Clazz.declarePackage("J.adapter.readers.quantum");
Clazz.load(null, "J.adapter.readers.quantum.NBOParser", ["java.util.Hashtable", "JU.Lst", "$.PT"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.haveBeta = false;
Clazz.instantialize(this, arguments);}, J.adapter.readers.quantum, "NBOParser", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "set", 
function(vwr){
this.vwr = vwr;
return this;
}, "JV.Viewer");
Clazz.defineMethod(c$, "getAllStructures", 
function(output, list){
if (output == null) return null;
if (list == null) list =  new JU.Lst();
output = JU.PT.rep(output, "the $CHOOSE", "");
this.getStructures(this.getBlock(output, "$CHOOSE"), "CHOOSE", list);
this.getStructures(this.getBlock(output, "$NRTSTR"), "NRTSTR", list);
this.getStructures(this.getBlock(output, "$NRTSTRA"), "NRTSTRA", list);
this.getStructures(this.getBlock(output, "$NRTSTRB"), "NRTSTRB", list);
this.getStructuresTOPO(this.getData(output, "TOPO matrix", "* Total *", 1), "RSA", list);
this.getStructuresTOPO(this.getData(output, "TOPO matrix", "* Total *", 2), "RSB", list);
return list;
}, "~S,JU.Lst");
Clazz.defineMethod(c$, "getBlock", 
function(output, key){
var pt = output.indexOf(key);
var pt1 = output.indexOf("$END", pt + 1);
return (pt < 0 || pt1 < 0 ? null : output.substring(pt + key.length, pt1));
}, "~S,~S");
c$.getStructures46 = Clazz.defineMethod(c$, "getStructures46", 
function(tokens, type, structures, nAtoms){
if (tokens == null) return;
var htData =  new java.util.Hashtable();
structures.addLast(htData);
var matrix =  Clazz.newIntArray (nAtoms, nAtoms, 0);
htData.put("matrix", matrix);
htData.put("type", type);
htData.put("spin", type);
htData.put("index", Integer.$valueOf(0));
for (var n = tokens.length, i = 0; i < n; i++) {
var org = tokens[i];
if (org.contains("(ry)") || org.contains("Ryd") || org.contains("RY")) break;
if (org.contains("*") || org.contains("(cr)") || org.startsWith("CR(") || org.contains("Cor(")) continue;
if (org.startsWith("LP(")) {
var ia = J.adapter.readers.quantum.NBOParser.getAtomIndex(org.substring(org.indexOf(")") + 1));
matrix[ia][ia] += 1;
continue;
}var isLP = org.endsWith("(lp)");
if (isLP || org.endsWith("(lv)")) {
var ia = J.adapter.readers.quantum.NBOParser.getAtomIndex(org.substring(0, org.length - 4));
matrix[ia][ia] += (isLP ? 1 : 10);
continue;
}var names = JU.PT.split(org, "-");
switch (names.length) {
case 3:
System.out.println("NBOParser 3-center bonnd " + org + " ignored for Kekule structure");
continue;
case 2:
if (names[0].startsWith("BD(")) {
names[0] = names[0].substring(names[0].indexOf(")") + 1);
}var ia = J.adapter.readers.quantum.NBOParser.getAtomIndex(names[0]);
var ib = J.adapter.readers.quantum.NBOParser.getAtomIndex(names[1]);
matrix[ia][ib]++;
break;
}
}
J.adapter.readers.quantum.NBOParser.dumpMatrix(type, 0, matrix);
}, "~A,~S,JU.Lst,~N");
c$.getAtomIndex = Clazz.defineMethod(c$, "getAtomIndex", 
function(xx99){
for (var n = xx99.length, i = n, val = 0, pow = 1, ch = 0; --i >= 0; ) {
if ((ch = (xx99.charAt(i)).charCodeAt(0)) < 48 || ch > 57) return val - 1;
val += (ch - 48) * pow;
pow *= 10;
}
return 0;
}, "~S");
Clazz.defineMethod(c$, "getStructuresTOPO", 
function(data, nrtType, list){
if (data == null || data.length == 0) return;
var parts = JU.PT.split(data, "Resonance");
if (parts.length < 2) return;
var pt = parts[0].lastIndexOf(".");
var nAtoms = JU.PT.parseInt(parts[0].substring(pt - 3, pt));
if (nAtoms < 0) return;
var tokens = JU.PT.getTokens(JU.PT.rep(JU.PT.rep(parts[0], ".", ".1"), "Atom", "-1"));
var raw =  Clazz.newFloatArray (tokens.length, 0);
var n = JU.PT.parseFloatArrayInfested(tokens, raw);
var table =  Clazz.newIntArray (nAtoms, nAtoms, 0);
var atom1 = -1;
var atom2 = 0;
var atom0 = 0;
for (var i = 0; i < n; i++) {
var f = raw[i];
if (f < 0) {
atom1 = -1;
continue;
}if (f % 1 == 0) {
if (atom1 == -1) {
atom0 = Clazz.floatToInt(f);
atom1 = -2;
}if (atom1 < 0) continue;
table[atom1][atom2++] = Clazz.floatToInt(f);
} else {
atom1 = Clazz.floatToInt(f - 1);
atom2 = atom0 - 1;
}}
var matrix = null;
tokens = parts[1].$plit("\n");
var s = "";
for (var i = 3; i < tokens.length; i++) if (tokens[i].indexOf("--") < 0) s += tokens[i].substring(10) + "\n";

s = s.$replace('-', ' ');
s = JU.PT.rep(s, ".", ".1");
s = JU.PT.rep(s, "(", " -1 ");
s = JU.PT.rep(s, ")", " -2 ");
s = JU.PT.rep(s, ",", " -3 ");
tokens = JU.PT.getTokens(s);
raw =  Clazz.newFloatArray (tokens.length, 0);
n = JU.PT.parseFloatArrayInfested(tokens, raw);
var htData = null;
var dir = 1;
atom1 = atom2 = -1;
for (var i = 0, index = 0; i < n; i++) {
var f = raw[i];
var remain = f % 1;
if (remain == 0) {
var v = Clazz.floatToInt(f);
switch (v) {
case -1:
dir = -1;
atom1 = atom2 = -1;
continue;
case -2:
break;
case -3:
if (atom1 < 0) continue;
break;
default:
if (atom1 < 0) {
atom1 = atom2 = v - 1;
} else {
atom2 = v - 1;
}continue;
}
matrix[atom1][atom2] += dir;
atom1 = atom2 = -1;
dir = 1;
} else {
if (htData == null) matrix = table;
J.adapter.readers.quantum.NBOParser.dumpMatrix(nrtType, index, matrix);
if (raw[i + 2] == 0) break;
list.addLast(htData =  new java.util.Hashtable());
s = "" + (Clazz.floatToInt(f) * 100 + Clazz.doubleToInt((remain - 0.0999999) * 1000));
var len = s.length;
s = (len == 2 ? "0" : "") + s.substring(0, len - 2) + "." + s.substring(len - 2);
htData.put("weight", s);
htData.put("index", Integer.$valueOf(index++));
htData.put("type", nrtType.toLowerCase());
htData.put("spin", nrtType.indexOf("B") >= 0 ? "beta" : "alpha");
matrix =  Clazz.newIntArray (nAtoms, nAtoms, 0);
htData.put("matrix", matrix);
for (var j = 0; j < nAtoms; j++) for (var k = 0; k < nAtoms; k++) matrix[j][k] = table[j][k];


}}
}, "~S,~S,JU.Lst");
c$.dumpMatrix = Clazz.defineMethod(c$, "dumpMatrix", 
function(nrtType, index, matrix){
System.out.println("NBOParser matrix " + nrtType + " " + index);
for (var j = 0, nAtoms = matrix.length; j < nAtoms; j++) System.out.println(JU.PT.toJSON(null, matrix[j]));

System.out.println("-------------------");
}, "~S,~N,~A");
Clazz.defineMethod(c$, "getData", 
function(output, start, end, n){
var pt = 0;
var pt1 = 0;
for (var i = 0; i < n; i++) {
pt = output.indexOf(start, pt1 + 1);
pt1 = output.indexOf(end, pt + 1);
}
return (pt < 0 || pt1 < 0 ? null : output.substring(pt, pt1));
}, "~S,~S,~S,~N");
Clazz.defineMethod(c$, "getStructures", 
function(data, nrtType, list){
if (data == null || data.length == 0) return 0;
var n = 0;
try {
var ignoreSTR = (data.indexOf("ALPHA") >= 0);
if (!ignoreSTR && !data.contains("STR")) data = "STR " + data + " END";
nrtType = nrtType.toLowerCase();
var spin = (nrtType.equals("nrtstrb") ? "beta" : "alpha");
if (nrtType.equals("choose")) nrtType = null;
var htData = null;
var tokens = JU.PT.getTokens(data.$replace('\r', ' ').$replace('\n', ' ').$replace('\t', ' '));
var lastType = "";
var index = 0;
for (var i = 0, nt = tokens.length; i < nt; i++) {
var tok = tokens[i];
switch ("STR  =    ALPHABETA LONE BOND 3C".indexOf(tok)) {
case 0:
if (ignoreSTR) continue;
tok = spin;
case 10:
case 15:
list.addLast(htData =  new java.util.Hashtable());
if (!lastType.equals(tok)) {
lastType = tok;
index = 0;
}htData.put("index", Integer.$valueOf(index++));
htData.put("spin", spin = tok.toLowerCase());
if (spin.equals("beta")) this.haveBeta = true;
htData.put("type", nrtType == null ? "choose" + spin.substring(0, 1) : nrtType);
n++;
break;
case 5:
htData.put("weight", tokens[++i]);
break;
case 20:
var lone =  new JU.Lst();
htData.put("lone", lone);
while (!(tok = tokens[++i]).equals("END")) {
var at1 = Integer.parseInt(tok);
var nlp = Integer.parseInt(tokens[++i]);
lone.addLast( Clazz.newIntArray(-1, [nlp, at1]));
}
break;
case 25:
var bonds =  new JU.Lst();
htData.put("bond", bonds);
while (!(tok = tokens[++i]).equals("END")) {
var order = "DTQ".indexOf(tok.charAt(0)) + 2;
var at1 = Integer.parseInt(tokens[++i]);
var at2 = Integer.parseInt(tokens[++i]);
bonds.addLast( Clazz.newIntArray(-1, [order, at1, at2]));
}
break;
case 30:
var threeCenter =  new JU.Lst();
htData.put("3c", threeCenter);
while (!(tok = tokens[++i]).equals("END")) {
var order = "DTQ".indexOf(tok.charAt(0)) + 2;
var at1 = Integer.parseInt(tokens[++i]);
var at2 = Integer.parseInt(tokens[++i]);
var at3 = Integer.parseInt(tokens[++i]);
threeCenter.addLast( Clazz.newIntArray(-1, [order, at1, at2, at3]));
}
break;
}
}
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
e.printStackTrace();
list.clear();
return -1;
} else {
throw e;
}
}
return n;
}, "~S,~S,JU.Lst");
Clazz.defineMethod(c$, "isOpenShell", 
function(){
return this.haveBeta;
});
c$.getStructureMap = Clazz.defineMethod(c$, "getStructureMap", 
function(structureList, type, index){
if (type == null || structureList == null) return null;
type = type.toLowerCase();
var spin = (type.indexOf("b") < 0 ? "alpha" : "beta");
for (var i = 0; i < structureList.size(); i++) {
var map = structureList.get(i);
if (spin.equals(map.get("spin")) && type.equals(map.get("type")) && (index < 0 || index == (map.get("index")).intValue())) {
return map;
}}
return null;
}, "JU.Lst,~S,~N");
Clazz.defineMethod(c$, "connectNBO", 
function(modelIndex, type){
try {
if (type == null) type = "alpha";
type = type.toLowerCase();
if (type.length == 0 || type.equals("46")) type = "alpha";
var map = this.vwr.ms.getModelAuxiliaryInfo(modelIndex);
this.haveBeta = map.containsKey("isOpenShell");
var list = map.get("nboStructures");
if (list == null || list.size() == 0) return false;
type = type.toLowerCase();
var index = type.indexOf("_");
if (index > 0) {
if (list.size() <= 2) {
var fname = map.get("fileName");
if (fname != null && !fname.endsWith(".nbo")) {
fname = fname.substring(0, fname.lastIndexOf(".")) + ".nbo";
this.getAllStructures(this.vwr.getAsciiFileOrNull(fname), list);
}}var tokens = JU.PT.split(type, "_");
index = JU.PT.parseInt(tokens[1]) - 1;
type = tokens[0];
} else {
index = 0;
}var structureMap = J.adapter.readers.quantum.NBOParser.getStructureMap(list, type, index);
if (structureMap == null || !this.setJmolLewisStructure(structureMap, modelIndex, index + 1)) {
return false;
}map.put("nboStructure", structureMap);
} catch (e) {
e.printStackTrace();
return false;
}
return true;
}, "~N,~S");
Clazz.defineMethod(c$, "setJmolLewisStructure", 
function(structureMap, modelIndex, resNo){
if (structureMap == null || modelIndex < 0) return false;
var type = structureMap.get("type");
System.out.println("creating structure " + modelIndex + " " + type);
var bonds = structureMap.get("bond");
var lonePairs = structureMap.get("lone");
var matrix = structureMap.get("matrix");
var lplv = structureMap.get("lplv");
var bondCounts = structureMap.get("bondCounts");
var needLP = (lplv == null);
var bsAtoms = this.vwr.ms.getModelAtomBitSetIncludingDeleted(modelIndex, false);
var atomCount = bsAtoms.cardinality();
var iatom0 = bsAtoms.nextSetBit(0);
if (matrix != null && atomCount != matrix.length) return false;
if (matrix != null) J.adapter.readers.quantum.NBOParser.dumpMatrix(type, resNo, matrix);
if (needLP) {
structureMap.put("lplv", lplv =  Clazz.newIntArray (atomCount, 0));
structureMap.put("bondCounts", bondCounts =  Clazz.newIntArray (atomCount, 0));
}if (needLP) {
if (lonePairs != null) {
for (var i = lonePairs.size(); --i >= 0; ) {
var na = lonePairs.get(i);
var nlp = na[0];
var a1 = na[1] - 1;
lplv[a1] = nlp;
}
} else if (matrix != null) {
for (var i = atomCount; --i >= 0; ) {
lplv[i] = matrix[i][i];
}
}}this.vwr.ms.deleteModelBonds(modelIndex);
var mad = this.vwr.ms.getDefaultMadFromOrder(1);
if (bonds != null) {
for (var i = bonds.size(); --i >= 0; ) {
var oab = bonds.get(i);
var a1 = iatom0 + oab[1] - 1;
var a2 = iatom0 + oab[2] - 1;
var order = oab[0];
if (needLP) {
bondCounts[a1] += order;
bondCounts[a2] += order;
}this.vwr.ms.bondAtoms(this.vwr.ms.at[a1], this.vwr.ms.at[a2], order, mad, null, 0, true, true);
}
} else if (matrix != null) {
for (var i = 0; i < atomCount - 1; i++) {
var m = matrix[i];
for (var j = i + 1; j < atomCount; j++) {
var order = m[j];
if (order == 0) continue;
System.out.println("adding bond " + this.vwr.ms.at[i + iatom0] + " " + this.vwr.ms.at[j + iatom0]);
this.vwr.ms.bondAtoms(this.vwr.ms.at[i + iatom0], this.vwr.ms.at[j + iatom0], order, mad, null, 0, false, true);
if (needLP) {
bondCounts[i] += order;
bondCounts[j] += order;
}}
}
}for (var i = 0, ia = bsAtoms.nextSetBit(0); ia >= 0; ia = bsAtoms.nextSetBit(ia + 1), i++) {
var a = this.vwr.ms.at[ia];
a.setValence(bondCounts[i]);
a.setFormalCharge(0);
var nH = this.vwr.ms.getMissingHydrogenCount(a, true);
if (a.getElementNumber() == 6 && nH == 1) {
if (bondCounts[i] == 3 && lplv[i] % 10 == 0 || bondCounts[i] == 2) nH -= 2;
}a.setFormalCharge(-nH);
}
return true;
}, "java.util.Map,~N,~N");
Clazz.defineMethod(c$, "getNBOAtomLabel", 
function(a){
var name = a.getAtomName();
var modelIndex = a.getModelIndex();
var structureMap = this.vwr.ms.getModelAuxiliaryInfo(modelIndex).get("nboStructure");
if (this.vwr == null || structureMap == null) return name;
var lplv = structureMap.get("lplv");
var i = a.i - this.vwr.ms.am[modelIndex].firstAtomIndex;
var addFormalCharge = this.vwr.getBoolean(603979891);
var charge = (addFormalCharge ? this.vwr.ms.at[i].getFormalCharge() : 0);
if (lplv[i] == 0 && charge == 0) return name;
if (lplv[i] % 10 > 0) name = "<sup>(" + (lplv[i] % 10) + ")</sup>" + name;
if (lplv[i] >= 10) name = "*" + name;
if (addFormalCharge) {
if (charge != 0) name += "<sup>" + Math.abs(charge) + (charge > 0 ? "+" : charge < 0 ? "-" : "") + "</sup>";
}return name;
}, "JM.Atom");
});
;//5.0.1-v7 Mon Aug 17 10:07:10 MDT 2026
