(function(Za,Vb,Wb,Xb,C,Yb,E,I,H,K,N,F,Zb,T,$b,U,v,aa,y,wa,$,ba,f,Ea,ha,qa,W,ia,ja,oa,B,ac,bc,$a,cc,dc,ec,fc,ab,bb,gc,hc,ic,jc,kc,lc,mc,nc,oc,pc,qc,rc,sc,tc,uc,vc,wc,xc,e,k){E("JS");H(null,"JS.ScriptExt",["JU.AU"],function(){c$=N(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;K(this,arguments)},JS,"ScriptExt");e(c$,"init",function(a){this.e=a;this.vwr=this.e.vwr;return this},"~O");e(c$,"atomExpressionAt",function(a){return this.e.atomExpressionAt(a)},"~N");e(c$,"checkLength",
function(a){this.e.checkLength(a)},"~N");e(c$,"error",function(a){this.e.error(a)},"~N");e(c$,"invArg",function(){this.e.invArg()});e(c$,"invPO",function(){this.error(23)});e(c$,"getShapeProperty",function(a,b){return this.e.getShapeProperty(a,b)},"~N,~S");e(c$,"paramAsStr",function(a){return this.e.paramAsStr(a)},"~N");e(c$,"centerParameter",function(a){return this.e.centerParameter(a,null)},"~N");e(c$,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");e(c$,"getPoint3f",function(a,
b){return this.e.getPoint3f(a,b,!0)},"~N,~B");e(c$,"intParameter",function(a){return this.e.intParameter(a)},"~N");e(c$,"isFloatParameter",function(a){switch(this.e.tokAt(a)){case 2:case 3:return!0}return!1},"~N");e(c$,"setShapeProperty",function(a,b,c){this.e.setShapeProperty(a,b,c)},"~N,~S,~O");e(c$,"showString",function(a){this.e.showString(a)},"~S");e(c$,"stringParameter",function(a){return this.e.stringParameter(a)},"~N");e(c$,"getToken",function(a){return this.e.getToken(a)},"~N");e(c$,"tokAt",
function(a){return this.e.tokAt(a)},"~N");e(c$,"setShapeId",function(a,b,c){c&&this.invArg();b=this.e.setShapeNameParameter(b).toLowerCase();this.setShapeProperty(a,"thisID",b);return b},"~N,~N,~B");e(c$,"getColorTrans",function(a,b,c,d){c=3.4028235E38;1765808134!=a.theTok&&--b;switch(this.tokAt(b+1)){case 603979967:b++;c=this.isFloatParameter(b+1)?a.getTranslucentLevel(++b):this.vwr.getFloat(570425354);break;case 1073742074:b++,c=0}a.isColorParam(b+1)?d[0]=a.getArgbParam(++b):1073742333==this.tokAt(b+
1)?(d[0]=0,a.iToken=b+1):3.4028235E38==c?this.invArg():d[0]=-2147483648;return c},"JS.ScriptEval,~N,~B,~A");e(c$,"finalizeObject",function(a,b,c,d,h,j,g,e){h&&this.setShapeProperty(a,"set",j);-2147483648!=b&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(b),e);3.4028235E38!=c&&this.e.setShapeTranslucency(a,"","translucent",c,e);0!=d&&this.setShapeProperty(a,"scale",Integer.$valueOf(d));0<g&&(this.e.setMeshDisplayProperty(a,g,0)||this.invArg())},"~N,~N,~N,~N,~B,~O,~N,JU.BS");e(c$,"getIntArray2",
function(a){a=this.e.getToken(a).getList();for(var b=JU.AU.newInt2(a.size()),c=b.length;0<=--c;){var d=a.get(c).getList();null==d&&this.invArg();b[c]=v(d.size(),0);for(var h=b[c].length;0<=--h;)b[c][h]=d.get(h).intValue}return b},"~N");e(c$,"getAllPoints",function(a){var b=null,c=null;try{switch(this.e.tokAt(a)){case 7:b=this.e.getPointArray(a,-1,!1);break;case 12290:case 10:case 1073742325:c=this.atomExpressionAt(a)}if(null==b){null==c&&(c=this.vwr.getAllAtoms());var b=Array(c.cardinality()),d=c.nextSetBit(0);
for(a=0;0<=d;d=c.nextSetBit(d+1))b[a++]=this.vwr.ms.at[d]}}catch(h){if(!U(h,Exception))throw h;}3>b.length&&this.invArg();return b},"~N")});E("JS");H(["JS.ScriptExt"],"JS.IsoExt","java.lang.Boolean $.Float $.Short JU.AU $.BS $.Lst $.M4 $.P3 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.c.VDW JS.SV $.ScriptEval $.ScriptInterruption $.T JU.BSUtil $.BoxInfo $.C $.Escape $.Logger $.Parser $.TempArray $.Triangulator".split(" "),function(){c$=wa(JS,"IsoExt",JS.ScriptExt);T(c$,function(){ba(this,
JS.IsoExt,[])});k(c$,"dispatch",function(a,b,c){this.chk=this.e.chk;this.slen=this.e.slen;this.st=c;switch(a){case 23:this.cgo();break;case 25:this.contact();break;case 17:this.dipole();break;case 22:this.draw();break;case 24:case 30:case 29:this.isosurface(a);break;case 26:this.lcaoCartoon();break;case 27:case 28:this.mo(b,a)}return null},"~N,~B,~A");e(c$,"dipole",function(){var a=this.e,b=null,c=null,d=!1,h=!1,j=!1,g=!1,e=null;a.sm.loadShape(17);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(17)))if(this.setShapeProperty(17,
"init",null),1==this.slen)this.setShapeProperty(17,"thisID",null);else{for(var m=1;m<this.slen;++m){c=b=null;switch(this.getToken(m).tok){case 1073742327:b="all";g=!0;break;case 1073742335:b="on";break;case 1073742334:b="off";break;case 12291:b="delete";break;case 2:case 3:b="value";c=Float.$valueOf(this.floatParameter(m));break;case 10:10==this.tokAt(m+1)?this.setShapeProperty(17,"startSet",this.atomExpressionAt(m++)):b="atomBitset";case 1073742325:null==b&&(b=d||h?"endSet":"startSet");c=e=this.atomExpressionAt(m);
m=a.iToken;0==this.tokAt(m+1)&&"startSet"===b&&(b="atomBitset");g=d=!0;break;case 1073742332:case 8:c=this.getPoint3f(m,!0);m=a.iToken;b=d||h?"endCoord":"startCoord";h=!0;break;case 1677721602:b="bonds";g=!0;break;case 4102:g=!0;b="calculate";a.isAtomExpression(m+1)&&(c=e=this.atomExpressionAt(++m),m=a.iToken);break;case 1073741974:this.setShapeId(17,++m,j);m=a.iToken;break;case 1275069442:b="cross";c=Boolean.TRUE;break;case 1073742040:b="cross";c=Boolean.FALSE;break;case 1073742066:this.isFloatParameter(m+
1)?(c=this.floatParameter(++m),2==a.theTok?(b="offsetPercent",c=Integer.$valueOf(F(c))):(b="offset",c=Float.$valueOf(c))):(b="offsetPt",c=this.centerParameter(++m),m=a.iToken);break;case 1073742068:b="offsetSide";c=Float.$valueOf(this.floatParameter(++m));break;case 1073742188:b="value";c=Float.$valueOf(this.floatParameter(++m));break;case 1073742196:b="width";c=Float.$valueOf(this.floatParameter(++m));break;default:if(268435633==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(17,m,j);
m=a.iToken;break}this.invArg()}j=12291!=a.theTok&&4102!=a.theTok;g&&(this.chk||a.getPartialCharges(e),g=!1);null!=b&&this.setShapeProperty(17,b,c)}(h||d)&&this.setShapeProperty(17,"set",null)}});e(c$,"draw",function(){var a=this.e;a.sm.loadShape(22);switch(this.tokAt(1)){case 1073742001:if(this.listIsosurface(22))return;break;case 136314895:case 134221850:case 4138:this.e.getCmdExt().dispatch(4133,!1,this.st);return}for(var b=!1,c=!1,d=!1,h=!1,j=!1,g,e=0,m=3.4028235E38,p=v(-1,[-2147483648]),f=0,q=
"",r=0,w=null,u=this.initIsosurface(22),M=null!=u,k=M&&null==this.getShapeProperty(22,"ID"),y=null,Fa=0,pa=-1,R=null,s=a.iToken;s<this.slen;++s){var G=null,z=null;g=this.getToken(s).tok;switch(g){case 134217762:f=a.isArrayParameter(++s)?a.getPointArray(s,-1,!1):null;null!=f&&(s=a.iToken+1,12289==this.tokAt(s)&&(w=a.centerParameter(++s,null),s=a.iToken+1));switch(this.tokAt(s)){case 1073742138:c="";break;case 1111490563:c="Cs";break;case 1073742330:f=B(-1,[a.objectNameParameter(++s),null]);if(this.chk)return;
this.vwr.shm.getShapePropertyData(21,"points",f);f=f[1];null==f&&this.invArg();c="";break;case 1275203608:c=":poly";break;case 1073742152:null==w&&(w=new JU.P3);c=this.vwr.ms.generateCrystalClass(this.vwr.bsA().nextSetBit(0),JU.P3.new3(NaN,NaN,NaN));null!=f&&this.invArg();f=Array(c.size());for(g=c.size();0<=--g;)f[g]=c.get(g);s++;c="";break;default:c=a.optParameterAsString(s)}d=1;h=0;0<c.length&&(++s,this.isFloatParameter(s+1)&&(h=this.intParameter(s++)));1073742138==this.tokAt(s)&&(d=this.floatParameter(++s));
this.chk||a.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),c,h,d,f,w,null==u?"":u));return;case 1814695966:case 1678381065:if(this.chk)break;1678381065==g&&1073741864==this.tokAt(s+1)&&(g=1814695966);1814695966==g&&(a.isArrayParameter(s+1)?(s=a.getPointArray(s+1,-1,!1),R=this.vwr.getSymTemp().getUnitCell(s,!1,null),s=a.iToken):1073741864==this.tokAt(s+1)?(s++,R=this.vwr.getSymTemp().getUnitCell(this.vwr.getOrientationText(1814695966,"array",null),!1,null)):R=this.vwr.getCurrentUnitCell(),
null==R&&this.invArg());b=this.getPlaneIntersection(g,null,R,f/100,0);f=0;G="polygon";z=b;b=!0;break;case 4106:y=v(4,0);Fa=4;b=a.floatParameterSet(++s,4,4);s=a.iToken;for(g=0;4>g;g++)y[g]=F(b[g]);b=!0;break;case 1677721602:case 1140850689:if(null==y||Fa>(1228931587==a.theTok?2:3))Fa=0,y=v(-1,[-1,-1,-1,-1]);y[Fa++]=this.atomExpressionAt(++s).nextSetBit(0);s=a.iToken;y[Fa++]=1677721602==a.theTok?this.atomExpressionAt(++s).nextSetBit(0):-1;s=a.iToken;b=!0;break;case 554176565:switch(this.getToken(++s).tok){case 1073742330:G=
"slab";z=a.objectNameParameter(++s);s=a.iToken;b=!0;break;default:this.invArg()}break;case 134217763:switch(this.getToken(s+1).tok){case 1814695966:case 1678381065:e=a.theTok;h=!0;continue;case 1073742330:G="intersect";z=a.objectNameParameter(++s);s=a.iToken;b=h=!0;break;default:this.invArg()}break;case 1275203608:case 134217751:case 1073742106:g=a.theTok;var C=134217751==g,G="polygon",b=!0,z=new JU.Lst,E=0,M=0,I=null,K=null,P=null;if(a.isArrayParameter(++s)){I=a.getPointArray(s,-1,!0);if(0<I.length&&
null==I[0]){1275203608==g?E=this.getIntArray2(s):(E=JU.AU.newInt2(1),E[0]=a.expandFloatArray(a.floatParameterSet(s,-1,2147483647),-1));I=this.getAllPoints(this.e.iToken+1);try{P=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulateFaces(E,I,null)}catch(N){this.invArg()}}E=I.length}1275203608==g&&(E=I.length);if(null==I){E=Math.max(0,this.intParameter(s));I=Array(E);for(g=0;g<E;g++)I[g]=this.centerParameter(++a.iToken)}s=a.iToken;switch(this.tokAt(s+1)){case 11:case 12:K=
JS.SV.newT(this.getToken(++s)).toArray().getList();M=K.size();break;case 7:K=this.getToken(++s).getList();M=K.size();break;case 2:M=this.intParameter(++s);0>M&&(C=!0);break;default:null==P&&(!C&&!this.chk)&&(P=J.api.Interface.getInterface("JU.MeshCapper",this.vwr,"script").set(null).triangulatePolygon(I,-1))}if(null==P&&!C){P=JU.AU.newInt2(M);for(g=0;g<M;g++)C=null==K?a.floatParameterSet(++a.iToken,3,4):JS.SV.flistValue(K.get(g),0),(3>C.length||4<C.length)&&this.invArg(),P[g]=v(-1,[F(C[0]),F(C[1]),
F(C[2]),3==C.length?7:F(C[3])])}0<E?(z.addLast(I),z.addLast(P)):z=null;s=a.iToken;break;case 1073742152:case 1296041986:c=null;d=2147483647;j=h=null;if(1296041986==g)switch(d=0,this.tokAt(++s)){case 4:c=this.stringParameter(s);break;case 12:c=JS.SV.sValue(this.getToken(s));break;default:a.isCenterParameter(s)||(d=this.intParameter(s++));e=B(-1,[null,this.vwr.getFrameAtoms()]);a.isCenterParameter(s)&&(w=a.centerParameter(s,e));a.isCenterParameter(a.iToken+1)&&(h=a.centerParameter(++a.iToken,e));if(this.chk)return;
s=a.iToken}null==w&&s+1<this.slen&&(w=this.centerParameter(++s),j=a.isAtomExpression(s)?this.atomExpressionAt(s):null,s=a.iToken);s=null!=h&&2==this.tokAt(s+1)?a.getToken(++s).intValue:-1;a.checkLast(a.iToken);this.chk||(e="",null==j&&0<=this.vwr.am.cmi&&(j=this.vwr.getModelUndeletedAtomsBitSet(this.vwr.am.cmi)),null!=j&&(e=this.vwr.getSymTemp().getSymmetryInfoAtom(this.vwr.ms,j.nextSetBit(0),c,d,w,h,u,135176,f/100,s)),a.runScript(0<e.length?e:'draw ID "sym_'+u+'*" delete'));return;case 4115:j=!0;
continue;case 1073742332:case 9:case 8:if(9==a.theTok||!a.isPoint3f(s)){z=a.getPoint4f(s);if(j){a.checkLast(a.iToken);this.chk||a.runScript(JU.Escape.drawQuat(JU.Quat.newP4(z),null==u?"frame":u," "+q,null==w?new JU.P3:w,f/100));return}G="planedef"}else z=w=this.getPoint3f(s,!0),G="coord";s=a.iToken;b=!0;break;case 134219265:case 134217750:if(!b&&!h&&0==e){134219265==a.theTok?(b=!0,a.hklParameter(++s),s=a.iToken,G="coords",g=new JU.Lst,g.addLast(JU.P3.newP(a.pt1)),g.addLast(JU.P3.newP(a.pt2)),g.addLast(JU.P3.newP(a.pt3)),
z=g):(G="plane",pa=s+1);break}g=134217750==a.theTok?a.planeParameter(s):a.hklParameter(++s);s=a.iToken;if(0==e)z=g,G="planedef";else{if(this.chk)break;b=this.getPlaneIntersection(e,g,R,f/100,0);f=0;G="polygon";z=b}b=!0;break;case 1073742E3:G="lineData";z=a.floatParameterSet(++s,0,2147483647);s=a.iToken;b=!0;break;case 12290:case 10:case 1073742325:G="atomSet";z=this.atomExpressionAt(s);j&&(w=this.centerParameter(s));s=a.iToken;b=!0;break;case 7:b=!0;G=pa==s?"coords":"modelBasedPoints";z=a.theToken.value;
break;case 1073742195:case 268435504:break;case 268435520:z=a.xypParameter(s);if(null!=z){s=a.iToken;G="coord";b=!0;break}d&&this.invArg();d=!0;break;case 268435521:d||this.invArg();d=!1;break;case 1140850693:G="reverse";break;case 4:z=this.stringParameter(s);G="title";break;case 135198:G="vector";break;case 1140850691:z=Float.$valueOf(this.floatParameter(++s));G="length";break;case 3:z=Float.$valueOf(this.floatParameter(s));G="length";break;case 1094713359:G="modelIndex";z=Integer.$valueOf(this.intParameter(++s));
break;case 2:d?(G="modelIndex",z=Integer.$valueOf(this.intParameter(s))):f=this.intParameter(s);break;case 1073742138:f=Math.round(this.floatParameter(++s)*(2==this.getToken(s).tok?1:100));continue;case 1073741974:u=this.setShapeId(22,++s,M);k=null==this.getShapeProperty(22,"ID");s=a.iToken;break;case 1073742027:G="fixed";z=Boolean.FALSE;break;case 12293:G="fixed";z=Boolean.TRUE;break;case 1073742066:g=this.getPoint3f(++s,!0);s=a.iToken;G="offset";z=g;break;case 1073741906:G="crossed";break;case 1073742196:z=
Float.$valueOf(this.floatParameter(++s));G="width";q=G+" "+z;break;case 1073741998:G="line";z=Boolean.TRUE;pa=s+1;break;case 1073741908:G="curve";pa=s+1;break;case 1073741840:G="arc";pa=s+1;break;case 1073741846:G="arrow";pa=s+1;break;case 1073742194:G="vertices";pa=s+1;break;case 1073741880:G="circle";break;case 1073741912:G="cylinder";break;case 1073742048:G="nohead";break;case 1073741860:G="isbarb";break;case 1073742130:G="rotate45";break;case 1073742092:G="perp";break;case 1665140738:case 1073741917:q=
1665140738==a.theTok;C=this.floatParameter(++s);q&&(C*=2);z=Float.$valueOf(C);G=q||3==this.tokAt(s)?"width":"diameter";q=G+(3==this.tokAt(s)?" "+C:" "+F(C));break;case 1073742330:if(268435520==this.tokAt(s+2)||j){b=w=this.centerParameter(s);s=a.iToken;G="coord";z=b;b=!0;break}z=a.objectNameParameter(++s);G="identifier";b=!0;break;case 1765808134:case 603979967:case 1073742074:M=!0;m=this.getColorTrans(a,s,!1,p);s=a.iToken;continue;default:if(!a.setMeshDisplayProperty(22,0,a.theTok)){if(268435633==
a.theTok||JS.T.tokAttr(a.theTok,1073741824)){u=this.setShapeId(22,s,M);s=a.iToken;break}this.invArg()}0==r&&(r=s);s=a.iToken;continue}M=12291!=a.theTok;b&&(!c&&!j)&&(this.setShapeProperty(22,"points",Integer.$valueOf(f)),c=!0,f=0);b&&k&&this.invArg();null!=G&&this.setShapeProperty(22,G,z)}this.finalizeObject(22,p[0],m,f,b,y,r,null)});e(c$,"mo",function(a,b){var c=this.e,d=2147483647,h=!1,j=null,g=this.vwr.getVisibleFramesBitSet(),e=new JU.Lst,m=!1,f=1073877011==this.tokAt(0),n=1;if(f){var q=this.e.optParameterAsString(1).equals("view");
if(1==this.e.slen||q||this.e.optParameterAsString(1).equals("options")){this.chk||(c=q?"VIEW":this.e.optParameterAsString(2),this.vwr.startNBO(c));return}}if(1094717454==this.tokAt(1)||4115==this.tokAt(1))n=c.modelNumberParameter(2),0>n&&this.invArg(),g.clearAll(),g.set(n),n=3;c.sm.loadShape(b);for(q=g.nextSetBit(0);0<=q;q=g.nextSetBit(q+1)){var r=n;if(1073742001==this.tokAt(r)&&this.listIsosurface(b))break;this.setShapeProperty(b,"init",Integer.$valueOf(q));if(a)break;var w=null,u=this.getShapeProperty(b,
"moNumber").intValue(),M=this.getShapeProperty(b,"moLinearCombination"),k=this.getShapeProperty(b,"moSquareData"),v=null==M?null:this.getShapeProperty(b,"moSquareLinear");0==u&&(u=2147483647);var B=null,C=null,R=!1;switch(this.getToken(r).tok){case 1140850696:if(1073877010==b){this.mo(a,28);return}j=this.paramAsStr(++r).toUpperCase();break;case 1073741875:case 554176565:B=c.theToken.value;C=this.getCapSlabObject(r,!1);break;case 1073741914:v=Boolean.TRUE;M=y(-1,[1]);d=u=0;break;case 2:u=this.intParameter(r);
1073741865==this.tokAt(r+1)&&(m=!0);M=this.moCombo(e);null==M&&0>u&&(M=y(-1,[-100,-u]));R=!0;break;case 268435616:switch(this.tokAt(++r)){case 1073741973:case 1073742008:break;default:this.invArg()}h=!0;case 1073741973:case 1073742008:2147483647==(d=this.moOffset(r))&&this.invArg();u=0;M=this.moCombo(e);R=!0;break;case 1073742037:u=1073742037;m=!1;M=this.moCombo(e);R=!0;break;case 1073742108:u=1073742108;m=!1;M=this.moCombo(e);R=!0;break;case 1765808134:this.setColorOptions(null,r+1,b,2);break;case 134217750:B=
"plane";C=1073742333==this.tokAt(this.e.iToken=++r)?null:c.planeParameter(r);break;case 134217751:this.addShapeProperty(e,"randomSeed",2==this.tokAt(r+2)?Integer.$valueOf(this.intParameter(r+2)):null);B="monteCarloCount";C=Integer.$valueOf(this.intParameter(r+1));break;case 1073742138:B="scale";C=Float.$valueOf(this.floatParameter(r+1));break;case 1073741910:268435617==this.tokAt(r+1)?(B="cutoffPositive",C=Float.$valueOf(this.floatParameter(r+2))):(B="cutoff",C=Float.$valueOf(this.floatParameter(r+
1)));break;case 536870916:B="debug";break;case 1073742054:B="plane";break;case 1073742104:case 1073742122:B="resolution";C=Float.$valueOf(this.floatParameter(r+1));break;case 1073742156:null==M?k=Boolean.TRUE:v=Boolean.TRUE;R=!1;break;case 1073742168:r+1<this.slen&&4==this.tokAt(r+1)&&(B="titleFormat",C=this.paramAsStr(r+1));break;case 1073741824:this.invArg();break;default:if(c.isArrayParameter(r)){M=c.floatParameterSet(r,1,2147483647);1073742156==this.tokAt(c.iToken+1)&&(R=!1,v=Boolean.TRUE,c.iToken++);
break}d=c.iToken;c.setMeshDisplayProperty(b,0,c.theTok)||this.invArg();this.setShapeProperty(b,"setProperties",e);c.setMeshDisplayProperty(b,d,this.tokAt(d));return}null!=B&&this.addShapeProperty(e,B,C);r=2147483647!=u||null!=M;if(this.chk)break;if(null!=j||r)r&&4==this.tokAt(c.iToken+1)&&(w=this.paramAsStr(++c.iToken)),c.setCursorWait(!0),this.setMoData(e,u,M,d,h,q,w,j,m),r&&this.addShapeProperty(e,"finalize",null);R||(this.setShapeProperty(b,"squareLinear",v),this.setShapeProperty(b,"squareData",
k));0<e.size()&&this.setShapeProperty(b,"setProperties",e);r&&!c.tQuiet&&(w="",f?w=this.getShapeProperty(b,"moLabel"):(u=this.getShapeProperty(b,"moNumber").intValue(),w=""+u),this.showString(JS.T.nameOf(this.tokAt(0))+" "+w+" "+(m?"beta ":"")+this.getShapeProperty(b,"message")));e.clear()}},"~B,~N");e(c$,"setNBOType",function(a,b){0>";AO;  ;PNAO;;NAO; ;PNHO;;NHO; ;PNBO;;NBO; ;PNLMO;NLMO;;MO;  ;NO;".indexOf(";"+b+";")&&this.invArg();a.containsKey("nboLabels")||this.error(27);this.chk||J.api.Interface.getInterface("J.adapter.readers.quantum.GenNBOReader",
this.vwr,"script").readNBOCoefficients(a,b,this.vwr)||this.error(27)},"java.util.Map,~S");e(c$,"moCombo",function(a){if(1073742156!=this.tokAt(this.e.iToken+1))return null;this.addShapeProperty(a,"squareLinear",Boolean.TRUE);this.e.iToken++;return y(0,0)},"JU.Lst");e(c$,"moOffset",function(a){var b=1073741973==this.getToken(a).tok?0:1,c=this.tokAt(++a);2==c&&"-"==this.e.st[a].value.charAt(0)?b+=this.intParameter(a):268435617==c?b+=this.intParameter(++a):268435616==c&&(b-=this.intParameter(++a));return b},
"~N");e(c$,"setMoData",function(a,b,c,d,h,j,g,e,m){var f=this.e;0>j&&(j=this.vwr.am.cmi,0>j&&f.errorStr(30,"MO isosurfaces"));j=this.vwr.ms.getInfo(j,"moData");null==j&&this.error(27);this.vwr.checkMenuUpdate();if(null!=e&&(this.setNBOType(j,e),null==c&&2147483647==b))return;var n=null,q,r=0;e=null;if(null==c||2>c.length){null!=c&&1==c.length?d=0:m&&j.containsKey("firstBeta")&&(d=j.get("firstBeta").intValue());n=j.containsKey("lastMoNumber")?j.get("lastMoNumber").intValue():0;r=j.containsKey("lastMoCount")?
j.get("lastMoCount").intValue():1;1073742108==b?b=n-1:1073742037==b&&(b=n+r);n=j.get("mos");r=null==n?0:n.size();0==r&&this.error(25);1==r&&1<b&&this.error(29);if(2147483647!=d){if(!m)if(j.containsKey("HOMO"))b=j.get("HOMO").intValue()+d,d=0;else{b=r;for(m=0;m<r;m++)if(q=n.get(m),null!=(e=q.get("occupancy"))){if(0.5>e.floatValue()){b=m;break}}else if(null!=(e=q.get("energy"))){if(0<e.floatValue()){b=m;break}}else break;null==e&&this.error(28)}b+=d;this.chk||JU.Logger.info("MO "+b)}(1>b||b>r)&&f.errorStr(26,
""+r)}b=Math.abs(b);j.put("lastMoNumber",Integer.$valueOf(b));j.put("lastMoCount",Integer.$valueOf(1));h&&null==c&&(c=y(-1,[-100,b]));if(null!=c&&2>c.length){q=n.get(b-1);if(null==(e=q.get("energy")))c=y(-1,[100,b]);else{f=e.floatValue();d=JU.BS.newN(r);h=0;c=1==c.length&&1==c[0];for(m=0;m<r;m++)if(null!=(e=n.get(m).get("energy")))if(e=e.floatValue(),c?e<=f:e==f)d.set(m+1),h+=2;c=y(h,0);for(e=m=0;m<h;m+=2)c[m]=1,c[m+1]=e=d.nextSetBit(e+1);j.put("lastMoNumber",Integer.$valueOf(d.nextSetBit(0)));j.put("lastMoCount",
Integer.$valueOf(C(h/2)))}this.addShapeProperty(a,"squareLinear",Boolean.TRUE)}this.addShapeProperty(a,"moData",j);null!=g&&this.addShapeProperty(a,"title",g);this.addShapeProperty(a,"molecularOrbital",null!=c?c:Integer.$valueOf(Math.abs(b)));this.addShapeProperty(a,"clear",null)},"JU.Lst,~N,~A,~N,~B,~N,~S,~S,~B");e(c$,"isosurface",function(a){var b=this.e;b.sm.loadShape(a);if(!(1073742001==this.tokAt(1)&&this.listIsosurface(a))){var c=0,d=!1,h=24==a,j=29==a,g=30==a,e=26==a,m=e||12291==this.tokAt(1)||
b.$isStateScript,f=!1,n=!1,q=!1,r=!1,w=!1,u=!1,M=!1,k=!1,E=!1,K=!1,pa=!1,R=!1,s=!1,G=!1,z=!1,N=null,H=null,T=null,aa=-2147483648,P,Y,W,$,ba,xa=NaN,ha=NaN,qa=0,ya=null,ia=2147483647,Q=null,S=null,da=null,t=new JU.SB,O,ja=null,oa=null,wa=!1,X=null,la=0,fa=null,V=this.chk?0:-2147483648;b.setCursorWait(!0);var ua=null!=this.initIsosurface(a),cb=ua&&null==this.getShapeProperty(a,"ID"),Ea=!1,db=!1,Ga=!1,Ha=null,eb=null,fb=null,ka=null,gb=null,Ca=null,Ia=null,D=new JU.Lst,ub=!1;(j||g)&&this.addShapeProperty(D,
"fileType","Pmesh");for(var l=b.iToken;l<this.slen;++l){var A=null,x=null;this.getToken(l);1073741824==b.theTok&&(fa=this.paramAsStr(l));switch(b.theTok){case 1073742148:m=!0;t.append(" silent");A="silent";break;case 603979868:ya=1073742335==this.getToken(++l).tok?Boolean.TRUE:1073742334==b.theTok?Boolean.FALSE:null;null==ya&&this.invArg();continue;case 553648149:ia=this.intParameter(++l);continue;case 4128:A="moveIsosurface";12!=this.tokAt(++l)&&this.invArg();x=this.getToken(l++).value;break;case 1296041986:for(var vb=
this.floatArraySet(l+2,this.intParameter(l+1),16),Ca=Array(vb.length),Z=Ca.length;0<=--Z;)Ca[Z]=JU.M4.newA16(vb[Z]);l=b.iToken;break;case 1088421903:0>V&&(V=Math.min(this.vwr.am.cmi,0));var wb=null==da;null==S&&(S=JU.BSUtil.copy(this.vwr.bsA()));S.and(this.vwr.ms.getAtoms(1296041986,Integer.$valueOf(1)));wb||S.andNot(da);this.addShapeProperty(D,"select",S);wb&&(da=JU.BSUtil.copy(S),JU.BSUtil.invertInPlace(da,this.vwr.ms.ac),z=!0,this.addShapeProperty(D,"ignore",da),t.append(" ignore ").append(JU.Escape.eBS(da)));
t.append(" symmetry");0==la&&this.addShapeProperty(D,"colorRGB",Integer.$valueOf(1296041986));Ca=this.vwr.ms.getSymMatrices(V);break;case 1073742066:A="offset";x=this.centerParameter(++l);l=b.iToken;break;case 528432:A="rotate";x=1073742333==this.tokAt(b.iToken=++l)?null:b.getPoint4f(l);l=b.iToken;break;case 1610612740:A="scale3d";x=Float.$valueOf(this.floatParameter(++l));break;case 1073742090:t.append(" periodic");A="periodic";break;case 1073742078:case 266298:case 134217751:A=b.theToken.value.toString();
t.append(" ").appendO(b.theToken.value);x=this.centerParameter(++l);t.append(" ").append(JU.Escape.eP(x));l=b.iToken;break;case 1678381065:if(0<=b.fullCommand.indexOf("# BBOX="))var xb=JU.PT.split(JU.PT.getQuotedAttribute(b.fullCommand,"# BBOX"),","),X=B(-1,[JU.Escape.uP(xb[0]),JU.Escape.uP(xb[1])]);else b.isCenterParameter(l+1)?(X=B(-1,[this.getPoint3f(l+1,!0),this.getPoint3f(b.iToken+1,!0)]),l=b.iToken):X=this.vwr.ms.getBBoxVertices();t.append(" boundBox "+JU.Escape.eP(X[0])+" "+JU.Escape.eP(X[X.length-
1]));A="boundingBox";x=X;break;case 135188:j=!0;t.append(" pmesh");A="fileType";x="Pmesh";break;case 134217763:S=this.atomExpressionAt(++l);this.chk?Q=new JU.BS:1073742325==this.tokAt(b.iToken+1)||10==this.tokAt(b.iToken+1)?(Q=this.atomExpressionAt(++b.iToken),Q.and(this.vwr.ms.getAtomsWithinRadius(5,S,!1,null))):(Q=this.vwr.ms.getAtomsWithinRadius(5,S,!0,null),Q.andNot(this.vwr.ms.getAtoms(1094713360,S)));Q.andNot(S);t.append(" intersection ").append(JU.Escape.eBS(S)).append(" ").append(JU.Escape.eBS(Q));
l=b.iToken;if(134320141==this.tokAt(l+1)){l++;var Ja=this.getToken(++l).value;t.append(" function ").append(JU.PT.esc(Ja));this.chk||this.addShapeProperty(D,"func",Ja.equals("a+b")||Ja.equals("a-b")?Ja:this.createFunction("__iso__","a,b",Ja))}else G=!0;A="intersection";x=B(-1,[S,Q]);break;case 1610625028:case 134217759:if(d=1610625028==b.theTok){t.append(" display");var c=l,ra=this.tokAt(l+1);if(0==ra)continue;l++;this.addShapeProperty(D,"token",Integer.$valueOf(1073742335));if(10==ra||1073742327==
ra){A="bsDisplay";1073742327==ra?t.append(" all"):(x=this.st[l].value,t.append(" ").append(JU.Escape.eBS(x)));b.checkLast(l);break}else 134217759!=ra&&(b.iToken=l,this.invArg())}else qa=l;var Sa,za=null,Q=null,Ta=Array(1);1073742325==this.tokAt(l+1)?(Sa=this.floatParameter(l+3),b.isPoint3f(l+4)?(za=b.centerParameter(l+4,null),b.iToken+=2):b.isPoint3f(l+5)?(za=b.centerParameter(l+5,null),b.iToken+=2):(Q=b.atomExpression(this.st,l+5,this.slen,!0,!1,Ta,!0),null==Q&&this.invArg())):(Sa=this.floatParameter(++l),
za=b.centerParameter(++l,Ta),Q=I(Ta[0],JU.BS)?Ta[0]:null);d&&b.checkLast(b.iToken);l=b.iToken;0<=b.fullCommand.indexOf("# WITHIN=")&&(Q=JU.BS.unescape(JU.PT.getQuotedAttribute(b.fullCommand,"# WITHIN")));this.chk||(null!=Q&&0<=V&&Q.and(this.vwr.getModelUndeletedAtomsBitSet(V)),null==za&&(za=null==Q?new JU.P3:this.vwr.ms.getAtomSetCenter(Q)),X=this.getWithinDistanceVector(D,Sa,za,Q,d),t.append(" within ").appendF(Sa).append(" ").append(null==Q?JU.Escape.eP(za):JU.Escape.eBS(Q)));continue;case 1073742083:var A=
"parameters",yb=b.floatParameterSet(++l,1,10),l=b.iToken,x=yb;t.append(" parameters ").append(JU.Escape.eAF(yb));break;case 1715472409:case 1073742190:var Ha=b.theToken.value,Za=1073742190==b.theTok,Ka=this.tokAt(l+1);null==gb?(!f&&(!q&&!n)&&(this.addShapeProperty(D,"sasurface",Float.$valueOf(0)),t.append(" vdw"),f=!0),A="property",null==ya&&(ya=JS.T.tokAttr(Ka,1111490560)&&1==this.vwr.getIsosurfacePropertySmoothing(!1)?Boolean.TRUE:Boolean.FALSE),this.addShapeProperty(D,"propertySmoothing",ya),t.append(" isosurfacePropertySmoothing "+
ya),ya===Boolean.TRUE&&(2147483647==ia&&(ia=this.vwr.getIsosurfacePropertySmoothing(!0)),this.addShapeProperty(D,"propertySmoothingPower",Integer.$valueOf(ia)),t.append(" isosurfacePropertySmoothingPower "+ia)),this.vwr.g.rangeSelected&&this.addShapeProperty(D,"rangeSelected",Boolean.TRUE)):A=gb;fa=this.paramAsStr(l);t.append(" ").append(fa);if(0==fa.toLowerCase().indexOf("property_")){H=y(this.vwr.ms.ac,0);if(this.chk)continue;H=this.vwr.getDataObj(fa,null,1);null==H&&this.invArg();this.addShapeProperty(D,
A,H);continue}var La=this.vwr.ms.ac,H=y(La,0);if(Za){var zb=this.paramAsStr(++l);0==zb.length?H=b.floatParameterSet(l,La,La):(H=y(La,0),this.chk||JU.Parser.parseStringInfestedFloatArray(""+b.getParameter(zb,4,!0),null,H));this.chk||t.append(' "" ').append(JU.Escape.eAF(H))}else{this.getToken(++l);if(!this.chk){t.append(" "+b.theToken.value);var $a=this.vwr.ms.at;this.vwr.autoCalculate(Ka,null);if(1765808134!=Ka){O=new JU.P3;for(var hb=La;0<=--hb;)H[hb]=$a[hb].atomPropertyFloat(this.vwr,Ka,O)}}1765808134==
Ka&&(ka="inherit");if(134217759==this.tokAt(l+1)){var Ab=this.floatParameter(l+=2);t.append(" within "+Ab);this.addShapeProperty(D,"propertyDistanceMax",Float.$valueOf(Ab))}}x=H;break;case 1094713359:case 1094717454:f&&this.invArg();V=1094713359==b.theTok?this.intParameter(++l):b.modelNumberParameter(++l);t.append(" modelIndex "+V);if(0>V){A="fixed";x=Boolean.TRUE;break}A="modelIndex";x=Integer.$valueOf(V);break;case 1275082245:var A="select",ib=this.atomExpressionAt(++l),x=ib,l=b.iToken;1073742072==
this.tokAt(l+1)&&(l++,da=JU.BSUtil.copy(ib),JU.BSUtil.invertInPlace(da,this.vwr.ms.ac),this.addShapeProperty(D,"ignore",da),t.append(" ignore ").append(JU.Escape.eBS(da)),z=!0);f||q?t.append(" select "+JU.Escape.eBS(ib)):(S=x,0>V&&0<=S.nextSetBit(0)&&(V=this.vwr.ms.at[S.nextSetBit(0)].mi));break;case 36867:aa=this.intParameter(++l);break;case 12289:A="center";x=this.centerParameter(++l);t.append(" center "+JU.Escape.eP(x));l=b.iToken;break;case 1073742147:case 1765808134:ua=!0;if(1073742147==b.theTok)Ga=
!0,t.append(" sign"),this.addShapeProperty(D,"sign",Boolean.TRUE);else{if(1073741914==this.tokAt(l+1)){l++;A="colorDensity";t.append(" color density");if(this.isFloatParameter(l+1)){var Bb=this.floatParameter(++l);t.append(" "+Bb);x=Float.$valueOf(Bb)}break}if(4==this.getToken(l+1).tok)ka=this.paramAsStr(++l),0<ka.indexOf(" ")&&(Ia=JU.C.getColixArray(ka),null==Ia&&this.error(4));else if(1073742018==b.theTok){l++;t.append(" color mesh");la=b.getArgbParam(++l);this.addShapeProperty(D,"meshcolor",Integer.$valueOf(la));
t.append(" ").append(JU.Escape.escapeColor(la));l=b.iToken;continue}if(603979967==(b.theTok=this.tokAt(l+1))||1073742074==b.theTok){t.append(" color");fb=this.setColorOptions(t,l+1,24,-2);l=b.iToken;continue}switch(this.tokAt(l+1)){case 1073741826:case 1073742114:this.getToken(++l);t.append(" color range");this.addShapeProperty(D,"rangeAll",null);if(1073742327==this.tokAt(l+1)){l++;t.append(" all");continue}var Cb=this.floatParameter(++l),Db=this.floatParameter(++l);this.addShapeProperty(D,"red",
Float.$valueOf(Cb));this.addShapeProperty(D,"blue",Float.$valueOf(Db));t.append(" ").appendF(Cb).append(" ").appendF(Db);continue}if(b.isColorParam(l+1)&&(la=b.getArgbParam(l+1),1073742170==this.tokAt(l+2))){ka=b.getColorRange(l+1);l=b.iToken;break}t.append(" color")}b.isColorParam(l+1)?(la=b.getArgbParam(++l),t.append(" ").append(JU.Escape.escapeColor(la)),l=b.iToken,this.addShapeProperty(D,"colorRGB",Integer.$valueOf(la)),ua=!0,b.isColorParam(l+1)?(la=b.getArgbParam(++l),l=b.iToken,this.addShapeProperty(D,
"colorRGB",Integer.$valueOf(la)),t.append(" ").append(JU.Escape.escapeColor(la)),r=!0):Ga&&this.invPO()):!Ga&&(null==Ia&&null==ka)&&this.invPO();continue;case 134221829:h||this.invArg();pa=!this.chk;continue;case 1228935687:4!=this.tokAt(l+1)&&this.invPO();continue;case 1111492618:case 1648363544:t.append(" ").appendO(b.theToken.value);var Ma=b.encodeRadiusParameter(l,!1,!0);if(null==Ma)return;t.append(" ").appendO(Ma);Float.isNaN(Ma.value)&&(Ma.value=100);x=Ma;A="radius";K=!0;q&&(f=!1);l=b.iToken;
break;case 134217750:n=!0;A="plane";x=b.planeParameter(l);l=b.iToken;t.append(" plane ").append(JU.Escape.eP4(x));break;case 1073742138:A="scale";x=Float.$valueOf(this.floatParameter(++l));t.append(" scale ").appendO(x);break;case 1073742327:ua&&this.invArg();A="thisID";break;case 1112150020:f=!0;++l;x=b.getPoint4f(l);A="ellipsoid";l=b.iToken;t.append(" ellipsoid ").append(JU.Escape.eP4(x));break;case 134219265:n=!0;A="plane";x=b.hklParameter(++l);l=b.iToken;t.append(" plane ").append(JU.Escape.eP4(x));
break;case 135182:var f=!0,Ua=this.paramAsStr(++l);this.addShapeProperty(D,"lcaoType",Ua);t.append(" lcaocartoon ").append(JU.PT.esc(Ua));switch(this.getToken(++l).tok){case 12290:case 10:case 1073742325:A="lcaoCartoon";Q=this.atomExpressionAt(l);l=b.iToken;if(this.chk)continue;var Na=Q.nextSetBit(0);0>Na&&this.error(14);t.append(" ({").appendI(Na).append("})");V=this.vwr.ms.at[Na].mi;this.addShapeProperty(D,"modelIndex",Integer.$valueOf(V));var jb=B(-1,[new JU.V3,new JU.V3,JU.V3.newV(this.vwr.ms.at[Na]),
new JU.V3]);if(!Ua.equalsIgnoreCase("s")&&null==this.vwr.getHybridizationAndAxes(Na,jb[0],jb[1],Ua))return;x=jb;break;default:this.error(14)}break;case 1073877011:N=this.paramAsStr(++l).toUpperCase(),t.append(" nbo ").append(N).append(" ");case 1073877010:null==N&&t.append(" mo ");var Oa=2147483647,Da=2147483647,kb=268435616==this.tokAt(l+1);kb&&l++;var Pa=null;switch(this.tokAt(++l)){case 0:b.bad();break;case 1073741914:t.append("[1] squared ");this.addShapeProperty(D,"squareLinear",Boolean.TRUE);
Pa=y(-1,[1]);Da=Oa=0;l++;break;case 1073741973:case 1073742008:Da=this.moOffset(l);Oa=0;l=b.iToken;t.append((kb?"-":"")+"HOMO ");0<Da&&t.append("+");0!=Da&&t.appendI(Da);break;case 2:Oa=this.intParameter(l);t.appendI(Oa);1073741865==this.tokAt(l+1)&&(k=!0,l++);break;default:b.isArrayParameter(l)&&(Pa=b.floatParameterSet(l,1,2147483647),l=b.iToken)}if(1073742156==this.tokAt(l+1))this.addShapeProperty(D,"squareLinear",Boolean.TRUE),t.append(" squared"),null==Pa&&(Pa=y(0,0));else if(134217751==this.tokAt(l+
1)){++l;var Eb=this.intParameter(++l),Fb=2==this.tokAt(l+1)?this.intParameter(++l):-System.currentTimeMillis()%1E4;this.addShapeProperty(D,"monteCarloCount",Integer.$valueOf(Eb));this.addShapeProperty(D,"randomSeed",Integer.$valueOf(Fb));t.append(" points ").appendI(Eb).appendC(" ").appendI(Fb)}this.setMoData(D,Oa,Pa,Da,kb,V,null,N,k);f=!0;continue;case 1073742036:A="nci";t.append(" "+A);var ra=this.tokAt(l+1),Gb=1228935687!=ra&&4!=ra&&1073742032!=ra,x=Boolean.$valueOf(Gb);Gb&&(f=!0);break;case 1073742016:case 1073742022:var Hb=
1073742016==b.theTok,A=Hb?"mep":"mlp";t.append(" "+A);var Va=null,lb=-1,f=!0;2==this.tokAt(l+1)&&(lb=this.intParameter(++l),t.append(" "+lb),this.addShapeProperty(D,"mepCalcType",Integer.$valueOf(lb)));if(4==this.tokAt(l+1))Va=this.stringParameter(++l),t.append(" /*file*/"+JU.PT.esc(Va));else if(1715472409==this.tokAt(l+1)){gb=A;continue}if(!this.chk)try{H=null==Va&&Hb?this.vwr.getOrCalcPartialCharges(S,da):this.getAtomicPotentials(S,da,Va)}catch(Ib){if(U(Ib,JV.JmolAsyncException))throw new JS.ScriptInterruption(this.e,
"partialcharge",1);throw Ib;}!this.chk&&null==H&&this.error(32);x=H;break;case 1312817669:M=!this.chk;t.append(" volume");break;case 1073741974:this.setShapeId(a,++l,ua);cb=null==this.getShapeProperty(a,"ID");l=b.iToken;break;case 1073741888:603979967==this.tokAt(l+1)&&(Ea=!0,l++);ka=this.paramAsStr(++l).toLowerCase();ka.equals("sets")?t.append(' colorScheme "sets"'):b.isColorParam(l)&&(ka=b.getColorRange(l),l=b.iToken);break;case 1073741828:A="addHydrogens";x=Boolean.TRUE;t.append(" mp.addHydrogens");
break;case 1073741836:A="angstroms";t.append(" angstroms");break;case 1073741837:A="anisotropy";x=this.getPoint3f(++l,!1);t.append(" anisotropy").append(JU.Escape.eP(x));l=b.iToken;break;case 1073741842:u=!this.chk;t.append(" area");break;case 1073741850:case 1073742076:f=!0;r&&!w&&(t.append(' phase "_orb"'),this.addShapeProperty(D,"phase","_orb"));var ca=y(7,0);ca[0]=this.intParameter(++l);ca[1]=this.intParameter(++l);ca[2]=this.intParameter(++l);ca[3]=this.isFloatParameter(l+1)?this.floatParameter(++l):
6;t.append(" atomicOrbital ").appendI(F(ca[0])).append(" ").appendI(F(ca[1])).append(" ").appendI(F(ca[2])).append(" ").appendF(ca[3]);134217751==this.tokAt(l+1)&&(l+=2,ca[4]=this.intParameter(l),ca[5]=3==this.tokAt(l+1)?this.floatParameter(++l):0,ca[6]=2==this.tokAt(l+1)?this.intParameter(++l):-System.currentTimeMillis()%1E4,t.append(" points ").appendI(F(ca[4])).appendC(" ").appendF(ca[5]).appendC(" ").appendI(F(ca[6])));A="hydrogenOrbital";x=ca;break;case 1073741866:t.append(" binary");continue;
case 1073741868:t.append(" blockData");A="blockData";x=Boolean.TRUE;break;case 1073741875:case 554176565:s=!0;A=b.theToken.value;x=this.getCapSlabObject(l,!1);l=b.iToken;break;case 1073741876:h||this.invArg();var E=!0,Jb=this.isFloatParameter(l+1)?this.floatParameter(++l):1.2,mb=this.isFloatParameter(l+1)?this.floatParameter(++l):10;if(this.chk)continue;if(10<mb){b.integerOutOfRange(0,10);return}t.append(" cavity ").appendF(Jb).append(" ").appendF(mb);this.addShapeProperty(D,"envelopeRadius",Float.$valueOf(mb));
this.addShapeProperty(D,"cavityRadius",Float.$valueOf(Jb));A="cavity";break;case 1073741896:case 1073741900:A="contour";t.append(" contour");switch(this.tokAt(l+1)){case 1073741920:x=b.floatParameterSet(l+2,1,2147483647);t.append(" discrete ").append(JU.Escape.eAF(x));l=b.iToken;break;case 1073741981:O=this.getPoint3f(l+2,!1);(0>=O.z||O.y<O.x)&&this.invArg();O.z==F(O.z)&&O.z>O.y-O.x&&(O.z=(O.y-O.x)/O.z);x=O;l=b.iToken;t.append(" increment ").append(JU.Escape.eP(O));break;default:x=Integer.$valueOf(2==
this.tokAt(l+1)?this.intParameter(++l):0),t.append(" ").appendO(x),2==this.tokAt(l+1)&&(this.addShapeProperty(D,A,x),x=Integer.$valueOf(-Math.abs(this.intParameter(++l))),t.append(" ").appendO(x))}break;case 1073741910:t.append(" cutoff ");268435617==this.tokAt(++l)?(A="cutoffPositive",x=Float.$valueOf(ha=this.floatParameter(++l)),t.append("+").appendO(x)):this.isFloatParameter(l)?(A="cutoff",x=Float.$valueOf(ha=this.floatParameter(l)),t.appendO(x)):(A="cutoffRange",x=b.floatParameterSet(l,2,2),this.addShapeProperty(D,
"cutoff",Float.$valueOf(0)),t.append(JU.Escape.eAF(x)),l=b.iToken);break;case 1073741928:A="downsample";x=Integer.$valueOf(this.intParameter(++l));t.append(" downsample ").appendO(x);break;case 1073741931:A="eccentricity";x=b.getPoint4f(++l);t.append(" eccentricity ").append(JU.Escape.eP4(x));l=b.iToken;break;case 1073741932:t.append(" ed");this.setMoData(D,-1,null,0,!1,V,null,null,!1);f=!0;continue;case 536870916:case 1073742041:t.append(" ").appendO(b.theToken.value);A="debug";x=536870916==b.theTok?
Boolean.TRUE:Boolean.FALSE;break;case 12293:t.append(" fixed");A="fixed";x=Boolean.TRUE;break;case 1073741962:t.append(" fullPlane");A="fullPlane";x=Boolean.TRUE;break;case 1073741966:case 1073741968:var ab=1073741968==b.theTok,A=""+b.theToken.value,sa=new JU.Lst,x=sa,R=f=!0;t.append(" ").append(A);var ea=this.paramAsStr(++l);if(ea.equals("=")){t.append(" =");ea=this.paramAsStr(++l);t.append(" ").append(JU.PT.esc(ea));sa.addLast(ea);this.chk||this.addShapeProperty(D,"func",this.createFunction("__iso__",
"x,y,z",ea));break}var nb=JU.PT.getQuotedAttribute(b.fullCommand,"# DATA"+(R?"2":""));null==nb?nb="inline":ea=nb;var Kb=0==ea.indexOf("data2d_"),bb=0==ea.indexOf("data3d_"),db=ea.equals("inline");t.append(" inline");sa.addLast(ea);var Lb=this.getPoint3f(++l,!1);t.append(" ").append(JU.Escape.eP(Lb));sa.addLast(Lb);var ta;$=++b.iToken;sa.addLast(ta=b.getPoint4f($));t.append(" ").append(JU.Escape.eP4(ta));P=F(ta.x);ba=++b.iToken;sa.addLast(ta=b.getPoint4f(ba));t.append(" ").append(JU.Escape.eP4(ta));
Y=F(ta.x);sa.addLast(ta=b.getPoint4f(++b.iToken));t.append(" ").append(JU.Escape.eP4(ta));W=F(ta.x);(0==P||0==Y||0==W)&&this.invArg();if(!this.chk){var ga=null,ma=null;if(ab){db?(P=Math.abs(P),Y=Math.abs(Y),W=Math.abs(W),ma=this.floatArraySetXYZ(++b.iToken,P,Y,W)):ma=bb?this.vwr.getDataObj(ea,null,3):this.vwr.functionXYZ(ea,P,Y,W);P=Math.abs(P);Y=Math.abs(Y);W=Math.abs(W);null==ma&&(b.iToken=$,b.errorStr(53,"xyzdata is null."));if(ma.length!=P||ma[0].length!=Y||ma[0][0].length!=W)b.iToken=$,b.errorStr(53,
"xyzdata["+ma.length+"]["+ma[0].length+"]["+ma[0][0].length+"] is not of size ["+P+"]["+Y+"]["+W+"]");sa.addLast(ma);t.append(" ").append(JU.Escape.e(ma))}else{db?(P=Math.abs(P),Y=Math.abs(Y),ga=this.floatArraySet(++b.iToken,P,Y)):Kb?(ga=this.vwr.getDataObj(ea,null,2),P=null==ga?0:ga.length,Y=3):(ga=this.vwr.functionXY(ea,P,Y),P=Math.abs(P),Y=Math.abs(Y));null==ga&&(b.iToken=$,b.errorStr(53,"fdata is null."));ga.length!=P&&!Kb&&(b.iToken=$,b.errorStr(53,"fdata length is not correct: "+ga.length+" "+
P+"."));for(Z=0;Z<P;Z++)null==ga[Z]&&(b.iToken=ba,b.errorStr(53,"fdata["+Z+"] is null.")),ga[Z].length!=Y&&(b.iToken=ba,b.errorStr(53,"fdata["+Z+"] is not the right length: "+ga[Z].length+" "+Y+"."));sa.addLast(ga);t.append(" ").append(JU.Escape.e(ga))}}l=b.iToken;break;case 1073741970:A="gridPoints";t.append(" gridPoints");break;case 1073741976:A="ignore";x=da=this.atomExpressionAt(++l);t.append(" ignore ").append(JU.Escape.eBS(da));l=b.iToken;break;case 1073741985:A="insideOut";t.append(" insideout");
break;case 1073741988:case 1073741986:case 1073742100:t.append(" ").appendO(b.theToken.value);A="pocket";x=1073742100==b.theTok?Boolean.TRUE:Boolean.FALSE;break;case 1073742002:A="lobe";x=b.getPoint4f(++l);l=b.iToken;t.append(" lobe ").append(JU.Escape.eP4(x));f=!0;break;case 1073742004:case 1073742006:A="lp";x=b.getPoint4f(++l);l=b.iToken;t.append(" lp ").append(JU.Escape.eP4(x));f=!0;break;case 4125:(q||this.slen==l+1)&&this.invArg();q=!0;if((E||K||G)&&!f)f=!0,this.addShapeProperty(D,"bsSolvent",
K||G?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(D,"sasurface",Float.$valueOf(0));0==t.length()?(ja=this.getShapeProperty(24,"plane"),null==ja?null!=this.getShapeProperty(24,"contours")&&this.addShapeProperty(D,"nocontour",null):(this.addShapeProperty(D,"plane",ja),t.append("plane ").append(JU.Escape.eP4(ja)),n=!0,ja=null)):!f&&!n&&this.invArg();t.append("; isosurface map");this.addShapeProperty(D,"map",f?Boolean.TRUE:Boolean.FALSE);break;case 1073742014:A="maxset";x=Integer.$valueOf(this.intParameter(++l));
t.append(" maxSet ").appendO(x);break;case 1073742020:A="minset";x=Integer.$valueOf(this.intParameter(++l));t.append(" minSet ").appendO(x);break;case 1073742112:f=!0;A="rad";x=b.getPoint4f(++l);l=b.iToken;t.append(" radical ").append(JU.Escape.eP4(x));break;case 1073742027:A="fixed";x=Boolean.FALSE;t.append(" modelBased");break;case 1073742028:case 1073742135:case 1612709912:var Ha=b.theToken.value,Wa;1073742028==b.theTok?(A="molecular",t.append(" molecular"),Wa=this.isFloatParameter(l+1)?this.floatParameter(++l):
1.4):(this.addShapeProperty(D,"bsSolvent",b.lookupIdentifierValue("solvent")),A=1073742135==b.theTok?"sasurface":"solvent",t.append(" ").appendO(b.theToken.value),Wa=this.isFloatParameter(l+1)?this.floatParameter(++l):this.vwr.getFloat(570425394));t.append(" ").appendF(Wa);x=Float.$valueOf(Wa);1073741961==this.tokAt(l+1)&&(this.addShapeProperty(D,"doFullMolecular",null),t.append(" full"),l++);f=!0;break;case 1073742032:this.addShapeProperty(D,"fileType","Mrc");t.append(" mrc");continue;case 1073742064:case 1073742062:this.addShapeProperty(D,
"fileType","Obj");t.append(" obj");continue;case 1073742033:this.addShapeProperty(D,"fileType","Msms");t.append(" msms");continue;case 1073742094:f&&this.invArg();A="phase";w=!0;x=4==this.tokAt(l+1)?this.stringParameter(++l):"_orb";t.append(" phase ").append(JU.PT.esc(x));break;case 1073742104:case 1073742122:A="resolution";x=Float.$valueOf(this.floatParameter(++l));t.append(" resolution ").appendO(x);break;case 1073742124:A="reverseColor";x=Boolean.TRUE;t.append(" reversecolor");break;case 1073742127:case 1073742146:A=
"sigma";x=Float.$valueOf(xa=this.floatParameter(++l));t.append(" sigma ").appendO(x);break;case 1112150021:A="geodesic";x=Float.$valueOf(this.floatParameter(++l));t.append(" geosurface ").appendO(x);f=!0;break;case 1073742154:A="sphere";x=Float.$valueOf(this.floatParameter(++l));t.append(" sphere ").appendO(x);f=!0;break;case 1073742156:A="squareData";x=Boolean.TRUE;t.append(" squared");break;case 1073741984:A=!f&&!n&&!q?"readFile":"mapColor";fa=this.stringParameter(++l);null==fa&&this.invArg();j&&
(fa=JU.PT.replaceWithCharacter(fa,"{,}|"," "));b.debugHigh&&JU.Logger.debug("pmesh inline data:\n"+fa);x=this.chk?null:fa;this.addShapeProperty(D,"fileName","");t.append(" INLINE ").append(JU.PT.esc(fa));f=!0;break;case 268435520:case 1073742195:case 7:(null!=eb||cb)&&this.invArg();var Xa=b.listParameter4(l,2,2147483647,!0),l=b.iToken,Qa=C(Xa.size()/2);(0==Qa||2*Qa!=Xa.size())&&this.invArg();var ob=Array(Qa),pb=y(Qa,0);t.append("[");try{for(var Mb=Z=0;Z<Qa;Z++)pb[Z]=Xa.get(Mb++).floatValue(),ob[Z]=
this.e.checkFileExists("ISOSURFACE_"+Z+"_",!1,Xa.get(Mb++),l,!1),t.appendF(pb[Z]),t.append(" /*file*/").append(JU.PT.esc(ob[Z]));t.append("]")}catch(Nb){if(U(Nb,Exception))this.invArg();else throw Nb;}eb=B(-1,[ob,pb]);A=!f&&!n&&!q?"readFile":"mapColor";f=!0;if(this.chk)break;this.addShapeProperty(D,"filesData",eb);break;case 545259556:case 545259557:case 4:var qb=!f&&!n,L,A=qb&&!q?"readFile":"mapColor";if(4==b.theTok)L=this.paramAsStr(l);else{var Ob=this.vwr.getPdbID();null==Ob&&b.errorStr(22,"no PDBID available");
L="*"+(545259557==b.theTok?"*":"")+Ob}var Pb=!1,Qb=!1;L.startsWith("http://eds.bmc.uu.se/eds/dfs/cb/")&&L.endsWith(".omap")&&(L=(0<=L.indexOf("_diff")?"*":"")+"*"+L.substring(32,36));if(L.startsWith("*")||(Qb=L.startsWith("="))&&1<L.length){Qb&&(L=L.$replace("=","*"));var Rb=0<=L.indexOf("/full");0<=L.indexOf("/diff")&&(L="*"+L.substring(0,L.indexOf("/diff")));L.startsWith("**")&&(Float.isNaN(xa)&&this.addShapeProperty(D,"sigma",Float.$valueOf(xa=3)),Ga||(Ga=!0,t.append(" sign"),this.addShapeProperty(D,
"sign",Boolean.TRUE)));Float.isNaN(xa)||this.showString("using cutoff = "+xa+" sigma");L=this.vwr.setLoadFormat(L,Rb||null==X?"_":"-",!1);Pb=!Rb}Pb&&(null==X&&0==qa&&(Ha=L,0>V&&(V=this.vwr.am.cmi),Q=this.vwr.getModelUndeletedAtomsBitSet(V),0<=Q.nextSetBit(0)&&(X=this.getWithinDistanceVector(D,2,null,Q,!1),t.append(" within 2.0 ").append(JU.Escape.eBS(Q)))),null!=X&&0<=L.indexOf("/0,0,0/0,0,0?")&&(L=L.$replace("0,0,0/0,0,0",X[0].x+","+X[0].y+","+X[0].z+"/"+X[X.length-1].x+","+X[X.length-1].y+","+X[X.length-
1].z)),qb&&(ub=!0));qb&&(this.vwr.getP("_fileType").equals("Pdb")&&Float.isNaN(xa)&&Float.isNaN(ha))&&(this.addShapeProperty(D,"sigma",Float.$valueOf(-1)),t.append(" sigma -1.0"));0==L.length&&(0>V&&(V=this.vwr.am.cmi),L=b.getFullPathName(),x=this.vwr.ms.getInfo(V,"jmolSurfaceInfo"));var rb=-1;null==x&&2==this.tokAt(l+1)&&this.addShapeProperty(D,"fileIndex",Integer.$valueOf(rb=this.intParameter(++l)));var Ra=4==this.tokAt(l+1)?this.stringParameter(++l):null,f=!0;if(this.chk)break;var Sb,va=null;null==
x&&(0<=b.fullCommand.indexOf("# FILE0=")?(L=JU.PT.getQuotedAttribute(b.fullCommand,"# FILE0"),1073741848==this.tokAt(l+1)&&(l+=2)):1073741848==this.tokAt(l+1)&&(va=this.vwr.fm.getFilePath(this.stringParameter(b.iToken=l+=2),!1,!1),Sb=this.vwr.getFullPathNameOrError(va),va=Sb[0],""!==this.vwr.fm.getPathForAllFiles()?(L=va,va=null):this.addShapeProperty(D,"localName",va)));null==Ra&&(L=this.e.checkFileExists("ISOSURFACE_"+(q?"MAP_":""),!1,L,l,!1));this.showString("reading isosurface data from "+L);
null!=Ra&&(x=this.vwr.fm.cacheGet(L,!1),this.addShapeProperty(D,"calculationType",Ra));null==x&&(this.addShapeProperty(D,"fileName",L),null!=va&&(L=va),0<=rb&&t.append(" ").appendI(rb));t.append(" /*file*/").append(JU.PT.esc(L));null!=Ra&&t.append(" ").append(JU.PT.esc(Ra));break;case 4106:A="connections";switch(this.tokAt(++l)){case 12290:case 10:case 1073742325:x=v(-1,[this.atomExpressionAt(l).nextSetBit(0)]);break;default:x=v(-1,[F(b.floatParameterSet(l,1,1)[0])])}l=b.iToken;break;case 1094713347:A=
"atomIndex";x=Integer.$valueOf(this.intParameter(++l));break;case 1073741999:A="link";t.append(" link");break;case 1814695966:24!=a&&this.invArg();268435617==this.tokAt(l+1)&&l++;A="extendGrid";x=Float.$valueOf(this.floatParameter(++l));t.append(" unitcell "+x);break;case 1073741994:24!=a&&this.invArg();O=this.getPoint3f(++l,!1);l=b.iToken;if(0>=O.x||0>=O.y||0>=O.z)break;O.x=F(O.x);O.y=F(O.y);O.z=F(O.z);t.append(" lattice ").append(JU.Escape.eP(O));q?(A="mapLattice",x=O):(oa=O,12293==this.tokAt(l+
1)&&(t.append(" fixed"),wa=!0,l++));break;default:1073741824==b.theTok&&(A="thisID",x=fa);if(!b.setMeshDisplayProperty(a,0,b.theTok)){if(JS.T.tokAttr(b.theTok,1073741824)&&!ua){this.setShapeId(a,l,ua);l=b.iToken;break}this.invArg()}0==c&&(c=l);l=this.slen-1}ua=12291!=b.theTok;cb&&f&&this.invArg();null!=A&&this.addShapeProperty(D,A,x)}if(!this.chk){if((E||K)&&!f)f=!0,this.addShapeProperty(D,"bsSolvent",K?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(D,"sasurface",Float.$valueOf(0));
n&&(!f&&!q)&&(this.addShapeProperty(D,"nomap",Float.$valueOf(0)),f=!0);-1<=aa&&this.addShapeProperty(D,"getSurfaceSets",Integer.$valueOf(aa-1));if(null!=Ia)this.addShapeProperty(D,"colorDiscrete",Ia);else if("sets".equals(ka))this.addShapeProperty(D,"setColorScheme",null);else if(null!=ka){var Ya=this.vwr.cm.getColorEncoder(ka);null!=Ya&&(Ya.isTranslucent=Ea,Ya.hi=3.4028235E38,this.addShapeProperty(D,"remapColor",Ya))}if(f&&!e&&0!=t.indexOf(";")){D.add(0,B(-1,["newObject",null]));var Tb=null==S;Tb&&
(S=JU.BSUtil.copy(this.vwr.bsA()));0>V&&(V=this.vwr.am.cmi);S.and(this.vwr.getModelUndeletedAtomsBitSet(V));null!=Ha&&(1<this.vwr.ms.getModelBS(S,!1).cardinality()&&b.errorStr(30,"ISOSURFACE "+Ha),Tb&&(D.add(0,B(-1,["select",S])),0==t.indexOf("; isosurface map")&&(t=(new JU.SB).append("; isosurface map select ").append(JU.Escape.eBS(S)).append(t.substring(16)))))}G&&!s&&(f||this.addShapeProperty(D,"sasurface",Float.$valueOf(0)),q||(this.addShapeProperty(D,"map",Boolean.TRUE),this.addShapeProperty(D,
"select",Q),this.addShapeProperty(D,"sasurface",Float.$valueOf(0))),this.addShapeProperty(D,"slab",this.getCapSlabObject(-100,!1)));var Ub=f&&this.vwr.getBoolean(603979934);Ub&&JU.Logger.startTimer("isosurface");this.setShapeProperty(a,"setProperties",D);Ub&&this.showString(JU.Logger.getTimerMsg("isosurface",0));ub&&(this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,"token",Integer.$valueOf(1073742046)),z=!0,t.append(" mesh nofill frontOnly"))}null!=oa&&(this.setShapeProperty(a,
"lattice",oa),wa&&this.setShapeProperty(a,"fixLattice",Boolean.TRUE));null!=Ca&&this.setShapeProperty(a,"symops",Ca);z&&this.setShapeProperty(a,"token",Integer.$valueOf(1073741960));0<c&&(b.setMeshDisplayProperty(a,c,0)||this.invArg());if(!this.chk){var Aa=null,Ba=null;u&&(Aa=this.getShapeProperty(a,"area"),I(Aa,Float)?this.vwr.setFloatProperty("isosurfaceArea",Aa.floatValue()):this.vwr.g.setUserVariable("isosurfaceArea",JS.SV.getVariableAD(Aa)));M&&(Ba=M?this.getShapeProperty(a,"volume"):null,I(Ba,
Float)?this.vwr.setFloatProperty("isosurfaceVolume",Ba.floatValue()):this.vwr.g.setUserVariable("isosurfaceVolume",JS.SV.getVariableAD(Ba)));if(!e){var na=null;q&&!f?this.setShapeProperty(a,"finalize",t.toString()):f&&(T=t.toString(),this.setShapeProperty(a,"finalize",(0==T.indexOf("; isosurface map")?"":" select "+JU.Escape.eBS(S)+" ")+T),na=this.getShapeProperty(a,"ID"),null!=na&&(!b.tQuiet&&!m)&&(ha=this.getShapeProperty(a,"cutoff").floatValue(),Float.isNaN(ha)&&!Float.isNaN(xa)&&JU.Logger.error("sigma not supported"),
na+=" created "+this.getShapeProperty(a,"message")));var sb,tb;if(u||M)sb=u?"isosurfaceArea = "+(I(Aa,Float)?""+Aa:JU.Escape.eAD(Aa)):null,tb=M?"isosurfaceVolume = "+(I(Ba,Float)?""+Ba:JU.Escape.eAD(Ba)):null,null==na?(u&&this.showString(sb),M&&this.showString(tb)):(u&&(na+="\n"+sb),M&&(na+="\n"+tb));null!=na&&!m&&this.showString(na)}null!=fb&&this.setShapeProperty(a,"translucency",fb);this.setShapeProperty(a,"clear",null);pa&&this.setShapeProperty(a,"cache",null);!m&&(!d&&!s&&12291!=b.theTok)&&this.listIsosurface(a)}}},
"~N");e(c$,"lcaoCartoon",function(){var a=this.e;a.sm.loadShape(26);if(!(1073742001==a.tokAt(1)&&this.listIsosurface(26)))if(this.setShapeProperty(26,"init",a.fullCommand),1==this.slen)this.setShapeProperty(26,"lcaoID",null);else{for(var b=!1,c=null,c=1;c<this.slen;c++){var d=null,h=null;switch(this.getToken(c).tok){case 1073741875:case 554176565:d=a.theToken.value;1073742334==this.tokAt(c+1)&&(a.iToken=c+1);h=this.getCapSlabObject(c,!0);c=a.iToken;break;case 12289:this.isosurface(26);return;case 528432:var j=
h=0,g=0;switch(this.getToken(++c).tok){case 1111492629:h=0.017453292*this.floatParameter(++c);break;case 1111492630:j=0.017453292*this.floatParameter(++c);break;case 1111492631:g=0.017453292*this.floatParameter(++c);break;default:this.invArg()}d="rotationAxis";h=JU.V3.new3(h,j,g);break;case 1073742335:case 1610625028:case 2097192:d="on";break;case 1073742334:case 12294:case 2097194:d="off";break;case 12291:d="delete";break;case 12290:case 10:case 1073742325:d="select";h=this.atomExpressionAt(c);c=
a.iToken;break;case 1765808134:c=this.setColorOptions(null,c+1,26,-2);null!=c&&this.setShapeProperty(26,"settranslucency",c);c=a.iToken;b=!0;continue;case 603979967:case 1073742074:a.setMeshDisplayProperty(26,c,a.theTok);c=a.iToken;b=!0;continue;case 1112152075:case 4:h=this.paramAsStr(c).toLowerCase();h.equals("spacefill")&&(h="cpk");d="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,d="molecular");break;case 1275082245:a.isAtomExpression(c+1)?(d="select",h=this.atomExpressionAt(c+
1),c=a.iToken):(d="selectType",h=this.paramAsStr(++c),h.equals("spacefill")&&(h="cpk"));break;case 1073742138:d="scale";h=Float.$valueOf(this.floatParameter(++c));break;case 1073742004:case 1073742006:d="lonePair";break;case 1073742112:case 1073742111:d="radical";break;case 1073742028:d="molecular";break;case 1073741904:h=this.paramAsStr(++c);d="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,d="molecular");break;case 1073741974:h=a.setShapeNameParameter(++c);c=a.iToken;b&&
this.invArg();d="lcaoID";break;default:if(268435633==a.theTok||JS.T.tokAttr(a.theTok,1073741824))268435633!=a.theTok&&(h=this.paramAsStr(c)),b&&this.invArg(),d="lcaoID"}12291!=a.theTok&&(b=!0);null==d&&this.invArg();this.setShapeProperty(26,d,h)}this.setShapeProperty(26,"clear",null)}});e(c$,"contact",function(){var a=this.e;a.sm.loadShape(25);if(1073742001==this.tokAt(1)&&this.listIsosurface(25))return!1;var b=0;a.iToken=1;for(var c=null!=this.initIsosurface(25),d=c&&null==this.getShapeProperty(25,
"ID"),h=null,j=null,g=null,e=null,m=null,f=!1,n=new JU.SB,q=2147483647,r=134217750,w=0,u=NaN,k=NaN,v=!0,F=null,E=null,H=0,R=!1,s=-2147483648,G=1<a.iToken,z=a.iToken;z<this.slen;++z){switch(g=this.getToken(z).tok){default:G=!0;if(!a.setMeshDisplayProperty(25,0,a.theTok)){268435633!=a.theTok&&!JS.T.tokAttr(a.theTok,1073741824)&&this.invArg();this.setShapeId(25,z,c);z=a.iToken;break}0==b&&(b=z);z=a.iToken;continue;case 1073741974:G=!0;this.setShapeId(25,++z,c);d=null==this.getShapeProperty(25,"ID");
z=a.iToken;break;case 1765808134:switch(this.tokAt(z+1)){case 1073741914:g=0;f=!0;n.append(" color density");z++;break;case 1140850696:g=0,R=!0,n.append(" color type"),z++}if(0==g)break;case 603979967:case 1073742074:G=!0;0==H&&(H=z);a.setMeshDisplayProperty(25,z,a.theTok);z=a.iToken;break;case 554176565:G=!0;E=this.getCapSlabObject(z,!1);this.setShapeProperty(25,"slab",E);z=a.iToken;break;case 1073741914:f=!0;n.append(" density");this.isFloatParameter(z+1)&&(null==m&&(m=y(1,0)),m[0]=-Math.abs(this.floatParameter(++z)),
n.append(" "+-m[0]));break;case 1073742122:c=this.floatParameter(++z);0<c&&(n.append(" resolution ").appendF(c),this.setShapeProperty(25,"resolution",Float.$valueOf(c)));break;case 1094717454:case 1094713359:s=1094713359==a.theTok?this.intParameter(++z):a.modelNumberParameter(++z);n.append(" modelIndex "+s);break;case 134217759:case 1275069443:u=this.floatParameter(++z);n.append(" within ").appendF(u);break;case 268435617:case 2:case 3:e=a.encodeRadiusParameter(z,!1,!1);if(null==e)return!1;n.append(" ").appendO(e);
z=a.iToken;break;case 1073741990:case 1073741989:F=1073741989==g?Boolean.TRUE:Boolean.FALSE;n.append(" ").appendO(a.theToken.value);break;case 1073742020:q=this.intParameter(++z);break;case 1613238294:case 1073741881:case 1648363544:w=g;n.append(" ").appendO(a.theToken.value);break;case 1073742135:this.isFloatParameter(z+1)&&(k=this.floatParameter(++z));case 1073741875:case 1073742036:case 2097180:v=!1;case 1275068932:case 1073741961:case 134217750:case 4106:r=g;n.append(" ").appendO(a.theToken.value);
1073742135==g&&n.append(" ").appendF(k);break;case 1073742083:m=a.floatParameterSet(++z,1,10);z=a.iToken;break;case 12290:case 10:case 1073742325:(d||null!=j)&&this.invArg(),g=JU.BSUtil.copy(this.atomExpressionAt(z)),z=a.iToken,null==h?h=g:j=g,n.append(" ").append(JU.Escape.eBS(g))}c=12291!=a.theTok}!G&&null==h&&this.error(13);if(this.chk)return!1;if(null!=h){1648363544==w&&null==e&&(e=new J.atomdata.RadiusData(null,0,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO));z=null==e?new J.atomdata.RadiusData(null,
0.26,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO):e;j=1073742036==r&&null==j&&null!=F&&F.booleanValue()?h:a.getMathExt().setContactBitSets(h,j,v,u,z,!0);switch(r){case 1073741875:case 1073742135:z=a.lookupIdentifierValue("solvent");h.andNot(z);j.andNot(z);j.andNot(h);break;case 2097180:j.andNot(h);break;case 1073742036:2147483647==q&&(q=100),this.setShapeProperty(25,"minset",Integer.$valueOf(q)),n.append(" minSet ").appendI(q),null==m&&(m=y(-1,[0.5,2]))}null!=F&&(m=null==m?y(2,0):JU.AU.ensureLengthA(m,
2),m[1]=F.booleanValue()?1:2);null!=m&&n.append(" parameters ").append(JU.Escape.eAF(m));this.setShapeProperty(25,"set",B(-1,[Integer.$valueOf(w),Integer.$valueOf(r),Boolean.$valueOf(f),Boolean.$valueOf(R),h,j,e,Float.$valueOf(k),m,Integer.$valueOf(s),n.toString()]));0<H&&a.setMeshDisplayProperty(25,H,0)}0<b&&(a.setMeshDisplayProperty(25,b,0)||this.invArg());null!=E&&null!=h&&this.setShapeProperty(25,"slab",E);if(null!=h&&(1073742036==r||v)){h=this.getShapeProperty(25,"volume");b=1073741961==r;if(JU.AU.isAD(h))for(z=
a=0;z<h.length;z++)a+=b?h[z]:Math.abs(h[z]);else a=h.floatValue();a=Math.round(1E3*a)/1E3;if(f||1275068932!=r)f=this.getShapeProperty(25,"nSets").intValue(),f="Contacts: "+(0>f?C(-f/2):f),0!=a&&(f+=", with "+(b?"approx ":"net ")+"volume "+a+" A^3"),this.showString(f)}return!0});e(c$,"cgo",function(){var a=this.e;a.sm.loadShape(23);if(1073742001==this.tokAt(1)&&this.listIsosurface(23))return!1;for(var b=0,c=null!=this.initIsosurface(23),d=c&&null==this.getShapeProperty(23,"ID"),h=!1,j=-1,g=null,e=
3.4028235E38,f=v(-1,[-2147483648]),p=0,n=a.iToken;n<this.slen;++n){var q=null,j=null;switch(this.getToken(n).tok){case 268435520:case 1073742195:case 7:(null!=g||d)&&this.invArg();g=new JU.Lst;n=v(-1,[n,this.slen]);a.getShapePropertyData(23,"data",B(-1,[this.st,n,g,this.vwr]))||this.invArg();n=n[0];continue;case 1073742138:++n>=this.slen&&this.error(34);switch(this.getToken(n).tok){case 2:p=this.intParameter(n);continue;case 3:p=Math.round(100*this.floatParameter(n));continue}this.error(34);break;
case 12293:q="modelIndex";j=Integer.$valueOf(-1);break;case 1094713359:case 1094717454:j=1094713359==a.theTok?this.intParameter(++n):a.modelNumberParameter(++n);q="modelIndex";j=Integer.$valueOf(j);break;case 1765808134:case 603979967:case 1073742074:e=this.getColorTrans(a,n,!1,f);n=a.iToken;c=!0;continue;case 1073741974:this.setShapeId(23,++n,c);d=null==this.getShapeProperty(23,"ID");n=a.iToken;break;default:if(!a.setMeshDisplayProperty(23,0,a.theTok)){if(268435633==a.theTok||JS.T.tokAttr(a.theTok,
1073741824)){this.setShapeId(23,n,c);n=a.iToken;break}this.invArg()}0==b&&(b=n);n=a.iToken;continue}c=12291!=a.theTok;null!=g&&!h&&(q="points",j=Integer.$valueOf(p),h=!0,p=0);null!=q&&this.setShapeProperty(23,q,j)}this.finalizeObject(23,f[0],e,p,null!=g,g,b,null);return!0});e(c$,"getAtomicPotentials",function(a,b,c){var d=y(this.vwr.ms.ac,0),h=J.api.Interface.getOption("quantum.MlpCalculation",this.vwr,"script");h.set(this.vwr);c=null==c?null:this.vwr.getFileAsString3(c,!1,null);try{h.assignPotentials(this.vwr.ms.at,
d,this.vwr.getSmartsMatch("a",a),this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]",a),b,c)}catch(j){if(!U(j,Exception))throw j;}return d},"JU.BS,JU.BS,~S");e(c$,"getCapSlabObject",function(a,b){if(0>a)return JU.TempArray.getSlabWithinRange(a,0);var c=this.e,d=null,h=554176565==this.tokAt(a),j=this.tokAt(a+1),g=null,e=g=null,f=null,p=null;if(603979967==j)switch(f=this.isFloatParameter(++a+1)?this.floatParameter(++a):0.5,c.isColorParam(a+1)?(f=Short.$valueOf(JU.C.getColixTranslucent3(JU.C.getColix(c.getArgbParam(a+
1)),0!=f,f)),a=c.iToken):f=Short.$valueOf(JU.C.getColixTranslucent3(1,0!=f,f)),j=this.tokAt(a+1)){case 1073742018:case 1073741938:p=Integer.$valueOf(j);j=this.tokAt(++a+1);break;default:p=Integer.$valueOf(1073741938)}switch(j){case 1073742334:return c.iToken=a+1,Integer.$valueOf(-2147483648);case 1073742333:c.iToken=a+1;break;case 1073742330:a++;d=B(-1,[Float.$valueOf(1),this.paramAsStr(++a)]);j=1073742018;break;case 134217759:a++;if(1073742114==this.tokAt(++a))d=this.floatParameter(++a),j=this.floatParameter(++a),
d=B(-1,[Float.$valueOf(d),Float.$valueOf(j)]),j=1073742114;else if(this.isFloatParameter(a)){d=this.floatParameter(a);if(c.isCenterParameter(++a)){var g=Array(1),n=c.centerParameter(a,g);if(this.chk||!I(g[0],JU.BS))g=B(-1,[n]);else for(var n=this.vwr.ms.at,e=g[0],g=Array(e.cardinality()),q=0,r=e.nextSetBit(0);0<=r;r=e.nextSetBit(r+1),q++)g[q]=n[r]}else g=c.getPointArray(a,-1,!1);0==g.length&&(c.iToken=a,this.invArg());d=B(-1,[Float.$valueOf(d),g,e])}else d=c.getPointArray(a,4,!1),j=1678381065;break;
case 1678381065:c.iToken=a+1;d=JU.BoxInfo.toOABC(this.vwr.ms.getBBoxVertices(),null);break;case 1073741872:case 1814695966:c.iToken=a+1;c=this.vwr.getCurrentUnitCell();if(null==c)1814695966==j&&this.invArg();else{g=JU.BoxInfo.toOABC(c.getUnitCellVerticesNoOffset(),c.getCartesianOffset());c=F(c.getUnitCellInfoType(6));d=e=null;switch(c){case 1:d=JU.V3.newVsub(g[2],g[0]),d.scale(1E3);case 2:e=JU.V3.newVsub(g[1],g[0]),e.scale(1E3),g[0].sub(e),g[1].scale(2E3),1==c&&(g[0].sub(d),g[2].scale(2E3))}d=g}break;
case 12290:case 10:case 1073742325:if(d=this.atomExpressionAt(a+1),j=3,!c.isCenterParameter(++c.iToken)){h=!0;break}default:if(!b&&h&&this.isFloatParameter(a+1)){d=this.floatParameter(++a);if(!this.isFloatParameter(a+1))return Integer.$valueOf(F(d));j=this.floatParameter(++a);d=B(-1,[Float.$valueOf(d),Float.$valueOf(j)]);j=1073742114;break}g=c.planeParameter(++a);j=this.isFloatParameter(c.iToken+1)?this.floatParameter(++c.iToken):NaN;Float.isNaN(j)||(g.w-=j);d=g;j=134217750}f=null==p?null:B(-1,[p,
f]);return JU.TempArray.getSlabObjectType(j,d,!h,f)},"~N,~B");e(c$,"setColorOptions",function(a,b,c,d){var h=this.e;this.getToken(b);var j="opaque";if(603979967==h.theTok)if(j="translucent",0>d){var g=this.isFloatParameter(b+1)?this.floatParameter(++b):3.4028235E38;h.setShapeTranslucency(c,null,"translucent",g,null);null!=a&&(a.append(" translucent"),3.4028235E38!=g&&a.append(" ").appendF(g))}else h.setMeshDisplayProperty(c,b,h.theTok);else 1073742074==h.theTok?0<=d&&h.setMeshDisplayProperty(c,b,
h.theTok):h.iToken--;d=Math.abs(d);for(g=0;g<d;g++)if(h.isColorParam(h.iToken+1)){var e=h.getArgbParam(++h.iToken);this.setShapeProperty(c,"colorRGB",Integer.$valueOf(e));null!=a&&a.append(" ").append(JU.Escape.escapeColor(e))}else if(h.iToken<b)this.invArg();else break;return j},"JU.SB,~N,~N,~N");e(c$,"createFunction",function(a,b,c){var d=(new JS.ScriptEval).setViewer(this.vwr);try{d.compileScript(null,"function "+a+"("+b+") { return "+c+"}",!1);var h=new JU.Lst;for(a=0;a<b.length;a+=2)h.addLast(JS.SV.newF(0).setName(b.substring(a,
a+1)));return B(-1,[d.aatoken[0][1].value,h])}catch(j){if(U(j,Exception))return null;throw j;}},"~S,~S,~S");e(c$,"getWithinDistanceVector",function(a,b,c,d,h){var j=new JU.Lst,g=Array(2);if(null==d){var e=JU.P3.new3(b,b,b),f=JU.P3.newP(c);f.sub(e);e.add(c);g[0]=f;g[1]=e;j.addLast(c)}else c=this.vwr.ms.getBoxInfo(d,-Math.abs(2*b)),g[0]=c.getBoundBoxVertices()[0],g[1]=c.getBoundBoxVertices()[7],1==d.cardinality()&&j.addLast(this.vwr.ms.at[d.nextSetBit(0)]);1==j.size()&&!h&&(this.addShapeProperty(a,
"withinDistance",Float.$valueOf(b)),this.addShapeProperty(a,"withinPoint",j.get(0)));this.addShapeProperty(a,h?"displayWithin":"withinPoints",B(-1,[Float.$valueOf(b),g,d,j]));return g},"JU.Lst,~N,JU.P3,JU.BS,~B");e(c$,"addShapeProperty",function(a,b,c){this.chk||a.addLast(B(-1,[b,c]))},"JU.Lst,~S,~O");e(c$,"floatArraySetXYZ",function(a,b,c,d){var h=this.e,j=this.tokAt(a++);1073742195==j&&(j=this.tokAt(a++));(268435520!=j||0>=b)&&this.invArg();for(var g=JU.AU.newFloat3(b,-1),e=0;268435521!=j;)switch(j=
this.getToken(a).tok,j){case 1073742195:case 268435521:continue;case 268435504:a++;break;case 268435520:g[e++]=this.floatArraySet(a,c,d);a=++h.iToken;j=0;e==b&&268435521!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return g},"~N,~N,~N,~N");e(c$,"floatArraySet",function(a,b,c){var d=this.tokAt(a++);1073742195==d&&(d=this.tokAt(a++));268435520!=d&&this.invArg();for(var h=JU.AU.newFloat2(b),j=0;268435521!=d;)switch(d=this.getToken(a).tok,d){case 1073742195:case 268435521:continue;case 268435504:a++;
break;case 268435520:a++;d=y(c,0);h[j++]=d;for(var g=0;g<c;g++)d[g]=this.floatParameter(a++),268435504==this.tokAt(a)&&a++;268435521!=this.tokAt(a++)&&this.invArg();d=0;j==b&&268435521!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return h},"~N,~N,~N");e(c$,"initIsosurface",function(a){var b=this.e;this.setShapeProperty(a,"init",b.fullCommand);b.iToken=0;var c=this.tokAt(1),d=this.tokAt(2);if(12291==c||12291==d&&1073742327==this.tokAt(++b.iToken))return this.setShapeProperty(a,"delete",
null),b.iToken+=2,this.slen>b.iToken&&(this.setShapeProperty(a,"init",b.fullCommand),this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+")),null;b.iToken=1;return!b.setMeshDisplayProperty(a,0,c)&&(this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+"),22!=a&&this.setShapeProperty(a,"title",B(-1,[b.thisCommand])),1073741974!=c&&(268435633==d||268435633==c&&b.setMeshDisplayProperty(a,0,d)))?(a=this.setShapeId(a,1,!1),b.iToken++,a):null},"~N");e(c$,"listIsosurface",function(a){var b=3<this.slen?"0":0==this.tokAt(2)?
"":" "+this.getToken(2).value;this.chk||this.showString(this.getShapeProperty(a,"list"+b));return!0},"~N");e(c$,"getPlaneIntersection",function(a,b,c,d,h){var j=null;switch(a){case 1814695966:if(null==c)return null;j=c.getCanonicalCopy(d,!0);break;case 1678381065:j=JU.BoxInfo.getCanonicalCopy(this.vwr.ms.getBoxInfo().getBoundBoxVertices(),d)}a=this.vwr.getTriangulator();if(null!=b)return a.intersectPlane(b,j,h);b=new JU.Lst;b.addLast(j);b.addLast(JU.Triangulator.fullCubePolygon);return b},"~N,JU.P4,J.api.SymmetryInterface,~N,~N")});
E("JU");H(["JU.TriangleData"],"JU.Triangulator",["JU.AU","$.BS","$.Lst","$.P3"],function(){c$=wa(JU,"Triangulator",JU.TriangleData);e(c$,"intersectPlane",function(a,b,c){for(var d=new JU.Lst,h=Array(12),j=0,g=y(8,0),e=0;8>e;e++)g[e]=a.x*b[e].x+a.y*b[e].y+a.z*b[e].z+a.w,0>g[e]&&(j|=JU.TriangleData.Pwr2[e]);a=JU.TriangleData.triangleTable2[j];if(null==a)return null;for(e=0;24>e;e+=2){var j=JU.TriangleData.edgeVertexes[e],f=JU.TriangleData.edgeVertexes[e+1],p=JU.P3.newP(b[f]);p.sub(b[j]);p.scale(g[j]/
(g[j]-g[f]));p.add(b[j]);h[e>>1]=p}if(0==c){c=new JU.BS;for(e=0;e<a.length;e++)c.set(a[e]),2==e%4&&e++;e=c.cardinality();g=Array(e);d.addLast(g);b=v(12,0);for(e=j=0;e<a.length;e++)f=a[e],c.get(f)&&(c.clear(f),g[j]=h[f],b[f]=j++),2==e%4&&e++;h=JU.AU.newInt2(a.length>>2);d.addLast(h);for(e=0;e<a.length;e++)h[e>>2]=v(-1,[b[a[e++]],b[a[e++]],b[a[e++]],a[e]]);return d}for(e=0;e<a.length;e++)b=h[a[e++]],g=h[a[e++]],j=h[a[e++]],1==(c&1)&&d.addLast(B(-1,[b,g,j])),2==(c&2)&&(f=a[e],1==(f&1)&&d.addLast(B(-1,
[b,g])),2==(f&2)&&d.addLast(B(-1,[g,j])),4==(f&4)&&d.addLast(B(-1,[b,j])));return d},"JU.P4,~A,~N");aa(c$,"fullCubePolygon",B(-1,[v(-1,[0,4,5,3]),v(-1,[5,1,0,3]),v(-1,[1,5,6,2]),v(-1,[6,2,1,3]),v(-1,[2,6,7,2]),v(-1,[7,3,2,3]),v(-1,[3,7,4,2]),v(-1,[4,0,3,2]),v(-1,[6,5,4,0]),v(-1,[4,7,6,0]),v(-1,[0,1,2,0]),v(-1,[2,3,0,0])]))});E("JU");H(["JU.P3i"],"JU.TriangleData",null,function(){c$=wa(JU,"TriangleData");aa(c$,"Pwr2",v(-1,[1,2,4,8,16,32,64,128,256,512,1024,2048]));c$.cubeVertexOffsets=c$.prototype.cubeVertexOffsets=
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"JU.P3i","$.P4"],"J.shapesurface.Isosurface","java.io.BufferedReader java.lang.Boolean $.Float java.util.Hashtable JU.A4 $.AU $.BS $.CU $.Lst $.M3 $.M4 $.P3 $.PT $.Quat $.Rdr $.SB $.V3 J.jvxl.data.JvxlCoder $.JvxlData $.MeshData J.jvxl.readers.SurfaceGenerator J.shape.Mesh J.shapesurface.IsosurfaceMesh JU.C $.Escape $.Logger $.TempArray JV.JC $.Viewer".split(" "),function(){c$=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.jvxlData=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;K(this,arguments)},J.shapesurface,"Isosurface",
J.shape.MeshCollection,J.jvxl.api.MeshDataServer);$(c$,function(){this.isomeshes=Array(4);this.lcaoDir=new JU.P4;this.ptXY=new JU.P3i});k(c$,"allocMesh",function(a,b){var c=this.meshCount++;this.meshes=this.isomeshes=JU.AU.ensureLength(this.isomeshes,2*this.meshCount);this.currentMesh=this.thisMesh=this.isomeshes[c]=null==b?new J.shapesurface.IsosurfaceMesh(this.vwr,a,this.colix,c):b;this.currentMesh.index=c;null!=this.sg&&this.sg.setJvxlData(this.jvxlData=this.thisMesh.jvxlData)},"~S,J.shape.Mesh");
e(c$,"initShape",function(){$a(this,J.shapesurface.Isosurface,"initShape",[]);this.myType="isosurface";this.newSg()});e(c$,"newSg",function(){this.sg=new J.jvxl.readers.SurfaceGenerator(this.vwr,this,null,this.jvxlData=new J.jvxl.data.JvxlData);this.sg.params.showTiming=this.vwr.getBoolean(603979934);this.sg.version="Jmol "+JV.Viewer.getJmolVersion()});e(c$,"clearSg",function(){this.sg=null});k(c$,"setProperty",function(a,b,c){this.setPropI(a,b,c)},"~S,~O,JU.BS");e(c$,"setPropI",function(a,b,c){if("cache"===
a){if(null!=this.currentMesh){var d=this.currentMesh.thisID;c=this.currentMesh.modelIndex;this.vwr.cachePut("cache://isosurface_"+d,this.getPropI("jvxlDataXml",-1).getBytes());this.deleteMeshI(this.currentMesh.index);this.setPropI("init",null,null);this.setPropI("thisID",d,null);this.setPropI("modelIndex",Integer.$valueOf(c),null);this.setPropI("fileName","cache://isosurface_"+d,null);this.setPropI("readFile",null,null);this.setPropI("finalize","isosurface ID "+JU.PT.esc(d)+(0<=c?" modelIndex "+c:
"")+" /*file*/"+JU.PT.esc("cache://isosurface_"+d),null);this.setPropI("clear",null,null)}}else if("delete"===a)this.setPropertySuper(a,b,c),this.explicitID||(this.nLCAO=this.nUnnamed=0),this.currentMesh=this.thisMesh=null;else if("remapInherited"===a)for(d=this.meshCount;0<=--d;)null!=this.isomeshes[d]&&"#inherit;".equals(this.isomeshes[d].colorCommand)&&this.isomeshes[d].remapColors(this.vwr,null,NaN);else if("remapColor"===a)null!=this.thisMesh&&this.thisMesh.remapColors(this.vwr,b,this.translucentLevel);
else if("thisID"===a)null!=this.actualID&&(b=this.actualID),this.setPropertySuper("thisID",b,null);else if("params"===a){if(null!=this.thisMesh){this.ensureMeshSource();this.thisMesh.checkAllocColixes();a=b[0];var h=null;if(null!=a){for(d=0;d<a.length;d++)a[d]=a[d];h=v(c.length(),0);b=0;for(d=c.nextSetBit(0);0<=d;d=c.nextSetBit(d+1),b++)h[d]=b}this.thisMesh.setVertexColixesForAtoms(this.vwr,a,h,c);this.thisMesh.setVertexColorMap()}}else if("atomcolor"===a)null!=this.thisMesh&&(this.ensureMeshSource(),
this.thisMesh.colorVertices(JU.C.getColixO(b),c,!0));else if("pointSize"===a)null!=this.thisMesh&&(this.thisMesh.volumeRenderPointSize=b.floatValue());else if("vertexcolor"===a)null!=this.thisMesh&&this.thisMesh.colorVertices(JU.C.getColixO(b),c,!1);else if("colorPhase"===a){d=b;c=JU.C.getColix(d[0].intValue());b=JU.C.getColix(d[1].intValue());d=null!=this.thisMesh?this.thisMesh.thisID:JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null;h=this.getMeshList(d,!1);for(d=h.size();0<=--d;)this.setColorPhase(h.get(d),
c,b)}else if("color"===a){var j=JU.C.getHexCode(JU.C.getColixO(b));if(null!=this.thisMesh)this.setIsoMeshColor(this.thisMesh,j);else{h=this.getMeshList(JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,!1);for(d=h.size();0<=--d;)this.setIsoMeshColor(h.get(d),j)}this.setPropertySuper(a,b,c)}else if("nocontour"===a)null!=this.thisMesh&&this.thisMesh.deleteContours();else if("fixed"===a)this.isFixed=b.booleanValue(),this.setMeshI();else if("newObject"===a)null!=this.thisMesh&&this.thisMesh.clearType(this.thisMesh.meshType,
!1);else if("moveIsosurface"===a)null!=this.thisMesh&&!this.thisMesh.isModelConnected&&(this.thisMesh.updateCoordinates(b,null),this.thisMesh.altVertices=null);else if("refreshTrajectories"===a){c=b[0].intValue();for(d=this.meshCount;0<=--d;)this.meshes[d].modelIndex==c&&(null!=this.meshes[d].connectedAtoms||this.meshes[d].isModelConnected)&&this.meshes[d].updateCoordinates(b[2],b[1])}else if("modelIndex"===a)this.iHaveModelIndex||(this.modelIndex=b.intValue(),this.isFixed=0>this.modelIndex,this.sg.params.modelIndex=
Math.abs(this.modelIndex));else if("lcaoCartoon"===a||"lonePair"===a||"radical"===a)d=b,this.explicitID||this.setPropertySuper("thisID",null,null),this.sg.setProp("lcaoCartoonCenter",d[2],null)||this.drawLcaoCartoon(d[0],d[1],d[3],"lonePair"===a?2:"radical"===a?1:0);else if(!("select"===a&&this.iHaveBitSets||"ignore"===a&&this.iHaveBitSets))if("meshcolor"===a)d=b.intValue(),this.meshColix=JU.C.getColix(d),null!=this.thisMesh&&(this.thisMesh.meshColix=this.meshColix);else if("offset"===a)d=JU.P3.newP(b),
d.equals(JV.JC.center)&&(d=null),null!=this.thisMesh&&(this.thisMesh.rotateTranslate(null,d,!0),this.thisMesh.altVertices=null);else if("rotate"===a)null!=this.thisMesh&&(this.thisMesh.rotateTranslate(JU.Quat.newP4(b),null,!0),this.thisMesh.altVertices=null);else if("bsDisplay"===a)this.bsDisplay=b;else if("displayWithin"===a)d=b,this.displayWithinDistance2=d[0].floatValue(),this.isDisplayWithinNot=0>this.displayWithinDistance2,this.displayWithinDistance2*=this.displayWithinDistance2,this.displayWithinPoints=
d[3],0==this.displayWithinPoints.size()&&(this.displayWithinPoints=this.vwr.ms.getAtomPointVector(d[2]));else if("finalize"===a)null!=this.thisMesh&&(d=b,null!=d&&!d.startsWith("; isosurface map")&&(this.thisMesh.setDiscreteColixes(this.sg.params.contoursDiscrete,this.sg.params.contourColixes),this.setJvxlInfo()),this.setScriptInfo(d)),this.clearSg();else if("connections"===a)null!=this.currentMesh&&(this.connections=b,0<=this.connections[0]&&this.connections[0]<this.vwr.ms.ac?this.currentMesh.connectedAtoms=
this.connections:this.connections=this.currentMesh.connectedAtoms=null);else if("cutoffRange"===a)this.cutoffRange=b;else if("fixLattice"===a)null!=this.thisMesh&&this.thisMesh.fixLattice();else{if("slab"===a){if(I(b,Integer)){null!=this.thisMesh&&(this.thisMesh.jvxlData.slabValue=b.intValue());return}if(null!=this.thisMesh){switch(b[0].intValue()){case 1073742018:d=b[1];c=this.getMesh(d[1]);if(null==c)return;d[1]=c}this.slabPolygons(b);return}}if("cap"===a&&null!=this.thisMesh&&0!=this.thisMesh.pc)this.thisMesh.getMeshSlicer().slabPolygons(b,
!0),this.thisMesh.initialize(this.thisMesh.lighting,null,null);else{if("map"===a&&(null!=this.sg&&(this.sg.params.isMapped=!0),this.setProperty("squareData",Boolean.FALSE,null),null==this.thisMesh||0==this.thisMesh.vc))return;if("deleteVdw"===a){for(d=this.meshCount;0<=--d;)null!=this.isomeshes[d].bsVdw&&(null==c||c.intersects(this.isomeshes[d].bsVdw))&&this.deleteMeshI(d);this.currentMesh=this.thisMesh=null}else{if("mapColor"===a||"readFile"===a){if(null==b){if(null==this.sg.params.filesData)b=this.getFileReader(this.sg.params.fileName);
else{b=this.sg.params.filesData;h=this.sg.params.filesData[0];j=Array(h.length);for(d=j.length;0<=--d&&null!=b;)if(null==(j[d]=this.getFileReader(h[d])))b=null;null!=b&&(this.sg.params.filesData[0]=j)}if(null==b)return}}else if("atomIndex"===a)this.atomIndex=b.intValue(),null!=this.thisMesh&&(this.thisMesh.atomIndex=this.atomIndex);else if("center"===a)this.center.setT(b);else if("colorRGB"===a)d=b.intValue(),1296041986==d?this.colorType=d:(this.colorType=0,this.defaultColix=JU.C.getColix(d));else if("contour"===
a)this.explicitContours=!0;else if("functionXY"===a)2==this.sg.params.state&&this.setScriptInfo(null);else if("init"===a)this.newSg();else if("getSurfaceSets"===a)null!=this.thisMesh&&(this.thisMesh.jvxlData.thisSet=b.intValue(),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(),I(b,Integer)?(this.moNumber=b.intValue(),this.moLinearCombination=
null):(this.moLinearCombination=b,this.moNumber=0),this.isColorExplicit||(this.isPhaseColored=!0),null==this.sg||!this.sg.params.isMapped)d=this.ms.am[this.currentMesh.modelIndex].mat4,null!=d&&(d=JU.M4.newM4(d),d.invert(),this.setPropI("modelInvRotation",d,null))}else if("phase"===a)this.isPhaseColored=!0;else if("plane"!==a&&"pocket"!==a)if("scale3d"===a)this.scale3d=b.floatValue(),null!=this.thisMesh&&(this.thisMesh.scale3d=this.thisMesh.jvxlData.scale3d=this.scale3d,this.thisMesh.altVertices=
null);else if("title"===a)I(b,String)&&"-".equals(b)&&(b=null),this.setPropertySuper(a,b,c),b=this.title;else if("withinPoints"===a)d=b,this.withinDistance2=d[0].floatValue(),this.isWithinNot=0>this.withinDistance2,this.withinDistance2*=this.withinDistance2,this.withinPoints=d[3],0==this.withinPoints.size()&&(this.withinPoints=this.vwr.ms.getAtomPointVector(d[2]));else if(("nci"===a||"orbital"===a)&&null!=this.sg)this.sg.params.testFlags=this.vwr.getBoolean(603979962)?2:0;if(null!=this.sg&&this.sg.setProp(a,
b,c)){if(this.sg.isValid){"molecularOrbital"===a&&(this.currentMesh.isModelConnected=!0,this.currentMesh.mat4=this.ms.am[this.currentMesh.modelIndex].mat4);return}a="delete"}if("init"===a)this.explicitID=!1,this.scriptAppendix="",d=I(b,String)?b:null,b=null==d?-1:d.indexOf("# ID="),this.actualID=0<=b?JU.PT.getQuotedStringAt(d,b):null,this.setPropertySuper("thisID","+PREVIOUS_MESH+",null),null!=d&&!(this.iHaveBitSets=this.getScriptBitSets(d,null))&&this.sg.setProp("select",c,null),this.initializeIsosurface(),
this.sg.params.modelIndex=this.isFixed?-1:this.modelIndex;else if("clear"===a)this.discardTempData(!0);else if("colorDensity"===a)null!=b&&null!=this.currentMesh&&(this.currentMesh.volumeRenderPointSize=b.floatValue());else if("deleteModelAtoms"===a){a=b[2][0];h=b[2][1];b=b[2][2];for(d=this.meshCount;0<=--d;)c=this.meshes[d],null!=c&&(null!=c.connectedAtoms&&(j=c.connectedAtoms[0],j>=h+b?c.connectedAtoms[0]=j-b:j>=h&&(c.connectedAtoms=null)),c.connectedAtoms=null,c.modelIndex==a?(this.meshCount--,
c===this.currentMesh&&(this.currentMesh=this.thisMesh=null),this.meshes=this.isomeshes=JU.AU.deleteElements(this.meshes,d,1)):c.modelIndex>a&&(c.modelIndex--,c.atomIndex>=h&&(c.atomIndex-=b)))}else this.setPropertySuper(a,b,c)}}}},"~S,~O,JU.BS");e(c$,"getFileReader",function(a){var b=this.vwr.fm.getBufferedReaderOrErrorMessageFromName(a,null,!0,!0);if(I(b,String))return JU.Logger.error("Isosurface: could not open file "+a+" -- "+b),null;if(!I(b,java.io.BufferedReader))try{b=JU.Rdr.getBufferedReader(b,
"ISO-8859-1")}catch(c){if(!U(c,java.io.IOException))throw c;}return b},"~S");e(c$,"setIsoMeshColor",function(a,b){a.jvxlData.baseColor=b;a.isColorSolid=!0;a.pcs=null;a.colorsExplicit=!1;a.colorEncoder=null;a.vertexColorMap=null},"J.shapesurface.IsosurfaceMesh,~S");e(c$,"setColorPhase",function(a,b,c){a.colorPhased=!0;a.colix=a.jvxlData.minColorIndex=b;a.jvxlData.maxColorIndex=c;a.jvxlData.isBicolorMap=!0;a.jvxlData.colorDensity=!1;a.isColorSolid=!1;a.remapColors(this.vwr,null,this.translucentLevel)},
"J.shapesurface.IsosurfaceMesh,~N,~N");e(c$,"ensureMeshSource",function(){var a=null!=this.thisMesh.vertexSource;if(a)for(var b=this.thisMesh.vc;0<=--b;)if(0>this.thisMesh.vertexSource[b]){a=!1;break}if(!a){var a=this.thisMesh.vertexSource,c=this.thisMesh.vcs,b=this.thisMesh.isColorSolid?this.thisMesh.colix:0;this.setProperty("init",null,null);this.setProperty("map",Boolean.FALSE,null);this.setProperty("property",y(this.vwr.ms.ac,0),null);0!=b&&(this.thisMesh.colorCommand="color isosurface "+JU.C.getHexCode(b),
this.setProperty("color",Integer.$valueOf(JU.C.getArgb(b)),null));if(null!=a){for(b=this.thisMesh.vc;0<=--b;)0>a[b]&&(a[b]=this.thisMesh.vertexSource[b]);this.thisMesh.vertexSource=a;this.thisMesh.vcs=c}}});e(c$,"slabPolygons",function(a){this.thisMesh.calculatedVolume=null;this.thisMesh.calculatedArea=null;this.thisMesh.getMeshSlicer().slabPolygons(a,!1);this.thisMesh.reinitializeLightingAndColor(this.vwr)},"~A");e(c$,"setPropertySuper",function(a,b,c){"thisID"===a&&null!=this.currentMesh&&null!=
this.currentMesh.thisID&&this.currentMesh.thisID.equals(b)?this.checkExplicit(b):(this.currentMesh=this.thisMesh,this.setPropMC(a,b,c),this.thisMesh=this.currentMesh,this.jvxlData=null==this.thisMesh?null:this.thisMesh.jvxlData,null!=this.sg&&this.sg.setJvxlData(this.jvxlData))},"~S,~O,JU.BS");k(c$,"getPropertyData",function(a,b){if("keys"===a){var c=I(b[1],JU.Lst)?b[1]:new JU.Lst;b[1]=c;c.addLast("info");c.addLast("data");c.addLast("atoms")}if("colorEncoder"===a)return c=this.getMesh(b[0]),null!=
c&&null!=(b[1]=c.colorEncoder);if("intersectPlane"===a){c=this.getMesh(b[0]);if(null==c||4>b.length)return!1;b[3]=Integer.$valueOf(c.modelIndex);c.getMeshSlicer().getIntersection(0,b[1],null,b[2],null,null,null,!1,!1,134217750,!1);return!0}if("getBoundingBox"===a){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;b[2]=c.jvxlData.boundingBox;if(null!=c.mat4){var d=Array(2);d[0]=JU.P3.newP(c.jvxlData.boundingBox[0]);d[1]=JU.P3.newP(c.jvxlData.boundingBox[1]);var h=new JU.V3;c.mat4.getTranslation(h);
d[0].add(h);d[1].add(h);b[2]=d}return!0}if("unitCell"===a)return c=this.getMesh(b[0]),null!=c&&null!=(b[1]=c.getUnitCell());if("getCenter"===a&&-2147483648==b[1].intValue()){c=b[0];c=this.getMesh(c);if(null==c||null==c.vs)return!1;d=JU.P3.newP(c.jvxlData.boundingBox[0]);d.add(c.jvxlData.boundingBox[1]);d.scale(0.5);null!=c.mat4&&(h=new JU.V3,c.mat4.getTranslation(h),d.add(h));b[2]=d;return!0}return this.getPropDataMC(a,b)},"~S,~A");k(c$,"getProperty",function(a,b){return this.getPropI(a,b)},"~S,~N");
e(c$,"getPropI",function(a,b){var c=this.thisMesh;if(0<=b&&(b>=this.meshCount||null==(c=this.isomeshes[b])))return null;var d=this.getPropMC(a,b);if(null!=d)return d;if("message"===a){c="";if(!this.jvxlData.isValid)return"invalid! (no atoms selected?)";Float.isNaN(this.jvxlData.integration)||(c+="integration "+this.jvxlData.integration);if(24==this.shapeID||27==this.shapeID||28==this.shapeID)c+=" with cutoff="+this.jvxlData.cutoff;if(27==this.shapeID||28==this.shapeID)return c;3.4028235E38!=this.jvxlData.dataMin&&
(c+=" min="+this.jvxlData.dataMin+" max="+this.jvxlData.dataMax);c+="; "+JV.JC.shapeClassBases[this.shapeID].toLowerCase()+" count: "+this.getPropMC("count",b);return c+this.getPropI("dataRangeStr",b)+this.jvxlData.msg}if("dataRange"===a)return this.getDataRange(c);if("dataRangeStr"===a)return c=this.getDataRange(c),null!=c&&3.4028235E38!=c[0]&&c[0]!=c[1]?"\nisosurface full data range "+c[0]+" to "+c[1]+" with color scheme spanning "+c[2]+" to "+c[3]:"";if("moNumber"===a)return Integer.$valueOf(this.moNumber);
if("moLinearCombination"===a)return this.moLinearCombination;if("nSets"===a)return Integer.$valueOf(null==c?0:c.nSets);if("area"===a)return null==c?Float.$valueOf(NaN):this.calculateVolumeOrArea(c,!0);if("volume"===a)return null==c?Float.$valueOf(NaN):this.calculateVolumeOrArea(c,!1);if(null==c)return null;if("cutoff"===a)return Float.$valueOf(this.jvxlData.cutoff);if("minMaxInfo"===a)return y(-1,[this.jvxlData.dataMin,this.jvxlData.dataMax]);if("plane"===a)return this.jvxlData.jvxlPlane;if("contours"===
a)return c.getContours();if("pmesh"===a||"pmeshbin"===a)return c.getPmeshData("pmeshbin"===a);if("jvxlDataXml"===a||"jvxlMeshXml"===a){var h=null;this.jvxlData.slabInfo=null;"jvxlMeshXml"===a||this.jvxlData.vertexDataOnly||null!=c.bsSlabDisplay&&null==c.bsSlabGhost?(h=new J.jvxl.data.MeshData,this.fillMeshData(h,1,c),h.polygonColorData=J.shapesurface.Isosurface.getPolygonColorData(h.pc,h.pcs,h.colorsExplicit?h.pis:null,h.bsSlabDisplay)):null!=c.bsSlabGhost&&(this.jvxlData.slabInfo=c.slabOptions.toString());
d=new JU.SB;this.getMeshCommand(d,c.index);c.setJvxlColorMap(!0);return J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,h,this.title,"",!0,1,d.toString(),null)}if("jvxlFileInfo"===a)return J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);if("command"===a){d=new JU.SB;for(c=this.getMeshList(0>b?this.previousMeshID:c.thisID,!1).size();0<=--c;)this.getMeshCommand(d,c);return d.toString()}return"atoms"===a?c.surfaceAtoms:"colorEncoder"===a?c.colorEncoder:null},"~S,~N");e(c$,"getDataRange",function(a){return null==
a?null:a.getDataRange()},"J.shapesurface.IsosurfaceMesh");e(c$,"calculateVolumeOrArea",function(a,b){if(b){if(null!=a.calculatedArea)return a.calculatedArea}else if(null!=a.calculatedVolume)return a.calculatedVolume;var c=new J.jvxl.data.MeshData;this.fillMeshData(c,1,a);c.nSets=a.nSets;c.vertexSets=a.vertexSets;if(!b&&a.jvxlData.colorDensity)return c=a.jvxlData.voxelVolume,c*=null==a.bsSlabDisplay?a.vc:a.bsSlabDisplay.cardinality(),a.calculatedVolume=Float.$valueOf(c);var d=J.jvxl.data.MeshData.calculateVolumeOrArea(c,
a.jvxlData.thisSet,b,!1);0>=a.nSets&&(a.nSets=-c.nSets);b?a.calculatedArea=d:a.calculatedVolume=d;return d},"J.shapesurface.IsosurfaceMesh,~B");c$.getPolygonColorData=e(c$,"getPolygonColorData",function(a,b,c,d){var h=null!=c;if(null==b&&null==c)return null;for(var j=new JU.SB,g=0,e=0,f=0,p=0,n=!1,q=0;q<a||!0==(n=!0);q++)if(n||null==d||d.get(q))if(n||(h?(p=c[q][4])!=f:b[q]!=e)){0!=g&&j.append(" ").appendI(g).append(" ").appendI(h?f:0==e?0:JU.C.getArgb(e));if(n)break;h?f=p:e=b[q];g=1}else g++;j.append("\n");
return j.toString()},"~N,~A,~A,JU.BS");k(c$,"getShapeState",function(){this.clean();var a=new JU.SB;a.append("\n");for(var b=0;b<this.meshCount;b++)this.getMeshCommand(a,b);return a.toString()});e(c$,"getMeshCommand",function(a,b){var c=this.meshes[b];if(!(null==c||null==c.scriptCommand)){var d=c.scriptCommand;1<this.vwr.ms.mc&&J.shape.Shape.appendCmd(a,"frame "+this.vwr.getModelNumberDotted(c.modelIndex));var d=JU.PT.rep(d,";; isosurface map"," map"),d=JU.PT.rep(d,"; isosurface map"," map"),d=d.$replace("\t",
" "),d=JU.PT.rep(d,";#","; #"),h=d.indexOf("; #");0<=h&&(d=d.substring(0,h));null!=c.connectedAtoms&&(d+=" connect "+JU.Escape.eAI(c.connectedAtoms));d=JU.PT.trim(d,";");null!=c.linkedMesh&&(d+=" LINK");"lcaoCartoon"===this.myType&&0<=c.atomIndex&&(d+=" ATOMINDEX "+c.atomIndex);J.shape.Shape.appendCmd(a,d);h=this.myType+" ID "+JU.PT.esc(c.thisID);0<=c.jvxlData.thisSet&&J.shape.Shape.appendCmd(a,h+" set "+(c.jvxlData.thisSet+1));null!=c.mat4&&!c.isModelConnected&&J.shape.Shape.appendCmd(a,h+" move "+
JU.Escape.matrixToScript(c.mat4));0!=c.scale3d&&J.shape.Shape.appendCmd(a,h+" scale3d "+c.scale3d);-2147483648!=c.jvxlData.slabValue&&J.shape.Shape.appendCmd(a,h+" slab "+c.jvxlData.slabValue);null!=c.slabOptions&&J.shape.Shape.appendCmd(a,c.slabOptions.toString());if("#"!=d.charAt(0)&&(this.allowMesh&&J.shape.Shape.appendCmd(a,c.getState(this.myType)),!c.isColorSolid&&(0==c.colorType&&JU.C.isColixTranslucent(c.colix))&&J.shape.Shape.appendCmd(a,"color "+this.myType+" "+J.shape.Shape.getTranslucentLabel(c.colix)),
null!=c.colorCommand&&(0==c.colorType&&!c.colorCommand.equals("#inherit;"))&&J.shape.Shape.appendCmd(a,c.colorCommand),d=c.isColorSolid&&null!=c.pcs,c.isColorSolid&&0==c.colorType&&!c.colorsExplicit&&!d?J.shape.Shape.appendCmd(a,J.shape.Shape.getColorCommandUnk(this.myType,c.colix,this.translucentAllowed)):c.jvxlData.isBicolorMap&&c.colorPhased&&J.shape.Shape.appendCmd(a,"color isosurface phase "+J.shape.Shape.encodeColor(c.jvxlData.minColorIndex)+" "+J.shape.Shape.encodeColor(c.jvxlData.maxColorIndex)),
null!=c.vertexColorMap))for(var j,c=c.vertexColorMap.entrySet().iterator();c.hasNext()&&((j=c.next())||1);)d=j.getValue(),d.isEmpty()||J.shape.Shape.appendCmd(a,"color "+this.myType+" "+JU.Escape.eBS(d)+" "+j.getKey())}},"JU.SB,~N");e(c$,"getScriptBitSets",function(a,b){this.script=a;var c;this.iHaveModelIndex=!1;this.modelIndex=-1;if(null!=a&&0<=(c=a.indexOf("MODEL({"))){var d=a.indexOf("})",c);0<d&&(c=JU.BS.unescape(a.substring(c+3,d+1)),this.modelIndex=null==c?-1:c.nextSetBit(0),this.iHaveModelIndex=
0<=this.modelIndex)}if(null==a)return!1;this.getCapSlabInfo(a);c=a.indexOf("# ({");if(0>c)return!1;d=a.indexOf("})",c);if(0>d)return!1;c=JU.BS.unescape(a.substring(c+2,d+2));null==b?this.sg.setProp("select",c,null):b[0]=c;if(0>(c=a.indexOf("({",d)))return!0;d=a.indexOf("})",c);if(0>d)return!1;c=JU.BS.unescape(a.substring(c+1,d+1));null==b?this.sg.setProp("ignore",c,null):b[1]=c;if((c=a.indexOf("/({",d))==d+2){if(0>(d=a.indexOf("})",c)))return!1;c=JU.BS.unescape(a.substring(c+3,d+1));null==b?this.vwr.ms.setTrajectoryBs(c):
b[2]=c}return!0},"~S,~A");e(c$,"getCapSlabInfo",function(a){var b=a.indexOf("# SLAB=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!1),null);b=a.indexOf("# CAP=");0<=b&&this.sg.setProp("slab",this.getCapSlabObject(JU.PT.getQuotedStringAt(a,b),!0),null)},"~S");e(c$,"getCapSlabObject",function(a,b){try{if(0==a.indexOf("array")){var c=JU.PT.split(a.substring(6,a.length-1),",");return JU.TempArray.getSlabObjectType(1678381065,B(-1,[JU.Escape.uP(c[0]),JU.Escape.uP(c[1]),
JU.Escape.uP(c[2]),JU.Escape.uP(c[3])]),b,null)}var d=JU.Escape.uP(a);if(I(d,JU.P4))return JU.TempArray.getSlabObjectType(134217750,d,b,null)}catch(h){if(!U(h,Exception))throw h;}return null},"~S,~B");e(c$,"initializeIsosurface",function(){this.iHaveModelIndex||(this.modelIndex=this.vwr.am.cmi);this.atomIndex=-1;this.bsDisplay=null;this.center=JU.P3.new3(NaN,0,0);this.colix=5;this.cutoffRange=this.connections=null;this.colorType=this.defaultColix=this.meshColix=0;this.displayWithinPoints=null;this.explicitContours=
!1;this.isFixed=0>this.modelIndex;this.isPhaseColored=this.isColorExplicit=!1;this.linkedMesh=null;0>this.modelIndex&&(this.modelIndex=0);this.scale3d=0;this.title=null;this.translucentLevel=0;this.withinPoints=null;this.initState()});e(c$,"initState",function(){this.associateNormals=!0;this.sg.initState()});e(c$,"setMeshI",function(){this.thisMesh.visible=!0;this.thisMesh.modelIndex=0<=(this.thisMesh.atomIndex=this.atomIndex)?this.vwr.ms.at[this.atomIndex].mi:this.isFixed?-1:0<=this.modelIndex?this.modelIndex:
this.vwr.am.cmi;this.thisMesh.scriptCommand=this.script;this.thisMesh.ptCenter.setT(this.center);this.thisMesh.scale3d=null==this.thisMesh.jvxlData.jvxlPlane?0:this.scale3d});e(c$,"discardTempData",function(a){a&&(this.title=null,null!=this.thisMesh&&(this.thisMesh.surfaceSet=null))},"~B");e(c$,"getDefaultColix",function(){return 0!=this.defaultColix?this.defaultColix:!this.sg.jvxlData.wasCubic?this.colix:JU.C.getColix(0<=this.sg.params.cutoff?-11525984:-6283184)});e(c$,"drawLcaoCartoon",function(a,
b,c,d){var h=this.sg.setLcao(),j=c.x+c.y+c.z;this.defaultColix=JU.C.getColix(this.sg.params.colorPos);var g=JU.C.getColix(this.sg.params.colorNeg),e=new JU.V3,f=0<h.length&&"-"==h.charAt(0);f&&(h=h.substring(1));f=f?-1:1;e.cross(a,b);if(0!=j){var p=new JU.A4;0!=c.x?p.setVA(b,j):0!=c.y?p.setVA(e,j):p.setVA(a,j);c=(new JU.M3).setAA(p);c.rotate(b);c.rotate(e);c.rotate(a)}null==this.thisMesh&&0==this.nLCAO&&(this.nLCAO=this.meshCount);c=null==this.thisMesh?(0<d?"lp":"lcao")+ ++this.nLCAO+"_"+h:this.thisMesh.thisID;
null==this.thisMesh&&this.allocMesh(c,null);h.equals("px")?(this.thisMesh.thisID+="a",h=this.thisMesh,this.createLcaoLobe(b,f,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(b,-f,d),this.thisMesh.colix=g,this.linkedMesh=this.thisMesh.linkedMesh=h)):h.equals("py")?(this.thisMesh.thisID+="a",h=this.thisMesh,this.createLcaoLobe(e,f,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(e,-f,d),this.thisMesh.colix=g,this.linkedMesh=this.thisMesh.linkedMesh=h)):h.equals("pz")?
(this.thisMesh.thisID+="a",h=this.thisMesh,this.createLcaoLobe(a,f,d),0<d||(this.setProperty("thisID",c+"b",null),this.createLcaoLobe(a,-f,d),this.thisMesh.colix=g,this.linkedMesh=this.thisMesh.linkedMesh=h)):h.equals("pza")||0==h.indexOf("sp")||0==h.indexOf("d")||0==h.indexOf("lp")?this.createLcaoLobe(a,f,d):h.equals("pzb")?this.createLcaoLobe(a,-f,d):h.equals("pxa")?this.createLcaoLobe(b,f,d):h.equals("pxb")?this.createLcaoLobe(b,-f,d):h.equals("pya")?this.createLcaoLobe(e,f,d):h.equals("pyb")?
this.createLcaoLobe(e,-f,d):h.equals("spacefill")||h.equals("cpk")?this.createLcaoLobe(null,2*this.vwr.ms.at[this.atomIndex].getRadius(),d):this.createLcaoLobe(null,1,d)},"JU.V3,JU.V3,JU.V3,~N");e(c$,"createLcaoLobe",function(a,b,c){this.initState();JU.Logger.debugging&&JU.Logger.debug("creating isosurface ID "+this.thisMesh.thisID);null==a?this.setProperty("sphere",Float.$valueOf(b/2),null):(this.lcaoDir.x=a.x*b,this.lcaoDir.y=a.y*b,this.lcaoDir.z=a.z*b,this.lcaoDir.w=0.7,this.setProperty(2==c?"lp":
1==c?"rad":"lobe",this.lcaoDir,null));this.thisMesh.colix=this.defaultColix;this.setScriptInfo(null)},"JU.V3,~N,~N");k(c$,"invalidateTriangles",function(){this.thisMesh.invalidatePolygons()});k(c$,"setOutputChannel",function(a,b){a.setOutputChannel(b)},"javajs.api.GenericBinaryDocument,JU.OC");k(c$,"fillMeshData",function(a,b,c){if(null==a){if(null==this.thisMesh&&this.allocMesh(null,null),this.thisMesh.isMerged||this.thisMesh.clearType(this.myType,this.sg.params.iAddGridPoints),this.thisMesh.connectedAtoms=
this.connections,this.thisMesh.colix=this.getDefaultColix(),this.thisMesh.colorType=this.colorType,this.thisMesh.meshColix=this.meshColix,this.isPhaseColored||this.thisMesh.jvxlData.isBicolorMap)this.thisMesh.isColorSolid=!1}else if(null==c&&(c=this.thisMesh),null!=c)switch(b){case 1:a.mergeVertexCount0=c.mergeVertexCount0;a.vs=c.vs;a.vertexSource=c.vertexSource;a.vvs=c.vvs;a.vc=c.vc;a.vertexIncrement=c.vertexIncrement;a.pc=c.pc;a.pis=c.pis;a.pcs=c.pcs;a.bsSlabDisplay=c.bsSlabDisplay;a.bsSlabGhost=
c.bsSlabGhost;a.slabColix=c.slabColix;a.slabMeshType=c.slabMeshType;a.polygonCount0=c.polygonCount0;a.vertexCount0=c.vertexCount0;a.slabOptions=c.slabOptions;a.colorsExplicit=c.colorsExplicit;break;case 2:if(null==c.vcs||c.vc>c.vcs.length)c.vcs=W(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");k(c$,"notifySurfaceGenerationCompleted",function(){this.setMeshI();this.setBsVdw();this.thisMesh.surfaceAtoms=this.sg.params.bsSelected;this.thisMesh.insideOut=this.sg.params.isInsideOut();
this.thisMesh.isModelConnected=this.sg.params.isModelConnected;this.thisMesh.vertexSource=this.sg.params.vertexSource;this.thisMesh.oabc=this.sg.getOriginVaVbVc();this.thisMesh.calculatedArea=null;this.thisMesh.calculatedVolume=null;if(!this.thisMesh.isMerged)return this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane),null!=this.jvxlData.fixedLattice&&(this.thisMesh.lattice=this.jvxlData.fixedLattice,this.thisMesh.fixLattice()),this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);
this.sg.params.allowVolumeRender||(this.thisMesh.jvxlData.allowVolumeRender=!1);this.thisMesh.setColorsFromJvxlData(this.sg.params.colorRgb);null!=this.thisMesh.jvxlData.slabInfo&&this.vwr.runScriptCautiously("isosurface "+this.thisMesh.jvxlData.slabInfo);0<this.sg.params.psi_monteCarloCount&&(this.thisMesh.diameter=-1);return!1});k(c$,"notifySurfaceMappingCompleted",function(){this.thisMesh.isMerged||this.thisMesh.initialize(this.sg.params.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane);
this.setBsVdw();this.thisMesh.isColorSolid=!1;this.thisMesh.colorDensity=this.jvxlData.colorDensity;this.thisMesh.volumeRenderPointSize=this.jvxlData.pointSize;this.thisMesh.colorEncoder=this.sg.params.colorEncoder;this.thisMesh.getContours();0!=this.thisMesh.jvxlData.nContours&&-1!=this.thisMesh.jvxlData.nContours&&(this.explicitContours=!0);this.explicitContours&&null!=this.thisMesh.jvxlData.jvxlPlane&&(this.thisMesh.havePlanarContours=!0);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?
1073742046:1073741938),null);this.setPropertySuper("token",Integer.$valueOf(this.explicitContours?1073741898:1073742039),null);this.thisMesh.isMerged||this.thisMesh.setJvxlDataRendering();null!=this.sg.params.slabInfo&&(this.thisMesh.slabPolygonsList(this.sg.params.slabInfo,!1),this.thisMesh.reinitializeLightingAndColor(this.vwr));this.thisMesh.setColorCommand()});e(c$,"setBsVdw",function(){null!=this.sg.bsVdw&&(null==this.thisMesh.bsVdw&&(this.thisMesh.bsVdw=new JU.BS),this.thisMesh.bsVdw.or(this.sg.bsVdw))});
k(c$,"calculateGeodesicSurface",function(a,b){return this.vwr.calculateSurface(a,b)},"JU.BS,~N");k(c$,"getSurfacePointIndexAndFraction",function(){return 0},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");k(c$,"addVertexCopy",function(a,b,c,d){return null!=this.cutoffRange&&(b<this.cutoffRange[0]||b>this.cutoffRange[1])?-1:null!=this.withinPoints&&!J.shape.Mesh.checkWithin(a,this.withinPoints,this.withinDistance2,this.isWithinNot)?-1:this.thisMesh.addVertexCopy(a,b,c,this.associateNormals,
d)},"JU.T3,~N,~N,~B");k(c$,"addTriangleCheck",function(a,b,c,d,h,j,g){return 0>a||0>b||0>c||j&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.thisMesh.vvs)?-1:this.thisMesh.addTriangleCheck(a,b,c,d,h,g)},"~N,~N,~N,~N,~N,~B,~N");e(c$,"setScriptInfo",function(a){a=null==a?this.sg.params.script:a;var b=null==a?-1:a.indexOf("; isosurface map");if(0==b)null!=this.thisMesh.scriptCommand&&(b=this.thisMesh.scriptCommand.indexOf("; isosurface map"),0<=b&&(this.thisMesh.scriptCommand=this.thisMesh.scriptCommand.substring(0,
b)),this.thisMesh.scriptCommand+=a);else if(this.thisMesh.title=this.sg.params.title,this.thisMesh.dataType=this.sg.params.dataType,this.thisMesh.scale3d=this.sg.params.scale3d,null!=a&&(null!=this.oldFileName&&(a=a.$replace(this.oldFileName,this.newFileName))," "==a.charAt(0)&&(a=this.myType+" ID "+JU.PT.esc(this.thisMesh.thisID)+a,b=a.indexOf("; isosurface map"))),this.thisMesh.scriptCommand=0<b&&0<this.scriptAppendix.length?a.substring(0,b)+this.scriptAppendix+a.substring(b):a+this.scriptAppendix,
!this.explicitID&&null!=a&&0<=(b=a.indexOf("# ID=")))this.thisMesh.thisID=JU.PT.getQuotedStringAt(a,b)},"~S");k(c$,"addRequiredFile",function(a){a=' # /*file*/"'+a+'"';0>this.scriptAppendix.indexOf(a)&&(this.scriptAppendix+=a)},"~S");k(c$,"setRequiredFile",function(a,b){this.oldFileName=a;this.newFileName=b},"~S,~S");e(c$,"setJvxlInfo",function(){if(this.sg.jvxlData!==this.jvxlData||this.sg.jvxlData!==this.thisMesh.jvxlData)this.jvxlData=this.thisMesh.jvxlData=this.sg.jvxlData});k(c$,"getShapeDetail",
function(){for(var a=new JU.Lst,b=0;b<this.meshCount;b++){var c=new java.util.Hashtable,d=this.isomeshes[b];null==d||(null==d.vs||0==d.vc&&0==d.pc)||(this.addMeshInfo(d,c),a.addLast(c))}return a});e(c$,"addMeshInfo",function(a,b){b.put("ID",null==a.thisID?"<noid>":a.thisID);b.put("visible",Boolean.$valueOf(a.visible));b.put("vertexCount",Integer.$valueOf(a.vc));null!=a.calculatedVolume&&b.put("volume",a.calculatedVolume);null!=a.calculatedArea&&b.put("area",a.calculatedArea);Float.isNaN(a.ptCenter.x)||
b.put("center",a.ptCenter);null!=a.mat4&&b.put("mat4",a.mat4);0!=a.scale3d&&b.put("scale3d",Float.$valueOf(a.scale3d));b.put("xyzMin",a.jvxlData.boundingBox[0]);b.put("xyzMax",a.jvxlData.boundingBox[1]);var c=J.jvxl.data.JvxlCoder.jvxlGetInfo(a.jvxlData);null!=c&&b.put("jvxlInfo",c.$replace("\n"," "));b.put("modelIndex",Integer.$valueOf(a.modelIndex));b.put("color",JU.CU.colorPtFromInt(JU.C.getArgb(a.colix),null));null!=a.colorEncoder&&b.put("colorKey",a.colorEncoder.getColorKey());null!=a.title&&
b.put("title",a.title);(null!=a.jvxlData.contourValues||null!=a.jvxlData.contourValuesUsed)&&b.put("contours",a.getContourList(this.vwr))},"J.shapesurface.IsosurfaceMesh,java.util.Map");k(c$,"getPlane",function(){return null},"~N");k(c$,"getValue",function(){return 0},"~N,~N,~N,~N");k(c$,"checkObjectHovered",function(a,b,c){if(null!=this.keyXy&&a>=this.keyXy[0]&&b>=this.keyXy[1]&&a<this.keyXy[2]&&b<this.keyXy[3])return this.hoverKey(a,b),!0;if(!this.vwr.getDrawHover())return!1;c=this.findValue(a,
b,!1,c);if(null==c)return!1;this.vwr.gdata.antialiasEnabled&&(a<<=1,b<<=1);this.vwr.hoverOnPt(a,b,c,this.pickedMesh.thisID,this.pickedPt);return!0},"~N,~N,JU.BS");e(c$,"hoverKey",function(a,b){try{var c,d=1-1*(b-this.keyXy[1])/(this.keyXy[3]-this.keyXy[1]);if(this.thisMesh.showContourLines){var h=this.thisMesh.getContours();if(null==h){if(null==this.thisMesh.jvxlData.contourValues)return;var j=C(Math.floor(d*this.thisMesh.jvxlData.contourValues.length));if(0>j||j>this.thisMesh.jvxlData.contourValues.length)return;
c=""+this.thisMesh.jvxlData.contourValues[j]}else{j=C(Math.floor(d*h.length));if(0>j||j>h.length)return;c=""+h[j].get(2).floatValue()}}else{var g=this.thisMesh.colorEncoder.quantize(d,!0),d=this.thisMesh.colorEncoder.quantize(d,!1);c=""+g+" - "+d}this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1);this.vwr.hoverOnPt(a,b,c,null,null)}catch(e){if(!U(e,Exception))throw e;}},"~N,~N");k(c$,"checkObjectClicked",function(a,b,c,d,h){if(!h||!this.vwr.isBound(c,18))return null;c=100;this.vwr.gdata.isAntialiased()&&
(a<<=1,b<<=1,c<<=1);for(var j=h=-1,g=-2147483648,e=2147483647,f=0;f<this.meshCount;f++){var p=this.isomeshes[f];if(this.isPickable(p,d)&&(p=p.vs,null!=p))for(var n=p.length;0<=--n;){var q=p[n];null!=q&&0<=this.coordinateInRange(a,b,q,c,this.ptXY)&&(this.ptXY.z<e&&(h=f,e=this.ptXY.z,j=n),this.ptXY.z>g&&(g=this.ptXY.z))}}if(0>h)return null;this.pickedMesh=this.isomeshes[h];this.setPropertySuper("thisID",this.pickedMesh.thisID,null);this.pickedVertex=j;a=new JU.P3;a.setT(this.pickedMesh.vs[this.pickedVertex]);
this.pickedModel=this.pickedMesh.modelIndex;b=this.getPickedPoint(a,this.pickedModel);this.setStatusPicked(-4,a,b);return b},"~N,~N,~N,JU.BS,~B");e(c$,"isPickable",function(a,b){return 0!=a.visibilityFlags&&(0>a.modelIndex||b.get(a.modelIndex))&&!JU.C.isColixTranslucent(a.colix)},"J.shapesurface.IsosurfaceMesh,JU.BS");e(c$,"findValue",function(a,b,c,d){c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var h=-1,j=null,g=null,e=0;e<this.meshCount;e++)if(g=this.isomeshes[e],this.isPickable(g,
d)){var f=g.jvxlData.vContours,p=0>g.firstRealVertex?0:g.firstRealVertex,n=0;if(null!=f&&0<f.length){for(p=0;p<f.length;p++)for(var q=f[p],r=q.size()-1,w=6;w<r;w++){var u=q.get(w),k=this.coordinateInRange(a,b,u,c,this.ptXY);0<=k&&(c=k,j=q,n=p,this.pickedMesh=g,this.pickedPt=u)}if(null!=j)return j.get(2).toString()+(JU.Logger.debugging?" "+n:"")}else if(null!=g.jvxlData.jvxlPlane&&null!=g.vvs){f=null==g.mat4&&0==g.scale3d?g.vs:g.getOffsetVertices(g.jvxlData.jvxlPlane);for(w=g.vc;--w>=p;)u=f[w],k=this.coordinateInRange(a,
b,u,c,this.ptXY),0<=k&&(c=k,h=w,this.pickedMesh=g,this.pickedPt=u);if(-1!=h)break}else if(null!=g.vvs){if(null!=g.bsSlabDisplay)for(w=g.bsSlabDisplay.nextSetBit(0);0<=w;w=g.bsSlabDisplay.nextSetBit(w+1)){if(f=g.pis[w],null!=f)for(n=0;3>n;n++)u=g.vs[f[n]],k=this.coordinateInRange(a,b,u,c,this.ptXY),0<=k&&(c=k,h=f[n],this.pickedMesh=g,this.pickedPt=u)}else for(w=g.vc;--w>=p;)u=g.vs[w],k=this.coordinateInRange(a,b,u,c,this.ptXY),0<=k&&(c=k,h=w,this.pickedMesh=g,this.pickedPt=u);if(-1!=h)break}}return-1==
h?null:(JU.Logger.debugging?"$"+g.thisID+"["+(h+1)+"] "+g.vs[h]+": ":g.thisID+": ")+g.vvs[h]},"~N,~N,~B,JU.BS");e(c$,"getCmd",function(a){var b=(new JU.SB).append("\n");this.getMeshCommand(b,a);return b.toString()},"~N");aa(c$,"MAX_OBJECT_CLICK_DISTANCE_SQUARED",100)});E("J.jvxl.data");H(null,"J.jvxl.data.JvxlCoder","java.lang.Float JU.BS $.Lst $.P3 $.PT $.SB J.api.Interface J.jvxl.data.VolumeData JU.BSUtil $.C $.Escape $.Logger JV.Viewer".split(" "),function(){c$=wa(J.jvxl.data,"JvxlCoder");c$.jvxlGetFile=
e(c$,"jvxlGetFile",function(a,b,c,d,h,j,g,e){J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var f=new JU.SB;if("TRAILERONLY".equals(d))return JU.XmlUtil.closeTag(f,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(f,"jvxl"),f.toString();var p=null!=b,n="HEADERONLY".equals(d);if(h){JU.XmlUtil.openDocument(f);JU.XmlUtil.openTagAttr(f,"jvxl",B(-1,["version","2.3","jmolVersion",a.version,"xmlns","http://jmol.org/jvxl_schema","xmlns:cml","http://www.xml-cml.org/schema"]));JU.XmlUtil.appendCdata(f,"jvxlFileTitle",null,null==
a.jvxlFileTitle?"\n":"\n"+a.jvxlFileTitle);null!=a.moleculeXml&&f.append(a.moleculeXml);var q=p?null:a.jvxlVolumeDataXml;null==q&&(q=(new J.jvxl.data.VolumeData).setVolumetricXml());f.append(q);JU.XmlUtil.openTagAttr(f,"jvxlSurfaceSet",B(-1,["count",""+(0<j?j:1)]));if(n)return f.toString()}j=p?"pmesh":null==a.jvxlPlane?"isosurface":"plane";null!=a.jvxlColorData&&0<a.jvxlColorData.length&&(j="mapped "+j);JU.XmlUtil.openTagAttr(f,"jvxlSurface",B(-1,["type",j]));f.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,
p));J.jvxl.data.JvxlCoder.jvxlAppendCommandState(f,e,g);if(null!=c||null!=d&&0<d.length){g=new JU.SB;null!=d&&0<d.length&&g.append(d).append("\n");if(null!=c)for(d=0;d<c.length;d++)g.append(c[d]).appendC("\n");JU.XmlUtil.appendCdata(f,"jvxlSurfaceTitle",null,g.toString())}g=new JU.SB;JU.XmlUtil.openTagAttr(g,"jvxlSurfaceData",p||null==a.jvxlPlane?null:null==a.mapLattice?B(-1,["plane",JU.Escape.eP4(a.jvxlPlane)]):B(-1,["plane",JU.Escape.eP4(a.jvxlPlane),"maplattice",JU.Escape.eP(a.mapLattice)]));if(p)J.jvxl.data.JvxlCoder.appendXmlVertexOnlyData(g,
a,b,!0);else{if(null==a.jvxlPlane){if(null==a.jvxlEdgeData)return"";J.jvxl.data.JvxlCoder.appendXmlEdgeData(g,a)}J.jvxl.data.JvxlCoder.appendXmlColorData(g,a.jvxlColorData,!0,a.isJvxlPrecisionColor,a.valueMappedToRed,a.valueMappedToBlue)}J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(g,"jvxlInvalidatedVertexData",a.jvxlExcluded[1],-1,null);0<a.excludedVertexCount&&(J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(g,"jvxlExcludedVertexData",a.jvxlExcluded[0],a.excludedVertexCount,null),J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(g,
"jvxlExcludedPlaneData",a.jvxlExcluded[2],-1,null));J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(g,"jvxlExcludedTriangleData",a.jvxlExcluded[3],a.excludedTriangleCount,null);JU.XmlUtil.closeTag(g,"jvxlSurfaceData");b=g.length();f.appendSB(g);null!=a.vContours&&0<a.vContours.length&&J.jvxl.data.JvxlCoder.jvxlEncodeContourData(a.vContours,f);if(null!=a.vertexColorMap){null==a.baseColor?JU.XmlUtil.openTag(f,"jvxlVertexColorData"):JU.XmlUtil.openTagAttr(f,"jvxlVertexColorData",B(-1,["baseColor",a.baseColor]));
var r;for(c=a.vertexColorMap.entrySet().iterator();c.hasNext()&&((r=c.next())||1);)J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,"jvxlColorMap",r.getValue(),-1,B(-1,["color",r.getKey()]));a.vertexColorMap=null;JU.XmlUtil.closeTag(f,"jvxlVertexColorData")}JU.XmlUtil.closeTag(f,"jvxlSurface");h&&(JU.XmlUtil.closeTag(f,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(f,"jvxl"));return J.jvxl.data.JvxlCoder.jvxlSetCompressionRatio(f,a,b)},"J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~A,~S,~B,~N,~S,~S");c$.checkHaveXMLUtil=
e(c$,"checkHaveXMLUtil",function(){J.jvxl.data.JvxlCoder.haveXMLUtil||(JV.Viewer.isJS&&J.api.Interface.getInterface("JU.XmlUtil",null,"show"),J.jvxl.data.JvxlCoder.haveXMLUtil=!0)});c$.appendEncodedBitSetTag=e(c$,"appendEncodedBitSetTag",function(a,b,c,d,h){0>d&&(d=JU.BSUtil.cardinalityOf(c));if(0!=d){var j=new JU.SB;j.append("\n ");J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(c,-1,j);JU.XmlUtil.appendTagObj(a,b,B(-1,[h,"bsEncoding","base90+35","count",""+d,"len",""+c.length()]),J.jvxl.data.JvxlCoder.jvxlCompressString(j.toString(),
!0))}},"JU.SB,~S,JU.BS,~N,~A");c$.jvxlSetCompressionRatio=e(c$,"jvxlSetCompressionRatio",function(a,b,c){a=a.toString();b=F(0<b.nBytes?b.nBytes/c:13*b.nPointsX*b.nPointsY*b.nPointsZ/c);return JU.PT.rep(a,'"not calculated"',0<b?'"'+b+':1"':'"?"')},"JU.SB,J.jvxl.data.JvxlData,~N");c$.appendXmlEdgeData=e(c$,"appendXmlEdgeData",function(a,b){JU.XmlUtil.appendTagObj(a,"jvxlEdgeData",B(-1,["count",""+(b.jvxlEdgeData.length-1),"encoding","base90f1","bsEncoding","base90+35c","isXLowToHigh",""+b.isXLowToHigh,
"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlEdgeData,!0)]),"\n"+J.jvxl.data.JvxlCoder.jvxlCompressString(b.jvxlSurfaceData,!0))},"JU.SB,J.jvxl.data.JvxlData");c$.jvxlAppendCommandState=e(c$,"jvxlAppendCommandState",function(a,b,c){null!=b&&JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceCommand",null,"\n"+(0>b.indexOf("#")?b:b.substring(0,b.indexOf("#")))+"\n");null!=c&&(0<=c.indexOf("** XML ** ")?(c=JU.PT.split(c,"** XML **")[1].trim(),JU.XmlUtil.appendTag(a,"jvxlIsosurfaceState","\n"+c+"\n")):
JU.XmlUtil.appendCdata(a,"jvxlIsosurfaceState",null,"\n"+c))},"JU.SB,~S,~S");c$.appendXmlColorData=e(c$,"appendXmlColorData",function(a,b,c,d,h,j){var g;if(!(null==b||0>(g=b.length-1)))d&&(g/=2),JU.XmlUtil.appendTagObj(a,"jvxlColorData",B(-1,["count",""+g,"encoding",c?"base90f"+(d?"2":"1"):"none","min",""+h,"max",""+j,"data",J.jvxl.data.JvxlCoder.jvxlCompressString(b,!0)]),null)},"JU.SB,~S,~B,~B,~N,~N");c$.jvxlGetInfo=e(c$,"jvxlGetInfo",function(a){return J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,a.vertexDataOnly)},
"J.jvxl.data.JvxlData");c$.jvxlGetInfoData=e(c$,"jvxlGetInfoData",function(a,b){if(null==a.jvxlSurfaceData)return"";J.jvxl.data.JvxlCoder.checkHaveXMLUtil();var c=new JU.Lst,d=a.nSurfaceInts,h=b?0:a.jvxlEdgeData.length-1,j=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",""+a.cutoff);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isCutoffAbsolute",""+a.isCutoffAbsolute);J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  pointsPerAngstrom",""+a.pointsPerAngstrom);var g=a.jvxlSurfaceData.length+h+j+1;0<g&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesData",""+g);J.jvxl.data.JvxlCoder.addAttrib(c,"\n  isXLowToHigh",""+a.isXLowToHigh);null==a.jvxlPlane&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nSurfaceInts",""+d),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedEdgeData",""+h));0<j&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedColorData",""+j)}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);g=JU.BSUtil.cardinalityOf(a.jvxlExcluded[1]);0<g&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nInvalidatedVertexes",""+g);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<j&&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<j&&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);0<=a.thisSet&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  set",""+(a.thisSet+1));-2147483648!=a.slabValue&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  slabValue",""+a.slabValue);a.isSlabbable&&J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  slabbable","true");0<a.nVertexColors&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nVertexColors",""+a.nVertexColors);d=3.4028235E38==a.mappedDataMin?0:a.mappedDataMin;h=a.isColorReversed?a.valueMappedToRed:a.valueMappedToBlue;j=a.isColorReversed?a.valueMappedToBlue:a.valueMappedToRed;null!=a.jvxlColorData&&(0<a.jvxlColorData.length&&!a.isBicolorMap)&&(J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMinimum",""+d),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  dataMaximum",""+a.mappedDataMax),J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  valueMappedToRed",""+j),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  valueMappedToBlue",""+h));a.isContoured&&(null==a.contourValues||null==a.contourColixes?null==a.vContours&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+Math.abs(a.nContours)):(null!=a.jvxlPlane&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contoured","true"),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nContours",""+a.contourValues.length),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourValues",JU.Escape.eAF(null==a.contourValuesUsed?a.contourValues:
a.contourValuesUsed)),J.jvxl.data.JvxlCoder.addAttrib(c,"\n  contourColors",a.contourColors)),0<a.thisContour&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  thisContour",""+a.thisContour));a.insideOut&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  insideOut","true");a.vertexDataOnly?J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","vertex/face data only"):a.isXLowToHigh&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  note","progressive JVXL+ -- X values read from low(0) to high("+(a.nPointsX-1)+")");J.jvxl.data.JvxlCoder.addAttrib(c,
"\n  xyzMin",JU.Escape.eP(a.boundingBox[0]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  xyzMax",JU.Escape.eP(a.boundingBox[1]));J.jvxl.data.JvxlCoder.addAttrib(c,"\n  approximateCompressionRatio","not calculated");J.jvxl.data.JvxlCoder.addAttrib(c,"\n  jmolVersion",a.version);d=new JU.SB;JU.XmlUtil.openTagAttr(d,"jvxlSurfaceInfo",c.toArray(Array(c.size())));JU.XmlUtil.closeTag(d,"jvxlSurfaceInfo");return d.toString()},"J.jvxl.data.JvxlData,~B");c$.addAttrib=e(c$,"addAttrib",function(a,b,c){a.addLast(B(-1,
[b,c]))},"JU.Lst,~S,~S");c$.jvxlEncodeContourData=e(c$,"jvxlEncodeContourData",function(a,b){JU.XmlUtil.openTagAttr(b,"jvxlContourData",B(-1,["count",""+a.length]));for(var c=0;c<a.length;c++)if(!(6>a[c].size())){var d=a[c].get(0).intValue(),h=new JU.SB;h.append("\n");var j=a[c].get(1);J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(j,d,h);JU.XmlUtil.appendTagObj(b,"jvxlContour",B(-1,["index",""+c,"value",""+a[c].get(2),"color",JU.Escape.escapeColor(a[c].get(4)[0]),"count",""+j.length(),"encoding","base90iff1",
"bsEncoding","base90+35c","data",J.jvxl.data.JvxlCoder.jvxlCompressString(a[c].get(5).toString(),!0)]),J.jvxl.data.JvxlCoder.jvxlCompressString(h.toString(),!0))}JU.XmlUtil.closeTag(b,"jvxlContourData")},"~A,JU.SB");c$.set3dContourVector=e(c$,"set3dContourVector",function(a,b,c){if(!(6>a.size()))for(var d=a.get(5),h=a.get(1),j=0,g=d.length(),e=0,f=" ",p=" ",n=h.nextSetBit(0);0<=n;n=h.nextSetBit(n+1)){for(var q=b[n];j<g&&!JU.PT.isDigit(f=d.charAt(j++)););for(e=f.charCodeAt(0)-48;j<g&&JU.PT.isWhitespace(f=
d.charAt(j++)););for(;j<g&&JU.PT.isWhitespace(p=d.charAt(j++)););var r=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(f.charCodeAt(0),35,90,0),w=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(p.charCodeAt(0),35,90,0),u,k;0==(e&1)?(u=q[1],k=e=q[2],q=q[0]):(u=q[0],k=q[1],0!=(e&2)?(e=k,q=q[2]):(e=q[2],q=u));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,u,k,r));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,e,q,w))}},"JU.Lst,~A,~A");c$.getContourPoint=e(c$,"getContourPoint",function(a,b,c,d){var h=
new JU.P3;h.sub2(a[c],a[b]);h.scaleAdd2(d,h,a[b]);return h},"~A,~N,~N,~N");c$.appendContourTriangleIntersection=e(c$,"appendContourTriangleIntersection",function(a,b,c,d){d.appendI(a);d.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(b));d.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(c))},"~N,~N,~N,JU.SB");c$.jvxlCreateColorData=e(c$,"jvxlCreateColorData",function(a,b){if(null==b)a.jvxlColorData="";else{var c=a.isJvxlPrecisionColor,d=a.isTruncated,h=a.colorFractionBase,j=a.colorFractionRange,
g=a.valueMappedToBlue,e=a.valueMappedToRed,f=0<a.saveVertexCount?a.saveVertexCount:a.vertexCount;f>b.length&&System.out.println("JVXLCODER ERROR");var p=a.mappedDataMin,n=a.mappedDataMax,q=new JU.SB,r=new JU.SB;b.length<f&&System.out.println("JVXLCOLOR OHOHO");for(var w=0;w<f;w++){var u=b[w];Float.isNaN(u)&&(u=p);d&&(u=0<u?0.999:-0.999);c?J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(u,p,n,h,j,q,r):q.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(u,e,g,h,j))}a.jvxlColorData=q.appendSB(r).appendC("\n").toString()}},
"J.jvxl.data.JvxlData,~A");c$.appendXmlVertexOnlyData=e(c$,"appendXmlVertexOnlyData",function(a,b,c,d){var h=v(c.vc,0);J.jvxl.data.JvxlCoder.appendXmlTriangleData(a,c.pis,c.pc,c.bsSlabDisplay,h,d)&&J.jvxl.data.JvxlCoder.appendXmlVertexData(a,b,h,c.vs,c.vvs,c.vc,c.polygonColorData,c.pc,c.bsSlabDisplay,b.vertexColors,0<b.jvxlColorData.length,d)},"JU.SB,J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~B");c$.appendXmlTriangleData=e(c$,"appendXmlTriangleData",function(a,b,c,d,h,j){for(var g=new JU.SB,e=new JU.SB,
f=1,p=0,n=0,q=!1,r=0,w=null!=d,u=0;u<c;)if(null==b[u]||w&&!d.get(u))u++;else{var k=b[u][p],k=0<h[k]?h[k]:h[k]=++n,v=k-f,f=k;0==v?(g.appendC("!"),q=!1):32<v?(q&&g.appendC("+"),g.appendI(v),q=!0):-32>v?(g.appendI(v),q=!0):(g.appendC(String.fromCharCode(92+v)),q=!1);0==++p%3&&(e.appendI(b[u][3]),p=0,u++,r++)}if(0==g.length())return!0;JU.XmlUtil.appendTagObj(a,"jvxlTriangleData",B(-1,["count",""+r,"encoding","jvxltdiff","data",J.jvxl.data.JvxlCoder.jvxlCompressString(g.toString(),j)]),null);JU.XmlUtil.appendTagObj(a,
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k=d[0==e?s:H[s]],J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(k.x,y.x,C.x,r,w,F,E),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(k.y,y.y,C.y,r,w,F,E),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(k.z,y.z,C.z,r,w,F,E);F.appendSB(E);JU.XmlUtil.appendTagObj(a,"jvxlVertexData",B(-1,["count",""+c,"min",JU.Escape.eP(y),"max",JU.Escape.eP(C),"encoding","base90xyz2","data",J.jvxl.data.JvxlCoder.jvxlCompressString(F.toString(),q)]),null);null!=g&&JU.XmlUtil.appendTagObj(a,"jvxlPolygonColorData",B(-1,["encoding","jvxlnc",
"count",""+e]),"\n"+g);if(n){F=new JU.SB;E=new JU.SB;if(null==p)for(s=0;s<j;s++){if(!R||f.get(s))J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(h[0==e?s:H[s]],b.mappedDataMin,b.mappedDataMax,r,w,F,E)}else{d=0;F.appendI(c).append(" ");for(s=0;s<j;s++)if(!R||f.get(s))h=p[0==e?s:H[s]],h==d?h=0:d=h,F.appendI(h),F.append(" ")}J.jvxl.data.JvxlCoder.appendXmlColorData(a,F.appendSB(E).append("\n").toString(),null==p,!0,b.valueMappedToRed,b.valueMappedToBlue)}},"JU.SB,J.jvxl.data.JvxlData,~A,~A,~A,~N,~S,~N,JU.BS,~A,~B,~B");
c$.jvxlFractionAsCharacter=e(c$,"jvxlFractionAsCharacter",function(a){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,35,90)},"~N");c$.jvxlFractionAsCharacterRange=e(c$,"jvxlFractionAsCharacterRange",function(a,b,c){0.9999<a?a=0.9999:Float.isNaN(a)&&(a=1.0001);a=C(Math.floor(a*c+b));return a<b?String.fromCharCode(b):92==a?"!":String.fromCharCode(a)},"~N,~N,~N");c$.jvxlAppendCharacter2=e(c$,"jvxlAppendCharacter2",function(a,b,c,d,h,j,g){a=b==c?a:(a-b)/(c-b);b=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,
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b,c){var d=0,h=-1,j=0;0>b&&(b=a.length());for(var g=0,e=!1,f=b-1,p=0;p<b;++p)e==a.get(p)?d++:(d==h&&p!=f?j++:(0<j&&(c.appendC(" ").appendI(-j),j=0,g++),c.appendC(" ").appendI(d),g++,h=d),d=1,e=!e);c.appendC(" ").appendI(d).appendC("\n");return g},"JU.BS,~N,JU.SB");c$.jvxlEncodeBitSet=e(c$,"jvxlEncodeBitSet",function(a){var b=new JU.SB;J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,-1,b);return b.toString()},"JU.BS");c$.jvxlEncodeBitSetBuffer=e(c$,"jvxlEncodeBitSetBuffer",function(a,b,c){var d=0,h=
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for(p&&g++;g<e&&!JU.PT.isWhitespace(a.charAt(g));){h=a.charCodeAt(g);h<b&&(h=92);j+=(h-b)*f;h=!0;++g;if(!p)break;f*=c}h||(j=-2147483648);d[0]=g;return j},"~S,~N,~N,~A");c$.jvxlDecodeBitSet=e(c$,"jvxlDecodeBitSet",function(a){if(a.startsWith("-"))return J.jvxl.data.JvxlCoder.jvxlDecodeBitSetRange(J.jvxl.data.JvxlCoder.jvxlDecompressString(a.substring(1)),35,90);for(var b=new JU.BS,c=0,d=0,h=0,j=0,g=!1,e=v(1,0);;){c=0>h++?c:JU.PT.parseIntNext(a,e);if(-2147483648==c)break;0>c?(h=c,c=d):(g&&b.setBits(j,
j+c),j+=c,d=c,g=!g)}return b},"~S");c$.jvxlCompressString=e(c$,"jvxlCompressString",function(a,b){if(0<=a.indexOf("~"))return a;for(var c=new JU.SB,d="\x00",h=!1,j=!1,e=0,f=a.length,m=0;m<=f;m++){var p=m==f?"\x00":a.charAt(m);switch(p){case "\n":case "\r":continue;case "&":case "<":h=b;break;default:h=!1}if(p==d)++e,p="\x00";else if(0<e||j){if(4>e&&!j||" "==d||"\t"==d)for(;0<=--e;)c.appendC(d);else j?j=!1:c.appendC("~"),c.appendI(e),c.appendC(" ");e=0}"\x00"!=p&&(h?(j=!0,c.appendC("~"),d=p,p=String.fromCharCode(p.charCodeAt(0)-
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"2.3","haveXMLUtil",!1,"CONTOUR_NPOLYGONS",0,"CONTOUR_BITSET",1,"CONTOUR_VALUE",2,"CONTOUR_COLIX",3,"CONTOUR_COLOR",4,"CONTOUR_FDATA",5,"CONTOUR_POINTS",6,"defaultEdgeFractionBase",35,"defaultEdgeFractionRange",90,"defaultColorFractionBase",35,"defaultColorFractionRange",90)});E("J.jvxl.data");H(["JU.M3","$.P3","$.V3"],"J.jvxl.data.VolumeData",["java.lang.Float","java.util.Hashtable","JU.SB","JU.Escape","$.Logger"],function(){c$=N(function(){this.sr=null;this.doIterate=!0;this.voxelCounts=this.volumetricVectors=
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arguments)},J.jvxl.data,"VolumeData");$(c$,function(){this.volumetricOrigin=new JU.P3;this.origin=y(3,0);this.volumetricVectors=Array(3);this.voxelCounts=v(3,0);this.volumetricVectorLengths=y(3,0);this.unitVolumetricVectors=Array(3);this.volumetricMatrix=new JU.M3;this.inverseMatrix=new JU.M3;this.ptXyzTemp=new JU.P3;this.edgeVector=new JU.V3;this.ptTemp=new JU.P3});e(c$,"getVoxelData",function(){return this.voxelData});e(c$,"setVoxelDataAsArray",function(a){this.voxelData=a;null!=a&&(this.sr=null)},
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this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[1].length());this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[2].length());this.nPoints=this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2];return this.yzCount=this.voxelCounts[1]*this.voxelCounts[2]});e(c$,"getVolumetricVectorLengths",function(){return this.volumetricVectorLengths});e(c$,"setVolumetricVector",function(a,b,c,d){this.volumetricVectors[a].x=b;this.volumetricVectors[a].y=c;this.volumetricVectors[a].z=d;this.setUnitVectors()},
"~N,~N,~N,~N");e(c$,"getVoxelCounts",function(){return this.voxelCounts});e(c$,"setVoxelCounts",function(a,b,c){this.voxelCounts[0]=a;this.voxelCounts[1]=b;this.voxelCounts[2]=c;return a*b*c},"~N,~N,~N");e(c$,"getVoxelDataAt",function(a){var b=C(a/this.yzCount);a-=b*this.yzCount;var c=C(a/this.voxelCounts[2]);return this.voxelData[b][c][a-c*this.voxelCounts[2]]},"~N");e(c$,"getPointIndex",function(a,b,c){return a*this.yzCount+b*this.voxelCounts[2]+c},"~N,~N,~N");e(c$,"getPoint",function(a,b){var c=
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Exception))return JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? "),!1;throw b;}return!0});e(c$,"transform",function(a,b){this.volumetricMatrix.rotate2(a,b)},"JU.V3,JU.V3");e(c$,"setPlaneParameters",function(a){this.thePlane=a;this.thePlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z)},"JU.P4");e(c$,"calcVoxelPlaneDistance",function(a,b,c){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.distancePointToPlane(this.ptXyzTemp)},"~N,~N,~N");e(c$,"getToPlaneParameter",function(){return Math.sqrt(this.thePlane.x*
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function(a,b,c,d){d.scaleAdd2(a,this.volumetricVectors[0],this.volumetricOrigin);d.scaleAdd2(b,this.volumetricVectors[1],d);d.scaleAdd2(c,this.volumetricVectors[2],d)},"~N,~N,~N,JU.T3");e(c$,"setUnitVectors",function(){this.maxVectorLength=0;this.voxelVolume=1;for(var a=0;3>a;a++){var b=this.volumetricVectorLengths[a]=this.volumetricVectors[a].length();if(0==b)return!1;b>this.maxVectorLength&&(this.maxVectorLength=b);this.voxelVolume*=b;this.unitVolumetricVectors[a].setT(this.volumetricVectors[a]);
this.unitVolumetricVectors[a].normalize()}this.minToPlaneDistance=2*this.maxVectorLength;this.origin[0]=this.volumetricOrigin.x;this.origin[1]=this.volumetricOrigin.y;this.origin[2]=this.volumetricOrigin.z;this.oabc=Array(4);this.oabc[0]=JU.V3.newV(this.volumetricOrigin);for(a=0;3>a;a++)b=this.oabc[a+1]=new JU.V3,b.scaleAdd2(this.voxelCounts[a]-1,this.volumetricVectors[a],b);return this.setMatrix()});e(c$,"xyzToVoxelPt",function(a,b,c,d){this.ptXyzTemp.set(a,b,c);this.ptXyzTemp.sub(this.volumetricOrigin);
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1),e=this.indexUpper(this.ptXyzTemp.x,h,d),g=this.indexLower(this.ptXyzTemp.y,d=this.voxelCounts[1]-1),f=this.indexUpper(this.ptXyzTemp.y,g,d),c=this.indexLower(this.ptXyzTemp.z,d=this.voxelCounts[2]-1),m=this.indexUpper(this.ptXyzTemp.z,c,d);d=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-h),this.mantissa(this.ptXyzTemp.y-g),this.getVoxelValue(h,g,c),this.getVoxelValue(e,g,c),this.getVoxelValue(h,f,c),this.getVoxelValue(e,f,c));h=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-
h),this.mantissa(this.ptXyzTemp.y-g),this.getVoxelValue(h,g,m),this.getVoxelValue(e,g,m),this.getVoxelValue(h,f,m),this.getVoxelValue(e,f,m));return d+this.mantissa(this.ptXyzTemp.z-c)*(h-d)},"JU.T3,~B");e(c$,"mantissa",function(a){return this.isPeriodic?a-Math.floor(a):a},"~N");e(c$,"getVoxelValue",function(a,b,c){if(null==this.voxelMap)return this.voxelData[a][b][c];a=this.voxelMap.get(Integer.$valueOf(this.getPointIndex(a,b,c)));return null==a?NaN:a.floatValue()},"~N,~N,~N");c$.getFractional2DValue=
e(c$,"getFractional2DValue",function(a,b,c,d,h,e){c+=a*(d-c);return c+b*(h+a*(e-h)-c)},"~N,~N,~N,~N,~N,~N");e(c$,"indexLower",function(a,b){if(this.isPeriodic&&0<b){for(;0>a;)a+=b;for(;a>=b;)a-=b;return C(Math.floor(a))}if(0>a)return 0;var c=C(Math.floor(a));return c>b?b:c},"~N,~N");e(c$,"indexUpper",function(a,b,c){return!this.isPeriodic&&0>a||b==c?b:b+1},"~N,~N,~N");e(c$,"offsetCenter",function(a){var b=new JU.P3;b.scaleAdd2((this.voxelCounts[0]-1)/2,this.volumetricVectors[0],b);b.scaleAdd2((this.voxelCounts[1]-
1)/2,this.volumetricVectors[1],b);b.scaleAdd2((this.voxelCounts[2]-1)/2,this.volumetricVectors[2],b);this.volumetricOrigin.sub2(a,b)},"JU.P3");e(c$,"setDataDistanceToPlane",function(a){this.setPlaneParameters(a);a=this.voxelCounts[0];var b=this.voxelCounts[1],c=this.voxelCounts[2];this.voxelData=y(a,b,c,0);for(var d=0;d<a;d++)for(var h=0;h<b;h++)for(var e=0;e<c;e++)this.voxelData[d][h][e]=this.calcVoxelPlaneDistance(d,h,e)},"JU.P4");e(c$,"filterData",function(a,b){var c=!Float.isNaN(b);if(null!=this.sr)this.isSquared=
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d;f++)for(var m=0;m<h;m++){var p=this.voxelData[g][f][m]-b;this.voxelPtToXYZ(g,f,m,this.ptXyzTemp);var n=(this.ptXyzTemp.x*e.x+this.ptXyzTemp.y*e.y+this.ptXyzTemp.z*e.z+a.w-b)/1;if(0<=n||n>p)this.voxelData[g][f][m]=n}}},"JU.P4,~N");e(c$,"setVolumetricXml",function(){var a=new JU.SB;if(0==this.voxelCounts[0])a.append("<jvxlVolumeData>\n");else{a.append('<jvxlVolumeData origin="'+JU.Escape.eP(this.volumetricOrigin)+'">\n');for(var b=0;3>b;b++)a.append('<jvxlVolumeVector type="'+b+'" count="'+this.voxelCounts[b]+
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this.edgeVector.length())return a;b=0;this.ptTemp.setT(e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1);for(h=NaN;10>++b;){var m=(c-d)/g;if(0>m||1<m)break;m=(a-c)/g/2;f+=m;if(0>f||1<f)break;e.setT(this.ptTemp);h=c;if(0.005>Math.abs(m))break;this.ptTemp.scaleAdd2(m,this.edgeVector,e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1)}return h},"~N,JU.P3,JU.P3,~N,~N,JU.P3")});E("J.jvxl.data");H(null,"J.jvxl.data.JvxlData",["java.lang.Float","JU.SB","J.jvxl.data.JvxlCoder"],function(){c$=N(function(){this.msg=
"";this.wasCubic=this.wasJvxl=!1;this.jvxlPlane=this.jvxlExcluded=this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData=this.jvxlFileMessage=this.jvxlFileTitle=null;this.isColorReversed=this.jvxlDataIsColorDensity=this.jvxlDataIs2dContour=this.jvxlDataIsColorMapped=this.isJvxlPrecisionColor=!1;this.thisSet=-2147483648;this.edgeFractionBase=35;this.edgeFractionRange=90;this.colorFractionBase=35;this.colorFractionRange=90;this.isValid=!0;this.vertexDataOnly=this.isModelConnected=
this.isCutoffAbsolute=this.isTruncated=this.isBicolorMap=this.isContoured=this.isXLowToHigh=this.insideOut=!1;this.vertexCount=this.nSurfaceInts=this.nEdges=this.nContours=this.nBytes=this.nPointsZ=this.nPointsY=this.nPointsX=this.pointsPerAngstrom=this.cutoff=this.valueMappedToBlue=this.valueMappedToRed=this.mappedDataMax=this.mappedDataMin=0;this.contourValuesUsed=this.contourValues=this.contourColors=this.contourColixes=this.vContours=null;this.thisContour=-1;this.scale3d=0;this.minColorIndex=
-1;this.maxColorIndex=0;this.boundingBox=this.version=this.title=null;this.excludedVertexCount=this.excludedTriangleCount=0;this.colorDensity=!1;this.pointSize=0;this.moleculeXml=null;this.saveVertexCount=this.dataMax=this.dataMin=0;this.vertexColorMap=null;this.nVertexColors=0;this.meshColor=this.color=this.vertexColors=null;this.translucency=0;this.rendering=this.colorScheme=null;this.slabValue=-2147483648;this.isSlabbable=!1;this.diameter=0;this.slabInfo=null;this.allowVolumeRender=!1;this.voxelVolume=
0;this.baseColor=this.fixedLattice=this.mapLattice=null;this.integration=NaN;K(this,arguments)},J.jvxl.data,"JvxlData");$(c$,function(){this.jvxlExcluded=Array(4)});T(c$,function(){});e(c$,"clear",function(){this.allowVolumeRender=!0;this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData="";this.colorScheme=this.color=null;this.colorDensity=!1;this.pointSize=NaN;this.contourColors=this.contourColixes=this.contourValuesUsed=this.contourValues=null;this.integration=NaN;this.isSlabbable=
!1;this.isValid=!0;this.meshColor=this.mapLattice=null;this.msg="";this.nVertexColors=this.nPointsX=0;this.slabInfo=this.fixedLattice=null;this.thisSet=this.slabValue=-2147483648;this.rendering=null;this.thisContour=-1;this.translucency=0;this.vertexColors=this.vertexColorMap=this.vContours=null;this.voxelVolume=0});e(c$,"setSurfaceInfo",function(a,b,c,d){this.jvxlSurfaceData=d;0==this.jvxlSurfaceData.indexOf("--")&&(this.jvxlSurfaceData=this.jvxlSurfaceData.substring(2));this.jvxlPlane=a;this.mapLattice=
b;this.nSurfaceInts=c},"JU.P4,JU.P3,~N,~S");e(c$,"setSurfaceInfoFromBitSet",function(a,b){this.setSurfaceInfoFromBitSetPts(a,b,null)},"JU.BS,JU.P4");e(c$,"setSurfaceInfoFromBitSetPts",function(a,b,c){var d=new JU.SB;a=null!=b?0:J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(a,this.nPointsX*this.nPointsY*this.nPointsZ,d);this.setSurfaceInfo(b,c,a,d.toString())},"JU.BS,JU.P4,JU.P3");e(c$,"jvxlUpdateInfo",function(a,b){this.title=a;this.nBytes=b},"~A,~N");c$.updateSurfaceData=e(c$,"updateSurfaceData",
function(a,b,c,d,h){if(0==a.length)return"";a=a.toCharArray();for(var e=0,g=0;e<c;e+=d,g++)Float.isNaN(b[e])&&(a[g]=h);return String.copyValueOf(a)},"~S,~A,~N,~N,~S")});E("J.jvxl.data");H(["JU.MeshSurface"],"J.jvxl.data.MeshData",["java.lang.Float","java.util.Arrays","JU.AU","$.BS","$.V3"],function(){c$=N(function(){this.setsSuccessful=!1;this.vertexIncrement=1;this.polygonColorData=null;ja("J.jvxl.data.MeshData.SSet")||J.jvxl.data.MeshData.$MeshData$SSet$();ja("J.jvxl.data.MeshData.SortSet")||J.jvxl.data.MeshData.$MeshData$SortSet$();
K(this,arguments)},J.jvxl.data,"MeshData",JU.MeshSurface);e(c$,"addVertexCopy",function(a,b,c,d){0>c&&(this.vertexIncrement=-c);return this.addVCVal(a,b,d)},"JU.T3,~N,~N,~B");e(c$,"getSurfaceSet",function(){return null==this.surfaceSet?this.getSurfaceSetForLevel(0):this.surfaceSet});e(c$,"getSurfaceSetForLevel",function(a){0==a&&(this.surfaceSet=Array(100),this.nSets=0);this.setsSuccessful=!0;for(var b=0;b<this.pc;b++)if(null!=this.pis[b]&&(null==this.bsSlabDisplay||this.bsSlabDisplay.get(b))){var c=
this.pis[b],d=this.findSet(c[0]),h=this.findSet(c[1]),e=this.findSet(c[2]);0>d&&0>h&&0>e?this.createSet(c[0],c[1],c[2]):d==h&&h==e||(0<=d?(this.surfaceSet[d].set(c[1]),this.surfaceSet[d].set(c[2]),0<=h&&h!=d&&this.mergeSets(d,h),0<=e&&(e!=d&&e!=h)&&this.mergeSets(d,e)):0<=h?(this.surfaceSet[h].set(c[0]),this.surfaceSet[h].set(c[2]),0<=e&&e!=h&&this.mergeSets(h,e)):(this.surfaceSet[e].set(c[0]),this.surfaceSet[e].set(c[1])))}for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&c++;d=Array(this.surfaceSet.length);
for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&(d[c++]=this.surfaceSet[b]);this.nSets=c;this.surfaceSet=d;!this.setsSuccessful&&2>a&&this.getSurfaceSetForLevel(a+1);if(0==a){a=Array(this.nSets);for(b=0;b<this.nSets;b++)a[b]=ia(J.jvxl.data.MeshData.SSet,this,null,this.surfaceSet[b]);java.util.Arrays.sort(a,ia(J.jvxl.data.MeshData.SortSet,this,null));for(b=0;b<this.nSets;b++)this.surfaceSet[b]=a[b].bs;this.setVertexSets(!1)}return this.surfaceSet},"~N");e(c$,"setVertexSets",function(a){if(null!=
this.surfaceSet){for(var b=0,c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&0>this.surfaceSet[c].nextSetBit(0)&&(this.surfaceSet[c]=null),null==this.surfaceSet[c]&&b++;if(0<b){a=Array(this.nSets-b);for(var d=c=0;c<this.nSets;c++)null!=this.surfaceSet[c]&&(a[d++]=this.surfaceSet[c]);this.surfaceSet=a;this.nSets-=b}else if(a)return;this.vertexSets=v(this.vc,0);for(c=0;c<this.nSets;c++)for(b=this.surfaceSet[c].nextSetBit(0);0<=b;b=this.surfaceSet[c].nextSetBit(b+1))this.vertexSets[b]=c}},"~B");e(c$,
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b){this.surfaceSet[a].or(this.surfaceSet[b]);this.surfaceSet[b]=null},"~N,~N");e(c$,"invalidateSurfaceSet",function(a){for(var b=this.surfaceSet[a].nextSetBit(0);0<=b;b=this.surfaceSet[a].nextSetBit(b+1))this.vvs[b]=NaN;this.surfaceSet[a]=null},"~N");c$.checkCutoff=e(c$,"checkCutoff",function(a,b,c,d){if(0>a||0>b||0>c)return!1;a=d[a];b=d[b];c=d[c];return 0<=a&&0<=b&&0<=c||0>=a&&0>=b&&0>=c},"~N,~N,~N,~A");c$.calculateVolumeOrArea=e(c$,"calculateVolumeOrArea",function(a,b,c,d){(d||0>=a.nSets)&&a.getSurfaceSet();
for(var h=(d=-1<=b)||0>=a.nSets?1:a.nSets,e=ab(h,0),g=new JU.V3,f=new JU.V3,m=new JU.V3,p=a.pc;0<=--p;)if(null!=a.setABC(p)){var n=0>=a.nSets?0:a.vertexSets[a.iA];0<=b&&n!=b||(c?(g.sub2(a.vs[a.iB],a.vs[a.iA]),f.sub2(a.vs[a.iC],a.vs[a.iA]),m.cross(g,f),e[d?0:n]+=m.length()):(g.setT(a.vs[a.iB]),f.setT(a.vs[a.iC]),m.cross(g,f),f.setT(a.vs[a.iA]),e[d?0:n]+=f.dot(m)))}a=c?2:6;for(p=0;p<h;p++)e[p]/=a;return d?Float.$valueOf(e[0]):e},"J.jvxl.data.MeshData,~N,~B,~B");e(c$,"updateInvalidatedVertices",function(a){a.clearAll();
for(var b=0;b<this.vc;b+=this.vertexIncrement)Float.isNaN(this.vvs[b])&&a.set(b)},"JU.BS");e(c$,"invalidateVertices",function(a){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.vvs[b]=NaN},"JU.BS");c$.$MeshData$SSet$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);this.bs=null;this.n=0;K(this,arguments)},J.jvxl.data.MeshData,"SSet");T(c$,function(a){this.bs=a;this.n=a.cardinality()},"JU.BS");c$=ha()};c$.$MeshData$SortSet$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);
K(this,arguments)},J.jvxl.data.MeshData,"SortSet",null,java.util.Comparator);k(c$,"compare",function(a,b){return a.n>b.n?-1:a.n<b.n?1:0},"J.jvxl.data.MeshData.SSet,J.jvxl.data.MeshData.SSet");c$=ha()};aa(c$,"MODE_GET_VERTICES",1,"MODE_GET_COLOR_INDEXES",2,"MODE_PUT_SETS",3,"MODE_PUT_VERTICES",4)});E("J.jvxl.readers");H(null,"J.jvxl.readers.XmlReader",["JU.P3","$.PT","$.SB","JU.Escape"],function(){c$=N(function(){this.line=this.br=null;K(this,arguments)},J.jvxl.readers,"XmlReader");e(c$,"getLine",
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"<"+b+">","</"+b+">",!1)},"~S,~S");c$.extractTag=e(c$,"extractTag",function(a,b,c,d){b=a.indexOf(b);if(0>b)return"";var h=a.indexOf(c,b);0>h&&(h=a.indexOf("/>",b),c="/>");if(0>h)return"";if(d)return h+=c.length,a.substring(b,h);for(c=!1;b<h;b++)if('"'==(d=a.charAt(b)))c=!c;else if(c&&"\\"==d)b++;else if(!c&&(">"==d||"/"==d))break;if(b>=h)return"";for(;JU.PT.isWhitespace(a.charAt(++b)););return J.jvxl.readers.XmlReader.unwrapCdata(a.substring(b,h))},"~S,~S,~S,~B");c$.unwrapCdata=e(c$,"unwrapCdata",
function(a){return a.startsWith("<![CDATA[")&&a.endsWith("]]\x3e")?JU.PT.rep(a.substring(9,a.length-3),"]]]]\x3e<![CDATA[>","]]\x3e"):a},"~S");c$.getXmlAttrib=e(c$,"getXmlAttrib",function(a,b){var c=v(1,0),d=J.jvxl.readers.XmlReader.setNext(a,b,c,1);if(2>d||2>(d=J.jvxl.readers.XmlReader.setNext(a,'"',c,0)))return"";c=J.jvxl.readers.XmlReader.setNext(a,'"',c,-1);return 0>=c?"":a.substring(d,c)},"~S,~S");e(c$,"getXmlPoint",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,b).$replace("(",
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0<=this.line.indexOf("</")&&this.line.indexOf("</")==this.line.indexOf("<"))this.line=this.br.readLine();return 0<=this.line.indexOf("<"+a)},"~S")});E("J.jvxl.readers");H(["JU.P3","$.V3"],"J.jvxl.readers.SurfaceGenerator","java.lang.Float java.util.Map JU.AU $.BS $.Measure $.P4 $.PT $.Rdr J.jvxl.data.JvxlCoder $.JvxlData $.MeshData $.VolumeData J.jvxl.readers.Parameters $.SurfaceReader JU.Logger JV.FileManager".split(" "),function(){c$=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;K(this,arguments)},J.jvxl.readers,"SurfaceGenerator");$(c$,function(){this.vAB=new JU.V3;this.vNorm=new JU.V3;this.ptRef=JU.P3.new3(0,0,1E15)});T(c$,function(a,b,c,d){this.atomDataServer=a;this.meshDataServer=b;this.params=new J.jvxl.readers.Parameters;this.meshData=null==c?
new J.jvxl.data.MeshData:c;this.jvxlData=null==d?new J.jvxl.data.JvxlData:d;this.volumeDataTemp=new J.jvxl.data.VolumeData;this.initializeIsosurface()},"J.atomdata.AtomDataServer,J.jvxl.api.MeshDataServer,J.jvxl.data.MeshData,J.jvxl.data.JvxlData");e(c$,"setJvxlData",function(a){this.jvxlData=a;null!=a&&(a.version=this.version)},"J.jvxl.data.JvxlData");e(c$,"setProp",function(a,b){if("debug"===a){var c=b.booleanValue();this.params.logMessages=c;this.params.logCube=c;return!0}if("init"===a)return this.initializeIsosurface(),
I(b,J.jvxl.readers.Parameters)?this.params=b:(this.params.script=b,null!=this.params.script&&0<=this.params.script.indexOf(";#")&&(this.params.script=JU.PT.rep(this.params.script,";#","; #"))),!1;if("silent"===a)return this.params.isSilent=!0;if("map"===a)return this.params.resetForMapping(b.booleanValue()),null!=this.surfaceReader&&(this.surfaceReader.minMax=null),!0;if("finalize"===a)return this.initializeIsosurface(),!0;if("clear"===a)return null!=this.surfaceReader&&this.surfaceReader.discardTempData(!0),
!1;if("fileIndex"===a)return this.params.fileIndex=b.intValue(),0>this.params.fileIndex&&(this.params.fileIndex=0),this.params.readAllData=!1,!0;if("blockData"===a)return this.params.blockCubeData=b.booleanValue(),!0;if("withinPoints"===a)return this.params.boundingBox=b[1],!0;if("boundingBox"===a)return this.params.boundingBox=B(-1,[JU.P3.newP(b[0]),JU.P3.newP(b[b.length-1])]),!0;if("func"===a)return this.params.func=b,!0;if("intersection"===a)return this.params.intersection=b,!0;if("bsSolvent"===
a)return this.params.bsSolvent=b,!0;if("select"===a)return this.params.bsSelected=b,!0;if("ignore"===a)return this.params.bsIgnore=b,!0;if("propertySmoothing"===a)return this.params.propertySmoothing=b.booleanValue(),!0;if("propertyDistanceMax"===a)return this.params.propertyDistanceMax=b.floatValue(),!0;if("propertySmoothingPower"===a)return this.params.propertySmoothingPower=b.intValue(),!0;if("title"===a){if(null==b)this.params.title=null;else if(JU.AU.isAS(b)&&(this.params.title=b,JU.Logger.debugging))for(var d=
0;d<this.params.title.length;d++)0<this.params.title[d].length&&JU.Logger.info(this.params.title[d]);return!0}if("sigma"===a)return this.params.cutoff=this.params.sigma=b.floatValue(),this.params.isPositiveOnly=!1,this.params.cutoffAutomatic=!1,!0;if("cutoff"===a)return this.params.cutoff=b.floatValue(),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("cutoffPositive"===a)return this.params.cutoff=b.floatValue(),this.params.isPositiveOnly=!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=!0,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(I(b,JU.P3)){var c=this.params.contourIncrements=b,d=c.x,h=c.y,e=c.z;0>=e&&(e=1);for(var c=0,g=d;g<=h+e/10;g+=e,c++);this.params.contoursDiscrete=
y(c,0);g=d;for(d=0;d<c;d++,g+=e)this.params.contoursDiscrete[d]=g;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.$valueOf(this.params.distance),this.surfaceReader=
this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("ellipsoid"===a){if(I(b,JU.P4))this.params.setEllipsoidP4(b);else if(JU.AU.isAF(b))this.params.setEllipsoidAF(b);else return!0;this.readerData=Float.$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=y(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("rad"===a)return this.params.setRadical(b),this.readerData=y(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lobe"===a)return this.params.setLobe(b),this.readerData=y(-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=y(-1,[this.params.psi_n,this.params.psi_l,this.params.psi_m,this.params.psi_Znuc,this.params.psi_monteCarloCount]);this.surfaceReader=this.newReader("IsoShapeReader");this.processState();return!0}if("functionXY"===a)return this.params.setFunctionXY(b),this.params.isContoured&&this.volumeDataTemp.setPlaneParameters(null==this.params.thePlane?this.params.thePlane=JU.P4.new4(0,0,1,0):this.params.thePlane),0<=this.params.functionInfo.get(0).indexOf("_xyz")&&this.getFunctionZfromXY(),
this.processState(),!0;if("functionXYZ"===a)return this.params.setFunctionXYZ(b),this.processState(),!0;if("lcaoType"===a)return this.params.setLcao(b,this.colorPtr),!0;if("lcaoCartoonCenter"===a){if(2!=++this.params.state)return!0;Float.isNaN(this.params.center.x)&&this.params.center.setT(b);return!1}if("molecular"===a||"solvent"===a||"sasurface"===a||"nomap"===a)return this.params.setSolvent(a,b.floatValue()),this.params.isSilent||JU.Logger.info(this.params.calculationType),this.processState(),
!0;if("moData"===a)return this.params.moData=b,!0;if("mepCalcType"===a)return this.params.mep_calcType=b.intValue(),!0;if("mep"===a)return this.params.setMep(b,!1),this.processState(),!0;if("mlp"===a)return this.params.setMep(b,!0),this.processState(),!0;if("nci"===a)return c=b.booleanValue(),this.params.setNci(c),c&&this.processState(),!0;if("calculationType"===a)return this.params.calculationType=b,!0;if("charges"===a)return this.params.theProperty=b,!0;if("randomSeed"===a)return this.params.randomSeed=
b.intValue(),!0;if("molecularOrbital"===a)return c=0,d=null,I(b,Integer)?c=b.intValue():d=b,this.params.setMO(c,d),JU.Logger.info(this.params.calculationType),this.processState(),!0;if("fileType"===a)return this.fileType=b,!0;if("fileName"===a)return this.params.fileName=b,!0;if("filesData"===a)return this.params.filesData=b,!0;if("outputChannel"===a)return this.out=b,!0;if("readFile"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,b)))return JU.Logger.error("Could not set the surface data"),
!0;this.surfaceReader.setOutputChannel(this.out);this.generateSurface();return!0}if("mapColor"===a){if(null==(this.surfaceReader=this.setFileData(this.atomDataServer,b)))return JU.Logger.error("Could not set the mapping data"),!0;this.surfaceReader.setOutputChannel(this.out);this.mapSurface();return!0}if("getSurfaceSets"===a)return this.getSurfaceSets(),!0;"periodic"===a&&(this.params.isPeriodic=!0);return!1},"~S,~O,JU.BS");e(c$,"newReader",function(a){a=J.jvxl.readers.SurfaceGenerator.getInterface(a);
null!=a&&a.init(this);return a},"~S");e(c$,"newReaderBr",function(a,b){var c=J.jvxl.readers.SurfaceGenerator.getInterface(a);null!=c&&c.init2(this,b);return c},"~S,java.io.BufferedReader");c$.getInterface=e(c$,"getInterface",function(a){try{var b=Za._4Name("J.jvxl.readers."+a);return null==b?null:b.newInstance()}catch(c){if(U(c,Exception))return JU.Logger.error("Interface.java Error creating instance for "+a+": \n"+c.toString()),null;throw c;}},"~S");e(c$,"getSurfaceSets",function(){null==this.meshDataServer?
this.meshData.getSurfaceSet():(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.getSurfaceSet(),this.meshDataServer.fillMeshData(this.meshData,3,null))});e(c$,"processState",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;2<=this.params.state?this.mapSurface():this.generateSurface()});e(c$,"setReader",function(){this.readerData=null;if(null!=this.surfaceReader)return!this.surfaceReader.vertexDataOnly;switch(this.params.dataType){case 1207:this.surfaceReader=
this.newReader("IsoPlaneReader");break;case 1208:this.surfaceReader=this.newReader("AtomPropertyMapper");break;case 1328:case 1329:this.readerData=1328==this.params.dataType?"Mep":"Mlp";this.surfaceReader=3==this.params.state?this.newReader("AtomPropertyMapper"):this.newReader("Iso"+this.readerData+"Reader");break;case 1334:this.surfaceReader=this.newReader("IsoIntersectFileReader");break;case 1333:this.surfaceReader=this.newReader("IsoIntersectAtomReader");break;case 1195:case 1203:case 1196:this.surfaceReader=
this.newReader("IsoSolventReader");break;case 1844:case 1837:this.surfaceReader=this.newReader("IsoMOReader");break;case 8:this.surfaceReader=this.newReader("IsoFxyReader");break;case 9:this.surfaceReader=this.newReader("IsoFxyzReader")}JU.Logger.debugging&&JU.Logger.info("Using surface reader "+this.surfaceReader);this.params.isSilent&&null!=this.surfaceReader&&(this.surfaceReader.isQuiet=!0);return!0});e(c$,"generateSurface",function(){if(2==++this.params.state){this.setReader();var a=null!=this.meshDataServer;
this.params.colorBySign&&(this.params.isBicolorMap=!0);if(null==this.surfaceReader)JU.Logger.error("surfaceReader is null for "+this.params.dataType);else if(this.surfaceReader.createIsosurface(!1)){null!=this.params.pocket&&a&&this.surfaceReader.selectPocket(!this.params.pocket.booleanValue());0<this.params.minSet&&this.surfaceReader.excludeMinimumSet();0<this.params.maxSet&&this.surfaceReader.excludeMaximumSet();null!=this.params.slabInfo&&this.surfaceReader.slabIsosurface(this.params.slabInfo);
a&&this.meshDataServer.notifySurfaceGenerationCompleted()&&(this.surfaceReader.hasColorData=!1);0<=this.jvxlData.thisSet&&this.getSurfaceSets();this.jvxlData.jvxlDataIs2dContour&&(this.surfaceReader.colorIsosurface(),this.params.state=3);this.jvxlData.jvxlDataIsColorDensity&&(this.params.state=3);if(this.params.colorBySign||this.params.isBicolorMap)this.params.state=3,this.surfaceReader.applyColorScale();null!=this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=null,this.surfaceReader.hasColorData=
!1);this.surfaceReader.jvxlUpdateInfo();this.marchingSquares=this.surfaceReader.marchingSquares;this.surfaceReader.discardTempData(!1);this.params.mappedDataMin=3.4028235E38;this.surfaceReader.closeReader();if(3!=this.params.state&&(this.surfaceReader.hasColorData||this.params.colorDensity))this.params.state=3,this.colorIsosurface();this.surfaceReader=null}else JU.Logger.error("Could not create isosurface"),this.params.cutoff=NaN,this.surfaceReader.closeReader()}});e(c$,"mapSurface",function(){1==
this.params.state&&null!=this.params.thePlane&&this.params.state++;if(!(3>++this.params.state)&&this.setReader()){this.params.isPeriodic&&(this.surfaceReader.volumeData.isPeriodic=!0);if(null!=this.params.thePlane){var a=this.params.isSquared;this.params.isSquared=!1;this.params.cutoff=0;this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);this.surfaceReader.createIsosurface(!this.params.isPeriodic);this.surfaceReader.volumeData.setMappingPlane(null);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted();
if(1207==this.params.dataType){this.surfaceReader.discardTempData(!0);return}this.params.isSquared=a;this.params.mappedDataMin=3.4028235E38;this.surfaceReader.readVolumeData(!0);null!=this.params.mapLattice&&(this.surfaceReader.volumeData.isPeriodic=!0)}else!this.params.colorBySets&&!this.params.colorDensity&&(this.surfaceReader.readAndSetVolumeParameters(!0),this.params.mappedDataMin=3.4028235E38,this.surfaceReader.readVolumeData(!0));this.colorIsosurface();this.surfaceReader.closeReader();this.surfaceReader=
null}});e(c$,"colorIsosurface",function(){this.surfaceReader.colorIsosurface();this.surfaceReader.jvxlUpdateInfo();this.surfaceReader.updateTriangles();this.surfaceReader.discardTempData(!0);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted()});e(c$,"getProperty",function(a,b){return"jvxlFileData"===a?J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,null,this.params.title,"",!0,b,null,null):"jvxlFileInfo"===a?J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData):null},"~S,~N");
e(c$,"setFileData",function(a,b){var c=this.fileType;this.fileType=null;if(I(b,java.util.Map)){var d=b;if(d.containsKey("__pymolSurfaceData__"))return this.readerData=d,this.newReaderBr("PyMOLMeshReader",null);b=d.get("volumeData")}if(I(b,J.jvxl.data.VolumeData))return this.volumeDataTemp=b,this.newReader("VolumeDataReader");d=null;I(b,String)&&(d=b,b=JU.Rdr.getBR(b));if(I(b,Array)){for(var c=b[0],d=Array(c.length),h=0;h<c.length;h++)d[h]=this.setFileData(a,c[h]);b[0]=d;this.readerData=b;return this.newReader("IsoIntersectGridReader")}h=
b;null==c&&(c=JV.FileManager.determineSurfaceFileType(h));if(null!=c&&c.startsWith("UPPSALA")){var e=this.params.fileName,e=e.substring(0,e.indexOf("/",10)),e=e+JU.PT.getQuotedStringAt(c,c.indexOf("A HREF")+1);this.params.fileName=e;b=this.atomDataServer.getBufferedInputStream(e);if(null==b)return JU.Logger.error("Isosurface: could not open file "+e),null;try{h=JU.Rdr.getBufferedReader(b,null)}catch(g){if(!U(g,Exception))throw g;}c=JV.FileManager.determineSurfaceFileType(h)}null==c&&(c="UNKNOWN");
JU.Logger.info("data file type was determined to be "+c);if(c.equals("Jvxl+"))return this.newReaderBr("JvxlReader",h);this.readerData=B(-1,[this.params.fileName,d]);0<="MRC DELPHI DSN6".indexOf(c.toUpperCase())&&(c+="Binary");return this.newReaderBr(c+"Reader",h)},"JV.Viewer,~O");e(c$,"getReaderData",function(){var a=this.readerData;this.readerData=null;return a});e(c$,"initializeIsosurface",function(){this.params.initialize();this.colorPtr=0;this.marchingSquares=this.surfaceReader=null;this.initState()});
e(c$,"initState",function(){this.params.state=1;this.params.dataType=this.params.surfaceType=0});e(c$,"setLcao",function(){this.params.colorPos=this.params.colorPosLCAO;this.params.colorNeg=this.params.colorNegLCAO;return this.params.lcaoType});e(c$,"getFunctionZfromXY",function(){for(var a=this.params.functionInfo.get(1),b=v(3,0),c=v(3,0),d=Array(3),h=0;3>h;h++){var e=this.params.functionInfo.get(h+2);b[h]=Math.abs(F(e.x));d[h]=JU.V3.new3(e.y,e.z,e.w)}for(var e=b[0],b=b[1],g=new JU.P3,f=new JU.P3,
m=new JU.P3,p=new JU.P3,n=this.params.functionInfo.get(5),q=y(e,b,0),r,h=0;h<e;h++)for(var k=0;k<b;k++){g.scaleAdd2(h,d[0],a);g.scaleAdd2(k,d[1],g);var u=J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(g.x,g.y,n,c);f.set((r=n[c[0]])[0],r[1],r[2]);1E-5>u?g.z=r[2]:(m.set((r=n[c[1]])[0],r[1],r[2]),p.set((r=n[c[2]])[0],r[1],r[2]),g.z=this.distanceVerticalToPlane(g.x,g.y,f,m,p));q[h][k]=g.z}this.params.functionInfo.set(5,q)});e(c$,"distanceVerticalToPlane",function(a,b,c,d,h){c=JU.Measure.getDirectedNormalThroughPoints(c,
d,h,this.ptRef,this.vNorm,this.vAB);return(this.vNorm.x*a+this.vNorm.y*b+c)/-this.vNorm.z},"~N,~N,JU.P3,JU.P3,JU.P3");c$.findNearestThreePoints=e(c$,"findNearestThreePoints",function(a,b,c,d){var h,e,g,f,m,p,n;m=p=n=-1;e=g=f=3.4028235E38;for(var q=c.length;0<=--q;)h=(h=c[q][0]-a)*h+(h=c[q][1]-b)*h,h<e?(f=g,g=e,e=h,n=p,p=m,m=q):h<g?(f=g,g=h,n=p,p=q):h<f&&(f=h,n=q);d[0]=m;d[1]=p;d[2]=n;return e},"~N,~N,~A,~A");e(c$,"addRequiredFile",function(a){null!=this.meshDataServer&&this.meshDataServer.addRequiredFile(a)},
"~S");e(c$,"setRequiredFile",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setRequiredFile(a,b)},"~S,~S");e(c$,"log",function(a){null==this.atomDataServer?System.out.println(a):this.atomDataServer.log(a)},"~S");e(c$,"setOutputChannel",function(a,b){null!=this.meshDataServer&&this.meshDataServer.setOutputChannel(a,b)},"javajs.api.GenericBinaryDocument,JU.OC");e(c$,"fillAtomData",function(a,b){0!=(b&2)&&null!=a.bsSelected&&(null==this.bsVdw&&(this.bsVdw=new JU.BS),this.bsVdw.or(a.bsSelected));
this.atomDataServer.fillAtomData(a,b)},"J.atomdata.AtomData,~N");e(c$,"getOriginVaVbVc",function(){return null==this.surfaceReader.volumeData?null:this.surfaceReader.volumeData.oabc})});E("J.jvxl.readers");H(null,"J.jvxl.readers.Parameters","java.lang.Float java.util.Hashtable JU.A4 $.Lst $.M3 $.P3 $.P4 $.V3 JU.Escape $.Logger".split(" "),function(){c$=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.sigma=this.cutoff=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.isModelConnected=!1;this.filesData=this.surfaceAtoms=null;K(this,arguments)},J.jvxl.readers,"Parameters");$(c$,function(){this.anisotropy=y(3,0)});e(c$,"initialize",function(){this.addHydrogens=!1;this.allowVolumeRender=!0;this.atomRadiusData=null;this.atomIndex=-1;this.blockCubeData=!1;this.boundingBox=null;this.bsExcluded=Array(4);this.bsSolvent=this.bsSelected=this.bsIgnore=
null;this.calculationType="";this.center=new JU.P3;this.resetForMapping(!0);this.colorBySign=this.colorByPhase=this.colorBySets=!1;this.colorEncoder=null;this.colorNeg=-65536;this.colorNegLCAO=-8388480;this.colorPos=-16776961;this.colorPosLCAO=-23296;this.colorRgb=-2147483648;this.colorSchemeTranslucent=!1;this.contourColixes=this.contoursDiscrete=this.contourIncrements=this.contactPair=null;this.contourFromZero=!0;this.cutoff=3.4028235E38;this.cutoffAutomatic=!0;this.dataXYReversed=!1;this.distance=
3.4028235E38;this.doFullMolecular=!1;this.envelopeRadius=10;this.extendGrid=0;this.fileIndex=1;this.readAllData=!0;this.fileName="";this.filesData=null;this.fullyLit=!1;this.functionInfo=null;this.logCube=this.logCompression=this.isSilent=this.isPeriodic=this.isMapped=this.isEccentric=this.isContoured=this.isSquaredLinear=this.isSquared=this.isModelConnected=this.isColorReversed=this.isCavity=this.isBicolorMap=this.isCutoffAbsolute=this.isPositiveOnly=this.isAngstroms=this.insideOut=this.iAddGridPoints=
!1;this.logMessages=JU.Logger.debugging;this.mapLattice=null;this.mep_calcType=-1;this.minSet=0;this.modelIndex=-1;this.modelInvRotation=null;this.nContours=0;this.pocket=null;this.pointSize=NaN;this.propertyDistanceMax=2147483647;this.propertySmoothing=!1;this.propertySmoothingPower=4;this.rangeSelected=this.rangeAll=this.rangeDefined=!1;this.resolution=3.4028235E38;this.scale=NaN;this.scale3d=0;this.sigma=NaN;this.slabInfo=null;this.solventExtendedAtomRadius=0;this.state=1;this.testFlags=0;this.theProperty=
this.thePlane=null;this.thisContour=-1;this.title=null;this.usePropertyForColorRange=!0;this.vertexSource=null});e(c$,"resetForMapping",function(a){a||(this.state=2);this.center.x=NaN;this.colorDensity=!1;this.intersection=this.func=null;this.isAnisotropic=!1;this.isMapped=!0;this.mappedDataMin=3.4028235E38;this.points=this.parameters=this.origin=null;this.qmOrbitalType=0;this.volumeData=this.steps=null},"~B");e(c$,"setAnisotropy",function(a){this.anisotropy[0]=a.x;this.anisotropy[1]=a.y;this.anisotropy[2]=
a.z;this.isAnisotropic=!0;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P3");e(c$,"setEccentricity",function(a){var b=JU.V3.new3(a.x,a.y,a.z),c=0<this.scale?this.scale:0>a.w?1:b.length();a=Math.abs(a.w);b.normalize();var d=JU.V3.new3(0,0,1);b.add(d);b.normalize();Float.isNaN(b.x)&&b.set(1,0,0);this.eccentricityMatrixInverse=new JU.M3;this.eccentricityMatrixInverse.invertM(this.eccentricityMatrix=(new JU.M3).setAA(JU.A4.newVA(b,3.141592653589793)));this.isEccentric=this.isAnisotropic=!0;
this.eccentricityScale=c;this.eccentricityRatio=a;1<a&&(this.eccentricityScale*=a);this.anisotropy[0]=a*c;this.anisotropy[1]=a*c;this.anisotropy[2]=c;Float.isNaN(this.center.x)&&this.center.set(0,0,0)},"JU.P4");e(c$,"setPlane",function(a){this.thePlane=a;0==this.thePlane.x&&(0==this.thePlane.y&&0==this.thePlane.z)&&(this.thePlane.z=1);this.isContoured=!0},"JU.P4");e(c$,"setSphere",function(a,b){this.dataType=b?74:65;this.distance=a;this.setEccentricity(JU.P4.new4(0,0,1,1));this.cutoff=1.4E-45;this.isCutoffAbsolute=
!1;this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" SPHERE "+a+";"},"~N,~B");e(c$,"setEllipsoidP4",function(a){this.dataType=66;this.distance=1;this.setEccentricity(a);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages},"JU.P4");e(c$,"setEllipsoidAF",function(a){this.anisoB=a;this.dataType=67;this.distance=0.3*(Float.isNaN(this.scale)?1:this.scale);this.cutoff=1.4E-45;this.isCutoffAbsolute=!1;this.isSilent=!this.logMessages;Float.isNaN(this.center.x)&&
this.center.set(0,0,0);3.4028235E38==this.resolution&&(this.resolution=6)},"~A");e(c$,"setLobe",function(a){this.dataType=68;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=this.getScriptParams()+" LOBE {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(c$,"getScriptParams",function(){return" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)});e(c$,"setLp",function(a){this.dataType=
70;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" LP {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(c$,"setRadical",function(a){this.dataType=71;this.setEccentricity(a);3.4028235E38==this.cutoff&&(this.cutoff=0.14,this.isSquared&&(this.cutoff*=this.cutoff));this.isSilent=!this.logMessages;this.script=
" center "+JU.Escape.eP(this.center)+(Float.isNaN(this.scale)?"":" scale "+this.scale)+" RAD {"+a.x+" "+a.y+" "+a.z+" "+a.w+"};"},"JU.P4");e(c$,"setLcao",function(a,b){this.lcaoType=a;1==b&&(this.colorPosLCAO=this.colorNegLCAO);this.isSilent=!this.logMessages},"~S,~N");e(c$,"setSolvent",function(a,b){this.isEccentric=this.isAnisotropic=!1;this.solventRadius=Math.abs(b);this.dataType=null!=this.intersection?1333:"nomap"===a?1207:"molecular"===a?1203:"sasurface"===a||0==this.solventRadius?1196:1195;
if(2>this.state&&(this.cutoffAutomatic||!this.colorDensity)&&(null==this.intersection||3.4028235E38==this.cutoff))this.cutoff=0;switch(this.dataType){case 1333:this.calculationType="VDW intersection";break;case 1207:this.calculationType="unmapped plane";break;case 1203:this.calculationType="molecular surface with radius "+this.solventRadius;break;case 1195:this.calculationType="solvent-excluded surface with radius "+this.solventRadius;break;case 1196:this.calculationType="solvent-accessible surface with radius "+
this.solventRadius}switch(this.dataType){case 1207:this.solventExtendedAtomRadius=this.solventRadius;this.solventRadius=0;this.isContoured=!1;break;case 1203:this.solventExtendedAtomRadius=0;break;case 1195:this.solventExtendedAtomRadius=0;null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent);break;case 1196:this.solventExtendedAtomRadius=this.solventRadius,this.solventRadius=0,null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&
this.bsIgnore.or(this.bsSolvent)}},"~S,~N");e(c$,"setFunctionXY",function(a){this.dataType=8;this.functionInfo=a;this.cutoff=1.4E-45;this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setFunctionXYZ",function(a){this.dataType=9;this.functionInfo=a;3.4028235E38==this.cutoff&&(this.cutoff=1.4E-45);this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setAtomicOrbital",function(a){this.dataType=1294;this.setEccentricity(JU.P4.new4(0,0,1,1));this.psi_n=F(a[0]);this.psi_l=F(a[1]);this.psi_m=F(a[2]);
this.psi_Znuc=a[3];this.psi_monteCarloCount=F(a[4]);this.distance=a[5];if(0!=this.distance||null!=this.thePlane)this.allowVolumeRender=!1;this.randomSeed=F(a[6]);this.psi_ptsPerAngstrom=10;if(3.4028235E38==this.cutoff||0.14==this.cutoff)this.cutoff=0<this.psi_monteCarloCount?0:0.04,this.isSquared&&(this.cutoff*=this.cutoff);this.isCutoffAbsolute=!0;2>this.state&&(null==this.thePlane&&this.colorBySign)&&(this.isBicolorMap=!0);return 0<this.psi_Znuc&&Math.abs(this.psi_m)<=this.psi_l&&this.psi_l<this.psi_n},
"~A");e(c$,"setMep",function(a,b){this.dataType=b?1329:1328;this.theProperty=a;this.isEccentric=this.isAnisotropic=this.usePropertyForColorRange=!1;3.4028235E38==this.cutoff&&(this.cutoff=0.1,this.isSquared&&(this.cutoff*=this.cutoff));this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;this.contourFromZero=!1;2<=this.state||null!=this.thePlane?!this.rangeDefined&&!this.rangeAll&&(this.valueMappedToRed=-0.1,this.valueMappedToBlue=0.1,this.rangeDefined=!0):this.isBicolorMap=this.colorBySign=
!0},"~A,~B");e(c$,"setNci",function(a){this.fullyLit=!0;this.qm_gridMax=200;a&&(this.dataType=1844);this.qm_marginAngstroms=2;this.qmOrbitalType=a?3:4;if(a&&(null==this.parameters||2>this.parameters.length))this.parameters=y(-1,[this.cutoff,2]);if(3.4028235E38==this.cutoff||0==this.cutoff)this.cutoff=0.3;this.isSquared&&(this.cutoff*=this.cutoff);null==this.title&&(this.title=[]);this.moData=new java.util.Hashtable},"~B");e(c$,"setMO",function(a,b){this.isModelConnected=!0;this.qm_moLinearCombination=
b;this.qm_moNumber=null==b?Math.abs(a):F(b[1]);this.qmOrbitalType=this.moData.containsKey("haveVolumeData")?5:this.moData.containsKey("gaussians")?1:this.moData.containsKey("slaters")?2:0;var c=0>=a&&null==b;0==this.qmOrbitalType?(JU.Logger.error("MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?)"),this.title=B(-1,["no basis functions found in file"])):(this.qmOrbitalCount=this.moData.get("mos").size(),this.calculationType=this.moData.get("calculationType"),
this.calculationType="Molecular orbital #"+this.qm_moNumber+"/"+this.qmOrbitalCount+" "+(null==this.calculationType?"":this.calculationType),!c&&null==this.title&&(this.title=Array(5),this.title[0]="%F",this.title[1]="Model %M  MO %I/%N %T",this.title[2]="?Energy = %E %U",this.title[3]="?Symmetry = %S",this.title[4]="?Occupancy = %O"));this.dataType=1837;3.4028235E38==this.cutoff&&(this.cutoff=c?0.01:0.05);if(this.isSquared||this.isSquaredLinear)this.cutoff*=this.cutoff;this.isEccentric=this.isAnisotropic=
!1;this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;2<=this.state||null!=this.thePlane||(this.colorBySign=!0,this.colorByPhase&&0==this.colorPhase&&(this.colorByPhase=!1),this.isBicolorMap=!0)},"~N,~A");e(c$,"setMapRanges",function(a,b){if(!this.colorDensity&&(this.colorByPhase||this.colorBySign||(null!=this.thePlane||this.isBicolorMap)&&!this.isContoured))this.mappedDataMin=-1,this.mappedDataMax=1;if(3.4028235E38==this.mappedDataMin||this.mappedDataMin==this.mappedDataMax){var c=a.getMinMaxMappedValues(b);
System.out.println("parameters - setmapranges "+c[0]+" "+c[1]);this.mappedDataMin=c[0];this.mappedDataMax=c[1]}0==this.mappedDataMin&&0==this.mappedDataMax&&(this.mappedDataMin=-1,this.mappedDataMax=1);this.rangeDefined||(this.valueMappedToRed=this.mappedDataMin,this.valueMappedToBlue=this.mappedDataMax)},"J.jvxl.readers.SurfaceReader,~B");e(c$,"addSlabInfo",function(a){null==this.slabInfo&&(this.slabInfo=new JU.Lst);this.slabInfo.addLast(a)},"~A");e(c$,"isInsideOut",function(){return this.insideOut!=
this.dataXYReversed});e(c$,"isFullyLit",function(){return null!=this.thePlane||this.fullyLit});aa(c$,"STATE_UNINITIALIZED",0,"STATE_INITIALIZED",1,"STATE_DATA_READ",2,"STATE_DATA_COLORED",3,"NO_ANISOTROPY",32,"IS_SILENT",64,"IS_SOLVENTTYPE",128,"HAS_MAXGRID",256,"IS_POINTMAPPABLE",512,"IS_SLABBABLE",1024,"SURFACE_NONE",0,"SURFACE_SPHERE",65,"SURFACE_ELLIPSOID2",66,"SURFACE_ELLIPSOID3",67,"SURFACE_LOBE",68,"SURFACE_LCAOCARTOON",69,"SURFACE_LONEPAIR",70,"SURFACE_RADICAL",71,"SURFACE_FUNCTIONXY",8,"SURFACE_FUNCTIONXYZ",
9,"SURFACE_GEODESIC",74,"SURFACE_SOLVENT",1195,"SURFACE_SASURFACE",1196,"SURFACE_MOLECULARORBITAL",1837,"SURFACE_ATOMICORBITAL",1294,"SURFACE_MEP",1328,"SURFACE_MLP",1329,"SURFACE_MOLECULAR",1203,"SURFACE_NCI",1844,"SURFACE_INTERSECT_ATOM",1333,"SURFACE_INTERSECT_FILE",1334,"SURFACE_NOMAP",1207,"SURFACE_PROPERTY",1208,"ANGSTROMS_PER_BOHR",0.5291772,"defaultEdgeFractionBase",35,"defaultEdgeFractionRange",90,"defaultColorFractionBase",35,"defaultColorFractionRange",90,"defaultMappedDataMin",0,"defaultMappedDataMax",
1,"defaultCutoff",0.02,"defaultOrbitalCutoff",0.04,"defaultLobeCutoff",0.14,"defaultOrbitalCutoffOld",0.14,"defaultQMOrbitalCutoff",0.05,"defaultQMElectronDensityCutoff",0.01,"defaultContourCount",11,"nContourMax",100,"defaultColorNegative",4294901760,"defaultColorPositive",4278190335,"defaultColorNegativeLCAO",4286578816,"defaultColorPositiveLCAO",4294944E3,"defaultSolventRadius",1.2,"defaultMepCutoff",0.1,"defaultMepMin",-0.1,"defaultMepMax",0.1,"MEP_MAX_GRID",40,"QM_TYPE_UNKNOWN",0,"QM_TYPE_GAUSSIAN",
1,"QM_TYPE_SLATER",2,"QM_TYPE_NCI_PRO",3,"QM_TYPE_NCI_SCF",4,"QM_TYPE_VOLUME_DATA",5,"MO_MAX_GRID",80)});E("J.jvxl.readers");H(["J.jvxl.api.VertexDataServer","JU.P3"],"J.jvxl.readers.SurfaceReader","java.lang.Float JU.AU $.BS J.jvxl.calc.MarchingCubes $.MarchingSquares J.jvxl.data.JvxlCoder $.MeshData JU.BoxInfo $.C $.ColorEncoder $.Escape $.Logger".split(" "),function(){c$=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.jvxlNSurfaceInts=this.jvxlCutoff=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;K(this,arguments)},J.jvxl.readers,"SurfaceReader",null,J.jvxl.api.VertexDataServer);$(c$,function(){this.ptTemp=new JU.P3});T(c$,function(){});e(c$,"initSR",function(a){this.sg=a;this.params=a.params;this.assocCutoff=this.params.assocCutoff;this.isXLowToHigh=this.params.isXLowToHigh;this.center=this.params.center;this.anisotropy=this.params.anisotropy;this.isAnisotropic=
this.params.isAnisotropic;this.eccentricityMatrix=this.params.eccentricityMatrix;this.eccentricityMatrixInverse=this.params.eccentricityMatrixInverse;this.isEccentric=this.params.isEccentric;this.eccentricityScale=this.params.eccentricityScale;this.eccentricityRatio=this.params.eccentricityRatio;this.marchingSquares=a.marchingSquares;this.meshData=a.meshData;this.jvxlData=a.jvxlData;this.setVolumeDataV(a.volumeDataTemp);this.meshDataServer=a.meshDataServer;this.cJvxlEdgeNaN=String.fromCharCode(125)},
"J.jvxl.readers.SurfaceGenerator");e(c$,"setOutputChannel",function(){},"JU.OC");e(c$,"newVoxelDataCube",function(){this.volumeData.setVoxelDataAsArray(this.voxelData=y(this.nPointsX,this.nPointsY,this.nPointsZ,0))});e(c$,"setVolumeDataV",function(a){this.nBytes=0;this.volumetricOrigin=a.volumetricOrigin;this.volumetricVectors=a.volumetricVectors;this.voxelCounts=a.voxelCounts;this.voxelData=a.getVoxelData();this.volumeData=a},"J.jvxl.data.VolumeData");e(c$,"jvxlUpdateInfo",function(){this.jvxlData.jvxlUpdateInfo(this.params.title,
this.nBytes)});e(c$,"readAndSetVolumeParameters",function(a){return!this.readVolumeParameters(a)?!1:this.vertexDataOnly?!0:this.volumeData.setUnitVectors()},"~B");e(c$,"createIsosurface",function(a){this.resetIsosurface();this.params.showTiming&&JU.Logger.startTimer("isosurface creation");this.jvxlData.cutoff=NaN;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="";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)}null==this.params.contactPair&&this.setBBoxAll();this.jvxlData.isValid=3.4028235E38!=this.xyzMin.x;this.params.isSilent||(this.jvxlData.isValid?JU.Logger.info("boundbox corners "+JU.Escape.eP(this.xyzMin)+" "+JU.Escape.eP(this.xyzMax)):JU.Logger.error("no isosurface points were found!"));this.jvxlData.boundingBox=B(-1,[this.xyzMin,this.xyzMax]);this.jvxlData.dataMin=this.dataMin;this.jvxlData.dataMax=this.dataMax;this.jvxlData.cutoff=
this.isJvxl?this.jvxlCutoff:this.params.cutoff;this.jvxlData.isCutoffAbsolute=this.params.isCutoffAbsolute;this.jvxlData.isModelConnected=this.params.isModelConnected;this.jvxlData.pointsPerAngstrom=1/this.volumeData.volumetricVectorLengths[0];this.jvxlData.jvxlColorData="";this.jvxlData.jvxlPlane=this.params.thePlane;this.jvxlData.jvxlEdgeData=this.edgeData;this.jvxlData.isBicolorMap=this.params.isBicolorMap;this.jvxlData.isContoured=this.params.isContoured;this.jvxlData.colorDensity=this.params.colorDensity;
this.jvxlData.pointSize=this.params.pointSize;null!=this.jvxlData.vContours&&(this.params.nContours=this.jvxlData.vContours.length);this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.nEdges=this.edgeCount;this.jvxlData.edgeFractionBase=this.edgeFractionBase;this.jvxlData.edgeFractionRange=this.edgeFractionRange;this.jvxlData.colorFractionBase=this.colorFractionBase;this.jvxlData.colorFractionRange=
this.colorFractionRange;this.jvxlData.jvxlDataIs2dContour=this.jvxlDataIs2dContour;this.jvxlData.jvxlDataIsColorMapped=this.jvxlDataIsColorMapped;this.jvxlData.jvxlDataIsColorDensity=this.jvxlDataIsColorDensity;this.jvxlData.isXLowToHigh=this.isXLowToHigh;this.jvxlData.vertexDataOnly=this.vertexDataOnly;this.jvxlData.saveVertexCount=0;if(this.jvxlDataIsColorMapped||0<this.jvxlData.nVertexColors)null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshDataServer.fillMeshData(this.meshData,
2,null)),this.jvxlData.jvxlColorData=this.readColorData(),this.updateSurfaceData(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceMappingCompleted();this.params.showTiming&&JU.Logger.checkTimer("isosurface creation",!1);return!0},"~B");e(c$,"resetIsosurface",function(){this.meshData=new J.jvxl.data.MeshData;this.xyzMin=this.xyzMax=null;this.jvxlData.isBicolorMap=this.params.isBicolorMap;null!=this.meshDataServer&&this.meshDataServer.fillMeshData(null,0,null);this.contourVertexCount=0;
3.4028235E38==this.params.cutoff&&(this.params.cutoff=0.02);this.jvxlData.jvxlSurfaceData="";this.jvxlData.jvxlEdgeData="";this.jvxlData.jvxlColorData="";this.edgeCount=0;this.edgeFractionBase=35;this.edgeFractionRange=90;this.colorFractionBase=35;this.colorFractionRange=90;this.params.mappedDataMin=3.4028235E38});e(c$,"discardTempData",function(a){this.discardTempDataSR(a)},"~B");e(c$,"discardTempDataSR",function(a){a&&(this.voxelData=null,this.marchingCubes=this.sg.marchingSquares=this.marchingSquares=
null)},"~B");e(c$,"initializeVolumetricData",function(){this.nPointsX=this.voxelCounts[0];this.nPointsY=this.voxelCounts[1];this.nPointsZ=this.voxelCounts[2];this.setVolumeDataV(this.volumeData)});e(c$,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0<this.nPointsX&&0<this.nPointsY&&0<this.nPointsZ)try{this.gotoData(this.params.fileIndex-1,this.nPointsX*this.nPointsY*this.nPointsZ),this.readSurfaceData(a)}catch(b){if(U(b,Exception))return JU.Logger.error(b.toString()),!1;throw b;
}return!0},"~B");e(c$,"gotoData",function(){},"~N,~N");e(c$,"readColorData",function(){if(null==this.jvxlData.vertexColors)return"";var a=this.jvxlData.vertexCount,b=this.meshData.vcs,c=this.meshData.vvs;if(null==b||b.length<a)this.meshData.vcs=b=W(a,0);if(null==c||c.length<a)this.meshData.vvs=y(a,0);for(c=0;c<a;c++)b[c]=JU.C.getColix(this.jvxlData.vertexColors[c]);return"-"});k(c$,"getPlane",function(a){return this.getPlaneSR(a)},"~N");e(c$,"getPlaneSR",function(a){0==this.yzCount&&this.initPlanes();
null!=this.qpc&&this.qpc.getPlane(a,this.yzPlanes[a%2]);return this.yzPlanes[a%2]},"~N");e(c$,"initPlanes",function(){this.yzCount=this.nPointsY*this.nPointsZ;this.isQuiet||JU.Logger.info("reading data progressively -- yzCount = "+this.yzCount);this.yzPlanes=JU.AU.newFloat2(2);this.yzPlanes[0]=y(this.yzCount,0);this.yzPlanes[1]=y(this.yzCount,0)});k(c$,"getValue",function(a,b,c,d){return this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(c$,"getValue2",function(a,b,c,d){return null==this.yzPlanes?this.voxelData[a][b][c]:
this.yzPlanes[a%2][d]},"~N,~N,~N,~N");e(c$,"generateSurfaceData",function(){this.edgeData="";if(this.vertexDataOnly)try{this.readSurfaceData(!1)}catch(a){if(U(a,Exception))System.out.println(a.toString()),JU.Logger.error("Exception in SurfaceReader::readSurfaceData: "+a.toString());else throw a;}else{this.contourVertexCount=0;var b=-1;this.marchingSquares=null;if(null!=this.params.thePlane||this.params.isContoured)this.marchingSquares=new J.jvxl.calc.MarchingSquares(this,this.volumeData,this.params.thePlane,
this.params.contoursDiscrete,this.params.nContours,this.params.thisContour,this.params.contourFromZero),b=this.marchingSquares.contourType,this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue);this.params.contourType=b;this.params.isXLowToHigh=this.isXLowToHigh;this.marchingCubes=new J.jvxl.calc.MarchingCubes(this,this.volumeData,this.params,this.jvxlVoxelBitSet);b=this.marchingCubes.getEdgeData();null==this.params.thePlane&&(this.edgeData=b);this.jvxlData.setSurfaceInfoFromBitSetPts(this.marchingCubes.bsVoxels,
this.params.thePlane,this.params.mapLattice);this.jvxlData.jvxlExcluded=this.params.bsExcluded;this.isJvxl&&(this.edgeData=this.jvxlEdgeDataRead);this.postProcessVertices()}});e(c$,"postProcessVertices",function(){});k(c$,"getSurfacePointIndexAndFraction",function(a,b,c,d,h,e,g,f,m,p,n,q,r,k){b=this.getSurfacePointAndFraction(a,b,m,p,n,q,c,d,h,g,f,k,this.ptTemp);if(null!=this.marchingSquares&&this.params.isContoured)return this.marchingSquares.addContourVertex(this.ptTemp,a);a=0<this.assocCutoff?
k[0]<this.assocCutoff?g:k[0]>1-this.assocCutoff?f:-1:-1;0<=a&&(a=this.marchingCubes.getLinearOffset(c,d,h,a));a=this.addVertexCopy(this.ptTemp,b,a,!0);0<=a&&this.params.iAddGridPoints&&(this.marchingCubes.calcVertexPoint(c,d,h,f,this.ptTemp),this.addVertexCopy(m<p?n:this.ptTemp,Math.min(m,p),-3,!0),this.addVertexCopy(m<p?this.ptTemp:n,Math.max(m,p),-3,!0));return a},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");e(c$,"getSurfacePointAndFraction",function(a,b,c,d,h,e,g,f,m,p,n,q,r){return this.getSPF(a,
b,c,d,h,e,g,f,m,p,n,q,r)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPF",function(a,b,c,d,h,e,g,f,m,p,n,q,r){d-=c;g=(a-c)/d;if(b&&(0>g||1<g))g=(-a-c)/d;if(0>g||1<g)g=NaN;q[0]=g;r.scaleAdd2(g,e,h);return c+g*d},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"addVertexCopy",function(a,b,c,d){return this.addVC(a,b,c,d)},"JU.T3,~N,~N,~B");e(c$,"addVC",function(a,b,c,d){return Float.isNaN(b)&&-3!=c?-1:null==this.meshDataServer?this.meshData.addVertexCopy(a,b,c,d):this.meshDataServer.addVertexCopy(a,
b,c,d)},"JU.T3,~N,~N,~B");e(c$,"addTriangleCheck",function(a,b,c,d,h,e,g){if(null!=this.marchingSquares&&this.params.isContoured){if(0==g)return this.marchingSquares.addTriangle(a,b,c,d,h);g=0}return null!=this.meshDataServer?this.meshDataServer.addTriangleCheck(a,b,c,d,h,e,g):e&&!J.jvxl.data.MeshData.checkCutoff(a,b,c,this.meshData.vvs)?-1:this.meshData.addTriangleCheck(a,b,c,d,h,g)},"~N,~N,~N,~N,~N,~B,~N");e(c$,"colorIsosurface",function(){this.params.isSquared&&null!=this.volumeData&&this.volumeData.filterData(!0,
NaN);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.jvxlData.saveVertexCount=0;this.params.isContoured&&null!=this.marchingSquares&&(this.initializeMapping(),this.params.setMapRanges(this,!1),this.marchingSquares.setMinMax(this.params.valueMappedToRed,this.params.valueMappedToBlue),this.jvxlData.saveVertexCount=this.marchingSquares.contourVertexCount,this.contourVertexCount=this.marchingSquares.generateContourData(this.jvxlDataIs2dContour,this.params.isSquared?
1E-8:1E-4),this.jvxlData.contourValuesUsed=this.marchingSquares.contourValuesUsed,this.minMax=this.marchingSquares.getMinMax(),null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted(),this.finalizeMapping());this.applyColorScale();this.jvxlData.nContours=this.params.contourFromZero?this.params.nContours:-1-this.params.nContours;this.jvxlData.thisContour=this.params.thisContour;this.jvxlData.jvxlFileMessage="mapped: min = "+this.params.valueMappedToRed+"; max = "+this.params.valueMappedToBlue});
e(c$,"applyColorScale",function(){this.colorFractionBase=this.jvxlData.colorFractionBase=35;this.colorFractionRange=this.jvxlData.colorFractionRange=90;0==this.params.colorPhase&&(this.params.colorPhase=1);null==this.meshDataServer?this.meshData.vcs=W(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=v(this.meshData.vc,0));var b=3.4028235E38,c=-3.4028235E38,d;this.initializeMapping();for(var h=this.meshData.vc;--h>=this.meshData.mergeVertexCount0;){if(this.params.colorBySets)d=this.meshData.vertexSets[h];else if(this.params.colorByPhase)d=this.getPhase(this.meshData.vs[h]);else{var e=this.haveSurfaceAtoms;d=this.volumeData.lookupInterpolatedVoxelValue(this.meshData.vs[h],e);e&&(this.meshData.vertexSource[h]=
this.getSurfaceAtomIndex())}d<b&&(b=d);d>c&&3.4028235E38!=d&&(c=d);this.meshData.vvs[h]=d}this.params.rangeSelected&&null==this.minMax&&(this.minMax=y(-1,[b,c]));this.finalizeMapping()}this.params.setMapRanges(this,!0);this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;null==this.params.contactPair&&null==this.jvxlData.vertexColors&&
this.colorData();J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,a?this.meshData.vvs:null);this.haveSurfaceAtoms&&null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null);null!=this.meshDataServer&&this.params.colorBySets&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(c$,"colorData",function(){var a=this.meshData.vvs,b=this.meshData.vcs;this.meshData.pcs=null;var c=this.jvxlData.valueMappedToBlue,d=this.jvxlData.valueMappedToRed,h=this.jvxlData.minColorIndex,
e=this.jvxlData.maxColorIndex;null==this.params.colorEncoder&&(this.params.colorEncoder=new JU.ColorEncoder(null,null));this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(var g=this.meshData.vc;0<=--g;){var f=a[g];0<=h?0>=f?b[g]=h:0<f&&(b[g]=e):(f<=d&&(f=d),f>=c&&(f=c),b[g]=this.params.colorEncoder.getColorIndex(f))}if((0<this.params.nContours||null!=this.jvxlData.contourValues)&&null==this.jvxlData.contourColixes){a=null==
this.jvxlData.contourValues?this.params.nContours:this.jvxlData.contourValues.length;b=this.jvxlData.contourColixes=W(a,0);h=this.jvxlData.contourValues;null==h&&(h=this.jvxlData.contourValuesUsed);null==this.jvxlData.contourValuesUsed&&(this.jvxlData.contourValuesUsed=null==h?y(a,0):h);c=(c-d)/(a+1);this.params.colorEncoder.setRange(this.params.valueMappedToRed,this.params.valueMappedToBlue,this.params.isColorReversed);for(g=0;g<a;g++)e=null==h?d+(g+1)*c:h[g],this.jvxlData.contourValuesUsed[g]=e,
b[g]=JU.C.getColixTranslucent(this.params.colorEncoder.getArgb(e));this.jvxlData.contourColors=JU.C.getHexCodes(b)}});c$.getColorPhaseIndex=e(c$,"getColorPhaseIndex",function(a){for(var b=-1,c=0;c<J.jvxl.readers.SurfaceReader.colorPhases.length;c++)if(a.equalsIgnoreCase(J.jvxl.readers.SurfaceReader.colorPhases[c])){b=c;break}return b},"~S");e(c$,"getPhase",function(a){switch(this.params.colorPhase){case 0:case -1:case 1:return 0<a.x?1:-1;case 2:return 0<a.y?1:-1;case 3:return 0<a.z?1:-1;case 4:return 0<
a.x*a.y?1:-1;case 5:return 0<a.y*a.z?1:-1;case 6:return 0<a.x*a.z?1:-1;case 7:return 0<a.x*a.x-a.y*a.y?1:-1;case 8:return 0<2*a.z*a.z-a.x*a.x-a.y*a.y?1:-1}return 1},"JU.T3");e(c$,"getMinMaxMappedValues",function(a){if(null!=this.minMax&&3.4028235E38!=this.minMax[0])return this.minMax;if(this.params.colorBySets)return this.minMax=y(-1,[0,Math.max(this.meshData.nSets-1,0)]);var b=3.4028235E38,c=-3.4028235E38;if(this.params.usePropertyForColorRange&&null!=this.params.theProperty){for(a=this.params.theProperty.length;0<=
--a;)if(!this.params.rangeSelected||this.params.bsSelected.get(a)){var d=this.params.theProperty[a];Float.isNaN(d)||(d<b&&(b=d),d>c&&(c=d))}return this.minMax=y(-1,[b,c])}var d=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc,e=this.meshData.vs,j=a||this.jvxlDataIs2dContour||this.vertexDataOnly||this.params.colorDensity;for(a=this.meshData.mergeVertexCount0;a<d;a++){var g;g=j?this.meshData.vvs[a]:this.volumeData.lookupInterpolatedVoxelValue(e[a],!1);g<b&&(b=g);g>c&&3.4028235E38!=
g&&(c=g)}return this.minMax=y(-1,[b,c])},"~B");e(c$,"updateTriangles",function(){null==this.meshDataServer?this.meshData.invalidatePolygons():this.meshDataServer.invalidateTriangles()});e(c$,"updateSurfaceData",function(){this.meshData.setVertexSets(!0);this.updateTriangles();null==this.params.bsExcluded[1]&&(this.params.bsExcluded[1]=new JU.BS);this.meshData.updateInvalidatedVertices(this.params.bsExcluded[1])});e(c$,"selectPocket",function(){},"~B");e(c$,"excludeMinimumSet",function(){null!=this.meshDataServer&&
this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()<this.params.minSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(c$,"excludeMaximumSet",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.getSurfaceSet();for(var a,
b=this.meshData.nSets;0<=--b;)null!=(a=this.meshData.surfaceSet[b])&&a.cardinality()>this.params.maxSet&&this.meshData.invalidateSurfaceSet(b);this.updateSurfaceData();null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,3,null)});e(c$,"slabIsosurface",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.meshData.slabPolygonsList(a,!0);null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,4,null)},"JU.Lst");e(c$,
"setVertexAnisotropy",function(a){a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2];a.add(this.center)},"JU.T3");e(c$,"setVectorAnisotropy",function(a){this.haveSetAnisotropy=!0;a.x*=this.anisotropy[0];a.y*=this.anisotropy[1];a.z*=this.anisotropy[2]},"JU.T3");e(c$,"setVolumetricAnisotropy",function(){this.haveSetAnisotropy||(this.setVolumetricOriginAnisotropy(),this.setVectorAnisotropy(this.volumetricVectors[0]),this.setVectorAnisotropy(this.volumetricVectors[1]),this.setVectorAnisotropy(this.volumetricVectors[2]))});
e(c$,"setVolumetricOriginAnisotropy",function(){this.volumetricOrigin.setT(this.center)});e(c$,"setBBoxAll",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);this.xyzMin=new JU.P3;this.xyzMax=new JU.P3;this.meshData.setBox(this.xyzMin,this.xyzMax)});e(c$,"setBBox",function(a,b){null==this.xyzMin&&(this.xyzMin=JU.P3.new3(3.4028235E38,3.4028235E38,3.4028235E38),this.xyzMax=JU.P3.new3(-3.4028235E38,-3.4028235E38,-3.4028235E38));JU.BoxInfo.addPoint(a,this.xyzMin,
this.xyzMax,b)},"JU.T3,~N");e(c$,"getValueAtPoint",function(){return 0},"JU.T3,~B");e(c$,"initializeMapping",function(){});e(c$,"finalizeMapping",function(){});e(c$,"getSurfaceAtomIndex",function(){return-1});aa(c$,"ANGSTROMS_PER_BOHR",0.5291772,"defaultMappedDataMin",0,"defaultMappedDataMax",1,"defaultCutoff",0.02,"colorPhases",B(-1,"_orb x y z xy yz xz x2-y2 z2".split(" ")))});E("J.jvxl.calc");H(["JU.TriangleData","JU.BS","$.P3","$.SB","$.V3"],"J.jvxl.calc.MarchingCubes",["java.lang.Float","J.jvxl.data.JvxlCoder"],
function(){c$=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.mode=0;this.vertexValues=null;this.edgeCount=0;this.mappingPlane=
this.yzPlanes=this.isoPointIndexPlanes=this.edgePointIndexes=this.edgeVectors=this.voxelVertexVectors=null;this.$isInside=this.allInside=!1;this.voxelData=this.offset=null;this.nTriangles=0;this.linearOffsets=this.fReturn=this.edgeVertexPlanes=this.edgeVertexPointers=this.pointA=this.pt0=this.bsValues=null;K(this,arguments)},J.jvxl.calc,"MarchingCubes",JU.TriangleData);$(c$,function(){this.edgeData=new JU.SB;this.vertexValues=y(8,0);this.voxelVertexVectors=Array(8);this.edgeVectors=Array(12);for(var a=
12;0<=--a;)this.edgeVectors[a]=new JU.V3;this.edgePointIndexes=v(12,0);this.bsValues=new JU.BS;this.pt0=new JU.P3;this.pointA=new JU.P3;this.fReturn=y(1,0);this.linearOffsets=v(8,0)});T(c$,function(){ba(this,J.jvxl.calc.MarchingCubes,[])});T(c$,function(a,b,c,d){ba(this,J.jvxl.calc.MarchingCubes,[]);this.excludePartialCubes=!0;this.surfaceReader=a;this.bsVoxels=d;a=c.bsExcluded;this.bsExcludedVertices=null==a[0]?a[0]=new JU.BS:a[0];this.bsExcludedPlanes=null==a[2]?a[2]=new JU.BS:a[2];this.bsExcludedTriangles=
null==a[3]?a[3]=new JU.BS:a[3];this.mode=null!=b.getVoxelData()||null!=b.mappingPlane?1:null!=d?2:3;this.setParameters(b,c)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");e(c$,"setParameters",function(a,b){this.volumeData=a;this.colorDensity=b.colorDensity;this.isContoured=null==b.thePlane&&b.isContoured&&!this.colorDensity;this.cutoff=b.cutoff;this.isCutoffAbsolute=b.isCutoffAbsolute;this.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=v(2,this.yzCount,3,0);this.yzPlanes=3==this.mode?y(2,this.yzCount,0):null;this.setLinearOffsets();this.calcVoxelVertexVectors()},"J.jvxl.data.VolumeData,J.jvxl.readers.Parameters");e(c$,"calcVoxelVertexVectors",function(){for(var a=8;0<=--a;)this.volumeData.transform(J.jvxl.calc.MarchingCubes.cubeVertexVectors[a],
this.voxelVertexVectors[a]=new JU.V3);for(a=12;0<=--a;)this.edgeVectors[a].sub2(this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a+1]],this.voxelVertexVectors[JU.TriangleData.edgeVertexes[a+a]])});e(c$,"resetIndexPlane",function(a){for(var b=0;b<this.yzCount;b++)for(var c=0;3>c;c++)a[b][c]=-2147483648;return a},"~A");e(c$,"getEdgeData",function(){if(0>this.cubeCountX||0>this.cubeCountY||0>this.cubeCountZ)return"";this.mappingPlane=this.volumeData.mappingPlane;this.edgeCount=0;var a,b,c,d,e,
j;this.isXLowToHigh?(a=0,this.colorDensity?(b=this.cubeCountX+1,j=this.yzCount-1):(b=this.cubeCountX,j=this.yzCount-1-this.nZ-1),c=1,d=this.yzCount):(this.colorDensity?(a=this.cubeCountX,j=(this.cubeCountX+1)*this.yzCount-1):(a=this.cubeCountX-1,j=this.cubeCountX*this.yzCount-1-this.nZ-1),c=b=-1,d=-this.yzCount);e=j;this.resetIndexPlane(this.isoPointIndexPlanes[1]);this.voxelData=null;var g=this.cubeCountY+(this.colorDensity?1:0),f=this.cubeCountZ+(this.colorDensity?1:0);switch(this.mode){case 3:this.getPlane(a,
!1);break;case 1:this.voxelData=this.volumeData.getVoxelData()}this.allInside=this.colorDensity&&(0==this.cutoff||2==this.mode&&0>this.bsVoxels.nextSetBit(0));for(var m=this.colorDensity&&0==this.cutoff,p=0;a!=b;a+=c,j+=d,e=j)if(3==this.mode&&a+c<=b&&this.getPlane(a+c,!0),!this.bsExcludedPlanes.get(a)||!this.bsExcludedPlanes.get(a+c))if(this.colorDensity)for(var n=g;0<=--n;)for(var q=f;0<=--q;e--)p=this.getValue(a,n,q,e,0),(m||this.$isInside)&&this.addVertex(a,n,q,e,p);else{n=this.isoPointIndexPlanes[0];
this.isoPointIndexPlanes[0]=this.isoPointIndexPlanes[1];this.isoPointIndexPlanes[1]=this.resetIndexPlane(n);for(var r=!0,n=g;0<=--n;e--)for(q=f;0<=--q;e--){for(var k=0,u=8;0<=--u;)p=this.getValue(a,n,q,e,u),this.$isInside&&(k|=JU.TriangleData.Pwr2[u]);r&&!Float.isNaN(p)&&(r=!1);0!=k&&255!=k&&this.processOneCubical(k,a,n,q,e)&&(!this.isContoured&&!this.colorDensity)&&this.processTriangles(k)}r&&this.bsExcludedPlanes.set(a)}return this.edgeData.toString()});e(c$,"getValue",function(a,b,c,d,e){this.offset=
JU.TriangleData.cubeVertexOffsets[e];d+=this.linearOffsets[e];switch(this.mode){case 3:a=this.vertexValues[e]=this.getValueArray(a+this.offset.x,b+this.offset.y,c+this.offset.z,d,this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[e]]);this.$isInside=this.allInside||this.bsVoxels.get(d);break;case 2:this.$isInside=this.allInside||this.bsVoxels.get(d);a=this.vertexValues[e]=this.bsExcludedVertices.get(d)?NaN:this.$isInside?1:0;break;default:case 1:null==this.mappingPlane?a=this.vertexValues[e]=this.voxelData[a+
this.offset.x][b+this.offset.y][c+this.offset.z]:(this.volumeData.voxelPtToXYZ(a+this.offset.x,b+this.offset.y,c+this.offset.z,this.pt0),a=this.vertexValues[e]=this.volumeData.distanceToMappingPlane(this.pt0)),this.isSquared&&(this.vertexValues[e]*=this.vertexValues[e]),(this.$isInside=this.allInside?!0:J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[e],this.cutoff,this.isCutoffAbsolute))&&this.bsVoxels.set(d)}return a},"~N,~N,~N,~N,~N");e(c$,"getPlane",function(a,b){if(!(0>a||a>this.cubeCountX))if(this.surfaceReader.getPlane(a),
b){var c=this.yzPlanes[0];this.yzPlanes[0]=this.yzPlanes[1];this.yzPlanes[1]=c}},"~N,~B");e(c$,"processTriangles",function(a){a=JU.TriangleData.triangleTable2[a];for(var b=a.length;0<=(b-=4);)this.addTriangle(a[b],a[b+1],a[b+2],a[b+3])},"~N");e(c$,"addVertex",function(a,b,c,d,e){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);0>this.surfaceReader.addVertexCopy(this.pt0,e,-4,!0)&&this.bsExcludedVertices.set(d)},"~N,~N,~N,~N,~N");e(c$,"addTriangle",function(a,b,c,d){!this.bsExcludedTriangles.get(this.nTriangles)&&
0>this.surfaceReader.addTriangleCheck(this.edgePointIndexes[a],this.edgePointIndexes[b],this.edgePointIndexes[c],d,0,this.isCutoffAbsolute,0)&&this.bsExcludedTriangles.set(this.nTriangles);this.nTriangles++},"~N,~N,~N,~N");e(c$,"getValueArray",function(a,b,c,d,e){var j=d%this.yzCount;this.bsValues.set(d);a=this.surfaceReader.getValue(a,b,c,j);this.isSquared&&(a*=a);e[j]=a;J.jvxl.calc.MarchingCubes.isInside(a,this.cutoff,this.isCutoffAbsolute)&&this.bsVoxels.set(d);return a},"~N,~N,~N,~N,~A");c$.isInside=
e(c$,"isInside",function(a,b,c){return 0<b&&(c?Math.abs(a):a)>=b||0>=b&&a<=b},"~N,~N,~B");e(c$,"processOneCubical",function(a,b,c,d,e){a=J.jvxl.calc.MarchingCubes.insideMaskTable[a];for(var j=!1,g=12;0<=--g;)if(0!=(a&JU.TriangleData.Pwr2[g])){var f=this.edgeVertexPlanes[g],m=(e+this.linearOffsets[this.edgeVertexPointers[g]])%this.yzCount,p=J.jvxl.calc.MarchingCubes.edgeTypeTable[g],n=this.edgePointIndexes[g]=this.isoPointIndexPlanes[f][m][p];if(-2147483648!=n)-1==n&&(j=this.excludePartialCubes);else{var n=
JU.TriangleData.edgeVertexes[g<<1],q=JU.TriangleData.edgeVertexes[(g<<1)+1],r=this.vertexValues[n],k=this.vertexValues[q];this.calcVertexPoint(b,c,d,n,this.pointA);this.edgeCount++;f=this.edgePointIndexes[g]=this.isoPointIndexPlanes[f][m][p]=this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff,this.isCutoffAbsolute,b,c,d,JU.TriangleData.cubeVertexOffsets[n],n,q,r,k,this.pointA,this.edgeVectors[g],p==this.contourType,this.fReturn);this.addEdgeData(0>f?NaN:this.fReturn[0]);if(Float.isNaN(this.fReturn[0])||
0>f)j=this.excludePartialCubes}}return!j},"~N,~N,~N,~N,~N");e(c$,"addEdgeData",function(a){a=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(a);this.edgeData.appendC(a)},"~N");e(c$,"calcVertexPoint",function(a,b,c,d,e){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);e.add2(this.pt0,this.voxelVertexVectors[d])},"~N,~N,~N,~N,JU.P3");e(c$,"setLinearOffsets",function(){this.linearOffsets[0]=0;this.linearOffsets[1]=this.yzCount;this.linearOffsets[2]=this.yzCount+1;this.linearOffsets[3]=1;this.linearOffsets[4]=
this.nZ;this.linearOffsets[5]=this.yzCount+this.nZ;this.linearOffsets[6]=this.yzCount+this.nZ+1;this.linearOffsets[7]=this.nZ+1});e(c$,"getLinearOffset",function(a,b,c,d){return a*this.yzCount+b*this.nZ+c+this.linearOffsets[d]},"~N,~N,~N,~N");aa(c$,"MODE_CUBE",1,"MODE_JVXL",2,"MODE_PLANES",3);aa(c$,"yzPlanePts",v(-1,[0,1,1,0,0,1,1,0]),"edgeVertexPointersLowToHigh",v(-1,[1,1,2,0,5,5,6,4,0,1,2,3]),"edgeVertexPointersHighToLow",v(-1,[0,1,3,0,4,5,7,4,0,1,2,3]),"edgeVertexPlanesLowToHigh",v(-1,[1,1,1,
0,1,1,1,0,0,1,1,0]),"edgeVertexPlanesHighToLow",v(-1,[1,0,1,1,1,0,1,1,1,0,0,1]));c$.cubeVertexVectors=c$.prototype.cubeVertexVectors=B(-1,[JU.V3.new3(0,0,0),JU.V3.new3(1,0,0),JU.V3.new3(1,0,1),JU.V3.new3(0,0,1),JU.V3.new3(0,1,0),JU.V3.new3(1,1,0),JU.V3.new3(1,1,1),JU.V3.new3(0,1,1)]);aa(c$,"edgeTypeTable",v(-1,[0,2,0,2,0,2,0,2,1,1,1,1]),"insideMaskTable",W(-1,[0,265,515,778,1030,1295,1541,1804,2060,2309,2575,2822,3082,3331,3593,3840,400,153,915,666,1430,1183,1941,1692,2460,2197,2975,2710,3482,3219,
3993,3728,560,825,51,314,1590,1855,1077,1340,2620,2869,2111,2358,3642,3891,3129,3376,928,681,419,170,1958,1711,1445,1196,2988,2725,2479,2214,4010,3747,3497,3232,1120,1385,1635,1898,102,367,613,876,3180,3429,3695,3942,2154,2403,2665,2912,1520,1273,2035,1786,502,255,1013,764,3580,3317,4095,3830,2554,2291,3065,2800,1616,1881,1107,1370,598,863,85,348,3676,3925,3167,3414,2650,2899,2137,2384,1984,1737,1475,1226,966,719,453,204,4044,3781,3535,3270,3018,2755,2505,2240,2240,2505,2755,3018,3270,3535,3781,4044,
204,453,719,966,1226,1475,1737,1984,2384,2137,2899,2650,3414,3167,3925,3676,348,85,863,598,1370,1107,1881,1616,2800,3065,2291,2554,3830,4095,3317,3580,764,1013,255,502,1786,2035,1273,1520,2912,2665,2403,2154,3942,3695,3429,3180,876,613,367,102,1898,1635,1385,1120,3232,3497,3747,4010,2214,2479,2725,2988,1196,1445,1711,1958,170,419,681,928,3376,3129,3891,3642,2358,2111,2869,2620,1340,1077,1855,1590,314,51,825,560,3728,3993,3219,3482,2710,2975,2197,2460,1692,1941,1183,1430,666,915,153,400,3840,3593,
3331,3082,2822,2575,2309,2060,1804,1541,1295,1030,778,515,265,0]))});E("J.jvxl.calc");H(["JU.P3","java.util.Hashtable"],"J.jvxl.calc.MarchingSquares",["java.lang.Float","JU.AU","JU.Logger"],function(){c$=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;ja("J.jvxl.calc.MarchingSquares.ContourVertex")||
J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$();this.contourPlaneMaximumValue=this.contourPlaneMinimumValue=0;this.ptTemp=this.contourValuesUsed=null;this.triangleCount=0;this.htPts=this.triangles=null;ja("J.jvxl.calc.MarchingSquares.Triangle")||J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$();K(this,arguments)},J.jvxl.calc,"MarchingSquares");$(c$,function(){this.pointA=new JU.P3;this.pointB=new JU.P3;this.contourVertexes=Array(1E3);this.ptTemp=new JU.P3;this.triangles=Array(1E3);
this.htPts=new java.util.Hashtable});T(c$,function(a,b,c,d,e,j,g){this.surfaceReader=a;this.volumeData=b;this.thisContour=j;this.contoursDiscrete=d;this.contourFromZero=g;null==d?(this.nContourSegments=(0==e?9:e)+0,100<this.nContourSegments&&(this.nContourSegments=100)):(this.nContourSegments=e=d.length,this.contourFromZero=!1)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,JU.P4,~A,~N,~N,~B");e(c$,"setMinMax",function(a,b){this.valueMin=a;this.valueMax=b},"~N,~N");e(c$,"addContourVertex",function(a,
b){this.contourVertexCount==this.contourVertexes.length&&(this.contourVertexes=JU.AU.doubleLength(this.contourVertexes));var c=this.surfaceReader.addVertexCopy(a,b,-2,!0);this.contourVertexes[this.contourVertexCount++]=ia(J.jvxl.calc.MarchingSquares.ContourVertex,this,null,a);return c},"JU.P3,~N");e(c$,"setContourData",function(a,b){this.contourVertexes[a].setValue(b)},"~N,~N");e(c$,"calcContourPoint",function(a,b,c,d){return this.volumeData.calculateFractionalPoint(a,this.pointA,this.pointB,b,c,
d)},"~N,~N,~N,JU.P3");e(c$,"addTriangle",function(a,b,c,d,e){this.triangleCount==this.triangles.length&&(this.triangles=JU.AU.doubleLength(this.triangles));this.triangles[this.triangleCount++]=ia(J.jvxl.calc.MarchingSquares.Triangle,this,null,a,b,c,d,e);return 0},"~N,~N,~N,~N,~N");e(c$,"generateContourData",function(a,b){JU.Logger.info("generateContours: "+this.nContourSegments+" segments");this.getVertexValues(a);this.createContours(this.valueMin,this.valueMax,b);this.addAllTriangles();return this.contourVertexCount},
"~B,~N");e(c$,"getVertexValues",function(a){this.contourPlaneMinimumValue=3.4028235E38;this.contourPlaneMaximumValue=-3.4028235E38;for(var b=0;b<this.contourVertexCount;b++){var c=this.contourVertexes[b],d;a?d=c.value:(d=this.volumeData.lookupInterpolatedVoxelValue(c,!1),c.setValue(d));d<this.contourPlaneMinimumValue&&(this.contourPlaneMinimumValue=d);d>this.contourPlaneMaximumValue&&(this.contourPlaneMaximumValue=d)}},"~B");e(c$,"createContours",function(a,b,c){b-=a;this.contourValuesUsed=y(this.nContourSegments,
0);for(var d=this.triangleCount;0<=--d;)this.triangles[d].check=0;for(var e=-3.4028235E38,d=0;d<this.nContourSegments;d++){e=null!=this.contoursDiscrete?this.contoursDiscrete[d]:this.contourFromZero?a+1*d/this.nContourSegments*b:0==d?-3.4028235E38:d==this.nContourSegments-1?3.4028235E38:a+1*(d-1)/(this.nContourSegments-1)*b;null==this.contoursDiscrete&&Math.abs(e)<c&&(e=0>e?-c:c);this.contourValuesUsed[d]=e;JU.Logger.info("#contour "+(d+1)+" "+e+" "+this.triangleCount);this.htPts.clear();for(var j=
this.triangleCount;0<=--j;)this.triangles[j].isValid&&this.checkContour(this.triangles[j],d,e)}this.valueMin=this.contourValuesUsed[0];this.valueMax=0==this.contourValuesUsed.length?this.valueMin:this.contourValuesUsed[this.contourValuesUsed.length-1];return!0},"~N,~N,~N");e(c$,"intercept",function(a,b,c){var d=a.pts[b];a=a.pts[(b+1)%3];if(2147483647==d||2147483647==a)return-1;b=d<a?d+"_"+a:a+"_"+d;if(this.htPts.containsKey(b))return this.htPts.get(b).intValue();var e=this.contourVertexes[d].value,
j=this.contourVertexes[a].value,g=-1;if(e!=j){var f=(c-e)/(j-e);if(0<=f&&1>=f&&(this.pointA.setT(this.contourVertexes[d]),this.pointB.setT(this.contourVertexes[a]),c=this.calcContourPoint(c,e,j,this.ptTemp),!Float.isNaN(c))){g=this.addContourVertex(this.ptTemp,c);if(0>g)return-1;this.contourVertexes[g].setValue(c)}}this.htPts.put(b,Integer.$valueOf(g));return g},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"checkContour",function(a,b,c){if(!(0<this.thisContour&&b+1!=this.thisContour)){var d=
this.intercept(a,0,c),e=this.intercept(a,1,c);c=this.intercept(a,2,c);var j=a.pts,g=0;0<=d&&(g+=1);0<=e&&(g+=2);0<=c&&(g+=4);switch(g){case 3:this.addTriangle(j[0],d,e,2|a.check&1,b);this.addTriangle(d,j[1],e,4|a.check&3,b);this.addTriangle(j[0],e,j[2],a.check&6,b);break;case 5:this.addTriangle(j[0],d,c,2|a.check&5,b);this.addTriangle(d,j[1],c,4|a.check&1,b);this.addTriangle(c,j[1],j[2],a.check&6,b);break;case 6:this.addTriangle(j[0],j[1],c,a.check&5,b);this.addTriangle(c,j[1],e,4|a.check&2,b);this.addTriangle(c,
e,j[2],1|a.check&6,b);break;default:return}a.isValid=!1}},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"getMinMax",function(){return y(-1,[this.valueMin,this.valueMax])});e(c$,"addAllTriangles",function(){for(var a=0;a<this.triangleCount;a++)if(this.triangles[a].isValid){var b=this.triangles[a];this.surfaceReader.addTriangleCheck(b.pts[0],b.pts[1],b.pts[2],b.check,b.contourIndex,!1,-1)}});c$.$MarchingSquares$ContourVertex$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);this.value=
0;K(this,arguments)},J.jvxl.calc.MarchingSquares,"ContourVertex",JU.P3);T(c$,function(a){ba(this,J.jvxl.calc.MarchingSquares.ContourVertex,[]);this.setT(a)},"JU.P3");e(c$,"setValue",function(a){this.value=a},"~N");k(c$,"toString",function(){return this.value+" "+this.x+" "+this.y+" "+this.z});c$=ha()};c$.$MarchingSquares$Triangle$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);this.pts=null;this.check=0;this.isValid=!0;this.contourIndex=0;K(this,arguments)},J.jvxl.calc.MarchingSquares,
"Triangle");T(c$,function(a,b,c,d,e){this.pts=v(-1,[a,b,c]);this.check=d;this.contourIndex=e},"~N,~N,~N,~N,~N");c$=ha()};aa(c$,"CONTOUR_POINT",-1,"VERTEX_POINT",-2,"EDGE_POINT",-3,"nContourMax",100,"defaultContourCount",9)});E("J.shapesurface");H(["J.shape.Mesh"],"J.shapesurface.IsosurfaceMesh","java.lang.Float java.util.Hashtable JU.AU $.BS $.CU $.Lst $.M4 $.P3 $.P3i $.PT $.SB $.V3 J.api.Interface J.jvxl.data.JvxlCoder $.JvxlData JS.T JU.C $.ColorEncoder $.Logger $.SimpleUnitCell JV.Viewer".split(" "),
function(){c$=N(function(){this.jvxlData=null;this.vertexIncrement=1;this.firstRealVertex=-1;this.dataType=0;this.hasGridPoints=!1;this.assocGridPointNormals=this.assocGridPointMap=this.info=this.calculatedVolume=this.calculatedArea=null;this.mergeAssociatedNormalCount=0;this.bsVdw=this.colorEncoder=this.contourColixes=this.contourValues=this.centers=null;this.colorPhased=!1;K(this,arguments)},J.shapesurface,"IsosurfaceMesh",J.shape.Mesh);k(c$,"getResolution",function(){return 1/this.jvxlData.pointsPerAngstrom});
T(c$,function(a,b,c,d){this.mesh1(a,b,c,d);this.jvxlData=new J.jvxl.data.JvxlData;this.checkByteCount=2;this.jvxlData.version=JV.Viewer.getJmolVersion()},"JV.Viewer,~S,~N,~N");e(c$,"clearType",function(a,b){this.clear(a);this.jvxlData.clear();this.colorEncoder=this.centers=this.calculatedArea=this.calculatedVolume=this.bsVdw=this.assocGridPointNormals=this.assocGridPointMap=null;this.colorsExplicit=this.colorPhased=!1;this.firstRealVertex=-1;this.hasGridPoints=b;this.isColorSolid=!0;this.nSets=this.mergeAssociatedNormalCount=
0;this.pcs=null;this.showPoints=b;this.vertexColorMap=this.vcs=this.surfaceSet=null;this.vertexIncrement=1;this.vvs=this.vertexSets=null},"~S,~B");e(c$,"allocVertexColixes",function(){if(null==this.vcs){this.vcs=W(this.vc,0);for(var a=this.vc;0<=--a;)this.vcs[a]=this.colix}this.isColorSolid=!1});e(c$,"addVertexCopy",function(a,b,c,d,e){a=this.addVCVal(a,b,e);switch(c){case -1:0>this.firstRealVertex&&(this.firstRealVertex=a);break;case -2:this.hasGridPoints=!0;break;case -3:this.vertexIncrement=3;
break;default:0>this.firstRealVertex&&(this.firstRealVertex=a),d&&(null==this.assocGridPointMap&&(this.assocGridPointMap=new java.util.Hashtable),this.assocGridPointMap.put(Integer.$valueOf(a),Integer.$valueOf(c+this.mergeAssociatedNormalCount)))}return a},"JU.T3,~N,~N,~B,~B");k(c$,"setTranslucent",function(a,b){this.colix=JU.C.getColixTranslucent3(this.colix,a,b);if(null!=this.vcs)for(var c=this.vc;0<=--c;)this.vcs[c]=JU.C.getColixTranslucent3(this.vcs[c],a,b)},"~B,~N");e(c$,"setMerged",function(a){this.mergePolygonCount0=
(this.isMerged=a)?this.pc:0;this.mergeVertexCount0=a?this.vc:0;a&&(this.mergeAssociatedNormalCount+=this.jvxlData.nPointsX*this.jvxlData.nPointsY*this.jvxlData.nPointsZ,this.assocGridPointNormals=null)},"~B");k(c$,"sumVertexNormals",function(a,b){J.shape.Mesh.sumVertexNormals2(this,a,b);if(null!=this.assocGridPointMap&&0<b.length&&!this.isMerged){null==this.assocGridPointNormals&&(this.assocGridPointNormals=new java.util.Hashtable);for(var c,d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&
((c=d.next())||1);){var e=c.getValue();this.assocGridPointNormals.containsKey(e)||this.assocGridPointNormals.put(e,JU.V3.new3(0,0,0));this.assocGridPointNormals.get(e).add(b[c.getKey().intValue()])}for(d=this.assocGridPointMap.entrySet().iterator();d.hasNext()&&((c=d.next())||1);)b[c.getKey().intValue()]=this.assocGridPointNormals.get(c.getValue())}},"~A,~A");e(c$,"getCenters",function(){if(null!=this.centers)return this.centers;this.centers=Array(this.pc);for(var a=0;a<this.pc;a++){var b=this.pis[a];
if(null!=b){var c=this.centers[a]=JU.P3.newP(this.vs[b[0]]);c.add(this.vs[b[1]]);c.add(this.vs[b[2]]);c.scale(0.33333334)}}return this.centers});e(c$,"getContours",function(){var a=this.jvxlData.nContours;if(0==a||null==this.pis||(this.havePlanarContours=null!=this.jvxlData.jvxlPlane))return null;0>a&&(a=-1-a);var b=this.jvxlData.vContours;if(null!=b){for(var c=0;c<a&&!(6<b[c].size());c++)J.jvxl.data.JvxlCoder.set3dContourVector(b[c],this.pis,this.vs);return this.jvxlData.vContours}b=Array(a);for(c=
0;c<a;c++)b[c]=new JU.Lst;if(null==this.jvxlData.contourValuesUsed){for(var d=(this.jvxlData.valueMappedToBlue-this.jvxlData.valueMappedToRed)/(a+1),c=0;c<a;c++){var e=this.jvxlData.valueMappedToRed+(c+1)*d;J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c])}JU.Logger.info(a+" contour lines; separation = "+d)}else for(c=0;c<a;c++)e=this.jvxlData.contourValuesUsed[c],J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],e,this.jvxlData.contourColixes[c]);this.jvxlData.contourColixes=
W(a,0);this.jvxlData.contourValues=y(a,0);for(c=0;c<a;c++)this.jvxlData.contourValues[c]=b[c].get(2).floatValue(),this.jvxlData.contourColixes[c]=b[c].get(3)[0];return this.jvxlData.vContours=b});e(c$,"getPmeshData",function(a){return J.api.Interface.getInterface("J.shapesurface.PMeshWriter",this.vwr,"script").write(this,a)},"~B");c$.get3dContour=e(c$,"get3dContour",function(a,b,c,d){var e=JU.BS.newN(a.pc),j=new JU.SB,g=JU.C.getArgb(d);J.shapesurface.IsosurfaceMesh.setContourVector(b,a.pc,e,c,d,g,
j);for(d=0;d<a.pc;d++)null!=a.setABC(d)&&J.shapesurface.IsosurfaceMesh.addContourPoints(b,e,d,j,a.vs,a.vvs,a.iA,a.iB,a.iC,c)},"J.shapesurface.IsosurfaceMesh,JU.Lst,~N,~N");c$.setContourVector=e(c$,"setContourVector",function(a,b,c,d,e,j,g){a.add(0,Integer.$valueOf(b));a.add(1,c);a.add(2,Float.$valueOf(d));a.add(3,W(-1,[e]));a.add(4,v(-1,[j]));a.add(5,g)},"JU.Lst,~N,JU.BS,~N,~N,~N,JU.SB");c$.addContourPoints=e(c$,"addContourPoints",function(a,b,c,d,e,j,g,f,m,p){var n=null,q=null,r=0,k=J.shapesurface.IsosurfaceMesh.checkPt(j,
g,f,p);Float.isNaN(k)||(n=J.shapesurface.IsosurfaceMesh.getContourPoint(e,g,f,k),r|=1);var u=1==k?NaN:J.shapesurface.IsosurfaceMesh.checkPt(j,f,m,p);Float.isNaN(u)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,f,m,u),0==r&&(n=q,k=u),r|=2);switch(r){case 0:return;case 1:if(0==k)return;case 2:u=1==u?NaN:J.shapesurface.IsosurfaceMesh.checkPt(j,m,g,p),Float.isNaN(u)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,m,g,u),r|=4)}switch(r){case 3:case 5:case 6:break;default:return}b.set(c);J.jvxl.data.JvxlCoder.appendContourTriangleIntersection(r,
k,u,d);a.addLast(n);a.addLast(q)},"JU.Lst,JU.BS,~N,JU.SB,~A,~A,~N,~N,~N,~N");c$.checkPt=e(c$,"checkPt",function(a,b,c,d){var e,f;return d==(e=a[b])?0:d==(f=a[c])?1:e<d==d<f?(d-e)/(f-e):NaN},"~A,~N,~N,~N");c$.getContourPoint=e(c$,"getContourPoint",function(a,b,c,d){var e=new JU.P3;e.sub2(a[c],a[b]);e.scaleAdd2(d,e,a[b]);return e},"~A,~N,~N,~N");e(c$,"setDiscreteColixes",function(a,b){null!=a&&(this.jvxlData.contourValues=a);if(null==a||0==a.length)a=this.jvxlData.contourValues=this.jvxlData.contourValuesUsed;
null==b&&null!=this.jvxlData.contourColixes?b=this.jvxlData.contourColixes:(this.jvxlData.contourColixes=b,this.jvxlData.contourColors=JU.C.getHexCodes(b));if(!(null==this.vs||null==this.vvs||null==a)){var c=a.length,d=a[c-1];this.colorCommand=null;var e=null!=b&&0<b.length;this.isColorSolid=e&&null!=this.jvxlData.jvxlPlane;if(null!=this.jvxlData.vContours){if(e)for(var 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=W(this.pc,0);this.colorsExplicit=!1;for(f=0;f<this.pc;f++){var g=this.pis[f];if(null!=g){this.pcs[f]=0;for(var g=(this.vvs[g[0]]+this.vvs[g[1]]+this.vvs[g[2]])/3,k=c;0<=--k;)if(g>=a[k]&&g<d){this.pcs[f]=e?b[k%b.length]:0;break}}}}}},"~A,~A");e(c$,"getContourList",function(){var a=new java.util.Hashtable;a.put("values",null==this.jvxlData.contourValuesUsed?this.jvxlData.contourValues:this.jvxlData.contourValuesUsed);var b=new JU.Lst;if(null!=this.jvxlData.contourColixes){for(var c=
0;c<this.jvxlData.contourColixes.length;c++)b.addLast(JU.CU.colorPtFromInt(JU.C.getArgb(this.jvxlData.contourColixes[c]),null));a.put("colors",b)}return a},"JV.Viewer");e(c$,"deleteContours",function(){this.jvxlData.contourValuesUsed=null;this.jvxlData.contourValues=null;this.jvxlData.contourColixes=null;this.jvxlData.vContours=null});e(c$,"setVertexColorMap",function(){this.vertexColorMap=new java.util.Hashtable;for(var a=-999,b=null,c=this.vc;0<=--c;){var d=this.vcs[c];d!=a&&(d=JU.C.getHexCode(a=
d),b=this.vertexColorMap.get(d),null==b&&this.vertexColorMap.put(d,b=new JU.BS));b.set(c)}});e(c$,"setVertexColixesForAtoms",function(a,b,c,d){this.jvxlData.vertexDataOnly=!0;this.jvxlData.vertexColors=v(this.vc,0);this.jvxlData.nVertexColors=this.vc;var e=a.ms.at;a=a.gdata;for(var f=this.mergeVertexCount0;f<this.vc;f++){var g=this.vertexSource[f];if(!(0>g)&&d.get(g)){this.jvxlData.vertexColors[f]=a.getColorArgbOrGray(this.vcs[f]=JU.C.copyColixTranslucency(this.colix,e[g].colixAtom));var k=null==
b?0:b[c[g]];0==k&&(k=e[g].colixAtom);this.vcs[f]=JU.C.copyColixTranslucency(this.colix,k)}}},"JV.Viewer,~A,~A,JU.BS");e(c$,"colorVertices",function(a,b,c){if(null!=this.vertexSource){a=JU.C.copyColixTranslucency(this.colix,a);var d=c?new JU.BS:b;this.checkAllocColixes();if(c)for(var e=0;e<this.vc;e++){var f=this.vertexSource[e];0<=f&&b.get(f)&&(this.vcs[e]=a,null!=d&&d.set(e))}else for(e=0;e<this.vc;e++)d.get(e)&&(this.vcs[e]=a);c&&(a=JU.C.getHexCode(a),null==this.vertexColorMap&&(this.vertexColorMap=
new java.util.Hashtable),J.shapesurface.IsosurfaceMesh.addColorToMap(this.vertexColorMap,a,b))}},"~N,JU.BS,~B");e(c$,"checkAllocColixes",function(){(null==this.vcs||null==this.vertexColorMap&&this.isColorSolid)&&this.allocVertexColixes();this.isColorSolid=!1});c$.addColorToMap=e(c$,"addColorToMap",function(a,b,c){for(var d=null,e,f=a.entrySet().iterator();f.hasNext()&&((e=f.next())||1);)e.getKey()===b?(d=e.getValue(),d.or(c)):e.getValue().andNot(c);null==d&&a.put(b,c)},"java.util.Map,~S,JU.BS");e(c$,
"setJvxlColorMap",function(a){this.jvxlData.diameter=this.diameter;this.jvxlData.color=JU.C.getHexCode(this.colix);this.jvxlData.meshColor=0==this.meshColix?null:JU.C.getHexCode(this.meshColix);this.jvxlData.translucency=30720==(this.colix&30720)?-1:JU.C.getColixTranslucencyFractional(this.colix);this.jvxlData.rendering=this.getRendering().substring(1);this.jvxlData.colorScheme=null==this.colorEncoder?null:this.colorEncoder.getColorScheme();null==this.jvxlData.vertexColors&&(this.jvxlData.nVertexColors=
null==this.vertexColorMap?0:this.vertexColorMap.size());if(!(null==this.vertexColorMap||null==this.vertexSource||!a)){null==this.jvxlData.vertexColorMap&&(this.jvxlData.vertexColorMap=new java.util.Hashtable);var b;for(a=this.vertexColorMap.entrySet().iterator();a.hasNext()&&((b=a.next())||1);){var c=b.getValue();if(!c.isEmpty()){for(var d=b.getKey(),e=new JU.BS,f=0;f<this.vc;f++)c.get(this.vertexSource[f])&&e.set(f);J.shapesurface.IsosurfaceMesh.addColorToMap(this.jvxlData.vertexColorMap,d,e)}}this.jvxlData.nVertexColors=
this.jvxlData.vertexColorMap.size();0==this.jvxlData.vertexColorMap.size()&&(this.jvxlData.vertexColorMap=null)}},"~B");e(c$,"setColorCommand",function(){if(!(null==this.colorEncoder||null==(this.colorCommand=this.colorEncoder.getColorScheme())))this.colorCommand=this.colorCommand.equals("inherit")?"#inherit;":"color $"+JU.PT.esc(this.thisID)+JU.PT.esc(this.colorCommand)+" range "+(this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue+" "+this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToRed+
" "+this.jvxlData.valueMappedToBlue)});e(c$,"setColorsFromJvxlData",function(a){this.diameter=this.jvxlData.diameter;-1!=a&&(-2147483648!=a&&2147483647!=a?this.colix=JU.C.getColix(a):null!=this.jvxlData.color&&(this.colix=JU.C.getColixS(this.jvxlData.color)));0==this.colix&&(this.colix=5);this.colix=JU.C.getColixTranslucent3(this.colix,0!=this.jvxlData.translucency,this.jvxlData.translucency);a=0==this.jvxlData.translucency?NaN:this.jvxlData.translucency;null!=this.jvxlData.meshColor&&(this.meshColix=
JU.C.getColixS(this.jvxlData.meshColor));this.setJvxlDataRendering();this.isColorSolid=!this.jvxlData.isBicolorMap&&null==this.jvxlData.vertexColors&&null==this.jvxlData.vertexColorMap;if(null==this.colorEncoder)return!1;if(null==this.jvxlData.vertexColorMap){if(null!=this.jvxlData.colorScheme){var b=this.jvxlData.colorScheme,c=b.startsWith("translucent ");c&&(b=b.substring(12),a=NaN);this.colorEncoder.setColorScheme(b,c);this.remapColors(null,null,a)}}else{if(null!=this.jvxlData.baseColor)for(a=
this.vc;0<=--a;)this.vcs[a]=this.colix;for(c=this.jvxlData.vertexColorMap.entrySet().iterator();c.hasNext()&&((b=c.next())||1);){var d=b.getValue(),e=JU.C.copyColixTranslucency(this.colix,JU.C.getColixS(b.getKey()));for(a=d.nextSetBit(0);0<=a;a=d.nextSetBit(a+1))this.vcs[a]=e}}return!0},"~N");e(c$,"setJvxlDataRendering",function(){if(null!=this.jvxlData.rendering)for(var a=JU.PT.getTokens(this.jvxlData.rendering),b=0;b<a.length;b++)this.setTokenProperty(JS.T.getTokFromName(a[b]),!0)});e(c$,"remapColors",
function(a,b,c){null==b&&(b=this.colorEncoder);null==b&&(b=this.colorEncoder=new JU.ColorEncoder(null,a));this.colorEncoder=b;this.setColorCommand();Float.isNaN(c)?c=JU.C.getColixTranslucencyLevel(this.colix):this.colix=JU.C.getColixTranslucent3(this.colix,!0,c);var d=b.lo,e=b.hi,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.vertexDataOnly=!0;this.jvxlData.vertexColors=v(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=W(this.contourValues.length,0);for(a=0;a<this.contourValues.length;a++)this.contourColixes[a]=b.getColorIndex(this.contourValues[a]);
this.setDiscreteColixes(null,null)}this.jvxlData.isJvxlPrecisionColor=!0;J.jvxl.data.JvxlCoder.jvxlCreateColorData(this.jvxlData,this.vvs);this.setColorCommand();this.isColorSolid=!1}},"JV.Viewer,JU.ColorEncoder,~N");e(c$,"reinitializeLightingAndColor",function(a){this.initialize(this.lighting,null,null);if(null!=this.colorEncoder||this.jvxlData.isBicolorMap)this.vcs=null,this.remapColors(a,null,NaN)},"JV.Viewer");k(c$,"getBoundingBox",function(){return this.jvxlData.boundingBox});k(c$,"setBoundingBox",
function(a){this.jvxlData.boundingBox=a},"~A");e(c$,"merge",function(a){var b=this.vc+(null==a?0:a.vc);null==this.pis&&(this.pis=v(0,0,0));null!=a&&null==a.pis&&(a.pis=v(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");c$.mergePolygons=e(c$,"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 g=0;3>g;g++)e[g]+=c;return b},"JU.MeshSurface,~N,~N,~A");k(c$,"getUnitCell",function(){return null!=this.unitCell||null!=(this.unitCell=this.vwr.ms.am[this.modelIndex].biosymmetry)||null!=(this.unitCell=this.vwr.ms.getUnitCell(this.modelIndex))||null!=this.oabc&&null!=(this.unitCell=J.api.Interface.getSymmetry(this.vwr,"symmetry").getUnitCell(this.oabc,!0,null))?
this.unitCell:null});e(c$,"fixLattice",function(){if(null!=this.getUnitCell()){var a=new JU.P3i,b=JU.P3i.new3(F(this.lattice.x),F(this.lattice.y),F(this.lattice.z));this.jvxlData.fixedLattice=this.lattice;this.lattice=null;JU.SimpleUnitCell.setMinMaxLatticeParameters(F(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 g=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 k=a.y;k<b.y;k++)for(var m=a.z;m<b.z;m++)if(!(0==f&&0==k&&0==m)){d.set(f,k,m);this.unitCell.toCartesian(d,!1);for(var p=0;p<e;p++){this.normixes[this.vc]=this.normixes[p];var n=JU.P3.newP(this.vs[p]);n.add(d);this.addVCVal(n,this.vvs[p],!1)}c+=e;for(p=0;p<g;p++)n=JU.AU.arrayCopyI(this.pis[p],-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=B(-1,[a,b])}});k(c$,"getMinDistance2ForVertexGrouping",function(){return null!=this.jvxlData.boundingBox&&null!=this.jvxlData.boundingBox[0]&&5>this.jvxlData.boundingBox[1].distanceSquared(this.jvxlData.boundingBox[0])?1E-10:1E-8});k(c$,"getVisibleVertexBitSet",function(){var a=this.getVisibleVBS();if(0<=this.jvxlData.thisSet)for(var b=0;b<this.vc;b++)this.vertexSets[b]!=this.jvxlData.thisSet&&a.clear(b);return a});e(c$,"updateCoordinates",function(a,b){var c=null==b||
this.isModelConnected;if(!c)for(var d=0;d<this.connectedAtoms.length;d++)if(0<=this.connectedAtoms[d]&&b.get(this.connectedAtoms[d])){c=!0;break}c&&(this.isModelConnected?this.mat4=this.vwr.ms.am[this.modelIndex].mat4:(null==this.mat4&&(this.mat4=JU.M4.newM4(null)),this.mat4.mul2(a,this.mat4)),this.recalcAltVertices=!0)},"JU.M4,JU.BS");e(c$,"getDataMinMax",function(){for(var a=3.4028235E38,b=1.4E-45,c=this.vvs.length;0<=--c;){var d=this.vvs[c];d<a&&(a=d);d>b&&(b=d)}return y(-1,[a,b])});e(c$,"getDataRange",
function(){return null!=this.jvxlData.jvxlPlane&&null==this.colorEncoder?null:y(-1,[this.jvxlData.mappedDataMin,this.jvxlData.mappedDataMax,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue:this.jvxlData.valueMappedToRed,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToBlue])})});E("J.jvxl.readers");H(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.VolumeDataReader",["java.lang.Float","JU.AU","$.SB","J.jvxl.data.JvxlCoder","JU.Logger"],function(){c$=
N(function(){this.dataType=0;this.allowMapData=this.precalculateVoxelData=!1;this.point=null;this.maxGrid=this.ptsPerAngstrom=0;this.useOriginStepsPoints=!1;K(this,arguments)},J.jvxl.readers,"VolumeDataReader",J.jvxl.readers.SurfaceReader);T(c$,function(){ba(this,J.jvxl.readers.VolumeDataReader,[])});k(c$,"init",function(a){this.initVDR(a)},"J.jvxl.readers.SurfaceGenerator");e(c$,"initVDR",function(a){this.initSR(a);this.useOriginStepsPoints=null!=this.params.origin&&null!=this.params.points&&null!=
this.params.steps;this.dataType=this.params.dataType;this.allowMapData=this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");e(c$,"setup",function(){this.jvxlFileHeaderBuffer=(new JU.SB).append("volume data read from file\n\n");J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData,this.jvxlFileHeaderBuffer)},"~B");k(c$,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();return!0},"~B");k(c$,"readVolumeData",function(a){try{this.readSurfaceData(a)}catch(b){if(U(b,
Exception))return System.out.println(b.toString()),!1;throw b;}return!0},"~B");e(c$,"readVoxelDataIndividually",function(a){if(!a||this.allowMapData)if(!a||null!=this.volumeData.sr)this.volumeData.setVoxelDataAsArray(this.voxelData=null);else{this.newVoxelDataCube();for(a=0;a<this.nPointsX;++a){var b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(var c=0,d=0;d<this.nPointsY;++d)for(var e=b[d]=y(this.nPointsZ,0),f=0;f<this.nPointsZ;++f,++c)e[f]=this.getValue(a,d,f,c)}}},"~B");e(c$,"setVolumeData",
function(){});e(c$,"setVolumeDataParams",function(){if(null!=this.params.volumeData)return this.setVolumeDataV(this.params.volumeData),!0;if(!this.useOriginStepsPoints)return!1;this.volumetricOrigin.setT(this.params.origin);this.volumetricVectors[0].set(this.params.steps.x,0,0);this.volumetricVectors[1].set(0,this.params.steps.y,0);this.volumetricVectors[2].set(0,0,this.params.steps.z);this.voxelCounts[0]=F(this.params.points.x);this.voxelCounts[1]=F(this.params.points.y);this.voxelCounts[2]=F(this.params.points.z);
if(1>this.voxelCounts[0]||1>this.voxelCounts[1]||1>this.voxelCounts[2])return!1;this.showGridInfo();return!0});e(c$,"showGridInfo",function(){JU.Logger.info("grid origin  = "+this.params.origin);JU.Logger.info("grid steps   = "+this.params.steps);JU.Logger.info("grid points  = "+this.params.points);this.ptTemp.x=this.params.steps.x*this.params.points.x;this.ptTemp.y=this.params.steps.y*this.params.points.y;this.ptTemp.z=this.params.steps.z*this.params.points.z;JU.Logger.info("grid lengths = "+this.ptTemp);
this.ptTemp.add(this.params.origin);JU.Logger.info("grid max xyz = "+this.ptTemp)});e(c$,"setVoxelRange",function(a,b,c,d,e,f){-1E-4<=b-c&&(b=-10,c=10);var g=c-b,k=this.params.resolution;3.4028235E38!=k&&(d=k);c=C(Math.floor(g*d))+1;c>e&&(0<(this.dataType&256)?3.4028235E38==k?(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==k&&(c=e));1==c&&(c=2);d=(c-
1)/g;d<f&&(c=C(Math.floor(f*g+1)),d=(c-1)/g);e=this.volumeData.volumetricVectorLengths[a]=1/d;this.voxelCounts[a]=c;this.isQuiet||JU.Logger.info("isosurface resolution for axis "+(a+1)+" set to "+d+" points/Angstrom; "+this.voxelCounts[a]+" voxels");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)}this.isEccentric&&this.eccentricityMatrix.rotate(this.volumetricVectors[a]);return this.voxelCounts[a]},"~N,~N,~N,~N,~N,~N");k(c$,"readSurfaceData",function(a){this.readSurfaceDataVDR(a)},"~B");e(c$,"readSurfaceDataVDR",function(a){this.isProgressive&&!a?(this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null):this.precalculateVoxelData?this.generateCube():
this.readVoxelDataIndividually(a)},"~B");e(c$,"generateCube",function(){JU.Logger.info("data type: user volumeData");JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);for(var a=0;3>a;++a)JU.Logger.info("voxel grid vector:"+this.volumetricVectors[a]);JU.Logger.info("Read "+this.nPointsX+" x "+this.nPointsY+" x "+this.nPointsZ+" data points")});k(c$,"closeReader",function(){})});E("J.jvxl.readers");H(["J.jvxl.readers.VolumeDataReader","JU.BS","$.P3","$.P3i","J.atomdata.AtomData"],"J.jvxl.readers.AtomDataReader",
"java.lang.Float java.util.Date JU.AU $.SB $.V3 J.atomdata.RadiusData J.c.VDW J.jvxl.data.JvxlCoder JU.BSUtil $.Logger".split(" "),function(){c$=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;K(this,arguments)},J.jvxl.readers,"AtomDataReader",J.jvxl.readers.VolumeDataReader);$(c$,function(){this.atomData=new J.atomdata.AtomData;this.bsMySelected=
new JU.BS;this.bsMyIgnored=new JU.BS;this.ptY0=new JU.P3;this.ptZ0=new JU.P3;this.pt0=new JU.P3i;this.pt1=new JU.P3i;this.ptV=new JU.P3});T(c$,function(){ba(this,J.jvxl.readers.AtomDataReader,[])});e(c$,"initADR",function(a){this.initVDR(a);this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");k(c$,"setup",function(){this.setup2()},"~B");e(c$,"setup2",function(){this.contactPair=this.params.contactPair;this.doAddHydrogens=null!=this.sg.atomDataServer&&this.params.addHydrogens;this.modelIndex=
this.params.modelIndex;null!=this.params.bsIgnore&&(this.bsMyIgnored=this.params.bsIgnore);if(null!=this.params.volumeData){this.setVolumeDataV(this.params.volumeData);this.setBBox(this.volumeData.volumetricOrigin,0);this.ptV.setT(this.volumeData.volumetricOrigin);for(var a=0;3>a;a++)this.ptV.scaleAdd2(this.volumeData.voxelCounts[a]-1,this.volumeData.volumetricVectors[a],this.ptV);this.setBBox(this.ptV,0)}(this.havePlane=null!=this.params.thePlane)&&this.volumeData.setPlaneParameters(this.params.thePlane)});
e(c$,"markPlaneVoxels",function(a,b){for(var c=0,d=this.thisX*this.yzCount,e=d+this.yzCount;d<e;d++,c++)this.volumeData.getPoint(d,this.ptV),this.thisPlane[c]=this.ptV.distance(a)-b},"JU.P3,~N");e(c$,"setVolumeForPlane",function(){this.useOriginStepsPoints?(this.xyzMin=JU.P3.newP(this.params.origin),this.xyzMax=JU.P3.newP(this.params.origin),this.xyzMax.add3((this.params.points.x-1)*this.params.steps.x,(this.params.points.y-1)*this.params.steps.y,(this.params.points.z-1)*this.params.steps.z)):null==
this.params.boundingBox?(this.getAtoms(this.params.bsSelected,!1,!0,!1,!1,!1,!1,this.params.mep_marginAngstroms,this.params.modelInvRotation),null==this.xyzMin&&(this.xyzMin=JU.P3.new3(-10,-10,-10),this.xyzMax=JU.P3.new3(10,10,10))):(this.xyzMin=JU.P3.newP(this.params.boundingBox[0]),this.xyzMax=JU.P3.newP(this.params.boundingBox[1]));this.setRanges(this.params.plane_ptsPerAngstrom,this.params.plane_gridMax,0)});e(c$,"getAtoms",function(a,b,c,d,e,f,g,k,m){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!=m&&this.atomData.transformXYZ(m,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,k)))continue;this.bsMySelected.set(d);e=!this.havePlane}if(c&&(f||e))this.atomData.atomRadius[d]=this.getWorkingRadius(d,k)}e=c&&b?this.getWorkingRadius(-1,k):0;this.myAtomCount=
JU.BSUtil.cardinalityOf(this.bsMySelected);k=JU.BSUtil.copy(this.bsMySelected);g=0;this.atomProp=null;this.theProperty=3.4028235E38;this.haveOneProperty=!1;a=this.params.theProperty;if(0<this.myAtomCount){m=null;if(b){this.atomData.bsSelected=k;this.sg.atomDataServer.fillAtomData(this.atomData,8);m=Array(g=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;)m[--g]=this.atomData.hAtoms[d][b];g=m.length;
JU.Logger.info(g+" attached hydrogens added")}b=g+this.myAtomCount;c&&(this.atomRadius=y(b,0));this.atomXyzTruncated=Array(b);null!=this.params.theProperty&&(this.atomProp=y(b,0));this.atomNo=v(b,0);this.atomIndex=v(b,0);this.myIndex=v(this.ac,0);for(d=0;d<g;d++)c&&(this.atomRadius[d]=e),this.atomXyzTruncated[d]=m[d],this.atomNo[d]=-1,null!=this.atomProp&&this.addAtomProp(d,NaN);this.myAtomCount=g;for(d=k.nextSetBit(0);0<=d;d=k.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++)!k.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(c$,"setRadii",
function(){if(null==this.rs){this.maxRS=0;this.rs=y(this.myAtomCount,0);this.rs2=y(this.myAtomCount,0);for(var a=0;a<this.myAtomCount;a++){var b=this.rs[a]=this.atomRadius[a]+this.sr;b>this.maxRS&&(this.maxRS=b);this.rs2[a]=this.rs[a]*this.rs[a]}}});e(c$,"addAtomProp",function(a,b){this.atomProp[a]=b;!Float.isNaN(this.theProperty)&&b!=this.theProperty&&(this.theProperty=3.4028235E38==this.theProperty?b:NaN)},"~N,~N");e(c$,"getWorkingRadius",function(a,b){var c=0>a?this.atomData.hAtomRadius:this.atomData.atomRadius[a];
return Float.isNaN(b)?Math.max(c,0.1):c+b},"~N,~N");e(c$,"setHeader",function(a,b){this.jvxlFileHeaderBuffer=new JU.SB;null!=this.atomData.programInfo&&this.jvxlFileHeaderBuffer.append("#created by ").append(this.atomData.programInfo).append(" on ").append(""+new java.util.Date).append("\n");this.jvxlFileHeaderBuffer.append(a).append("\n").append(b).append("\n")},"~S,~S");e(c$,"setRanges",function(a,b,c){null!=this.xyzMin&&(this.ptsPerAngstrom=a,this.maxGrid=b,this.minPtsPerAng=c,this.setVolumeData(),
J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData,this.jvxlFileHeaderBuffer))},"~N,~N,~N");k(c$,"setVolumeData",function(){this.setVolumeDataADR()});e(c$,"setVolumeDataADR",function(){this.setVolumeDataParams()||(this.setVoxelRange(0,this.xyzMin.x,this.xyzMax.x,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(1,this.xyzMin.y,this.xyzMax.y,this.ptsPerAngstrom,this.maxGrid,this.minPtsPerAng),this.setVoxelRange(2,this.xyzMin.z,this.xyzMax.z,this.ptsPerAngstrom,this.maxGrid,
this.minPtsPerAng))});e(c$,"setVertexSource",function(){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);if(null!=this.params.vertexSource){this.params.vertexSource=JU.AU.arrayCopyI(this.params.vertexSource,this.meshData.vc);for(var a=0;a<this.meshData.vc;a++)this.params.vertexSource[a]=Math.abs(this.params.vertexSource[a])-1}});e(c$,"resetPlane",function(a){for(var b=0;b<this.yzCount;b++)this.thisPlane[b]=a},"~N");e(c$,"resetVoxelData",function(a){for(var b=0;b<this.nPointsX;++b)for(var c=
0;c<this.nPointsY;++c)for(var d=0;d<this.nPointsZ;++d)this.voxelData[b][c][d]=a},"~N");e(c$,"getVoxel",function(a,b,c,d){return this.isProgressive?this.thisPlane[d%this.yzCount]:this.voxelData[a][b][c]},"~N,~N,~N,~N");e(c$,"unsetVoxelData",function(){this.unsetVoxelData2()});e(c$,"unsetVoxelData2",function(){if(this.isProgressive)for(var a=0;a<this.yzCount;a++)3.4028235E38==this.thisPlane[a]&&(this.thisPlane[a]=NaN);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)3.4028235E38==
this.voxelData[a][b][c]&&(this.voxelData[a][b][c]=NaN)});e(c$,"setGridLimitsForAtom",function(a,b,c,d){b+=this.margin;this.volumeData.xyzToVoxelPt(a.x,a.y,a.z,c);a=C(Math.floor(b/this.volumeData.volumetricVectorLengths[0]));var e=C(Math.floor(b/this.volumeData.volumetricVectorLengths[1]));b=C(Math.floor(b/this.volumeData.volumetricVectorLengths[2]));d.set(c.x+a,c.y+e,c.z+b);c.set(c.x-a,c.y-e,c.z-b);c.x=Math.max(c.x-1,0);c.y=Math.max(c.y-1,0);c.z=Math.max(c.z-1,0);d.x=Math.min(d.x+1,this.nPointsX);
d.y=Math.min(d.y+1,this.nPointsY);d.z=Math.min(d.z+1,this.nPointsZ)},"JU.P3,~N,JU.P3i,JU.P3i");e(c$,"getAtomMinMax",function(a,b){for(var c=0;c<this.nPointsX;c++)b[c]=new JU.BS;for(var d=this.myAtomCount;0<=--d;)if(null==a||a.get(d)){this.setGridLimitsForAtom(this.atomXyzTruncated[d],this.atomRadius[d],this.pt0,this.pt1);for(c=this.pt0.x;c<this.pt1.x;c++)b[c].set(d)}},"JU.BS,~A");e(c$,"markSphereVoxels",function(a,b){for(var c=3.4028235E38!=b&&null!=this.point,d=this.volumetricVectors[0],e=this.volumetricVectors[1],
f=this.volumetricVectors[2],g=this.thisAtomSet.nextSetBit(0);0<=g;g=this.thisAtomSet.nextSetBit(g+1))if(this.havePlane||null==this.validSpheres||this.validSpheres.get(g)){var k=null!=this.noFaceSpheres&&this.noFaceSpheres.get(g),m=g>=this.firstNearbyAtom,p=this.atomXyzTruncated[g],n=this.atomRadius[g];if(!(c&&p.distance(this.point)>b+n+0.5)){var q=n+a;this.setGridLimitsForAtom(p,q,this.pt0,this.pt1);this.isProgressive&&(this.pt0.x=this.thisX,this.pt1.x=this.thisX+1);this.volumeData.voxelPtToXYZ(this.pt0.x,
this.pt0.y,this.pt0.z,this.ptV);for(var r=this.pt0.x;r<this.pt1.x;r++,this.ptV.add2(d,this.ptY0)){this.ptY0.setT(this.ptV);for(var w=this.pt0.y;w<this.pt1.y;w++,this.ptV.add2(e,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var u=this.pt0.z;u<this.pt1.z;u++,this.ptV.add(f)){var v=this.ptV.distance(p)-n,y=this.volumeData.getPointIndex(r,w,u);if((0==a||v<=q)&&v<this.getVoxel(r,w,u,y)){if(m||c&&this.ptV.distance(this.point)>b)v=NaN;this.setVoxel(r,w,u,y,v);Float.isNaN(v)||(null!=this.voxelSource&&(this.voxelSource[y]=
g+1),0>v&&k&&this.bsSurfaceVoxels.set(y))}}}}}}},"~N,~N");e(c$,"setVoxel",function(a,b,c,d,e){this.isProgressive?this.thisPlane[d%this.yzCount]=e:this.voxelData[a][b][c]=e},"~N,~N,~N,~N,~N")});E("J.jvxl.readers");H(["JU.P3","J.jvxl.readers.AtomDataReader","JU.P4","$.V3"],"J.jvxl.readers.IsoSolventReader","java.lang.Float java.util.Hashtable JU.BS $.Lst $.Measure J.jvxl.data.MeshData JU.BSUtil $.Logger $.MeshSurface $.TempArray".split(" "),function(){c$=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;ja("J.jvxl.readers.IsoSolventReader.Edge")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$();ja("J.jvxl.readers.IsoSolventReader.Face")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$();
this.ecosASB2=this.dAB2=this.dAB=this.rBS2=this.rAS2=this.rBS=this.rAS=0;K(this,arguments)},J.jvxl.readers,"IsoSolventReader",J.jvxl.readers.AtomDataReader);$(c$,function(){this.ptS1=new JU.P3;this.ptS2=new JU.P3;this.vTemp=new JU.V3;this.plane=new JU.P4;this.ptTemp2=new JU.P3;this.vTemp2=new JU.V3;this.p=new JU.P3});T(c$,function(){ba(this,J.jvxl.readers.IsoSolventReader,[])});k(c$,"init",function(a){this.initADR(a)},"J.jvxl.readers.SurfaceGenerator");k(c$,"readVolumeParameters",function(a){this.setup(a);
this.initializeVolumetricData();this.volumeData.setUnitVectors();this.vl0=this.volumeData.volumetricVectorLengths[0];this.vl1=this.volumeData.volumetricVectorLengths[1];this.vl2=this.volumeData.volumetricVectorLengths[2];this.isProgressive&&(this.volumeData.getYzCount(),this.bsAtomMinMax=Array(this.nPointsX),this.getAtomMinMax(null,this.bsAtomMinMax),this.voxelSource=v(this.volumeData.nPoints,0));return!0},"~B");k(c$,"setup",function(a){this.setup2();if(null==this.contactPair){this.cavityRadius=this.params.cavityRadius;
this.envelopeRadius=this.params.envelopeRadius;this.sr=this.params.solventRadius;this.point=this.params.point;this.isCavity=this.params.isCavity&&null!=this.meshDataServer;this.isPocket=null!=this.params.pocket&&null!=this.meshDataServer;this.doUseIterator=this.doCalculateTroughs=!a&&null!=this.sg.atomDataServer&&!this.isCavity&&0<this.sr&&(1195==this.dataType||1203==this.dataType);this.getAtoms(this.params.bsSelected,this.doAddHydrogens,!0,!1,!1,!0,!1,NaN,null);if(this.isCavity||this.isPocket)this.dots=
this.meshDataServer.calculateGeodesicSurface(this.bsMySelected,this.envelopeRadius);this.setHeader("solvent/molecular surface",this.params.calculationType);if(this.havePlane||!a)this.setRanges(this.params.solvent_ptsPerAngstrom,this.params.solvent_gridMax,0),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");k(c$,"generateCube",function(){if(!(this.isCavity&&null!=this.params.theProperty)){this.isCavity&&1207!=this.dataType&&1208!=this.dataType?(this.params.vertexSource=null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(this.cavityRadius,this.params.distance),this.generateSolventCavity(),this.resetVoxelData(3.4028235E38),this.markSphereVoxels(0,
NaN)):(this.voxelSource=v(this.volumeData.nPoints,0),this.generateSolventCube());this.unsetVoxelData();var a=this.params.slabInfo;if(null!=a)for(var b=0;b<a.size();b++)a.get(b)[2].booleanValue()&&I(a.get(b)[0],JU.P4)&&(this.volumeData.capData(a.get(b)[0],this.params.cutoff),a.removeItemAt(b--))}});k(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,f,g,k,m,p,n,q,r){p=this.marchingCubes.getLinearOffset(g,k,m,p);n=this.marchingCubes.getLinearOffset(g,k,m,n);this.isSurfacePoint=null!=this.bsSurfaceVoxels&&
(this.bsSurfaceVoxels.get(p)||this.bsSurfaceVoxels.get(n));if(null!=this.voxelSource){var w=Math.abs(Float.isNaN(d)||c<d?this.voxelSource[p]:this.voxelSource[n]);0<w&&(this.iAtomSurface=this.atomIndex[w-1])}if(J.jvxl.readers.IsoSolventReader.testLinear||null==this.voxelSource||0==this.voxelSource[p]||this.voxelSource[p]!=this.voxelSource[n])return this.getSPF(a,b,c,d,e,f,g,k,m,p,n,q,r);a=q[0]=JU.MeshSurface.getSphericalInterpolationFraction(0>this.voxelSource[p]?this.sr:this.atomRadius[this.voxelSource[p]-
1],c,d,f.length());r.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");k(c$,"addVertexCopy",function(a,b,c,d){a=this.addVC(a,b,c,d);if(0>a)return a;this.isSurfacePoint&&this.bsSurfacePoints.set(a);null!=this.params.vertexSource&&(this.params.vertexSource[a]=this.iAtomSurface);return a},"JU.T3,~N,~N,~B");k(c$,"selectPocket",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);for(var b=this.meshData.vs,c=this.meshData.vc,
d=this.meshData.vvs,e=this.dots.length,f=0;f<c;f++)for(var g=0;g<e;g++)this.dots[g].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(g=d.nextSetBit(0);0<=g;g=d.nextSetBit(g+1))if(Float.isNaN(this.meshData.vvs[g])){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");k(c$,"postProcessVertices",function(){this.setVertexSource();if(this.doCalculateTroughs&&null!=this.bsSurfacePoints){var a=new JU.BS,b=this.meshData.getSurfaceSet(),c=null,d=this.isPocket?null:J.jvxl.data.MeshData.calculateVolumeOrArea(this.meshData,-2147483648,!1,!1),e=this.isCavity?4.71238898038469*Math.pow(this.sr,3):0,f=0,g=!1;if(null!=d&&!this.isCavity)for(var k=
0;k<this.meshData.nSets;k++){var m=d[k];Math.abs(m)>f&&(f=Math.abs(m),g=0>m)}f=g?-1:1;for(k=0;k<this.meshData.nSets;k++)if(g=b[k],g.intersects(this.bsSurfacePoints)&&(null==d||d[k]*f>e)&&null!=this.params.vertexSource){m=new JU.BS;null==c&&(c=Array(b.length));for(var p=g.nextSetBit(0);0<=p;p=g.nextSetBit(p+1)){var n=this.params.vertexSource[p];if(!(0>n)){if(a.get(n)){this.meshData.invalidateSurfaceSet(k);break}m.set(n)}}a.or(m)}else this.meshData.invalidateSurfaceSet(k);this.updateSurfaceData();null!=
this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)}null!=this.params.thePlane&&null==this.params.slabInfo&&this.params.addSlabInfo(JU.TempArray.getSlabWithinRange(-100,0))});e(c$,"generateSolventCavity",function(){for(var a=JU.BS.newN(this.nPointsX*this.nPointsY*this.nPointsZ),b=0,c=this.dots.length,d=0,e,f=this.envelopeRadius,g=0;g<this.nPointsX;++g)for(var k=0;k<this.nPointsY;++k){var m=0;a:for(;m<this.nPointsZ;++m,++b)if(3.4028235E38>
(e=this.voxelData[g][k][m])&&e>=this.cavityRadius){this.volumeData.voxelPtToXYZ(g,k,m,this.ptV);for(var p=0;p<c;p++)if(this.dots[p].distance(this.ptV)<f)continue a;a.set(b);d++}}JU.Logger.info("cavities include "+d+" voxel points");this.atomRadius=y(d,0);this.atomXyzTruncated=Array(d);for(c=b=g=0;g<this.nPointsX;++g)for(k=0;k<this.nPointsY;++k)for(m=0;m<this.nPointsZ;++m)a.get(b++)&&(this.volumeData.voxelPtToXYZ(g,k,m,this.atomXyzTruncated[c]=new JU.P3),this.atomRadius[c++]=this.voxelData[g][k][m]);
this.myAtomCount=this.firstNearbyAtom=d;this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount);this.rs=null;this.setRadii()});e(c$,"generateSolventCube",function(){1207!=this.dataType&&(this.params.vertexSource=v(this.volumeData.nPoints,0),this.bsSurfaceDone=new JU.BS,this.bsSurfaceVoxels=new JU.BS,this.bsSurfacePoints=new JU.BS,this.doCalculateTroughs?(this.iter=this.sg.atomDataServer.getSelectedAtomIterator(this.bsMySelected,!0,!1,!1),this.vEdges=new JU.Lst,this.bsLocale=Array(this.myAtomCount),this.htEdges=
new java.util.Hashtable,this.getEdges(),JU.Logger.info(this.vEdges.size()+" edges"),this.vFaces=new JU.Lst,this.getFaces(),JU.Logger.info(this.vFaces.size()+" faces"),this.htEdges=this.bsLocale=null,this.iter.release(),this.iter=null,this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38),this.markFaceVoxels(!0),this.markToroidVoxels(),this.validSpheres.or(this.noFaceSpheres),this.vEdges=null,this.markFaceVoxels(!1),this.vFaces=null):(this.newVoxelDataCube(),this.resetVoxelData(3.4028235E38)),this.markSphereVoxels(0,
this.doCalculateTroughs?3.4028235E38:this.params.distance),this.validSpheres=this.noFaceSpheres=null)});e(c$,"getEdges",function(){for(var a=0;a<this.myAtomCount;a++)this.bsLocale[a]=new JU.BS;for(a=0;a<this.myAtomCount;a++){var b=this.atomXyzTruncated[a],c=this.rs[a];for(this.sg.atomDataServer.setIteratorForAtom(this.iter,this.atomIndex[a],c+this.maxRS);this.iter.hasNext();){var d=this.iter.next(),d=this.myIndex[d];if(!(a>=this.firstNearbyAtom&&d>=this.firstNearbyAtom)){var e=this.rs[d],f=b.distance(this.atomXyzTruncated[d]);
f>=c+e||(e=ia(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(c$,"findEdge",function(a,b){return this.htEdges.get(a<b?a+"_"+b:b+"_"+a)},"~N,~N");e(c$,"getFaces",function(){var a=new JU.BS;this.params.surfaceAtoms=this.validSpheres=new JU.BS;this.noFaceSpheres=JU.BSUtil.setAll(this.myAtomCount);for(var b=this.vEdges.size();0<=--b;){var c=this.vEdges.get(b),d=c.ia,e=c.ib;a.clearAll();
a.or(this.bsLocale[d]);a.and(this.bsLocale[e]);for(var f=a.nextSetBit(e+1);0<=f;f=a.nextSetBit(f+1))if(this.getSolventPoints(c,d,e,f)){var g,k=!1;if(null!=(g=this.validateFace(d,e,f,c,this.ptS1)))this.vFaces.addLast(g),k=!0;if(null!=(g=this.validateFace(d,e,f,c,this.ptS2)))this.vFaces.addLast(g),k=!0;k&&(this.noFaceSpheres.clear(d),this.noFaceSpheres.clear(e),this.noFaceSpheres.clear(f))}}});e(c$,"validateFace",function(a,b,c,d,e){this.sg.atomDataServer.setIteratorForPoint(this.iter,this.modelIndex,
e,this.maxRS);for(var f=!0;this.iter.hasNext();){var g=this.iter.next(),k=this.myIndex[g];if(!(k==a||k==b||k==c)&&this.atomData.atoms[g].distance(e)<this.atomData.atomRadius[g]+this.sr){f=!1;break}}g=this.findEdge(b,c);k=this.findEdge(a,c);e=f?ia(J.jvxl.readers.IsoSolventReader.Face,this,null,a,b,c,e):null;d.addFace(e);g.addFace(e);k.addFace(e);if(!f)return null;this.validSpheres.set(a);this.validSpheres.set(b);this.validSpheres.set(c);return e},"~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");
e(c$,"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 g=this.vFaces.get(f),k=this.atomXyzTruncated[g.ia],m=this.atomXyzTruncated[g.ib],p=this.atomXyzTruncated[g.ic],n=g.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 q=this.pt0.x;q<this.pt1.x;q++,this.ptV.add2(c,this.ptY0)){this.ptY0.setT(this.ptV);
for(var r=this.pt0.y;r<this.pt1.y;r++,this.ptV.add2(d,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var w=this.pt0.z;w<this.pt1.z;w++,this.ptV.add(e)){var u=this.sr-this.ptV.distance(n),v=this.voxelData[q][r][w],y=this.volumeData.getPointIndex(q,r,w);a&&0<u&&this.bsSurfaceDone.set(y);if(JU.Measure.isInTetrahedron(this.ptV,k,m,p,n,this.plane,this.vTemp,this.vTemp2,!1)&&(!a?!this.bsSurfaceDone.get(y)&&0>u&&u>1.8*-this.volumeData.maxGrid&&u>v==b.get(y):0<u&&(0>v||3.4028235E38==v||u>v==b.get(y))))b.set(y),
this.setVoxel(q,r,w,y,u),null!=this.voxelSource&&(this.voxelSource[y]=-1-g.ia),0<u&&this.bsSurfaceVoxels.set(y)}}}}},"~B");e(c$,"markToroidVoxels",function(){for(var a=this.volumetricVectors[0],b=this.volumetricVectors[1],c=this.volumetricVectors[2],d=this.vEdges.size();0<=--d;){var e=this.vEdges.get(d);if(e.isValid()){var f=e.ia,g=e.ib,k=this.atomXyzTruncated[f],m=this.atomXyzTruncated[g];this.rAS=this.rs[f];this.rBS=this.rs[g];this.rAS2=this.rs2[f];this.rBS2=this.rs2[g];this.dAB=e.d;this.dAB2=e.d2;
this.ecosASB2=e.cosASB2;this.setGridLimitsForAtom(e,e.maxr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,this.pt0.y,this.pt0.z,this.ptV);for(e=this.pt0.x;e<this.pt1.x;e++,this.ptV.add2(a,this.ptY0)){this.ptY0.setT(this.ptV);for(g=this.pt0.y;g<this.pt1.y;g++,this.ptV.add2(b,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var p=this.pt0.z;p<this.pt1.z;p++,this.ptV.add(c)){var n=this.checkSpecialVoxel(k,m,this.ptV);if(!Float.isNaN(n)&&(n=this.sr-n,n<this.voxelData[e][g][p])){var q=this.volumeData.getPointIndex(e,
g,p);this.setVoxel(e,g,p,q,n);null!=this.voxelSource&&(this.voxelSource[q]=-1-f)}}}}}}});k(c$,"unsetVoxelData",function(){if(this.havePlane)if(this.isProgressive)for(var a=0;a<this.yzCount;a++)0.001>this.thisPlane[a]||(this.thisPlane[a]=0.001);else for(a=0;a<this.nPointsX;++a)for(var b=0;b<this.nPointsY;++b)for(var c=0;c<this.nPointsZ;++c)0.001>this.voxelData[a][b][c]||(this.voxelData[a][b][c]=0.001);else this.unsetVoxelData2()});e(c$,"getSolventPoints",function(a,b,c,d){var e=this.rs[b],f=a.v;a=
(a.d2+this.rs2[b]-this.rs2[c])/(2*a.d*e);c=Math.acos(a);this.p.scaleAdd2(a*e,f,this.atomXyzTruncated[b]);JU.Measure.getPlaneThroughPoint(this.p,f,this.plane);b=Math.sin(c)*e;a=this.atomXyzTruncated[d];c=this.rs[d];e=JU.Measure.distanceToPlane(this.plane,a);if(Math.abs(e)>=0.9*c)return!1;this.ptTemp.scaleAdd2(-e,f,a);a=this.p.distance(this.ptTemp);d=(b*b+a*a-(this.rs2[d]-e*e))/(2*b*a);if(0.99<=Math.abs(d))return!1;e=this.vTemp2;e.sub2(this.ptTemp,this.p);e.normalize();this.ptTemp.scaleAdd2(b*d,e,this.p);
e.cross(f,e);e.normalize();e.scale(Math.sqrt(1-d*d)*b);this.ptS1.add2(this.ptTemp,e);this.ptS2.sub2(this.ptTemp,e);return!0},"J.jvxl.readers.IsoSolventReader.Edge,~N,~N,~N");e(c$,"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(c$,"solventDistance",function(a,b,c,d,e,f){f=Math.acos((e+this.dAB2-f)/(2*d*this.dAB));c=Math.acos((b+this.dAB2-c)/(2*a*this.dAB));e=b+e-2*a*d*Math.cos(c-f);c=Math.sqrt(e);return this.ecosASB2<(b+e-d*d)/(c*a)?c:NaN},"~N,~N,~N,~N,~N,~N");e(c$,"dumpLine",function(a,b,c,d){this.sg.log('draw ID "x'+c+this.nTest++ +
'" '+JU.P3.newP(a)+" "+JU.P3.newP(b)+" color "+d)},"JU.P3,JU.T3,~S,~S");e(c$,"dumpLine2",function(a,b,c,d,e,f){var g=new JU.V3;g.setT(b);g.sub(a);g.normalize();g.scale(d);g.add(a);this.sg.log('draw ID "'+c+this.nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(g)+" color "+e);this.sg.log('draw ID "'+c+this.nTest++ +'"'+JU.P3.newP(g)+" "+JU.P3.newP(b)+" color "+f+'"'+c+'"')},"JU.P3,JU.P3,~S,~N,~S,~S");e(c$,"dumpPoint",function(a,b,c){this.sg.log('draw ID "'+b+this.nTest++ +'"'+JU.P3.newP(a)+" color "+c)},
"JU.P3,~S,~S");k(c$,"getValueAtPoint",function(a){if(null!=this.contactPair)return a.distance(this.contactPair.myAtoms[1])-this.contactPair.radii[1];for(var b=3.4028235E38,c=0;c<this.firstNearbyAtom;c++){var d=a.distance(this.atomXyzTruncated[c])-this.rs[c];d<b&&(b=d)}return 3.4028235E38==b?NaN:b},"JU.T3,~B");k(c$,"discardTempData",function(a){this.rs2=this.rs=null;this.discardTempDataSR(a)},"~B");k(c$,"getPlane",function(a){0==this.yzCount&&this.initPlanes();this.thisX=a;this.thisPlane=this.yzPlanes[a%
2];null==this.contactPair?(this.resetPlane(3.4028235E38),this.thisAtomSet=this.bsAtomMinMax[a],this.markSphereVoxels(0,this.params.distance),this.unsetVoxelData()):this.markPlaneVoxels(this.contactPair.myAtoms[0],this.contactPair.radii[0]);return this.thisPlane},"~N");c$.$IsoSolventReader$Edge$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);this.cosASB2=this.maxr=this.d2=this.d=this.nInvalid=this.nFaces=this.ib=this.ia=0;this.v=null;K(this,arguments)},J.jvxl.readers.IsoSolventReader,"Edge",
JU.P3);bb(c$,function(a,b,c,d){this.ia=Math.min(b,c);this.ib=Math.max(b,c);this.d=d;this.d2=d*d;this.maxr=Math.sqrt(this.d2/4+Math.max(a.rs2[b],a.rs2[c]));this.ave(a.atomXyzTruncated[b],a.atomXyzTruncated[c]);this.cosASB2=(a.rs2[b]+a.rs2[c]-this.d2)/(a.rs[c]*a.rs[b]);this.v=JU.V3.newVsub(a.atomXyzTruncated[c],a.atomXyzTruncated[b]);this.v.normalize()},"J.jvxl.readers.IsoSolventReader,~N,~N,~N");e(c$,"addFace",function(a){this.nFaces++;null==a&&this.nInvalid++},"J.jvxl.readers.IsoSolventReader.Face");
e(c$,"isValid",function(){return 0==this.nFaces||this.nInvalid!=this.nFaces});k(c$,"toString",function(){return this.ia+"_"+this.ib});c$=ha()};c$.$IsoSolventReader$Face$=function(){qa(self.c$);c$=N(function(){oa(this,arguments);this.ic=this.ib=this.ia=0;this.pS=null;K(this,arguments)},J.jvxl.readers.IsoSolventReader,"Face");T(c$,function(a,b,c,d){this.ia=a;this.ib=b;this.ic=c;this.pS=JU.P3.newP(d)},"~N,~N,~N,JU.P3");k(c$,"toString",function(){return this.ia+"_"+this.ib+"_"+this.ic+"_"+this.pS});c$=
ha()};aa(c$,"testLinear",!1)});E("J.jvxl.readers");H(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.SurfaceFileReader",["JU.PT","J.api.Interface"],function(){c$=N(function(){this.next=this.line=this.out=this.binarydoc=this.br=null;K(this,arguments)},J.jvxl.readers,"SurfaceFileReader",J.jvxl.readers.SurfaceReader);$(c$,function(){this.next=v(1,0)});T(c$,function(){ba(this,J.jvxl.readers.SurfaceFileReader,[])});e(c$,"setStream",function(a,b){if(null==a)this.binarydoc.setStream(null,b);else try{if(I(this.br,
JU.Rdr.StreamReader)){var c=this.br.getStream();c.reset();this.binarydoc.setStream(c,!0)}}catch(d){if(U(d,Exception))System.out.println("BCifDensityReader "+d),this.binarydoc.setStream(this.sg.atomDataServer.getBufferedInputStream(a),b);else throw d;}},"~S,~B");k(c$,"init",function(a){this.initSR(a)},"J.jvxl.readers.SurfaceGenerator");e(c$,"init2",function(a,b){this.init2SFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2SFR",function(a,b){this.br=b;this.init(a)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
e(c$,"newBinaryDocument",function(){return J.api.Interface.getInterface("JU.BinaryDocument",this.sg.atomDataServer,"file")});k(c$,"setOutputChannel",function(a){null==this.binarydoc?this.out=a:this.sg.setOutputChannel(this.binarydoc,a)},"JU.OC");k(c$,"closeReader",function(){this.closeReaderSFR()});e(c$,"closeReaderSFR",function(){if(null!=this.br)try{this.br.close()}catch(a){if(!U(a,java.io.IOException))throw a;}null!=this.out&&this.out.closeChannel();null!=this.binarydoc&&this.binarydoc.close()});
k(c$,"discardTempData",function(a){this.closeReader();this.discardTempDataSR(a)},"~B");e(c$,"getTokens",function(){return JU.PT.getTokensAt(this.line,0)});e(c$,"parseFloat",function(){return JU.PT.parseFloatNext(this.line,this.next)});e(c$,"parseFloatStr",function(a){this.next[0]=0;return JU.PT.parseFloatNext(a,this.next)},"~S");e(c$,"parseFloatRange",function(a,b,c){this.next[0]=b;return JU.PT.parseFloatRange(a,c,this.next)},"~S,~N,~N");e(c$,"parseInt",function(){return JU.PT.parseIntNext(this.line,
this.next)});e(c$,"parseIntStr",function(a){this.next[0]=0;return JU.PT.parseIntNext(a,this.next)},"~S");e(c$,"parseIntNext",function(a){return JU.PT.parseIntNext(a,this.next)},"~S");e(c$,"parseFloatArrayStr",function(a){this.next[0]=0;return JU.PT.parseFloatArrayNext(a,this.next,null,null,null)},"~S");e(c$,"parseFloatArray",function(a,b,c){return JU.PT.parseFloatArrayNext(this.line,this.next,a,b,c)},"~A,~S,~S");e(c$,"getQuotedStringNext",function(){return JU.PT.getQuotedStringNext(this.line,this.next)});
e(c$,"skipTo",function(a,b){if(null!=a)for(;0>this.rd().indexOf(a););null!=b&&(this.next[0]=this.line.indexOf(b)+b.length+2)},"~S,~S");e(c$,"rd",function(){this.line=this.br.readLine();if(null!=this.line&&(this.nBytes+=this.line.length,null!=this.out)){var a=this.line.getBytes();this.out.write(a,0,a.length);this.out.writeByteAsInt(10)}return this.line})});E("J.jvxl.readers");H(["J.jvxl.readers.SurfaceFileReader"],"J.jvxl.readers.VolumeFileReader","java.lang.Float JU.AU $.PT $.SB J.api.Interface J.atomdata.AtomData JU.Logger".split(" "),
function(){c$=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;K(this,arguments)},J.jvxl.readers,"VolumeFileReader",J.jvxl.readers.SurfaceFileReader);T(c$,function(){ba(this,J.jvxl.readers.VolumeFileReader,
[])});k(c$,"init2",function(a,b){this.init2VFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2VFR",function(a,b){this.init2SFR(a,b);this.canDownsample=this.isProgressive=this.isXLowToHigh=!0;this.jvxlData.wasCubic=!0;this.boundingBox=this.params.boundingBox;4==this.params.qmOrbitalType&&(this.hasColorData=null==this.params.parameters||0<=this.params.parameters[1],this.getNCIPlanes=!0,this.params.insideOut=!this.params.insideOut)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");
e(c$,"recordData",function(a){if(Float.isNaN(a))return a;a<this.dataMin&&(this.dataMin=a);a>this.dataMax&&(this.dataMax=a);this.dataMean+=a;this.nData++;return a},"~N");k(c$,"closeReader",function(){this.readerClosed||(this.readerClosed=!0,this.closeReaderSFR(),0==this.nData||-3.4028235E38==this.dataMax||(this.dataMean/=this.nData,JU.Logger.info("VolumeFileReader closing file: "+this.nData+" points read \ndata min/max/mean = "+this.dataMin+"/"+this.dataMax+"/"+this.dataMean)))});k(c$,"readVolumeParameters",
function(){this.endOfData=!1;this.nSurfaces=this.readVolumetricHeader();if(0==this.nSurfaces)return!1;this.nSurfaces<this.params.fileIndex&&(JU.Logger.warn("not enough surfaces in file -- resetting params.fileIndex to "+this.nSurfaces),this.params.fileIndex=this.nSurfaces);return!0},"~B");k(c$,"readVolumeData",function(a){return this.readVolumeDataVFR(a)},"~B");e(c$,"readVolumeDataVFR",function(a){if(!this.gotoAndReadVoxelData(a))return!1;this.vertexDataOnly||JU.Logger.info("JVXL read: "+this.nPointsX+
" x "+this.nPointsY+" x "+this.nPointsZ+" data points");return!0},"~B");e(c$,"readVolumetricHeader",function(){try{this.readParameters();if(-2147483648==this.ac)return 0;this.vertexDataOnly||JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);var a=this.params.downsampleFactor,b=this.canDownsample&&1<a;1<a&&!this.canDownsample&&(this.jvxlData.msg+="\ncannot downsample this file type");if(b){this.downsampleRemainders=v(3,0);JU.Logger.info("downsample factor = "+a);for(var c=0;3>c;++c){var d=
this.voxelCounts[c];this.downsampleRemainders[c]=d%a;this.voxelCounts[c]/=a;this.isPeriodic&&(this.voxelCounts[c]++,this.downsampleRemainders[c]--);this.volumetricVectors[c].scale(a);JU.Logger.info("downsampling axis "+(c+1)+" from "+d+" to "+this.voxelCounts[c])}}if(!this.vertexDataOnly)for(c=0;3>c;++c)this.isAngstroms||this.volumetricVectors[c].scale(0.5291772),this.line=this.voxelCounts[c]+" "+this.volumetricVectors[c].x+" "+this.volumetricVectors[c].y+" "+this.volumetricVectors[c].z,this.jvxlFileHeaderBuffer.append(this.line).appendC("\n"),
JU.Logger.info("voxel grid count/vector:"+this.line);this.scaleIsosurface(this.params.scale);this.volumeData.setVolumetricXml();return this.nSurfaces}catch(e){if(U(e,Exception))return JU.Logger.error(e.toString()),0;throw e;}});e(c$,"skipComments",function(a){for(var b=new JU.SB;null!=this.rd()&&(a&&0==this.line.length||0==this.line.indexOf("#"));)b.append(this.line).appendC("\n");return b.toString()},"~B");e(c$,"readVoxelVector",function(a){this.rd();var b=this.volumetricVectors[a];if(-2147483648==
(this.voxelCounts[a]=this.parseIntStr(this.line)))this.next[0]=this.line.indexOf(" ");b.set(this.parseFloat(),this.parseFloat(),this.parseFloat());this.isAnisotropic&&this.setVectorAnisotropy(b)},"~N");e(c$,"initializeSurfaceData",function(){this.downsampleFactor=this.params.downsampleFactor;this.nSkipZ=this.nSkipY=this.nSkipX=0;this.canDownsample&&0<this.downsampleFactor&&(this.nSkipX=this.downsampleFactor-1,this.nSkipY=this.downsampleRemainders[2]+(this.downsampleFactor-1)*(this.nSkipZ=(this.nPointsZ-
(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[2]),this.nSkipZ=this.downsampleRemainders[1]*this.nSkipZ+(this.downsampleFactor-1)*this.nSkipZ*((this.nPointsY-(this.isPeriodic?1:0))*this.downsampleFactor+this.downsampleRemainders[1]));null!=this.params.thePlane?this.params.cutoff=0:this.isJvxl&&(this.params.cutoff=this.params.isBicolorMap||this.params.colorBySign?0.01:0.5);this.nDataPoints=0;this.next[0]=0;this.line="";this.jvxlNSurfaceInts=0});k(c$,"readSurfaceData",function(a){this.readSurfaceDataVFR(a)},
"~B");e(c$,"readSurfaceDataVFR",function(a){this.initializeSurfaceData();if(this.isProgressive&&!a||this.isJvxl)this.nDataPoints=this.volumeData.setVoxelCounts(this.nPointsX,this.nPointsY,this.nPointsZ),this.voxelData=null,this.isJvxl&&(this.jvxlVoxelBitSet=this.getVoxelBitSet(this.nDataPoints));else if(a&&this.volumeData.hasPlane()){this.volumeData.setVoxelMap();var b=this.volumeData.getToPlaneParameter();for(a=0;a<this.nPointsX;++a){for(var c=0;c<this.nPointsY;++c){for(var d=0;d<this.nPointsZ;++d){var e=
this.recordData(this.getNextVoxelValue());this.volumeData.isNearPlane(a,c,d,b)&&this.volumeData.setVoxelMapValue(a,c,d,e);0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}}else{this.voxelData=JU.AU.newFloat3(this.nPointsX,-1);for(a=0;a<this.nPointsX;++a){b=JU.AU.newFloat2(this.nPointsY);this.voxelData[a]=b;for(c=0;c<this.nPointsY;++c){e=y(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");k(c$,"getPlane",function(a){0==a&&this.initPlanes();if(this.getNCIPlanes)return this.getPlaneNCI(a);a=this.getPlaneSR(a);null==this.qpc&&this.getPlaneVFR(a,!0);return a},"~N");e(c$,"getPlaneNCI",function(a){var b;if(0==this.iPlaneNCI){this.qpc=J.api.Interface.getOption("quantum.NciCalculation",this.sg.atomDataServer,
null);b=new J.atomdata.AtomData;b.modelIndex=-1;b.bsSelected=this.params.bsSelected;this.sg.fillAtomData(b,1);this.qpc.setupCalculation(this.volumeData,this.sg.params.bsSelected,null,null,b.atoms,-1,!0,null,this.params.parameters,this.params.testFlags);this.iPlaneNCI=1;this.qpc.setPlanes(this.yzPlanesRaw=y(4,this.yzCount,0));if(this.hasColorData){this.getPlaneVFR(this.yzPlanesRaw[0],!1);this.getPlaneVFR(this.yzPlanesRaw[1],!1);b=this.yzPlanes[0];for(a=0;a<this.yzCount;a++)b[a]=NaN;return b}this.iPlaneNCI=
-1}var c=this.qpc.getNoValue(),d=this.nPointsX-1;switch(this.iPlaneNCI){case -1:b=this.yzPlanes[a%2];d++;break;case 3:b=this.yzPlanesRaw[0];this.yzPlanesRaw[0]=this.yzPlanesRaw[1];this.yzPlanesRaw[1]=this.yzPlanesRaw[2];this.yzPlanesRaw[2]=this.yzPlanesRaw[3];this.yzPlanesRaw[3]=b;b=this.yzPlanesRaw[this.iPlaneNCI];break;default:this.iPlaneNCI++,b=this.yzPlanesRaw[this.iPlaneNCI]}if(a<d){this.getPlaneVFR(b,!1);this.qpc.calcPlane(a,b=this.yzPlanes[a%2]);for(a=0;a<this.yzCount;a++)b[a]!=c&&this.recordData(b[a])}else for(a=
0;a<this.yzCount;a++)b[a]=NaN;return b},"~N");e(c$,"getPlaneVFR",function(a,b){try{for(var c=0,d=0;c<this.nPointsY;++c){for(var e=0;e<this.nPointsZ;++e){var f=this.getNextVoxelValue();b&&this.recordData(f);a[d++]=f;0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}catch(g){if(!U(g,Exception))throw g;}},"~A,~B");k(c$,"getValue",function(a,b,c,d){return null!=this.boundingBox&&(this.volumeData.voxelPtToXYZ(a,b,c,this.ptTemp),
this.ptTemp.x<this.boundingBox[0].x||this.ptTemp.x>this.boundingBox[1].x||this.ptTemp.y<this.boundingBox[0].y||this.ptTemp.y>this.boundingBox[1].y||this.ptTemp.z<this.boundingBox[0].z||this.ptTemp.z>this.boundingBox[1].z)?NaN:this.getValue2(a,b,c,d)},"~N,~N,~N,~N");e(c$,"skipVoxels",function(a){for(;0<=--a;)this.getNextVoxelValue()},"~N");e(c$,"getVoxelBitSet",function(){return null},"~N");e(c$,"getNextVoxelValue",function(){var a=0;if(1<this.nSurfaces&&!this.params.blockCubeData){for(var b=1;b<this.params.fileIndex;b++)this.nextVoxel();
a=this.nextVoxel();for(b=this.params.fileIndex;b<this.nSurfaces;b++)this.nextVoxel()}else a=this.nextVoxel();return a});e(c$,"nextVoxel",function(){var a=this.parseFloat();if(Float.isNaN(a)){for(;null!=this.rd()&&Float.isNaN(a=this.parseFloatStr(this.line)););null==this.line&&(this.endOfData||JU.Logger.warn("end of file reading cube voxel data? nBytes="+this.nBytes+" nDataPoints="+this.nDataPoints+" (line):"+this.line),this.endOfData=!0,this.line="0 0 0 0 0 0 0 0 0 0")}return a});k(c$,"gotoData",
function(a,b){if(this.params.blockCubeData){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");for(var c=0;c<a;c++)this.skipData(b)}},"~N,~N");e(c$,"skipData",function(a){this.skipDataVFR(a)},"~N");e(c$,"skipDataVFR",function(a){for(var b=0;b<a;)b+=this.countData(this.rd())},"~N");e(c$,"countData",function(a){for(var b=0,c=0,d=a.length,e;c<d;){for(;c<d&&(" "==(e=a.charAt(c))||"\t"==e);)++c;for(c<d&&++b;c<d&&" "!=(e=a.charAt(c))&&"\t"!=e;)++c}return b},"~S");c$.checkAtomLine=e(c$,"checkAtomLine",
function(a,b,c,d,e){0<=d.indexOf("ANGSTROMS")&&(b=!0);c=null==c?2147483647:JU.PT.parseInt(c);switch(c){case -2147483648:c=0;d=" "+d.substring(d.indexOf(" ")+1);break;case 2147483647:c=-2147483648;break;default:var 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");k(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,f,g,k,m,p,n,q,r){return this.getSPFv(a,
b,c,d,e,f,g,k,m,p,n,q,r)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPFv",function(a,b,c,d,e,f,g,k,m,p,n,q,r){a=this.getSPF(a,b,c,d,e,f,g,k,m,p,n,q,r);if(null==this.qpc||Float.isNaN(a)||!this.hasColorData)return a;p=this.marchingCubes.getLinearOffset(g,k,m,p);n=this.marchingCubes.getLinearOffset(g,k,m,n);return this.qpc.process(p,n,q[0])},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"scaleIsosurface",function(a){this.isScaledAlready||(this.isScaledAlready=!0,this.isAnisotropic&&
this.setVolumetricAnisotropy(),Float.isNaN(a)||(JU.Logger.info("applying scaling factor of "+a),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[0],this.volumetricOrigin),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[1],this.volumetricOrigin),this.volumetricOrigin.scaleAdd2((1-a)/2,this.volumetricVectors[2],this.volumetricOrigin),this.volumetricVectors[0].scale(a),this.volumetricVectors[1].scale(a),this.volumetricVectors[2].scale(a)))},"~N");e(c$,"swapXZ",function(){var a=
this.volumetricVectors[0];this.volumetricVectors[0]=this.volumetricVectors[2];this.volumetricVectors[2]=a;a=this.voxelCounts[0];this.voxelCounts[0]=this.voxelCounts[2];this.voxelCounts[2]=a;this.params.insideOut=!this.params.insideOut})});E("J.jvxl.readers");H(["J.jvxl.readers.VolumeFileReader"],"J.jvxl.readers.JvxlXmlReader","java.lang.Float $.NullPointerException java.util.Hashtable JU.AU $.BS $.CU $.Lst $.P3 $.P4 $.PT $.SB J.jvxl.data.JvxlCoder $.MeshData J.jvxl.readers.XmlReader J.shapesurface.IsosurfaceMesh JU.C $.ColorEncoder $.Escape $.Logger".split(" "),
function(){c$=N(function(){this.JVXL_VERSION="2.3";this.invalidatedVertexCount=this.excludedVertexCount=this.excludedTriangleCount=this.colorDataCount=this.edgeDataCount=this.surfaceDataCount=0;this.haveContourData=!1;this.xr=null;this.isXmlFile=!0;this.thisInside=!1;this.bsVoxelBitSet=this.tempDataXml=null;this.includeValueNaN=!0;this.valueCount=0;this.valueRange=this.valueMin=NaN;this.colorPtr=this.fractionPtr=0;this.strFractionTemp="";this.haveReadColorData=!1;this.jvxlColorEncodingRead=null;K(this,
arguments)},J.jvxl.readers,"JvxlXmlReader",J.jvxl.readers.VolumeFileReader);T(c$,function(){ba(this,J.jvxl.readers.JvxlXmlReader,[])});k(c$,"init2",function(a,b){this.init2JXR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2JXR",function(a,b){this.init2VFR(a,b);this.jvxlData.wasJvxl=this.isJvxl=!0;this.isXLowToHigh=this.canDownsample=!1;this.xr=new J.jvxl.readers.XmlReader(b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");k(c$,"readVolumeData",function(a){if(!this.readVolumeDataVFR(a))return!1;
this.strFractionTemp=this.jvxlEdgeDataRead;this.fractionPtr=0;return!0},"~B");k(c$,"gotoAndReadVoxelData",function(a){this.initializeVolumetricData();if(0>this.nPointsX||0>this.nPointsY||0>this.nPointsZ)return!0;try{this.gotoData(this.params.fileIndex-1,this.nPointsX*this.nPointsY*this.nPointsZ);if(this.vertexDataOnly)return!0;this.volumeData.setMappingPlane(this.params.thePlane);this.readSurfaceData(a);this.volumeData.setMappingPlane(null);0<this.edgeDataCount&&(this.jvxlEdgeDataRead=this.jvxlReadFractionData("edge",
this.edgeDataCount));this.params.bsExcluded=this.jvxlData.jvxlExcluded=Array(4);if(this.hasColorData=0<this.colorDataCount)this.jvxlColorDataRead=this.jvxlReadFractionData("color",this.colorDataCount);0<this.excludedVertexCount&&(this.jvxlData.jvxlExcluded[0]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedVertexData",null,!1,!1)),this.xr.isNext("jvxlExcludedPlaneData")&&(this.jvxlData.jvxlExcluded[2]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedPlaneData",
null,!1,!1))));0<this.excludedTriangleCount&&(this.jvxlData.jvxlExcluded[3]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlExcludedTriangleData",null,!1,!1)));0<this.invalidatedVertexCount&&(this.jvxlData.jvxlExcluded[1]=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlInvalidatedVertexData",null,!1,!1)));this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1));if(this.jvxlDataIsColorMapped&&0<this.jvxlData.nVertexColors){this.jvxlData.vertexColorMap=
new java.util.Hashtable;var b=this.xr.getXmlData("jvxlVertexColorData",null,!0,!1),c=J.jvxl.readers.XmlReader.getXmlAttrib(b,"baseColor");this.jvxlData.baseColor=0<c.length?c:null;for(a=0;a<this.jvxlData.nVertexColors;a++){var d=this.xr.getXmlData("jvxlColorMap",b,!0,!1),e=J.jvxl.readers.XmlReader.getXmlAttrib(d,"color"),f=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlColorMap",d,!1,!1));this.jvxlData.vertexColorMap.put(e,f)}}}catch(g){if(U(g,Exception))return JU.Logger.error(g.toString()),
!1;throw g;}return!0},"~B");k(c$,"readParameters",function(){var a=this.xr.getXmlData("jvxlFileTitle",null,!1,!1);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)});e(c$,"readVector",function(a){var b=this.xr.getXmlData("jvxlVolumeVector",this.tempDataXml,!0,!0);this.tempDataXml=this.tempDataXml.substring(this.tempDataXml.indexOf(b)+b.length);var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,
"count"));-2147483648==c&&(this.vertexDataOnly=!0);this.voxelCounts[a]=0>c?0:c;this.volumetricVectors[a].setT(this.xr.getXmlPoint(b,"vector"));this.isAnisotropic&&this.setVectorAnisotropy(this.volumetricVectors[a])},"~N");k(c$,"gotoData",function(a,b){0<a&&JU.Logger.info("skipping "+a+" data sets, "+b+" points each");this.vertexDataOnly=this.jvxlData.vertexDataOnly=0==b;for(var c=0;c<a;c++)this.jvxlSkipData(b,!0);this.xr.toTag("jvxlSurface");this.jvxlReadSurfaceInfo()},"~N,~N");e(c$,"jvxlSkipData",
function(){this.rd();this.xr.skipTag("jvxlSurface")},"~N,~B");e(c$,"jvxlReadSurfaceInfo",function(){var a,b=this.xr.getXmlData("jvxlSurfaceInfo",null,!0,!0);this.isXLowToHigh=J.jvxl.readers.XmlReader.getXmlAttrib(b,"isXLowToHigh").equals("true");this.jvxlCutoff=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"cutoff"));Float.isNaN(this.jvxlCutoff)||JU.Logger.info("JVXL read: cutoff "+this.jvxlCutoff);var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nContourData"));this.haveContourData=
0<c;this.params.isContoured=this.jvxlData.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(b,"contoured").equals("true");this.params.isModelConnected=J.jvxl.readers.XmlReader.getXmlAttrib(b,"isModelConnected").equals("true");if(this.params.isContoured){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nContours"));0>=d?d=0:(0>this.params.thisContour&&(this.params.thisContour=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"thisContour"))),a=J.jvxl.readers.XmlReader.getXmlAttrib(b,
"contourValues"),0<a.length&&(a=a.$replace("["," ").$replace("]"," "),this.jvxlData.contourValues=this.params.contoursDiscrete=this.parseFloatArrayStr(a),JU.Logger.info("JVXL read: contourValues "+JU.Escape.eAF(this.jvxlData.contourValues))),a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"contourColors"),0<a.length&&(this.jvxlData.contourColixes=this.params.contourColixes=JU.C.getColixArray(a),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(b,"contourFromZero").equals("true"));this.params.nContours=this.haveContourData?c:d}this.jvxlData.nVertexColors=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nVertexColors"));this.params.isBicolorMap=J.jvxl.readers.XmlReader.getXmlAttrib(b,"bicolorMap").equals("true");this.params.isBicolorMap&&(a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"colorPositive"),0<a.length&&(-2147483648==
this.params.colorRgb&&-16776961==this.params.colorPos)&&(this.params.colorPos=JU.CU.getArgbFromString(a)),a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"colorNegative"),0<a.length&&(-2147483648==this.params.colorRgb&&-65536==this.params.colorNeg)&&(this.params.colorNeg=JU.CU.getArgbFromString(a)));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(b,
"colorMapped").equals("true"));this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.XmlReader.getXmlAttrib(b,"precisionColor").equals("true");this.jvxlData.jvxlDataIsColorDensity=this.params.colorDensity=-2147483648==this.params.colorRgb&&J.jvxl.readers.XmlReader.getXmlAttrib(b,"colorDensity").equals("true");this.jvxlData.jvxlDataIsColorDensity&&Float.isNaN(this.params.pointSize)&&(a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"pointSize"),0<a.length&&(this.jvxlData.pointSize=this.params.pointSize=this.parseFloatStr(a)));
a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"allowVolumeRender");this.jvxlData.allowVolumeRender=this.params.allowVolumeRender=0==a.length||a.equalsIgnoreCase("true");a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"plane");if(0<=a.indexOf("{")){this.params.thePlane=null;this.params.mapLattice=null;try{this.params.thePlane=JU.Escape.uP(a),a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"maplattice"),JU.Logger.info("JVXL read: plane "+this.params.thePlane),0<=a.indexOf("{")&&(this.params.mapLattice=JU.Escape.uP(a),
JU.Logger.info("JVXL read: mapLattice "+this.params.mapLattice)),0==this.params.scale3d&&(this.params.scale3d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"scale3d"))),Float.isNaN(this.params.scale3d)&&(this.params.scale3d=0)}catch(e){if(U(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(b,"nSurfaceInts")),this.edgeDataCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nBytesUncompressedEdgeData")),a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"fixedLattice"),0<=a.indexOf("{")&&(this.jvxlData.fixedLattice=JU.Escape.uP(a));this.excludedVertexCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nExcludedVertexes"));
this.excludedTriangleCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nExcludedTriangles"));this.invalidatedVertexCount=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nInvalidatedVertexes"));a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"slabInfo");0<a.length&&(this.jvxlData.slabInfo=a);this.colorDataCount=Math.max(0,this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"nBytesUncompressedColorData")));this.jvxlDataIs2dContour=null!=this.params.thePlane&&this.jvxlDataIsColorMapped;
this.jvxlData.color=J.jvxl.readers.XmlReader.getXmlAttrib(b,"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(b,"translucency"));Float.isNaN(this.jvxlData.translucency)&&(this.jvxlData.translucency=0);a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"meshColor");0<a.length&&(this.jvxlData.meshColor=a);a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"rendering");0<a.length&&
(this.jvxlData.rendering=a);this.jvxlData.colorScheme=J.jvxl.readers.XmlReader.getXmlAttrib(b,"colorScheme");0==this.jvxlData.colorScheme.length&&(this.jvxlData.colorScheme=this.jvxlDataIsColorMapped?"roygb":null);0>this.jvxlData.thisSet&&(a=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"set")),0<a&&(this.jvxlData.thisSet=a-1));this.jvxlData.slabValue=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"slabValue"));this.jvxlData.isSlabbable=J.jvxl.readers.XmlReader.getXmlAttrib(b,
"slabbable").equalsIgnoreCase("true");this.jvxlData.diameter=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"diameter"));-2147483648==this.jvxlData.diameter&&(this.jvxlData.diameter=0);this.jvxlDataIs2dContour&&(this.params.isContoured=!0);this.params.colorBySign&&(this.params.isBicolorMap=!0);a=J.jvxl.readers.XmlReader.getXmlAttrib(b,"insideOut").equals("true");var f=d=c=NaN,g=NaN;this.jvxlDataIsColorMapped&&(c=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"dataMinimum")),
d=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"dataMaximum")),f=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"valueMappedToRed")),g=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,"valueMappedToBlue")),Float.isNaN(c)&&(c=f=-1,d=g=1));this.jvxlSetColorRanges(c,d,f,g,a)});e(c$,"jvxlSetColorRanges",function(a,b,c,d,e){this.jvxlDataIsColorMapped&&(!Float.isNaN(a)&&!Float.isNaN(b)&&(0==b&&0==a&&(a=-1,b=1),this.params.mappedDataMin=a,this.params.mappedDataMax=b,JU.Logger.info("JVXL read: data_min/max "+
this.params.mappedDataMin+"/"+this.params.mappedDataMax)),this.params.rangeDefined||(!Float.isNaN(c)&&!Float.isNaN(d)?(0==c&&0==d&&(c=-1,d=1),this.params.valueMappedToRed=Math.min(c,d),this.params.valueMappedToBlue=Math.max(c,d),this.params.isColorReversed=c>d):(this.params.valueMappedToRed=0,this.params.valueMappedToBlue=1),this.params.rangeDefined=!0),JU.Logger.info("JVXL read: color red/blue: "+this.params.valueMappedToRed+"/"+this.params.valueMappedToBlue));this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;
this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.isColorReversed=this.params.isColorReversed;this.params.insideOut&&(e=!e);this.params.insideOut=this.jvxlData.insideOut=e},"~N,~N,~N,~N,~B");k(c$,"readSurfaceData",function(){this.thisInside=!this.params.isContoured;this.readSurfaceDataXML()||(this.tempDataXml=this.xr.getXmlData("jvxlEdgeData",null,!0,!1),this.bsVoxelBitSet=
J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlEdgeData",this.tempDataXml,!1,!1)),this.readSurfaceDataJXR())},"~B");e(c$,"readSurfaceDataXML",function(){return this.vertexDataOnly?(this.getEncodedVertexData(),!0):null!=this.params.thePlane?(this.volumeData.setDataDistanceToPlane(this.params.thePlane),this.setVolumeDataV(this.volumeData),this.params.cutoff=0,this.jvxlData.setSurfaceInfo(this.params.thePlane,this.params.mapLattice,0,""),this.jvxlData.scale3d=this.params.scale3d,!0):
!1});e(c$,"readSurfaceDataJXR",function(){this.readSurfaceDataVFR(!1);this.volumeData.setMappingPlane(null)});e(c$,"jvxlReadFractionData",function(a){var b;try{if(a.equals("edge"))b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml,"data"));else{var c=this.xr.getXmlData("jvxlColorData",null,!0,!1);this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.JvxlXmlReader.getEncoding(c).endsWith("2");b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(c,
"data"))}}catch(d){if(U(d,Exception))throw JU.Logger.error("Error reading "+a+" data "+d),new NullPointerException;throw d;}return b},"~S,~N");k(c$,"getVoxelBitSet",function(a){if(null!=this.bsVoxelBitSet)return this.bsVoxelBitSet;var b=new JU.BS,c=0;if(0>=this.surfaceDataCount)return b;for(var d=0;c<a;){d=this.parseInt();if(-2147483648==d&&(this.rd(),null==this.line||-2147483648==(d=this.parseIntStr(this.line))))this.endOfData||JU.Logger.error("end of file in JvxlReader? line="+this.line),this.endOfData=
!0,d=1E4;this.thisInside=!this.thisInside;++this.jvxlNSurfaceInts;this.thisInside&&b.setBits(c,c+d);c+=d}return b},"~N");k(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,f,g,k,m,p,n,q,r){if(0>=this.edgeDataCount)return this.getSPFv(a,b,c,d,e,f,g,k,m,p,n,q,r);r.scaleAdd2(q[0]=this.jvxlGetNextFraction(this.edgeFractionBase,this.edgeFractionRange,0.5),f,e);Float.isNaN(this.valueMin)&&this.setValueMinMax();return 0==this.valueCount||this.includeValueNaN&&Float.isNaN(q[0])?q[0]:this.getNextValue()},
"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getNextValue",function(){for(var a=NaN;this.colorPtr<this.valueCount&&Float.isNaN(a);){a=this.jvxlData.isJvxlPrecisionColor?J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(this.jvxlColorDataRead.charCodeAt(this.colorPtr),this.jvxlColorDataRead.charCodeAt(this.colorPtr++ +this.valueCount),this.colorFractionBase,this.colorFractionRange):J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.jvxlColorDataRead.charCodeAt(this.colorPtr++),this.colorFractionBase,
this.colorFractionRange,0.5);break}return this.valueMin+a*this.valueRange});e(c$,"setValueMinMax",function(){this.valueCount=this.jvxlColorDataRead.length;this.jvxlData.isJvxlPrecisionColor&&(this.valueCount/=2);this.includeValueNaN=this.valueCount!=this.jvxlEdgeDataRead.length;this.valueMin=!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToRed:3.4028235E38==this.params.mappedDataMin?0:this.params.mappedDataMin;this.valueRange=(!this.jvxlData.isJvxlPrecisionColor?this.params.valueMappedToBlue:
3.4028235E38==this.params.mappedDataMin?1:this.params.mappedDataMax)-this.valueMin;this.haveReadColorData=!0});e(c$,"jvxlGetNextFraction",function(a,b,c){this.fractionPtr>=this.strFractionTemp.length&&(this.endOfData||JU.Logger.error("end of file reading compressed fraction data"),this.endOfData=!0,this.strFractionTemp=""+String.fromCharCode(a),this.fractionPtr=0);return J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(this.strFractionTemp.charCodeAt(this.fractionPtr++),a,b,c)},"~N,~N,~N");k(c$,"readColorData",
function(){if(!this.jvxlDataIsColorMapped)return"";var a=this.jvxlData.vertexCount=this.meshData.vc,b=this.meshData.vcs,c=this.meshData.vvs;if("none".equals(this.jvxlColorEncodingRead)){this.jvxlData.vertexColors=v(a,0);for(var d=v(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,g=0,d=0;d<c;d++)try{var k=J.jvxl.readers.JvxlXmlReader.getColor(a[d]);0==k?k=g:g=k;b[d]=JU.C.getColixTranslucent(this.jvxlData.vertexColors[d]=
k);JU.C.isColixTranslucent(b[d])?e=!0:0!=f&&(b[d]=JU.C.getColixTranslucent3(b[d],!0,f))}catch(m){if(U(m,Exception))JU.Logger.info("JvxlXmlReader: Cannot interpret color code: "+a[d]);else throw m;}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 p=Float.isNaN(this.valueMin);p&&this.setValueMinMax();var n=3.4028235E38,q=-3.4028235E38;if(null==b||b.length<a)this.meshData.vcs=
b=W(a,0);e=k=0;this.params.colorBySign&&(e=JU.C.getColix(this.params.isColorReversed?this.params.colorNeg:this.params.colorPos),k=JU.C.getColix(this.params.isColorReversed?this.params.colorPos:this.params.colorNeg));for(var f=this.meshData.vertexIncrement,r=3.4028235E38==this.params.mappedDataMin,d=0;d<a;d+=f)g=p?c[d]=this.getNextValue():c[d],r&&(g<n&&(n=g),g>q&&(q=g));r&&(this.params.mappedDataMin=n,this.params.mappedDataMax=q);if(null!=this.jvxlData.colorScheme){p=null!=this.marchingSquares&&this.params.isContoured;
for(d=0;d<a;d+=f)g=c[d],p?this.marchingSquares.setContourData(d,g):(g=!this.params.colorBySign?this.params.colorEncoder.getColorIndex(g):(this.params.isColorReversed?0<g:0>=g)?k:e,b[d]=JU.C.getColixTranslucent3(g,!0,this.jvxlData.translucency))}return this.jvxlColorDataRead+"\n"});c$.getColor=e(c$,"getColor",function(a){var b=0;try{switch(a.charAt(0)){case "[":b=JU.CU.getArgbFromString(a);break;case "0":b=JU.PT.parseIntRadix(a.substring(2),16);break;default:b=JU.PT.parseIntRadix(a,10)}}catch(c){if(!U(c,
Exception))throw c;}return b},"~S");e(c$,"getEncodedVertexData",function(){var a=this.xr.getXmlData("jvxlSurfaceData",null,!0,!1);this.jvxlDecodeVertexData(this.xr.getXmlData("jvxlVertexData",a,!0,!1),!1);var b=this.xr.getXmlData("jvxlTriangleData",a,!0,!1),c=this.xr.getXmlData("jvxlTriangleEdgeData",a,!0,!1),d=this.xr.getXmlData("jvxlPolygonColorData",a,!1,!1);this.jvxlDecodeTriangleData(b,c,d);a=this.xr.getXmlData("jvxlColorData",a,!0,!1);this.jvxlColorEncodingRead=J.jvxl.readers.JvxlXmlReader.getEncoding(a);
this.jvxlData.isJvxlPrecisionColor=this.jvxlColorEncodingRead.endsWith("2");a=this.getData(a,"jvxlColorData");this.jvxlColorDataRead=this.jvxlColorEncodingRead.equals("none")?a:J.jvxl.data.JvxlCoder.jvxlDecompressString(a);this.jvxlDataIsColorMapped=(-2147483648==this.params.colorRgb||2147483647==this.params.colorRgb)&&0<this.jvxlColorDataRead.length;this.haveContourData&&this.jvxlDecodeContourData(this.jvxlData,this.xr.getXmlData("jvxlContourData",null,!1,!1))});e(c$,"getData",function(a,b){var c=
J.jvxl.readers.XmlReader.getXmlAttrib(a,"data");0==c.length&&(c=this.xr.getXmlData(b,a,!1,!1));return c},"~S,~S");c$.getEncoding=e(c$,"getEncoding",function(a){if(0<J.jvxl.readers.XmlReader.getXmlAttrib(a,"len").length)return"";a=J.jvxl.readers.XmlReader.getXmlAttrib(a,"encoding");return 0==a.length?"none":a},"~S");e(c$,"jvxlDecodeVertexData",function(a,b){var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));b||JU.Logger.info("Reading "+c+" vertices");var d=3*c,e=b?Array(c):null,
f,g=J.jvxl.readers.XmlReader.getXmlAttrib(a,"data"),k=J.jvxl.readers.JvxlXmlReader.getEncoding(a);if("none".equals(k)){0==g.length&&(g=this.xr.getXmlData("jvxlVertexData",a,!1,!1));d=JU.PT.parseFloatArray(g);d[0]!=3*c&&JU.Logger.info("JvxlXmlReader: vertexData count="+F(d[0])+"; expected "+3*c);g=0;for(k=1;g<c;g++){var m=JU.P3.new3(d[k++],d[k++],d[k++]);b?e[g]=m:this.addVertexCopy(m,0,g,!1)}}else{var p=this.xr.getXmlPoint(a,"min"),n=this.xr.getXmlPoint(a,"max");n.sub(p);var q=this.jvxlData.colorFractionBase,
r=this.jvxlData.colorFractionRange,w=J.jvxl.data.JvxlCoder.jvxlDecompressString(g);0==w.length&&(w=this.xr.getXmlData("jvxlVertexData",a,!1,!1));g=0;for(k=-1;g<c;g++)m=new JU.P3,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(w.charCodeAt(++k),w.charCodeAt(k+d),q,r),m.x=p.x+f*n.x,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(w.charCodeAt(++k),w.charCodeAt(k+d),q,r),m.y=p.y+f*n.y,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(w.charCodeAt(++k),w.charCodeAt(k+d),q,r),m.z=p.z+f*n.z,b?e[g]=
m:this.addVertexCopy(m,0,g,!1)}return e},"~S,~B");e(c$,"jvxlDecodeTriangleData",function(a,b,c){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));if(!(0>d)){var e=v(1,0),f=null==c?-1:1,g=0;JU.Logger.info("Reading "+d+" triangles");var k=J.jvxl.readers.JvxlXmlReader.getEncoding(a);a=this.getData(a,"jvxlTriangleData");b=this.getData(b,"jvxlTriangleEdgeData");var m=v(3,0),p=v(1,0),n=null,q=7,r=!"none".equals(k);if(r)a=J.jvxl.data.JvxlCoder.jvxlDecompressString(a),b=J.jvxl.data.JvxlCoder.jvxlDecompressString(b).trim(),
k=b.length==d;else{var w=JU.PT.parseIntNext(a,p);(k=0<b.length)?(n=v(1,0),JU.PT.parseIntNext(b,n)):0<w&&JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count="+w+"; expected "+d)}for(var u=w=0,y=0,C=-1;w<d;){if(r){var B=a.charAt(++C);switch(B){case "!":B=0;break;case "+":case ".":case " ":case "\n":case "\r":case "\t":case ",":continue;case "-":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":p[0]=C;B=JU.PT.parseIntNext(a,p);C=p[0]-1;break;default:B=B.charCodeAt(0)-
92}u+=B}else u=JU.PT.parseIntNext(a,p)-1;m[y]=u;if(3==++y){y=0;if(k&&(q=null==n?b.charCodeAt(w)-48:JU.PT.parseIntNext(b,n),0>q||7<q))q=7;0==--f&&(f=JU.PT.parseIntNext(c,e),B=JU.PT.parseIntNext(c,e),-2147483648==B?f=0:g=B|4278190080);this.addTriangleCheck(m[0],m[1],m[2],q,g,!1,g);w++}}}},"~S,~S,~S");e(c$,"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 g=new JU.Lst,k=this.xr.getXmlData("jvxlContour",
b.substring(f),!0,!1),m=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(k,"value"));d.append(" ").appendF(m);var p=J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(k,"color")),n=JU.C.getColix(p);e.append(" ").append(JU.Escape.escapeColor(p));var q=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(k,"data")),r=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour",k,!1,!1)),k=r.length();J.shapesurface.IsosurfaceMesh.setContourVector(g,
k,r,m,n,p,JU.SB.newS(q));c.addLast(g)}k=c.size();if(0<k){a.vContours=JU.AU.createArrayOfArrayList(k);a.contourColixes=this.params.contourColixes=W(k,0);a.contourValues=this.params.contoursDiscrete=y(k,0);for(f=0;f<k;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: "+k+" discrete contours");JU.Logger.info("JVXL read: contour values: "+d);JU.Logger.info("JVXL read: contour colors: "+
e)}}},"J.jvxl.data.JvxlData,~S");k(c$,"postProcessVertices",function(){var a=this.params.bsExcluded[1];null!=a&&(null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null),this.meshData.invalidateVertices(a),null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,4,null),this.meshData=new J.jvxl.data.MeshData),this.updateTriangles())})});E("J.rendersurface");H(["J.render.MeshRenderer"],"J.rendersurface.IsosurfaceRenderer",["java.lang.Boolean","$.Float","JU.V3",
"JU.C","$.Normix"],function(){c$=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;K(this,arguments)},J.rendersurface,"IsosurfaceRenderer",J.render.MeshRenderer);k(c$,"render",function(){return this.renderIso()});e(c$,"renderIso",function(){this.setGlobals();
for(var a=this.isosurface.meshCount;0<=--a;)if(this.mesh=this.imesh=this.isosurface.meshes[a],null==this.imesh.connectedAtoms||this.vwr.ms.at[this.imesh.connectedAtoms[0]].checkVisible())this.hasColorRange=!1,this.renderMeshSlab()&&(this.renderInfo(),this.isExport&&this.isGhostPass&&(this.exportPass=1,this.renderMeshSlab(),this.exportPass=2));return this.needTranslucent});e(c$,"setGlobals",function(){this.needTranslucent=!1;this.antialias=this.g3d.isAntialiased();this.iShowNormals=this.vwr.getBoolean(603979965);
this.showNumbers=this.vwr.getBoolean(603979964);this.isosurface=this.shape;this.exportPass=this.isExport?2:0;this.isNavigationMode=this.vwr.getBoolean(603979889);this.showKey=this.vwr.getBoolean(603979867)?Boolean.TRUE:null;this.isosurface.keyXy=null;this.meshScale=-1;this.globalSlabValue=this.vwr.gdata.slab;this.mySlabValue=this.isNavigationMode?F(this.tm.getNavigationOffset().z):2147483647});e(c$,"renderInfo",function(){if(!this.isExport&&this.hasColorRange&&!(null==this.imesh.colorEncoder||Boolean.TRUE!==
this.showKey)){this.showKey=Boolean.FALSE;var a=null,b=null,c=null,d=0,e=0;if(this.imesh.showContourLines)if(c=this.imesh.getContours(),null==c){b=this.imesh.jvxlData.contourColixes;if(null==b)return;d=b.length}else d=c.length,e=1;else a=this.imesh.colorEncoder.getColorSchemeArray(this.imesh.colorEncoder.currentPalette),d=null==a?0:a.length,e=2;if(!(2>d)){var f=this.antialias?2:1,g=this.vwr.getScreenHeight()*f,k=C(C(g/2)/(d-1)),g=3*C(g/4)-k,m=10*f,p=20*f;this.isosurface.keyXy=v(-1,[C(m/f),0,C((m+
p)/f),C((g+k)/f),C(k/f)]);for(var n=0;n<d;n++,g-=k){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(m,g,5,-2147483648,p,k)}this.isosurface.keyXy[1]=C((g+k)/f)}}});e(c$,"renderMeshSlab",function(){this.volumeRender=this.imesh.jvxlData.colorDensity&&this.imesh.jvxlData.allowVolumeRender;var a=this.mySlabValue;this.frontOnly=this.mesh.frontOnly||26==this.shapeID;this.isShell=this.mesh.isShell&&
26!=this.shapeID;if(!this.isNavigationMode&&(this.meshSlabValue=this.imesh.jvxlData.slabValue,-2147483648!=this.meshSlabValue&&this.imesh.jvxlData.isSlabbable)){for(var b=this.imesh.jvxlData.boundingBox,a=3.4028235E38,c=1.4E-45,d=b.length;0<=--d;)this.pt2f.setT(b[d]),this.tm.transformPt3f(this.pt2f,this.pt2f),this.pt2f.z<a&&(a=this.pt2f.z),this.pt2f.z>c&&(c=this.pt2f.z);a=Math.round(a+(c-a)*(100-this.meshSlabValue)/100);this.frontOnly=(new Boolean(this.frontOnly&100<=this.meshSlabValue)).valueOf();
this.isShell=(new Boolean(this.isShell&100<=this.meshSlabValue)).valueOf()}b=this.vwr.gdata.translucentCoverOnly;this.vwr.gdata.translucentCoverOnly=this.frontOnly||!this.vwr.getBoolean(603979967);this.thePlane=this.imesh.jvxlData.jvxlPlane;this.vertexValues=this.mesh.vvs;2147483647!=a&&this.imesh.jvxlData.isSlabbable?(this.g3d.setSlab(a),a=this.renderMesh2(this.mesh),this.g3d.setSlab(this.globalSlabValue)):a=this.renderMesh2(this.mesh);this.vwr.gdata.translucentCoverOnly=b;return a});k(c$,"render2",
function(a){if(this.volumeRender)this.renderPoints();else{switch(this.imesh.dataType){case 70:this.renderLonePair(!1);return;case 71:this.renderLonePair(!0);return}this.isBicolorMap=this.imesh.jvxlData.isBicolorMap;this.render2b(a);this.g3d.setC(4)&&this.imesh.showContourLines&&this.renderContourLines()}},"~B");e(c$,"renderLonePair",function(a){this.pt2f.setT(this.vertices[1]);this.tm.transformPt3f(this.pt2f,this.pt2f);var b=F(this.vwr.tm.scaleToScreen(F(this.pt2f.z),100));1>b&&(b=1);if(!a){var c=
new JU.V3;a=new JU.V3;this.pt1f.setT(this.vertices[0]);this.tm.transformPt3f(this.pt1f,this.pt1f);c.sub2(this.pt2f,this.pt1f);a.set(c.x,c.y,c.z+1);a.cross(a,c);a.normalize();c=this.vwr.tm.scaleToScreen(F(this.pt1f.z),100);a.scale(c);this.pt1f.add2(this.pt2f,a);this.pt2f.sub(a);this.screens[0].set(Math.round(this.pt1f.x),Math.round(this.pt1f.y),Math.round(this.pt1f.z));this.g3d.fillSphereI(b,this.screens[0])}this.screens[1].set(Math.round(this.pt2f.x),Math.round(this.pt2f.y),Math.round(this.pt2f.z));
this.g3d.fillSphereI(b,this.screens[1])},"~B");e(c$,"renderContourLines",function(){var a=this.imesh.getContours();if(null==a)null!=this.imesh.jvxlData.contourValues&&(this.hasColorRange=!0);else{this.hasColorRange=0==this.mesh.meshColix;for(var b=a.length;0<=--b;){var c=a[b];if(!(6>c.size())){this.colix=0==this.mesh.meshColix?c.get(3)[0]:this.mesh.meshColix;if(!this.g3d.setC(this.colix))break;for(var d=c.size()-1,e=this.getDiameter(),f=6;f<d;f++){var g=c.get(f),k=c.get(++f);if(Float.isNaN(g.x)||
Float.isNaN(k.x))break;this.tm.transformPtScrT3(g,this.pt1f);this.tm.transformPtScrT3(k,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)}}}}});k(c$,"renderPoints",function(){try{this.volumeRender&&this.g3d.volumeRender(!0);var a=(this.volumeRender||0==this.mesh.pc)&&this.selectedPolyOnly,b=this.imesh.vertexIncrement,c;0>=this.mesh.diameter?(c=this.vwr.getInt(553648143),this.frontOnly=this.isShell=
!1):c=C(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?C(this.vwr.getScreenWidth()/2):0,f=this.showNumbers?C(this.vwr.getScreenHeight()/2):0;this.showNumbers&&this.vwr.gdata.setFontFid(this.vwr.gdata.getFontFidFS("Monospaced",24));for(var g=!this.imesh.hasGridPoints||0>this.imesh.firstRealVertex?0:this.imesh.firstRealVertex;g<this.vertexCount;g+=b)if(!(null!=
this.vertexValues&&Float.isNaN(this.vertexValues[g])||this.frontOnly&&!this.isVisibleNormix(this.normixes[g])||0<=this.imesh.jvxlData.thisSet&&this.mesh.vertexSets[g]!=this.imesh.jvxlData.thisSet||!this.mesh.isColorSolid&&null!=this.mesh.vcs&&!this.setColix(this.mesh.vcs[g])||this.haveBsDisplay&&!this.mesh.bsDisplay.get(g)||a&&!this.bsPolygons.get(g))){this.hasColorRange=!0;if(this.showNumbers&&10<this.screens[g].z&&150>Math.abs(this.screens[g].x-e)&&150>Math.abs(this.screens[g].y-f)){var k=g+(this.mesh.isColorSolid?
"":" "+this.mesh.vvs[g]);this.g3d.setC(4);this.g3d.drawStringNoSlab(k,null,this.screens[g].x,this.screens[g].y,this.screens[g].z-30,0)}this.volumeRender?(c=F(this.vwr.tm.scaleToScreen(this.screens[g].z,d)),1>c&&(c=1),this.g3d.volumeRender4(c,this.screens[g].x,this.screens[g].y,this.screens[g].z)):this.g3d.fillSphereI(c,this.screens[g])}if(3==b){this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(12,!0,0.5):12);for(g=1;g<this.vertexCount;g+=3)this.g3d.fillCylinder(3,C(c/4),this.screens[g],this.screens[g+
1]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(21,!0,0.5):21);for(g=1;g<this.vertexCount;g+=3)this.g3d.fillSphereI(c,this.screens[g]);this.g3d.setC(this.isTranslucent?JU.C.getColixTranslucent3(7,!0,0.5):7);for(g=2;g<this.vertexCount;g+=3)this.g3d.fillSphereI(c,this.screens[g])}}catch(m){}this.volumeRender&&this.g3d.volumeRender(!1)});k(c$,"renderTriangles",function(a,b,c){this.g3d.addRenderer(1073742182);var d=this.mesh.pis;this.colix=this.isGhostPass?this.mesh.slabColix:!a&&0!=this.mesh.meshColix?
this.mesh.meshColix:this.mesh.colix;var e=!a&&0!=this.mesh.meshColix?null:this.mesh.vcs;this.isTranslucentInherit&&(this.colix=JU.C.copyColixTranslucency(this.mesh.slabColix,this.mesh.colix));this.g3d.setC(this.colix);c&&(this.frontOnly&&a&&(this.frontOnly=!1),this.bsPolygonsToExport.clearAll());1==this.exportType&&(this.frontOnly=!1);var f=this.isGhostPass&&!this.isBicolorMap||null==e||this.mesh.isColorSolid,g=this.isGhostPass&&!this.isBicolorMap||null==e||!a&&0!=this.mesh.meshColix,k=this.colix;
null!=this.imesh.jvxlData.jvxlPlane&&(!f&&!a&&this.mesh.fillTriangles)&&(f=!0,k=4);var m=f&&null!=this.mesh.pcs;m&&(!a&&this.mesh.fillTriangles)&&(m=!1);var p=this.imesh.jvxlData.contourColixes;this.hasColorRange=!f&&!this.isBicolorMap;for(var n=this.getDiameter(),q=this.mesh.pc;0<=--q;){var r=d[q];if(!(null==r||this.selectedPolyOnly&&!this.bsPolygons.get(q))){var w=r[0],u=r[1],v=r[2];if(!(0<=this.imesh.jvxlData.thisSet&&null!=this.mesh.vertexSets&&this.mesh.vertexSets[w]!=this.imesh.jvxlData.thisSet)&&
(!this.haveBsDisplay||this.mesh.bsDisplay.get(w)&&this.mesh.bsDisplay.get(u)&&this.mesh.bsDisplay.get(v))){var y=this.normixes[w],B=this.normixes[u],C=this.normixes[v],F=this.frontOnly||this.isShell?this.checkFront(y,B,C):7;if(!(a&&0==F)){var E,s,G;if(f){if(m&&q<this.mesh.pcs.length){E=this.mesh.pcs[q];if(0==E)continue;k=E}b&&(k=Math.round(10*Math.random())+5);E=s=G=k}else if(E=e[w],s=e[u],G=e[v],this.isBicolorMap){if(E!=s||s!=G)continue;this.isGhostPass&&(E=s=G=JU.C.copyColixTranslucency(this.mesh.slabColix,
E))}if(a)c?this.bsPolygonsToExport.set(q):(u==v?(this.setColix(E),w==u?this.g3d.fillSphereI(n,this.screens[w]):this.g3d.fillCylinder(3,n,this.screens[w],this.screens[u])):this.mesh.colorsExplicit?(this.vwr.gdata.setColor(r[4]),E=JU.C.copyColixTranslucency(this.mesh.colix,2047),this.g3d.setC(E),this.g3d.fillTriangle3CN(this.screens[w],E,y,this.screens[u],E,B,this.screens[v],E,C)):(this.isTranslucentInherit&&null!=e&&(E=JU.C.copyColixTranslucency(this.mesh.slabColix,e[w]),s=JU.C.copyColixTranslucency(this.mesh.slabColix,
e[u]),G=JU.C.copyColixTranslucency(this.mesh.slabColix,e[v])),this.g3d.fillTriangle3CN(this.screens[w],E,y,this.screens[u],s,B,this.screens[v],G,C)),this.iShowNormals&&this.renderNormals());else if(F&=r[3],0!=F){b&&(F=7);this.pt1i.setT(this.screens[w]);this.pt2i.setT(this.screens[u]);this.pt3i.setT(this.screens[v]);this.pt1i.z-=2;this.pt2i.z-=2;this.pt3i.z-=2;if(!g)if(m)this.g3d.setC(this.mesh.fillTriangles?4:p[r[4]%p.length]);else{this.drawTriangle(this.pt1i,E,this.pt2i,s,this.pt3i,G,F,n);continue}this.drawTriangle(this.pt1i,
k,this.pt2i,k,this.pt3i,k,F,n)}}}}}c&&this.exportSurface(f?k:0)},"~B,~B,~B");e(c$,"getDiameter",function(){var a;0>=this.mesh.diameter?(a=0>this.meshScale?this.meshScale=this.vwr.getInt(553648151):this.meshScale,this.antialias&&(a*=2)):a=C(this.vwr.getScreenDim()/100);1>a&&(a=1);return a});e(c$,"renderNormals",function(){if(this.g3d.setC(JU.C.copyColixTranslucency(this.mesh.colix,8))){this.vwr.gdata.setFontFid(this.vwr.gdata.getFontFidFS("Monospaced",24));for(var a=JU.Normix.getVertexVectors(),b=
this.vertexCount;0<=--b;)if(!(null!=this.vertexValues&&Float.isNaN(this.vertexValues[b]))){this.pt1f.setT(this.vertices[b]);var c=this.mesh.normixes[b];0<=c&&(this.pt2f.scaleAdd2(0.3,a[c],this.pt1f),this.tm.transformPtScrT3(this.pt2f,this.pt2f),this.pt1f.set(this.screens[b].x,this.screens[b].y,this.screens[b].z),this.g3d.drawLineAB(this.pt1f,this.pt2f))}}})})})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,
Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,
Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAB,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.cloneFinals);
