(function(Wa,Nb,Ob,E,Pb,H,V,K,G,C,y,Qb,Q,Rb,U,p,R,u,wa,W,Y,f,sa,fa,la,Z,ma,na,oa,w,Sb,Tb,Xa,Ub,Vb,Wb,Xb,Ya,Za,Yb,Zb,$b,ac,bc,cc,dc,ec,fc,gc,hc,ic,jc,kc,lc,mc,nc,e,j){H("JS");c$=C(function(){this.e=this.vwr=null;this.chk=!1;this.st=null;this.slen=0;G(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$,"centerParameter",function(a){return this.e.centerParameter(a)},"~N");e(c$,"floatParameter",function(a){return this.e.floatParameter(a)},"~N");e(c$,"getPoint3f",function(a,b){return this.e.getPoint3f(a,b)},"~N,~B");e(c$,"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;1766856708!=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):1048587==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$,"finalizeObject",function(a,b,c,d,h,m,g,M){h&&this.setShapeProperty(a,"set",m);-2147483648!=b&&this.e.setShapePropertyBs(a,"color",Integer.$valueOf(b),M);3.4028235E38!=c&&this.e.setShapeTranslucency(a,"","translucent",c,M);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");H("JS");K(["JS.ScriptExt"],"JS.IsoExt","java.lang.Boolean $.Float $.Short java.util.Hashtable JU.AU $.BS $.Lst $.M4 $.P3 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.c.VDW JS.SV $.ScriptEval $.T JU.BSUtil $.BoxInfo $.C $.Escape $.Logger $.Parser $.TempArray".split(" "),
function(){c$=wa(JS,"IsoExt",JS.ScriptExt);Q(c$,function(){Y(this,JS.IsoExt,[])});j(c$,"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$,"dipole",function(){var a=this.e,b=null,c=null,d=!1,h=!1,m=!1;a.sm.loadShape(17);
if(!(1073742001==this.tokAt(1)&&this.listIsosurface(17)))if(this.setShapeProperty(17,"init",null),1==this.slen)this.setShapeProperty(17,"thisID",null);else{for(var g=1;g<this.slen;++g){c=b=null;switch(this.getToken(g).tok){case 1048579:b="all";break;case 1048589:b="on";break;case 1048588:b="off";break;case 12291:b="delete";break;case 2:case 3:b="value";c=Float.$valueOf(this.floatParameter(g));break;case 10:10==this.tokAt(g+1)?this.setShapeProperty(17,"startSet",this.atomExpressionAt(g++)):b="atomBitset";
case 1048577:null==b&&(b=d||h?"endSet":"startSet");c=this.atomExpressionAt(g);g=a.iToken;0==this.tokAt(g+1)&&"startSet"===b&&(b="atomBitset");d=!0;break;case 1048586:case 8:c=this.getPoint3f(g,!0);g=a.iToken;b=d||h?"endCoord":"startCoord";h=!0;break;case 1678770178:b="bonds";break;case 4102:b="calculate";if(10==this.tokAt(g+1)||1048577==this.tokAt(g+1))c=this.atomExpressionAt(++g),g=a.iToken;break;case 1074790550:this.setShapeId(17,++g,m);g=a.iToken;break;case 135267329:b="cross";c=Boolean.TRUE;break;
case 1073742040:b="cross";c=Boolean.FALSE;break;case 1073742066:this.isFloatParameter(g+1)?(c=this.floatParameter(++g),2==a.theTok?(b="offsetPercent",c=Integer.$valueOf(y(c))):(b="offset",c=Float.$valueOf(c))):(b="offsetPt",c=this.centerParameter(++g),g=a.iToken);break;case 1073742068:b="offsetSide";c=Float.$valueOf(this.floatParameter(++g));break;case 1073742188:b="value";c=Float.$valueOf(this.floatParameter(++g));break;case 1073742196:b="width";c=Float.$valueOf(this.floatParameter(++g));break;default:if(269484209==
a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(17,g,m);g=a.iToken;break}this.invArg()}m=12291!=a.theTok&&4102!=a.theTok;null!=b&&this.setShapeProperty(17,b,c)}(h||d)&&this.setShapeProperty(17,"set",null)}});e(c$,"draw",function(){var a=this.e;a.sm.loadShape(22);switch(this.tokAt(1)){case 1073742001:if(this.listIsosurface(22))return!1;break;case 1073742102:var b=2,c=1073742138==this.tokAt(b)?"":a.optParameterAsString(b);c.equalsIgnoreCase("chemicalShift")?c="cs":c.equalsIgnoreCase("polyhedra")&&
(c=":poly");var d=1,h=0;0<c.length&&this.isFloatParameter(++b)&&(h=this.intParameter(b++));1073742138==this.tokAt(b)&&(d=this.floatParameter(++b));this.chk||a.runScript(this.vwr.ms.getPointGroupAsString(this.vwr.bsA(),!0,c,h,d));return!1;case 137363467:case 135270418:case 1052714:return this.e.getCmdExt().plot(this.st),!1}for(var m=!1,g=!1,M=!1,e=!1,k=!1,f=0,q=3.4028235E38,t=p(-1,[-2147483648]),r=0,L="",j=0,d=null,c=this.initIsosurface(22),u=(b=null!=c)&&null==this.getShapeProperty(22,"ID"),w=null,
E=0,h=a.iToken;h<this.slen;++h){var B=null,D=null;switch(this.getToken(h).tok){case 1614417948:case 1679429641:if(this.chk)break;m=this.vwr.getPlaneIntersection(a.theTok,null,r/100,0);r=0;B="polygon";D=m;m=!0;break;case 4106:w=p(4,0);E=4;m=a.floatParameterSet(++h,4,4);h=a.iToken;for(b=0;4>b;b++)w[b]=y(m[b]);m=!0;break;case 1678770178:case 1141899265:if(null==w||E>(1229980163==a.theTok?2:3))E=0,w=p(-1,[-1,-1,-1,-1]);w[E++]=this.atomExpressionAt(++h).nextSetBit(0);h=a.iToken;w[E++]=1678770178==a.theTok?
this.atomExpressionAt(++h).nextSetBit(0):-1;h=a.iToken;m=!0;break;case 554176565:switch(this.getToken(++h).tok){case 1048582:B="slab";D=a.objectNameParameter(++h);h=a.iToken;m=!0;break;default:this.invArg()}break;case 135267842:switch(this.getToken(++h).tok){case 1614417948:case 1679429641:f=a.theTok;e=!0;continue;case 1048582:B="intersect";D=a.objectNameParameter(++h);h=a.iToken;m=e=!0;break;default:this.invArg()}break;case 135266320:case 1073742106:var A=135266320==a.theTok,B="polygon",m=!0,D=new JU.Lst,
H=0,F=0,N=null,P=null;if(a.isArrayParameter(++h))N=a.getPointArray(h,-1,!1),H=N.length;else{H=Math.max(0,this.intParameter(h));N=Array(H);for(b=0;b<H;b++)N[b]=this.centerParameter(++a.iToken);h=a.iToken}var G=null;switch(this.tokAt(h+1)){case 11:case 12:h=JS.SV.newT(this.getToken(++h));h.toArray();P=h.getList();F=P.size();break;case 7:P=this.getToken(++h).getList();F=P.size();break;case 2:F=this.intParameter(++h);0>F&&(A=!0);break;default:!A&&!this.chk&&(G=J.api.Interface.getInterface("JU.MeshCapper",
this.vwr,"script").set(null).triangulatePolygon(N))}if(null==G&&!A){G=JU.AU.newInt2(F);for(b=0;b<F;b++)A=null==P?a.floatParameterSet(++a.iToken,3,4):JS.SV.flistValue(P.get(b),0),(3>A.length||4<A.length)&&this.invArg(),G[b]=p(-1,[y(A[0]),y(A[1]),y(A[2]),3==A.length?7:y(A[3])])}0<H?(D.addLast(N),D.addLast(G)):D=null;h=a.iToken;break;case 1297090050:g=null;M=0;e=null;switch(this.tokAt(++h)){case 4:g=this.stringParameter(h);break;case 12:g=JS.SV.sValue(this.getToken(h));break;default:a.isCenterParameter(h)||
(M=this.intParameter(h++));a.isCenterParameter(h)&&(d=this.centerParameter(h));a.isCenterParameter(a.iToken+1)&&(e=this.centerParameter(++a.iToken));if(this.chk)return!1;h=a.iToken}k=null;null==d&&h+1<this.slen&&(d=this.centerParameter(++h),k=10==this.tokAt(h)||1048577==this.tokAt(h)?this.atomExpressionAt(h):null);a.checkLast(a.iToken);this.chk||(d=this.vwr.ms.getSymTemp(!1).getSymmetryInfoAtom(this.vwr.ms,k,g,M,d,e,c,135176),this.showString(d.substring(0,d.indexOf("\n")+1)),a.runScript(0<d.length?
d:'draw ID "sym_'+c+'*" delete'));return!1;case 4115:k=!0;continue;case 1048586:case 9:case 8:if(9==a.theTok||!a.isPoint3f(h)){D=a.getPoint4f(h);if(k)return a.checkLast(a.iToken),this.chk||a.runScript(JU.Escape.drawQuat(JU.Quat.newP4(D),null==c?"frame":c," "+L,null==d?new JU.P3:d,r/100)),!1;B="planedef"}else D=d=this.getPoint3f(h,!0),B="coord";h=a.iToken;m=!0;break;case 135267841:case 135266319:if(!m&&!e&&0==f&&135267841!=a.theTok){B="plane";break}b=135266319==a.theTok?a.planeParameter(h):a.hklParameter(++h);
h=a.iToken;if(0!=f){if(this.chk)break;m=this.vwr.getPlaneIntersection(f,b,r/100,0);r=0;B="polygon";D=m}else D=b,B="planedef";m=!0;break;case 1073742E3:B="lineData";D=a.floatParameterSet(++h,0,2147483647);h=a.iToken;m=!0;break;case 10:case 1048577:B="atomSet";D=this.atomExpressionAt(h);k&&(d=this.centerParameter(h));h=a.iToken;m=!0;break;case 7:B="modelBasedPoints";D=a.theToken.value;m=!0;break;case 1073742195:case 269484080:break;case 269484096:D=a.xypParameter(h);if(null!=D){h=a.iToken;B="coord";
m=!0;break}M&&this.invArg();M=!0;break;case 269484097:M||this.invArg();M=!1;break;case 1141899269:B="reverse";break;case 4:D=this.stringParameter(h);B="title";break;case 135198:B="vector";break;case 1141899267:D=Float.$valueOf(this.floatParameter(++h));B="length";break;case 3:D=Float.$valueOf(this.floatParameter(h));B="length";break;case 1095761935:B="modelIndex";D=Integer.$valueOf(this.intParameter(++h));break;case 2:M?(B="modelIndex",D=Integer.$valueOf(this.intParameter(h))):r=this.intParameter(h);
break;case 1073742138:++h>=this.slen&&this.error(34);switch(this.getToken(h).tok){case 2:r=this.intParameter(h);continue;case 3:r=Math.round(100*this.floatParameter(h));continue}this.error(34);break;case 1074790550:c=this.setShapeId(22,++h,b);u=null==this.getShapeProperty(22,"ID");h=a.iToken;break;case 1073742027:B="fixed";D=Boolean.FALSE;break;case 1060869:B="fixed";D=Boolean.TRUE;break;case 1073742066:b=this.getPoint3f(++h,!0);h=a.iToken;B="offset";D=b;break;case 1073741906:B="crossed";break;case 1073742196:D=
Float.$valueOf(this.floatParameter(++h));B="width";L=B+" "+D;break;case 1073741998:B="line";D=Boolean.TRUE;break;case 1073741908:B="curve";break;case 1074790416:B="arc";break;case 1073741846:B="arrow";break;case 1073741880:B="circle";break;case 1073741912:B="cylinder";break;case 1073742194:B="vertices";break;case 1073742048:B="nohead";break;case 1073741861:B="isbarb";break;case 1073742130:B="rotate45";break;case 1073742092:B="perp";break;case 1666189314:case 1073741917:L=1666189314==a.theTok;A=this.floatParameter(++h);
L&&(A*=2);D=Float.$valueOf(A);B=L||3==this.tokAt(h)?"width":"diameter";L=B+(3==this.tokAt(h)?" "+A:" "+y(A));break;case 1048582:if(269484096==this.tokAt(h+2)||k){m=d=this.centerParameter(h);h=a.iToken;B="coord";D=m;m=!0;break}D=a.objectNameParameter(++h);B="identifier";m=!0;break;case 1766856708:case 603979967:case 1073742074:b=!0;q=this.getColorTrans(a,h,!1,t);h=a.iToken;continue;default:if(!a.setMeshDisplayProperty(22,0,a.theTok)){if(269484209==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){c=this.setShapeId(22,
h,b);h=a.iToken;break}this.invArg()}0==j&&(j=h);h=a.iToken;continue}b=12291!=a.theTok;m&&(!g&&!k)&&(this.setShapeProperty(22,"points",Integer.$valueOf(r)),g=!0,r=0);m&&u&&this.invArg();null!=B&&this.setShapeProperty(22,B,D)}this.finalizeObject(22,t[0],q,r,m,w,j,null);return!0});e(c$,"mo",function(a,b){var c=this.e,d=2147483647,h=!1,m=null,g=this.vwr.getVisibleFramesBitSet(),M=new JU.Lst,e=1;if(1073877011==this.tokAt(0)&&1==this.e.slen)this.chk||(c=new java.util.Hashtable,c.put("service","nbo"),c.put("action",
"showPanel"),this.vwr.sm.processService(c));else{if(1095766030==this.tokAt(1)||4115==this.tokAt(1))e=c.modelNumberParameter(2),0>e&&this.invArg(),g.clearAll(),g.set(e),e=3;c.sm.loadShape(b);for(var k=g.nextSetBit(0);0<=k;k=g.nextSetBit(k+1)){var f=e;if(1073742001==this.tokAt(f)&&this.listIsosurface(b))break;this.setShapeProperty(b,"init",Integer.$valueOf(k));var q=null,t=this.getShapeProperty(b,"moNumber").intValue(),r=this.getShapeProperty(b,"moLinearCombination");if(a)break;0==t&&(t=2147483647);
var L=null,j=null;switch(this.getToken(f).tok){case 1141899272:if(1073877010==b){this.mo(a,28);return}m=this.paramAsStr(++f).toUpperCase();break;case 1074790451:case 554176565:L=c.theToken.value;j=this.getCapSlabObject(f,!1);break;case 1073741914:L="squareLinear";j=Boolean.TRUE;r=u(-1,[1]);d=t=0;break;case 2:t=this.intParameter(f);r=this.moCombo(M);null==r&&0>t&&(r=u(-1,[-100,-t]));break;case 269484192:switch(this.tokAt(++f)){case 1073741973:case 1073742008:break;default:this.invArg()}h=!0;case 1073741973:case 1073742008:2147483647==
(d=this.moOffset(f))&&this.invArg();t=0;r=this.moCombo(M);break;case 1073742037:t=1073742037;r=this.moCombo(M);break;case 1073742108:t=1073742108;r=this.moCombo(M);break;case 1766856708:this.setColorOptions(null,f+1,b,2);break;case 135266319:L="plane";j=1048587==this.tokAt(this.e.iToken=++f)?null:c.planeParameter(f);break;case 135266320:this.addShapeProperty(M,"randomSeed",2==this.tokAt(f+2)?Integer.$valueOf(this.intParameter(f+2)):null);L="monteCarloCount";j=Integer.$valueOf(this.intParameter(f+
1));break;case 1073742138:L="scale";j=Float.$valueOf(this.floatParameter(f+1));break;case 1073741910:269484193==this.tokAt(f+1)?(L="cutoffPositive",j=Float.$valueOf(this.floatParameter(f+2))):(L="cutoff",j=Float.$valueOf(this.floatParameter(f+1)));break;case 536870916:L="debug";break;case 1073742054:L="plane";break;case 1073742104:case 1073742122:L="resolution";j=Float.$valueOf(this.floatParameter(f+1));break;case 1073742156:L="squareData";j=Boolean.TRUE;break;case 1073742168:f+1<this.slen&&4==this.tokAt(f+
1)&&(L="titleFormat",j=this.paramAsStr(f+1));break;case 1073741824:this.invArg();break;default:if(c.isArrayParameter(f)){r=c.floatParameterSet(f,1,2147483647);1073742156==this.tokAt(c.iToken+1)&&(this.addShapeProperty(M,"squareLinear",Boolean.TRUE),c.iToken++);break}d=c.iToken;c.setMeshDisplayProperty(b,0,c.theTok)||this.invArg();this.setShapeProperty(b,"setProperties",M);c.setMeshDisplayProperty(b,d,this.tokAt(d));return}null!=L&&this.addShapeProperty(M,L,j);f=2147483647!=t||null!=r;if(this.chk)break;
if(null!=m||f)f&&4==this.tokAt(c.iToken+1)&&(q=this.paramAsStr(++c.iToken)),c.setCursorWait(!0),this.setMoData(M,t,r,d,h,k,q,m),f&&this.addShapeProperty(M,"finalize",null);0<M.size()&&this.setShapeProperty(b,"setProperties",M);M.clear()}}},"~B,~N");e(c$,"setNBOType",function(a,b){var c=";AO;  ;PNAO;;NAO; ;PNHO;;NHO; ;PNBO;;NBO; ;PNLMO;NLMO;;MO;  ;NO;".indexOf(";"+b+";");0>c&&this.invArg();var c=E(c/6)+31,d=a.get("nboLabels");null==d&&this.error(27);if(!this.chk)try{var h=a.get(b+"_coefs");if(null==
h){var m=a.get("nboRoot")+"."+c,g=this.vwr.getFileAsString3(m,!0,null);null==g&&this.error(27);for(var h=a.get("mos"),M=h.get(0).get("dfCoefMaps"),e=h.size(),h=new JU.Lst,c=e;0<=--c;){var f=new java.util.Hashtable;h.addLast(f);f.put("dfCoefMaps",M)}J.api.Interface.getInterface("J.quantum.QS",this.vwr,"script").setNboLabels(d,e,h,0,b);for(var g=g.substring(g.lastIndexOf("--")+2),n=g.length,q=p(1,0),c=0;c<e;c++){var f=h.get(c),t=u(e,0);f.put("coefficients",t);for(var r=0;r<e;r++)t[r]=JU.PT.parseFloatChecked(g,
n,q,!1)}if(b.equals("NBO")){for(var j=u(e,0),r=0;r<e;r++)j[r]=JU.PT.parseFloatChecked(g,n,q,!1);for(c=0;c<e;c++)f=h.get(c),f.put("occupancy",Float.$valueOf(j[c]))}a.put(b+"_coefs",h)}a.put("nboType",b);a.put("mos",h)}catch(ta){if(U(ta,Exception))this.error(27);else throw ta;}},"java.util.Map,~S");e(c$,"moCombo",function(a){if(1073742156!=this.tokAt(this.e.iToken+1))return null;this.addShapeProperty(a,"squareLinear",Boolean.TRUE);this.e.iToken++;return u(0,0)},"JU.Lst");e(c$,"moOffset",function(a){var b=
1073741973==this.getToken(a).tok?0:1,c=this.tokAt(++a);2==c&&0>this.intParameter(a)?b+=this.intParameter(a):269484193==c?b+=this.intParameter(++a):269484192==c&&(b-=this.intParameter(++a));return b},"~N");e(c$,"setMoData",function(a,b,c,d,h,m,g,e){var f=this.e;0>m&&(m=this.vwr.am.cmi,0>m&&f.errorStr(30,"MO isosurfaces"));m=this.vwr.ms.getInfo(m,"moData");null==m&&this.error(27);this.vwr.checkMenuUpdate();if(null!=e&&(this.setNBOType(m,e),null==c&&2147483647==b))return;var k=null,n,q,t=0;if(null==
c||2>c.length){null!=c&&1==c.length&&(d=0);e=m.containsKey("lastMoNumber")?m.get("lastMoNumber").intValue():0;k=m.containsKey("lastMoCount")?m.get("lastMoCount").intValue():1;1073742108==b?b=e-1:1073742037==b&&(b=e+k);k=m.get("mos");t=null==k?0:k.size();0==t&&this.error(25);1==t&&1<b&&this.error(29);if(2147483647!=d){if(m.containsKey("HOMO"))b=m.get("HOMO").intValue()+d;else{b=-1;for(e=0;e<t;e++)if(n=k.get(e),null!=(q=n.get("occupancy"))){if(0.5>q.floatValue()){b=e;break}}else if(null!=(q=n.get("energy"))){if(0<
q.floatValue()){b=e;break}}else break;0>b&&this.error(28);b+=d}JU.Logger.info("MO "+b)}(1>b||b>t)&&f.errorStr(26,""+t)}b=Math.abs(b);m.put("lastMoNumber",Integer.$valueOf(b));m.put("lastMoCount",Integer.$valueOf(1));h&&null==c&&(c=u(-1,[-100,b]));if(null!=c&&2>c.length){n=k.get(b-1);if(null==(q=n.get("energy")))c=u(-1,[100,b]);else{f=q.floatValue();d=JU.BS.newN(t);h=0;c=1==c.length&&1==c[0];for(e=0;e<t;e++)if(null!=(q=k.get(e).get("energy")))if(q=q.floatValue(),c?q<=f:q==f)d.set(e+1),h+=2;c=u(h,0);
for(k=e=0;e<h;e+=2)c[e]=1,c[e+1]=k=d.nextSetBit(k+1);m.put("lastMoNumber",Integer.$valueOf(d.nextSetBit(0)));m.put("lastMoCount",Integer.$valueOf(E(h/2)))}this.addShapeProperty(a,"squareLinear",Boolean.TRUE)}this.addShapeProperty(a,"moData",m);null!=g&&this.addShapeProperty(a,"title",g);this.addShapeProperty(a,"molecularOrbital",null!=c?c:Integer.$valueOf(Math.abs(b)));this.addShapeProperty(a,"clear",null)},"JU.Lst,~N,~A,~N,~B,~N,~S,~S");e(c$,"isosurface",function(a){var b=this.e;b.sm.loadShape(a);
if(!(1073742001==this.tokAt(1)&&this.listIsosurface(a))){var c=0,d=24==a,h=29==a,m=30==a,g=26==a,e=!1,f=!1,k=!1,n=!1,q=!1,t=!1,r=!1,j=!1,ta=!1,pb=!1,E=!1,H=!1,B=!1,D=!1,A=null,G=null,F=-2147483648,N,P,C,K,Q,R=NaN,aa=NaN,Z=0,W=null,Y=2147483647,O=null,S=null,ca=null,s=new JU.SB,I,fa=null,la=null,ma=!1,xa,ga=0,da=null,T=this.chk?0:-2147483648;b.setCursorWait(!0);var ua=null!=this.initIsosurface(a),na=ua&&null==this.getShapeProperty(a,"ID"),oa=!1,sa=!1,Ea=null,wa=null,ha=null,$a=null,Ba=null,Fa=null,
z=new JU.Lst,qb=!1;(h||m)&&this.addShapeProperty(z,"fileType","Pmesh");for(var l=b.iToken;l<this.slen;++l){var x=null,v=null;this.getToken(l);1073741824==b.theTok&&(da=this.paramAsStr(l));switch(b.theTok){case 603979870:W=1048589==this.getToken(++l).tok?Boolean.TRUE:1048588==b.theTok?Boolean.FALSE:null;null==W&&this.invArg();continue;case 553648149:Y=this.intParameter(++l);continue;case 4128:x="moveIsosurface";12!=this.tokAt(++l)&&this.invArg();v=this.getToken(l++).value;break;case 1297090050:for(var rb=
this.floatArraySet(l+2,this.intParameter(l+1),16),Ba=Array(rb.length),ia=Ba.length;0<=--ia;)Ba[ia]=JU.M4.newA16(rb[ia]);l=b.iToken;break;case 1089470478:0>T&&(T=Math.min(this.vwr.am.cmi,0));var sb=null==ca;null==S&&(S=JU.BSUtil.copy(this.vwr.bsA()));S.and(this.vwr.ms.getAtoms(1297090050,Integer.$valueOf(1)));sb||S.andNot(ca);this.addShapeProperty(z,"select",S);sb&&(ca=JU.BSUtil.copy(S),JU.BSUtil.invertInPlace(ca,this.vwr.ms.ac),D=!0,this.addShapeProperty(z,"ignore",ca),s.append(" ignore ").append(JU.Escape.eBS(ca)));
s.append(" symmetry");0==ga&&this.addShapeProperty(z,"colorRGB",Integer.$valueOf(1297090050));Ba=this.vwr.ms.getSymMatrices(T);break;case 1073742066:x="offset";v=this.centerParameter(++l);l=b.iToken;break;case 528432:x="rotate";v=1048587==this.tokAt(b.iToken=++l)?null:b.getPoint4f(l);l=b.iToken;break;case 1610612740:x="scale3d";v=Float.$valueOf(this.floatParameter(++l));break;case 1073742090:s.append(" periodic");x="periodic";break;case 1073742078:case 266298:case 135266320:x=b.theToken.value.toString();
s.append(" ").appendO(b.theToken.value);v=this.centerParameter(++l);s.append(" ").append(JU.Escape.eP(v));l=b.iToken;break;case 1679429641:if(0<=b.fullCommand.indexOf("# BBOX=")){var tb=JU.PT.split(JU.PT.getQuotedAttribute(b.fullCommand,"# BBOX"),",");xa=w(-1,[JU.Escape.uP(tb[0]),JU.Escape.uP(tb[1])])}else b.isCenterParameter(l+1)?(xa=w(-1,[this.getPoint3f(l+1,!0),this.getPoint3f(b.iToken+1,!0)]),l=b.iToken):xa=this.vwr.ms.getBBoxVertices();s.append(" boundBox "+JU.Escape.eP(xa[0])+" "+JU.Escape.eP(xa[xa.length-
1]));x="boundingBox";v=xa;break;case 135188:h=!0;s.append(" pmesh");x="fileType";v="Pmesh";break;case 135267842:S=this.atomExpressionAt(++l);this.chk?O=new JU.BS:1048577==this.tokAt(b.iToken+1)||10==this.tokAt(b.iToken+1)?(O=this.atomExpressionAt(++b.iToken),O.and(this.vwr.ms.getAtomsWithinRadius(5,S,!1,null))):(O=this.vwr.ms.getAtomsWithinRadius(5,S,!0,null),O.andNot(this.vwr.ms.getAtoms(1095761936,S)));O.andNot(S);s.append(" intersection ").append(JU.Escape.eBS(S)).append(" ").append(JU.Escape.eBS(O));
l=b.iToken;if(135368713==this.tokAt(l+1)){l++;var Ga=this.getToken(++l).value;s.append(" function ").append(JU.PT.esc(Ga));this.chk||this.addShapeProperty(z,"func",Ga.equals("a+b")||Ga.equals("a-b")?Ga:this.createFunction("__iso__","a,b",Ga))}else B=!0;x="intersection";v=w(-1,[S,O]);break;case 1610625028:case 135266325:var ab=1610625028==b.theTok;if(ab){s.append(" display");var c=l,pa=this.tokAt(l+1);if(0==pa)continue;l++;this.addShapeProperty(z,"token",Integer.$valueOf(1048589));if(10==pa||1048579==
pa){x="bsDisplay";1048579==pa?s.append(" all"):(v=this.st[l].value,s.append(" ").append(JU.Escape.eBS(v)));b.checkLast(l);break}else 135266325!=pa&&(b.iToken=l,this.invArg())}else Z=l;var Pa,ya=null,O=null,bb=!1;1048577==this.tokAt(l+1)?(Pa=this.floatParameter(l+3),b.isPoint3f(l+4)?(ya=this.centerParameter(l+4),bb=!0,b.iToken+=2):b.isPoint3f(l+5)?(ya=this.centerParameter(l+5),bb=!0,b.iToken+=2):(O=b.atomExpression(this.st,l+5,this.slen,!0,!1,!1,!0),null==O&&this.invArg())):(Pa=this.floatParameter(++l),
ya=this.centerParameter(++l));ab&&b.checkLast(b.iToken);l=b.iToken;0<=b.fullCommand.indexOf("# WITHIN=")?O=JU.BS.unescape(JU.PT.getQuotedAttribute(b.fullCommand,"# WITHIN")):bb||(O=V(b.expressionResult,JU.BS)?b.expressionResult:null);this.chk||(null!=O&&0<=T&&O.and(this.vwr.getModelUndeletedAtomsBitSet(T)),null==ya&&(ya=null==O?new JU.P3:this.vwr.ms.getAtomSetCenter(O)),this.getWithinDistanceVector(z,Pa,ya,O,ab),s.append(" within ").appendF(Pa).append(" ").append(null==O?JU.Escape.eP(ya):JU.Escape.eBS(O)));
continue;case 1073742083:var x="parameters",ub=b.floatParameterSet(++l,1,10),l=b.iToken,v=ub;s.append(" parameters ").append(JU.Escape.eAF(ub));break;case 1716520985:case 1073742190:var Ea=b.theToken.value,Wa=1073742190==b.theTok,Ha=this.tokAt(l+1);null==$a?(!e&&(!k&&!f)&&(this.addShapeProperty(z,"sasurface",Float.$valueOf(0)),s.append(" vdw"),e=!0),x="property",null==W&&(W=JS.T.tokAttr(Ha,1112539136)&&1==this.vwr.getIsosurfacePropertySmoothing(!1)?Boolean.TRUE:Boolean.FALSE),this.addShapeProperty(z,
"propertySmoothing",W),s.append(" isosurfacePropertySmoothing "+W),W===Boolean.TRUE&&(2147483647==Y&&(Y=this.vwr.getIsosurfacePropertySmoothing(!0)),this.addShapeProperty(z,"propertySmoothingPower",Integer.$valueOf(Y)),s.append(" isosurfacePropertySmoothingPower "+Y)),this.vwr.g.rangeSelected&&this.addShapeProperty(z,"rangeSelected",Boolean.TRUE)):x=$a;da=this.paramAsStr(l);s.append(" ").append(da);if(0==da.toLowerCase().indexOf("property_")){A=u(this.vwr.ms.ac,0);if(this.chk)continue;A=this.vwr.getDataFloat(da);
null==A&&this.invArg();this.addShapeProperty(z,x,A);continue}var Ia=this.vwr.ms.ac,A=u(Ia,0);if(Wa){var vb=this.paramAsStr(++l);0==vb.length?A=b.floatParameterSet(l,Ia,Ia):(A=u(Ia,0),this.chk||JU.Parser.parseStringInfestedFloatArray(""+b.getParameter(vb,4,!0),null,A));this.chk||s.append(' "" ').append(JU.Escape.eAF(A))}else{this.getToken(++l);if(!this.chk){s.append(" "+b.theToken.value);var Xa=this.vwr.ms.at;this.vwr.autoCalculate(Ha);if(1766856708!=Ha){I=new JU.P3;for(var cb=Ia;0<=--cb;)A[cb]=Xa[cb].atomPropertyFloat(this.vwr,
Ha,I)}}1766856708==Ha&&(ha="inherit");if(135266325==this.tokAt(l+1)){var wb=this.floatParameter(l+=2);s.append(" within "+wb);this.addShapeProperty(z,"propertyDistanceMax",Float.$valueOf(wb))}}v=A;break;case 1095761935:case 1095766030:e&&this.invArg();T=1095761935==b.theTok?this.intParameter(++l):b.modelNumberParameter(++l);s.append(" modelIndex "+T);if(0>T){x="fixed";v=Boolean.TRUE;break}x="modelIndex";v=Integer.$valueOf(T);break;case 135280133:var x="select",db=this.atomExpressionAt(++l),v=db,l=
b.iToken;1073742072==this.tokAt(l+1)&&(l++,ca=JU.BSUtil.copy(db),JU.BSUtil.invertInPlace(ca,this.vwr.ms.ac),this.addShapeProperty(z,"ignore",ca),s.append(" ignore ").append(JU.Escape.eBS(ca)),D=!0);e||k?s.append(" select "+JU.Escape.eBS(db)):(S=v,0>T&&0<=S.nextSetBit(0)&&(T=this.vwr.ms.at[S.nextSetBit(0)].mi));break;case 1085443:F=this.intParameter(++l);break;case 12289:x="center";v=this.centerParameter(++l);s.append(" center "+JU.Escape.eP(v));l=b.iToken;break;case 1073742147:case 1766856708:var ua=
!0,eb=1073742147==b.theTok;if(eb)s.append(" sign"),this.addShapeProperty(z,"sign",Boolean.TRUE);else{if(1073741914==this.tokAt(l+1)){l++;x="colorDensity";s.append(" color density");if(this.isFloatParameter(l+1)){var xb=this.floatParameter(++l);s.append(" "+xb);v=Float.$valueOf(xb)}break}if(4==this.getToken(l+1).tok)ha=this.paramAsStr(++l),0<ha.indexOf(" ")&&(Fa=JU.C.getColixArray(ha),null==Fa&&this.error(4));else if(1073742018==b.theTok){l++;s.append(" color mesh");ga=b.getArgbParam(++l);this.addShapeProperty(z,
"meshcolor",Integer.$valueOf(ga));s.append(" ").append(JU.Escape.escapeColor(ga));l=b.iToken;continue}if(603979967==(b.theTok=this.tokAt(l+1))||1073742074==b.theTok){s.append(" color");wa=this.setColorOptions(s,l+1,24,-2);l=b.iToken;continue}switch(this.tokAt(l+1)){case 1073741826:case 1073742114:this.getToken(++l);s.append(" color range");this.addShapeProperty(z,"rangeAll",null);if(1048579==this.tokAt(l+1)){l++;s.append(" all");continue}var yb=this.floatParameter(++l),zb=this.floatParameter(++l);
this.addShapeProperty(z,"red",Float.$valueOf(yb));this.addShapeProperty(z,"blue",Float.$valueOf(zb));s.append(" ").appendF(yb).append(" ").appendF(zb);continue}if(b.isColorParam(l+1)&&(ga=b.getArgbParam(l+1),1074790746==this.tokAt(l+2))){ha=b.getColorRange(l+1);l=b.iToken;break}s.append(" color")}b.isColorParam(l+1)?(ga=b.getArgbParam(++l),s.append(" ").append(JU.Escape.escapeColor(ga)),l=b.iToken,this.addShapeProperty(z,"colorRGB",Integer.$valueOf(ga)),ua=!0,b.isColorParam(l+1)?(ga=b.getArgbParam(++l),
l=b.iToken,this.addShapeProperty(z,"colorRGB",Integer.$valueOf(ga)),s.append(" ").append(JU.Escape.escapeColor(ga)),n=!0):eb&&this.invPO()):!eb&&null==Fa&&this.invPO();continue;case 135270423:d||this.invArg();pb=!this.chk;continue;case 1229984263:4!=this.tokAt(l+1)&&this.invPO();continue;case 1112541194:case 1649412120:s.append(" ").appendO(b.theToken.value);var Ja=b.encodeRadiusParameter(l,!1,!0);if(null==Ja)return;s.append(" ").appendO(Ja);Float.isNaN(Ja.value)&&(Ja.value=100);v=Ja;x="radius";ta=
!0;k&&(e=!1);l=b.iToken;break;case 135266319:f=!0;x="plane";v=b.planeParameter(l);l=b.iToken;s.append(" plane ").append(JU.Escape.eP4(v));break;case 1073742138:x="scale";v=Float.$valueOf(this.floatParameter(++l));s.append(" scale ").appendO(v);break;case 1048579:ua&&this.invArg();x="thisID";break;case 1113198596:e=!0;++l;v=b.getPoint4f(l);x="ellipsoid";l=b.iToken;s.append(" ellipsoid ").append(JU.Escape.eP4(v));break;case 135267841:f=!0;x="plane";v=b.hklParameter(++l);l=b.iToken;s.append(" plane ").append(JU.Escape.eP4(v));
break;case 135182:var e=!0,Qa=this.paramAsStr(++l);this.addShapeProperty(z,"lcaoType",Qa);s.append(" lcaocartoon ").append(JU.PT.esc(Qa));switch(this.getToken(++l).tok){case 10:case 1048577:x="lcaoCartoon";O=this.atomExpressionAt(l);l=b.iToken;if(this.chk)continue;var Ka=O.nextSetBit(0);0>Ka&&this.error(14);s.append(" ({").appendI(Ka).append("})");T=this.vwr.ms.at[Ka].mi;this.addShapeProperty(z,"modelIndex",Integer.$valueOf(T));var fb=w(-1,[new JU.V3,new JU.V3,JU.V3.newV(this.vwr.ms.at[Ka]),new JU.V3]);
if(!Qa.equalsIgnoreCase("s")&&null==this.vwr.getHybridizationAndAxes(Ka,fb[0],fb[1],Qa))return;v=fb;break;default:this.error(14)}break;case 1073877010:var La=2147483647,Ca=2147483647,gb=269484192==this.tokAt(l+1);gb&&l++;var Ma=null;switch(this.tokAt(++l)){case 0:b.bad();break;case 1073741914:s.append("mo [1] squared ");this.addShapeProperty(z,"squareLinear",Boolean.TRUE);Ma=u(-1,[1]);Ca=La=0;l++;break;case 1073741973:case 1073742008:Ca=this.moOffset(l);La=0;l=b.iToken;s.append(" mo "+(gb?"-":"")+
"HOMO ");0<Ca&&s.append("+");0!=Ca&&s.appendI(Ca);break;case 2:La=this.intParameter(l);s.append(" mo ").appendI(La);break;default:b.isArrayParameter(l)&&(Ma=b.floatParameterSet(l,1,2147483647),l=b.iToken)}if(1073742156==this.tokAt(l+1))this.addShapeProperty(z,"squareLinear",Boolean.TRUE),s.append(" squared"),null==Ma&&(Ma=u(0,0));else if(135266320==this.tokAt(l+1)){++l;var Ab=this.intParameter(++l),Bb=2==this.tokAt(l+1)?this.intParameter(++l):-System.currentTimeMillis()%1E4;this.addShapeProperty(z,
"monteCarloCount",Integer.$valueOf(Ab));this.addShapeProperty(z,"randomSeed",Integer.$valueOf(Bb));s.append(" points ").appendI(Ab).appendC(" ").appendI(Bb)}this.setMoData(z,La,Ma,Ca,gb,T,null,null);e=!0;continue;case 1073742036:x="nci";s.append(" "+x);var pa=this.tokAt(l+1),Cb=1229984263!=pa&&4!=pa&&1073742033!=pa,v=Boolean.$valueOf(Cb);Cb&&(e=!0);break;case 1073742016:case 1073742022:var Db=1073742016==b.theTok,x=Db?"mep":"mlp";s.append(" "+x);var Ra=null,hb=-1,e=!0;2==this.tokAt(l+1)&&(hb=this.intParameter(++l),
s.append(" "+hb),this.addShapeProperty(z,"mepCalcType",Integer.$valueOf(hb)));if(4==this.tokAt(l+1))Ra=this.stringParameter(++l),s.append(" /*file*/"+JU.PT.esc(Ra));else if(1716520985==this.tokAt(l+1)){$a=x;continue}if(!this.chk)try{A=null==Ra&&Db?this.vwr.getPartialCharges():this.getAtomicPotentials(S,ca,Ra)}catch(Eb){if(!U(Eb,Exception))throw Eb;}!this.chk&&null==A&&this.error(32);v=A;break;case 1313866249:r=!this.chk;s.append(" volume");break;case 1074790550:this.setShapeId(a,++l,ua);na=null==
this.getShapeProperty(a,"ID");l=b.iToken;break;case 1073741888:603979967==this.tokAt(l+1)&&(oa=!0,l++);ha=this.paramAsStr(++l).toLowerCase();ha.equals("sets")?s.append(' colorScheme "sets"'):b.isColorParam(l)&&(ha=b.getColorRange(l),l=b.iToken);break;case 1073741828:x="addHydrogens";v=Boolean.TRUE;s.append(" mp.addHydrogens");break;case 1073741836:x="angstroms";s.append(" angstroms");break;case 1073741837:x="anisotropy";v=this.getPoint3f(++l,!1);s.append(" anisotropy").append(JU.Escape.eP(v));l=b.iToken;
break;case 1073741842:t=!this.chk;s.append(" area");break;case 1073741850:case 1073742076:e=!0;n&&!q&&(s.append(' phase "_orb"'),this.addShapeProperty(z,"phase","_orb"));var $=u(7,0);$[0]=this.intParameter(++l);$[1]=this.intParameter(++l);$[2]=this.intParameter(++l);$[3]=this.isFloatParameter(l+1)?this.floatParameter(++l):6;s.append(" atomicOrbital ").appendI(y($[0])).append(" ").appendI(y($[1])).append(" ").appendI(y($[2])).append(" ").appendF($[3]);135266320==this.tokAt(l+1)&&(l+=2,$[4]=this.intParameter(l),
$[5]=3==this.tokAt(l+1)?this.floatParameter(++l):0,$[6]=2==this.tokAt(l+1)?this.intParameter(++l):-System.currentTimeMillis()%1E4,s.append(" points ").appendI(y($[4])).appendC(" ").appendF($[5]).appendC(" ").appendI(y($[6])));x="hydrogenOrbital";v=$;break;case 1073741866:s.append(" binary");continue;case 1073741868:s.append(" blockData");x="blockData";v=Boolean.TRUE;break;case 1074790451:case 554176565:H=!0;x=b.theToken.value;v=this.getCapSlabObject(l,!1);l=b.iToken;break;case 1073741876:d||this.invArg();
var j=!0,Fb=this.isFloatParameter(l+1)?this.floatParameter(++l):1.2,ib=this.isFloatParameter(l+1)?this.floatParameter(++l):10;if(this.chk)continue;if(10<ib){b.integerOutOfRange(0,10);return}s.append(" cavity ").appendF(Fb).append(" ").appendF(ib);this.addShapeProperty(z,"envelopeRadius",Float.$valueOf(ib));this.addShapeProperty(z,"cavityRadius",Float.$valueOf(Fb));x="cavity";break;case 1073741896:case 1073741900:x="contour";s.append(" contour");switch(this.tokAt(l+1)){case 1073741920:v=b.floatParameterSet(l+
2,1,2147483647);s.append(" discrete ").append(JU.Escape.eAF(v));l=b.iToken;break;case 1073741981:I=this.getPoint3f(l+2,!1);(0>=I.z||I.y<I.x)&&this.invArg();I.z==y(I.z)&&I.z>I.y-I.x&&(I.z=(I.y-I.x)/I.z);v=I;l=b.iToken;s.append(" increment ").append(JU.Escape.eP(I));break;default:v=Integer.$valueOf(2==this.tokAt(l+1)?this.intParameter(++l):0),s.append(" ").appendO(v),2==this.tokAt(l+1)&&(this.addShapeProperty(z,x,v),v=Integer.$valueOf(-Math.abs(this.intParameter(++l))),s.append(" ").appendO(v))}break;
case 1073741910:s.append(" cutoff ");269484193==this.tokAt(++l)?(x="cutoffPositive",v=Float.$valueOf(aa=this.floatParameter(++l)),s.append("+").appendO(v)):this.isFloatParameter(l)?(x="cutoff",v=Float.$valueOf(aa=this.floatParameter(l)),s.appendO(v)):(x="cutoffRange",v=b.floatParameterSet(l,2,2),this.addShapeProperty(z,"cutoff",Float.$valueOf(0)),s.append(JU.Escape.eAF(v)),l=b.iToken);break;case 1073741928:x="downsample";v=Integer.$valueOf(this.intParameter(++l));s.append(" downsample ").appendO(v);
break;case 1073741931:x="eccentricity";v=b.getPoint4f(++l);s.append(" eccentricity ").append(JU.Escape.eP4(v));l=b.iToken;break;case 1074790508:s.append(" ed");this.setMoData(z,-1,null,0,!1,T,null,null);e=!0;continue;case 536870916:case 1073742041:s.append(" ").appendO(b.theToken.value);x="debug";v=536870916==b.theTok?Boolean.TRUE:Boolean.FALSE;break;case 1060869:s.append(" fixed");x="fixed";v=Boolean.TRUE;break;case 1073741962:s.append(" fullPlane");x="fullPlane";v=Boolean.TRUE;break;case 1073741966:case 1073741968:var Ya=
1073741968==b.theTok,x=""+b.theToken.value,qa=new JU.Lst,v=qa,E=e=!0;s.append(" ").append(x);var ba=this.paramAsStr(++l);if(ba.equals("=")){s.append(" =");ba=this.paramAsStr(++l);s.append(" ").append(JU.PT.esc(ba));qa.addLast(ba);this.chk||this.addShapeProperty(z,"func",this.createFunction("__iso__","x,y,z",ba));break}var jb=JU.PT.getQuotedAttribute(b.fullCommand,"# DATA"+(E?"2":""));null==jb?jb="inline":ba=jb;var Gb=0==ba.indexOf("data2d_"),Za=0==ba.indexOf("data3d_"),sa=ba.equals("inline");s.append(" inline");
qa.addLast(ba);var Hb=this.getPoint3f(++l,!1);s.append(" ").append(JU.Escape.eP(Hb));qa.addLast(Hb);var ra;K=++b.iToken;qa.addLast(ra=b.getPoint4f(K));s.append(" ").append(JU.Escape.eP4(ra));N=y(ra.x);Q=++b.iToken;qa.addLast(ra=b.getPoint4f(Q));s.append(" ").append(JU.Escape.eP4(ra));P=y(ra.x);qa.addLast(ra=b.getPoint4f(++b.iToken));s.append(" ").append(JU.Escape.eP4(ra));C=y(ra.x);(0==N||0==P||0==C)&&this.invArg();if(!this.chk){var ea=null,ja=null;if(Ya){sa?(N=Math.abs(N),P=Math.abs(P),C=Math.abs(C),
ja=this.floatArraySetXYZ(++b.iToken,N,P,C)):ja=Za?this.vwr.getDataFloat3D(ba):this.vwr.functionXYZ(ba,N,P,C);N=Math.abs(N);P=Math.abs(P);C=Math.abs(C);null==ja&&(b.iToken=K,b.errorStr(53,"xyzdata is null."));if(ja.length!=N||ja[0].length!=P||ja[0][0].length!=C)b.iToken=K,b.errorStr(53,"xyzdata["+ja.length+"]["+ja[0].length+"]["+ja[0][0].length+"] is not of size ["+N+"]["+P+"]["+C+"]");qa.addLast(ja);s.append(" ").append(JU.Escape.e(ja))}else{sa?(N=Math.abs(N),P=Math.abs(P),ea=this.floatArraySet(++b.iToken,
N,P)):Gb?(ea=this.vwr.getDataFloat2D(ba),N=null==ea?0:ea.length,P=3):(ea=this.vwr.functionXY(ba,N,P),N=Math.abs(N),P=Math.abs(P));null==ea&&(b.iToken=K,b.errorStr(53,"fdata is null."));ea.length!=N&&!Gb&&(b.iToken=K,b.errorStr(53,"fdata length is not correct: "+ea.length+" "+N+"."));for(ia=0;ia<N;ia++)null==ea[ia]&&(b.iToken=Q,b.errorStr(53,"fdata["+ia+"] is null.")),ea[ia].length!=P&&(b.iToken=Q,b.errorStr(53,"fdata["+ia+"] is not the right length: "+ea[ia].length+" "+P+"."));qa.addLast(ea);s.append(" ").append(JU.Escape.e(ea))}}l=
b.iToken;break;case 1073741970:x="gridPoints";s.append(" gridPoints");break;case 1073741976:x="ignore";v=ca=this.atomExpressionAt(++l);s.append(" ignore ").append(JU.Escape.eBS(ca));l=b.iToken;break;case 1073741984:x="insideOut";s.append(" insideout");break;case 1073741988:case 1073741986:case 1073742100:s.append(" ").appendO(b.theToken.value);x="pocket";v=1073742100==b.theTok?Boolean.TRUE:Boolean.FALSE;break;case 1073742002:x="lobe";v=b.getPoint4f(++l);l=b.iToken;s.append(" lobe ").append(JU.Escape.eP4(v));
e=!0;break;case 1073742004:case 1073742006:x="lp";v=b.getPoint4f(++l);l=b.iToken;s.append(" lp ").append(JU.Escape.eP4(v));e=!0;break;case 1052701:(k||this.slen==l+1)&&this.invArg();k=!0;if((j||ta||B)&&!e)e=!0,this.addShapeProperty(z,"bsSolvent",ta||B?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(z,"sasurface",Float.$valueOf(0));0==s.length()?(fa=this.getShapeProperty(24,"plane"),null==fa?null!=this.getShapeProperty(24,"contours")&&this.addShapeProperty(z,"nocontour",null):(this.addShapeProperty(z,
"plane",fa),s.append("plane ").append(JU.Escape.eP4(fa)),f=!0,fa=null)):!e&&!f&&this.invArg();s.append("; isosurface map");this.addShapeProperty(z,"map",e?Boolean.TRUE:Boolean.FALSE);break;case 1073742014:x="maxset";v=Integer.$valueOf(this.intParameter(++l));s.append(" maxSet ").appendO(v);break;case 1073742020:x="minset";v=Integer.$valueOf(this.intParameter(++l));s.append(" minSet ").appendO(v);break;case 1073742112:e=!0;x="rad";v=b.getPoint4f(++l);l=b.iToken;s.append(" radical ").append(JU.Escape.eP4(v));
break;case 1073742027:x="fixed";v=Boolean.FALSE;s.append(" modelBased");break;case 1073742028:case 1073742135:case 1613758488:var Ea=b.theToken.value,Sa;1073742028==b.theTok?(x="molecular",s.append(" molecular"),Sa=this.isFloatParameter(l+1)?this.floatParameter(++l):1.4):(this.addShapeProperty(z,"bsSolvent",b.lookupIdentifierValue("solvent")),x=1073742135==b.theTok?"sasurface":"solvent",s.append(" ").appendO(b.theToken.value),Sa=this.isFloatParameter(l+1)?this.floatParameter(++l):this.vwr.getFloat(570425394));
s.append(" ").appendF(Sa);v=Float.$valueOf(Sa);1073741961==this.tokAt(l+1)&&(this.addShapeProperty(z,"doFullMolecular",null),s.append(" full"),l++);e=!0;break;case 1073742033:this.addShapeProperty(z,"fileType","Mrc");s.append(" mrc");continue;case 1073742064:case 1073742062:this.addShapeProperty(z,"fileType","Obj");s.append(" obj");continue;case 1073742034:this.addShapeProperty(z,"fileType","Msms");s.append(" msms");continue;case 1073742094:e&&this.invArg();x="phase";q=!0;v=4==this.tokAt(l+1)?this.stringParameter(++l):
"_orb";s.append(" phase ").append(JU.PT.esc(v));break;case 1073742104:case 1073742122:x="resolution";v=Float.$valueOf(this.floatParameter(++l));s.append(" resolution ").appendO(v);break;case 1073742124:x="reverseColor";v=Boolean.TRUE;s.append(" reversecolor");break;case 1073742127:case 1073742146:x="sigma";v=Float.$valueOf(R=this.floatParameter(++l));s.append(" sigma ").appendO(v);break;case 1113198597:x="geodesic";v=Float.$valueOf(this.floatParameter(++l));s.append(" geosurface ").appendO(v);e=!0;
break;case 1073742154:x="sphere";v=Float.$valueOf(this.floatParameter(++l));s.append(" sphere ").appendO(v);e=!0;break;case 1073742156:x="squareData";v=Boolean.TRUE;s.append(" squared");break;case 1073741983:x=!e&&!f&&!k?"readFile":"mapColor";da=this.stringParameter(++l);null==da&&this.invArg();h&&(da=JU.PT.replaceWithCharacter(da,"{,}|"," "));b.debugHigh&&JU.Logger.debug("pmesh inline data:\n"+da);v=this.chk?null:da;this.addShapeProperty(z,"fileName","");s.append(" INLINE ").append(JU.PT.esc(da));
e=!0;break;case 4:var Ta=!e&&!f,x=Ta&&!k?"readFile":"mapColor",X=this.paramAsStr(l);if(X.startsWith("=")&&1<X.length){var kb=this.vwr.setLoadFormat(X,"_",!1),X=kb[0],lb=!Ta||!Float.isNaN(aa)?null:kb[1],Ib=kb[2];if(null!=lb&&!this.chk){var aa=NaN,Jb=null==Ib?"MAP_SIGMA_DENS":"DIFF_SIGMA_DENS";try{var Ua=this.vwr.getFileAsString3(lb,!1,null);JU.Logger.info(Ua);Ua=JU.PT.split(Ua,Jb)[1];aa=JU.PT.parseFloat(Ua)}catch(Kb){if(U(Kb,Exception))JU.Logger.error(Jb+" -- could  not read "+lb);else throw Kb;}0<
aa&&(null!=Ib&&(Float.isNaN(R)&&(R=3),this.addShapeProperty(z,"sign",Boolean.TRUE)),this.showString("using cutoff = "+aa+(Float.isNaN(R)?"":" sigma="+R)),Float.isNaN(R)||(aa*=R,R=NaN,this.addShapeProperty(z,"sigma",Float.$valueOf(R))),this.addShapeProperty(z,"cutoff",Float.$valueOf(aa)),s.append(" cutoff ").appendF(aa))}0==Z&&(Ea="=xxxx",0>T&&(T=this.vwr.am.cmi),O=this.vwr.getModelUndeletedAtomsBitSet(T),0<=O.nextSetBit(0)&&(this.getWithinDistanceVector(z,2,null,O,!1),s.append(" within 2.0 ").append(JU.Escape.eBS(O))));
Ta&&(qb=!0)}Ta&&(this.vwr.getP("_fileType").equals("Pdb")&&Float.isNaN(R)&&Float.isNaN(aa))&&(this.addShapeProperty(z,"sigma",Float.$valueOf(-1)),s.append(" sigma -1.0"));0==X.length&&(0>T&&(T=this.vwr.am.cmi),X=b.getFullPathName(),v=this.vwr.ms.getInfo(T,"jmolSurfaceInfo"));var mb=-1;null==v&&2==this.tokAt(l+1)&&this.addShapeProperty(z,"fileIndex",Integer.$valueOf(mb=this.intParameter(++l)));var Na=4==this.tokAt(l+1)?this.stringParameter(++l):null,e=!0;if(this.chk)break;var Da,va=null;null==v&&(0<=
b.fullCommand.indexOf("# FILE0=")?(X=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),Da=this.vwr.getFullPathNameOrError(va),va=Da[0],""!==this.vwr.fm.getPathForAllFiles()?(X=va,va=null):this.addShapeProperty(z,"localName",va)));!X.startsWith("cache://")&&null==Na&&(Da=this.vwr.getFullPathNameOrError(X),X=Da[0],null!=Da[1]&&b.errorStr(17,X+":"+Da[1]));this.showString("reading isosurface data from "+
X);null!=Na&&(v=this.vwr.fm.cacheGet(X,!1),this.addShapeProperty(z,"calculationType",Na));null==v&&(this.addShapeProperty(z,"fileName",X),null!=va&&(X=va),0<=mb&&s.append(" ").appendI(mb));s.append(" /*file*/").append(JU.PT.esc(X));null!=Na&&s.append(" ").append(JU.PT.esc(Na));break;case 4106:x="connections";switch(this.tokAt(++l)){case 10:case 1048577:v=p(-1,[this.atomExpressionAt(l).nextSetBit(0)]);break;default:v=p(-1,[y(b.floatParameterSet(l,1,1)[0])])}l=b.iToken;break;case 1095761923:x="atomIndex";
v=Integer.$valueOf(this.intParameter(++l));break;case 1073741999:x="link";s.append(" link");break;case 1614417948:24!=a&&this.invArg();269484193==this.tokAt(l+1)&&l++;x="extendGrid";v=Float.$valueOf(this.floatParameter(++l));s.append(" unitcell "+v);break;case 1073741994:24!=a&&this.invArg();I=this.getPoint3f(++l,!1);l=b.iToken;if(0>=I.x||0>=I.y||0>=I.z)break;I.x=y(I.x);I.y=y(I.y);I.z=y(I.z);s.append(" lattice ").append(JU.Escape.eP(I));k?(x="mapLattice",v=I):(la=I,1060869==this.tokAt(l+1)&&(s.append(" fixed"),
ma=!0,l++));break;default:1073741824==b.theTok&&(x="thisID",v=da);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;na&&e&&this.invArg();null!=x&&this.addShapeProperty(z,x,v)}if(!this.chk){if((j||ta)&&!e)e=!0,this.addShapeProperty(z,"bsSolvent",ta?new JU.BS:b.lookupIdentifierValue("solvent")),this.addShapeProperty(z,"sasurface",Float.$valueOf(0));f&&(!e&&!k)&&(this.addShapeProperty(z,
"nomap",Float.$valueOf(0)),e=!0);-1<=F&&this.addShapeProperty(z,"getSurfaceSets",Integer.$valueOf(F-1));if(null!=Fa)this.addShapeProperty(z,"colorDiscrete",Fa);else if("sets".equals(ha))this.addShapeProperty(z,"setColorScheme",null);else if(null!=ha){var Va=this.vwr.cm.getColorEncoder(ha);null!=Va&&(Va.isTranslucent=oa,Va.hi=3.4028235E38,this.addShapeProperty(z,"remapColor",Va))}if(e&&!g&&0!=s.indexOf(";")){z.add(0,w(-1,["newObject",null]));var Lb=null==S;Lb&&(S=JU.BSUtil.copy(this.vwr.bsA()));0>
T&&(T=this.vwr.am.cmi);S.and(this.vwr.getModelUndeletedAtomsBitSet(T));null!=Ea&&(1<this.vwr.ms.getModelBS(S,!1).cardinality()&&b.errorStr(30,"ISOSURFACE "+Ea),Lb&&(z.add(0,w(-1,["select",S])),0==s.indexOf("; isosurface map")&&(s=(new JU.SB).append("; isosurface map select ").append(JU.Escape.eBS(S)).append(s.substring(16)))))}B&&!H&&(e||this.addShapeProperty(z,"sasurface",Float.$valueOf(0)),k||(this.addShapeProperty(z,"map",Boolean.TRUE),this.addShapeProperty(z,"select",O),this.addShapeProperty(z,
"sasurface",Float.$valueOf(0))),this.addShapeProperty(z,"slab",this.getCapSlabObject(-100,!1)));var Mb=e&&this.vwr.getBoolean(603979934);Mb&&JU.Logger.startTimer("isosurface");this.setShapeProperty(a,"setProperties",z);Mb&&this.showString(JU.Logger.getTimerMsg("isosurface",0));qb&&(this.setShapeProperty(a,"token",Integer.$valueOf(1073742018)),this.setShapeProperty(a,"token",Integer.$valueOf(1073742046)),D=!0,s.append(" mesh nofill frontOnly"))}null!=la&&(this.setShapeProperty(a,"lattice",la),ma&&
this.setShapeProperty(a,"fixLattice",Boolean.TRUE));null!=Ba&&this.setShapeProperty(a,"symops",Ba);D&&this.setShapeProperty(a,"token",Integer.$valueOf(1073741960));0<c&&(b.setMeshDisplayProperty(a,c,0)||this.invArg());if(!this.chk){var za=null,Aa=null;t&&(za=this.getShapeProperty(a,"area"),V(za,Float)?this.vwr.setFloatProperty("isosurfaceArea",za.floatValue()):this.vwr.g.setUserVariable("isosurfaceArea",JS.SV.getVariableAD(za)));r&&(Aa=r?this.getShapeProperty(a,"volume"):null,V(Aa,Float)?this.vwr.setFloatProperty("isosurfaceVolume",
Aa.floatValue()):this.vwr.g.setUserVariable("isosurfaceVolume",JS.SV.getVariableAD(Aa)));if(!g){var ka=null;k&&!e?this.setShapeProperty(a,"finalize",s.toString()):e&&(G=s.toString(),this.setShapeProperty(a,"finalize",(0==G.indexOf("; isosurface map")?"":" select "+JU.Escape.eBS(S)+" ")+G),ka=this.getShapeProperty(a,"ID"),null!=ka&&!b.tQuiet&&(aa=this.getShapeProperty(a,"cutoff").floatValue(),Float.isNaN(aa)&&!Float.isNaN(R)&&JU.Logger.error("sigma not supported"),ka+=" created "+this.getShapeProperty(a,
"message")));var nb,ob;if(t||r)nb=t?"isosurfaceArea = "+(V(za,Float)?""+za:JU.Escape.eAD(za)):null,ob=r?"isosurfaceVolume = "+(V(Aa,Float)?""+Aa:JU.Escape.eAD(Aa)):null,null==ka?(t&&this.showString(nb),r&&this.showString(ob)):(t&&(ka+="\n"+nb),r&&(ka+="\n"+ob));null!=ka&&this.showString(ka)}null!=wa&&this.setShapeProperty(a,"translucency",wa);this.setShapeProperty(a,"clear",null);pb&&this.setShapeProperty(a,"cache",null);26!=a&&this.listIsosurface(a)}}},"~N");e(c$,"lcaoCartoon",function(){var a=this.e;
a.sm.loadShape(26);if(!(1073742001==a.tokAt(1)&&this.listIsosurface(26)))if(this.setShapeProperty(26,"init",a.fullCommand),1==this.slen)this.setShapeProperty(26,"lcaoID",null);else{for(var b=!1,c=null,c=1;c<this.slen;c++){var d=null,h=null;switch(this.getToken(c).tok){case 1074790451:case 554176565:d=a.theToken.value;1048588==this.tokAt(c+1)&&(a.iToken=c+1);h=this.getCapSlabObject(c,!0);c=a.iToken;break;case 12289:this.isosurface(26);return;case 528432:var m=h=0,g=0;switch(this.getToken(++c).tok){case 1112541205:h=
0.017453292*this.floatParameter(++c);break;case 1112541206:m=0.017453292*this.floatParameter(++c);break;case 1112541207:g=0.017453292*this.floatParameter(++c);break;default:this.invArg()}d="rotationAxis";h=JU.V3.new3(h,m,g);break;case 1048589:case 1610625028:case 3145768:d="on";break;case 1048588:case 12294:case 3145770:d="off";break;case 12291:d="delete";break;case 10:case 1048577:d="select";h=this.atomExpressionAt(c);c=a.iToken;break;case 1766856708:c=this.setColorOptions(null,c+1,26,-2);null!=
c&&this.setShapeProperty(26,"settranslucency",c);c=a.iToken;b=!0;continue;case 603979967:case 1073742074:a.setMeshDisplayProperty(26,c,a.theTok);c=a.iToken;b=!0;continue;case 1113200651:case 4:h=this.paramAsStr(c).toLowerCase();h.equals("spacefill")&&(h="cpk");d="create";a.optParameterAsString(c+1).equalsIgnoreCase("molecular")&&(c++,d="molecular");break;case 135280133:10==this.tokAt(c+1)||1048577==this.tokAt(c+1)?(d="select",h=this.atomExpressionAt(c+1),c=a.iToken):(d="selectType",h=this.paramAsStr(++c),
h.equals("spacefill")&&(h="cpk"));break;case 1073742138:d="scale";h=Float.$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 1074790550:h=a.setShapeNameParameter(++c);c=a.iToken;b&&this.invArg();d="lcaoID";break;default:if(269484209==
a.theTok||JS.T.tokAttr(a.theTok,1073741824))269484209!=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$,"contact",function(){var a=this.e;a.sm.loadShape(25);if(1073742001==this.tokAt(1)&&this.listIsosurface(25))return!1;var b=0;a.iToken=1;for(var c=null!=this.initIsosurface(25),d=c&&null==this.getShapeProperty(25,"ID"),h=null,m=null,g=null,e=null,f=null,k=!1,n=new JU.SB,
q=2147483647,t=135266319,r=0,j=NaN,p=NaN,y=!0,C=null,H=null,B=0,D=!1,A=-2147483648,G=1<a.iToken,F=a.iToken;F<this.slen;++F){switch(g=this.getToken(F).tok){default:G=!0;if(!a.setMeshDisplayProperty(25,0,a.theTok)){269484209!=a.theTok&&!JS.T.tokAttr(a.theTok,1073741824)&&this.invArg();this.setShapeId(25,F,c);F=a.iToken;break}0==b&&(b=F);F=a.iToken;continue;case 1074790550:G=!0;this.setShapeId(25,++F,c);d=null==this.getShapeProperty(25,"ID");F=a.iToken;break;case 1766856708:switch(this.tokAt(F+1)){case 1073741914:g=
0;k=!0;n.append(" color density");F++;break;case 1141899272:g=0,D=!0,n.append(" color type"),F++}if(0==g)break;case 603979967:case 1073742074:G=!0;0==B&&(B=F);a.setMeshDisplayProperty(25,F,a.theTok);F=a.iToken;break;case 554176565:G=!0;H=this.getCapSlabObject(F,!1);this.setShapeProperty(25,"slab",H);F=a.iToken;break;case 1073741914:k=!0;n.append(" density");this.isFloatParameter(F+1)&&(null==f&&(f=u(1,0)),f[0]=-Math.abs(this.floatParameter(++F)),n.append(" "+-f[0]));break;case 1073742122:c=this.floatParameter(++F);
0<c&&(n.append(" resolution ").appendF(c),this.setShapeProperty(25,"resolution",Float.$valueOf(c)));break;case 1095766030:case 1095761935:A=1095761935==a.theTok?this.intParameter(++F):a.modelNumberParameter(++F);n.append(" modelIndex "+A);break;case 135266325:case 1276118018:j=this.floatParameter(++F);n.append(" within ").appendF(j);break;case 269484193:case 2:case 3:e=a.encodeRadiusParameter(F,!1,!1);if(null==e)return!1;n.append(" ").appendO(e);F=a.iToken;break;case 1073741990:case 1073741989:C=
1073741989==g?Boolean.TRUE:Boolean.FALSE;n.append(" ").appendO(a.theToken.value);break;case 1073742020:q=this.intParameter(++F);break;case 1612189718:case 1073741881:case 1649412120:r=g;n.append(" ").appendO(a.theToken.value);break;case 1073742135:this.isFloatParameter(F+1)&&(p=this.floatParameter(++F));case 1074790451:case 1073742036:case 3145756:y=!1;case 1276117512:case 1073741961:case 135266319:case 4106:t=g;n.append(" ").appendO(a.theToken.value);1073742135==g&&n.append(" ").appendF(p);break;
case 1073742083:f=a.floatParameterSet(++F,1,10);F=a.iToken;break;case 10:case 1048577:(d||null!=m)&&this.invArg(),g=JU.BSUtil.copy(this.atomExpressionAt(F)),F=a.iToken,null==h?h=g:m=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){1649412120==r&&null==e&&(e=new J.atomdata.RadiusData(null,0,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO));F=null==e?new J.atomdata.RadiusData(null,0.26,J.atomdata.RadiusData.EnumType.OFFSET,J.c.VDW.AUTO):
e;m=1073742036==t&&null==m&&null!=C&&C.booleanValue()?h:a.getMathExt().setContactBitSets(h,m,y,j,F,!0);switch(t){case 1074790451:case 1073742135:F=a.lookupIdentifierValue("solvent");h.andNot(F);m.andNot(F);m.andNot(h);break;case 3145756:m.andNot(h);break;case 1073742036:2147483647==q&&(q=100),this.setShapeProperty(25,"minset",Integer.$valueOf(q)),n.append(" minSet ").appendI(q),null==f&&(f=u(-1,[0.5,2]))}null!=C&&(f=null==f?u(2,0):JU.AU.ensureLengthA(f,2),f[1]=C.booleanValue()?1:2);null!=f&&n.append(" parameters ").append(JU.Escape.eAF(f));
this.setShapeProperty(25,"set",w(-1,[Integer.$valueOf(r),Integer.$valueOf(t),Boolean.$valueOf(k),Boolean.$valueOf(D),h,m,e,Float.$valueOf(p),f,Integer.$valueOf(A),n.toString()]));0<B&&a.setMeshDisplayProperty(25,B,0)}0<b&&(a.setMeshDisplayProperty(25,b,0)||this.invArg());null!=H&&null!=h&&this.setShapeProperty(25,"slab",H);if(null!=h&&(1073742036==t||y)){h=this.getShapeProperty(25,"volume");b=1073741961==t;if(JU.AU.isAD(h))for(F=a=0;F<h.length;F++)a+=b?h[F]:Math.abs(h[F]);else a=h.floatValue();a=
Math.round(1E3*a)/1E3;if(k||1276117512!=t)k=this.getShapeProperty(25,"nSets").intValue(),k="Contacts: "+(0>k?E(-k/2):k),0!=a&&(k+=", with "+(b?"approx ":"net ")+"volume "+a+" A^3"),this.showString(k)}return!0});e(c$,"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,m=null,g=3.4028235E38,e=p(-1,[-2147483648]),f=0,k=a.iToken;k<this.slen;++k){var n=
null,q=null;switch(this.getToken(k).tok){case 269484096:case 1073742195:case 7:(null!=m||d)&&this.invArg();m=new JU.Lst;k=p(-1,[k,this.slen]);a.getShapePropertyData(23,"data",w(-1,[this.st,k,m,this.vwr]))||this.invArg();k=k[0];continue;case 1073742138:++k>=this.slen&&this.error(34);switch(this.getToken(k).tok){case 2:f=this.intParameter(k);continue;case 3:f=Math.round(100*this.floatParameter(k));continue}this.error(34);break;case 1766856708:case 603979967:case 1073742074:g=this.getColorTrans(a,k,
!1,e);k=a.iToken;c=!0;continue;case 1074790550:this.setShapeId(23,++k,c);d=null==this.getShapeProperty(23,"ID");k=a.iToken;break;default:if(!a.setMeshDisplayProperty(23,0,a.theTok)){if(269484209==a.theTok||JS.T.tokAttr(a.theTok,1073741824)){this.setShapeId(23,k,c);k=a.iToken;break}this.invArg()}0==b&&(b=k);k=a.iToken;continue}c=12291!=a.theTok;null!=m&&!h&&(n="points",q=Integer.$valueOf(f),h=!0,f=0);null!=n&&this.setShapeProperty(23,n,q)}this.finalizeObject(23,e[0],g,f,null!=m,m,b,null);return!0});
e(c$,"getAtomicPotentials",function(a,b,c){var d=u(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);h.assignPotentials(this.vwr.ms.at,d,this.vwr.getSmartsMatch("a",a),this.vwr.getSmartsMatch("/noAromatic/[$(C=O),$(O=C),$(NC=O)]",a),b,c);return d},"JU.BS,JU.BS,~S");e(c$,"getCapSlabObject",function(a,b){if(0>a)return JU.TempArray.getSlabWithinRange(a,0);var c=this.e,d=null,h=554176565==this.tokAt(a),
m=this.tokAt(a+1),g=null,e=g=null,f=null,k=null;if(603979967==m)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)),m=this.tokAt(a+1)){case 1073742018:case 1073741938:k=Integer.$valueOf(m);m=this.tokAt(++a+1);break;default:k=Integer.$valueOf(1073741938)}switch(m){case 1048588:return c.iToken=a+1,Integer.$valueOf(-2147483648);
case 1048587:c.iToken=a+1;break;case 1048582:a++;d=w(-1,[Float.$valueOf(1),this.paramAsStr(++a)]);m=1073742018;break;case 135266325:a++;if(1073742114==this.tokAt(++a))d=this.floatParameter(++a),m=this.floatParameter(++a),d=w(-1,[Float.$valueOf(d),Float.$valueOf(m)]),m=1073742114;else if(this.isFloatParameter(a)){d=this.floatParameter(a);if(c.isCenterParameter(++a))if(g=this.centerParameter(a),this.chk||!V(c.expressionResult,JU.BS))g=w(-1,[g]);else for(var n=this.vwr.ms.at,e=c.expressionResult,g=Array(e.cardinality()),
q=0,t=e.nextSetBit(0);0<=t;t=e.nextSetBit(t+1),q++)g[q]=n[t];else g=c.getPointArray(a,-1,!1);0==g.length&&(c.iToken=a,this.invArg());d=w(-1,[Float.$valueOf(d),g,e])}else d=c.getPointArray(a,4,!1),m=1679429641;break;case 1679429641:c.iToken=a+1;d=JU.BoxInfo.getUnitCellPoints(this.vwr.ms.getBBoxVertices(),null);break;case 1073741872:case 1614417948:c.iToken=a+1;c=this.vwr.getCurrentUnitCell();if(null==c)1614417948==m&&this.invArg();else{g=JU.BoxInfo.getUnitCellPoints(c.getUnitCellVerticesNoOffset(),
c.getCartesianOffset());c=y(c.getUnitCellInfoType(6));d=e=null;switch(c){case 1:d=JU.V3.newVsub(g[2],g[0]),d.scale(1E3);case 2:e=JU.V3.newVsub(g[1],g[0]),e.scale(1E3),g[0].sub(e),g[1].scale(2E3),1==c&&(g[0].sub(d),g[2].scale(2E3))}d=g}break;case 10:case 1048577:if(d=this.atomExpressionAt(a+1),m=3,!c.isCenterParameter(++c.iToken)){h=!0;break}default:if(!b&&h&&this.isFloatParameter(a+1)){d=this.floatParameter(++a);if(!this.isFloatParameter(a+1))return Integer.$valueOf(y(d));m=this.floatParameter(++a);
d=w(-1,[Float.$valueOf(d),Float.$valueOf(m)]);m=1073742114;break}g=c.planeParameter(++a);m=this.isFloatParameter(c.iToken+1)?this.floatParameter(++c.iToken):NaN;Float.isNaN(m)||(g.w-=m);d=g;m=135266319}f=null==k?null:w(-1,[k,f]);return JU.TempArray.getSlabObjectType(m,d,!h,f)},"~N,~B");e(c$,"setColorOptions",function(a,b,c,d){var h=this.e;this.getToken(b);var m="opaque";if(603979967==h.theTok)if(m="translucent",0>d){var g=this.isFloatParameter(b+1)?this.floatParameter(++b):3.4028235E38;h.setShapeTranslucency(c,
null,"translucent",g,null);null!=a&&(a.append(" translucent"),3.4028235E38!=g&&a.append(" ").appendF(g))}else h.setMeshDisplayProperty(c,b,h.theTok);else 1073742074==h.theTok?0<=d&&h.setMeshDisplayProperty(c,b,h.theTok):h.iToken--;d=Math.abs(d);for(g=0;g<d;g++)if(h.isColorParam(h.iToken+1)){var e=h.getArgbParam(++h.iToken);this.setShapeProperty(c,"colorRGB",Integer.$valueOf(e));null!=a&&a.append(" ").append(JU.Escape.escapeColor(e))}else if(h.iToken<b)this.invArg();else break;return m},"JU.SB,~N,~N,~N");
e(c$,"createFunction",function(a,b,c){var d=(new JS.ScriptEval).setViewer(this.vwr);try{d.compileScript(null,"function "+a+"("+b+") { return "+c+"}",!1);var h=new JU.Lst;for(a=0;a<b.length;a+=2)h.addLast(JS.SV.newV(3,Float.$valueOf(0)).setName(b.substring(a,a+1)));return w(-1,[d.aatoken[0][1].value,h])}catch(m){if(U(m,Exception))return null;throw m;}},"~S,~S,~S");e(c$,"getWithinDistanceVector",function(a,b,c,d,h){var m=new JU.Lst,g=Array(2);if(null==d){var e=JU.P3.new3(b,b,b),f=JU.P3.newP(c);f.sub(e);
e.add(c);g[0]=f;g[1]=e;m.addLast(c)}else c=this.vwr.ms.getBoxInfo(d,-Math.abs(b)),g[0]=c.getBoundBoxVertices()[0],g[1]=c.getBoundBoxVertices()[7],1==d.cardinality()&&m.addLast(this.vwr.ms.at[d.nextSetBit(0)]);1==m.size()&&!h&&(this.addShapeProperty(a,"withinDistance",Float.$valueOf(b)),this.addShapeProperty(a,"withinPoint",m.get(0)));this.addShapeProperty(a,h?"displayWithin":"withinPoints",w(-1,[Float.$valueOf(b),g,d,m]))},"JU.Lst,~N,JU.P3,JU.BS,~B");e(c$,"addShapeProperty",function(a,b,c){this.chk||
a.addLast(w(-1,[b,c]))},"JU.Lst,~S,~O");e(c$,"floatArraySetXYZ",function(a,b,c,d){var h=this.e,m=this.tokAt(a++);1073742195==m&&(m=this.tokAt(a++));(269484096!=m||0>=b)&&this.invArg();for(var g=JU.AU.newFloat3(b,-1),e=0;269484097!=m;)switch(m=this.getToken(a).tok,m){case 1073742195:case 269484097:continue;case 269484080:a++;break;case 269484096:g[e++]=this.floatArraySet(a,c,d);a=++h.iToken;m=0;e==b&&269484097!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return g},"~N,~N,~N,~N");e(c$,
"floatArraySet",function(a,b,c){var d=this.tokAt(a++);1073742195==d&&(d=this.tokAt(a++));269484096!=d&&this.invArg();for(var h=JU.AU.newFloat2(b),m=0;269484097!=d;)switch(d=this.getToken(a).tok,d){case 1073742195:case 269484097:continue;case 269484080:a++;break;case 269484096:a++;d=u(c,0);h[m++]=d;for(var g=0;g<c;g++)d[g]=this.floatParameter(a++),269484080==this.tokAt(a)&&a++;269484097!=this.tokAt(a++)&&this.invArg();d=0;m==b&&269484097!=this.tokAt(a)&&this.invArg();break;default:this.invArg()}return h},
"~N,~N,~N");e(c$,"initIsosurface",function(a){var b=this.e;this.setShapeProperty(a,"init",b.fullCommand);b.iToken=0;var c=this.tokAt(1),d=this.tokAt(2);if(12291==c||12291==d&&1048579==this.tokAt(++b.iToken))return this.setShapeProperty(a,"delete",null),b.iToken+=2,this.slen>b.iToken&&(this.setShapeProperty(a,"init",b.fullCommand),this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+")),null;b.iToken=1;return!b.setMeshDisplayProperty(a,0,c)&&(this.setShapeProperty(a,"thisID","+PREVIOUS_MESH+"),22!=a&&
this.setShapeProperty(a,"title",w(-1,[b.thisCommand])),1074790550!=c&&(269484209==d||269484209==c&&b.setMeshDisplayProperty(a,0,d)))?(a=this.setShapeId(a,1,!1),b.iToken++,a):null},"~N");e(c$,"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")});H("JU");sa(JU,"Triangulator");H("JU");K(["JU.Triangulator","JU.P3i"],"JU.TriangleData",["JU.AU","$.BS","$.P3","JU.BSUtil"],function(){c$=
wa(JU,"TriangleData",null,JU.Triangulator);j(c$,"intersectPlane",function(a,b,c){if(null==a)return b.addLast(JU.TriangleData.fullCubePolygon),b;var d=b.get(0);0!=c&&b.clear();for(var h=u(8,0),m=Array(12),g=0,e=0;8>e;e++)h[e]=a.x*d[e].x+a.y*d[e].y+a.z*d[e].z+a.w,0>h[e]&&(g|=JU.TriangleData.Pwr2[e]);a=JU.TriangleData.triangleTable2[g];if(null==a)return null;for(e=0;24>e;e+=2){var g=JU.TriangleData.edgeVertexes[e],f=JU.TriangleData.edgeVertexes[e+1],k=JU.P3.newP(d[f]);k.sub(d[g]);k.scale(h[g]/(h[g]-
h[f]));k.add(d[g]);m[e>>1]=k}if(0==c){c=new JU.BS;b.clear();for(e=0;e<a.length;e++)c.set(a[e]),2==e%4&&e++;e=JU.BSUtil.cardinalityOf(c);h=Array(e);b.addLast(h);d=p(12,0);for(e=g=0;e<a.length;e++)f=a[e],c.get(f)&&(c.clear(f),h[g]=m[f],d[f]=g++),2==e%4&&e++;m=JU.AU.newInt2(a.length>>2);b.addLast(m);for(e=0;e<a.length;e++)m[e>>2]=p(-1,[d[a[e++]],d[a[e++]],d[a[e++]],a[e]]);return b}for(e=0;e<a.length;e++)d=m[a[e++]],h=m[a[e++]],g=m[a[e++]],1==(c&1)&&b.addLast(w(-1,[d,h,g])),2==(c&2)&&(f=a[e],1==(f&1)&&
b.addLast(w(-1,[d,h])),2==(f&2)&&b.addLast(w(-1,[h,g])),4==(f&4)&&b.addLast(w(-1,[d,g])));return b},"JU.P4,JU.Lst,~N");R(c$,"Pwr2",p(-1,[1,2,4,8,16,32,64,128,256,512,1024,2048]),"fullCubePolygon",w(-1,[p(-1,[0,4,5,3]),p(-1,[5,1,0,3]),p(-1,[1,5,6,2]),p(-1,[6,2,1,3]),p(-1,[2,6,7,2]),p(-1,[7,3,2,3]),p(-1,[3,7,4,2]),p(-1,[4,0,3,2]),p(-1,[6,5,4,0]),p(-1,[4,7,6,0]),p(-1,[0,1,2,0]),p(-1,[2,3,0,0])]));c$.cubeVertexOffsets=c$.prototype.cubeVertexOffsets=w(-1,[JU.P3i.new3(0,0,0),JU.P3i.new3(1,0,0),JU.P3i.new3(1,
0,1),JU.P3i.new3(0,0,1),JU.P3i.new3(0,1,0),JU.P3i.new3(1,1,0),JU.P3i.new3(1,1,1),JU.P3i.new3(0,1,1)]);R(c$,"edgeVertexes",f(-1,[0,1,1,2,2,3,3,0,4,5,5,6,6,7,7,4,0,4,1,5,2,6,3,7]),"triangleTable2",w(-1,[null,f(-1,[0,8,3,7]),f(-1,[0,1,9,7]),f(-1,[1,8,3,6,9,8,1,5]),f(-1,[1,2,10,7]),f(-1,[0,8,3,7,1,2,10,7]),f(-1,[9,2,10,6,0,2,9,5]),f(-1,[2,8,3,6,2,10,8,1,10,9,8,3]),f(-1,[3,11,2,7]),f(-1,[0,11,2,6,8,11,0,5]),f(-1,[1,9,0,7,2,3,11,7]),f(-1,[1,11,2,6,1,9,11,1,9,8,11,3]),f(-1,[3,10,1,6,11,10,3,5]),f(-1,[0,
10,1,6,0,8,10,1,8,11,10,3]),f(-1,[3,9,0,6,3,11,9,1,11,10,9,3]),f(-1,[9,8,10,5,10,8,11,6]),f(-1,[4,7,8,7]),f(-1,[4,3,0,6,7,3,4,5]),f(-1,[0,1,9,7,8,4,7,7]),f(-1,[4,1,9,6,4,7,1,1,7,3,1,3]),f(-1,[1,2,10,7,8,4,7,7]),f(-1,[3,4,7,6,3,0,4,3,1,2,10,7]),f(-1,[9,2,10,6,9,0,2,3,8,4,7,7]),f(-1,[2,10,9,3,2,9,7,0,2,7,3,6,7,9,4,6]),f(-1,[8,4,7,7,3,11,2,7]),f(-1,[11,4,7,6,11,2,4,1,2,0,4,3]),f(-1,[9,0,1,7,8,4,7,7,2,3,11,7]),f(-1,[4,7,11,3,9,4,11,1,9,11,2,2,9,2,1,6]),f(-1,[3,10,1,6,3,11,10,3,7,8,4,7]),f(-1,[1,11,10,
6,1,4,11,0,1,0,4,3,7,11,4,5]),f(-1,[4,7,8,7,9,0,11,1,9,11,10,6,11,0,3,6]),f(-1,[4,7,11,3,4,11,9,4,9,11,10,6]),f(-1,[9,5,4,7]),f(-1,[9,5,4,7,0,8,3,7]),f(-1,[0,5,4,6,1,5,0,5]),f(-1,[8,5,4,6,8,3,5,1,3,1,5,3]),f(-1,[1,2,10,7,9,5,4,7]),f(-1,[3,0,8,7,1,2,10,7,4,9,5,7]),f(-1,[5,2,10,6,5,4,2,1,4,0,2,3]),f(-1,[2,10,5,3,3,2,5,1,3,5,4,2,3,4,8,6]),f(-1,[9,5,4,7,2,3,11,7]),f(-1,[0,11,2,6,0,8,11,3,4,9,5,7]),f(-1,[0,5,4,6,0,1,5,3,2,3,11,7]),f(-1,[2,1,5,3,2,5,8,0,2,8,11,6,4,8,5,5]),f(-1,[10,3,11,6,10,1,3,3,9,5,4,
7]),f(-1,[4,9,5,7,0,8,1,5,8,10,1,2,8,11,10,3]),f(-1,[5,4,0,3,5,0,11,0,5,11,10,6,11,0,3,6]),f(-1,[5,4,8,3,5,8,10,4,10,8,11,6]),f(-1,[9,7,8,6,5,7,9,5]),f(-1,[9,3,0,6,9,5,3,1,5,7,3,3]),f(-1,[0,7,8,6,0,1,7,1,1,5,7,3]),f(-1,[1,5,3,5,3,5,7,6]),f(-1,[9,7,8,6,9,5,7,3,10,1,2,7]),f(-1,[10,1,2,7,9,5,0,5,5,3,0,2,5,7,3,3]),f(-1,[8,0,2,3,8,2,5,0,8,5,7,6,10,5,2,5]),f(-1,[2,10,5,3,2,5,3,4,3,5,7,6]),f(-1,[7,9,5,6,7,8,9,3,3,11,2,7]),f(-1,[9,5,7,3,9,7,2,0,9,2,0,6,2,7,11,6]),f(-1,[2,3,11,7,0,1,8,5,1,7,8,2,1,5,7,3]),
f(-1,[11,2,1,3,11,1,7,4,7,1,5,6]),f(-1,[9,5,8,5,8,5,7,6,10,1,3,3,10,3,11,6]),f(-1,[5,7,0,1,5,0,9,6,7,11,0,1,1,0,10,5,11,10,0,1]),f(-1,[11,10,0,1,11,0,3,6,10,5,0,1,8,0,7,5,5,7,0,1]),f(-1,[11,10,5,3,7,11,5,5]),f(-1,[10,6,5,7]),f(-1,[0,8,3,7,5,10,6,7]),f(-1,[9,0,1,7,5,10,6,7]),f(-1,[1,8,3,6,1,9,8,3,5,10,6,7]),f(-1,[1,6,5,6,2,6,1,5]),f(-1,[1,6,5,6,1,2,6,3,3,0,8,7]),f(-1,[9,6,5,6,9,0,6,1,0,2,6,3]),f(-1,[5,9,8,3,5,8,2,0,5,2,6,6,3,2,8,5]),f(-1,[2,3,11,7,10,6,5,7]),f(-1,[11,0,8,6,11,2,0,3,10,6,5,7]),f(-1,
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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 $.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 $.Viewer".split(" "),function(){c$=C(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=null;G(this,arguments)},J.shapesurface,"Isosurface",J.shape.MeshCollection,
J.jvxl.api.MeshDataServer);W(c$,function(){this.isomeshes=Array(4);this.lcaoDir=new JU.P4;this.ptXY=new JU.P3i});j(c$,"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$,"initShape",function(){Xa(this,
J.shapesurface.Isosurface,"initShape",[]);this.myType="isosurface";this.newSg()});e(c$,"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$,"clearSg",function(){this.sg=null});j(c$,"setProperty",function(a,b,c){this.setPropI(a,b,c)},"~S,~O,JU.BS");e(c$,"setPropI",function(a,b,c){if("cache"===a){if(null!=this.currentMesh){var d=
this.currentMesh.thisID;c=this.currentMesh.modelIndex;this.vwr.cachePut("cache://isosurface_"+d,this.getPropI("jvxlDataXml"));this.deleteMeshI(this.currentMesh.index);this.setPropI("init",null,null);this.setPropI("thisID",d,null);this.setPropI("modelIndex",Integer.$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=p(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 m=JU.C.getHexCode(JU.C.getColixO(b));if(null!=this.thisMesh)this.setIsoMeshColor(this.thisMesh,m);else{h=this.getMeshList(JU.PT.isWild(this.previousMeshID)?this.previousMeshID:null,!1);for(d=h.size();0<=--d;)this.setIsoMeshColor(h.get(d),m)}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.updateCoordinates(b,null),this.thisMesh.altVertices=null);else if("refreshTrajectories"===a)for(d=this.meshCount;0<=--d;)null!=this.meshes[d].connections&&this.meshes[d].modelIndex==b[0].intValue()&&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.connections=this.connections:this.connections=this.currentMesh.connections=null);else if("cutoffRange"===a)this.cutoffRange=
b;else if("fixLattice"===a)null!=this.thisMesh&&this.thisMesh.fixLattice();else{if("slab"===a){if(V(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){b=this.vwr.fm.getBufferedReaderOrErrorMessageFromName(this.sg.params.fileName,null,!0,!0);if(V(b,String)){JU.Logger.error("Isosurface: could not open file "+
this.sg.params.fileName+" -- "+b);return}if(!V(b,java.io.BufferedReader))try{b=JU.Rdr.getBufferedReader(b,"ISO-8859-1")}catch(g){if(!U(g,java.io.IOException))throw g;}}}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(),1297090050==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)V(b,Integer)?(this.moNumber=b.intValue(),this.moLinearCombination=null):(this.moLinearCombination=b,this.moNumber=0),this.isColorExplicit||(this.isPhaseColored=
!0);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)V(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.getTestFlag(2)?2:0;if(null!=this.sg&&this.sg.setProp(a,b,c)){if(this.sg.isValid)return;a="delete"}if("init"===a)this.explicitID=!1,this.scriptAppendix="",d=V(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.connections&&(m=c.connections[0],m>=h+b?c.connections[0]=m-b:m>=
h&&(c.connections=null)),c.connections=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$,"setIsoMeshColor",function(a,b){a.jvxlData.baseColor=b;a.isColorSolid=!0;a.pcs=null;a.colorsExplicit=!1;a.colorEncoder=null;a.vertexColorMap=null},"J.shapesurface.IsosurfaceMesh,~S");
e(c$,"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$,"ensureMeshSource",function(){var a=null!=this.thisMesh.vertexSource;if(a)for(var b=this.thisMesh.vc;0<=--b;)if(0>this.thisMesh.vertexSource[b]){a=!1;break}if(!a){var a=this.thisMesh.vertexSource,c=this.thisMesh.vcs,b=
this.thisMesh.isColorSolid?this.thisMesh.colix:0;this.setProperty("init",null,null);this.setProperty("map",Boolean.FALSE,null);this.setProperty("property",u(this.vwr.ms.ac,0),null);0!=b&&(this.thisMesh.colorCommand="color isosurface "+JU.C.getHexCode(b),this.setProperty("color",Integer.$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$,"slabPolygons",function(a){this.thisMesh.getMeshSlicer().slabPolygons(a,
!1);this.thisMesh.reinitializeLightingAndColor(this.vwr)},"~A");e(c$,"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");j(c$,"getPropertyData",function(a,b){if("colorEncoder"===a){var c=
this.getMesh(b[0]);return null==c||null==(b[1]=c.colorEncoder)?!1:!0}if("intersectPlane"===a){c=this.getMesh(b[0]);if(null==c)return!1;b[3]=Integer.$valueOf(c.modelIndex);c.getMeshSlicer().getIntersection(0,b[1],null,b[2],null,null,null,!1,!1,135266319,!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");j(c$,"getProperty",function(a){return this.getPropI(a)},
"~S,~N");e(c$,"getPropI",function(a){var b=this.getPropMC(a);if(null!=b)return b;if("message"===a)return a="",24==this.shapeID&&(a+=" with cutoff="+this.jvxlData.cutoff),3.4028235E38!=this.jvxlData.dataMin&&(a+=" min="+this.jvxlData.dataMin+" max="+this.jvxlData.dataMax),a+="; "+JV.JC.shapeClassBases[this.shapeID].toLowerCase()+" count: "+this.getPropMC("count"),a+this.getPropI("dataRangeStr")+this.jvxlData.msg;if("dataRange"===a)return this.getDataRange();if("dataRangeStr"===a)return a=this.getDataRange(),
null!=a&&3.4028235E38!=a[0]&&a[0]!=a[1]?"\nisosurface full data range "+a[0]+" to "+a[1]+" with color scheme spanning "+a[2]+" to "+a[3]:"";if("moNumber"===a)return Integer.$valueOf(this.moNumber);if("moLinearCombination"===a)return this.moLinearCombination;if("nSets"===a)return Integer.$valueOf(null==this.thisMesh?0:this.thisMesh.nSets);if("area"===a)return null==this.thisMesh?Float.$valueOf(NaN):this.calculateVolumeOrArea(!0);if("volume"===a)return null==this.thisMesh?Float.$valueOf(NaN):this.calculateVolumeOrArea(!1);
if(null==this.thisMesh)return null;if("cutoff"===a)return Float.$valueOf(this.jvxlData.cutoff);if("minMaxInfo"===a)return u(-1,[this.jvxlData.dataMin,this.jvxlData.dataMax]);if("plane"===a)return this.jvxlData.jvxlPlane;if("contours"===a)return this.thisMesh.getContours();if("jvxlDataXml"===a||"jvxlMeshXml"===a)return b=null,this.jvxlData.slabInfo=null,"jvxlMeshXml"===a||this.jvxlData.vertexDataOnly||null!=this.thisMesh.bsSlabDisplay&&null==this.thisMesh.bsSlabGhost?(b=new J.jvxl.data.MeshData,this.fillMeshData(b,
1,null),b.polygonColorData=J.shapesurface.Isosurface.getPolygonColorData(b.pc,b.pcs,b.colorsExplicit?b.pis:null,b.bsSlabDisplay)):null!=this.thisMesh.bsSlabGhost&&(this.jvxlData.slabInfo=this.thisMesh.slabOptions.toString()),a=new JU.SB,this.getMeshCommand(a,this.thisMesh.index),this.thisMesh.setJvxlColorMap(!0),J.jvxl.data.JvxlCoder.jvxlGetFile(this.jvxlData,b,this.title,"",!0,1,a.toString(),null);if("jvxlFileInfo"===a)return this.thisMesh.setJvxlColorMap(!1),J.jvxl.data.JvxlCoder.jvxlGetInfo(this.jvxlData);
if("command"===a){a=new JU.SB;for(b=this.getMeshList(this.previousMeshID,!1).size();0<=--b;)this.getMeshCommand(a,b);return a.toString()}return null},"~S");e(c$,"getDataRange",function(){return null==this.thisMesh||null!=this.jvxlData.jvxlPlane&&null==this.thisMesh.colorEncoder?null:u(-1,[this.jvxlData.mappedDataMin,this.jvxlData.mappedDataMax,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue:this.jvxlData.valueMappedToRed,this.jvxlData.isColorReversed?this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToBlue])});
e(c$,"calculateVolumeOrArea",function(a){if(a){if(null!=this.thisMesh.calculatedArea)return this.thisMesh.calculatedArea}else if(null!=this.thisMesh.calculatedVolume)return this.thisMesh.calculatedVolume;var b=new J.jvxl.data.MeshData;this.fillMeshData(b,1,null);b.nSets=this.thisMesh.nSets;b.vertexSets=this.thisMesh.vertexSets;if(!a&&this.thisMesh.jvxlData.colorDensity)return a=this.thisMesh.jvxlData.voxelVolume,a*=null==this.thisMesh.bsSlabDisplay?this.thisMesh.vc:this.thisMesh.bsSlabDisplay.cardinality(),
this.thisMesh.calculatedVolume=Float.$valueOf(a);var c=J.jvxl.data.MeshData.calculateVolumeOrArea(b,this.thisMesh.jvxlData.thisSet,a,!1);0>=this.thisMesh.nSets&&(this.thisMesh.nSets=-b.nSets);a?this.thisMesh.calculatedArea=c:this.thisMesh.calculatedVolume=c;return c},"~B");c$.getPolygonColorData=e(c$,"getPolygonColorData",function(a,b,c,d){var h=null!=c;if(null==b&&null==c)return null;for(var m=new JU.SB,g=0,e=0,f=0,k=0,n=!1,q=0;q<a||!0==(n=!0);q++)if(n||null==d||d.get(q))if(n||(h?(k=c[q][4])!=f:
b[q]!=e)){0!=g&&m.append(" ").appendI(g).append(" ").appendI(h?f:0==e?0:JU.C.getArgb(e));if(n)break;h?f=k:e=b[q];g=1}else g++;m.append("\n");return m.toString()},"~N,~A,~A,JU.BS");j(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.$replace("\t"," "),d=JU.PT.rep(d,";#","; #"),h=d.indexOf("; #");0<=h&&(d=d.substring(0,h));null!=c.connections&&(d+=" connect "+JU.Escape.eAI(c.connections));d=JU.PT.trim(d,";");null!=c.linkedMesh&&(d+=" LINK");"lcaoCartoon"===this.myType&&0<=c.atomIndex&&(d+=" ATOMINDEX "+c.atomIndex);J.shape.Shape.appendCmd(a,d);h=this.myType+" ID "+JU.PT.esc(c.thisID);0<=c.jvxlData.thisSet&&
J.shape.Shape.appendCmd(a,h+" set "+(c.jvxlData.thisSet+1));null!=c.mat4&&J.shape.Shape.appendCmd(a,h+" move "+JU.Escape.matrixToScript(c.mat4));0!=c.scale3d&&J.shape.Shape.appendCmd(a,h+" scale3d "+c.scale3d);-2147483648!=c.jvxlData.slabValue&&J.shape.Shape.appendCmd(a,h+" slab "+c.jvxlData.slabValue);null!=c.slabOptions&&J.shape.Shape.appendCmd(a,c.slabOptions.toString());if("#"!=d.charAt(0)&&(this.allowMesh&&J.shape.Shape.appendCmd(a,c.getState(this.myType)),!c.isColorSolid&&(0==c.colorType&&JU.C.isColixTranslucent(c.colix))&&
J.shape.Shape.appendCmd(a,"color "+this.myType+" "+J.shape.Shape.getTranslucentLabel(c.colix)),null!=c.colorCommand&&(0==c.colorType&&!c.colorCommand.equals("#inherit;"))&&J.shape.Shape.appendCmd(a,c.colorCommand),d=c.isColorSolid&&null!=c.pcs,c.isColorSolid&&0==c.colorType&&!c.colorsExplicit&&!d?J.shape.Shape.appendCmd(a,J.shape.Shape.getColorCommandUnk(this.myType,c.colix,this.translucentAllowed)):c.jvxlData.isBicolorMap&&c.colorPhased&&J.shape.Shape.appendCmd(a,"color isosurface phase "+J.shape.Shape.encodeColor(c.jvxlData.minColorIndex)+
" "+J.shape.Shape.encodeColor(c.jvxlData.maxColorIndex)),null!=c.vertexColorMap))for(var m,c=c.vertexColorMap.entrySet().iterator();c.hasNext()&&((m=c.next())||1);)d=m.getValue(),d.isEmpty()||J.shape.Shape.appendCmd(a,"color "+this.myType+" "+JU.Escape.eBS(d)+" "+m.getKey())}},"JU.SB,~N");e(c$,"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(1679429641,
w(-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(V(d,JU.P4))return JU.TempArray.getSlabObjectType(135266319,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(),m=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!=m){var k=new JU.A4;0!=c.x?k.setVA(b,m):0!=c.y?k.setVA(e,m):k.setVA(a,m);c=(new JU.M3).setAA(k);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");j(c$,"invalidateTriangles",function(){this.thisMesh.invalidatePolygons()});j(c$,"setOutputChannel",function(a,b){a.setOutputChannel(b)},"javajs.api.GenericBinaryDocument,JU.OC");j(c$,"fillMeshData",function(a,b,c){if(null==a){if(null==this.thisMesh&&this.allocMesh(null,null),this.thisMesh.isMerged||this.thisMesh.clearType(this.myType,
this.sg.params.iAddGridPoints),this.thisMesh.connections=this.connections,this.thisMesh.colix=this.getDefaultColix(),this.thisMesh.colorType=this.colorType,this.thisMesh.meshColix=this.meshColix,this.isPhaseColored||this.thisMesh.jvxlData.isBicolorMap)this.thisMesh.isColorSolid=!1}else if(null==c&&(c=this.thisMesh),null!=c)switch(b){case 1:a.mergeVertexCount0=c.mergeVertexCount0;a.vs=c.vs;a.vertexSource=c.vertexSource;a.vvs=c.vvs;a.vc=c.vc;a.vertexIncrement=c.vertexIncrement;a.pc=c.pc;a.pis=c.pis;
a.pcs=c.pcs;a.bsSlabDisplay=c.bsSlabDisplay;a.bsSlabGhost=c.bsSlabGhost;a.slabColix=c.slabColix;a.slabMeshType=c.slabMeshType;a.polygonCount0=c.polygonCount0;a.vertexCount0=c.vertexCount0;a.slabOptions=c.slabOptions;a.colorsExplicit=c.colorsExplicit;break;case 2:if(null==c.vcs||c.vc>c.vcs.length)c.vcs=Z(c.vc,0);a.vcs=c.vcs;break;case 3:c.surfaceSet=a.surfaceSet;c.vertexSets=a.vertexSets;c.nSets=a.nSets;break;case 4:c.vs=a.vs,c.vvs=a.vvs,c.vc=a.vc,c.vertexIncrement=a.vertexIncrement,c.vertexSource=
a.vertexSource,c.pc=a.pc,c.pis=a.pis,c.pcs=a.pcs,c.bsSlabDisplay=a.bsSlabDisplay,c.bsSlabGhost=a.bsSlabGhost,c.slabColix=a.slabColix,c.slabMeshType=a.slabMeshType,c.polygonCount0=a.polygonCount0,c.vertexCount0=a.vertexCount0,c.mergeVertexCount0=a.mergeVertexCount0,c.slabOptions=a.slabOptions,c.colorsExplicit=a.colorsExplicit}},"J.jvxl.data.MeshData,~N,J.shapesurface.IsosurfaceMesh");j(c$,"notifySurfaceGenerationCompleted",function(){this.setMeshI();this.setBsVdw();this.thisMesh.insideOut=this.sg.isInsideOut();
this.thisMesh.vertexSource=this.sg.params.vertexSource;this.thisMesh.spanningVectors=this.sg.getSpanningVectors();this.thisMesh.calculatedArea=null;this.thisMesh.calculatedVolume=null;if(!this.thisMesh.isMerged)return this.thisMesh.initialize(this.sg.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.runScript("isosurface "+this.thisMesh.jvxlData.slabInfo);0<this.sg.params.psi_monteCarloCount&&(this.thisMesh.diameter=-1);return!1});j(c$,"notifySurfaceMappingCompleted",function(){this.thisMesh.isMerged||this.thisMesh.initialize(this.sg.isFullyLit()?1073741964:1073741958,null,this.sg.params.thePlane);this.setBsVdw();this.thisMesh.isColorSolid=
!1;this.thisMesh.colorDensity=this.jvxlData.colorDensity;this.thisMesh.volumeRenderPointSize=this.jvxlData.pointSize;this.thisMesh.colorEncoder=this.sg.params.colorEncoder;this.thisMesh.getContours();0!=this.thisMesh.jvxlData.nContours&&-1!=this.thisMesh.jvxlData.nContours&&(this.explicitContours=!0);this.explicitContours&&null!=this.thisMesh.jvxlData.jvxlPlane&&(this.thisMesh.havePlanarContours=!0);this.setPropertySuper("token",Integer.$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))});j(c$,"calculateGeodesicSurface",
function(a,b){return this.vwr.calculateSurface(a,b)},"JU.BS,~N");j(c$,"getSurfacePointIndexAndFraction",function(){return 0},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");j(c$,"addVertexCopy",function(a,b,c,d){return null!=this.cutoffRange&&(b<this.cutoffRange[0]||b>this.cutoffRange[1])?-1:null!=this.withinPoints&&!J.shape.Mesh.checkWithin(a,this.withinPoints,this.withinDistance2,this.isWithinNot)?-1:this.thisMesh.addVertexCopy(a,b,c,this.associateNormals,d)},"JU.T3,~N,~N,~B");j(c$,"addTriangleCheck",
function(a,b,c,d,h,m,g){return 0>a||0>b||0>c||m&&!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$,"setScriptInfo",function(a){a=null==a?this.sg.params.script:a;var b=null==a?-1:a.indexOf("; isosurface map");if(0==b)null!=this.thisMesh.scriptCommand&&(b=this.thisMesh.scriptCommand.indexOf("; isosurface map"),0<=b&&(this.thisMesh.scriptCommand=this.thisMesh.scriptCommand.substring(0,b)),this.thisMesh.scriptCommand+=
a);else if(this.thisMesh.title=this.sg.params.title,this.thisMesh.dataType=this.sg.params.dataType,this.thisMesh.scale3d=this.sg.params.scale3d,null!=a&&" "==a.charAt(0)&&(a=this.myType+" ID "+JU.PT.esc(this.thisMesh.thisID)+a,b=a.indexOf("; isosurface map")),this.thisMesh.scriptCommand=0<b&&0<this.scriptAppendix.length?a.substring(0,b)+this.scriptAppendix+a.substring(b):a+this.scriptAppendix,!this.explicitID&&null!=a&&0<=(b=a.indexOf("# ID=")))this.thisMesh.thisID=JU.PT.getQuotedStringAt(a,b)},"~S");
j(c$,"addRequiredFile",function(a){a=' # /*file*/"'+a+'"';0>this.scriptAppendix.indexOf(a)&&(this.scriptAppendix+=a)},"~S");e(c$,"setJvxlInfo",function(){if(this.sg.jvxlData!==this.jvxlData||this.sg.jvxlData!==this.thisMesh.jvxlData)this.jvxlData=this.thisMesh.jvxlData=this.sg.jvxlData});j(c$,"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");j(c$,"getPlane",
function(){return null},"~N");j(c$,"getValue",function(){return 0},"~N,~N,~N,~N");j(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 m=E(Math.floor(d*this.thisMesh.jvxlData.contourValues.length));if(0>m||m>this.thisMesh.jvxlData.contourValues.length)return;c=""+this.thisMesh.jvxlData.contourValues[m]}else{m=E(Math.floor(d*h.length));if(0>m||m>h.length)return;c=""+h[m].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");j(c$,"checkObjectClicked",function(a,b,c,d,h){if(!h||!this.vwr.isBound(c,18))return null;c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var m=h=-1,g=-2147483648,e=2147483647,f=0;f<this.meshCount;f++){var k=this.isomeshes[f];if(this.isPickable(k,d)&&(k=k.vs,null!=k))for(var n=k.length;0<=--n;){var q=
k[n];null!=q&&0<=this.coordinateInRange(a,b,q,c,this.ptXY)&&(this.ptXY.z<e&&(h=f,e=this.ptXY.z,m=n),this.ptXY.z>g&&(g=this.ptXY.z))}}if(0>h)return null;this.pickedMesh=this.isomeshes[h];this.setPropertySuper("thisID",this.pickedMesh.thisID,null);this.pickedVertex=m;a=new JU.P3;a.setT(this.pickedMesh.vs[this.pickedVertex]);this.pickedModel=this.pickedMesh.modelIndex;b=this.getPickedPoint(a,this.pickedModel);this.setStatusPicked(-4,a,b);return b},"~N,~N,~N,JU.BS,~B");e(c$,"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$,"findValue",function(a,b,c,d){c=100;this.vwr.gdata.isAntialiased()&&(a<<=1,b<<=1,c<<=1);for(var h=-1,m=null,g=null,e=0;e<this.meshCount;e++)if(g=this.isomeshes[e],this.isPickable(g,d)){var f=g.jvxlData.vContours,k=0>g.firstRealVertex?0:g.firstRealVertex,n=0;if(null!=f&&0<f.length){for(k=0;k<f.length;k++)for(var q=f[k],t=q.size()-1,r=6;r<t;r++){var j=q.get(r),p=this.coordinateInRange(a,
b,j,c,this.ptXY);0<=p&&(c=p,m=q,n=k,this.pickedMesh=g,this.pickedPt=j)}if(null!=m)return m.get(2).toString()+(JU.Logger.debugging?" "+n:"")}else if(null!=g.jvxlData.jvxlPlane&&null!=g.vvs){f=null==g.mat4&&0==g.scale3d?g.vs:g.getOffsetVertices(g.jvxlData.jvxlPlane);for(r=g.vc;--r>=k;)j=f[r],p=this.coordinateInRange(a,b,j,c,this.ptXY),0<=p&&(c=p,h=r,this.pickedMesh=g,this.pickedPt=j);if(-1!=h)break}else if(null!=g.vvs){if(null!=g.bsSlabDisplay)for(r=g.bsSlabDisplay.nextSetBit(0);0<=r;r=g.bsSlabDisplay.nextSetBit(r+
1)){f=g.pis[r];for(n=0;3>n;n++)j=g.vs[f[n]],p=this.coordinateInRange(a,b,j,c,this.ptXY),0<=p&&(c=p,h=f[n],this.pickedMesh=g,this.pickedPt=j)}else for(r=g.vc;--r>=k;)j=g.vs[r],p=this.coordinateInRange(a,b,j,c,this.ptXY),0<=p&&(c=p,h=r,this.pickedMesh=g,this.pickedPt=j);if(-1!=h)break}}return-1==h?null:(JU.Logger.debugging?"$"+g.thisID+"["+(h+1)+"] "+g.vs[h]+": ":g.thisID+": ")+g.vvs[h]},"~N,~N,~B,JU.BS");e(c$,"getCmd",function(a){var b=(new JU.SB).append("\n");this.getMeshCommand(b,a);return b.toString()},
"~N");R(c$,"MAX_OBJECT_CLICK_DISTANCE_SQUARED",100)});H("J.jvxl.data");K(null,"J.jvxl.data.JvxlCoder","java.lang.Float JU.BS $.Lst $.P3 $.PT $.SB $.XmlUtil J.jvxl.data.VolumeData JU.BSUtil $.C $.Escape $.Logger".split(" "),function(){c$=wa(J.jvxl.data,"JvxlCoder");c$.jvxlGetFile=e(c$,"jvxlGetFile",function(a,b,c){var d=a.getVoxelCounts();b.nPointsX=d[0];b.nPointsY=d[1];b.nPointsZ=d[2];b.jvxlVolumeDataXml=a.setVolumetricXml();return J.jvxl.data.JvxlCoder.jvxlGetFile(b,null,c,null,!0,1,null,null)},
"J.jvxl.data.VolumeData,J.jvxl.data.JvxlData,~A");c$.jvxlGetFile=e(c$,"jvxlGetFile",function(a,b,c,d,h,m,g,e){return J.jvxl.data.JvxlCoder.jvxlGetFileXml(a,b,c,d,h,m,g,e)},"J.jvxl.data.JvxlData,J.jvxl.data.MeshData,~A,~S,~B,~N,~S,~S");c$.jvxlGetFileXml=e(c$,"jvxlGetFileXml",function(a,b,c,d,h,m,g,e){var f=new JU.SB;if("TRAILERONLY".equals(d))return JU.XmlUtil.closeTag(f,"jvxlSurfaceSet"),JU.XmlUtil.closeTag(f,"jvxl"),f.toString();var k=null!=b,n="HEADERONLY".equals(d);if(h){JU.XmlUtil.openDocument(f);
JU.XmlUtil.openTagAttr(f,"jvxl",w(-1,["version","2.3","jmolVersion",a.version,"xmlns","http://jmol.org/jvxl_schema","xmlns:cml","http://www.xml-cml.org/schema"]));null!=a.jvxlFileTitle&&JU.XmlUtil.appendCdata(f,"jvxlFileTitle",null,"\n"+a.jvxlFileTitle);null!=a.moleculeXml&&f.append(a.moleculeXml);var q=k?null:a.jvxlVolumeDataXml;null==q&&(q=(new J.jvxl.data.VolumeData).setVolumetricXml());f.append(q);JU.XmlUtil.openTagAttr(f,"jvxlSurfaceSet",w(-1,["count",""+(0<m?m:1)]));if(n)return f.toString()}m=
k?"pmesh":null==a.jvxlPlane?"isosurface":"plane";null!=a.jvxlColorData&&0<a.jvxlColorData.length&&(m="mapped "+m);JU.XmlUtil.openTagAttr(f,"jvxlSurface",w(-1,["type",m]));f.append(J.jvxl.data.JvxlCoder.jvxlGetInfoData(a,k));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",k||null==a.jvxlPlane?null:null==a.mapLattice?w(-1,["plane",JU.Escape.eP4(a.jvxlPlane)]):w(-1,["plane",JU.Escape.eP4(a.jvxlPlane),"maplattice",JU.Escape.eP(a.mapLattice)]));if(k)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",w(-1,["baseColor",a.baseColor]));var t;for(c=a.vertexColorMap.entrySet().iterator();c.hasNext()&&((t=c.next())||1);)J.jvxl.data.JvxlCoder.appendEncodedBitSetTag(f,"jvxlColorMap",t.getValue(),-1,w(-1,["color",t.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$.appendEncodedBitSetTag=e(c$,"appendEncodedBitSetTag",function(a,b,c,d,h){0>d&&(d=JU.BSUtil.cardinalityOf(c));if(0!=d){var m=new JU.SB;m.append("\n ");J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(c,-1,m);JU.XmlUtil.appendTagObj(a,b,w(-1,[h,"bsEncoding","base90+35","count",""+d,"len",""+
c.length()]),J.jvxl.data.JvxlCoder.jvxlCompressString(m.toString(),!0))}},"JU.SB,~S,JU.BS,~N,~A");c$.jvxlSetCompressionRatio=e(c$,"jvxlSetCompressionRatio",function(a,b,c){a=a.toString();b=y(0<b.nBytes?b.nBytes/c:13*b.nPointsX*b.nPointsY*b.nPointsZ/c);return JU.PT.rep(a,'"not calculated"',0<b?'"'+b+':1"':'"?"')},"JU.SB,J.jvxl.data.JvxlData,~N");c$.appendXmlEdgeData=e(c$,"appendXmlEdgeData",function(a,b){JU.XmlUtil.appendTagObj(a,"jvxlEdgeData",w(-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,m){var g;if(!(null==b||0>(g=b.length-1)))d&&(g/=2),JU.XmlUtil.appendTagObj(a,"jvxlColorData",w(-1,["count",""+g,"encoding",c?"base90f"+(d?"2":"1"):"none","min",""+h,"max",""+m,"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"";var c=new JU.Lst,d=a.nSurfaceInts,h=b?0:a.jvxlEdgeData.length-1,m=null==a.jvxlColorData?-1:a.jvxlColorData.length-1;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+m+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<m&&J.jvxl.data.JvxlCoder.addAttrib(c,"\n  nBytesUncompressedColorData",""+m)}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<m&&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<m&&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;m=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",""+m),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(w(-1,[b,c]))},"JU.Lst,~S,~S");c$.jvxlEncodeContourData=e(c$,"jvxlEncodeContourData",
function(a,b){JU.XmlUtil.openTagAttr(b,"jvxlContourData",w(-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 m=a[c].get(1);J.jvxl.data.JvxlCoder.jvxlEncodeBitSetBuffer(m,d,h);JU.XmlUtil.appendTagObj(b,"jvxlContour",w(-1,["index",""+c,"value",""+a[c].get(2),"color",JU.Escape.escapeColor(a[c].get(4)[0]),"count",""+m.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),m=0,g=d.length(),e=0,f=" ",k=" ",n=h.nextSetBit(0);0<=n;n=h.nextSetBit(n+1)){for(var q=b[n];m<g&&!JU.PT.isDigit(f=d.charAt(m++)););for(e=f.charCodeAt(0)-48;m<g&&JU.PT.isWhitespace(f=d.charAt(m++)););for(;m<g&&JU.PT.isWhitespace(k=d.charAt(m++)););var t=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(f.charCodeAt(0),
35,90,0),r=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(k.charCodeAt(0),35,90,0),j,p;0==(e&1)?(j=q[1],p=e=q[2],q=q[0]):(j=q[0],p=q[1],0!=(e&2)?(e=p,q=q[2]):(e=q[2],q=j));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,j,p,t));a.addLast(J.jvxl.data.JvxlCoder.getContourPoint(c,e,q,r))}},"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,m=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 k=a.mappedDataMin,n=a.mappedDataMax,q=new JU.SB,j=new JU.SB;b.length<f&&System.out.println("JVXLCOLOR OHOHO");for(var r=0;r<f;r++){var p=b[r];Float.isNaN(p)&&(p=k);d&&(p=0<p?0.999:-0.999);c?J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(p,k,n,h,m,q,j):q.appendC(J.jvxl.data.JvxlCoder.jvxlValueAsCharacter(p,e,g,h,m))}a.jvxlColorData=q.appendSB(j).appendC("\n").toString()}},"J.jvxl.data.JvxlData,~A");c$.appendXmlVertexOnlyData=e(c$,"appendXmlVertexOnlyData",function(a,b,c,d){var h=p(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,m){for(var g=new JU.SB,e=new JU.SB,f=1,k=0,n=0,q=!1,j=0,r=null!=d,p=0;p<c;)if(null==b[p]||r&&!d.get(p))p++;else{var u=b[p][k],u=0<h[u]?h[u]:h[u]=++n,y=u-f,f=u;0==y?(g.appendC("!"),q=!1):32<y?(q&&
g.appendC("+"),g.appendI(y),q=!0):-32>y?(g.appendI(y),q=!0):(g.appendC(String.fromCharCode(92+y)),q=!1);0==++k%3&&(e.appendI(b[p][3]),k=0,p++,j++)}if(0==g.length())return!0;JU.XmlUtil.appendTagObj(a,"jvxlTriangleData",w(-1,["count",""+j,"encoding","jvxltdiff","data",J.jvxl.data.JvxlCoder.jvxlCompressString(g.toString(),m)]),null);JU.XmlUtil.appendTagObj(a,"jvxlTriangleEdgeData",w(-1,["count",""+j,"encoding","jvxlsc","data",J.jvxl.data.JvxlCoder.jvxlCompressString(e.toString(),m)]),null);return!0},
"JU.SB,~A,~N,JU.BS,~A,~B");c$.appendXmlVertexData=e(c$,"appendXmlVertexData",function(a,b,c,d,h,m,g,e,f,k,n,q){var j=b.colorFractionBase,r=b.colorFractionRange,L,u=b.boundingBox[0],y=b.boundingBox[1],E=new JU.SB,C=new JU.SB,B=null,D=null!=f;if(0<e){D&&(e=f.cardinality());for(var D=!1,B=p(m,0),A=0;A<m;A++)0<c[A]&&(B[c[A]-1]=A)}for(A=c=0;A<m;A++)if(!D||f.get(A))c++,L=d[0==e?A:B[A]],J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(L.x,u.x,y.x,j,r,E,C),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(L.y,u.y,y.y,
j,r,E,C),J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(L.z,u.z,y.z,j,r,E,C);E.appendSB(C);JU.XmlUtil.appendTagObj(a,"jvxlVertexData",w(-1,["count",""+c,"min",JU.Escape.eP(u),"max",JU.Escape.eP(y),"encoding","base90xyz2","data",J.jvxl.data.JvxlCoder.jvxlCompressString(E.toString(),q)]),null);null!=g&&JU.XmlUtil.appendTagObj(a,"jvxlPolygonColorData",w(-1,["encoding","jvxlnc","count",""+e]),"\n"+g);if(n){E=new JU.SB;C=new JU.SB;if(null==k)for(A=0;A<m;A++){if(!D||f.get(A))J.jvxl.data.JvxlCoder.jvxlAppendCharacter2(h[0==
e?A:B[A]],b.mappedDataMin,b.mappedDataMax,j,r,E,C)}else{d=0;E.appendI(c).append(" ");for(A=0;A<m;A++)if(!D||f.get(A))h=k[0==e?A:B[A]],h==d?h=0:d=h,E.appendI(h),E.append(" ")}J.jvxl.data.JvxlCoder.appendXmlColorData(a,E.appendSB(C).append("\n").toString(),null==k,!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=E(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,m,g){a=b==c?a:(a-b)/(c-b);b=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a,d,h);m.appendC(b);a-=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b.charCodeAt(0),d,h,0);g.appendC(J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(a*
h,d,h))},"~N,~N,~N,~N,~N,JU.SB,JU.SB");c$.jvxlFractionFromCharacter=e(c$,"jvxlFractionFromCharacter",function(a,b,c,d){if(a==b+c)return NaN;a<b&&(a=92);a=(a-b+d)/c;return 0>a?0:1<a?0.999999:a},"~N,~N,~N,~N");c$.jvxlFractionFromCharacter2=e(c$,"jvxlFractionFromCharacter2",function(a,b,c,d){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(a,c,d,0);b=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter(b,c,d,0.5);return a+b/d},"~N,~N,~N,~N");c$.jvxlValueAsCharacter=e(c$,"jvxlValueAsCharacter",function(a,
b,c,d,h){return J.jvxl.data.JvxlCoder.jvxlFractionAsCharacterRange(b==c?a:(a-b)/(c-b),d,h)},"~N,~N,~N,~N,~N");c$.jvxlValueFromCharacter2=e(c$,"jvxlValueFromCharacter2",function(a,b,c,d,h,m){a=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(a,b,h,m);return d==c?a:c+a*(d-c)},"~N,~N,~N,~N,~N,~N");c$.jvxlEncodeBitSet0=e(c$,"jvxlEncodeBitSet0",function(a,b,c){var d=0,h=-1,m=0;0>b&&(b=a.length());for(var g=0,e=!1,f=b-1,k=0;k<b;++k)e==a.get(k)?d++:(d==h&&k!=f?m++:(0<m&&(c.appendC(" ").appendI(-m),m=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=0,m=!1;0>b&&(b=a.length());if(0==b)return 0;c.append("-");for(var e=0;e<b;++e)m==a.get(e)?d++:(J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,d,35,90),
h++,d=1,m=!m);J.jvxl.data.JvxlCoder.jvxlAppendEncodedNumber(c,d,35,90);c.appendC("\n");return h},"JU.BS,~N,JU.SB");c$.jvxlAppendEncodedNumber=e(c$,"jvxlAppendEncodedNumber",function(a,b,c,d){var h=b<d;for(0==b?a.appendC(String.fromCharCode(c)):h||a.appendC(String.fromCharCode(c+d));0<b;){var e=E(b/d);b=c+b-e*d;92==b&&(b=33);a.appendC(String.fromCharCode(b));b=e}h||a.append(" ")},"JU.SB,~N,~N,~N");c$.jvxlDecodeBitSetRange=e(c$,"jvxlDecodeBitSetRange",function(a,b,c){for(var d=new JU.BS,h=0,e=0,g=!1,
f=p(1,0);-2147483648!=(h=J.jvxl.data.JvxlCoder.jvxlParseEncodedInt(a,b,c,f));)g&&d.setBits(e,e+h),e+=h,g=!g;return d},"~S,~N,~N");c$.jvxlParseEncodedInt=e(c$,"jvxlParseEncodedInt",function(a,b,c,d){var h=!1,e=0,g=d[0],f=a.length;if(0>g)return-2147483648;for(;g<f&&JU.PT.isWhitespace(a.charAt(g));)++g;if(g>=f)return-2147483648;var j=1,k=a.charCodeAt(g)==b+c;for(k&&g++;g<f&&!JU.PT.isWhitespace(a.charAt(g));){h=a.charCodeAt(g);h<b&&(h=92);e+=(h-b)*j;h=!0;++g;if(!k)break;j*=c}h||(e=-2147483648);d[0]=g;
return e},"~S,~N,~N,~A");c$.jvxlDecodeBitSet=e(c$,"jvxlDecodeBitSet",function(a){if(a.startsWith("-"))return J.jvxl.data.JvxlCoder.jvxlDecodeBitSetRange(J.jvxl.data.JvxlCoder.jvxlDecompressString(a.substring(1)),35,90);for(var b=new JU.BS,c=0,d=0,h=0,e=0,g=!1,f=p(1,0);;){c=0>h++?c:JU.PT.parseIntNext(a,f);if(-2147483648==c)break;0>c?(h=c,c=d):(g&&b.setBits(e,e+c),e+=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,e=!1,g=0,f=a.length,j=0;j<=f;j++){var k=j==f?"\x00":a.charAt(j);switch(k){case "\n":case "\r":continue;case "&":case "<":h=b;break;default:h=!1}if(k==d)++g,k="\x00";else if(0<g||e){if(4>g&&!e||" "==d||"\t"==d)for(;0<=--g;)c.appendC(d);else e?e=!1:c.appendC("~"),c.appendI(g),c.appendC(" ");g=0}"\x00"!=k&&(h?(e=!0,c.appendC("~"),d=k,k=String.fromCharCode(k.charCodeAt(0)-1)):d=k,c.appendC(k))}return c.toString()},"~S,~B");c$.jvxlDecompressString=e(c$,"jvxlDecompressString",function(a){if(0>
a.indexOf("~"))return a;for(var b=new JU.SB,c="\x00",d=p(1,0),h=0;h<a.length;h++){var e=a.charAt(h);if("~"==e)switch(d[0]=++h,e=a.charAt(h)){case ";":case "%":d[0]++,b.appendC(c=String.fromCharCode(e.charCodeAt(0)+1));case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":h=JU.PT.parseIntNext(a,d);for(e=0;e<h;e++)b.appendC(c);h=d[0];continue;case "~":--h;break;default:JU.Logger.error("Error uncompressing string "+a.substring(0,h)+"?")}b.appendC(e);c=e}return b.toString()},
"~S");c$.jvxlCreateHeaderWithoutTitleOrAtoms=e(c$,"jvxlCreateHeaderWithoutTitleOrAtoms",function(a,b){J.jvxl.data.JvxlCoder.jvxlCreateHeader(a,b)},"J.jvxl.data.VolumeData,JU.SB");c$.jvxlCreateHeader=e(c$,"jvxlCreateHeader",function(a,b){a.setVolumetricXml();0==b.length()&&b.append("Line 1\nLine 2\n")},"J.jvxl.data.VolumeData,JU.SB");R(c$,"JVXL_VERSION1","2.0","JVXL_VERSION_XML","2.3","CONTOUR_NPOLYGONS",0,"CONTOUR_BITSET",1,"CONTOUR_VALUE",2,"CONTOUR_COLIX",3,"CONTOUR_COLOR",4,"CONTOUR_FDATA",5,"CONTOUR_POINTS",
6,"defaultEdgeFractionBase",35,"defaultEdgeFractionRange",90,"defaultColorFractionBase",35,"defaultColorFractionRange",90)});H("J.jvxl.data");K(["J.api.VolumeDataInterface","JU.M3","$.P3","$.V3"],"J.jvxl.data.VolumeData",["java.lang.Float","java.util.Hashtable","JU.SB","JU.Escape","$.Logger"],function(){c$=C(function(){this.sr=null;this.doIterate=!0;this.voxelCounts=this.volumetricVectors=this.origin=this.volumetricOrigin=null;this.nPoints=0;this.volumetricVectorLengths=this.voxelMap=this.voxelData=
null;this.yzCount=this.minToPlaneDistance=this.maxVectorLength=0;this.thePlane=this.inverseMatrix=this.volumetricMatrix=this.unitVolumetricVectors=null;this.thePlaneNormalMag=0;this.mappingPlane=this.xmlData=this.ptXyzTemp=null;this.voxelVolume=this.maxGrid=this.minGrid=this.mappingPlaneNormalMag=0;this.spanningVectors=null;this.isSquared=this.isPeriodic=!1;this.ptTemp=this.edgeVector=null;G(this,arguments)},J.jvxl.data,"VolumeData",null,J.api.VolumeDataInterface);W(c$,function(){this.volumetricOrigin=
new JU.P3;this.origin=u(3,0);this.volumetricVectors=Array(3);this.voxelCounts=p(3,0);this.volumetricVectorLengths=u(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});j(c$,"getVoxelData",function(){return this.voxelData});j(c$,"setVoxelDataAsArray",function(a){this.voxelData=a;null!=a&&(this.sr=null)},"~A");e(c$,"hasPlane",function(){return null!=this.thePlane});Q(c$,function(){this.volumetricVectors[0]=
new JU.V3;this.volumetricVectors[1]=new JU.V3;this.volumetricVectors[2]=new JU.V3;this.unitVolumetricVectors[0]=new JU.V3;this.unitVolumetricVectors[1]=new JU.V3;this.unitVolumetricVectors[2]=new JU.V3});e(c$,"setMappingPlane",function(a){this.mappingPlane=a;null!=a&&(this.mappingPlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z))},"JU.P4");e(c$,"distanceToMappingPlane",function(a){return(this.mappingPlane.x*a.x+this.mappingPlane.y*a.y+this.mappingPlane.z*a.z+this.mappingPlane.w)/this.mappingPlaneNormalMag},
"JU.T3");j(c$,"setVolumetricOrigin",function(a,b,c){this.volumetricOrigin.set(a,b,c)},"~N,~N,~N");j(c$,"getOriginFloat",function(){return this.origin});e(c$,"getYzCount",function(){this.minGrid=this.volumetricVectors[0].length();this.minGrid=Math.min(this.minGrid,this.volumetricVectors[1].length());this.minGrid=Math.min(this.minGrid,this.volumetricVectors[2].length());this.maxGrid=this.volumetricVectors[0].length();this.maxGrid=Math.max(this.maxGrid,this.volumetricVectors[1].length());this.maxGrid=
Math.max(this.maxGrid,this.volumetricVectors[2].length());this.nPoints=this.voxelCounts[0]*this.voxelCounts[1]*this.voxelCounts[2];return this.yzCount=this.voxelCounts[1]*this.voxelCounts[2]});j(c$,"getVolumetricVectorLengths",function(){return this.volumetricVectorLengths});j(c$,"setVolumetricVector",function(a,b,c,d){this.volumetricVectors[a].x=b;this.volumetricVectors[a].y=c;this.volumetricVectors[a].z=d;this.setUnitVectors()},"~N,~N,~N,~N");j(c$,"getVoxelCounts",function(){return this.voxelCounts});
j(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=E(a/this.yzCount);a-=b*this.yzCount;var c=E(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=E(a/this.yzCount);a-=c*this.yzCount;var d=E(a/this.voxelCounts[2]);this.voxelPtToXYZ(c,
d,a-d*this.voxelCounts[2],b)},"~N,JU.P3");e(c$,"setVoxelData",function(a,b){var c=E(a/this.yzCount);a-=c*this.yzCount;var d=E(a/this.voxelCounts[2]);this.voxelData[c][d][a-d*this.voxelCounts[2]]=b},"~N,~N");e(c$,"setVoxelMap",function(){this.voxelMap=new java.util.Hashtable;this.getYzCount()});e(c$,"setMatrix",function(){for(var a=0;3>a;a++)this.volumetricMatrix.setColumnV(a,this.volumetricVectors[a]);try{this.inverseMatrix.invertM(this.volumetricMatrix)}catch(b){if(U(b,Exception))return JU.Logger.error("VolumeData error setting matrix -- bad unit vectors? "),
!1;throw b;}return!0});j(c$,"transform",function(a,b){this.volumetricMatrix.rotate2(a,b)},"JU.V3,JU.V3");j(c$,"setPlaneParameters",function(a){this.thePlane=a;this.thePlaneNormalMag=Math.sqrt(a.x*a.x+a.y*a.y+a.z*a.z)},"JU.P4");j(c$,"calcVoxelPlaneDistance",function(a,b,c){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.distancePointToPlane(this.ptXyzTemp)},"~N,~N,~N");e(c$,"getToPlaneParameter",function(){return Math.sqrt(this.thePlane.x*this.thePlane.x+this.thePlane.y*this.thePlane.y+this.thePlane.z*
this.thePlane.z)*this.minToPlaneDistance});e(c$,"isNearPlane",function(a,b,c,d){this.voxelPtToXYZ(a,b,c,this.ptXyzTemp);return this.thePlane.x*this.ptXyzTemp.x+this.thePlane.y*this.ptXyzTemp.y+this.thePlane.z*this.ptXyzTemp.z+this.thePlane.w<d},"~N,~N,~N,~N");j(c$,"distancePointToPlane",function(a){return(this.thePlane.x*a.x+this.thePlane.y*a.y+this.thePlane.z*a.z+this.thePlane.w)/this.thePlaneNormalMag},"JU.T3");j(c$,"voxelPtToXYZ",function(a,b,c,d){d.scaleAdd2(a,this.volumetricVectors[0],this.volumetricOrigin);
d.scaleAdd2(b,this.volumetricVectors[1],d);d.scaleAdd2(c,this.volumetricVectors[2],d)},"~N,~N,~N,JU.T3");e(c$,"setUnitVectors",function(){this.maxVectorLength=0;this.voxelVolume=1;for(var a=0;3>a;a++){var b=this.volumetricVectorLengths[a]=this.volumetricVectors[a].length();if(0==b)return!1;b>this.maxVectorLength&&(this.maxVectorLength=b);this.voxelVolume*=b;this.unitVolumetricVectors[a].setT(this.volumetricVectors[a]);this.unitVolumetricVectors[a].normalize()}this.minToPlaneDistance=2*this.maxVectorLength;
this.origin[0]=this.volumetricOrigin.x;this.origin[1]=this.volumetricOrigin.y;this.origin[2]=this.volumetricOrigin.z;this.spanningVectors=Array(4);this.spanningVectors[0]=JU.V3.newV(this.volumetricOrigin);for(a=0;3>a;a++)b=this.spanningVectors[a+1]=new JU.V3,b.scaleAdd2(this.voxelCounts[a]-1,this.volumetricVectors[a],b);return this.setMatrix()});j(c$,"xyzToVoxelPt",function(a,b,c,d){this.ptXyzTemp.set(a,b,c);this.ptXyzTemp.sub(this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);d.set(Math.round(this.ptXyzTemp.x),
Math.round(this.ptXyzTemp.y),Math.round(this.ptXyzTemp.z))},"~N,~N,~N,JU.T3i");j(c$,"lookupInterpolatedVoxelValue",function(a,b){if(null!=this.mappingPlane)return this.distanceToMappingPlane(a);if(null!=this.sr){var c=this.sr.getValueAtPoint(a,b);return this.isSquared?c*c:c}this.ptXyzTemp.sub2(a,this.volumetricOrigin);this.inverseMatrix.rotate(this.ptXyzTemp);var d,h=this.indexLower(this.ptXyzTemp.x,d=this.voxelCounts[0]-1),e=this.indexUpper(this.ptXyzTemp.x,h,d),g=this.indexLower(this.ptXyzTemp.y,
d=this.voxelCounts[1]-1),f=this.indexUpper(this.ptXyzTemp.y,g,d),c=this.indexLower(this.ptXyzTemp.z,d=this.voxelCounts[2]-1),j=this.indexUpper(this.ptXyzTemp.z,c,d);d=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-h),this.mantissa(this.ptXyzTemp.y-g),this.getVoxelValue(h,g,c),this.getVoxelValue(e,g,c),this.getVoxelValue(h,f,c),this.getVoxelValue(e,f,c));h=J.jvxl.data.VolumeData.getFractional2DValue(this.mantissa(this.ptXyzTemp.x-h),this.mantissa(this.ptXyzTemp.y-g),this.getVoxelValue(h,
g,j),this.getVoxelValue(e,g,j),this.getVoxelValue(h,f,j),this.getVoxelValue(e,f,j));return d+this.mantissa(this.ptXyzTemp.z-c)*(h-d)},"JU.T3,~B");e(c$,"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$,"indexLower",function(a,b){if(this.isPeriodic&&0<b){for(;0>a;)a+=b;for(;a>=b;)a-=b;return E(Math.floor(a))}if(0>a)return 0;var c=E(Math.floor(a));return c>b?b:c},"~N,~N");e(c$,"indexUpper",function(a,b,c){return!this.isPeriodic&&0>a||b==c?b:b+1},"~N,~N,~N");e(c$,"offsetCenter",function(a){var b=new JU.P3;b.scaleAdd2((this.voxelCounts[0]-1)/2,this.volumetricVectors[0],b);b.scaleAdd2((this.voxelCounts[1]-1)/2,this.volumetricVectors[1],b);b.scaleAdd2((this.voxelCounts[2]-
1)/2,this.volumetricVectors[2],b);this.volumetricOrigin.sub2(a,b)},"JU.P3");j(c$,"setDataDistanceToPlane",function(a){this.setPlaneParameters(a);a=this.voxelCounts[0];var b=this.voxelCounts[1],c=this.voxelCounts[2];this.voxelData=u(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");j(c$,"filterData",function(a,b){var c=!Float.isNaN(b);if(null!=this.sr)this.isSquared=a;else{var d=this.voxelCounts[0],h=this.voxelCounts[1],
e=this.voxelCounts[2];if(a)for(var g=0;g<d;g++)for(var f=0;f<h;f++)for(var j=0;j<e;j++)this.voxelData[g][f][j]*=this.voxelData[g][f][j];if(c)for(g=0;g<d;g++)for(f=0;f<h;f++)for(j=0;j<e;j++)this.voxelData[g][f][j]=b-this.voxelData[g][f][j]}},"~B,~N");j(c$,"capData",function(a,b){if(null!=this.voxelData){var c=this.voxelCounts[0],d=this.voxelCounts[1],h=this.voxelCounts[2],e=JU.V3.new3(a.x,a.y,a.z);e.normalize();for(var g=0;g<c;g++)for(var f=0;f<d;f++)for(var j=0;j<h;j++){var k=this.voxelData[g][f][j]-
b;this.voxelPtToXYZ(g,f,j,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>k)this.voxelData[g][f][j]=n}}},"JU.P4,~N");e(c$,"setVolumetricXml",function(){var a=new JU.SB;if(0==this.voxelCounts[0])a.append("<jvxlVolumeData>\n");else{a.append('<jvxlVolumeData origin="'+JU.Escape.eP(this.volumetricOrigin)+'">\n');for(var b=0;3>b;b++)a.append('<jvxlVolumeVector type="'+b+'" count="'+this.voxelCounts[b]+'" vector="'+JU.Escape.eP(this.volumetricVectors[b])+
'"></jvxlVolumeVector>\n')}a.append("</jvxlVolumeData>\n");return this.xmlData=a.toString()});e(c$,"setVoxelMapValue",function(a,b,c,d){null!=this.voxelMap&&this.voxelMap.put(Integer.$valueOf(this.getPointIndex(a,b,c)),Float.$valueOf(d))},"~N,~N,~N,~N");e(c$,"calculateFractionalPoint",function(a,b,c,d,h,e){var g=h-d,f=(a-d)/g;this.edgeVector.sub2(c,b);e.scaleAdd2(f,this.edgeVector,b);if(null==this.sr||!this.doIterate||h==d||0.01>f||0.99<f||0.01>this.edgeVector.length())return a;b=0;this.ptTemp.setT(e);
c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1);for(h=NaN;10>++b;){var j=(c-d)/g;if(0>j||1<j)break;j=(a-c)/g/2;f+=j;if(0>f||1<f)break;e.setT(this.ptTemp);h=c;if(0.005>Math.abs(j))break;this.ptTemp.scaleAdd2(j,this.edgeVector,e);c=this.lookupInterpolatedVoxelValue(this.ptTemp,!1)}return h},"~N,JU.P3,JU.P3,~N,~N,JU.P3")});H("J.jvxl.data");K(null,"J.jvxl.data.JvxlData",["java.lang.Float","JU.SB","J.jvxl.data.JvxlCoder"],function(){c$=C(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.vertexDataOnly=this.isCutoffAbsolute=this.isTruncated=this.isBicolorMap=this.isContoured=this.isXLowToHigh=
this.insideOut=this.dataXYReversed=!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;G(this,arguments)},J.jvxl.data,
"JvxlData");W(c$,function(){this.jvxlExcluded=Array(4)});Q(c$,function(){});e(c$,"clear",function(){this.allowVolumeRender=!0;this.jvxlVolumeDataXml=this.jvxlColorData=this.jvxlEdgeData=this.jvxlSurfaceData="";this.colorScheme=this.color=null;this.colorDensity=!1;this.pointSize=NaN;this.contourColors=this.contourColixes=this.contourValuesUsed=this.contourValues=null;this.isSlabbable=!1;this.meshColor=this.mapLattice=null;this.msg="";this.nVertexColors=this.nPointsX=0;this.slabInfo=this.fixedLattice=
null;this.thisSet=this.slabValue=-2147483648;this.rendering=null;this.thisContour=-1;this.translucency=0;this.vertexColors=this.vertexColorMap=this.vContours=null;this.voxelVolume=0});e(c$,"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$,"updateSurfaceData",function(a,b,c,d,h){if(0==a.length)return"";a=a.toCharArray();for(var e=0,g=0;e<c;e+=d,g++)Float.isNaN(b[e])&&(a[g]=h);return String.copyValueOf(a)},
"~S,~A,~N,~N,~S")});H("J.jvxl.data");K(["JU.MeshSurface"],"J.jvxl.data.MeshData",["java.lang.Float","java.util.Arrays","JU.AU","$.BS","$.V3"],function(){c$=C(function(){this.setsSuccessful=!1;this.vertexIncrement=1;this.polygonColorData=null;na("J.jvxl.data.MeshData.SSet")||J.jvxl.data.MeshData.$MeshData$SSet$();na("J.jvxl.data.MeshData.SortSet")||J.jvxl.data.MeshData.$MeshData$SortSet$();G(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$,"getSurfaceSetForLevel",function(a){0==a&&(this.surfaceSet=Array(100),this.nSets=0);this.setsSuccessful=!0;for(var b=0;b<this.pc;b++)if(null!=this.pis[b]&&(null==this.bsSlabDisplay||this.bsSlabDisplay.get(b))){var c=this.pis[b],d=this.findSet(c[0]),h=this.findSet(c[1]),e=this.findSet(c[2]);0>d&&0>h&&0>e?this.createSet(c[0],c[1],c[2]):
d==h&&h==e||(0<=d?(this.surfaceSet[d].set(c[1]),this.surfaceSet[d].set(c[2]),0<=h&&h!=d&&this.mergeSets(d,h),0<=e&&(e!=d&&e!=h)&&this.mergeSets(d,e)):0<=h?(this.surfaceSet[h].set(c[0]),this.surfaceSet[h].set(c[2]),0<=e&&e!=h&&this.mergeSets(h,e)):(this.surfaceSet[e].set(c[0]),this.surfaceSet[e].set(c[1])))}for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&c++;d=Array(this.surfaceSet.length);for(b=c=0;b<this.nSets;b++)null!=this.surfaceSet[b]&&(d[c++]=this.surfaceSet[b]);this.nSets=c;this.surfaceSet=
d;!this.setsSuccessful&&2>a&&this.getSurfaceSetForLevel(a+1);if(0==a){a=Array(this.nSets);for(b=0;b<this.nSets;b++)a[b]=ma(J.jvxl.data.MeshData.SSet,this,null,this.surfaceSet[b]);java.util.Arrays.sort(a,ma(J.jvxl.data.MeshData.SortSet,this,null));for(b=0;b<this.nSets;b++)this.surfaceSet[b]=a[b].bs;this.setVertexSets(!1)}return this.surfaceSet},"~N");e(c$,"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=p(this.vc,0);for(c=0;c<this.nSets;c++)for(b=this.surfaceSet[c].nextSetBit(0);0<=b;b=this.surfaceSet[c].nextSetBit(b+1))this.vertexSets[b]=c}},"~B");e(c$,"findSet",function(a){for(var b=0;b<this.nSets;b++)if(null!=this.surfaceSet[b]&&this.surfaceSet[b].get(a))return b;
return-1},"~N");e(c$,"createSet",function(a,b,c){var d;for(d=0;d<this.nSets&&null!=this.surfaceSet[d];d++);d==this.surfaceSet.length&&(this.surfaceSet=JU.AU.ensureLength(this.surfaceSet,this.surfaceSet.length+100));this.surfaceSet[d]=new JU.BS;this.surfaceSet[d].set(a);this.surfaceSet[d].set(b);this.surfaceSet[d].set(c);d==this.nSets&&this.nSets++},"~N,~N,~N");e(c$,"mergeSets",function(a,b){this.surfaceSet[a].or(this.surfaceSet[b]);this.surfaceSet[b]=null},"~N,~N");e(c$,"invalidateSurfaceSet",function(a){for(var b=
this.surfaceSet[a].nextSetBit(0);0<=b;b=this.surfaceSet[a].nextSetBit(b+1))this.vvs[b]=NaN;this.surfaceSet[a]=null},"~N");c$.checkCutoff=e(c$,"checkCutoff",function(a,b,c,d){if(0>a||0>b||0>c)return!1;a=d[a];b=d[b];c=d[c];return 0<=a&&0<=b&&0<=c||0>=a&&0>=b&&0>=c},"~N,~N,~N,~A");c$.calculateVolumeOrArea=e(c$,"calculateVolumeOrArea",function(a,b,c,d){(d||0>=a.nSets)&&a.getSurfaceSet();for(var h=(d=-1<=b)||0>=a.nSets?1:a.nSets,e=Ya(h,0),g=new JU.V3,f=new JU.V3,j=new JU.V3,k=a.pc;0<=--k;)if(null!=a.setABC(k)){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]),j.cross(g,f),e[d?0:n]+=j.length()):(g.setT(a.vs[a.iB]),f.setT(a.vs[a.iC]),j.cross(g,f),f.setT(a.vs[a.iA]),e[d?0:n]+=f.dot(j)))}a=c?2:6;for(k=0;k<h;k++)e[k]/=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$=function(){la(self.c$);c$=C(function(){oa(this,arguments);this.bs=null;this.n=0;G(this,arguments)},J.jvxl.data.MeshData,"SSet");Q(c$,function(a){this.bs=a;this.n=a.cardinality()},"JU.BS");c$=fa()};c$.$MeshData$SortSet$=function(){la(self.c$);c$=C(function(){oa(this,arguments);G(this,arguments)},J.jvxl.data.MeshData,"SortSet",null,java.util.Comparator);j(c$,"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$=fa()};R(c$,"MODE_GET_VERTICES",1,"MODE_GET_COLOR_INDEXES",2,"MODE_PUT_SETS",3,"MODE_PUT_VERTICES",4)});H("J.jvxl.readers");K(null,"J.jvxl.readers.XmlReader",["JU.P3","$.PT","$.SB","$.XmlUtil","JU.Escape"],function(){c$=C(function(){this.line=this.br=null;G(this,arguments)},J.jvxl.readers,"XmlReader");e(c$,"getLine",function(){return this.line});Q(c$,function(a){this.br=a},"java.io.BufferedReader");e(c$,"toTag",function(a){this.skipTo("<"+
a);if(null==this.line)return"";var b=this.line.indexOf("<"+a)+a.length+1;if(b==this.line.length||" "==this.line.charAt(b)||">"==this.line.charAt(b))return this.line;this.line=null;return this.toTag(a)},"~S");e(c$,"skipTag",function(a){this.skipTo("</"+a+">")},"~S");e(c$,"getXmlData",function(a,b,c,d){var h="</"+a+">";a="<"+a;if(null==b){b=new JU.SB;try{null==this.line&&(this.line=this.br.readLine());for(;0>this.line.indexOf(a);)this.line=this.br.readLine()}catch(e){if(U(e,Exception))return null;throw e;
}b.append(this.line);var g=!1,f=this.line.indexOf("/>"),j=this.line.indexOf(">");if(0>j||f==j-1)g=d;for(;0>this.line.indexOf(h)&&(!g||0>this.line.indexOf("/>"));)b.append(this.line=this.br.readLine());b=b.toString()}return J.jvxl.readers.XmlReader.extractTag(b,a,h,c)},"~S,~S,~B,~B");c$.extractTagOnly=e(c$,"extractTagOnly",function(a,b){return J.jvxl.readers.XmlReader.extractTag(a,"<"+b+">","</"+b+">",!1)},"~S,~S");c$.extractTag=e(c$,"extractTag",function(a,b,c,d){b=a.indexOf(b);if(0>b)return"";var h=
a.indexOf(c,b);0>h&&(h=a.indexOf("/>",b),c="/>");if(0>h)return"";if(d)return h+=c.length,a.substring(b,h);for(c=!1;b<h;b++)if('"'==(d=a.charAt(b)))c=!c;else if(c&&"\\"==d)b++;else if(!c&&(">"==d||"/"==d))break;if(b>=h)return"";for(;JU.PT.isWhitespace(a.charAt(++b)););return JU.XmlUtil.unwrapCdata(a.substring(b,h))},"~S,~S,~S,~B");c$.getXmlAttrib=e(c$,"getXmlAttrib",function(a,b){var c=p(1,0),d=J.jvxl.readers.XmlReader.setNext(a,b,c,1);if(2>d||2>(d=J.jvxl.readers.XmlReader.setNext(a,'"',c,0)))return"";
c=J.jvxl.readers.XmlReader.setNext(a,'"',c,-1);return 0>=c?"":a.substring(d,c)},"~S,~S");e(c$,"getXmlPoint",function(a,b){var c=J.jvxl.readers.XmlReader.getXmlAttrib(a,b).$replace("(","{").$replace(")","}"),c=JU.Escape.uP(c);return V(c,JU.P3)?c:new JU.P3},"~S,~S");c$.setNext=e(c$,"setNext",function(a,b,c,d){var h=c[0];if(0>h||0>(h=a.indexOf(b,c[0])))return-1;h+=b.length;c[0]=h+d;return 0<d&&h<a.length&&"="!=a.charAt(h)?J.jvxl.readers.XmlReader.setNext(a,b,c,d):c[0]},"~S,~S,~A,~N");e(c$,"skipTo",function(a){null==
this.line&&(this.line=this.br.readLine());for(;null!=this.line&&0>this.line.indexOf(a);)this.line=this.br.readLine()},"~S");e(c$,"isNext",function(a){if(null==this.line||0<=this.line.indexOf("</")&&this.line.indexOf("</")==this.line.indexOf("<"))this.line=this.br.readLine();return 0<=this.line.indexOf("<"+a)},"~S")});H("J.jvxl.readers");K(["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 $.SurfaceReader JU.Logger JV.FileManager".split(" "),
function(){c$=C(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;G(this,arguments)},J.jvxl.readers,"SurfaceGenerator");W(c$,function(){this.vAB=new JU.V3;this.vNorm=new JU.V3;this.ptRef=JU.P3.new3(0,0,1E15)});Q(c$,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$,"setJvxlData",function(a){this.jvxlData=a;null!=a&&(a.version=this.version)},"J.jvxl.data.JvxlData");e(c$,"isInsideOut",function(){return this.params.insideOut!=this.params.dataXYReversed});
e(c$,"isFullyLit",function(){return null!=this.params.thePlane||this.params.fullyLit});e(c$,"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(),V(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("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=w(-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;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("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(V(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=u(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=1206,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(V(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=u(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("rad"===a)return this.params.setRadical(b),this.readerData=u(-1,[3,2,0,15,0]),this.surfaceReader=this.newReader("IsoShapeReader"),this.generateSurface(),!0;if("lobe"===a)return this.params.setLobe(b),this.readerData=
u(-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=u(-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()),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,V(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("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=Wa._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$,"setReader",function(){this.readerData=null;if(null!=this.surfaceReader)return!this.surfaceReader.vertexDataOnly;
switch(this.params.dataType){case 1205:this.surfaceReader=this.newReader("IsoPlaneReader");break;case 1206:this.surfaceReader=this.newReader("AtomPropertyMapper");break;case 1328:case 1329:this.readerData=1328==this.params.dataType?"Mep":"Mlp";this.surfaceReader=3==this.params.state?this.newReader("AtomPropertyMapper"):this.newReader("Iso"+this.readerData+"Reader");break;case 1333:this.surfaceReader=this.newReader("IsoIntersectReader");break;case 1195:case 1203:case 1196:this.surfaceReader=this.newReader("IsoSolventReader");
break;case 1844:case 1837:this.surfaceReader=this.newReader("IsoMOReader");break;case 8:this.surfaceReader=this.newReader("IsoFxyReader");break;case 9:this.surfaceReader=this.newReader("IsoFxyzReader")}JU.Logger.info("Using surface reader "+this.surfaceReader);return!0});e(c$,"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$,"mapSurface",function(){1==this.params.state&&null!=this.params.thePlane&&this.params.state++;if(!(3>++this.params.state)&&this.setReader()){this.params.isPeriodic&&
(this.surfaceReader.volumeData.isPeriodic=!0);if(null!=this.params.thePlane){var a=this.params.isSquared;this.params.isSquared=!1;this.params.cutoff=0;this.surfaceReader.volumeData.setMappingPlane(this.params.thePlane);this.surfaceReader.createIsosurface(!this.params.isPeriodic);this.surfaceReader.volumeData.setMappingPlane(null);null!=this.meshDataServer&&this.meshDataServer.notifySurfaceGenerationCompleted();if(1205==this.params.dataType){this.surfaceReader.discardTempData(!0);return}this.params.isSquared=
a;this.params.mappedDataMin=3.4028235E38;this.surfaceReader.readVolumeData(!0);null!=this.params.mapLattice&&(this.surfaceReader.volumeData.isPeriodic=!0)}else!this.params.colorBySets&&!this.params.colorDensity&&(this.surfaceReader.readAndSetVolumeParameters(!0),this.params.mappedDataMin=3.4028235E38,this.surfaceReader.readVolumeData(!0));this.colorIsosurface();this.surfaceReader.closeReader();this.surfaceReader=null}});e(c$,"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(V(b,java.util.Map)){var d=b;if(d.containsKey("__pymolSurfaceData__"))return this.readerData=
d,this.newReaderBr("PyMOLMeshReader",null);b=d.get("volumeData")}if(V(b,J.jvxl.data.VolumeData))return this.volumeDataTemp=b,this.newReader("VolumeDataReader");d=null;V(b,String)&&(d=b,b=JU.Rdr.getBR(b));var 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=w(-1,[this.params.fileName,d]);if(0<="MRC DELPHI DSN6".indexOf(c.toUpperCase())){try{h.close()}catch(f){if(!U(f,java.io.IOException))throw f;}h=null;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$,"getFunctionZfromXY",
function(){for(var a=this.params.functionInfo.get(1),b=p(3,0),c=p(3,0),d=Array(3),h=0;3>h;h++){var e=this.params.functionInfo.get(h+2);b[h]=Math.abs(y(e.x));d[h]=JU.V3.new3(e.y,e.z,e.w)}for(var e=b[0],b=b[1],g=new JU.P3,f=new JU.P3,j=new JU.P3,k=new JU.P3,n=this.params.functionInfo.get(5),q=u(e,b,0),t,h=0;h<e;h++)for(var r=0;r<b;r++){g.scaleAdd2(h,d[0],a);g.scaleAdd2(r,d[1],g);var L=J.jvxl.readers.SurfaceGenerator.findNearestThreePoints(g.x,g.y,n,c);f.set((t=n[c[0]])[0],t[1],t[2]);1E-5>L?g.z=t[2]:
(j.set((t=n[c[1]])[0],t[1],t[2]),k.set((t=n[c[2]])[0],t[1],t[2]),g.z=this.distanceVerticalToPlane(g.x,g.y,f,j,k));q[h][r]=g.z}this.params.functionInfo.set(5,q)});e(c$,"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,j,k,n;j=k=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=k,k=j,j=q):h<g?(f=g,g=h,n=k,k=q):h<f&&(f=h,n=q);d[0]=j;d[1]=k;d[2]=n;return e},"~N,~N,~A,~A");e(c$,"addRequiredFile",function(a){null!=this.meshDataServer&&this.meshDataServer.addRequiredFile(a)},"~S");e(c$,"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$,"getSpanningVectors",function(){return null==this.surfaceReader.volumeData?null:this.surfaceReader.volumeData.spanningVectors})});H("J.jvxl.readers");K(null,"J.jvxl.readers.Parameters","java.lang.Float java.util.Hashtable JU.A4 $.Lst $.M3 $.P3 $.P4 $.V3 JU.Escape $.Logger".split(" "),function(){c$=
C(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.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;G(this,arguments)},J.jvxl.readers,"Parameters");W(c$,function(){this.anisotropy=u(3,0)});e(c$,"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.fullyLit=!1;this.functionInfo=null;this.logCube=this.logCompression=this.isSilent=this.isPeriodic=this.isMapped=this.isEccentric=this.isContoured=this.isSquaredLinear=this.isSquared=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.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$,"setSolvent",function(a,b){this.isEccentric=this.isAnisotropic=!1;this.solventRadius=Math.abs(b);this.dataType=null!=this.intersection?1333:"nomap"===a?1205:"molecular"===a?1203:"sasurface"===a||0==this.solventRadius?1196:1195;
if(2>this.state&&(this.cutoffAutomatic||!this.colorDensity)&&(null==this.intersection||3.4028235E38==this.cutoff))this.cutoff=0;switch(this.dataType){case 1333:this.calculationType="VDW intersection";break;case 1205:this.calculationType="unmapped plane";break;case 1203:this.calculationType="molecular surface with radius "+this.solventRadius;break;case 1195:this.calculationType="solvent-excluded surface with radius "+this.solventRadius;break;case 1196:this.calculationType="solvent-accessible surface with radius "+
this.solventRadius}switch(this.dataType){case 1205:this.solventExtendedAtomRadius=this.solventRadius;this.solventRadius=0;this.isContoured=!1;break;case 1203:this.solventExtendedAtomRadius=0;break;case 1195:this.solventExtendedAtomRadius=0;null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&this.bsIgnore.or(this.bsSolvent);break;case 1196:this.solventExtendedAtomRadius=this.solventRadius,this.solventRadius=0,null==this.bsIgnore?this.bsIgnore=this.bsSolvent:null!=this.bsSolvent&&
this.bsIgnore.or(this.bsSolvent)}},"~S,~N");e(c$,"setFunctionXY",function(a){this.dataType=8;this.functionInfo=a;this.cutoff=1.4E-45;this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setFunctionXYZ",function(a){this.dataType=9;this.functionInfo=a;3.4028235E38==this.cutoff&&(this.cutoff=1.4E-45);this.isEccentric=this.isAnisotropic=!1},"JU.Lst");e(c$,"setAtomicOrbital",function(a){this.dataType=1294;this.setEccentricity(JU.P4.new4(0,0,1,1));this.psi_n=y(a[0]);this.psi_l=y(a[1]);this.psi_m=y(a[2]);
this.psi_Znuc=a[3];this.psi_monteCarloCount=y(a[4]);this.distance=a[5];if(0!=this.distance||null!=this.thePlane)this.allowVolumeRender=!1;this.randomSeed=y(a[6]);this.psi_ptsPerAngstrom=10;if(3.4028235E38==this.cutoff||0.14==this.cutoff)this.cutoff=0<this.psi_monteCarloCount?0:0.04,this.isSquared&&(this.cutoff*=this.cutoff);this.isCutoffAbsolute=!0;2>this.state&&(null==this.thePlane&&this.colorBySign)&&(this.isBicolorMap=!0);return 0<this.psi_Znuc&&Math.abs(this.psi_m)<=this.psi_l&&this.psi_l<this.psi_n},
"~A");e(c$,"setMep",function(a,b){this.dataType=b?1329:1328;this.theProperty=a;this.isEccentric=this.isAnisotropic=this.usePropertyForColorRange=!1;3.4028235E38==this.cutoff&&(this.cutoff=0.1,this.isSquared&&(this.cutoff*=this.cutoff));this.isCutoffAbsolute=0<this.cutoff&&!this.isPositiveOnly;this.contourFromZero=!1;2<=this.state||null!=this.thePlane?!this.rangeDefined&&!this.rangeAll&&(this.valueMappedToRed=-0.1,this.valueMappedToBlue=0.1,this.rangeDefined=!0):this.isBicolorMap=this.colorBySign=
!0},"~A,~B");e(c$,"setNci",function(a){this.fullyLit=!0;this.qm_gridMax=200;a&&(this.dataType=1844);this.qm_marginAngstroms=2;this.qmOrbitalType=a?3:4;if(a&&(null==this.parameters||2>this.parameters.length))this.parameters=u(-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$,"setMO",function(a,b){this.qm_moLinearCombination=b;this.qm_moNumber=null==
b?Math.abs(a):y(b[1]);this.qmOrbitalType=this.moData.containsKey("haveVolumeData")?5:this.moData.containsKey("gaussians")?1:this.moData.containsKey("slaters")?2:0;var c=0>=a&&null==b;0==this.qmOrbitalType?(JU.Logger.error("MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?)"),this.title=w(-1,["no basis functions found in file"])):(this.qmOrbitalCount=this.moData.get("mos").size(),this.calculationType=this.moData.get("calculationType"),this.calculationType=
"Molecular orbital #"+this.qm_moNumber+"/"+this.qmOrbitalCount+" "+(null==this.calculationType?"":this.calculationType),!c&&null==this.title&&(this.title=Array(5),this.title[0]="%F",this.title[1]="Model %M  MO %I/%N %T",this.title[2]="?Energy = %E %U",this.title[3]="?Symmetry = %S",this.title[4]="?Occupancy = %O"));this.dataType=1837;3.4028235E38==this.cutoff&&(this.cutoff=c?0.01:0.05);if(this.isSquared||this.isSquaredLinear)this.cutoff*=this.cutoff;this.isEccentric=this.isAnisotropic=!1;this.isCutoffAbsolute=
0<this.cutoff&&!this.isPositiveOnly;2<=this.state||null!=this.thePlane||(this.colorBySign=!0,this.colorByPhase&&0==this.colorPhase&&(this.colorByPhase=!1),this.isBicolorMap=!0)},"~N,~A");e(c$,"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);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$,"addSlabInfo",function(a){null==this.slabInfo&&(this.slabInfo=new JU.Lst);this.slabInfo.addLast(a)},"~A");R(c$,"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",
1333,"SURFACE_NOMAP",1205,"SURFACE_PROPERTY",1206,"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)});H("J.jvxl.readers");K(["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 $.Logger".split(" "),
function(){c$=C(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;G(this,arguments)},J.jvxl.readers,"SurfaceReader",null,J.jvxl.api.VertexDataServer);W(c$,function(){this.ptTemp=new JU.P3});Q(c$,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$,"newVoxelDataCube",function(){this.volumeData.setVoxelDataAsArray(this.voxelData=u(this.nPointsX,this.nPointsY,this.nPointsZ,0))});e(c$,"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.insideOut;this.jvxlData.dataXYReversed=
this.params.dataXYReversed;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){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.params.isSilent||JU.Logger.info("boundbox corners "+JU.Escape.eP(this.xyzMin)+" "+JU.Escape.eP(this.xyzMax));this.jvxlData.boundingBox=w(-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.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=Z(a,0);if(null==c||c.length<a)this.meshData.vvs=u(a,0);for(c=0;c<a;c++)b[c]=JU.C.getColix(this.jvxlData.vertexColors[c]);return"-"});j(c$,"getPlane",function(a){return this.getPlane2(a)},"~N");e(c$,"getPlane2",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$,"initPlanes",function(){this.yzCount=this.nPointsY*this.nPointsZ;this.isQuiet||JU.Logger.info("reading data progressively -- yzCount = "+this.yzCount);this.yzPlanes=JU.AU.newFloat2(2);this.yzPlanes[0]=u(this.yzCount,0);this.yzPlanes[1]=u(this.yzCount,0)});j(c$,"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$,"postProcessVertices",function(){});j(c$,"getSurfacePointIndexAndFraction",function(a,b,c,d,h,e,g,f,j,k,n,q,t,r){b=this.getSurfacePointAndFraction(a,b,j,k,n,q,c,d,h,g,f,r,this.ptTemp);if(null!=this.marchingSquares&&this.params.isContoured)return this.marchingSquares.addContourVertex(this.ptTemp,a);a=0<this.assocCutoff?
r[0]<this.assocCutoff?g:r[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(j<k?n:this.ptTemp,Math.min(j,k),-3,!0),this.addVertexCopy(j<k?this.ptTemp:n,Math.max(j,k),-3,!0));return a},"~N,~B,~N,~N,~N,JU.P3i,~N,~N,~N,~N,JU.T3,JU.V3,~B,~A");e(c$,"getSurfacePointAndFraction",function(a,b,c,d,h,e,g,f,j,k,n,q,t){return this.getSPF(a,
b,c,d,h,e,g,f,j,k,n,q,t)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPF",function(a,b,c,d,h,e,g,f,j,k,n,q,t){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;t.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=Z(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=p(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=u(-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=Z(a,0);h=this.jvxlData.contourValues;null==h&&(h=this.jvxlData.contourValuesUsed);null==this.jvxlData.contourValuesUsed&&(this.jvxlData.contourValuesUsed=null==h?u(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=u(-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=u(-1,[b,c])}var d=0<this.contourVertexCount?this.contourVertexCount:this.meshData.vc,h=this.meshData.vs,e=a||this.jvxlDataIs2dContour||this.vertexDataOnly||this.params.colorDensity;for(a=this.meshData.mergeVertexCount0;a<d;a++){var g;g=e?this.meshData.vvs[a]:this.volumeData.lookupInterpolatedVoxelValue(h[a],!1);g<b&&(b=g);g>c&&3.4028235E38!=
g&&(c=g)}return this.minMax=u(-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});R(c$,"ANGSTROMS_PER_BOHR",0.5291772,"defaultMappedDataMin",0,"defaultMappedDataMax",1,"defaultCutoff",0.02,"colorPhases",w(-1,"_orb x y z xy yz xz x2-y2 z2".split(" ")))});H("J.jvxl.calc");K(["JU.TriangleData","JU.BS","$.P3","$.SB","$.V3"],"J.jvxl.calc.MarchingCubes",["java.lang.Float","J.jvxl.data.JvxlCoder"],
function(){c$=C(function(){this.volumeData=this.surfaceReader=null;this.contourType=0;this.isContoured=!1;this.cutoff=0;this.isXLowToHigh=this.isSquared=this.isCutoffAbsolute=!1;this.yzCount=this.nZ=this.nY=this.cubeCountZ=this.cubeCountY=this.cubeCountX=0;this.colorDensity=!1;this.integrateSquared=!0;this.edgeData=this.bsExcludedPlanes=this.bsExcludedTriangles=this.bsExcludedVertices=this.bsVoxels=null;this.excludePartialCubes=!0;this.mode=0;this.vertexValues=null;this.edgeCount=0;this.mappingPlane=
this.yzPlanes=this.isoPointIndexPlanes=this.edgePointIndexes=this.edgeVectors=this.voxelVertexVectors=null;this.$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;G(this,arguments)},J.jvxl.calc,"MarchingCubes",JU.TriangleData);W(c$,function(){this.edgeData=new JU.SB;this.vertexValues=u(8,0);this.voxelVertexVectors=Array(8);this.edgeVectors=Array(12);for(var a=
12;0<=--a;)this.edgeVectors[a]=new JU.V3;this.edgePointIndexes=p(12,0);this.bsValues=new JU.BS;this.pt0=new JU.P3;this.pointA=new JU.P3;this.fReturn=u(1,0);this.linearOffsets=p(8,0)});Q(c$,function(){Y(this,J.jvxl.calc.MarchingCubes,[])});Q(c$,function(a,b,c,d){Y(this,J.jvxl.calc.MarchingCubes,[]);this.excludePartialCubes=!0;this.surfaceReader=a;this.bsVoxels=d;a=c.bsExcluded;this.bsExcludedVertices=null==a[0]?a[0]=new JU.BS:a[0];this.bsExcludedPlanes=null==a[2]?a[2]=new JU.BS:a[2];this.bsExcludedTriangles=
null==a[3]?a[3]=new JU.BS:a[3];this.mode=null!=b.getVoxelData()||null!=b.mappingPlane?1:null!=d?2:3;this.setParameters(b,c)},"J.jvxl.api.VertexDataServer,J.jvxl.data.VolumeData,J.jvxl.readers.Parameters,JU.BS");e(c$,"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=p(2,this.yzCount,3,0);this.yzPlanes=3==this.mode?u(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$,"getEdgeData",function(){if(0>this.cubeCountX||0>this.cubeCountY||0>this.cubeCountZ)return"";this.mappingPlane=this.volumeData.mappingPlane;this.edgeCount=0;var a,b,c,d,h,
e;this.isXLowToHigh?(a=0,this.colorDensity?(b=this.cubeCountX+1,e=this.yzCount-1):(b=this.cubeCountX,e=this.yzCount-1-this.nZ-1),c=1,d=this.yzCount):(this.colorDensity?(a=this.cubeCountX,e=(this.cubeCountX+1)*this.yzCount-1):(a=this.cubeCountX-1,e=this.cubeCountX*this.yzCount-1-this.nZ-1),c=b=-1,d=-this.yzCount);h=e;this.resetIndexPlane(this.isoPointIndexPlanes[1]);this.voxelData=null;var g=this.cubeCountY+(this.colorDensity?1:0),f=this.cubeCountZ+(this.colorDensity?1:0);switch(this.mode){case 3:this.getPlane(a,
!1);break;case 1:this.voxelData=this.volumeData.getVoxelData()}this.allInside=this.colorDensity&&(0==this.cutoff||2==this.mode&&0>this.bsVoxels.nextSetBit(0));for(var j=this.colorDensity&&0==this.cutoff,k=0;a!=b;a+=c,e+=d,h=e)if(3==this.mode&&a+c<=b&&this.getPlane(a+c,!0),!this.bsExcludedPlanes.get(a)||!this.bsExcludedPlanes.get(a+c))if(this.colorDensity)for(var n=g;0<=--n;)for(var q=f;0<=--q;h--)k=this.getValue(a,n,q,h,0),(j||this.$isInside)&&this.addVertex(a,n,q,h,k);else{n=this.isoPointIndexPlanes[0];
this.isoPointIndexPlanes[0]=this.isoPointIndexPlanes[1];this.isoPointIndexPlanes[1]=this.resetIndexPlane(n);for(var t=!0,n=g;0<=--n;h--)for(q=f;0<=--q;h--){for(var r=0,p=8;0<=--p;)k=this.getValue(a,n,q,h,p),this.$isInside&&(r|=JU.TriangleData.Pwr2[p]);t&&!Float.isNaN(k)&&(t=!1);0!=r&&255!=r&&this.processOneCubical(r,a,n,q,h)&&(!this.isContoured&&!this.colorDensity)&&this.processTriangles(r)}t&&this.bsExcludedPlanes.set(a)}return this.edgeData.toString()});e(c$,"getValue",function(a,b,c,d,h){this.offset=
JU.TriangleData.cubeVertexOffsets[h];d+=this.linearOffsets[h];switch(this.mode){case 3:a=this.vertexValues[h]=this.getValueArray(a+this.offset.x,b+this.offset.y,c+this.offset.z,d,this.yzPlanes[J.jvxl.calc.MarchingCubes.yzPlanePts[h]]);this.$isInside=this.allInside||this.bsVoxels.get(d);break;case 2:this.$isInside=this.allInside||this.bsVoxels.get(d);a=this.vertexValues[h]=this.bsExcludedVertices.get(d)?NaN:this.$isInside?1:0;break;default:case 1:null==this.mappingPlane?a=this.vertexValues[h]=this.voxelData[a+
this.offset.x][b+this.offset.y][c+this.offset.z]:(this.volumeData.voxelPtToXYZ(a+this.offset.x,b+this.offset.y,c+this.offset.z,this.pt0),a=this.vertexValues[h]=this.volumeData.distanceToMappingPlane(this.pt0)),this.isSquared&&(this.vertexValues[h]*=this.vertexValues[h]),(this.$isInside=this.allInside?!0:J.jvxl.calc.MarchingCubes.isInside(this.vertexValues[h],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$,"addVertex",function(a,b,c,d,h){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);0>this.surfaceReader.addVertexCopy(this.pt0,h,-4,!0)&&this.bsExcludedVertices.set(d)},"~N,~N,~N,~N,~N");e(c$,"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$,"getValueArray",function(a,b,c,d,h){var e=d%this.yzCount;this.bsValues.set(d);a=this.surfaceReader.getValue(a,b,c,e);this.isSquared&&(a*=a);h[e]=a;J.jvxl.calc.MarchingCubes.isInside(a,this.cutoff,this.isCutoffAbsolute)&&this.bsVoxels.set(d);return a},"~N,~N,~N,~N,~A");c$.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,h){a=J.jvxl.calc.MarchingCubes.insideMaskTable[a];for(var e=!1,g=12;0<=--g;)if(0!=(a&JU.TriangleData.Pwr2[g])){var f=this.edgeVertexPlanes[g],j=(h+this.linearOffsets[this.edgeVertexPointers[g]])%this.yzCount,k=J.jvxl.calc.MarchingCubes.edgeTypeTable[g],n=this.edgePointIndexes[g]=this.isoPointIndexPlanes[f][j][k];if(-2147483648!=n)-1==n&&(e=this.excludePartialCubes);else{var n=
JU.TriangleData.edgeVertexes[g<<1],q=JU.TriangleData.edgeVertexes[(g<<1)+1],t=this.vertexValues[n],r=this.vertexValues[q];this.calcVertexPoint(b,c,d,n,this.pointA);this.edgeCount++;f=this.edgePointIndexes[g]=this.isoPointIndexPlanes[f][j][k]=this.surfaceReader.getSurfacePointIndexAndFraction(this.cutoff,this.isCutoffAbsolute,b,c,d,JU.TriangleData.cubeVertexOffsets[n],n,q,t,r,this.pointA,this.edgeVectors[g],k==this.contourType,this.fReturn);this.addEdgeData(0>f?NaN:this.fReturn[0]);if(Float.isNaN(this.fReturn[0])||
0>f)e=this.excludePartialCubes}}return!e},"~N,~N,~N,~N,~N");e(c$,"addEdgeData",function(a){a=J.jvxl.data.JvxlCoder.jvxlFractionAsCharacter(a);this.edgeData.appendC(a)},"~N");e(c$,"calcVertexPoint",function(a,b,c,d,h){this.volumeData.voxelPtToXYZ(a,b,c,this.pt0);h.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");R(c$,"MODE_CUBE",1,"MODE_JVXL",2,"MODE_PLANES",3);R(c$,"yzPlanePts",p(-1,[0,1,1,0,0,1,1,0]),"edgeVertexPointersLowToHigh",p(-1,[1,1,2,0,5,5,6,4,0,1,2,3]),"edgeVertexPointersHighToLow",p(-1,[0,1,3,0,4,5,7,4,0,1,2,3]),"edgeVertexPlanesLowToHigh",p(-1,[1,1,1,0,
1,1,1,0,0,1,1,0]),"edgeVertexPlanesHighToLow",p(-1,[1,0,1,1,1,0,1,1,1,0,0,1]));c$.cubeVertexVectors=c$.prototype.cubeVertexVectors=w(-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)]);R(c$,"edgeTypeTable",p(-1,[0,2,0,2,0,2,0,2,1,1,1,1]),"insideMaskTable",Z(-1,[0,265,515,778,1030,1295,1541,1804,2060,2309,2575,2822,3082,3331,3593,3840,400,153,915,666,1430,1183,1941,1692,2460,2197,2975,2710,3482,3219,3993,
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453,719,966,1226,1475,1737,1984,2384,2137,2899,2650,3414,3167,3925,3676,348,85,863,598,1370,1107,1881,1616,2800,3065,2291,2554,3830,4095,3317,3580,764,1013,255,502,1786,2035,1273,1520,2912,2665,2403,2154,3942,3695,3429,3180,876,613,367,102,1898,1635,1385,1120,3232,3497,3747,4010,2214,2479,2725,2988,1196,1445,1711,1958,170,419,681,928,3376,3129,3891,3642,2358,2111,2869,2620,1340,1077,1855,1590,314,51,825,560,3728,3993,3219,3482,2710,2975,2197,2460,1692,1941,1183,1430,666,915,153,400,3840,3593,3331,
3082,2822,2575,2309,2060,1804,1541,1295,1030,778,515,265,0]))});H("J.jvxl.calc");K(["JU.P3","java.util.Hashtable"],"J.jvxl.calc.MarchingSquares",["java.lang.Float","JU.AU","JU.Logger"],function(){c$=C(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;na("J.jvxl.calc.MarchingSquares.ContourVertex")||
J.jvxl.calc.MarchingSquares.$MarchingSquares$ContourVertex$();this.contourPlaneMaximumValue=this.contourPlaneMinimumValue=0;this.ptTemp=this.contourValuesUsed=null;this.triangleCount=0;this.htPts=this.triangles=null;na("J.jvxl.calc.MarchingSquares.Triangle")||J.jvxl.calc.MarchingSquares.$MarchingSquares$Triangle$();G(this,arguments)},J.jvxl.calc,"MarchingSquares");W(c$,function(){this.pointA=new JU.P3;this.pointB=new JU.P3;this.contourVertexes=Array(1E3);this.ptTemp=new JU.P3;this.triangles=Array(1E3);
this.htPts=new java.util.Hashtable});Q(c$,function(a,b,c,d,h,e,g){this.surfaceReader=a;this.volumeData=b;this.thisContour=e;this.contoursDiscrete=d;this.contourFromZero=g;null==d?(this.nContourSegments=(0==h?9:h)+0,100<this.nContourSegments&&(this.nContourSegments=100)):(this.nContourSegments=h=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++]=ma(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$,"addTriangle",function(a,b,c,d,h){this.triangleCount==this.triangles.length&&(this.triangles=JU.AU.doubleLength(this.triangles));this.triangles[this.triangleCount++]=ma(J.jvxl.calc.MarchingSquares.Triangle,this,null,a,b,c,d,h);return 0},"~N,~N,~N,~N,~N");e(c$,"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=u(this.nContourSegments,
0);for(var d=this.triangleCount;0<=--d;)this.triangles[d].check=0;for(var h=-3.4028235E38,d=0;d<this.nContourSegments;d++){h=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(h)<c&&(h=0>h?-c:c);this.contourValuesUsed[d]=h;JU.Logger.info("#contour "+(d+1)+" "+h+" "+this.triangleCount);this.htPts.clear();for(var e=
this.triangleCount;0<=--e;)this.triangles[e].isValid&&this.checkContour(this.triangles[e],d,h)}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$,"intercept",function(a,b,c){var d=a.pts[b];a=a.pts[(b+1)%3];if(2147483647==d||2147483647==a)return-1;b=d<a?d+"_"+a:a+"_"+d;if(this.htPts.containsKey(b))return this.htPts.get(b).intValue();var h=this.contourVertexes[d].value,
e=this.contourVertexes[a].value,g=-1;if(h!=e){var f=(c-h)/(e-h);if(0<=f&&1>=f&&(this.pointA.setT(this.contourVertexes[d]),this.pointB.setT(this.contourVertexes[a]),c=this.calcContourPoint(c,h,e,this.ptTemp),!Float.isNaN(c))){g=this.addContourVertex(this.ptTemp,c);if(0>g)return-1;this.contourVertexes[g].setValue(c)}}this.htPts.put(b,Integer.$valueOf(g));return g},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"checkContour",function(a,b,c){if(!(0<this.thisContour&&b+1!=this.thisContour)){var d=
this.intercept(a,0,c),h=this.intercept(a,1,c);c=this.intercept(a,2,c);var e=a.pts,g=0;0<=d&&(g+=1);0<=h&&(g+=2);0<=c&&(g+=4);switch(g){case 3:this.addTriangle(e[0],d,h,2|a.check&1,b);this.addTriangle(d,e[1],h,4|a.check&3,b);this.addTriangle(e[0],h,e[2],a.check&6,b);break;case 5:this.addTriangle(e[0],d,c,2|a.check&5,b);this.addTriangle(d,e[1],c,4|a.check&1,b);this.addTriangle(c,e[1],e[2],a.check&6,b);break;case 6:this.addTriangle(e[0],e[1],c,a.check&5,b);this.addTriangle(c,e[1],h,4|a.check&2,b);this.addTriangle(c,
h,e[2],1|a.check&6,b);break;default:return}a.isValid=!1}},"J.jvxl.calc.MarchingSquares.Triangle,~N,~N");e(c$,"getMinMax",function(){return u(-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$=function(){la(self.c$);c$=C(function(){oa(this,arguments);this.value=
0;G(this,arguments)},J.jvxl.calc.MarchingSquares,"ContourVertex",JU.P3);Q(c$,function(a){Y(this,J.jvxl.calc.MarchingSquares.ContourVertex,[]);this.setT(a)},"JU.P3");e(c$,"setValue",function(a){this.value=a},"~N");j(c$,"toString",function(){return this.value+" "+this.x+" "+this.y+" "+this.z});c$=fa()};c$.$MarchingSquares$Triangle$=function(){la(self.c$);c$=C(function(){oa(this,arguments);this.pts=null;this.check=0;this.isValid=!0;this.contourIndex=0;G(this,arguments)},J.jvxl.calc.MarchingSquares,"Triangle");
Q(c$,function(a,b,c,d,h){this.pts=p(-1,[a,b,c]);this.check=d;this.contourIndex=h},"~N,~N,~N,~N,~N");c$=fa()};R(c$,"CONTOUR_POINT",-1,"VERTEX_POINT",-2,"EDGE_POINT",-3,"nContourMax",100,"defaultContourCount",9)});H("J.shapesurface");K(["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 $.Logger JV.Viewer".split(" "),function(){c$=C(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;G(this,arguments)},J.shapesurface,"IsosurfaceMesh",J.shape.Mesh);j(c$,"getResolution",function(){return 1/this.jvxlData.pointsPerAngstrom});Q(c$,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=Z(this.vc,0);for(var a=this.vc;0<=--a;)this.vcs[a]=this.colix}this.isColorSolid=!1});e(c$,"addVertexCopy",function(a,b,c,d,h){a=this.addVCVal(a,b,h);switch(c){case -1:0>this.firstRealVertex&&(this.firstRealVertex=a);break;case -2:this.hasGridPoints=!0;break;case -3:this.vertexIncrement=3;break;default:0>
this.firstRealVertex&&(this.firstRealVertex=a),d&&(null==this.assocGridPointMap&&(this.assocGridPointMap=new java.util.Hashtable),this.assocGridPointMap.put(Integer.$valueOf(a),Integer.$valueOf(c+this.mergeAssociatedNormalCount)))}return a},"JU.T3,~N,~N,~B,~B");j(c$,"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$,"setMerged",function(a){this.mergePolygonCount0=
(this.isMerged=a)?this.pc:0;this.mergeVertexCount0=a?this.vc:0;a&&(this.mergeAssociatedNormalCount+=this.jvxlData.nPointsX*this.jvxlData.nPointsY*this.jvxlData.nPointsZ,this.assocGridPointNormals=null)},"~B");j(c$,"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 h=c.getValue();this.assocGridPointNormals.containsKey(h)||this.assocGridPointNormals.put(h,JU.V3.new3(0,0,0));this.assocGridPointNormals.get(h).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 h=this.jvxlData.valueMappedToRed+(c+1)*d;J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],h,this.jvxlData.contourColixes[c])}JU.Logger.info(a+" contour lines; separation = "+d)}else for(c=0;c<a;c++)h=this.jvxlData.contourValuesUsed[c],J.shapesurface.IsosurfaceMesh.get3dContour(this,b[c],h,this.jvxlData.contourColixes[c]);this.jvxlData.contourColixes=
Z(a,0);this.jvxlData.contourValues=u(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});c$.get3dContour=e(c$,"get3dContour",function(a,b,c,d){var h=JU.BS.newN(a.pc),e=new JU.SB,g=JU.C.getArgb(d);J.shapesurface.IsosurfaceMesh.setContourVector(b,a.pc,h,c,d,g,e);for(d=0;d<a.pc;d++)null!=a.setABC(d)&&J.shapesurface.IsosurfaceMesh.addContourPoints(b,h,d,e,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,h,e,g){a.add(0,Integer.$valueOf(b));a.add(1,c);a.add(2,Float.$valueOf(d));a.add(3,Z(-1,[h]));a.add(4,p(-1,[e]));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,f,g,j,p,k){var n=null,q=null,t=0,r=J.shapesurface.IsosurfaceMesh.checkPt(f,g,j,k);Float.isNaN(r)||(n=J.shapesurface.IsosurfaceMesh.getContourPoint(e,g,j,r),t|=1);var u=1==r?NaN:J.shapesurface.IsosurfaceMesh.checkPt(f,j,
p,k);Float.isNaN(u)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,j,p,u),0==t&&(n=q,r=u),t|=2);switch(t){case 0:return;case 1:if(0==r)return;case 2:u=1==u?NaN:J.shapesurface.IsosurfaceMesh.checkPt(f,p,g,k),Float.isNaN(u)||(q=J.shapesurface.IsosurfaceMesh.getContourPoint(e,p,g,u),t|=4)}switch(t){case 3:case 5:case 6:break;default:return}b.set(c);J.jvxl.data.JvxlCoder.appendContourTriangleIntersection(t,r,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$,"setDiscreteColixes",function(a,b){null!=a&&(this.jvxlData.contourValues=a);if(null==a||0==a.length)a=this.jvxlData.contourValues=this.jvxlData.contourValuesUsed;null==b&&null!=this.jvxlData.contourColixes?b=this.jvxlData.contourColixes:(this.jvxlData.contourColixes=
b,this.jvxlData.contourColors=JU.C.getHexCodes(b));if(!(null==this.vs||null==this.vvs||null==a)){var c=a.length,d=a[c-1];this.colorCommand=null;var e=null!=b&&0<b.length;this.isColorSolid=e&&null!=this.jvxlData.jvxlPlane;if(null!=this.jvxlData.vContours){if(e)for(var f=0;f<this.jvxlData.vContours.length;f++)c=b[f%b.length],this.jvxlData.vContours[f].get(3)[0]=c,this.jvxlData.vContours[f].get(4)[0]=JU.C.getArgb(c)}else{this.pcs=Z(this.pc,0);this.colorsExplicit=!1;for(f=0;f<this.pc;f++){var g=this.pis[f];
if(null!=g){this.pcs[f]=0;for(var g=(this.vvs[g[0]]+this.vvs[g[1]]+this.vvs[g[2]])/3,j=c;0<=--j;)if(g>=a[j]&&g<d){this.pcs[f]=e?b[j%b.length]:0;break}}}}}},"~A,~A");e(c$,"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$,"setVertexColixesForAtoms",
function(a,b,c,d){this.jvxlData.vertexDataOnly=!0;this.jvxlData.vertexColors=p(this.vc,0);this.jvxlData.nVertexColors=this.vc;var e=a.ms.at;a=a.gdata;for(var f=this.mergeVertexCount0;f<this.vc;f++){var g=this.vertexSource[f];if(!(0>g)&&d.get(g)){this.jvxlData.vertexColors[f]=a.getColorArgbOrGray(this.vcs[f]=JU.C.copyColixTranslucency(this.colix,e[g].colixAtom));var j=null==b?0:b[c[g]];0==j&&(j=e[g].colixAtom);this.vcs[f]=JU.C.copyColixTranslucency(this.colix,j)}}},"JV.Viewer,~A,~A,JU.BS");e(c$,"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(){null!=this.colorEncoder&&(this.colorCommand=this.colorEncoder.getColorScheme(),this.colorCommand.equals("inherit")?this.colorCommand="#inherit;":null!=this.colorCommand&&(this.colorCommand="color $"+(JU.PT.isLetter(this.thisID.charAt(0))&&0>this.thisID.indexOf(" ")?this.thisID:'"'+this.thisID+'"')+' "'+this.colorCommand+'" range '+(this.jvxlData.isColorReversed?this.jvxlData.valueMappedToBlue+" "+this.jvxlData.valueMappedToRed:this.jvxlData.valueMappedToRed+" "+this.jvxlData.valueMappedToBlue)))});
e(c$,"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=p(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=Z(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$,"reinitializeLightingAndColor",function(a){this.initialize(this.lighting,null,null);if(null!=this.colorEncoder||this.jvxlData.isBicolorMap)this.vcs=null,this.remapColors(a,null,NaN)},"JV.Viewer");j(c$,"getBoundingBox",function(){return this.jvxlData.boundingBox});j(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=p(0,0,0));null!=a&&null==a.pis&&(a.pis=p(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");j(c$,"getUnitCell",function(){return null!=this.unitCell||null!=(this.unitCell=this.vwr.ms.am[this.modelIndex].biosymmetry)||null!=(this.unitCell=this.vwr.ms.getUnitCell(this.modelIndex))||null!=this.spanningVectors&&null!=(this.unitCell=J.api.Interface.getSymmetry(this.vwr,"symmetry").getUnitCell(this.spanningVectors,!0,null))?this.unitCell:null});e(c$,"fixLattice",function(){if(null!=
this.getUnitCell()){var a=new JU.P3i,b=JU.P3i.new3(y(this.lattice.x),y(this.lattice.y),y(this.lattice.z));this.jvxlData.fixedLattice=this.lattice;this.lattice=null;this.unitCell.setMinMaxLatticeParameters(a,b);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 j=a.y;j<b.y;j++)for(var p=a.z;p<b.z;p++)if(!(0==f&&0==j&&0==p)){d.set(f,j,p);this.unitCell.toCartesian(d,!1);for(var k=0;k<e;k++){this.normixes[this.vc]=this.normixes[k];var n=JU.P3.newP(this.vs[k]);n.add(d);this.addVCVal(n,this.vvs[k],!1)}c+=e;for(k=0;k<g;k++)n=JU.AU.arrayCopyI(this.pis[k],-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=w(-1,[a,b])}});j(c$,"getMinDistance2ForVertexGrouping",function(){return null!=
this.jvxlData.boundingBox&&null!=this.jvxlData.boundingBox[0]&&5>this.jvxlData.boundingBox[1].distanceSquared(this.jvxlData.boundingBox[0])?1E-10:1E-8});j(c$,"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$,"updateCoordinates",function(a,b){var c=null==b;if(!c)for(var d=0;d<this.connections.length;d++)if(0<=this.connections[d]&&b.get(this.connections[d])){c=!0;
break}c&&(null==this.mat4&&(this.mat4=JU.M4.newM4(null)),this.mat4.mul2(a,this.mat4),this.recalcAltVertices=!0)},"JU.M4,JU.BS")});H("J.jvxl.readers");K(["J.jvxl.readers.SurfaceReader"],"J.jvxl.readers.VolumeDataReader",["java.lang.Float","JU.AU","$.SB","J.jvxl.data.JvxlCoder","JU.Logger"],function(){c$=C(function(){this.dataType=0;this.allowMapData=this.precalculateVoxelData=!1;this.point=null;this.maxGrid=this.ptsPerAngstrom=0;this.useOriginStepsPoints=!1;G(this,arguments)},J.jvxl.readers,"VolumeDataReader",
J.jvxl.readers.SurfaceReader);Q(c$,function(){Y(this,J.jvxl.readers.VolumeDataReader,[])});j(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$,"setup",function(){this.jvxlFileHeaderBuffer=(new JU.SB).append("volume data read from file\n\n");
J.jvxl.data.JvxlCoder.jvxlCreateHeaderWithoutTitleOrAtoms(this.volumeData,this.jvxlFileHeaderBuffer)},"~B");j(c$,"readVolumeParameters",function(a){this.setup(a);this.initializeVolumetricData();return!0},"~B");j(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]=u(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]=y(this.params.points.x);this.voxelCounts[1]=y(this.params.points.y);this.voxelCounts[2]=y(this.params.points.z);if(1>this.voxelCounts[0]||1>this.voxelCounts[1]||1>this.voxelCounts[2])return!1;this.showGridInfo();return!0});e(c$,"showGridInfo",function(){JU.Logger.info("grid origin  = "+this.params.origin);JU.Logger.info("grid steps   = "+
this.params.steps);JU.Logger.info("grid points  = "+this.params.points);this.ptTemp.x=this.params.steps.x*this.params.points.x;this.ptTemp.y=this.params.steps.y*this.params.points.y;this.ptTemp.z=this.params.steps.z*this.params.points.z;JU.Logger.info("grid lengths = "+this.ptTemp);this.ptTemp.add(this.params.origin);JU.Logger.info("grid max xyz = "+this.ptTemp)});e(c$,"setVoxelRange",function(a,b,c,d,e,f){b>=c&&(b=-10,c=10);var g=c-b,j=this.params.resolution;3.4028235E38!=j&&(d=j);c=E(Math.floor(g*
d))+1;c>e&&(0<(this.dataType&256)?3.4028235E38==j?(this.isQuiet||JU.Logger.info("Maximum number of voxels for index="+a+" exceeded ("+c+") -- set to "+e),c=e):this.isQuiet||JU.Logger.info("Warning -- high number of grid points: "+c):3.4028235E38==j&&(c=e));d=(c-1)/g;d<f&&(c=E(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");j(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$,"generateCube",function(){JU.Logger.info("data type: user volumeData");JU.Logger.info("voxel grid origin:"+this.volumetricOrigin);for(var a=0;3>
a;++a)JU.Logger.info("voxel grid vector:"+this.volumetricVectors[a]);JU.Logger.info("Read "+this.nPointsX+" x "+this.nPointsY+" x "+this.nPointsZ+" data points")});j(c$,"closeReader",function(){})});H("J.jvxl.readers");K(["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 $.Logger".split(" "),function(){c$=C(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.atomXyz=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;G(this,arguments)},J.jvxl.readers,"AtomDataReader",J.jvxl.readers.VolumeDataReader);W(c$,function(){this.atomData=new J.atomdata.AtomData;this.bsMySelected=new JU.BS;this.bsMyIgnored=new JU.BS;this.ptY0=new JU.P3;this.ptZ0=new JU.P3;this.pt0=new JU.P3i;this.pt1=new JU.P3i;this.ptV=new JU.P3});Q(c$,function(){Y(this,J.jvxl.readers.AtomDataReader,
[])});e(c$,"initADR",function(a){this.initVDR(a);this.precalculateVoxelData=!0},"J.jvxl.readers.SurfaceGenerator");j(c$,"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$,"setVolumeForPlane",
function(){this.useOriginStepsPoints?(this.xyzMin=JU.P3.newP(this.params.origin),this.xyzMax=JU.P3.newP(this.params.origin),this.xyzMax.add3((this.params.points.x-1)*this.params.steps.x,(this.params.points.y-1)*this.params.steps.y,(this.params.points.z-1)*this.params.steps.z)):null==this.params.boundingBox?(this.getAtoms(this.params.bsSelected,!1,!0,!1,!1,!1,!1,this.params.mep_marginAngstroms),null==this.xyzMin&&(this.xyzMin=JU.P3.new3(-10,-10,-10),this.xyzMax=JU.P3.new3(10,10,10))):(this.xyzMin=
JU.P3.newP(this.params.boundingBox[0]),this.xyzMax=JU.P3.newP(this.params.boundingBox[1]));this.setRanges(this.params.plane_ptsPerAngstrom,this.params.plane_gridMax,0)});e(c$,"getAtoms",function(a,b,c,d,e,f,g,j){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;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.atomXyz[d]))>
2*(this.atomData.atomRadius[d]=this.getWorkingRadius(d,j)))continue;this.bsMySelected.set(d);e=!this.havePlane}if(c&&(f||e))this.atomData.atomRadius[d]=this.getWorkingRadius(d,j)}e=c&&b?this.getWorkingRadius(-1,j):0;this.myAtomCount=JU.BSUtil.cardinalityOf(this.bsMySelected);j=JU.BSUtil.copy(this.bsMySelected);g=0;this.atomProp=null;this.theProperty=3.4028235E38;this.haveOneProperty=!1;a=this.params.theProperty;if(0<this.myAtomCount){var Oa=null;if(b){this.atomData.bsSelected=j;this.sg.atomDataServer.fillAtomData(this.atomData,
8);Oa=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;)Oa[--g]=this.atomData.hAtoms[d][b];g=Oa.length;JU.Logger.info(g+" attached hydrogens added")}b=g+this.myAtomCount;c&&(this.atomRadius=u(b,0));this.atomXyz=Array(b);null!=this.params.theProperty&&(this.atomProp=u(b,0));this.atomNo=p(b,0);this.atomIndex=p(b,0);this.myIndex=p(this.ac,0);for(d=0;d<g;d++)c&&(this.atomRadius[d]=e),this.atomXyz[d]=
Oa[d],this.atomNo[d]=-1,null!=this.atomProp&&this.addAtomProp(d,NaN);this.myAtomCount=g;for(d=j.nextSetBit(0);0<=d;d=j.nextSetBit(d+1))null!=this.atomProp&&this.addAtomProp(this.myAtomCount,null!=a&&d<a.length?a[d]:NaN),this.atomXyz[this.myAtomCount]=this.atomData.atomXyz[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;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.atomXyz[d],c?this.atomRadius[d]+0.5:0);Float.isNaN(this.params.scale)||(b=JU.V3.newVsub(this.xyzMax,this.xyzMin),b.scale(0.5),this.xyzMin.add(b),b.scale(this.params.scale),this.xyzMax.add2(this.xyzMin,b),this.xyzMin.sub(b));if(f&&0!=this.myAtomCount){f=
new JU.P3;this.bsNearby=new JU.BS;for(d=0;d<this.ac;d++)!j.get(d)&&!this.bsMyIgnored.get(d)&&(b=this.atomData.atomRadius[d],null!=this.params.thePlane&&Math.abs(this.volumeData.distancePointToPlane(this.atomData.atomXyz[d]))>2*b||(null!=this.params.theProperty&&(b+=this.maxDistance),f=this.atomData.atomXyz[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.atomXyz=JU.AU.arrayCopyObject(this.atomXyz,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.atomXyz[this.myAtomCount]=
this.atomData.atomXyz[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");e(c$,"setRadii",function(){if(null==this.rs){this.maxRS=0;this.rs=u(this.myAtomCount,0);this.rs2=u(this.myAtomCount,0);for(var a=0;a<this.myAtomCount;a++){var b=this.rs[a]=this.atomRadius[a]+this.sr;b>this.maxRS&&(this.maxRS=b);this.rs2[a]=this.rs[a]*this.rs[a]}}});e(c$,"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$,"setRanges",function(a,b,c){null!=this.xyzMin&&(this.ptsPerAngstrom=a,this.maxGrid=b,this.minPtsPerAng=c,this.setVolumeData(),J.jvxl.data.JvxlCoder.jvxlCreateHeader(this.volumeData,this.jvxlFileHeaderBuffer))},"~N,~N,~N");j(c$,"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=E(Math.floor(b/this.volumeData.volumetricVectorLengths[0]));var e=E(Math.floor(b/this.volumeData.volumetricVectorLengths[1]));
b=E(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$,"getAtomMinMax",function(a,b){for(var c=0;c<this.nPointsX;c++)b[c]=new JU.BS;for(var d=this.myAtomCount;0<=--d;)if(null==a||a.get(d)){this.setGridLimitsForAtom(this.atomXyz[d],this.atomRadius[d],
this.pt0,this.pt1);for(c=this.pt0.x;c<this.pt1.x;c++)b[c].set(d)}},"JU.BS,~A");e(c$,"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 j=null!=this.noFaceSpheres&&this.noFaceSpheres.get(g),p=g>=this.firstNearbyAtom,k=this.atomXyz[g],n=this.atomRadius[g];
if(!(c&&k.distance(this.point)>b+n+0.5)){var q=n+a;this.setGridLimitsForAtom(k,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 t=this.pt0.x;t<this.pt1.x;t++,this.ptV.add2(d,this.ptY0)){this.ptY0.setT(this.ptV);for(var r=this.pt0.y;r<this.pt1.y;r++,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 y=this.ptV.distance(k)-
n,w=this.volumeData.getPointIndex(t,r,u);if((0==a||y<=q)&&y<this.getVoxel(t,r,u,w)){if(p||c&&this.ptV.distance(this.point)>b)y=NaN;this.setVoxel(t,r,u,w,y);Float.isNaN(y)||(null!=this.voxelSource&&(this.voxelSource[w]=g+1),0>y&&j&&this.bsSurfaceVoxels.set(w))}}}}}}},"~N,~N");e(c$,"setVoxel",function(a,b,c,d,e){this.isProgressive?this.thisPlane[d%this.yzCount]=e:this.voxelData[a][b][c]=e},"~N,~N,~N,~N,~N")});H("J.jvxl.readers");K(["JU.P3","J.jvxl.readers.AtomDataReader","JU.P4","$.V3"],"J.jvxl.readers.IsoSolventReader",
"java.lang.Float java.util.Hashtable JU.BS $.Lst $.Measure J.jvxl.data.MeshData JU.BSUtil $.Logger $.MeshSurface $.TempArray".split(" "),function(){c$=C(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;na("J.jvxl.readers.IsoSolventReader.Edge")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Edge$();na("J.jvxl.readers.IsoSolventReader.Face")||J.jvxl.readers.IsoSolventReader.$IsoSolventReader$Face$();this.ecosASB2=this.dAB2=this.dAB=this.rBS2=this.rAS2=this.rBS=this.rAS=0;G(this,arguments)},J.jvxl.readers,"IsoSolventReader",J.jvxl.readers.AtomDataReader);W(c$,function(){this.ptS1=new JU.P3;this.ptS2=new JU.P3;this.vTemp=new JU.V3;this.plane=new JU.P4;this.ptTemp2=new JU.P3;
this.vTemp2=new JU.V3;this.p=new JU.P3});Q(c$,function(){Y(this,J.jvxl.readers.IsoSolventReader,[])});j(c$,"init",function(a){this.initADR(a)},"J.jvxl.readers.SurfaceGenerator");j(c$,"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=p(this.volumeData.nPoints,0));return!0},"~B");j(c$,"setup",function(a){this.setup2();if(null==this.contactPair){this.cavityRadius=this.params.cavityRadius;this.envelopeRadius=this.params.envelopeRadius;this.sr=this.params.solventRadius;this.point=this.params.point;this.isCavity=this.params.isCavity&&null!=this.meshDataServer;this.isPocket=null!=this.params.pocket&&null!=this.meshDataServer;this.doUseIterator=
this.doCalculateTroughs=!a&&null!=this.sg.atomDataServer&&!this.isCavity&&0<this.sr&&(1195==this.dataType||1203==this.dataType);this.getAtoms(this.params.bsSelected,this.doAddHydrogens,!0,!1,!1,!0,!1,NaN);if(this.isCavity||this.isPocket)this.dots=this.meshDataServer.calculateGeodesicSurface(this.bsMySelected,this.envelopeRadius);this.setHeader("solvent/molecular surface",this.params.calculationType);if(this.havePlane||!a)this.setRanges(this.params.solvent_ptsPerAngstrom,this.params.solvent_gridMax,
0),this.volumeData.getYzCount(),this.margin=2*this.volumeData.maxGrid;null!=this.bsNearby&&this.bsMySelected.or(this.bsNearby)}else a||this.setVolumeData();this.doCalculateTroughs||(a?(this.precalculateVoxelData=!1,this.volumeData.sr=this):this.isCavity||(this.isProgressive=this.isXLowToHigh=!0));null==this.thisAtomSet&&(this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount))},"~B");j(c$,"generateCube",function(){if(!(this.isCavity&&null!=this.params.theProperty)){this.isCavity&&1205!=this.dataType&&
1206!=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=p(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()&&V(a.get(b)[0],JU.P4)&&(this.volumeData.capData(a.get(b)[0],
this.params.cutoff),a.remove(b--))}});j(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,f,g,j,p,k,n,q,t){k=this.marchingCubes.getLinearOffset(g,j,p,k);n=this.marchingCubes.getLinearOffset(g,j,p,n);this.isSurfacePoint=null!=this.bsSurfaceVoxels&&(this.bsSurfaceVoxels.get(k)||this.bsSurfaceVoxels.get(n));if(null!=this.voxelSource){var r=Math.abs(Float.isNaN(d)||c<d?this.voxelSource[k]:this.voxelSource[n]);0<r&&(this.iAtomSurface=this.atomIndex[r-1])}if(J.jvxl.readers.IsoSolventReader.testLinear||
null==this.voxelSource||0==this.voxelSource[k]||this.voxelSource[k]!=this.voxelSource[n])return this.getSPF(a,b,c,d,e,f,g,j,p,k,n,q,t);a=q[0]=JU.MeshSurface.getSphericalInterpolationFraction(0>this.voxelSource[k]?this.sr:this.atomRadius[this.voxelSource[k]-1],c,d,f.length());t.scaleAdd2(a,f,e);return c+a*(d-c)},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");j(c$,"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");j(c$,"selectPocket",function(a){null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,1,null);for(var b=this.meshData.vs,c=this.meshData.vc,d=this.meshData.vvs,e=this.dots.length,f=0;f<c;f++)for(var g=0;g<e;g++)this.dots[g].distance(b[f])<this.envelopeRadius&&(d[f]=NaN);this.meshData.getSurfaceSet();b=this.meshData.nSets;c=JU.BS.newN(b);for(f=0;f<b;f++)if(null!=(d=this.meshData.surfaceSet[f]))for(g=d.nextSetBit(0);0<=
g;g=d.nextSetBit(g+1))if(Float.isNaN(this.meshData.vvs[g])){c.set(f);break}for(f=0;f<b;f++)null!=this.meshData.surfaceSet[f]&&c.get(f)==a&&this.meshData.invalidateSurfaceSet(f);this.updateSurfaceData();a||(this.meshData.surfaceSet=null);null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)},"~B");j(c$,"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 j=0;j<this.meshData.nSets;j++){var p=d[j];Math.abs(p)>f&&(f=Math.abs(p),g=0>p)}f=g?-1:1;for(j=0;j<this.meshData.nSets;j++)if(g=b[j],g.intersects(this.bsSurfacePoints)&&(null==d||d[j]*f>e)&&null!=this.params.vertexSource){p=new JU.BS;null==c&&(c=Array(b.length));for(var k=
g.nextSetBit(0);0<=k;k=g.nextSetBit(k+1)){var n=this.params.vertexSource[k];if(!(0>n)){if(a.get(n)){this.meshData.invalidateSurfaceSet(j);break}p.set(n)}}a.or(p)}else this.meshData.invalidateSurfaceSet(j);this.updateSurfaceData();null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,3,null),this.meshData=new J.jvxl.data.MeshData)}null!=this.params.thePlane&&null==this.params.slabInfo&&this.params.addSlabInfo(JU.TempArray.getSlabWithinRange(-100,0))});e(c$,"generateSolventCavity",
function(){for(var a=JU.BS.newN(this.nPointsX*this.nPointsY*this.nPointsZ),b=0,c=this.dots.length,d=0,e,f=this.envelopeRadius,g=0;g<this.nPointsX;++g)for(var j=0;j<this.nPointsY;++j){var p=0;a:for(;p<this.nPointsZ;++p,++b)if(3.4028235E38>(e=this.voxelData[g][j][p])&&e>=this.cavityRadius){this.volumeData.voxelPtToXYZ(g,j,p,this.ptV);for(var k=0;k<c;k++)if(this.dots[k].distance(this.ptV)<f)continue a;a.set(b);d++}}JU.Logger.info("cavities include "+d+" voxel points");this.atomRadius=u(d,0);this.atomXyz=
Array(d);for(c=b=g=0;g<this.nPointsX;++g)for(j=0;j<this.nPointsY;++j)for(p=0;p<this.nPointsZ;++p)a.get(b++)&&(this.volumeData.voxelPtToXYZ(g,j,p,this.atomXyz[c]=new JU.P3),this.atomRadius[c++]=this.voxelData[g][j][p]);this.myAtomCount=this.firstNearbyAtom=d;this.thisAtomSet=JU.BSUtil.setAll(this.myAtomCount);this.rs=null;this.setRadii()});e(c$,"generateSolventCube",function(){1205!=this.dataType&&(this.params.vertexSource=p(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$,"getEdges",function(){for(var a=0;a<this.myAtomCount;a++)this.bsLocale[a]=new JU.BS;for(a=0;a<this.myAtomCount;a++){var b=this.atomXyz[a],c=this.rs[a];for(this.sg.atomDataServer.setIteratorForAtom(this.iter,
this.atomIndex[a],c+this.maxRS);this.iter.hasNext();){var d=this.iter.next(),d=this.myIndex[d];if(!(a>=this.firstNearbyAtom&&d>=this.firstNearbyAtom)){var e=this.rs[d],f=b.distance(this.atomXyz[d]);f>=c+e||(e=ma(J.jvxl.readers.IsoSolventReader.Edge,this,null,this,a,d,f),this.vEdges.addLast(e),this.bsLocale[a].set(d),this.bsLocale[d].set(a),this.htEdges.put(e.toString(),e))}}}});e(c$,"findEdge",function(a,b){return this.htEdges.get(a<b?a+"_"+b:b+"_"+a)},"~N,~N");e(c$,"getFaces",function(){var a=new JU.BS;
this.validSpheres=new JU.BS;this.noFaceSpheres=JU.BSUtil.setAll(this.myAtomCount);for(var b=this.vEdges.size();0<=--b;){var c=this.vEdges.get(b),d=c.ia,e=c.ib;a.clearAll();a.or(this.bsLocale[d]);a.and(this.bsLocale[e]);for(var f=a.nextSetBit(e+1);0<=f;f=a.nextSetBit(f+1))if(this.getSolventPoints(c,d,e,f)){var g,j=!1;if(null!=(g=this.validateFace(d,e,f,c,this.ptS1)))this.vFaces.addLast(g),j=!0,g.dump();if(null!=(g=this.validateFace(d,e,f,c,this.ptS2)))this.vFaces.addLast(g),j||g.dump(),j=!0;j&&(this.noFaceSpheres.clear(d),
this.noFaceSpheres.clear(e),this.noFaceSpheres.clear(f))}}});e(c$,"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(),j=this.myIndex[g];if(!(j==a||j==b||j==c)&&this.atomData.atomXyz[g].distance(e)<this.atomData.atomRadius[g]+this.sr){f=!1;break}}g=this.findEdge(b,c);j=this.findEdge(a,c);e=f?ma(J.jvxl.readers.IsoSolventReader.Face,this,null,a,b,c,e):null;d.addFace(e);g.addFace(e);
j.addFace(e);if(!f)return null;this.validSpheres.set(a);this.validSpheres.set(b);this.validSpheres.set(c);return e},"~N,~N,~N,J.jvxl.readers.IsoSolventReader.Edge,JU.P3");e(c$,"markFaceVoxels",function(a){for(var b=new JU.BS,c=this.volumetricVectors[0],d=this.volumetricVectors[1],e=this.volumetricVectors[2],f=this.vFaces.size();0<=--f;){var g=this.vFaces.get(f),j=this.atomXyz[g.ia],p=this.atomXyz[g.ib],k=this.atomXyz[g.ic],n=g.pS;this.setGridLimitsForAtom(n,this.sr,this.pt0,this.pt1);this.volumeData.voxelPtToXYZ(this.pt0.x,
this.pt0.y,this.pt0.z,this.ptV);for(var q=this.pt0.x;q<this.pt1.x;q++,this.ptV.add2(c,this.ptY0)){this.ptY0.setT(this.ptV);for(var t=this.pt0.y;t<this.pt1.y;t++,this.ptV.add2(d,this.ptZ0)){this.ptZ0.setT(this.ptV);for(var r=this.pt0.z;r<this.pt1.z;r++,this.ptV.add(e)){var u=this.sr-this.ptV.distance(n),y=this.voxelData[q][t][r],w=this.volumeData.getPointIndex(q,t,r);a&&0<u&&this.bsSurfaceDone.set(w);if(JU.Measure.isInTetrahedron(this.ptV,j,p,k,n,this.plane,this.vTemp,this.vTemp2,!1)&&(!a?!this.bsSurfaceDone.get(w)&&
0>u&&u>1.8*-this.volumeData.maxGrid&&u>y==b.get(w):0<u&&(0>y||3.4028235E38==y||u>y==b.get(w))))b.set(w),this.setVoxel(q,t,r,w,u),null!=this.voxelSource&&(this.voxelSource[w]=-1-g.ia),0<u&&this.bsSurfaceVoxels.set(w)}}}}},"~B");e(c$,"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,j=this.atomXyz[f],p=this.atomXyz[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 k=this.pt0.z;k<this.pt1.z;k++,this.ptV.add(c)){var n=this.checkSpecialVoxel(j,p,this.ptV);
if(!Float.isNaN(n)&&(n=this.sr-n,n<this.voxelData[e][g][k])){var q=this.volumeData.getPointIndex(e,g,k);this.setVoxel(e,g,k,q,n);null!=this.voxelSource&&(this.voxelSource[q]=-1-f)}}}}}}});j(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.atomXyz[b]);JU.Measure.getPlaneThroughPoint(this.p,f,this.plane);b=Math.sin(c)*e;a=this.atomXyz[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$,"dumpPoint",function(a,b,
c){this.sg.log('draw ID "'+b+this.nTest++ +'"'+JU.P3.newP(a)+" color "+c)},"JU.P3,~S,~S");j(c$,"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.atomXyz[c])-this.rs[c];d<b&&(b=d)}return 3.4028235E38==b?NaN:b},"JU.T3,~B");j(c$,"discardTempData",function(a){this.rs2=this.rs=null;this.discardTempDataSR(a)},"~B");j(c$,"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(){la(self.c$);c$=C(function(){oa(this,arguments);this.cosASB2=this.maxr=this.d2=this.d=this.nInvalid=this.nFaces=this.ib=this.ia=0;this.v=
null;G(this,arguments)},J.jvxl.readers.IsoSolventReader,"Edge",JU.P3);Za(c$,function(a,b,c,d){this.ia=Math.min(b,c);this.ib=Math.max(b,c);this.d=d;this.d2=d*d;this.maxr=Math.sqrt(this.d2/4+Math.max(a.rs2[b],a.rs2[c]));this.ave(a.atomXyz[b],a.atomXyz[c]);this.cosASB2=(a.rs2[b]+a.rs2[c]-this.d2)/(a.rs[c]*a.rs[b]);this.v=JU.V3.newVsub(a.atomXyz[c],a.atomXyz[b]);this.v.normalize()},"J.jvxl.readers.IsoSolventReader,~N,~N,~N");e(c$,"addFace",function(a){this.nFaces++;null==a&&this.nInvalid++},"J.jvxl.readers.IsoSolventReader.Face");
e(c$,"isValid",function(){return 0==this.nFaces||this.nInvalid!=this.nFaces});j(c$,"toString",function(){return this.ia+"_"+this.ib});c$=fa()};c$.$IsoSolventReader$Face$=function(){la(self.c$);c$=C(function(){oa(this,arguments);this.ic=this.ib=this.ia=0;this.pS=null;G(this,arguments)},J.jvxl.readers.IsoSolventReader,"Face");Q(c$,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");e(c$,"dump",function(){var a=this.b$["J.jvxl.readers.IsoSolventReader"].atomXyz[this.ia],
b=this.b$["J.jvxl.readers.IsoSolventReader"].atomXyz[this.ib],c=this.b$["J.jvxl.readers.IsoSolventReader"].atomXyz[this.ic];this.b$["J.jvxl.readers.IsoSolventReader"].sg.log('draw ID "x'+("f"+this.ia+"_"+this.ib+"_"+this.ic+"_")+this.b$["J.jvxl.readers.IsoSolventReader"].nTest++ +'" '+JU.P3.newP(a)+" "+JU.P3.newP(b)+" "+JU.P3.newP(c)+" color red")});j(c$,"toString",function(){return this.ia+"_"+this.ib+"_"+this.ic+"_"+this.pS});c$=fa()};R(c$,"testLinear",!1)});H("J.jvxl.readers");K(["J.jvxl.readers.SurfaceReader"],
"J.jvxl.readers.SurfaceFileReader",["JU.PT","J.api.Interface"],function(){c$=C(function(){this.next=this.line=this.out=this.binarydoc=this.br=null;G(this,arguments)},J.jvxl.readers,"SurfaceFileReader",J.jvxl.readers.SurfaceReader);W(c$,function(){this.next=p(1,0)});Q(c$,function(){Y(this,J.jvxl.readers.SurfaceFileReader,[])});e(c$,"setStream",function(a,b){this.binarydoc.setStream(this.sg.atomDataServer.getJzt(),null==a?null:this.sg.atomDataServer.getBufferedInputStream(a),b)},"~S,~B");j(c$,"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.init(a);this.br=b},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"newBinaryDocument",function(){return J.api.Interface.getInterface("JU.BinaryDocument",this.sg.atomDataServer,"file")});j(c$,"setOutputChannel",function(a){null==this.binarydoc?this.out=a:this.sg.setOutputChannel(this.binarydoc,
a)},"JU.OC");j(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()});j(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})});H("J.jvxl.readers");K(["J.jvxl.readers.SurfaceFileReader"],"J.jvxl.readers.VolumeFileReader","java.lang.Float JU.AU $.PT $.SB J.api.Interface J.atomdata.AtomData JU.Logger".split(" "),function(){c$=C(function(){this.negativeAtomCount=this.endOfData=!1;this.nSurfaces=this.ac=0;this.canDownsample=this.isAngstroms=!1;this.downsampleRemainders=null;this.preProcessPlanes=!1;this.nData=
0;this.readerClosed=!1;this.nSkipZ=this.nSkipY=this.nSkipX=this.downsampleFactor=0;this.yzPlanesRaw=null;this.iPlaneRaw=0;this.boundingBox=null;this.isScaledAlready=!1;G(this,arguments)},J.jvxl.readers,"VolumeFileReader",J.jvxl.readers.SurfaceFileReader);Q(c$,function(){Y(this,J.jvxl.readers.VolumeFileReader,[])});j(c$,"init2",function(a,b){this.init2VFR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2VFR",function(a,b){this.init2SFR(a,b);this.canDownsample=this.isProgressive=
this.isXLowToHigh=!0;this.jvxlData.wasCubic=!0;this.boundingBox=this.params.boundingBox;4==this.params.qmOrbitalType&&(this.hasColorData=null==this.params.parameters||0<=this.params.parameters[1],this.preProcessPlanes=!0,this.params.insideOut=!this.params.insideOut)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"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");j(c$,"closeReader",
function(){this.readerClosed||(this.readerClosed=!0,this.closeReaderSFR(),0==this.nData||-3.4028235E38==this.dataMax||(this.dataMean/=this.nData,JU.Logger.info("VolumeFileReader closing file: "+this.nData+" points read \ndata min/max/mean = "+this.dataMin+"/"+this.dataMax+"/"+this.dataMean)))});j(c$,"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");j(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$,"readVolumetricHeader",function(){try{this.readParameters();if(-2147483648==this.ac)return 0;this.vertexDataOnly||JU.Logger.info("voxel grid origin:"+
this.volumetricOrigin);var a=this.params.downsampleFactor,b=this.canDownsample&&1<a;1<a&&!this.canDownsample&&(this.jvxlData.msg+="\ncannot downsample this file type");if(b){this.downsampleRemainders=p(3,0);JU.Logger.info("downsample factor = "+a);for(var c=0;3>c;++c){var d=this.voxelCounts[c];this.downsampleRemainders[c]=d%a;this.voxelCounts[c]/=a;this.isPeriodic&&(this.voxelCounts[c]++,this.downsampleRemainders[c]--);this.volumetricVectors[c].scale(a);JU.Logger.info("downsampling axis "+(c+1)+" from "+
d+" to "+this.voxelCounts[c])}}if(!this.vertexDataOnly)for(c=0;3>c;++c)this.isAngstroms||this.volumetricVectors[c].scale(0.5291772),this.line=this.voxelCounts[c]+" "+this.volumetricVectors[c].x+" "+this.volumetricVectors[c].y+" "+this.volumetricVectors[c].z,this.jvxlFileHeaderBuffer.append(this.line).appendC("\n"),JU.Logger.info("voxel grid count/vector:"+this.line);this.scaleIsosurface(this.params.scale);this.volumeData.setVolumetricXml();return this.nSurfaces}catch(e){if(U(e,Exception))return JU.Logger.error(e.toString()),
0;throw e;}});e(c$,"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});j(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=u(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");
e(c$,"getPlane",function(a){0==a&&this.initPlanes();if(this.preProcessPlanes)return this.getPlaneProcessed(a);a=this.getPlane2(a);null==this.qpc&&this.getPlane(a,!0);return a},"~N");e(c$,"getPlaneProcessed",function(a){var b;if(0==this.iPlaneRaw){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,null,b.atomXyz,-1,null,null,null,null,null,null,this.params.isSquaredLinear,null,this.params.theProperty,!0,null,this.params.parameters,this.params.testFlags);this.iPlaneRaw=1;this.qpc.setPlanes(this.yzPlanesRaw=u(4,this.yzCount,0));if(this.hasColorData){this.getPlane(this.yzPlanesRaw[0],!1);this.getPlane(this.yzPlanesRaw[1],!1);b=this.yzPlanes[0];for(a=0;a<this.yzCount;a++)b[a]=NaN;return b}this.iPlaneRaw=-1}var c=this.qpc.getNoValue(),d=this.nPointsX-1;switch(this.iPlaneRaw){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.iPlaneRaw];break;default:this.iPlaneRaw++,b=this.yzPlanesRaw[this.iPlaneRaw]}if(a<d){this.getPlane(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$,"getPlane",
function(a,b){try{for(var c=0,d=0;c<this.nPointsY;++c){for(var e=0;e<this.nPointsZ;++e){var f=this.getNextVoxelValue();b&&this.recordData(f);a[d++]=f;0!=this.nSkipX&&this.skipVoxels(this.nSkipX)}0!=this.nSkipY&&this.skipVoxels(this.nSkipY)}0!=this.nSkipZ&&this.skipVoxels(this.nSkipZ)}catch(g){if(!U(g,Exception))throw g;}},"~A,~B");j(c$,"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});j(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");j(c$,"getSurfacePointAndFraction",function(a,b,c,d,e,f,g,j,p,k,n,q,t){return this.getSPFv(a,b,c,d,e,f,g,j,p,k,n,q,t)},
"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"getSPFv",function(a,b,c,d,e,f,g,j,p,k,n,q,t){a=this.getSPF(a,b,c,d,e,f,g,j,p,k,n,q,t);if(null==this.qpc||Float.isNaN(a)||!this.hasColorData)return a;k=this.marchingCubes.getLinearOffset(g,j,p,k);n=this.marchingCubes.getLinearOffset(g,j,p,n);return this.qpc.process(k,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})});H("J.jvxl.readers");K(["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 $.Logger".split(" "),
function(){c$=C(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;G(this,
arguments)},J.jvxl.readers,"JvxlXmlReader",J.jvxl.readers.VolumeFileReader);Q(c$,function(){Y(this,J.jvxl.readers.JvxlXmlReader,[])});j(c$,"init2",function(a,b){this.init2JXR(a,b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");e(c$,"init2JXR",function(a,b){this.init2VFR(a,b);this.jvxlData.wasJvxl=this.isJvxl=!0;this.isXLowToHigh=this.canDownsample=!1;this.xr=new J.jvxl.readers.XmlReader(b)},"J.jvxl.readers.SurfaceGenerator,java.io.BufferedReader");j(c$,"readVolumeData",function(a){if(!this.readVolumeDataVFR(a))return!1;
this.strFractionTemp=this.jvxlEdgeDataRead;this.fractionPtr=0;return!0},"~B");j(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");j(c$,"readParameters",function(){var a=this.xr.getXmlData("jvxlFileTitle",null,!1,!1);this.jvxlFileHeaderBuffer=JU.SB.newS(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$,"readVector",function(a){var b=this.xr.getXmlData("jvxlVolumeVector",this.tempDataXml,!0,!0);this.tempDataXml=this.tempDataXml.substring(this.tempDataXml.indexOf(b)+b.length);var c=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(b,
"count"));-2147483648==c&&(this.vertexDataOnly=!0);this.voxelCounts[a]=0>c?0:c;this.volumetricVectors[a].setT(this.xr.getXmlPoint(b,"vector"));this.isAnisotropic&&this.setVectorAnisotropy(this.volumetricVectors[a])},"~N");j(c$,"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=J.jvxl.readers.XmlReader.getXmlAttrib(b,"contoured").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=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$,"jvxlSetColorRanges",function(a,b,c,d,e){this.jvxlDataIsColorMapped&&(!Float.isNaN(a)&&!Float.isNaN(b)&&(0==b&&0==a&&(a=-1,b=1),this.params.mappedDataMin=a,this.params.mappedDataMax=b,JU.Logger.info("JVXL read: data_min/max "+this.params.mappedDataMin+"/"+this.params.mappedDataMax)),this.params.rangeDefined||(!Float.isNaN(c)&&!Float.isNaN(d)?(0==c&&0==d&&(c=-1,d=1),this.params.valueMappedToRed=Math.min(c,d),this.params.valueMappedToBlue=Math.max(c,
d),this.params.isColorReversed=c>d):(this.params.valueMappedToRed=0,this.params.valueMappedToBlue=1),this.params.rangeDefined=!0),JU.Logger.info("JVXL read: color red/blue: "+this.params.valueMappedToRed+"/"+this.params.valueMappedToBlue));this.jvxlData.valueMappedToRed=this.params.valueMappedToRed;this.jvxlData.valueMappedToBlue=this.params.valueMappedToBlue;this.jvxlData.mappedDataMin=this.params.mappedDataMin;this.jvxlData.mappedDataMax=this.params.mappedDataMax;this.jvxlData.isColorReversed=this.params.isColorReversed;
this.jvxlData.insideOut=e;this.params.insideOut&&(this.jvxlData.insideOut=!this.jvxlData.insideOut);this.params.insideOut=this.jvxlData.insideOut},"~N,~N,~N,~N,~B");j(c$,"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$,"jvxlReadFractionData",function(a){var b;try{if(a.equals("edge"))b=
J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(this.tempDataXml,"data"));else{var c=this.xr.getXmlData("jvxlColorData",null,!0,!1);this.jvxlData.isJvxlPrecisionColor=J.jvxl.readers.JvxlXmlReader.getEncoding(c).endsWith("2");b=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(c,"data"))}}catch(d){if(U(d,Exception))throw JU.Logger.error("Error reading "+a+" data "+d),new NullPointerException;throw d;}return b},"~S,~N");j(c$,"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");j(c$,"getSurfacePointAndFraction",function(a,
b,c,d,e,f,g,j,p,k,n,q,t){if(0>=this.edgeDataCount)return this.getSPFv(a,b,c,d,e,f,g,j,p,k,n,q,t);t.scaleAdd2(q[0]=this.jvxlGetNextFraction(this.edgeFractionBase,this.edgeFractionRange,0.5),f,e);Float.isNaN(this.valueMin)&&this.setValueMinMax();return 0==this.valueCount||this.includeValueNaN&&Float.isNaN(q[0])?q[0]:this.getNextValue()},"~N,~B,~N,~N,JU.T3,JU.V3,~N,~N,~N,~N,~N,~A,JU.T3");e(c$,"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");j(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=
p(a,0);for(var d=p(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 j=J.jvxl.readers.JvxlXmlReader.getColor(a[d]);0==j?j=g:g=j;b[d]=JU.C.getColixTranslucent(this.jvxlData.vertexColors[d]=j);JU.C.isColixTranslucent(b[d])?e=!0:0!=f&&(b[d]=JU.C.getColixTranslucent3(b[d],!0,f))}catch(u){if(U(u,Exception))JU.Logger.info("JvxlXmlReader: Cannot interpret color code: "+a[d]);
else throw u;}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 k=Float.isNaN(this.valueMin);k&&this.setValueMinMax();var n=3.4028235E38,q=-3.4028235E38;if(null==b||b.length<a)this.meshData.vcs=b=Z(a,0);e=j=0;this.params.colorBySign&&(e=JU.C.getColix(this.params.isColorReversed?this.params.colorNeg:this.params.colorPos),j=JU.C.getColix(this.params.isColorReversed?this.params.colorPos:
this.params.colorNeg));for(var f=this.meshData.vertexIncrement,t=3.4028235E38==this.params.mappedDataMin,d=0;d<a;d+=f)g=k?c[d]=this.getNextValue():c[d],t&&(g<n&&(n=g),g>q&&(q=g));t&&(this.params.mappedDataMin=n,this.params.mappedDataMax=q);if(null!=this.jvxlData.colorScheme){k=null!=this.marchingSquares&&this.params.isContoured;for(d=0;d<a;d+=f)g=c[d],k?this.marchingSquares.setContourData(d,g):(g=!this.params.colorBySign?this.params.colorEncoder.getColorIndex(g):(this.params.isColorReversed?0<g:0>=
g)?j: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"),j=J.jvxl.readers.JvxlXmlReader.getEncoding(a);if("none".equals(j)){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="+y(d[0])+"; expected "+3*c);g=0;for(j=1;g<c;g++){var p=JU.P3.new3(d[j++],d[j++],d[j++]);b?e[g]=p:this.addVertexCopy(p,0,g,!1)}}else{var k=this.xr.getXmlPoint(a,"min"),n=this.xr.getXmlPoint(a,"max");n.sub(k);var q=this.jvxlData.colorFractionBase,t=this.jvxlData.colorFractionRange,r=J.jvxl.data.JvxlCoder.jvxlDecompressString(g);0==r.length&&(r=this.xr.getXmlData("jvxlVertexData",a,!1,!1));g=0;for(j=-1;g<c;g++)p=new JU.P3,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(r.charCodeAt(++j),
r.charCodeAt(j+d),q,t),p.x=k.x+f*n.x,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(r.charCodeAt(++j),r.charCodeAt(j+d),q,t),p.y=k.y+f*n.y,f=J.jvxl.data.JvxlCoder.jvxlFractionFromCharacter2(r.charCodeAt(++j),r.charCodeAt(j+d),q,t),p.z=k.z+f*n.z,b?e[g]=p:this.addVertexCopy(p,0,g,!1)}return e},"~S,~B");e(c$,"jvxlDecodeTriangleData",function(a,b,c){var d=this.parseIntStr(J.jvxl.readers.XmlReader.getXmlAttrib(a,"count"));if(!(0>d)){var e=p(1,0),f=null==c?-1:1,g=0;JU.Logger.info("Reading "+d+" triangles");
var j=J.jvxl.readers.JvxlXmlReader.getEncoding(a);a=this.getData(a,"jvxlTriangleData");b=this.getData(b,"jvxlTriangleEdgeData");var u=p(3,0),k=p(1,0),n=null,q=7,t=!"none".equals(j);if(t)a=J.jvxl.data.JvxlCoder.jvxlDecompressString(a),b=J.jvxl.data.JvxlCoder.jvxlDecompressString(b).trim(),j=b.length==d;else{var r=JU.PT.parseIntNext(a,k);(j=0<b.length)?(n=p(1,0),JU.PT.parseIntNext(b,n)):0<r&&JU.Logger.info("JvxlXmlReader: jvxlTriangleEdgeData count="+r+"; expected "+d)}for(var w=r=0,y=0,E=-1;r<d;){if(t){var C=
a.charAt(++E);switch(C){case "!":C=0;break;case "+":case ".":case " ":case "\n":case "\r":case "\t":case ",":continue;case "-":case "0":case "1":case "2":case "3":case "4":case "5":case "6":case "7":case "8":case "9":k[0]=E;C=JU.PT.parseIntNext(a,k);E=k[0]-1;break;default:C=C.charCodeAt(0)-92}w+=C}else w=JU.PT.parseIntNext(a,k)-1;u[y]=w;if(3==++y){y=0;if(j&&(q=null==n?b.charCodeAt(r)-48:JU.PT.parseIntNext(b,n),0>q||7<q))q=7;0==--f&&(f=JU.PT.parseIntNext(c,e),C=JU.PT.parseIntNext(c,e),-2147483648==
C?f=0:g=C|4278190080);this.addTriangleCheck(u[0],u[1],u[2],q,g,!1,g);r++}}}},"~S,~S,~S");e(c$,"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,j=this.xr.getXmlData("jvxlContour",b.substring(f),!0,!1),p=this.parseFloatStr(J.jvxl.readers.XmlReader.getXmlAttrib(j,"value"));d.append(" ").appendF(p);var k=J.jvxl.readers.JvxlXmlReader.getColor(J.jvxl.readers.XmlReader.getXmlAttrib(j,
"color")),n=JU.C.getColix(k);e.append(" ").append(JU.Escape.escapeColor(k));var q=J.jvxl.data.JvxlCoder.jvxlDecompressString(J.jvxl.readers.XmlReader.getXmlAttrib(j,"data")),t=J.jvxl.data.JvxlCoder.jvxlDecodeBitSet(this.xr.getXmlData("jvxlContour",j,!1,!1)),j=t.length();J.shapesurface.IsosurfaceMesh.setContourVector(g,j,t,p,n,k,JU.SB.newS(q));c.addLast(g)}j=c.size();if(0<j){a.vContours=JU.AU.createArrayOfArrayList(j);a.contourColixes=this.params.contourColixes=Z(j,0);a.contourValues=this.params.contoursDiscrete=
u(j,0);for(f=0;f<j;f++)a.vContours[f]=c.get(f),a.contourValues[f]=a.vContours[f].get(2).floatValue(),a.contourColixes[f]=a.vContours[f].get(3)[0];a.contourColors=JU.C.getHexCodes(a.contourColixes);JU.Logger.info("JVXL read: "+j+" discrete contours");JU.Logger.info("JVXL read: contour values: "+d);JU.Logger.info("JVXL read: contour colors: "+e)}}},"J.jvxl.data.JvxlData,~S");j(c$,"postProcessVertices",function(){var a=this.params.bsExcluded[1];null!=a&&(null!=this.meshDataServer&&this.meshDataServer.fillMeshData(this.meshData,
1,null),this.meshData.invalidateVertices(a),null!=this.meshDataServer&&(this.meshDataServer.fillMeshData(this.meshData,4,null),this.meshData=new J.jvxl.data.MeshData),this.updateTriangles())})});H("J.rendersurface");K(["J.render.MeshRenderer"],"J.rendersurface.IsosurfaceRenderer",["java.lang.Boolean","$.Float","JU.V3","JU.C","$.Normix"],function(){c$=C(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;G(this,arguments)},J.rendersurface,"IsosurfaceRenderer",J.render.MeshRenderer);j(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.connections||this.vwr.ms.at[this.imesh.connections[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$,"setGlobals",function(){this.needTranslucent=!1;this.antialias=this.g3d.isAntialiased();this.iShowNormals=this.vwr.getTestFlag(4);this.showNumbers=this.vwr.getTestFlag(3);this.isosurface=this.shape;this.exportPass=this.isExport?2:0;this.isNavigationMode=this.vwr.getBoolean(603979888);this.showKey=this.vwr.getBoolean(603979869)?
Boolean.TRUE:null;this.isosurface.keyXy=null;this.meshScale=-1;this.globalSlabValue=this.vwr.gdata.slab;this.mySlabValue=this.isNavigationMode?y(this.tm.getNavigationOffset().z):2147483647});e(c$,"renderInfo",function(){if(!this.isExport&&this.hasColorRange&&!(null==this.imesh.colorEncoder||Boolean.TRUE!==this.showKey)){this.showKey=Boolean.FALSE;var a=null,b=null,c=null,d=0,e=0;if(this.imesh.showContourLines)if(c=this.imesh.getContours(),null==c){b=this.imesh.jvxlData.contourColixes;if(null==b)return;
d=b.length}else d=c.length,e=1;else a=this.imesh.colorEncoder.getColorSchemeArray(this.imesh.colorEncoder.currentPalette),d=null==a?0:a.length,e=2;if(!(2>d)){var f=this.antialias?2:1,g=this.vwr.getScreenHeight()*f,j=E(E(g/2)/(d-1)),g=3*E(g/4)-j,u=10*f,k=20*f;this.isosurface.keyXy=p(-1,[E(u/f),0,E((u+k)/f),E((g+j)/f),E(j/f)]);for(var n=0;n<d;n++,g-=j){switch(e){case 0:if(!this.g3d.setC(b[n]))return;break;case 1:if(!this.g3d.setC(c[n].get(3)[0]))return;break;case 2:this.vwr.gdata.setColor(a[n])}this.g3d.fillTextRect(u,
g,5,-2147483648,k,j)}this.isosurface.keyXy[1]=E((g+j)/f)}}});e(c$,"renderMeshSlab",function(){this.volumeRender=this.imesh.jvxlData.colorDensity&&this.imesh.jvxlData.allowVolumeRender;var a=this.mySlabValue;this.frontOnly=this.mesh.frontOnly||26==this.shapeID;if(!this.isNavigationMode&&(this.meshSlabValue=this.imesh.jvxlData.slabValue,-2147483648!=this.meshSlabValue&&this.imesh.jvxlData.isSlabbable)){for(var b=this.imesh.jvxlData.boundingBox,a=3.4028235E38,c=1.4E-45,d=b.length;0<=--d;)this.pt2f.setT(b[d]),
this.tm.transformPt3f(this.pt2f,this.pt2f),this.pt2f.z<a&&(a=this.pt2f.z),this.pt2f.z>c&&(c=this.pt2f.z);a=Math.round(a+(c-a)*(100-this.meshSlabValue)/100);this.frontOnly=(new Boolean(this.frontOnly&100<=this.meshSlabValue)).valueOf()}b=this.vwr.gdata.translucentCoverOnly;this.vwr.gdata.translucentCoverOnly=this.frontOnly||!this.vwr.getBoolean(603979967);this.thePlane=this.imesh.jvxlData.jvxlPlane;this.vertexValues=this.mesh.vvs;2147483647!=a&&this.imesh.jvxlData.isSlabbable?(this.g3d.setSlab(a),
a=this.renderMesh2(this.mesh),this.g3d.setSlab(this.globalSlabValue)):a=this.renderMesh2(this.mesh);this.vwr.gdata.translucentCoverOnly=b;return a});j(c$,"render2",function(a){if(this.volumeRender)this.renderPoints();else{switch(this.imesh.dataType){case 70:this.renderLonePair(!1);return;case 71:this.renderLonePair(!0);return}this.isBicolorMap=this.imesh.jvxlData.isBicolorMap;this.render2b(a);this.g3d.setC(4)&&this.imesh.showContourLines&&this.renderContourLines()}},"~B");e(c$,"renderLonePair",function(a){this.pt2f.setT(this.vertices[1]);
this.tm.transformPt3f(this.pt2f,this.pt2f);var b=y(this.vwr.tm.scaleToScreen(y(this.pt2f.z),100));1>b&&(b=1);if(!a){var c=new JU.V3;a=new JU.V3;this.pt1f.setT(this.vertices[0]);this.tm.transformPt3f(this.pt1f,this.pt1f);c.sub2(this.pt2f,this.pt1f);a.set(c.x,c.y,c.z+1);a.cross(a,c);a.normalize();c=this.vwr.tm.scaleToScreen(y(this.pt1f.z),100);a.scale(c);this.pt1f.add2(this.pt2f,a);this.pt2f.sub(a);this.screens[0].set(Math.round(this.pt1f.x),Math.round(this.pt1f.y),Math.round(this.pt1f.z));this.g3d.fillSphereI(b,
this.screens[0])}this.screens[1].set(Math.round(this.pt2f.x),Math.round(this.pt2f.y),Math.round(this.pt2f.z));this.g3d.fillSphereI(b,this.screens[1])},"~B");e(c$,"renderContourLines",function(){var a=this.imesh.getContours();if(null==a)null!=this.imesh.jvxlData.contourValues&&(this.hasColorRange=!0);else{this.hasColorRange=0==this.mesh.meshColix;for(var b=a.length;0<=--b;){var c=a[b];if(!(6>c.size())){this.colix=0==this.mesh.meshColix?c.get(3)[0]:this.mesh.meshColix;if(!this.g3d.setC(this.colix))break;
for(var d=c.size()-1,e=this.getDiameter(),f=6;f<d;f++){var g=c.get(f),j=c.get(++f);if(Float.isNaN(g.x)||Float.isNaN(j.x))break;this.tm.transformPtScrT3(g,this.pt1f);this.tm.transformPtScrT3(j,this.pt2f);this.pt1f.z-=2;this.pt2f.z-=2;!this.antialias&&1==e?this.g3d.drawLineAB(this.pt1f,this.pt2f):this.g3d.fillCylinderBits(1,e,this.pt1f,this.pt2f)}}}}});j(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(553648144),this.frontOnly=!1):c=E(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?E(this.vwr.getScreenWidth()/2):0,f=this.showNumbers?E(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&&0>this.transformedVectors[this.normixes[g]].z||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 j=g+(this.mesh.isColorSolid?"":" "+this.mesh.vvs[g]);this.g3d.setC(4);this.g3d.drawStringNoSlab(j,null,this.screens[g].x,this.screens[g].y,this.screens[g].z-30,0)}this.volumeRender?(c=y(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,E(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(p){}this.volumeRender&&this.g3d.volumeRender(!1)});j(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,j=this.colix;null!=this.imesh.jvxlData.jvxlPlane&&(!f&&!a&&this.mesh.fillTriangles)&&(f=!0,j=4);var p=f&&null!=this.mesh.pcs;p&&(!a&&this.mesh.fillTriangles)&&(p=!1);var k=this.imesh.jvxlData.contourColixes;this.hasColorRange=!f&&!this.isBicolorMap;for(var n=this.getDiameter(),q=this.mesh.pc;0<=--q;){var t=d[q];if(!(null==t||this.selectedPolyOnly&&!this.bsPolygons.get(q))){var r=t[0],u=t[1],w=t[2];if(!(0<=this.imesh.jvxlData.thisSet&&
null!=this.mesh.vertexSets&&this.mesh.vertexSets[r]!=this.imesh.jvxlData.thisSet)&&(!this.haveBsDisplay||this.mesh.bsDisplay.get(r)&&this.mesh.bsDisplay.get(u)&&this.mesh.bsDisplay.get(w))){var y=this.normixes[r],C=this.normixes[u],E=this.normixes[w],B=this.checkNormals(y,C,E);if(!(a&&0==B)){var D,A,G;if(f){if(p&&q<this.mesh.pcs.length){D=this.mesh.pcs[q];if(0==D)continue;j=D}b&&(j=Math.round(10*Math.random())+5);D=A=G=j}else if(D=e[r],A=e[u],G=e[w],this.isBicolorMap){if(D!=A||A!=G)continue;this.isGhostPass&&
(D=A=G=JU.C.copyColixTranslucency(this.mesh.slabColix,D))}if(a)c?this.bsPolygonsToExport.set(q):(u==w?(this.setColix(D),r==u?this.g3d.fillSphereI(n,this.screens[r]):this.g3d.fillCylinder(3,n,this.screens[r],this.screens[u])):this.mesh.colorsExplicit?(this.vwr.gdata.setColor(t[4]),D=JU.C.copyColixTranslucency(this.mesh.colix,2047),this.g3d.setC(D),this.g3d.fillTriangle3CN(this.screens[r],D,y,this.screens[u],D,C,this.screens[w],D,E)):(this.isTranslucentInherit&&null!=e&&(D=JU.C.copyColixTranslucency(this.mesh.slabColix,
e[r]),A=JU.C.copyColixTranslucency(this.mesh.slabColix,e[u]),G=JU.C.copyColixTranslucency(this.mesh.slabColix,e[w])),this.g3d.fillTriangle3CN(this.screens[r],D,y,this.screens[u],A,C,this.screens[w],G,E)),this.iShowNormals&&this.renderNormals());else if(B&=t[3],0!=B){b&&(B=7);this.pt1i.setT(this.screens[r]);this.pt2i.setT(this.screens[u]);this.pt3i.setT(this.screens[w]);this.pt1i.z-=2;this.pt2i.z-=2;this.pt3i.z-=2;if(!g)if(p)this.g3d.setC(this.mesh.fillTriangles?4:k[t[4]%k.length]);else{this.drawTriangle(this.pt1i,
D,this.pt2i,A,this.pt3i,G,B,n);continue}this.drawTriangle(this.pt1i,j,this.pt2i,j,this.pt3i,j,B,n)}}}}}c&&this.exportSurface(f?j:0)},"~B,~B,~B");e(c$,"getDiameter",function(){var a;0>=this.mesh.diameter?(a=0>this.meshScale?this.meshScale=this.vwr.getInt(553648151):this.meshScale,this.antialias&&(a*=2)):a=E(this.vwr.getScreenDim()/100);1>a&&(a=1);return a});e(c$,"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]))&&!(100<b)){this.pt1f.setT(this.vertices[b]);var c=this.mesh.normixes[b];0<=c&&(this.pt1f.scaleAdd2(3,a[c],this.pt1f),this.tm.transformPtScrT3(this.pt1f,this.pt1f),this.pt1f.set(this.screens[b].x,this.screens[b].y,this.screens[b].z),this.g3d.drawLineAB(this.pt1f,this.pt1f))}}})})})(Clazz,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.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);
