Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.Wien2kReader", ["JU.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.isrhombohedral = false;
this.latticeCode = '\0';
this.doSymmetry = true;
this.cxyz = " x y z";
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "Wien2kReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.doSymmetry = !this.sgName.equals("none");
this.setFractionalCoordinates(true);
this.asc.setCollectionName(this.rd());
this.readUnitCell();
this.readAtoms();
this.readSymmetry();
this.readEmbeddedScript();
this.continuing = false;
});
Clazz.defineMethod(c$, "readUnitCell", 
function(){
this.rd();
this.isrhombohedral = ((this.latticeCode = this.line.charAt(0)) == 'R');
if (this.line.startsWith("CYZ")) this.latticeCode = 'A';
 else if (this.line.startsWith("CXZ")) this.latticeCode = 'B';
 else if (this.line.startsWith("B")) this.latticeCode = 'I';
if (this.latticeCode != 'R' && this.latticeCode != 'H') this.asc.getXSymmetry().setLatticeParameter(this.latticeCode.charCodeAt(0));
if (this.line.length > 32) {
var name = this.line.substring(32).trim();
if (name.indexOf(" ") >= 0) name = name.substring(name.indexOf(" ") + 1);
if (name.indexOf("_") >= 0) name = name.substring(name.indexOf("_") + 1);
this.setSpaceGroupName(name);
}var factor = (this.rd().toLowerCase().indexOf("ang") >= 0 ? 1 : 0.5291772);
this.rd();
var a = this.parseFloatRange(this.line, 0, 10) * factor;
var b = this.parseFloatRange(this.line, 10, 20) * factor;
var c = this.parseFloatRange(this.line, 20, 30) * factor;
var l = this.line.length;
var alpha = (l >= 40 ? this.parseFloatRange(this.line, 30, 40) : 0);
var beta = (l >= 50 ? this.parseFloatRange(this.line, 40, 50) : 0);
var gamma = (l >= 60 ? this.parseFloatRange(this.line, 50, 60) : 0);
if (this.isrhombohedral) {
var ar = Math.sqrt(a * a / 3 + c * c / 9);
alpha = beta = gamma = (Math.acos((2 * c * c - 3 * a * a) / (2 * c * c + 6 * a * a)) * 180 / 3.141592653589793);
a = b = c = ar;
}if (Float.isNaN(alpha) || alpha == 0) alpha = 90;
if (Float.isNaN(beta) || beta == 0) beta = 90;
if (Float.isNaN(gamma) || gamma == 0) gamma = 90;
this.setUnitCell(a, b, c, alpha, beta, gamma);
});
Clazz.defineMethod(c$, "readAtoms", 
function(){
this.rd();
while (this.line != null && (this.line.indexOf("ATOM") == 0 || !this.doSymmetry && this.line.indexOf(":") == 8)) {
var thisAtom = this.asc.ac;
this.addAtom();
if (this.rd().indexOf("MULT=") == 10) for (var i = this.parseIntRange(this.line, 15, 18); --i >= 0; ) {
this.rd();
if (!this.doSymmetry) this.addAtom();
}
var atomName = this.line.substring(0, 10);
var sym = atomName.substring(0, 2).trim();
if (sym.length == 2 && JU.PT.isDigit(sym.charAt(1))) sym = sym.substring(0, 1);
atomName = JU.PT.rep(atomName, " ", "");
var n = 0;
for (var i = this.asc.ac; --i >= thisAtom; ) {
var atom = this.asc.atoms[i];
atom.elementSymbol = sym;
atom.atomName = atomName + "_" + (n++);
}
while (this.rd() != null && this.line.indexOf("ATOM") < 0 && this.line.indexOf("SYMMETRY") < 0) {
}
}
});
Clazz.defineMethod(c$, "addAtom", 
function(){
var a = this.parseFloatRange(this.line, 12, 22);
var b = this.parseFloatRange(this.line, 25, 35);
var c = this.parseFloatRange(this.line, 38, 48);
var atom = this.asc.addNewAtom();
this.setAtomCoordXYZ(atom, a, b, c);
});
Clazz.defineMethod(c$, "readSymmetry", 
function(){
if (this.line.indexOf("SYMMETRY") < 0) return;
var n = this.parseIntRange(this.line, 0, 4);
for (var i = n; --i >= 0; ) {
var xyz = this.getJones() + "," + this.getJones() + "," + this.getJones();
if (this.doSymmetry) this.setSymmetryOperator(xyz);
this.rd();
}
});
Clazz.defineMethod(c$, "getJones", 
function(){
this.rd();
var xyz = "";
var trans = this.parseFloatStr(this.line.substring(6));
for (var i = 0; i < 6; i++) {
if (this.line.charAt(i) == '-') xyz += "-";
if (this.line.charAt(++i) == '1') {
xyz += " x y z".charAt(i);
if (trans > 0) xyz += "+";
if (trans != 0) xyz += trans;
}}
return xyz;
});
Clazz.defineMethod(c$, "readEmbeddedScript", 
function(){
while (this.line != null) {
this.checkCurrentLineForScript();
this.rd();
}
});
});
;//5.0.1-v2 Mon Mar 04 12:59:58 CST 2024
