Clazz.declarePackage("JS");
Clazz.load(["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"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.atoms = null;
this.ac = 0;
this.bsSelected = null;
this.bsAromatic = null;
this.flags = 0;
this.explicitHydrogen = 0;
this.ringSets = null;
this.vTemp = null;
this.nPairs = 0;
this.nPairsMax = 0;
this.bsBondsUp = null;
this.bsBondsDn = null;
this.bsToDo = null;
this.bsIgnoreHydrogen =  new JU.BS();
this.prevAtom = null;
this.prevSp2Atoms = null;
this.alleneStereo = null;
this.htRingsSequence = null;
this.htRings = null;
this.bsRingKeys = null;
this.bsIncludingH = null;
this.topologyOnly = false;
this.getAromatic = true;
this.addAtomComment = false;
this.noBioComment = false;
this.aromaticDouble = false;
this.noStereo = false;
this.openSMILES = false;
this.polySmilesCenter = null;
this.smilesStereo = null;
this.isPolyhedral = false;
this.aromaticRings = null;
this.sm = null;
this.iHypervalent = 0;
this.is2D = false;
this.haveSmilesAtoms = false;
this.noBranches = false;
this.allComponents = false;
this.ptAtom = 0;
this.ptSp2Atom0 = 0;
this.atemp = null;
this.chainCheck = 0;
Clazz.instantialize(this, arguments);}, JS, "SmilesGenerator", null);
Clazz.prepareFields (c$, function(){
this.vTemp =  new JS.VTemp();
this.bsBondsUp =  new JU.BS();
this.bsBondsDn =  new JU.BS();
this.htRingsSequence =  new java.util.Hashtable();
this.htRings =  new java.util.Hashtable();
this.bsRingKeys =  new JU.BS();
});
Clazz.defineMethod(c$, "getSmiles", 
function(sm, atoms, ac, bsSelected, comment, flags){
var ipt = bsSelected.nextSetBit(0);
if (ipt < 0) return "";
this.haveSmilesAtoms = (Clazz.instanceOf(atoms[ipt],"JS.SmilesAtom") && (atoms[ipt]).definesStereo());
this.sm = sm;
this.flags = flags;
this.atoms = atoms;
this.ac = ac;
bsSelected = JU.BSUtil.copy(bsSelected);
this.bsSelected = JU.BS.copy(bsSelected);
this.flags = flags = JS.SmilesSearch.addFlags(flags, comment == null ? "" : comment.toUpperCase());
if ((flags & 1048576) == 1048576) return this.getBioSmiles(bsSelected, comment, flags);
this.openSMILES = ((flags & 5) == 5);
this.addAtomComment = ((flags & 131072) == 131072);
this.aromaticDouble = ((flags & 512) == 512);
this.explicitHydrogen = ((flags & 8192) == 8192 ? 8192 : (flags & 4096) == 4096 ? 4096 : 0);
if (this.explicitHydrogen == 8192) {
var bsHa =  new JU.BS();
for (var i = bsSelected.nextSetBit(0); i >= 0; i = bsSelected.nextSetBit(i + 1)) {
var a = atoms[i];
if (a.getCovalentHydrogenCount() == 3 && (a.getCovalentBondCount() == 4)) {
var doIgnore = true;
bsHa.clearAll();
for (var j = a.getBondCount(); --j >= 0; ) {
var aj = a.getBondedAtomIndex(j);
if (atoms[aj].getElementNumber() == 1) {
doIgnore = (atoms[aj].getElementNumber() == 1);
if (doIgnore) bsHa.set(aj);
 else break;
}if (doIgnore) {
this.bsIgnoreHydrogen.set(i);
bsSelected.andNot(bsHa);
}}
}}
}this.topologyOnly = ((flags & 16384) == 16384);
this.getAromatic = !((flags & 16) == 16);
this.noStereo = ((flags & 32) == 32);
this.isPolyhedral = ((flags & 65536) == 65536);
this.is2D = ((flags & 134217728) == 134217728);
this.noBranches = false;
this.allComponents = ((flags & 32768) == 32768);
return this.getSmilesComponent(atoms[ipt], bsSelected, true, false, false);
}, "JS.SmilesMatcher,~A,~N,JU.BS,~S,~N");
Clazz.defineMethod(c$, "getBioSmiles", 
function(bsSelected, comment, flags){
this.addAtomComment = ((flags & 131072) == 131072);
var allowUnmatchedRings = ((flags & 3145728) == 3145728);
var noBioComments = ((flags & 34603008) == 34603008);
var crosslinkCovalent = ((flags & 5242880) == 5242880);
var crosslinkHBonds = ((flags & 9437184) == 9437184);
var addCrosslinks = (crosslinkCovalent || crosslinkHBonds);
var sb =  new JU.SB();
var bs = bsSelected;
if (comment != null && !this.noBioComment) sb.append("//* Jmol bioSMILES ").append(comment.$replace('*', '_')).append(" *//");
var end = (this.noBioComment ? "" : "\n");
var bsIgnore =  new JU.BS();
var lastComponent = null;
var groupString = "";
var s;
var vLinks =  new JU.Lst();
try {
var len = 0;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
var a = this.atoms[i];
var ch = a.getGroup1('?');
var bioStructureName = a.getBioStructureTypeName();
var unknown = (ch === ch.toLowerCase());
if (end != null) {
if (sb.length() > 0) sb.append(end);
end = null;
len = 0;
if (bioStructureName.length > 0) {
var id = a.getChainID();
if (id != 0 && !noBioComments) {
s = "//* chain " + a.getChainIDStr() + " " + bioStructureName + " " + a.getResno() + " *// ";
len = s.length;
sb.append(s);
}len++;
sb.append("~").appendC(bioStructureName.toLowerCase().charAt(0)).append("~");
} else {
s = this.getSmilesComponent(a, bs, false, true, true);
if (s.equals(lastComponent)) {
end = "";
continue;
}lastComponent = s;
var groupName = a.getGroup3(true);
var key;
if (noBioComments) {
key = "/" + s + "/";
} else {
if (groupName != null) {
s = "//* " + groupName + " *//" + s;
}key = s + "//";
}if (groupString.indexOf(key) >= 0) {
end = "";
continue;
}groupString += key;
sb.append(s);
end = (noBioComments ? "." : ".\n");
continue;
}}if (len >= 75 && !noBioComments) {
sb.append("\n  ");
len = 2;
}if (this.addAtomComment) sb.append("\n//* [" + a.getGroup3(false) + "#" + a.getResno() + "] *//\t");
if (unknown) {
this.addBracketedBioName(sb, a, bioStructureName.length > 0 ? ".0" : null, false);
} else {
sb.append(ch);
}len++;
if (addCrosslinks) {
a.getCrossLinkVector(vLinks, crosslinkCovalent, crosslinkHBonds);
for (var j = 0; j < vLinks.size(); j += 3) {
sb.append(":");
s = this.getRingCache(vLinks.get(j).intValue(), vLinks.get(j + 1).intValue(), this.htRingsSequence);
sb.append(s);
len += 1 + s.length;
}
vLinks.clear();
}a.getGroupBits(bsIgnore);
bs.andNot(bsIgnore);
var i2 = a.getOffsetResidueAtom("\0", 1);
if (i2 < 0 || !bs.get(i2)) {
if (!noBioComments) sb.append(" //* ").appendI(a.getResno()).append(" *//");
if (i2 < 0 && (i2 = bs.nextSetBit(i + 1)) < 0) break;
if (len > 0) end = (noBioComments ? "." : ".\n");
}i = i2 - 1;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
throw  new JS.InvalidSmilesException("//* error: " + e.getMessage() + " *//");
} else {
throw e;
}
}
if (!allowUnmatchedRings && !this.htRingsSequence.isEmpty()) {
this.dumpRingKeys(sb, this.htRingsSequence);
throw  new JS.InvalidSmilesException("//* ?ring error? *//");
}s = sb.toString();
if (s.endsWith(".\n")) s = s.substring(0, s.length - 2);
 else if (noBioComments && s.endsWith(".")) s = s.substring(0, s.length - 1);
return s;
}, "JU.BS,~S,~N");
Clazz.defineMethod(c$, "addBracketedBioName", 
function(sb, atom, atomName, addComment){
sb.append("[");
if (atomName != null) {
var chain = atom.getChainIDStr();
sb.append(atom.getGroup3(false));
if (!atomName.equals(".0")) sb.append(atomName).append("#").appendI(atom.getElementNumber());
if (addComment) {
sb.append("//* ").appendI(atom.getResno());
if (chain.length > 0) sb.append(":").append(chain);
sb.append(" *//");
}} else {
sb.append(JU.Elements.elementNameFromNumber(atom.getElementNumber()));
}sb.append("]");
}, "JU.SB,JU.Node,~S,~B");
Clazz.defineMethod(c$, "getSmilesComponent", 
function(atom, bs, allowBioResidues, allowConnectionsToOutsideWorld, forceBrackets){
var ret = "";
while (true) {
if (atom == null) atom = this.atoms[bs.nextSetBit(0)];
atom = this.checkFirstAtom(atom);
this.bsSelected = JU.JmolMolecule.getBranchBitSet(this.atoms, atom.getIndex(), JU.BSUtil.copy(bs), null, -1, true, allowBioResidues);
bs.andNot(this.bsSelected);
this.iHypervalent = -1;
for (var i = this.bsSelected.nextSetBit(0); i >= 0 && this.iHypervalent < 0; i = this.bsSelected.nextSetBit(i + 1)) {
if (this.atoms[i].getCovalentBondCount() > 4 || this.isPolyhedral) {
this.iHypervalent = i;
}}
this.bsIncludingH = JU.BSUtil.copy(this.bsSelected);
if (this.explicitHydrogen == 0) {
for (var j = this.bsSelected.nextSetBit(0); j >= 0; j = this.bsSelected.nextSetBit(j + 1)) {
var a = this.atoms[j];
if (a.getAtomicAndIsotopeNumber() == 1 && a.getBondCount() > 0 && a.getBondedAtomIndex(0) != this.iHypervalent && !this.isExplicitOnly(this.atoms[a.getBondedAtomIndex(0)])) this.bsSelected.clear(j);
}
}this.bsAromatic =  new JU.BS();
if (!this.topologyOnly && this.bsSelected.cardinality() > 2) {
this.generateRingData();
this.setBondDirections();
}this.bsToDo = JU.BSUtil.copy(this.bsSelected);
var sb =  new JU.SB();
for (var i = this.bsToDo.nextSetBit(0); i >= 0; i = this.bsToDo.nextSetBit(i + 1)) {
if (this.atoms[i].getCovalentBondCount() > 4 || this.isPolyhedral || this.noBranches) {
if (atom == null) sb.append(".");
this.getSmilesAt(sb, this.atoms[i], allowConnectionsToOutsideWorld, false, forceBrackets, false);
atom = null;
}}
if (atom != null) while ((atom = this.getSmilesAt(sb, atom, allowConnectionsToOutsideWorld, true, forceBrackets, false)) != null) {
}
while (!this.bsToDo.isEmpty() || !this.htRings.isEmpty()) {
var e = this.htRings.values().iterator();
if (e.hasNext()) {
atom = this.atoms[(e.next()[1]).intValue()];
if (!this.bsToDo.get(atom.getIndex())) break;
} else {
atom = this.atoms[this.bsToDo.nextSetBit(0)];
}sb.append(".");
this.prevSp2Atoms = this.alleneStereo = null;
this.prevAtom = null;
while ((atom = this.getSmilesAt(sb, atom, allowConnectionsToOutsideWorld, true, forceBrackets, false)) != null) {
}
}
if (!this.htRings.isEmpty()) {
this.dumpRingKeys(sb, this.htRings);
throw  new JS.InvalidSmilesException("//* ?ring error? *//\n" + sb);
}var s = sb.toString();
if (s.indexOf("^-") >= 0) {
var s0 = s;
try {
var keys = this.sm.getAtropisomerKeys(s, this.atoms, this.ac, this.bsSelected, this.bsAromatic, this.flags);
for (var i = 1; i < keys.length; ) {
var pt = s.indexOf("^-");
if (pt < 0) break;
s = s.substring(0, pt + 1) + keys.substring(i, i + 3).trim() + s.substring(pt + 1);
i += 3;
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
e.printStackTrace();
s = s0;
} else {
throw e;
}
}
}ret += s;
var ipt = bs.nextSetBit(0);
if (ipt < 0 || !this.allComponents) break;
ret += ".";
atom = null;
}
return ret;
}, "JU.Node,JU.BS,~B,~B,~B");
Clazz.defineMethod(c$, "checkFirstAtom", 
function(atom){
if (this.explicitHydrogen == 0 && atom.getAtomicAndIsotopeNumber() == 1 && atom.getEdges().length > 0) atom = this.atoms[atom.getBondedAtomIndex(0)];
var a = atom;
var aprev = null;
while (true) {
if (a.getCovalentBondCount() != 2) break;
var bonds = a.getEdges();
if (bonds[0].getBondType() != 2 || bonds[1].getBondType() != 2) break;
var anext = bonds[0].getOtherNode(a);
if (anext === aprev) anext = bonds[1].getOtherNode(a);
aprev = a;
a = anext;
}
return (a == null ? atom : a);
}, "JU.Node");
Clazz.defineMethod(c$, "generateRingData", 
function(){
var search = JS.SmilesParser.newSearch("[r500]", true, true);
search.target.setAtoms(this.atoms, this.ac, this.bsSelected);
search.setFlags(this.flags);
if (!search.needRingData && search.target.hasDoubleBonds()) search.needRingData = true;
search.ringDataMax = 7;
search.flags = this.flags;
var vRings = JU.AU.createArrayOfArrayList(4);
search.setRingData(null, vRings, true);
this.bsAromatic = search.target.bsAromatic;
this.ringSets = search.target.ringSets;
this.aromaticRings = vRings[3];
});
Clazz.defineMethod(c$, "getBondStereochemistry", 
function(bond, atomFrom){
if (bond == null) return '\0';
var i = bond.index;
var isFirst = (atomFrom == null || bond.getAtomIndex1() == atomFrom.getIndex());
return (this.bsBondsUp.get(i) ? (isFirst ? '/' : '\\') : this.bsBondsDn.get(i) ? (isFirst ? '\\' : '/') : '\0');
}, "JU.Edge,JU.SimpleNode");
Clazz.defineMethod(c$, "setBondDirections", 
function(){
var bsDone =  new JU.BS();
var edges =  Clazz.newArray(2, 3, null);
for (var i = this.bsSelected.nextSetBit(0); i >= 0; i = this.bsSelected.nextSetBit(i + 1)) {
var atom1 = this.atoms[i];
var bonds = atom1.getEdges();
for (var k = 0; k < bonds.length; k++) {
var bond = bonds[k];
var index = bond.index;
var atom2;
if (bsDone.get(index) || bond.getCovalentOrder() != 2 || JS.SmilesSearch.isRingBond(this.ringSets, null, i, (atom2 = bond.getOtherNode(atom1)).getIndex())) continue;
bsDone.set(index);
var nCumulene = 0;
var a10 = atom1;
while (atom2.getCovalentBondCount() == 2 && atom2.getValence() == 4) {
var e2 = atom2.getEdges();
var e = e2[e2[0].getOtherNode(atom2) === a10 ? 1 : 0];
bsDone.set(e.index);
a10 = atom2;
atom2 = e.getOtherNode(atom2);
nCumulene++;
}
if (nCumulene % 2 == 1) continue;
var b0 = null;
var a0 = null;
var i0 = 0;
var atom12 =  Clazz.newArray(-1, [atom1, atom2]);
var edgeCount = 1;
for (var j = 0; j < 2 && edgeCount > 0 && edgeCount < 3; j++) {
edgeCount = 0;
var atomA = atom12[j];
var bb = (atomA).getEdges();
var explicitH = this.explicitHydrogen > 0 || this.isExplicitOnly(atomA);
for (var b = 0; b < bb.length; b++) {
var other;
if (bb[b].getCovalentOrder() != 1 || !explicitH && (other = bb[b].getOtherNode(atomA)).getElementNumber() == 1 && other.getIsotopeNumber() == 0) continue;
edges[j][edgeCount++] = bb[b];
if (this.getBondStereochemistry(bb[b], atomA) != '\0') {
b0 = bb[b];
i0 = j;
}}
}
if (edgeCount == 3 || edgeCount == 0) continue;
if (b0 == null) {
i0 = 0;
b0 = edges[i0][0];
this.bsBondsUp.set(b0.index);
}var aA = atom12[i0];
var c0 = this.getBondStereochemistry(b0, aA);
a0 = b0.getOtherNode(aA);
if (a0 == null) continue;
for (var j = 0; j < 2; j++) {
var aB = atom12[j];
for (var jj = 0; jj < 2; jj++) {
var b1 = edges[j][jj];
if (b1 == null || b1 === b0) continue;
var bi = b1.index;
var a1 = b1.getOtherNode(aB);
if (a1 == null) continue;
var c1 = this.getBondStereochemistry(b1, aB);
var isOpposite;
if (this.haveSmilesAtoms) {
var isop = (a0).isStereoOpposite(a1.getIndex(), aA.getIndex(), aB.getIndex());
if (isop == null) {
if (JU.Logger.debugging) JU.Logger.debug("SmilesGenerator could not find stereo for " + a0 + "/" + a1);
continue;
}isOpposite = isop.booleanValue();
} else {
isOpposite = JS.SmilesStereo.isDiaxial(aA, aB, a0, a1, this.vTemp, 0);
}if (c1 == '\0' || (c1 != c0) == isOpposite) {
var isUp = (c0 == '\\' && isOpposite || c0 == '/' && !isOpposite);
if (isUp == (b1.getAtomIndex1() != a1.getIndex())) {
this.bsBondsUp.set(bi);
} else {
this.bsBondsDn.set(bi);
}} else {
this.bsBondsUp.clear(bi);
this.bsBondsDn.clear(bi);
JU.Logger.error("BOND STEREOCHEMISTRY PARITY ERROR-stereochemistry for bond " + bi + "");
}if (JU.Logger.debugging) JU.Logger.debug(this.getBondStereochemistry(b0, aA) + " " + a0.getIndex() + " " + a1.getIndex() + " " + this.getBondStereochemistry(b1, aB));
}
}
}
}
});
Clazz.defineMethod(c$, "getSmilesAt", 
function(sb, atom, allowConnectionsToOutsideWorld, allowBranches, forceBrackets, isBranch){
var atomIndex = atom.getIndex();
if (!this.bsToDo.get(atomIndex)) return null;
this.ptAtom++;
this.bsToDo.clear(atomIndex);
var includeHs = (atomIndex == this.iHypervalent || this.explicitHydrogen != 0 && !this.bsIgnoreHydrogen.get(atomIndex));
var explicitHs = this.isExplicitOnly(atom);
var isAromatic = this.bsAromatic.get(atomIndex);
var isExtension = (!this.bsSelected.get(atomIndex));
var prevIndex = (this.prevAtom == null ? -1 : this.prevAtom.getIndex());
var sp2Atoms = this.prevSp2Atoms;
var havePreviousSp2Atoms = (sp2Atoms != null);
var atomicNumber = atom.getElementNumber();
var nH = 0;
var prevStereo = this.alleneStereo;
this.alleneStereo = null;
var v =  new JU.Lst();
var bondNext = null;
var bondPrev = null;
var bonds = atom.getEdges();
if (!isBranch && this.polySmilesCenter != null) {
allowBranches = false;
this.sortPolyBonds(atom, this.prevAtom, this.polySmilesCenter);
}var aH = null;
var stereoFlag = (isAromatic ? 10 : 0);
if (JU.Logger.debugging) JU.Logger.debug(sb.toString());
if (bonds != null) {
for (var i = 0, nb = bonds.length; i < nb; i++) {
var bond = bonds[i];
if (!bond.isCovalent()) continue;
var atom1 = bonds[i].getOtherNode(atom);
var index1 = atom1.getIndex();
if (index1 == prevIndex) {
bondPrev = bonds[i];
continue;
}var isH = !includeHs && !explicitHs && (atom1.getElementNumber() == 1 && atom1.getIsotopeNumber() <= 0);
if (!this.bsIncludingH.get(index1)) {
if (isH || !allowConnectionsToOutsideWorld || !this.bsSelected.get(atomIndex)) continue;
this.bsToDo.set(index1);
}if (isH) {
aH = atom1;
nH++;
if (nH > 1) stereoFlag = 10;
} else {
v.addLast(bonds[i]);
}}
}if (nH > 1) sp2Atoms = null;
var nSp2Atoms = (sp2Atoms != null ? 2 : 0);
if (sp2Atoms == null && !isAromatic && nH <= 1) sp2Atoms =  new Array(5);
var strPrev = null;
if (bondPrev != null) {
strPrev = this.getBondOrder(bondPrev, atomIndex, prevIndex, isAromatic);
if (sp2Atoms != null && !havePreviousSp2Atoms) {
sp2Atoms[nSp2Atoms++] = this.prevAtom;
}}if (sp2Atoms != null && !havePreviousSp2Atoms) {
this.ptSp2Atom0 = this.ptAtom;
}if (sp2Atoms != null && nH == 1) sp2Atoms[nSp2Atoms++] = aH;
var nMax = 0;
var bsBranches =  new JU.BS();
var nBonds = v.size();
if (allowBranches) {
for (var i = 0; i < nBonds; i++) {
var bond = v.get(i);
var a = bond.getOtherNode(atom);
var n = a.getCovalentBondCount() - (includeHs || this.isExplicitOnly(a) ? 0 : (a).getCovalentHydrogenCount());
var order = bond.getCovalentOrder();
var isEndPoint = this.htRings.containsKey(JS.SmilesGenerator.getRingKey(a.getIndex(), atomIndex));
if (isEndPoint) continue;
var check = (bondNext != null || i < nBonds - 1);
if (n == 1 && check) {
bsBranches.set(bond.index);
} else if ((order > 1 || n > nMax)) {
nMax = (order > 1 ? 1000 + order : n);
bondNext = bond;
}}
}var atomNext = (bondNext == null ? null : bondNext.getOtherNode(atom));
var orderNext = (bondNext == null ? 0 : bondNext.getCovalentOrder());
var stereo =  new Array(7);
if (stereoFlag < 7 && bondPrev != null) {
if (havePreviousSp2Atoms && bondPrev.getCovalentOrder() == 2 && orderNext == 2 && sp2Atoms[1] != null) {
stereo[stereoFlag++] = sp2Atoms[0];
stereo[stereoFlag++] = sp2Atoms[1];
} else {
stereo[stereoFlag++] = this.prevAtom;
}}if (stereoFlag < 7 && nH == 1) stereo[stereoFlag++] = aH;
var deferStereo = false;
var chBond = this.getBondStereochemistry(bondPrev, this.prevAtom);
if (strPrev != null || chBond != '\0') {
if (chBond != '\0') strPrev = "" + chBond;
sb.append(strPrev);
}var stereoFlag0 = stereoFlag;
var nSp2Atoms0 = nSp2Atoms;
var sbBranches =  new JU.SB();
var vBranches =  new JU.Lst();
for (var i = 0; i < v.size(); i++) {
var bond = v.get(i);
if (!bsBranches.get(bond.index)) continue;
var a = bond.getOtherNode(atom);
var s2 =  new JU.SB();
this.prevAtom = atom;
this.prevSp2Atoms = this.alleneStereo = null;
var bond0t = bondNext;
var ptSp2Atom0t = this.ptSp2Atom0;
var ptAtomt = this.ptAtom;
this.getSmilesAt(s2, a, allowConnectionsToOutsideWorld, allowBranches, forceBrackets, true);
bondNext = bond0t;
this.ptAtom = ptAtomt;
this.ptSp2Atom0 = ptSp2Atom0t;
var branch = s2.toString();
v.removeItemAt(i--);
if (bondNext == null) vBranches.addLast(branch);
 else sbBranches.append("(").append(branch).append(")");
if (stereoFlag < 7) stereo[stereoFlag++] = a;
if (sp2Atoms != null && nSp2Atoms < 5) sp2Atoms[nSp2Atoms++] = a;
}
var sbRings =  new JU.SB();
var stereoFlag1 = stereoFlag;
var nSp2Atoms1 = nSp2Atoms;
var atat = null;
if (!allowBranches && !this.noStereo && this.polySmilesCenter == null && (v.size() == 5 || v.size() == 6)) {
atat = this.sortInorganic(atom, v, this.vTemp);
}for (var i = 0; i < v.size(); i++) {
var bond = v.get(i);
if (bond === bondNext) continue;
var a = bond.getOtherNode(atom);
var ia = a.getIndex();
strPrev = this.getBondOrder(bond, atomIndex, ia, isAromatic);
chBond = this.getBondStereochemistry(bond, atom);
if (!deferStereo && chBond != '\0') {
strPrev = "" + chBond;
}sbRings.append(strPrev);
sbRings.append(this.getRingCache(atomIndex, ia, this.htRings));
if (stereoFlag < 7) stereo[stereoFlag++] = a;
if (sp2Atoms != null && nSp2Atoms < 5) sp2Atoms[nSp2Atoms++] = a;
}
if (stereoFlag0 != stereoFlag1 && stereoFlag1 != stereoFlag) this.swapArray(stereo, stereoFlag0, stereoFlag1, stereoFlag);
if (nSp2Atoms0 != nSp2Atoms1 && nSp2Atoms1 != nSp2Atoms) this.swapArray(sp2Atoms, nSp2Atoms0, nSp2Atoms1, nSp2Atoms);
if (havePreviousSp2Atoms && stereoFlag == 2 && orderNext == 2) {
var nc = (this.ptAtom - this.ptSp2Atom0);
var nb = atomNext.getCovalentBondCount();
var lastIsN = (atomNext.getElementNumber() == 7);
if (nc % 2 == 0) {
stereoFlag = 8;
} else {
if (nb == 3 || nb == 2 && lastIsN) {
bonds = atomNext.getEdges();
for (var k = 0; k < bonds.length; k++) {
var index = atomNext.getBondedAtomIndex(k);
if (bonds[k].isCovalent() && index != atomIndex) stereo[stereoFlag++] = this.atoms[index];
}
if (nb == 2) stereo[stereoFlag++] = atomNext;
if (stereoFlag == 4) {
this.alleneStereo = stereo;
if ((stereo[3]).getAtomicAndIsotopeNumber() == 1) {
var n = stereo[3];
stereo[3] = stereo[2];
stereo[2] = n;
}}}}nSp2Atoms = 0;
} else if (atomNext != null && stereoFlag < 7) {
stereo[stereoFlag++] = atomNext;
}if (prevStereo != null) {
if (prevStereo[3] !== stereo[2]) {
var ptat = sb.lastIndexOf("@]=");
if (ptat > 0) {
var trail = sb.substring(ptat);
sb.setLength(sb.charAt(ptat - 1) == '@' ? ptat - 1 : ptat + 1);
sb.append(trail);
}}prevStereo = null;
}if (this.haveSmilesAtoms && atat == null && (stereoFlag == 4)) {
atat = (atom).getStereoAtAt(stereo);
}var charge = atom.getFormalCharge();
var isotope = atom.getIsotopeNumber();
var valence = atom.getValence();
var osclass = (this.openSMILES ? (atom).getFloatProperty("property_atomclass") : NaN);
var atomName = atom.getAtomName();
var groupType = (atom).getBioStructureTypeName();
if (this.addAtomComment) sb.append("\n//* " + atom.toString() + " *//\t");
if (this.topologyOnly) {
sb.append("*");
} else if (isExtension && groupType.length != 0 && atomName.length != 0) {
this.addBracketedBioName(sb, atom, "." + atomName, false);
} else {
sb.append(JS.SmilesAtom.getAtomLabel(atomicNumber, isotope, (forceBrackets ? -1 : valence), charge, osclass, nH, isAromatic, atat != null ? atat : this.noStereo ? null : this.checkStereoPairs(atom, this.alleneStereo == null ? atomIndex : -1, stereo, stereoFlag, prevIndex == -1), this.is2D));
}sb.appendSB(sbRings);
if (bondNext != null) {
sb.appendSB(sbBranches);
} else {
var n = vBranches.size() - 1;
if (n >= 0) {
for (var i = 0; i < n; i++) sb.append("(").append(vBranches.get(i)).append(")");

sb.append(vBranches.get(n));
}return null;
}if (sp2Atoms != null && orderNext == 2 && (nSp2Atoms == 1 || nSp2Atoms == 2)) {
if (sp2Atoms[0] == null) sp2Atoms[0] = atom;
if (sp2Atoms[1] == null) sp2Atoms[1] = atom;
} else {
sp2Atoms = null;
nSp2Atoms = 0;
}this.prevSp2Atoms = sp2Atoms;
this.prevAtom = atom;
return atomNext;
}, "JU.SB,JU.SimpleNode,~B,~B,~B,~B");
Clazz.defineMethod(c$, "isExplicitOnly", 
function(atom){
return (atom.getElementNumber() == 7 && atom.getCovalentBondCount() == 2 || atom.getElementNumber() == 6 && atom.getIsotopeNumber() == 17);
}, "JU.SimpleNode");
Clazz.defineMethod(c$, "swapArray", 
function(a, i0, i1, i2){
var n = i1 - i0;
if (this.atemp == null || this.atemp.length < n) this.atemp =  new Array(n);
for (var p = n, i = i1; p > 0; ) this.atemp[--p] = a[--i];

for (var i = i1; i < i2; i++) a[i - n] = a[i];

for (var p = n, i = i2; p > 0; ) a[--i] = this.atemp[--p];

}, "~A,~N,~N,~N");
Clazz.defineMethod(c$, "getBondOrder", 
function(bondPrev, atomIndex, prevIndex, isAromatic){
if (this.topologyOnly) return "";
if ((bondPrev.order & 65537) == 65537) {
return "^-";
}var border = Math.max(bondPrev.isPartial() ? 1 : 0, bondPrev.getCovalentOrder());
return (!isAromatic || !this.bsAromatic.get(prevIndex) ? JS.SmilesBond.getBondOrderString(border) : border == 1 && !this.isSameAromaticRing(atomIndex, prevIndex) ? "-" : this.aromaticDouble && (border == 2 || border == 514) ? "=" : "");
}, "JU.Edge,~N,~N,~B");
Clazz.defineMethod(c$, "isSameAromaticRing", 
function(a1, a2){
var bs;
for (var i = this.aromaticRings.size(); --i >= 0; ) if ((bs = this.aromaticRings.get(i)).get(a1) && bs.get(a2)) return true;

return false;
}, "~N,~N");
Clazz.defineMethod(c$, "sortPolyBonds", 
function(atom, refAtom, center){
if (this.smilesStereo == null) try {
this.smilesStereo = JS.SmilesStereo.newStereo(null);
} catch (e) {
if (Clazz.exceptionOf(e,"JS.InvalidSmilesException")){
} else {
throw e;
}
}
this.smilesStereo.sortPolyBondsByStereo(atom, refAtom, center, atom.getEdges(), this.vTemp.vA);
}, "JU.SimpleNode,JU.SimpleNode,JU.P3");
Clazz.defineMethod(c$, "sortInorganic", 
function(atom, v, vTemp){
var atomIndex = atom.getIndex();
var n = v.size();
var axialPairs =  new JU.Lst();
var bonds =  new JU.Lst();
var a1;
var a2;
var a01 = null;
var a02 = null;
var bond1;
var bond2;
var bsDone =  new JU.BS();
var pair0 = null;
var stereo =  new Array(6);
var isOK = true;
var s = "";
var naxial = 0;
for (var i = 0; i < n; i++) {
bond1 = v.get(i);
stereo[0] = a1 = bond1.getOtherNode(atom);
if (i == 0) s = this.addStereoCheck(0, atomIndex, a1, "", null);
 else if (isOK && this.addStereoCheck(0, atomIndex, a1, s, null) != null) isOK = false;
if (bsDone.get(i)) continue;
bsDone.set(i);
var isAxial = false;
for (var j = i + 1; j < n; j++) {
if (bsDone.get(j)) continue;
bond2 = v.get(j);
a2 = bond2.getOtherNode(atom);
if (JS.SmilesStereo.isDiaxial(atom, atom, a1, a2, vTemp, -0.95)) {
switch (++naxial) {
case 1:
a01 = a1;
break;
case 2:
a02 = a1;
break;
case 3:
if (JS.SmilesStereo.getHandedness(a02, a01, a1, atom, vTemp) == 2) {
var b = bond1;
bond1 = bond2;
bond2 = b;
}break;
}
axialPairs.addLast( Clazz.newArray(-1, [bond1, bond2]));
isAxial = true;
bsDone.set(j);
break;
}}
if (!isAxial) bonds.addLast(bond1);
}
var npAxial = axialPairs.size();
if (isOK || n == 6 && npAxial != 3 || n == 5 && npAxial == 0) return "";
pair0 = axialPairs.get(0);
bond1 = pair0[0];
stereo[0] = bond1.getOtherNode(atom);
v.clear();
v.addLast(bond1);
if (npAxial > 1) bonds.addLast(axialPairs.get(1)[0]);
if (npAxial == 3) bonds.addLast(axialPairs.get(2)[0]);
if (npAxial > 1) bonds.addLast(axialPairs.get(1)[1]);
if (npAxial == 3) bonds.addLast(axialPairs.get(2)[1]);
for (var i = 0; i < bonds.size(); i++) {
bond1 = bonds.get(i);
v.addLast(bond1);
stereo[i + 1] = bond1.getOtherNode(atom);
}
v.addLast(pair0[1]);
stereo[n - 1] = pair0[1].getOtherNode(atom);
return JS.SmilesStereo.getStereoFlag(atom, stereo, n, vTemp, this.is2D);
}, "JU.SimpleNode,JU.Lst,JS.VTemp");
Clazz.defineMethod(c$, "checkStereoPairs", 
function(atom, atomIndex, stereo, stereoFlag, isFirst){
if (stereoFlag == 10 || stereoFlag < (this.is2D ? 3 : 4)) return "";
if (this.explicitHydrogen == 0 && atomIndex >= 0 && stereoFlag == 4) {
if (atom.getElementNumber() <= 17) {
var s = "";
for (var i = 0; i < 4; i++) {
if ((s = this.addStereoCheck(0, atomIndex, stereo[i], s, JU.BSUtil.newAndSetBit(atomIndex))) == null) {
return "";
}}
}}if (this.is2D) {
var dir = (stereoFlag == 4 || !isFirst ? 1 : -1);
var bonds = atom.getEdges();
var c = null;
for (var i = atom.getBondCount(); --i >= 0; ) {
var b = bonds[i];
if (atom === b.getAtom(0)) {
switch (b.getBondType()) {
case 1025:
c = JS.SmilesGenerator.setStereoTemp(null, stereo, b.getAtom(1), dir);
break;
case 1041:
c = JS.SmilesGenerator.setStereoTemp(null, stereo, b.getAtom(1), -dir);
break;
}
}}
if (c == null) return "";
if (stereoFlag == 3) {
stereo[stereoFlag++] = JS.SmilesGenerator.setStereoTemp(atom, stereo, c, 0);
}}return JS.SmilesStereo.getStereoFlag(atom, stereo, stereoFlag, this.vTemp, this.is2D);
}, "JU.SimpleNode,~N,~A,~N,~B");
c$.setStereoTemp = Clazz.defineMethod(c$, "setStereoTemp", 
function(atom, stereo, a, z){
var b =  new JS.SmilesAtom();
for (var i = 0; i < 4; i++) {
var isA = (stereo[i] === a);
if (atom == null) {
if (isA) {
var c = a.getXYZ();
b.set(c.x, c.y, z);
return stereo[i] = b;
}} else if (i < 3) {
b.add(stereo[i]);
}}
if (atom == null) return null;
b.scale(-0.33333334);
b.scaleAdd2(2, atom, b);
return b;
}, "JU.SimpleNode,~A,JU.SimpleNode,~N");
Clazz.defineMethod(c$, "addStereoCheck", 
function(level, atomIndex, atom, s, bsDone){
if (bsDone != null) bsDone.set(atomIndex);
var n = (atom).getAtomicAndIsotopeNumber();
if (n == 1 && this.explicitHydrogen == 0) return "H";
var nx = atom.getCovalentBondCount();
var nhcov = (atom).getCovalentHydrogenCount();
var nh = (n == 6 && this.explicitHydrogen != 0 ? nhcov : 0);
if (n == 6 || n == 16 ? nx != 4 : n == 1 || nx > 1) return s + (++this.chainCheck);
var sa = ";" + level + "/" + n + "/" + nh + "/" + nx + (level == 0 ? "," : "_");
if (n == 6 || n == 16) {
switch (nh) {
case 1:
return s + sa + (++this.chainCheck);
case 0:
case 2:
if (bsDone == null) return s;
var edges = (atom).getEdges();
var s2 = "";
var sa2 = "";
var nunique = (nh == 2 ? 0 : 3);
for (var j = atom.getBondCount(); --j >= 0; ) {
var a2 = edges[j].getOtherNode(atom);
var i2 = a2.getIndex();
if (bsDone.get(i2) || !edges[j].isCovalent()) continue;
bsDone.set(i2);
sa2 = this.addStereoCheck(level + 1, atom.getIndex(), a2, "", bsDone.clone());
if (s2.indexOf(sa2) >= 0) nunique--;
s2 += sa2;
}
if (nunique == 3) {
return s + sa + (++this.chainCheck);
}sa = (sa + s2).$replace(',', '_');
if (level > 0) return s + sa;
break;
case 3:
break;
}
}if (s.indexOf(sa) >= 0) {
if (nhcov == 3) {
var ndt = 0;
for (var j = 0; j < nx && ndt < 3; j++) {
var ia = (atom).getBondedAtomIndex(j);
if (ia == atomIndex) continue;
ndt += this.atoms[ia].getAtomicAndIsotopeNumber();
}
if (ndt > 3) return s;
}return null;
}return s + sa;
}, "~N,~N,JU.SimpleNode,~S,JU.BS");
Clazz.defineMethod(c$, "getRingCache", 
function(i0, i1, ht){
var key = JS.SmilesGenerator.getRingKey(i0, i1);
var o = ht.get(key);
var s = (o == null ? null : o[0]);
if (s == null) {
this.bsRingKeys.set(++this.nPairs);
this.nPairsMax = Math.max(this.nPairs, this.nPairsMax);
ht.put(key,  Clazz.newArray(-1, [s = this.getRingPointer(this.nPairs), Integer.$valueOf(i1), Integer.$valueOf(this.nPairs)]));
if (JU.Logger.debugging) JU.Logger.debug("adding for " + i0 + " ring key " + this.nPairs + ": " + key);
} else {
ht.remove(key);
var nPair = (o[2]).intValue();
this.bsRingKeys.clear(nPair);
if (this.bsRingKeys.nextSetBit(0) < 0 && (this.nPairsMax == 2 || this.nPairsMax == 99)) {
this.nPairsMax = this.nPairs = (this.nPairsMax == 99 ? 10 : 0);
}if (JU.Logger.debugging) JU.Logger.debug("using ring key " + key);
}return s;
}, "~N,~N,java.util.Map");
Clazz.defineMethod(c$, "getRingPointer", 
function(i){
return (i < 10 ? "" + i : i < 100 ? "%" + i : "%(" + i + ")");
}, "~N");
Clazz.defineMethod(c$, "dumpRingKeys", 
function(sb, ht){
JU.Logger.info(sb.toString() + "\n\n");
for (var key, $key = ht.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) JU.Logger.info("unmatched connection: " + key);

}, "JU.SB,java.util.Map");
c$.getRingKey = Clazz.defineMethod(c$, "getRingKey", 
function(i0, i1){
return Math.min(i0, i1) + "_" + Math.max(i0, i1);
}, "~N,~N");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
