Clazz.declarePackage("J.adapter.writers");
Clazz.load(null, "J.adapter.writers.MOLWriter", ["java.util.Arrays", "$.Hashtable", "JU.Lst", "$.Measure", "$.P3", "$.PT", "$.SB", "$.V3", "JS.T", "JU.Elements", "$.Escape", "JV.PropertyManager", "$.Viewer"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.vwr = null;
this.ptTemp = null;
this.vNorm = null;
this.vTemp = null;
this.connections = null;
Clazz.instantialize(this, arguments);}, J.adapter.writers, "MOLWriter", null);
/*LV!1824 unnec constructor*/Clazz.defineMethod(c$, "setViewer", 
function(vwr){
this.vwr = vwr;
return this;
}, "JV.Viewer");
Clazz.defineMethod(c$, "addMolFile", 
function(title, iModel, mol, bsAtoms, bsBonds, asV3000, asJSON, noAromatic, q, is2d){
var nAtoms = bsAtoms.cardinality();
var nBonds = bsBonds.cardinality();
if (!asV3000 && !asJSON && (nAtoms > 999 || nBonds > 999)) return false;
if (!asJSON) {
if (title.length > 80) title = title.substring(0, 77) + "...";
mol.append(title).append("\n");
var version = JV.Viewer.getJmolVersion();
mol.append(JV.PropertyManager.getSDFDateLine("__Jmol-" + version, is2d));
mol.append("Jmol version ").append(version).append(" EXTRACT: ").append(JU.Escape.eBS(bsAtoms)).append("\n");
}var asSDF = (iModel >= 0);
var molData = (asSDF ? this.vwr.ms.getInfo(iModel, "molData") : null);
var _keyList = (asSDF ? this.vwr.ms.getInfo(iModel, "molDataKeys") : null);
var ms = this.vwr.ms;
var atomMap =  Clazz.newIntArray (ms.ac, 0);
var pTemp =  new JU.P3();
if (asV3000) {
mol.append("  0  0  0  0  0  0            999 V3000");
} else if (asJSON) {
mol.append("{\"mol\":{\"createdBy\":\"Jmol " + JV.Viewer.getJmolVersion() + "\",\"a\":[");
} else {
JU.PT.rightJustify(mol, "   ", "" + nAtoms);
JU.PT.rightJustify(mol, "   ", "" + nBonds);
mol.append("  0  0  0  0            999 V2000");
}if (!asJSON) mol.append("\n");
if (asV3000) {
mol.append("M  V30 BEGIN CTAB\nM  V30 COUNTS ").appendI(nAtoms).append(" ").appendI(nBonds).append(" 0 0 0\n").append("M  V30 BEGIN ATOM\n");
}var o = (molData == null ? null : molData.get("atom_value_name"));
if (Clazz.instanceOf(o,"JS.SV")) o = (o).asString();
var valueType = (o == null ? 0 : JS.T.getTokFromName("" + o));
var atomValues = (valueType == 0 && !asSDF ? null :  new JU.SB());
for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
this.getAtomRecordMOL(iModel, ms, mol, atomMap[i] = ++n, ms.at[i], q, pTemp, asV3000, asJSON, atomValues, valueType, asSDF);
}
if (asV3000) {
mol.append("M  V30 END ATOM\nM  V30 BEGIN BOND\n");
} else if (asJSON) {
mol.append("],\"b\":[");
}for (var i = bsBonds.nextSetBit(0), n = 0; i >= 0; i = bsBonds.nextSetBit(i + 1)) {
this.getBondRecordMOL(mol, ++n, ms.bo[i], atomMap, asV3000, asJSON, noAromatic, is2d);
}
if (asV3000) {
mol.append("M  V30 END BOND\nM  V30 END CTAB\n");
}if (asJSON) mol.append("]}}");
 else {
if (atomValues != null && atomValues.length() > 0) mol.append(atomValues.toString());
mol.append("M  END\n");
}if (asSDF) {
try {
var pc = ms.getPartialCharges();
if (molData == null) molData =  new java.util.Hashtable();
var sb =  new JU.SB();
if (pc != null) {
sb.appendI(nAtoms).appendC('\n');
for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) sb.appendI(++n).append(" ").appendF(pc[i]).appendC('\n');

molData.put("jmol_partial_charges", sb.toString());
}sb.setLength(0);
sb.appendI(nAtoms).appendC('\n');
for (var i = bsAtoms.nextSetBit(0), n = 0; i >= 0; i = bsAtoms.nextSetBit(i + 1)) {
var name = ms.at[i].getAtomName().trim();
if (name.length == 0) name = ".";
sb.appendI(++n).append(" ").append(name.$replace(' ', '_')).appendC('\n');
}
molData.put("jmol_atom_names", sb.toString());
if (_keyList == null) _keyList =  new JU.Lst();
for (var key, $key = molData.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) if (!_keyList.contains(key)) _keyList.addLast(key);

for (var i = 0, n = _keyList.size(); i < n; i++) {
var key = _keyList.get(i);
if (key.startsWith(">")) continue;
o = molData.get(key);
if (Clazz.instanceOf(o,"JS.SV")) o = (o).asString();
mol.append("> <" + key.toUpperCase() + ">\n");
this.output80CharWrap(mol, o.toString(), 80);
mol.append("\n\n");
}
} catch (e) {
}
mol.append("$$$$\n");
}return true;
}, "~S,~N,JU.SB,JU.BS,JU.BS,~B,~B,~B,JU.Quat,~B");
Clazz.defineMethod(c$, "getAtomRecordMOL", 
function(iModel, ms, mol, n, a, q, pTemp, asV3000, asJSON, atomValues, tokValue, asSDF){
ms.getPointTransf(iModel, a, q, pTemp);
var elemNo = a.getElementNumber();
var sym = (a.isDeleted() ? "Xx" : JU.Elements.elementSymbolFromNumber(elemNo));
var isotope = a.getIsotopeNumber();
var charge = a.getFormalCharge();
var o =  Clazz.newArray(-1, [pTemp]);
if (asV3000) {
mol.append("M  V30 ").appendI(n).append(" ").append(sym).append(JU.PT.sprintf(" %12.5p %12.5p %12.5p 0", "p", o));
if (charge != 0) mol.append(" CHG=").appendI(charge);
if (isotope != 0) mol.append(" MASS=").appendI(isotope);
mol.append("\n");
} else if (asJSON) {
if (n != 1) mol.append(",");
mol.append("{");
if (a.getElementNumber() != 6) mol.append("\"l\":\"").append(a.getElementSymbol()).append("\",");
if (charge != 0) mol.append("\"c\":").appendI(charge).append(",");
if (isotope != 0) mol.append("\"m\":").appendI(isotope).append(",");
mol.append("\"x\":").appendF(a.x).append(",\"y\":").appendF(a.y).append(",\"z\":").appendF(a.z).append("}");
} else {
mol.append(JU.PT.sprintf("%10.4p%10.4p%10.4p", "p", o));
mol.append(" ").append(sym);
if (sym.length == 1) mol.append(" ");
JU.PT.rightJustify(mol, "   ", "" + (isotope > 0 ? isotope - JU.Elements.getNaturalIsotope(a.getElementNumber()) : 0));
if (asSDF && isotope > 0) {
atomValues.append("M  ISO  1");
JU.PT.rightJustify(atomValues, "    ", "" + n);
JU.PT.rightJustify(atomValues, "    ", "" + isotope);
atomValues.append("\n");
}JU.PT.rightJustify(mol, "   ", "" + (charge == 0 ? 0 : 4 - charge));
mol.append("  ").append(this.getAtomParity(a));
mol.append("  0  0  0\n");
var label = (tokValue == 0 || asV3000 ? null : this.getAtomPropertyAsString(a, tokValue));
if (label != null && (label = label.trim()).length > 0) {
var sn = "   " + n + " ";
atomValues.append("V  ").append(sn.substring(sn.length - 4));
this.output80CharWrap(atomValues, label, 73);
}}}, "~N,JM.ModelSet,JU.SB,~N,JM.Atom,JU.Quat,JU.P3,~B,~B,JU.SB,~N,~B");
Clazz.defineMethod(c$, "getAtomParity", 
function(a){
if (a.getCovalentBondCount() == 4) {
if (this.connections == null) {
this.connections =  Clazz.newIntArray (4, 0);
this.vTemp =  new JU.V3();
this.vNorm =  new JU.V3();
}var isWavy = false;
var bonds = a.bonds;
var nH = 0;
for (var pt = 0, i = bonds.length; --i >= 0; ) {
if (bonds[i].isCovalent()) {
if (bonds[i].order == 1057) {
isWavy = true;
break;
}var b = bonds[i].getOtherAtom(a);
if (b.getAtomicAndIsotopeNumber() == 1) nH++;
this.connections[pt++] = b.i;
}}
if (nH < 3) {
if (isWavy) return "3";
java.util.Arrays.sort(this.connections);
var atoms = this.vwr.ms.at;
JU.Measure.getNormalThroughPoints(atoms[this.connections[0]], atoms[this.connections[1]], atoms[this.connections[2]], this.vNorm, this.vTemp);
this.vTemp.sub2(atoms[this.connections[3]], atoms[this.connections[0]]);
return (this.vTemp.dot(this.vNorm) > 0 ? "1" : "2");
}}return "0";
}, "JM.Atom");
Clazz.defineMethod(c$, "getAtomPropertyAsString", 
function(a, tok){
switch (tok & 1136656384) {
case 1094713344:
var i = a.atomPropertyInt(tok);
return (tok == 1765808134 ? JU.PT.trim(JU.Escape.escapeColor(i), "[x]").toUpperCase() : "" + i);
case 1086324736:
return a.atomPropertyString(this.vwr, tok);
case 1111490560:
var f = a.atomPropertyFloat(this.vwr, tok, null);
return (Float.isNaN(f) ? null : "" + f);
default:
if (this.ptTemp == null) this.ptTemp =  new JU.P3();
a.atomPropertyTuple(this.vwr, tok, this.ptTemp);
return (this.ptTemp == null ? null : this.ptTemp.toString());
}
}, "JM.Atom,~N");
Clazz.defineMethod(c$, "getBondRecordMOL", 
function(mol, n, b, atomMap, asV3000, asJSON, noAromatic, is2d){
if (b == null) return;
var a1 = atomMap[b.atom1.i];
var a2 = atomMap[b.atom2.i];
var order = b.getValence();
var cfg = "";
if (order > 3) order = 1;
if (!asJSON && b.order == 1057) {
cfg = (asV3000 ? "  CFG=3" : "  4");
}if (is2d) {
if (asJSON) {
} else {
switch (b.order) {
case 1057:
cfg = (asV3000 ? "  CFG=3" : "  4");
break;
case 1025:
cfg = (asV3000 ? "  CFG=1" : "  1");
break;
case 1041:
cfg = (asV3000 ? "  CFG=2" : "  6");
break;
default:
cfg = "  0";
break;
}
}}switch (b.order & 131071) {
case 515:
order = (asJSON ? -3 : 4);
break;
case 66:
order = (asJSON ? -3 : 5);
break;
case 513:
order = (asJSON || noAromatic ? 1 : 6);
break;
case 514:
order = (asJSON || noAromatic ? 2 : 7);
break;
case 33:
order = (asJSON ? -1 : 8);
break;
}
if (asV3000) {
mol.append("M  V30 ").appendI(n).append(" ").appendI(order).append(" ").appendI(a1).append(" ").appendI(a2).append(cfg).appendC('\n');
} else if (asJSON) {
if (n != 1) mol.append(",");
mol.append("{\"b\":").appendI(a1 - 1).append(",\"e\":").appendI(a2 - 1);
if (order != 1) {
mol.append(",\"o\":");
if (order < 0) {
mol.appendF(-order / 2);
} else {
mol.appendI(order);
}}mol.append("}");
} else {
JU.PT.rightJustify(mol, "   ", "" + a1);
JU.PT.rightJustify(mol, "   ", "" + a2);
mol.append("  ").appendI(order).append(cfg).append("\n");
}}, "JU.SB,~N,JM.Bond,~A,~B,~B,~B,~B");
Clazz.defineMethod(c$, "output80CharWrap", 
function(mol, data, maxN){
if (maxN < 80) data = JU.PT.rep(data, "\n", "|");
var lines = JU.PT.split(JU.PT.trim(JU.PT.rep(data, "\n\n", "\n"), "\n"), "\n");
for (var i = 0; i < lines.length; i++) this.outputLines(mol, lines[i], maxN);

}, "JU.SB,~S,~N");
Clazz.defineMethod(c$, "outputLines", 
function(mol, data, maxN){
var done = false;
for (var i = 0, n = data.length; i < n && !done; i += 80) {
mol.append(data.substring(i, Math.min(i + maxN, n)));
if (!(done = (maxN != 80)) && i + 80 < n) mol.append("+");
mol.append("\n");
}
}, "JU.SB,~S,~N");
});
;//5.0.1-v7 Mon Jul 28 06:27:19 CDT 2025
