?this.mesh.meshColix:this.mesh.colix;var e=!a&&0!=this.mesh.meshColix?null:this.mesh.vcs;this.isTranslucentInherit&&(this.colix=JU.C.copyColixTranslucency(this.mesh.slabColix,this.mesh.colix));this.g3d.setC(this.colix);
c&&(this.frontOnly&&a&&(this.frontOnly=!1),this.bsPolygonsToExport.clearAll());1==this.exportType&&(this.frontOnly=!1);var f=this.isGhostPass&&!this.isBicolorMap||null==e||this.mesh.isColorSolid,h=this.isGhostPass&&!this.isBicolorMap||null==e||!a&&0!=this.mesh.meshColix,j=this.colix;null!=this.imesh.jvxlData.jvxlPlane&&(!f&&!a&&this.mesh.fillTriangles)&&(f=!0,j=4);var k=f&&null!=this.mesh.pcs;k&&(!a&&this.mesh.fillTriangles)&&(k=!1);var l=this.imesh.jvxlData.contourColixes;this.hasColorRange=!f&&
!this.isBicolorMap;for(var n=this.getDiameter(),r=this.mesh.hasTranslucentVertices,q=this.mesh.pc;0<=--q;){var t=d[q];if(!(null==t||this.selectedPolyOnly&&!this.bsPolygons.get(q))){var v=t[0],w=t[1],y=t[2];if(!(null!=this.imesh.jvxlData.thisSet&&null!=this.mesh.vertexSets&&!this.imesh.jvxlData.thisSet.get(this.mesh.vertexSets[v]))&&(!this.haveBsDisplay||this.mesh.bsDisplay.get(v)&&this.mesh.bsDisplay.get(w)&&this.mesh.bsDisplay.get(y))){var C=this.normixes[v],D=this.normixes[w],L=this.normixes[y],
N=this.frontOnly||this.isShell?this.checkFront(C,D,L):7;if(!(a&&0==N)){var E,M,G;if(f){if(k&&q<this.mesh.pcs.length){E=this.mesh.pcs[q];if(0==E)continue;j=E}b&&(j=Math.round(10*Math.random())+5);E=M=G=j}else{E=e[v];M=e[w];G=e[y];if(r){var R=(this.g3d.setC(E)?1:0)+(this.g3d.setC(M)?2:0);if(0==R||3!=R&&!this.g3d.setC(G))continue}if(this.isBicolorMap){if(E!=M||M!=G)continue;this.isGhostPass&&(E=M=G=JU.C.copyColixTranslucency(this.mesh.slabColix,E))}}if(a)c?this.bsPolygonsToExport.set(q):(w==y?(this.setColix(E),
v==w?this.g3d.fillSphereI(n,this.screens[v]):this.g3d.fillCylinder(3,n,this.screens[v],this.screens[w])):this.mesh.colorsExplicit?(this.vwr.gdata.setColor(t[4]),E=JU.C.copyColixTranslucency(this.mesh.colix,2047),this.g3d.setC(E),this.g3d.fillTriangle3CN(this.screens[v],E,C,this.screens[w],E,D,this.screens[y],E,L)):(this.isTranslucentInherit&&null!=e&&(E=JU.C.copyColixTranslucency(this.mesh.slabColix,e[v]),M=JU.C.copyColixTranslucency(this.mesh.slabColix,e[w]),G=JU.C.copyColixTranslucency(this.mesh.slabColix,
e[y])),this.g3d.fillTriangle3CN(this.screens[v],E,C,this.screens[w],M,D,this.screens[y],G,L)),this.iShowNormals&&this.renderNormals());else if(N&=t[3],0!=N){b&&(N=7);this.pt1i.setT(this.screens[v]);this.pt2i.setT(this.screens[w]);this.pt3i.setT(this.screens[y]);this.pt1i.z-=2;this.pt2i.z-=2;this.pt3i.z-=2;if(!h)if(k)this.g3d.setC(this.mesh.fillTriangles?4:l[t[4]%l.length]);else{this.drawTriangle(this.pt1i,E,this.pt2i,M,this.pt3i,G,N,n);continue}this.drawTriangle(this.pt1i,j,this.pt2i,j,this.pt3i,
j,N,n)}}}}}c&&this.exportSurface(f?j:0)},"~B,~B,~B");e(d,"getDiameter",function(){var a;0>=this.mesh.diameter?(a=0>this.meshScale?this.meshScale=this.vwr.getInt(553648149):this.meshScale,this.antialias&&(a*=2)):a=D(this.vwr.getScreenDim()/100);1>a&&(a=1);return a});e(d,"renderNormals",function(){if(this.g3d.setC(JU.C.copyColixTranslucency(this.mesh.colix,8))){this.vwr.gdata.setFontBold("Monospaced",24);for(var a=JU.Normix.getVertexVectors(),b=this.vertexCount;0<=--b;)if(!(null!=this.vertexValues&&
Float.isNaN(this.vertexValues[b]))){this.pt1f.setT(this.vertices[b]);var c=this.mesh.normixes[b];0<=c&&(this.pt2f.scaleAdd2(0.3,a[c],this.pt1f),this.tm.transformPtScrT3(this.pt2f,this.pt2f),this.pt1f.set(this.screens[b].x,this.screens[b].y,this.screens[b].z),this.g3d.drawLineAB(this.pt1f,this.pt2f))}}})})})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,
Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,
Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAB,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.cloneFinals);
