Clazz.declarePackage("J.adapter.readers.xtal");
Clazz.load(["J.adapter.smarter.AtomSetCollectionReader", "JU.V3"], "J.adapter.readers.xtal.CgdReader", ["java.util.Hashtable", "JU.Lst", "$.M3", "$.P3", "$.PT", "J.adapter.smarter.Bond", "JU.Logger"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.noBondSym = false;
this.tokens = null;
this.htEdges = null;
this.lastName = null;
this.edgeData = null;
Clazz.instantialize(this, arguments);}, J.adapter.readers.xtal, "CgdReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod(c$, "initializeReader", 
function(){
this.setFractionalCoordinates(true);
this.asc.setNoAutoBond();
this.asc.vibScale = 1;
this.forceSymmetry(!this.noPack);
this.noBondSym = this.checkFilterKey("NOBONDSYM");
});
Clazz.overrideMethod(c$, "checkLine", 
function(){
this.line = this.line.trim();
if (this.line.length == 0 || this.line.startsWith("#")) return true;
if (!Character.isLetter(this.line.charAt(0))) this.line = this.lastName + " " + this.line;
this.tokens = this.getTokens();
if (this.tokens.length > 0) {
this.lastName = this.tokens[0].toUpperCase();
var pt = "NAME |CELL |GROUP|ATOM |EDGE |".indexOf(this.lastName);
if (this.tokens.length > 1 && (pt == 0 || this.doProcessLines)) switch (pt) {
case 0:
if (!this.doGetModel(++this.modelNumber, null)) return this.checkLastModel();
this.applySymmetryAndSetTrajectory();
this.setFractionalCoordinates(true);
this.asc.newAtomSet();
this.asc.setAtomSetName(this.line.substring(6).trim());
this.htEdges = null;
this.edgeData = null;
break;
case 6:
for (var i = 0; i < 6; i++) this.setUnitCellItem(i, (i < 3 ? 10 : 1) * this.parseFloatStr(this.tokens[i + 1]));

break;
case 12:
this.setSpaceGroupName("bilbao:" + this.group(this.tokens[1]));
break;
case 18:
this.atom();
break;
case 24:
if (!this.doApplySymmetry) break;
if (this.edgeData == null) this.edgeData =  new JU.Lst();
this.edgeData.addLast(this.line);
break;
}
}return true;
});
Clazz.defineMethod(c$, "group", 
function(name){
var name0 = null;
if (name.charAt(0) == '"') name = name.substring(1, name.length - 1);
var pt = ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf(";" + name + "=");
if (pt >= 0) {
name0 = name;
name = ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".substring(";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf("=", pt) + 1, ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;".indexOf(";", pt + 1));
}JU.Logger.info("CgdReader using GROUP " + name + (name0 == null ? "" : " alias of " + name0));
return name;
}, "~S");
Clazz.defineMethod(c$, "atom", 
function(){
var name = this.getName(this.tokens[1]);
var edgeCount = this.parseIntStr(this.tokens[2]);
for (var i = 3; i < 6; i++) if (this.tokens[i].indexOf("/") >= 0) this.tokens[i] = "" + JU.PT.parseFloatFraction(this.tokens[i]);

var a = this.addAtomXYZSymName(this.tokens, 3, null, name);
if (!this.doApplySymmetry) return;
this.asc.atomSymbolicMap.put(name, a);
this.asc.addVibrationVector(a.index, 1, 3, 7);
if (this.htEdges == null) this.htEdges =  new java.util.Hashtable();
this.htEdges.put(a,  new Array(edgeCount));
});
Clazz.defineMethod(c$, "getName", 
function(name){
return (name.charAt(0) == '"' ? name.substring(1, name.length - 1) : Character.isDigit(name.charAt(0)) ? "C" + name : name);
}, "~S");
Clazz.overrideMethod(c$, "finalizeSubclassReader", 
function(){
this.finalizeReaderASCR();
if (this.doApplySymmetry) this.finalizeNet();
});
Clazz.defineMethod(c$, "finalizeEdges", 
function(){
var p;
var name;
var a;
var atomEdges;
for (var j = 0; j < this.edgeData.size(); j++) {
this.tokens = JU.PT.getTokens(this.line = this.edgeData.get(j));
switch (this.tokens.length) {
case 3:
name = this.getName(this.tokens[1]);
a = this.asc.getAtomFromName(name);
atomEdges = this.htEdges.get(a);
p = this.asc.getAtomFromName(this.getName(this.tokens[2]));
break;
case 5:
name = this.getName(this.tokens[1]);
a = this.asc.getAtomFromName(name);
atomEdges = this.htEdges.get(a);
p = this.getCoord(2);
break;
case 7:
atomEdges = this.htEdges.get(this.findAtom(this.getCoord(1)));
p = this.getCoord(4);
break;
default:
JU.Logger.error("EDGE record skipped: " + this.line);
continue;
}
for (var i = 0, n = atomEdges.length; i < n; i++) if (atomEdges[i] == null) {
atomEdges[i] = JU.V3.newV(p);
break;
}
}
});
Clazz.defineMethod(c$, "getCoord", 
function(i){
return JU.P3.new3(JU.PT.parseFloatFraction(this.tokens[i++]), JU.PT.parseFloatFraction(this.tokens[i++]), JU.PT.parseFloatFraction(this.tokens[i++]));
}, "~N");
Clazz.defineMethod(c$, "finalizeNet", 
function(){
this.finalizeEdges();
var m =  new JU.M3();
var pt =  new JU.P3();
for (var i = 0, n = this.asc.ac; i < n; i++) {
var a = this.asc.atoms[i];
var a0 = this.asc.atoms[a.atomSite];
if (this.noBondSym && a !== a0) continue;
var edges = this.htEdges.get(a0);
if (edges == null) continue;
var ix = Clazz.floatToInt(a.vib.x) + 7;
var iy = Clazz.floatToInt(a.vib.y) + 7;
var iz = Clazz.floatToInt(a.vib.z) + 7;
m.setRowV(0, J.adapter.readers.xtal.CgdReader.vecs[ix]);
m.setRowV(1, J.adapter.readers.xtal.CgdReader.vecs[iy]);
m.setRowV(2, J.adapter.readers.xtal.CgdReader.vecs[iz]);
for (var j = 0, n1 = edges.length; j < n1; j++) {
pt.sub2(edges[j], a0);
m.rotate(pt);
pt.add(a);
var b = this.findAtom(pt);
if (b != null) this.asc.addBond( new J.adapter.smarter.Bond(a.index, b.index, 1));
 else if (pt.x >= 0 && pt.x <= 1 && pt.y >= 0 && pt.y <= 1 && pt.z >= 0 && pt.z <= 1) JU.Logger.error(" not found: i=" + i + "  pt=" + pt + " for a=" + a + "\n a0=" + a0 + " edge[" + j + "]=" + edges[j] + "\n a.vib=" + a.vib + "\n m=" + m);
}
a.vib = null;
}
});
Clazz.defineMethod(c$, "findAtom", 
function(pt){
for (var i = this.asc.ac; --i >= 0; ) if (this.asc.atoms[i].distanceSquared(pt) < 0.00001) return this.asc.atoms[i];

return null;
}, "JU.P3");
c$.vecs =  Clazz.newArray(-1, [JU.V3.new3(0, 0, -1), JU.V3.new3(1, 0, -1), null, JU.V3.new3(0, 1, -1), JU.V3.new3(0, -1, 0), JU.V3.new3(1, -1, 0), JU.V3.new3(-1, 0, 0), null, JU.V3.new3(1, 0, 0), JU.V3.new3(-1, 1, 0), JU.V3.new3(0, 1, 0), JU.V3.new3(0, -1, 1), null, JU.V3.new3(-1, 0, 1), JU.V3.new3(0, 0, 1)]);
});
;//5.0.1-v7 Mon Jul 21 08:59:16 CDT 2025
