Clazz.declarePackage ("JS");
Clazz.load (["JU.BS"], "JS.CIPChirality", ["java.util.Arrays", "$.Collections", "$.Hashtable", "JU.Lst", "$.PT", "JU.Elements", "$.Logger", "JV.JC"], function () {
var c$ = Clazz.decorateAsClass (function () {
this.currentRule = 1;
this.root = null;
this.data = null;
this.doTrack = false;
this.isAux = false;
this.bsNeedRule = null;
this.havePseudoAuxiliary = false;
this.ptIDLogger = 0;
if (!Clazz.isClassDefined ("JS.CIPChirality.CIPAtom")) {
JS.CIPChirality.$CIPChirality$CIPAtom$ ();
}
Clazz.instantialize (this, arguments);
}, JS, "CIPChirality");
Clazz.prepareFields (c$, function () {
this.bsNeedRule =  new JU.BS ();
});
Clazz.defineMethod (c$, "getRuleName", 
function (rule) {
return JS.CIPChirality.ruleNames[rule];
}, "~N");
Clazz.makeConstructor (c$, 
function () {
});
Clazz.defineMethod (c$, "getChiralityForAtoms", 
function (data) {
if (data.bsAtoms.isEmpty ()) return;
this.data = data;
this.doTrack = data.isTracker ();
this.ptIDLogger = 0;
var bsToDo = data.bsMolecule.clone ();
var haveAlkenes = this.preFilterAtomList (data.atoms, bsToDo, data.bsEnes);
if (!data.bsEnes.isEmpty ()) data.getEneKekule ();
this.logInfo ("bsKekule:" + data.bsKekuleAmbiguous);
bsToDo = data.bsAtoms.clone ();
for (var i = bsToDo.nextSetBit (0); i >= 0; i = bsToDo.nextSetBit (i + 1)) {
var a = data.atoms[i];
a.setCIPChirality (0);
this.ptIDLogger = 0;
var c = this.getAtomChiralityLimited (a, null, null);
a.setCIPChirality (c == 0 ? 3 : c | ((this.currentRule - 1) << 5));
if (this.doTrack && c != 0) data.getRootTrackerResult (this.root);
}
if (haveAlkenes) {
var lstEZ =  new JU.Lst ();
for (var i = bsToDo.nextSetBit (0); i >= 0; i = bsToDo.nextSetBit (i + 1)) this.getAtomBondChirality (data.atoms[i], lstEZ, bsToDo);

if (data.lstSmallRings.length > 0 && lstEZ.size () > 0) this.clearSmallRingEZ (data.atoms, lstEZ);
this.setStereoFromSmiles (data.bsHelixM, 17, data.atoms);
this.setStereoFromSmiles (data.bsHelixP, 18, data.atoms);
}if (JU.Logger.debugging) {
this.logInfo ("Kekule ambiguous = " + data.bsKekuleAmbiguous);
this.logInfo ("small rings = " + JU.PT.toJSON (null, data.lstSmallRings));
}}, "JS.CIPData");
Clazz.defineMethod (c$, "setStereoFromSmiles", 
function (bsHelix, stereo, atoms) {
if (bsHelix != null) for (var i = bsHelix.nextSetBit (0); i >= 0; i = bsHelix.nextSetBit (i + 1)) atoms[i].setCIPChirality (stereo);

}, "JU.BS,~N,~A");
Clazz.defineMethod (c$, "preFilterAtomList", 
function (atoms, bsToDo, bsEnes) {
var haveAlkenes = false;
for (var i = bsToDo.nextSetBit (0); i >= 0; i = bsToDo.nextSetBit (i + 1)) {
if (!this.data.couldBeChiralAtom (atoms[i])) {
bsToDo.clear (i);
continue;
}switch (this.data.couldBeChiralAlkene (atoms[i], null)) {
case -1:
break;
case 13:
bsEnes.set (i);
case 17:
haveAlkenes = true;
break;
}
}
return haveAlkenes;
}, "~A,JU.BS,JU.BS");
c$.isFirstRow = Clazz.defineMethod (c$, "isFirstRow", 
function (a) {
var n = a.getElementNumber ();
return (n > 2 && n <= 10);
}, "JU.SimpleNode");
Clazz.defineMethod (c$, "clearSmallRingEZ", 
function (atoms, lstEZ) {
for (var j = this.data.lstSmallRings.length; --j >= 0; ) this.data.lstSmallRings[j].andNot (this.data.bsAtropisomeric);

for (var i = lstEZ.size (); --i >= 0; ) {
var ab = lstEZ.get (i);
for (var j = this.data.lstSmallRings.length; --j >= 0; ) {
var ring = this.data.lstSmallRings[j];
if (ring.get (ab[0]) && ring.get (ab[1])) {
atoms[ab[0]].setCIPChirality (3);
atoms[ab[1]].setCIPChirality (3);
}}
}
}, "~A,JU.Lst");
Clazz.defineMethod (c$, "getAtomBondChirality", 
function (atom, lstEZ, bsToDo) {
var index = atom.getIndex ();
var bonds = atom.getEdges ();
var c = 0;
var isAtropic = this.data.bsAtropisomeric.get (index);
for (var j = bonds.length; --j >= 0; ) {
var bond = bonds[j];
var atom1;
var index1;
if (isAtropic) {
atom1 = bonds[j].getOtherNode (atom);
index1 = atom1.getIndex ();
if (!this.data.bsAtropisomeric.get (index1)) continue;
c = this.setBondChirality (atom, atom1, atom, atom1, true);
} else if (this.data.getBondOrder (bond) == 2) {
atom1 = this.getLastCumuleneAtom (bond, atom, null, null);
index1 = atom1.getIndex ();
if (index1 < index) continue;
c = this.getBondChiralityLimited (bond, atom);
} else {
continue;
}if (c != 0) {
if (!isAtropic) lstEZ.addLast ( Clazz.newIntArray (-1, [index, index1]));
bsToDo.clear (index);
bsToDo.clear (index1);
}if (isAtropic) break;
}
}, "JU.SimpleNode,JU.Lst,JU.BS");
Clazz.defineMethod (c$, "getLastCumuleneAtom", 
function (bond, atom, nSP2, parents) {
var atom2 = bond.getOtherNode (atom);
if (parents != null) {
parents[0] = atom2;
parents[1] = atom;
}if (nSP2 != null) nSP2[0] = 2;
var ppt = 0;
while (true) {
if (atom2.getCovalentBondCount () != 2) return atom2;
var edges = atom2.getEdges ();
for (var i = edges.length; --i >= 0; ) {
var atom3 = (bond = edges[i]).getOtherNode (atom2);
if (atom3 === atom) continue;
if (this.data.getBondOrder (bond) != 2) return atom2;
if (parents != null) {
if (ppt == 0) {
parents[0] = atom2;
ppt = 1;
}parents[1] = atom2;
}if (nSP2 != null) nSP2[0]++;
atom = atom2;
atom2 = atom3;
break;
}
}
}, "JU.SimpleEdge,JU.SimpleNode,~A,~A");
Clazz.defineMethod (c$, "getAtomChiralityLimited", 
function (atom, cipAtom, parentAtom) {
var rs = 0;
this.bsNeedRule.clearAll ();
this.bsNeedRule.set (1);
try {
var isAlkeneEndCheck = (atom == null);
if (isAlkeneEndCheck) {
atom = (this.root = cipAtom).atom;
cipAtom.htPathPoints = (cipAtom.parent = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (parentAtom, null, true, false, false)).htPathPoints;
} else {
if (!(this.root = cipAtom = (cipAtom == null ? Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (atom, null, false, false, false) : cipAtom)).isSP3) {
return 0;
}}if (cipAtom.setNode ()) {
for (this.currentRule = 1; this.currentRule <= 9; this.currentRule++) {
var nPrioritiesPrev = cipAtom.nPriorities;
switch (this.currentRule) {
case 3:
if (cipAtom.rule6refIndex >= 0) this.bsNeedRule.set (3);
break;
case 4:
this.isAux = true;
this.doTrack = false;
this.havePseudoAuxiliary = false;
cipAtom.createAuxiliaryDescriptors (null, null);
this.doTrack = this.data.isTracker ();
this.isAux = false;
break;
case 5:
if (!this.bsNeedRule.get (5)) {
this.currentRule = 8;
continue;
}case 6:
case 7:
cipAtom.sortSubstituents (-2147483648);
this.bsNeedRule.set (this.currentRule);
break;
case 8:
if (this.havePseudoAuxiliary) cipAtom.clearRule4Lists ();
cipAtom.sortSubstituents (-2147483648);
this.bsNeedRule.set (this.currentRule);
break;
case 9:
this.bsNeedRule.setBitTo (9, (cipAtom.rule6refIndex < 0 && (rs = cipAtom.getRule6Descriptor (false)) != 0));
break;
}
if (!this.bsNeedRule.get (this.currentRule)) continue;
if (rs == 0 && cipAtom.sortSubstituents (0)) {
if (JU.Logger.debuggingHigh && cipAtom.h1Count < 2) {
for (var i = 0; i < cipAtom.bondCount; i++) {
if (cipAtom.atoms[i] != null) this.logInfo (cipAtom.atoms[i] + " " + cipAtom.priorities[i]);
}
}if (isAlkeneEndCheck) return cipAtom.getEneTop ();
rs = this.data.checkHandedness (cipAtom);
if (this.currentRule == 8) {
if (cipAtom.nPriorities == 4 && nPrioritiesPrev == 2) cipAtom.isRule5Pseudo = !cipAtom.isRule5Pseudo;
if (cipAtom.isRule5Pseudo) rs |= 8;
}if (JU.Logger.debugging) this.logInfo (atom + " " + JV.JC.getCIPChiralityName (rs) + " by Rule " + this.getRuleName (this.currentRule) + "\n----------------------------------");
return rs;
}}
}} catch (e) {
System.out.println (e + " in CIPChirality " + this.currentRule);
{
alert(e);
}return 3;
}
return rs;
}, "JU.SimpleNode,JS.CIPChirality.CIPAtom,JU.SimpleNode");
Clazz.defineMethod (c$, "getBondChiralityLimited", 
function (bond, a) {
if (a == null) a = bond.getOtherNode (null);
if (this.data.couldBeChiralAlkene (a, bond) == -1) return 0;
var nSP2 =  Clazz.newIntArray (1, 0);
var parents =  new Array (2);
var b = this.getLastCumuleneAtom (bond, a, nSP2, parents);
var isAxial = nSP2[0] % 2 == 1;
if (!isAxial && this.data.bsAromatic.get (a.getIndex ())) return -1;
var c = this.setBondChirality (a, parents[0], parents[1], b, isAxial);
if (JU.Logger.debugging) this.logInfo ("get Bond Chirality " + JV.JC.getCIPChiralityName (c) + " " + bond);
return c;
}, "JU.SimpleEdge,JU.SimpleNode");
Clazz.defineMethod (c$, "setBondChirality", 
function (a, pa, pb, b, isAxial) {
var a1 = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (a, null, true, false, false);
var b2 = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (b, null, true, false, false);
var atop = this.getAtomChiralityLimited (null, a1, pa) - 1;
var ruleA = this.currentRule;
var btop = this.getAtomChiralityLimited (null, b2, pb) - 1;
var ruleB = this.currentRule;
if (isAxial && a1.nRootDuplicates > 3 && atop < 0 && btop < 0) {
ruleA = ruleB = this.currentRule = 9;
b2.rule6refIndex = a1.atoms[atop = a1.getEneTop () - 1].atomIndex;
if (b2.sortSubstituents (0)) btop = b2.getEneTop () - 1;
}var c = (atop >= 0 && btop >= 0 ? this.getEneChirality (b2.atoms[btop], b2, a1, a1.atoms[atop], isAxial, true) : 0);
if (c != 0 && (isAxial || !this.data.bsAtropisomeric.get (a.getIndex ()) && !this.data.bsAtropisomeric.get (b.getIndex ()))) {
if (isAxial == (ruleA == 8) == (ruleB == 8)) c &= -9;
 else c |= 8;
a.setCIPChirality (c | ((ruleA - 1) << 5));
b.setCIPChirality (c | ((ruleB - 1) << 5));
if (JU.Logger.debugging) this.logInfo (a + "-" + b + " " + JV.JC.getCIPChiralityName (c));
}return c;
}, "JU.SimpleNode,JU.SimpleNode,JU.SimpleNode,JU.SimpleNode,~B");
Clazz.defineMethod (c$, "getEneChirality", 
function (winner1, end1, end2, winner2, isAxial, allowPseudo) {
return (winner1 == null || winner2 == null || winner1.atom == null || winner2.atom == null ? 0 : isAxial ? this.data.isPositiveTorsion (winner1, end1, end2, winner2) : this.data.isCis (winner1, end1, end2, winner2));
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,~B,~B");
Clazz.defineMethod (c$, "logInfo", 
function (msg) {
JU.Logger.info (msg);
}, "~S");
c$.$CIPChirality$CIPAtom$ = function () {
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
this.isRule5Pseudo = true;
this.id = 0;
this.sphere = 0;
this.rootDistance = 0;
this.isSet = false;
this.isDuplicate = true;
this.isTerminal = false;
this.isAlkene = false;
this.atom = null;
this.atomIndex = -1;
this.bondCount = 0;
this.elemNo = 0;
this.mass = -1;
this.parent = null;
this.rootSubstituent = null;
this.h1Count = 0;
this.atoms = null;
this.nAtoms = 0;
this.bsPath = null;
this.myPath = "";
this.oldPriorities = null;
this.priorities =  Clazz.newIntArray (4, 0);
this.oldNPriorities = 0;
this.nPriorities = 0;
this.priority = 0;
this.chiralPath = null;
this.nRootDuplicates = 0;
this.htPathPoints = null;
this.rule6refIndex = -1;
this.bsRule6Subs = null;
this.alkeneParent = null;
this.alkeneChild = null;
this.isAlkeneAtom2 = false;
this.isKekuleAmbiguous = false;
this.nextSP2 = null;
this.multipleBondDuplicate = false;
this.isEvenEne = true;
this.auxEZ = -1;
this.isSP3 = true;
this.auxChirality = '~';
this.nextChiralBranch = null;
this.isChiralPath = false;
this.rule4Type = 0;
this.bsTemp = null;
this.rule4Ref = 0;
this.listRS = null;
Clazz.instantialize (this, arguments);
}, JS.CIPChirality, "CIPAtom", null, [Comparable, Cloneable]);
Clazz.prepareFields (c$, function () {
this.atoms =  new Array (4);
this.bsTemp =  new JU.BS ();
});
Clazz.makeConstructor (c$, 
function () {
});
Clazz.defineMethod (c$, "create", 
function (atom, parent, isAlkene, isDuplicate, isParentBond) {
this.id = ++this.b$["JS.CIPChirality"].ptIDLogger;
this.parent = parent;
if (atom == null) return this;
this.isAlkene = isAlkene;
this.atom = atom;
this.atomIndex = atom.getIndex ();
if (atom.getIsotopeNumber () > 0) this.b$["JS.CIPChirality"].bsNeedRule.set (3);
this.isDuplicate = this.multipleBondDuplicate = isDuplicate;
this.isKekuleAmbiguous = (this.b$["JS.CIPChirality"].data.bsKekuleAmbiguous != null && this.b$["JS.CIPChirality"].data.bsKekuleAmbiguous.get (this.atomIndex));
this.elemNo = (isDuplicate && this.isKekuleAmbiguous ? parent.getKekuleElementNumber () : atom.getElementNumber ());
this.bondCount = atom.getCovalentBondCount ();
this.isSP3 = (this.bondCount == 4 || this.bondCount == 3 && !isAlkene && (this.elemNo > 10 || this.b$["JS.CIPChirality"].data.bsAzacyclic != null && this.b$["JS.CIPChirality"].data.bsAzacyclic.get (this.atomIndex)));
if (parent != null) this.sphere = parent.sphere + 1;
if (this.sphere == 1) {
this.rootSubstituent = this;
} else if (parent != null && parent.htPathPoints != null) {
this.rootSubstituent = parent.rootSubstituent;
this.htPathPoints = (parent.htPathPoints).clone ();
}if (this.htPathPoints == null) this.htPathPoints =  new java.util.Hashtable ();
this.bsPath = (parent == null ?  new JU.BS () : parent.bsPath.clone ());
if (isDuplicate) this.b$["JS.CIPChirality"].bsNeedRule.set (4);
this.rootDistance = this.sphere;
if (parent == null) {
this.bsPath.set (this.atomIndex);
} else if (this.multipleBondDuplicate) {
this.rootDistance--;
} else if (this.bsPath.get (this.atomIndex)) {
this.b$["JS.CIPChirality"].bsNeedRule.setBitTo (2, (this.isDuplicate = true));
if ((this.rootDistance = (atom === this.b$["JS.CIPChirality"].root.atom ? 0 : isParentBond ? parent.sphere : this.htPathPoints.get (Integer.$valueOf (this.atomIndex)).intValue ())) == 0) {
this.b$["JS.CIPChirality"].root.nRootDuplicates++;
}} else {
this.bsPath.set (this.atomIndex);
this.htPathPoints.put (Integer.$valueOf (this.atomIndex), Integer.$valueOf (this.rootDistance));
}if (this.b$["JS.CIPChirality"].doTrack) {
if (this.sphere < 50) this.myPath = (parent != null ? parent.myPath + "-" : "") + this;
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo ("new CIPAtom " + this.myPath);
}return this;
}, "JU.SimpleNode,JS.CIPChirality.CIPAtom,~B,~B,~B");
Clazz.defineMethod (c$, "getEneTop", 
function () {
return (this.atoms[0].isDuplicate ? 2 : 1);
});
Clazz.defineMethod (c$, "getRule6Descriptor", 
function (isAux) {
if (this.nPriorities > 2 || (isAux ? this.countAuxDuplicates (this.atomIndex) : this.nRootDuplicates) <= 2) return 0;
var i1 = (this.priorities[0] == this.priorities[1] ? 0 : 1);
var i2 = (this.priorities[2] != this.priorities[3] ? 3 : 4);
var istep = (this.priorities[2] == this.priorities[1] ? 1 : 2);
var rsRM = 0;
var rsSP = 0;
var bsSubs =  new JU.BS ();
for (var i = i1; i < i2; i++) bsSubs.set (this.atoms[i].atomIndex);

if (this.nPriorities == 1) i2 = 2;
var cipAtom = null;
var rs;
for (var i = i1; i < i2; i += istep) {
if (this.b$["JS.CIPChirality"].data.testRule6Full) {
cipAtom = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (this.atom, null, false, false, false);
cipAtom.rule6refIndex = this.atoms[i].atomIndex;
cipAtom.setNode ();
for (var j = 0; j < 4; j++) {
cipAtom.atoms[j] = this.atoms[j].clone ();
cipAtom.priorities[j] = this.priorities[j];
}
cipAtom.bsRule6Subs = bsSubs;
rs = this.b$["JS.CIPChirality"].getAtomChiralityLimited (this.atom, cipAtom, null);
this.b$["JS.CIPChirality"].currentRule = 9;
if (rs == 0) return 0;
} else {
this.b$["JS.CIPChirality"].root.bsRule6Subs =  new JU.BS ();
this.b$["JS.CIPChirality"].root.rule6refIndex = this.atoms[i].atomIndex;
this.saveRestorePriorities (false);
this.sortSubstituents (-2147483648);
if (!this.sortSubstituents (0)) return 0;
rs = this.b$["JS.CIPChirality"].data.checkHandedness (this);
this.saveRestorePriorities (true);
}if ((rs & 8) == 0) {
if (rs == 1 || rs == 17) {
if (rsRM == 0) {
rsRM = rs;
continue;
}} else if (rsSP == 0) {
rsSP = rs;
continue;
}}return rs;
}
return 0;
}, "~B");
Clazz.defineMethod (c$, "saveRestorePriorities", 
function (isRestore) {
if (isRestore) {
this.priorities = this.oldPriorities;
this.nPriorities = this.oldNPriorities;
} else {
this.oldPriorities = java.util.Arrays.copyOf (this.priorities, 4);
this.oldNPriorities = this.nPriorities;
}for (var i = 0; i < this.nAtoms; i++) this.atoms[i].saveRestorePriorities (isRestore);

}, "~B");
Clazz.defineMethod (c$, "countAuxDuplicates", 
function (index) {
var n = 0;
for (var i = 0; i < 4; i++) {
if (this.atoms[i] == null) continue;
if (this.atoms[i].isDuplicate) {
if (this.atoms[i].atomIndex == index) n++;
} else {
n += this.atoms[i].countAuxDuplicates (index);
}}
return n;
}, "~N");
Clazz.defineMethod (c$, "getMass", 
function () {
if (this.isDuplicate) return 0;
if (this.mass == -1) {
if (this.isDuplicate || (this.mass = this.atom.getMass ()) != Clazz.floatToInt (this.mass) || this.isType (";9Be;19F;23Na;27Al;31P;45Sc;55Mn;59Co;75As;89Y;93Nb;98Tc;103Rh;127I;133Cs;141Pr;145Pm;159Tb;165Ho;169Tm;197Au;209Bi;209Po;210At;222Rn;223Fr;226Ra;227Ac;231Pa;232Th;and all > U (atomno > 92)")) return (this.mass == -1 ? this.mass = JU.Elements.getAtomicMass (Clazz.floatToInt (this.elemNo)) : this.mass);
if (this.isType (";16O;52Cr;96Mo;175Lu;")) this.mass -= 0.1;
}return this.mass;
});
Clazz.defineMethod (c$, "isType", 
function (rule2Type) {
return JU.PT.isOneOf (Clazz.floatToInt (this.mass) + JU.Elements.elementSymbolFromNumber (Clazz.floatToInt (this.elemNo)), rule2Type);
}, "~S");
Clazz.defineMethod (c$, "getKekuleElementNumber", 
function () {
var edges = this.atom.getEdges ();
var bond;
var ave = 0;
var n = 0;
for (var i = edges.length; --i >= 0; ) if ((bond = edges[i]).isCovalent ()) {
var other = bond.getOtherNode (this.atom);
if (this.b$["JS.CIPChirality"].data.bsKekuleAmbiguous.get (other.getIndex ())) {
n++;
ave += other.getElementNumber ();
}}
return ave / n;
});
Clazz.defineMethod (c$, "setNode", 
function () {
if (this.isSet || (this.isSet = true) && this.isDuplicate) return true;
var index = this.atom.getIndex ();
var bonds = this.atom.getEdges ();
var nBonds = bonds.length;
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo ("set " + this);
var pt = 0;
for (var i = 0; i < nBonds; i++) {
var bond = bonds[i];
if (!bond.isCovalent ()) continue;
var other = bond.getOtherNode (this.atom);
var isParentBond = (this.parent != null && this.parent.atom === other);
var order = this.b$["JS.CIPChirality"].data.getBondOrder (bond);
if (order == 2) {
if (this.elemNo > 10 || !JS.CIPChirality.isFirstRow (other)) order = 1;
 else {
this.isAlkene = true;
if (isParentBond) this.setEne ();
}}if (nBonds == 1 && order == 1 && isParentBond) return this.isTerminal = true;
switch (order) {
case 3:
if (this.addAtom (pt++, other, isParentBond, false, isParentBond) == null) return !(this.isTerminal = true);
case 2:
if (this.addAtom (pt++, other, order != 2 || isParentBond, order == 2, isParentBond) == null) return !(this.isTerminal = true);
case 1:
if (isParentBond || this.addAtom (pt++, other, order != 1 && this.elemNo <= 10, false, false) != null) break;
default:
return !(this.isTerminal = true);
}
}
this.nAtoms = pt;
switch (pt) {
case 2:
case 3:
if (this.elemNo == 6 && this.b$["JS.CIPChirality"].data.bsNegativeAromatic.get (index) || this.b$["JS.CIPChirality"].data.bsXAromatic.get (index)) {
this.nAtoms++;
this.addAtom (pt++, this.atom, true, false, false);
}break;
}
this.fillAtoms (pt);
try {
java.util.Arrays.sort (this.atoms);
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
e.printStackTrace ();
} else {
throw e;
}
}
return true;
});
Clazz.defineMethod (c$, "fillAtoms", 
function (pt) {
if (pt < 4) for (; pt < this.atoms.length; pt++) if (this.atoms[pt] == null) this.atoms[pt] = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (null, this, false, true, false);

}, "~N");
Clazz.defineMethod (c$, "setEne", 
function () {
this.parent.alkeneChild = null;
this.alkeneParent = (this.parent.alkeneParent == null ? this.parent : this.parent.alkeneParent);
this.alkeneParent.alkeneChild = this;
this.nextSP2 = this.parent;
if (this.parent.alkeneParent == null) this.parent.nextSP2 = this;
if (this.atom.getCovalentBondCount () == 2 && this.atom.getValence () == 4) {
this.parent.isAlkeneAtom2 = false;
this.alkeneParent.isEvenEne = !this.alkeneParent.isEvenEne;
} else {
this.isAlkeneAtom2 = true;
}});
Clazz.defineMethod (c$, "addAtom", 
function (i, other, isDuplicate, isAlkene, isParentBond) {
if (i >= this.atoms.length) {
if (JU.Logger.debugging) this.b$["JS.CIPChirality"].logInfo (" too many bonds on " + this.atom);
return null;
}if (other.getElementNumber () == 1 && other.getIsotopeNumber () == 0) {
if (++this.h1Count > 1) {
if (this.parent == null) {
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo (" second H atom found on " + this.atom);
return null;
}}}return this.atoms[i] = Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (other, this, isAlkene, isDuplicate, isParentBond);
}, "~N,JU.SimpleNode,~B,~B,~B");
Clazz.defineMethod (c$, "sortSubstituents", 
function (sphere) {
if (this.nPriorities == (sphere < 1 ? 4 : 3)) return true;
var ignoreTies = (sphere == -2147483648);
if (ignoreTies) {
if (this.isTerminal) return false;
switch (this.b$["JS.CIPChirality"].currentRule) {
case 5:
case 7:
for (var i = 0; i < 4; i++) if (this.atoms[i] != null && (this.atoms[i].isChiralPath || this.atoms[i].nextChiralBranch != null)) this.atoms[i].sortSubstituents (-2147483648);

if (this.isAlkene) return false;
break;
case 9:
for (var i = 0; i < 4; i++) if (this.atoms[i] != null && !this.atoms[i].isDuplicate && this.atoms[i].atom != null && this.atoms[i].setNode ()) this.atoms[i].sortSubstituents (-2147483648);

break;
}
}ignoreTies = new Boolean (ignoreTies | (this.b$["JS.CIPChirality"].currentRule == 6 || this.b$["JS.CIPChirality"].currentRule == 8)).valueOf ();
var indices =  Clazz.newIntArray (4, 0);
var newPriorities =  Clazz.newIntArray (4, 0);
if (JU.Logger.debuggingHigh && this.h1Count < 2) {
this.b$["JS.CIPChirality"].logInfo (this.b$["JS.CIPChirality"].root + "---sortSubstituents---" + this);
for (var i = 0; i < 4; i++) {
this.b$["JS.CIPChirality"].logInfo (this.b$["JS.CIPChirality"].getRuleName (this.b$["JS.CIPChirality"].currentRule) + ": " + this + "[" + i + "]=" + this.atoms[i].myPath + " " + Integer.toHexString (this.priorities[i]));
}
this.b$["JS.CIPChirality"].logInfo ("---" + this.nPriorities);
}var loser;
for (var i = 0; i < 3; i++) {
var a = this.atoms[i];
var aLoses = a.isDuplicate && this.b$["JS.CIPChirality"].currentRule > 2;
for (var j = i + 1; j < 4; j++) {
var b = this.atoms[loser = j];
var score = 0;
switch (b.atom == null || this.priorities[i] < this.priorities[j] ? -1 : aLoses || a.atom == null || this.priorities[j] < this.priorities[i] ? 1 : (score = a.checkCurrentRule (b)) != 0 && score != -2147483648 || ignoreTies ? score : this.sign (a.breakTie (b, sphere + 1))) {
case 1:
loser = i;
case -1:
newPriorities[loser]++;
if (this.b$["JS.CIPChirality"].doTrack && score != 0 && (sphere == 0 || ignoreTies)) this.b$["JS.CIPChirality"].data.track (this.b$["JS.CIPChirality"], a, b, 1, score, false);
case -2147483648:
case 0:
indices[loser]++;
continue;
}
}
}
this.bsTemp.clearAll ();
var newAtoms =  new Array (4);
for (var i = 0; i < 4; i++) {
var pt = indices[i];
var a = newAtoms[pt] = this.atoms[i];
var p = newPriorities[i];
if (a.atom != null) this.bsTemp.set (p);
a.priority = this.priorities[pt] = p;
}
this.atoms = newAtoms;
this.nPriorities = this.bsTemp.cardinality ();
if (JU.Logger.debuggingHigh && this.atoms[2].atom != null && this.atoms[2].elemNo != 1) {
this.b$["JS.CIPChirality"].logInfo (this.dots () + this.atom + " nPriorities = " + this.nPriorities);
for (var i = 0; i < 4; i++) {
this.b$["JS.CIPChirality"].logInfo (this.dots () + this.myPath + "[" + i + "]=" + this.atoms[i] + " " + this.priorities[i] + " " + Integer.toHexString (this.priorities[i]));
}
this.b$["JS.CIPChirality"].logInfo (this.dots () + "-------" + this.nPriorities);
}return (this.nPriorities == this.bondCount);
}, "~N");
Clazz.defineMethod (c$, "dots", 
function () {
return ".....................".substring (0, Math.min (20, this.sphere));
});
Clazz.defineMethod (c$, "breakTie", 
function (b, sphere) {
var finalScore = 0;
while (true) {
if (this.isDuplicate && (this.b$["JS.CIPChirality"].currentRule > 2 || b.isDuplicate && this.atom === b.atom && this.rootDistance == b.rootDistance) || !this.setNode () || !b.setNode () || this.isTerminal && b.isTerminal || this.isDuplicate && b.isDuplicate) break;
if (this.isTerminal != b.isTerminal) {
finalScore = (this.isTerminal ? 1 : -1) * (sphere + (b.isDuplicate || this.isDuplicate ? 0 : 1));
if (this.b$["JS.CIPChirality"].doTrack) this.b$["JS.CIPChirality"].data.track (this.b$["JS.CIPChirality"], this, b, sphere, finalScore, true);
break;
}var score = (this.b$["JS.CIPChirality"].currentRule > 2 ? 0 : this.unlikeDuplicates (b));
if (score != 0) {
finalScore = score * (sphere + 1);
if (this.b$["JS.CIPChirality"].doTrack) this.b$["JS.CIPChirality"].data.track (this.b$["JS.CIPChirality"], this, b, sphere, finalScore, false);
break;
}for (var i = 0; i < this.nAtoms; i++) if ((score = this.atoms[i].checkCurrentRule (b.atoms[i])) != 0) {
finalScore = score * (sphere + 1);
if (this.b$["JS.CIPChirality"].doTrack) this.b$["JS.CIPChirality"].data.track (this.b$["JS.CIPChirality"], this.atoms[i], b.atoms[i], sphere, finalScore, false);
break;
}
if (finalScore != 0) {
break;
}this.sortSubstituents (sphere);
b.sortSubstituents (sphere);
for (var i = 0, abs, absScore = 2147483647; i < this.nAtoms; i++) {
if ((score = this.atoms[i].breakTie (b.atoms[i], sphere + 1)) != 0 && (abs = Math.abs (score)) < absScore) {
absScore = abs;
finalScore = score;
}}
break;
}
return finalScore;
}, "JS.CIPChirality.CIPAtom,~N");
Clazz.overrideMethod (c$, "compareTo", 
function (b) {
var score;
return (this.b$["JS.CIPChirality"].root.rule4Ref == 0 ? (b == null ? -1 : (this.atom == null) != (b.atom == null) ? (this.atom == null ? 1 : -1) : (score = this.compareRule1a (b)) != 0 ? score : (score = this.unlikeDuplicates (b)) != 0 ? score : this.isDuplicate ? this.compareRule1b (b) : this.compareRule2 (b)) : this.sphere < b.sphere ? -1 : this.sphere > b.sphere ? 1 : this.chiralPath.compareTo (b.chiralPath));
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "checkCurrentRule", 
function (b) {
switch (this.b$["JS.CIPChirality"].currentRule) {
default:
case 1:
return this.compareRule1a (b);
case 2:
return this.compareRule1b (b);
case 3:
return this.compareRule2 (b);
case 4:
return this.compareRule3 (b);
case 5:
return this.compareRules4ac (b, " sr SR PM");
case 6:
case 8:
return (this.isTerminal || b.isTerminal ? 0 : this.compareRule4b5 (b));
case 7:
return this.compareRules4ac (b, " s r p m");
case 9:
return this.compareRule6 (b);
}
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "unlikeDuplicates", 
function (b) {
return b.isDuplicate == this.isDuplicate ? 0 : this.isDuplicate ? 1 : -1;
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRule1a", 
function (b) {
return b.atom == null ? -1 : this.atom == null ? 1 : b.elemNo < this.elemNo ? -1 : b.elemNo > this.elemNo ? 1 : 0;
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRule1b", 
function (b) {
return Integer.compare (this.rootDistance, b.rootDistance);
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRule2", 
function (b) {
return (this.atomIndex == b.atomIndex ? 0 : this.getMass () > b.getMass () ? -1 : this.mass < b.mass ? 1 : this.b$["JS.CIPChirality"].root.rule6refIndex < 0 ? 0 : !this.b$["JS.CIPChirality"].root.bsRule6Subs.get (this.atomIndex) || !this.b$["JS.CIPChirality"].root.bsRule6Subs.get (b.atomIndex) ? 0 : this.b$["JS.CIPChirality"].root.rule6refIndex == this.atomIndex ? -1 : this.b$["JS.CIPChirality"].root.rule6refIndex == b.atomIndex ? 1 : 0);
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRule3", 
function (b) {
return (this.isDuplicate || b.isDuplicate || !this.parent.isAlkeneAtom2 || !b.parent.isAlkeneAtom2 || !this.parent.alkeneParent.isEvenEne || !b.parent.alkeneParent.isEvenEne || this.parent === b.parent ? 0 : this.parent.auxEZ < b.parent.auxEZ ? -1 : 1);
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRules4ac", 
function (b, test) {
if (this.isTerminal || this.isDuplicate) return 0;
var isRa = test.indexOf (this.auxChirality);
var isRb = test.indexOf (b.auxChirality);
return (isRa > isRb + 1 ? -1 : isRb > isRa + 1 ? 1 : 0);
}, "JS.CIPChirality.CIPAtom,~S");
Clazz.defineMethod (c$, "compareRule4b5", 
function (b) {
var bsA = this.getBetter4bList ();
var bsB = b.getBetter4bList ();
var best = this.compareLikeUnlike (bsA, bsB);
var score = (best == null ? -2147483648 : best === bsA ? -1 : 1);
if (best != null) {
if (this.b$["JS.CIPChirality"].currentRule == 8) {
if ((this.compareLikeUnlike (this.listRS[2], b.listRS[2]) === this.listRS[2]) == (best === bsA)) this.parent.isRule5Pseudo = !this.parent.isRule5Pseudo;
}if (this.b$["JS.CIPChirality"].doTrack) this.b$["JS.CIPChirality"].data.track (this.b$["JS.CIPChirality"], this, b, 1, score, false);
}return score;
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "compareRule6", 
function (b) {
return ((this.atomIndex == this.b$["JS.CIPChirality"].root.rule6refIndex) == (b.atomIndex == this.b$["JS.CIPChirality"].root.rule6refIndex) ? 0 : this.atomIndex == this.b$["JS.CIPChirality"].root.rule6refIndex ? -1 : 1);
}, "JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "clearRule4Lists", 
function () {
this.listRS = null;
for (var i = 0; i < 4 && this.atoms[i] != null; i++) this.atoms[i].clearRule4Lists ();

});
Clazz.defineMethod (c$, "getBetter4bList", 
function () {
if (this.listRS != null) return this.listRS[this.b$["JS.CIPChirality"].currentRule == 8 ? 1 : 0];
var bs;
this.listRS =  Clazz.newArray (-1, [null, bs = this.rank4bAndRead (null), this.rank4bAndRead (bs)]);
this.b$["JS.CIPChirality"].logInfo ("getBest " + this.b$["JS.CIPChirality"].currentRule + " " + this + " " + this.listRS[1] + this.listRS[2] + " " + this.myPath);
bs = this.compareLikeUnlike (this.listRS[1], this.listRS[2]);
return this.listRS[0] = (this.b$["JS.CIPChirality"].currentRule == 8 || bs == null ? this.listRS[1] : bs);
});
Clazz.defineMethod (c$, "rank4bAndRead", 
function (bsR) {
var isS = (bsR != null);
var ref = (isS ? 2 : 1);
var list =  new JU.BS ();
var chiralAtoms =  new JU.Lst ();
this.b$["JS.CIPChirality"].root.rule4Ref = ref;
this.addChiralAtoms (chiralAtoms, ref);
java.util.Collections.sort (chiralAtoms);
this.b$["JS.CIPChirality"].root.rule4Ref = 0;
for (var i = 0, n = chiralAtoms.size (); i < n; i++) {
if (JU.Logger.debugging) this.b$["JS.CIPChirality"].logInfo ("" + ref + " " + this + " " + chiralAtoms.get (i).chiralPath);
if (chiralAtoms.get (i).rule4Type == ref) list.set (i);
}
return list;
}, "JU.BS");
Clazz.defineMethod (c$, "addChiralAtoms", 
function (chiralAtoms, ref) {
if (this.atom == null || this.isTerminal || this.isDuplicate) return;
if (this.rule4Type != 0) {
var s = "";
var a = this;
while (a != null) {
s = String.fromCharCode (64 + (a.priority << 2) + (a.rule4Type == 0 ? 0 : a.rule4Type == ref ? 1 : 2)) + s;
if ((a = a.parent) != null && a.chiralPath != null) {
s = a.chiralPath + s;
break;
}}
this.chiralPath = s;
chiralAtoms.addLast (this);
}for (var i = 0; i < 4; i++) if (this.atoms[i] != null) this.atoms[i].addChiralAtoms (chiralAtoms, ref);

}, "JU.Lst,~N");
Clazz.defineMethod (c$, "compareLikeUnlike", 
function (bsA, bsB) {
var bsXOR = bsB.clone ();
bsXOR.xor (bsA);
var l = bsXOR.nextSetBit (0);
return (l < 0 ? null : bsA.get (l) ? bsA : bsB);
}, "JU.BS,JU.BS");
Clazz.defineMethod (c$, "createAuxiliaryDescriptors", 
function (node1, ret) {
var isChiralPath = false;
var c = '~';
if (this.atom == null) return false;
this.setNode ();
var rs = -1;
var nRS = 0;
var ret1 =  new Array (1);
var skipRules4And5 = false;
var prevIsChiral = true;
var allowTwoSame = (!this.isAlkene && this.nPriorities <= (node1 == null ? 2 : 1));
for (var i = 0; i < 4; i++) {
var a = this.atoms[i];
if (a != null && !a.isDuplicate && !a.isTerminal) {
ret1[0] = null;
var aIsChiralPath = a.createAuxiliaryDescriptors (node1 == null ? a : node1, ret1);
if (ret1[0] != null && ret != null) ret[0] = this.nextChiralBranch = a.nextChiralBranch;
if (a.nextChiralBranch != null || aIsChiralPath) {
nRS++;
isChiralPath = aIsChiralPath;
prevIsChiral = true;
} else {
if (!allowTwoSame && !prevIsChiral && this.priorities[i] == this.priorities[i - 1]) {
return false;
}prevIsChiral = false;
}}}
var isBranch = (nRS >= 2);
switch (nRS) {
case 0:
isChiralPath = false;
case 1:
skipRules4And5 = true;
break;
case 2:
case 3:
case 4:
isChiralPath = false;
if (ret != null) ret[0] = this.nextChiralBranch = this;
break;
}
if (this.isAlkene) {
if (this.alkeneChild != null) {
if (!this.isEvenEne || (this.auxEZ == 15 || this.auxEZ == -1) && !this.isKekuleAmbiguous && this.alkeneChild.bondCount >= 2) {
var rule2 = (this.isEvenEne ?  Clazz.newIntArray (1, 0) : null);
rs = this.getAuxEneWinnerChirality (this, this.alkeneChild, !this.isEvenEne, rule2);
if (rs == 0) {
this.auxEZ = this.alkeneChild.auxEZ = 15;
} else {
isChiralPath = true;
if (rule2 != null && rule2[0] != 8) {
this.auxEZ = this.alkeneChild.auxEZ = rs;
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo ("alkene type " + this + " " + (this.auxEZ == 14 ? "E" : "Z"));
} else if (!isBranch) {
switch (rs) {
case 17:
case 13:
rs = 1;
c = 'R';
isChiralPath = true;
break;
case 18:
case 14:
rs = 2;
c = 'S';
isChiralPath = true;
break;
}
this.auxChirality = c;
this.rule4Type = rs;
}}}}} else if (this.isSP3 && ret != null) {
var atom1 = this.clone ();
if (atom1.setNode ()) {
atom1.addReturnPath (null, this);
var rule = 1;
for (; rule <= 9; rule++) if ((!skipRules4And5 || rule < 5 || rule > 8) && atom1.auxSort (rule)) break;

if (rule > 9) {
c = '~';
} else {
rs = this.b$["JS.CIPChirality"].data.checkHandedness (atom1);
isChiralPath = new Boolean (isChiralPath | (rs != 0)).valueOf ();
c = (rs == 1 ? 'R' : rs == 2 ? 'S' : '~');
if (rule == 8) {
c = (c == 'R' ? 'r' : c == 'S' ? 's' : '~');
if (rs != 0) this.b$["JS.CIPChirality"].havePseudoAuxiliary = true;
} else {
this.rule4Type = rs;
}}}this.auxChirality = c;
}if (node1 == null) this.b$["JS.CIPChirality"].bsNeedRule.setBitTo (5, nRS > 0);
if (c != '~') {
this.b$["JS.CIPChirality"].logInfo ("creating aux " + c + " for " + this + (this.myPath.length == 0 ? "" : " = " + this.myPath));
}return (this.isChiralPath = isChiralPath);
}, "JS.CIPChirality.CIPAtom,~A");
Clazz.defineMethod (c$, "auxSort", 
function (rule) {
var current = this.b$["JS.CIPChirality"].currentRule;
this.b$["JS.CIPChirality"].currentRule = rule;
var rule6ref = this.b$["JS.CIPChirality"].root.rule6refIndex;
var nDup = this.b$["JS.CIPChirality"].root.nRootDuplicates;
var isChiral = (rule == 9 ? this.getRule6Descriptor (true) != 0 : this.sortSubstituents (0));
this.b$["JS.CIPChirality"].root.nRootDuplicates = nDup;
this.b$["JS.CIPChirality"].root.rule6refIndex = rule6ref;
this.b$["JS.CIPChirality"].currentRule = current;
return isChiral;
}, "~N");
Clazz.defineMethod (c$, "getAuxEneWinnerChirality", 
function (end1, end2, isAxial, retRule2) {
if (isAxial && end1.nextSP2 === end2) return 0;
var winner1 = this.getAuxEneEndWinner (end1, end1.nextSP2, null);
var winner2 = (winner1 == null || winner1.atom == null ? null : this.getAuxEneEndWinner (end2, end2.nextSP2, retRule2));
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo (this + " alkene end winners " + winner1 + winner2);
return this.b$["JS.CIPChirality"].getEneChirality (winner1, end1, end2, winner2, isAxial, false);
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,~B,~A");
Clazz.defineMethod (c$, "getAuxEneEndWinner", 
function (end, prevSP2, retRule) {
var atom1 = end.clone ();
if (atom1.parent !== prevSP2) {
atom1.addReturnPath (prevSP2, end);
}var a;
for (var rule = 1; rule <= 9; rule++) {
if (atom1.auxSort (rule)) {
for (var i = 0; i < 4; i++) {
a = atom1.atoms[i];
if (!a.multipleBondDuplicate) {
if (atom1.priorities[i] != atom1.priorities[i + 1]) {
if (retRule != null) retRule[0] = rule;
return (a.atom == null ? null : a);
}}}
}}
return null;
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,~A");
Clazz.defineMethod (c$, "addReturnPath", 
function (newParent, fromAtom) {
var path =  new JU.Lst ();
var thisAtom = this;
var newSub;
var oldParent = fromAtom;
var oldSub = newParent;
while (oldParent.parent != null && oldParent.parent.atoms[0] != null) {
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo ("path:" + oldParent.parent + "->" + oldParent);
path.addLast (oldParent = oldParent.parent);
}
if (oldParent.parent != null && newParent != null) path.add (oldParent.parent);
path.addLast (null);
for (var i = 0, n = path.size (); i < n; i++) {
oldParent = path.get (i);
newSub = (oldParent == null ? Clazz.innerTypeInstance (JS.CIPChirality.CIPAtom, this, null).create (null, this, thisAtom.isAlkene, true, false) : oldParent.clone ());
newSub.nPriorities = 0;
newSub.sphere = thisAtom.sphere + 1;
if (thisAtom.atoms[0] == null) thisAtom.atoms[0] = oldSub;
thisAtom.replaceParentSubstituent (oldSub, newParent, newSub);
if (i > 0 && thisAtom.isAlkene && !thisAtom.isAlkeneAtom2) {
if (newParent.isAlkeneAtom2) {
if (newParent.alkeneChild == null || newParent.alkeneChild.atom === thisAtom.atom) {
newParent.isAlkeneAtom2 = false;
thisAtom.alkeneParent = newParent;
thisAtom.setEne ();
}}}newParent = thisAtom;
thisAtom = newSub;
oldSub = fromAtom;
fromAtom = oldParent;
}
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "replaceParentSubstituent", 
function (oldSub, newParent, newSub) {
for (var i = 0; i < 4; i++) if (this.atoms[i] === oldSub || newParent == null && this.atoms[i].atom == null) {
if (JU.Logger.debuggingHigh) this.b$["JS.CIPChirality"].logInfo ("reversed: " + newParent + "->" + this + "->" + newSub);
this.parent = newParent;
this.atoms[i] = newSub;
this.fillAtoms (++i);
java.util.Arrays.sort (this.atoms);
break;
}
}, "JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom,JS.CIPChirality.CIPAtom");
Clazz.defineMethod (c$, "sign", 
function (score) {
return (score < 0 ? -1 : score > 0 ? 1 : 0);
}, "~N");
Clazz.defineMethod (c$, "clone", 
function () {
var a = null;
try {
a = Clazz.superCall (this, JS.CIPChirality.CIPAtom, "clone", []);
} catch (e) {
if (Clazz.exceptionOf(e,"CloneNotSupportedException")){
} else {
throw e;
}
}
a.id = this.b$["JS.CIPChirality"].ptIDLogger++;
a.atoms =  new Array (4);
for (var i = 0; i < 4; i++) a.atoms[i] = this.atoms[i];

a.priorities =  Clazz.newIntArray (4, 0);
a.htPathPoints = this.htPathPoints;
a.alkeneParent = null;
a.auxEZ = -1;
a.rule4Type = 0;
a.listRS = null;
if (JU.Logger.debuggingHigh) a.myPath = a.toString ();
return a;
});
Clazz.overrideMethod (c$, "toString", 
function () {
if (this.atom == null) return "<null>";
if (JU.Logger.debuggingHigh) return ("[" + this.b$["JS.CIPChirality"].currentRule + "." + this.sphere + "," + this.id + "." + (this.isDuplicate ? this.parent.atom : this.atom).getAtomName () + (this.isDuplicate ? "*(" + this.rootDistance + ")" : "") + (this.auxChirality == '~' ? "" : "" + this.auxChirality) + " " + this.elemNo + "]");
return (this.isDuplicate ? "(" + this.atom.getAtomName () + "." + this.rootDistance + ")" : this.atom.getAtomName ());
});
/*eoif4*/})();
};
Clazz.defineStatics (c$,
"ruleNames",  Clazz.newArray (-1, ["", "1a", "1b", "2", "3", "4a", "4b", "4c", "5", "6"]));
});
;//5.0.1-v2 Sat Nov 25 17:51:22 CST 2023
