Clazz.declarePackage("J.adapter.readers.molxyz");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.molxyz.MolReader", ["java.util.Hashtable", "JU.BS", "$.Lst", "$.PT", "J.adapter.smarter.Atom", "J.api.JmolAdapter", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.haveAtomSerials = false;
this.allow2D = true;
this.iatom0 = 0;
this.vr = null;
this.atomCount = 0;
this.atomData = null;
this.bsDeleted = null;
this.haveNonzeroZ = false;
this.fixN = false;
this.is3D = false;
this.nDouble = 0;
this.nH = 0;
this.nC = 0;
Clazz.instantialize(this, arguments);}, J.adapter.readers.molxyz, "MolReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.fixN = this.checkFilterKey("FIXN");
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
var isMDL = (this.line.startsWith("$MDL"));
if (isMDL) {
this.discardLinesUntilStartsWith("$HDR");
this.rd();
if (this.line == null) {
JU.Logger.warn("$HDR not found in MDL RG file");
this.continuing = false;
return false;
}} else if (this.line.equals("M  END")) {
return true;
}if (this.doGetModel(++this.modelNumber, null)) {
this.iatom0 = this.asc.ac;
this.processMolSdHeader();
this.processCtab(isMDL);
this.vr = null;
if (this.isLastModel(this.modelNumber)) {
this.continuing = false;
return false;
}}if (this.line != null && this.line.indexOf("$$$$") < 0) this.discardLinesUntilStartsWith("$$$$");
return true;
});
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.finalizeReaderMR();
});
Clazz.defineMethod(c$, "finalizeReaderMR", 
function(){
if (this.fixN) {
this.addJmolScript("{search('[Nv4+0,nv4+0]')}.formalCharge=1;{search('{[Ov1-0]}[Nv4+1,nv4+1]')}.formalCharge=-1;");
}this.check2D3D();
if (this.bsDeleted != null) {
this.asc.getBSAtoms(-1).andNot(this.bsDeleted);
}this.isTrajectory = false;
this.finalizeReaderASCR();
});
Clazz.defineMethod(c$, "check2D3D", 
function(){
if (this.haveNonzeroZ) {
if (this.is2D) {
this.is2D = this.optimize2D = false;
}} else if (!this.is2D && !this.is3D) {
if (this.nC > 0 && this.nH == 0 && this.nDouble != 0) {
this.is2D = true;
}}if (this.is2D) {
if (!this.allow2D) {
throw  new Exception("File is 2D, not 3D");
}this.set2D();
}});
Clazz.defineMethod(c$, "processMolSdHeader", 
function(){
var thisDataSetName = this.line.trim();
this.asc.setCollectionName(thisDataSetName);
var header = this.line + "\n";
this.rd();
if (this.line == null) return;
header += this.line + "\n";
var dim = (this.line.length >= 22 ? this.line.substring(20, 22) : null);
this.is3D = "3D".equals(dim);
this.is2D = !this.is3D && ("2D".equals(dim) || this.line.startsWith("JME "));
this.rd();
if (this.line == null) return;
this.line = this.line.trim();
header += this.line + "\n";
JU.Logger.info(header);
this.checkCurrentLineForScript();
this.asc.setInfo("fileHeader", header);
this.newAtomSet(thisDataSetName);
});
Clazz.defineMethod(c$, "processCtab", 
function(isMDL){
if (isMDL) this.discardLinesUntilStartsWith("$CTAB");
if (this.rd() == null) return;
if (this.line.indexOf("V3000") >= 0) {
this.optimize2D = this.is2D && !this.noHydrogens;
this.vr = (this.getInterface("J.adapter.readers.molxyz.V3000Rdr")).set(this);
this.discardLinesUntilContains("COUNTS");
this.vr.readAtomsAndBonds(this.getTokens());
} else {
this.readAtomsAndBonds(this.parseIntRange(this.line, 0, 3), this.parseIntRange(this.line, 3, 6));
}this.applySymmetryAndSetTrajectory();
}, "~B");
Clazz.defineMethod(c$, "readAtomsAndBonds", 
function(ac, bc){
this.atomCount = ac;
for (var i = 0; i < ac; ++i) {
this.rd();
var len = this.line.length;
var elementSymbol;
var x;
var y;
var z;
var charge = 0;
var isotope = 0;
var iAtom = -2147483648;
x = this.parseFloatRange(this.line, 0, 10);
y = this.parseFloatRange(this.line, 10, 20);
z = this.parseFloatRange(this.line, 20, 30);
if (len < 34) {
elementSymbol = this.line.substring(31).trim();
} else {
elementSymbol = this.line.substring(31, 34).trim();
if (elementSymbol.equals("H1")) {
elementSymbol = "H";
isotope = 1;
}if (len >= 39) {
var code = this.parseIntRange(this.line, 36, 39);
if (code >= 1 && code <= 7) charge = 4 - code;
code = this.parseIntRange(this.line, 34, 36);
if (code != 0 && code >= -3 && code <= 4) {
isotope = J.api.JmolAdapter.getNaturalIsotope(J.api.JmolAdapter.getElementNumber(elementSymbol)) + code;
}if (iAtom == -2147483648 && this.haveAtomSerials) iAtom = i + 1;
}}this.addMolAtom(iAtom, isotope, elementSymbol, charge, x, y, z);
}
this.asc.setModelInfoForSet("dimension", (this.is2D ? "2D" : "3D"), this.asc.iSet);
this.rd();
if (this.line.startsWith("V  ")) {
this.readAtomValues();
}if (bc == 0) this.asc.setNoAutoBond();
for (var i = 0; i < bc; ++i) {
if (i > 0) this.rd();
var iAtom1;
var iAtom2;
var stereo = 0;
iAtom1 = this.line.substring(0, 3).trim();
iAtom2 = this.line.substring(3, 6).trim();
var order = this.parseIntRange(this.line, 6, 9);
if (order == 1 && this.line.length >= 12) stereo = this.parseIntRange(this.line, 9, 12);
if (stereo != 0 && !this.is3D) this.is2D = true;
order = this.fixOrder(order, stereo);
if (this.haveAtomSerials) this.asc.addNewBondFromNames(iAtom1, iAtom2, order);
 else this.asc.addNewBondWithOrder(this.iatom0 + this.parseIntStr(iAtom1) - 1, this.iatom0 + this.parseIntStr(iAtom2) - 1, order);
}
var molData =  new java.util.Hashtable();
var _keyList =  new JU.Lst();
this.rd();
while (this.line != null && this.line.indexOf("$$$$") != 0) {
if (this.line.indexOf(">") == 0) {
this.readMolData(molData, _keyList);
continue;
}if (this.line.startsWith("M  ISO")) {
this.readIsotopes();
continue;
}if (this.line.startsWith("M  CHG")) {
this.readCharges();
continue;
}this.rd();
}
if (this.atomData != null) {
var atomValueName = molData.get("atom_value_name");
molData.put(atomValueName == null ? "atom_values" : atomValueName.toString(), this.atomData);
}if (!molData.isEmpty()) {
this.asc.setCurrentModelInfo("molDataKeys", _keyList);
this.asc.setCurrentModelInfo("molData", molData);
}}, "~N,~N");
Clazz.defineMethod(c$, "readAtomValues", 
function(){
this.atomData =  new Array(this.atomCount);
for (var i = this.atomData.length; --i >= 0; ) this.atomData[i] = "";

while (this.line.indexOf("V  ") == 0) {
var iAtom = this.parseIntAt(this.line, 3);
if (iAtom < 1 || iAtom > this.atomCount) {
JU.Logger.error("V  nnn does not evalute to a valid atom number: " + iAtom);
return;
}var s = this.line.substring(6).trim();
this.atomData[iAtom - 1] = s;
this.rd();
}
});
Clazz.defineMethod(c$, "readIsotopes", 
function(){
try {
var n = this.parseIntAt(this.line, 6);
var i0 = this.asc.getLastAtomSetAtomIndex();
for (var i = 0, pt = 9; i < n; i++) {
var ipt = this.parseIntAt(this.line, pt);
var atom = this.asc.atoms[ipt + i0 - 1];
var iso = this.parseIntAt(this.line, pt + 4);
pt += 8;
var sym = JU.PT.replaceAllCharacters(atom.elementSymbol, "0123456789", "");
if (iso == 17 && sym.equals("C")) {
atom.elementSymbol = "N";
} else if (iso == 5 && sym.equals("H")) {
this.deleteAtom(atom);
} else {
atom.elementSymbol = "" + iso + sym;
}}
} catch (e) {
}
this.rd();
});
Clazz.defineMethod(c$, "readCharges", 
function(){
try {
var n = this.parseIntAt(this.line, 6);
var i0 = this.asc.getLastAtomSetAtomIndex();
for (var i = this.asc.ac; --i >= i0; ) {
this.asc.atoms[i].formalCharge = 0;
}
for (var i = 0, pt = 9; i < n; i++, pt += 8) {
this.asc.atoms[this.parseIntAt(this.line, pt) + i0 - 1].formalCharge = this.parseIntAt(this.line, pt + 4);
}
} catch (e) {
}
this.rd();
});
Clazz.defineMethod(c$, "deleteAtom", 
function(atom){
if (this.bsDeleted == null) this.bsDeleted =  new JU.BS();
this.bsDeleted.set(atom.index);
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "readMolData", 
function(molData, _keyList){
var atoms = this.asc.atoms;
var dataName = JU.PT.trim(this.line, "> <").toLowerCase();
var data = "";
var fdata = null;
while (this.rd() != null && !this.line.equals("$$$$") && this.line.length > 0) data += (this.line.length == 81 && this.line.charAt(80) == '+' ? this.line.substring(0, 80) : this.line + "\n");

data = JU.PT.trim(data, "\n");
JU.Logger.info(dataName + ":" + JU.PT.esc(data));
molData.put(dataName, data);
_keyList.addLast(dataName);
var ndata = 0;
if (dataName.toUpperCase().contains("_PARTIAL_CHARGES")) {
try {
fdata = JU.PT.parseFloatArray(data);
for (var i = this.asc.getLastAtomSetAtomIndex(), n = this.asc.ac; i < n; i++) atoms[i].partialCharge = 0;

var pt = 0;
for (var i = Clazz.floatToInt(fdata[pt++]); --i >= 0; ) {
var atomIndex = Clazz.floatToInt(fdata[pt++]) + this.iatom0 - 1;
var partialCharge = fdata[pt++];
atoms[atomIndex].partialCharge = partialCharge;
ndata++;
}
} catch (e) {
for (var i = this.asc.getLastAtomSetAtomIndex(), n = this.asc.ac; i < n; i++) atoms[i].partialCharge = 0;

JU.Logger.error("error reading " + dataName + " field -- partial charges cleared");
}
JU.Logger.info(ndata + " partial charges read");
} else if (dataName.toUpperCase().contains("ATOM_NAMES")) {
ndata = 0;
try {
var tokens = JU.PT.getTokens(data);
var pt = 0;
for (var i = this.parseIntStr(tokens[pt++]); --i >= 0; ) {
var iatom;
while ((iatom = this.parseIntStr(tokens[pt++])) == -2147483648) {
}
var atomIndex = iatom + this.iatom0 - 1;
var name = tokens[pt++];
if (!name.equals(".")) atoms[atomIndex].atomName = name;
ndata++;
}
} catch (e) {
JU.Logger.error("error reading " + dataName + " field");
}
JU.Logger.info(ndata + " atom names read");
}}, "java.util.Map,JU.Lst");
Clazz.defineMethod(c$, "addMolAtom", 
function(iAtom, isotope, elementSymbol, charge, x, y, z){
if ("H".equals(elementSymbol)) this.nH++;
 else if ("C".equals(elementSymbol)) this.nC++;
this.haveNonzeroZ = new Boolean (this.haveNonzeroZ | (Math.abs(z) > 0.001)).valueOf();
switch (isotope) {
case 0:
break;
case 1:
elementSymbol = "1H";
break;
case 2:
elementSymbol = "2H";
break;
case 3:
elementSymbol = "3H";
break;
default:
elementSymbol = isotope + elementSymbol;
}
var atom =  new J.adapter.smarter.Atom();
atom.elementSymbol = elementSymbol;
atom.formalCharge = charge;
this.setAtomCoordXYZ(atom, x, y, z);
if (iAtom == -2147483648) {
this.asc.addAtom(atom);
} else {
this.haveAtomSerials = true;
atom.atomSerial = iAtom;
this.asc.addAtomWithMappedSerialNumber(atom);
}return atom;
}, "~N,~N,~S,~N,~N,~N,~N");
Clazz.defineMethod(c$, "fixOrder", 
function(order, stereo){
switch (order) {
default:
case 0:
case -10:
return 1;
case 1:
switch (stereo) {
case 1:
this.is2D = true;
return 1025;
case 3:
case 6:
this.is2D = true;
return 1041;
case 2:
case 4:
this.is2D = true;
return 1057;
}
break;
case 2:
case 3:
this.nDouble++;
break;
case 4:
return 515;
case 5:
return 66;
case 6:
return 513;
case 7:
return 514;
case 8:
case 9:
return 33;
case 14:
return 4;
case 15:
return 5;
case 16:
return 6;
}
return order;
}, "~N,~N");
Clazz.defineMethod(c$, "addMolBond", 
function(iAtom1, iAtom2, order, stereo){
order = this.fixOrder(order, stereo);
if (this.haveAtomSerials) return this.asc.addNewBondFromNames(iAtom1, iAtom2, order);
return this.asc.addNewBondWithOrder(this.iatom0 + this.parseIntStr(iAtom1) - 1, this.iatom0 + this.parseIntStr(iAtom2) - 1, order);
}, "~S,~S,~N,~N");
});
;//5.0.1-v7 Sat Feb 21 18:17:38 CST 2026
