Clazz.declarePackage ("JS");
Clazz.load (null, "JS.ScriptTokenParser", ["java.lang.Boolean", "$.Float", "JU.Lst", "$.P3", "$.PT", "J.i18n.GT", "JS.ScriptParam", "$.T", "JU.Logger", "$.SimpleUnitCell"], function () {
c$ = Clazz.decorateAsClass (function () {
this.vwr = null;
this.script = null;
this.isStateScript = false;
this.lineCurrent = 0;
this.iCommand = 0;
this.ichCurrentCommand = 0;
this.ichComment = 0;
this.ichEnd = 0;
this.ichToken = 0;
this.theToken = null;
this.lastFlowCommand = null;
this.tokenCommand = null;
this.lastToken = null;
this.tokenAndEquals = null;
this.theTok = 0;
this.nTokens = 0;
this.tokCommand = 0;
this.ptNewSetModifier = 0;
this.isNewSet = false;
this.haveMacro = false;
this.logMessages = true;
this.atokenInfix = null;
this.itokenInfix = 0;
this.isSetBrace = false;
this.isMathExpressionCommand = false;
this.isSetOrDefine = false;
this.ltokenPostfix = null;
this.isEmbeddedExpression = false;
this.isCommaAsOrAllowed = false;
this.theValue = null;
this.htUserFunctions = null;
this.haveString = false;
this.residueSpecCodeGenerated = false;
this.errorMessage = null;
this.errorMessageUntranslated = null;
this.errorLine = null;
this.errorType = null;
Clazz.instantialize (this, arguments);
}, JS, "ScriptTokenParser");
Clazz.defineMethod (c$, "compileExpressions", 
function () {
var isScriptExpression = ((this.tokCommand == 134222850 || this.tokCommand == 4124) && this.tokAt (2) == 268435472);
this.isEmbeddedExpression = (isScriptExpression || (this.tokCommand != 0 && (this.tokCommand != 134320141 && this.tokCommand != 102436 && this.tokCommand != 364558 && this.tokCommand != 102412 || this.tokenCommand.intValue != 2147483647) && this.tokCommand != 102409 && !JS.T.tokAttr (this.tokCommand, 12288) && (this.nTokens > 2 || !JS.T.tokAttr (this.tokCommand, 20480))));
this.isMathExpressionCommand = (this.tokCommand == 1073741824 || isScriptExpression || JS.T.tokAttr (this.tokCommand, 36864));
var checkExpression = this.isEmbeddedExpression || (JS.T.tokAttr (this.tokCommand, 12288));
if (this.tokAt (1) == 1073742330 && JS.T.tokAttr (this.tokCommand, 12288)) checkExpression = false;
if (checkExpression && !this.compileExpression ()) return false;
var size = this.atokenInfix.length;
var nDefined = 0;
for (var i = 1; i < size; i++) {
if (this.tokAt (i) == 12290) nDefined++;
}
size -= nDefined;
if (this.isNewSet) {
if (size == 1) {
this.atokenInfix[0] = JS.T.tv (134320141, 0, this.atokenInfix[0].value);
this.isNewSet = false;
}}if ((this.isNewSet || this.isSetBrace) && this.ptNewSetModifier != 2147483647 && size < this.ptNewSetModifier + 2) {
if (!this.isNewSet || !this.haveMacro) return this.commandExpected ();
this.htUserFunctions.put (this.atokenInfix[0].value, Boolean.TRUE);
}return (size == 1 || !JS.T.tokAttr (this.tokCommand, 262144) ? true : this.error (0));
});
Clazz.defineMethod (c$, "compileExpression", 
function () {
var firstToken = (this.isSetOrDefine && !this.isSetBrace ? 2 : 1);
this.ltokenPostfix =  new JU.Lst ();
this.itokenInfix = 0;
var tokenBegin = null;
var tok = this.tokAt (1);
switch (this.tokCommand) {
case 12290:
var i = (this.tokAt (1) == 12290 ? 2 : 1);
if (this.tokAt (i) == 2 && this.tokAt (i + 1) == 1073742336 && this.tokAt (i + 3) == 268435860) {
this.tokCommand = 36867;
this.isSetBrace = true;
this.ptNewSetModifier = i + 3;
this.isMathExpressionCommand = true;
this.isEmbeddedExpression = true;
this.addTokenToPostfixToken (JS.T.tokenSetProperty);
this.addTokenToPostfixToken (JS.T.tokenExpressionBegin);
for (var j = 0; j++ <= i; ) this.addNextToken ();

this.addTokenToPostfixToken (JS.T.tokenExpressionEnd);
firstToken = 0;
}break;
case 12295:
if (tok == 1677721602) firstToken = 2;
break;
case 1275082245:
switch (tok) {
case 1073742335:
case 1073742334:
tok = this.tokAt (++firstToken);
break;
}
case 12294:
case 1610625028:
switch (tok) {
case 1275069441:
case 1073742119:
tok = this.tokAt (++firstToken);
break;
}
if (tok == 1086324742 && !JS.T.tokAttr (this.tokAt (firstToken + 1), 268435456)) firstToken++;
}
for (var i = 0; i < firstToken && this.addNextToken (); i++) {
}
while (this.moreTokens ()) {
if (this.isEmbeddedExpression) {
while (!this.isExpressionNext ()) {
if (this.tokPeekIs (1073741824) && !(this.tokCommand == 134222849 && this.itokenInfix == 1)) {
var name = this.atokenInfix[this.itokenInfix].value;
var t = JS.T.getTokenFromName (name);
if (t != null) if (!this.isMathExpressionCommand && this.lastToken.tok != 12290 || (this.lastToken.tok == 1073742336 || this.tokAt (this.itokenInfix + 1) == 268435472) && !this.isUserFunction (name)) {
this.atokenInfix[this.itokenInfix] = t;
}}if (!this.addNextToken ()) break;
}
if (!this.moreTokens ()) break;
}if (this.lastToken.tok == 12290) {
if (!this.clauseDefine (true, false)) return false;
continue;
}if (!this.isMathExpressionCommand) this.addTokenToPostfixToken (tokenBegin = JS.T.o (1073742325, "implicitExpressionBegin"));
if (!this.clauseOr (this.isCommaAsOrAllowed || !this.isMathExpressionCommand && this.tokPeekIs (268435472))) return false;
if (!this.isMathExpressionCommand && !(this.isEmbeddedExpression && this.lastToken === JS.T.tokenCoordinateEnd)) {
this.addTokenToPostfixToken (JS.T.tokenExpressionEnd);
}if (this.moreTokens ()) {
if (this.tokCommand != 1275082245 && this.tokCommand != 12291 && !this.isEmbeddedExpression) return this.error (5);
if (this.tokCommand == 1275082245) {
tokenBegin.intValue = 0;
this.tokCommand = 0;
this.isEmbeddedExpression = true;
this.isMathExpressionCommand = true;
this.isCommaAsOrAllowed = false;
}}}
this.atokenInfix = this.ltokenPostfix.toArray ( new Array (this.ltokenPostfix.size ()));
return true;
});
Clazz.defineMethod (c$, "isUserFunction", 
function (name) {
name = name.toLowerCase ();
return (!this.isStateScript && (this.vwr.isFunction (name) || this.htUserFunctions.containsKey (name)));
}, "~S");
Clazz.defineMethod (c$, "isExpressionNext", 
 function () {
return this.tokPeekIs (1073742332) && !(this.tokAt (this.itokenInfix + 1) == 4 && this.tokAt (this.itokenInfix + 2) == 268435490) || !this.isMathExpressionCommand && this.tokPeekIs (268435472);
});
c$.tokenAttr = Clazz.defineMethod (c$, "tokenAttr", 
function (token, tok) {
return token != null && JS.T.tokAttr (token.tok, tok);
}, "JS.T,~N");
Clazz.defineMethod (c$, "moreTokens", 
 function () {
return (this.itokenInfix < this.atokenInfix.length);
});
Clazz.defineMethod (c$, "tokAt", 
function (i) {
return (i < this.atokenInfix.length ? this.atokenInfix[i].tok : 0);
}, "~N");
Clazz.defineMethod (c$, "tokPeek", 
 function () {
return (this.itokenInfix >= this.atokenInfix.length ? 0 : this.atokenInfix[this.itokenInfix].tok);
});
Clazz.defineMethod (c$, "tokPeekIs", 
 function (tok) {
return (this.tokAt (this.itokenInfix) == tok);
}, "~N");
Clazz.defineMethod (c$, "intPeek", 
 function () {
return (this.itokenInfix >= this.atokenInfix.length ? 2147483647 : this.atokenInfix[this.itokenInfix].intValue);
});
Clazz.defineMethod (c$, "valuePeek", 
 function () {
return (this.moreTokens () ? this.atokenInfix[this.itokenInfix].value : "");
});
Clazz.defineMethod (c$, "tokenNext", 
 function () {
return (this.itokenInfix >= this.atokenInfix.length ? null : this.atokenInfix[this.itokenInfix++]);
});
Clazz.defineMethod (c$, "tokenNextTok", 
 function (tok) {
var token = this.tokenNext ();
return (token != null && token.tok == tok);
}, "~N");
Clazz.defineMethod (c$, "returnToken", 
 function () {
this.itokenInfix--;
return false;
});
Clazz.defineMethod (c$, "getToken", 
 function () {
this.theValue = ((this.theToken = this.tokenNext ()) == null ? null : this.theToken.value);
return this.theToken;
});
Clazz.defineMethod (c$, "getNumericalToken", 
 function () {
return (this.getToken () != null && (this.theToken.tok == 2 || this.theToken.tok == 3));
});
Clazz.defineMethod (c$, "floatValue", 
 function () {
switch (this.theToken.tok) {
case 2:
return this.theToken.intValue;
case 3:
return (this.theValue).floatValue ();
}
return 0;
});
Clazz.defineMethod (c$, "addTokenToPostfix", 
 function (tok, value) {
return this.addTokenToPostfixToken (JS.T.o (tok, value));
}, "~N,~O");
Clazz.defineMethod (c$, "addTokenToPostfixInt", 
 function (tok, intValue, value) {
return this.addTokenToPostfixToken (JS.T.tv (tok, intValue, value));
}, "~N,~N,~O");
Clazz.defineMethod (c$, "addTokenToPostfixToken", 
 function (token) {
if (token == null) return false;
if (this.logMessages) JU.Logger.debug ("addTokenToPostfix" + token);
if (token.tok == 268435520 && (this.lastToken.tok == 1073742336 || this.lastToken.tok == 1073742337)) {
var ipt = this.ltokenPostfix.size () - 1;
this.ltokenPostfix.removeItemAt (ipt);
this.ltokenPostfix.addLast (JS.T.tokenRightParen);
var pcount = 0;
var tok;
for (var i = this.ltokenPostfix.size (); --i >= 0 && pcount >= 0; ) {
switch (tok = this.ltokenPostfix.get (i).tok) {
case 268435473:
case 268435521:
pcount++;
break;
case 268435472:
case 268435520:
pcount--;
var tok2;
if (pcount == 1 && (tok2 = this.ltokenPostfix.get (i - 1).tok) != 268435473 && tok2 != 268435521) {
ipt = (tok == 268435520 ? i - 1 : i);
pcount = -10;
}break;
default:
tok2 = (i == 0 ? 0 : this.ltokenPostfix.get (i - 1).tok);
if (tok2 == 1073742336 || tok2 == 1073742337) {
ipt = i - 1;
break;
}if (i == ipt - 1) {
ipt = i;
pcount = -10;
}break;
}
}
if (pcount == -10) {
this.ltokenPostfix.add (ipt, JS.T.tokenLeftParen);
}}this.ltokenPostfix.addLast (token);
this.lastToken = token;
return true;
}, "JS.T");
Clazz.defineMethod (c$, "addNextToken", 
 function () {
return this.addTokenToPostfixToken (this.tokenNext ());
});
Clazz.defineMethod (c$, "addNextTokenIf", 
 function (tok) {
return (this.tokPeekIs (tok) && this.addNextToken ());
}, "~N");
Clazz.defineMethod (c$, "addSubstituteTokenIf", 
 function (tok, token) {
if (!this.tokPeekIs (tok)) return false;
this.itokenInfix++;
return this.addTokenToPostfixToken (token);
}, "~N,JS.T");
Clazz.defineMethod (c$, "clauseOr", 
 function (allowCommaAsOr) {
this.haveString = false;
if (!this.clauseAnd ()) return false;
if (this.isEmbeddedExpression && this.lastToken.tok == 1073742326) return true;
var tok;
while ((tok = this.tokPeek ()) == 268435536 || tok == 268435537 || tok == 268435538 || allowCommaAsOr && tok == 268435504) {
if (tok == 268435504 && !this.haveString) this.addSubstituteTokenIf (268435504, JS.T.tokenOr);
 else this.addNextToken ();
if (!this.clauseAnd ()) return false;
if (allowCommaAsOr && (this.lastToken.tok == 1073742338 || this.lastToken.tok == 10)) this.haveString = true;
}
return true;
}, "~B");
Clazz.defineMethod (c$, "clauseAnd", 
 function () {
if (!this.clauseNot ()) return false;
if (this.isEmbeddedExpression && this.lastToken.tok == 1073742326) return true;
while (this.tokPeekIs (268435552)) {
this.addNextToken ();
if (!this.clauseNot ()) return false;
}
return true;
});
Clazz.defineMethod (c$, "clauseNot", 
 function () {
if (this.tokPeekIs (268435568)) {
this.addNextToken ();
return this.clauseNot ();
}return (this.clausePrimitive ());
});
Clazz.defineMethod (c$, "clausePrimitive", 
 function () {
var tok = this.tokPeek ();
switch (tok) {
case 1073742195:
this.itokenInfix++;
return this.clausePrimitive ();
case 0:
return this.error (4);
case 1073742327:
case 10:
case 268435632:
case 136314895:
case 2097160:
case 2097159:
case 2097162:
case 1073742331:
case 1073742333:
case 2097184:
return this.addNextToken ();
case 4:
this.haveString = true;
return this.addNextToken ();
case 3:
return this.addTokenToPostfixInt (1073742359, this.fixModelSpec (this.getToken ()), this.theValue);
case 1094713349:
case 1094713350:
return this.clauseCell (tok);
case 134217736:
case 1275203608:
return this.clauseConnected (tok == 1275203608);
case 134218756:
case 134218757:
return this.clauseSubstructure ();
case 134217759:
case 134353926:
return this.clauseWithin (tok == 134217759);
case 12290:
return this.clauseDefine (false, false);
case 1677721602:
case 1745489939:
this.addNextToken ();
if (this.tokPeekIs (10)) this.addNextToken ();
 else if (this.tokPeekIs (12290)) return this.clauseDefine (false, false);
return true;
case 268435472:
this.addNextToken ();
if (!this.clauseOr (true)) return false;
if (!this.addNextTokenIf (268435473)) return this.errorStr (15, ")");
return this.checkForItemSelector (true);
case 1073742332:
return this.checkForCoordinate (this.isMathExpressionCommand);
default:
if (this.clauseResidueSpec ()) return true;
if (this.isError ()) return false;
if (JS.T.tokAttr (tok, 1077936128)) {
var itemp = this.itokenInfix;
var isOK = this.clauseComparator (true);
if (isOK || this.itokenInfix != itemp) return isOK;
if (tok == 1237320707) {
return this.clauseSubstructure ();
}}return this.addNextToken ();
}
});
Clazz.defineMethod (c$, "checkForCoordinate", 
 function (isImplicitExpression) {
var isCoordinate = false;
var pt = this.ltokenPostfix.size ();
if (isImplicitExpression) {
this.addTokenToPostfixToken (JS.T.tokenExpressionBegin);
this.tokenNext ();
} else if (this.isEmbeddedExpression) {
this.tokenNext ();
pt--;
} else {
this.addNextToken ();
}var isHash = this.tokPeekIs (4);
if (isHash) {
isImplicitExpression = false;
this.returnToken ();
this.ltokenPostfix.removeItemAt (this.ltokenPostfix.size () - 1);
this.addNextToken ();
var nBrace = 1;
while (nBrace != 0) {
if (this.tokPeekIs (1073742332)) {
if (this.isExpressionNext ()) {
this.addTokenToPostfixToken (JS.T.o (1073742325, "implicitExpressionBegin"));
if (!this.clauseOr (false)) return false;
if (this.lastToken !== JS.T.tokenCoordinateEnd) {
this.addTokenToPostfixToken (JS.T.tokenExpressionEnd);
}} else {
nBrace++;
}}if (this.tokPeekIs (1073742338)) nBrace--;
this.addNextToken ();
}
} else {
if (!this.tokPeekIs (1073742338) && !this.clauseOr (false)) return false;
var n = 1;
while (!this.tokPeekIs (1073742338)) {
var haveComma = this.addNextTokenIf (268435504);
if (!this.clauseOr (false)) return (haveComma || n < 3 ? false : this.errorStr (15, "}"));
n++;
}
isCoordinate = (n >= 2);
}if (isCoordinate && (isImplicitExpression || this.isEmbeddedExpression)) {
this.ltokenPostfix.set (pt, JS.T.tokenCoordinateBegin);
this.addTokenToPostfixToken (JS.T.tokenCoordinateEnd);
this.tokenNext ();
} else if (isImplicitExpression) {
this.addTokenToPostfixToken (JS.T.tokenExpressionEnd);
this.tokenNext ();
} else if (this.isEmbeddedExpression) {
if (!isHash) this.tokenNext ();
} else {
this.addNextToken ();
}return this.checkForItemSelector (!isHash);
}, "~B");
Clazz.defineMethod (c$, "checkForItemSelector", 
 function (allowNumeric) {
var tok;
if ((tok = this.tokAt (this.itokenInfix + 1)) == 268435520 || allowNumeric && tok == 1073742332) return true;
while (true) {
if (!this.addNextTokenIf (268435520)) break;
if (!this.clauseItemSelector ()) return false;
if (!this.addNextTokenIf (268435521)) return this.errorStr (15, "]");
}
return true;
}, "~B");
Clazz.defineMethod (c$, "clauseWithin", 
 function (isWithin) {
this.addNextToken ();
if (!this.addNextTokenIf (268435472)) return false;
if (this.getToken () == null) return false;
var distance = 3.4028235E38;
var key = null;
var allowComma = isWithin;
var tok;
var tok0 = this.theToken.tok;
if (!isWithin) {
tok = -1;
for (var i = this.itokenInfix; tok != 0; i++) {
switch (tok = this.tokAt (i)) {
case 268435504:
tok = 0;
break;
case 1073742332:
case 268435472:
case 268435473:
distance = 100;
this.returnToken ();
tok0 = tok = 0;
break;
}
}
}switch (tok0) {
case 268435616:
if (this.getToken () == null) return false;
if (this.theToken.tok != 2) return this.error (12);
distance = -this.theToken.intValue;
break;
case 2:
case 3:
distance = this.floatValue ();
break;
case 12290:
this.addTokenToPostfixToken (this.theToken);
if (!this.clauseDefine (true, false)) return false;
key = "";
allowComma = false;
break;
}
if (isWithin && distance == 3.4028235E38) switch (tok0) {
case 12290:
break;
case 1111490587:
case 1073742128:
case 134218756:
case 134218757:
case 1237320707:
case 1073741925:
case 1073742189:
this.addTokenToPostfix (4, this.theValue);
if (!this.addNextTokenIf (268435504)) return false;
allowComma = false;
tok = this.tokPeek ();
switch (tok) {
case 0:
return false;
case 4:
this.addNextToken ();
key = "";
break;
case 12290:
if (!this.clauseDefine (false, true)) return false;
key = "";
break;
default:
return false;
}
break;
case 1073742328:
allowComma = false;
case 1086326785:
case 1086326786:
case 1073741863:
case 1678381065:
case 1086326788:
case 1073742329:
case 1086326789:
case 1086324742:
case 1814695966:
case 136314895:
case 1094717454:
case 1094713360:
case 134217750:
case 134219265:
case 1094713362:
case 1086324744:
case 2097184:
case 1094713366:
case 1639976963:
case 4:
case 1648363544:
key = this.theValue;
break;
default:
key = (this.theValue).toLowerCase ();
break;
}
if (key == null) this.addTokenToPostfix (3, Float.$valueOf (distance));
 else if (key.length > 0) this.addTokenToPostfix (4, key);
var done = false;
while (!done) {
if (tok0 != 0 && !this.addNextTokenIf (268435504)) break;
if (tok0 == 0) tok0 = 134353926;
var isCoordOrPlane = false;
tok = this.tokPeek ();
if (isWithin) {
switch (tok0) {
case 2:
case 3:
if (tok == 1073742335 || tok == 1073742334) {
this.addTokenToPostfixToken (this.getToken ());
if (!this.addNextTokenIf (268435504)) break;
tok = this.tokPeek ();
}break;
}
if (key == null) {
switch (tok) {
case 134219265:
case 1073742329:
case 134217750:
isCoordOrPlane = true;
this.addNextToken ();
break;
case 1073742330:
this.getToken ();
this.getToken ();
this.addTokenToPostfix (4, "$" + this.theValue);
done = true;
break;
case 1086324742:
case 1648363544:
case 1814695966:
this.getToken ();
this.addTokenToPostfix (4, JS.T.nameOf (tok));
break;
case 1073742332:
this.returnToken ();
isCoordOrPlane = true;
this.addTokenToPostfixToken (JS.T.getTokenFromName (distance == 3.4028235E38 ? "plane" : "coord"));
}
if (!done) this.addNextTokenIf (268435504);
}}tok = this.tokPeek ();
if (done) break;
if (isCoordOrPlane) {
while (!this.tokPeekIs (268435473)) {
switch (this.tokPeek ()) {
case 0:
return this.error (4);
case 268435472:
this.addTokenToPostfixToken (JS.T.tokenExpressionBegin);
this.addNextToken ();
if (!this.clauseOr (false)) return this.errorIntStr2 (18, "WITHIN", ": ?");
if (!this.addNextTokenIf (268435473)) return this.errorStr (15, ", / )");
this.addTokenToPostfixToken (JS.T.tokenExpressionEnd);
break;
case 12290:
if (!this.clauseDefine (false, false)) return false;
break;
default:
this.addTokenToPostfixToken (this.getToken ());
}
}
} else if (!this.clauseOr (allowComma)) {
}}
if (!this.addNextTokenIf (268435473)) return this.errorStr (15, ")");
return true;
}, "~B");
Clazz.defineMethod (c$, "clauseConnected", 
 function (isPolyhedra) {
this.addNextToken ();
if (!this.addNextTokenIf (268435472)) {
this.addTokenToPostfixToken (JS.T.tokenLeftParen);
this.addTokenToPostfixToken (JS.T.tokenRightParen);
return true;
}while (true) {
if (this.addNextTokenIf (2)) {
if (!this.addNextTokenIf (268435504)) {
break;
}if (isPolyhedra) {
this.returnToken ();
break;
}} else if (isPolyhedra && (this.addNextTokenIf (4) || this.addNextTokenIf (1073741824))) {
break;
}if (this.addNextTokenIf (2)) if (!this.addNextTokenIf (268435504)) break;
if (this.addNextTokenIf (3)) if (!this.addNextTokenIf (268435504)) break;
if (this.addNextTokenIf (3)) if (!this.addNextTokenIf (268435504)) break;
var o = this.getToken ().value;
var strOrder = (Clazz.instanceOf (o, String) ? o : " ");
var intType = JS.ScriptParam.getBondOrderFromString (strOrder);
if (intType == 131071) {
this.returnToken ();
} else {
this.addTokenToPostfix (4, strOrder);
if (!this.addNextTokenIf (268435504)) break;
}if (this.addNextTokenIf (268435473)) return true;
if (!this.clauseOr (this.tokPeekIs (268435472))) return false;
if (this.addNextTokenIf (268435473)) return true;
if (!this.addNextTokenIf (268435504)) return false;
if (!this.clauseOr (this.tokPeekIs (268435472))) return false;
break;
}
if (!this.addNextTokenIf (268435473)) return this.errorStr (15, ")");
return true;
}, "~B");
Clazz.defineMethod (c$, "clauseSubstructure", 
 function () {
this.addNextToken ();
if (!this.addNextTokenIf (268435472)) return false;
if (this.tokPeekIs (12290)) {
if (!this.clauseDefine (false, true)) return false;
} else if (!this.addNextTokenIf (4)) {
return this.errorStr (15, "\"...\"");
}if (this.addNextTokenIf (268435504)) if (!this.clauseOr (this.tokPeekIs (268435472))) return false;
if (!this.addNextTokenIf (268435473)) return this.errorStr (15, ")");
return true;
});
Clazz.defineMethod (c$, "clauseItemSelector", 
 function () {
var tok;
var nparen = 0;
while ((tok = this.tokPeek ()) != 0 && tok != 268435521) {
this.addNextToken ();
if (tok == 268435520) nparen++;
if (this.tokPeek () == 268435521 && nparen-- > 0) this.addNextToken ();
}
return true;
});
Clazz.defineMethod (c$, "clauseComparator", 
 function (isOptional) {
var tokenAtomProperty = this.tokenNext ();
var tokenComparator = this.tokenNext ();
if (!JS.ScriptTokenParser.tokenAttr (tokenComparator, 268435712)) {
if (!isOptional) return this.errorStr (15, "== != < > <= >=");
if (tokenComparator != null) this.returnToken ();
this.returnToken ();
return false;
}if (JS.ScriptTokenParser.tokenAttr (tokenAtomProperty, 1086324736) && tokenComparator.tok != 268435860 && tokenComparator.tok != 268435862 && tokenComparator.tok != 268435861) return this.errorStr (15, "== !=");
if (this.tokPeek () == 268435520) {
this.getToken ();
this.addTokenToPostfixToken (JS.T.tokenLeftParen);
while (true) {
if (!this.addCompare (tokenAtomProperty, tokenComparator)) return false;
if (this.tokPeek () == 268435504) this.getToken ();
 else if (this.tokPeek () == 268435521) break;
this.addTokenToPostfixToken (tokenComparator.tok == 268435861 ? JS.T.tokenAnd : JS.T.tokenOr);
}
this.getToken ();
this.addTokenToPostfixToken (JS.T.tokenRightParen);
return true;
}return this.addCompare (tokenAtomProperty, tokenComparator);
}, "~B");
Clazz.defineMethod (c$, "addCompare", 
 function (tokenAtomProperty, tokenComparator) {
if (this.getToken () == null) return this.errorStr (17, "" + this.valuePeek ());
var isNegative = (this.theToken.tok == 268435616);
if (isNegative && this.getToken () == null) return this.error (12);
switch (this.theToken.tok) {
case 2:
case 3:
case 1073741824:
case 4:
case 1073742332:
case 12290:
break;
default:
if (!JS.T.tokAttr (this.theToken.tok, 1073741824)) return this.error (13);
}
this.addTokenToPostfixInt (tokenComparator.tok, tokenAtomProperty.tok, tokenComparator.value + (isNegative ? " -" : ""));
if (tokenAtomProperty.tok == 1715472409) this.addTokenToPostfixToken (tokenAtomProperty);
if (this.theToken.tok == 1073742332) {
this.returnToken ();
return this.clausePrimitive ();
}this.addTokenToPostfixToken (this.theToken);
if (this.theToken.tok == 12290) return this.clauseDefine (true, false);
return true;
}, "JS.T,JS.T");
Clazz.defineMethod (c$, "clauseCell", 
 function (tok) {
var cell =  new JU.P3 ();
this.tokenNext ();
if (!this.tokenNextTok (268435860)) return this.errorStr (15, "=");
if (this.getToken () == null) return this.error (3);
if (this.theToken.tok == 2) {
JU.SimpleUnitCell.ijkToPoint3f (this.theToken.intValue, cell, 1, 0);
return this.addTokenToPostfix (tok, cell);
}if (this.theToken.tok != 1073742332 || !this.getNumericalToken ()) return this.error (3);
cell.x = this.floatValue ();
if (this.tokPeekIs (268435504)) this.tokenNext ();
if (!this.getNumericalToken ()) return this.error (3);
cell.y = this.floatValue ();
if (this.tokPeekIs (268435504)) this.tokenNext ();
if (!this.getNumericalToken () || !this.tokenNextTok (1073742338)) return this.error (3);
cell.z = this.floatValue ();
return this.addTokenToPostfix (tok, cell);
}, "~N");
Clazz.defineMethod (c$, "clauseDefine", 
 function (haveToken, forceString) {
if (!haveToken) {
var token = this.tokenNext ();
if (forceString) token = JS.T.tokenDefineString;
this.addTokenToPostfixToken (token);
}if (this.tokPeekIs (0)) return this.error (4);
if (!this.addSubstituteTokenIf (1073742332, JS.T.tokenExpressionBegin)) {
if (this.tokPeek () == 12290) this.addNextToken ();
return this.addNextToken () && this.checkForItemSelector (true);
}while (this.moreTokens () && !this.tokPeekIs (1073742338)) {
if (this.tokPeekIs (1073742332)) {
if (!this.checkForCoordinate (true)) return false;
} else {
this.addNextToken ();
}}
return this.addSubstituteTokenIf (1073742338, JS.T.tokenExpressionEnd) && this.checkForItemSelector (true);
}, "~B,~B");
Clazz.defineMethod (c$, "generateResidueSpecCode", 
 function (token) {
if (this.residueSpecCodeGenerated) this.addTokenToPostfixToken (JS.T.tokenAndSpec);
this.addTokenToPostfixToken (token);
this.residueSpecCodeGenerated = true;
return true;
}, "JS.T");
Clazz.defineMethod (c$, "clauseResidueSpec", 
 function () {
var tok = this.tokPeek ();
this.residueSpecCodeGenerated = false;
var checkResNameSpec = false;
switch (tok) {
case 0:
case 2097156:
case 2097174:
return false;
case 2:
case 268435490:
case 268435634:
case 5:
break;
case 268435633:
case 268435520:
case 1073741824:
checkResNameSpec = true;
break;
default:
if (JS.T.tokAttr (tok, 268435712)) return false;
var str = "" + this.valuePeek ();
checkResNameSpec = (str.length == 2 || str.length == 3);
if (!checkResNameSpec) return false;
}
var specSeen = false;
if (checkResNameSpec) {
if (!this.clauseResNameSpec ()) return false;
specSeen = true;
tok = this.tokPeek ();
}if (tok == 2 || tok == 268435633 || tok == 5) {
if (!this.clauseSequenceSpec ()) return false;
specSeen = true;
tok = this.tokPeek ();
}if (tok == 268435490) {
if (!this.clauseChainSpec (tok)) return false;
specSeen = true;
tok = this.tokPeek ();
}if (tok == 1073742336) {
if (!this.clauseAtomSpec ()) return false;
specSeen = true;
tok = this.tokPeek ();
}if (tok == 268435634) {
if (!this.clauseAlternateSpec ()) return false;
specSeen = true;
tok = this.tokPeek ();
}if (tok == 268435632) {
if (!this.clauseModelSpec ()) return false;
specSeen = true;
tok = this.tokPeek ();
}if (!specSeen) return this.error (14);
if (!this.residueSpecCodeGenerated) {
this.addTokenToPostfixToken (JS.T.tokenAll);
}return true;
});
Clazz.defineMethod (c$, "clauseResNameSpec", 
 function () {
this.getToken ();
var tok = this.tokPeek ();
switch (this.theToken.tok) {
case 268435633:
return true;
case 268435520:
var strSpec = "";
while (this.getToken () != null && this.theToken.tok != 268435521) strSpec += this.theValue;

if (this.theToken == null) return false;
if (strSpec === "") return true;
var pt;
return (strSpec.length > 0 && (pt = strSpec.indexOf ("*")) >= 0 && pt != strSpec.length - 1 ? this.error (14) : this.generateResidueSpecCode (JS.T.o (1073742360, strSpec.toUpperCase ())));
default:
if (JS.T.tokAttr (tok, 268435712)) {
this.returnToken ();
return false;
}var res = this.theValue;
if (tok == 268435633) {
res = this.theValue + "*";
this.getToken ();
}return this.generateResidueSpecCode (JS.T.o (1073741824, res));
}
});
Clazz.defineMethod (c$, "clauseSequenceSpec", 
 function () {
if (this.tokPeek () == 268435633) return (this.getToken () != null);
var seqToken = this.getSequenceCode (false);
if (seqToken == null) return false;
var tok = this.tokPeek ();
if (tok == 268435616 || tok == 2 && this.intPeek () < 0) {
if (tok == 268435616) {
this.tokenNext ();
} else {
var i = -this.intPeek ();
this.tokenNext ().intValue = i;
this.returnToken ();
}seqToken.tok = 1073742363;
this.generateResidueSpecCode (seqToken);
return this.addTokenToPostfixToken (this.getSequenceCode (true));
}return this.generateResidueSpecCode (seqToken);
});
Clazz.defineMethod (c$, "getSequenceCode", 
 function (isSecond) {
var seqcode = 2147483647;
var seqvalue = 2147483647;
switch (this.tokPeek ()) {
case 5:
seqcode = this.tokenNext ().intValue;
break;
case 2:
seqvalue = this.tokenNext ().intValue;
break;
default:
if (!isSecond) return null;
}
return JS.T.tv (1073742362, seqvalue, Integer.$valueOf (seqcode));
}, "~B");
Clazz.defineMethod (c$, "clauseChainSpec", 
 function (tok) {
this.tokenNext ();
tok = this.tokPeek ();
var strChain;
if (this.isTerminator (tok)) {
strChain = " ";
} else {
switch (tok) {
case 268435633:
return (this.getToken () != null);
case 2:
this.getToken ();
var val = this.theToken.intValue;
if (val < 0 || val > 9999) return this.error (8);
strChain = "" + val;
break;
case 4:
this.vwr.getChainID ("a", true);
default:
strChain = "" + this.getToken ().value;
break;
}
if (strChain.length == 0) strChain = " ";
 else if (strChain.equals ("?")) return true;
}var chain = this.vwr.getChainID (strChain, false);
return this.generateResidueSpecCode (JS.T.tv (1073742357, chain, "spec_chain"));
}, "~N");
Clazz.defineMethod (c$, "clauseAlternateSpec", 
 function () {
this.tokenNext ();
if (this.isTerminator (this.tokPeek ())) return this.generateResidueSpecCode (JS.T.o (1073742355, null));
switch (this.getToken ().tok) {
case 268435633:
case 4:
case 2:
case 1073741824:
case 805306401:
case 1111492629:
case 1111492630:
case 1111492631:
case 1140850705:
break;
default:
return this.error (10);
}
return this.generateResidueSpecCode (JS.T.o (1073742355, this.theToken.value));
});
Clazz.defineMethod (c$, "isTerminator", 
 function (tok) {
switch (tok) {
case 0:
case 268435632:
case 268435552:
case 268435536:
case 268435568:
case 268435504:
case 268435473:
case 1073742338:
return true;
default:
return false;
}
}, "~N");
Clazz.defineMethod (c$, "clauseModelSpec", 
 function () {
this.getToken ();
switch (this.tokPeek ()) {
case 268435633:
this.getToken ();
return true;
case 2:
return this.generateResidueSpecCode (JS.T.o (1073742358, Integer.$valueOf (this.getToken ().intValue)));
case 3:
return this.generateResidueSpecCode (JS.T.tv (1073742358, this.fixModelSpec (this.getToken ()), this.theValue));
case 268435504:
case 1073742338:
case 0:
return this.generateResidueSpecCode (JS.T.o (1073742358, Integer.$valueOf (1)));
}
return this.error (10);
});
Clazz.defineMethod (c$, "fixModelSpec", 
 function (token) {
var ival = token.intValue;
if (ival == 2147483647) {
var f = (this.theValue).floatValue ();
if (f == Clazz.floatToInt (f)) ival = (Clazz.floatToInt (f)) * 1000000;
if (ival < 0) ival = 2147483647;
}return ival;
}, "JS.T");
Clazz.defineMethod (c$, "clauseAtomSpec", 
 function () {
if (!this.tokenNextTok (1073742336)) return this.error (7);
if (this.getToken () == null) return true;
var atomSpec = "";
if (this.theToken.tok == 2) {
atomSpec += "" + this.theToken.intValue;
if (this.getToken () == null) return this.error (7);
}if (this.theToken.tok == 268435633) return true;
atomSpec += "" + this.theToken.value;
if (this.tokPeekIs (268435633)) {
this.tokenNext ();
atomSpec += "'";
}return this.generateResidueSpecCode (JS.T.tv (1073742356, this.vwr.getJBR ().lookupSpecialAtomID (atomSpec.toUpperCase ()), atomSpec));
});
c$.errorString = Clazz.defineMethod (c$, "errorString", 
function (iError, value, more, translated) {
var doTranslate = false;
if (!translated && (doTranslate = J.i18n.GT.getDoTranslate ()) == true) J.i18n.GT.setDoTranslate (false);
var msg;
switch (iError) {
default:
msg = "Unknown compiler error message number: " + iError;
break;
case 0:
msg = J.i18n.GT.$ ("bad argument count");
break;
case 1:
msg = J.i18n.GT.$ ("invalid context for {0}");
break;
case 2:
msg = J.i18n.GT.$ ("command expected");
break;
case 3:
msg = J.i18n.GT.$ ("{ number number number } expected");
break;
case 4:
msg = J.i18n.GT.$ ("unexpected end of script command");
break;
case 5:
msg = J.i18n.GT.$ ("end of expression expected");
break;
case 6:
msg = J.i18n.GT.$ ("identifier or residue specification expected");
break;
case 7:
msg = J.i18n.GT.$ ("invalid atom specification");
break;
case 8:
msg = J.i18n.GT.$ ("invalid chain specification");
break;
case 9:
msg = J.i18n.GT.$ ("invalid expression token: {0}");
break;
case 10:
msg = J.i18n.GT.$ ("invalid model specification");
break;
case 11:
msg = J.i18n.GT.$ ("missing END for {0}");
break;
case 12:
msg = J.i18n.GT.$ ("number expected");
break;
case 13:
msg = J.i18n.GT.$ ("number or variable name expected");
break;
case 14:
msg = J.i18n.GT.$ ("residue specification (ALA, AL?, A*) expected");
break;
case 15:
msg = J.i18n.GT.$ ("{0} expected");
break;
case 16:
msg = J.i18n.GT.$ ("{0} unexpected");
break;
case 17:
msg = J.i18n.GT.$ ("unrecognized expression token: {0}");
break;
case 18:
msg = J.i18n.GT.$ ("unrecognized {0} parameter");
break;
case 19:
msg = J.i18n.GT.$ ("unrecognized token: {0}");
break;
}
if (msg.indexOf ("{0}") < 0) {
if (value != null) msg += ": " + value;
} else {
msg = JU.PT.rep (msg, "{0}", value);
if (msg.indexOf ("{1}") >= 0) msg = JU.PT.rep (msg, "{1}", more);
 else if (more != null) msg += ": " + more;
}if (!translated) J.i18n.GT.setDoTranslate (doTranslate);
return msg;
}, "~N,~S,~S,~B");
Clazz.defineMethod (c$, "commandExpected", 
function () {
this.ichToken = this.ichCurrentCommand;
return this.error (2);
});
Clazz.defineMethod (c$, "error", 
function (error) {
return this.errorIntStr2 (error, null, null);
}, "~N");
Clazz.defineMethod (c$, "errorStr", 
function (error, value) {
return this.errorIntStr2 (error, value, null);
}, "~N,~S");
Clazz.defineMethod (c$, "errorIntStr2", 
function (iError, value, more) {
var strError = JS.ScriptTokenParser.errorString (iError, value, more, true);
var strUntranslated = (J.i18n.GT.getDoTranslate () ? JS.ScriptTokenParser.errorString (iError, value, more, false) : null);
return this.errorStr2 (strError, strUntranslated);
}, "~N,~S,~S");
Clazz.defineMethod (c$, "isError", 
 function () {
return this.errorMessage != null;
});
Clazz.defineMethod (c$, "errorStr2", 
function (errorMessage, strUntranslated) {
this.errorMessage = errorMessage;
this.errorMessageUntranslated = strUntranslated;
return false;
}, "~S,~S");
Clazz.defineStatics (c$,
"ERROR_badArgumentCount", 0,
"ERROR_badContext", 1,
"ERROR_commandExpected", 2,
"ERROR_endOfCommandUnexpected", 4,
"ERROR_invalidExpressionToken", 9,
"ERROR_missingEnd", 11,
"ERROR_tokenExpected", 15,
"ERROR_tokenUnexpected", 16,
"ERROR_unrecognizedParameter", 18,
"ERROR_unrecognizedToken", 19,
"ERROR_coordinateExpected", 3,
"ERROR_endOfExpressionExpected", 5,
"ERROR_identifierOrResidueSpecificationExpected", 6,
"ERROR_invalidAtomSpecification", 7,
"ERROR_invalidChainSpecification", 8,
"ERROR_invalidModelSpecification", 10,
"ERROR_numberExpected", 12,
"ERROR_numberOrVariableNameExpected", 13,
"ERROR_residueSpecificationExpected", 14,
"ERROR_unrecognizedExpressionToken", 17);
});
