Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.BilbaoReader", ["JU.PT", "$.SB", "$.V3", "JU.Vibration"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.getHigh = false;
this.getSym = false;
this.normDispl = false;
this.doDisplace = false;
this.kvec = null;
this.i0 = 0;
this.nAtoms = 0;
this.isBCSfile = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "BilbaoReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.normDispl = !this.checkFilterKey("NONORM");
this.doDisplace = this.isTrajectory;
this.getSym = true;
this.getHigh = this.checkFilterKey("HIGH") && !this.doDisplace;
this.asc.vibScale = 1;
this.appendLoadNote("Bilbao Crystallographic Server\ncryst@wm.lc.ehu.es");
if (this.rd().indexOf("<") < 0) {
this.readBilbaoDataFile();
this.continuing = false;
}});
Clazz.overrideMethod(c$, "checkLine", 
function(){
if (this.line.contains(">Bilbao Crystallographic Server<")) {
this.line = this.line.substring(this.line.lastIndexOf(">") + 1).trim();
if (this.line.length > 0) this.appendLoadNote(this.line + "\n");
} else if (this.line.contains("High symmetry structure<")) {
if (this.getHigh) this.readBilbaoFormat("high symmetry", NaN);
} else if (this.line.contains("Low symmetry structure<")) {
if (!this.doDisplace) this.readBilbaoFormat("low symmetry", NaN);
} else if (this.line.contains("structure in the subgroup basis<")) {
if (!this.doDisplace) this.readBilbaoFormat("high symmetry in the subgroup basis", NaN);
} else if (this.line.contains("Low symmetry structure after the origin shift<")) {
this.readBilbaoFormat("low symmetry after origin shift", NaN);
} else if (this.line.contains("<h3>Irrep:")) {
this.readVirtual();
}return true;
});
Clazz.defineMethod(c$, "readBilbaoDataFile", 
function(){
this.isBCSfile = true;
this.checkComment();
while (this.line != null) {
this.readBilbaoFormat(null, NaN);
if (this.rdLine() == null || this.line.indexOf("##disp-par##") < 0) {
this.applySymmetryAndSetTrajectory();
} else {
this.readDisplacements(1);
this.rdLine();
}}
});
Clazz.defineMethod(c$, "checkComment", 
function(){
if (!this.line.startsWith("#") || this.line.indexOf("disp-par") >= 0) return false;
if (this.isBCSfile) {
this.appendLoadNote(this.line);
if (this.line.startsWith("# Title:")) this.asc.setAtomSetName(this.line.substring(8).trim());
}return true;
});
Clazz.defineMethod(c$, "readBilbaoFormat", 
function(title, fAmp){
this.setFractionalCoordinates(true);
if (!this.doGetModel(++this.modelNumber, title)) return;
this.asc.newAtomSet();
if (this.line.startsWith("#")) this.rdLine();
if (this.line.startsWith("Bilbao Crys:")) {
title = this.line.substring(13).trim();
this.rdLine();
}this.setTitle(title);
var ptPre = this.line.indexOf("<pre>");
if (ptPre >= 0) this.line = this.line.substring(ptPre + 5);
var intTableNo = this.parseIntStr(this.line);
if (intTableNo == 0) {
this.setSpaceGroupName(this.line.substring(2));
} else {
while (intTableNo < 0 && this.rdLine() != null) intTableNo = this.parseIntStr(this.line);

this.setSpaceGroupName("" + intTableNo);
}var data =  Clazz.newFloatArray (/*org.eclipse.jdt.core.dom.NumberLiteral*/6, 0);
this.fillFloatArray(this.rdLine(), 0, data);
for (var i = 0; i < 6; i++) this.setUnitCellItem(i, data[i]);

this.i0 = this.asc.ac;
this.nAtoms = this.parseIntStr(this.rdLine());
for (var i = this.nAtoms; --i >= 0; ) {
var tokens = JU.PT.getTokens(this.rdLine());
if (!this.getSym && tokens[1].contains("_")) continue;
if (tokens.length == 3) this.addAtomXYZSymName(tokens, 0, "Be", "Be1");
 else this.addAtomXYZSymName(tokens, 3, tokens[0], tokens[0] + tokens[1]);
}
if (Float.isNaN(fAmp)) {
if (ptPre >= 0) this.applySymmetryAndSetTrajectory();
return;
}this.line = null;
this.readDisplacements(fAmp);
}, "~S,~N");
Clazz.defineMethod(c$, "setSpaceGroupName", 
function(name){
if (!this.ignoreFileSpaceGroupName) {
name = "bilbao:" + name;
} else if (this.sgName.startsWith(":")) {
var pt = name.indexOf(':');
if (pt < 0) pt = name.length;
name = name.substring(0, pt);
var s = this.htParams.get("loadScript");
if (s != null) {
pt = s.indexOf("spacegroup \":");
if (pt > 0) s.insert(pt + 12, name);
}name += this.sgName;
this.ignoreFileSpaceGroupName = false;
}Clazz.superCall(this, J.adapter.readers.xtal.BilbaoReader, "setSpaceGroupName", [name]);
}, "~S");
Clazz.defineMethod(c$, "readDisplacements", 
function(fAmp){
for (var i = 0; i < this.nAtoms; i++) {
if (this.line == null) this.rdLine();
var tokens = JU.PT.split(this.line, "x|x");
if (this.getSym || !tokens[0].contains("_")) this.asc.atoms[this.i0 + i].vib = JU.V3.new3(this.parseFloatStr(tokens[1]), this.parseFloatStr(tokens[2]), this.parseFloatStr(tokens[3]));
this.line = null;
}
this.applySymmetryAndSetTrajectory();
for (var i = this.asc.ac; --i >= this.i0; ) {
var a = this.asc.atoms[i];
if (a.vib != null) {
var v =  new JU.Vibration();
v.setT(a.vib);
a.vib = v;
this.asc.getSymmetry().toCartesian(v, true);
v.scale(1 / fAmp);
}}
this.appendLoadNote((this.asc.ac - this.i0) + " displacements");
}, "~N");
Clazz.defineMethod(c$, "setTitle", 
function(title){
if (title != null) {
this.asc.setAtomSetName(title);
this.appendLoadNote(title);
}}, "~S");
Clazz.defineMethod(c$, "rdLine", 
function(){
while (this.rd() != null && (this.line.trim().length == 0 || this.checkComment())) {
}
return this.line;
});
Clazz.defineMethod(c$, "readVirtual", 
function(){
if (this.line.contains("<h3>K-vector:")) this.kvec = this.line.substring(this.line.indexOf("("), this.line.indexOf(")") + 1);
var s = this.getLinesUntil("\"BCS\"");
var pt = s.indexOf("The amplitude");
pt = s.indexOf("=", pt);
var amp = s.substring(pt + 2, s.indexOf(" ", pt + 2));
var fAmp = (this.normDispl ? this.parseFloatStr(amp) : 1);
var irrep = this.getAttr(s, "irrep");
if (irrep.indexOf(":") >= 0) irrep = irrep.substring(0, irrep.indexOf(":"));
this.line = this.line.substring(this.line.indexOf("value=") + 7);
this.readBilbaoFormat(this.kvec + " " + irrep + " (" + amp + " Ang.)", fAmp);
});
Clazz.defineMethod(c$, "getAttr", 
function(s, key){
var pt = s.indexOf("value", s.indexOf("\"" + key + "\""));
s = JU.PT.getQuotedStringAt(s, pt);
s = JU.PT.rep(s, "<i>", "");
s = JU.PT.rep(s, "</i>", "");
return s.trim();
}, "~S,~S");
Clazz.defineMethod(c$, "getLinesUntil", 
function(key){
var sb =  new JU.SB();
do {
sb.append(this.line);
} while (!this.rd().contains(key));
return sb.toString();
}, "~S");
});
;//5.0.1-v4 Thu Feb 20 12:29:54 CST 2025
