Clazz.declarePackage("J.adapter.smarter");
Clazz.load(["javajs.api.GenericLineReader", "JU.SB", "JV.Viewer"], "J.adapter.smarter.AtomSetCollectionReader", ["JU.BS", "$.Lst", "$.M3", "$.P3", "$.PT", "$.Quat", "$.V3", "J.adapter.smarter.Atom", "$.AtomSetCollection", "J.api.Interface", "$.JmolAdapter", "JU.BSUtil", "$.Logger", "$.SimpleUnitCell", "JV.FileManager", "$.JC"], function(){
var c$ = Clazz.decorateAsClass(function(){
this.isBinary = false;
this.debugging = false;
this.requiresBSFilter = false;
this.primitiveToCrystal = null;
this.asc = null;
this.reader = null;
this.binaryDoc = null;
this.readerName = null;
this.htParams = null;
this.trajectorySteps = null;
this.domains = null;
this.validation = null;
this.dssr = null;
this.openVarna = false;
this.isConcatenated = false;
this.addedData = null;
this.addedDataKey = null;
this.thisBiomolecule = null;
this.lstNCS = null;
this.floatifyJavaDouble = true;
this.line = null;
this.prevline = null;
this.next = null;
this.ptLine = 0;
this.checkNearAtoms = true;
this.latticeType = null;
this.latticeCells = null;
this.fillRange = null;
this.doProcessLines = false;
this.iHaveUnitCell = false;
this.iHaveSymmetryOperators = false;
this.continuing = true;
this.vwr = null;
this.doApplySymmetry = false;
this.ignoreFileSymmetryOperators = false;
this.isTrajectory = false;
this.applySymmetryToBonds = false;
this.doCheckUnitCell = false;
this.getHeader = false;
this.isSequential = false;
this.optimize2D = false;
this.noHydrogens = false;
this.noMinimize = false;
this.is2D = false;
this.isMolecular = false;
this.templateAtomCount = 0;
this.modelNumber = 0;
this.vibrationNumber = 0;
this.desiredVibrationNumber = -2147483648;
this.bsModels = null;
this.useFileModelNumbers = false;
this.havePartialChargeFilter = false;
this.calculationType = "?";
this.sgName = null;
this.ignoreFileUnitCell = false;
this.ignoreFileSpaceGroupName = false;
this.unitCellParams = null;
this.desiredModelNumber = -2147483648;
this.symmetry = null;
this.out = null;
this.iHaveFractionalCoordinates = false;
this.doPackUnitCell = false;
this.ptSupercell = null;
this.mustFinalizeModelSet = false;
this.forcePacked = false;
this.packingRange = null;
this.cellSlop = 1.0E-4;
this.rotateHexCell = false;
this.isPrimitive = false;
this.modDim = 0;
this.lowPrecision = false;
this.highprecision0 = false;
this.loadNote = null;
this.doConvertToFractional = false;
this.fileCoordinatesAreFractional = false;
this.merging = false;
this.symmetryRange = 0;
this.firstLastStep = null;
this.lastModelNumber = 2147483647;
this.desiredSpaceGroupIndex = -1;
this.latticeScaling = NaN;
this.unitCellOffset = null;
this.unitCellOffsetFractional = false;
this.moreUnitCellInfo = null;
this.paramsLattice = null;
this.paramsCentroid = false;
this.paramsPacked = false;
this.fileScaling = null;
this.fileOffset = null;
this.fileOffsetFractional = null;
this.filePath = null;
this.fileName = null;
this.baseAtomIndex = 0;
this.baseBondIndex = 0;
this.stateScriptVersionInt = 2147483647;
this.isFinalized = false;
this.noPack = false;
this.isSUPERCELL = false;
this.precision = 0;
this.haveModel = false;
this.previousSpaceGroup = null;
this.previousUnitCell = null;
this.nMatrixElements = 0;
this.ucItems = null;
this.matUnitCellOrientation = null;
this.bsFilter = null;
this.filter = null;
this.filterCased = null;
this.haveAtomFilter = false;
this.filterAltLoc = false;
this.filterGroup3 = false;
this.filterChain = false;
this.filterAtomName = false;
this.filterAtomType = false;
this.filterAtomTypeStr = null;
this.filterAtomNameTerminator = ";";
this.filterElement = false;
this.filterHetero = false;
this.filterAllHetero = false;
this.filterEveryNth = false;
this.filterSymop = null;
this.filterN = 0;
this.nFiltered = 0;
this.doSetOrientation = false;
this.doCentralize = false;
this.addVibrations = false;
this.useAltNames = false;
this.ignoreStructure = false;
this.isDSSP1 = false;
this.allowPDBFilter = false;
this.doReadMolecularOrbitals = false;
this.reverseModels = false;
this.modelNameRequired = null;
this.doCentroidUnitCell = false;
this.centroidPacked = false;
this.strSupercell = null;
this.allow_a_len_1 = false;
this.slabXY = false;
this.polymerX = false;
this.filteredPrecision = false;
this.filter1 = null;
this.filter2 = null;
this.filter1Cased = null;
this.filter2Cased = null;
this.matRot = null;
this.ms = null;
this.vibsFractional = false;
this.previousScript = null;
this.siteScript = null;
Clazz.instantialize(this, arguments);}, J.adapter.smarter, "AtomSetCollectionReader", null, javajs.api.GenericLineReader);
Clazz.prepareFields (c$, function(){
this.next =  Clazz.newIntArray (1, 0);
this.highprecision0 = JV.Viewer.isHighPrecision;
this.loadNote =  new JU.SB();
});
Clazz.defineMethod(c$, "getPackingRangeValue", 
function(def){
return (this.packingRange != null ? this.packingRange.floatValue() : def != 0 ? def : 0.02);
}, "~N");
Clazz.defineMethod(c$, "setup", 
function(fullPath, htParams, readerOrDocument){
this.setupASCR(fullPath, htParams, readerOrDocument);
}, "~S,java.util.Map,~O");
Clazz.defineMethod(c$, "setupASCR", 
function(fullPath, htParams, readerOrDocument){
if (fullPath == null) return;
this.debugging = JU.Logger.debugging;
this.htParams = htParams;
this.filePath = JV.FileManager.stripTypePrefix("" + htParams.get("fullPathName"));
var i = this.filePath.lastIndexOf('/');
this.fileName = this.filePath.substring(i + 1);
if (Clazz.instanceOf(readerOrDocument,"java.io.BufferedReader")) this.reader = readerOrDocument;
 else if (Clazz.instanceOf(readerOrDocument,"javajs.api.GenericBinaryDocument")) this.binaryDoc = readerOrDocument;
}, "~S,java.util.Map,~O");
Clazz.defineMethod(c$, "readData", 
function(){
this.initialize();
this.asc =  new J.adapter.smarter.AtomSetCollection(this.readerName, this, null, null);
try {
this.initializeReader();
if (this.binaryDoc == null) {
if (this.line == null && this.continuing) this.rd();
while (this.line != null && this.continuing) if (this.checkLine()) this.rd();

} else {
this.binaryDoc.setOutputChannel(this.out);
this.processBinaryDocument();
}this.finalizeSubclassReader();
if (!this.isFinalized) this.finalizeReaderASCR();
} catch (e) {
JU.Logger.info("Reader error: " + e);
e.printStackTrace();
this.setError(e);
}
if (this.reader != null) this.reader.close();
if (this.binaryDoc != null) this.binaryDoc.close();
return this.finish();
});
Clazz.defineMethod(c$, "fixBaseIndices", 
function(){
try {
var ii = this.htParams.get("baseModelIndex");
if (ii == null) return;
var baseModelIndex = ii.intValue();
this.baseAtomIndex += this.asc.ac;
this.baseBondIndex += this.asc.bondCount;
baseModelIndex += this.asc.atomSetCount;
this.htParams.put("baseAtomIndex", Integer.$valueOf(this.baseAtomIndex));
this.htParams.put("baseBondIndex", Integer.$valueOf(this.baseBondIndex));
this.htParams.put("baseModelIndex", Integer.$valueOf(baseModelIndex));
} catch (e) {
if (Clazz.exceptionOf(e, Exception)){
} else {
throw e;
}
}
});
Clazz.defineMethod(c$, "readDataObject", 
function(node){
this.initialize();
this.asc =  new J.adapter.smarter.AtomSetCollection(this.readerName, this, null, null);
this.initializeReader();
this.processDOM(node);
return this.finish();
}, "~O");
Clazz.defineMethod(c$, "processDOM", 
function(DOMNode){
}, "~O");
Clazz.defineMethod(c$, "processBinaryDocument", 
function(){
});
Clazz.defineMethod(c$, "initializeReader", 
function(){
});
Clazz.defineMethod(c$, "checkLine", 
function(){
return true;
});
Clazz.defineMethod(c$, "checkLastModel", 
function(){
if (this.isLastModel(this.modelNumber) && this.doProcessLines) return (this.continuing = this.doProcessLines = false);
this.doProcessLines = false;
return true;
});
Clazz.defineMethod(c$, "isLastModel", 
function(modelNumber){
return (this.desiredModelNumber > 0 || modelNumber >= this.lastModelNumber);
}, "~N");
Clazz.defineMethod(c$, "appendLoadNote", 
function(info){
if (info == null) {
this.loadNote =  new JU.SB();
return;
}this.loadNote.append(info).append("\n");
JU.Logger.info(info);
}, "~S");
Clazz.defineMethod(c$, "initializeTrajectoryFile", 
function(){
this.asc.addAtom( new J.adapter.smarter.Atom());
this.trajectorySteps = this.htParams.get("trajectorySteps");
if (this.trajectorySteps == null) this.htParams.put("trajectorySteps", this.trajectorySteps =  new JU.Lst());
});
Clazz.defineMethod(c$, "finalizeSubclassReader", 
function(){
});
Clazz.defineMethod(c$, "finalizeReaderASCR", 
function(){
this.isFinalized = true;
if (this.asc.atomSetCount > 0) {
if (this.asc.atomSetCount == 1) {
this.asc.setCurrentModelInfo("dbName", this.htParams.get("dbName"));
this.asc.setCurrentModelInfo("auxFiles", this.htParams.get("auxFiles"));
}this.applySymmetryAndSetTrajectory();
this.asc.finalizeStructures();
if (this.doCentralize) this.asc.centralize();
if (this.fillRange != null) this.asc.setInfo("boundbox", this.fillRange);
var info = this.asc.getAtomSetAuxiliaryInfo(0);
if (info != null) {
if (this.domains != null) {
this.asc.setGlobalBoolean(5);
var s = (this.domains).getMapKeys(2, true);
var pt = s.indexOf("{ ", 2);
if (pt >= 0) s = s.substring(pt + 2);
pt = s.indexOf("_metadata");
if (pt < 0) pt = s.indexOf("metadata");
if (pt >= 0) s = s.substring(0, pt);
s = JU.PT.rep(JU.PT.replaceAllCharacters(s, "{}", "").trim(), "\n", "\n  ") + "\n\nUse SHOW DOMAINS for details.";
this.appendLoadNote("\nDomains loaded:\n   " + s);
for (var i = this.asc.atomSetCount; --i >= 0; ) {
info = this.asc.getAtomSetAuxiliaryInfo(i);
info.put("domains", this.domains);
}
}if (this.validation != null) {
for (var i = this.asc.atomSetCount; --i >= 0; ) {
info = this.asc.getAtomSetAuxiliaryInfo(i);
info.put("validation", this.validation);
}
}if (this.dssr != null) {
info.put("dssrJSON", Boolean.TRUE);
info.put("dssr", this.dssr);
if (this.openVarna) this.vwr.plugin("VARNA", "show", "dssr");
this.addJmolScript("set cartoonblocks;cartoons only;color structure");
} else if (this.openVarna) {
this.addJmolScript("calculate structure dssr;set cartoonblocks;cartoons only;color structure");
}}}if (!this.floatifyJavaDouble) this.asc.setInfo("highPrecision", Boolean.TRUE);
this.setLoadNote();
});
Clazz.defineMethod(c$, "setLoadNote", 
function(){
var s = this.loadNote.toString();
if (this.loadNote.length() > 0) this.asc.setInfo("modelLoadNote", s);
return s;
});
Clazz.defineMethod(c$, "setIsPDB", 
function(){
this.asc.setGlobalBoolean(4);
if (this.htParams.get("pdbNoHydrogens") != null) this.asc.setInfo("pdbNoHydrogens", this.htParams.get("pdbNoHydrogens"));
if (this.checkFilterKey("ADDHYDROGENS")) this.asc.setInfo("pdbAddHydrogens", Boolean.TRUE);
});
Clazz.defineMethod(c$, "setModelPDB", 
function(isPDB){
if (isPDB) this.asc.setGlobalBoolean(4);
 else this.asc.clearGlobalBoolean(4);
this.asc.setCurrentModelInfo(JV.JC.getBoolName(4), isPDB ? Boolean.TRUE : null);
}, "~B");
Clazz.defineMethod(c$, "finish", 
function(){
if (false != this.highprecision0) this.vwr.setBooleanPropertyTok("doubleprecision", 603979831, this.highprecision0);
var s = this.htParams.get("loadState");
this.asc.setInfo("loadState", s == null ? "" : s);
s = this.htParams.get("smilesString");
if (s != null) this.asc.setInfo("smilesString", s);
if (!this.htParams.containsKey("templateAtomCount")) this.htParams.put("templateAtomCount", Integer.$valueOf(this.asc.ac));
if (this.bsFilter != null) {
this.htParams.put("filteredAtomCount", Integer.$valueOf(JU.BSUtil.cardinalityOf(this.bsFilter)));
this.htParams.put("bsFilter", this.bsFilter);
}if (!this.calculationType.equals("?")) this.asc.setInfo("calculationType", this.calculationType);
var name = this.asc.fileTypeName;
var fileType = name;
if (fileType.indexOf("(") >= 0) fileType = fileType.substring(0, fileType.indexOf("("));
for (var i = this.asc.atomSetCount; --i >= 0; ) {
this.asc.setModelInfoForSet("fileName", this.filePath, i);
this.asc.setModelInfoForSet("fileType", fileType, i);
}
this.asc.freeze(this.reverseModels);
if (this.asc.errorMessage != null) return this.asc.errorMessage + "\nfor file " + this.filePath + "\ntype " + name;
if (!this.merging && (this.asc.bsAtoms == null ? this.asc.ac == 0 : this.asc.bsAtoms.nextSetBit(0) < 0) && fileType.indexOf("DataOnly") < 0 && this.asc.atomSetInfo.get("dataOnly") == null) return "No atoms found\nfor file " + this.filePath + "\ntype " + name;
this.fixBaseIndices();
return this.asc;
});
Clazz.defineMethod(c$, "setError", 
function(e){
var s = e.getMessage();
if (this.line == null) this.asc.errorMessage = "Error reading file at end of file \n" + s;
 else this.asc.errorMessage = "Error reading file at line " + this.ptLine + ":\n" + this.line + "\n" + s;
e.printStackTrace();
}, "Throwable");
Clazz.defineMethod(c$, "initialize", 
function(){
if (this.htParams.containsKey("baseAtomIndex")) this.baseAtomIndex = (this.htParams.get("baseAtomIndex")).intValue();
if (this.htParams.containsKey("baseBondIndex")) this.baseBondIndex = (this.htParams.get("baseBondIndex")).intValue();
this.initializeSymmetry();
this.vwr = this.htParams.remove("vwr");
if (this.htParams.containsKey("stateScriptVersionInt")) this.stateScriptVersionInt = (this.htParams.get("stateScriptVersionInt")).intValue();
this.packingRange = this.htParams.get("packingRange");
var isHighPrecision = (this.htParams.get("highPrecision") != null);
if (this.packingRange == null && isHighPrecision) {
this.floatifyJavaDouble = false;
this.packingRange = Float.$valueOf(1.0E-4);
}this.merging = this.htParams.containsKey("merging");
this.getHeader = this.htParams.containsKey("getHeader");
this.isSequential = this.htParams.containsKey("isSequential");
this.readerName = this.htParams.get("readerName");
if (this.htParams.containsKey("outputChannel")) this.out = this.htParams.get("outputChannel");
if (this.htParams.containsKey("vibrationNumber")) this.desiredVibrationNumber = (this.htParams.get("vibrationNumber")).intValue();
 else if (this.htParams.containsKey("modelNumber")) this.desiredModelNumber = (this.htParams.get("modelNumber")).intValue();
this.applySymmetryToBonds = this.htParams.containsKey("applySymmetryToBonds");
this.bsFilter = (this.requiresBSFilter ? this.htParams.get("bsFilter") : null);
this.setFilter(null);
this.fillRange = this.htParams.get("fillRange");
this.paramsLattice = this.htParams.get("lattice");
var o = this.htParams.get("supercell");
if (this.strSupercell != null && !this.noPack) {
this.forcePacked = true;
}if (Clazz.instanceOf(o,"JU.P3")) {
var s = this.ptSupercell = o;
if (s.length() != 1) {
this.strSupercell = (Clazz.floatToInt(s.x)) + "a," + (Clazz.floatToInt(s.y)) + "b," + (Clazz.floatToInt(s.z)) + "c";
this.isSUPERCELL = true;
}} else if ((typeof(o)=='string')) {
this.strSupercell = o;
this.isSUPERCELL = true;
}var ptFile = (this.htParams.containsKey("ptFile") ? (this.htParams.get("ptFile")).intValue() : -1);
this.isTrajectory = this.htParams.containsKey("isTrajectory");
if (ptFile > 0 && this.htParams.containsKey("firstLastSteps")) {
var val = (this.htParams.get("firstLastSteps")).get(ptFile - 1);
if (Clazz.instanceOf(val,"JU.BS")) {
this.bsModels = val;
} else {
this.firstLastStep = val;
}} else if (this.htParams.containsKey("firstLastStep")) {
this.firstLastStep = this.htParams.get("firstLastStep");
} else if (this.htParams.containsKey("bsModels")) {
this.bsModels = this.htParams.get("bsModels");
}this.useFileModelNumbers = this.htParams.containsKey("useFileModelNumbers") || this.checkFilterKey("USEFILEMODELNUMBERS");
if (this.htParams.containsKey("templateAtomCount")) this.templateAtomCount = (this.htParams.get("templateAtomCount")).intValue();
if (this.bsModels != null || this.firstLastStep != null) this.desiredModelNumber = -2147483648;
if (this.bsModels == null && this.firstLastStep != null) {
if (this.firstLastStep[0] < 0) this.firstLastStep[0] = 0;
if (this.firstLastStep[2] == 0 || this.firstLastStep[1] < this.firstLastStep[0]) this.firstLastStep[1] = -1;
if (this.firstLastStep[2] < 1) this.firstLastStep[2] = 1;
this.bsModels = JU.BSUtil.newAndSetBit(this.firstLastStep[0]);
if (this.firstLastStep[1] > this.firstLastStep[0]) {
for (var i = this.firstLastStep[0]; i <= this.firstLastStep[1]; i += this.firstLastStep[2]) this.bsModels.set(i);

}}if (this.bsModels != null && (this.firstLastStep == null || this.firstLastStep[1] != -1)) this.lastModelNumber = this.bsModels.length();
this.symmetryRange = (this.htParams.containsKey("symmetryRange") ? (this.htParams.get("symmetryRange")).floatValue() : 0);
this.paramsCentroid = this.htParams.containsKey("centroid");
this.paramsPacked = this.htParams.containsKey("packed");
this.initializeSymmetryOptions();
if (this.htParams.containsKey("spaceGroupIndex")) {
this.desiredSpaceGroupIndex = (this.htParams.get("spaceGroupIndex")).intValue();
if (this.desiredSpaceGroupIndex == -2) this.sgName = this.htParams.get("spaceGroupName");
this.ignoreFileSpaceGroupName = (this.desiredSpaceGroupIndex == -2 || this.desiredSpaceGroupIndex >= 0);
this.ignoreFileSymmetryOperators = (this.desiredSpaceGroupIndex != -1);
}if (this.htParams.containsKey("unitCellOffset")) {
this.fileScaling = JU.P3.new3(1, 1, 1);
this.fileOffset = this.htParams.get("unitCellOffset");
this.fileOffsetFractional = JU.P3.newP(this.fileOffset);
this.unitCellOffsetFractional = this.htParams.containsKey("unitCellOffsetFractional");
}if (this.htParams.containsKey("unitcell")) {
var fParams = this.htParams.get("unitcell");
if (this.merging) this.setFractionalCoordinates(true);
if (fParams.length == 9) {
this.addExplicitLatticeVector(0, fParams, 0);
this.addExplicitLatticeVector(1, fParams, 3);
this.addExplicitLatticeVector(2, fParams, 6);
} else {
this.setUnitCell(fParams[0], fParams[1], fParams[2], fParams[3], fParams[4], fParams[5]);
}this.ignoreFileUnitCell = this.iHaveUnitCell;
if (this.merging && !this.iHaveUnitCell) this.setFractionalCoordinates(false);
}this.domains = this.htParams.get("domains");
this.validation = this.htParams.get("validation");
this.dssr = this.htParams.get("dssr");
this.isConcatenated = this.htParams.containsKey("concatenate");
});
Clazz.defineMethod(c$, "parsePrecision", 
function(s){
if (!this.filteredPrecision) {
var pt = s.indexOf('.') + 1;
if (pt >= 0) {
var n = s.indexOf('(');
if (n < 0) {
this.precision = Math.max(this.precision, s.length - 1 - pt);
} else {
if (this.precision == 0) this.precision = n;
this.precision = Math.min(this.precision, n - 1 - pt);
}}}return this.parseFloatStr(s);
}, "~S");
Clazz.defineMethod(c$, "setLowPrecision", 
function(){
this.lowPrecision = true;
this.cellSlop = 1.0E-4;
if (this.packingRange == null) this.packingRange = Double.$valueOf(1.0E-4);
});
Clazz.defineMethod(c$, "setPrecision", 
function(){
var isHigh;
if (this.lowPrecision) {
isHigh = false;
this.precision = 4;
} else {
if (this.precision > 1000) {
this.precision -= 1000;
} else {
this.precision = Math.min(12, Math.max(4, this.precision));
}isHigh = (this.precision >= 7);
if (isHigh) {
this.vwr.setBooleanProperty("doubleprecision", true);
if (JV.Viewer.isHighPrecision) {
this.cellSlop = 1.0E-12;
if (!this.paramsPacked) this.packingRange = Double.$valueOf(this.cellSlop);
this.asc.setInfo("highPrecision", Boolean.TRUE);
} else {
isHigh = false;
this.precision = 6;
this.appendLoadNote("Structure read has high precision but this version of Jmol uses float precision.\nUse JmolD.jar or JavaScript for full precision.");
}}}if (!isHigh) {
if (this.precision < 10) {
this.cellSlop = Math.pow(10, -this.precision);
}}this.symmetry.setPrecision(this.cellSlop);
this.unitCellParams[26] = this.cellSlop;
if (this.fileCoordinatesAreFractional) {
for (var i = this.asc.ac, n = this.asc.getLastAtomSetAtomIndex(); --i >= n; ) {
this.symmetry.twelfthify(this.asc.atoms[i]);
}
}this.appendLoadNote("Precision set to " + this.precision + "; packing set to " + (this.packingRange == null ? 0.02 : this.packingRange.floatValue()));
});
Clazz.defineMethod(c$, "initializeSymmetryOptions", 
function(){
this.latticeCells =  Clazz.newIntArray (4, 0);
this.doApplySymmetry = false;
var pt = this.paramsLattice;
if (pt == null || pt.length() == 0) {
if (!this.forcePacked && this.strSupercell == null) return;
pt = JU.P3.new3(1, 1, 1);
}this.latticeCells[0] = Clazz.floatToInt(pt.x);
this.latticeCells[1] = Clazz.floatToInt(pt.y);
this.latticeCells[2] = Clazz.floatToInt(pt.z);
if (Clazz.instanceOf(pt,"JU.T4")) this.latticeCells[3] = Clazz.floatToInt((pt).w);
this.doCentroidUnitCell = this.paramsCentroid;
if (this.doCentroidUnitCell && (this.latticeCells[2] == -1 || this.latticeCells[2] == 0)) this.latticeCells[2] = 1;
var isPacked = this.forcePacked || this.paramsPacked;
this.centroidPacked = this.doCentroidUnitCell && isPacked;
this.doPackUnitCell = !this.doCentroidUnitCell && (isPacked || this.latticeCells[2] < 0);
this.doApplySymmetry = (this.latticeCells[0] > 0 && this.latticeCells[1] > 0);
if (!this.doApplySymmetry) this.latticeCells =  Clazz.newIntArray (3, 0);
});
Clazz.defineMethod(c$, "doGetModel", 
function(modelNumber, title){
if (title != null && this.modelNameRequired != null && this.modelNameRequired.length > 0 && title.toUpperCase().indexOf(this.modelNameRequired) < 0) return false;
var isOK = (this.bsModels == null ? this.desiredModelNumber < 1 || modelNumber == this.desiredModelNumber : modelNumber > this.lastModelNumber ? false : modelNumber > 0 && this.bsModels.get(modelNumber - 1) || this.haveModel && this.firstLastStep != null && this.firstLastStep[1] < 0 && (this.firstLastStep[2] < 2 || (modelNumber - 1 - this.firstLastStep[0]) % this.firstLastStep[2] == 0));
if (isOK && this.desiredModelNumber == 0) this.discardPreviousAtoms();
this.haveModel = new Boolean (this.haveModel | isOK).valueOf();
if (isOK) this.doProcessLines = true;
return isOK;
}, "~N,~S");
Clazz.defineMethod(c$, "discardPreviousAtoms", 
function(){
this.asc.discardPreviousAtoms();
});
Clazz.defineMethod(c$, "initializeSymmetry", 
function(){
this.previousSpaceGroup = this.sgName;
this.previousUnitCell = this.unitCellParams;
this.iHaveUnitCell = this.ignoreFileUnitCell;
if (!this.ignoreFileUnitCell) {
this.unitCellParams =  Clazz.newFloatArray (27, 0);
for (var i = 27; --i >= 0; ) this.unitCellParams[i] = NaN;

this.unitCellParams[25] = this.latticeScaling;
this.unitCellParams[26] = this.cellSlop;
this.symmetry = null;
}if (!this.ignoreFileSpaceGroupName) this.sgName = "unspecified!";
this.doCheckUnitCell = false;
});
Clazz.defineMethod(c$, "newAtomSet", 
function(name){
if (this.asc.iSet >= 0) {
this.asc.newAtomSet();
this.asc.setCollectionName("<collection of " + (this.asc.iSet + 1) + " models>");
} else {
this.asc.setCollectionName(name);
}this.asc.setModelInfoForSet("name", name, Math.max(0, this.asc.iSet));
this.asc.setAtomSetName(name);
}, "~S");
Clazz.defineMethod(c$, "cloneLastAtomSet", 
function(ac, pts){
var lastAtomCount = this.asc.getLastAtomSetAtomCount();
this.asc.cloneLastAtomSetFromPoints(ac, pts);
if (this.asc.haveUnitCell) {
this.iHaveUnitCell = true;
this.doCheckUnitCell = true;
this.sgName = this.previousSpaceGroup;
this.unitCellParams = this.previousUnitCell;
}return lastAtomCount;
}, "~N,~A");
Clazz.defineMethod(c$, "setSpaceGroupName", 
function(name){
if (this.ignoreFileSpaceGroupName || name == null) return;
var s = name.trim();
if (s.length == 0 || s.equals("HM:") || s.equals(this.sgName)) return;
if (!s.equals("P1")) JU.Logger.info("Setting space group name to " + s);
this.sgName = s;
}, "~S");
Clazz.defineMethod(c$, "setSymmetryOperator", 
function(xyz){
if (this.ignoreFileSymmetryOperators) return -1;
var isym = this.asc.getXSymmetry().addSpaceGroupOperation(xyz, true);
if (isym < 0) this.warnSkippingOperation(xyz);
this.iHaveSymmetryOperators = true;
return isym;
}, "~S");
Clazz.defineMethod(c$, "warnSkippingOperation", 
function(xyz){
JU.Logger.warn("Skipping symmetry operation " + xyz);
}, "~S");
Clazz.defineMethod(c$, "initializeCartesianToFractional", 
function(){
for (var i = 0; i < 16; i++) if (!Float.isNaN(this.unitCellParams[6 + i])) return;

for (var i = 0; i < 16; i++) this.unitCellParams[6 + i] = ((i % 5 == 0 ? 1 : 0));

this.nMatrixElements = 0;
});
Clazz.defineMethod(c$, "clearUnitCell", 
function(){
if (this.ignoreFileUnitCell) return;
for (var i = 6; i < 22; i++) this.unitCellParams[i] = NaN;

this.checkUnitCell(6);
});
Clazz.defineMethod(c$, "setUnitCellItem", 
function(i, x){
if (this.ignoreFileUnitCell) return;
if (i == 0 && x == 1 && !this.allow_a_len_1 || i == 3 && x == 0) {
if (this.ucItems == null) this.ucItems =  Clazz.newFloatArray (6, 0);
this.ucItems[i] = x;
return;
}if (this.ucItems != null && i < 6) this.ucItems[i] = x;
if (!Float.isNaN(x) && i >= 6 && Float.isNaN(this.unitCellParams[6])) this.initializeCartesianToFractional();
this.unitCellParams[i] = x;
if (this.debugging) {
JU.Logger.debug("setunitcellitem " + i + " " + x);
}if (i < 6 || Float.isNaN(x)) this.iHaveUnitCell = this.checkUnitCell(6);
 else if (++this.nMatrixElements == 12) this.iHaveUnitCell = this.checkUnitCell(22);
}, "~N,~N");
Clazz.defineMethod(c$, "setUnitCell", 
function(a, b, c, alpha, beta, gamma){
if (this.ignoreFileUnitCell) return;
this.clearUnitCell();
this.unitCellParams[0] = a;
this.unitCellParams[1] = b;
this.unitCellParams[2] = c;
if (alpha != 0) this.unitCellParams[3] = alpha;
if (beta != 0) this.unitCellParams[4] = beta;
if (gamma != 0) this.unitCellParams[5] = gamma;
this.iHaveUnitCell = this.checkUnitCell(6);
}, "~N,~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "addExplicitLatticeVector", 
function(i, xyz, i0){
if (this.ignoreFileUnitCell) return;
if (i == 0) for (var j = 0; j < 6; j++) this.unitCellParams[j] = 0;

i = 6 + i * 3;
this.unitCellParams[i++] = xyz[i0++];
this.unitCellParams[i++] = xyz[i0++];
this.unitCellParams[i] = xyz[i0];
if (Float.isNaN(this.unitCellParams[0])) {
for (i = 0; i < 6; i++) this.unitCellParams[i] = -1;

}this.iHaveUnitCell = this.checkUnitCell(15);
if (this.iHaveUnitCell) {
if (this.slabXY || this.polymerX) this.unitCellParams[2] = -1;
if (this.polymerX) this.unitCellParams[1] = -1;
}}, "~N,~A,~N");
Clazz.defineMethod(c$, "checkUnitCell", 
function(n){
for (var i = 0; i < n; i++) if (Float.isNaN(this.unitCellParams[i])) return false;

this.fixFloatA(this.unitCellParams);
if (n == 22 && this.unitCellParams[0] == 1) {
if (this.unitCellParams[1] == 1 && this.unitCellParams[2] == 1 && this.unitCellParams[6] == 1 && this.unitCellParams[11] == 1 && this.unitCellParams[16] == 1) {
return false;
}}if (n == 6 && Float.isNaN(this.unitCellParams[6])) {
if (this.slabXY && this.unitCellParams[2] > 0) {
JU.SimpleUnitCell.addVectors(this.unitCellParams);
this.unitCellParams[2] = -1;
} else if (this.polymerX && this.unitCellParams[1] > 0) {
JU.SimpleUnitCell.addVectors(this.unitCellParams);
this.unitCellParams[1] = this.unitCellParams[2] = -1;
}}if (this.doApplySymmetry) {
this.getSymmetry();
this.doConvertToFractional = !this.fileCoordinatesAreFractional;
}return true;
}, "~N");
Clazz.defineMethod(c$, "getSymmetry", 
function(){
if (!this.iHaveUnitCell) return null;
if (this.symmetry == null) {
(this.symmetry = this.asc.newFileSymmetry()).setUnitCellFromParams(this.unitCellParams, false, this.cellSlop);
this.checkUnitCellOffset();
}if (this.symmetry == null) this.iHaveUnitCell = false;
 else this.symmetry.setSpaceGroupName(this.sgName);
return this.symmetry;
});
Clazz.defineMethod(c$, "checkUnitCellOffset", 
function(){
if (this.fileOffsetFractional == null || this.symmetry == null) return;
this.fileOffset.setT(this.fileOffsetFractional);
if (this.unitCellOffsetFractional != this.fileCoordinatesAreFractional) {
if (this.unitCellOffsetFractional) this.symmetry.toCartesian(this.fileOffset, false);
 else this.symmetry.toFractional(this.fileOffset, false);
}});
Clazz.defineMethod(c$, "fractionalizeCoordinates", 
function(toFrac){
if (this.getSymmetry() == null) return;
var a = this.asc.atoms;
if (toFrac) for (var i = this.asc.ac; --i >= 0; ) this.symmetry.toFractional(a[i], false);

 else for (var i = this.asc.ac; --i >= 0; ) this.symmetry.toCartesian(a[i], false);

this.setFractionalCoordinates(toFrac);
}, "~B");
Clazz.defineMethod(c$, "setFractionalCoordinates", 
function(TF){
this.iHaveFractionalCoordinates = this.fileCoordinatesAreFractional = TF;
this.checkUnitCellOffset();
}, "~B");
Clazz.defineMethod(c$, "setFilterAtomTypeStr", 
function(s){
this.filterAtomTypeStr = s;
this.filterAtomNameTerminator = "\0";
}, "~S");
Clazz.defineMethod(c$, "setFilter", 
function(filter0){
if (filter0 == null) {
filter0 = this.htParams.get("filter");
} else {
this.bsFilter = null;
this.filterCased = null;
}if (this.filterCased == null) this.filterCased = (filter0 == null ? null : filter0 + ";");
if (filter0 != null) filter0 = filter0.toUpperCase();
this.filter = filter0;
if (this.filter == null) return;
this.checkFilterKeys();
this.filterSymmetry();
this.filterModelName();
this.filterAtoms();
var s = this.getFilter("FILESCALING=");
if (s != null) {
var fs = this.parseFloatStr(s);
this.fileScaling = JU.P3.new3(fs, fs, fs);
this.fileOffset =  new JU.P3();
}}, "~S");
Clazz.defineMethod(c$, "filterAtoms", 
function(){
if (this.checkFilterKey("HETATM")) {
this.filterHetero = true;
this.filter = JU.PT.rep(this.filter, "HETATM", "HETATM-Y");
this.filterCased = JU.PT.rep(this.filterCased, "HETATM", "HETATM-Y");
}if (this.checkFilterKey("ATOM")) {
this.filterHetero = true;
this.filter = JU.PT.rep(this.filter, "ATOM", "HETATM-N");
this.filterCased = JU.PT.rep(this.filterCased, "ATOM", "HETATM-N");
}this.filterAtomName = this.checkFilterKey("*.") || this.checkFilterKey("!.");
if (this.filter.startsWith("_") || this.filter.startsWith("!_") || this.filter.indexOf(";_") >= 0 || this.filter.indexOf(";!_") >= 0) this.filterElement = this.checkFilterKey("_");
this.filterGroup3 = this.checkFilterKey("[");
this.filterChain = this.checkFilterKey(":");
this.filterAltLoc = this.checkFilterKey("%");
this.filterEveryNth = this.checkFilterKey("/=");
this.filterAllHetero = this.checkFilterKey("ALLHET");
if (this.filterEveryNth) this.filterN = this.parseIntAt(this.filter, this.filter.indexOf("/=") + 2);
 else if (this.filter.startsWith("=") || this.filter.indexOf(";=") >= 0) this.filterAtomType = this.checkFilterKey("=");
if (this.filterN == -2147483648) this.filterEveryNth = false;
this.haveAtomFilter = this.filterAtomName || this.filterAtomType || this.filterElement || this.filterGroup3 || this.filterChain || this.filterAltLoc || this.filterHetero || this.filterEveryNth || this.checkFilterKey("/=");
if (this.bsFilter == null) {
this.bsFilter =  new JU.BS();
this.htParams.put("bsFilter", this.bsFilter);
if (this.haveAtomFilter) {
var ipt;
this.filter1Cased = this.filterCased;
this.filter2Cased = "";
if ((ipt = this.filter.indexOf("|")) >= 0) {
this.filter1Cased = this.filter.substring(0, ipt).trim() + ";";
this.filter2Cased = ";" + this.filter.substring(ipt).trim();
}this.filter1 = this.filter1Cased.toUpperCase();
this.filter2 = (this.filter2Cased.length == 0 ? null : this.filter2Cased.toUpperCase());
}}});
Clazz.defineMethod(c$, "filterModelName", 
function(){
this.modelNameRequired = JU.PT.getQuotedAttribute(this.filter, "NAME");
if (this.modelNameRequired == null) return;
if (this.modelNameRequired.length == 0) {
this.modelNameRequired = this.getFilter("NAME=");
if (this.modelNameRequired.startsWith("'")) this.modelNameRequired = JU.PT.split(this.modelNameRequired, "'")[1];
}this.filter = JU.PT.rep(this.filter, this.modelNameRequired, "");
this.filter = JU.PT.rep(this.filter, "NAME=", "");
this.filter = JU.PT.rep(this.filter, "\"\"", "");
this.filter = JU.PT.rep(this.filter, "''", "");
});
Clazz.defineMethod(c$, "filterSymmetry", 
function(){
if (this.checkFilterKey("CELL=")) this.strSupercell = this.filter.substring(this.filter.indexOf("CELL=") + 5).toLowerCase();
this.filter = ";" + this.filter + ";";
JU.Logger.info("filtering with " + this.filter);
var s = this.getFilter("SYMOP=");
if (s != null) this.filterSymop = " " + s.$replace(',', ' ') + " ";
this.filter = this.filter.$replace(',', ';');
var p = this.getFilter("PRECISION=");
if (p != null) {
var prec = JU.PT.parseInt(p);
if (prec > 0 && prec <= 16) {
this.precision = 1000 + prec;
this.filteredPrecision = true;
}}s = this.getFilter("LATTICESCALING=");
if (s != null && this.unitCellParams.length > 25) this.unitCellParams[25] = this.latticeScaling = this.parseFloatStr(s);
});
Clazz.defineMethod(c$, "checkFilterKeys", 
function(){
this.doSetOrientation = !this.checkFilterKey("NOORIENT");
this.doCentralize = (!this.checkFilterKey("NOCENTER") && this.checkFilterKey("CENTER"));
this.addVibrations = !this.checkFilterKey("NOVIB");
this.ignoreStructure = this.checkFilterKey("DSSP");
this.isDSSP1 = this.checkFilterKey("DSSP1");
this.doReadMolecularOrbitals = !this.checkFilterKey("NOMO");
this.useAltNames = this.checkFilterKey("ALTNAME");
this.reverseModels = this.checkFilterKey("REVERSEMODELS");
this.allow_a_len_1 = this.checkFilterKey("TOPOS");
this.slabXY = this.checkFilterKey("SLABXY");
this.polymerX = !this.slabXY && this.checkFilterKey("POLYMERX");
this.noHydrogens = this.checkFilterKey("NOH");
this.noMinimize = this.checkFilterKey("NOMIN");
this.optimize2D = this.checkFilterKey("2D") && !this.noHydrogens && !this.noMinimize;
this.noPack = this.checkFilterKey("NOPACK");
this.openVarna = this.checkFilterKey("VARNA");
if (this.checkFilterKey("LOWPRECISION")) {
this.setLowPrecision();
}if (this.checkFilterKey("HETATM")) {
this.filterHetero = true;
this.filter = JU.PT.rep(this.filter, "HETATM", "HETATM-Y");
this.filterCased = JU.PT.rep(this.filterCased, "HETATM", "HETATM-Y");
}if (this.checkFilterKey("ATOM")) {
this.filterHetero = true;
this.filter = JU.PT.rep(this.filter, "ATOM", "HETATM-N");
this.filterCased = JU.PT.rep(this.filterCased, "ATOM", "HETATM-N");
}});
Clazz.defineMethod(c$, "getFilterWithCase", 
function(key){
var pt = (this.filterCased == null ? -1 : this.filterCased.toUpperCase().indexOf(key.toUpperCase()));
return (pt < 0 ? null : this.filterCased.substring(pt + key.length, this.filterCased.indexOf(";", pt)));
}, "~S");
Clazz.defineMethod(c$, "getFilter", 
function(key){
var pt = (this.filter == null ? -1 : this.filter.indexOf(key));
return (pt < 0 ? null : this.filter.substring(pt + key.length, this.filter.indexOf(";", pt)));
}, "~S");
Clazz.defineMethod(c$, "checkFilterKey", 
function(key){
return (this.filter != null && this.filter.indexOf(key) >= 0);
}, "~S");
Clazz.defineMethod(c$, "checkAndRemoveFilterKey", 
function(key){
if (!this.checkFilterKey(key)) return false;
this.filter = JU.PT.rep(this.filter, key, "");
if (this.filter.length < 3) this.filter = null;
return true;
}, "~S");
Clazz.defineMethod(c$, "filterAtom", 
function(atom, iAtom){
if (!this.haveAtomFilter) return true;
var isOK = this.checkFilter(atom, this.filter1, this.filter1Cased);
if (this.filter2 != null) isOK = new Boolean (isOK | this.checkFilter(atom, this.filter2, this.filter2Cased)).valueOf();
if (isOK && this.filterEveryNth && (!atom.isHetero || !this.filterAllHetero)) isOK = (((this.nFiltered++) % this.filterN) == 0);
this.bsFilter.setBitTo(iAtom >= 0 ? iAtom : this.asc.ac, isOK);
return isOK;
}, "J.adapter.smarter.Atom,~N");
Clazz.defineMethod(c$, "checkFilter", 
function(atom, f, fCased){
if (atom.isHetero && this.filterAllHetero) return true;
return (!this.filterGroup3 || atom.group3 == null || !this.filterReject(f, "[", atom.group3.toUpperCase() + "]")) && (!this.filterAtomName || this.allowAtomName(atom.atomName, f)) && (this.filterAtomTypeStr == null || atom.atomName == null || atom.atomName.toUpperCase().indexOf("\0" + this.filterAtomTypeStr) >= 0) && (!this.filterElement || atom.elementSymbol == null || !this.filterReject(f, "_", atom.elementSymbol.toUpperCase() + ";")) && (!this.filterChain || atom.chainID == 0 || !this.filterReject(fCased, ":", "" + this.vwr.getChainIDStr(atom.chainID))) && (!this.filterAltLoc || atom.altLoc == '\0' || !this.filterReject(f, "%", "" + atom.altLoc)) && (!this.filterHetero || !this.allowPDBFilter || !this.filterReject(f, "HETATM", atom.isHetero ? "-Y" : "-N"));
}, "J.adapter.smarter.Atom,~S,~S");
Clazz.defineMethod(c$, "rejectAtomName", 
function(name){
return this.filterAtomName && !this.allowAtomName(name, this.filter);
}, "~S");
Clazz.defineMethod(c$, "allowAtomName", 
function(atomName, f){
return (atomName == null || !this.filterReject(f, ".", atomName.toUpperCase() + this.filterAtomNameTerminator));
}, "~S,~S");
Clazz.defineMethod(c$, "filterReject", 
function(f, code, atomCode){
return (f.indexOf(code) >= 0 && (f.indexOf("!" + code) >= 0) == (f.indexOf(code + atomCode) >= 0));
}, "~S,~S,~S");
Clazz.defineMethod(c$, "set2D", 
function(){
this.asc.setInfo("is2D", Boolean.TRUE);
this.asc.getBSAtoms(-1);
if (this.noHydrogens) {
this.asc.setInfo("noHydrogen", Boolean.TRUE);
this.optimize2D = false;
}if (this.optimize2D) {
this.asc.fix2Stereo();
this.asc.setInfo("doMinimize", Boolean.TRUE);
this.appendLoadNote("This model is 2D. Its 3D structure was generated.");
} else {
this.appendLoadNote("This model is 2D. Its 3D structure has not been generated; use LOAD \"\" FILTER \"2D\" to optimize 3D.");
this.addJmolScript("select thismodel;wireframe only");
}});
Clazz.defineMethod(c$, "doGetVibration", 
function(vibrationNumber){
return this.addVibrations && (this.desiredVibrationNumber <= 0 || vibrationNumber == this.desiredVibrationNumber);
}, "~N");
Clazz.defineMethod(c$, "setTransform", 
function(x1, y1, z1, x2, y2, z2, x3, y3, z3){
if (this.matRot != null || !this.doSetOrientation) return;
this.matRot =  new JU.M3();
var v = JU.V3.new3(x1, y1, z1);
v.normalize();
this.matRot.setColumnV(0, v);
v.set(x2, y2, z2);
v.normalize();
this.matRot.setColumnV(1, v);
v.set(x3, y3, z3);
v.normalize();
this.matRot.setColumnV(2, v);
this.asc.setInfo("defaultOrientationMatrix", JU.M3.newM3(this.matRot));
var q = JU.Quat.newM(this.matRot);
this.asc.setInfo("defaultOrientationQuaternion", q);
JU.Logger.info("defaultOrientationMatrix = " + this.matRot);
}, "~N,~N,~N,~N,~N,~N,~N,~N,~N");
Clazz.defineMethod(c$, "setAtomCoordXYZ", 
function(atom, x, y, z){
atom.set(x, y, z);
this.setAtomCoord(atom);
}, "J.adapter.smarter.Atom,~N,~N,~N");
Clazz.defineMethod(c$, "setAtomCoordScaled", 
function(atom, tokens, i, f){
if (atom == null) atom = this.asc.addNewAtom();
this.setAtomCoordXYZ(atom, this.parsePrecision(tokens[i]) * f, this.parsePrecision(tokens[i + 1]) * f, this.parsePrecision(tokens[i + 2]) * f);
return atom;
}, "J.adapter.smarter.Atom,~A,~N,~N");
Clazz.defineMethod(c$, "setAtomCoordTokens", 
function(atom, tokens, i){
this.setAtomCoordXYZ(atom, this.parsePrecision(tokens[i]), this.parsePrecision(tokens[i + 1]), this.parsePrecision(tokens[i + 2]));
}, "J.adapter.smarter.Atom,~A,~N");
Clazz.defineMethod(c$, "addAtomXYZSymName", 
function(tokens, i, sym, name){
var atom = this.asc.addNewAtom();
if (sym != null) atom.elementSymbol = sym;
if (name != null) atom.atomName = name;
this.setAtomCoordTokens(atom, tokens, i);
return atom;
}, "~A,~N,~S,~S");
Clazz.defineMethod(c$, "setAtomCoord", 
function(atom){
var mustFractionalize = (this.doConvertToFractional && !this.fileCoordinatesAreFractional && this.getSymmetry() != null);
if (this.fileScaling != null) {
atom.x = atom.x * this.fileScaling.x + this.fileOffset.x;
atom.y = atom.y * this.fileScaling.y + this.fileOffset.y;
atom.z = atom.z * this.fileScaling.z + this.fileOffset.z;
}if (mustFractionalize) {
if (!this.symmetry.haveUnitCell()) this.symmetry.setUnitCellFromParams(this.unitCellParams, false, NaN);
this.symmetry.toFractional(atom, false);
this.iHaveFractionalCoordinates = true;
}if (this.floatifyJavaDouble && this.fileCoordinatesAreFractional) this.fixFloatPt(atom, 100000.0);
this.doCheckUnitCell = true;
}, "J.adapter.smarter.Atom");
Clazz.defineMethod(c$, "addSites", 
function(htSites){
this.asc.setCurrentModelInfo("pdbSites", htSites);
var sites = "";
for (var entry, $entry = htSites.entrySet().iterator (); $entry.hasNext()&& ((entry = $entry.next ()) || true);) {
var name = entry.getKey();
var htSite = entry.getValue();
var ch;
for (var i = name.length; --i >= 0; ) if (!JU.PT.isLetterOrDigit(ch = name.charAt(i)) && ch != '\'') name = name.substring(0, i) + "_" + name.substring(i + 1);

var groups = htSite.get("groups");
if (groups.length == 0) continue;
this.addSiteScript("@site_" + name + " " + groups);
this.addSiteScript("site_" + name + " = [\"" + JU.PT.rep(groups, ",", "\",\"") + "\"]");
sites += ",\"site_" + name + "\"";
}
if (sites.length > 0) this.addSiteScript("site_list = [" + sites.substring(1) + "]");
}, "java.util.Map");
Clazz.defineMethod(c$, "applySymmetryAndSetTrajectory", 
function(){
this.applySymTrajASCR();
});
Clazz.defineMethod(c$, "applySymTrajASCR", 
function(){
if (this.forcePacked) this.initializeSymmetryOptions();
var doApply = (this.iHaveUnitCell && this.doCheckUnitCell);
var sym = null;
if (doApply) {
sym = this.getSymmetry();
this.setPrecision();
sym = this.asc.getXSymmetry().applySymmetryFromReader(sym);
} else {
this.asc.setTensors();
}if (this.isTrajectory) this.asc.setTrajectory();
if (this.moreUnitCellInfo != null) {
this.setMoreInfo();
this.moreUnitCellInfo = null;
}this.finalizeSubclassSymmetry(sym != null);
if (this.merging && sym != null && this.iHaveFractionalCoordinates && this.iHaveUnitCell && this.iHaveSymmetryOperators) {
this.fractionalizeCoordinates(false);
this.addJmolScript("modelkit spacegroup P1");
}this.initializeSymmetry();
return sym;
});
Clazz.defineMethod(c$, "setMoreInfo", 
function(){
this.asc.setCurrentModelInfo("moreUnitCellInfo", this.moreUnitCellInfo);
for (var i = this.moreUnitCellInfo.size(); --i >= 0; ) {
var s = this.moreUnitCellInfo.get(i).$plit("=");
this.asc.setCurrentModelInfo(s[0], s[1]);
}
});
Clazz.defineMethod(c$, "finalizeSubclassSymmetry", 
function(haveSymmetry){
}, "~B");
Clazz.defineMethod(c$, "doPreSymmetry", 
function(doApplySymmetry){
}, "~B");
Clazz.defineMethod(c$, "finalizeMOData", 
function(moData){
this.asc.setCurrentModelInfo("moData", moData);
if (moData == null) return;
var orbitals = moData.get("mos");
if (orbitals != null) JU.Logger.info(orbitals.size() + " molecular orbitals read in model " + this.asc.atomSetCount);
}, "java.util.Map");
c$.getElementSymbol = Clazz.defineMethod(c$, "getElementSymbol", 
function(elementNumber){
return J.api.JmolAdapter.getElementSymbol(elementNumber);
}, "~N");
Clazz.defineMethod(c$, "fillDataBlock", 
function(data, minLineLen){
var nLines = data.length;
for (var i = 0; i < nLines; i++) {
data[i] = JU.PT.getTokens(this.discardLinesUntilNonBlank());
if (data[i].length < minLineLen) --i;
}
}, "~A,~N");
Clazz.defineMethod(c$, "fill3x3", 
function(tokens, pt){
var a =  Clazz.newDoubleArray (3, 3, 0);
var needTokens = (tokens == null);
var pt0 = pt;
for (var i = 0; i < 3; i++) {
if (needTokens || pt >= tokens.length) {
while ((tokens = JU.PT.getTokens(this.rd())).length < 3) {
}
pt = (pt0 < 0 ? tokens.length + pt0 : pt0);
}for (var j = 0; j < 3; j++) a[i][j] = Double.$valueOf(tokens[pt++]).doubleValue();

}
return a;
}, "~A,~N");
Clazz.defineMethod(c$, "fillFloatArray", 
function(s, width, data){
var tokens =  new Array(0);
var pt = 0;
for (var i = 0; i < data.length; i++) {
while (tokens != null && pt >= tokens.length) {
if (s == null) s = this.rd();
if (width == 0) {
tokens = JU.PT.getTokens(s);
} else {
tokens =  new Array(Clazz.doubleToInt(s.length / width));
for (var j = 0; j < tokens.length; j++) tokens[j] = s.substring(j * width, (j + 1) * width);

}s = null;
pt = 0;
}
if (tokens == null) break;
data[i] = this.parseFloatStr(tokens[pt++]);
}
return data;
}, "~S,~N,~A");
Clazz.defineMethod(c$, "fillFrequencyData", 
function(iAtom0, ac, modelAtomCount, ignore, isWide, col0, colWidth, atomIndexes, minLineLen, data){
var withSymmetry = (ac != 0 && modelAtomCount != ac && data == null);
if (ac == 0 && atomIndexes != null) ac = atomIndexes.length;
var nLines = (isWide ? ac : ac * 3);
var nFreq = ignore.length;
if (data == null) {
data =  new Array(nLines);
this.fillDataBlockFixed(data, col0, colWidth, minLineLen);
} else if (!isWide) {
var ptNonblank = minLineLen;
this.fillDataBlockFixed(data, col0, colWidth, -ptNonblank);
if (data[0] == null) return;
iAtom0 += this.parseIntAt(this.line, ptNonblank - 5) - 1;
}for (var i = 0, atomPt = 0; i < nLines; i++, atomPt++) {
var values = data[i];
var valuesY = (isWide ? null : data[++i]);
var valuesZ = (isWide ? null : data[++i]);
var dataPt = values.length - (isWide ? nFreq * 3 : nFreq) - 1;
for (var j = 0, jj = 0; jj < nFreq; jj++) {
++dataPt;
var x = values[dataPt];
if (x.charAt(0) == ')') x = x.substring(1);
var vx = this.parseFloatStr(x);
var vy = this.parseFloatStr(isWide ? values[++dataPt] : valuesY[dataPt]);
var vz = this.parseFloatStr(isWide ? values[++dataPt] : valuesZ[dataPt]);
if (ignore[jj]) continue;
var iAtom = (atomIndexes == null ? atomPt : atomIndexes[atomPt]);
if (iAtom < 0) continue;
iAtom += iAtom0 + modelAtomCount * j++;
if (this.debugging) JU.Logger.debug("atom " + iAtom + " vib" + j + ": " + vx + " " + vy + " " + vz);
this.asc.addVibrationVectorWithSymmetry(iAtom, vx, vy, vz, withSymmetry);
}
}
}, "~N,~N,~N,~A,~B,~N,~N,~A,~N,~A");
Clazz.defineMethod(c$, "fillDataBlockFixed", 
function(data, col0, colWidth, minLineLen){
if (colWidth == 0) {
this.fillDataBlock(data, minLineLen);
return;
}var nLines = data.length;
for (var i = 0; i < nLines; i++) {
this.discardLinesUntilNonBlank();
if (minLineLen < 0 && this.line.charAt(-minLineLen) == ' ') {
data[0] = null;
return;
}var nFields = Clazz.doubleToInt((this.line.length - col0 + 1) / colWidth);
data[i] =  new Array(nFields);
for (var j = 0, start = col0; j < nFields; j++, start += colWidth) data[i][j] = this.line.substring(start, Math.min(this.line.length, start + colWidth));

}
}, "~A,~N,~N,~N");
Clazz.defineMethod(c$, "readLines", 
function(nLines){
for (var i = nLines; --i >= 0; ) this.rd();

return this.line;
}, "~N");
Clazz.defineMethod(c$, "discardLinesUntilStartsWith", 
function(startsWith){
while (this.rd() != null && !this.line.startsWith(startsWith)) {
}
return this.line;
}, "~S");
Clazz.defineMethod(c$, "discardLinesUntilContains", 
function(containsMatch){
while (this.rd() != null && this.line.indexOf(containsMatch) < 0) {
}
return this.line;
}, "~S");
Clazz.defineMethod(c$, "discardLinesUntilContains2", 
function(s1, s2){
while (this.rd() != null && this.line.indexOf(s1) < 0 && this.line.indexOf(s2) < 0) {
}
return this.line;
}, "~S,~S");
Clazz.defineMethod(c$, "discardLinesUntilBlank", 
function(){
while (this.rd() != null && this.line.trim().length != 0) {
}
return this.line;
});
Clazz.defineMethod(c$, "discardLinesUntilNonBlank", 
function(){
while (this.rd() != null && this.line.trim().length == 0) {
}
return this.line;
});
Clazz.defineMethod(c$, "checkLineForScript", 
function(line){
this.line = line;
this.checkCurrentLineForScript();
}, "~S");
Clazz.defineMethod(c$, "checkCurrentLineForScript", 
function(){
if (this.line.endsWith("#noautobond")) {
this.line = this.line.substring(0, this.line.lastIndexOf('#')).trim();
this.asc.setNoAutoBond();
}var pt = this.line.indexOf("jmolscript:");
if (pt >= 0) {
var script = this.line.substring(pt + 11, this.line.length);
if (script.indexOf("#") >= 0) {
script = script.substring(0, script.indexOf("#"));
}this.addJmolScript(script);
this.line = this.line.substring(0, pt).trim();
}});
Clazz.defineMethod(c$, "addJmolScript", 
function(script){
JU.Logger.info("#jmolScript: " + script);
if (this.previousScript == null) this.previousScript = "";
 else if (!this.previousScript.endsWith(";")) this.previousScript += ";";
this.previousScript += script;
this.asc.setInfo("jmolscript", this.previousScript);
}, "~S");
Clazz.defineMethod(c$, "addSiteScript", 
function(script){
if (this.siteScript == null) this.siteScript = "";
 else if (!this.siteScript.endsWith(";")) this.siteScript += ";";
this.siteScript += script;
this.asc.setInfo("sitescript", this.siteScript);
}, "~S");
Clazz.defineMethod(c$, "rd", 
function(){
return this.RL();
});
Clazz.defineMethod(c$, "RL", 
function(){
this.prevline = this.line;
this.line = this.reader.readLine();
if (this.out != null && this.line != null) this.out.append(this.line).append("\n");
this.ptLine++;
if (this.debugging && this.line != null) JU.Logger.info(this.line);
return this.line;
});
c$.getStrings = Clazz.defineMethod(c$, "getStrings", 
function(sinfo, nFields, width){
var fields =  new Array(nFields);
for (var i = 0, pt = 0; i < nFields; i++, pt += width) fields[i] = sinfo.substring(pt, pt + width);

return fields;
}, "~S,~N,~N");
Clazz.defineMethod(c$, "getTokens", 
function(){
return JU.PT.getTokens(this.line);
});
c$.getTokensFloat = Clazz.defineMethod(c$, "getTokensFloat", 
function(s, f, n){
if (f == null) f =  Clazz.newFloatArray (n, 0);
JU.PT.parseFloatArrayDataN(JU.PT.getTokens(s), f, n);
return f;
}, "~S,~A,~N");
Clazz.defineMethod(c$, "parseFloat", 
function(){
return JU.PT.parseFloatNext(this.line, this.next);
});
Clazz.defineMethod(c$, "parseFloatStr", 
function(s){
this.next[0] = 0;
return JU.PT.parseFloatNext(s, this.next);
}, "~S");
Clazz.defineMethod(c$, "parseFloatRange", 
function(s, iStart, iEnd){
this.next[0] = iStart;
return JU.PT.parseFloatRange(s, iEnd, this.next);
}, "~S,~N,~N");
Clazz.defineMethod(c$, "parseInt", 
function(){
return JU.PT.parseIntNext(this.line, this.next);
});
Clazz.defineMethod(c$, "parseIntStr", 
function(s){
this.next[0] = 0;
return JU.PT.parseIntNext(s, this.next);
}, "~S");
Clazz.defineMethod(c$, "parseIntAt", 
function(s, iStart){
this.next[0] = iStart;
return JU.PT.parseIntNext(s, this.next);
}, "~S,~N");
Clazz.defineMethod(c$, "parseIntRange", 
function(s, iStart, iEnd){
this.next[0] = iStart;
return JU.PT.parseIntRange(s, iEnd, this.next);
}, "~S,~N,~N");
Clazz.defineMethod(c$, "parseToken", 
function(){
return JU.PT.parseTokenNext(this.line, this.next);
});
Clazz.defineMethod(c$, "parseTokenStr", 
function(s){
this.next[0] = 0;
return JU.PT.parseTokenNext(s, this.next);
}, "~S");
Clazz.defineMethod(c$, "parseTokenNext", 
function(s){
return JU.PT.parseTokenNext(s, this.next);
}, "~S");
Clazz.defineMethod(c$, "parseTokenRange", 
function(s, iStart, iEnd){
this.next[0] = iStart;
return JU.PT.parseTokenRange(s, iEnd, this.next);
}, "~S,~N,~N");
c$.getFortranFormatLengths = Clazz.defineMethod(c$, "getFortranFormatLengths", 
function(s){
var vdata =  new JU.Lst();
var n = 0;
var c = 0;
var factor = 1;
var inN = false;
var inCount = true;
s += ",";
for (var i = 0; i < s.length; i++) {
var ch = s.charAt(i);
switch ((ch).charCodeAt(0)) {
case 46:
inN = false;
continue;
case 44:
for (var j = 0; j < c; j++) vdata.addLast(Integer.$valueOf(n * factor));

inN = false;
inCount = true;
c = 0;
continue;
case 88:
n = c;
c = 1;
factor = -1;
continue;
}
var isDigit = JU.PT.isDigit(ch);
if (isDigit) {
if (inN) n = n * 10 + ch.charCodeAt(0) - 48;
 else if (inCount) c = c * 10 + ch.charCodeAt(0) - 48;
} else if (JU.PT.isLetter(ch)) {
n = 0;
inN = true;
inCount = false;
factor = 1;
} else {
inN = false;
}}
return vdata;
}, "~S");
Clazz.defineMethod(c$, "read3Vectors", 
function(isBohr){
var vectors =  new Array(3);
var f =  Clazz.newFloatArray (3, 0);
for (var i = 0; i < 3; i++) {
if (i > 0 || Float.isNaN(this.parseFloatStr(this.line))) {
this.rd();
if (i == 0 && this.line != null) {
i = -1;
continue;
}}this.fillFloatArray(this.line, 0, f);
vectors[i] =  new JU.V3();
vectors[i].setA(f);
if (isBohr) vectors[i].scale(0.5291772);
}
return vectors;
}, "~B");
Clazz.defineMethod(c$, "setElementAndIsotope", 
function(atom, str){
var isotope = this.parseIntStr(str);
if (isotope == -2147483648) {
atom.elementSymbol = str;
} else {
str = str.substring(("" + isotope).length);
atom.elementNumber = (str.length == 0 ? isotope : ((isotope << 7) + J.api.JmolAdapter.getElementNumber(str)));
}}, "J.adapter.smarter.Atom,~S");
Clazz.defineMethod(c$, "finalizeModelSet", 
function(){
});
Clazz.defineMethod(c$, "setChainID", 
function(atom, label){
atom.chainID = this.vwr.getChainID(label, true);
}, "J.adapter.smarter.Atom,~S");
Clazz.overrideMethod(c$, "readNextLine", 
function(){
if (this.rd() != null && this.line.indexOf("#jmolscript:") >= 0) this.checkCurrentLineForScript();
return this.line;
});
Clazz.defineMethod(c$, "addMoreUnitCellInfo", 
function(info){
if (this.moreUnitCellInfo == null) this.moreUnitCellInfo =  new JU.Lst();
this.moreUnitCellInfo.addLast(info);
}, "~S");
Clazz.defineMethod(c$, "getInterface", 
function(className){
var o = J.api.Interface.getInterface(className, this.vwr, "file");
if (o == null) throw  new NullPointerException("Interface");
return o;
}, "~S");
Clazz.defineMethod(c$, "forceSymmetry", 
function(andPack){
if (andPack) this.doPackUnitCell = andPack;
if (!this.doApplySymmetry) {
this.doApplySymmetry = true;
this.latticeCells[0] = this.latticeCells[1] = this.latticeCells[2] = 1;
}}, "~B");
Clazz.defineMethod(c$, "fixFloatA", 
function(pts){
if (this.floatifyJavaDouble) for (var i = pts.length; --i >= 0; ) if (!Float.isNaN(pts[i])) pts[i] = JU.PT.fixFloat(pts[i], 100000.0);

}, "~A");
Clazz.defineMethod(c$, "fixDoubleA", 
function(pts){
if (this.floatifyJavaDouble) for (var i = pts.length; --i >= 0; ) if (!Double.isNaN(pts[i])) pts[i] = JU.PT.fixDouble(pts[i], 100000.0);

}, "~A");
Clazz.defineMethod(c$, "fixFloatPt", 
function(pt, prec){
if (this.floatifyJavaDouble) JU.PT.fixPtFloats(pt, prec);
}, "JU.P3,~N");
});
;//5.0.1-v7 Mon Aug 24 10:01:38 CDT 2026
