Clazz.declarePackage("J.adapter.readers.simple");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.AmpacReader", ["JU.P3"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ac = 0;
this.freqAtom0 = -1;
this.partialCharges = null;
this.atomPositions = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.simple, "AmpacReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.indexOf("CARTESIAN COORDINATES") >= 0) {
if (!this.doGetModel(++this.modelNumber, null)) return this.checkLastModel();
this.readCoordinates();
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf("NET ATOMIC CHARGES") >= 0) {
this.readPartialCharges();
return true;
}if (this.line.indexOf("VIBRATIONAL FREQUENCIES") >= 0) {
this.readFrequencies();
return true;
}return true;
});
Clazz.defineMethod(c$, "readCoordinates", 
function(){
var haveFreq = (this.freqAtom0 >= 0);
if (haveFreq) {
this.atomPositions =  new Array(this.ac);
} else {
this.asc.newAtomSet();
}this.rd();
this.ac = 0;
while (this.rd() != null) {
var tokens = this.getTokens();
if (tokens.length < 5) break;
if (haveFreq) {
this.atomPositions[this.ac] = JU.P3.new3(this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]), this.parseFloatStr(tokens[4]));
} else {
this.addAtomXYZSymName(tokens, 2, tokens[1], null);
}this.ac++;
}
if (haveFreq) this.setPositions();
});
Clazz.defineMethod(c$, "setPositions", 
function(){
var maxAtom = this.asc.ac;
var atoms = this.asc.atoms;
for (var i = this.freqAtom0; i < maxAtom; i++) {
atoms[i].setT(this.atomPositions[i % this.ac]);
atoms[i].partialCharge = this.partialCharges[i % this.ac];
}
});
Clazz.defineMethod(c$, "readPartialCharges", 
function(){
this.rd();
this.partialCharges =  Clazz.newFloatArray (/*org.eclipse.jdt.core.dom.SimpleName*/this.ac, 0);
var tokens;
for (var i = 0; i < this.ac; i++) {
if (this.rd() == null || (tokens = this.getTokens()).length < 4) break;
this.partialCharges[i] = this.parseFloatStr(tokens[2]);
}
});
Clazz.defineMethod(c$, "readFrequencies", 
function(){
while (this.rd() != null && this.line.indexOf("FREQ  :") < 0) {
}
while (this.line != null && this.line.indexOf("FREQ  :") >= 0) {
var frequencies = this.getTokens();
while (this.rd() != null && this.line.indexOf("IR I") < 0) {
}
var iAtom0 = this.asc.ac;
if (this.vibrationNumber == 0) this.freqAtom0 = iAtom0;
var frequencyCount = frequencies.length - 2;
var ignore =  Clazz.newBooleanArray(frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration(++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneLastAtomSet();
this.asc.setAtomSetName(frequencies[i + 2] + " cm^-1");
this.asc.setAtomSetModelProperty("Frequency", frequencies[i + 2] + " cm^-1");
this.asc.setAtomSetModelProperty(".PATH", "Frequencies");
}
this.fillFrequencyData(iAtom0, this.ac, this.ac, ignore, false, 8, 9, null, 0, null);
this.rd();
this.rd();
}
});
});
;//5.0.1-v4 Thu Feb 20 12:29:54 CST 2025
