(function(U,V,W,X,R,Y,D,L,B,E,G,S,Z,I,$,H,v,M,P,Q,N,O,aa,T,ba,ca,da,ea,fa,ga,K,ha,ia,ja,ka,la,ma,na,oa,pa,qa,ra,sa,ta,ua,va,wa,xa,ya,za,Aa,Ba,Ca,Da,Ea,Fa,Ga,Ha,h,p){D("JS");B(["JU.BS","$.V3"],"JS.VTemp",null,function(){c$=G(function(){this.bsTemp=this.vNorm4=this.vNorm3=this.vNorm2=this.vTemp2=this.vTemp1=this.vB=this.vA=this.vTemp=null;E(this,arguments)},JS,"VTemp");N(c$,function(){this.vTemp=new JU.V3;this.vA=new JU.V3;this.vB=new JU.V3;this.vTemp1=new JU.V3;this.vTemp2=new JU.V3;this.vNorm2=new JU.V3;
this.vNorm3=new JU.V3;this.vNorm4=new JU.V3;this.bsTemp=new JU.BS})});D("J.api");T(J.api,"SmilesMatcherInterface");D("JS");B(["J.api.SmilesMatcherInterface"],"JS.SmilesMatcher","JU.AU $.BS $.PT JS.InvalidSmilesException $.SmilesAtom $.SmilesBond $.SmilesGenerator $.SmilesParser $.SmilesSearch JU.BSUtil $.Elements $.Logger $.Node $.Point3fi".split(" "),function(){c$=G(function(){this.okMF=!0;E(this,arguments)},JS,"SmilesMatcher",null,J.api.SmilesMatcherInterface);p(c$,"getLastException",function(){return!0==
this.okMF?JS.InvalidSmilesException.getLastError():"MF_FAILED"});p(c$,"getMolecularFormula",function(a,b){this.clearExceptions();var c=JS.SmilesParser.newSearch("/nostereo/"+a,b,!0);c.createTopoMap(null);c.nodes=c.targetAtoms;return c.getMolecularFormula(!b,null,!1)},"~S,~B");h(c$,"clearExceptions",function(){this.okMF=!0;JS.InvalidSmilesException.clear()});p(c$,"getSmiles",function(a,b,c,d,e){this.clearExceptions();return(new JS.SmilesGenerator).getSmiles(this,a,b,c,d,e)},"~A,~N,JU.BS,~S,~N");p(c$,
"areEqual",function(a,b){this.clearExceptions();var c=0<=a.indexOf("*");if(!c&&a.equals(b))return 1;c=this.matchPriv(a,null,0,null,null,!1,(c?2:1)|8,2,JS.SmilesParser.newSearch(b,!1,!0));return null==c?-1:c.length},"~S,~S");h(c$,"areEqualTest",function(a,b){b.set();var c=this.matchPriv(a,null,0,null,null,!1,9,2,b);return null!=c&&1==c.length},"~S,JS.SmilesSearch");p(c$,"find",function(a,b,c){this.clearExceptions();b=JS.SmilesParser.cleanPattern(b);a=JS.SmilesParser.cleanPattern(a);b=JS.SmilesParser.newSearch(b,
!1,!0);a=this.matchPriv(a,null,0,null,null,!1,c,3,b);for(c=a.length;0<=--c;)for(var d=a[c],e=d.length;0<=--e;)d[e]=b.targetAtoms[d[e]].mapIndex;return a},"~S,~S,~N");p(c$,"getAtoms",function(a){this.clearExceptions();a=JS.SmilesParser.cleanPattern(a);a=JS.SmilesParser.newSearch(a,!1,!0);a.createTopoMap(new JU.BS);return a.targetAtoms},"~S");p(c$,"getRelationship",function(a,b){if(null==a||null==b||0==a.length||0==b.length)return"";var c=this.getMolecularFormula(a,!1),d=this.getMolecularFormula(b,
!1);if(!c.equals(d))return"none";var e,c=JU.PT.countChar(JU.PT.rep(a,"@@","@"),"@"),d=JU.PT.countChar(JU.PT.rep(b,"@@","@"),"@");e=c==d&&0<this.areEqual(b,a);if(!e){e=a+b;if(0<=e.indexOf("/")||0<=e.indexOf("\\")||0<=e.indexOf("@")){if(c==d&&(0<c&&0>e.indexOf("@SP"))&&(e=0<this.areEqual("/invertstereo/"+b,a)))return"enantiomers";if(e=0<this.areEqual("/nostereo/"+b,a))return c==d?"diastereomers":"ambiguous stereochemistry!"}return"constitutional isomers"}return"identical"},"~S,~S");p(c$,"reverseChirality",
function(a){a=JU.PT.rep(a,"@@","!@");a=JU.PT.rep(a,"@","@@");return a=JU.PT.rep(a,"!@@","@")},"~S");p(c$,"getSubstructureSet",function(a,b,c,d,e){return this.matchPriv(a,b,c,d,null,!0,e|JS.SmilesParser.getFlags(a),1,null)},"~S,~A,~N,JU.BS,~N");p(c$,"getMMFF94AtomTypes",function(a,b,c,d,e,f){this.clearExceptions();var g=new JS.SmilesParser(!0,!0),j=null,j=g.parse("");j.exitFirstMatch=!1;j.targetAtoms=b;j.targetAtomCount=Math.abs(c);j.setSelected(d);j.flags=770;j.getRingData(f,!0,!0);j.asVector=!1;
j.subSearches=Array(1);j.getSelections();b=new JU.BS;for(d=0;d<a.length;d++)if(null==a[d]||0==a[d].length||a[d].startsWith("#"))e.addLast(null);else if(j.clear(),j.subSearches[0]=g.getSubsearch(j,JS.SmilesParser.cleanPattern(a[d]),770),f=JU.BSUtil.copy(j.search()),e.addLast(f),b.or(f),b.cardinality()==c)break},"~A,~A,~N,JU.BS,JU.Lst,~A");p(c$,"getSubstructureSetArray",function(a,b,c,d,e,f){return this.matchPriv(a,b,c,d,e,!0,f,2,null)},"~S,~A,~N,JU.BS,JU.BS,~N");h(c$,"getAtropisomerKeys",function(a,
b,c,d,e,f){return this.matchPriv(a,b,c,d,e,!1,f,4,null)},"~S,~A,~N,JU.BS,JU.BS,~N");p(c$,"polyhedronToSmiles",function(a,b,c,d,e,f){for(var g=Array(c),j=0;j<c;j++){g[j]=new JS.SmilesAtom;var m=null==d?null:d[j];L(m,JU.Node)?(g[j].elementNumber=m.getElementNumber(),g[j].bioAtomName=m.getAtomName(),g[j].atomNumber=m.getAtomNumber(),g[j].setT(m)):(g[j].elementNumber=L(m,JU.Point3fi)?m.sD:-2,null!=m&&g[j].setT(m));g[j].index=j}m=0;for(j=b.length;0<=--j;)for(var n=b[j],k=n.length,l,h,r=k;0<=--r;)if(!((l=
n[r])>=c||(h=n[(r+1)%k])>=c)&&null==g[l].getBondTo(g[h]))(new JS.SmilesBond(g[l],g[h],1,!1)).index=m++;for(j=0;j<c;j++)if(k=g[j].bondCount,0==k||k!=g[j].bonds.length)g[j].bonds=JU.AU.arrayCopyObject(g[j].bonds,k);b=null;b=new JS.SmilesGenerator;null!=d&&(b.polySmilesCenter=a);this.clearExceptions();b=b.getSmiles(this,g,c,JU.BSUtil.newBitSet2(0,c),null,e|4144);65536==(e&65536)&&(b=(0==(e&131072)?"":"//* "+a+" *//\t")+"["+JU.Elements.elementSymbolFromNumber(a.getElementNumber())+"@PH"+c+(null==f?"":
"/"+f+"/")+"]."+b);return b},"JU.Node,~A,~N,~A,~N,~S");p(c$,"getCorrelationMaps",function(a,b,c,d,e){return this.matchPriv(a,b,c,d,null,!0,e,3,null)},"~S,~A,~N,JU.BS,~N");h(c$,"matchPriv",function(a,b,c,d,e,f,g,j,m){this.clearExceptions();try{var n=2==(g&2),k=JS.SmilesParser.newSearch(a,n,!1),l=16384==(g&16384);if(null!=m){k.haveTopo=!0;e=new JU.BS;m.setFlags(m.flags|JS.SmilesParser.getFlags(a));m.createTopoMap(e);b=m.targetAtoms;c=m.targetAtoms.length;if(n)for(var h=m.elementCounts,r=k.elementCounts,
s=Math.max(m.elementNumberMax,k.elementNumberMax);0<s;s--){if(h[s]<r[s]){this.okMF=!1;break}}else{var q=l?null:k.getMolecularFormulaImpl(!0,null,!1),p=m.getMolecularFormulaImpl(!0,null,!1);this.okMF=null==q||q.equals(p);this.okMF||(System.out.println("\n"+a+"\n"+q+" \n"+p),m.getMolecularFormulaImpl(!0,null,!1))}m.mf=k.mf=null}if(this.okMF&&(!n&&!k.patternAromatic&&(null==e&&(e=new JU.BS),k.normalizeAromaticity(e),k.isNormalized=!0),k.targetAtoms=b,k.targetAtomCount=c,k.setSelected(d),0!=c&&(null==
d||!d.isEmpty()))){var u=!L(b[0],JS.SmilesAtom);k.getSelections();f||(k.bsAromatic=e);k.setRingData(null,null,u||f);k.exitFirstMatch=8==(g&8);k.mapUnique=128==(g&128)}switch(j){case 1:return k.asVector=!1,this.okMF?k.search():new JU.BS;case 2:if(!this.okMF)return[];k.asVector=!0;var t=k.search();return t.toArray(Array(t.size()));case 4:if(!this.okMF)return"";k.exitFirstMatch=!0;k.setAtropicity=!0;k.search();return k.atropKeys;case 3:if(!this.okMF)return v(0,0,0);k.getMaps=!0;k.setFlags(g|k.flags);
var x=k.search();return x.toArray(JU.AU.newInt2(x.size()))}}catch(w){if(H(w,Exception))throw JU.Logger.debugging&&w.printStackTrace(),null==JS.InvalidSmilesException.getLastError()&&this.clearExceptions(),new JS.InvalidSmilesException(JS.InvalidSmilesException.getLastError());throw w;}return null},"~S,~A,~N,JU.BS,JU.BS,~B,~N,~N,JS.SmilesSearch");p(c$,"cleanSmiles",function(a){return JS.SmilesParser.cleanPattern(a)},"~S");p(c$,"getMapForJME",function(a,b,c){var d=new JS.SmilesSearch,e=JU.PT.getTokens(a);
a=JU.PT.parseInt(e[0]);for(var f=JU.PT.parseInt(e[1]),g=2,j=0;j<a;j++,g+=3){var m=e[g],n=d.addAtom(),k=m.indexOf("+"),l=0;if(0<=k)l=k==m.length-1?1:JU.PT.parseInt(m.substring(k+1));else if(0<=(k=m.indexOf("-")))l=JU.PT.parseInt(m.substring(k));n.setCharge(l);n.setSymbol(0>k?m:m.substring(0,k))}for(j=0;j<f;j++){n=JU.PT.parseInt(e[g++])-1;k=JU.PT.parseInt(e[g++])-1;m=JU.PT.parseInt(e[g++]);n=d.patternAtoms[n];k=d.patternAtoms[k];l=1;switch(m){case 2:l=2;break;case 3:l=3}(new JS.SmilesBond(n,k,l,!1)).index=
j}e="";try{d.isSmarts=!0;d.set();var h=JU.BSUtil.newBitSet2(0,a),e=this.getSmiles(d.patternAtoms,d.ac,h,null,34),r=this.getCorrelationMaps(e,d.patternAtoms,a,h,42),s=this.getCorrelationMaps(e,b,c.cardinality(),c,42);return K(-1,[r[0],s[0]])}catch(q){if(H(q,Exception))q.printStackTrace();else throw q;}return null},"~S,~A,JU.BS");M(c$,"MODE_BITSET",1,"MODE_ARRAY",2,"MODE_MAP",3,"MODE_ATROP",4)});D("JS");B(["java.lang.Exception"],"JS.InvalidSmilesException",null,function(){c$=Q(JS,"InvalidSmilesException",
Exception);c$.getLastError=h(c$,"getLastError",function(){return JS.InvalidSmilesException.lastError});c$.clear=h(c$,"clear",function(){JS.InvalidSmilesException.lastError=null});p(c$,"getMessage",function(){return JS.InvalidSmilesException.lastError});I(c$,function(a){O(this,JS.InvalidSmilesException,[a]);JS.InvalidSmilesException.lastError=a.startsWith("Jmol SMILES")?a:"Jmol SMILES Exception: "+a},"~S");M(c$,"lastError",null)});D("JS");B(["JU.JmolMolecule","JU.BS","$.Lst"],"JS.SmilesSearch","java.lang.Float java.util.Hashtable JU.AU $.SB JS.InvalidSmilesException $.SmilesAromatic $.SmilesAtom $.SmilesBond $.SmilesMeasure $.SmilesParser $.SmilesStereo $.VTemp JU.BSUtil $.Logger".split(" "),
function(){c$=G(function(){this.isSmarts=!1;this.targetAtoms=this.patternAtoms=this.pattern=this.top=null;this.targetAtomCount=0;this.v=this.bsSelected=null;this.patternBioSequence=this.isTopology=this.haveTopo=this.patternAromatic=this.setAtropicity=this.groupByModel=this.exitFirstMatch=this.invertStereochemistry=this.ignoreStereochemistry=this.ignoreElement=this.ignoreAtomClass=this.noAromatic=this.aromaticUnknown=this.aromaticDefined=this.aromaticMMFF94=this.aromaticDouble=this.aromaticPlanar=
this.aromaticStrict=this.aromaticOpen=!1;this.subSearches=null;this.haveBondStereochemistry=this.haveSelected=!1;this.stereo=null;this.needRingData=!1;this.needAromatic=!0;this.needRingMemberships=!1;this.nDouble=0;this.ringDataMax=-2147483648;this.ringSets=null;this.ringCount=0;this.measures=null;this.flags=0;this.lastChainAtom=this.atropKeys=this.bsAromatic6=this.bsAromatic5=this.bsAromatic=null;this.isRingCheck=this.isSilent=this.haveComponents=this.isNormalized=this.getMaps=this.asVector=!1;this.selectedAtomCount=
0;this.htNested=this.bsFound=this.ringConnections=this.ringCounts=this.ringData=null;this.nNested=0;this.bsCheck=this.bsReturn=this.uniqueList=this.vReturn=this.nestedBond=null;this.mapUnique=!1;this.polyAtom=this.polyhedronStereo=this.bsAromaticRings=null;this.autoAddImplicitH=!0;E(this,arguments)},JS,"SmilesSearch",JU.JmolMolecule);N(c$,function(){this.patternAtoms=Array(16);this.measures=new JU.Lst;this.bsAromatic=new JU.BS;this.bsAromatic5=new JU.BS;this.bsAromatic6=new JU.BS;this.bsFound=new JU.BS;
this.bsReturn=new JU.BS});I(c$,function(){O(this,JS.SmilesSearch,[]);this.top=this;this.v=new JS.VTemp});h(c$,"setTop",function(a){for(;a.top!==a;)a=a.top;this.top=a},"JS.SmilesSearch");c$.addFlags=h(c$,"addFlags",function(a,b){0<=b.indexOf("OPEN")&&(a|=5);0<=b.indexOf("BIO")&&(a|=1048576);0<=b.indexOf("HYDROGEN2")?a|=8192:0<=b.indexOf("HYDROGEN")&&(a|=4096);0<=b.indexOf("FIRSTMATCHONLY")&&(a|=8);0<=b.indexOf("STRICT")&&(a|=256);0<=b.indexOf("PLANAR")&&(a|=1024);if(0<=b.indexOf("NOAROMATIC")||0<=
b.indexOf("NONAROMATIC"))a|=16;0<=b.indexOf("AROMATICDOUBLE")&&(a|=512);0<=b.indexOf("AROMATICDEFINED")&&(a|=128);0<=b.indexOf("MMFF94")&&(a|=768);0<=b.indexOf("TOPOLOGY")&&(a|=16384);0<=b.indexOf("NOATOMCLASS")&&(a|=2048);0<=b.indexOf("NOSTEREO")?a|=32:0<=b.indexOf("INVERTSTEREO")&&(a=0!=(a&64)?a&-65:a|64);0<=b.indexOf("ATOMCOMMENT")&&(a|=131072);0<=b.indexOf("GROUPBYMODEL")&&(a|=67108864);1048576==(a&1048576)&&(0<=b.indexOf("NOCOMMENT")&&(a|=34603008),0<=b.indexOf("UNMATCHED")&&(a|=3145728),0<=
b.indexOf("COVALENT")&&(a|=5242880),0<=b.indexOf("HBOND")&&(a|=9437184));return a},"~N,~S");h(c$,"setFlags",function(a){this.flags=a;this.exitFirstMatch=(new Boolean(this.exitFirstMatch|8==(a&8))).valueOf();this.aromaticOpen=5==(a&5);this.aromaticDouble=512==(a&512);this.aromaticStrict=256==(a&256);this.aromaticPlanar=1024==(a&1024);this.aromaticMMFF94=768==(a&768);this.aromaticDefined=128==(a&128);this.noAromatic=(new Boolean(this.noAromatic|16==(a&16))).valueOf();this.aromaticUnknown=!this.noAromatic&&
!this.aromaticOpen&&!this.aromaticDouble&&!this.aromaticStrict&&!this.aromaticPlanar&&!this.aromaticMMFF94&&!this.aromaticDefined;this.groupByModel=67108864==(a&67108864);this.ignoreAtomClass=2048==(a&2048);this.ignoreStereochemistry=32==(a&32);this.invertStereochemistry=!this.ignoreStereochemistry&&64==(a&64);this.ignoreElement=16384==(a&16384)},"~N");h(c$,"set",function(){this.patternAtoms.length>this.ac&&(this.patternAtoms=JU.AU.arrayCopyObject(this.patternAtoms,this.ac));this.nodes=this.patternAtoms;
this.isTopology=!0;this.patternAromatic=!1;this.patternBioSequence=!0;for(var a=this.ac;0<=--a;){var b=this.patternAtoms[a];this.isTopology&&b.isDefined()&&(this.isTopology=!1);b.isBioResidue||(this.patternBioSequence=!1);b.isAromatic&&(this.patternAromatic=!0);b.setBondArray();if(this.autoAddImplicitH&&!this.isSmarts&&"\x00"==b.bioType&&!b.setHydrogenCount())throw new JS.InvalidSmilesException("unbracketed atoms must be one of: B, C, N, O, P, S, F, Cl, Br, I, *,");}if(this.haveComponents)for(a=this.ac;0<=
--a;)for(var b=this.patternAtoms[a],c=b.bonds,d=b.component,e=b.bondCount;0<=--e;){var f=c[e],g;if(f.isConnection&&f.atom2===b&&(g=f.atom1.component)!=d)for(f=this.ac;0<=--f;)this.patternAtoms[f].component==d&&(this.patternAtoms[f].component=g)}});h(c$,"setSelected",function(a){this.selectedAtomCount=null==a?this.targetAtomCount:a.cardinality();null==a&&(a=JU.BS.newN(this.targetAtomCount),a.setBits(0,this.targetAtomCount));this.bsSelected=a},"JU.BS");h(c$,"addAtom",function(){return this.appendAtom(new JS.SmilesAtom)});
h(c$,"appendAtom",function(a){this.ac>=this.patternAtoms.length&&(this.patternAtoms=JU.AU.doubleLength(this.patternAtoms));return this.patternAtoms[this.ac]=a.setIndex(this.ac++)},"JS.SmilesAtom");h(c$,"addNested",function(a){null==this.htNested&&(this.htNested=new java.util.Hashtable);this.setNested(++this.nNested,a);return this.nNested},"~S");h(c$,"clear",function(){this.bsReturn.clearAll();this.nNested=0;this.nestedBond=this.htNested=null;this.clearBsFound(-1)});h(c$,"clearBsFound",function(a){0>
a?null==this.bsCheck&&this.bsFound.clearAll():this.bsFound.clear(a)},"~N");h(c$,"setNested",function(a,b){this.top.htNested.put("_"+a,b)},"~N,~O");h(c$,"getNested",function(a){return this.top.htNested.get("_"+a)},"~N");h(c$,"getMissingHydrogenCount",function(){for(var a=0,b,c=0;c<this.ac;c++)if(0<=(b=this.patternAtoms[c].explicitHydrogenCount))a+=b;return a});h(c$,"setRingData",function(a,b,c){if(this.isTopology||this.patternBioSequence)this.needAromatic=!1;if(this.needAromatic=(new Boolean(this.needAromatic&
(new Boolean(null==a&!this.noAromatic)).valueOf())).valueOf())this.needRingData=!0;if(!this.needAromatic&&(this.bsAromatic.clearAll(),null!=a&&this.bsAromatic.or(a),!this.needRingMemberships&&!this.needRingData))return;this.getRingData(b,this.needRingData,c)},"JU.BS,~A,~B");h(c$,"getRingData",function(a,b,c){var d=this.needAromatic&&(this.aromaticStrict||!this.aromaticOpen&&!this.aromaticPlanar);d&&this.aromaticUnknown&&0<this.targetAtomCount&&this.targetAtoms[this.bsSelected.nextSetBit(0)].modelIsRawPDB()&&
(d=!1);var e=this.needAromatic&&this.aromaticOpen&&!this.aromaticStrict,f=this.needAromatic&&!d,g=this.needAromatic&&c&&(d||e),j=this.needAromatic&&!this.aromaticDefined,m=null==a?new JU.Lst:a[3]=new JU.Lst,n=g?new JU.Lst:null,k=!d?0:this.aromaticMMFF94?2:1;this.needAromatic&&this.aromaticDefined&&(JS.SmilesAromatic.checkAromaticDefined(this.targetAtoms,this.bsSelected,this.bsAromatic),k=0);0>this.ringDataMax&&(this.ringDataMax=8);0<k&&6>this.ringDataMax&&(this.ringDataMax=6);b&&(this.ringCounts=
v(this.targetAtomCount,0),this.ringConnections=v(this.targetAtomCount,0),this.ringData=Array(this.ringDataMax+1));this.ringSets=new JU.Lst;if(!(3>this.selectedAtomCount)){for(var l="****",h=this.ringDataMax;l.length<h;)l+=l;for(var r=g&&j?v(this.targetAtomCount,0):null,s=j&&L(this.targetAtoms[0],JS.SmilesAtom),q=3;q<=h&&!(q>this.targetAtomCount);q++){var p="*1"+l.substring(0,q-2)+"*1",p=JS.SmilesParser.newSearch(p,!0,!0),p=this.subsearch(p,2);if(null!=a&&5>=q){for(var u=new JU.Lst,t=p.size();0<=--t;)u.addLast(p.get(t));
a[q-3]=u}if(0!=p.size()&&(j&&(4<=q&&7>=q)&&JS.SmilesAromatic.setAromatic(q,this.targetAtoms,this.bsSelected,p,this.bsAromatic,k,e,s,f,this.v,m,n,r,c),b)){this.ringData[q]=new JU.BS;for(u=p.size();0<=--u;){var x=p.get(u);this.ringData[q].or(x);for(t=x.nextSetBit(0);0<=t;t=x.nextSetBit(t+1))this.ringCounts[t]++}}}if(this.needAromatic){g&&JS.SmilesAromatic.finalizeAromatic(this.targetAtoms,this.bsAromatic,m,n,r,e,d);this.bsAromatic5.clearAll();this.bsAromatic6.clearAll();for(q=m.size();0<=--q;)switch(a=
m.get(q),a.and(this.bsAromatic),a.cardinality()){case 5:this.bsAromatic5.or(a);break;case 6:this.bsAromatic6.or(a)}}if(b)for(q=this.bsSelected.nextSetBit(0);0<=q;q=this.bsSelected.nextSetBit(q+1)){b=this.targetAtoms[q];for(u=b.getBondCount();0<=--u;)0<this.ringCounts[b.getBondedAtomIndex(u)]&&this.ringConnections[q]++}}},"~A,~B,~B");h(c$,"subsearch",function(a,b){a.ringSets=this.ringSets;a.mapUnique=this.mapUnique;a.targetAtoms=this.targetAtoms;a.targetAtomCount=this.targetAtomCount;a.bsSelected=
this.bsSelected;a.selectedAtomCount=this.selectedAtomCount;a.htNested=this.htNested;a.haveTopo=this.haveTopo;a.bsCheck=this.bsCheck;a.isSmarts=!0;a.bsAromatic=this.bsAromatic;a.bsAromatic5=this.bsAromatic5;a.bsAromatic6=this.bsAromatic6;a.ringData=this.ringData;a.ringCounts=this.ringCounts;a.ringConnections=this.ringConnections;switch(b){case 1:a.exitFirstMatch=!1;break;case 2:a.isRingCheck=!0;a.isSilent=!0;a.asVector=!0;break;case 3:a.ignoreAtomClass=this.ignoreAtomClass,a.aromaticDouble=this.aromaticDouble,
a.haveSelected=this.haveSelected,a.exitFirstMatch=this.exitFirstMatch,a.getMaps=this.getMaps,a.asVector=this.asVector,a.vReturn=this.vReturn,a.bsReturn=this.bsReturn,a.haveBondStereochemistry=this.haveBondStereochemistry}return a.search2(1==b)},"JS.SmilesSearch,~N");h(c$,"search",function(){return this.search2(!1)});h(c$,"search2",function(a){this.setFlags(this.flags);!this.isRingCheck&&(JU.Logger.debuggingHigh&&!this.isSilent)&&JU.Logger.debug("SmilesSearch processing "+this.pattern);if(null==this.vReturn&&
(this.asVector||this.getMaps))this.vReturn=new JU.Lst;if(null!=this.subSearches)for(a=0;a<this.subSearches.length&&!(null!=this.subSearches[a]&&(this.subsearch(this.subSearches[a],3),this.exitFirstMatch&&(null==this.vReturn?0<=this.bsReturn.nextSetBit(0):0<this.vReturn.size())));a++);else 0<this.ac&&this.ac<=this.selectedAtomCount&&(null==this.nestedBond?this.clearBsFound(-1):this.bsReturn.clearAll(),this.nextPatternAtom(-1,-1,a,-1));return this.asVector||this.getMaps?this.vReturn:this.bsReturn},
"~B");h(c$,"nextPatternAtom",function(a,b,c,d){var e,f;if(++a<this.ac){var g=this.patternAtoms[a],j=0<=b?g.getBondTo(null):0==a?this.nestedBond:null;if(null==j){b=JU.BSUtil.copy(this.bsFound);var m=JU.BSUtil.copy(this.bsFound);if(0<=g.notBondedIndex)if(e=this.patternAtoms[g.notBondedIndex],j=e.getMatchingAtom(),e.isBioAtom)e=j.getOffsetResidueAtom("\x00",1),0<=e&&b.set(e),e=j.getOffsetResidueAtom("\x00",-1),0<=e&&b.set(e);else if(e===this.polyAtom)b.set(e.getMatchingAtomIndex());else{f=j.getEdges();
for(e=0;e<f.length;e++)b.set(f[e].getOtherNode(j).getIndex())}f=g.isBioAtomWild;e=this.bsSelected.nextSetBit(0);e=f&&0<=e?this.targetAtoms[e].getOffsetResidueAtom("\x00",e):e;for(var n,k=(0<a?this.patternAtoms[a-1]:g).component,l=g.component,h=this.haveComponents&&-2147483648!=l,j=e;0<=j;j=this.bsSelected.nextSetBit(j+1)){if(!b.get(j)&&!this.bsFound.get(j)){e=this.targetAtoms[j];if(h&&!this.isRingCheck&&(d=this.groupByModel?e.getModelIndex():e.getMoleculeNumber(!1),n=0<a?this.patternAtoms[a-1].matchingComponent:
d,k==l!=(n==d)))continue;if(!this.nextTargetAtom(g,e,a,j,c,d))return!1}f&&(e=this.targetAtoms[j].getOffsetResidueAtom(g.bioAtomName,1),0<=e&&(j=e-1))}this.bsFound=m;return!0}e=j.atom1.getMatchingAtom();switch(j.order){case 96:j=e.getOffsetResidueAtom(g.bioAtomName,1);if(0<=j){b=JU.BSUtil.copy(this.bsFound);e.getGroupBits(this.bsFound);if(this.doCheckAtom(j)&&!this.nextTargetAtom(g,this.targetAtoms[j],a,j,c,d))return!1;this.bsFound=b}return!0;case 112:f=new JU.Lst;e.getCrossLinkVector(f,!0,!0);b=JU.BSUtil.copy(this.bsFound);
e.getGroupBits(this.bsFound);for(j=2;j<f.size();j+=3)if(m=f.get(j).intValue(),this.doCheckAtom(m)&&!this.nextTargetAtom(g,this.targetAtoms[m],a,m,c,d))return!1;this.bsFound=b;return!0}f=e.getEdges();if(null!=f)for(j=0;j<f.length;j++)if(m=e.getBondedAtomIndex(j),this.doCheckAtom(m)&&!this.nextTargetAtom(g,this.targetAtoms[m],a,m,c,d))return!1;this.clearBsFound(b);return!0}if(!this.ignoreStereochemistry&&!this.isRingCheck){if(JU.Logger.debuggingHigh){for(g=0;g<a;g++)JU.Logger.debug("pattern atoms "+
this.patternAtoms[g]+" "+this.patternAtoms[g].matchingComponent);JU.Logger.debug("--ss-- "+this.bsFound.cardinality())}if(!this.checkStereochemistry())return!0}b=new JU.BS;for(j=d=0;j<this.ac;j++)if(g=this.patternAtoms[j].getMatchingAtomIndex(),c||!this.top.haveSelected||this.patternAtoms[j].selected){d++;b.set(g);this.patternAtoms[j].isBioAtomWild&&this.targetAtoms[g].getGroupBits(b);if(c)break;if(!this.isSmarts&&!this.setAtropicity&&0<this.patternAtoms[j].explicitHydrogenCount){g=this.targetAtoms[g];
e=0;for(f=g.getEdges().length;e<f;e++)m=g.getBondedAtomIndex(e),1==this.targetAtoms[m].getElementNumber()&&b.set(m)}}if(!this.isSmarts&&b.cardinality()!=this.selectedAtomCount)return!0;if(null!=this.bsCheck)if(c){this.bsCheck.clearAll();for(j=0;j<this.ac;j++)this.bsCheck.set(this.patternAtoms[j].getMatchingAtomIndex());if(this.bsCheck.cardinality()!=this.ac)return!0}else if(b.cardinality()!=this.ac)return!0;this.bsReturn.or(b);if(this.getMaps){if(this.mapUnique){null==this.uniqueList&&(this.uniqueList=
new JU.Lst);for(j=this.uniqueList.size();0<=--j;)if(this.uniqueList.get(j).equals(b))return!0;this.uniqueList.addLast(b)}a=v(d,0);for(b=j=0;j<this.ac;j++)if(c||!this.top.haveSelected||this.patternAtoms[j].selected)a[b++]=this.patternAtoms[j].getMatchingAtomIndex();this.vReturn.addLast(a);return!this.exitFirstMatch}if(this.asVector){c=!0;for(j=this.vReturn.size();0<=--j&&c;)c=!this.vReturn.get(j).equals(b);if(!c)return!0;this.vReturn.addLast(b)}if(this.isRingCheck){c=new JU.BS;for(e=3*a+2;--e>a;)c.set(this.patternAtoms[(e<=
2*a?2*a-e+1:e-1)%a].getMatchingAtomIndex());this.ringSets.addLast(c);return!0}return this.exitFirstMatch?!1:b.cardinality()!=this.selectedAtomCount},"~N,~N,~B,~N");h(c$,"doCheckAtom",function(a){return this.bsSelected.get(a)&&!this.bsFound.get(a)},"~N");h(c$,"nextTargetAtom",function(a,b,c,d,e,f){if(!this.isRingCheck&&!this.isTopology)if(null==a.subAtoms){if(!this.checkPrimitiveAtom(a,d))return!0}else if(a.isAND)for(var g=0;g<a.nSubAtoms;g++){if(!this.checkPrimitiveAtom(a.subAtoms[g],d))return!0}else{for(g=
0;g<a.nSubAtoms;g++)if(!this.nextTargetAtom(a.subAtoms[g],b,c,d,e,f))return!1;return!0}b=b.getEdges();for(g=a.getBondCount();0<=--g;){var j=a.getBond(g);if(j.getAtomIndex2()==a.index){var m=j.atom1,n=m.getMatchingAtomIndex();switch(j.order){case 96:case 112:if(!this.checkMatchBond(a,m,j,d,n,null))return!0;break;default:for(var k=0,l=null;k<b.length&&(!(l=b[k]).isCovalent()||!(l.getAtomIndex1()==n||l.getAtomIndex2()==n));k++);if(k==b.length||!this.checkMatchBond(a,m,j,d,n,l))return!0}}}a=this.patternAtoms[a.index];
a.setMatchingAtom(this.targetAtoms[d],d);a.matchingComponent=f;this.bsFound.set(d);if(!this.nextPatternAtom(c,d,e,f))return!1;0<=d&&this.clearBsFound(d);return!0},"JS.SmilesAtom,JU.Node,~N,~N,~B,~N");h(c$,"checkPrimitiveAtom",function(a,b){if(0<a.nSubAtoms){for(var c=0;c<a.nSubAtoms;c++)if(this.checkPrimitiveAtom(a.subAtoms[c],b))return!0;return!1}for(var d=this.targetAtoms[b],c=a.not;;){if(0<a.iNested){c=this.getNested(a.iNested);L(c,JS.SmilesSearch)&&(a.isBioAtom&&(c.nestedBond=a.getBondTo(null)),
c=this.subsearch(c,1),null==c&&(c=new JU.BS),a.isBioAtom||this.setNested(a.iNested,c));c=a.not!=c.get(b);break}var e=d.getElementNumber(),f=a.elementNumber;if(0<=e&&0<=f&&f!=e&&!this.ignoreElement)break;if(a.isBioResidue){if(null!=a.bioAtomName&&(a.isLeadAtom()?!d.isLeadAtom():!a.bioAtomName.equals(d.getAtomName().toUpperCase())))break;if(null!=a.residueName&&!a.residueName.equals(d.getGroup3(!1).toUpperCase()))break;if(-2147483648!=a.residueNumber&&a.residueNumber!=d.getResno())break;if("\x00"!=
a.insCode&&a.insCode!=d.getInsertionCode())break;if(null!=a.residueChar||-2==a.elementNumber){var e=d.getBioSmilesType(),g=a.getBioSmilesType(),j=!0,f=!1;switch(g){case "\x00":case "*":j=!0;break;case "n":j="r"==e||"c"==e;f=!0;break;case "r":case "c":f=!0;default:j=e==g}if(!j)break;j=d.getGroup1("\x00").toUpperCase();g=null==a.residueChar?"*":a.residueChar.charAt(0);j=g==j.charAt(0);switch(g){case "*":j=!0;break;case "N":j=f?"r"==e||"c"==e:j;break;case "R":j=f?d.isPurine():j;break;case "Y":j=f?d.isPyrimidine():
j}if(!j)break}if(a.isBioAtom&&a.notCrossLinked&&d.getCrossLinkVector(null,!0,!0))break}else{if(-2147483648!=a.atomNumber&&a.atomNumber!=d.getAtomNumber())break;if(0<=a.jmolIndex&&d.getIndex()!=a.jmolIndex)break;if(null!=a.atomType&&!a.atomType.equals(d.getAtomType()))break;if(-2147483648!=(f=a.getAtomicMass())&&(0<=f&&f!=(e=d.getIsotopeNumber())||0>f&&0!=e&&-f!=e))break;if(!this.noAromatic&&!a.aromaticAmbiguous&&a.isAromatic!=this.bsAromatic.get(b))break;if(-2147483648!=(f=a.getCharge())&&f!=d.getFormalCharge())break;
f=a.getCovalentHydrogenCount()+a.explicitHydrogenCount;if(0<=f&&f!=d.getTotalHydrogenCount())break;if(-2147483648!=(f=a.implicitHydrogenCount))if(e=d.getImplicitHydrogenCount(),-1==f?0==e:f!=e)break;if(0<a.degree&&a.degree!=d.getCovalentBondCount())break;if(0<a.nonhydrogenDegree&&a.nonhydrogenDegree!=d.getCovalentBondCount()-d.getCovalentHydrogenCount())break;if(this.isSmarts&&0<a.valence&&a.valence!=d.getTotalValence())break;if(0<a.connectivity&&a.connectivity!=d.getCovalentBondCountPlusMissingH())break;
if(-2147483648!=a.atomNumber&&a.atomNumber!=d.getAtomNumber())break;if(0<=a.jmolIndex&&d.getIndex()!=a.jmolIndex)break;if(null!=a.atomType&&!a.atomType.equals(d.getAtomType()))break;if((!this.ignoreAtomClass||this.isSmarts)&&!Float.isNaN(a.atomClass)&&a.atomClass!=d.getFloatProperty("property_atomclass"))break;if(null!=this.ringData){if(-1<=a.ringSize)if(0>=a.ringSize){if(0==this.ringCounts[b]!=(0==a.ringSize))break}else{d=this.ringData[500==a.ringSize?5:600==a.ringSize?6:a.ringSize];if(null==d||
!d.get(b))break;if(!this.noAromatic)if(500==a.ringSize){if(!this.bsAromatic5.get(b))break}else if(600==a.ringSize&&!this.bsAromatic6.get(b))break}if(-1<=a.ringMembership&&(-1==a.ringMembership?0==this.ringCounts[b]:this.ringCounts[b]!=a.ringMembership))break;if(0<=a.ringConnectivity&&(f=this.ringConnections[b],-1==a.ringConnectivity&&0==f||-1!=a.ringConnectivity&&f!=a.ringConnectivity))break}}c=!c;break}return c},"JS.SmilesAtom,~N");h(c$,"checkMatchBond",function(a,b,c,d,e,f){if(null!=c.bondsOr){for(var g=
0;g<c.nBondsOr;g++)if(this.checkMatchBond(a,b,c.bondsOr[g],d,e,f))return!0;return!1}if(!this.isRingCheck&&!this.isTopology)if(0==c.nPrimitives){if(!this.checkPrimitiveBond(c,d,e,f))return!1}else for(a=0;a<c.nPrimitives;a++)if(b=c.setPrimitive(a),!this.checkPrimitiveBond(b,d,e,f))return!1;c.matchingBond=f;return!0},"JS.SmilesAtom,JS.SmilesAtom,JS.SmilesBond,~N,~N,JU.Edge");h(c$,"checkPrimitiveBond",function(a,b,c,d){var e=!1;switch(a.order){case 96:return a.isNot!=(this.targetAtoms[c].getOffsetResidueAtom("\x00",
1)==this.targetAtoms[b].getOffsetResidueAtom("\x00",0));case 112:return a.isNot!=this.targetAtoms[b].isCrossLinked(this.targetAtoms[c])}var f=!this.noAromatic&&this.bsAromatic.get(b),g=!this.noAromatic&&this.bsAromatic.get(c);d=d.getCovalentOrder();var j=a.order;if(f&&g)switch(j){case 17:case 65:e=JS.SmilesSearch.isRingBond(this.ringSets,null,b,c);break;case 1:e=!this.isSmarts||!JS.SmilesSearch.isRingBond(this.ringSets,this.getBSAromaticRings(),b,c);break;case 2:e=this.isNormalized||this.aromaticDouble&&
(2==d||514==d);break;case 65537:case 65538:e=!a.isNot;break;case 81:case -1:e=!0}else switch(j){case 17:if(!this.noAromatic)break;case 81:case -1:e=!0;break;case 1:case 1025:case 1041:switch(d){case 1:case 1025:case 1041:e=!0}break;case 65537:case 65538:switch(d){case 1:case 65537:case 65538:e=!a.isNot}break;case 2:case 3:case 4:e=d==j;break;case 65:e=JS.SmilesSearch.isRingBond(this.ringSets,null,b,c)}return e!=a.isNot},"JS.SmilesBond,~N,~N,JU.Edge");h(c$,"getBSAromaticRings",function(){if(null==
this.bsAromaticRings&&(this.bsAromaticRings=new JU.BS,null!=this.ringSets&&null!=this.bsAromatic))for(var a=this.ringSets.size();0<=--a;){var b=this.ringSets.get(a).clone();b.andNot(this.bsAromatic);b.isEmpty()&&this.bsAromaticRings.set(a)}return this.bsAromaticRings});c$.isRingBond=h(c$,"isRingBond",function(a,b,c,d){if(null!=a)for(var e=a.size();0<=--e;){var f=a.get(e);if(f.get(c)&&f.get(d)&&(null==b||b.get(e)))return!0}return!1},"JU.Lst,JU.BS,~N,~N");h(c$,"checkStereochemistry",function(){for(var a=
0;a<this.measures.size();a++)if(!this.measures.get(a).check())return!1;if(null!=this.stereo&&!this.stereo.checkStereoChemistry(this,this.v))return!1;if(!this.haveBondStereochemistry)return!0;for(var b=null,a=null,c=0;c<this.ac;c++){for(var d=this.patternAtoms[c],e=null,f=null,g=null,j=0,m=0,n=0,k=d.getBondCount(),l=!1,h=!0,r=0;r<k;r++){var a=d.getBond(r),s=a.atom2===d,h=a.atom1.index<a.atom2.index,q=a.getBondType();switch(q){case 65537:case 65538:if(!h)continue;case 2:if(s)continue;e=a.atom2;n=q;
(l=2!=q)&&(j=a.isNot?-1:1);break;case 1025:case 1041:f=s?a.atom1:a.atom2,j=s!=(1025==q)?1:-1}}if(l){if(this.setAtropicity){null==b&&(b=new JU.Lst);b.addLast(a);continue}g=d.getBond(a.atropType[0]);if(null==g)return!1;f=g.getOtherAtom(d);g=e.getBond(a.atropType[1]);if(null==g)return!1;g=g.getOtherAtom(e);JU.Logger.debugging&&JU.Logger.info("atropisomer check for atoms "+f+d+" "+e+g)}else{if(null==e||0==j)continue;k=d;for(r=0;2==e.getBondCount()&&4==e.getValence();)r++,s=e.getEdges(),s=s[s[0].getOtherNode(e)===
k?1:0],k=e,e=s.getOtherNode(e);if(1==r%2)continue;k=e.getBondCount();for(r=0;r<k&&0==m;r++)switch(a=e.getBond(r),q=a.getBondType(),q){case 1025:case 1041:g=(s=a.atom2===e)?a.atom1:a.atom2,m=s!=(1025==q)?1:-1}if(0==m)continue}k=d.getMatchingAtom();r=e.getMatchingAtom();f=f.getMatchingAtom();g=g.getMatchingAtom();if(null==f||null==g)return!1;this.haveTopo&&JS.SmilesSearch.setTopoCoordinates(k,r,f,g,n);f=JS.SmilesMeasure.setTorsionData(f,k,r,g,this.v,l);if(l){if(f*=-1*j*(65537==n?1:-1)*(h?1:-1),JU.Logger.debugging&&
JU.Logger.info("atrop dihedral "+f+" "+d+" "+e+" "+a),1>f)return!1}else if(0>this.v.vTemp1.dot(this.v.vTemp2)*j*m)return!1}if(this.setAtropicity){this.atropKeys="";for(a=0;a<b.size();a++)this.atropKeys+=","+this.getAtropIndex(b.get(a))}return!0});h(c$,"getAtropIndex",function(a){var b=Array(4),c="";b[1]=a.atom1.getMatchingAtom();b[2]=a.atom2.getMatchingAtom();for(var d=a.atom1.bonds,e,f=a.atom1.getBondCount();0<=--f;)if((e=d[f].getOtherNode(a.atom1))!==a.atom2){c+=f+1;b[0]=e.getMatchingAtom();break}d=
a.atom2.bonds;for(f=0;f<=a.atom2.getBondCount();f++)if((e=d[f].getOtherNode(a.atom2))!==a.atom1){c+=f+1;b[3]=e.getMatchingAtom();break}c.equals("22")&&(c="");c=(1==JS.SmilesStereo.getAtropicStereoFlag(b)?"":"^")+c;return(c+"   ").substring(0,3)},"JS.SmilesBond");c$.setTopoCoordinates=h(c$,"setTopoCoordinates",function(a,b,c,d,e){a.set(-1,0,0);b.set(1,0,0);if(2!=e)e=a.getBondTo(b),a=a.getBondedAtomIndex(e.atropType[0])==c.index,b=b.getBondedAtomIndex(e.atropType[1])==d.index,b=(65537==e.order?1:-1)*
(a==b?1:-1),c.set(-1,1,0),d.set(1,1,-1*(b/2));else{d=c=0;for(var f=a.getEdges(),g=f.length;0<=--g;)if(e=f[g],2!=e.order){var j=e.getOtherNode(a);j.set(-1,0==c++?-1:1,0);j=e.getAtomIndex2()==a.getIndex()?c:-c;switch(e.order){case 1025:d=j;break;case 1041:d=-j}}var m=0;c=0;a=Array(2);f=b.getEdges();for(g=f.length;0<=--g;)if(e=f[g],2!=e.order)switch(j=e.getOtherNode(b),a[c]=j,j.set(1,0==c++?1:-1,0),j=e.getAtomIndex2()==b.getIndex()?c:-c,e.order){case 1025:m=j;break;case 1041:m=-j}0<d*m==(Math.abs(d)%
2==Math.abs(m)%2)&&(b=a[0].y,a[0].y=a[1].y,a[1].y=b)}},"JS.SmilesAtom,JS.SmilesAtom,JS.SmilesAtom,JS.SmilesAtom,~N");h(c$,"createTopoMap",function(a){var b=null==a,c=this.autoAddImplicitH?this.getMissingHydrogenCount():0,c=this.ac+c,d=Array(c);this.targetAtoms=d;for(var e=0,f=0;e<this.ac;e++,f++){var g=this.patternAtoms[e],j=g.explicitHydrogenCount;if(0>j||!this.autoAddImplicitH)j=0;var m=d[f]=(new JS.SmilesAtom).setTopoAtom(g.component,f,g.symbol,g.getCharge(),e);m.implicitHydrogenCount=j;if(!b){m.mapIndex=
e;m.stereo=g.stereo;m.setAtomicMass(g.getAtomicMass());m.bioAtomName=g.bioAtomName;m.residueName=g.residueName;m.residueChar=g.residueChar;m.residueNumber=g.residueNumber;m.atomNumber=g.residueNumber;m.insCode=g.insCode;m.atomClass=g.atomClass;m.explicitHydrogenCount=0;m.isBioAtom=g.isBioAtom;m.bioType=g.bioType;m.$isLeadAtom=g.$isLeadAtom;!b&&g.isAromatic&&a.set(f);g.setMatchingAtom(null,f);g=Array(g.getBondCount()+j);for(m.setBonds(g);0<=--j;){g=d[++f]=(new JS.SmilesAtom).setTopoAtom(m.component,
f,"H",0,-1);g.mapIndex=-e-1;g.setBonds(Array(1));var n=new JS.SmilesBond(m,g,1,!1);JU.Logger.debugging&&JU.Logger.info(""+n)}}}if(!b){for(e=0;e<this.ac;e++){g=this.patternAtoms[e];j=g.getMatchingAtomIndex();a=d[j];j=g.getBondCount();for(b=0;b<j;b++)if(f=g.getBond(b),f.atom1===g){n=1;switch(f.order){case 1:case 2:case 3:case 4:case 1025:case 1041:case 65537:case 65538:case 112:case 96:n=f.order;break;case 17:n=514}m=d[f.atom2.getMatchingAtomIndex()];n=new JS.SmilesBond(a,m,n,!1);n.isConnection=f.isConnection;
n.atropType=f.atropType;n.isNot=f.isNot;m.bondCount--;JU.Logger.debugging&&JU.Logger.info(""+n)}else m=d[f.atom1.getMatchingAtomIndex()],n=m.getBondTo(a),a.addBond(n)}for(e=0;e<c;e++)if(n=d[e],g=n.bonds,!(2>g.length||g[0].isFromPreviousTo(n)))for(j=g.length;1<=--j;)if(g[j].isFromPreviousTo(n)){n=g[j];g[j]=g[0];g[0]=n;break}if(!this.ignoreStereochemistry)for(e=this.ac;0<=--e;)g=this.patternAtoms[e],null!=g.stereo&&g.stereo.fixStereo(g)}},"JU.BS");h(c$,"normalizeAromaticity",function(a){var b=this.patternAtoms,
c=new JS.SmilesSearch;c.noAromatic=this.noAromatic;c.setFlags(this.flags);c.targetAtoms=b;c.targetAtomCount=b.length;c.bsSelected=JU.BSUtil.newBitSet2(0,b.length);var d=JU.AU.createArrayOfArrayList(4);c.setRingData(null,d,!0);a.or(c.bsAromatic);if(!a.isEmpty()){a=d[3];for(c=a.size();0<=--c;)for(var d=a.get(c),e=d.nextSetBit(0);0<=e;e=d.nextSetBit(e+1)){var f=b[e];!f.isAromatic&&!(-2==f.elementNumber||0==f.elementNumber)&&f.setSymbol(f.symbol.toLowerCase())}}},"JU.BS");h(c$,"getSelections",function(){var a=
this.top.htNested;if(!(null==a||0==this.targetAtoms.length))for(var b=new java.util.Hashtable,c,a=a.entrySet().iterator();a.hasNext()&&((c=a.next())||1);){var d=c.getValue().toString();if(d.startsWith("select")){var e=b.containsKey(d)?b.get(d):this.targetAtoms[0].findAtomsLike(d.substring(6));null==e&&(e=new JU.BS);b.put(d,e);c.setValue(e)}}});h(c$,"findImplicitHydrogen",function(a){for(var b=a.getEdges().length;0<=--b;){var c=a.getBondedAtomIndex(b);if(1==this.targetAtoms[c].getElementNumber()&&
!this.bsFound.get(c))return this.targetAtoms[c]}return null},"JU.Node");h(c$,"toString",function(){var a=(new JU.SB).append(this.pattern);a.append("\nmolecular formula: "+this.getMolecularFormula(!0,null,!1));return a.toString()});M(c$,"SUBMODE_NESTED",1,"SUBMODE_RINGCHECK",2,"SUBMODE_OR",3,"ATROPIC_SWITCH",1)});D("JS");B(["java.util.Hashtable","JU.BS","JS.VTemp"],"JS.SmilesGenerator","JU.AU $.Lst $.SB JS.InvalidSmilesException $.SmilesAtom $.SmilesBond $.SmilesParser $.SmilesSearch $.SmilesStereo JU.BSUtil $.Elements $.JmolMolecule $.Logger".split(" "),
function(){c$=G(function(){this.atoms=null;this.ac=0;this.bsAromatic=this.bsSelected=null;this.explicitHydrogen=this.flags=0;this.vTemp=this.ringSets=null;this.nPairsMax=this.nPairs=0;this.bsToDo=this.bsBondsDn=this.bsBondsUp=null;this.bsIgnoreHydrogen=new JU.BS;this.bsIncludingH=this.bsRingKeys=this.htRings=this.htRingsSequence=this.alleneStereo=this.prevSp2Atoms=this.prevAtom=null;this.topologyOnly=!1;this.getAromatic=!0;this.openSMILES=this.noStereo=this.aromaticDouble=this.noBioComment=this.addAtomComment=
!1;this.smilesStereo=this.polySmilesCenter=null;this.isPolyhedral=!1;this.sm=this.aromaticRings=null;this.iHypervalent=0;this.haveSmilesAtoms=this.is2D=!1;this.ptSp2Atom0=this.ptAtom=0;this.atemp=null;this.chainCheck=0;E(this,arguments)},JS,"SmilesGenerator");N(c$,function(){this.vTemp=new JS.VTemp;this.bsBondsUp=new JU.BS;this.bsBondsDn=new JU.BS;this.htRingsSequence=new java.util.Hashtable;this.htRings=new java.util.Hashtable;this.bsRingKeys=new JU.BS});h(c$,"getSmiles",function(a,b,c,d,e,f){var g=
d.nextSetBit(0);if(0>g)return"";this.haveSmilesAtoms=L(b[g],JS.SmilesAtom)&&b[g].definesStereo();this.sm=a;this.flags=f;this.atoms=b;this.ac=c;d=JU.BSUtil.copy(d);this.bsSelected=JU.BS.copy(d);this.flags=f=JS.SmilesSearch.addFlags(f,null==e?"":e.toUpperCase());if(1048576==(f&1048576))return this.getBioSmiles(d,e,f);this.openSMILES=5==(f&5);this.addAtomComment=131072==(f&131072);this.aromaticDouble=512==(f&512);this.explicitHydrogen=8192==(f&8192)?8192:4096==(f&4096)?4096:0;if(8192==this.explicitHydrogen){a=
new JU.BS;for(c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))if(e=b[c],3==e.getCovalentHydrogenCount()&&4==e.getCovalentBondCount()){var j=!0;a.clearAll();for(var m=e.getBondCount();0<=--m;){var n=e.getBondedAtomIndex(m);if(1==b[n].getElementNumber())if(j=1==b[n].getElementNumber())a.set(n);else break;j&&(this.bsIgnoreHydrogen.set(c),d.andNot(a))}}}this.topologyOnly=16384==(f&16384);this.getAromatic=16!=(f&16);this.noStereo=32==(f&32);this.isPolyhedral=65536==(f&65536);this.is2D=134217728==(f&134217728);
return this.getSmilesComponent(b[g],d,!0,!1,!1)},"JS.SmilesMatcher,~A,~N,JU.BS,~S,~N");h(c$,"getBioSmiles",function(a,b,c){this.addAtomComment=131072==(c&131072);var d=3145728==(c&3145728),e=34603008==(c&34603008),f=5242880==(c&5242880);c=9437184==(c&9437184);var g=f||c,j=new JU.SB;null!=b&&!this.noBioComment&&j.append("//* Jmol bioSMILES ").append(b.$replace("*","_")).append(" *//");b=this.noBioComment?"":"\n";var m=new JU.BS,n=null,k="",l,h=new JU.Lst;try{for(var r=0,s=a.nextSetBit(0);0<=s;s=a.nextSetBit(s+
1)){var q=this.atoms[s],p=q.getGroup1("?"),u=q.getBioStructureTypeName(),t=p===p.toLowerCase();if(null!=b)if(0<j.length()&&j.append(b),b=null,r=0,0<u.length)0!=q.getChainID()&&!e&&(l="//* chain "+q.getChainIDStr()+" "+u+" "+q.getResno()+" *// ",r=l.length,j.append(l)),r++,j.append("~").appendC(u.toLowerCase().charAt(0)).append("~");else{l=this.getSmilesComponent(q,a,!1,!0,!0);if(l.equals(n)){b="";continue}var n=l,x=q.getGroup3(!0),w;e?w="/"+l+"/":(null!=x&&(l="//* "+x+" *//"+l),w=l+"//");if(0<=k.indexOf(w)){b=
"";continue}k+=w;j.append(l);b=e?".":".\n";continue}75<=r&&!e&&(j.append("\n  "),r=2);this.addAtomComment&&j.append("\n//* ["+q.getGroup3(!1)+"#"+q.getResno()+"] *//\t");t?this.addBracketedBioName(j,q,0<u.length?".0":null,!1):j.append(p);r++;if(g){q.getCrossLinkVector(h,f,c);for(var y=0;y<h.size();y+=3)j.append(":"),l=this.getRingCache(h.get(y).intValue(),h.get(y+1).intValue(),this.htRingsSequence),j.append(l),r+=1+l.length;h.clear()}q.getGroupBits(m);a.andNot(m);var z=q.getOffsetResidueAtom("\x00",
1);if(0>z||!a.get(z)){e||j.append(" //* ").appendI(q.getResno()).append(" *//");if(0>z&&0>(z=a.nextSetBit(s+1)))break;0<r&&(b=e?".":".\n")}s=z-1}}catch(A){if(H(A,Exception))throw new JS.InvalidSmilesException("//* error: "+A.getMessage()+" *//");throw A;}if(!d&&!this.htRingsSequence.isEmpty())throw this.dumpRingKeys(j,this.htRingsSequence),new JS.InvalidSmilesException("//* ?ring error? *//");l=j.toString();l.endsWith(".\n")?l=l.substring(0,l.length-2):e&&l.endsWith(".")&&(l=l.substring(0,l.length-
1));return l},"JU.BS,~S,~N");h(c$,"addBracketedBioName",function(a,b,c,d){a.append("[");if(null!=c){var e=b.getChainIDStr();a.append(b.getGroup3(!1));c.equals(".0")||a.append(c).append("#").appendI(b.getElementNumber());d&&(a.append("//* ").appendI(b.getResno()),0<e.length&&a.append(":").append(e),a.append(" *//"))}else a.append(JU.Elements.elementNameFromNumber(b.getElementNumber()));a.append("]")},"JU.SB,JU.Node,~S,~B");h(c$,"getSmilesComponent",function(a,b,c,d,e){a=this.checkFirstAtom(a);this.bsSelected=
JU.JmolMolecule.getBranchBitSet(this.atoms,a.getIndex(),JU.BSUtil.copy(b),null,-1,!0,c);b.andNot(this.bsSelected);this.iHypervalent=-1;for(b=this.bsSelected.nextSetBit(0);0<=b&&0>this.iHypervalent;b=this.bsSelected.nextSetBit(b+1))if(4<this.atoms[b].getCovalentBondCount()||this.isPolyhedral)this.iHypervalent=b;this.bsIncludingH=JU.BSUtil.copy(this.bsSelected);if(0==this.explicitHydrogen)for(b=this.bsSelected.nextSetBit(0);0<=b;b=this.bsSelected.nextSetBit(b+1))c=this.atoms[b],1==c.getAtomicAndIsotopeNumber()&&
(0<c.getBondCount()&&c.getBondedAtomIndex(0)!=this.iHypervalent&&!this.isExplicitOnly(this.atoms[c.getBondedAtomIndex(0)]))&&this.bsSelected.clear(b);this.bsAromatic=new JU.BS;!this.topologyOnly&&2<this.bsSelected.cardinality()&&(this.generateRingData(),this.setBondDirections());this.bsToDo=JU.BSUtil.copy(this.bsSelected);c=new JU.SB;for(b=this.bsToDo.nextSetBit(0);0<=b;b=this.bsToDo.nextSetBit(b+1))if(4<this.atoms[b].getCovalentBondCount()||this.isPolyhedral)null==a&&c.append("."),this.getSmilesAt(c,
this.atoms[b],d,!1,e),a=null;if(null!=a)for(;null!=(a=this.getSmilesAt(c,a,d,!0,e)););for(;0<this.bsToDo.cardinality()||!this.htRings.isEmpty();){a=this.htRings.values().iterator();if(a.hasNext()){if(a=this.atoms[a.next()[1].intValue()],!this.bsToDo.get(a.getIndex()))break}else a=this.atoms[this.bsToDo.nextSetBit(0)];c.append(".");for(this.prevAtom=this.prevSp2Atoms=this.alleneStereo=null;null!=(a=this.getSmilesAt(c,a,d,!0,e)););}if(!this.htRings.isEmpty())throw this.dumpRingKeys(c,this.htRings),
new JS.InvalidSmilesException("//* ?ring error? *//\n"+c);d=c.toString();if(0<=d.indexOf("^-")){e=d;try{var f=this.sm.getAtropisomerKeys(d,this.atoms,this.ac,this.bsSelected,this.bsAromatic,this.flags);for(b=1;b<f.length;){var g=d.indexOf("^-");if(0>g)break;d=d.substring(0,g+1)+f.substring(b,b+3).trim()+d.substring(g+1);b+=3}}catch(j){if(H(j,Exception))j.printStackTrace(),d=e;else throw j;}}return d},"JU.Node,JU.BS,~B,~B,~B");h(c$,"checkFirstAtom",function(a){0==this.explicitHydrogen&&(1==a.getAtomicAndIsotopeNumber()&&
0<a.getEdges().length)&&(a=this.atoms[a.getBondedAtomIndex(0)]);for(var b=a,c=null;2==b.getCovalentBondCount();){var d=b.getEdges();if(2!=d[0].getBondType()||2!=d[1].getBondType())break;var e=d[0].getOtherNode(b);e===c&&(e=d[1].getOtherNode(b));c=b;b=e}return null==b?a:b},"JU.Node");h(c$,"generateRingData",function(){var a=JS.SmilesParser.newSearch("[r500]",!0,!0);a.targetAtoms=this.atoms;a.setSelected(this.bsSelected);a.setFlags(this.flags);a.targetAtomCount=this.ac;a.ringDataMax=7;a.flags=this.flags;
var b=JU.AU.createArrayOfArrayList(4);a.setRingData(null,b,!0);this.bsAromatic=a.bsAromatic;this.ringSets=a.ringSets;this.aromaticRings=b[3]});h(c$,"getBondStereochemistry",function(a,b){if(null==a)return"\x00";var c=a.index,d=null==b||a.getAtomIndex1()==b.getIndex();return this.bsBondsUp.get(c)?d?"/":"\\":this.bsBondsDn.get(c)?d?"\\":"/":"\x00"},"JU.Edge,JU.SimpleNode");h(c$,"setBondDirections",function(){for(var a=new JU.BS,b=K(2,3,null),c=this.bsSelected.nextSetBit(0);0<=c;c=this.bsSelected.nextSetBit(c+
1))for(var d=this.atoms[c],e=d.getEdges(),f=0;f<e.length;f++){var g=e[f],j=g.index,m;if(!a.get(j)&&!(2!=g.getCovalentOrder()||JS.SmilesSearch.isRingBond(this.ringSets,null,c,(m=g.getOtherNode(d)).getIndex()))){a.set(j);g=0;for(j=d;2==m.getCovalentBondCount()&&4==m.getValence();){var n=m.getEdges(),n=n[n[0].getOtherNode(m)===j?1:0];a.set(n.index);j=m;m=n.getOtherNode(m);g++}if(1!=g%2){for(var k=g=null,k=0,j=K(-1,[d,m]),l=1,n=0;2>n&&0<l&&3>l;n++)for(var l=0,h=j[n],r=h.getEdges(),s=0<this.explicitHydrogen||
this.isExplicitOnly(h),q=0;q<r.length;q++){var p;if(!(1!=r[q].getCovalentOrder()||!s&&1==(p=r[q].getOtherNode(h)).getElementNumber()&&0==p.getIsotopeNumber()))b[n][l++]=r[q],"\x00"!=this.getBondStereochemistry(r[q],h)&&(g=r[q],k=n)}if(!(3==l||0==l))if(null==g&&(k=0,g=b[k][0],this.bsBondsUp.set(g.index)),l=j[k],h=this.getBondStereochemistry(g,l),k=g.getOtherNode(l),null!=k)for(n=0;2>n;n++){r=j[n];for(s=0;2>s;s++)if(q=b[n][s],!(null==q||q===g)){var u=q.index,t=q.getOtherNode(r);if(null!=t){var x=this.getBondStereochemistry(q,
r),w;if(this.haveSmilesAtoms){w=k.isStereoOpposite(t.getIndex(),l.getIndex(),r.getIndex());if(null==w){JU.Logger.debugging&&JU.Logger.debug("SmilesGenerator could not find stereo for "+k+"/"+t);continue}w=w.booleanValue()}else w=JS.SmilesStereo.isDiaxial(l,r,k,t,this.vTemp,0);"\x00"==x||x!=h==w?("\\"==h&&w||"/"==h&&!w)==(q.getAtomIndex1()!=t.getIndex())?this.bsBondsUp.set(u):this.bsBondsDn.set(u):(this.bsBondsUp.clear(u),this.bsBondsDn.clear(u),JU.Logger.error("BOND STEREOCHEMISTRY PARITY ERROR-stereochemistry for bond "+
u+""));JU.Logger.debugging&&JU.Logger.debug(this.getBondStereochemistry(g,l)+" "+k.getIndex()+" "+t.getIndex()+" "+this.getBondStereochemistry(q,r))}}}}}}});h(c$,"getSmilesAt",function(a,b,c,d,e){var f=b.getIndex();if(!this.bsToDo.get(f))return null;this.ptAtom++;this.bsToDo.clear(f);var g=f==this.iHypervalent||0!=this.explicitHydrogen&&!this.bsIgnoreHydrogen.get(f),j=this.isExplicitOnly(b),m=!this.bsSelected.get(f),n=null==this.prevAtom?-1:this.prevAtom.getIndex(),k=this.bsAromatic.get(f),l=this.prevSp2Atoms,
h=null!=l,r=b.getElementNumber(),s=0,q=this.alleneStereo;this.alleneStereo=null;var p=new JU.Lst,u=null,t=null,x=b.getEdges();null!=this.polySmilesCenter&&(d=!1,this.sortPolyBonds(b,this.prevAtom,this.polySmilesCenter));var w=null,y=k?10:0;JU.Logger.debugging&&JU.Logger.debug(a.toString());if(null!=x)for(var z=x.length;0<=--z;){var A=x[z];if(A.isCovalent()){var C=x[z].getOtherNode(b),v=C.getIndex();if(v==n)t=x[z];else{var F=!g&&!j&&1==C.getElementNumber()&&0>=C.getIsotopeNumber();if(!this.bsIncludingH.get(v))if(!F&&
c&&this.bsSelected.get(f))this.bsToDo.set(v);else continue;F?(w=C,s++,1<s&&(y=10)):p.addLast(x[z])}}}1<s&&(l=null);x=null!=l?2:0;null==l&&(!k&&1>=s)&&(l=Array(5));var D=null;null!=t&&(D=this.getBondOrder(t,f,n,k),null!=l&&!h&&(l[x++]=this.prevAtom));null!=l&&!h&&(this.ptSp2Atom0=this.ptAtom);null!=l&&1==s&&(l[x++]=w);j=0;v=new JU.BS;C=p.size();if(d)for(z=0;z<C;z++){var A=p.get(z),F=A.getOtherNode(b),B=F.getCovalentBondCount()-(g||this.isExplicitOnly(F)?0:F.getCovalentHydrogenCount()),E=A.getCovalentOrder();
if(1==B&&(null!=u||z<C-1))v.set(A.index);else if((1<E||B>j)&&!this.htRings.containsKey(JS.SmilesGenerator.getRingKey(F.getIndex(),f)))j=1<E?1E3+E:B,u=A}g=null==u?null:u.getOtherNode(b);j=null==u?0:u.getCovalentOrder();C=Array(7);7>y&&null!=t&&(h&&2==t.getCovalentOrder()&&2==j&&null!=l[1]?(C[y++]=l[0],C[y++]=l[1]):C[y++]=this.prevAtom);7>y&&1==s&&(C[y++]=w);A=this.getBondStereochemistry(t,this.prevAtom);if(null!=D||"\x00"!=A)"\x00"!=A&&(D=""+A),a.append(D);B=y;E=x;t=new JU.SB;w=new JU.Lst;for(z=0;z<
p.size();z++)if(A=p.get(z),v.get(A.index)){F=A.getOtherNode(b);A=new JU.SB;this.prevAtom=b;this.prevSp2Atoms=this.alleneStereo=null;var D=this.ptSp2Atom0,G=this.ptAtom;this.getSmilesAt(A,F,c,d,e);this.ptAtom=G;this.ptSp2Atom0=D;A=A.toString();p.removeItemAt(z--);null==u?w.addLast(A):t.append("(").append(A).append(")");7>y&&(C[y++]=F);null!=l&&5>x&&(l[x++]=F)}c=new JU.SB;var G=y,H=x,v=null;if(!d&&!this.noStereo&&null==this.polySmilesCenter&&(5==p.size()||6==p.size()))v=this.sortInorganic(b,p,this.vTemp);
for(z=0;z<p.size();z++)A=p.get(z),A!==u&&(F=A.getOtherNode(b),D=this.getBondOrder(A,f,F.getIndex(),k),A=this.getBondStereochemistry(A,b),"\x00"!=A&&(D=""+A),c.append(D),c.append(this.getRingCache(f,F.getIndex(),this.htRings)),7>y&&(C[y++]=F),null!=l&&5>x&&(l[x++]=F));B!=G&&G!=y&&this.swapArray(C,B,G,y);E!=H&&H!=x&&this.swapArray(l,E,H,x);if(h&&2==y&&2==j){x=this.ptAtom-this.ptSp2Atom0;d=g.getCovalentBondCount();h=7==g.getElementNumber();if(0==x%2)y=8;else if(3==d||2==d&&h){x=g.getEdges();for(h=0;h<
x.length;h++)p=g.getBondedAtomIndex(h),x[h].isCovalent()&&p!=f&&(C[y++]=this.atoms[p]);2==d&&(C[y++]=g);4==y&&(this.alleneStereo=C,1==C[3].getAtomicAndIsotopeNumber()&&(B=C[3],C[3]=C[2],C[2]=B))}x=0}else null!=g&&7>y&&(C[y++]=g);null!=q&&q[3]!==C[2]&&(q=a.lastIndexOf("@]="),0<q&&(d=a.substring(q),a.setLength("@"==a.charAt(q-1)?q-1:q+1),a.append(d)));this.haveSmilesAtoms&&(null==v&&4==y)&&(v=b.getStereoAtAt(C));q=b.getFormalCharge();d=b.getIsotopeNumber();h=b.getValence();p=this.openSMILES?b.getFloatProperty("property_atomclass"):
NaN;z=b.getAtomName();F=b.getBioStructureTypeName();this.addAtomComment&&a.append("\n//* "+b.toString()+" *//\t");this.topologyOnly?a.append("*"):m&&0!=F.length&&0!=z.length?this.addBracketedBioName(a,b,"."+z,!1):a.append(JS.SmilesAtom.getAtomLabel(r,d,e?-1:h,q,p,s,k,null!=v?v:this.noStereo?null:this.checkStereoPairs(b,null==this.alleneStereo?f:-1,C,y,-1==n),this.is2D));a.appendSB(c);if(null!=u)a.appendSB(t);else{B=w.size()-1;if(0<=B){for(z=0;z<B;z++)a.append("(").append(w.get(z)).append(")");a.append(w.get(B))}return null}null!=
l&&2==j&&(1==x||2==x)?(null==l[0]&&(l[0]=b),null==l[1]&&(l[1]=b)):l=null;this.prevSp2Atoms=l;this.prevAtom=b;return g},"JU.SB,JU.SimpleNode,~B,~B,~B");h(c$,"isExplicitOnly",function(a){return 7==a.getElementNumber()||6==a.getElementNumber()&&17==a.getIsotopeNumber()},"JU.SimpleNode");h(c$,"swapArray",function(a,b,c,d){b=c-b;if(null==this.atemp||this.atemp.length<b)this.atemp=Array(b);for(var e=b,f=c;0<e;)this.atemp[--e]=a[--f];for(f=c;f<d;f++)a[f-b]=a[f];e=b;for(f=d;0<e;)a[--f]=this.atemp[--e]},"~A,~N,~N,~N");
h(c$,"getBondOrder",function(a,b,c,d){if(this.topologyOnly)return"";if(65537==(a.order&65537))return"^-";a=a.getCovalentOrder();return!d||!this.bsAromatic.get(c)?JS.SmilesBond.getBondOrderString(a):1==a&&!this.isSameAromaticRing(b,c)?"-":this.aromaticDouble&&(2==a||514==a)?"=":""},"JU.Edge,~N,~N,~B");h(c$,"isSameAromaticRing",function(a,b){for(var c,d=this.aromaticRings.size();0<=--d;)if((c=this.aromaticRings.get(d)).get(a)&&c.get(b))return!0;return!1},"~N,~N");h(c$,"sortPolyBonds",function(a,b,c){if(null==
this.smilesStereo)try{this.smilesStereo=JS.SmilesStereo.newStereo(null)}catch(d){if(!H(d,JS.InvalidSmilesException))throw d;}this.smilesStereo.sortPolyBondsByStereo(a,b,c,a.getEdges(),this.vTemp.vA)},"JU.SimpleNode,JU.SimpleNode,JU.P3");h(c$,"sortInorganic",function(a,b,c){for(var d=a.getIndex(),e=b.size(),f=new JU.Lst,g=new JU.Lst,j,m,h=null,k=null,l,p,r=new JU.BS,s=null,q=Array(6),s=!0,v="",u=0,t=0;t<e;t++)if(l=b.get(t),q[0]=j=l.getOtherNode(a),0==t?v=this.addStereoCheck(0,d,j,"",null):s&&null!=
this.addStereoCheck(0,d,j,v,null)&&(s=!1),!r.get(t)){r.set(t);for(var x=!1,w=t+1;w<e;w++)if(!r.get(w)&&(p=b.get(w),m=p.getOtherNode(a),JS.SmilesStereo.isDiaxial(a,a,j,m,c,-0.95))){switch(++u){case 1:h=j;break;case 2:k=j;break;case 3:2==JS.SmilesStereo.getHandedness(k,h,j,a,c)&&(j=l,l=p,p=j)}f.addLast(K(-1,[l,p]));x=!0;r.set(w);break}x||g.addLast(l)}d=f.size();if(s||6==e&&3!=d||5==e&&0==d)return"";s=f.get(0);l=s[0];q[0]=l.getOtherNode(a);b.clear();b.addLast(l);1<d&&g.addLast(f.get(1)[0]);3==d&&g.addLast(f.get(2)[0]);
1<d&&g.addLast(f.get(1)[1]);3==d&&g.addLast(f.get(2)[1]);for(t=0;t<g.size();t++)l=g.get(t),b.addLast(l),q[t+1]=l.getOtherNode(a);b.addLast(s[1]);q[e-1]=s[1].getOtherNode(a);return JS.SmilesStereo.getStereoFlag(a,q,e,c,this.is2D)},"JU.SimpleNode,JU.Lst,JS.VTemp");h(c$,"checkStereoPairs",function(a,b,c,d,e){if(10==d||d<(this.is2D?3:4))return"";if(0==this.explicitHydrogen&&0<=b&&4==d&&6==a.getElementNumber())for(var f="",g=0;4>g;g++)if(null==(f=this.addStereoCheck(0,b,c[g],f,JU.BSUtil.newAndSetBit(b))))return"";
if(this.is2D){b=4==d||!e?1:-1;e=a.getEdges();f=null;for(g=a.getBondCount();0<=--g;){var j=e[g];if(a===j.getAtom(0))switch(j.getBondType()){case 1025:this.setStereoTemp(c,f=j.getAtom(1),b);break;case 1041:this.setStereoTemp(c,f=j.getAtom(1),-b)}}if(null==f)return"";3==d&&(c[d++]=f)}return JS.SmilesStereo.getStereoFlag(a,c,d,this.vTemp,this.is2D)},"JU.SimpleNode,~N,~A,~N,~B");h(c$,"setStereoTemp",function(a,b,c){for(var d=0;4>d;d++)if(a[d]===b){var e=new JS.SmilesAtom;b=b.getXYZ();e.set(b.x,b.y,c);
a[d]=e;break}},"~A,JU.SimpleNode,~N");h(c$,"addStereoCheck",function(a,b,c,d,e){null!=e&&e.set(b);var f=c.getAtomicAndIsotopeNumber(),g=c.getCovalentBondCount(),j=6==f&&0!=this.explicitHydrogen?c.getCovalentHydrogenCount():0;if(6==f?4!=g:1==f||1<g)return d+ ++this.chainCheck;var m=";"+a+"/"+f+"/"+j+"/"+g+(0==a?",":"_");if(6==f)switch(j){case 1:return d+m+ ++this.chainCheck;case 0:case 2:if(null==e)return d;for(var h=c.getEdges(),k="",l="",p=2==j?0:3,f=c.getBondCount();0<=--f;){var l=h[f].getOtherNode(c),
r=l.getIndex();!e.get(r)&&(h[f].isCovalent()&&1!=l.getElementNumber())&&(e.set(r),l=this.addStereoCheck(a+1,c.getIndex(),l,"",e.clone()),0<=k.indexOf(l)&&p--,k+=l)}if(3==p)return d+m+ ++this.chainCheck;m=(m+k).$replace(",","_");if(0<a)return d+m}if(0<=d.indexOf(m)){if(3==j){for(f=a=0;f<g&&3>a;f++)e=c.getBondedAtomIndex(f),e!=b&&(a+=this.atoms[e].getAtomicAndIsotopeNumber());if(3<a)return d}return null}return d+m},"~N,~N,JU.SimpleNode,~S,JU.BS");h(c$,"getRingCache",function(a,b,c){var d=JS.SmilesGenerator.getRingKey(a,
b),e=c.get(d),f=null==e?null:e[0];if(null==f)this.bsRingKeys.set(++this.nPairs),this.nPairsMax=Math.max(this.nPairs,this.nPairsMax),c.put(d,K(-1,[f=this.getRingPointer(this.nPairs),Integer.$valueOf(b),Integer.$valueOf(this.nPairs)])),JU.Logger.debugging&&JU.Logger.debug("adding for "+a+" ring key "+this.nPairs+": "+d);else{c.remove(d);a=e[2].intValue();this.bsRingKeys.clear(a);if(0>this.bsRingKeys.nextSetBit(0)&&(2==this.nPairsMax||99==this.nPairsMax))this.nPairsMax=this.nPairs=99==this.nPairsMax?
10:0;JU.Logger.debugging&&JU.Logger.debug("using ring key "+d)}return f},"~N,~N,java.util.Map");h(c$,"getRingPointer",function(a){return 10>a?""+a:100>a?"%"+a:"%("+a+")"},"~N");h(c$,"dumpRingKeys",function(a,b){JU.Logger.info(a.toString()+"\n\n");for(var c,d=b.keySet().iterator();d.hasNext()&&((c=d.next())||1);)JU.Logger.info("unmatched connection: "+c)},"JU.SB,java.util.Map");c$.getRingKey=h(c$,"getRingKey",function(a,b){return Math.min(a,b)+"_"+Math.max(a,b)},"~N,~N")});D("JS");B(null,"JS.SmilesAromatic",
"java.util.Hashtable JU.BS $.Lst $.Measure $.V3 JS.SmilesRing $.SmilesRingSet JU.BSUtil $.Logger".split(" "),function(){c$=Q(JS,"SmilesAromatic");c$.setAromatic=h(c$,"setAromatic",function(a,b,c,d,e,f,g,j,m,h,k,l,p,r){g=g||0<f;if(r)for(w=d.size();0<=--w;){if(y=d.get(w),r=JS.SmilesAromatic.isSp2Ring(a,b,c,y,j?3.4028235E38:0<f?0.1:0.01,m,0==f)){e.or(y);if(g){h=new JU.Lst;for(var s=y.nextSetBit(0);0<=s;s=y.nextSetBit(s+1))for(var q=b[s],v=q.getEdges(),u=q.getIndex(),t=v.length;0<=--t;){var x=v[t].getOtherNode(q).getIndex();
x>u&&y.get(x)&&h.addLast(v[t])}switch(JS.SmilesAromatic.checkHueckelAromatic(a,b,e,y,f,p)){case -1:continue;case 0:r=!1;case 1:if(null!=l&&l.addLast(new JS.SmilesRing(a,y,h,r)),!r)continue}}k.addLast(y)}}else for(var w=d.size();0<=--w;){var y=JU.BSUtil.copy(d.get(w));y.and(e);y.cardinality()==a&&k.addLast(y)}},"~N,~A,JU.BS,JU.Lst,JU.BS,~N,~B,~B,~B,JS.VTemp,JU.Lst,JU.Lst,~A,~B");c$.checkAromaticDefined=h(c$,"checkAromaticDefined",function(a,b,c){for(var d=b.nextSetBit(0);0<=d;d=b.nextSetBit(d+1))for(var e=
a[d].getEdges(),f=0;f<e.length;f++)switch(e[f].getBondType()){case 515:case 514:case 513:c.set(e[f].getAtomIndex1()),c.set(e[f].getAtomIndex2())}},"~A,JU.BS,JU.BS");c$.isSp2Ring=h(c$,"isSp2Ring",function(a,b,c,d,e,f,g){if(f)for(var j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1)){if(3<b[j].getCovalentBondCount())return!1}else for(j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))if(3<b[j].getCovalentBondCountPlusMissingH())return!1;if(3.4028235E38==e)return!0;0>=e&&(e=0.01);for(var m=f=a=null,j=d.cardinality(),
h=Array(2*j),k=0,l=1-5*e,j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1)){for(var p=b[j],r=-1,s=-1,q=-1,v=p.getEdges().length;0<=--v;){var u=p.getBondedAtomIndex(v);if(c.get(u))if(d.get(u))0>s?s=u:q=u;else{if(16==p.getElementNumber()){if(!g)return!1;u=-1}r=u}}null==m&&(m=new JU.V3,a=new JU.V3,f=new JU.V3);v=0;for(p=j;2>v;v++){JU.Measure.getNormalThroughPoints(b[s],b[p],b[q],a,f);if(!JS.SmilesAromatic.addNormal(a,m,l))return!1;h[k++]=JU.V3.newV(a);if(0>(p=r))break}}return JS.SmilesAromatic.checkStandardDeviation(h,
m,k,e)},"~N,~A,JU.BS,JU.BS,~N,~B,~B");c$.addNormal=h(c$,"addNormal",function(a,b,c){var d=b.dot(a);if(0!=d&&Math.abs(d)<c)return!1;0>d&&a.scale(-1);b.add(a);b.normalize();return!0},"JU.V3,JU.V3,~N");c$.checkStandardDeviation=h(c$,"checkStandardDeviation",function(a,b,c,d){for(var e=0,f=0,g=0;g<c;g++)var j=a[g].dot(b),e=e+j,f=f+j*j;e=Math.sqrt((f-e*e/c)/(c-1));return e<d},"~A,JU.V3,~N,~N");c$.checkHueckelAromatic=h(c$,"checkHueckelAromatic",function(a,b,c,d,e,f){for(var g=0,j=0,m=d.nextSetBit(0);0<=
m&&0<=g;m=d.nextSetBit(m+1)){var h=b[m],k=h.getElementNumber(),l=h.getCovalentBondCountPlusMissingH(),l=l+h.getValence(),l=l-4;if(6==k){var p=h.getFormalCharge();-2147483648!=p&&(l+=p)}k=5<=k&&8>=k?k-5:15==k?2:34==k?3:33==k?4:16==k?5:-1;if(0<=k){k=JS.SmilesAromatic.OS_PI_COUNTS[k];if(0>l||l>=k.length)return-1;switch(l=k[l]){case -2:return-1;case -1:k=h.getEdges();l=0;for(p=k.length;0<=--p;){var r=k[p];if(2==r.getCovalentOrder()){l=r.getOtherNode(h);l=6==l.getElementNumber()||c.get(l.getIndex())?1:
0<e?-100:0;break}}default:if(0>l)return-1;null!=f&&(f[m]=l);g+=l;1==l&&j++;JU.Logger.debuggingHigh&&JU.Logger.info("atom "+h+" pi="+l+" npi="+g)}}}return 0==(g-2)%4&&(2>e||5==a||6==j)?1:0},"~N,~A,JU.BS,JU.BS,~N,~A");c$.finalizeAromatic=h(c$,"finalizeAromatic",function(a,b,c,d,e,f,g){g&&JS.SmilesAromatic.removeBridgingRings(c,d);JS.SmilesAromatic.checkFusedRings(d,e,c);b.clearAll();for(e=c.size();0<=--e;)b.or(c.get(e));if(g||f)for(e=b.nextSetBit(0);0<=e;e=b.nextSetBit(e+1)){c=a[e].getEdges();f=0;for(var j=
c.length;0<=--j;){var m=c[j].getOtherNode(a[e]),h=c[j].getCovalentOrder(),k=m.getIndex();if(b.get(k)){if(2==h){m=!1;for(h=d.size();0<=--h;){var l=d.get(h);if(l.get(e)&&l.get(k)){m=!0;break}}if(!m){f=-1;break}}f++}else if(g&&6==m.getElementNumber()&&2==h){f=-1;break}}2>f&&(b.clear(e),e=-1)}},"~A,JU.BS,JU.Lst,JU.Lst,~A,~B,~B");c$.removeBridgingRings=h(c$,"removeBridgingRings",function(a,b){var c=new JU.BS,d=new JU.BS,e=new JU.BS;JS.SmilesAromatic.checkBridges(a,d,a,d,c);JS.SmilesAromatic.checkBridges(b,
e,b,e,c);JS.SmilesAromatic.checkBridges(a,d,b,e,c);for(c=a.size();0<=--c;)d.get(c)&&a.removeItemAt(c);for(c=b.size();0<=--c;)e.get(c)&&b.removeItemAt(c)},"JU.Lst,JU.Lst");c$.checkBridges=h(c$,"checkBridges",function(a,b,c,d,e){for(var f=a===c,g=a.size();0<=--g;)for(var j=a.get(g),m=f?g+1:0,h=c.size();--h>=m;){var k=c.get(h);k.equals(j)||(e.clearAll(),e.or(j),e.and(k),2<e.cardinality()&&(b.set(g),d.set(h)))}},"JU.Lst,JU.BS,JU.Lst,JU.BS,JU.BS");c$.checkFusedRings=h(c$,"checkFusedRings",function(a,b,
c){for(var d=new java.util.Hashtable,e=a.size();0<=--e;){for(var f=a.get(e),g=f.edges,j=g.size();0<=--j;){var m=JS.SmilesRing.getSetByEdge(g.get(j),d);null==m||m===f.$set||(null!=f.$set?m.addSet(f.$set,d):m.addRing(f))}(null==f.$set?f.$set=new JS.SmilesRingSet:f.$set).addRing(f);f.addEdges(d)}for(e=a.size();0<=--e;)if(!(f=a.get(e)).isOK&&!(null==(m=f.$set)||m.isEmpty())){if(2==m.getElectronCount(b)%4)for(j=m.size();0<=--j;)(f=m.get(j)).isOK||c.addLast(f);m.clear()}},"JU.Lst,~A,JU.Lst");M(c$,"OS_PI_COUNTS",
K(-1,[v(-1,[-2,1,0]),v(-1,[1,2,1,-1]),v(-1,[2,1,2,1,1]),v(-1,[2,1]),v(-1,[-2,1,2,1,-2]),v(-1,[2,1,2,2])]))});D("JS");B(["JU.BS"],"JS.SmilesRing",null,function(){c$=G(function(){this.bsEdgesToCheck=this.edges=this.$set=null;this.isOK=!1;this.n=0;E(this,arguments)},JS,"SmilesRing",JU.BS);I(c$,function(a,b,c,d){O(this,JS.SmilesRing,[]);this.or(b);this.edges=c;this.isOK=d;this.n=a},"~N,JU.BS,JU.Lst,~B");h(c$,"addEdges",function(a){for(var b=this.edges.size();0<=--b;)a.put(JS.SmilesRing.getKey(this.edges.get(b)),
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"addSet",function(a,b){for(var c=a.size();0<=--c;){var d=a.get(c);this.addRing(d);d.addEdges(b)}},"JS.SmilesRingSet,java.util.Hashtable");h(c$,"addRing",function(a){this.addLast(a);a.$set=this;this.bs.or(a)},"JS.SmilesRing");h(c$,"getElectronCount",function(a){for(var b=0,c=this.bs.nextSetBit(0);0<=c;c=this.bs.nextSetBit(c+1))b+=a[c];return b},"~A")});D("JS");B(["JU.P3","JU.Node"],"JS.SmilesAtom",["java.lang.Float","JU.AU","JU.Elements","$.Logger","JV.JC"],function(){c$=G(function(){this.patternIndex=
-1;this.pattern=null;this.primitiveType=0;this.isAND=!1;this.subAtoms=null;this.index=this.nSubAtoms=0;this.residueChar=this.residueName=this.referance=null;this.insCode="\x00";this.isBioAtomWild=this.isBioResidue=this.isBioAtom=!1;this.bioType="\x00";this.$isLeadAtom=!1;this.notBondedIndex=-1;this.notCrossLinked=!1;this.aromaticAmbiguous=!0;this.covalentHydrogenCount=-1;this.elementDefined=this.hasSymbol=this.selected=this.not=!1;this.bioAtomName=this.atomType=null;this.isFirst=!0;this.jmolIndex=
-1;this.elementNumber=-2;this.implicitHydrogenCount=this.explicitHydrogenCount=this.residueNumber=this.atomNumber=-2147483648;this.bonds=this.parent=null;this.iNested=this.bondCount=0;this.isAromatic=!1;this.charge=this.atomicMass=-2147483648;this.matchingIndex=-1;this.stereo=null;this.component=-2147483648;this.atomSite=this.matchingComponent=0;this.nonhydrogenDegree=this.degree=-1;this.valence=0;this.connectivity=-1;this.ringSize=this.ringMembership=-2147483648;this.ringConnectivity=-1;this.matchingNode=
null;this.hasSubpattern=!1;this.mapIndex=-1;this.atomClass=NaN;this.symbol=null;this.isTopoAtom=!1;this.cipChirality=this.missingHydrogenCount=0;E(this,arguments)},JS,"SmilesAtom",JU.P3,JU.Node);N(c$,function(){this.bonds=Array(4)});c$.allowSmilesUnbracketed=h(c$,"allowSmilesUnbracketed",function(a){return 0<="B, C, N, O, P, S, F, Cl, Br, I, *,".indexOf(a+",")},"~S");I(c$,function(){O(this,JS.SmilesAtom,[])});p(c$,"getAtomType",function(){return null==this.atomType?this.bioAtomName:this.atomType});
h(c$,"getChiralClass",function(){return null==this.stereo?-2147483648:this.stereo.getChiralClass(this)});h(c$,"isDefined",function(){return this.hasSubpattern||0!=this.iNested||this.isBioAtom||-2147483648!=this.component||-2!=this.elementNumber||0<this.nSubAtoms});h(c$,"setBioAtom",function(a){this.isBioAtom="\x00"!=a;this.bioType=a;null!=this.parent&&(this.parent.bioType=a,this.parent.isBioAtom=this.isBioAtom,this.parent.isBioAtomWild=this.isBioAtomWild)},"~S");h(c$,"setAtomName",function(a){null!=
a&&(0<a.length&&(this.bioAtomName=a),a.equals("\x00")&&(this.$isLeadAtom=!0),null!=this.parent&&(this.parent.bioAtomName=a))},"~S");h(c$,"setBonds",function(a){this.bonds=a},"~A");h(c$,"addSubAtom",function(a,b){this.isAND=b;null==this.subAtoms&&(this.subAtoms=Array(2));this.nSubAtoms>=this.subAtoms.length&&(this.subAtoms=JU.AU.doubleLength(this.subAtoms));a.setIndex(this.index);a.parent=this;this.subAtoms[this.nSubAtoms++]=a;this.setSymbol("*");this.hasSymbol=!1;return a},"JS.SmilesAtom,~B");h(c$,
"setIndex",function(a){this.index=a;return this},"~N");h(c$,"setTopoAtom",function(a,b,c,d,e){this.component=a;this.index=b;this.patternIndex=e;this.setSymbol(c);this.charge=d;this.isTopoAtom=!0;return this},"~N,~N,~S,~N,~N");h(c$,"setHydrogenCount",function(){this.missingHydrogenCount=this.explicitHydrogenCount;if(-2147483648!=this.explicitHydrogenCount)return!0;var a=JS.SmilesAtom.getDefaultCount(this.elementNumber,this.isAromatic);if(0>a)return this.missingHydrogenCount=0,-1==a;7==this.elementNumber&&
this.isAromatic&&2==this.bondCount&&1==this.bonds[0].getBondType()&&1==this.bonds[1].getBondType()&&a++;for(var b=0;b<this.bondCount;b++){var c=this.bonds[b];switch(c.getBondType()){case 81:7==this.elementNumber&&JU.Logger.info("Ambiguous bonding to aromatic N found -- MF may be in error");a-=1;break;case 1025:case 1041:case 65537:case 65538:a-=1;break;case 2:a-=this.isAromatic&&6==this.elementNumber?1:2;break;case 1:case 3:case 4:a-=c.getBondType()}}0<=a&&(this.missingHydrogenCount=this.explicitHydrogenCount=
a);return!0});c$.getDefaultCount=h(c$,"getDefaultCount",function(a,b){switch(a){case 0:case -1:case -2:return-1;case 1:return 1;case 6:return b?3:4;case 8:case 16:return 2;case 7:return b?2:3;case 5:case 15:return 3;case 9:case 17:case 35:case 53:return 1;default:return 0}},"~N,~B");p(c$,"getIndex",function(){return this.index});h(c$,"setSymbol",function(a){this.symbol=a;this.isAromatic=a.equals(a.toLowerCase());this.elementDefined=this.hasSymbol=!0;if(a.equals("*"))return this.isAromatic=!1,this.elementNumber=
-2,!0;if(a.equals("Xx"))return this.elementNumber=0,!0;this.aromaticAmbiguous=!1;if(a.equals("a")||a.equals("A"))return 0>this.elementNumber&&(this.elementNumber=-1),!0;this.isAromatic&&(a=a.substring(0,1).toUpperCase()+(1==a.length?"":a.substring(1)));this.elementNumber=JU.Elements.elementNumberFromSymbol(a,!0);return 0!=this.elementNumber},"~S");p(c$,"getElementNumber",function(){return this.elementNumber});h(c$,"getAtomicMass",function(){return this.atomicMass});p(c$,"getAtomNumber",function(){return this.atomNumber});
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p(c$,"getGroup3",function(){return null==this.residueName?"":this.residueName},"~B");p(c$,"getGroup1",function(){return null==this.residueChar?"":this.residueChar},"~S");h(c$,"addBond",function(a){this.bondCount>=this.bonds.length&&(this.bonds=JU.AU.doubleLength(this.bonds));this.bonds[this.bondCount]=a;this.bondCount++},"JS.SmilesBond");h(c$,"setBondArray",function(){this.bonds.length>this.bondCount&&(this.bonds=JU.AU.arrayCopyObject(this.bonds,this.bondCount));null!=this.subAtoms&&this.subAtoms.length>
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p(c$,"getBondCount",function(){return null!=this.parent?this.parent.getBondCount():this.bondCount});p(c$,"getCovalentBondCountPlusMissingH",function(){return this.getBondCount()+(this.isTopoAtom?0:this.missingHydrogenCount)});p(c$,"getTotalHydrogenCount",function(){return this.getCovalentHydrogenCount()+(this.isTopoAtom?0:this.missingHydrogenCount)});p(c$,"getImplicitHydrogenCount",function(){return this.implicitHydrogenCount});p(c$,"getExplicitHydrogenCount",function(){return this.explicitHydrogenCount});
h(c$,"getMatchingBondedAtom",function(a){if(null!=this.parent)return this.parent.getMatchingBondedAtom(a);if(a>=this.bondCount)return-1;a=this.bonds[a];return(a.atom1===this?a.atom2:a.atom1).matchingIndex},"~N");p(c$,"getBondedAtomIndex",function(a){return null!=this.parent?this.parent.getBondedAtomIndex(a):this.bonds[a].getOtherAtom(this).index},"~N");p(c$,"getCovalentHydrogenCount",function(){if(0<=this.covalentHydrogenCount)return this.covalentHydrogenCount;if(null!=this.parent)return this.covalentHydrogenCount=
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p(c$,"getOffsetResidueAtom",function(a,b){if(this.isBioAtom){if(0==b)return this.index;for(var c=0;c<this.bonds.length;c++)if(this.bonds[c].getAtomIndex1()==this.index&&96==this.bonds[c].getBondType())return this.bonds[c].getOtherAtom(this).index}return-1},"~S,~N");p(c$,"getGroupBits",function(a){a.set(this.index)},"JU.BS");p(c$,"isCrossLinked",function(a){return this.getBondTo(a).isHydrogen()},"JU.Node");p(c$,"getCrossLinkVector",function(a){for(var b=!1,c=0;c<this.bonds.length;c++)if(112==this.bonds[c].order){if(null==
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function(a,b,c,d,e,f,g,j,m){var h=JU.Elements.elementSymbolFromNumber(a);if(1==a||g&&!(h=h.toLowerCase()).equals("c"))c=2147483647;g=2147483647!=c&&0>=b&&0==d&&Float.isNaN(e)&&(null==j||0==j.length);var k=JS.SmilesAtom.getDefaultCount(a,!1);if(m&&0==f){if(g&&6==a)return h;f=k-c}return g&&k==c?h:"["+(0>=b?"":""+b)+h+(null==j?"":j)+(1<f?"H"+f:1==f?"H":"")+(0>d&&-2147483648!=d?""+d:0<d?"+"+d:"")+(Float.isNaN(e)?"":":"+S(e))+"]"},"~N,~N,~N,~N,~N,~N,~B,~S,~B");p(c$,"getBioSmilesType",function(){return this.bioType});
h(c$,"isNucleic",function(){return"n"==this.bioType||"r"==this.bioType||"d"==this.bioType});p(c$,"isPurine",function(){return null!=this.residueChar&&this.isNucleic()&&0<="AG".indexOf(this.residueChar)});p(c$,"isPyrimidine",function(){return null!=this.residueChar&&this.isNucleic()&&0<="CTUI".indexOf(this.residueChar)});p(c$,"isDeleted",function(){return!1});p(c$,"findAtomsLike",function(){return null},"~S");p(c$,"toString",function(){var a=null!=this.residueChar||null!=this.residueName?(null==this.residueChar?
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new JU.SB;j.append("||").append(a.substring(0,g));for(l=0;l<f;l++)j.append(k);j.append(a.substring(h));b.appendSB(j)}}}}}return e?this.parseVariableLength(b.substring(2)):2>b.length()?a:b.substring(2)},"~S");h(c$,"getSubsearch",function(a,b,c){this.htMeasures=new java.util.Hashtable;var d=new JS.SmilesSearch;d.setTop(a);d.isSmarts=this.isSmarts;d.pattern=b;d.setFlags(c);0<=b.indexOf("$(")&&(b=this.parseNested(d,b,""));this.parseSmiles(d,b,null,!1);if(0!=this.braceCount)throw new JS.InvalidSmilesException("unmatched '{'");
if(!this.connections.isEmpty())throw new JS.InvalidSmilesException("Open connection");d.set();if(this.isSmarts)for(a=d.ac;0<=--a;)this.checkNested(d,d.patternAtoms[a],c);else this.isBioSequence||(d.elementCounts[1]=d.getMissingHydrogenCount());!this.ignoreStereochemistry&&!this.isTarget&&this.fixChirality(d);return d},"JS.SmilesSearch,~S,~N");h(c$,"checkNested",function(a,b,c){if(0<b.iNested){var d=a.getNested(b.iNested);if(L(d,String)){if(d.startsWith("select"))return;"~"!=d.charAt(0)&&"\x00"!=b.bioType&&
(d="~"+b.bioType+"~"+d);d=this.getSubsearch(a,d,c);0<d.ac&&d.patternAtoms[0].selected&&(b.selected=!0);a.setNested(b.iNested,d)}}for(d=0;d<b.nSubAtoms;d++)this.checkNested(a,b.subAtoms[d],c)},"JS.SmilesSearch,JS.SmilesAtom,~N");h(c$,"fixChirality",function(a){for(var b=a.ac;0<=--b;){var c=a.patternAtoms[b];null!=c.stereo&&c.stereo.fixStereo(c)}},"JS.SmilesSearch");h(c$,"parseSmiles",function(a,b,c,d){var e=v(1,0),f=0,g,j=null,h=!1;a:for(;null!=b&&0!=b.length;){var n=0;null==c&&(n=this.checkBioType(b,
0),n==b.length&&(b+="*"),this.isBioSequence&&(a.needAromatic=a.top.needAromatic=!1));g=JS.SmilesParser.getChar(b,n);var k=this.checkBrace(a,g,"{");k&&(g=JS.SmilesParser.getChar(b,++n));if("("==g)if(j=JS.SmilesParser.getSubPattern(b,n,"("),g="."==JS.SmilesParser.getChar(b,n+1),null==c){if(g||!this.isSmarts)throw new JS.InvalidSmilesException("No previous atom for measure");a.haveComponents=!0;do this.componentCount++,this.componentParenCount++,g=JS.SmilesParser.getChar(b=b.substring(1),0);while("("==
g);if(!k&&!0==(k=this.checkBrace(a,g,"{")))g=JS.SmilesParser.getChar(b=b.substring(1),0)}else h=!1,j.startsWith(".")?(this.parseMeasure(a,j.substring(1),c),h=!0):0==j.length&&this.isBioSequence?c.notCrossLinked=!0:(this.branchLevel++,this.parseSmiles(a,j,c,!0),this.branchLevel--),n=j.length+2,g=JS.SmilesParser.getChar(b,n),"}"==g&&this.checkBrace(a,g,"}")&&n++,g="\x00";if("\x00"!=g){f=n;b:for(;"\x00"!=g;){switch(JS.SmilesBond.isBondType(g,this.isSmarts,this.isBioSequence)){case 0:break b;case -1:if(!((JU.PT.isDigit(JS.SmilesParser.getChar(b,
++n))&&0<n++?JU.PT.isDigit(JS.SmilesParser.getChar(b,n++)):1)&&"-"==(g=JS.SmilesParser.getChar(b,n))))throw new JS.InvalidSmilesException("malformed atropisomerism bond ^nn-  or ^^nn-");continue}g=JS.SmilesParser.getChar(b,++n)}g=JS.SmilesParser.getChar(b,n);if(")"==g){switch(JS.SmilesParser.getChar(b,++n)){case "\x00":case ")":case ".":if(b=b.substring(n),this.componentParenCount--,0<=this.componentParenCount)continue a}throw new JS.InvalidSmilesException("invalid continuation after component grouping (SMARTS).(SMARTS)");
}j=this.parseBond(a,null,b.substring(f,n),null,c,!1,d,n-f,e);k&&-1!=j.order&&(g=JS.SmilesParser.getChar(b,n=f));this.checkBrace(a,g,"{")&&(g=JS.SmilesParser.getChar(b,++n));switch(g){case "~":0==j.order&&(n=this.checkBioType(b,n),n==b.length&&(b+="*"));break;case "(":do this.componentCount++,this.componentParenCount++,g=JS.SmilesParser.getChar(b,++n);while("("==g);break;case "\x00":if(0==j.order)return}k=JU.PT.isDigit(g)||"%"==g;f=!k&&("_"==g||"["==g||"*"==g||JU.PT.isLetter(g));if(k){if(h)throw new JS.InvalidSmilesException("connection number must immediately follow its connecting atom");
n=JS.SmilesParser.getRingNumber(b,n,g,e);this.parseConnection(a,e[0],c,j)}else if(f)switch(h=!1,g){case "[":case "_":k=JS.SmilesParser.getSubPattern(b,n,g);n+=k.length+("["==g?2:0);this.isBioSequence&&("["==g&&0>k.indexOf(".")&&0>k.indexOf("_"))&&(k+=".0");c=this.parseAtom(a,null,k,c,j,"["==g,!1,d);c.hasSubpattern=!0;-1!=j.order&&0!=j.order&&this.setBondAtom(j,null,c,a);break;default:k=!this.isBioSequence&&JU.PT.isUpperCase(g)?JS.SmilesParser.getChar(b,n+1):"\x00";if("X"!=g||"x"!=k)if(!JU.PT.isLowerCase(k)||
0==JU.Elements.elementNumberFromSymbol(b.substring(n,n+2),!0))k="\x00";"\x00"!=k&&0<="NA CA BA PA SC AC".indexOf(b.substring(n,n+2))&&(k="\x00");g=JU.PT.isUpperCase(g)&&JU.PT.isLowerCase(k)?2:1;c=this.parseAtom(a,null,b.substring(n,n+g),c,j,!1,!1,d);n+=g}else throw new JS.InvalidSmilesException("Unexpected character: "+JS.SmilesParser.getChar(b,n));g=JS.SmilesParser.getChar(b,n);"}"==g&&this.checkBrace(a,g,"}")&&n++}b=b.substring(n);d=!1}},"JS.SmilesSearch,~S,JS.SmilesAtom,~B");h(c$,"parseConnection",
function(a,b,c,d){b=Integer.$valueOf(b);var e=this.connections.get(b);if(null==e)this.connections.put(b,d),a.top.ringCount++;else{this.connections.remove(b);switch(d.order){case -1:d.order=-1!=e.order?e.order:this.isSmarts||c.isAromatic&&e.atom1.isAromatic?81:1;break;case 1025:d.order=1041;break;case 1041:d.order=1025}if(-1!=e.order&&e.order!=d.order||c===e.atom1||null!=e.atom1.getBondTo(c))throw new JS.InvalidSmilesException("Bad connection type or atom");e.set(d);c.bondCount--;e.setAtom2(c,a)}},
"JS.SmilesSearch,~N,JS.SmilesAtom,JS.SmilesBond");h(c$,"setBondAtom",function(a,b,c,d){a.set2a(b,c);null!=d&&(2==a.order&&null!=a.atom1&&null!=a.atom2&&a.atom1.isAromatic&&a.atom2.isAromatic&&0==(this.flags&512))&&d.setFlags(this.flags|=512)},"JS.SmilesBond,JS.SmilesAtom,JS.SmilesAtom,JS.SmilesSearch");c$.getRingNumber=h(c$,"getRingNumber",function(a,b,c,d){switch(c){case "%":if("("==JS.SmilesParser.getChar(a,b+1)){if(a=JS.SmilesParser.getSubPattern(a,b+1,"("),JS.SmilesParser.getDigits(a,0,d),b+=
a.length+3,0>d[0])throw new JS.InvalidSmilesException("Invalid number designation: "+a);}else if(b+3<=a.length&&(b=JS.SmilesParser.getDigits(a.substring(0,b+3),b+1,d)),10>d[0])throw new JS.InvalidSmilesException("Two digits must follow the % sign");a=d[0];break;default:a=c.charCodeAt(0)-48,b++}d[0]=a;return b},"~S,~N,~S,~A");h(c$,"checkBioType",function(a,b){if(this.isBioSequence="~"==a.charAt(b)){b++;this.bioType="*";var c=JS.SmilesParser.getChar(a,2);if("~"==c&&("*"==(c=a.charAt(1))||JU.PT.isLowerCase(c)))this.bioType=
c,b=3}return b},"~S,~N");h(c$,"parseMeasure",function(a,b,c){for(var d=b.indexOf(":"),e=0>d?b:b.substring(0,d);0!=d;){var f=e.length;1==f&&(e+="0");var g=this.htMeasures.get(e);if(null==g==0>d||0==f)break;try{if(0<d){var j="__dat".indexOf(e.charAt(0));if(2>j)break;var h=v(1,0);JS.SmilesParser.getDigits(e,1,h);var n=h[0];b=b.substring(d+1);var k=b.startsWith("!");k&&(b=b.substring(1));var l=b.startsWith("-");l&&(b=b.substring(1));b=JU.PT.rep(b,"-",",");b=JU.PT.rep(b,",,",",-");l&&(b="-"+b);var p=JU.PT.split(b,
",");if(1==p.length%2||k&&2!=p.length)break;for(var r=P(p.length,0),s=p.length;0<=--s&&!Float.isNaN(r[s]=Float.parseFloat(p[s])););if(0<=s)break;g=new JS.SmilesMeasure(a,n,j,k,r);a.measures.addLast(g);0<n?this.htMeasures.put(e,g):0==n&&JU.Logger.debugging&&JU.Logger.debug("measure created: "+g)}else{if(!g.addPoint(c.index))break;g.nPoints==g.type&&(this.htMeasures.remove(e),JU.Logger.debugging&&JU.Logger.debug("measure created: "+g));return}if(!g.addPoint(c.index))break}catch(q){if(H(q,NumberFormatException))break;
else throw q;}return}throw new JS.InvalidSmilesException("invalid measure: "+b);},"JS.SmilesSearch,~S,JS.SmilesAtom");h(c$,"checkBrace",function(a,b,c){switch(b){case "{":if(b!=c)break;this.braceCount++;return a.top.haveSelected=!0;case "}":if(b!=c)break;if(0<this.braceCount)return this.braceCount--,!0;break;default:return!1}throw new JS.InvalidSmilesException("Unmatched '}'");},"JS.SmilesSearch,~S,~S");h(c$,"parseNested",function(a,b,c){var d;for(c="$("+c;0<=(d=b.lastIndexOf(c));){var e=JS.SmilesParser.getSubPattern(b,
d+1,"("),f=d+e.length+3,g=b.substring(f);b=b.substring(0,d);var j="";if(b.endsWith("]"))throw new JS.InvalidSmilesException("$(...) must be enclosed in brackets: "+b+"$("+e+")");if(1<d&&2==c.length&&1<(f=b.length)&&0>",;&![".indexOf(b.substring(f-1)))j="&";1<g.length&&0>",;&!)]".indexOf(g.charAt(0))&&(g="&"+g);b=b+j+"_"+a.top.addNested(e)+"_"+g}return b},"JS.SmilesSearch,~S,~S");h(c$,"parseVariables",function(a){var b=new JU.Lst,c=new JU.Lst,d,e=0,f=-1;for(JU.Logger.debugging&&JU.Logger.info(a);0<=
(d=a.indexOf("$",e))&&"("!=JS.SmilesParser.getChar(a,d+1);){e=JS.SmilesParser.skipTo(a,d,"=");if(e<=d+1||'"'!=JS.SmilesParser.getChar(a,e+1))break;d=a.substring(d,e);if(0<d.lastIndexOf("$")||0<d.indexOf("]"))throw new JS.InvalidSmilesException("Invalid variable name: "+d);f=JS.SmilesParser.getSubPattern(a,e+1,'"');b.addLast("["+d+"]");c.addLast(f);e+=f.length+2;e=JS.SmilesParser.skipTo(a,e,";");f=++e}if(0>f)return a;a=a.substring(f);for(e=b.size();0<=--e;)d=b.get(e),f=c.get(e),f.equals(d)||(a=JU.PT.rep(a,
d,f));JU.Logger.debugging&&JU.Logger.info(a);return a},"~S");h(c$,"parseAtom",function(a,b,c,d,e,f,g,j){if(null==c||0==c.length)throw new JS.InvalidSmilesException("Empty atom definition");var h=new JS.SmilesAtom;0<this.componentParenCount&&(h.component=this.componentCount);null==b&&a.appendAtom(h);if(!this.checkLogic(a,c,h,null,d,g,j,null)){var n=v(1,0);this.isBioSequence&&1==c.length&&(c+=".0");var k=c.charAt(0),l=0,p=!1;if(this.isSmarts&&"!"==k){k=JS.SmilesParser.getChar(c,++l);if("\x00"==k)throw new JS.InvalidSmilesException("invalid '!'");
h.not=p=!0}var r=0<=c.indexOf("@PH")?-1:c.indexOf(".");if(0<=r){h.isBioResidue=!0;var s=c.substring(l,r);c=c.substring(r+1).toUpperCase();var q=s.length;if(0<=(r=s.indexOf("^")))r==q-2&&(k=s.charAt(q-1),"*"!=k&&(h.insCode=k)),s=s.substring(0,r);if(0<=(r=s.indexOf("#")))JS.SmilesParser.getDigits(s,r+1,n),h.residueNumber=n[0],s=s.substring(0,r);0==s.length&&(s="*");1<s.length?h.residueName=s.toUpperCase():s.equals("*")||(h.residueChar=s);s=c;if(0<=(r=s.indexOf("#")))JS.SmilesParser.getDigits(s,r+1,
n),h.elementNumber=n[0],s=s.substring(0,r);0==s.length?s="*":s.equals("0")&&(s="\x00");s.equals("*")?h.isBioAtomWild=!0:h.setAtomName(s);k="\x00"}h.setBioAtom(this.bioType);for(r=-2147483648;"\x00"!=k;){h.setAtomName(this.isBioSequence?"\x00":"");if(JU.PT.isDigit(k)){l=JS.SmilesParser.getDigits(c,l,n);k=n[0];if(-2147483648==k)throw new JS.InvalidSmilesException("Non numeric atomic mass");"?"==JS.SmilesParser.getChar(c,l)&&(l++,k=-k);if(h.elementDefined)throw new JS.InvalidSmilesException('atom mass must precede atom symbol or be separated from it with ";"');
h.setAtomicMass(k)}else switch(k){case '"':k=JU.PT.getQuotedStringAt(c,l);l+=k.length+2;h.atomType=k;break;case "_":l=JS.SmilesParser.getDigits(c,l+1,n)+1;if(-2147483648==n[0])throw new JS.InvalidSmilesException("Invalid SEARCH primitive: "+c.substring(l));h.iNested=n[0];if(!f)throw new JS.InvalidSmilesException("nesting must appear in [...]: $("+a.getNested(n[0])+")");if(this.isBioSequence&&l!=c.length)throw new JS.InvalidSmilesException("invalid characters: "+c.substring(l));break;case "=":l=JS.SmilesParser.getDigits(c,
l+1,n);h.jmolIndex=n[0];break;case "#":k="-"==c.charAt(l+1);l=JS.SmilesParser.getDigits(c,l+(k?2:1),n);k?h.atomNumber=n[0]:h.elementNumber=n[0];break;case "-":case "+":l=this.checkCharge(c,l,h);break;case "@":null==a.stereo&&(a.stereo=JS.SmilesStereo.newStereo(a));l=JS.SmilesStereo.checkChirality(a,c,l,a.patternAtoms[h.index]);break;case ":":l=JS.SmilesParser.getDigits(c,++l,n);if(-2147483648==n[0])throw new JS.InvalidSmilesException("Invalid atom class");h.atomClass=n[0];break;default:var s=JS.SmilesParser.getChar(c,
l+1),q=l+(JU.PT.isLowerCase(s)&&(!f||!JU.PT.isDigit(JS.SmilesParser.getChar(c,l+2)))?2:1),B=c.substring(l+1,q),u=Character.toUpperCase(k)+B,t=!0;f&&JU.PT.isLetter(k)&&(!p&&(g?b:h).hasSymbol?t=!1:"H"==k?t=1==c.length||!JU.PT.isDigit(s):JU.PT.isDigit(s)?t=!1:!u.equals("A")&&!u.equals("Xx")&&(t=("h"==k?2==q:!0)&&0<JU.Elements.elementNumberFromSymbol(u,!0),!t&&2==q&&(B="",u=u.substring(0,1),t=0<JU.Elements.elementNumberFromSymbol(u,!0))));if(t){if(!f&&!this.isSmarts&&!this.isBioSequence&&!JS.SmilesAtom.allowSmilesUnbracketed(u)||
!h.setSymbol(u=k+B))throw new JS.InvalidSmilesException("Invalid atom symbol: "+u);g&&(b.hasSymbol=!0);l+=u.length}else switch(l=JS.SmilesParser.getDigits(c,l+1,n),q=n[0],k){default:throw new JS.InvalidSmilesException("Invalid SEARCH primitive: "+c.substring(l));case "D":h.setDegree(-2147483648==q?1:q);break;case "d":h.setNonhydrogenDegree(-2147483648==q?1:q);break;case "H":r=-2147483648==q?1:q;break;case "h":h.setImplicitHydrogenCount(-2147483648==q?-1:q);break;case "R":-2147483648==q&&(q=-1);h.setRingMembership(q);
a.top.needRingData=!0;break;case "r":if(-2147483648==q)q=-1,h.setRingMembership(q);else{h.setRingSize(q);switch(q){case 500:q=5;break;case 600:q=6}q>a.ringDataMax&&(a.ringDataMax=q)}a.top.needRingData=!0;break;case "v":h.setValence(-2147483648==q?1:q);break;case "X":h.setConnectivity(-2147483648==q?1:q);break;case "x":h.setRingConnectivity(-2147483648==q?-1:q),a.top.needRingData=!0}}k=JS.SmilesParser.getChar(c,l);if(p&&"\x00"!=k)throw new JS.InvalidSmilesException("'!' may only involve one primitive.");
}-2147483648==r&&f&&(r=-2147483647);h.setExplicitHydrogenCount(r);a.patternAtoms[h.index].setExplicitHydrogenCount(r)}0<this.braceCount&&(h.selected=!0);null!=b&&b.addSubAtom(h,g);null!=d&&0==e.order&&(h.notBondedIndex=d.index);null!=d&&0!=e.order&&(-1==e.order&&(e.order=this.isBioSequence&&j?112:this.isSmarts||d.isAromatic&&h.isAromatic?81:1),f||this.setBondAtom(e,null,h,a),0==this.branchLevel&&(17==e.getBondType()||112==e.order)&&this.branchLevel++);0==this.branchLevel&&(a.lastChainAtom=h);return h},
"JS.SmilesSearch,JS.SmilesAtom,~S,JS.SmilesAtom,JS.SmilesBond,~B,~B,~B");h(c$,"checkCharge",function(a,b,c){var d=a.length,e=a.charAt(b),f=1;++b;if(b<d){var g=a.charAt(b);if(JU.PT.isDigit(g)){if(d=v(1,0),b=JS.SmilesParser.getDigits(a,b,d),f=d[0],-2147483648==f)throw new JS.InvalidSmilesException("Non numeric charge");}else for(;b<d&&a.charAt(b)==e;)b++,f++}c.setCharge("+"==e?f:-f);return b},"~S,~N,JS.SmilesAtom");h(c$,"parseBond",function(a,b,c,d,e,f,g,j,h){var n;if(0<j)switch(n=c.charAt(0)){case ">":if(!c.equals(">>")){j=
-1;break}case ".":if(null==d&&null==b)return this.isBioSequence="~"==JS.SmilesParser.getChar(c,1),new JS.SmilesBond(null,null,0,!1);j=-1;break;case "+":null!=b&&(j=-1)}else n="\x00";d=null==b?null==d?new JS.SmilesBond(e,null,this.isBioSequence&&null!=e?g?112:96:-1,!1):d:f?b.addPrimitive():b.addBondOr();if(0<j&&!this.checkLogic(a,c,null,d,e,f,!1,h)){if(f="!"==n)if(n=JS.SmilesParser.getChar(c,1),"\x00"==n||"!"==n)throw new JS.InvalidSmilesException("invalid '!'");g=JS.SmilesBond.getBondTypeFromCode(n);
65==g&&(a.top.needRingMemberships=!0);if(null==e&&0!=g)throw new JS.InvalidSmilesException("Bond without a previous atom");switch(g){case 65537:case 65538:(j=c.length)<(f?3:2)||"-"!=c.charAt(j-1)?j=0:j==(f?3:2)?d.setAtropType(22):(JS.SmilesParser.getDigits(c,f?2:1,h),d.setAtropType(h[0]));a.haveBondStereochemistry=!0;break;case 1025:case 1041:this.bondDirectionPaired=!this.bondDirectionPaired;a.haveBondStereochemistry=!0;break;case 2:a.top.nDouble++;case 1:e.isAromatic&&(a.top.needRingData=!0)}d.set2(g,
f);this.isBioSequence&&null!=b&&b.set2(g,f)}if(-1==j)throw new JS.InvalidSmilesException("invalid bond:"+n);return d},"JS.SmilesSearch,JS.SmilesBond,~S,JS.SmilesBond,JS.SmilesAtom,~B,~B,~N,~A");h(c$,"checkLogic",function(a,b,c,d,e,f,g,j){var h=b.lastIndexOf("!");null!=c&&(c.pattern=b);for(;0<h;)0>",;&!(".indexOf(b.charAt(h-1))&&(b=b.substring(0,h)+"&"+b.substring(h)),h=b.lastIndexOf("!",h-1);var h=b.indexOf(","),n=b.length,k="&";a:for(;;){var l=0<h;if(l&&!this.isSmarts||0==h)break;h=b.indexOf(";");
if(0<=h){if(!this.isSmarts||0==h)break;l?(k=";",l=!1):b=b.$replace(";","&")}var p=0;if(l)for(b+=",";0<(h=b.indexOf(",",p))&&h<=n;){p=b.substring(p,h);if(0==p.length)throw new JS.InvalidSmilesException("missing "+(null==d?"atom":"bond")+" token");null==d?this.parseAtom(a,c,p,null,null,!0,!1,g):this.parseBond(a,d,p,null,e,!1,!1,p.length,j);p=h+1}else if(0<=(h=b.indexOf(k))||null!=d&&1<n&&!f){if(0==h||null==d&&!this.isSmarts)break;if(null!=d&&0>h&&1<n){f=new JU.SB;for(l=0;l<n;){var r=b.charAt(l++);f.appendC(r);
switch(r){case "!":if(!this.isSmarts)break a;continue;case "^":case "`":for(;"-"!=(r=b.charAt(l++))&&"\x00"!=r;)f.appendC(r);f.appendC("-")}if(l<n){if(!this.isSmarts)break a;f.append(k)}}b=f.toString();n=b.length}for(b+=k;0<(h=b.indexOf(k,p))&&h<=n;)p=b.substring(p,h),null==d?this.parseAtom(a,c,p,null,null,!0,!0,g):this.parseBond(a,this.isSmarts?d:null,p,this.isSmarts?null:d,e,!0,!1,p.length,j),p=h+1}else return!1;return!0}r=b.charAt(h);throw new JS.InvalidSmilesException((this.isSmarts?"invalid placement for '"+
r+"'":"["+r+"] notation only valid with SMARTS, not SMILES,")+" in "+b);},"JS.SmilesSearch,~S,JS.SmilesAtom,JS.SmilesBond,JS.SmilesAtom,~B,~B,~A");c$.getSubPattern=h(c$,"getSubPattern",function(a,b,c){var d,e=1;switch(c){case "[":d="]";break;case '"':case "%":case "/":d=c;break;case "(":d=")";break;default:d=c,e=0}for(var f=a.length,g=1,h=b+1;h<f;h++){var m=a.charAt(h);if(m==d){if(g--,0==g)return a.substring(b+e,h+1-e)}else m==c&&g++}throw new JS.InvalidSmilesException("Unmatched "+c);},"~S,~N,~S");
c$.getChar=h(c$,"getChar",function(a,b){return b<a.length?a.charAt(b):"\x00"},"~S,~N");c$.getDigits=h(c$,"getDigits",function(a,b,c){for(var d=b,e=a.length;d<e&&JU.PT.isDigit(a.charAt(d));)d++;if(d>b)try{return c[0]=Integer.parseInt(a.substring(b,d)),d}catch(f){if(!H(f,NumberFormatException))throw f;}c[0]=-2147483648;return d},"~S,~N,~A");c$.skipTo=h(c$,"skipTo",function(a,b,c){for(var d;(d=JS.SmilesParser.getChar(a,++b))!=c&&"\x00"!=d;);return"\x00"==d?-1:b},"~S,~N,~S");c$.cleanPattern=h(c$,"cleanPattern",
function(a){a=JU.PT.replaceAllCharacters(a," \t\n\r","");a=JU.PT.rep(a,"^^","`");for(var b=0,c=0;0<=(b=a.indexOf("//*"))&&(c=a.indexOf("*//"))>=b;)a=a.substring(0,b)+a.substring(c+3);return a=JU.PT.rep(a,"//","")},"~S");c$.extractFlags=h(c$,"extractFlags",function(a,b){a=JS.SmilesParser.cleanPattern(a);for(var c=0;a.startsWith("/");){var d=JS.SmilesParser.getSubPattern(a,0,"/").toUpperCase();a=a.substring(d.length+2);c=JS.SmilesSearch.addFlags(c,d)}b[0]=c;return a},"~S,~A");c$.getFlags=h(c$,"getFlags",
function(a){var b=v(1,0);JS.SmilesParser.extractFlags(a,b);return b[0]},"~S")});D("JS");B(null,"JS.SmilesExt","java.lang.Float JU.AU $.BS $.Lst $.M4 $.Measure $.P3 J.api.Interface JU.Logger".split(" "),function(){c$=G(function(){this.e=null;E(this,arguments)},JS,"SmilesExt");I(c$,function(){});h(c$,"init",function(a){this.e=a;return this},"~O");h(c$,"getSmilesCorrelation",function(a,b,c,d,e,f,g,h,m,n,k,l){var p=null==m?0.1:3.4028235E38;try{null==d&&(d=new JU.Lst,e=new JU.Lst);var r=new JU.M4,s=new JU.P3,
q=this.e.vwr.ms.at,v=this.e.vwr.ms.ac,u=this.e.vwr.getSmilesMatcher(),t=u.getCorrelationMaps(c,q,v,a,l|8);null==t&&this.e.evalError(u.getLastException(),null);if(0==t.length)return NaN;var x=t[0];for(a=0;a<x.length;a++)d.addLast(q[x[a]]);t=u.getCorrelationMaps(c,q,v,b,l);null==t&&this.e.evalError(u.getLastException(),null);if(0==t.length)return NaN;JU.Logger.info(t.length+" mappings found");if(k||!h){b=3.4028235E38;c=null;for(a=0;a<t.length;a++){e.clear();for(var w=0;w<t[a].length;w++)e.addLast(q[t[a][w]]);
J.api.Interface.getInterface("JU.Eigen",this.e.vwr,"script");var y=1==e.size()?0:JU.Measure.getTransformMatrix4(d,e,r,null);JU.Logger.info("getSmilesCorrelation stddev="+y);if(null!=g&&y<p){for(var z=new JU.BS,w=0;w<t[a].length;w++)z.set(t[a][w]);g.addLast(z)}y<b&&(c=t[a],null!=f&&f.setM4(r),null!=n&&n.setT(s),b=y)}null!=m&&(m[0]=x,m[1]=c);e.clear();for(a=0;a<c.length;a++)e.addLast(q[c[a]]);return b}for(a=0;a<t.length;a++)for(w=0;w<t[a].length;w++)e.addLast(q[t[a][w]])}catch(A){if(H(A,Exception))this.e.evalError(A.getMessage(),
null);else throw A;}return 0},"JU.BS,JU.BS,~S,JU.Lst,JU.Lst,JU.M4,JU.Lst,~B,~A,JU.P3,~B,~N");h(c$,"getSmilesMatches",function(a,b,c,d,e,f,g){if(0==a.length||a.endsWith("///")||a.equals("H")||a.equals("H2")||a.equals("top")||a.equalsIgnoreCase("NOAROMATIC"))try{return this.e.vwr.getSmilesOpt(c,0,0,e|(a.equals("H2")?8192:0)|(a.equals("H")?4096:0)|(a.equals("top")?16384:0)|(a.equalsIgnoreCase("NOAROMATIC")?16:0),a.endsWith("///")?a:null)}catch(h){if(H(h,Exception))this.e.evalError(h.getMessage(),null);
else throw h;}var m;if(null==d)try{if(null==b)m=this.e.vwr.getSubstructureSetArray(a,c,e);else{if(a.equals("chirality"))return this.e.vwr.calculateChiralityForSmiles(b);m=2==(e&2);e=16384==(e&16384);var n=this.e.vwr.getSmilesMatcher().find(a,b,(m?2:1)|(g?8:0)|(e?16384:0));if(!f)return!g?n:0==n.length?v(0,0):n[0];var k=new JU.BS;for(f=0;f<n.length;f++)for(var l=n[f],p=l.length;0<=--p;)0<=l[p]&&k.set(l[p]);if(!m)return v(k.cardinality(),0);var r=v(k.cardinality(),0);f=0;for(var s=k.nextSetBit(0);0<=
s;s=k.nextSetBit(s+1))r[f++]=s;return r}}catch(q){if(H(q,Exception))return this.e.evalError(q.getMessage(),null),null;throw q;}else{k=new JU.Lst;r=this.getSmilesCorrelation(d,c,a,null,null,null,k,!1,null,null,!1,e);if(Float.isNaN(r))return f?new JU.BS:K(-1,[]);this.e.showString("RMSD "+r+" Angstroms");m=k.toArray(Array(k.size()))}if(f){k=new JU.BS;for(f=0;f<m.length;f++)k.or(m[f]);return k}k=new JU.Lst;for(f=0;f<m.length;f++)k.addLast(m[f]);return k},"~S,~S,JU.BS,JU.BS,~N,~B,~B");h(c$,"getFlexFitList",
function(a,b,c,d){var e=JU.AU.newInt2(2);this.getSmilesCorrelation(a,b,c,null,null,null,null,!1,e,null,!1,d?2:1);if(null==e[0])return null;a=this.e.vwr.ms.getDihedralMap(e[0]);b=null==a?null:this.e.vwr.ms.getDihedralMap(e[1]);if(null==b||b.length!=a.length)return null;e=P(a.length,3,0);c=this.e.vwr.ms.at;JS.SmilesExt.getTorsions(c,b,e,0);JS.SmilesExt.getTorsions(c,a,e,1);b=P(6*a.length,0);for(d=c=0;c<a.length;c++){var f=a[c];b[d++]=f[0];b[d++]=f[1];b[d++]=f[2];b[d++]=f[3];b[d++]=e[c][0];b[d++]=e[c][1]}return b},
"JU.BS,JU.BS,~S,~B");c$.getTorsions=h(c$,"getTorsions",function(a,b,c,d){for(var e=b.length;0<=--e;){var f=b[e],f=JU.Measure.computeTorsion(a[f[0]],a[f[1]],a[f[2]],a[f[3]],!0);1==d&&(180<f-c[e][0]?f-=360:-180>=f-c[e][0]&&(f+=360));c[e][d]=f}},"~A,~A,~A,~N");h(c$,"mapPolyhedra",function(a,b,c,d){var e=new JU.Lst,f=new JU.Lst,g;g=K(-1,[Integer.$valueOf(a),null]);this.e.getShapePropertyData(21,"syminfo",g);a=g[1];g[0]=Integer.$valueOf(b);g[1]=null;this.e.getShapePropertyData(21,"syminfo",g);b=g[1];if(null==
a||null==b)return NaN;g=a.get("polySmiles");var h=b.get("polySmiles");c=this.getSmilesMatches(h,g,null,null,c?1:16385,!1,!0);if(0==c.length)return NaN;e.addLast(a.get("center"));a=a.get("vertices");g=0;for(h=a.length;g<h;g++)e.add(a[c[g+1]-1]);f.addLast(b.get("center"));a=b.get("vertices");g=0;for(h=a.length;g<h;g++)f.add(a[g]);J.api.Interface.getInterface("JU.Eigen",this.e.vwr,"script");return JU.Measure.getTransformMatrix4(e,f,d,null)},"~N,~N,~B,JU.M4")})})(Clazz,Clazz.getClassName,Clazz.newLongArray,
Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.defineStatics,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,Clazz.declareInterface,Clazz.p0p,Clazz.pu$h,Clazz.newShortArray,Clazz.innerTypeInstance,Clazz.isClassDefined,Clazz.prepareCallback,
Clazz.newArray,Clazz.castNullAs,Clazz.floatToShort,Clazz.superCall,Clazz.decorateAsType,Clazz.newBooleanArray,Clazz.newCharArray,Clazz.implementOf,Clazz.newDoubleArray,Clazz.overrideConstructor,Clazz.clone,Clazz.doubleToShort,Clazz.getInheritedLevel,Clazz.getParamsType,Clazz.isAF,Clazz.isAB,Clazz.isAI,Clazz.isAS,Clazz.isASS,Clazz.isAP,Clazz.isAFloat,Clazz.isAII,Clazz.isAFF,Clazz.isAFFF,Clazz.tryToSearchAndExecute,Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,
Clazz.declareAnonymous,Clazz.cloneFinals);
