Clazz.declarePackage("JS");
Clazz.load(["java.util.Hashtable"], "JS.SmilesParser", ["JU.Lst", "$.PT", "$.SB", "JS.InvalidSmilesException", "$.SmilesAtom", "$.SmilesBond", "$.SmilesMeasure", "$.SmilesSearch", "$.SmilesStereo", "JU.Elements", "$.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.connections = null;
this.htMeasures = null;
this.flags = 0;
this.isSmarts = false;
this.isBioSequence = false;
this.bioType = '\0';
this.braceCount = 0;
this.branchLevel = 0;
this.componentCount = 0;
this.componentParenCount = 0;
this.ignoreStereochemistry = false;
this.bondDirectionPaired = true;
this.isTarget = false;
Clazz.instantialize(this, arguments);}, JS, "SmilesParser", null);
Clazz.prepareFields (c$, function(){
this.connections =  new java.util.Hashtable();
this.htMeasures =  new java.util.Hashtable();
});
Clazz.makeConstructor(c$, 
function(isSmarts, isTarget){
this.isSmarts = isSmarts;
this.isTarget = isTarget;
}, "~B,~B");
c$.newSearch = Clazz.defineMethod(c$, "newSearch", 
function(pattern, isSmarts, isTarget){
return ( new JS.SmilesParser(isSmarts, isTarget)).parse(pattern);
}, "~S,~B,~B");
Clazz.defineMethod(c$, "parse", 
function(pattern){
if (pattern == null) throw  new JS.InvalidSmilesException("expression must not be null");
var search =  new JS.SmilesSearch();
if (this.isSmarts && !this.isTarget) search.pattern0 = pattern;
if (pattern.indexOf("$(select") >= 0) pattern = this.parseNested(search, pattern, "select");
var ret =  Clazz.newIntArray (1, 0);
pattern = JS.SmilesParser.extractFlags(pattern, ret);
this.flags = ret[0];
search.setFlags(this.flags);
if (pattern.indexOf("$") >= 0) pattern = this.parseVariables(pattern);
if (this.isSmarts && pattern.indexOf("[$") >= 0) pattern = this.parseVariableLength(pattern);
if (pattern.indexOf("||") < 0) return this.getSubsearch(search, pattern, this.flags);
var patterns = JU.PT.split(pattern, "||");
var toDo = "";
search.subSearches =  new Array(patterns.length);
for (var i = 0; i < patterns.length; i++) {
var key = "|" + patterns[i] + "|";
if (toDo.indexOf(key) < 0) {
search.subSearches[i] = this.getSubsearch(search, patterns[i], this.flags);
toDo += key;
}}
return search;
}, "~S");
Clazz.defineMethod(c$, "parseVariableLength", 
function(pattern){
var sout =  new JU.SB();
var len = pattern.length - 1;
var nParen = 0;
var haveInternalOr = false;
for (var i = 0; i < len; i++) {
switch ((pattern.charAt(i)).charCodeAt(0)) {
case 40:
nParen++;
break;
case 41:
nParen--;
break;
case 124:
if (nParen > 0) {
haveInternalOr = true;
if (pattern.charAt(i + 1) == '|') {
pattern = pattern.substring(0, i) + pattern.substring(i + 1);
len--;
}}break;
}
}
if (pattern.indexOf("||") >= 0) {
var patterns = JU.PT.split(pattern, "||");
for (var i = 0; i < patterns.length; i++) sout.append("||").append(this.parseVariableLength(patterns[i]));

} else {
var pt = -1;
var ret =  Clazz.newIntArray (1, 0);
var isOK = true;
var bracketed = null;
while ((pt = pattern.indexOf("[$", pt + 1)) >= 0) {
var pt0 = pt;
var min = -2147483648;
var max = -2147483648;
pt = JS.SmilesParser.getDigits(pattern, pt + 2, ret);
min = ret[0];
if (min != -2147483648) {
if (JS.SmilesParser.getChar(pattern, pt) == '-') {
pt = JS.SmilesParser.getDigits(pattern, pt + 1, ret);
max = ret[0];
}}if (JS.SmilesParser.getChar(pattern, pt) != '(') continue;
bracketed = JS.SmilesParser.getSubPattern(pattern, pt0, '[');
if (!bracketed.endsWith(")")) continue;
var pt1 = pt0 + bracketed.length + 2;
var repeat = JS.SmilesParser.getSubPattern(pattern, pt, '(');
var pt2 = pt;
bracketed = JS.SmilesParser.getSubPattern(pattern, pt, '[');
pt += 1 + repeat.length;
if (repeat.indexOf(':') >= 0 && repeat.indexOf('|') < 0) {
var parenCount = 0;
var n = repeat.length;
var ptColon = -1;
for (var i = 0; i < n; i++) {
switch ((repeat.charAt(i)).charCodeAt(0)) {
case 91:
case 40:
parenCount++;
break;
case 41:
case 93:
parenCount--;
break;
case 46:
if (ptColon >= 0 && parenCount == 0) n = i;
break;
case 58:
if (ptColon < 0 && parenCount == 0) ptColon = i;
break;
}
}
if (ptColon > 0) repeat = repeat.substring(0, ptColon) + "(" + repeat.substring(ptColon, n) + ")" + repeat.substring(n);
}if (min == -2147483648) {
var ptOr = repeat.indexOf("|");
if (ptOr >= 0) return this.parseVariableLength(pattern.substring(0, pt0) + "[$1" + pattern.substring(pt2, pt2 + ptOr + 1) + ")]" + pattern.substring(pt1) + "||" + pattern.substring(0, pt0) + "[$1(" + pattern.substring(pt2 + ptOr + 2) + pattern.substring(pt1));
continue;
}if (max == -2147483648) max = min;
if (repeat.indexOf("|") >= 0) repeat = "[$(" + repeat + ")]";
for (var i = min; i <= max; i++) {
var sb =  new JU.SB();
sb.append("||").append(pattern.substring(0, pt0));
for (var j = 0; j < i; j++) sb.append(repeat);

sb.append(pattern.substring(pt1));
sout.appendSB(sb);
}
}
if (!isOK) throw  new JS.InvalidSmilesException("bad variable expression: " + bracketed);
}return (haveInternalOr ? this.parseVariableLength(sout.substring(2)) : sout.length() < 2 ? pattern : sout.substring(2));
}, "~S");
Clazz.defineMethod(c$, "getSubsearch", 
function(parent, pattern, flags){
this.htMeasures =  new java.util.Hashtable();
var search =  new JS.SmilesSearch();
search.setTop(parent);
search.isSmarts = this.isSmarts;
search.pattern = pattern;
search.pattern0 = parent.pattern0;
search.setFlags(flags);
if (pattern.indexOf("$(") >= 0) pattern = this.parseNested(search, pattern, "");
this.parseSmiles(search, pattern, null, false);
if (this.braceCount != 0) throw  new JS.InvalidSmilesException("unmatched '{'");
if (!this.connections.isEmpty()) throw  new JS.InvalidSmilesException("Open connection");
search.set();
if (this.isSmarts) for (var i = search.ac; --i >= 0; ) this.checkNested(search, search.patternAtoms[i], flags);

 else if (!this.isBioSequence) search.elementCounts[1] = search.getMissingHydrogenCount();
if (!this.ignoreStereochemistry && !this.isTarget) this.fixChirality(search);
return search;
}, "JS.SmilesSearch,~S,~N");
Clazz.defineMethod(c$, "checkNested", 
function(search, atom, flags){
if (atom.iNested > 0) {
var o = search.getNested(atom.iNested);
if ((typeof(o)=='string')) {
var s = o;
if (s.startsWith("select")) return;
if (s.charAt(0) != '~' && atom.bioType != '\0') s = "~" + atom.bioType + "~" + s;
var nested = this.getSubsearch(search, s, flags);
if (nested.ac > 0 && nested.patternAtoms[0].selected) atom.selected = true;
search.setNested(atom.iNested, nested);
}}for (var i = 0; i < atom.nSubAtoms; i++) this.checkNested(search, atom.subAtoms[i], flags);

}, "JS.SmilesSearch,JS.SmilesAtom,~N");
Clazz.defineMethod(c$, "fixChirality", 
function(search){
for (var i = search.ac; --i >= 0; ) {
var sAtom = search.patternAtoms[i];
if (sAtom.stereo != null) sAtom.stereo.fixStereo(sAtom);
}
}, "JS.SmilesSearch");
Clazz.defineMethod(c$, "parseSmiles", 
function(search, pattern, currentAtom, isBranchAtom){
var ret =  Clazz.newIntArray (1, 0);
var pt = 0;
var ch;
var bond = null;
var wasMeasure = false;
var wasBranch = false;
loop : while (pattern != null && pattern.length != 0) {
var index = 0;
if (currentAtom == null) {
index = this.checkBioType(pattern, 0);
if (index == pattern.length) pattern += "*";
if (this.isBioSequence) search.needAromatic = search.top.needAromatic = false;
}ch = JS.SmilesParser.getChar(pattern, index);
var haveOpen = this.checkBrace(search, ch, '{');
if (haveOpen) ch = JS.SmilesParser.getChar(pattern, ++index);
if (ch == '(') {
var subString = JS.SmilesParser.getSubPattern(pattern, index, '(');
var isMeasure = (JS.SmilesParser.getChar(pattern, index + 1) == '.');
if (currentAtom == null) {
if (isMeasure || !this.isSmarts) throw  new JS.InvalidSmilesException("No previous atom for measure");
search.haveComponents = true;
do {
this.componentCount++;
this.componentParenCount++;
ch = JS.SmilesParser.getChar(pattern = pattern.substring(1), 0);
} while (ch == '(');
if (!haveOpen && (haveOpen = this.checkBrace(search, ch, '{')) == true) ch = JS.SmilesParser.getChar(pattern = pattern.substring(1), 0);
} else {
wasMeasure = wasBranch = false;
if (subString.startsWith(".")) {
this.parseMeasure(search, subString.substring(1), currentAtom);
wasMeasure = true;
} else if (subString.length == 0 && this.isBioSequence) {
currentAtom.notCrossLinked = true;
} else {
this.branchLevel++;
this.parseSmiles(search, subString, currentAtom, true);
wasBranch = true;
this.branchLevel--;
}index = subString.length + 2;
ch = JS.SmilesParser.getChar(pattern, index);
if (ch == '}' && this.checkBrace(search, ch, '}')) index++;
ch = '\0';
}}if (ch != '\0') {
pt = index;
out : while (ch != '\0') {
switch (JS.SmilesBond.isBondType(ch, this.isSmarts, this.isBioSequence)) {
case 1:
break;
case 0:
break out;
case -1:
if (!((JU.PT.isDigit(JS.SmilesParser.getChar(pattern, ++index)) && index++ > 0 ? JU.PT.isDigit(JS.SmilesParser.getChar(pattern, index++)) : true) && (ch = JS.SmilesParser.getChar(pattern, index)) == '-')) throw  new JS.InvalidSmilesException("malformed atropisomerism bond ^nn-  or ^^nn-");
continue;
}
ch = JS.SmilesParser.getChar(pattern, ++index);
}
ch = JS.SmilesParser.getChar(pattern, index);
if (ch == ')') {
switch ((ch = JS.SmilesParser.getChar(pattern, ++index)).charCodeAt(0)) {
case 0:
case 41:
case 46:
pattern = pattern.substring(index);
this.componentParenCount--;
if (this.componentParenCount >= 0) continue loop;
}
throw  new JS.InvalidSmilesException("invalid continuation after component grouping (SMARTS).(SMARTS)");
}bond = this.parseBond(search, null, pattern.substring(pt, index), null, currentAtom, false, isBranchAtom, index - pt, ret);
if (haveOpen && bond.order != -1) ch = JS.SmilesParser.getChar(pattern, index = pt);
if (this.checkBrace(search, ch, '{')) ch = JS.SmilesParser.getChar(pattern, ++index);
switch ((ch).charCodeAt(0)) {
case 126:
if (bond.order == 0) {
index = this.checkBioType(pattern, index);
if (index == pattern.length) pattern += "*";
}break;
case 40:
do {
this.componentCount++;
this.componentParenCount++;
ch = JS.SmilesParser.getChar(pattern, ++index);
} while (ch == '(');
break;
case 0:
if (bond.order == 0) return;
}
var isConnect = (JU.PT.isDigit(ch) || ch == '%');
var isAtom = (!isConnect && (ch == '_' || ch == '[' || ch == '*' || JU.PT.isLetter(ch)));
if (isConnect) {
if (wasMeasure) throw  new JS.InvalidSmilesException("connection number must immediately follow its connecting atom");
index = JS.SmilesParser.getRingNumber(pattern, index, ch, ret);
var ringNumber = ret[0];
this.parseConnection(search, ringNumber, currentAtom, bond);
bond = null;
} else if (isAtom) {
wasMeasure = wasBranch = false;
switch ((ch).charCodeAt(0)) {
case 91:
case 95:
var subPattern = JS.SmilesParser.getSubPattern(pattern, index, ch);
index += subPattern.length + (ch == '[' ? 2 : 0);
if (this.isBioSequence && ch == '[' && subPattern.indexOf(".") < 0 && subPattern.indexOf("_") < 0) subPattern += ".0";
currentAtom = this.parseAtom(search, null, subPattern, currentAtom, bond, ch == '[', false, isBranchAtom);
currentAtom.hasSubpattern = true;
if (bond.order != -1 && bond.order != 0) this.setBondAtom(bond, null, currentAtom, search);
bond = null;
break;
default:
var ch2 = (!this.isBioSequence && JU.PT.isUpperCase(ch) ? JS.SmilesParser.getChar(pattern, index + 1) : '\0');
if (ch != 'X' || ch2 != 'x') if (!JU.PT.isLowerCase(ch2) || JU.Elements.elementNumberFromSymbol(pattern.substring(index, index + 2), true) == 0) ch2 = '\0';
if (ch2 != '\0' && "NA CA BA PA SC AC Na Ca Ba Pa Sc Ac".indexOf(pattern.substring(index, index + 2)) >= 0) {
ch2 = '\0';
}var size = (JU.PT.isUpperCase(ch) && JU.PT.isLowerCase(ch2) ? 2 : 1);
currentAtom = this.parseAtom(search, null, pattern.substring(index, index + size), currentAtom, bond, false, false, isBranchAtom);
bond = null;
index += size;
}
} else {
throw  new JS.InvalidSmilesException("Unexpected character: " + JS.SmilesParser.getChar(pattern, index));
}ch = JS.SmilesParser.getChar(pattern, index);
if (ch == '}' && this.checkBrace(search, ch, '}')) index++;
}pattern = pattern.substring(index);
isBranchAtom = false;
}
}, "JS.SmilesSearch,~S,JS.SmilesAtom,~B");
Clazz.defineMethod(c$, "parseConnection", 
function(search, ringNum, currentAtom, bond){
var r = Integer.$valueOf(ringNum);
var bond0 = this.connections.get(r);
if (bond0 == null) {
this.connections.put(r, bond);
search.target.ringCount++;
return;
}this.connections.remove(r);
switch (bond.order) {
case -1:
bond.order = (bond0.order != -1 ? bond0.order : this.isSmarts || currentAtom.isAromatic && bond0.atom1.isAromatic ? 81 : 1);
break;
case 1025:
bond.order = 1041;
break;
case 1041:
bond.order = 1025;
break;
}
if (bond0.order != -1 && bond0.order != bond.order || currentAtom === bond0.atom1 || bond0.atom1.getBondTo(currentAtom) != null) throw  new JS.InvalidSmilesException("Bad connection type or atom");
bond0.set(bond);
currentAtom.bondCount--;
bond0.setAtom2(currentAtom, search);
}, "JS.SmilesSearch,~N,JS.SmilesAtom,JS.SmilesBond");
Clazz.defineMethod(c$, "setBondAtom", 
function(bond, a1, a2, search){
bond.set2a(a1, a2);
if (search != null && bond.order == 2 && bond.atom1 != null && bond.atom2 != null && bond.atom1.isAromatic && bond.atom2.isAromatic && ((this.flags & 512) == 0)) search.setFlags(this.flags = (this.flags | 512));
}, "JS.SmilesBond,JS.SmilesAtom,JS.SmilesAtom,JS.SmilesSearch");
c$.getRingNumber = Clazz.defineMethod(c$, "getRingNumber", 
function(pattern, index, ch, ret){
var ringNumber;
switch ((ch).charCodeAt(0)) {
case 37:
if (JS.SmilesParser.getChar(pattern, index + 1) == '(') {
var subPattern = JS.SmilesParser.getSubPattern(pattern, index + 1, '(');
JS.SmilesParser.getDigits(subPattern, 0, ret);
index += subPattern.length + 3;
if (ret[0] < 0) throw  new JS.InvalidSmilesException("Invalid number designation: " + subPattern);
} else {
if (index + 3 <= pattern.length) index = JS.SmilesParser.getDigits(pattern.substring(0, index + 3), index + 1, ret);
if (ret[0] < 10) throw  new JS.InvalidSmilesException("Two digits must follow the % sign");
}ringNumber = ret[0];
break;
default:
ringNumber = ch.charCodeAt(0) - 48;
index++;
}
ret[0] = ringNumber;
return index;
}, "~S,~N,~S,~A");
Clazz.defineMethod(c$, "checkBioType", 
function(pattern, index){
this.isBioSequence = (pattern.charAt(index) == '~');
if (this.isBioSequence) {
index++;
this.bioType = '*';
var ch = JS.SmilesParser.getChar(pattern, 2);
if (ch == '~' && ((ch = pattern.charAt(1)) == '*' || JU.PT.isLowerCase(ch))) {
this.bioType = ch;
index = 3;
}}return index;
}, "~S,~N");
Clazz.defineMethod(c$, "parseMeasure", 
function(search, strMeasure, currentAtom){
var pt = strMeasure.indexOf(":");
var id = (pt < 0 ? strMeasure : strMeasure.substring(0, pt));
while (pt != 0) {
var len = id.length;
if (len == 1) id += "0";
var m = this.htMeasures.get(id);
if ((m == null) == (pt < 0) || len == 0) break;
try {
if (pt > 0) {
var type = ("__dat".indexOf(id.charAt(0)));
if (type < 2) break;
var ret =  Clazz.newIntArray (1, 0);
JS.SmilesParser.getDigits(id, 1, ret);
var index = ret[0];
strMeasure = strMeasure.substring(pt + 1);
var isNot = strMeasure.startsWith("!");
if (isNot) strMeasure = strMeasure.substring(1);
var isNegative = (strMeasure.startsWith("-"));
if (isNegative) strMeasure = strMeasure.substring(1);
strMeasure = JU.PT.rep(strMeasure, "-", ",");
strMeasure = JU.PT.rep(strMeasure, ",,", ",-");
if (isNegative) strMeasure = "-" + strMeasure;
var tokens = JU.PT.split(strMeasure, ",");
if (tokens.length % 2 == 1 || isNot && tokens.length != 2) break;
var vals =  Clazz.newFloatArray (tokens.length, 0);
var i = tokens.length;
for (; --i >= 0; ) if (Float.isNaN(vals[i] = Float.parseFloat(tokens[i]))) break;

if (i >= 0) break;
m =  new JS.SmilesMeasure(search, index, type, isNot, vals);
search.measures.addLast(m);
if (index > 0) this.htMeasures.put(id, m);
 else if (index == 0 && JU.Logger.debugging) JU.Logger.debug("measure created: " + m);
} else {
if (!m.addPoint(currentAtom.index)) break;
if (m.nPoints == m.type) {
this.htMeasures.remove(id);
if (JU.Logger.debugging) JU.Logger.debug("measure created: " + m);
}return;
}if (!m.addPoint(currentAtom.index)) break;
} catch (e) {
if (Clazz.exceptionOf(e,"NumberFormatException")){
break;
} else {
throw e;
}
}
return;
}
throw  new JS.InvalidSmilesException("invalid measure: " + strMeasure);
}, "JS.SmilesSearch,~S,JS.SmilesAtom");
Clazz.defineMethod(c$, "checkBrace", 
function(search, ch, type){
switch ((ch).charCodeAt(0)) {
case 123:
if (ch != type) break;
this.braceCount++;
search.top.haveSelected = true;
return true;
case 125:
if (ch != type) break;
if (this.braceCount > 0) {
this.braceCount--;
return true;
}break;
default:
return false;
}
throw  new JS.InvalidSmilesException("Unmatched '}'");
}, "JS.SmilesSearch,~S,~S");
Clazz.defineMethod(c$, "parseNested", 
function(search, pattern, prefix){
var index;
prefix = "$(" + prefix;
while ((index = pattern.lastIndexOf(prefix)) >= 0) {
var s = JS.SmilesParser.getSubPattern(pattern, index + 1, '(');
var pt = index + s.length + 3;
var ext = pattern.substring(pt);
pattern = pattern.substring(0, index);
var op = "";
if (pattern.endsWith("]")) throw  new JS.InvalidSmilesException("$(...) must be enclosed in brackets: " + pattern + "$(" + s + ")");
if (index > 1 && prefix.length == 2 && ((pt = pattern.length) > 1 && ",;&![".indexOf(pattern.substring(pt - 1)) < 0)) op = "&";
if (ext.length > 1 && ",;&!)]".indexOf(ext.charAt(0)) < 0) ext = "&" + ext;
pattern = pattern + op + "_" + search.top.addNested(s) + "_" + ext;
}
return pattern;
}, "JS.SmilesSearch,~S,~S");
Clazz.defineMethod(c$, "parseVariables", 
function(pattern){
var keys =  new JU.Lst();
var values =  new JU.Lst();
var index;
var ipt = 0;
var iptLast = -1;
if (JU.Logger.debugging) JU.Logger.info(pattern);
while ((index = pattern.indexOf("$", ipt)) >= 0) {
if (JS.SmilesParser.getChar(pattern, index + 1) == '(') break;
ipt = JS.SmilesParser.skipTo(pattern, index, '=');
if (ipt <= index + 1 || JS.SmilesParser.getChar(pattern, ipt + 1) != '\"') break;
var key = pattern.substring(index, ipt);
if (key.lastIndexOf('$') > 0 || key.indexOf(']') > 0) throw  new JS.InvalidSmilesException("Invalid variable name: " + key);
var s = JS.SmilesParser.getSubPattern(pattern, ipt + 1, '\"');
keys.addLast("[" + key + "]");
values.addLast(s);
ipt += s.length + 2;
ipt = JS.SmilesParser.skipTo(pattern, ipt, ';');
iptLast = ++ipt;
}
if (iptLast < 0) return pattern;
pattern = pattern.substring(iptLast);
for (var i = keys.size(); --i >= 0; ) {
var k = keys.get(i);
var v = values.get(i);
if (!v.equals(k)) pattern = JU.PT.rep(pattern, k, v);
}
if (JU.Logger.debugging) JU.Logger.info(pattern);
return pattern;
}, "~S");
Clazz.defineMethod(c$, "parseAtom", 
function(search, atomSet, pattern, atom, bond, isBracketed, isAND, isBranchAtom){
if (pattern == null || pattern.length == 0) throw  new JS.InvalidSmilesException("Empty atom definition");
var newAtom =  new JS.SmilesAtom();
if (this.componentParenCount > 0) newAtom.component = this.componentCount;
if (atomSet == null) search.appendAtom(newAtom);
var isNewAtom = true;
if (!this.checkLogic(search, pattern, newAtom, null, atom, isAND, isBranchAtom, null)) {
var ret =  Clazz.newIntArray (1, 0);
if (this.isBioSequence && pattern.length == 1) pattern += ".0";
var ch = pattern.charAt(0);
var index = 0;
var isNot = false;
if (this.isSmarts && ch == '!') {
ch = JS.SmilesParser.getChar(pattern, ++index);
if (ch == '\0') throw  new JS.InvalidSmilesException("invalid '!'");
newAtom.not = isNot = true;
}var biopt = (pattern.indexOf("@PH") >= 0 ? -1 : pattern.indexOf('.'));
if (biopt >= 0) {
newAtom.isBioResidue = true;
var resOrName = pattern.substring(index, biopt);
pattern = pattern.substring(biopt + 1).toUpperCase();
var len = resOrName.length;
if ((biopt = resOrName.indexOf("^")) >= 0) {
if (biopt == len - 2) {
ch = resOrName.charAt(len - 1);
if (ch != '*') newAtom.insCode = ch;
}resOrName = resOrName.substring(0, biopt);
}if ((biopt = resOrName.indexOf("#")) >= 0) {
JS.SmilesParser.getDigits(resOrName, biopt + 1, ret);
newAtom.residueNumber = ret[0];
resOrName = resOrName.substring(0, biopt);
}if (resOrName.length == 0) resOrName = "*";
if (resOrName.length > 1) newAtom.residueName = resOrName.toUpperCase();
 else if (!resOrName.equals("*")) newAtom.residueChar = resOrName;
resOrName = pattern;
if ((biopt = resOrName.indexOf("#")) >= 0) {
JS.SmilesParser.getDigits(resOrName, biopt + 1, ret);
newAtom.elementNumber = ret[0];
resOrName = resOrName.substring(0, biopt);
}if (resOrName.length == 0) resOrName = "*";
 else if (resOrName.equals("0")) resOrName = "\0";
if (resOrName.equals("*")) newAtom.isBioAtomWild = true;
 else newAtom.setAtomName(resOrName);
ch = '\0';
}newAtom.setBioAtom(this.bioType);
var hydrogenCount = -2147483648;
while (ch != '\0' && isNewAtom) {
newAtom.setAtomName(this.isBioSequence ? "\0" : "");
if (JU.PT.isDigit(ch)) {
index = JS.SmilesParser.getDigits(pattern, index, ret);
var mass = ret[0];
if (mass == -2147483648) throw  new JS.InvalidSmilesException("Non numeric atomic mass");
if (JS.SmilesParser.getChar(pattern, index) == '?') {
index++;
mass = -mass;
}if (newAtom.elementDefined) throw  new JS.InvalidSmilesException("atom mass must precede atom symbol or be separated from it with \";\"");
newAtom.setAtomicMass(mass);
} else {
switch ((ch).charCodeAt(0)) {
case 34:
var type = JU.PT.getQuotedStringAt(pattern, index);
index += type.length + 2;
newAtom.atomType = type;
break;
case 95:
index = JS.SmilesParser.getDigits(pattern, index + 1, ret) + 1;
if (ret[0] == -2147483648) throw  new JS.InvalidSmilesException("Invalid SEARCH primitive: " + pattern.substring(index));
newAtom.iNested = ret[0];
if (!isBracketed) throw  new JS.InvalidSmilesException("nesting must appear in [...]: $(" + search.getNested(ret[0]) + ")");
if (this.isBioSequence && index != pattern.length) throw  new JS.InvalidSmilesException("invalid characters: " + pattern.substring(index));
break;
case 61:
index = JS.SmilesParser.getDigits(pattern, index + 1, ret);
newAtom.jmolIndex = ret[0];
break;
case 35:
var isAtomNo = (pattern.charAt(index + 1) == '-');
index = JS.SmilesParser.getDigits(pattern, index + (isAtomNo ? 2 : 1), ret);
if (isAtomNo) newAtom.atomNumber = ret[0];
 else newAtom.elementNumber = ret[0];
break;
case 45:
case 43:
index = this.checkCharge(pattern, index, newAtom);
break;
case 64:
if (search.stereo == null) search.stereo = JS.SmilesStereo.newStereo(search);
index = JS.SmilesStereo.checkChirality(search, pattern, index, search.patternAtoms[newAtom.index]);
break;
case 58:
index = JS.SmilesParser.getDigits(pattern, ++index, ret);
if (ret[0] == -2147483648) throw  new JS.InvalidSmilesException("Invalid atom class");
newAtom.atomClass = ret[0];
break;
default:
var nextChar = JS.SmilesParser.getChar(pattern, index + 1);
var len = index + (JU.PT.isLowerCase(nextChar) && (!isBracketed || !JU.PT.isDigit(JS.SmilesParser.getChar(pattern, index + 2))) ? 2 : 1);
var sym2 = pattern.substring(index + 1, len);
var symbol = Character.toUpperCase(ch) + sym2;
var mustBeSymbol = true;
var checkForPrimitive = (isBracketed && JU.PT.isLetter(ch));
if (checkForPrimitive) {
if (!isNot && (isAND ? atomSet : newAtom).hasSymbol) {
mustBeSymbol = false;
} else if (ch == 'H') {
mustBeSymbol = (pattern.length == 1 || !JU.PT.isDigit(nextChar));
} else if (JU.PT.isDigit(nextChar)) {
mustBeSymbol = false;
} else if (!symbol.equals("A") && !symbol.equals("Xx")) {
mustBeSymbol = ((ch == 'h' ? len == 2 : true) && JU.Elements.elementNumberFromSymbol(symbol, true) > 0);
if (!mustBeSymbol && len == 2) {
sym2 = "";
symbol = symbol.substring(0, 1);
mustBeSymbol = (JU.Elements.elementNumberFromSymbol(symbol, true) > 0);
}}}if (mustBeSymbol) {
if (!isBracketed && !this.isSmarts && !this.isBioSequence && !JS.SmilesAtom.allowSmilesUnbracketed(symbol) || !newAtom.setSymbol(symbol = ch + sym2)) throw  new JS.InvalidSmilesException("Invalid atom symbol: " + symbol);
if (isAND) atomSet.hasSymbol = true;
index += symbol.length;
} else {
index = JS.SmilesParser.getDigits(pattern, index + 1, ret);
var val = ret[0];
switch ((ch).charCodeAt(0)) {
default:
throw  new JS.InvalidSmilesException("Invalid SEARCH primitive: " + pattern.substring(index));
case 68:
newAtom.setDegree(val == -2147483648 ? 1 : val);
break;
case 100:
newAtom.setNonhydrogenDegree(val == -2147483648 ? 1 : val);
break;
case 72:
hydrogenCount = (val == -2147483648 ? 1 : val);
break;
case 104:
newAtom.setImplicitHydrogenCount(val == -2147483648 ? -1 : val);
break;
case 82:
if (val == -2147483648) val = -1;
newAtom.setRingMembership(val);
search.top.needRingData = true;
break;
case 114:
if (val == -2147483648) {
val = -1;
newAtom.setRingMembership(val);
} else {
newAtom.setRingSize(val);
switch (val) {
case 500:
val = 5;
break;
case 600:
val = 6;
break;
}
if (val > search.ringDataMax) search.ringDataMax = val;
}search.top.needRingData = true;
break;
case 118:
newAtom.setValence(val == -2147483648 ? 1 : val);
break;
case 88:
newAtom.setConnectivity(val == -2147483648 ? 1 : val);
break;
case 120:
newAtom.setRingConnectivity(val == -2147483648 ? -1 : val);
search.top.needRingData = true;
break;
}
}}
}ch = JS.SmilesParser.getChar(pattern, index);
if (isNot && ch != '\0') throw  new JS.InvalidSmilesException("'!' may only involve one primitive.");
}
if (hydrogenCount == -2147483648 && isBracketed) hydrogenCount = -2147483647;
newAtom.setExplicitHydrogenCount(hydrogenCount);
search.patternAtoms[newAtom.index].setExplicitHydrogenCount(hydrogenCount);
}if (this.braceCount > 0) newAtom.selected = true;
if (isNewAtom && atomSet != null) atomSet.addSubAtom(newAtom, isAND);
if (atom != null && bond.order == 0) {
newAtom.notBondedIndex = atom.index;
}if (atom != null && bond.order != 0) {
if (bond.order == -1) bond.order = (this.isBioSequence && isBranchAtom ? 112 : this.isSmarts || atom.isAromatic && newAtom.isAromatic ? 81 : 1);
if (!isBracketed) this.setBondAtom(bond, null, newAtom, search);
if (this.branchLevel == 0 && (bond.getBondType() == 17 || bond.order == 112)) this.branchLevel++;
}if (this.branchLevel == 0) search.lastChainAtom = newAtom;
return newAtom;
}, "JS.SmilesSearch,JS.SmilesAtom,~S,JS.SmilesAtom,JS.SmilesBond,~B,~B,~B");
Clazz.defineMethod(c$, "checkCharge", 
function(pattern, index, newAtom){
var len = pattern.length;
var ch = pattern.charAt(index);
var count = 1;
++index;
if (index < len) {
var nextChar = pattern.charAt(index);
if (JU.PT.isDigit(nextChar)) {
var ret =  Clazz.newIntArray (1, 0);
index = JS.SmilesParser.getDigits(pattern, index, ret);
count = ret[0];
if (count == -2147483648) throw  new JS.InvalidSmilesException("Non numeric charge");
} else {
while (index < len && pattern.charAt(index) == ch) {
index++;
count++;
}
}}newAtom.setCharge(ch == '+' ? count : -count);
return index;
}, "~S,~N,JS.SmilesAtom");
Clazz.defineMethod(c$, "parseBond", 
function(search, bondSet, pattern, bond, currentAtom, isAND, isBranchAtom, len, ret){
var ch;
if (len > 0) {
switch ((ch = pattern.charAt(0)).charCodeAt(0)) {
case 62:
if (!pattern.equals(">>")) {
len = -1;
break;
}case 46:
if (bond == null && bondSet == null) {
this.isBioSequence = (JS.SmilesParser.getChar(pattern, 1) == '~');
return  new JS.SmilesBond(null, null, 0, false);
}len = -1;
break;
case 43:
if (bondSet != null) len = -1;
break;
}
} else {
ch = '\0';
}var newBond = (bondSet == null ? (bond == null ?  new JS.SmilesBond(currentAtom, null, (this.isBioSequence && currentAtom != null ? (isBranchAtom ? 112 : 96) : -1), false) : bond) : isAND ? bondSet.addPrimitive() : bondSet.addBondOr());
if (len > 0 && !this.checkLogic(search, pattern, null, newBond, currentAtom, isAND, false, ret)) {
var isBondNot = (ch == '!');
if (isBondNot) {
ch = JS.SmilesParser.getChar(pattern, 1);
if (ch == '\0' || ch == '!') throw  new JS.InvalidSmilesException("invalid '!'");
}var bondType = JS.SmilesBond.getBondTypeFromCode(ch);
if (bondType == 65) search.top.needRingMemberships = true;
if (currentAtom == null && bondType != 0) throw  new JS.InvalidSmilesException("Bond without a previous atom");
switch (bondType) {
case 65537:
case 65538:
if ((len = pattern.length) < (isBondNot ? 3 : 2) || pattern.charAt(len - 1) != '-') {
len = 0;
} else {
if (len == (isBondNot ? 3 : 2)) {
newBond.setAtropType(22);
} else {
JS.SmilesParser.getDigits(pattern, (isBondNot ? 2 : 1), ret);
newBond.setAtropType(ret[0]);
}}search.haveBondStereochemistry = true;
break;
case 1025:
case 1041:
this.bondDirectionPaired = !this.bondDirectionPaired;
search.haveBondStereochemistry = true;
break;
case 17:
break;
case 2:
search.top.nDouble++;
case 1:
if (currentAtom.isAromatic) search.top.needRingData = true;
break;
}
newBond.set2(bondType, isBondNot);
if (this.isBioSequence && bondSet != null) bondSet.set2(bondType, isBondNot);
}if (len == -1) throw  new JS.InvalidSmilesException("invalid bond:" + ch);
return newBond;
}, "JS.SmilesSearch,JS.SmilesBond,~S,JS.SmilesBond,JS.SmilesAtom,~B,~B,~N,~A");
Clazz.defineMethod(c$, "checkLogic", 
function(search, pattern, atom, bond, currentAtom, isAND, isBranchAtom, ret){
var pt = pattern.lastIndexOf("!");
if (atom != null) atom.pattern = pattern;
while (pt > 0) {
if (",;&!(".indexOf(pattern.charAt(pt - 1)) < 0) pattern = pattern.substring(0, pt) + "&" + pattern.substring(pt);
pt = pattern.lastIndexOf("!", pt - 1);
}
pt = pattern.indexOf(',');
var len = pattern.length;
var and = "&";
out : while (true) {
var haveOr = (pt > 0);
if (haveOr && !this.isSmarts || pt == 0) break;
pt = pattern.indexOf(';');
if (pt >= 0) {
if (!this.isSmarts || pt == 0) break;
if (haveOr) {
and = ";";
haveOr = false;
} else {
pattern = pattern.$replace(';', '&');
}}var index = 0;
if (haveOr) {
pattern += ",";
while ((pt = pattern.indexOf(',', index)) > 0 && pt <= len) {
var s = pattern.substring(index, pt);
if (s.length == 0) throw  new JS.InvalidSmilesException("missing " + (bond == null ? "atom" : "bond") + " token");
if (bond == null) this.parseAtom(search, atom, s, null, null, true, false, isBranchAtom);
 else this.parseBond(search, bond, s, null, currentAtom, false, false, s.length, ret);
index = pt + 1;
}
} else if ((pt = pattern.indexOf(and)) >= 0 || bond != null && len > 1 && !isAND) {
if (pt == 0 || bond == null && !this.isSmarts) break;
if (bond != null && pt < 0) {
if (len > 1) {
var sNew =  new JU.SB();
for (var i = 0; i < len; ) {
var ch = pattern.charAt(i++);
sNew.appendC(ch);
switch ((ch).charCodeAt(0)) {
case 33:
if (!this.isSmarts) break out;
continue;
case 94:
case 96:
while ((ch = pattern.charAt(i++)) != '-' && ch != '\0') {
sNew.appendC(ch);
}
sNew.appendC('-');
break;
}
if (i < len) {
if (!this.isSmarts) break out;
sNew.append(and);
}}
pattern = sNew.toString();
len = pattern.length;
}}pattern += and;
while ((pt = pattern.indexOf(and, index)) > 0 && pt <= len) {
var s = pattern.substring(index, pt);
if (bond == null) this.parseAtom(search, atom, s, null, null, true, true, isBranchAtom);
 else this.parseBond(search, this.isSmarts ? bond : null, s, this.isSmarts ? null : bond, currentAtom, true, false, s.length, ret);
index = pt + 1;
}
} else {
return false;
}return true;
}
var ch = pattern.charAt(pt);
throw  new JS.InvalidSmilesException((this.isSmarts ? "invalid placement for '" + ch + "'" : "[" + ch + "] notation only valid with SMARTS, not SMILES,") + " in " + pattern);
}, "JS.SmilesSearch,~S,JS.SmilesAtom,JS.SmilesBond,JS.SmilesAtom,~B,~B,~A");
c$.getSubPattern = Clazz.defineMethod(c$, "getSubPattern", 
function(pattern, index, ch){
var ch2;
var margin = 1;
switch ((ch).charCodeAt(0)) {
case 91:
ch2 = ']';
break;
case 34:
case 37:
case 47:
ch2 = ch;
break;
case 40:
ch2 = ')';
break;
default:
ch2 = ch;
margin = 0;
}
var len = pattern.length;
var pCount = 1;
for (var pt = index + 1; pt < len; pt++) {
var ch1 = pattern.charAt(pt);
if (ch1 == ch2) {
pCount--;
if (pCount == 0) return pattern.substring(index + margin, pt + 1 - margin);
} else if (ch1 == ch) {
pCount++;
}}
throw  new JS.InvalidSmilesException("Unmatched " + ch);
}, "~S,~N,~S");
c$.getChar = Clazz.defineMethod(c$, "getChar", 
function(pattern, i){
return (i < pattern.length ? pattern.charAt(i) : '\0');
}, "~S,~N");
c$.getDigits = Clazz.defineMethod(c$, "getDigits", 
function(pattern, index, ret){
var pt = index;
var len = pattern.length;
while (pt < len && JU.PT.isDigit(pattern.charAt(pt))) pt++;

if (pt > index) try {
ret[0] = Integer.parseInt(pattern.substring(index, pt));
return pt;
} catch (e) {
if (Clazz.exceptionOf(e,"NumberFormatException")){
} else {
throw e;
}
}
ret[0] = -2147483648;
return pt;
}, "~S,~N,~A");
c$.skipTo = Clazz.defineMethod(c$, "skipTo", 
function(pattern, index, ch0){
var pt = index;
var ch;
while ((ch = JS.SmilesParser.getChar(pattern, ++pt)) != ch0 && ch != '\0') {
}
return (ch == '\0' ? -1 : pt);
}, "~S,~N,~S");
c$.cleanPattern = Clazz.defineMethod(c$, "cleanPattern", 
function(pattern){
pattern = JU.PT.replaceAllCharacters(pattern, " \t\n\r", "");
pattern = JU.PT.rep(pattern, "^^", "`");
var i = 0;
var i2 = 0;
while ((i = pattern.indexOf("//*")) >= 0 && (i2 = pattern.indexOf("*//")) >= i) pattern = pattern.substring(0, i) + pattern.substring(i2 + 3);

pattern = JU.PT.rep(pattern, "//", "");
return pattern;
}, "~S");
c$.extractFlags = Clazz.defineMethod(c$, "extractFlags", 
function(pattern, ret){
pattern = JS.SmilesParser.cleanPattern(pattern);
var flags = 0;
while (pattern.startsWith("/")) {
var strFlags = JS.SmilesParser.getSubPattern(pattern, 0, '/').toUpperCase();
pattern = pattern.substring(strFlags.length + 2);
flags = JS.SmilesSearch.addFlags(flags, strFlags);
}
ret[0] = flags;
return pattern;
}, "~S,~A");
c$.getFlags = Clazz.defineMethod(c$, "getFlags", 
function(pattern){
var ret =  Clazz.newIntArray (1, 0);
JS.SmilesParser.extractFlags(pattern, ret);
return ret[0];
}, "~S");
});
;//5.0.1-v7 Mon Jul 21 08:59:16 CDT 2025
