Clazz.declarePackage("J.adapter.readers.more");
Clazz.load(["J.adapter.readers.more.ForceFieldReader"], "J.adapter.readers.more.Mol2Reader", ["JU.PT", "J.adapter.smarter.Bond"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.nAtoms = 0;
this.ac = 0;
this.isPDB = false;
this.lastSequenceNumber = 2147483647;
this.chainID = 64;
Clazz.instantialize(this, arguments);}, J.adapter.readers.more, "Mol2Reader", J.adapter.readers.more.ForceFieldReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.setUserAtomTypes();
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.equals("@<TRIPOS>MOLECULE")) {
if (!this.processMolecule()) {
return true;
}this.continuing = !this.isLastModel(this.modelNumber);
return false;
}if (this.line.length != 0 && this.line.charAt(0) == '#') {
this.checkCurrentLineForScript();
}return true;
});
Clazz.defineMethod(c$, "processMolecule", 
function(){
this.isPDB = false;
var thisDataSetName = this.rd().trim();
if (!this.doGetModel(++this.modelNumber, thisDataSetName)) {
return false;
}this.lastSequenceNumber = 2147483647;
this.chainID = 64;
this.rd();
this.line += " 0 0 0 0 0 0";
this.ac = this.parseIntStr(this.line);
var bondCount = this.parseInt();
if (bondCount == 0) this.asc.setNoAutoBond();
var resCount = this.parseInt();
this.rd();
this.rd();
if (this.rd() != null && (this.line.length == 0 || this.line.charAt(0) != '@')) {
if (this.rd() != null && this.line.length != 0 && this.line.charAt(0) != '@') {
if (this.line.indexOf("jmolscript:") >= 0) {
this.checkCurrentLineForScript();
if (this.line.equals("#")) {
this.line = "";
}}if (this.line.length != 0) {
thisDataSetName += ": " + this.line.trim();
}}}this.newAtomSet(thisDataSetName);
while (this.line != null && !this.line.equals("@<TRIPOS>MOLECULE")) {
if (this.line.equals("@<TRIPOS>ATOM")) {
this.readAtoms(this.ac);
this.asc.setAtomSetName(thisDataSetName);
} else if (this.line.equals("@<TRIPOS>BOND")) {
this.readBonds(bondCount);
} else if (this.line.equals("@<TRIPOS>SUBSTRUCTURE")) {
this.readResInfo(resCount);
} else if (this.line.equals("@<TRIPOS>CRYSIN")) {
this.readCrystalInfo();
}this.rd();
}
this.nAtoms += this.ac;
if (this.isPDB) {
this.setIsPDB();
this.setModelPDB(true);
}this.applySymmetryAndSetTrajectory();
return true;
});
Clazz.defineMethod(c$, "readAtoms", 
function(ac){
if (ac == 0) return;
var i0 = this.asc.ac;
for (var i = 0; i < ac; ++i) {
var atom = this.asc.addNewAtom();
var tokens = JU.PT.getTokens(this.rd());
var atomType = tokens[5];
var name = tokens[1];
var pt = atomType.indexOf(".");
if (pt >= 0) {
atom.elementSymbol = atomType.substring(0, pt);
} else {
atom.atomName = name;
atom.elementSymbol = atom.getElementSymbol();
}atom.atomName = name + '\0' + atomType;
atom.set(this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[4]));
if (tokens.length > 6) {
atom.sequenceNumber = this.parseIntStr(tokens[6]);
if (atom.sequenceNumber < this.lastSequenceNumber) {
if (this.chainID == 90) this.chainID = 96;
this.chainID++;
}this.lastSequenceNumber = atom.sequenceNumber;
this.setChainID(atom, "" + String.fromCharCode(this.chainID));
}if (tokens.length > 7) atom.group3 = tokens[7];
if (tokens.length > 8) {
atom.partialCharge = this.parseFloatStr(tokens[8]);
if (atom.partialCharge == Clazz.floatToInt(atom.partialCharge)) atom.formalCharge = Clazz.floatToInt(atom.partialCharge);
}}
var atoms = this.asc.atoms;
var g3 = atoms[i0].group3;
if (g3 == null) return;
var isPDB = false;
if (!g3.equals("UNK") && !g3.startsWith("RES")) {
for (var i = this.asc.ac; --i >= i0; ) if (!g3.equals(atoms[this.asc.ac - 1].group3)) {
isPDB = true;
break;
}
if (isPDB) {
isPDB = false;
for (var i = this.asc.ac; --i >= i0; ) {
var pt = this.getPDBGroupLength(atoms[i].group3);
if (pt == 0 || pt > 3) break;
if (this.vwr.getJBR().isKnownPDBGroup(g3.substring(0, pt), 2147483647)) {
isPDB = this.isPDB = true;
break;
}}
}}for (var i = this.asc.ac; --i >= i0; ) {
if (isPDB) {
g3 = atoms[i].group3;
g3 = g3.substring(0, this.getPDBGroupLength(g3));
atoms[i].isHetero = this.vwr.getJBR().isHetero(g3);
} else {
g3 = null;
}atoms[i].group3 = g3;
}
}, "~N");
Clazz.defineMethod(c$, "getPDBGroupLength", 
function(g3){
var pt0 = g3.length;
var pt = pt0;
while (--pt > 0 && Character.isDigit(g3.charAt(pt))) {
}
return ++pt;
}, "~S");
Clazz.defineMethod(c$, "readBonds", 
function(bondCount){
for (var i = 0; i < bondCount; ++i) {
var tokens = JU.PT.getTokens(this.rd());
var atomIndex1 = this.parseIntStr(tokens[1]);
var atomIndex2 = this.parseIntStr(tokens[2]);
var order = this.parseIntStr(tokens[3]);
if (order == -2147483648) order = (tokens[3].equals("ar") ? 515 : tokens[3].equals("am") ? 1 : 17);
this.asc.addBond( new J.adapter.smarter.Bond(this.nAtoms + atomIndex1 - 1, this.nAtoms + atomIndex2 - 1, order));
}
}, "~N");
Clazz.defineMethod(c$, "readResInfo", 
function(resCount){
for (var i = 0; i < resCount; ++i) {
this.rd();
}
}, "~N");
Clazz.defineMethod(c$, "readCrystalInfo", 
function(){
this.rd();
var tokens = this.getTokens();
if (tokens.length < 6) return;
var name = "";
for (var i = 6; i < tokens.length; i++) name += " " + tokens[i];

if (name === "") name = " P1";
 else name += " *";
name = name.substring(1);
this.setSpaceGroupName(name);
if (this.ignoreFileUnitCell) return;
for (var i = 0; i < 6; i++) this.setUnitCellItem(i, this.parseFloatStr(tokens[i]));

var atoms = this.asc.atoms;
for (var i = 0; i < this.ac; ++i) this.setAtomCoord(atoms[this.nAtoms + i]);

});
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
