Clazz.declarePackage("J.adapter.writers");
Clazz.load(["JU.SB", "J.api.JmolWriter", "JU.JSONWriter", "java.util.Hashtable"], "J.adapter.writers.QCJSONWriter", ["java.util.Date", "JU.DF", "$.P3", "$.PT", "org.qcschema.QCSchemaUnits"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.moBases = null;
this.htBasisMap = null;
this.filterMOs = false;
this.vwr = null;
this.basisID = 0;
this.shells = null;
this.dfCoefMaps = null;
if (!Clazz.isClassDefined("J.adapter.writers.QCJSONWriter.SparseArray")) {
J.adapter.writers.QCJSONWriter.$QCJSONWriter$SparseArray$ ();
}
Clazz.instantialize(this, arguments);}, J.adapter.writers, "QCJSONWriter", JU.JSONWriter, J.api.JmolWriter);
Clazz.prepareFields (c$, function(){
this.moBases =  new java.util.Hashtable();
this.htBasisMap =  new java.util.Hashtable();
});
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor (this, J.adapter.writers.QCJSONWriter, []);
});
Clazz.overrideMethod(c$, "set", 
function(viewer, oc, data){
this.vwr = viewer;
this.oc = (oc == null ? this.vwr.getOutputChannel(null, null) : oc);
this.setWriteNullAsString(false);
this.setStream(oc);
}, "JV.Viewer,JU.OC,~A");
Clazz.overrideMethod(c$, "write", 
function(bs){
this.writeJSON();
return this.toString();
}, "JU.BS");
Clazz.defineMethod(c$, "toString", 
function(){
return (this.oc == null ? "{}" : this.oc.toString());
});
Clazz.defineMethod(c$, "writeJSON", 
function(){
this.openSchema();
this.writeMagic();
this.oc.append(",\n");
this.writeSchemaMetadata();
this.writeJobs();
this.closeSchema();
});
Clazz.defineMethod(c$, "writeSchemaMetadata", 
function(){
this.mapOpen();
this.mapAddKeyValue("__jmol_created",  new java.util.Date(), ",\n");
this.mapAddKeyValue("__jmol_source", this.vwr.getP("_modelFile"), "");
this.mapClose();
});
Clazz.defineMethod(c$, "openSchema", 
function(){
this.arrayOpen(false);
});
Clazz.defineMethod(c$, "writeMagic", 
function(){
this.writeString(org.qcschema.QCSchemaUnits.version);
});
Clazz.defineMethod(c$, "closeSchema", 
function(){
this.oc.append("\n");
this.arrayClose(false);
this.closeStream();
});
Clazz.defineMethod(c$, "writeJobs", 
function(){
this.writeJob(1);
});
Clazz.defineMethod(c$, "writeJob", 
function(iJob){
this.append(",\n");
this.mapOpen();
{
this.mapAddKeyValue("__jmol_block", "Job " + iJob, ",\n");
this.writeJobMetadata();
this.writeModels();
this.writeMOBases();
}this.mapClose();
}, "~N");
Clazz.defineMethod(c$, "writeJobMetadata", 
function(){
this.mapAddKey("metadata");
this.mapOpen();
{
this.mapAddMapAllExcept("__jmol_info", this.vwr.getModelSetAuxiliaryInfo(), ";group3Counts;properties;group3Lists;models;unitCellParams;");
}this.mapClose();
});
Clazz.defineMethod(c$, "writeModels", 
function(){
var nModels = this.vwr.ms.mc;
this.oc.append(",\n");
this.mapAddKey("steps");
this.arrayOpen(true);
{
this.oc.append("\n");
for (var i = 0; i < nModels; ) {
if (i > 0) this.append(",\n");
i = this.writeModel(i);
}
}this.arrayClose(true);
});
Clazz.defineMethod(c$, "writeModel", 
function(modelIndex){
var nextModel = modelIndex + 1;
this.append("");
this.mapOpen();
{
this.mapAddKeyValue("__jmol_block", "Model " + (modelIndex + 1), ",\n");
this.writeTopology(modelIndex);
if (this.isVibration(modelIndex)) {
this.oc.append(",\n");
nextModel = this.writeVibrations(modelIndex);
}if (this.haveMOData(modelIndex)) {
this.oc.append(",\n");
this.writeMOData(modelIndex);
}this.oc.append(",\n");
this.writeModelMetadata(modelIndex);
}this.mapClose();
this.oc.append("\n");
return nextModel;
}, "~N");
Clazz.defineMethod(c$, "writeTopology", 
function(modelIndex){
this.mapAddKey("topology");
this.mapOpen();
{
this.writeAtoms(modelIndex);
this.writeBonds(modelIndex);
}this.mapClose();
}, "~N");
Clazz.defineMethod(c$, "getProperty", 
function(modelIndex, key){
var props = (modelIndex >= this.vwr.ms.am.length ? null : this.vwr.ms.am[modelIndex].auxiliaryInfo.get("modelProperties"));
return (props == null ? null : props.get(key));
}, "~N,~S");
Clazz.defineMethod(c$, "isVibration", 
function(modelIndex){
return (this.vwr.ms.getLastVibrationVector(modelIndex, 0) >= 0);
}, "~N");
Clazz.defineMethod(c$, "writeModelMetadata", 
function(modelIndex){
this.mapAddKey("metadata");
this.mapOpen();
{
this.mapAddMapAllExcept("__jmol_info", this.vwr.ms.am[modelIndex].auxiliaryInfo, ";.PATH;PATH;fileName;moData;unitCellParams;");
}this.mapClose();
}, "~N");
Clazz.defineMethod(c$, "writeAtoms", 
function(modelIndex){
var symbols = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
var numbers = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
var charges = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
var names = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
var types = Clazz.innerTypeInstance(J.adapter.writers.QCJSONWriter.SparseArray, this, null, "_RLE_");
this.mapAddKey("atoms");
this.mapOpen();
{
var unitCell = this.vwr.ms.getUnitCell(modelIndex);
var isFractional = (unitCell != null && !unitCell.isBio());
if (isFractional) {
var params = unitCell.getUnitCellAsArray(false);
this.writePrefix_Units("unit_cell", "angstroms");
this.mapAddKeyValue("unit_cell", params, ",\n");
}this.writePrefix_Units("coords", isFractional ? "fractional" : "angstroms");
this.mapAddKey("coords");
this.arrayOpen(true);
{
this.oc.append("\n");
var bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
var last = bs.length() - 1;
var pt =  new JU.P3();
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
var a = this.vwr.ms.at[i];
this.append("");
pt.setT(a);
if (isFractional) unitCell.toFractional(pt, false);
this.oc.append(this.formatNumber(pt.x)).append(",\t").append(this.formatNumber(pt.y)).append(",\t").append(this.formatNumber(pt.z)).append(i < last ? ",\n" : "\n");
symbols.add(JU.PT.esc(a.getElementSymbol()));
numbers.add("" + a.getElementNumber());
charges.add("" + a.getPartialCharge());
var name = a.getAtomName();
names.add(name);
var type = a.getAtomType();
types.add(type.equals(name) ? null : type);
}
}this.arrayClose(true);
this.oc.append(",\n");
if (charges.isNumericAndNonZero()) {
this.mapAddKeyValueRaw("charge", charges, ",\n");
}if (types.hasValues()) {
this.mapAddKeyValueRaw("types", types, ",\n");
}this.mapAddKeyValueRaw("symbol", symbols, ",\n");
this.mapAddKeyValueRaw("atom_number", numbers, "\n");
}this.mapClose();
}, "~N");
Clazz.defineMethod(c$, "formatNumber", 
function(x){
return (x < 0 ? "" : " ") + JU.DF.formatDecimal(x, -6);
}, "~N");
Clazz.defineMethod(c$, "writePrefix_Units", 
function(prefix, units){
this.mapAddKeyValueRaw(prefix + "_units", org.qcschema.QCSchemaUnits.getUnitsJSON(units, false), ",\n");
}, "~S,~S");
Clazz.defineMethod(c$, "writeBonds", 
function(modelIndex){
}, "~N");
Clazz.defineMethod(c$, "writeVibrations", 
function(modelIndex){
this.mapAddKey("vibrations");
this.arrayOpen(true);
{
this.oc.append("\n");
var sep = null;
var ivib = 0;
modelIndex--;
while (this.isVibration(++modelIndex)) {
if (sep != null) this.oc.append(sep);
sep = ",\n";
this.append("");
this.mapOpen();
{
this.mapAddKeyValue("__jmol_block", "Vibration " + (++ivib), ",\n");
var value = this.getProperty(modelIndex, "FreqValue");
var freq = this.getProperty(modelIndex, "Frequency");
var intensity = this.getProperty(modelIndex, "IRIntensity");
var tokens;
if (value == null) {
System.out.println("model " + modelIndex + " has no _M.properties.FreqValue");
}if (freq == null) {
System.out.println("model " + modelIndex + " has no _M.properties.Frequency");
} else {
tokens = JU.PT.split(freq, " ");
if (tokens.length == 1) {
System.out.println("model " + modelIndex + " has no frequency units");
}this.writeMapKeyValueUnits("frequency", value, tokens[1]);
}if (intensity != null) {
tokens = JU.PT.split(intensity, " ");
this.writeMapKeyValueUnits("ir_intensity", tokens[0], tokens[1]);
}var label = this.getProperty(modelIndex, "FrequencyLabel");
if (label != null) this.mapAddKeyValue("label", label, ",\n");
this.mapAddKey("vectors");
this.arrayOpen(true);
{
this.oc.append("\n");
var bs = this.vwr.getModelUndeletedAtomsBitSet(modelIndex);
var last = bs.length() - 1;
for (var i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
var a = this.vwr.ms.at[i];
var v = a.getVibrationVector();
this.append("");
this.oc.append(this.formatNumber(v.x)).append(",\t").append(this.formatNumber(v.y)).append(",\t").append(this.formatNumber(v.z)).append(i < last ? ",\n" : "\n");
}
}this.arrayClose(true);
}this.append("");
this.mapClose();
}
}this.oc.append("\n");
this.arrayClose(true);
return modelIndex;
}, "~N");
Clazz.defineMethod(c$, "writeMapKeyValueUnits", 
function(key, value, units){
this.mapAddKeyValueRaw(key, "{\"value\":" + value + ",\"units\":" + org.qcschema.QCSchemaUnits.getUnitsJSON(units, false) + "}", ",\n");
}, "~S,~O,~S");
Clazz.defineMethod(c$, "haveMOData", 
function(modelIndex){
return (this.getAuxiliaryData(modelIndex, "moData") != null);
}, "~N");
Clazz.defineMethod(c$, "getAuxiliaryData", 
function(modelIndex, key){
return this.vwr.ms.am[modelIndex].auxiliaryInfo.get(key);
}, "~N,~S");
Clazz.defineMethod(c$, "writeMOData", 
function(modelIndex){
var moData = this.getAuxiliaryData(modelIndex, "moData");
var moDataJSON =  new java.util.Hashtable();
moDataJSON.put("orbitals", moData.get("mos"));
var units = moData.get("EnergyUnits");
if (units == null) units = "?";
moDataJSON.put("orbitals_energy_units", org.qcschema.QCSchemaUnits.getUnitsJSON(units, true));
moDataJSON.put("__jmol_normalized", Boolean.$valueOf(moData.get("isNormalized") === Boolean.TRUE));
var type = moData.get("calculationType");
moDataJSON.put("__jmol_calculation_type", type == null ? "?" : type);
this.setDFCoord(moData);
moDataJSON.put("basis_id", this.addBasis(moData));
this.filterMOs = true;
this.setModifyKeys(J.adapter.writers.QCJSONWriter.fixIntegration());
this.mapAddKeyValue("molecular_orbitals", moDataJSON, "\n");
this.setModifyKeys(null);
this.filterMOs = false;
this.append("");
}, "~N");
c$.fixIntegration = Clazz.defineMethod(c$, "fixIntegration", 
function(){
if (J.adapter.writers.QCJSONWriter.integrationKeyMap == null) {
J.adapter.writers.QCJSONWriter.integrationKeyMap =  new java.util.Hashtable();
J.adapter.writers.QCJSONWriter.integrationKeyMap.put("integration", "__jmol_integration");
}return J.adapter.writers.QCJSONWriter.integrationKeyMap;
});
Clazz.overrideMethod(c$, "getAndCheckValue", 
function(map, key){
if (this.filterMOs) {
if (key.equals("dfCoefMaps")) return null;
if (key.equals("symmetry")) return (map.get(key)).$replace('_', ' ').trim();
if (key.equals("coefficients") && this.dfCoefMaps != null) {
return this.fixCoefficients(map.get(key));
}}return map.get(key);
}, "java.util.Map,~S");
Clazz.defineMethod(c$, "fixCoefficients", 
function(coeffs){
var c =  Clazz.newDoubleArray (coeffs.length, 0);
for (var i = 0, n = this.shells.size(); i < n; i++) {
var shell = this.shells.get(i);
var type = shell[1];
var map = this.dfCoefMaps[type];
for (var j = 0, coefPtr = 0; j < map.length; j++, coefPtr++) c[coefPtr + j] = coeffs[coefPtr + map[j]];

}
return c;
}, "~A");
Clazz.defineMethod(c$, "setDFCoord", 
function(moData){
this.dfCoefMaps = moData.get("dfCoefMaps");
if (this.dfCoefMaps != null) {
var haveMap = false;
for (var i = 0; !haveMap && i < this.dfCoefMaps.length; i++) {
var m = this.dfCoefMaps[i];
for (var j = 0; j < m.length; j++) if (m[j] != 0) {
haveMap = true;
break;
}
}
if (!haveMap) this.dfCoefMaps = null;
}}, "java.util.Map");
Clazz.defineMethod(c$, "addBasis", 
function(moData){
var hash = 1;
var gaussians = moData.get("gaussians");
if (gaussians != null) {
hash ^= gaussians.hashCode();
}this.shells = moData.get("shells");
if (this.shells != null) {
hash ^= this.shells.hashCode();
}var slaters = moData.get("slaters");
if (slaters != null) {
hash ^= slaters.hashCode();
}var strHash = "" + hash;
var key = this.htBasisMap.get(strHash);
if (key == null) {
this.htBasisMap.put(strHash, key = "MOBASIS_" + ++this.basisID);
var map =  new java.util.Hashtable();
if (gaussians != null) map.put("gaussians", gaussians);
if (this.shells != null) {
map.put("shells", this.shells);
}if (slaters != null) map.put("slaters", slaters);
this.moBases.put(key, map);
}return key;
}, "java.util.Map");
Clazz.defineMethod(c$, "writeMOBases", 
function(){
if (this.moBases.isEmpty()) return;
this.oc.append(",\n");
this.mapAddKey("mo_bases");
this.mapOpen();
{
var sep = null;
for (var key, $key = this.moBases.keySet().iterator (); $key.hasNext()&& ((key = $key.next ()) || true);) {
if (key.startsWith("!")) continue;
this.append(sep);
this.mapAddKeyValue(key, this.moBases.get(key), "\n");
sep = ",\n";
}
}this.mapClose();
this.moBases.clear();
});
Clazz.defineMethod(c$, "writeObject", 
function(o){
if (Clazz.instanceOf(o,"J.quantum.SlaterData")) {
this.oc.append(o.toString());
} else {
Clazz.superCall(this, J.adapter.writers.QCJSONWriter, "writeObject", [o]);
}}, "~O");
c$.$QCJSONWriter$SparseArray$ = function(){
/*if4*/;(function(){
var c$ = Clazz.decorateAsClass(function(){
Clazz.prepareCallback(this, arguments);
this.repeatCount = 0;
this.elementCount = 0;
this.$lastElement = null;
this.sep = "";
this.type = null;
this.isRLE = false;
Clazz.instantialize(this, arguments);}, J.adapter.writers.QCJSONWriter, "SparseArray", JU.SB);
Clazz.makeConstructor(c$, 
function(type){
Clazz.superConstructor (this, J.adapter.writers.QCJSONWriter.SparseArray, []);
this.type = type;
this.isRLE = (type.equals("_RLE_"));
}, "~S");
Clazz.defineMethod(c$, "add", 
function(element){
if (element == null) element = "null";
if (!this.isRLE) {
this.append(this.sep);
this.append(element);
this.sep = ",";
return;
}if (this.repeatCount > 0 && !element.equals(this.$lastElement)) {
this.append(this.sep);
this.appendI(this.repeatCount);
this.sep = ",";
this.append(this.sep);
this.append(this.$lastElement);
this.repeatCount = 0;
}this.$lastElement = element;
this.repeatCount++;
this.elementCount++;
}, "~S");
Clazz.defineMethod(c$, "lastElement", 
function(){
return this.$lastElement;
});
Clazz.defineMethod(c$, "isEmpty", 
function(){
return (this.elementCount == 0);
});
Clazz.defineMethod(c$, "allNaN", 
function(){
return (this.allSame() && JU.PT.parseFloat(this.$lastElement) == NaN);
});
Clazz.defineMethod(c$, "allNull", 
function(){
return (this.allSame() && this.$lastElement.equals("null"));
});
Clazz.defineMethod(c$, "allEmptyString", 
function(){
return (this.allSame() && this.$lastElement.equals(""));
});
Clazz.defineMethod(c$, "allSame", 
function(){
return (!this.isEmpty() && this.elementCount == this.repeatCount);
});
Clazz.defineMethod(c$, "allZero", 
function(){
return (this.allSame() && JU.PT.parseFloat(this.$lastElement) != NaN);
});
Clazz.defineMethod(c$, "hasValues", 
function(){
return (!this.allSame() || !this.allNull() && !this.allEmptyString());
});
Clazz.defineMethod(c$, "isNumericAndNonZero", 
function(){
return (this.allSame() && !this.allNaN() && !this.allZero());
});
Clazz.defineMethod(c$, "toString", 
function(){
var s = Clazz.superCall(this, J.adapter.writers.QCJSONWriter.SparseArray, "toString", []);
return (s.length == 0 ? "[]" : "[\"" + this.type + "\"," + s + (this.repeatCount > 0 ? this.sep + this.repeatCount + "," + this.$lastElement : "") + "]");
});
/*eoif4*/})();
};
c$.integrationKeyMap = null;
});
;//5.0.1-v2 Mon Mar 04 12:59:58 CST 2024
