Clazz.declarePackage("J.adapter.readers.molxyz");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.molxyz.XyzReader", ["JU.Logger"], function(){
var c$ = Clazz.declareType(J.adapter.readers.molxyz, "XyzReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "checkLine", 
function(){
var modelAtomCount = this.parseIntStr(this.line);
if (modelAtomCount == -2147483648) {
this.continuing = false;
return false;
}this.vibrationNumber = ++this.modelNumber;
if (this.desiredVibrationNumber <= 0 ? this.doGetModel(this.modelNumber, null) : this.doGetVibration(this.vibrationNumber)) {
this.rd();
this.checkCurrentLineForScript();
this.asc.newAtomSet();
var name = this.line.trim();
this.readAtoms(modelAtomCount);
this.applySymmetryAndSetTrajectory();
this.asc.setAtomSetName(name);
if (this.isLastModel(this.modelNumber)) {
this.continuing = false;
return false;
}} else {
this.skipAtomSet(modelAtomCount);
}this.discardLinesUntilNonBlank();
return false;
});
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.isTrajectory = false;
this.finalizeReaderASCR();
});
Clazz.defineMethod(c$, "skipAtomSet", 
function(modelAtomCount){
this.rd();
for (var i = modelAtomCount; --i >= 0; ) this.rd();

}, "~N");
Clazz.defineMethod(c$, "readAtoms", 
function(modelAtomCount){
for (var i = 0; i < modelAtomCount; ++i) {
this.rd();
var tokens = this.getTokens();
if (tokens.length < 4) {
JU.Logger.warn("line cannot be read for XYZ atom data: " + this.line);
continue;
}var atom = this.addAtomXYZSymName(tokens, 1, null, null);
this.setElementAndIsotope(atom, tokens[0]);
var vpt = 4;
switch (tokens.length) {
case 4:
continue;
case 5:
case 6:
case 8:
case 9:
if (tokens[4].indexOf(".") >= 0) {
atom.partialCharge = this.parseFloatStr(tokens[4]);
} else {
var charge = this.parseIntStr(tokens[4]);
if (charge != -2147483648) atom.formalCharge = charge;
}switch (tokens.length) {
case 5:
continue;
case 6:
atom.radius = this.parseFloatStr(tokens[5]);
continue;
case 9:
atom.atomSerial = this.parseIntStr(tokens[8]);
}
vpt++;
default:
var vx = this.parseFloatStr(tokens[vpt++]);
var vy = this.parseFloatStr(tokens[vpt++]);
var vz = this.parseFloatStr(tokens[vpt++]);
if (Float.isNaN(vx) || Float.isNaN(vy) || Float.isNaN(vz)) continue;
this.asc.addVibrationVector(atom.index, vx, vy, vz);
}
}
}, "~N");
});
;//5.0.1-v7 Tue Jul 22 18:14:29 CDT 2025
