Clazz.declarePackage("J.adapter.readers.simple");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.CubeReader", ["JU.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.ac = 0;
this.isAngstroms = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.simple, "CubeReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.asc.newAtomSet();
this.readTitleLines();
this.readAtomCountAndOrigin();
this.readLines(3);
this.readAtoms();
this.applySymmetryAndSetTrajectory();
this.continuing = false;
});
Clazz.defineMethod(c$, "readTitleLines", 
function(){
if (this.rd().indexOf("#JVXL") == 0) while (this.rd().indexOf("#") == 0) {
}
this.checkCurrentLineForScript();
var name = this.line.trim();
this.rd();
this.checkCurrentLineForScript();
this.asc.setAtomSetName(name + " - " + this.line.trim());
});
Clazz.defineMethod(c$, "readAtomCountAndOrigin", 
function(){
this.rd();
this.isAngstroms = (this.line.indexOf("ANGSTROMS") >= 0);
var tokens = this.getTokens();
if (tokens[0].charAt(0) == '+') tokens[0] = tokens[0].substring(1);
this.ac = Math.abs(this.parseIntStr(tokens[0]));
});
Clazz.defineMethod(c$, "readAtoms", 
function(){
var f = (this.isAngstroms ? 1 : 0.5291772);
for (var i = 0; i < this.ac; ++i) {
var tokens = JU.PT.getTokens(this.rd());
this.setAtomCoordScaled(null, tokens, 2, f).elementNumber = this.parseIntStr(tokens[0]);
}
});
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
