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Curo
2025-12-04 09:57:17 +01:00
commit 0054cc02b1
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3
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/Jmol.properties Normal file
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Jmol.___JmolDate="$Date: 2018-02-07 23:40:37 -0600 (Wed, 07 Feb 2018) $"
Jmol.___fullJmolProperties="src/org/jmol/viewer/Jmol.properties"
Jmol.___JmolVersion="14.29.4"

210
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/aflow/AFLOWReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.aflow");
Clazz.load (["J.adapter.readers.xtal.VaspPoscarReader", "java.util.Hashtable"], "J.adapter.readers.aflow.AFLOWReader", ["java.lang.Float", "java.util.Arrays", "JU.BS", "$.Lst", "$.PT", "$.SB", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.aabb = null;
this.readPRE = false;
this.fracB = NaN;
this.compositions = null;
this.getComposition = false;
this.listKey = null;
this.listKeyCase = null;
this.fileModelNumber = 0;
this.havePRE = false;
this.titleMsg = null;
this.keyMap = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.aflow, "AFLOWReader", J.adapter.readers.xtal.VaspPoscarReader);
Clazz.prepareFields (c$, function () {
this.keyMap = new java.util.Hashtable ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.readPRE = this.checkFilterKey ("PRE");
var s;
s = this.getFilter ("CA=");
if (s != null) this.fracB = (1 - this.parseFloatStr (s));
s = this.getFilter ("CB=");
if (s != null) this.fracB = this.parseFloatStr (s);
s = this.getFilter ("LIST=");
this.listKey = (s == null ? "HF" : s);
this.listKeyCase = this.listKey;
this.getComposition = !Float.isNaN (this.fracB);
this.discardLinesUntilStartsWith ("[");
this.aabb = this.line.substring (1, this.line.indexOf ("]"));
var pt = (JU.PT.isUpperCase (this.aabb.charAt (1)) ? 1 : 2);
this.defaultLabels = Clazz.newArray (-1, [this.aabb.substring (0, pt), this.aabb.substring (pt)]);
while (this.rd ().indexOf ("] REFERENCE:") >= 0) this.appendLoadNote (this.line);
this.compositions = new java.util.Hashtable ();
this.quiet = true;
this.asc.bsAtoms = new JU.BS ();
this.addJmolScript ("unitcell off;axes off;");
this.havePRE = (this.line.indexOf ("Structure PRE") >= 0);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (!this.havePRE) this.discardLinesUntilContains ("Structure PRE");
this.havePRE = false;
if (this.line == null) return false;
this.continuing = new Boolean (this.continuing & this.readPrePost ()).valueOf ();
return this.continuing;
});
Clazz.defineMethod (c$, "readPrePost",
function () {
this.fileModelNumber++;
this.titleMsg = "#" + (this.modelNumber + 1) + (this.getComposition ? "," + this.fileModelNumber + ", Cb=" + this.fracB : "");
this.elementLabel = null;
var n0 = this.asc.bsAtoms.cardinality ();
if (this.readPRE) {
this.readStructure (this.titleMsg);
} else {
this.readElementLabelsOnly ();
this.discardLinesUntilContains ("Structure POST");
this.readStructure (this.titleMsg);
}if (this.getData ()) {
this.applySymmetryAndSetTrajectory ();
} else {
this.asc.bsAtoms.clearBits (this.asc.getLastAtomSetAtomIndex (), this.asc.ac);
this.doCheckUnitCell = false;
}this.finalizeModel ();
if (n0 != this.asc.bsAtoms.cardinality ()) JU.Logger.info ("AFLOW: file#, saved#, atoms: " + this.fileModelNumber + " " + this.modelNumber + " " + (this.asc.bsAtoms.cardinality () - n0));
return !this.haveModel || this.modelNumber != this.desiredModelNumber;
});
Clazz.defineMethod (c$, "finalizeModel",
function () {
var n = this.asc.ac;
var nremoved = 0;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var nnow = 0;
for (var i = i0; i < n; i++) {
if (!this.asc.bsAtoms.get (i)) {
nremoved++;
this.asc.ac--;
this.asc.atoms[i] = null;
continue;
}if (nremoved > 0) {
this.asc.atoms[this.asc.atoms[i].index = i - nremoved] = this.asc.atoms[i];
this.asc.atoms[i] = null;
}nnow++;
}
this.asc.atomSetAtomCounts[this.asc.iSet] = nnow;
if (nnow == 0) {
this.asc.iSet--;
this.asc.atomSetCount--;
} else {
this.asc.bsAtoms.setBits (i0, i0 + nnow);
}});
Clazz.defineMethod (c$, "readElementLabelsOnly",
function () {
this.readLines (5);
this.rdline ();
var n = this.getTokens ().length;
this.elementLabel = new Array (n);
this.rdline ();
this.line = "";
var s = null;
var last = null;
for (var i = 0; i < n; i++) {
while (s == null || s.equals (last)) {
this.rdline ();
var tokens = this.getTokens ();
if (tokens.length != 4 || (s = this.elementLabel[i] = this.getElement (tokens[3])) == null) {
i = n + 1;
break;
}}
last = s;
}
if (s == null) this.elementLabel = this.defaultLabels;
});
Clazz.defineMethod (c$, "getData",
function () {
this.discardLinesUntilContains ("- DATA -");
var htAFLOW = new java.util.Hashtable ();
htAFLOW.put ("fileModelNumber", Integer.$valueOf (this.fileModelNumber));
htAFLOW.put ("modelNumber", Integer.$valueOf (this.modelNumber + 1));
htAFLOW.put ("AaBb", this.aabb);
var pt = 0;
var sb = new JU.SB ();
var listVal = 3.4028235E38;
var strcb = "?";
var listValStr = null;
var cb = 0;
while (this.rdline () != null && (pt = this.line.indexOf (" # ")) >= 0) {
var key = this.line.substring (pt + 3).trim ();
var val = this.line.substring (0, pt).trim ();
sb.append (key).append ("=").append (val).append (" | ");
if (key.toUpperCase ().startsWith (this.listKey)) {
this.listKey = key.toUpperCase ();
this.listKeyCase = key;
listValStr = val;
listVal = this.parseFloatStr (val);
}if (key.equals ("Ca")) {
var ca = this.parseFloatStr (val);
if (this.getComposition && Math.abs ((1 - ca) - this.fracB) > 0.01) return false;
} else if (key.equals ("Cb")) {
cb = this.parseFloatStr (strcb = val);
if (this.getComposition && Math.abs (cb - this.fracB) > 0.01) return false;
} else if (key.equals ("Hf_atom [eV] (VASP)")) {
var e = this.parseFloatStr (val);
this.asc.setAtomSetEnergy (val, e);
}}
this.asc.setAtomSetName (this.titleMsg + (this.getComposition ? "" : " Cb=" + cb) + " " + this.listKey + "=" + listValStr);
var count_min = this.compositions.get (strcb);
if (!this.doGetModel (++this.modelNumber, null)) return false;
if (count_min == null) this.compositions.put (strcb, count_min = Clazz.newFloatArray (-1, [0, 3.4028235E38, 0]));
count_min[0]++;
if (listVal < count_min[1]) {
count_min[1] = listVal;
count_min[2] = this.fileModelNumber;
}while (this.line.indexOf ("- URL -") < 0) this.rdline ();
sb.append ("URL=" + this.rdline () + "|");
while (this.line.indexOf ("aurl=") < 0) this.rdline ();
sb.append (this.line);
var pairs = JU.PT.split (sb.toString (), " | ");
for (var i = pairs.length; --i >= 0; ) {
var kv = pairs[i].$plit ("=");
if (kv.length < 2) continue;
var f = this.parseFloatStr (kv[1]);
var o = Float.isNaN (f) ? kv[1] : Float.$valueOf (f);
htAFLOW.put (kv[0], o);
var kvclean = this.cleanKey (kv[0]);
if (kvclean !== kv[0]) htAFLOW.put (kvclean, o);
}
this.asc.setCurrentModelInfo ("aflowInfo", htAFLOW);
return true;
});
Clazz.defineMethod (c$, "cleanKey",
function (key) {
var kclean = this.keyMap.get (key);
if (kclean != null) return kclean;
var chars = key.toCharArray ();
for (var i = chars.length; --i >= 0; ) if (!JU.PT.isLetterOrDigit (chars[i])) chars[i] = '_';
this.keyMap.put (key, kclean = JU.PT.trim (JU.PT.rep ( String.instantialize (chars), "__", "_"), "_"));
return kclean;
}, "~S");
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.alignUnitCells ();
this.listCompositions ();
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "listCompositions",
function () {
var list = new JU.Lst ();
for (var e, $e = this.compositions.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var count_min = e.getValue ();
list.addLast (e.getKey () + "\t" + (Clazz.floatToInt (count_min[0])) + "\t" + Clazz.floatToInt (count_min[2]) + "\t" + this.listKeyCase + "\t" + count_min[1]);
}
var a = new Array (list.size ());
list.toArray (a);
java.util.Arrays.sort (a);
for (var i = 0, n = a.length; i < n; i++) this.appendLoadNote (this.aabb + "\t" + a[i]);
});
Clazz.defineMethod (c$, "alignUnitCells",
function () {
});
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/cif/Cif2DataParser.js Normal file
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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["JU.CifDataParser"], "J.adapter.readers.cif.Cif2DataParser", ["java.lang.Float", "java.util.Hashtable", "JU.Lst", "$.PT"], function () {
c$ = Clazz.declareType (J.adapter.readers.cif, "Cif2DataParser", JU.CifDataParser);
Clazz.overrideMethod (c$, "getVersion",
function () {
return 2;
});
Clazz.overrideMethod (c$, "toUnicode",
function (data) {
return data;
}, "~S");
Clazz.overrideMethod (c$, "isQuote",
function (ch) {
switch (ch) {
case '\1':
case '\'':
case '\"':
case '[':
case ']':
case '{':
case '}':
case ';':
return true;
}
return false;
}, "~S");
Clazz.overrideMethod (c$, "getQuotedStringOrObject",
function (ch) {
return this.processQuotedString ();
}, "~S");
Clazz.overrideMethod (c$, "preprocessString",
function () {
this.line = (this.ich == 0 ? this.str : this.str.substring (this.ich));
return this.setString (this.processSemiString ());
});
Clazz.defineMethod (c$, "processQuotedString",
function () {
var str = null;
var quoteChar = this.str.charAt (this.ich);
var tripleChar = null;
try {
switch (quoteChar) {
case '\1':
str = this.str.substring (1, (this.ich = this.str.indexOf ("\1", this.ich + 1)));
this.ich++;
break;
case '[':
return this.readList ();
case ']':
this.ich++;
return "]";
case '{':
return this.readTable ();
case '}':
this.ich++;
return "}";
case '\'':
case '"':
if (this.str.indexOf ("'''") == this.ich) tripleChar = "'''";
else if (this.str.indexOf ("\"\"\"") == this.ich) tripleChar = "\"\"\"";
var nchar = (tripleChar == null ? 1 : 3);
var pt = this.ich + nchar;
var pt1 = 0;
while ((pt1 = (tripleChar == null ? this.str.indexOf (quoteChar, pt) : this.str.indexOf (tripleChar, pt))) < 0) {
if (this.readLine () == null) break;
this.str += this.line;
}
this.ich = pt1 + nchar;
this.cch = this.str.length;
str = this.str.substring (pt, pt1);
break;
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
System.out.println ("exception in Cif2DataParser ; " + e);
} else {
throw e;
}
}
return (this.cterm == '\0' || this.asObject ? str : JU.PT.esc (str));
});
Clazz.defineMethod (c$, "processSemiString",
function () {
var pt1;
var pt2;
var str = this.preprocessSemiString ();
if (str.indexOf (';') != 1 && (pt1 = str.indexOf ('\\')) > 1 && ((pt2 = str.indexOf ('\n')) > pt1 || pt2 < 0)) {
var prefix = str.substring (1, pt1);
str = JU.PT.rep (str, "\n" + prefix, "\n");
str = "\1" + str.substring (str.charAt (pt1 + 1) == '\\' ? pt1 + 1 : pt2 < 0 ? str.length - 1 : pt2 + 1);
}this.ich = 0;
return this.fixLineFolding (str);
});
Clazz.defineMethod (c$, "readList",
function () {
this.ich++;
var cterm0 = this.cterm;
this.cterm = ']';
var ns = this.nullString;
this.nullString = null;
var lst = (this.asObject ? new JU.Lst () : null);
var n = 0;
var str = "";
while (true) {
var value = (this.asObject ? this.getNextTokenObject () : this.getNextToken ());
if (value == null || value.equals ("]")) break;
if (this.asObject) {
lst.addLast (value);
} else {
if (n++ > 0) str += ",";
str += value;
}}
this.cterm = cterm0;
this.nullString = ns;
return (this.asObject ? lst : "[" + str + "]");
});
Clazz.defineMethod (c$, "readTable",
function () {
this.ich++;
var cterm0 = this.cterm;
this.cterm = '}';
var ns = this.nullString;
this.nullString = null;
var map = (this.asObject ? new java.util.Hashtable () : null);
var n = 0;
var str = "";
while (true) {
var key = this.getNextToken ();
if (key == null || key.equals ("}")) break;
while (this.isSpaceOrColon (this.ich)) this.ich++;
if (this.asObject) {
map.put (key, this.getNextTokenObject ());
} else {
if (n++ > 0) str += ",";
str += key + " : " + this.getNextToken ();
}}
this.cterm = cterm0;
this.nullString = ns;
return (this.asObject ? map : "{" + str + "}");
});
Clazz.defineMethod (c$, "isSpaceOrColon",
function (ich) {
if (ich < this.cch) switch (this.line.charAt (ich)) {
case ' ':
case '\t':
case '\n':
case ':':
return true;
}
return false;
}, "~N");
Clazz.overrideMethod (c$, "unquoted",
function (s) {
if (this.cterm == '\0' && !this.asObject) return s;
var n = s.length;
if (n > 0) {
var c = s.charAt (0);
if (JU.PT.isDigit (c) || c == '-' || c == '.' && n > 1) {
var pt = s.indexOf ('(');
var isFloat = (s.indexOf (".") >= 0);
if (n > 1 && pt > 0 && s.indexOf (')', pt + 1) == n - 1) s = s.substring (0, pt);
try {
if (isFloat) {
var f = Float.parseFloat (s);
if (this.asObject) return Float.$valueOf (f);
s = "" + f;
if (s.indexOf (".") < 0 && s.indexOf ("E") < 0) s += ".0";
return s;
}var i = Integer.parseInt (s);
return (this.asObject ? Integer.$valueOf (i) : "" + i);
} catch (e) {
}
}}return (this.asObject ? s : JU.PT.esc (s));
}, "~S");
Clazz.defineMethod (c$, "fixLineFolding",
function (str) {
if (str.indexOf ('\\') < 0) return str;
var n = str.length;
if (str.endsWith ("\\\1")) str = str.substring (0, n - 1) + "\n\1";
var pt = 0;
while ((pt = str.indexOf ('\\', pt + 1)) >= 0) {
var eol = str.indexOf ('\n', pt);
if (eol < 0) break;
for (var i = eol; --i > pt; ) {
var ch = str.charAt (i);
if (!JU.PT.isWhitespace (ch)) {
if (ch == '\\') {
pt = i;
break;
}pt = eol;
break;
}}
if (pt < eol) str = str.substring (0, pt) + str.substring (eol + 1);
}
return str;
}, "~S");
});

8
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/cif/Cif2Reader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["J.adapter.readers.cif.CifReader"], "J.adapter.readers.cif.Cif2Reader", ["J.adapter.readers.cif.Cif2DataParser"], function () {
c$ = Clazz.declareType (J.adapter.readers.cif, "Cif2Reader", J.adapter.readers.cif.CifReader);
Clazz.overrideMethod (c$, "getCifDataParser",
function () {
return new J.adapter.readers.cif.Cif2DataParser ().set (this, null, this.debugging);
});
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/cif/CifReader.js Normal file
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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/cif/MMCifReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["J.adapter.readers.cif.CifReader"], "J.adapter.readers.cif.MMCifReader", ["java.lang.Boolean", "java.util.Hashtable", "JU.BS", "$.Lst", "$.M4", "$.P3", "$.PT", "$.SB", "J.adapter.smarter.Atom", "$.Structure", "J.c.STR", "JU.BSUtil", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.isBiomolecule = false;
this.byChain = false;
this.bySymop = false;
this.chainAtomMap = null;
this.chainAtomCounts = null;
this.vBiomolecules = null;
this.htBiomts = null;
this.htSites = null;
this.htHetero = null;
this.htBondMap = null;
this.assemblyIdAtoms = null;
this.thisChain = -1;
this.modelIndex = 0;
this.chainSum = null;
this.chainAtomCount = null;
this.isLigandBondBug = false;
this.mident = null;
this.requiresSorting = false;
this.structConnMap = null;
this.structConnList = "";
this.doSetBonds = false;
this.modelStrings = "";
this.done = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "MMCifReader", J.adapter.readers.cif.CifReader);
Clazz.overrideMethod (c$, "initSubclass",
function () {
this.setIsPDB ();
this.mident = JU.M4.newM4 (null);
this.isMMCIF = true;
if (this.isDSSP1) this.asc.setInfo ("isDSSP1", Boolean.TRUE);
if (this.htParams.containsKey ("isMutate")) this.asc.setInfo ("isMutate", Boolean.TRUE);
this.doSetBonds = this.checkFilterKey ("ADDBONDS");
this.byChain = this.checkFilterKey ("BYCHAIN");
if (this.checkFilterKey ("BIOMOLECULE")) this.filter = JU.PT.rep (this.filter, "BIOMOLECULE", "ASSEMBLY");
this.isBiomolecule = this.checkFilterKey ("ASSEMBLY");
if (this.isBiomolecule) {
this.filter = this.filter.$replace (':', ' ');
this.bySymop = this.checkFilterKey ("BYSYMOP");
}this.isCourseGrained = this.byChain || this.bySymop;
if (this.isCourseGrained) {
this.chainAtomMap = new java.util.Hashtable ();
this.chainAtomCounts = new java.util.Hashtable ();
}this.isLigandBondBug = (this.stateScriptVersionInt >= 140204 && this.stateScriptVersionInt <= 140208 || this.stateScriptVersionInt >= 140304 && this.stateScriptVersionInt <= 140308);
});
Clazz.overrideMethod (c$, "processSubclassEntry",
function () {
if (this.key0.startsWith ("_pdbx_struct_assembly_gen.") || this.key0.startsWith ("_struct_conn.") || this.key0.startsWith ("_struct_ref_seq_dif.") || this.key0.startsWith ("_struct_conf.") || this.key0.startsWith ("_struct_sheet_range.")) this.processSubclassLoopBlock ();
else if (this.key.equals ("_rna3d")) {
this.addedData = this.data;
this.addedDataKey = this.key;
} else if (this.key.equals ("_dssr")) {
this.dssr = this.vwr.parseJSONMap (this.reader.readLine ());
this.reader.readLine ();
}});
Clazz.overrideMethod (c$, "processSubclassLoopBlock",
function () {
if (this.key0.startsWith ("_struct_ncs_oper.")) return this.processStructOperListBlock (true);
if (this.key0.startsWith ("_pdbx_struct_oper_list.")) return this.processStructOperListBlock (false);
if (this.key0.startsWith ("_pdbx_struct_assembly_gen.")) return this.processAssemblyGenBlock ();
if (this.key0.startsWith ("_struct_ref_seq_dif.")) return this.processSequence ();
if (this.isCourseGrained) return false;
if (this.key0.startsWith ("_struct_site_gen.")) return this.processStructSiteBlock ();
if (this.key0.startsWith ("_chem_comp.")) return this.processChemCompLoopBlock ();
if (this.key0.startsWith ("_struct_conf.")) return this.processStructConfLoopBlock ();
if (this.key0.startsWith ("_struct_sheet_range.")) return this.processStructSheetRangeLoopBlock ();
if (this.isLigandBondBug) return false;
if (this.key0.startsWith ("_chem_comp_bond.")) return this.processCompBondLoopBlock ();
if (this.key0.startsWith ("_struct_conn.")) return this.processStructConnLoopBlock ();
return false;
});
Clazz.defineMethod (c$, "sortAssemblyModels",
function () {
var natoms = this.asc.ac;
var lastSet = -1;
var atoms = this.asc.atoms;
var newAtoms = new Array (natoms);
var ids = JU.PT.split ("," + this.modelStrings + ",", ",,");
var bsAtomsNew = (this.asc.bsAtoms == null ? null : JU.BS.newN (this.asc.bsAtoms.size ()));
for (var im = 1, n = 0; im < ids.length; im++) {
var sModel = ids[im];
var modelIndex = -1;
for (var is = 0; is < this.asc.atomSetCount; is++) {
var ia0 = this.asc.getAtomSetAtomIndex (is);
var ia1 = ia0 + this.asc.getAtomSetAtomCount (is);
var am = "" + this.modelMap.get ("_" + is);
if (am.equals (sModel)) {
if (modelIndex < 0 && (modelIndex = is) > lastSet) lastSet = is;
for (var i = ia0; i < ia1; i++) {
if (bsAtomsNew == null || this.asc.bsAtoms.get (i)) {
if (bsAtomsNew != null) bsAtomsNew.set (n);
atoms[i].atomSetIndex = modelIndex;
newAtoms[n++] = atoms[i];
}}
}}
}
this.asc.atoms = newAtoms;
this.asc.bsAtoms = bsAtomsNew;
if (++lastSet < this.asc.atomSetCount) this.asc.atomSetCount = lastSet;
});
Clazz.overrideMethod (c$, "finalizeSubclass",
function () {
if (this.byChain && !this.isBiomolecule) for (var id, $id = this.chainAtomMap.keySet ().iterator (); $id.hasNext () && ((id = $id.next ()) || true);) this.createParticle (id);
var haveBiomolecule = (this.isBiomolecule && this.vBiomolecules != null && this.vBiomolecules.size () > 0);
if (!this.isCourseGrained && this.asc.ac == this.nAtoms) {
this.asc.removeCurrentAtomSet ();
} else {
if ((this.dssr != null || this.validation != null || this.addedData != null) && !this.isCourseGrained && !this.requiresSorting) {
var vs = (this.getInterface ("J.adapter.readers.cif.MMCifValidationParser")).set (this);
var note = null;
if (this.addedData == null) {
if (this.validation != null || this.dssr != null) note = vs.finalizeValidations (this.vwr, this.modelMap);
} else if (this.addedDataKey.equals ("_rna3d")) {
note = vs.finalizeRna3d (this.modelMap);
}if (note != null) this.appendLoadNote (note);
}this.setHetero ();
if (this.doSetBonds) this.setBonds ();
}if (this.asc.ac == 0 && !this.isCourseGrained) return false;
var spaceGroup = this.sgName;
if (this.htSites != null) this.addSites (this.htSites);
if (haveBiomolecule) {
this.asc.setCurrentModelInfo ("biomolecules", this.vBiomolecules);
this.setBiomolecules ();
if (this.thisBiomolecule != null) {
if (this.iHaveFractionalCoordinates) this.fractionalizeCoordinates (false);
this.asc.getXSymmetry ().applySymmetryBio (this.thisBiomolecule, this.applySymmetryToBonds, this.filter);
this.asc.xtalSymmetry = null;
}this.doCheckUnitCell = new Boolean (this.doCheckUnitCell & (this.iHaveUnitCell && this.doApplySymmetry)).valueOf ();
if (this.doCheckUnitCell) {
this.ignoreFileSpaceGroupName = true;
this.sgName = spaceGroup;
this.fractionalizeCoordinates (true);
this.asc.setCurrentModelInfo ("biosymmetry", null);
this.asc.setCurrentModelInfo ("biosymmetryCount", null);
this.asc.checkSpecial = false;
if (this.byChain) return true;
}}if (this.latticeCells != null && this.latticeCells[0] != 0) this.addJmolScript ("unitcell;axes on;axes unitcell;");
if (this.requiresSorting) this.sortAssemblyModels ();
return true;
});
Clazz.overrideMethod (c$, "checkSubclassSymmetry",
function () {
this.asc.checkSpecial = false;
var modelIndex = this.asc.iSet;
this.asc.setCurrentModelInfo ("PDB_CONECT_firstAtom_count_max", Clazz.newIntArray (-1, [this.asc.getAtomSetAtomIndex (modelIndex), this.asc.getAtomSetAtomCount (modelIndex), this.maxSerial]));
return false;
});
Clazz.defineMethod (c$, "setBonds",
function () {
if (this.htBondMap == null) return;
var bsAtoms = this.asc.bsAtoms;
if (bsAtoms == null) bsAtoms = JU.BSUtil.newBitSet2 (0, this.asc.ac);
var atoms = this.asc.atoms;
var seqid = -1;
var comp = null;
var map = null;
for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) {
var a = atoms[i];
var pt = (a.vib == null ? a.sequenceNumber : a.vib.x);
if (pt != seqid) {
seqid = pt;
if (comp != null) this.processBonds (this.htBondMap.get (comp), map, false);
map = new java.util.Hashtable ();
comp = atoms[i].group3;
if (!this.htBondMap.containsKey (comp)) {
comp = null;
continue;
}}if (comp == null) continue;
map.put (a.atomName, Integer.$valueOf (a.index));
}
if (comp != null) this.processBonds (this.htBondMap.get (comp), map, false);
if (this.structConnMap != null) {
map = new java.util.Hashtable ();
seqid = -1;
comp = null;
for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) {
var a = atoms[i];
var pt = (a.vib == null ? a.sequenceNumber : a.vib.x);
if (pt != seqid) {
seqid = pt;
var ckey = a.chainID + a.group3 + seqid;
if (this.structConnList.indexOf (ckey) < 0) {
comp = null;
continue;
}comp = ckey;
}if (comp == null) continue;
map.put (comp + a.atomName + a.altLoc, Integer.$valueOf (a.index));
}
this.processBonds (this.structConnMap, map, true);
}this.appendLoadNote (this.asc.bondCount + " bonds added");
});
Clazz.defineMethod (c$, "processBonds",
function (cmap, map, isStructConn) {
var i1;
var i2;
for (var i = 0, n = cmap.size (); i < n; i++) {
var o = cmap.get (i);
if ((i1 = map.get (o[0])) == null || (i2 = map.get (o[1])) == null) continue;
if (this.debugging) JU.Logger.debug ((isStructConn ? "_struct_conn" : "_comp_bond") + " adding bond " + i1 + " " + i2 + " order=" + o[2]);
this.asc.addNewBondWithOrder (i1.intValue (), i2.intValue (), (o[2]).intValue ());
}
}, "JU.Lst,java.util.Map,~B");
Clazz.defineMethod (c$, "processSequence",
function () {
this.parseLoopParameters (J.adapter.readers.cif.MMCifReader.structRefFields);
var g1;
var g3;
while (this.parser.getData ()) {
if (this.isNull (g1 = this.getField (1).toLowerCase ()) || g1.length != 1 || this.isNull (g3 = this.getField (0))) continue;
if (this.htGroup1 == null) this.asc.setInfo ("htGroup1", this.htGroup1 = new java.util.Hashtable ());
this.htGroup1.put (g3, g1);
}
return true;
});
Clazz.defineMethod (c$, "processAssemblyGenBlock",
function () {
this.parseLoopParameters (J.adapter.readers.cif.MMCifReader.assemblyFields);
while (this.parser.getData ()) {
var assem = new Array (3);
var count = 0;
var p;
var n = this.parser.getColumnCount ();
for (var i = 0; i < n; ++i) {
switch (p = this.fieldProperty (i)) {
case 0:
case 1:
case 2:
count++;
assem[p] = this.field;
break;
}
}
if (count == 3) this.addAssembly (assem);
}
return true;
});
Clazz.defineMethod (c$, "addAssembly",
function (assem) {
var id = assem[0];
var list = assem[2];
var operators = assem[1];
var name = "biomolecule " + id;
JU.Logger.info (name + " operators " + operators + " ASYM_IDs " + list);
this.appendLoadNote ("found " + name + ": " + list);
if (this.vBiomolecules == null) this.vBiomolecules = new JU.Lst ();
var info = null;
for (var i = this.vBiomolecules.size (); --i >= 0; ) if (this.vBiomolecules.get (i).get ("name").equals (name)) {
info = this.vBiomolecules.get (i);
break;
}
if (info == null) {
info = new java.util.Hashtable ();
info.put ("name", name);
var iMolecule = this.parseIntStr (id);
info.put ("molecule", iMolecule == -2147483648 ? id : Integer.$valueOf (iMolecule));
info.put ("biomts", new JU.Lst ());
info.put ("chains", new JU.Lst ());
info.put ("assemblies", new JU.Lst ());
info.put ("operators", new JU.Lst ());
this.vBiomolecules.addLast (info);
}(info.get ("assemblies")).addLast ("$" + list.$replace (',', '$'));
(info.get ("operators")).addLast (this.decodeAssemblyOperators (operators));
this.checkFilterAssembly (id, info);
}, "~A");
Clazz.defineMethod (c$, "checkFilterAssembly",
function (id, info) {
if (this.checkFilterKey ("ASSEMBLY " + id + ";") || this.checkFilterKey ("ASSEMBLY=" + id + ";")) this.thisBiomolecule = info;
}, "~S,java.util.Map");
Clazz.defineMethod (c$, "decodeAssemblyOperators",
function (ops) {
var pt = ops.indexOf (")(");
if (pt >= 0) return this.crossBinary (this.decodeAssemblyOperators (ops.substring (0, pt + 1)), this.decodeAssemblyOperators (ops.substring (pt + 1)));
if (ops.startsWith ("(")) {
if (ops.indexOf ("-") >= 0) ops = JU.BS.unescape ("({" + ops.substring (1, ops.length - 1).$replace ('-', ':').$replace (',', ' ') + "})").toJSON ();
ops = JU.PT.rep (ops, " ", "");
ops = ops.substring (1, ops.length - 1);
}return ops;
}, "~S");
Clazz.defineMethod (c$, "crossBinary",
function (ops1, ops2) {
var sb = new JU.SB ();
var opsLeft = JU.PT.split (ops1, ",");
var opsRight = JU.PT.split (ops2, ",");
for (var i = 0; i < opsLeft.length; i++) for (var j = 0; j < opsRight.length; j++) sb.append (",").append (opsLeft[i]).append ("|").append (opsRight[j]);
return sb.toString ().substring (1);
}, "~S,~S");
Clazz.defineMethod (c$, "processStructOperListBlock",
function (isNCS) {
this.parseLoopParametersFor ((isNCS ? "_struct_ncs_oper" : "_pdbx_struct_oper_list"), isNCS ? J.adapter.readers.cif.MMCifReader.ncsoperFields : J.adapter.readers.cif.MMCifReader.operFields);
var m = Clazz.newFloatArray (16, 0);
m[15] = 1;
while (this.parser.getData ()) {
var count = 0;
var id = null;
var xyz = null;
var n = this.parser.getColumnCount ();
for (var i = 0; i < n; ++i) {
var p = this.fieldProperty (i);
switch (p) {
case -1:
break;
case 12:
id = this.field;
break;
case 13:
xyz = this.field;
break;
default:
m[p] = this.parseFloatStr (this.field);
++count;
}
}
if (id != null && (count == 12 || xyz != null && this.symmetry != null)) {
JU.Logger.info ((isNCS ? "noncrystallographic symmetry operator " : "assembly operator ") + id + " " + xyz);
var m4 = new JU.M4 ();
if (count != 12) {
this.symmetry.getMatrixFromString (xyz, m, false, 0);
m[3] *= this.symmetry.getUnitCellInfoType (0) / 12;
m[7] *= this.symmetry.getUnitCellInfoType (1) / 12;
m[11] *= this.symmetry.getUnitCellInfoType (2) / 12;
}m4.setA (m);
this.addMatrix (id, m4, isNCS);
}}
return true;
}, "~B");
Clazz.defineMethod (c$, "addMatrix",
function (id, m4, isNCS) {
if (isNCS) {
if (m4.equals (this.mident)) return;
m4.m33 = 0;
if (this.lstNCS == null) this.lstNCS = new JU.Lst ();
this.lstNCS.addLast (m4);
} else {
if (this.htBiomts == null) this.htBiomts = new java.util.Hashtable ();
this.htBiomts.put (id, m4);
}}, "~S,JU.M4,~B");
Clazz.defineMethod (c$, "processChemCompLoopBlock",
function () {
this.parseLoopParameters (J.adapter.readers.cif.MMCifReader.chemCompFields);
var groupName;
var hetName;
while (this.parser.getData ()) if (!this.isNull (groupName = this.getField (0)) && !this.isNull (hetName = this.getField (1))) this.addHetero (groupName, hetName, true, true);
return true;
});
Clazz.defineMethod (c$, "addHetero",
function (groupName, hetName, doCheck, addNote) {
if (doCheck && !this.vwr.getJBR ().isHetero (groupName)) return;
if (this.htHetero == null) this.htHetero = new java.util.Hashtable ();
if (doCheck && this.htHetero.containsKey (groupName)) return;
this.htHetero.put (groupName, hetName);
if (addNote) this.appendLoadNote (groupName + " = " + hetName);
}, "~S,~S,~B,~B");
Clazz.defineMethod (c$, "processStructConfLoopBlock",
function () {
if (this.ignoreStructure) {
this.parser.skipLoop (false);
return false;
}this.parseLoopParametersFor ("_struct_conf", J.adapter.readers.cif.MMCifReader.structConfFields);
if (!this.checkAllFieldsPresent (J.adapter.readers.cif.MMCifReader.structConfFields, -1, true)) {
this.parser.skipLoop (true);
return false;
}while (this.parser.getData ()) {
var structure = new J.adapter.smarter.Structure (-1, J.c.STR.HELIX, J.c.STR.HELIX, null, 0, 0, null);
var type = this.getField (0);
if (type.startsWith ("TURN")) structure.structureType = structure.substructureType = J.c.STR.TURN;
else if (!type.startsWith ("HELX")) structure.structureType = structure.substructureType = J.c.STR.NONE;
else structure.substructureType = J.adapter.smarter.Structure.getHelixType (this.parseIntStr (this.getField (9)));
structure.serialID = this.parseIntStr (this.getField (8));
structure.structureID = this.getField (7);
this.addStructure (structure);
}
return true;
});
Clazz.defineMethod (c$, "addStructure",
function (structure) {
structure.startChainID = this.vwr.getChainID (structure.startChainStr = this.getField (1), true);
structure.startSequenceNumber = this.parseIntStr (this.getField (2));
structure.startInsertionCode = this.getField (3).charAt (0);
structure.endChainID = this.vwr.getChainID (structure.endChainStr = this.getField (4), true);
structure.endSequenceNumber = this.parseIntStr (this.getField (5));
structure.endInsertionCode = this.getField (6).charAt (0);
this.asc.addStructure (structure);
}, "J.adapter.smarter.Structure");
Clazz.defineMethod (c$, "processStructSheetRangeLoopBlock",
function () {
if (this.ignoreStructure) {
this.parser.skipLoop (false);
return false;
}this.parseLoopParametersFor ("_struct_sheet_range", J.adapter.readers.cif.MMCifReader.structSheetRangeFields);
if (!this.checkAllFieldsPresent (J.adapter.readers.cif.MMCifReader.structSheetRangeFields, -1, true)) {
this.parser.skipLoop (true);
return false;
}while (this.parser.getData ()) this.addStructure ( new J.adapter.smarter.Structure (-1, J.c.STR.SHEET, J.c.STR.SHEET, this.getField (0), this.parseIntStr (this.getField (7)), 1, null));
return true;
});
Clazz.defineMethod (c$, "processStructSiteBlock",
function () {
this.parseLoopParametersFor ("_struct_site_gen", J.adapter.readers.cif.MMCifReader.structSiteFields);
var htSite = null;
this.htSites = new java.util.Hashtable ();
var seqNum;
var resID;
while (this.parser.getData ()) {
if (this.isNull (seqNum = this.getField (3)) || this.isNull (resID = this.getField (1))) continue;
var siteID = this.getField (0);
htSite = this.htSites.get (siteID);
if (htSite == null) {
htSite = new java.util.Hashtable ();
htSite.put ("groups", "");
this.htSites.put (siteID, htSite);
}var insCode = this.getField (4);
var chainID = this.getField (2);
var group = "[" + resID + "]" + seqNum + (this.isNull (insCode) ? "" : "^" + insCode) + (this.isNull (chainID) ? "" : ":" + chainID);
var groups = htSite.get ("groups");
groups += (groups.length == 0 ? "" : ",") + group;
htSite.put ("groups", groups);
}
return true;
});
Clazz.defineMethod (c$, "setBiomolecules",
function () {
if (this.assemblyIdAtoms == null && this.chainAtomCounts == null) return;
var bsAll = new JU.BS ();
for (var i = this.vBiomolecules.size (); --i >= 0; ) {
var biomolecule = this.vBiomolecules.get (i);
this.setBiomolecule (biomolecule, (biomolecule === this.thisBiomolecule ? bsAll : null));
}
if (this.isBiomolecule && bsAll.cardinality () < this.asc.ac) {
if (this.asc.bsAtoms != null) this.asc.bsAtoms.and (bsAll);
else if (!this.isCourseGrained) this.asc.bsAtoms = bsAll;
}});
Clazz.defineMethod (c$, "setBiomolecule",
function (biomolecule, bsAll) {
var biomtchains = biomolecule.get ("chains");
var biomts = biomolecule.get ("biomts");
var operators = biomolecule.get ("operators");
var assemblies = biomolecule.get ("assemblies");
var sum = new JU.P3 ();
var count = 0;
var bsAtoms = new JU.BS ();
var nAtomsTotal = 0;
var isBioCourse = (this.isBiomolecule && this.isCourseGrained);
for (var i = operators.size (); --i >= 0; ) {
var ops = JU.PT.split (operators.get (i), ",");
var ids = JU.PT.split (assemblies.get (i), "$");
var chainlist = "";
var nAtoms = 0;
for (var j = 1; j < ids.length; j++) {
var id = ids[j];
chainlist += ":" + id + ";";
if (this.assemblyIdAtoms != null) {
biomolecule.put ("asemblyIdAtoms", this.assemblyIdAtoms);
var bs = this.assemblyIdAtoms.get (id);
if (bs != null) {
bsAtoms.or (bs);
if (bsAll != null) bsAll.or (bs);
nAtoms += bs.cardinality ();
}} else if (isBioCourse) {
var asum = this.chainAtomMap.get (id);
if (asum != null) {
if (this.bySymop) {
sum.add (asum);
count += this.chainAtomCounts.get (id)[0];
} else {
this.createParticle (id);
nAtoms++;
}}}}
if (!this.isBiomolecule) continue;
for (var j = 0; j < ops.length; j++) {
var m = this.getOpMatrix (ops[j]);
if (m == null) return 0;
if (m.equals (this.mident)) {
biomts.add (0, this.mident);
biomtchains.add (0, chainlist);
} else {
biomts.addLast (m);
biomtchains.addLast (chainlist);
}}
if (this.bySymop && bsAll != null) {
nAtoms = 1;
var a1 = new J.adapter.smarter.Atom ();
a1.setT (sum);
a1.scale (1 / count);
a1.radius = 16;
this.asc.addAtom (a1);
}nAtoms *= ops.length;
nAtomsTotal += nAtoms;
}
biomolecule.put ("atomCount", Integer.$valueOf (nAtomsTotal));
return nAtomsTotal;
}, "java.util.Map,JU.BS");
Clazz.defineMethod (c$, "createParticle",
function (id) {
var asum = this.chainAtomMap.get (id);
var c = this.chainAtomCounts.get (id)[0];
var a = new J.adapter.smarter.Atom ();
a.setT (asum);
a.scale (1 / c);
a.elementSymbol = "Pt";
this.setChainID (a, id);
a.radius = 16;
this.asc.addAtom (a);
}, "~S");
Clazz.defineMethod (c$, "getOpMatrix",
function (ops) {
if (this.htBiomts == null) return JU.M4.newM4 (null);
var pt = ops.indexOf ("|");
if (pt >= 0) {
var m = JU.M4.newM4 (this.htBiomts.get (ops.substring (0, pt)));
m.mul (this.htBiomts.get (ops.substring (pt + 1)));
return m;
}return this.htBiomts.get (ops);
}, "~S");
Clazz.defineMethod (c$, "processStructConnLoopBlock",
function () {
this.parseLoopParametersFor ("_struct_conn", J.adapter.readers.cif.MMCifReader.structConnFields);
while (this.parser.getData ()) {
var sym1 = this.getField (5);
var sym2 = this.getField (11);
if (!sym1.equals (sym2) || !this.isNull (sym1) && !sym1.equals ("1_555")) continue;
var type = this.getField (12);
if (!type.startsWith ("covale") && !type.equals ("disulf") && !type.equals ("metalc")) continue;
if (this.htBondMap == null) this.htBondMap = new java.util.Hashtable ();
var key1 = this.vwr.getChainID (this.getField (0), true) + this.getField (2) + this.parseFloatStr (this.getField (1)) + this.getField (3) + this.getField (4);
var key2 = this.vwr.getChainID (this.getField (6), true) + this.getField (8) + this.parseFloatStr (this.getField (7)) + this.getField (9) + this.getField (10);
var order = this.getBondOrder (this.getField (13));
if (this.structConnMap == null) this.structConnMap = new JU.Lst ();
this.structConnMap.addLast ( Clazz.newArray (-1, [key1, key2, Integer.$valueOf (order)]));
if (this.structConnList.indexOf (key1) < 0) this.structConnList += key1;
if (this.structConnList.indexOf (key2) < 0) this.structConnList += key2;
}
return true;
});
Clazz.defineMethod (c$, "processCompBondLoopBlock",
function () {
this.doSetBonds = true;
this.parseLoopParametersFor ("_chem_comp_bond", J.adapter.readers.cif.MMCifReader.chemCompBondFields);
while (this.parser.getData ()) {
var comp = this.getField (0);
var atom1 = this.getField (1);
var atom2 = this.getField (2);
var order = this.getBondOrder (this.getField (3));
if ((this.getField (4).charAt (0) == 'Y')) switch (order) {
case 1:
order = 513;
break;
case 2:
order = 514;
break;
}
if (this.isLigand) {
this.asc.addNewBondWithOrderA (this.asc.getAtomFromName (atom1), this.asc.getAtomFromName (atom2), order);
} else if (this.haveHAtoms || this.htHetero != null && this.htHetero.containsKey (comp)) {
if (this.htBondMap == null) this.htBondMap = new java.util.Hashtable ();
var cmap = this.htBondMap.get (comp);
if (cmap == null) this.htBondMap.put (comp, cmap = new JU.Lst ());
cmap.addLast ( Clazz.newArray (-1, [atom1, atom2, Integer.$valueOf (this.haveHAtoms ? order : 1)]));
}}
return true;
});
Clazz.overrideMethod (c$, "processSubclassAtom",
function (atom, assemblyId, strChain) {
if (this.isBiomolecule) {
if (this.isCourseGrained) {
var sum = this.chainAtomMap.get (assemblyId);
if (sum == null) {
this.chainAtomMap.put (assemblyId, sum = new JU.P3 ());
this.chainAtomCounts.put (assemblyId, Clazz.newIntArray (1, 0));
}this.chainAtomCounts.get (assemblyId)[0]++;
sum.add (atom);
return false;
}} else if (this.byChain) {
if (this.thisChain != atom.chainID) {
this.thisChain = atom.chainID;
this.chainSum = this.chainAtomMap.get (strChain);
if (this.chainSum == null) {
this.chainAtomMap.put (strChain, this.chainSum = new JU.P3 ());
this.chainAtomCounts.put (strChain, this.chainAtomCount = Clazz.newIntArray (1, 0));
}}this.chainSum.add (atom);
this.chainAtomCount[0]++;
return false;
}if (assemblyId != null) {
if (this.assemblyIdAtoms == null) this.assemblyIdAtoms = new java.util.Hashtable ();
var bs = this.assemblyIdAtoms.get (assemblyId);
if (bs == null) this.assemblyIdAtoms.put (assemblyId, bs = new JU.BS ());
bs.set (this.ac);
}return true;
}, "J.adapter.smarter.Atom,~S,~S");
Clazz.overrideMethod (c$, "checkPDBModelField",
function (modelField, currentModelNo) {
this.fieldProperty (modelField);
var modelNo = this.parseIntStr (this.field);
return (modelNo == currentModelNo ? modelNo : this.incrementModel (modelNo));
}, "~N,~N");
Clazz.defineMethod (c$, "incrementModel",
function (modelNo) {
var isAssembly = (this.thisDataSetName != null && this.thisDataSetName.indexOf ("-assembly-") >= 0);
if (isAssembly) {
this.useFileModelNumbers = true;
var key = "," + modelNo + ",";
if (this.modelStrings.indexOf (key) >= 0) {
this.requiresSorting = true;
} else {
this.modelStrings += key;
}}if (this.iHaveDesiredModel && this.asc.atomSetCount > 0 && !isAssembly) {
this.done = true;
if (this.parser != null) {
this.parser.skipLoop (false);
this.skipping = false;
}this.continuing = true;
return -2147483648;
}var modelNumberToUse = (this.useFileModelNumbers ? modelNo : ++this.modelIndex);
this.setHetero ();
this.newModel (modelNumberToUse);
if (!this.skipping) {
this.nextAtomSet ();
if (this.modelMap == null || this.asc.ac == 0) this.modelMap = new java.util.Hashtable ();
this.modelMap.put ("" + modelNo, Integer.$valueOf (Math.max (0, this.asc.iSet)));
this.modelMap.put ("_" + Math.max (0, this.asc.iSet), Integer.$valueOf (modelNo));
}return modelNo;
}, "~N");
Clazz.defineMethod (c$, "setHetero",
function () {
if (this.htHetero != null) {
this.asc.setCurrentModelInfo ("hetNames", this.htHetero);
this.asc.setInfo ("hetNames", this.htHetero);
}});
Clazz.defineStatics (c$,
"OPER_ID", 12,
"OPER_XYZ", 13,
"FAMILY_NCS_CAT", "_struct_ncs_oper.",
"FAMILY_NCS", "_struct_ncs_oper",
"ncsoperFields", Clazz.newArray (-1, ["*_matrix[1][1]", "*_matrix[1][2]", "*_matrix[1][3]", "*_vector[1]", "*_matrix[2][1]", "*_matrix[2][2]", "*_matrix[2][3]", "*_vector[2]", "*_matrix[3][1]", "*_matrix[3][2]", "*_matrix[3][3]", "*_vector[3]", "*_id", "*_symmetry_operation"]),
"FAMILY_OPER_CAT", "_pdbx_struct_oper_list.",
"FAMILY_OPER", "_pdbx_struct_oper_list",
"operFields", Clazz.newArray (-1, ["*_matrix[1][1]", "*_matrix[1][2]", "*_matrix[1][3]", "*_vector[1]", "*_matrix[2][1]", "*_matrix[2][2]", "*_matrix[2][3]", "*_vector[2]", "*_matrix[3][1]", "*_matrix[3][2]", "*_matrix[3][3]", "*_vector[3]", "*_id", "*_symmetry_operation"]),
"ASSEM_ID", 0,
"ASSEM_OPERS", 1,
"ASSEM_LIST", 2,
"FAMILY_ASSEM_CAT", "_pdbx_struct_assembly_gen.",
"assemblyFields", Clazz.newArray (-1, ["_pdbx_struct_assembly_gen_assembly_id", "_pdbx_struct_assembly_gen_oper_expression", "_pdbx_struct_assembly_gen_asym_id_list"]),
"FAMILY_SEQUENCEDIF_CAT", "_struct_ref_seq_dif.",
"STRUCT_REF_G3", 0,
"STRUCT_REF_G1", 1,
"structRefFields", Clazz.newArray (-1, ["_struct_ref_seq_dif_mon_id", "_struct_ref_seq_dif_db_mon_id"]),
"CHEM_COMP_ID", 0,
"CHEM_COMP_NAME", 1,
"FAMILY_CHEMCOMP_CAT", "_chem_comp.",
"chemCompFields", Clazz.newArray (-1, ["_chem_comp_id", "_chem_comp_name"]),
"CONF_TYPE_ID", 0,
"BEG_ASYM_ID", 1,
"BEG_SEQ_ID", 2,
"BEG_INS_CODE", 3,
"END_ASYM_ID", 4,
"END_SEQ_ID", 5,
"END_INS_CODE", 6,
"STRUCT_ID", 7,
"SERIAL_NO", 8,
"HELIX_CLASS", 9,
"FAMILY_STRUCTCONF_CAT", "_struct_conf.",
"FAMILY_STRUCTCONF", "_struct_conf",
"structConfFields", Clazz.newArray (-1, ["*_conf_type_id", "*_beg_auth_asym_id", "*_beg_auth_seq_id", "*_pdbx_beg_pdb_ins_code", "*_end_auth_asym_id", "*_end_auth_seq_id", "*_pdbx_end_pdb_ins_code", "*_id", "*_pdbx_pdb_helix_id", "*_pdbx_pdb_helix_class"]),
"SHEET_ID", 0,
"STRAND_ID", 7,
"FAMILY_SHEET_CAT", "_struct_sheet_range.",
"FAMILY_SHEET", "_struct_sheet_range",
"structSheetRangeFields", Clazz.newArray (-1, ["*_sheet_id", "*_beg_auth_asym_id", "*_beg_auth_seq_id", "*_pdbx_beg_pdb_ins_code", "*_end_auth_asym_id", "*_end_auth_seq_id", "*_pdbx_end_pdb_ins_code", "*_id"]),
"SITE_ID", 0,
"SITE_COMP_ID", 1,
"SITE_ASYM_ID", 2,
"SITE_SEQ_ID", 3,
"SITE_INS_CODE", 4,
"FAMILY_STRUCSITE_CAT", "_struct_site_gen.",
"FAMILY_STRUCSITE", "_struct_site_gen",
"structSiteFields", Clazz.newArray (-1, ["*_site_id", "*_auth_comp_id", "*_auth_asym_id", "*_auth_seq_id", "*_label_alt_id"]),
"STRUCT_CONN_ASYM1", 0,
"STRUCT_CONN_SEQ1", 1,
"STRUCT_CONN_COMP1", 2,
"STRUCT_CONN_ATOM1", 3,
"STRUCT_CONN_ALT1", 4,
"STRUCT_CONN_SYMM1", 5,
"STRUCT_CONN_ASYM2", 6,
"STRUCT_CONN_SEQ2", 7,
"STRUCT_CONN_COMP2", 8,
"STRUCT_CONN_ATOM2", 9,
"STRUCT_CONN_ALT2", 10,
"STRUCT_CONN_SYMM2", 11,
"STRUCT_CONN_TYPE", 12,
"STRUCT_CONN_ORDER", 13,
"FAMILY_STRUCTCONN_CAT", "_struct_conn.",
"FAMILY_STRUCTCONN", "_struct_conn",
"structConnFields", Clazz.newArray (-1, ["*_ptnr1_auth_asym_id", "*_ptnr1_auth_seq_id", "*_ptnr1_auth_comp_id", "*_ptnr1_label_atom_id", "*_pdbx_ptnr1_label_alt_id", "*_ptnr1_symmetry", "*_ptnr2_auth_asym_id", "*_ptnr2_auth_seq_id", "*_ptnr2_auth_comp_id", "*_ptnr2_label_atom_id", "*_pdbx_ptnr2_label_alt_id", "*_ptnr2_symmetry", "*_conn_type_id", "*_pdbx_value_order"]),
"CHEM_COMP_BOND_ID", 0,
"CHEM_COMP_BOND_ATOM_ID_1", 1,
"CHEM_COMP_BOND_ATOM_ID_2", 2,
"CHEM_COMP_BOND_VALUE_ORDER", 3,
"CHEM_COMP_BOND_AROMATIC_FLAG", 4,
"FAMILY_COMPBOND_CAT", "_chem_comp_bond.",
"FAMILY_COMPBOND", "_chem_comp_bond",
"chemCompBondFields", Clazz.newArray (-1, ["*_comp_id", "*_atom_id_1", "*_atom_id_2", "*_value_order", "*_pdbx_aromatic_flag"]));
});

132
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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (null, "J.adapter.readers.cif.MMCifValidationParser", ["java.lang.Character", "java.util.Hashtable", "JU.Lst", "$.PT", "JS.SV", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.asResidues = false;
this.reader = null;
this.resMap = null;
this.atomMap = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "MMCifValidationParser");
Clazz.makeConstructor (c$,
function () {
});
Clazz.defineMethod (c$, "set",
function (reader) {
this.reader = reader;
this.asResidues = reader.checkFilterKey ("ASRES");
return this;
}, "J.adapter.smarter.AtomSetCollectionReader");
Clazz.defineMethod (c$, "finalizeValidations",
function (vwr, modelMap) {
var map = this.reader.dssr;
if (map != null) return vwr.getAnnotationParser (true).fixDSSRJSONMap (map);
this.mapAtomResIDs (modelMap);
var svMap = this.reader.validation;
var retProps = this.reader.vwr.getAnnotationParser (false).catalogValidations (this.reader.vwr, svMap, this.getModelAtomIndices (), this.resMap, (this.asResidues ? null : this.atomMap), modelMap);
var note = (retProps == null || retProps.size () == 0 ? null : this.setProperties (retProps));
svMap.mapPut ("_note", JS.SV.newS (note));
return note;
}, "JV.Viewer,java.util.Map");
Clazz.defineMethod (c$, "finalizeRna3d",
function (modelMap) {
this.mapAtomResIDs (modelMap);
var svMap = this.getRna3dMap (this.reader.addedData);
var note = this.reader.vwr.getAnnotationParser (false).catalogStructureUnits (this.reader.vwr, svMap, this.getModelAtomIndices (), this.resMap, null, modelMap);
svMap.mapPut ("_note", JS.SV.newS (note));
for (var i = this.reader.asc.atomSetCount; --i >= 0; ) {
var info = this.reader.asc.getAtomSetAuxiliaryInfo (i);
info.put ("rna3d", svMap);
}
return note;
}, "java.util.Map");
Clazz.defineMethod (c$, "getRna3dMap",
function (addedData) {
var map = new java.util.Hashtable ();
var next = Clazz.newIntArray (1, 0);
var id = "";
while ((id = JU.PT.getQuotedStringNext (addedData, next)).length > 0) {
var units = JU.PT.getQuotedStringNext (addedData, next);
var type = "?";
switch (id.charAt (0)) {
case 'H':
type = "hairpinLoops";
break;
case 'I':
type = "internalLoops";
break;
case 'J':
type = "junctions";
break;
default:
JU.Logger.error ("MMCif could not read: " + id + " " + units);
continue;
}
var list = map.get (type);
if (list == null) map.put (type, list = new JU.Lst ());
var m = new java.util.Hashtable ();
m.put ("index", Integer.$valueOf (JU.PT.parseInt (id.substring (id.lastIndexOf ("_") + 1))));
m.put ("units", units);
list.addLast (m);
}
return JS.SV.getVariableMap (map);
}, "~S");
Clazz.defineMethod (c$, "mapAtomResIDs",
function (modelMap) {
var atoms = this.reader.asc.atoms;
this.resMap = new java.util.Hashtable ();
this.atomMap = new java.util.Hashtable ();
var iresLast = -1;
var resLast = null;
var smodel = "" + modelMap.get ("_0");
for (var i = 0, model = 1, i0 = 0, n = this.reader.asc.getAtomSetAtomCount (0); i < n; i++) {
var a = atoms[i];
var ires = a.sequenceNumber;
var res = smodel + "_" + a.chainID + "_" + ires + "_" + (a.insertionCode == '\0' ? "" : "" + a.insertionCode);
var atom = res + "_" + a.atomName.toUpperCase () + "_" + (a.altLoc == '\0' ? "" : "" + Character.toLowerCase (a.altLoc));
var ia = Integer.$valueOf (i - i0);
if (ires != iresLast) {
iresLast = ires;
if (resLast != null) resLast[1] = i - i0;
this.resMap.put (res, resLast = Clazz.newIntArray (-1, [i - i0, n]));
}this.atomMap.put (atom, ia);
if (i == n - 1) {
i0 += n;
n = this.reader.asc.getAtomSetAtomCount (model++);
}}
}, "java.util.Map");
Clazz.defineMethod (c$, "getModelAtomIndices",
function () {
var indices = Clazz.newIntArray (this.reader.asc.atomSetCount + 1, 0);
for (var m = indices.length - 1; --m >= 0; ) indices[m] = this.reader.baseAtomIndex + this.reader.asc.getAtomSetAtomIndex (m);
indices[indices.length - 1] = this.reader.asc.ac;
return indices;
});
Clazz.defineMethod (c$, "setProperties",
function (propList) {
var note = "Validations loaded:";
for (var i = 0, n = propList.size (); i < n; ) {
var key = propList.get (i++);
var f = propList.get (i++);
var model = (propList.get (i++)).intValue ();
var isGroup = (propList.get (i++)).booleanValue ();
var count = 0;
var max = 0;
var reslast = -1;
var i0 = this.reader.asc.getAtomSetAtomIndex (model);
for (var j = f.length; --j >= 0; ) if (f[j] != 0) {
if (isGroup) {
var res = this.reader.asc.atoms[i0 + j].sequenceNumber;
if (res != reslast) {
reslast = res;
count++;
}} else {
count++;
}max = Math.max (f[j], max);
}
note += "\n property_" + key + " (" + (isGroup ? "residues: " : "atoms: ") + count + (max == 1 ? "" : ", max: " + (Clazz.floatToInt (max * 100)) / 100) + ")";
this.reader.asc.setAtomProperties (key, f, model, isGroup);
}
return note;
}, "JU.Lst");
});

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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["J.adapter.readers.cif.MMCifReader"], "J.adapter.readers.cif.MMTFReader", ["java.lang.Boolean", "java.util.Hashtable", "JU.BS", "$.Lst", "$.M4", "$.MessagePackReader", "$.PT", "$.SB", "J.adapter.smarter.Atom", "$.Bond", "$.Structure", "JS.SV", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.haveStructure = false;
this.$pdbID = null;
this.map = null;
this.fileAtomCount = 0;
this.opCount = 0;
this.groupModels = null;
this.groupMap = null;
this.groupDSSP = null;
this.atomGroup = null;
this.labelAsymList = null;
this.atomMap = null;
this.entities = null;
this.groupCount = 0;
this.ac0 = 0;
this.bsStructures = null;
this.lastGroup = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "MMTFReader", J.adapter.readers.cif.MMCifReader);
Clazz.overrideMethod (c$, "addHeader",
function () {
});
Clazz.overrideMethod (c$, "setup",
function (fullPath, htParams, reader) {
this.isBinary = true;
this.isMMCIF = true;
this.iHaveFractionalCoordinates = false;
this.setupASCR (fullPath, htParams, reader);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod (c$, "processBinaryDocument",
function () {
var doDoubleBonds = (!this.isCourseGrained && !this.checkFilterKey ("NODOUBLE"));
this.isDSSP1 = !this.checkFilterKey ("DSSP2");
var mmtfImplementsDSSP2 = false;
this.applySymmetryToBonds = true;
this.map = ( new JU.MessagePackReader (this.binaryDoc, true)).readMap ();
this.entities = this.map.get ("entityList");
if (JU.Logger.debugging) {
for (var s, $s = this.map.keySet ().iterator (); $s.hasNext () && ((s = $s.next ()) || true);) JU.Logger.info (s);
}this.asc.setInfo ("noAutoBond", Boolean.TRUE);
JU.Logger.info ("MMTF version " + this.map.get ("mmtfVersion"));
JU.Logger.info ("MMTF Producer " + this.map.get ("mmtfProducer"));
var title = this.map.get ("title");
if (title != null) this.appendLoadNote (title);
this.$pdbID = this.map.get ("structureId");
if (this.$pdbID == null) this.$pdbID = this.map.get ("pdbId");
this.fileAtomCount = (this.map.get ("numAtoms")).intValue ();
var nBonds = (this.map.get ("numBonds")).intValue ();
this.groupCount = (this.map.get ("numGroups")).intValue ();
this.groupModels = Clazz.newIntArray (this.groupCount, 0);
this.groupDSSP = Clazz.newIntArray (this.groupCount, 0);
this.groupMap = Clazz.newIntArray (this.groupCount, 0);
var modelCount = (this.map.get ("numModels")).intValue ();
this.appendLoadNote ("id=" + this.$pdbID + " numAtoms=" + this.fileAtomCount + " numBonds=" + nBonds + " numGroups=" + this.groupCount + " numModels=" + modelCount);
this.getMMTFAtoms (doDoubleBonds);
if (!this.isCourseGrained) {
var bo = this.decode ("bondOrderList");
var bi = this.decode ("bondAtomList");
this.addMMTFBonds (bo, bi, 0, doDoubleBonds, true);
if (this.isDSSP1 || mmtfImplementsDSSP2) this.getStructure ();
}this.setMMTFSymmetry ();
this.getMMTFBioAssembly ();
this.setModelPDB (true);
if (JU.Logger.debuggingHigh) JU.Logger.info (JS.SV.getVariable (this.map).asString ());
});
Clazz.defineMethod (c$, "applySymmetryAndSetTrajectory",
function () {
this.ac0 = this.ac;
Clazz.superCall (this, J.adapter.readers.cif.MMTFReader, "applySymmetryAndSetTrajectory", []);
if (this.haveStructure) this.addStructureSymmetry ();
});
Clazz.defineMethod (c$, "getMMTFAtoms",
function (doMulti) {
var chainsPerModel = this.map.get ("chainsPerModel");
var groupsPerChain = this.map.get ("groupsPerChain");
this.labelAsymList = this.decode ("chainIdList");
var authAsymList = this.decode ("chainNameList");
var groupTypeList = this.decode ("groupTypeList");
var groupIdList = this.decode ("groupIdList");
var groupList = this.map.get ("groupList");
var insCodes = this.decode ("insCodeList");
var atomId = this.decode ("atomIdList");
var haveSerial = (atomId != null);
var altloc = this.decode ("altLocList");
var occ = this.decode ("occupancyList");
var x = this.decode ("xCoordList");
var y = this.decode ("yCoordList");
var z = this.decode ("zCoordList");
var bf = this.decode ("bFactorList");
var nameList = (this.useAuthorChainID ? authAsymList : this.labelAsymList);
var iModel = -1;
var iChain = 0;
var nChain = 0;
var iGroup = 0;
var nGroup = 0;
var chainpt = 0;
var seqNo = 0;
var iatom = 0;
var chainID = "";
var authAsym = "";
var labelAsym = "";
var insCode = '\u0000';
this.atomMap = new Array (this.fileAtomCount);
this.atomGroup = Clazz.newIntArray (this.fileAtomCount, 0);
for (var j = 0, thisGroup = -1; j < this.groupCount; j++) {
if (++iGroup >= nGroup) {
chainID = nameList[chainpt];
authAsym = authAsymList[chainpt];
labelAsym = this.labelAsymList[chainpt];
nGroup = groupsPerChain[chainpt++];
iGroup = 0;
if (++iChain >= nChain) {
this.groupModels[j] = ++iModel;
nChain = chainsPerModel[iModel];
iChain = 0;
this.setModelPDB (true);
this.incrementModel (iModel + 1);
this.asc.setCurrentModelInfo ("pdbID", this.$pdbID);
this.nAtoms0 = this.asc.ac;
if (this.done) return;
}}var g = groupList[groupTypeList[j]];
var atomNameList = g.get ("atomNameList");
var len = atomNameList.length;
if (this.skipping) {
iatom += len;
continue;
}var a0 = iatom;
if (insCodes != null) insCode = insCodes[j];
seqNo = groupIdList[j];
var group3 = g.get ("groupName");
var isHetero = this.vwr.getJBR ().isHetero (group3);
if (isHetero) {
var hetName = "" + g.get ("chemCompType");
if (this.htHetero == null || !this.htHetero.containsKey (group3)) {
if (this.entities != null && hetName.equals ("NON-POLYMER")) out : for (var i = this.entities.length; --i >= 0; ) {
var entity = this.entities[i];
var chainList = entity.get ("chainIndexList");
for (var k = chainList.length; --k >= 0; ) if (chainList[k] == iChain) {
hetName = "a component of the entity \"" + entity.get ("description") + "\"";
break out;
}
}
this.addHetero (group3, hetName, false, true);
}}var elementList = g.get ("elementList");
var haveAtom = false;
for (var ia = 0, pt = 0; ia < len; ia++, iatom++) {
var a = new J.adapter.smarter.Atom ();
a.isHetero = isHetero;
if (insCode.charCodeAt (0) != 0) a.insertionCode = insCode;
this.setAtomCoordXYZ (a, x[iatom], y[iatom], z[iatom]);
a.elementSymbol = elementList[pt];
a.atomName = atomNameList[pt++];
if (seqNo >= 0) this.maxSerial = Math.max (this.maxSerial, a.sequenceNumber = seqNo);
a.group3 = group3;
this.setChainID (a, chainID);
if (bf != null) a.bfactor = bf[iatom];
if (altloc != null) a.altLoc = altloc[iatom];
if (occ != null) a.foccupancy = occ[iatom];
if (haveSerial) a.atomSerial = atomId[iatom];
if (!this.filterAtom (a, -1) || !this.processSubclassAtom (a, labelAsym, authAsym)) continue;
if (!haveAtom) {
thisGroup++;
haveAtom = true;
}if (haveSerial) {
this.asc.addAtomWithMappedSerialNumber (a);
} else {
this.asc.addAtom (a);
}this.atomMap[iatom] = a;
this.atomGroup[this.ac] = j;
this.groupMap[j] = this.lastGroup = thisGroup;
this.ac++;
}
if (!this.isCourseGrained) {
var bo = g.get ("bondOrderList");
var bi = g.get ("bondAtomList");
this.addMMTFBonds (bo, bi, a0, doMulti, false);
}}
this.asc.setCurrentModelInfo ("pdbID", this.$pdbID);
}, "~B");
Clazz.defineMethod (c$, "addMMTFBonds",
function (bo, bi, a0, doMulti, isInter) {
if (bi == null) return;
doMulti = new Boolean (doMulti & (bo != null)).valueOf ();
for (var bj = 0, pt = 0, nj = Clazz.doubleToInt (bi.length / 2); bj < nj; bj++) {
var a1 = this.atomMap[bi[pt++] + a0];
var a2 = this.atomMap[bi[pt++] + a0];
if (a1 != null && a2 != null) {
var bond = new J.adapter.smarter.Bond (a1.index, a2.index, doMulti ? bo[bj] : 1);
this.asc.addBond (bond);
if (JU.Logger.debugging && isInter) {
JU.Logger.info ("inter-group (" + (a1.atomSetIndex + 1) + "." + a1.index + "/" + (a2.atomSetIndex + 1) + "." + a2.index + ") bond " + a1.group3 + a1.sequenceNumber + "." + a1.atomName + " - " + a2.group3 + a2.sequenceNumber + "." + a2.atomName + " " + bond.order);
}}}
}, "~A,~A,~N,~B,~B");
Clazz.defineMethod (c$, "setMMTFSymmetry",
function () {
this.setSpaceGroupName (this.map.get ("spaceGroup"));
var o = this.map.get ("unitCell");
if (o != null) for (var i = 0; i < 6; i++) this.setUnitCellItem (i, o[i]);
});
Clazz.defineMethod (c$, "getMMTFBioAssembly",
function () {
var o = this.map.get ("bioAssemblyList");
if (o == null) return;
if (this.vBiomolecules == null) this.vBiomolecules = new JU.Lst ();
for (var i = o.length; --i >= 0; ) {
var info = new java.util.Hashtable ();
this.vBiomolecules.addLast (info);
var iMolecule = i + 1;
this.checkFilterAssembly ("" + iMolecule, info);
info.put ("name", "biomolecule " + iMolecule);
info.put ("molecule", Integer.$valueOf (iMolecule));
var assemb = new JU.Lst ();
var ops = new JU.Lst ();
info.put ("biomts", new JU.Lst ());
info.put ("chains", new JU.Lst ());
info.put ("assemblies", assemb);
info.put ("operators", ops);
var m = o[i];
var tlist = m.get ("transformList");
var chlist = new JU.SB ();
for (var j = 0, n = tlist.length; j < n; j++) {
var t = tlist[j];
chlist.setLength (0);
var chainList = t.get ("chainIndexList");
for (var k = 0, kn = chainList.length; k < kn; k++) chlist.append ("$").append (this.labelAsymList[chainList[k]]);
assemb.addLast (chlist.append ("$").toString ());
var id = "" + (++this.opCount);
this.addMatrix (id, JU.M4.newA16 (t.get ("matrix")), false);
ops.addLast (id);
}
}
});
Clazz.defineMethod (c$, "getStructure",
function () {
var a = this.decode ("secStructList");
if (JU.Logger.debugging) JU.Logger.info (JU.PT.toJSON ("secStructList", a));
this.bsStructures = Clazz.newArray (-1, [ new JU.BS (), null, new JU.BS (), new JU.BS (), new JU.BS (), null, new JU.BS ()]);
var lastGroup = -1;
for (var j = 0; j < a.length; j++) {
var type = a[j];
switch (type) {
case 0:
case 2:
case 3:
case 4:
case 6:
var igroup = this.groupMap[j];
this.bsStructures[type].set (igroup);
this.groupDSSP[igroup] = type + 1;
lastGroup = j;
}
}
var n = (this.isDSSP1 ? this.asc.iSet : this.groupModels[lastGroup]);
if (lastGroup >= 0) {
this.haveStructure = true;
this.asc.addStructure ( new J.adapter.smarter.Structure (n, null, null, null, 0, 0, this.bsStructures));
}});
Clazz.defineMethod (c$, "addStructureSymmetry",
function () {
if (this.asc.ac == 0) return;
var atoms = this.asc.atoms;
var bsAtoms = this.asc.bsAtoms;
var ptGroup = this.lastGroup;
var mygroup = -1;
for (var i = this.ac0, n = this.asc.ac; i < n; i++) {
if (bsAtoms == null || bsAtoms.get (i)) {
var a = atoms[i];
var igroup = this.atomGroup[a.atomSite];
if (igroup != mygroup) {
mygroup = igroup;
ptGroup++;
}var dssp = this.groupDSSP[igroup];
if (dssp > 0) {
this.bsStructures[dssp - 1].set (ptGroup);
}}}
});
Clazz.defineMethod (c$, "decode",
function (key) {
return JU.MessagePackReader.decode (this.map.get (key));
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["J.adapter.readers.cif.MSRdr"], "J.adapter.readers.cif.MSCifParser", ["java.lang.Character", "$.Double", "JU.M3", "$.Matrix", "$.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.field = null;
this.comSSMat = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "MSCifParser", J.adapter.readers.cif.MSRdr);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.cif.MSCifParser, []);
});
Clazz.defineMethod (c$, "processEntry",
function () {
var cr = this.cr;
if (cr.key.equals ("_cell_commen_t_section_1")) {
this.isCommensurate = true;
this.commensurateSection1 = cr.parseIntStr (cr.data);
}if (cr.key.startsWith ("_cell_commen_supercell_matrix")) {
this.isCommensurate = true;
if (this.comSSMat == null) this.comSSMat = JU.M3.newM3 (null);
var tokens = JU.PT.split (cr.key, "_");
var r = cr.parseIntStr (tokens[tokens.length - 2]);
var c = cr.parseIntStr (tokens[tokens.length - 1]);
if (r > 0 && c > 0) this.comSSMat.setElement (r - 1, c - 1, cr.parseFloatStr (cr.data));
}});
Clazz.defineMethod (c$, "processLoopBlock",
function () {
var cr = this.cr;
var key = cr.key;
if (key.equals ("_cell_subsystem_code")) return this.processSubsystemLoopBlock ();
if (!key.startsWith ("_cell_wave") && !key.contains ("fourier") && !key.contains ("legendre") && !key.contains ("_special_func")) {
if (key.contains ("crenel_ortho")) cr.appendLoadNote ("WARNING: Orthogonalized non-Legendre functions not supported.\nThe following block has been ignored. Use Legendre functions instead.\n\n" + cr.parser.skipLoop (true) + "=================================\n");
return 0;
}if (cr.asc.iSet < 0) cr.asc.newAtomSet ();
cr.parseLoopParametersFor ("_atom_site", J.adapter.readers.cif.MSCifParser.modulationFields);
var tok;
if (cr.key2col[8] != -1) {
cr.key2col[5] = cr.key2col[6] = cr.key2col[7] = -1;
}while (cr.parser.getData ()) {
var ignore = false;
var type_id = null;
var atomLabel = null;
var axis = null;
var pt = Clazz.newDoubleArray (-1, [NaN, NaN, NaN]);
var c = NaN;
var w = NaN;
var fid = null;
var n = cr.parser.getColumnCount ();
for (var i = 0; i < n; ++i) {
switch (tok = this.fieldProperty (cr, i)) {
case 1:
cr.haveCellWaveVector = true;
case 0:
case 40:
case 41:
case 42:
pt[0] = pt[1] = pt[2] = 0;
case 13:
case 25:
case 50:
case 35:
case 43:
case 44:
case 45:
switch (tok) {
case 1:
type_id = "W_";
break;
case 0:
type_id = "F_";
break;
case 40:
case 41:
case 42:
fid = "?" + this.field;
pt[2] = 1;
continue;
case 43:
case 44:
case 45:
atomLabel = axis = "*";
case 13:
case 25:
case 50:
case 35:
type_id = Character.toUpperCase (J.adapter.readers.cif.MSCifParser.modulationFields[tok].charAt (11)) + "_";
break;
}
type_id += this.field;
break;
case 46:
type_id = "J_O";
pt[0] = pt[2] = 1;
axis = "0";
atomLabel = this.field;
break;
case 30:
type_id = "O_0";
axis = "0";
atomLabel = this.field;
break;
case 18:
type_id = "D_S";
axis = "0";
atomLabel = this.field;
break;
case 55:
type_id = "M_T";
axis = "0";
atomLabel = this.field;
break;
case 61:
type_id = "D_L";
atomLabel = this.field;
break;
case 65:
type_id = "U_L";
atomLabel = this.field;
break;
case 69:
type_id = "O_L";
atomLabel = this.field;
break;
case 11:
case 24:
case 48:
case 33:
atomLabel = this.field;
break;
case 12:
case 49:
case 62:
axis = this.field;
if (this.modAxes != null && this.modAxes.indexOf (axis.toUpperCase ()) < 0) ignore = true;
break;
case 66:
case 34:
axis = this.field.toUpperCase ();
break;
default:
var f = cr.parseFloatStr (this.field);
switch (tok) {
case 64:
case 71:
case 68:
pt[0] = f;
if (f != 0) pt[2] = 0;
break;
case 27:
case 31:
case 15:
case 52:
case 37:
case 77:
case 73:
case 75:
pt[2] = 0;
case 2:
case 5:
case 19:
case 56:
pt[0] = f;
break;
case 8:
type_id += "_coefs_";
pt = Clazz.newDoubleArray (this.modDim, 0);
pt[0] = f;
break;
case 16:
case 28:
case 53:
case 38:
pt[0] = f;
pt[2] = 1;
break;
case 70:
case 74:
case 26:
axis = "0";
case 63:
case 67:
case 3:
case 6:
case 9:
case 17:
case 29:
case 54:
case 39:
case 32:
case 20:
case 57:
case 47:
case 14:
case 51:
case 36:
case 72:
case 76:
pt[1] = f;
break;
case 4:
case 7:
case 10:
case 21:
case 58:
pt[2] = f;
break;
case 22:
case 59:
c = f;
break;
case 23:
case 60:
w = f;
break;
}
break;
}
}
if (ignore || type_id == null || atomLabel != null && !atomLabel.equals ("*") && cr.rejectAtomName (atomLabel)) continue;
var ok = true;
for (var j = 0, nzero = pt.length; j < pt.length; j++) if (Double.isNaN (pt[j]) || pt[j] > 1e100 || pt[j] == 0 && --nzero == 0) {
ok = false;
break;
}
if (!ok) continue;
switch (type_id.charAt (0)) {
case 'C':
case 'D':
case 'O':
case 'M':
case 'U':
case 'J':
if (atomLabel == null || axis == null) continue;
if (type_id.equals ("D_S") || type_id.equals ("M_T")) {
if (Double.isNaN (c) || Double.isNaN (w)) continue;
if (pt[0] != 0) this.addMod (type_id + "#x;" + atomLabel, fid, Clazz.newDoubleArray (-1, [c, w, pt[0]]));
if (pt[1] != 0) this.addMod (type_id + "#y;" + atomLabel, fid, Clazz.newDoubleArray (-1, [c, w, pt[1]]));
if (pt[2] != 0) this.addMod (type_id + "#z;" + atomLabel, fid, Clazz.newDoubleArray (-1, [c, w, pt[2]]));
continue;
}if (type_id.indexOf ("_L") == 1) {
if (type_id.startsWith ("U")) type_id += Clazz.doubleToInt (pt[1]);
else axis += Clazz.doubleToInt (pt[1]);
}type_id += "#" + axis + ";" + atomLabel;
break;
}
this.addMod (type_id, fid, pt);
}
return 1;
});
Clazz.defineMethod (c$, "addMod",
function (id, fid, params) {
if (fid != null) id += fid;
this.addModulation (null, id, params, -1);
}, "~S,~S,~A");
Clazz.defineMethod (c$, "processSubsystemLoopBlock",
function () {
var cr = this.cr;
cr.parseLoopParameters (null);
while (cr.parser.getData ()) {
this.fieldProperty (cr, 0);
var id = this.field;
this.addSubsystem (id, this.getSparseMatrix (cr, "_w_", 1, 3 + this.modDim));
}
return 1;
});
Clazz.defineMethod (c$, "getSparseMatrix",
function (cr, term, i, dim) {
var m = new JU.Matrix (null, dim, dim);
var a = m.getArray ();
var key;
var p;
var n = cr.parser.getColumnCount ();
for (; i < n; ++i) {
if ((p = this.fieldProperty (cr, i)) < 0 || !(key = cr.parser.getColumnName (p)).contains (term)) continue;
var tokens = JU.PT.split (key, "_");
var r = cr.parseIntStr (tokens[tokens.length - 2]);
var c = cr.parseIntStr (tokens[tokens.length - 1]);
if (r > 0 && c > 0) a[r - 1][c - 1] = cr.parseFloatStr (this.field);
}
return m;
}, "J.adapter.readers.cif.CifReader,~S,~N,~N");
Clazz.defineMethod (c$, "fieldProperty",
function (cr, i) {
return ((this.field = cr.parser.getColumnData (i)).length > 0 && this.field.charAt (0) != '\0' ? cr.col2key[i] : -1);
}, "J.adapter.readers.cif.CifReader,~N");
Clazz.defineStatics (c$,
"FWV_ID", 0,
"WV_ID", 1,
"WV_X", 2,
"WV_Y", 3,
"WV_Z", 4,
"FWV_X", 5,
"FWV_Y", 6,
"FWV_Z", 7,
"JANA_FWV_Q1_COEF", 8,
"JANA_FWV_Q2_COEF", 9,
"JANA_FWV_Q3_COEF", 10,
"FWV_DISP_LABEL", 11,
"FWV_DISP_AXIS", 12,
"FWV_DISP_SEQ_ID", 13,
"FWV_DISP_COS", 14,
"FWV_DISP_SIN", 15,
"FWV_DISP_MODULUS", 16,
"FWV_DISP_PHASE", 17,
"DISP_SPEC_LABEL", 18,
"DISP_SAW_AX", 19,
"DISP_SAW_AY", 20,
"DISP_SAW_AZ", 21,
"DISP_SAW_C", 22,
"DISP_SAW_W", 23,
"FWV_OCC_LABEL", 24,
"FWV_OCC_SEQ_ID", 25,
"FWV_OCC_COS", 26,
"FWV_OCC_SIN", 27,
"FWV_OCC_MODULUS", 28,
"FWV_OCC_PHASE", 29,
"OCC_SPECIAL_LABEL", 30,
"OCC_CRENEL_C", 31,
"OCC_CRENEL_W", 32,
"FWV_U_LABEL", 33,
"FWV_U_TENS", 34,
"FWV_U_SEQ_ID", 35,
"FWV_U_COS", 36,
"FWV_U_SIN", 37,
"FWV_U_MODULUS", 38,
"FWV_U_PHASE", 39,
"FD_ID", 40,
"FO_ID", 41,
"FU_ID", 42,
"FDP_ID", 43,
"FOP_ID", 44,
"FUP_ID", 45,
"JANA_OCC_ABS_LABEL", 46,
"JANA_OCC_ABS_O_0", 47,
"FWV_SPIN_LABEL", 48,
"FWV_SPIN_AXIS", 49,
"FWV_SPIN_SEQ_ID", 50,
"FWV_SPIN_COS", 51,
"FWV_SPIN_SIN", 52,
"FWV_SPIN_MODULUS", 53,
"FWV_SPIN_PHASE", 54,
"SPIN_SPEC_LABEL", 55,
"SPIN_SAW_AX", 56,
"SPIN_SAW_AY", 57,
"SPIN_SAW_AZ", 58,
"SPIN_SAW_C", 59,
"SPIN_SAW_W", 60,
"LEG_DISP_LABEL", 61,
"LEG_DISP_AXIS", 62,
"LEG_DISP_ORDER", 63,
"LEG_DISP_COEF", 64,
"LEG_U_LABEL", 65,
"LEG_U_TENS", 66,
"LEG_U_ORDER", 67,
"LEG_U_COEF", 68,
"LEG_OCC_LABEL", 69,
"LEG_OCC_ORDER", 70,
"LEG_OCC_COEF", 71,
"DEPR_FD_COS", 72,
"DEPR_FD_SIN", 73,
"DEPR_FO_COS", 74,
"DEPR_FO_SIN", 75,
"DEPR_FU_COS", 76,
"DEPR_FU_SIN", 77,
"modulationFields", Clazz.newArray (-1, ["*_fourier_wave_vector_seq_id", "_cell_wave_vector_seq_id", "_cell_wave_vector_x", "_cell_wave_vector_y", "_cell_wave_vector_z", "*_fourier_wave_vector_x", "*_fourier_wave_vector_y", "*_fourier_wave_vector_z", "*_fourier_wave_vector_q1_coeff", "*_fourier_wave_vector_q2_coeff", "*_fourier_wave_vector_q3_coeff", "*_displace_fourier_atom_site_label", "*_displace_fourier_axis", "*_displace_fourier_wave_vector_seq_id", "*_displace_fourier_param_cos", "*_displace_fourier_param_sin", "*_displace_fourier_param_modulus", "*_displace_fourier_param_phase", "*_displace_special_func_atom_site_label", "*_displace_special_func_sawtooth_ax", "*_displace_special_func_sawtooth_ay", "*_displace_special_func_sawtooth_az", "*_displace_special_func_sawtooth_c", "*_displace_special_func_sawtooth_w", "*_occ_fourier_atom_site_label", "*_occ_fourier_wave_vector_seq_id", "*_occ_fourier_param_cos", "*_occ_fourier_param_sin", "*_occ_fourier_param_modulus", "*_occ_fourier_param_phase", "*_occ_special_func_atom_site_label", "*_occ_special_func_crenel_c", "*_occ_special_func_crenel_w", "*_u_fourier_atom_site_label", "*_u_fourier_tens_elem", "*_u_fourier_wave_vector_seq_id", "*_u_fourier_param_cos", "*_u_fourier_param_sin", "*_u_fourier_param_modulus", "*_u_fourier_param_phase", "*_displace_fourier_id", "*_occ_fourier_id", "*_u_fourier_id", "*_displace_fourier_param_id", "*_occ_fourier_param_id", "*_u_fourier_param_id", "*_occ_fourier_absolute_site_label", "*_occ_fourier_absolute", "*_moment_fourier_atom_site_label", "*_moment_fourier_axis", "*_moment_fourier_wave_vector_seq_id", "*_moment_fourier_param_cos", "*_moment_fourier_param_sin", "*_moment_fourier_param_modulus", "*_moment_fourier_param_phase", "*_moment_special_func_atom_site_label", "*_moment_special_func_sawtooth_ax", "*_moment_special_func_sawtooth_ay", "*_moment_special_func_sawtooth_az", "*_moment_special_func_sawtooth_c", "*_moment_special_func_sawtooth_w", "*_displace_legendre_atom_site_label", "*_displace_legendre_axis", "*_displace_legendre_param_order", "*_displace_legendre_param_coeff", "*_u_legendre_atom_site_label", "*_u_legendre_tens_elem", "*_u_legendre_param_order", "*_u_legendre_param_coeff", "*_occ_legendre_atom_site_label", "*_occ_legendre_param_order", "*_occ_legendre_param_coeff", "*_displace_fourier_cos", "*_displace_fourier_sin", "*_occ_fourier_cos", "*_occ_fourier_sin", "*_u_fourier_cos", "*_u_fourier_sin"]),
"NONE", -1);
});

593
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/cif/MSRdr.js Normal file
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@@ -0,0 +1,593 @@
Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (["J.adapter.smarter.MSInterface"], "J.adapter.readers.cif.MSRdr", ["java.lang.Boolean", "$.Exception", "$.Float", "java.util.Hashtable", "JU.Lst", "$.M3", "$.Matrix", "$.P3", "$.PT", "J.adapter.readers.cif.Subsystem", "J.adapter.smarter.AtomSetCollectionReader", "JU.BSUtil", "$.BoxInfo", "$.Escape", "$.Logger", "$.Modulation", "$.ModulationSet", "$.Vibration"], function () {
c$ = Clazz.decorateAsClass (function () {
this.cr = null;
this.modDim = 0;
this.modAxes = null;
this.modAverage = false;
this.isCommensurate = false;
this.commensurateSection1 = 0;
this.modPack = false;
this.modVib = false;
this.modType = null;
this.modCell = null;
this.modDebug = false;
this.modSelected = -1;
this.modLast = false;
this.sigma = null;
this.htModulation = null;
this.htAtomMods = null;
this.iopLast = -1;
this.gammaE = null;
this.nOps = 0;
this.haveOccupancy = false;
this.atoms = null;
this.ac = 0;
this.haveAtomMods = false;
this.modCoord = false;
this.finalized = false;
this.symmetry = null;
this.supercellSymmetry = null;
this.legendres = null;
this.atModel = "@0";
this.modMatrices = null;
this.qlist100 = null;
this.qs = null;
this.modCount = 0;
this.modTUV = null;
this.htSubsystems = null;
this.minXYZ0 = null;
this.maxXYZ0 = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "MSRdr", null, J.adapter.smarter.MSInterface);
Clazz.defineMethod (c$, "getSigma",
function () {
return this.sigma;
});
Clazz.makeConstructor (c$,
function () {
});
Clazz.overrideMethod (c$, "initialize",
function (r, modDim) {
this.cr = r;
this.modCoord = r.checkFilterKey ("MODCOORD");
this.modDebug = r.checkFilterKey ("MODDEBUG");
this.modPack = !r.checkFilterKey ("MODNOPACK");
this.modLast = r.checkFilterKey ("MODLAST");
this.modAxes = r.getFilter ("MODAXES=");
this.modType = r.getFilter ("MODTYPE=");
this.modCell = r.getFilter ("MODCELL=");
this.modSelected = r.parseIntStr ("" + r.getFilter ("MOD="));
this.modVib = r.checkFilterKey ("MODVIB");
this.modAverage = r.checkFilterKey ("MODAVE");
var smodTUV = r.getFilter ("MODT=");
if (smodTUV != null || (smodTUV = r.getFilter ("MODTUV=")) != null) {
this.modTUV = new JU.P3 ();
var tuv = (JU.PT.replaceAllCharacters (smodTUV, "{}()", "") + ",0,0,0").$plit (",");
this.modTUV.x = JU.PT.parseFloatFraction (tuv[0]);
this.modTUV.y = JU.PT.parseFloatFraction (tuv[1]);
this.modTUV.z = JU.PT.parseFloatFraction (tuv[2]);
if (Float.isNaN (this.modTUV.lengthSquared ())) {
JU.Logger.error ("MSRdr cannot read modTUV=" + smodTUV);
this.modTUV = null;
}}this.setModDim (modDim);
return modDim;
}, "J.adapter.smarter.AtomSetCollectionReader,~N");
Clazz.defineMethod (c$, "setSubsystemOptions",
function () {
this.cr.forceSymmetry (this.modPack);
if (this.modCell != null) this.cr.addJmolScript ("unitcell {%" + this.modCell + "}");
});
Clazz.defineMethod (c$, "setModDim",
function (ndim) {
this.htModulation = new java.util.Hashtable ();
this.modDim = ndim;
this.cr.appendLoadNote ("Modulation dimension = " + this.modDim);
}, "~N");
Clazz.overrideMethod (c$, "addModulation",
function (map, id, pt, iModel) {
var ch = id.charAt (0);
switch (ch) {
case 'O':
case 'D':
case 'M':
case 'U':
if (this.modType != null && this.modType.indexOf (ch) < 0 || this.modSelected > 0 && this.modSelected != 1) return;
break;
}
var isOK = false;
for (var i = pt.length; --i >= 0; ) {
if (this.modSelected > 0 && i + 1 != this.modSelected && id.contains ("_coefs_")) {
pt[i] = 0;
} else if (pt[i] != 0) {
isOK = true;
break;
}}
if (!isOK) return;
if (map == null) map = this.htModulation;
if (id.indexOf ("@") < 0) id += "@" + (iModel >= 0 ? iModel : this.cr.asc.iSet);
if (id.startsWith ("D_L#") || id.startsWith ("U_L")) {
if (this.legendres == null) this.legendres = new JU.Lst ();
this.legendres.addLast (id);
}JU.Logger.info ("Adding " + id + " " + JU.Escape.e (pt));
map.put (id, pt);
}, "java.util.Map,~S,~A,~N");
Clazz.overrideMethod (c$, "setModulation",
function (isPost, symmetry) {
if (this.modDim == 0 || this.htModulation == null) return;
if (this.modDebug) JU.Logger.debugging = JU.Logger.debuggingHigh = true;
this.cr.asc.setInfo ("someModelsAreModulated", Boolean.TRUE);
this.symmetry = symmetry;
this.setModulationForStructure (this.cr.asc.iSet, isPost);
if (this.modDebug) JU.Logger.debugging = JU.Logger.debuggingHigh = false;
}, "~B,J.api.SymmetryInterface");
Clazz.overrideMethod (c$, "finalizeModulation",
function () {
if (!this.finalized && this.modDim > 0 && !this.modVib) {
if (this.modTUV != null) this.cr.appendLoadNote ("modTUV=" + this.modTUV);
this.cr.asc.setInfo ("modulationOn", this.modTUV == null ? Boolean.TRUE : this.modTUV);
this.cr.addJmolScript ("set modulateOccupancy " + (this.haveOccupancy && !this.isCommensurate ? true : false));
}this.finalized = true;
});
Clazz.defineMethod (c$, "checkKey",
function (key, checkQ) {
var pt = key.indexOf (this.atModel);
return (pt < 0 || key.indexOf ("_pos#") >= 0 || key.indexOf ("*;*") >= 0 || checkQ && key.indexOf ("?") >= 0 ? null : key.substring (0, pt));
}, "~S,~B");
Clazz.overrideMethod (c$, "getMod",
function (key) {
return this.htModulation.get (key + this.atModel);
}, "~S");
Clazz.overrideMethod (c$, "getModulationMap",
function () {
return this.htModulation;
});
Clazz.defineMethod (c$, "setModulationForStructure",
function (iModel, isPost) {
this.atModel = "@" + iModel;
if (this.htModulation.containsKey ("X_" + this.atModel)) return;
if (!isPost) {
this.initModForStructure (iModel);
return;
}this.htModulation.put ("X_" + this.atModel, Clazz.newDoubleArray (0, 0));
this.cr.appendLoadNote (this.modCount + " modulations for " + this.ac + " modulated atoms");
if (!this.haveAtomMods) return;
var n = this.cr.asc.ac;
this.atoms = this.cr.asc.atoms;
if (this.symmetry != null) this.nOps = this.symmetry.getSpaceGroupOperationCount ();
this.supercellSymmetry = this.cr.asc.getXSymmetry ().symmetry;
if (this.supercellSymmetry === this.symmetry) this.supercellSymmetry = null;
this.iopLast = -1;
var i0 = this.cr.asc.getLastAtomSetAtomIndex ();
for (var i = i0; i < n; i++) this.modulateAtom (this.atoms[i]);
this.htAtomMods = null;
if (this.minXYZ0 != null) this.trimAtomSet ();
this.htSubsystems = null;
}, "~N,~B");
Clazz.defineMethod (c$, "initModForStructure",
function (iModel) {
var key;
if (this.legendres != null) this.fixLegendre ();
this.sigma = new JU.Matrix (null, this.modDim, 3);
this.qs = null;
this.modMatrices = Clazz.newArray (-1, [this.sigma, null]);
var pt;
for (var i = 0; i < this.modDim; i++) {
pt = this.getMod ("W_" + (i + 1));
if (pt == null) {
JU.Logger.info ("Not enough cell wave vectors for d=" + this.modDim);
return;
}this.fixDouble (pt);
this.cr.appendLoadNote ("W_" + (i + 1) + " = " + JU.Escape.e (pt));
this.cr.appendUunitCellInfo ("q" + (i + 1) + "=" + pt[0] + " " + pt[1] + " " + pt[2]);
this.sigma.getArray ()[i] = Clazz.newDoubleArray (-1, [pt[0], pt[1], pt[2]]);
}
var map = new java.util.Hashtable ();
for (var e, $e = this.htModulation.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
if ((key = this.checkKey (e.getKey (), false)) == null) continue;
pt = e.getValue ();
switch (key.charAt (0)) {
case 'O':
this.haveOccupancy = true;
case 'D':
case 'M':
case 'U':
if (pt[2] == 1 && key.charAt (2) != 'S' && key.charAt (2) != 'T' && key.charAt (2) != 'L') {
var ipt = key.indexOf ("?");
if (ipt >= 0) {
var s = key.substring (ipt + 1);
pt = this.getMod (key.substring (0, 2) + s + "#*;*");
if (pt != null) this.addModulation (map, key = key.substring (0, ipt), pt, iModel);
} else {
var a = pt[0];
var d = 2 * 3.141592653589793 * pt[1];
pt[0] = (a * Math.cos (d));
pt[1] = (a * Math.sin (-d));
pt[2] = 0;
JU.Logger.info ("msCIF setting " + key + " " + JU.Escape.e (pt));
}}break;
case 'W':
if (this.modDim > 1) {
continue;
}case 'F':
if (key.indexOf ("_coefs_") >= 0) {
this.cr.appendLoadNote ("Wave vector " + key + "=" + JU.Escape.eAD (pt));
} else {
var ptHarmonic = this.calculateQCoefs (pt);
if (ptHarmonic == null) {
this.cr.appendLoadNote ("Cannot match atom wave vector " + key + " " + JU.Escape.eAD (pt) + " to a cell wave vector or its harmonic");
} else {
var k2 = key + "_coefs_";
if (!this.htModulation.containsKey (k2 + this.atModel)) {
this.addModulation (map, k2, ptHarmonic, iModel);
if (key.startsWith ("F_")) this.cr.appendLoadNote ("atom wave vector " + key + " = " + JU.Escape.e (pt) + " fn = " + JU.Escape.e (ptHarmonic));
}}}break;
}
}
if (!map.isEmpty ()) this.htModulation.putAll (map);
if (this.htSubsystems == null) {
this.haveAtomMods = false;
} else {
this.cr.strSupercell = null;
this.haveAtomMods = true;
this.htAtomMods = new java.util.Hashtable ();
}for (var e, $e = this.htModulation.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
if ((key = this.checkKey (e.getKey (), true)) == null) continue;
var params = e.getValue ();
var atomName = key.substring (key.indexOf (";") + 1);
var pt_ = atomName.indexOf ("#=");
if (pt_ >= 0) {
params = this.getMod (atomName.substring (pt_ + 2));
atomName = atomName.substring (0, pt_);
}if (JU.Logger.debuggingHigh) JU.Logger.debug ("SetModulation: " + key + " " + JU.Escape.e (params));
var type = key.charAt (0);
pt_ = key.indexOf ("#") + 1;
var utens = null;
switch (type) {
case 'U':
utens = key.substring (pt_, key.indexOf (";"));
case 'O':
case 'D':
case 'M':
if (this.modAverage) break;
var axis = key.charAt (pt_);
type = this.getModType (key);
if (this.htAtomMods == null) this.htAtomMods = new java.util.Hashtable ();
var p = Clazz.newDoubleArray (params.length, 0);
for (var i = p.length; --i >= 0; ) p[i] = params[i];
var qcoefs = this.getQCoefs (key);
if (qcoefs == null) throw new Exception ("Missing cell wave vector for atom wave vector for " + key + " " + JU.Escape.e (params));
this.addAtomModulation (atomName, axis, type, p, utens, qcoefs);
this.haveAtomMods = true;
break;
}
}
}, "~N");
Clazz.defineMethod (c$, "fixLegendre",
function () {
for (var i = this.legendres.size (); --i >= 0; ) {
var key = this.legendres.get (i);
var pt = this.htModulation.get (key);
if (pt != null) {
var key1 = "O_0#0" + key.substring (key.indexOf (";"));
var pt1 = this.htModulation.get (key1);
if (pt1 == null) {
JU.Logger.error ("Crenel " + key1 + " not found for legendre modulation " + key);
pt[2] = NaN;
} else {
this.htModulation.put (key, Clazz.newDoubleArray (-1, [pt1[0], pt1[1], pt[0], pt[1]]));
}}}
});
Clazz.defineMethod (c$, "fixDouble",
function (pt) {
if (this.cr.fixJavaFloat) for (var i = pt.length; --i >= 0; ) pt[i] = JU.PT.fixDouble (pt[i], 100000.0);
}, "~A");
Clazz.overrideMethod (c$, "getQCoefs",
function (key) {
var fn = Math.max (0, this.cr.parseIntAt (key, 2));
if (fn == 0) {
if (this.qlist100 == null) {
this.qlist100 = Clazz.newDoubleArray (this.modDim, 0);
this.qlist100[0] = 1;
}return this.qlist100;
}return this.getMod ("F_" + fn + "_coefs_");
}, "~S");
Clazz.overrideMethod (c$, "getModType",
function (key) {
var type = key.charAt (0);
var id = key.charAt (2);
return (id == 'S' ? 's' : id == 'T' ? 't' : id == 'L' ? (type == 'D' ? 'l' : 'L') : id == '0' ? 'c' : type == 'D' ? 'f' : type == 'O' ? 'o' : type == 'M' ? 'm' : type == 'U' ? 'u' : '?');
}, "~S");
Clazz.defineMethod (c$, "calculateQCoefs",
function (p) {
if (this.qs == null) {
this.qs = new Array (this.modDim);
for (var i = 0; i < this.modDim; i++) {
this.qs[i] = this.toP3 (this.getMod ("W_" + (i + 1)));
}
}var pt = this.toP3 (p);
for (var i = 0; i < this.modDim; i++) if (this.qs[i] != null) {
var ifn = this.approxInt (pt.dot (this.qs[i]) / this.qs[i].dot (this.qs[i]));
if (ifn != 0) {
p = Clazz.newDoubleArray (this.modDim, 0);
p[i] = ifn;
return p;
}}
var p3 = this.toP3 (p);
var jmin = (this.modDim < 2 ? 0 : -3);
var jmax = (this.modDim < 2 ? 0 : 3);
var kmin = (this.modDim < 3 ? 0 : -3);
var kmax = (this.modDim < 3 ? 0 : 3);
for (var i = -3; i <= 3; i++) for (var j = jmin; j <= jmax; j++) for (var k = kmin; k <= kmax; k++) {
pt.setT (this.qs[0]);
pt.scale (i);
if (this.modDim > 1 && this.qs[1] != null) pt.scaleAdd2 (j, this.qs[1], pt);
if (this.modDim > 2 && this.qs[2] != null) pt.scaleAdd2 (k, this.qs[2], pt);
if (pt.distanceSquared (p3) < 0.0001) {
p = Clazz.newDoubleArray (this.modDim, 0);
switch (this.modDim) {
default:
p[2] = k;
case 2:
p[1] = j;
case 1:
p[0] = i;
break;
}
return p;
}pt.setT (this.qs[0]);
pt.scale (1 / i);
if (this.modDim > 1 && this.qs[1] != null) pt.scaleAdd2 (1 / j, this.qs[1], pt);
if (this.modDim > 2 && this.qs[2] != null) pt.scaleAdd2 (1 / k, this.qs[2], pt);
if (pt.distanceSquared (p3) < 0.0001) {
p = Clazz.newDoubleArray (this.modDim, 0);
switch (this.modDim) {
default:
p[2] = 1 / k;
case 2:
p[1] = 1 / j;
case 1:
p[0] = 1 / i;
break;
}
return p;
}}
pt = this.toP3 (p);
for (var i = 0; i < this.modDim; i++) if (this.qs[i] != null) {
p3 = this.qs[i];
var ifn = 0;
if (pt.x != 0) ifn = this.approxInt (pt.x / p3.x);
if (pt.y != 0) ifn = Math.max (this.approxInt (pt.y / p3.y), ifn);
if (ifn == 0 && pt.z != 0) ifn = Math.max (this.approxInt (pt.z / p3.z), ifn);
if (ifn == 0) continue;
if (p3.x != 0 && this.approxInt (10 + p3.x * ifn - pt.x) == 0 || p3.y != 0 && this.approxInt (10 + p3.y * ifn - pt.y) == 0 || p3.z != 0 && this.approxInt (10 + p3.z * ifn - pt.z) == 0) continue;
p = Clazz.newDoubleArray (this.modDim, 0);
p[i] = ifn;
return p;
}
return null;
}, "~A");
Clazz.defineMethod (c$, "approxInt",
function (fn) {
var ifn = Math.round (fn);
return (Math.abs (fn - ifn) < 0.001 ? ifn : 0);
}, "~N");
Clazz.defineMethod (c$, "toP3",
function (x) {
return JU.P3.new3 (x[0], x[1], x[2]);
}, "~A");
Clazz.defineMethod (c$, "addAtomModulation",
function (atomName, axis, type, params, utens, qcoefs) {
var list = this.htAtomMods.get (atomName);
if (list == null) {
this.ac++;
this.htAtomMods.put (atomName, list = new JU.Lst ());
}list.addLast ( new JU.Modulation (axis, type, params, utens, qcoefs));
this.modCount++;
}, "~S,~S,~S,~A,~S,~A");
Clazz.overrideMethod (c$, "addSubsystem",
function (code, w) {
if (code == null) return;
var ss = new J.adapter.readers.cif.Subsystem (this, code, w);
this.cr.appendLoadNote ("subsystem " + code + "\n" + w);
this.setSubsystem (code, ss);
}, "~S,JU.Matrix");
Clazz.defineMethod (c$, "addUStr",
function (atom, id, val) {
var i = Clazz.doubleToInt ("U11U22U33U12U13U23UISO".indexOf (id) / 3);
if (JU.Logger.debuggingHigh) JU.Logger.debug ("MOD RDR adding " + id + " " + i + " " + val + " to " + atom.anisoBorU[i]);
this.cr.asc.setU (atom, i, val + atom.anisoBorU[i]);
}, "J.adapter.smarter.Atom,~S,~N");
Clazz.defineMethod (c$, "modulateAtom",
function (a) {
if (this.modCoord && this.htSubsystems != null) {
var ptc = JU.P3.newP (a);
var spt = this.getSymmetry (a);
spt.toCartesian (ptc, true);
}var list = this.htAtomMods.get (a.atomName);
if (list == null && a.altLoc != '\0' && this.htSubsystems != null) {
list = new JU.Lst ();
}if (list == null || this.symmetry == null || a.bsSymmetry == null) return;
var iop = Math.max (a.bsSymmetry.nextSetBit (0), 0);
if (this.modLast) iop = Math.max ((a.bsSymmetry.length () - 1) % this.nOps, iop);
if (JU.Logger.debuggingHigh) JU.Logger.debug ("\nsetModulation: i=" + a.index + " " + a.atomName + " xyz=" + a + " occ=" + a.foccupancy);
if (iop != this.iopLast) {
this.iopLast = iop;
this.gammaE = new JU.M3 ();
this.getSymmetry (a).getSpaceGroupOperation (iop).getRotationScale (this.gammaE);
}if (JU.Logger.debugging) {
JU.Logger.debug ("setModulation iop = " + iop + " " + this.symmetry.getSpaceGroupXyz (iop, false) + " " + a.bsSymmetry);
}var ms = new JU.ModulationSet ().setMod (a.index + " " + a.atomName, this.getAtomR0 (this.cr.asc.atoms[a.atomSite]), this.getAtomR0 (a), this.modDim, list, this.gammaE, this.getMatrices (a), this.getSymmetry (a), this.nOps, iop, Clazz.instanceOf (a.vib, JU.Vibration) ? a.vib : null, this.isCommensurate);
ms.calculate (this.modTUV, false);
if (!Float.isNaN (ms.vOcc)) {
a.foccupancy = ms.setOccupancy (this.getMod ("J_O#0;" + a.atomName), a.foccupancy, (a.vib == null ? 0 : a.vib.x));
}if (ms.htUij != null) {
var t = (a.tensors == null ? null : a.tensors.get (0));
if (t != null && t.parBorU != null) {
a.anisoBorU = Clazz.newFloatArray (8, 0);
for (var i = 0; i < 8; i++) a.anisoBorU[i] = t.parBorU[i];
t.isUnmodulated = true;
}if (a.anisoBorU == null) {
JU.Logger.error ("MOD RDR cannot modulate nonexistent atom anisoBorU for atom " + a.atomName);
} else {
if (JU.Logger.debuggingHigh) {
JU.Logger.debug ("setModulation Uij(initial)=" + JU.Escape.eAF (a.anisoBorU));
JU.Logger.debug ("setModulation tensor=" + JU.Escape.e ((a.tensors.get (0)).getInfo ("all")));
}for (var e, $e = ms.htUij.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) this.addUStr (a, e.getKey (), e.getValue ().floatValue ());
var sym = this.getAtomSymmetry (a, this.symmetry);
t = this.cr.asc.getXSymmetry ().addRotatedTensor (a, sym.getTensor (this.cr.vwr, a.anisoBorU), iop, false, sym);
t.isModulated = true;
t.id = JU.Escape.e (a.anisoBorU);
a.bfactor = a.anisoBorU[7] * 100;
a.anisoBorU = null;
if (JU.Logger.debuggingHigh) {
JU.Logger.debug ("setModulation Uij(final)=" + JU.Escape.eAF (a.anisoBorU) + "\n");
JU.Logger.debug ("setModulation tensor=" + JU.Escape.e ((a.tensors.get (1)).getInfo ("all")));
}}}if (Float.isNaN (ms.x)) ms.set (0, 0, 0);
a.vib = ms;
}, "J.adapter.smarter.Atom");
Clazz.defineMethod (c$, "getAtomR0",
function (atom) {
var r0 = JU.P3.newP (atom);
if (this.supercellSymmetry != null) {
this.supercellSymmetry.toCartesian (r0, true);
this.symmetry.toFractional (r0, true);
}return r0;
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod (c$, "getAtomSymmetry",
function (a, defaultSymmetry) {
var ss;
return (this.htSubsystems == null || (ss = this.getSubsystem (a)) == null ? defaultSymmetry : ss.getSymmetry ());
}, "J.adapter.smarter.Atom,J.api.SymmetryInterface");
Clazz.defineMethod (c$, "setSubsystem",
function (code, system) {
if (this.htSubsystems == null) this.htSubsystems = new java.util.Hashtable ();
this.htSubsystems.put (code, system);
this.setSubsystemOptions ();
}, "~S,J.adapter.readers.cif.Subsystem");
Clazz.defineMethod (c$, "getMatrices",
function (a) {
var ss = this.getSubsystem (a);
return (ss == null ? this.modMatrices : ss.getModMatrices ());
}, "J.adapter.smarter.Atom");
Clazz.defineMethod (c$, "getSymmetry",
function (a) {
var ss = this.getSubsystem (a);
return (ss == null ? this.symmetry : ss.getSymmetry ());
}, "J.adapter.smarter.Atom");
Clazz.defineMethod (c$, "getSubsystem",
function (a) {
return (this.htSubsystems == null ? null : this.htSubsystems.get ("" + a.altLoc));
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod (c$, "setMinMax0",
function (minXYZ, maxXYZ) {
if (this.htSubsystems == null) return;
var symmetry = this.getDefaultUnitCell ();
this.minXYZ0 = JU.P3.newP (minXYZ);
this.maxXYZ0 = JU.P3.newP (maxXYZ);
var pt0 = JU.P3.newP (minXYZ);
var pt1 = JU.P3.newP (maxXYZ);
var pt = new JU.P3 ();
symmetry.toCartesian (pt0, true);
symmetry.toCartesian (pt1, true);
var pts = JU.BoxInfo.unitCubePoints;
if (this.sigma == null) {
JU.Logger.error ("Why are we in MSRdr.setMinMax0 without modulation init?");
return;
}for (var e, $e = this.htSubsystems.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var sym = e.getValue ().getSymmetry ();
for (var i = 8; --i >= 0; ) {
pt.x = (pts[i].x == 0 ? pt0.x : pt1.x);
pt.y = (pts[i].y == 0 ? pt0.y : pt1.y);
pt.z = (pts[i].z == 0 ? pt0.z : pt1.z);
this.expandMinMax (pt, sym, minXYZ, maxXYZ);
}
}
}, "JU.P3,JU.P3");
Clazz.defineMethod (c$, "expandMinMax",
function (pt, sym, minXYZ, maxXYZ) {
var pt2 = JU.P3.newP (pt);
var slop = 0.0001;
sym.toFractional (pt2, false);
if (minXYZ.x > pt2.x + slop) minXYZ.x = Clazz.doubleToInt (Math.floor (pt2.x)) - 1;
if (minXYZ.y > pt2.y + slop) minXYZ.y = Clazz.doubleToInt (Math.floor (pt2.y)) - 1;
if (minXYZ.z > pt2.z + slop) minXYZ.z = Clazz.doubleToInt (Math.floor (pt2.z)) - 1;
if (maxXYZ.x < pt2.x - slop) maxXYZ.x = Clazz.doubleToInt (Math.ceil (pt2.x)) + 1;
if (maxXYZ.y < pt2.y - slop) maxXYZ.y = Clazz.doubleToInt (Math.ceil (pt2.y)) + 1;
if (maxXYZ.z < pt2.z - slop) maxXYZ.z = Clazz.doubleToInt (Math.ceil (pt2.z)) + 1;
}, "JU.P3,J.api.SymmetryInterface,JU.P3,JU.P3");
Clazz.defineMethod (c$, "trimAtomSet",
function () {
if (!this.cr.doApplySymmetry) return;
var asc = this.cr.asc;
var bs = asc.bsAtoms;
var sym = this.getDefaultUnitCell ();
var atoms = asc.atoms;
var pt = new JU.P3 ();
if (bs == null) bs = asc.bsAtoms = JU.BSUtil.newBitSet2 (0, asc.ac);
for (var i = bs.nextSetBit (0); i >= 0; i = bs.nextSetBit (i + 1)) {
var a = atoms[i];
var isOK = (!this.isCommensurate || this.modAverage || a.foccupancy >= 0.5);
if (isOK) {
pt.setT (a);
if (a.vib != null) pt.add (a.vib);
this.getSymmetry (a).toCartesian (pt, false);
sym.toFractional (pt, false);
if (this.cr.fixJavaFloat) JU.PT.fixPtFloats (pt, 100000.0);
isOK = asc.xtalSymmetry.isWithinCell (3, pt, this.minXYZ0.x, this.maxXYZ0.x, this.minXYZ0.y, this.maxXYZ0.y, this.minXYZ0.z, this.maxXYZ0.z, 0.001);
}if (isOK) {
if (this.cr.fixJavaFloat) JU.PT.fixPtFloats (a, 100000.0);
} else {
bs.clear (i);
}}
});
Clazz.defineMethod (c$, "getDefaultUnitCell",
function () {
return (this.modCell != null && this.htSubsystems.containsKey (this.modCell) ? this.htSubsystems.get (this.modCell).getSymmetry () : this.cr.asc.getSymmetry ());
});
Clazz.overrideMethod (c$, "getSymmetryFromCode",
function (code) {
return this.htSubsystems.get (code).getSymmetry ();
}, "~S");
Clazz.overrideMethod (c$, "addLatticeVector",
function (lattvecs, data) {
var a = null;
var c = data.charAt (0);
var dim = this.modDim + 3;
switch (c) {
case 'P':
case 'X':
break;
case 'A':
case 'B':
case 'C':
case 'I':
a = Clazz.newFloatArray (-1, [0.5, 0.5, 0.5]);
if (c != 'I') a[c.charCodeAt (0) - 65] = 0;
break;
case 'F':
this.addLatticeVector (lattvecs, "A");
this.addLatticeVector (lattvecs, "B");
this.addLatticeVector (lattvecs, "C");
break;
case 'M':
dim++;
case '0':
if (data.indexOf (".") >= 0) a = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (data, null, dim);
break;
default:
return false;
}
if (a != null) lattvecs.addLast (a);
return true;
}, "JU.Lst,~S");
Clazz.defineStatics (c$,
"U_LIST", "U11U22U33U12U13U23UISO");
});

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Clazz.declarePackage ("J.adapter.readers.cif");
Clazz.load (null, "J.adapter.readers.cif.Subsystem", ["JU.Lst", "$.Matrix", "$.V3", "JU.Logger", "$.SimpleUnitCell"], function () {
c$ = Clazz.decorateAsClass (function () {
this.msRdr = null;
this.code = null;
this.d = 0;
this.w = null;
this.symmetry = null;
this.modMatrices = null;
this.isFinalized = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.cif, "Subsystem");
Clazz.makeConstructor (c$,
function (msRdr, code, w) {
this.msRdr = msRdr;
this.code = code;
this.w = w;
this.d = w.getArray ().length - 3;
}, "J.adapter.readers.cif.MSRdr,~S,JU.Matrix");
Clazz.defineMethod (c$, "getSymmetry",
function () {
if (!this.isFinalized) this.setSymmetry (true);
return this.symmetry;
});
Clazz.defineMethod (c$, "getModMatrices",
function () {
if (!this.isFinalized) this.setSymmetry (true);
return this.modMatrices;
});
Clazz.defineMethod (c$, "setSymmetry",
function (setOperators) {
var a;
JU.Logger.info ("[subsystem " + this.code + "]");
var winv = this.w.inverse ();
JU.Logger.info ("w=" + this.w);
JU.Logger.info ("w_inv=" + winv);
var w33 = this.w.getSubmatrix (0, 0, 3, 3);
var wd3 = this.w.getSubmatrix (3, 0, this.d, 3);
var w3d = this.w.getSubmatrix (0, 3, 3, this.d);
var wdd = this.w.getSubmatrix (3, 3, this.d, this.d);
var sigma = this.msRdr.getSigma ();
var sigma_nu = wdd.mul (sigma).add (wd3).mul (w3d.mul (sigma).add (w33).inverse ());
var tFactor = wdd.sub (sigma_nu.mul (w3d));
JU.Logger.info ("sigma_nu = " + sigma_nu);
var s0 = this.msRdr.cr.asc.getSymmetry ();
var vu43 = s0.getUnitCellVectors ();
var vr43 = JU.SimpleUnitCell.getReciprocal (vu43, null, 1);
var mard3 = new JU.Matrix (null, 3 + this.d, 3);
var mar3 = new JU.Matrix (null, 3, 3);
var mard3a = mard3.getArray ();
var mar3a = mar3.getArray ();
for (var i = 0; i < 3; i++) mard3a[i] = mar3a[i] = Clazz.newDoubleArray (-1, [vr43[i + 1].x, vr43[i + 1].y, vr43[i + 1].z]);
var sx = sigma.mul (mar3);
a = sx.getArray ();
for (var i = 0; i < this.d; i++) mard3a[i + 3] = a[i];
a = this.w.mul (mard3).getArray ();
var uc_nu = new Array (4);
uc_nu[0] = vu43[0];
for (var i = 0; i < 3; i++) uc_nu[i + 1] = JU.V3.new3 (a[i][0], a[i][1], a[i][2]);
uc_nu = JU.SimpleUnitCell.getReciprocal (uc_nu, null, 1);
this.symmetry = (this.msRdr.cr.getInterface ("JS.Symmetry")).getUnitCell (uc_nu, false, null);
this.modMatrices = Clazz.newArray (-1, [sigma_nu, tFactor]);
if (!setOperators) return;
this.isFinalized = true;
JU.Logger.info ("unit cell parameters: " + this.symmetry.getUnitCellInfo ());
this.symmetry.createSpaceGroup (-1, "[subsystem " + this.code + "]", new JU.Lst ());
var nOps = s0.getSpaceGroupOperationCount ();
for (var iop = 0; iop < nOps; iop++) {
var rv = s0.getOperationRsVs (iop);
var r0 = rv.getRotation ();
var v0 = rv.getTranslation ();
var r = this.w.mul (r0).mul (winv);
var v = this.w.mul (v0);
var code = this.code;
if (this.isMixed (r)) {
for (var e, $e = this.msRdr.htSubsystems.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var ss = e.getValue ();
if (ss === this) continue;
var rj = ss.w.mul (r0).mul (winv);
if (!this.isMixed (rj)) {
r = rj;
v = ss.w.mul (v0);
code = ss.code;
break;
}}
}var jf = this.symmetry.addOp (code, r, v, sigma_nu);
JU.Logger.info (this.code + "." + (iop + 1) + (this.code.equals (code) ? " " : ">" + code + " ") + jf);
}
}, "~B");
Clazz.defineMethod (c$, "isMixed",
function (r) {
var a = r.getArray ();
for (var i = 3; --i >= 0; ) for (var j = 3 + this.d; --j >= 3; ) if (a[i][j] != 0) return true;
return false;
}, "JU.Matrix");
Clazz.overrideMethod (c$, "toString",
function () {
return "Subsystem " + this.code + "\n" + this.w;
});
});

8
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Clazz.declarePackage ("J.adapter.readers.molxyz");
Clazz.load (["J.adapter.readers.molxyz.MolReader"], "J.adapter.readers.molxyz.Mol3DReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.molxyz, "Mol3DReader", J.adapter.readers.molxyz.MolReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.allow2D = false;
});
});

306
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Clazz.declarePackage ("J.adapter.readers.molxyz");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.molxyz.MolReader", ["java.lang.Exception", "java.util.Hashtable", "JU.PT", "J.adapter.smarter.Atom", "J.api.JmolAdapter", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.optimize2D = false;
this.haveAtomSerials = false;
this.dimension = null;
this.allow2D = true;
this.iatom0 = 0;
this.vr = null;
this.atomCount = 0;
this.atomData = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.molxyz, "MolReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.optimize2D = this.checkFilterKey ("2D");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var isMDL = (this.line.startsWith ("$MDL"));
if (isMDL) {
this.discardLinesUntilStartsWith ("$HDR");
this.rd ();
if (this.line == null) {
JU.Logger.warn ("$HDR not found in MDL RG file");
this.continuing = false;
return false;
}} else if (this.line.equals ("M END")) {
return true;
}if (this.doGetModel (++this.modelNumber, null)) {
this.iatom0 = this.asc.ac;
this.processMolSdHeader ();
this.processCtab (isMDL);
this.vr = null;
if (this.isLastModel (this.modelNumber)) {
this.continuing = false;
return false;
}}if (this.line != null && this.line.indexOf ("$$$$") < 0) this.discardLinesUntilStartsWith ("$$$$");
return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderMR ();
});
Clazz.defineMethod (c$, "finalizeReaderMR",
function () {
if (this.optimize2D) this.set2D ();
this.isTrajectory = false;
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "processMolSdHeader",
function () {
var header = "";
var thisDataSetName = this.line.trim ();
this.asc.setCollectionName (thisDataSetName);
header += this.line + "\n";
this.rd ();
if (this.line == null) return;
header += this.line + "\n";
this.dimension = (this.line.length < 22 ? "3D" : this.line.substring (20, 22));
if (this.dimension.equals ("2D")) {
if (!this.allow2D) throw new Exception ("File is 2D, not 3D");
this.appendLoadNote ("This model is 2D. Its 3D structure has not been generated.");
}this.asc.setInfo ("dimension", this.dimension);
this.rd ();
if (this.line == null) return;
this.line = this.line.trim ();
header += this.line + "\n";
JU.Logger.info (header);
this.checkCurrentLineForScript ();
this.asc.setInfo ("fileHeader", header);
this.newAtomSet (thisDataSetName);
});
Clazz.defineMethod (c$, "processCtab",
function (isMDL) {
if (isMDL) this.discardLinesUntilStartsWith ("$CTAB");
if (this.rd () == null) return;
if (this.line.indexOf ("V3000") >= 0) {
this.optimize2D = (this.dimension.equals ("2D"));
this.vr = (this.getInterface ("J.adapter.readers.molxyz.V3000Rdr")).set (this);
this.discardLinesUntilContains ("COUNTS");
this.vr.readAtomsAndBonds (this.getTokens ());
} else {
this.readAtomsAndBonds (this.parseIntRange (this.line, 0, 3), this.parseIntRange (this.line, 3, 6));
}this.applySymmetryAndSetTrajectory ();
}, "~B");
Clazz.defineMethod (c$, "readAtomsAndBonds",
function (ac, bc) {
this.atomCount = ac;
for (var i = 0; i < ac; ++i) {
this.rd ();
var len = this.line.length;
var elementSymbol;
var x;
var y;
var z;
var charge = 0;
var isotope = 0;
var iAtom = -2147483648;
x = this.parseFloatRange (this.line, 0, 10);
y = this.parseFloatRange (this.line, 10, 20);
z = this.parseFloatRange (this.line, 20, 30);
if (len < 34) {
elementSymbol = this.line.substring (31).trim ();
} else {
elementSymbol = this.line.substring (31, 34).trim ();
if (elementSymbol.equals ("H1")) {
elementSymbol = "H";
isotope = 1;
}if (len >= 39) {
var code = this.parseIntRange (this.line, 36, 39);
if (code >= 1 && code <= 7) charge = 4 - code;
code = this.parseIntRange (this.line, 34, 36);
if (code != 0 && code >= -3 && code <= 4) {
isotope = J.api.JmolAdapter.getNaturalIsotope (J.api.JmolAdapter.getElementNumber (elementSymbol)) + code;
}if (iAtom == -2147483648 && this.haveAtomSerials) iAtom = i + 1;
}}this.addMolAtom (iAtom, isotope, elementSymbol, charge, x, y, z);
}
this.rd ();
if (this.line.startsWith ("V ")) {
this.readAtomValues ();
}if (bc == 0) this.asc.setNoAutoBond ();
for (var i = 0; i < bc; ++i) {
if (i > 0) this.rd ();
var iAtom1;
var iAtom2;
var stereo = 0;
iAtom1 = this.line.substring (0, 3).trim ();
iAtom2 = this.line.substring (3, 6).trim ();
var order = this.parseIntRange (this.line, 6, 9);
if (this.optimize2D && order == 1 && this.line.length >= 12) stereo = this.parseIntRange (this.line, 9, 12);
order = this.fixOrder (order, stereo);
if (this.haveAtomSerials) this.asc.addNewBondFromNames (iAtom1, iAtom2, order);
else this.asc.addNewBondWithOrder (this.iatom0 + this.parseIntStr (iAtom1) - 1, this.iatom0 + this.parseIntStr (iAtom2) - 1, order);
}
var molData = new java.util.Hashtable ();
this.rd ();
while (this.line != null && this.line.indexOf ("$$$$") != 0) {
if (this.line.indexOf (">") == 0) {
this.readMolData (molData);
continue;
}if (this.line.startsWith ("M ISO")) {
this.readIsotopes ();
continue;
}this.rd ();
}
if (this.atomData != null) {
var atomValueName = molData.get ("atom_value_name");
molData.put (atomValueName == null ? "atom_values" : atomValueName.toString (), this.atomData);
}if (!molData.isEmpty ()) this.asc.setCurrentModelInfo ("molData", molData);
}, "~N,~N");
Clazz.defineMethod (c$, "readAtomValues",
function () {
this.atomData = new Array (this.atomCount);
for (var i = this.atomData.length; --i >= 0; ) this.atomData[i] = "";
while (this.line.indexOf ("V ") == 0) {
var iAtom = this.parseIntAt (this.line, 3);
if (iAtom < 1 || iAtom > this.atomCount) {
JU.Logger.error ("V nnn does not evalute to a valid atom number: " + iAtom);
return;
}var s = this.line.substring (6).trim ();
this.atomData[iAtom - 1] = s;
this.rd ();
}
});
Clazz.defineMethod (c$, "readIsotopes",
function () {
var n = this.parseIntAt (this.line, 6);
try {
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0, pt = 9; i < n; i++) {
var ipt = this.parseIntAt (this.line, pt);
var atom = this.asc.atoms[ipt + i0 - 1];
var iso = this.parseIntAt (this.line, pt + 4);
pt += 8;
atom.elementSymbol = "" + iso + JU.PT.replaceAllCharacters (atom.elementSymbol, "0123456789", "");
}
} catch (e) {
}
this.rd ();
});
Clazz.defineMethod (c$, "readMolData",
function (molData) {
var atoms = this.asc.atoms;
var dataName = JU.PT.trim (this.line, "> <").toLowerCase ();
var data = "";
var fdata = null;
while (this.rd () != null && !this.line.equals ("$$$$") && this.line.length > 0) data += this.line + "\n";
data = JU.PT.trim (data, "\n");
JU.Logger.info (dataName + ":" + JU.PT.esc (data));
molData.put (dataName, data);
var ndata = 0;
if (dataName.toUpperCase ().contains ("_PARTIAL_CHARGES")) {
try {
fdata = JU.PT.parseFloatArray (data);
for (var i = this.asc.getLastAtomSetAtomIndex (), n = this.asc.ac; i < n; i++) atoms[i].partialCharge = 0;
var pt = 0;
for (var i = Clazz.floatToInt (fdata[pt++]); --i >= 0; ) {
var atomIndex = Clazz.floatToInt (fdata[pt++]) + this.iatom0 - 1;
var partialCharge = fdata[pt++];
atoms[atomIndex].partialCharge = partialCharge;
ndata++;
}
} catch (e) {
for (var i = this.asc.getLastAtomSetAtomIndex (), n = this.asc.ac; i < n; i++) atoms[i].partialCharge = 0;
JU.Logger.error ("error reading " + dataName + " field -- partial charges cleared");
}
JU.Logger.info (ndata + " partial charges read");
} else if (dataName.toUpperCase ().contains ("ATOM_NAMES")) {
ndata = 0;
try {
var tokens = JU.PT.getTokens (data);
var pt = 0;
for (var i = this.parseIntStr (tokens[pt++]); --i >= 0; ) {
var iatom;
while ((iatom = this.parseIntStr (tokens[pt++])) == -2147483648) {
}
var atomIndex = iatom + this.iatom0 - 1;
var name = tokens[pt++];
if (!name.equals (".")) atoms[atomIndex].atomName = name;
ndata++;
}
} catch (e) {
JU.Logger.error ("error reading " + dataName + " field");
}
JU.Logger.info (ndata + " atom names read");
}}, "java.util.Map");
Clazz.defineMethod (c$, "addMolAtom",
function (iAtom, isotope, elementSymbol, charge, x, y, z) {
switch (isotope) {
case 0:
break;
case 1:
elementSymbol = "1H";
break;
case 2:
elementSymbol = "2H";
break;
case 3:
elementSymbol = "3H";
break;
default:
elementSymbol = isotope + elementSymbol;
}
if (this.optimize2D && z != 0) this.optimize2D = false;
var atom = new J.adapter.smarter.Atom ();
atom.elementSymbol = elementSymbol;
atom.formalCharge = charge;
this.setAtomCoordXYZ (atom, x, y, z);
if (iAtom == -2147483648) {
this.asc.addAtom (atom);
} else {
this.haveAtomSerials = true;
atom.atomSerial = iAtom;
this.asc.addAtomWithMappedSerialNumber (atom);
}}, "~N,~N,~S,~N,~N,~N,~N");
Clazz.defineMethod (c$, "fixOrder",
function (order, stereo) {
switch (order) {
default:
case 0:
case -10:
return 1;
case 1:
switch (stereo) {
case 1:
return 1025;
case 3:
case 6:
return 1041;
}
break;
case 2:
case 3:
break;
case 4:
return 515;
case 5:
return 66;
case 6:
return 513;
case 7:
return 514;
case 8:
case 9:
return 33;
case 14:
return 4;
case 15:
return 5;
case 16:
return 6;
}
return order;
}, "~N,~N");
Clazz.defineMethod (c$, "addMolBond",
function (iAtom1, iAtom2, order, stereo) {
order = this.fixOrder (order, stereo);
if (this.haveAtomSerials) this.asc.addNewBondFromNames (iAtom1, iAtom2, order);
else this.asc.addNewBondWithOrder (this.iatom0 + this.parseIntStr (iAtom1) - 1, this.iatom0 + this.parseIntStr (iAtom2) - 1, order);
}, "~S,~S,~N,~N");
});

158
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Clazz.declarePackage ("J.adapter.readers.molxyz");
Clazz.load (null, "J.adapter.readers.molxyz.V3000Rdr", ["java.util.Hashtable", "JU.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.mr = null;
this.line = null;
this.userData = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.molxyz, "V3000Rdr");
Clazz.makeConstructor (c$,
function () {
});
Clazz.defineMethod (c$, "set",
function (mr) {
this.mr = mr;
return this;
}, "J.adapter.smarter.AtomSetCollectionReader");
Clazz.defineMethod (c$, "readAtomsAndBonds",
function (tokens) {
var ac = this.mr.parseIntStr (tokens[3]);
this.readAtoms (ac);
this.readBonds (this.mr.parseIntStr (tokens[4]));
this.readUserData (ac);
}, "~A");
Clazz.defineMethod (c$, "readAtoms",
function (ac) {
this.mr.discardLinesUntilContains ("BEGIN ATOM");
for (var i = 0; i < ac; ++i) {
this.rd ();
this.checkLineContinuation ();
var tokens = this.mr.getTokens ();
var iAtom = this.mr.parseIntStr (tokens[2]);
var elementSymbol = tokens[3];
if (elementSymbol.equals ("*")) continue;
var x = this.mr.parseFloatStr (tokens[4]);
var y = this.mr.parseFloatStr (tokens[5]);
var z = this.mr.parseFloatStr (tokens[6]);
var charge = 0;
var isotope = 0;
for (var j = 7; j < tokens.length; j++) {
var s = tokens[j].toUpperCase ();
if (s.startsWith ("CHG=")) charge = this.mr.parseIntAt (tokens[j], 4);
else if (s.startsWith ("MASS=")) isotope = this.mr.parseIntAt (tokens[j], 5);
}
if (isotope > 1 && elementSymbol.equals ("H")) isotope = 1 - isotope;
this.mr.addMolAtom (iAtom, isotope, elementSymbol, charge, x, y, z);
}
this.mr.discardLinesUntilContains ("END ATOM");
}, "~N");
Clazz.defineMethod (c$, "readBonds",
function (bondCount) {
this.mr.discardLinesUntilContains ("BEGIN BOND");
if (bondCount == 0) this.mr.asc.setNoAutoBond ();
for (var i = 0; i < bondCount; ++i) {
this.rd ();
var stereo = 0;
this.checkLineContinuation ();
var tokens = this.mr.getTokens ();
var order = this.mr.parseIntStr (tokens[3]);
var iAtom1 = tokens[4];
var iAtom2 = tokens[5];
var cfg = this.getField ("CFG");
if (cfg == null) {
var endpts = this.getField ("ENDPTS");
if (endpts != null && this.line.indexOf ("ATTACH=ALL") >= 0) {
tokens = JU.PT.getTokens (endpts);
var n = this.mr.parseIntStr (tokens[0]);
var o = this.mr.fixOrder (order, 0);
for (var k = 1; k <= n; k++) this.mr.asc.addNewBondFromNames (iAtom1, tokens[k], o);
}} else {
stereo = this.mr.parseIntStr (cfg);
}this.mr.addMolBond (iAtom1, iAtom2, order, stereo);
}
this.mr.discardLinesUntilContains ("END BOND");
}, "~N");
Clazz.defineMethod (c$, "readUserData",
function (ac) {
this.userData = null;
var pc = null;
while (!this.rd ().contains ("END CTAB")) {
if (!this.line.contains ("BEGIN SGROUP")) continue;
var atoms;
var name;
var data;
while (!this.rd ().contains ("END SGROUP")) {
if (this.userData == null) this.userData = new java.util.Hashtable ();
if ((atoms = this.getField ("ATOMS")) == null || (name = this.getField ("FIELDNAME")) == null || (data = this.getField ("FIELDDATA")) == null) continue;
name = name.toLowerCase ();
var isPartial = (name.indexOf ("partial") >= 0);
if (isPartial) {
if (pc == null) pc = name;
else if (!pc.equals (name)) isPartial = false;
}if (isPartial) {
var at = this.mr.asc.atoms;
for (var i = this.mr.asc.getLastAtomSetAtomIndex (), n = this.mr.asc.ac; i < n; i++) at[i].partialCharge = 0;
}var a = null;
var f = 0;
if (isPartial) f = this.mr.parseFloatStr (data);
else if ((a = this.userData.get (name)) == null) this.userData.put (name, a = new Array (ac));
try {
var tokens = JU.PT.getTokens (atoms);
for (var i = tokens.length; --i >= 1; ) {
var atom = tokens[i];
if (isPartial) this.mr.asc.getAtomFromName (atom).partialCharge = f;
else a[this.mr.parseIntStr (atom) - 1] = data;
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}
}
if (this.userData == null) return;
for (var key, $key = this.userData.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
var a = this.userData.get (key);
var f = Clazz.newFloatArray (a.length, 0);
for (var i = 0; i < a.length; i++) f[i] = (a[i] == null ? 0 : this.mr.parseFloatStr (a[i]));
this.mr.asc.setAtomProperties (key, f, -1, false);
}
}, "~N");
Clazz.defineMethod (c$, "getField",
function (key) {
var pt = this.line.indexOf (key + "=");
if (pt < 0) return null;
pt += key.length + 1;
var term = ' ';
switch (this.line.charAt (pt)) {
case '"':
term = '"';
break;
case '(':
term = ')';
break;
case '+':
break;
default:
pt--;
break;
}
return this.line.substring (pt + 1, (this.line + term).indexOf (term, pt + 1));
}, "~S");
Clazz.defineMethod (c$, "rd",
function () {
return (this.line = this.mr.rd ());
});
Clazz.defineMethod (c$, "checkLineContinuation",
function () {
while (this.line.endsWith ("-")) {
var s = this.line;
this.rd ();
this.line = s + this.line;
}
});
});

80
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/molxyz/XyzReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.molxyz");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.molxyz.XyzReader", ["java.lang.Float", "JU.Logger"], function () {
c$ = Clazz.declareType (J.adapter.readers.molxyz, "XyzReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
var modelAtomCount = this.parseIntStr (this.line);
if (modelAtomCount == -2147483648) {
this.continuing = false;
return false;
}this.vibrationNumber = ++this.modelNumber;
if (this.desiredVibrationNumber <= 0 ? this.doGetModel (this.modelNumber, null) : this.doGetVibration (this.vibrationNumber)) {
this.rd ();
this.checkCurrentLineForScript ();
this.asc.newAtomSet ();
var name = this.line.trim ();
this.readAtoms (modelAtomCount);
this.applySymmetryAndSetTrajectory ();
this.asc.setAtomSetName (name);
if (this.isLastModel (this.modelNumber)) {
this.continuing = false;
return false;
}} else {
this.skipAtomSet (modelAtomCount);
}this.discardLinesUntilNonBlank ();
return false;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.isTrajectory = false;
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "skipAtomSet",
function (modelAtomCount) {
this.rd ();
for (var i = modelAtomCount; --i >= 0; ) this.rd ();
}, "~N");
Clazz.defineMethod (c$, "readAtoms",
function (modelAtomCount) {
for (var i = 0; i < modelAtomCount; ++i) {
this.rd ();
var tokens = this.getTokens ();
if (tokens.length < 4) {
JU.Logger.warn ("line cannot be read for XYZ atom data: " + this.line);
continue;
}var atom = this.addAtomXYZSymName (tokens, 1, null, null);
this.setElementAndIsotope (atom, tokens[0]);
var vpt = 4;
switch (tokens.length) {
case 4:
continue;
case 5:
case 6:
case 8:
case 9:
if (tokens[4].indexOf (".") >= 0) {
atom.partialCharge = this.parseFloatStr (tokens[4]);
} else {
var charge = this.parseIntStr (tokens[4]);
if (charge != -2147483648) atom.formalCharge = charge;
}switch (tokens.length) {
case 5:
continue;
case 6:
atom.radius = this.parseFloatStr (tokens[5]);
continue;
case 9:
atom.atomSerial = this.parseIntStr (tokens[8]);
}
vpt++;
default:
var vx = this.parseFloatStr (tokens[vpt++]);
var vy = this.parseFloatStr (tokens[vpt++]);
var vz = this.parseFloatStr (tokens[vpt++]);
if (Float.isNaN (vx) || Float.isNaN (vy) || Float.isNaN (vz)) continue;
this.asc.addVibrationVector (atom.index, vx, vy, vz);
}
}
}, "~N");
});

152
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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.BinaryDcdReader", ["java.lang.Boolean", "JU.BS", "$.P3", "$.SB", "JU.Escape", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.nModels = 0;
this.nAtoms = 0;
this.nFree = 0;
this.bsFree = null;
this.xAll = null;
this.yAll = null;
this.zAll = null;
this.crystGroup = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "BinaryDcdReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "setup",
function (fullPath, htParams, reader) {
this.isBinary = true;
this.requiresBSFilter = true;
this.setupASCR (fullPath, htParams, reader);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.initializeTrajectoryFile ();
this.asc.setInfo ("ignoreUnitCell", Boolean.TRUE);
});
Clazz.overrideMethod (c$, "processBinaryDocument",
function () {
var bytes = Clazz.newByteArray (40, 0);
this.binaryDoc.setStream (null, this.binaryDoc.readInt () == 0x54);
this.binaryDoc.readInt ();
this.nModels = this.binaryDoc.readInt ();
var nPriv = this.binaryDoc.readInt ();
var nSaveC = this.binaryDoc.readInt ();
var nStep = this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
var ndegf = this.binaryDoc.readInt ();
this.nFree = Clazz.doubleToInt (ndegf / 3);
var nFixed = this.binaryDoc.readInt ();
var delta4 = this.binaryDoc.readInt ();
this.crystGroup = this.binaryDoc.readInt ();
this.binaryDoc.readByteArray (bytes, 0, 32);
this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
var sb = new JU.SB ();
for (var i = 0, n = this.binaryDoc.readInt (); i < n; i++) sb.append (this.trimString (this.binaryDoc.readString (80))).appendC ('\n');
this.binaryDoc.readInt ();
JU.Logger.info ("BinaryDcdReadaer:\n" + sb);
this.binaryDoc.readInt ();
this.nAtoms = this.binaryDoc.readInt ();
this.binaryDoc.readInt ();
this.nFree = this.nAtoms - nFixed;
if (nFixed != 0) {
this.binaryDoc.readInt ();
this.bsFree = JU.BS.newN (this.nFree);
for (var i = 0; i < this.nFree; i++) this.bsFree.set (this.binaryDoc.readInt () - 1);
this.binaryDoc.readInt ();
JU.Logger.info ("free: " + this.bsFree.cardinality () + " " + JU.Escape.eBS (this.bsFree));
}this.readCoordinates ();
JU.Logger.info ("Total number of trajectory steps=" + this.trajectorySteps.size ());
});
Clazz.defineMethod (c$, "trimString",
function (s) {
var pt = s.indexOf ('\0');
if (pt >= 0) s = s.substring (0, pt);
return s.trim ();
}, "~S");
Clazz.defineMethod (c$, "readFloatArray",
function () {
var n = Clazz.doubleToInt (this.binaryDoc.readInt () / 4);
var data = Clazz.newFloatArray (n, 0);
for (var i = 0; i < n; i++) data[i] = this.binaryDoc.readFloat ();
this.binaryDoc.readInt ();
return data;
});
Clazz.defineMethod (c$, "readDoubleArray",
function () {
var n = Clazz.doubleToInt (this.binaryDoc.readInt () / 8);
var data = Clazz.newDoubleArray (n, 0);
for (var i = 0; i < n; i++) data[i] = this.binaryDoc.readDouble ();
this.binaryDoc.readInt ();
return data;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
var ac = (this.bsFilter == null ? this.templateAtomCount : (this.htParams.get ("filteredAtomCount")).intValue ());
for (var i = 0; i < this.nModels; i++) if (this.doGetModel (++this.modelNumber, null)) {
var trajectoryStep = new Array (ac);
if (!this.getTrajectoryStep (trajectoryStep)) return;
this.trajectorySteps.addLast (trajectoryStep);
if (this.isLastModel (this.modelNumber)) return;
} else {
if (this.crystGroup > 0) this.readDoubleArray ();
this.readFloatArray ();
this.readFloatArray ();
this.readFloatArray ();
}
});
Clazz.defineMethod (c$, "getTrajectoryStep",
function (trajectoryStep) {
try {
var ac = trajectoryStep.length;
var n = -1;
if (this.crystGroup > 0) this.calcUnitCell (this.readDoubleArray ());
var x = this.readFloatArray ();
var y = this.readFloatArray ();
var z = this.readFloatArray ();
var bs = (this.xAll == null ? null : this.bsFree);
if (bs == null) {
this.xAll = x;
this.yAll = y;
this.zAll = z;
}for (var i = 0, vpt = 0; i < this.nAtoms; i++) {
var pt = new JU.P3 ();
if (bs == null || bs.get (i)) {
pt.set (x[vpt], y[vpt], z[vpt]);
vpt++;
} else {
pt.set (this.xAll[i], this.yAll[i], this.zAll[i]);
}if (this.bsFilter == null || this.bsFilter.get (i)) {
if (++n == ac) return true;
trajectoryStep[n] = pt;
}}
return true;
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
return false;
} else {
throw e;
}
}
}, "~A");
Clazz.defineMethod (c$, "calcUnitCell",
function (abc) {
var a = abc[0];
var angle1 = abc[1];
var b = abc[2];
var angle2 = abc[3];
var angle3 = abc[4];
var c = abc[5];
var alpha = (1.5707963267948966 - Math.asin (angle3)) * 180 / 3.141592653589793;
var beta = (1.5707963267948966 - Math.asin (angle2)) * 180 / 3.141592653589793;
var gamma = (1.5707963267948966 - Math.asin (angle1)) * 180 / 3.141592653589793;
System.out.println ("unitcell:[" + a + " " + b + " " + c + " " + alpha + " " + beta + " " + gamma + "]");
return Clazz.newFloatArray (-1, [a, b, c, alpha, beta, gamma]);
}, "~A");
});

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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "java.util.Properties"], "J.adapter.readers.more.ForceFieldReader", ["java.lang.Character", "JU.PT", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.decorateAsClass (function () {
this.userAtomTypes = null;
this.atomTypes = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "ForceFieldReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.atomTypes = new java.util.Properties ();
});
Clazz.defineMethod (c$, "setUserAtomTypes",
function () {
this.userAtomTypes = this.htParams.get ("atomTypes");
if (this.userAtomTypes != null) this.userAtomTypes = ";" + this.userAtomTypes + ";";
});
Clazz.defineMethod (c$, "getElementSymbol",
function (atom, atomType) {
var elementSymbol = this.atomTypes.get (atomType);
if (elementSymbol != null) {
atom.elementSymbol = elementSymbol;
return true;
}var nChar = atomType.length;
var haveSymbol = (nChar < 2);
var ptType;
if (this.userAtomTypes != null && (ptType = this.userAtomTypes.indexOf (";" + atomType + "=>")) >= 0) {
ptType += nChar + 3;
elementSymbol = this.userAtomTypes.substring (ptType, this.userAtomTypes.indexOf (";", ptType)).trim ();
haveSymbol = true;
} else if (nChar == 1) {
elementSymbol = atomType.toUpperCase ();
haveSymbol = true;
} else {
var ch0 = atomType.charAt (0);
var ch1 = atomType.charAt (1);
var isXx = (JU.PT.isUpperCase (ch0) && JU.PT.isLowerCase (ch1));
if (" IM IP sz az sy ay ayt ".indexOf (atomType) >= 0) {
if (ch0 == 'I') {
elementSymbol = atom.atomName.substring (0, 2);
if (!JU.PT.isLowerCase (elementSymbol.charAt (1))) elementSymbol = elementSymbol.substring (0, 1);
} else {
elementSymbol = (ch0 == 's' ? "Si" : "Al");
}} else if (nChar == 2 && isXx) {
} else if (JU.PT.isLetter (ch0) && !JU.PT.isLetter (ch1)) {
elementSymbol = "" + Character.toUpperCase (ch0);
} else if (nChar > 2 && isXx && !JU.PT.isLetter (atomType.charAt (2))) {
elementSymbol = "" + ch0 + ch1;
} else {
ch0 = Character.toUpperCase (ch0);
var check = " " + atomType + " ";
if (" CA CB CC CD CE CF CG CH CI CJ CK CM CN CP CQ CR CT CV CW HA HP HC HO HS HW LP NA NB NC NT OH OS OW SH AH BH HT HY AC BC CS OA OB OE OT dw hc hi hn ho hp hs hw hscp htip ca cg ci cn co coh cp cr cs ct c3h c3m c4h c4m na nb nh nho nh+ ni nn np npc nr nt nz oc oe oh op oscp otip sc sh sp br cl ca+ ar si lp nu sz oz az pz ga ge tioc titd li+ na+ rb+ cs+ mg2+ ca2+ ba2+ cu2+ cl- br- so4 sy oy ay ayt nac+ mg2c fe2c mn4c mn3c co2c ni2c lic+ pd2+ ti4c sr2c ca2c cly- hocl py vy nh4+ so4y lioh naoh koh foh cloh beoh al CE1 CF1 CF2 CF3 CG CD2 CH1E CH2E CH3E CM CP3 CPH1 CPH2 CQ66 CR55 CR56 CR66 CS66 CT CT3 CT4 CUA1 CUA2 CUA3 CUY1 CUY2 HA HC HMU HO HT LP NC NC2 NO2 NP NR1 NR2 NR3 NR55 NR56 NR66 NT NX OA OAC OC OE OH2 OK OM OS OSH OSI OT OW PO3 PO4 PT PUA1 PUY1 SE SH1E SK SO1 SO2 SO3 SO4 ST ST2 ST2 br br- br1 cl cl- cl1 cl12 cl13 cl14 cl1p ca+ cu+2 fe+2 mg+2 zn+2 cs+ li+ na+ rb+ al4z si si4 si4c si4z ar he kr ne xe dw hi hw ca cg ci co coh cp cr cs ct ct3 na nb nh nho ni no np nt nt2 nz oa oc oh op os ot sp bt cl\' si4l si5l si5t si6 si6o si\' br ca cc cd ce cf cl cp cq cu cv cx cy ha hc hn ho hp hs na nb nc nd nh oh os pb pc pd pe pf px py sh ss sx sy hn2 ho2 cz oo oz si sio hsi osi ".indexOf (check) < 0) {
} else if (" AH BH AC BC ".indexOf (check) >= 0) {
elementSymbol = "" + ch1;
} else if (" al al4z ar ba2+ beoh br br- br1 ca+ ca2+ ca2c cl cl\' cl- cl1 cl12 cl13 cl14 cl1p cloh cly- co2c cs+ cu+2 cu2+ fe+2 fe2c ga ge he kr li+ lic+ lioh lp LP mg+2 mg2+ mg2c mn3c mn4c na+ nac+ naoh ne ni2c nu pd2+ rb+ si si\' si4 si4c si4l si4z si5l si5t si6 si6o sio sr2c ti4c tioc titd xe zn+2 ".indexOf (check) >= 0) {
elementSymbol = "" + ch0 + ch1;
} else {
elementSymbol = "" + ch0;
}}if (elementSymbol == null) {
elementSymbol = "" + ch0 + Character.toLowerCase (ch1);
} else {
haveSymbol = true;
}}atom.elementSymbol = elementSymbol;
if (haveSymbol) this.atomTypes.put (atomType, elementSymbol);
return haveSymbol;
}, "J.adapter.smarter.Atom,~S");
c$.deducePdbElementSymbol = Clazz.defineMethod (c$, "deducePdbElementSymbol",
function (isHetero, XX, group3) {
var i = XX.indexOf ('\0');
var atomType = null;
if (i >= 0) {
atomType = XX.substring (i + 1);
XX = XX.substring (0, i);
if (atomType != null && atomType.length == 1) return atomType;
}if (XX.equalsIgnoreCase (group3)) return XX;
var len = XX.length;
var ch1 = ' ';
i = 0;
while (i < len && (ch1 = XX.charAt (i++)) <= '9') {
}
var ch2 = (i < len ? XX.charAt (i) : ' ');
var full = group3 + "." + ch1 + ch2;
if (("OEC.CA ICA.CA OC1.CA OC2.CA OC4.CA").indexOf (full) >= 0) return "Ca";
if (XX.indexOf ("'") > 0 || XX.indexOf ("*") >= 0 || "HCNO".indexOf (ch1) >= 0 && ch2 <= 'H' || XX.startsWith ("CM")) return "" + ch1;
if (isHetero && J.adapter.smarter.Atom.isValidSymNoCase (ch1, ch2)) return ("" + ch1 + ch2).trim ();
if (J.adapter.smarter.Atom.isValidSym1 (ch1)) return "" + ch1;
if (J.adapter.smarter.Atom.isValidSym1 (ch2)) return "" + ch2;
return "Xx";
}, "~B,~S,~S");
Clazz.defineStatics (c$,
"ffTypes", " CA CB CC CD CE CF CG CH CI CJ CK CM CN CP CQ CR CT CV CW HA HP HC HO HS HW LP NA NB NC NT OH OS OW SH AH BH HT HY AC BC CS OA OB OE OT dw hc hi hn ho hp hs hw hscp htip ca cg ci cn co coh cp cr cs ct c3h c3m c4h c4m na nb nh nho nh+ ni nn np npc nr nt nz oc oe oh op oscp otip sc sh sp br cl ca+ ar si lp nu sz oz az pz ga ge tioc titd li+ na+ rb+ cs+ mg2+ ca2+ ba2+ cu2+ cl- br- so4 sy oy ay ayt nac+ mg2c fe2c mn4c mn3c co2c ni2c lic+ pd2+ ti4c sr2c ca2c cly- hocl py vy nh4+ so4y lioh naoh koh foh cloh beoh al CE1 CF1 CF2 CF3 CG CD2 CH1E CH2E CH3E CM CP3 CPH1 CPH2 CQ66 CR55 CR56 CR66 CS66 CT CT3 CT4 CUA1 CUA2 CUA3 CUY1 CUY2 HA HC HMU HO HT LP NC NC2 NO2 NP NR1 NR2 NR3 NR55 NR56 NR66 NT NX OA OAC OC OE OH2 OK OM OS OSH OSI OT OW PO3 PO4 PT PUA1 PUY1 SE SH1E SK SO1 SO2 SO3 SO4 ST ST2 ST2 br br- br1 cl cl- cl1 cl12 cl13 cl14 cl1p ca+ cu+2 fe+2 mg+2 zn+2 cs+ li+ na+ rb+ al4z si si4 si4c si4z ar he kr ne xe dw hi hw ca cg ci co coh cp cr cs ct ct3 na nb nh nho ni no np nt nt2 nz oa oc oh op os ot sp bt cl\' si4l si5l si5t si6 si6o si\' br ca cc cd ce cf cl cp cq cu cv cx cy ha hc hn ho hp hs na nb nc nd nh oh os pb pc pd pe pf px py sh ss sx sy hn2 ho2 cz oo oz si sio hsi osi ",
"twoChar", " al al4z ar ba2+ beoh br br- br1 ca+ ca2+ ca2c cl cl' cl- cl1 cl12 cl13 cl14 cl1p cloh cly- co2c cs+ cu+2 cu2+ fe+2 fe2c ga ge he kr li+ lic+ lioh lp LP mg+2 mg2+ mg2c mn3c mn4c na+ nac+ naoh ne ni2c nu pd2+ rb+ si si' si4 si4c si4l si4z si5l si5t si6 si6o sio sr2c ti4c tioc titd xe zn+2 ",
"specialTypes", " IM IP sz az sy ay ayt ",
"secondCharOnly", " AH BH AC BC ");
});

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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.GromacsReader", ["java.lang.Float", "JU.P3", "J.adapter.smarter.Atom", "JU.Logger"], function () {
c$ = Clazz.declareType (J.adapter.readers.more, "GromacsReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setIsPDB ();
this.asc.newAtomSet ();
this.setModelPDB (true);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
this.checkCurrentLineForScript ();
this.asc.setAtomSetName (this.line.trim ());
this.readAtoms ();
this.readUnitCell ();
this.continuing = false;
return false;
});
Clazz.defineMethod (c$, "readAtoms",
function () {
var modelAtomCount = this.parseIntStr (this.rd ());
for (var i = 0; i < modelAtomCount; ++i) {
this.rd ();
var len = this.line.length;
if (len != 44 && len != 68) {
JU.Logger.warn ("line cannot be read for GROMACS atom data: " + this.line);
continue;
}var atom = new J.adapter.smarter.Atom ();
atom.sequenceNumber = this.parseIntRange (this.line, 0, 5);
this.setAtomName (atom, this.parseTokenRange (this.line, 5, 9).trim (), this.line.substring (11, 15).trim ());
atom.atomSerial = this.parseIntRange (this.line, 15, 20);
atom.x = this.parseFloatRange (this.line, 20, 28) * 10;
atom.y = this.parseFloatRange (this.line, 28, 36) * 10;
atom.z = this.parseFloatRange (this.line, 36, 44) * 10;
if (Float.isNaN (atom.x) || Float.isNaN (atom.y) || Float.isNaN (atom.z)) {
JU.Logger.warn ("line cannot be read for GROMACS atom data: " + this.line);
atom.set (0, 0, 0);
}this.setAtomCoord (atom);
atom.elementSymbol = this.deduceElementSymbol (atom.group3, atom.atomName);
if (!this.filterAtom (atom, i)) continue;
atom.isHetero = false;
this.asc.addAtom (atom);
if (len < 69) continue;
var vx = this.parseFloatRange (this.line, 44, 52) * 10;
var vy = this.parseFloatRange (this.line, 52, 60) * 10;
var vz = this.parseFloatRange (this.line, 60, 68) * 10;
if (Float.isNaN (vx) || Float.isNaN (vy) || Float.isNaN (vz)) continue;
this.asc.addVibrationVector (atom.index, vx, vy, vz);
}
});
Clazz.defineMethod (c$, "setAtomName",
function (atom, gname, aname) {
atom.atomName = aname;
if (gname.equals ("SOL") && aname.length == 3 && "OW1;HW2;HW3".indexOf (aname) >= 0) gname = "WAT";
atom.group3 = gname;
}, "J.adapter.smarter.Atom,~S,~S");
Clazz.defineMethod (c$, "deduceElementSymbol",
function (group3, atomName) {
if (atomName.length <= 2 && group3.equals (atomName)) return atomName;
var ch1 = (atomName.length == 4 ? atomName.charAt (0) : '\0');
var ch2 = atomName.charAt (atomName.length == 4 ? 1 : 0);
var isHetero = this.vwr.getJBR ().isHetero (group3);
if (J.adapter.smarter.Atom.isValidSymNoCase (ch1, ch2)) return (isHetero || ch1 != 'H' ? "" + ch1 + ch2 : "H");
if (J.adapter.smarter.Atom.isValidSym1 (ch2)) return "" + ch2;
if (J.adapter.smarter.Atom.isValidSym1 (ch1)) return "" + ch1;
return "Xx";
}, "~S,~S");
Clazz.defineMethod (c$, "readUnitCell",
function () {
if (this.rd () == null) return;
var tokens = this.getTokens ();
if (tokens.length < 3 || !this.doApplySymmetry) return;
var a = 10 * this.parseFloatStr (tokens[0]);
var b = 10 * this.parseFloatStr (tokens[1]);
var c = 10 * this.parseFloatStr (tokens[2]);
this.setUnitCell (a, b, c, 90, 90, 90);
this.setSpaceGroupName ("P1");
var atoms = this.asc.atoms;
var pt = JU.P3.new3 (0.5, 0.5, 0.5);
for (var i = this.asc.ac; --i >= 0; ) {
this.setAtomCoord (atoms[i]);
atoms[i].add (pt);
}
});
});

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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.readers.molxyz.MolReader", "J.api.JmolJDXMOLReader", "JU.Lst"], "J.adapter.readers.more.JcampdxReader", ["java.lang.Float", "JU.BS", "$.PT", "$.Rdr", "J.adapter.smarter.SmarterJmolAdapter", "J.api.Interface", "JU.BSUtil", "$.Logger", "JV.JC"], function () {
c$ = Clazz.decorateAsClass (function () {
this.selectedModel = 0;
this.mpr = null;
this.acdMolFile = null;
this.nPeaks = 0;
this.acdAssignments = null;
this.title = null;
this.nucleus = "";
this.type = null;
this.peakData = null;
this.allTypes = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "JcampdxReader", J.adapter.readers.molxyz.MolReader, J.api.JmolJDXMOLReader);
Clazz.prepareFields (c$, function () {
this.peakData = new JU.Lst ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.vwr.setBooleanProperty ("_JSpecView".toLowerCase (), true);
if (this.isTrajectory) {
JU.Logger.warn ("TRAJECTORY keyword ignored");
this.isTrajectory = false;
}if (this.reverseModels) {
JU.Logger.warn ("REVERSE keyword ignored");
this.reverseModels = false;
}this.selectedModel = this.desiredModelNumber;
this.desiredModelNumber = -2147483648;
if (!this.checkFilterKey ("NOSYNC")) this.addJmolScript ("sync on");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var i = this.line.indexOf ("=");
if (i < 0 || !this.line.startsWith ("##")) return true;
var label = JU.PT.replaceAllCharacters (this.line.substring (0, i).trim (), " ", "").toUpperCase ();
if (label.length > 12) label = label.substring (0, 12);
var pt = ("##$MODELS ##$PEAKS ##$SIGNALS ##$MOLFILE ##NPOINTS ##TITLE ##PEAKASSIGN##$UVIR_ASSI##$MS_FRAGME##.OBSERVENU##DATATYPE ").indexOf (label);
if (pt < 0) return true;
if (this.mpr == null) this.mpr = (J.api.Interface.getOption ("jsv.JDXMOLParser", this.vwr, "file")).set (this, this.filePath, this.htParams);
var value = this.line.substring (i + 1).trim ();
this.mpr.setLine (value);
switch (pt) {
case 0:
this.mpr.readModels ();
break;
case 12:
case 24:
this.mpr.readPeaks (pt == 24, -1);
break;
case 36:
this.acdMolFile = this.mpr.readACDMolFile ();
this.processModelData (this.acdMolFile, this.title + " (assigned)", "MOL", "mol", "", 0.01, NaN, true);
if (this.asc.errorMessage != null) {
this.continuing = false;
return false;
}break;
case 48:
this.nPeaks = JU.PT.parseInt (value);
break;
case 60:
this.title = JU.PT.split (value, "$$")[0].trim ();
break;
case 72:
case 84:
case 96:
this.acdAssignments = this.mpr.readACDAssignments (this.nPeaks, pt == 72);
break;
case 108:
this.nucleus = value.substring (1);
break;
case 120:
this.type = value;
if ((pt = this.type.indexOf (" ")) >= 0) this.type = this.type.substring (0, pt);
break;
}
return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (this.mpr != null) this.processPeakData ();
this.finalizeReaderMR ();
});
Clazz.overrideMethod (c$, "processModelData",
function (data, id, type, base, last, modelScale, vibScale, isFirst) {
var model0 = this.asc.iSet;
var model = null;
while (true) {
var ret = J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollectionReader (this.filePath, type, JU.Rdr.getBR (data), this.htParams);
if (Clazz.instanceOf (ret, String)) {
JU.Logger.warn ("" + ret);
if ((ret).startsWith (JV.JC.READER_NOT_FOUND)) this.asc.errorMessage = ret;
break;
}ret = J.adapter.smarter.SmarterJmolAdapter.staticGetAtomSetCollection (ret);
if (Clazz.instanceOf (ret, String)) {
JU.Logger.warn ("" + ret);
break;
}model = ret;
var baseModel = base;
if (baseModel.length == 0) baseModel = last;
if (baseModel.length != 0) {
var ibase = this.findModelById (baseModel);
if (ibase >= 0) {
this.asc.setModelInfoForSet ("jdxModelID", baseModel, ibase);
for (var i = model.atomSetCount; --i >= 0; ) model.setModelInfoForSet ("jdxBaseModel", baseModel, i);
if (model.bondCount == 0) this.setBonding (model, ibase);
}}if (!Float.isNaN (vibScale)) {
JU.Logger.info ("JcampdxReader applying vibration scaling of " + vibScale + " to " + model.ac + " atoms");
var atoms = model.atoms;
for (var i = model.ac; --i >= 0; ) {
if (atoms[i].vib != null && !Float.isNaN (atoms[i].vib.z)) atoms[i].vib.scale (vibScale);
}
}if (!Float.isNaN (modelScale)) {
JU.Logger.info ("JcampdxReader applying model scaling of " + modelScale + " to " + model.ac + " atoms");
var atoms = model.atoms;
for (var i = model.ac; --i >= 0; ) atoms[i].scale (modelScale);
}JU.Logger.info ("jdx model=" + id + " type=" + model.fileTypeName);
this.asc.appendAtomSetCollection (-1, model);
break;
}
this.updateModelIDs (id, model0, isFirst);
}, "~S,~S,~S,~S,~S,~N,~N,~B");
Clazz.defineMethod (c$, "setBonding",
function (a, ibase) {
var n0 = this.asc.getAtomSetAtomCount (ibase);
var n = a.ac;
if (n % n0 != 0) {
JU.Logger.warn ("atom count in secondary model (" + n + ") is not a multiple of " + n0 + " -- bonding ignored");
return;
}var bonds = this.asc.bonds;
var b0 = 0;
for (var i = 0; i < ibase; i++) b0 += this.asc.getAtomSetBondCount (i);
var b1 = b0 + this.asc.getAtomSetBondCount (ibase);
var ii0 = this.asc.getAtomSetAtomIndex (ibase);
var nModels = a.atomSetCount;
for (var j = 0; j < nModels; j++) {
var i0 = a.getAtomSetAtomIndex (j) - ii0;
if (a.getAtomSetAtomCount (j) != n0) {
JU.Logger.warn ("atom set atom count in secondary model (" + a.getAtomSetAtomCount (j) + ") is not equal to " + n0 + " -- bonding ignored");
return;
}for (var i = b0; i < b1; i++) a.addNewBondWithOrder (bonds[i].atomIndex1 + i0, bonds[i].atomIndex2 + i0, bonds[i].order);
}
}, "J.adapter.smarter.AtomSetCollection,~N");
Clazz.defineMethod (c$, "updateModelIDs",
function (id, model0, isFirst) {
var n = this.asc.atomSetCount;
if (isFirst && n == model0 + 2) {
this.asc.setCurrentModelInfo ("modelID", id);
return;
}for (var pt = 0, i = model0; ++i < n; ) this.asc.setModelInfoForSet ("modelID", id + "." + (++pt), i);
}, "~S,~N,~B");
Clazz.overrideMethod (c$, "addPeakData",
function (info) {
this.peakData.addLast (info);
}, "~S");
Clazz.defineMethod (c$, "processPeakData",
function () {
if (this.acdAssignments != null) {
try {
this.mpr.setACDAssignments (this.title, this.nucleus + this.type, 0, this.acdAssignments, this.acdMolFile);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}var n = this.peakData.size ();
if (n == 0) return;
var bsModels = new JU.BS ();
var havePeaks = (n > 0);
for (var p = 0; p < n; p++) {
this.line = this.peakData.get (p);
var type = this.mpr.getAttribute (this.line, "type");
var id = this.mpr.getAttribute (this.line, "model");
var i = this.findModelById (id);
if (i < 0) {
JU.Logger.warn ("cannot find model " + id + " required for " + this.line);
continue;
}this.addType (i, type);
var title = type + ": " + this.mpr.getAttribute (this.line, "title");
var key = "jdxAtomSelect_" + this.mpr.getAttribute (this.line, "type");
bsModels.set (i);
var s;
if (this.mpr.getAttribute (this.line, "atoms").length != 0) {
this.processPeakSelectAtom (i, key, this.line);
s = type + ": ";
} else if (this.processPeakSelectModel (i, title)) {
s = "model: ";
} else {
s = "ignored: ";
}JU.Logger.info (s + this.line);
}
n = this.asc.atomSetCount;
for (var i = n; --i >= 0; ) {
var id = this.asc.getAtomSetAuxiliaryInfoValue (i, "modelID");
if (havePeaks && !bsModels.get (i) && id.indexOf (".") >= 0) {
this.removeAtomSet (i);
n--;
}}
if (this.selectedModel == -2147483648) {
if (this.allTypes != null) this.appendLoadNote (this.allTypes);
} else {
if (this.selectedModel == 0) this.selectedModel = n - 1;
for (var i = this.asc.atomSetCount; --i >= 0; ) if (i + 1 != this.selectedModel) this.removeAtomSet (i);
if (n > 0) this.appendLoadNote (this.asc.getAtomSetAuxiliaryInfoValue (0, "name"));
}for (var i = this.asc.atomSetCount; --i >= 0; ) this.asc.setAtomSetNumber (i, i + 1);
this.asc.centralize ();
});
Clazz.defineMethod (c$, "findModelById",
function (modelID) {
for (var i = this.asc.atomSetCount; --i >= 0; ) {
var id = this.asc.getAtomSetAuxiliaryInfoValue (i, "modelID");
if (modelID.equals (id)) return i;
}
return -1;
}, "~S");
Clazz.defineMethod (c$, "addType",
function (imodel, type) {
var types = this.addTypeStr (this.asc.getAtomSetAuxiliaryInfoValue (imodel, "spectrumTypes"), type);
if (types == null) return;
this.asc.setModelInfoForSet ("spectrumTypes", types, imodel);
var s = this.addTypeStr (this.allTypes, type);
if (s != null) this.allTypes = s;
}, "~N,~S");
Clazz.defineMethod (c$, "addTypeStr",
function (types, type) {
if (types != null && types.contains (type)) return null;
if (types == null) types = "";
else types += ",";
return types + type;
}, "~S,~S");
Clazz.defineMethod (c$, "processPeakSelectAtom",
function (i, key, data) {
var peaks = this.asc.getAtomSetAuxiliaryInfoValue (i, key);
if (peaks == null) this.asc.setModelInfoForSet (key, peaks = new JU.Lst (), i);
peaks.addLast (data);
}, "~N,~S,~S");
Clazz.defineMethod (c$, "processPeakSelectModel",
function (i, title) {
if (this.asc.getAtomSetAuxiliaryInfoValue (i, "jdxModelSelect") != null) return false;
this.asc.setModelInfoForSet ("name", title, i);
this.asc.setModelInfoForSet ("jdxModelSelect", this.line, i);
return true;
}, "~N,~S");
Clazz.overrideMethod (c$, "setSpectrumPeaks",
function (nH, piUnitsX, piUnitsY) {
}, "~N,~S,~S");
Clazz.defineMethod (c$, "removeAtomSet",
function (imodel) {
if (this.asc.bsAtoms == null) this.asc.bsAtoms = JU.BSUtil.newBitSet2 (0, this.asc.ac);
var i0 = this.asc.atomSetAtomIndexes[imodel];
var nAtoms = this.asc.atomSetAtomCounts[imodel];
var i1 = i0 + nAtoms;
this.asc.bsAtoms.clearBits (i0, i1);
for (var i = i1; i < this.asc.ac; i++) this.asc.atoms[i].atomSetIndex--;
for (var i = imodel + 1; i < this.asc.atomSetCount; i++) {
this.asc.atomSetAuxiliaryInfo[i - 1] = this.asc.atomSetAuxiliaryInfo[i];
this.asc.atomSetAtomIndexes[i - 1] = this.asc.atomSetAtomIndexes[i];
this.asc.atomSetBondCounts[i - 1] = this.asc.atomSetBondCounts[i];
this.asc.atomSetAtomCounts[i - 1] = this.asc.atomSetAtomCounts[i];
this.asc.atomSetNumbers[i - 1] = this.asc.atomSetNumbers[i];
}
for (var i = 0; i < this.asc.bondCount; i++) this.asc.bonds[i].atomSetIndex = this.asc.atoms[this.asc.bonds[i].atomIndex1].atomSetIndex;
this.asc.atomSetAuxiliaryInfo[--this.asc.atomSetCount] = null;
var n = 0;
for (var i = 0; i < this.asc.structureCount; i++) {
var s = this.asc.structures[i];
if (s.modelStartEnd[0] == imodel && s.modelStartEnd[1] == imodel) {
this.asc.structures[i] = null;
n++;
}}
if (n > 0) {
var ss = new Array (this.asc.structureCount - n);
for (var i = 0, pt = 0; i < this.asc.structureCount; i++) if (this.asc.structures[i] != null) ss[pt++] = this.asc.structures[i];
this.asc.structures = ss;
}}, "~N");
});

77
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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.MdCrdReader", ["java.lang.Float", "JU.P3", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.ptFloat = 0;
this.lenLine = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "MdCrdReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "setup",
function (fullPath, htParams, readerOrDocument) {
this.requiresBSFilter = true;
this.setupASCR (fullPath, htParams, readerOrDocument);
}, "~S,java.util.Map,~O");
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.initializeTrajectoryFile ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
this.readCoordinates ();
JU.Logger.info ("Total number of trajectory steps=" + this.trajectorySteps.size ());
this.continuing = false;
return false;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
this.line = null;
var ac = (this.bsFilter == null ? this.templateAtomCount : (this.htParams.get ("filteredAtomCount")).intValue ());
var isPeriodic = this.htParams.containsKey ("isPeriodic");
var floatCount = this.templateAtomCount * 3 + (isPeriodic ? 3 : 0);
while (true) if (this.doGetModel (++this.modelNumber, null)) {
var trajectoryStep = new Array (ac);
if (!this.getTrajectoryStep (trajectoryStep, isPeriodic)) return;
this.trajectorySteps.addLast (trajectoryStep);
if (this.isLastModel (this.modelNumber)) return;
} else {
if (!this.skipFloats (floatCount)) return;
}
});
Clazz.defineMethod (c$, "getFloat",
function () {
while (this.line == null || this.ptFloat >= this.lenLine) {
if (this.rd () == null) return NaN;
this.ptFloat = 0;
this.lenLine = this.line.length;
}
this.ptFloat += 8;
return this.parseFloatRange (this.line, this.ptFloat - 8, this.ptFloat);
});
Clazz.defineMethod (c$, "getPoint",
function () {
var x = this.getFloat ();
var y = this.getFloat ();
var z = this.getFloat ();
return (Float.isNaN (z) ? null : JU.P3.new3 (x, y, z));
});
Clazz.defineMethod (c$, "getTrajectoryStep",
function (trajectoryStep, isPeriodic) {
var ac = trajectoryStep.length;
var n = -1;
for (var i = 0; i < this.templateAtomCount; i++) {
var pt = this.getPoint ();
if (pt == null) return false;
if (this.bsFilter == null || this.bsFilter.get (i)) {
if (++n == ac) return false;
trajectoryStep[n] = pt;
}}
if (isPeriodic) this.getPoint ();
return (this.line != null);
}, "~A,~B");
Clazz.defineMethod (c$, "skipFloats",
function (n) {
var i = 0;
while (i < n && this.rd () != null) i += this.getTokens ().length;
return (this.line != null);
}, "~N");
});

133
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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.readers.more.ForceFieldReader"], "J.adapter.readers.more.MdTopReader", ["java.lang.Boolean", "JU.Lst", "J.adapter.smarter.Atom", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.nAtoms = 0;
this.ac = 0;
this.$atomTypes = null;
this.group3s = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "MdTopReader", J.adapter.readers.more.ForceFieldReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setIsPDB ();
this.setUserAtomTypes ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("%FLAG ") != 0) return true;
this.line = this.line.substring (6).trim ();
if (this.line.equals ("POINTERS")) this.getPointers ();
else if (this.line.equals ("ATOM_NAME")) this.getAtomNames ();
else if (this.line.equals ("CHARGE")) this.getCharges ();
else if (this.line.equals ("RESIDUE_LABEL")) this.getResidueLabels ();
else if (this.line.equals ("RESIDUE_POINTER")) this.getResiduePointers ();
else if (this.line.equals ("AMBER_ATOM_TYPE")) this.getAtomTypes ();
else if (this.line.equals ("MASS")) this.getMasses ();
return false;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderASCR ();
var atoms = this.asc.atoms;
var atom;
for (var i = 0; i < this.ac; i++) {
atom = atoms[i];
atom.isHetero = this.vwr.getJBR ().isHetero (atom.group3);
var atomType = this.$atomTypes[i];
if (!this.getElementSymbol (atom, atomType)) atom.elementSymbol = J.adapter.readers.more.ForceFieldReader.deducePdbElementSymbol (atom.isHetero, atom.atomName, atom.group3);
}
var atoms2 = null;
if (this.filter == null) {
this.nAtoms = this.ac;
} else {
atoms2 = new Array (atoms.length);
this.nAtoms = 0;
for (var i = 0; i < this.ac; i++) if (this.filterAtom (atoms[i], i)) atoms2[this.nAtoms++] = atoms[i];
}for (var i = 0, j = 0, k = 0; i < this.ac; i++) {
if (this.filter == null || this.bsFilter.get (i)) {
if (k % 100 == 0) j++;
this.setAtomCoordXYZ (atoms[i], (i % 100) * 2, j * 2, 0);
}}
if (atoms2 != null) {
this.discardPreviousAtoms ();
for (var i = 0; i < this.nAtoms; i++) this.asc.addAtom (atoms2[i]);
}JU.Logger.info ("Total number of atoms used=" + this.nAtoms);
this.setModelPDB (true);
this.htParams.put ("defaultType", "mdcrd");
});
Clazz.defineMethod (c$, "getDataBlock",
function () {
var vdata = new JU.Lst ();
this.discardLinesUntilContains ("FORMAT");
var n = J.adapter.smarter.AtomSetCollectionReader.getFortranFormatLengths (this.line.substring (this.line.indexOf ("("))).get (0).intValue ();
var i = 0;
var len = 0;
while (true) {
if (i >= len) {
if (this.rd () == null) break;
i = 0;
len = this.line.length;
if (len == 0 || this.line.indexOf ("FLAG") >= 0) break;
}vdata.addLast (this.line.substring (i, i + n).trim ());
i += n;
}
return vdata.toArray ( new Array (vdata.size ()));
});
Clazz.defineMethod (c$, "getPointers",
function () {
var tokens = this.getDataBlock ();
this.ac = this.parseIntStr (tokens[0]);
var isPeriodic = (tokens[27].charAt (0) != '0');
if (isPeriodic) {
JU.Logger.info ("Periodic type: " + tokens[27]);
this.htParams.put ("isPeriodic", Boolean.TRUE);
}JU.Logger.info ("Total number of atoms read=" + this.ac);
this.htParams.put ("templateAtomCount", Integer.$valueOf (this.ac));
for (var i = 0; i < this.ac; i++) this.asc.addAtom ( new J.adapter.smarter.Atom ());
});
Clazz.defineMethod (c$, "getAtomTypes",
function () {
this.$atomTypes = this.getDataBlock ();
});
Clazz.defineMethod (c$, "getCharges",
function () {
var data = this.getDataBlock ();
if (data.length != this.ac) return;
var atoms = this.asc.atoms;
for (var i = this.ac; --i >= 0; ) atoms[i].partialCharge = this.parseFloatStr (data[i]);
});
Clazz.defineMethod (c$, "getResiduePointers",
function () {
var resPtrs = this.getDataBlock ();
JU.Logger.info ("Total number of residues=" + resPtrs.length);
var pt1 = this.ac;
var pt2;
var atoms = this.asc.atoms;
for (var i = resPtrs.length; --i >= 0; ) {
var ptr = pt2 = this.parseIntStr (resPtrs[i]) - 1;
while (ptr < pt1) {
if (this.group3s != null) atoms[ptr].group3 = this.group3s[i];
atoms[ptr++].sequenceNumber = i + 1;
}
pt1 = pt2;
}
});
Clazz.defineMethod (c$, "getResidueLabels",
function () {
this.group3s = this.getDataBlock ();
});
Clazz.defineMethod (c$, "getAtomNames",
function () {
var names = this.getDataBlock ();
var atoms = this.asc.atoms;
for (var i = 0; i < this.ac; i++) atoms[i].atomName = names[i];
});
Clazz.defineMethod (c$, "getMasses",
function () {
});
});

171
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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.readers.more.ForceFieldReader"], "J.adapter.readers.more.Mol2Reader", ["java.lang.Character", "JU.PT", "J.adapter.smarter.Bond"], function () {
c$ = Clazz.decorateAsClass (function () {
this.nAtoms = 0;
this.ac = 0;
this.isPDB = false;
this.lastSequenceNumber = 2147483647;
this.chainID = 64;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "Mol2Reader", J.adapter.readers.more.ForceFieldReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setUserAtomTypes ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.equals ("@<TRIPOS>MOLECULE")) {
if (!this.processMolecule ()) {
return true;
}this.continuing = !this.isLastModel (this.modelNumber);
return false;
}if (this.line.length != 0 && this.line.charAt (0) == '#') {
this.checkCurrentLineForScript ();
}return true;
});
Clazz.defineMethod (c$, "processMolecule",
function () {
this.isPDB = false;
var thisDataSetName = this.rd ().trim ();
if (!this.doGetModel (++this.modelNumber, thisDataSetName)) {
return false;
}this.lastSequenceNumber = 2147483647;
this.chainID = 64;
this.rd ();
this.line += " 0 0 0 0 0 0";
this.ac = this.parseIntStr (this.line);
var bondCount = this.parseInt ();
if (bondCount == 0) this.asc.setNoAutoBond ();
var resCount = this.parseInt ();
this.rd ();
this.rd ();
if (this.rd () != null && (this.line.length == 0 || this.line.charAt (0) != '@')) {
if (this.rd () != null && this.line.length != 0 && this.line.charAt (0) != '@') {
if (this.line.indexOf ("jmolscript:") >= 0) {
this.checkCurrentLineForScript ();
if (this.line.equals ("#")) {
this.line = "";
}}if (this.line.length != 0) {
thisDataSetName += ": " + this.line.trim ();
}}}this.newAtomSet (thisDataSetName);
while (this.line != null && !this.line.equals ("@<TRIPOS>MOLECULE")) {
if (this.line.equals ("@<TRIPOS>ATOM")) {
this.readAtoms (this.ac);
this.asc.setAtomSetName (thisDataSetName);
} else if (this.line.equals ("@<TRIPOS>BOND")) {
this.readBonds (bondCount);
} else if (this.line.equals ("@<TRIPOS>SUBSTRUCTURE")) {
this.readResInfo (resCount);
} else if (this.line.equals ("@<TRIPOS>CRYSIN")) {
this.readCrystalInfo ();
}this.rd ();
}
this.nAtoms += this.ac;
if (this.isPDB) {
this.setIsPDB ();
this.setModelPDB (true);
}this.applySymmetryAndSetTrajectory ();
return true;
});
Clazz.defineMethod (c$, "readAtoms",
function (ac) {
if (ac == 0) return;
var i0 = this.asc.ac;
for (var i = 0; i < ac; ++i) {
var atom = this.asc.addNewAtom ();
var tokens = JU.PT.getTokens (this.rd ());
var atomType = tokens[5];
var name = tokens[1];
var pt = atomType.indexOf (".");
if (pt >= 0) {
atom.elementSymbol = atomType.substring (0, pt);
} else {
atom.atomName = name;
atom.elementSymbol = atom.getElementSymbol ();
}atom.atomName = name + '\0' + atomType;
atom.set (this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[4]));
if (tokens.length > 6) {
atom.sequenceNumber = this.parseIntStr (tokens[6]);
if (atom.sequenceNumber < this.lastSequenceNumber) {
if (this.chainID == 90) this.chainID = 96;
this.chainID++;
}this.lastSequenceNumber = atom.sequenceNumber;
this.setChainID (atom, "" + String.fromCharCode (this.chainID));
}if (tokens.length > 7) atom.group3 = tokens[7];
if (tokens.length > 8) {
atom.partialCharge = this.parseFloatStr (tokens[8]);
if (atom.partialCharge == Clazz.floatToInt (atom.partialCharge)) atom.formalCharge = Clazz.floatToInt (atom.partialCharge);
}}
var atoms = this.asc.atoms;
var g3 = atoms[i0].group3;
if (g3 == null) return;
var isPDB = false;
if (!g3.equals ("UNK") && !g3.startsWith ("RES")) {
for (var i = this.asc.ac; --i >= i0; ) if (!g3.equals (atoms[this.asc.ac - 1].group3)) {
isPDB = true;
break;
}
if (isPDB) {
isPDB = false;
for (var i = this.asc.ac; --i >= i0; ) {
var pt = this.getPDBGroupLength (atoms[i].group3);
if (pt == 0 || pt > 3) break;
if (this.vwr.getJBR ().isKnownPDBGroup (g3.substring (0, pt), 2147483647)) {
isPDB = this.isPDB = true;
break;
}}
}}for (var i = this.asc.ac; --i >= i0; ) {
if (isPDB) {
g3 = atoms[i].group3;
g3 = g3.substring (0, this.getPDBGroupLength (g3));
atoms[i].isHetero = this.vwr.getJBR ().isHetero (g3);
} else {
g3 = null;
}atoms[i].group3 = g3;
}
}, "~N");
Clazz.defineMethod (c$, "getPDBGroupLength",
function (g3) {
var pt0 = g3.length;
var pt = pt0;
while (--pt > 0 && Character.isDigit (g3.charAt (pt))) {
}
return ++pt;
}, "~S");
Clazz.defineMethod (c$, "readBonds",
function (bondCount) {
for (var i = 0; i < bondCount; ++i) {
var tokens = JU.PT.getTokens (this.rd ());
var atomIndex1 = this.parseIntStr (tokens[1]);
var atomIndex2 = this.parseIntStr (tokens[2]);
var order = this.parseIntStr (tokens[3]);
if (order == -2147483648) order = (tokens[3].equals ("ar") ? 515 : tokens[3].equals ("am") ? 1 : 17);
this.asc.addBond ( new J.adapter.smarter.Bond (this.nAtoms + atomIndex1 - 1, this.nAtoms + atomIndex2 - 1, order));
}
}, "~N");
Clazz.defineMethod (c$, "readResInfo",
function (resCount) {
for (var i = 0; i < resCount; ++i) {
this.rd ();
}
}, "~N");
Clazz.defineMethod (c$, "readCrystalInfo",
function () {
this.rd ();
var tokens = this.getTokens ();
if (tokens.length < 6) return;
var name = "";
for (var i = 6; i < tokens.length; i++) name += " " + tokens[i];
if (name === "") name = " P1";
else name += " *";
name = name.substring (1);
this.setSpaceGroupName (name);
if (this.ignoreFileUnitCell) return;
for (var i = 0; i < 6; i++) this.setUnitCellItem (i, this.parseFloatStr (tokens[i]));
var atoms = this.asc.atoms;
for (var i = 0; i < this.ac; ++i) this.setAtomCoord (atoms[this.nAtoms + i]);
});
});

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Clazz.declarePackage ("J.adapter.readers.more");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.more.TlsDataOnlyReader", ["java.lang.Float", "java.util.Hashtable", "JU.Lst", "$.P3", "$.PT", "$.SB", "JU.Escape", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.vTlsModels = null;
this.sbTlsErrors = null;
this.tlsGroupID = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.more, "TlsDataOnlyReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.readTlsData ();
this.continuing = false;
});
Clazz.defineMethod (c$, "readTlsData",
function () {
this.vTlsModels = new JU.Lst ();
var tlsGroups;
var tlsGroup = null;
var ranges = null;
var range = null;
tlsGroups = new JU.Lst ();
while (this.rd () != null) {
var tokens = JU.PT.getTokens (this.line.$replace ('\'', ' '));
if (tokens.length == 0) continue;
if (tokens[0].equals ("TLS")) {
tlsGroup = new java.util.Hashtable ();
ranges = new JU.Lst ();
tlsGroup.put ("ranges", ranges);
tlsGroups.addLast (tlsGroup);
tlsGroup.put ("id", Integer.$valueOf (++this.tlsGroupID));
} else if (tokens[0].equals ("RANGE")) {
range = new java.util.Hashtable ();
var chain1 = tokens[1].charAt (0);
var chain2 = tokens[3].charAt (0);
var res1 = JU.PT.parseInt (tokens[2]);
var res2 = JU.PT.parseInt (tokens[4]);
if (chain1 == chain2) {
range.put ("chains", "" + chain1 + chain2);
if (res1 <= res2) {
range.put ("residues", Clazz.newIntArray (-1, [res1, res2]));
ranges.addLast (range);
} else {
this.tlsAddError (" TLS group residues are not in order (range ignored)");
}} else {
this.tlsAddError (" TLS group chains are different (range ignored)");
}} else if (tokens[0].equals ("ORIGIN")) {
var origin = new JU.P3 ();
tlsGroup.put ("origin", origin);
origin.set (this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3]));
if (Float.isNaN (origin.x) || Float.isNaN (origin.y) || Float.isNaN (origin.z)) {
origin.set (NaN, NaN, NaN);
this.tlsAddError ("invalid origin: " + this.line);
}} else if (tokens[0].equals ("T") || tokens[0].equals ("L") || tokens[0].equals ("S")) {
var tensorType = tokens[0].charAt (0);
var nn = (tensorType == 'S' ? J.adapter.readers.more.TlsDataOnlyReader.Snn : J.adapter.readers.more.TlsDataOnlyReader.TLnn);
var tensor = Clazz.newFloatArray (3, 3, 0);
tlsGroup.put ("t" + tensorType, tensor);
for (var i = 1; i < tokens.length; i++) {
var ti = nn[i].charCodeAt (0) - 49;
var tj = nn[i].charCodeAt (1) - 49;
tensor[ti][tj] = this.parseFloatStr (tokens[++i]);
if (ti < tj) tensor[tj][ti] = tensor[ti][tj];
}
if (tensorType == 'S') tensor[0][0] = -tensor[0][0];
for (var i = 0; i < 3; i++) for (var j = 0; j < 3; j++) if (Float.isNaN (tensor[i][j])) {
this.tlsAddError ("invalid tensor: " + JU.Escape.escapeFloatAA (tensor, false));
}
}}
JU.Logger.info (this.tlsGroupID + " TLS groups read");
var groups = new java.util.Hashtable ();
groups.put ("groupCount", Integer.$valueOf (this.tlsGroupID));
groups.put ("groups", tlsGroups);
this.vTlsModels.addLast (groups);
this.htParams.put ("vTlsModels", this.vTlsModels);
});
Clazz.defineMethod (c$, "tlsAddError",
function (error) {
if (this.sbTlsErrors == null) this.sbTlsErrors = new JU.SB ();
this.sbTlsErrors.append (this.fileName).appendC ('\t').append ("TLS group ").appendI (this.tlsGroupID).appendC ('\t').append (error).appendC ('\n');
}, "~S");
c$.TLnn = c$.prototype.TLnn = Clazz.newArray (-1, ["11", "22", "33", "12", "13", "23"]);
c$.Snn = c$.prototype.Snn = Clazz.newArray (-1, ["22", "11", "12", "13", "23", "21", "31", "32"]);
});

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Clazz.declarePackage ("J.adapter.readers.pdb");
Clazz.load (["J.adapter.readers.pdb.PdbReader"], "J.adapter.readers.pdb.JmolDataReader", ["java.util.Hashtable", "JU.P3", "JU.Logger", "$.Parser"], function () {
c$ = Clazz.decorateAsClass (function () {
this.props = null;
this.residueNames = null;
this.atomNames = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.pdb, "JmolDataReader", J.adapter.readers.pdb.PdbReader);
Clazz.overrideMethod (c$, "checkRemark",
function () {
while (true) {
if (this.line.length < 30 || this.line.indexOf ("Jmol") != 11) break;
switch ("Ppard".indexOf (this.line.substring (16, 17))) {
case 0:
this.props = new java.util.Hashtable ();
this.asc.setInfo ("jmolData", this.line);
if (!this.line.endsWith ("#noautobond")) this.line += "#noautobond";
break;
case 1:
var pt1 = this.line.indexOf ("[");
var pt2 = this.line.indexOf ("]");
if (pt1 < 25 || pt2 <= pt1) return;
var name = this.line.substring (25, pt1).trim ();
this.line = this.line.substring (pt1 + 1, pt2).$replace (',', ' ');
var tokens = this.getTokens ();
JU.Logger.info ("reading " + name + " " + tokens.length);
var prop = Clazz.newFloatArray (tokens.length, 0);
for (var i = prop.length; --i >= 0; ) prop[i] = this.parseFloatStr (tokens[i]);
this.props.put (name, prop);
break;
case 2:
this.line = this.line.substring (27);
this.atomNames = this.getTokens ();
JU.Logger.info ("reading atom names " + this.atomNames.length);
break;
case 3:
this.line = this.line.substring (30);
this.residueNames = this.getTokens ();
JU.Logger.info ("reading residue names " + this.residueNames.length);
break;
case 4:
JU.Logger.info (this.line);
var data = Clazz.newFloatArray (15, 0);
JU.Parser.parseStringInfestedFloatArray (this.line.substring (10).$replace ('=', ' ').$replace ('{', ' ').$replace ('}', ' '), null, data);
var minXYZ = JU.P3.new3 (data[0], data[1], data[2]);
var maxXYZ = JU.P3.new3 (data[3], data[4], data[5]);
this.fileScaling = JU.P3.new3 (data[6], data[7], data[8]);
this.fileOffset = JU.P3.new3 (data[9], data[10], data[11]);
var plotScale = JU.P3.new3 (data[12], data[13], data[14]);
if (plotScale.x <= 0) plotScale.x = 100;
if (plotScale.y <= 0) plotScale.y = 100;
if (plotScale.z <= 0) plotScale.z = 100;
if (this.fileScaling.y == 0) this.fileScaling.y = 1;
if (this.fileScaling.z == 0) this.fileScaling.z = 1;
this.setFractionalCoordinates (true);
this.latticeCells = Clazz.newIntArray (3, 0);
this.asc.xtalSymmetry = null;
this.setUnitCell (plotScale.x * 2 / (maxXYZ.x - minXYZ.x), plotScale.y * 2 / (maxXYZ.y - minXYZ.y), plotScale.z * 2 / (maxXYZ.z == minXYZ.z ? 1 : maxXYZ.z - minXYZ.z), 90, 90, 90);
this.unitCellOffset = JU.P3.newP (plotScale);
this.unitCellOffset.scale (-1);
this.getSymmetry ();
this.symmetry.toFractional (this.unitCellOffset, false);
this.unitCellOffset.scaleAdd2 (-1.0, minXYZ, this.unitCellOffset);
this.symmetry.setOffsetPt (this.unitCellOffset);
this.asc.setInfo ("jmolDataScaling", Clazz.newArray (-1, [minXYZ, maxXYZ, plotScale]));
this.doApplySymmetry = true;
break;
}
break;
}
this.checkCurrentLineForScript ();
});
Clazz.overrideMethod (c$, "setAdditionalAtomParameters",
function (atom) {
if (this.residueNames != null && atom.index < this.residueNames.length) atom.group3 = this.residueNames[atom.index];
if (this.atomNames != null && atom.index < this.atomNames.length) atom.atomName = this.atomNames[atom.index];
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.asc.setCurrentModelInfo ("jmolDataProperties", this.props);
this.finalizeReaderPDB ();
});
});

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Clazz.declarePackage ("J.adapter.readers.pdb");
Clazz.load (["J.adapter.readers.pdb.PdbReader", "JU.Lst"], "J.adapter.readers.pdb.P2nReader", null, function () {
c$ = Clazz.decorateAsClass (function () {
this.altNames = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.pdb, "P2nReader", J.adapter.readers.pdb.PdbReader);
Clazz.prepareFields (c$, function () {
this.altNames = new JU.Lst ();
});
Clazz.overrideMethod (c$, "setAdditionalAtomParameters",
function (atom) {
var altName = this.line.substring (69, 72).trim ();
if (altName.length == 0) altName = atom.atomName;
if (this.useAltNames) atom.atomName = altName;
else this.altNames.addLast (altName);
}, "J.adapter.smarter.Atom");
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderPDB ();
if (!this.useAltNames) this.asc.setCurrentModelInfo ("altName", this.altNames.toArray ( new Array (this.altNames.size ())));
});
});

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15
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/pdb/PqrReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.pdb");
Clazz.load (["J.adapter.readers.pdb.PdbReader"], "J.adapter.readers.pdb.PqrReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.pdb, "PqrReader", J.adapter.readers.pdb.PdbReader);
Clazz.overrideMethod (c$, "setAdditionalAtomParameters",
function (atom) {
if (this.gromacsWideFormat) {
atom.partialCharge = this.parseFloatRange (this.line, 60, 68);
atom.radius = J.adapter.readers.pdb.PdbReader.fixRadius (this.parseFloatRange (this.line, 68, 76));
} else {
var tokens = this.getTokens ();
var pt = tokens.length - 2 - (this.line.length > 75 ? 1 : 0);
atom.partialCharge = this.parseFloatStr (tokens[pt++]);
atom.radius = J.adapter.readers.pdb.PdbReader.fixRadius (this.parseFloatStr (tokens[pt]));
}}, "J.adapter.smarter.Atom");
});

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Clazz.declarePackage ("J.adapter.readers.pymol");
Clazz.load (null, "J.adapter.readers.pymol.JmolObject", ["java.lang.Float", "JU.P3", "$.PT", "$.SB", "J.adapter.readers.pymol.PyMOLReader", "JU.BSUtil", "$.Escape"], function () {
c$ = Clazz.decorateAsClass (function () {
this.id = 0;
this.bsAtoms = null;
this.info = null;
this.size = -1;
this.colors = null;
this.modelIndex = -2147483648;
this.jmolName = null;
this.argb = 0;
this.translucency = 0;
this.visible = true;
this.rd = null;
this.cacheID = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.pymol, "JmolObject");
Clazz.makeConstructor (c$,
function (id, branchNameID, bsAtoms, info) {
this.id = id;
this.bsAtoms = bsAtoms;
this.info = info;
this.jmolName = branchNameID;
}, "~N,~S,JU.BS,~O");
Clazz.defineMethod (c$, "offset",
function (modelOffset, atomOffset) {
if (modelOffset > 0) {
if (this.modelIndex != -2147483648) this.modelIndex += modelOffset;
switch (this.id) {
case 1610625028:
case 12294:
return;
case 4115:
var i = (this.info).intValue ();
if (i >= 0) this.info = Integer.$valueOf (modelOffset + i);
return;
case 1073742031:
var movie = this.info;
var frames = movie.get ("frames");
for (var j = frames.length; --j >= 0; ) frames[j] += modelOffset;
return;
}
}if (atomOffset <= 0) return;
if (this.id == 12290) {
var map = (this.info).values ();
for (var o, $o = map.iterator (); $o.hasNext () && ((o = $o.next ()) || true);) JU.BSUtil.offset (o, 0, atomOffset);
return;
}if (this.bsAtoms != null) JU.BSUtil.offset (this.bsAtoms, 0, atomOffset);
if (this.colors != null) {
var colixes = this.colors[0];
var c = Clazz.newShortArray (colixes.length + atomOffset, 0);
System.arraycopy (colixes, 0, c, atomOffset, colixes.length);
this.colors[0] = c;
}}, "~N,~N");
Clazz.defineMethod (c$, "finalizeObject",
function (pymolScene, m, mepList, doCache) {
var sm = m.sm;
var color = "color";
var sID;
var sb = null;
if (this.bsAtoms != null) this.modelIndex = this.getModelIndex (m);
switch (this.id) {
case 2097194:
sm.vwr.displayAtoms (this.bsAtoms, false, false, 1275069441, true);
return;
case 12295:
var bs = sm.vwr.getModelUndeletedAtomsBitSet (this.argb);
JU.BSUtil.invertInPlace (bs, sm.vwr.ms.ac);
sm.vwr.select (bs, false, 0, true);
sm.restrictSelected (false, true);
return;
case 1610625028:
case 12294:
if (this.bsAtoms == null) {
if (this.info == null) {
sm.vwr.displayAtoms (null, true, false, 0, true);
}sm.vwr.setObjectProp (this.info, this.id);
} else {
sm.vwr.displayAtoms (this.bsAtoms, this.id == 1610625028, false, 1275069441, true);
}return;
case 12290:
sm.vwr.defineAtomSets (this.info);
return;
case 1073742031:
sm.vwr.am.setMovie (this.info);
return;
case 4115:
var frame = (this.info).intValue ();
if (frame >= 0) {
sm.vwr.setCurrentModelIndex (frame);
} else {
sm.vwr.setAnimationRange (-1, -1);
sm.vwr.setCurrentModelIndex (-1);
}return;
case 1073742139:
sm.vwr.stm.saveScene (this.jmolName, this.info);
sm.vwr.stm.saveOrientation (this.jmolName, (this.info).get ("pymolView"));
return;
case 5:
sm.loadShape (this.id);
sm.setShapePropertyBs (this.id, "pymolLabels", this.info, this.bsAtoms);
return;
case 1677721602:
break;
case 659488:
case 1:
if (this.size != -1) {
sm.setShapeSizeBs (1, this.size, null, this.bsAtoms);
var bsBonds = (sm.getShapePropertyIndex (1, "sets", 0))[1];
pymolScene.setUniqueBonds (bsBonds, this.id == 1);
this.size = -1;
}this.id = 1;
break;
case 1140850689:
this.id = 0;
break;
case 0:
break;
case 10:
case 9:
sm.loadShape (this.id);
var bsCarb = m.getAtoms (2097188, null);
JU.BSUtil.andNot (this.bsAtoms, bsCarb);
break;
case 16:
sm.loadShape (this.id);
sm.setShapePropertyBs (this.id, "ignore", JU.BSUtil.copyInvert (this.bsAtoms, sm.vwr.ms.ac), null);
break;
default:
if (!this.visible) return;
break;
}
switch (this.id) {
case 23:
sm.vwr.setCGO (this.info);
break;
case 16:
case 0:
case 7:
case 20:
case 11:
case 9:
case 10:
case 24:
if (Clazz.instanceOf (this.info, Array)) {
sm.loadShape (this.id);
sm.setShapePropertyBs (this.id, "params", this.info, this.bsAtoms);
}break;
case 6:
if (this.modelIndex < 0) return;
sm.loadShape (this.id);
var md = this.info;
md.setModelSet (m);
var points = md.points;
for (var i = points.size (); --i >= 0; ) (points.get (i)).mi = this.modelIndex;
sm.setShapePropertyBs (this.id, "measure", md, this.bsAtoms);
return;
case 135180:
sID = (this.bsAtoms == null ? this.info : this.jmolName);
if (sm.getShapeIdFromObjectName (sID) >= 0) {
sm.vwr.setObjectProp (sID, 1610625028);
return;
}sb = new JU.SB ();
sb.append ("isosurface ID ").append (JU.PT.esc (sID));
if (this.modelIndex < 0) this.modelIndex = sm.vwr.am.cmi;
if (this.bsAtoms == null) {
sb.append (" model ").append (m.getModelNumberDotted (this.modelIndex)).append (" color density sigma 1.0 ").append (JU.PT.esc (this.cacheID)).append (" ").append (JU.PT.esc (sID));
if (doCache) sb.append (";isosurface cache");
} else {
var lighting = (this.info)[0];
var only = (this.info)[1];
only = " only";
var bsCarve = (this.info)[2];
var carveDistance = ((this.info)[3]).floatValue ();
var resolution = "";
if (lighting == null) {
lighting = "mesh nofill";
resolution = " resolution 1.5";
}var haveMep = JU.PT.isOneOf (sID, mepList);
var model = m.getModelNumberDotted (this.modelIndex);
var ignore = "";
var type = (this.size < 0 ? " sasurface " : " solvent ");
sb.append (" model ").append (model).append (resolution).append (" select ").append (JU.Escape.eBS (this.bsAtoms)).append (only).append (ignore).append (type).appendF (Math.abs (this.size / 1000));
if (!haveMep) {
if (this.argb == 0) sb.append (" map property color");
else sb.append (";color isosurface ").append (JU.Escape.escapeColor (this.argb));
}sb.append (";isosurface frontOnly ").append (lighting);
if (this.translucency > 0) sb.append (";color isosurface translucent " + this.translucency);
if (bsCarve != null && !bsCarve.isEmpty ()) sb.append (";isosurface slab within " + carveDistance + " {" + model + " and " + JU.Escape.eBS (bsCarve) + "}");
if (doCache && !haveMep) sb.append (";isosurface cache");
}break;
case 1073742016:
var mep = this.info;
sID = mep.get (mep.size () - 2).toString ();
var mapID = mep.get (mep.size () - 1).toString ();
var min = J.adapter.readers.pymol.PyMOLReader.floatAt (J.adapter.readers.pymol.PyMOLReader.listAt (mep, 3), 0);
var max = J.adapter.readers.pymol.PyMOLReader.floatAt (J.adapter.readers.pymol.PyMOLReader.listAt (mep, 3), 2);
sb = new JU.SB ();
sb.append (";isosurface ID ").append (JU.PT.esc (sID)).append (" map ").append (JU.PT.esc (this.cacheID)).append (" ").append (JU.PT.esc (mapID)).append (";color isosurface range " + min + " " + max + ";isosurface colorscheme rwb;set isosurfacekey true");
if (this.translucency > 0) sb.append (";color isosurface translucent " + this.translucency);
if (doCache) sb.append (";isosurface cache");
break;
case 1073742018:
this.modelIndex = sm.vwr.am.cmi;
var mesh = this.info;
sID = mesh.get (mesh.size () - 2).toString ();
sb = new JU.SB ();
sb.append ("isosurface ID ").append (JU.PT.esc (sID)).append (" model ").append (m.getModelNumberDotted (this.modelIndex)).append (" color ").append (JU.Escape.escapeColor (this.argb)).append (" ").append (JU.PT.esc (this.cacheID)).append (" ").append (JU.PT.esc (sID)).append (" mesh nofill frontonly");
var list = J.adapter.readers.pymol.PyMOLReader.sublistAt (mesh, [2, 0]);
var within = J.adapter.readers.pymol.PyMOLReader.floatAt (list, 11);
list = J.adapter.readers.pymol.PyMOLReader.listAt (list, 12);
if (within > 0) {
var pt = new JU.P3 ();
sb.append (";isosurface slab within ").appendF (within).append (" [ ");
for (var j = list.size () - 3; j >= 0; j -= 3) {
J.adapter.readers.pymol.PyMOLReader.pointAt (list, j, pt);
sb.append (JU.Escape.eP (pt));
}
sb.append (" ]");
}if (doCache && !JU.PT.isOneOf (sID, mepList)) sb.append (";isosurface cache");
sb.append (";set meshScale ").appendI (Clazz.doubleToInt (this.size / 500));
break;
case 134222850:
sb = this.info;
break;
case 1112152078:
sm.loadShape (this.id = 10);
sm.setShapePropertyBs (this.id, "putty", this.info, this.bsAtoms);
break;
}
if (sb != null) {
sm.vwr.runScriptCautiously (sb.toString ());
return;
}if (this.size != -1 || this.rd != null) sm.setShapeSizeBs (this.id, this.size, this.rd, this.bsAtoms);
if (this.argb != 0) sm.setShapePropertyBs (this.id, color, Integer.$valueOf (this.argb), this.bsAtoms);
if (this.translucency > 0) {
sm.setShapePropertyBs (this.id, "translucentLevel", Float.$valueOf (this.translucency), this.bsAtoms);
sm.setShapePropertyBs (this.id, "translucency", "translucent", this.bsAtoms);
} else if (this.colors != null) sm.setShapePropertyBs (this.id, "colors", this.colors, this.bsAtoms);
}, "J.adapter.readers.pymol.PyMOLScene,JM.ModelSet,~S,~B");
Clazz.defineMethod (c$, "getModelIndex",
function (m) {
if (this.bsAtoms == null) return -1;
var iAtom = this.bsAtoms.nextSetBit (0);
if (iAtom >= m.at.length) System.out.println ("PyMOL LOADING ERROR IN MERGE");
return (iAtom < 0 ? -1 : m.at[iAtom].mi);
}, "JM.ModelSet");
Clazz.defineMethod (c$, "setColors",
function (colixes, translucency) {
this.colors = Clazz.newArray (-1, [colixes, Float.$valueOf (translucency)]);
}, "~A,~N");
Clazz.defineMethod (c$, "setSize",
function (size) {
this.size = Clazz.floatToInt (size * 1000);
}, "~N");
});

318
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/pymol/PickleReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.pymol");
Clazz.load (["java.util.Hashtable", "JU.Lst"], "J.adapter.readers.pymol.PickleReader", ["java.lang.Double", "$.Long", "JU.AU", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.vwr = null;
this.binaryDoc = null;
this.stack = null;
this.marks = null;
this.build = null;
this.memo = null;
this.logging = false;
this.id = 0;
this.markCount = 0;
this.filePt = 0;
this.emptyListPt = 0;
this.thisSection = null;
this.inMovie = false;
this.inNames = false;
this.thisName = null;
this.lastMark = 0;
this.retrieveCount = 0;
this.ipt = 0;
this.aTemp = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.pymol, "PickleReader");
Clazz.prepareFields (c$, function () {
this.stack = new JU.Lst ();
this.marks = new JU.Lst ();
this.build = new JU.Lst ();
this.memo = new java.util.Hashtable ();
this.aTemp = Clazz.newByteArray (16, 0);
});
Clazz.makeConstructor (c$,
function (doc, vwr) {
this.binaryDoc = doc;
this.vwr = vwr;
this.stack.ensureCapacity (1000);
}, "javajs.api.GenericBinaryDocument,JV.Viewer");
Clazz.defineMethod (c$, "log",
function (s) {
this.vwr.log (s + "\0");
}, "~S");
Clazz.defineMethod (c$, "getMap",
function (logging) {
this.logging = logging;
var b;
var i;
var mark;
var d;
var o;
var a;
var map;
var l;
this.ipt = 0;
var going = true;
while (going) {
b = this.binaryDoc.readByte ();
this.ipt++;
switch (b) {
case 125:
this.push ( new java.util.Hashtable ());
break;
case 97:
o = this.pop ();
(this.peek ()).addLast (o);
break;
case 101:
l = this.getObjects (this.getMark ());
if (this.inNames && this.markCount == 2) {
var pt = this.binaryDoc.getPosition ();
var l2 = new JU.Lst ();
l2.addLast (Integer.$valueOf (this.filePt));
l2.addLast (Integer.$valueOf (pt - this.filePt));
l.addLast (l2);
}(this.peek ()).addAll (l);
break;
case 71:
d = this.binaryDoc.readDouble ();
this.push (Double.$valueOf (d));
break;
case 74:
i = this.binaryDoc.readIntLE ();
this.push (Integer.$valueOf (i));
break;
case 75:
i = this.binaryDoc.readByte () & 0xff;
this.push (Integer.$valueOf (i));
break;
case 77:
i = (this.binaryDoc.readByte () & 0xff | ((this.binaryDoc.readByte () & 0xff) << 8)) & 0xffff;
this.push (Integer.$valueOf (i));
break;
case 113:
i = this.binaryDoc.readByte ();
this.putMemo (i, false);
break;
case 114:
i = this.binaryDoc.readIntLE ();
this.putMemo (i, true);
break;
case 104:
i = this.binaryDoc.readByte ();
o = this.getMemo (i);
this.push (o == null ? "BINGET" + (++this.id) : o);
break;
case 106:
i = this.binaryDoc.readIntLE ();
o = this.getMemo (i);
this.push (o == null ? "LONG_BINGET" + (++this.id) : o);
break;
case 85:
i = this.binaryDoc.readByte () & 0xff;
a = Clazz.newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
if (this.inNames && this.markCount == 3 && this.lastMark == this.stack.size ()) {
this.thisName = this.bytesToString (a);
this.filePt = this.emptyListPt;
}this.push (a);
break;
case 84:
i = this.binaryDoc.readIntLE ();
a = Clazz.newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
this.push (a);
break;
case 87:
i = this.binaryDoc.readIntLE ();
a = Clazz.newByteArray (i, 0);
this.binaryDoc.readByteArray (a, 0, i);
this.push (a);
break;
case 93:
this.emptyListPt = this.binaryDoc.getPosition () - 1;
this.push ( new JU.Lst ());
break;
case 99:
l = new JU.Lst ();
l.addLast ("global");
l.addLast (this.readStringAsBytes ());
l.addLast (this.readStringAsBytes ());
this.push (l);
break;
case 98:
o = this.pop ();
this.build.addLast (o);
break;
case 40:
this.putMark (this.stack.size ());
break;
case 78:
this.push (null);
break;
case 111:
this.push (this.getObjects (this.getMark ()));
break;
case 115:
o = this.pop ();
var s = this.bytesToString (this.pop ());
(this.peek ()).put (s, o);
break;
case 117:
mark = this.getMark ();
l = this.getObjects (mark);
o = this.peek ();
if (Clazz.instanceOf (o, JU.Lst)) {
for (i = 0; i < l.size (); i++) (o).addLast (l.get (i));
} else {
map = o;
for (i = l.size (); --i >= 0; ) {
o = l.get (i);
map.put (this.bytesToString (l.get (--i)), o);
}
}break;
case 46:
going = false;
break;
case 116:
this.push (this.getObjects (this.getMark ()));
break;
case 73:
s = this.bytesToString (this.readStringAsBytes ());
try {
this.push (Integer.$valueOf (Integer.parseInt (s)));
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
var ll = Long.parseLong (s);
this.push (Integer.$valueOf ((ll & 0xFFFFFFFF)));
} else {
throw e;
}
}
break;
default:
JU.Logger.error ("Pickle reader error: " + b + " " + this.binaryDoc.getPosition ());
}
}
if (logging) this.log ("");
JU.Logger.info ("PyMOL Pickle reader cached " + this.memo.size () + " tokens; retrieved " + this.retrieveCount);
map = this.stack.removeItemAt (0);
if (map.size () == 0) for (i = this.stack.size (); --i >= 0; ) {
o = this.stack.get (i--);
a = this.stack.get (i);
map.put (this.bytesToString (a), o);
}
this.memo = null;
return map;
}, "~B");
Clazz.defineMethod (c$, "bytesToString",
function (o) {
try {
return (JU.AU.isAB (o) ? String.instantialize (o, "UTF-8") : o.toString ());
} catch (e) {
if (Clazz.exceptionOf (e, java.io.UnsupportedEncodingException)) {
return "";
} else {
throw e;
}
}
}, "~O");
Clazz.defineMethod (c$, "putMemo",
function (i, doCheck) {
var o = this.peek ();
if (JU.AU.isAB (o)) o = this.bytesToString (o);
if (Clazz.instanceOf (o, String)) {
if (doCheck && this.markCount >= 6 || this.markCount == 3 && this.inMovie) return;
this.memo.put (Integer.$valueOf (i), o);
}}, "~N,~B");
Clazz.defineMethod (c$, "getMemo",
function (i) {
var o = this.memo.get (Integer.$valueOf (i));
if (o == null) return o;
this.retrieveCount++;
return o;
}, "~N");
Clazz.defineMethod (c$, "getObjects",
function (mark) {
var n = this.stack.size () - mark;
var args = new JU.Lst ();
args.ensureCapacity (n);
for (var i = mark; i < this.stack.size (); ++i) args.addLast (this.stack.get (i));
for (var i = this.stack.size (); --i >= mark; ) this.stack.removeItemAt (i);
return args;
}, "~N");
Clazz.defineMethod (c$, "readStringAsBytes",
function () {
var n = 0;
var a = this.aTemp;
while (true) {
var b = this.binaryDoc.readByte ();
if (b == 0xA) break;
if (n >= a.length) a = this.aTemp = JU.AU.arrayCopyByte (a, a.length * 2);
a[n++] = b;
}
return JU.AU.arrayCopyByte (a, n);
});
Clazz.defineMethod (c$, "putMark",
function (i) {
if (this.logging) this.log ("\n " + Integer.toHexString (this.binaryDoc.getPosition ()) + " [");
this.marks.addLast (Integer.$valueOf (this.lastMark = i));
this.markCount++;
switch (this.markCount) {
case 2:
var o = this.stack.get (i - 2);
if (JU.AU.isAB (o)) {
this.thisSection = this.bytesToString (o);
this.inMovie = "movie".equals (this.thisSection);
this.inNames = "names".equals (this.thisSection);
}break;
default:
break;
}
}, "~N");
Clazz.defineMethod (c$, "getMark",
function () {
return this.marks.removeItemAt (--this.markCount).intValue ();
});
Clazz.defineMethod (c$, "push",
function (o) {
if (this.logging && (Clazz.instanceOf (o, String) || Clazz.instanceOf (o, Double) || Clazz.instanceOf (o, Integer))) this.log ((Clazz.instanceOf (o, String) ? "'" + o + "'" : o) + ", ");
this.stack.addLast (o);
}, "~O");
Clazz.defineMethod (c$, "peek",
function () {
return this.stack.get (this.stack.size () - 1);
});
Clazz.defineMethod (c$, "pop",
function () {
return this.stack.removeItemAt (this.stack.size () - 1);
});
Clazz.defineStatics (c$,
"APPEND", 97,
"APPENDS", 101,
"BINFLOAT", 71,
"BININT", 74,
"BININT1", 75,
"BININT2", 77,
"BINPUT", 113,
"BINSTRING", 84,
"BINUNICODE", 87,
"BUILD", 98,
"EMPTY_DICT", 125,
"EMPTY_LIST", 93,
"GLOBAL", 99,
"LONG_BINPUT", 114,
"MARK", 40,
"NONE", 78,
"OBJ", 111,
"SETITEM", 115,
"SETITEMS", 117,
"SHORT_BINSTRING", 85,
"STOP", 46,
"BINGET", 104,
"LONG_BINGET", 106,
"TUPLE", 116,
"INT", 73);
});

1023
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Clazz.declarePackage ("J.adapter.readers.pymol");
Clazz.load (["java.util.Hashtable", "JU.BS"], "J.adapter.readers.pymol.PyMOLGroup", null, function () {
c$ = Clazz.decorateAsClass (function () {
this.name = null;
this.objectNameID = null;
this.list = null;
this.object = null;
this.visible = true;
this.occluded = false;
this.bsAtoms = null;
this.firstAtom = 0;
this.type = 0;
this.parent = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.pymol, "PyMOLGroup");
Clazz.prepareFields (c$, function () {
this.list = new java.util.Hashtable ();
this.bsAtoms = new JU.BS ();
});
Clazz.makeConstructor (c$,
function (name) {
this.name = name;
}, "~S");
Clazz.defineMethod (c$, "addList",
function (child) {
var group = this.list.get (child.name);
if (group != null) return;
this.list.put (child.name, child);
child.parent = this;
}, "J.adapter.readers.pymol.PyMOLGroup");
Clazz.defineMethod (c$, "set",
function () {
if (this.parent != null) return;
});
Clazz.defineMethod (c$, "addGroupAtoms",
function (bs) {
this.bsAtoms.or (bs);
if (this.parent != null) this.parent.addGroupAtoms (this.bsAtoms);
}, "JU.BS");
Clazz.overrideMethod (c$, "toString",
function () {
return this.name;
});
});

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250
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.SlaterReader"], "J.adapter.readers.quantum.AdfReader", ["java.lang.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.api.JmolAdapter", "J.quantum.SlaterData", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.htSymmetries = null;
this.vSymmetries = null;
this.energy = null;
this.nXX = 0;
this.symLine = null;
if (!Clazz.isClassDefined ("J.adapter.readers.quantum.AdfReader.SymmetryData")) {
J.adapter.readers.quantum.AdfReader.$AdfReader$SymmetryData$ ();
}
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "AdfReader", J.adapter.readers.quantum.SlaterReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("Irreducible Representations, including subspecies") >= 0) {
this.readSymmetries ();
return true;
}if (this.line.indexOf ("S F O s *** (Symmetrized Fragment Orbitals) ***") >= 0) {
this.readSlaterBasis ();
return true;
}if (this.line.indexOf (" Coordinates (Cartesian, in Input Orientation)") >= 0 || this.line.indexOf ("G E O M E T R Y ***") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.readCoordinates ();
return true;
}if (this.line.indexOf (" ====== Eigenvectors (rows) in BAS representation") >= 0) {
if (this.doReadMolecularOrbitals) this.readMolecularOrbitals (JU.PT.getTokens (this.symLine)[1]);
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("Energy:") >= 0) {
var tokens = JU.PT.getTokens (this.line.substring (this.line.indexOf ("Energy:")));
this.energy = tokens[1];
return true;
}if (this.line.indexOf ("Vibrations") >= 0) {
this.readFrequencies ();
return true;
}if (this.line.indexOf (" === ") >= 0) {
this.symLine = this.line;
return true;
}if (this.line.indexOf (" ====== Eigenvectors (rows) in BAS representation") >= 0) {
this.readMolecularOrbitals (JU.PT.getTokens (this.symLine)[1]);
return true;
}return true;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
var isGeometry = (this.line.indexOf ("G E O M E T R Y") >= 0);
this.asc.newAtomSet ();
this.asc.setAtomSetName ("" + this.energy);
this.discardLinesUntilContains ("----");
var pt0 = (isGeometry ? 2 : 5);
this.nXX = 0;
var tokens;
while (this.rd () != null && !this.line.startsWith (" -----")) {
tokens = this.getTokens ();
if (tokens.length < 5) break;
var symbol = tokens[1];
var name = null;
if (symbol.indexOf (".") >= 0) {
name = symbol;
symbol = symbol.substring (0, symbol.indexOf ("."));
}if (J.api.JmolAdapter.getElementNumber (symbol) < 1) this.nXX++;
else this.addAtomXYZSymName (tokens, pt0, symbol, name);
}
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
this.rd ();
while (this.rd () != null) {
while (this.rd () != null && this.line.indexOf (".") < 0 && this.line.indexOf ("====") < 0) {
}
if (this.line == null || this.line.indexOf (".") < 0) return;
var frequencies = this.getTokens ();
this.rd ();
var iAtom0 = this.asc.ac;
var ac = this.asc.getLastAtomSetAtomCount ();
var frequencyCount = frequencies.length;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneLastAtomSet ();
this.asc.setAtomSetFrequency (null, null, frequencies[i], null);
}
this.readLines (this.nXX);
this.fillFrequencyData (iAtom0, ac, ac, ignore, true, 0, 0, null, 0);
}
});
Clazz.defineMethod (c$, "readSymmetries",
function () {
this.vSymmetries = new JU.Lst ();
this.htSymmetries = new java.util.Hashtable ();
this.rd ();
var index = 0;
var syms = "";
while (this.rd () != null && this.line.length > 1) syms += this.line;
var tokens = JU.PT.getTokens (syms);
for (var i = 0; i < tokens.length; i++) {
var sd = Clazz.innerTypeInstance (J.adapter.readers.quantum.AdfReader.SymmetryData, this, null, index++, tokens[i]);
this.htSymmetries.put (tokens[i], sd);
this.vSymmetries.addLast (sd);
}
});
Clazz.defineMethod (c$, "readSlaterBasis",
function () {
if (this.vSymmetries == null) return;
var nBF = 0;
for (var i = 0; i < this.vSymmetries.size (); i++) {
var sd = this.vSymmetries.get (i);
JU.Logger.info (sd.sym);
this.discardLinesUntilContains ("=== " + sd.sym + " ===");
if (this.line == null) {
JU.Logger.error ("Symmetry slater basis section not found: " + sd.sym);
return;
}sd.nSFO = this.parseIntAt (this.rd (), 15);
sd.nBF = this.parseIntAt (this.rd (), 75);
var funcList = "";
while (this.rd () != null && this.line.length > 1) funcList += this.line;
var tokens = JU.PT.getTokens (funcList);
if (tokens.length != sd.nBF) return;
sd.basisFunctions = Clazz.newIntArray (tokens.length, 0);
for (var j = tokens.length; --j >= 0; ) {
var n = this.parseIntStr (tokens[j]);
if (n > nBF) nBF = n;
sd.basisFunctions[j] = n - 1;
}
}
this.slaterArray = new Array (nBF);
this.discardLinesUntilContains ("(power of)");
this.readLines (2);
while (this.rd () != null && this.line.length > 3 && this.line.charAt (3) == ' ') {
var data = this.line;
while (this.rd ().indexOf ("---") < 0) data += this.line;
var tokens = JU.PT.getTokens (data);
var nAtoms = tokens.length - 1;
var atomList = Clazz.newIntArray (nAtoms, 0);
for (var i = 1; i <= nAtoms; i++) atomList[i - 1] = this.parseIntStr (tokens[i]) - 1;
this.rd ();
while (this.line.length >= 10) {
data = this.line;
while (this.rd ().length > 35 && this.line.substring (0, 35).trim ().length == 0) data += this.line;
tokens = JU.PT.getTokens (data);
var isCore = tokens[0].equals ("Core");
var pt = (isCore ? 1 : 0);
var x = this.parseIntStr (tokens[pt++]);
var y = this.parseIntStr (tokens[pt++]);
var z = this.parseIntStr (tokens[pt++]);
var r = this.parseIntStr (tokens[pt++]);
var zeta = this.parseFloatStr (tokens[pt++]);
for (var i = 0; i < nAtoms; i++) {
var ptBF = this.parseIntStr (tokens[pt++]) - 1;
this.slaterArray[ptBF] = new J.quantum.SlaterData (atomList[i], x, y, z, r, zeta, 1);
this.slaterArray[ptBF].index = ptBF;
}
}
}
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function (sym) {
var sd = this.htSymmetries.get (sym);
if (sd == null) return;
var ptSym = sd.index;
var isLast = (ptSym == this.vSymmetries.size () - 1);
var n = 0;
var nBF = this.slaterArray.length;
sd.coefs = Clazz.newFloatArray (sd.nSFO, nBF, 0);
while (n < sd.nBF) {
this.rd ();
var nLine = JU.PT.getTokens (this.rd ()).length;
this.rd ();
sd.mos = JU.AU.createArrayOfHashtable (sd.nSFO);
var data = new Array (sd.nSFO);
this.fillDataBlock (data, 0);
for (var j = 1; j < nLine; j++) {
var pt = sd.basisFunctions[n++];
for (var i = 0; i < sd.nSFO; i++) sd.coefs[i][pt] = this.parseFloatStr (data[i][j]);
}
}
for (var i = 0; i < sd.nSFO; i++) {
var mo = new java.util.Hashtable ();
mo.put ("coefficients", sd.coefs[i]);
mo.put ("id", sym + " " + (i + 1));
sd.mos[i] = mo;
}
if (!isLast) return;
var nSym = this.htSymmetries.size ();
this.discardLinesUntilContains (nSym == 1 ? "Orbital Energies, per Irrep" : "Orbital Energies, all Irreps");
this.readLines (4);
var pt = (nSym == 1 ? 0 : 1);
if (nSym == 1) sym = this.rd ().trim ();
while (this.rd () != null && this.line.length > 10) {
this.line = this.line.$replace ('(', ' ').$replace (')', ' ');
var tokens = this.getTokens ();
var len = tokens.length;
if (nSym > 1) sym = tokens[0];
var moPt = this.parseIntStr (tokens[pt]);
var occ = this.parseFloatStr (tokens[len - 4 + pt]);
var energy = this.parseFloatStr (tokens[len - 2 + pt]);
this.addMo (sym, moPt, occ, energy);
}
var iAtom0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0; i < nBF; i++) this.slaterArray[i].atomNo += iAtom0 + 1;
this.setSlaters (true, true);
this.sortOrbitals ();
this.setMOs ("eV");
}, "~S");
Clazz.defineMethod (c$, "addMo",
function (sym, moPt, occ, energy) {
var sd = this.htSymmetries.get (sym);
if (sd == null) {
for (var entry, $entry = this.htSymmetries.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) if (entry.getKey ().startsWith (sym + ":")) {
sd = entry.getValue ();
break;
}
if (sd == null) return;
}var mo = sd.mos[moPt - 1];
mo.put ("occupancy", Float.$valueOf (occ > 2 ? 2 : occ));
mo.put ("energy", Float.$valueOf (energy));
mo.put ("symmetry", sd.sym + "_" + moPt);
this.setMO (mo);
}, "~S,~N,~N,~N");
c$.$AdfReader$SymmetryData$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
this.index = 0;
this.sym = null;
this.nSFO = 0;
this.nBF = 0;
this.coefs = null;
this.mos = null;
this.basisFunctions = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum.AdfReader, "SymmetryData");
Clazz.makeConstructor (c$,
function (a, b) {
JU.Logger.info ("ADF reader creating SymmetryData " + b + " " + a);
this.index = a;
this.sym = b;
}, "~N,~S");
c$ = Clazz.p0p ();
};
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "java.util.Hashtable", "JU.Lst"], "J.adapter.readers.quantum.BasisFunctionReader", ["java.util.Arrays", "JU.PT", "J.quantum.QS", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.shells = null;
this.moData = null;
this.orbitals = null;
this.nOrbitals = 0;
this.ignoreMOs = false;
this.alphaBeta = "";
this.dfCoefMaps = null;
this.filterTokens = null;
this.filterIsNot = false;
this.spin = null;
if (!Clazz.isClassDefined ("J.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter")) {
J.adapter.readers.quantum.BasisFunctionReader.$BasisFunctionReader$MOEnergySorter$ ();
}
this.orbitalMaps = null;
this.nCoef = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "BasisFunctionReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.moData = new java.util.Hashtable ();
this.orbitals = new JU.Lst ();
this.orbitalMaps = new java.util.Hashtable ();
});
Clazz.defineMethod (c$, "filterMO",
function () {
var isHeader = (this.line.indexOf ('\n') == 0);
if (!isHeader && !this.doReadMolecularOrbitals) return false;
var isOK = true;
this.line += " " + this.alphaBeta;
var ucline = this.line.toUpperCase ();
if (this.filter != null) {
var nOK = 0;
if (this.filterTokens == null) {
this.filterIsNot = (this.filter.indexOf ("!") >= 0);
this.filterTokens = JU.PT.getTokens (this.filter.$replace ('!', ' ').$replace (',', ' ').$replace (';', ' '));
}for (var i = 0; i < this.filterTokens.length; i++) if (ucline.indexOf (this.filterTokens[i]) >= 0) {
if (!this.filterIsNot) {
nOK = this.filterTokens.length;
break;
}} else if (this.filterIsNot) {
nOK++;
}
isOK = (nOK == this.filterTokens.length);
if (!isHeader) JU.Logger.info ("filter MOs: " + isOK + " for \"" + this.line + "\"");
}this.spin = (ucline.indexOf ("ALPHA") >= 0 ? "alpha" : ucline.indexOf ("BETA") >= 0 ? "beta" : null);
return isOK;
});
Clazz.defineMethod (c$, "setMO",
function (mo) {
if (this.dfCoefMaps != null) mo.put ("dfCoefMaps", this.dfCoefMaps);
this.orbitals.addLast (mo);
mo.put ("index", Integer.$valueOf (this.orbitals.size ()));
if (this.spin != null) mo.put ("spin", this.spin);
}, "java.util.Map");
Clazz.defineMethod (c$, "getDFMap",
function (shell, fileList, shellType, jmolList, minLength) {
this.orbitalMaps.put (shell, fileList);
this.moData.put ("orbitalMaps", this.orbitalMaps);
if (fileList.equals (jmolList)) return true;
this.getDfCoefMaps ();
var isOK = J.quantum.QS.createDFMap (this.dfCoefMaps[shellType], fileList, jmolList, minLength);
if (!isOK) JU.Logger.error ("Disabling orbitals of type " + shellType + " -- Cannot read orbital order for: " + fileList + "\n expecting: " + jmolList);
return isOK;
}, "~S,~S,~N,~S,~N");
Clazz.defineMethod (c$, "getDfCoefMaps",
function () {
return (this.dfCoefMaps == null ? (this.dfCoefMaps = J.quantum.QS.getNewDfCoefMap ()) : this.dfCoefMaps);
});
c$.canonicalizeQuantumSubshellTag = Clazz.defineMethod (c$, "canonicalizeQuantumSubshellTag",
function (tag) {
var firstChar = tag.charAt (0);
if (firstChar == 'X' || firstChar == 'Y' || firstChar == 'Z') {
var sorted = tag.toCharArray ();
java.util.Arrays.sort (sorted);
return String.instantialize (sorted);
}return tag;
}, "~S");
Clazz.defineMethod (c$, "fixSlaterTypes",
function (typeOld, typeNew) {
if (this.shells == null) return 0;
this.nCoef = 0;
for (var i = this.shells.size (); --i >= 0; ) {
var slater = this.shells.get (i);
if (slater[1] == typeOld) slater[1] = typeNew;
var m = this.getDfCoefMaps ()[slater[1]].length;
this.nCoef += m;
}
return this.nCoef;
}, "~N,~N");
c$.getQuantumShellTagIDSpherical = Clazz.defineMethod (c$, "getQuantumShellTagIDSpherical",
function (tag) {
return J.quantum.QS.getQuantumShellTagIDSpherical (tag);
}, "~S");
c$.getQuantumShellTagID = Clazz.defineMethod (c$, "getQuantumShellTagID",
function (tag) {
return J.quantum.QS.getQuantumShellTagID (tag);
}, "~S");
c$.getQuantumShellTag = Clazz.defineMethod (c$, "getQuantumShellTag",
function (id) {
return J.quantum.QS.getQuantumShellTag (id);
}, "~N");
Clazz.overrideMethod (c$, "discardPreviousAtoms",
function () {
this.asc.discardPreviousAtoms ();
this.moData.remove ("mos");
this.orbitals.clear ();
});
Clazz.defineMethod (c$, "clearOrbitals",
function () {
this.orbitals = new JU.Lst ();
this.moData = new java.util.Hashtable ();
this.alphaBeta = "";
});
c$.$BasisFunctionReader$MOEnergySorter$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum.BasisFunctionReader, "MOEnergySorter", null, java.util.Comparator);
Clazz.overrideMethod (c$, "compare",
function (a, b) {
var c = ((a).get ("energy")).floatValue ();
var d = ((b).get ("energy")).floatValue ();
return (c < d ? -1 : c > d ? 1 : 0);
}, "~O,~O");
c$ = Clazz.p0p ();
};
});

437
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/quantum/CsfReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MopacSlaterReader", "java.util.Hashtable"], "J.adapter.readers.quantum.CsfReader", ["java.lang.Float", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.Atom", "$.Bond", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.nAtoms = 0;
this.strAtomicNumbers = "";
this.fieldCount = 0;
this.nVibrations = 0;
this.nGaussians = 0;
this.nSlaters = 0;
this.htBonds = null;
this.propertyItemCounts = null;
this.fieldTypes = null;
this.connectors = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "CsfReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.prepareFields (c$, function () {
this.propertyItemCounts = new java.util.Hashtable ();
this.fieldTypes = Clazz.newIntArray (100, 0);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.equals ("local_transform")) {
this.processLocalTransform ();
return true;
}if (this.line.startsWith ("object_class")) {
if (this.line.equals ("object_class connector")) {
this.processConnectorObject ();
return false;
}if (this.line.equals ("object_class atom")) {
this.processAtomObject ();
return false;
}if (this.line.equals ("object_class bond")) {
this.processBondObject ();
return false;
}if (this.line.equals ("object_class vibrational_level")) {
this.processVibrationObject ();
return false;
}if (this.line.equals ("object_class mol_orbital")) {
this.processMolecularOrbitalObject ();
return false;
}if (this.line.equals ("object_class sto_basis_fxn")) {
this.processBasisObject ("sto");
return false;
}if (this.line.equals ("object_class gto_basis_fxn")) {
this.processBasisObject ("gto");
return false;
}}return true;
});
Clazz.defineMethod (c$, "processLocalTransform",
function () {
var tokens = JU.PT.getTokens (this.rd () + " " + this.rd () + " " + this.rd () + " " + this.rd ());
this.setTransform (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[4]), this.parseFloatStr (tokens[5]), this.parseFloatStr (tokens[6]), this.parseFloatStr (tokens[8]), this.parseFloatStr (tokens[9]), this.parseFloatStr (tokens[10]));
});
Clazz.defineMethod (c$, "getPropertyCount",
function (what) {
var count = this.propertyItemCounts.get (what);
return (what.equals ("ID") ? 1 : count == null ? 0 : count.intValue ());
}, "~S");
Clazz.defineMethod (c$, "parseLineParameters",
function (fields, fieldMap) {
for (var i = 0; i < this.fieldCount; i++) this.fieldTypes[i] = 0;
this.fieldCount = -1;
if (this.line == null || this.line.startsWith ("property_flags:")) this.rd ();
if (this.line == null || this.line.startsWith ("object_class")) return this.fieldCount;
var tokens = new Array (0);
while (this.line != null) {
tokens = this.getTokens ();
if (this.line.indexOf ("property ") == 0) this.propertyItemCounts.put (tokens[1], Integer.$valueOf ((tokens[6].equals ("STRING") ? 1 : this.parseIntStr (tokens[5]))));
else if (this.line.indexOf ("ID") == 0) break;
this.rd ();
}
for (var ipt = 0, fpt = 0; ipt < tokens.length; ipt++) {
var field = tokens[ipt];
for (var i = fields.length; --i >= 0; ) if (field.equals (fields[i])) {
this.fieldTypes[fpt] = fieldMap[i];
this.fieldCount = fpt + 1;
break;
}
fpt += this.getPropertyCount (field);
}
return this.fieldCount;
}, "~A,~A");
Clazz.defineMethod (c$, "fillCsfArray",
function (property, tokens, i0, f, isInteger) {
var n = this.getPropertyCount (property);
var ioffset = i0;
for (var i = 0; i < n; i++) {
var ipt = ioffset + i;
if (ipt == tokens.length) {
tokens = JU.PT.getTokens (this.rd ());
ioffset -= ipt - i0;
ipt = i0;
}if (isInteger) (f)[i] = this.parseIntStr (tokens[ipt]);
else (f)[i] = this.parseFloatStr (tokens[ipt]);
}
}, "~S,~A,~N,~O,~B");
Clazz.defineMethod (c$, "processConnectorObject",
function () {
this.connectors = new java.util.Hashtable ();
this.rd ();
this.parseLineParameters (J.adapter.readers.quantum.CsfReader.connectorFields, J.adapter.readers.quantum.CsfReader.connectorFieldMap);
out : for (; this.rd () != null; ) {
if (this.line.startsWith ("property_flags:")) break;
var thisAtomID = null;
var thisBondID = null;
var tokens = this.getTokens ();
var field2 = "";
var isVibration = false;
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case 1:
if (!field.equals ("atom")) continue out;
break;
case 3:
field2 = field;
if (field.equals ("sto_basis_fxn")) this.nSlaters++;
else if (field.equals ("gto_basis_fxn")) this.nGaussians++;
else if (field.equals ("vibrational_level")) isVibration = true;
else if (!field.equals ("bond")) continue out;
break;
case 2:
thisAtomID = field;
break;
case 4:
thisBondID = field2 + field;
if (isVibration) this.nVibrations = Math.max (this.nVibrations, this.parseIntStr (field));
break;
default:
}
}
if (thisAtomID != null && thisBondID != null) {
if (this.connectors.containsKey (thisBondID)) {
var connect = this.connectors.get (thisBondID);
connect[1] = thisAtomID;
if (this.htBonds != null) this.setBond (this.htBonds.get (thisBondID), connect);
} else {
var connect = new Array (2);
connect[0] = thisAtomID;
this.connectors.put (thisBondID, connect);
}}}
});
Clazz.defineMethod (c$, "setBond",
function (bond, connect) {
bond.atomIndex1 = this.asc.getAtomIndex (connect[0]);
bond.atomIndex2 = this.asc.getAtomIndex (connect[1]);
this.asc.addBond (bond);
}, "J.adapter.smarter.Bond,~A");
Clazz.defineMethod (c$, "processAtomObject",
function () {
this.rd ();
this.parseLineParameters (J.adapter.readers.quantum.CsfReader.atomFields, J.adapter.readers.quantum.CsfReader.atomFieldMap);
this.nAtoms = 0;
for (; this.rd () != null; ) {
if (this.line.startsWith ("property_flags:")) break;
var tokens = this.getTokens ();
var atom = new J.adapter.smarter.Atom ();
var field;
for (var i = 0; i < this.fieldCount; i++) {
var type = this.fieldTypes[i];
if (type == 0) continue;
if ((field = tokens[i]) == null) JU.Logger.warn ("field == null in " + this.line);
switch (type) {
case -1:
atom.atomSerial = JU.PT.parseInt (field);
break;
case 1:
atom.elementSymbol = field;
atom.atomName = field + atom.atomSerial;
break;
case 2:
this.strAtomicNumbers += field + " ";
break;
case 3:
atom.formalCharge = this.parseIntStr (field);
break;
case 5:
atom.partialCharge = this.parseFloatStr (field);
break;
case 4:
this.setAtomCoordTokens (atom, tokens, i);
i += 2;
break;
}
}
if (Float.isNaN (atom.x) || Float.isNaN (atom.y) || Float.isNaN (atom.z)) {
JU.Logger.warn ("atom " + atom.atomName + " has invalid/unknown coordinates");
} else {
this.nAtoms++;
this.asc.addAtomWithMappedSerialNumber (atom);
}}
});
Clazz.defineMethod (c$, "processBondObject",
function () {
this.rd ();
this.parseLineParameters (J.adapter.readers.quantum.CsfReader.bondFields, J.adapter.readers.quantum.CsfReader.bondFieldMap);
for (; this.rd () != null; ) {
if (this.line.startsWith ("property_flags:")) break;
var thisBondID = null;
var tokens = this.getTokens ();
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
thisBondID = "bond" + field;
break;
case 1:
var order = 1;
if (field.equals ("single")) order = 1;
else if (field.equals ("double")) order = 2;
else if (field.equals ("triple")) order = 3;
else JU.Logger.warn ("unknown CSF bond order: " + field);
var bond = new J.adapter.smarter.Bond (-1, -1, 1);
bond.order = order;
if (this.connectors == null) {
if (this.htBonds == null) this.htBonds = new java.util.Hashtable ();
this.htBonds.put (thisBondID, bond);
} else {
this.setBond (bond, this.connectors.get (thisBondID));
}break;
}
}
}
});
Clazz.defineMethod (c$, "processVibrationObject",
function () {
var vibData = Clazz.newFloatArray (this.nVibrations, this.nAtoms * 3, 0);
var energies = new Array (this.nVibrations);
this.rd ();
while (this.line != null && this.parseLineParameters (J.adapter.readers.quantum.CsfReader.vibFields, J.adapter.readers.quantum.CsfReader.vibFieldMap) > 0) {
while (this.rd () != null && !this.line.startsWith ("property_flags:")) {
var tokens = this.getTokens ();
var thisvib = -1;
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
thisvib = this.parseIntStr (field) - 1;
break;
case 1:
this.fillCsfArray ("normalMode", tokens, i, vibData[thisvib], false);
break;
case 2:
energies[thisvib] = field;
break;
}
}
}
}
for (var i = 0; i < this.nVibrations; i++) {
if (!this.doGetVibration (i + 1)) continue;
this.asc.cloneAtomSetWithBonds (false);
this.asc.setAtomSetFrequency (null, null, energies[i], null);
var ipt = 0;
var baseAtom = this.nAtoms * (i + 1);
for (var iAtom = 0; iAtom < this.nAtoms; iAtom++) this.asc.addVibrationVector (baseAtom + iAtom, vibData[i][ipt++], vibData[i][ipt++], vibData[i][ipt++]);
}
});
Clazz.defineMethod (c$, "processMolecularOrbitalObject",
function () {
if (this.nSlaters == 0 && this.nGaussians == 0 || !this.doReadMolecularOrbitals) {
this.rd ();
return;
}this.nOrbitals = (this.nSlaters + this.nGaussians);
JU.Logger.info ("Reading CSF data for " + this.nOrbitals + " molecular orbitals");
var energy = Clazz.newFloatArray (this.nOrbitals, 0);
var occupancy = Clazz.newFloatArray (this.nOrbitals, 0);
var list = Clazz.newFloatArray (this.nOrbitals, this.nOrbitals, 0);
var listCompressed = null;
var coefIndices = null;
var ipt = 0;
var isCompressed = false;
this.rd ();
while (this.line != null && this.parseLineParameters (J.adapter.readers.quantum.CsfReader.moFields, J.adapter.readers.quantum.CsfReader.moFieldMap) > 0) while (this.rd () != null && !this.line.startsWith ("property_flags:")) {
var tokens = this.getTokens ();
for (var i = 0; i < this.fieldCount; ++i) {
switch (this.fieldTypes[i]) {
case -1:
ipt = this.parseIntStr (tokens[i]) - 1;
break;
case 1:
energy[ipt] = this.parseFloatStr (tokens[i]);
break;
case 2:
occupancy[ipt] = this.parseFloatStr (tokens[i]);
break;
case 3:
this.fillCsfArray ("eig_vec", tokens, i, list[ipt], false);
break;
case 4:
isCompressed = true;
if (listCompressed == null) listCompressed = Clazz.newFloatArray (this.nOrbitals, this.nOrbitals, 0);
this.fillCsfArray ("eig_vec_compressed", tokens, i, listCompressed[ipt], false);
break;
case 5:
if (coefIndices == null) coefIndices = Clazz.newIntArray (this.nOrbitals, this.nOrbitals, 0);
this.fillCsfArray ("coef_indices", tokens, i, coefIndices[ipt], true);
break;
}
}
}
for (var iMo = 0; iMo < this.nOrbitals; iMo++) {
if (isCompressed) {
for (var i = 0; i < coefIndices[iMo].length; i++) {
var pt = coefIndices[iMo][i] - 1;
if (pt < 0) break;
list[iMo][pt] = listCompressed[iMo][i];
}
}for (var i = 0; i < this.nOrbitals; i++) if (Math.abs (list[iMo][i]) < 1.0E-4) list[iMo][i] = 0;
var mo = new java.util.Hashtable ();
mo.put ("energy", Float.$valueOf (energy[iMo]));
mo.put ("occupancy", Float.$valueOf (occupancy[iMo]));
mo.put ("coefficients", list[iMo]);
this.setMO (mo);
}
this.setMOs ("eV");
});
Clazz.defineMethod (c$, "processBasisObject",
function (sto_gto) {
var atomNos = JU.PT.getTokens (this.strAtomicNumbers);
this.atomicNumbers = Clazz.newIntArray (atomNos.length, 0);
for (var i = 0; i < this.atomicNumbers.length; i++) this.atomicNumbers[i] = this.parseIntStr (atomNos[i]);
this.nOrbitals = (this.nSlaters + this.nGaussians);
var isGaussian = (sto_gto.equals ("gto"));
var zetas = JU.AU.newFloat2 (this.nOrbitals);
var contractionCoefs = null;
var types = new Array (this.nOrbitals);
var shells = Clazz.newIntArray (this.nOrbitals, 0);
var nZetas = 0;
this.rd ();
while (this.line != null && this.parseLineParameters (J.adapter.readers.quantum.CsfReader.moFields, J.adapter.readers.quantum.CsfReader.moFieldMap) > 0) {
if (nZetas == 0) nZetas = this.getPropertyCount (sto_gto + "_exp");
var ipt = 0;
while (this.rd () != null && !this.line.startsWith ("property_flags:")) {
var tokens = this.getTokens ();
for (var i = 0; i < this.fieldCount; ++i) {
var field = tokens[i];
switch (this.fieldTypes[i]) {
case -1:
ipt = this.parseIntStr (field) - 1;
break;
case 6:
types[ipt] = field;
break;
case 7:
case 9:
zetas[ipt] = Clazz.newFloatArray (nZetas, 0);
this.fillCsfArray (sto_gto + "_exp", tokens, i, zetas[ipt], false);
break;
case 10:
shells[ipt] = this.parseIntStr (field);
break;
case 8:
if (contractionCoefs == null) contractionCoefs = Clazz.newFloatArray (this.nOrbitals, nZetas, 0);
this.fillCsfArray ("contractions", tokens, i, contractionCoefs[ipt], false);
}
}
}
}
if (isGaussian) {
var sdata = new JU.Lst ();
var gdata = new JU.Lst ();
var iShell = 0;
var gaussianCount = 0;
for (var ipt = 0; ipt < this.nGaussians; ipt++) {
if (shells[ipt] != iShell) {
iShell = shells[ipt];
var slater = Clazz.newIntArray (4, 0);
var iAtom = this.asc.getAtomIndex (this.connectors.get (sto_gto + "_basis_fxn" + (ipt + 1))[0]);
slater[0] = iAtom + 1;
slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (types[ipt].substring (0, 1));
var nZ = 0;
while (++nZ < nZetas && zetas[ipt][nZ] != 0) {
}
slater[2] = gaussianCount;
slater[3] = nZ;
sdata.addLast (slater);
gaussianCount += nZ;
for (var i = 0; i < nZ; i++) gdata.addLast ( Clazz.newFloatArray (-1, [zetas[ipt][i], contractionCoefs[ipt][i]]));
}}
var garray = JU.AU.newFloat2 (gaussianCount);
for (var i = 0; i < gaussianCount; i++) garray[i] = gdata.get (i);
this.moData.put ("shells", sdata);
this.moData.put ("gaussians", garray);
} else {
for (var ipt = 0; ipt < this.nSlaters; ipt++) {
var iAtom = this.asc.getAtomIndex (this.connectors.get (sto_gto + "_basis_fxn" + (ipt + 1))[0]);
for (var i = 0; i < nZetas; i++) {
if (zetas[ipt][i] == 0) break;
this.createSphericalSlaterByType (iAtom, this.atomicNumbers[iAtom], types[ipt], zetas[ipt][i] * (i == 0 ? 1 : -1), contractionCoefs == null ? 1 : contractionCoefs[ipt][i]);
}
}
this.setSlaters (true, false);
}}, "~S");
Clazz.defineStatics (c$,
"objCls1", 1,
"objID1", 2,
"objCls2", 3,
"objID2", 4,
"connectorFields", Clazz.newArray (-1, ["objCls1", "objID1", "objCls2", "objID2"]),
"connectorFieldMap", Clazz.newByteArray (-1, [1, 2, 3, 4]),
"ID", -1,
"SYM", 1,
"ANUM", 2,
"CHRG", 3,
"XYZ", 4,
"PCHRG", 5,
"atomFields", Clazz.newArray (-1, ["ID", "sym", "anum", "chrg", "xyz_coordinates", "pchrg"]),
"atomFieldMap", Clazz.newByteArray (-1, [-1, 1, 2, 3, 4, 5]),
"BTYPE", 1,
"bondFields", Clazz.newArray (-1, ["ID", "type"]),
"bondFieldMap", Clazz.newByteArray (-1, [-1, 1]),
"NORMAL_MODE", 1,
"VIB_ENERGY", 2,
"DIPOLE", 3,
"vibFields", Clazz.newArray (-1, ["ID", "normalMode", "Energy", "transitionDipole"]),
"vibFieldMap", Clazz.newByteArray (-1, [-1, 1, 2, 3]),
"EIG_VAL", 1,
"MO_OCC", 2,
"EIG_VEC", 3,
"EIG_VEC_COMPRESSED", 4,
"COEF_INDICES", 5,
"BFXN_ANGL", 6,
"STO_EXP", 7,
"CONTRACTIONS", 8,
"GTO_EXP", 9,
"SHELL", 10,
"moFields", Clazz.newArray (-1, ["ID", "eig_val", "mo_occ", "eig_vec", "eig_vec_compressed", "coef_indices", "bfxn_ang", "sto_exp", "contractions", "gto_exp", "shell"]),
"moFieldMap", Clazz.newByteArray (-1, [-1, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]));
});

172
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/quantum/DgridReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.SlaterReader", "java.util.Hashtable"], "J.adapter.readers.quantum.DgridReader", ["java.lang.Float", "JU.PT", "$.SB", "J.quantum.SlaterData", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.title = null;
this.htExponents = null;
this.htFuncMap = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "DgridReader", J.adapter.readers.quantum.SlaterReader);
Clazz.prepareFields (c$, function () {
this.htExponents = new java.util.Hashtable ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf (":title") == 0) {
this.title = this.rd ().substring (2);
return true;
}if (this.line.indexOf ("basis: CARTESIAN STO") >= 0) {
this.readSlaterBasis ();
return true;
}if (this.line.indexOf (":atom") == 0) {
this.readCoordinates ();
return true;
}if (this.line.indexOf (" MO DATA ") >= 0) {
if (this.doReadMolecularOrbitals) this.readMolecularOrbitals ();
return true;
}return true;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
this.asc.newAtomSet ();
this.asc.setAtomSetName (this.title);
this.discardLinesUntilContains ("----");
while (this.rd () != null && !this.line.startsWith (":-----")) {
var tokens = this.getTokens ();
if (tokens.length < 5) break;
this.setAtomCoordScaled (null, tokens, 2, 0.5291772).elementSymbol = tokens[0];
}
});
Clazz.defineMethod (c$, "readSlaterBasis",
function () {
this.discardLinesUntilContains (":-");
var ch = 'a';
while (this.rd () != null && this.line.indexOf (":-") < 0) {
var atomSymbol = this.line.substring (3, 6).trim ();
var xyz = this.line.substring (19, 21);
var code = atomSymbol + xyz;
if (this.htExponents.get (code) == null) {
ch = 'a';
} else {
code += "_" + ($c$ = ch, ch = String.fromCharCode (ch.charCodeAt (0) + 1), $c$);
}var exp = this.line.substring (34);
this.htExponents.put (code, Float.$valueOf (this.parseFloatStr (exp)));
}
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function () {
this.htFuncMap = new java.util.Hashtable ();
this.readLines (3);
while (this.line != null && this.line.indexOf (":") != 0) {
this.discardLinesUntilContains ("sym: ");
var symmetry = this.line.substring (4, 10).trim ();
if (symmetry.indexOf ("_FC") >= 0) break;
var data = new JU.SB ();
data.append (this.line.substring (15));
while (this.rd () != null && this.line.length >= 15) data.append (this.line);
var tokens = JU.PT.getTokens (data.toString ());
var nFuncs = Clazz.doubleToInt (tokens.length / 2);
var ptSlater = Clazz.newIntArray (nFuncs, 0);
var atoms = this.asc.atoms;
for (var i = 0, pt = 0; i < tokens.length; ) {
var iAtom = this.parseIntStr (tokens[i++]) - 1;
var code = tokens[i++];
var key = iAtom + "_" + code;
if (this.htFuncMap.containsKey (key)) {
ptSlater[pt++] = this.htFuncMap.get (key).intValue ();
} else {
var n = this.slaters.size ();
ptSlater[pt++] = n;
this.htFuncMap.put (key, Integer.$valueOf (n));
this.addSlater (this.createSlaterData (iAtom + 1, atoms[iAtom].elementSymbol, code), n);
}}
this.discardLinesUntilContains (":-");
this.rd ();
while (this.line != null && this.line.length >= 20) {
var iOrb = this.parseIntRange (this.line, 0, 10);
var energy = this.parseFloatRange (this.line, 10, 20);
var cData = new JU.SB ();
cData.append (this.line.substring (20));
while (this.rd () != null && this.line.length >= 10) {
if (this.line.charAt (3) != ' ') break;
cData.append (this.line);
}
var list = Clazz.newFloatArray (this.slaters.size (), 0);
tokens = JU.PT.getTokens (cData.toString ());
if (tokens.length != nFuncs) JU.Logger.error ("DgridReader: number of coefficients (" + tokens.length + ") does not equal number of functions (" + nFuncs + ")");
for (var i = 0; i < tokens.length; i++) {
var pt = ptSlater[i];
list[pt] = this.parseFloatStr (tokens[i]);
}
var mo = new java.util.Hashtable ();
mo.put ("energy", Float.$valueOf (energy));
mo.put ("coefficients", list);
mo.put ("symmetry", symmetry + "_" + iOrb);
this.setMO (mo);
}
}
this.discardLinesUntilContains (": # symmetry");
this.rd ();
for (var i = 0; i < this.orbitals.size (); i++) {
this.rd ();
var occupancy = this.parseFloatRange (this.line, 31, 45) + this.parseFloatRange (this.line, 47, 61);
this.orbitals.get (i).put ("occupancy", Float.$valueOf (occupancy));
}
this.sortOrbitals ();
this.setSlaters (true, true);
this.setMOs ("eV");
});
Clazz.defineMethod (c$, "createSlaterData",
function (iAtom, atomSymbol, xyz) {
var ch;
var abc = ' ';
var type = ' ';
var exp = 1;
var el = 0;
var x = 0;
var y = 0;
var z = 0;
for (var i = xyz.length; --i >= 0; ) {
switch (ch = xyz.charAt (i)) {
case '_':
type = abc;
break;
case '1':
case '2':
case '3':
case '4':
exp = ch.charCodeAt (0) - 48;
break;
case 'x':
x = exp;
el += exp;
exp = 1;
break;
case 'y':
y = exp;
el += exp;
exp = 1;
break;
case 'z':
z = exp;
el += exp;
exp = 1;
break;
case 's':
case 'p':
case 'd':
case 'f':
default:
abc = ch;
}
}
var r = (exp - el - 1);
var code = atomSymbol + xyz.substring (0, 2);
if (type != ' ') code += "_" + type;
var f = this.htExponents.get (code);
var zeta = 0;
if (f == null) JU.Logger.error ("Exponent for " + code + " not found");
else zeta = f.floatValue ();
return new J.quantum.SlaterData (iAtom, x, y, z, r, zeta, 1);
}, "~N,~S,~S");
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader"], "J.adapter.readers.quantum.GamessReader", ["java.lang.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.atomNames = null;
this.calcOptions = null;
this.isTypeSet = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GamessReader", J.adapter.readers.quantum.MOReader);
Clazz.defineMethod (c$, "readEnergy",
function () {
var tokens = JU.PT.getTokens (this.line.substring (this.line.indexOf ("ENERGY")));
if (tokens.length < 3) return;
var strEnergy = tokens[2];
var e = this.parseFloatStr (strEnergy);
if (!Float.isNaN (e)) this.asc.setAtomSetEnergy (strEnergy, e);
});
Clazz.defineMethod (c$, "readGaussianBasis",
function (initiator, terminator) {
var gdata = new JU.Lst ();
this.gaussianCount = 0;
var nGaussians = 0;
this.shellCount = 0;
var thisShell = "0";
var tokens;
this.discardLinesUntilContains (initiator);
this.rd ();
var slater = null;
var shellsByAtomType = new java.util.Hashtable ();
var slatersByAtomType = new JU.Lst ();
var atomType = null;
while (this.rd () != null && this.line.indexOf (terminator) < 0) {
if (this.line.indexOf ("(") >= 0) this.line = J.adapter.readers.quantum.GamessReader.fixBasisLine (this.line);
tokens = this.getTokens ();
switch (tokens.length) {
case 1:
if (atomType != null) {
if (slater != null) {
slater[2] = nGaussians;
slatersByAtomType.addLast (slater);
slater = null;
}shellsByAtomType.put (atomType, slatersByAtomType);
}slatersByAtomType = new JU.Lst ();
atomType = tokens[0];
break;
case 0:
break;
default:
if (!tokens[0].equals (thisShell)) {
if (slater != null) {
slater[2] = nGaussians;
slatersByAtomType.addLast (slater);
}thisShell = tokens[0];
this.shellCount++;
slater = Clazz.newIntArray (-1, [J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (this.fixShellTag (tokens[1])), this.gaussianCount, 0]);
nGaussians = 0;
}++nGaussians;
++this.gaussianCount;
gdata.addLast (tokens);
}
}
if (slater != null) {
slater[2] = nGaussians;
slatersByAtomType.addLast (slater);
}if (atomType != null) shellsByAtomType.put (atomType, slatersByAtomType);
this.gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) {
tokens = gdata.get (i);
this.gaussians[i] = Clazz.newFloatArray (tokens.length - 3, 0);
for (var j = 3; j < tokens.length; j++) this.gaussians[i][j - 3] = this.parseFloatStr (tokens[j]);
}
var ac = this.atomNames.size ();
if (this.shells == null && ac > 0) {
this.shells = new JU.Lst ();
for (var i = 0; i < ac; i++) {
atomType = this.atomNames.get (i);
var slaters = shellsByAtomType.get (atomType);
if (slaters == null) {
JU.Logger.error ("slater for atom " + i + " atomType " + atomType + " was not found in listing. Ignoring molecular orbitals");
return;
}for (var j = 0; j < slaters.size (); j++) {
slater = slaters.get (j);
this.shells.addLast ( Clazz.newIntArray (-1, [i + 1, slater[0], slater[1] + 1, slater[2]]));
}
}
}if (this.debugging) {
JU.Logger.debug (this.shellCount + " slater shells read");
JU.Logger.debug (this.gaussianCount + " gaussian primitives read");
}}, "~S,~S");
Clazz.defineMethod (c$, "readFrequencies",
function () {
this.discardLinesUntilContains ("FREQUENCY:");
var haveFreq = false;
while (this.line != null && this.line.indexOf ("FREQUENCY:") >= 0) {
var frequencyCount = 0;
var tokens = this.getTokens ();
var frequencies = Clazz.newFloatArray (tokens.length, 0);
for (var i = 0; i < tokens.length; i++) {
var frequency = this.parseFloatStr (tokens[i]);
if (tokens[i].equals ("I")) frequencies[frequencyCount - 1] = -frequencies[frequencyCount - 1];
if (Float.isNaN (frequency)) continue;
frequencies[frequencyCount++] = frequency;
if (this.debugging) {
JU.Logger.debug ((this.vibrationNumber + 1) + " frequency=" + frequency);
}}
var red_masses = null;
var intensities = null;
this.rd ();
if (this.line.indexOf ("MASS") >= 0) {
red_masses = this.getTokens ();
this.rd ();
}if (this.line.indexOf ("INTENS") >= 0) {
intensities = this.getTokens ();
}var ac = this.asc.getLastAtomSetAtomCount ();
var iAtom0 = this.asc.ac;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; i++) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
if (haveFreq) {
this.asc.cloneLastAtomSet ();
} else {
haveFreq = true;
iAtom0 -= ac;
}this.asc.setAtomSetFrequency (null, null, "" + frequencies[i], null);
if (red_masses != null) this.asc.setAtomSetModelProperty ("ReducedMass", red_masses[red_masses.length - frequencyCount + i] + " AMU");
if (intensities != null) this.asc.setAtomSetModelProperty ("IRIntensity", intensities[intensities.length - frequencyCount + i] + " D^2/AMU-Angstrom^2");
}
this.discardLinesUntilBlank ();
this.fillFrequencyData (iAtom0, ac, ac, ignore, false, 20, 12, null, 0);
this.readLines (13);
}
});
c$.fixBasisLine = Clazz.defineMethod (c$, "fixBasisLine",
function (line) {
var pt;
var pt1;
line = line.$replace (')', ' ');
while ((pt = line.indexOf ("(")) >= 0) {
pt1 = pt;
while (line.charAt (--pt1) == ' ') {
}
while (line.charAt (--pt1) != ' ') {
}
line = line.substring (0, ++pt1) + line.substring (pt + 1);
}
return line;
}, "~S");
Clazz.defineMethod (c$, "setCalculationType",
function () {
if (this.calcOptions == null || this.isTypeSet) return;
this.isTypeSet = true;
var SCFtype = this.calcOptions.get ("contrl_options_SCFTYP");
var Runtype = this.calcOptions.get ("contrl_options_RUNTYP");
var igauss = this.calcOptions.get ("basis_options_IGAUSS");
var gbasis = this.calcOptions.get ("basis_options_GBASIS");
var DFunc = !"0".equals (this.calcOptions.get ("basis_options_NDFUNC"));
var PFunc = !"0".equals (this.calcOptions.get ("basis_options_NPFUNC"));
var FFunc = !"0".equals (this.calcOptions.get ("basis_options_NFFUNC"));
var DFTtype = this.calcOptions.get ("contrl_options_DFTTYP");
var perturb = this.parseIntStr (this.calcOptions.get ("contrl_options_MPLEVL"));
var CItype = this.calcOptions.get ("contrl_options_CITYP");
var CCtype = this.calcOptions.get ("contrl_options_CCTYP");
if (igauss == null && SCFtype == null) return;
if (this.calculationType.equals ("?")) this.calculationType = "";
if (igauss != null) {
if ("0".equals (igauss)) {
var recognized = false;
if (this.calculationType.length > 0) this.calculationType += " ";
if (gbasis.startsWith ("ACC")) this.calculationType += "aug-cc-p";
if (gbasis.startsWith ("CC")) this.calculationType += "cc-p";
if ((gbasis.startsWith ("ACC") || gbasis.startsWith ("CC")) && gbasis.endsWith ("C")) this.calculationType += "C";
if (gbasis.indexOf ("CCD") >= 0) {
this.calculationType += "VDZ";
recognized = true;
}if (gbasis.indexOf ("CCT") >= 0) {
this.calculationType += "VTZ";
recognized = true;
}if (gbasis.indexOf ("CCQ") >= 0) {
this.calculationType += "VQZ";
recognized = true;
}if (gbasis.indexOf ("CC5") >= 0) {
this.calculationType += "V5Z";
recognized = true;
}if (gbasis.indexOf ("CC6") >= 0) {
this.calculationType += "V6Z";
recognized = true;
}if (!recognized) this.calculationType += gbasis;
} else {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += igauss + "-" + JU.PT.rep (gbasis, "N", "");
if ("T".equals (this.calcOptions.get ("basis_options_DIFFSP"))) {
if ("T".equals (this.calcOptions.get ("basis_options_DIFFS"))) this.calculationType += "+";
this.calculationType += "+";
}this.calculationType += "G";
if (DFunc || PFunc || FFunc) {
this.calculationType += "(";
if (FFunc) {
this.calculationType += "f";
if (DFunc || PFunc) this.calculationType += ",";
}if (DFunc) {
this.calculationType += "d";
if (PFunc) this.calculationType += ",";
}if (PFunc) this.calculationType += "p";
this.calculationType += ")";
}}if (DFTtype != null && DFTtype.indexOf ("NONE") < 0) {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += DFTtype;
}if (CItype != null && CItype.indexOf ("NONE") < 0) {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += CItype;
}if (CCtype != null && CCtype.indexOf ("NONE") < 0) {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += CCtype;
}if (perturb > 0) {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += "MP" + perturb;
}if (SCFtype != null) {
if (this.calculationType.length > 0) this.calculationType += " ";
this.calculationType += SCFtype + " " + Runtype;
}}});
Clazz.defineMethod (c$, "readControlInfo",
function () {
this.readCalculationInfo ("contrl_options_");
});
Clazz.defineMethod (c$, "readBasisInfo",
function () {
this.readCalculationInfo ("basis_options_");
});
Clazz.defineMethod (c$, "readCalculationInfo",
function (type) {
if (this.calcOptions == null) {
this.calcOptions = new java.util.Hashtable ();
this.asc.setInfo ("calculationOptions", this.calcOptions);
}while (this.rd () != null && (this.line = this.line.trim ()).length > 0) {
if (this.line.indexOf ("=") < 0) continue;
var tokens = JU.PT.getTokens (JU.PT.rep (this.line, "=", " = ") + " ?");
for (var i = 0; i < tokens.length; i++) {
if (!tokens[i].equals ("=")) continue;
try {
var key = type + tokens[i - 1];
var value = (key.equals ("basis_options_SPLIT3") ? tokens[++i] + " " + tokens[++i] + " " + tokens[++i] : tokens[++i]);
if (this.debugging) JU.Logger.debug (key + " = " + value);
this.calcOptions.put (key, value);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
}
}
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.GamessReader"], "J.adapter.readers.quantum.GamessUKReader", ["java.lang.Float", "JU.Lst", "$.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.symmetries = null;
this.occupancies = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GamessUKReader", J.adapter.readers.quantum.GamessReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("BASIS OPTIONS") >= 0) {
this.readBasisInfo ();
return true;
}if (this.line.indexOf ("$CONTRL OPTIONS") >= 0) {
this.readControlInfo ();
return true;
}if (this.line.indexOf ("contracted primitive functions") >= 0) {
this.readGaussianBasis ("======================================================", "======");
return false;
}if (this.line.indexOf ("molecular geometry") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.atomNames = new JU.Lst ();
this.readAtomsInBohrCoordinates ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("FREQUENCY_INFO_WOULD_BE_HERE") >= 0) {
return true;
}if (this.line.indexOf ("SYMMETRY ASSIGNMENT") >= 0) {
this.readOrbitalSymmetryAndOccupancy ();
return false;
}if (this.line.indexOf ("- ALPHA SET -") >= 0) this.alphaBeta = "alpha";
else if (this.line.indexOf ("- BETA SET -") >= 0) this.alphaBeta = "beta";
else if (this.line.indexOf ("eigenvectors") >= 0) {
this.readMolecularOrbitals (3);
this.setOrbitalSymmetryAndOccupancy ();
return false;
}return this.checkNboLine ();
});
Clazz.overrideMethod (c$, "readAtomsInBohrCoordinates",
function () {
this.discardLinesUntilContains ("*****");
this.discardLinesUntilContains ("atom");
this.discardLinesUntilContains ("*****");
this.asc.newAtomSet ();
while (this.rd () != null && this.line.indexOf ("*****") < 0) {
if (this.line.charAt (14) == ' ') continue;
var tokens = this.getTokens ();
var atomicNumber = Clazz.floatToInt (this.parseFloatStr (tokens[2]));
var atom = this.setAtomCoordScaled (null, tokens, 3, 0.5291772);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (atomicNumber);
this.atomNames.addLast (atom.atomName = tokens[1]);
}
});
Clazz.overrideMethod (c$, "fixShellTag",
function (tag) {
return tag.substring (1).toUpperCase ();
}, "~S");
Clazz.defineMethod (c$, "readOrbitalSymmetryAndOccupancy",
function () {
this.readLines (4);
this.symmetries = new JU.Lst ();
this.occupancies = new JU.Lst ();
while (this.rd () != null && this.line.indexOf ("====") < 0) {
var tokens = JU.PT.getTokens (this.line.substring (20));
this.symmetries.addLast (tokens[0] + " " + tokens[1]);
this.occupancies.addLast (Float.$valueOf (this.parseFloatStr (tokens[5])));
}
});
Clazz.defineMethod (c$, "setOrbitalSymmetryAndOccupancy",
function () {
if (this.symmetries.size () < this.orbitals.size ()) return;
for (var i = this.orbitals.size (); --i >= 0; ) {
var mo = this.orbitals.get (i);
mo.put ("symmetry", this.symmetries.get (i));
mo.put ("occupancy", this.occupancies.get (i));
}
});
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.GamessReader"], "J.adapter.readers.quantum.GamessUSReader", ["java.lang.Float", "JU.Lst", "$.PT", "$.V3", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.lowdenCharges = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GamessUSReader", J.adapter.readers.quantum.GamessReader);
Clazz.defineMethod (c$, "initializeReader",
function () {
this.lowdenCharges = this.checkAndRemoveFilterKey ("CHARGE=LOW");
Clazz.superCall (this, J.adapter.readers.quantum.GamessUSReader, "initializeReader", []);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.startsWith (" $DATA")) return this.readInputDeck ();
if (this.line.indexOf ("***************") >= 0) JU.Logger.info (this.rd ());
var isBohr;
if (this.line.indexOf ("FINAL ENERGY IS") >= 0 || this.line.indexOf ("TOTAL ENERGY = ") >= 0 || this.line.indexOf ("FINAL RHF ENERGY IS") >= 0) this.readEnergy ();
if (this.line.indexOf ("BASIS OPTIONS") >= 0) {
this.readBasisInfo ();
return true;
}if (this.line.indexOf ("$CONTRL OPTIONS") >= 0) {
this.readControlInfo ();
return true;
}if (this.line.indexOf ("ATOMIC BASIS SET") >= 0) {
this.readGaussianBasis ("SHELL TYPE", "TOTAL");
return false;
}if ((isBohr = this.line.indexOf ("COORDINATES (BOHR)") >= 0) || this.line.indexOf ("COORDINATES OF ALL ATOMS ARE (ANGS)") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.atomNames = new JU.Lst ();
if (isBohr) this.readAtomsInBohrCoordinates ();
else this.readAtomsInAngstromCoordinates ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("FREQUENCIES IN CM") >= 0) {
this.readFrequencies ();
return true;
}if (this.line.indexOf ("SUMMARY OF THE EFFECTIVE FRAGMENT") >= 0) {
this.readEFPInBohrCoordinates ();
return false;
}if (this.line.indexOf (" TOTAL MULLIKEN AND LOWDIN ATOMIC POPULATIONS") >= 0) {
this.readPartialCharges ();
return false;
}if (this.line.indexOf ("ELECTROSTATIC MOMENTS") >= 0) {
this.readDipoleMoment ();
return true;
}if (this.line.indexOf ("- ALPHA SET -") >= 0) this.alphaBeta = "alpha";
else if (this.line.indexOf ("- BETA SET -") >= 0) this.alphaBeta = "beta";
else if (this.line.indexOf (" EIGENVECTORS") >= 0 || this.line.indexOf (" INITIAL GUESS ORBITALS") >= 0 || this.line.indexOf (" MCSCF OPTIMIZED ORBITALS") >= 0 || this.line.indexOf (" MCSCF NATURAL ORBITALS") >= 0 || this.line.indexOf (" MOLECULAR ORBITALS") >= 0 && this.line.indexOf (" MOLECULAR ORBITALS LOCALIZED BY THE POPULATION METHOD") < 0) {
if (!this.filterMO ()) return true;
this.readMolecularOrbitals (1);
return false;
}if (this.line.indexOf ("EDMISTON-RUEDENBERG ENERGY LOCALIZED ORBITALS") >= 0 || this.line.indexOf (" THE PIPEK-MEZEY POPULATION LOCALIZED ORBITALS ARE") >= 0) {
if (!this.filterMO ()) return true;
this.readMolecularOrbitals (0);
return false;
}if (this.line.indexOf (" NATURAL ORBITALS IN ATOMIC ORBITAL BASIS") >= 0) {
if (!this.filterMO ()) return true;
this.readMolecularOrbitals (2);
return false;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "readInputDeck",
function () {
this.readLines (2);
this.asc.newAtomSet ();
while (this.rd ().indexOf ("$END") < 0) {
var tokens = this.getTokens ();
if (tokens.length > 4) this.addAtomXYZSymName (tokens, 2, tokens[0], null).elementNumber = this.parseIntStr (tokens[1]);
}
return (this.continuing = false);
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function (headerType) {
this.setCalculationType ();
Clazz.superCall (this, J.adapter.readers.quantum.GamessUSReader, "readMolecularOrbitals", [headerType]);
}, "~N");
Clazz.defineMethod (c$, "readEFPInBohrCoordinates",
function () {
var acInFirstModel = this.asc.ac;
this.discardLinesUntilContains ("MULTIPOLE COORDINATES");
this.rd ();
this.rd ();
while (this.rd () != null && this.line.length >= 72) {
var atomName = this.line.substring (1, 2);
if (atomName.charAt (0) == 'Z') atomName = this.line.substring (2, 3);
else if (this.parseFloatRange (this.line, 67, 73) == 0) continue;
var x = this.parseFloatRange (this.line, 8, 25);
var y = this.parseFloatRange (this.line, 25, 40);
var z = this.parseFloatRange (this.line, 40, 56);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) break;
var atom = this.asc.addNewAtom ();
atom.atomName = atomName + (++acInFirstModel);
this.setAtomCoordXYZ (atom, x * 0.5291772, y * 0.5291772, z * 0.5291772);
this.atomNames.addLast (atomName);
}
});
Clazz.overrideMethod (c$, "readAtomsInBohrCoordinates",
function () {
this.rd ();
var atomName;
this.asc.newAtomSet ();
var n = 0;
while (this.rd () != null && (atomName = this.parseTokenRange (this.line, 1, 11)) != null) {
var x = this.parseFloatRange (this.line, 17, 37);
var y = this.parseFloatRange (this.line, 37, 57);
var z = this.parseFloatRange (this.line, 57, 77);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) break;
var atom = this.asc.addNewAtom ();
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.parseIntRange (this.line, 11, 14));
atom.atomName = atom.elementSymbol + (++n);
this.setAtomCoordXYZ (atom, x * 0.5291772, y * 0.5291772, z * 0.5291772);
this.atomNames.addLast (atomName);
}
});
Clazz.defineMethod (c$, "readAtomsInAngstromCoordinates",
function () {
this.rd ();
this.rd ();
var atomName;
this.asc.newAtomSet ();
var n = 0;
while (this.rd () != null && (atomName = this.parseTokenRange (this.line, 1, 11)) != null) {
var x = this.parseFloatRange (this.line, 16, 31);
var y = this.parseFloatRange (this.line, 31, 46);
var z = this.parseFloatRange (this.line, 46, 61);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) break;
var atom = this.asc.addNewAtom ();
this.setAtomCoordXYZ (atom, x, y, z);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.parseIntRange (this.line, 11, 14));
atom.atomName = atom.elementSymbol + (++n);
this.atomNames.addLast (atomName);
}
if (this.line.indexOf ("COORDINATES OF FRAGMENT MULTIPOLE CENTERS (ANGS)") >= 0) {
this.rd ();
this.rd ();
this.rd ();
while (this.rd () != null && (atomName = this.parseTokenRange (this.line, 1, 2)) != null) {
if (this.parseTokenRange (this.line, 1, 2).equals ("Z")) atomName = this.parseTokenRange (this.line, 2, 3);
else if (this.parseTokenRange (this.line, 1, 9).equals ("FRAGNAME")) continue;
else atomName = this.parseTokenRange (this.line, 1, 2);
var x = this.parseFloatRange (this.line, 16, 31);
var y = this.parseFloatRange (this.line, 31, 46);
var z = this.parseFloatRange (this.line, 46, 61);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) break;
var atom = this.asc.addNewAtom ();
atom.atomName = atomName + (++n);
this.setAtomCoordXYZ (atom, x, y, z);
this.atomNames.addLast (atomName);
}
}});
Clazz.overrideMethod (c$, "fixShellTag",
function (tag) {
return tag;
}, "~S");
Clazz.defineMethod (c$, "readPartialCharges",
function () {
var tokens = null;
var searchstr = (this.lowdenCharges ? "LOW.POP." : "MULL.POP.");
while (this.rd () != null && ("".equals (this.line.trim ()) || this.line.indexOf ("ATOM") >= 0)) {
tokens = this.getTokens ();
}
var poploc = 0;
for (; ++poploc < tokens.length; ) if (searchstr.equals (tokens[poploc])) break;
if (++poploc >= tokens.length || !"CHARGE".equals (tokens[poploc++])) return;
var atoms = this.asc.atoms;
var startAtom = this.asc.getLastAtomSetAtomIndex ();
var endAtom = this.asc.ac;
for (var i = startAtom; i < endAtom && this.rd () != null; ++i) atoms[i].partialCharge = this.parseFloatStr (JU.PT.getTokens (this.prevline)[poploc]);
});
Clazz.defineMethod (c$, "readDipoleMoment",
function () {
var tokens = null;
this.rd ();
while (this.line != null && ("".equals (this.line.trim ()) || this.line.indexOf ("DX") < 0)) {
this.rd ();
}
tokens = this.getTokens ();
if (tokens.length != 5) return;
if ("DX".equals (tokens[0]) && "DY".equals (tokens[1]) && "DZ".equals (tokens[2])) {
tokens = JU.PT.getTokens (this.rd ());
var dipole = JU.V3.new3 (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]));
JU.Logger.info ("Molecular dipole for model " + this.asc.atomSetCount + " = " + dipole);
this.asc.setCurrentModelInfo ("dipole", dipole);
}});
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.GaussianReader"], "J.adapter.readers.quantum.GaussianFchkReader", ["java.lang.Double", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.V3", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.Bond", "JU.Escape", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.fileData = null;
this.atomCount = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GaussianFchkReader", J.adapter.readers.quantum.GaussianReader);
Clazz.defineMethod (c$, "initializeReader",
function () {
Clazz.superCall (this, J.adapter.readers.quantum.GaussianFchkReader, "initializeReader", []);
this.energyUnits = "";
this.fileData = new java.util.Hashtable ();
this.fileData.put ("title", this.rd ().trim ());
this.calculationType = JU.PT.rep (this.rd (), " ", " ");
this.asc.newAtomSet ();
this.asc.setCurrentModelInfo ("fileData", this.fileData);
this.readAllData ();
this.readAtoms ();
this.readBonds ();
this.readDipoleMoment ();
this.readPartialCharges ();
this.readBasis ();
this.readMolecularObitals ();
this.checkForFreq ();
this.continuing = false;
});
Clazz.defineMethod (c$, "checkForFreq",
function () {
var n = this.fileData.get ("Vib-NDim");
if (n == null) {
this.readFrequencies ("NumFreq", false);
return;
}try {
var nModes = n.intValue ();
var vibE2 = this.fileData.get ("Vib-E2");
var modes = this.fileData.get ("Vib-Modes");
var frequencies = this.fillFloat (vibE2, 0, nModes);
var red_masses = this.fillFloat (vibE2, nModes, nModes);
var frc_consts = this.fillFloat (vibE2, nModes * 2, nModes);
var intensities = this.fillFloat (vibE2, nModes * 3, nModes);
var ac = this.asc.getLastAtomSetAtomCount ();
var ignore = Clazz.newBooleanArray (nModes, false);
var fpt = 0;
for (var i = 0; i < nModes; ++i) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
var iAtom0 = this.asc.ac;
this.asc.cloneAtomSetWithBonds (true);
var name = this.asc.setAtomSetFrequency ("Calculation " + this.calculationNumber, null, "" + frequencies[i], null);
this.appendLoadNote ("model " + this.asc.atomSetCount + ": " + name);
this.namedSets.set (this.asc.iSet);
this.asc.setAtomSetModelProperty ("ReducedMass", red_masses[i] + " AMU");
this.asc.setAtomSetModelProperty ("ForceConstant", frc_consts[i] + " mDyne/A");
this.asc.setAtomSetModelProperty ("IRIntensity", intensities[i] + " KM/Mole");
for (var iAtom = 0; iAtom < ac; iAtom++) {
this.asc.addVibrationVectorWithSymmetry (iAtom0 + iAtom, modes[fpt++], modes[fpt++], modes[fpt++], false);
}
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
JU.Logger.error ("Could not read Vib-E2 section: " + e.getMessage ());
} else {
throw e;
}
}
});
Clazz.defineMethod (c$, "fillFloat",
function (f0, i, n) {
var f = Clazz.newFloatArray (n, 0);
for (var i1 = 0, ilast = i + n; i < ilast; i++, i1++) f[i1] = f0[i];
return f;
}, "~A,~N,~N");
Clazz.defineMethod (c$, "readAllData",
function () {
while ((this.line == null ? this.rd () : this.line) != null) {
if (this.line.length < 40) {
if (this.line.indexOf ("NumAtom") == 0) {
return;
}continue;
}var name = JU.PT.rep (this.line.substring (0, 40).trim (), " ", "");
var type = this.line.charAt (43);
var isArray = (this.line.indexOf ("N=") >= 0);
var v = this.line.substring (50).trim ();
JU.Logger.info (name + " = " + v + " " + isArray);
var o = null;
if (isArray) {
switch (type) {
case 'I':
case 'R':
o = this.fillFloatArray (null, 0, Clazz.newFloatArray (this.parseIntStr (v), 0));
this.line = null;
break;
default:
v = this.rd ().trim ();
while (this.rd () != null && this.line.indexOf (" N= ") < 0) v += " " + this.line.trim ();
o = v;
break;
}
} else {
switch (type) {
case 'I':
o = Integer.$valueOf (this.parseIntStr (v));
break;
case 'R':
o = Double.$valueOf (Double.parseDouble (v));
break;
case 'C':
case 'L':
o = v;
break;
}
this.line = null;
}if (o != null) this.fileData.put (name, o);
}
});
Clazz.overrideMethod (c$, "readAtoms",
function () {
var atomNumbers = this.fileData.get ("Atomicnumbers");
var data = this.fileData.get ("Currentcartesiancoordinates");
var e = "" + this.fileData.get ("TotalEnergy");
this.asc.setAtomSetEnergy (e, this.parseFloatStr (e));
this.atomCount = atomNumbers.length;
var f = 0.5291772;
for (var i = 0, pt = 0; i < this.atomCount; i++) {
var atom = this.asc.addNewAtom ();
atom.elementNumber = Clazz.floatToShort (atomNumbers[i]);
if (atom.elementNumber < 0) atom.elementNumber = 0;
this.setAtomCoordXYZ (atom, data[pt++] * f, data[pt++] * f, data[pt++] * f);
}
});
Clazz.defineMethod (c$, "readBonds",
function () {
try {
var nBond = this.fileData.get ("NBond");
var iBond = this.fileData.get ("IBond");
if (nBond.length == 0) return;
var rBond = this.fileData.get ("RBond");
var mxBond = Clazz.doubleToInt (rBond.length / nBond.length);
for (var ia = 0, pt = 0; ia < this.atomCount; ia++) for (var j = 0; j < mxBond; j++, pt++) {
var ib = Clazz.floatToInt (iBond[pt]) - 1;
if (ib <= ia) continue;
var order = rBond[pt];
var iorder = (order == 1.5 ? 515 : Clazz.floatToInt (order));
this.asc.addBond ( new J.adapter.smarter.Bond (ia, ib, iorder));
}
this.addJmolScript ("connect 1.1 {_H} {*} ");
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
JU.Logger.info ("GaussianFchkReader -- bonding ignored");
} else {
throw e;
}
}
});
Clazz.overrideMethod (c$, "readDipoleMoment",
function () {
var data = this.fileData.get ("DipoleMoment");
if (data == null) return;
var dipole = JU.V3.new3 (data[0], data[1], data[2]);
JU.Logger.info ("Molecular dipole for model " + this.asc.atomSetCount + " = " + dipole);
this.asc.setCurrentModelInfo ("dipole", dipole);
});
Clazz.overrideMethod (c$, "readPartialCharges",
function () {
var data = this.fileData.get ("Mulliken Charges");
if (data == null) return;
var atoms = this.asc.atoms;
for (var i = 0; i < this.atomCount; ++i) {
var c = data[i];
atoms[i].partialCharge = c;
if (Math.abs (c) > 0.8) atoms[i].formalCharge = Math.round (c);
}
JU.Logger.info ("Mulliken charges found for Model " + this.asc.atomSetCount);
});
Clazz.overrideMethod (c$, "readBasis",
function () {
var types = this.fileData.get ("Shelltypes");
this.gaussianCount = 0;
this.shellCount = 0;
if (types == null) return;
this.shellCount = types.length;
this.shells = new JU.Lst ();
var pps = this.fileData.get ("Numberofprimitivespershell");
var atomMap = this.fileData.get ("Shelltoatommap");
var exps = this.fileData.get ("Primitiveexponents");
var coefs = this.fileData.get ("Contractioncoefficients");
var spcoefs = this.fileData.get ("P(S=P)Contractioncoefficients");
this.gaussians = JU.AU.newFloat2 (exps.length);
for (var i = 0; i < this.shellCount; i++) {
var oType = J.adapter.readers.quantum.GaussianFchkReader.AO_TYPES[Clazz.floatToInt (types[i]) + 3];
var nGaussians = Clazz.floatToInt (pps[i]);
var iatom = Clazz.floatToInt (atomMap[i]);
var slater = Clazz.newIntArray (4, 0);
slater[0] = iatom;
if (oType.equals ("F7") || oType.equals ("D5")) slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagIDSpherical (oType.substring (0, 1));
else slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (oType);
slater[2] = this.gaussianCount + 1;
slater[3] = nGaussians;
if (this.debugging) JU.Logger.debug ("Slater " + this.shells.size () + " " + JU.Escape.eAI (slater));
this.shells.addLast (slater);
for (var j = 0; j < nGaussians; j++) {
var g = this.gaussians[this.gaussianCount] = Clazz.newFloatArray (3, 0);
g[0] = exps[this.gaussianCount];
g[1] = coefs[this.gaussianCount];
if (spcoefs != null) g[2] = spcoefs[this.gaussianCount];
this.gaussianCount++;
}
}
JU.Logger.info (this.shellCount + " slater shells read");
JU.Logger.info (this.gaussianCount + " gaussian primitives read");
});
Clazz.defineMethod (c$, "readMolecularObitals",
function () {
if (this.shells == null) return;
var nElec = (this.fileData.get ("Numberofelectrons")).intValue ();
var nAlpha = (this.fileData.get ("Numberofalphaelectrons")).intValue ();
var nBeta = (this.fileData.get ("Numberofbetaelectrons")).intValue ();
var aenergies = this.fileData.get ("AlphaOrbitalEnergies");
var benergies = this.fileData.get ("BetaOrbitalEnergies");
var acoefs = this.fileData.get ("AlphaMOcoefficients");
var bcoefs = this.fileData.get ("BetaMOcoefficients");
if (acoefs == null) return;
var occ = (bcoefs == null ? 2 : 1);
var n = (bcoefs == null ? nElec : nAlpha);
this.getOrbitals (aenergies, acoefs, occ, n);
if (bcoefs != null) this.getOrbitals (benergies, bcoefs, occ, nBeta);
this.setMOData (false);
});
Clazz.defineMethod (c$, "getOrbitals",
function (e, c, occ, nElec) {
var nOrb = e.length;
var nCoef = c.length;
nCoef /= nOrb;
this.alphaBeta = (occ == 2 ? "" : this.alphaBeta.equals ("alpha") ? "beta" : "alpha");
var pt = 0;
var n = 0;
for (var i = 0; i < nOrb; i++) {
var coefs = Clazz.newFloatArray (nCoef, 0);
for (var j = 0; j < nCoef; j++) coefs[j] = c[pt++];
var mo = new java.util.Hashtable ();
mo.put ("coefficients", coefs);
mo.put ("occupancy", Float.$valueOf (occ));
n += occ;
if (n >= nElec) occ = 0;
mo.put ("energy", Float.$valueOf (e[i]));
mo.put ("type", this.alphaBeta);
this.setMO (mo);
}
}, "~A,~A,~N,~N");
Clazz.defineStatics (c$,
"AO_TYPES", Clazz.newArray (-1, ["F7", "D5", "L", "S", "P", "D", "F", "G", "H"]));
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader", "JU.BS"], "J.adapter.readers.quantum.GaussianReader", ["java.lang.Exception", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.V3", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.SmarterJmolAdapter", "J.quantum.QS", "JU.Escape", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.energyString = "";
this.energyKey = "";
this.calculationNumber = 1;
this.scanPoint = -1;
this.equivalentAtomSets = 0;
this.stepNumber = 0;
this.moModelSet = -1;
this.namedSets = null;
this.isHighPrecision = false;
this.haveHighPrecision = false;
this.allowHighPrecision = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GaussianReader", J.adapter.readers.quantum.MOReader);
Clazz.prepareFields (c$, function () {
this.namedSets = new JU.BS ();
});
Clazz.defineMethod (c$, "initializeReader",
function () {
this.allowHighPrecision = !this.checkAndRemoveFilterKey ("NOHP");
Clazz.superCall (this, J.adapter.readers.quantum.GaussianReader, "initializeReader", []);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.startsWith (" Step number")) {
this.equivalentAtomSets = 0;
this.stepNumber++;
var scanPointIndex = this.line.indexOf ("scan point");
if (scanPointIndex > 0) {
this.scanPoint = this.parseIntAt (this.line, scanPointIndex + 10);
} else {
this.scanPoint = -1;
}return true;
}if (this.line.indexOf ("-- Stationary point found") > 0) {
if (this.scanPoint >= 0) this.scanPoint++;
return true;
}if (this.line.indexOf ("Input orientation:") >= 0 || this.line.indexOf ("Z-Matrix orientation:") >= 0 || this.line.indexOf ("Standard orientation:") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) {
return this.checkLastModel ();
}this.equivalentAtomSets++;
JU.Logger.info (this.asc.atomSetCount + " model " + this.modelNumber + " step " + this.stepNumber + " equivalentAtomSet " + this.equivalentAtomSets + " calculation " + this.calculationNumber + " scan point " + this.scanPoint + this.line);
this.readAtoms ();
return false;
}if (!this.doProcessLines) return true;
if (this.line.startsWith (" Energy=")) {
this.setEnergy ();
return true;
}if (this.line.startsWith (" SCF Done:")) {
this.readSCFDone ();
return true;
}if (this.line.startsWith (" Harmonic frequencies")) {
this.readFrequencies (":", true);
return true;
}if (this.line.startsWith (" Total atomic charges:") || this.line.startsWith (" Mulliken atomic charges:")) {
this.readPartialCharges ();
return true;
}if (this.line.startsWith (" Dipole moment")) {
this.readDipoleMoment ();
return true;
}if (this.line.startsWith (" Standard basis:") || this.line.startsWith (" General basis read from")) {
this.energyUnits = "";
this.calculationType = this.line.substring (this.line.indexOf (":") + 1).trim ();
return true;
}if (this.line.startsWith (" AO basis set")) {
this.readBasis ();
return true;
}if (this.line.indexOf ("Molecular Orbital Coefficients") >= 0 || this.line.indexOf ("Natural Orbital Coefficients") >= 0 || this.line.indexOf ("Natural Transition Orbitals") >= 0) {
if (!this.filterMO ()) return true;
this.readMolecularOrbitals ();
JU.Logger.info (this.orbitals.size () + " molecular orbitals read");
return true;
}if (this.line.startsWith (" Normal termination of Gaussian")) {
++this.calculationNumber;
this.equivalentAtomSets = 0;
return true;
}if (this.line.startsWith (" Mulliken atomic spin densities:")) {
this.getSpinDensities (11);
return true;
}if (this.line.startsWith (" Mulliken charges and spin densities:")) {
this.getSpinDensities (21);
return true;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "getSpinDensities",
function (pt) {
this.rd ();
var data = Clazz.newFloatArray (this.asc.getLastAtomSetAtomCount (), 0);
for (var i = 0; i < data.length; i++) data[i] = this.parseFloatStr (this.rd ().substring (pt, pt + 10));
this.asc.setAtomProperties ("spin", data, -1, false);
this.appendLoadNote (data.length + " spin densities loaded into model " + (this.asc.iSet + 1));
}, "~N");
Clazz.defineMethod (c$, "readSCFDone",
function () {
var tokens = JU.PT.getTokensAt (this.line, 11);
if (tokens.length < 4) return;
this.energyKey = tokens[0];
this.asc.setAtomSetEnergy (tokens[2], this.parseFloatStr (tokens[2]));
this.energyString = tokens[2] + " " + tokens[3];
this.setNames (this.energyKey + " = " + this.energyString, this.namedSets, this.equivalentAtomSets);
this.setProps (this.energyKey, this.energyString, this.equivalentAtomSets);
tokens = JU.PT.getTokens (this.rd ());
if (tokens.length > 2) {
this.setProps (tokens[0], tokens[2], this.equivalentAtomSets);
if (tokens.length > 5) this.setProps (tokens[3], tokens[5], this.equivalentAtomSets);
tokens = JU.PT.getTokens (this.rd ());
}if (tokens.length > 2) this.setProps (tokens[0], tokens[2], this.equivalentAtomSets);
});
Clazz.defineMethod (c$, "setProps",
function (key, value, n) {
for (var i = this.asc.iSet; --n >= 0 && i >= 0; --i) this.asc.setAtomSetModelPropertyForSet (key, value, i);
}, "~S,~S,~N");
Clazz.defineMethod (c$, "setNames",
function (atomSetName, namedSets, n) {
for (var i = this.asc.iSet; --n >= 0 && i >= 0; --i) if (namedSets == null || !namedSets.get (i)) this.asc.setModelInfoForSet ("name", atomSetName, i);
}, "~S,JU.BS,~N");
Clazz.defineMethod (c$, "setEnergy",
function () {
var tokens = this.getTokens ();
this.energyKey = "Energy";
this.energyString = tokens[1];
this.setNames ("Energy = " + tokens[1], this.namedSets, this.equivalentAtomSets);
this.asc.setAtomSetEnergy (this.energyString, this.parseFloatStr (this.energyString));
});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.asc.newAtomSet ();
this.haveHighPrecision = false;
if (this.energyKey.length != 0) this.asc.setAtomSetName (this.energyKey + " = " + this.energyString);
this.asc.setAtomSetEnergy (this.energyString, this.parseFloatStr (this.energyString));
var path = this.getTokens ()[0];
this.readLines (4);
var tokens;
while (this.rd () != null && !this.line.startsWith (" --")) {
tokens = this.getTokens ();
var atom = this.asc.addNewAtom ();
atom.elementNumber = this.parseIntStr (tokens[1]);
if (atom.elementNumber < 0) atom.elementNumber = 0;
this.setAtomCoordTokens (atom, tokens, tokens.length - 3);
}
this.asc.setAtomSetModelProperty (".PATH", "Calculation " + this.calculationNumber + (this.scanPoint >= 0 ? (J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Scan Point " + this.scanPoint) : "") + J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + path);
});
Clazz.defineMethod (c$, "readBasis",
function () {
this.shells = new JU.Lst ();
var gdata = new JU.Lst ();
var ac = 0;
this.gaussianCount = 0;
this.shellCount = 0;
var lastAtom = "";
var tokens;
var doSphericalD = (this.calculationType != null && (this.calculationType.indexOf ("5D") > 0));
var doSphericalF = (this.calculationType != null && (this.calculationType.indexOf ("7F") > 0));
var isGeneral = (this.line.indexOf ("general basis input") >= 0);
if (isGeneral) {
while (this.rd () != null && this.line.length > 0) {
this.shellCount++;
tokens = this.getTokens ();
ac++;
while (this.rd ().indexOf ("****") < 0) {
var slater = Clazz.newIntArray (4, 0);
slater[0] = ac;
tokens = this.getTokens ();
var oType = tokens[0];
if (doSphericalF && oType.indexOf ("F") >= 0 || doSphericalD && oType.indexOf ("D") >= 0) slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagIDSpherical (oType);
else slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (oType);
var nGaussians = this.parseIntStr (tokens[1]);
slater[2] = this.gaussianCount + 1;
slater[3] = nGaussians;
if (this.debugging) JU.Logger.debug ("Slater " + this.shells.size () + " " + JU.Escape.eAI (slater));
this.shells.addLast (slater);
this.gaussianCount += nGaussians;
for (var i = 0; i < nGaussians; i++) {
this.rd ();
this.line = JU.PT.rep (this.line, "D ", "D+");
tokens = this.getTokens ();
if (this.debugging) JU.Logger.debug ("Gaussians " + (i + 1) + " " + JU.Escape.eAS (tokens, true));
gdata.addLast (tokens);
}
}
}
} else {
while (this.rd () != null && this.line.startsWith (" Atom")) {
this.shellCount++;
tokens = this.getTokens ();
var slater = Clazz.newIntArray (4, 0);
if (!tokens[1].equals (lastAtom)) ac++;
lastAtom = tokens[1];
slater[0] = ac;
var oType = tokens[4];
if (doSphericalF && oType.indexOf ("F") >= 0 || doSphericalD && oType.indexOf ("D") >= 0) slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagIDSpherical (oType);
else slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (oType);
var nGaussians = this.parseIntStr (tokens[5]);
slater[2] = this.gaussianCount + 1;
slater[3] = nGaussians;
this.shells.addLast (slater);
this.gaussianCount += nGaussians;
for (var i = 0; i < nGaussians; i++) {
gdata.addLast (JU.PT.getTokens (this.rd ()));
}
}
}if (ac == 0) ac = 1;
this.gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) {
tokens = gdata.get (i);
this.gaussians[i] = Clazz.newFloatArray (tokens.length, 0);
for (var j = 0; j < tokens.length; j++) this.gaussians[i][j] = this.parseFloatStr (tokens[j]);
}
JU.Logger.info (this.shellCount + " slater shells read");
JU.Logger.info (this.gaussianCount + " gaussian primitives read");
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function () {
if (this.shells == null) return;
var mos = JU.AU.createArrayOfHashtable (5);
var data = JU.AU.createArrayOfArrayList (5);
var nThisLine = 0;
var isNOtype = this.line.contains ("Natural Orbital");
while (this.rd () != null && this.line.toUpperCase ().indexOf ("DENS") < 0) {
var tokens;
if (this.line.indexOf ("eta Molecular Orbital Coefficients") >= 0) {
this.addMOData (nThisLine, data, mos);
nThisLine = 0;
if (!this.filterMO ()) break;
}if (this.line.indexOf (" ") == 0) {
this.addMOData (nThisLine, data, mos);
if (isNOtype) {
tokens = this.getTokens ();
nThisLine = tokens.length;
tokens = JU.PT.getTokens (this.rd ());
} else {
tokens = JU.PT.getTokens (this.rd ());
nThisLine = tokens.length;
}for (var i = 0; i < nThisLine; i++) {
mos[i] = new java.util.Hashtable ();
data[i] = new JU.Lst ();
var sym;
if (isNOtype) {
mos[i].put ("occupancy", Float.$valueOf (JU.PT.parseFloat (tokens[i + 2])));
} else {
sym = tokens[i];
mos[i].put ("symmetry", sym);
if (sym.indexOf ("O") >= 0) mos[i].put ("occupancy", Float.$valueOf (2));
else if (sym.indexOf ("V") >= 0) mos[i].put ("occupancy", Float.$valueOf (0));
}}
if (isNOtype) continue;
this.line = this.rd ().substring (21);
tokens = this.getTokens ();
if (tokens.length != nThisLine) tokens = J.adapter.smarter.AtomSetCollectionReader.getStrings (this.line, nThisLine, 10);
for (var i = 0; i < nThisLine; i++) {
mos[i].put ("energy", Float.$valueOf (JU.PT.fVal (tokens[i])));
}
continue;
} else if (this.line.length < 21 || (this.line.charAt (5) != ' ' && !JU.PT.isDigit (this.line.charAt (5)))) {
continue;
}try {
this.line = JU.PT.rep (this.line, " 0 ", "0 ");
tokens = this.getTokens ();
var type = tokens[tokens.length - nThisLine - 1].substring (1);
if (JU.PT.isDigit (type.charAt (0))) type = type.substring (1);
if (!J.quantum.QS.isQuantumBasisSupported (type.charAt (0)) && "XYZ".indexOf (type.charAt (0)) >= 0) type = (type.length == 2 ? "D" : "F") + type;
if (!J.quantum.QS.isQuantumBasisSupported (type.charAt (0))) continue;
tokens = J.adapter.smarter.AtomSetCollectionReader.getStrings (this.line.substring (this.line.length - 10 * nThisLine), nThisLine, 10);
for (var i = 0; i < nThisLine; i++) data[i].addLast (tokens[i]);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
JU.Logger.error ("Error reading Gaussian file Molecular Orbitals at line: " + this.line);
break;
} else {
throw e;
}
}
}
this.addMOData (nThisLine, data, mos);
this.setMOData (this.moModelSet != this.asc.atomSetCount);
this.moModelSet = this.asc.atomSetCount;
});
Clazz.defineMethod (c$, "readFrequencies",
function (key, mustHave) {
this.discardLinesUntilContains2 (key, ":");
if (this.line == null && mustHave) throw ( new Exception ("No frequencies encountered"));
while ((this.line = this.rd ()) != null && this.line.length > 15) {
var symmetries = JU.PT.getTokens (this.rd ());
this.discardLinesUntilContains (" Frequencies");
this.isHighPrecision = (this.line.indexOf ("---") > 0);
if (this.isHighPrecision ? !this.allowHighPrecision : this.haveHighPrecision) return;
if (this.isHighPrecision && !this.haveHighPrecision) {
this.appendLoadNote ("high precision vibrational modes enabled. Use filter 'NOHP' to disable.");
this.haveHighPrecision = true;
}var width = (this.isHighPrecision ? 22 : 15);
var frequencies = JU.PT.getTokensAt (this.line, width);
var red_masses = JU.PT.getTokensAt (this.discardLinesUntilContains (this.isHighPrecision ? "Reduced masses" : "Red. masses"), width);
var frc_consts = JU.PT.getTokensAt (this.discardLinesUntilContains (this.isHighPrecision ? "Force constants" : "Frc consts"), width);
var intensities = JU.PT.getTokensAt (this.discardLinesUntilContains (this.isHighPrecision ? "IR Intensities" : "IR Inten"), width);
var iAtom0 = this.asc.ac;
var ac = this.asc.getLastAtomSetAtomCount ();
var frequencyCount = frequencies.length;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneAtomSetWithBonds (true);
var name = this.asc.setAtomSetFrequency ("Calculation " + this.calculationNumber, symmetries[i], frequencies[i], null);
this.appendLoadNote ("model " + this.asc.atomSetCount + ": " + name);
this.namedSets.set (this.asc.iSet);
this.asc.setAtomSetModelProperty ("ReducedMass", red_masses[i] + " AMU");
this.asc.setAtomSetModelProperty ("ForceConstant", frc_consts[i] + " mDyne/A");
this.asc.setAtomSetModelProperty ("IRIntensity", intensities[i] + " KM/Mole");
}
this.discardLinesUntilContains (" Atom ");
if (this.isHighPrecision) this.fillFrequencyData (iAtom0, ac, ac, ignore, false, 23, 10, null, 0);
else this.fillFrequencyData (iAtom0, ac, ac, ignore, true, 0, 0, null, 0);
}
}, "~S,~B");
Clazz.defineMethod (c$, "readDipoleMoment",
function () {
var tokens = JU.PT.getTokens (this.rd ());
if (tokens.length != 8) return;
var dipole = JU.V3.new3 (this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[5]));
JU.Logger.info ("Molecular dipole for model " + this.asc.atomSetCount + " = " + dipole);
this.asc.setCurrentModelInfo ("dipole", dipole);
});
Clazz.defineMethod (c$, "readPartialCharges",
function () {
this.rd ();
var ac = this.asc.ac;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var atoms = this.asc.atoms;
for (var i = i0; i < ac; ++i) {
while (atoms[i].elementNumber == 0) ++i;
var charge = this.parseFloatStr (JU.PT.getTokens (this.rd ())[2]);
atoms[i].partialCharge = charge;
}
JU.Logger.info ("Mulliken charges found for Model " + this.asc.atomSetCount);
});
Clazz.defineStatics (c$,
"STD_ORIENTATION_ATOMIC_NUMBER_OFFSET", 1);
});

8
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.quantum.GaussianWfnReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.quantum, "GaussianWfnReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.continuing = false;
});
});

396
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader"], "J.adapter.readers.quantum.GenNBOReader", ["java.lang.Boolean", "$.Exception", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.Rdr", "$.SB", "J.adapter.readers.quantum.NBOParser", "J.quantum.QS", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.isOutputFile = false;
this.nboType = "";
this.nOrbitals0 = 0;
this.is47File = false;
this.isOpenShell = false;
this.alphaOnly = false;
this.betaOnly = false;
this.nAOs = 0;
this.topoType = "A";
this.nStructures = 0;
this.nboParser = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "GenNBOReader", J.adapter.readers.quantum.MOReader);
Clazz.defineMethod (c$, "initializeReader",
function () {
var line1 = this.rd ().trim ();
this.is47File = (line1.indexOf ("$GENNBO") >= 0 || line1.indexOf ("$NBO") >= 0);
this.alphaOnly = this.is47File || this.checkFilterKey ("ALPHA");
this.betaOnly = !this.is47File && this.checkFilterKey ("BETA");
if (this.is47File) {
this.readData47 ();
return;
}var isOK;
var line2 = this.rd ();
this.line = line1 + line2;
this.isOutputFile = (line2.indexOf ("****") >= 0);
if (this.isOutputFile) {
isOK = this.getFile31 ();
Clazz.superCall (this, J.adapter.readers.quantum.GenNBOReader, "initializeReader", []);
this.moData.put ("isNormalized", Boolean.TRUE);
} else if (line2.indexOf ("s in the AO basis:") >= 0) {
this.nboType = line2.substring (1, line2.indexOf ("s"));
this.asc.setCollectionName (line1 + ": " + this.nboType + "s");
isOK = this.getFile31 ();
} else {
this.nboType = "AO";
this.asc.setCollectionName (line1 + ": " + this.nboType + "s");
isOK = this.readData31 (line1);
}if (!isOK) JU.Logger.error ("Unimplemented shell type -- no orbitals available: " + this.line);
if (this.isOutputFile) return;
if (isOK) this.readMOs ();
this.continuing = false;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.appendLoadNote ("NBO type " + this.nboType);
if (this.isOpenShell) this.asc.setCurrentModelInfo ("isOpenShell", Boolean.TRUE);
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "readMOs",
function () {
this.nOrbitals0 = this.orbitals.size ();
this.getFile46 ();
if (this.betaOnly) {
this.discardLinesUntilContains ("BETA");
this.filterMO ();
}var isAO = this.nboType.equals ("AO");
var isNBO = !isAO && !this.nboType.equals ("MO");
this.nOrbitals = this.orbitals.size ();
if (this.nOrbitals == 0) return;
this.line = null;
if (!isNBO) this.nOrbitals = this.nOrbitals0 + this.nAOs;
for (var i = this.nOrbitals0; i < this.nOrbitals; i++) {
var mo = this.orbitals.get (i);
var coefs = Clazz.newFloatArray (this.nAOs, 0);
mo.put ("coefficients", coefs);
if (!isAO) {
if (this.line == null) {
while (this.rd () != null && Float.isNaN (this.parseFloatStr (this.line))) {
this.filterMO ();
}
} else {
this.line = null;
}this.fillFloatArray (this.line, 0, coefs);
if (Float.isNaN (coefs[0])) System.out.println ("testing gennboreader");
this.line = null;
} else {
coefs[i] = 1;
}}
if (this.nboType.equals ("NBO")) {
var occupancies = Clazz.newFloatArray (this.nOrbitals - this.nOrbitals0, 0);
this.fillFloatArray (null, 0, occupancies);
for (var i = this.nOrbitals0; i < this.nOrbitals; i++) {
var mo = this.orbitals.get (i);
mo.put ("occupancy", Float.$valueOf (occupancies[i - this.nOrbitals0]));
}
}this.moData.put (this.nboType + "_coefs", this.orbitals);
this.setMOData (false);
this.moData.put ("isNormalized", Boolean.TRUE);
this.moData.put ("nboType", this.nboType);
JU.Logger.info ((this.orbitals.size () - this.nOrbitals0) + " orbitals read");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("SECOND ORDER PERTURBATION THEORY ANALYSIS") >= 0 && !this.orbitalsRead) {
this.nboType = "NBO";
var data = this.getFileData (".37");
if (data == null) return true;
var readerSave = this.reader;
this.reader = JU.Rdr.getBR (data);
this.rd ();
this.rd ();
this.readMOs ();
this.reader = readerSave;
this.orbitalsRead = false;
return true;
}if (this.line.indexOf ("$NRTSTRA") >= 0) {
this.getStructures ("NRTSTRA");
return true;
}if (this.line.indexOf ("$NRTSTRB") >= 0) {
this.getStructures ("NRTSTRB");
return true;
}if (this.line.indexOf ("$NRTSTR") >= 0) {
this.getStructures ("NRTSTR");
return true;
}if (this.line.indexOf (" TOPO ") >= 0) {
this.getStructures ("TOPO" + this.topoType);
this.topoType = "B";
return true;
}if (this.line.indexOf ("$CHOOSE") >= 0) {
this.getStructures ("CHOOSE");
return true;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "getStructures",
function (type) {
if (this.nboParser == null) this.nboParser = new J.adapter.readers.quantum.NBOParser ();
var structures = this.getStructureList ();
var sb = new JU.SB ();
while (!this.rd ().trim ().equals ("$END")) sb.append (this.line).append ("\n");
this.nStructures = this.nboParser.getStructures (sb.toString (), type, structures);
this.appendLoadNote (this.nStructures + " NBO " + type + " resonance structures");
}, "~S");
Clazz.defineMethod (c$, "getStructureList",
function () {
var structures = this.asc.getAtomSetAuxiliaryInfo (this.asc.iSet).get ("nboStructures");
if (structures == null) this.asc.setCurrentModelInfo ("nboStructures", structures = new JU.Lst ());
return structures;
});
Clazz.defineMethod (c$, "getFileData",
function (ext) {
var fileName = this.htParams.get ("fullPathName");
var pt = fileName.lastIndexOf (".");
if (pt < 0) pt = fileName.length;
fileName = fileName.substring (0, pt);
this.moData.put ("nboRoot", fileName);
fileName += ext;
var data = this.vwr.getFileAsString3 (fileName, false, null);
JU.Logger.info (data.length + " bytes read from " + fileName);
if (data.length == 0 || data.indexOf ("java.io.FileNotFound") >= 0 && this.nboType !== "AO") throw new Exception (" supplemental file " + fileName + " was not found");
return data;
}, "~S");
Clazz.defineMethod (c$, "getFile31",
function () {
var data = this.getFileData (".31");
var readerSave = this.reader;
this.reader = JU.Rdr.getBR (data);
return (this.readData31 (null) && (this.reader = readerSave) != null);
});
Clazz.defineMethod (c$, "getFile46",
function () {
var data = this.getFileData (".46");
var readerSave = this.reader;
this.reader = JU.Rdr.getBR (data);
this.readData46 ();
this.reader = readerSave;
});
Clazz.defineMethod (c$, "readData47",
function () {
this.allowNoOrbitals = true;
this.discardLinesUntilContains ("$COORD");
this.asc.newAtomSet ();
this.asc.setAtomSetName (this.rd ().trim ());
while (this.rd ().indexOf ("$END") < 0) {
var tokens = this.getTokens ();
this.addAtomXYZSymName (tokens, 2, null, null).elementNumber = this.parseIntStr (tokens[0]);
}
this.discardLinesUntilContains ("$BASIS");
var centers = this.getIntData ();
var labels = this.getIntData ();
this.discardLinesUntilContains ("NSHELL =");
this.shellCount = this.parseIntAt (this.line, 10);
this.gaussianCount = this.parseIntAt (this.rd (), 10);
this.rd ();
var ncomp = this.getIntData ();
var nprim = this.getIntData ();
var nptr = this.getIntData ();
this.shells = new JU.Lst ();
this.gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) this.gaussians[i] = Clazz.newFloatArray (6, 0);
this.nOrbitals = 0;
var ptCenter = 0;
var l = this.line;
for (var i = 0; i < this.shellCount; i++) {
var slater = Clazz.newIntArray (4, 0);
var nc = ncomp[i];
slater[0] = centers[ptCenter];
this.line = "";
for (var ii = 0; ii < nc; ii++) this.line += labels[ptCenter++] + " ";
if (!this.fillSlater (slater, nc, nptr[i] - 1, nprim[i])) return;
}
this.line = l;
this.getAlphasAndExponents ();
this.nboType = "AO";
this.readMOs ();
this.continuing = false;
});
Clazz.defineMethod (c$, "getIntData",
function () {
while (this.line.indexOf ("=") < 0) this.rd ();
var s = this.line.substring (this.line.indexOf ("=") + 1);
this.line = "";
while (this.rd ().indexOf ("=") < 0 && this.line.indexOf ("$") < 0) s += this.line;
var tokens = JU.PT.getTokens (s);
var f = Clazz.newIntArray (tokens.length, 0);
for (var i = f.length; --i >= 0; ) f[i] = this.parseIntStr (tokens[i]);
return f;
});
Clazz.defineMethod (c$, "fillSlater",
function (slater, n, pt, ng) {
this.nOrbitals += n;
switch (n) {
case 1:
slater[1] = 0;
break;
case 3:
if (!this.getDFMap ("P", this.line, 1, J.adapter.readers.quantum.GenNBOReader.$P_LIST, 3)) return false;
slater[1] = 1;
break;
case 4:
if (!this.getDFMap ("SP", this.line, 2, J.adapter.readers.quantum.GenNBOReader.SP_LIST, 1)) return false;
slater[1] = 2;
break;
case 5:
if (!this.getDFMap ("DS", this.line, 3, J.adapter.readers.quantum.GenNBOReader.$DS_LIST, 3)) return false;
slater[1] = 3;
break;
case 6:
if (!this.getDFMap ("DC", this.line, 4, J.adapter.readers.quantum.GenNBOReader.$DC_LIST, 3)) return false;
slater[1] = 4;
break;
case 7:
if (!this.getDFMap ("FS", this.line, 5, J.adapter.readers.quantum.GenNBOReader.$FS_LIST, 3)) return false;
slater[1] = 5;
break;
case 10:
if (!this.getDFMap ("FC", this.line, 6, J.adapter.readers.quantum.GenNBOReader.$FC_LIST, 3)) return false;
slater[1] = 6;
break;
}
slater[2] = pt + 1;
slater[3] = ng;
this.shells.addLast (slater);
return true;
}, "~A,~N,~N,~N");
Clazz.defineMethod (c$, "getAlphasAndExponents",
function () {
for (var j = 0; j < 5; j++) {
if (this.line.indexOf ("=") < 0) this.rd ();
if (this.line.indexOf ("$END") >= 0) break;
this.line = this.line.substring (this.line.indexOf ("=") + 1);
var temp = this.fillFloatArray (this.line, 0, Clazz.newFloatArray (this.gaussianCount, 0));
for (var i = 0; i < this.gaussianCount; i++) {
this.gaussians[i][j] = temp[i];
if (j > 1) this.gaussians[i][5] += temp[i];
}
}
for (var i = 0; i < this.gaussianCount; i++) {
if (this.gaussians[i][1] == 0) this.gaussians[i][1] = this.gaussians[i][5];
}
if (this.debugging) {
JU.Logger.debug (this.shells.size () + " slater shells read");
JU.Logger.debug (this.gaussians.length + " gaussian primitives read");
}});
Clazz.defineMethod (c$, "readData31",
function (line1) {
if (line1 == null) {
line1 = this.rd ();
this.rd ();
}this.rd ();
var tokens = JU.PT.getTokens (this.rd ());
var ac = this.parseIntStr (tokens[0]);
this.shellCount = this.parseIntStr (tokens[1]);
this.gaussianCount = this.parseIntStr (tokens[2]);
this.rd ();
this.asc.newAtomSet ();
this.asc.setAtomSetName (this.nboType + "s: " + line1.trim ());
this.asc.setCurrentModelInfo ("nboType", this.nboType);
for (var i = 0; i < ac; i++) {
tokens = JU.PT.getTokens (this.rd ());
var z = this.parseIntStr (tokens[0]);
if (z < 0) continue;
var atom = this.asc.addNewAtom ();
atom.elementNumber = z;
this.setAtomCoordTokens (atom, tokens, 1);
}
this.shells = new JU.Lst ();
this.gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) this.gaussians[i] = Clazz.newFloatArray (6, 0);
this.rd ();
this.nOrbitals = 0;
for (var i = 0; i < this.shellCount; i++) {
tokens = JU.PT.getTokens (this.rd ());
var slater = Clazz.newIntArray (4, 0);
slater[0] = this.parseIntStr (tokens[0]);
var n = this.parseIntStr (tokens[1]);
var pt = this.parseIntStr (tokens[2]) - 1;
var ng = this.parseIntStr (tokens[3]);
this.line = this.rd ().trim ();
if (!this.fillSlater (slater, n, pt, ng)) return false;
}
this.rd ();
this.getAlphasAndExponents ();
return true;
}, "~S");
Clazz.defineMethod (c$, "readData46",
function () {
var map = new java.util.Hashtable ();
var tokens = new Array (0);
this.rd ();
this.nAOs = this.nOrbitals;
while (this.line != null && this.line.length > 0) {
tokens = JU.PT.getTokens (this.line);
var type = tokens[0];
this.isOpenShell = (tokens.length == 3);
var ab = (this.isOpenShell ? tokens[1] : "");
var count = tokens[tokens.length - 1];
var key = (ab.equals ("BETA") ? "beta_" : "") + type;
if (this.parseIntStr (count) != this.nOrbitals) {
JU.Logger.error ("file 46 number of orbitals (" + count + ") does not match nOrbitals: " + this.nOrbitals);
return;
}var sb = new JU.SB ();
while (this.rd () != null && this.line.length > 4 && " NA NB AO NH".indexOf (this.line.substring (1, 4)) < 0) sb.append (this.line);
sb.appendC (' ');
var data = JU.PT.rep (sb.toString (), " )", ")");
sb = new JU.SB ();
for (var i = 0, n = data.length - 1; i < n; i++) {
var c = data.charAt (i);
switch (c) {
case '(':
case '-':
if (data.charAt (i + 1) == ' ') i++;
break;
case ' ':
if (JU.PT.isDigit (data.charAt (i + 1)) || data.charAt (i + 1) == '(') continue;
break;
}
sb.appendC (c);
}
tokens = JU.PT.getTokens (sb.toString ());
map.put (key, tokens);
}
var type = this.nboType;
if (type.charAt (0) == 'P') type = type.substring (1);
if (type.equals ("NLMO")) type = "NBO";
tokens = map.get ((this.betaOnly ? "beta_" : "") + type);
this.moData.put ("nboLabelMap", map);
if (tokens == null) {
tokens = new Array (this.nAOs);
for (var i = 0; i < this.nAOs; i++) tokens[i] = this.nboType + (i + 1);
map.put (this.nboType, tokens);
if (this.isOpenShell) map.put ("beta_" + this.nboType, tokens);
}this.moData.put ("nboLabels", tokens);
var addBetaSet = (this.isOpenShell && !this.betaOnly && !this.is47File);
if (addBetaSet) this.nOrbitals *= 2;
for (var i = 0; i < this.nOrbitals; i++) this.setMO ( new java.util.Hashtable ());
var qs = new J.quantum.QS ();
qs.setNboLabels (tokens, this.nAOs, this.orbitals, this.nOrbitals0, this.nboType);
if (addBetaSet) {
this.moData.put ("firstBeta", Integer.$valueOf (this.nAOs));
qs.setNboLabels (map.get ("beta_" + type), this.nAOs, this.orbitals, this.nOrbitals0 + this.nAOs, this.nboType);
}var structures = this.getStructureList ();
J.adapter.readers.quantum.NBOParser.getStructures46 (map.get ("NBO"), "alpha", structures, this.asc.ac);
J.adapter.readers.quantum.NBOParser.getStructures46 (map.get ("beta_NBO"), "beta", structures, this.asc.ac);
});
Clazz.defineStatics (c$,
"$P_LIST", "101 102 103",
"SP_LIST", "1 101 102 103",
"$DS_LIST", "255 252 253 254 251",
"$DC_LIST", "201 204 206 202 203 205",
"$FS_LIST", "351 352 353 354 355 356 357",
"$FC_LIST", "301 307 310 304 302 303 306 309 308 305");
});

249
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader"], "J.adapter.readers.quantum.JaguarReader", ["java.lang.Boolean", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.moCount = 0;
this.lumoEnergy = 3.4028235E38;
this.haveLine = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "JaguarReader", J.adapter.readers.quantum.MOReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.startsWith (" Input geometry:") || this.line.startsWith (" Symmetrized geometry:") || this.line.startsWith (" final geometry:")) {
this.readAtoms ();
return true;
}if (this.line.startsWith (" Atomic charges from electrostatic potential:")) {
this.readCharges ();
return true;
}if (this.line.startsWith (" number of basis functions....")) {
this.moCount = this.parseIntAt (this.line, 32);
return true;
}if (this.line.startsWith (" basis set:")) {
this.moData.put ("energyUnits", "");
this.moData.put ("calculationType", this.calculationType = this.line.substring (13).trim ());
if ("sto-3g".equals (this.calculationType)) {
JU.Logger.error ("STO-3G not supported for Jaguar -- unusual SP basis definition.");
}return true;
}if (this.line.indexOf ("XXXXXShell information") >= 0) {
this.readUnnormalizedBasis ();
return true;
}if (this.line.indexOf ("Normalized coefficients") >= 0) {
if (!"sto-3g".equals (this.calculationType)) this.readBasisNormalized ();
return true;
}if (this.line.startsWith (" LUMO energy:")) {
this.lumoEnergy = this.parseFloatStr (this.line.substring (13));
return true;
}if (this.line.indexOf ("final wvfn") >= 0) {
if (this.shells != null) this.readJaguarMolecularOrbitals ();
return true;
}if (this.line.startsWith (" harmonic frequencies in")) {
this.readFrequencies ();
this.continuing = false;
return false;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.discardPreviousAtoms ();
this.readLines (2);
while (this.rd () != null && this.line.length >= 60 && this.line.charAt (2) != ' ') {
var tokens = this.getTokens ();
var atomName = tokens[0];
if (atomName.length < 2) return;
var ch2 = atomName.charAt (1);
var elementSymbol = (ch2 >= 'a' && ch2 <= 'z' ? atomName.substring (0, 2) : atomName.substring (0, 1));
this.addAtomXYZSymName (tokens, 1, elementSymbol, atomName);
}
});
Clazz.defineMethod (c$, "readCharges",
function () {
var iAtom = 0;
while (this.rd () != null && this.line.indexOf ("sum") < 0) {
if (this.line.indexOf ("Charge") < 0) continue;
var tokens = this.getTokens ();
for (var i = 1; i < tokens.length; i++) this.asc.atoms[iAtom++].partialCharge = this.parseFloatStr (tokens[i]);
}
});
Clazz.defineMethod (c$, "readUnnormalizedBasis",
function () {
var lastAtom = "";
var iAtom = 0;
var sdata = Clazz.newIntArray (this.moCount, 4, 0);
var sgdata = JU.AU.createArrayOfArrayList (this.moCount);
var tokens;
this.gaussianCount = 0;
this.discardLinesUntilContains ("--------");
while (this.rd () != null && (tokens = this.getTokens ()).length == 9) {
var jCont = this.parseIntStr (tokens[2]);
if (jCont > 0) {
if (!tokens[0].equals (lastAtom)) iAtom++;
lastAtom = tokens[0];
var iFunc = this.parseIntStr (tokens[5]);
var iType = this.parseIntStr (tokens[4]);
if (iType <= 2) iType--;
if (sgdata[iFunc] == null) {
sdata[iFunc][0] = iAtom;
sdata[iFunc][1] = iType;
sdata[iFunc][2] = 0;
sdata[iFunc][3] = 0;
sgdata[iFunc] = new JU.Lst ();
}var factor = 1;
sgdata[iFunc].addLast ( Clazz.newFloatArray (-1, [this.parseFloatStr (tokens[6]), this.parseFloatStr (tokens[8]) * factor]));
this.gaussianCount += jCont;
for (var i = jCont - 1; --i >= 0; ) {
tokens = JU.PT.getTokens (this.rd ());
sgdata[iFunc].addLast ( Clazz.newFloatArray (-1, [this.parseFloatStr (tokens[6]), this.parseFloatStr (tokens[8]) * factor]));
}
}}
var garray = JU.AU.newFloat2 (this.gaussianCount);
var sarray = new JU.Lst ();
this.gaussianCount = 0;
for (var i = 0; i < this.moCount; i++) if (sgdata[i] != null) {
var n = sgdata[i].size ();
sdata[i][2] = this.gaussianCount;
sdata[i][3] = n;
for (var j = 0; j < n; j++) {
garray[this.gaussianCount++] = sgdata[i].get (j);
}
sarray.addLast (sdata[i]);
}
this.moData.put ("shells", sarray);
this.moData.put ("gaussians", garray);
if (this.debugging) {
JU.Logger.debug (sarray.size () + " slater shells read");
JU.Logger.debug (this.gaussianCount + " gaussian primitives read");
}});
Clazz.defineMethod (c$, "readBasisNormalized",
function () {
var lastAtom = "";
var iAtom = 0;
var id;
var iFunc = 0;
var iFuncLast = -1;
var sarray = new JU.Lst ();
var gdata = new JU.Lst ();
this.gaussianCount = 0;
var sdata = null;
this.discardLinesUntilContains ("--------");
while (this.rd () != null && this.line.length > 3) {
var tokens = this.getTokens ();
if (tokens.length == 4) {
id = tokens[0];
continue;
}if (!tokens[0].equals (lastAtom)) iAtom++;
lastAtom = tokens[0];
id = tokens[2];
var iType = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (id);
iFunc = this.parseIntStr (tokens[3]) - 1;
var gPtr = gdata.size ();
if (iFunc == iFuncLast) {
sdata[3]++;
} else if (iFunc < iFuncLast) {
for (var i = gdata.size (); --i >= 0; ) {
if (gdata.get (i)[2] == iFunc) {
gPtr = i + 1;
break;
}}
for (var i = sarray.size (); --i >= 0; ) {
if (sarray.get (i)[4] == iFunc) {
sarray.get (i)[3]++;
while (++i < sarray.size ()) {
sarray.get (i)[2]++;
}
break;
}}
} else {
sdata = Clazz.newIntArray (-1, [iAtom, iType, this.gaussianCount + 1, 1, iFunc]);
sarray.addLast (sdata);
iFuncLast = iFunc;
}this.gaussianCount++;
var z = this.parseFloatStr (tokens[4]);
var rCoef = this.parseFloatStr (tokens[5]);
if (id.equals ("XX")) rCoef *= 1.7320508;
gdata.add (gPtr, Clazz.newFloatArray (-1, [z, rCoef, iFunc]));
}
var garray = JU.AU.newFloat2 (this.gaussianCount);
for (var i = gdata.size (); --i >= 0; ) garray[i] = gdata.get (i);
this.moData.put ("shells", this.shells = sarray);
this.moData.put ("gaussians", garray);
if (this.debugging) {
JU.Logger.debug (sarray.size () + " slater shells read");
JU.Logger.debug (this.gaussianCount + " gaussian primitives read");
}this.moData.put ("isNormalized", Boolean.TRUE);
});
Clazz.defineMethod (c$, "readJaguarMolecularOrbitals",
function () {
var dataBlock = new Array (this.moCount);
this.rd ();
this.rd ();
this.rd ();
var nMo = 0;
while (this.line != null) {
this.rd ();
this.rd ();
this.rd ();
if (this.line == null || this.line.indexOf ("eigenvalues-") < 0) break;
var eigenValues = this.getTokens ();
var n = eigenValues.length - 1;
this.fillDataBlock (dataBlock, 0);
var occ = 2;
for (var iOrb = 0; iOrb < n; iOrb++) {
var coefs = Clazz.newFloatArray (this.moCount, 0);
var mo = new java.util.Hashtable ();
var energy = this.parseFloatStr (eigenValues[iOrb + 1]);
mo.put ("energy", Float.$valueOf (energy));
if (Math.abs (energy - this.lumoEnergy) < 0.0001) {
this.moData.put ("HOMO", Integer.$valueOf (nMo));
this.lumoEnergy = 3.4028235E38;
occ = 0;
}mo.put ("occupancy", Float.$valueOf (occ));
nMo++;
for (var i = 0, pt = 0; i < this.moCount; i++) {
coefs[pt++] = this.parseFloatStr (dataBlock[i][iOrb + 3]);
}
mo.put ("coefficients", coefs);
this.setMO (mo);
}
}
this.moData.put ("mos", this.orbitals);
this.finalizeMOData (this.moData);
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
var ac = this.asc.getLastAtomSetAtomCount ();
this.discardLinesUntilStartsWith (" frequencies ");
while (this.line != null && this.line.startsWith (" frequencies ")) {
var iAtom0 = this.asc.ac;
var frequencies = this.getTokens ();
var frequencyCount = frequencies.length - 1;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
var symmetries = null;
var intensities = null;
while (this.line != null && this.line.charAt (2) != ' ') {
if (this.line.indexOf ("symmetries") >= 0) symmetries = this.getTokens ();
else if (this.line.indexOf ("intensities") >= 0) intensities = this.getTokens ();
this.rd ();
}
for (var i = 0; i < frequencyCount; i++) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneFirstAtomSet (0);
this.asc.setAtomSetFrequency (null, symmetries == null ? null : symmetries[i + 1], frequencies[i + 1], null);
if (intensities != null) this.asc.setAtomSetModelProperty ("IRIntensity", intensities[i + 1] + " km/mol");
}
this.haveLine = true;
this.fillFrequencyData (iAtom0, ac, ac, ignore, false, 0, 0, null, 0);
this.rd ();
this.rd ();
}
});
Clazz.defineMethod (c$, "rd",
function () {
if (!this.haveLine) return Clazz.superCall (this, J.adapter.readers.quantum.JaguarReader, "rd", []);
this.haveLine = false;
return this.line;
});
Clazz.defineStatics (c$,
"ROOT3", 1.73205080756887729);
});

316
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.BasisFunctionReader"], "J.adapter.readers.quantum.MOReader", ["java.lang.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.quantum.QS", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.shellCount = 0;
this.gaussianCount = 0;
this.gaussians = null;
this.energyUnits = "";
this.moTypes = null;
this.getNBOs = false;
this.getNBOCharges = false;
this.haveNboCharges = false;
this.haveNboOrbitals = false;
this.orbitalsRead = false;
this.lastMoData = null;
this.allowNoOrbitals = false;
this.HEADER_GAMESS_UK_MO = 3;
this.HEADER_GAMESS_OCCUPANCIES = 2;
this.HEADER_GAMESS_ORIGINAL = 1;
this.HEADER_NONE = 0;
this.haveCoeffMap = false;
this.iMo0 = 1;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "MOReader", J.adapter.readers.quantum.BasisFunctionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.line = "\nNBOs";
this.getNBOs = (this.filter != null && this.filterMO ());
this.line = "\nNBOCHARGES";
this.getNBOCharges = (this.filter != null && this.filterMO ());
this.checkAndRemoveFilterKey ("NBOCHARGES");
});
Clazz.defineMethod (c$, "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$, "checkNboLine",
function () {
if (this.getNBOs) {
if (this.line.indexOf ("(Occupancy) Bond orbital/ Coefficients/ Hybrids") >= 0) {
this.getNboTypes ();
return false;
}if (this.line.indexOf ("NBOs in the AO basis:") >= 0) {
this.readMolecularOrbitals (0);
return false;
}if (this.line.indexOf (" SECOND ORDER PERTURBATION THEORY ANALYSIS") >= 0) {
this.readSecondOrderData ();
return false;
}}if (this.getNBOCharges && this.line.indexOf ("Summary of Natural Population Analysis:") >= 0) {
this.getNboCharges ();
return true;
}return true;
});
Clazz.defineMethod (c$, "getNboCharges",
function () {
if (this.haveNboCharges) return;
this.discardLinesUntilContains ("----");
this.discardLinesUntilContains ("----");
this.haveNboCharges = true;
var ac = this.asc.ac;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var atoms = this.asc.atoms;
for (var i = i0; i < ac; ++i) {
while (atoms[i].elementNumber == 0) ++i;
var tokens = JU.PT.getTokens (this.rd ());
var charge;
if (tokens == null || tokens.length < 3 || Float.isNaN (charge = this.parseFloatStr (tokens[2]))) {
JU.Logger.info ("Error reading NBO charges: " + this.line);
return;
}atoms[i].partialCharge = charge;
if (this.debugging) JU.Logger.debug ("Atom " + i + " using NBOcharge: " + charge);
}
JU.Logger.info ("Using NBO charges for Model " + this.asc.atomSetCount);
});
Clazz.defineMethod (c$, "getNboTypes",
function () {
this.moTypes = new JU.Lst ();
this.iMo0 = (this.orbitals == null ? 0 : this.orbitals.size ()) + 1;
this.rd ();
this.rd ();
var n = 0;
var pt = 0;
while (this.line != null && (pt = this.line.indexOf (".")) >= 0 && pt < 10) {
if (this.parseIntRange (this.line, 0, pt) != n + 1) break;
this.moTypes.add (n++, this.line.substring (pt + 1, Math.min (40, this.line.length)).trim ());
while (this.rd () != null && this.line.startsWith (" ")) {
}
}
JU.Logger.info (n + " natural bond AO basis functions found");
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function (headerType) {
if (this.ignoreMOs) {
this.rd ();
return;
}this.dfCoefMaps = null;
if (this.haveNboOrbitals) {
this.orbitals = new JU.Lst ();
this.alphaBeta = "";
}this.haveNboOrbitals = true;
this.orbitalsRead = true;
var mos = null;
var data = null;
var dCoeffLabels = "";
var fCoeffLabels = "";
var pCoeffLabels = "";
var ptOffset = -1;
var fieldSize = 0;
var nThisLine = 0;
this.rd ();
var moCount = 0;
var nBlank = 0;
var haveMOs = false;
if (this.line.indexOf ("---") >= 0) this.rd ();
while (this.rd () != null) {
var tokens = this.getTokens ();
if (this.debugging) {
JU.Logger.debug (tokens.length + " --- " + this.line);
}if (this.line.indexOf ("end") >= 0) break;
if (this.line.indexOf (" ALPHA SET ") >= 0) {
this.alphaBeta = "alpha";
if (this.rd () == null) break;
} else if (this.line.indexOf (" BETA SET ") >= 0) {
if (haveMOs) break;
this.alphaBeta = "beta";
if (this.rd () == null) break;
}var str = this.line.toUpperCase ();
if (str.length == 0 || str.indexOf ("--") >= 0 || str.indexOf (".....") >= 0 || str.indexOf ("NBO BASIS") >= 0 || str.indexOf ("CI EIGENVECTORS WILL BE LABELED") >= 0 || str.indexOf ("LZ VALUE") >= 0 || str.indexOf (" THIS LOCALIZATION HAD") >= 0) {
if (!this.haveCoeffMap) {
this.haveCoeffMap = true;
var isOK = true;
if (pCoeffLabels.length > 0) isOK = this.getDFMap ("P", pCoeffLabels, 1, "(PX) (PY) (PZ)", 4);
if (dCoeffLabels.length > 0) {
if (dCoeffLabels.indexOf ("X") >= 0) isOK = this.getDFMap ("DC", dCoeffLabels, 4, "DXX DYY DZZ DXY DXZ DYZ", 2);
else if (dCoeffLabels.indexOf ("(D6)") >= 0) isOK = this.getDFMap ("DC", dCoeffLabels, 4, "(D1) (D4) (D6) (D2) (D3) (D5)", 4);
else isOK = this.getDFMap ("DS", dCoeffLabels, 3, "(D5) (D2) (D3) (D4) (D1)", 4);
}if (fCoeffLabels.length > 0) {
if (fCoeffLabels.indexOf ("X") >= 0) isOK = this.getDFMap ("FC", fCoeffLabels, 6, "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ", 2);
else if (fCoeffLabels.indexOf ("(F10)") >= 0) isOK = this.getDFMap ("FC", fCoeffLabels, 6, J.adapter.readers.quantum.MOReader.FC_LIST, 5);
else isOK = this.getDFMap ("FS", fCoeffLabels, 5, "(F1) (F2) (F3) (F4) (F5) (F6) (F7)", 4);
}if (!isOK) {
}}if (str.length == 0) nBlank++;
else nBlank = 0;
if (nBlank == 2) break;
if (str.indexOf ("LZ VALUE") >= 0) this.discardLinesUntilBlank ();
for (var iMo = 0; iMo < nThisLine; iMo++) {
var coefs = Clazz.newFloatArray (data[iMo].size (), 0);
var iCoeff = 0;
while (iCoeff < coefs.length) {
coefs[iCoeff] = this.parseFloatStr (data[iMo].get (iCoeff));
iCoeff++;
}
haveMOs = true;
this.addCoef (mos[iMo], coefs, null, NaN, NaN, moCount++);
}
nThisLine = 0;
if (this.line.length == 0) continue;
break;
}nBlank = 0;
if (nThisLine == 0) {
nThisLine = tokens.length;
if (tokens[0].equals ("AO")) {
nThisLine--;
ptOffset = 16;
fieldSize = 8;
}if (mos == null || nThisLine > mos.length) {
mos = JU.AU.createArrayOfHashtable (nThisLine);
data = JU.AU.createArrayOfArrayList (nThisLine);
}for (var i = 0; i < nThisLine; i++) {
mos[i] = new java.util.Hashtable ();
data[i] = new JU.Lst ();
}
this.getMOHeader (headerType, tokens, mos, nThisLine);
continue;
}var nSkip = tokens.length - nThisLine;
var type = tokens[nSkip - 1];
var ch;
if (type.charAt (0) == '(') {
ch = type.charAt (1);
if (!this.haveCoeffMap) {
switch (ch) {
case 'p':
pCoeffLabels += " " + type.toUpperCase ();
break;
case 'd':
dCoeffLabels += " " + J.adapter.readers.quantum.BasisFunctionReader.canonicalizeQuantumSubshellTag (type.toUpperCase ());
break;
case 'f':
fCoeffLabels += " " + J.adapter.readers.quantum.BasisFunctionReader.canonicalizeQuantumSubshellTag (type.toUpperCase ());
break;
case 's':
}
}} else {
var nChar = type.length;
ch = (nChar < 4 ? 'S' : nChar == 4 ? 'G' : nChar == 5 ? 'H' : '?');
if (!this.haveCoeffMap && nChar == 3) fCoeffLabels += " " + J.adapter.readers.quantum.BasisFunctionReader.canonicalizeQuantumSubshellTag (type.toUpperCase ());
else if (!this.haveCoeffMap && nChar == 2) dCoeffLabels += " " + J.adapter.readers.quantum.BasisFunctionReader.canonicalizeQuantumSubshellTag (type.toUpperCase ());
}if (J.quantum.QS.isQuantumBasisSupported (ch)) {
if (ptOffset < 0) {
for (var i = 0; i < nThisLine; i++) data[i].addLast (tokens[i + nSkip]);
} else {
var pt = ptOffset;
for (var i = 0; i < nThisLine; i++, pt += fieldSize) data[i].addLast (this.line.substring (pt, pt + fieldSize).trim ());
}}this.line = "";
}
this.energyUnits = "a.u.";
this.setMOData (!this.alphaBeta.equals ("alpha"));
this.haveCoeffMap = false;
this.dfCoefMaps = null;
}, "~N");
Clazz.defineMethod (c$, "addCoef",
function (mo, coefs, type, energy, occ, moCount) {
mo.put ("coefficients", coefs);
if (this.moTypes != null) {
type = this.moTypes.get (moCount % this.moTypes.size ());
occ = (type.indexOf ("*") >= 0 ? 0 : 2);
} else if (this.alphaBeta.length > 0) {
type = this.alphaBeta;
}if (type != null) mo.put ("type", type);
if (!Float.isNaN (energy)) mo.put ("energy", Float.$valueOf (energy));
if (!Float.isNaN (occ)) mo.put ("occupancy", Float.$valueOf (occ));
this.setMO (mo);
}, "java.util.Map,~A,~S,~N,~N,~N");
Clazz.defineMethod (c$, "getMOHeader",
function (headerType, tokens, mos, nThisLine) {
this.rd ();
switch (headerType) {
default:
case 0:
return;
case 3:
for (var i = 0; i < nThisLine; i++) mos[i].put ("energy", Float.$valueOf (JU.PT.fVal (tokens[i])));
this.readLines (5);
return;
case 1:
tokens = this.getTokens ();
if (tokens.length == 0) tokens = JU.PT.getTokens (this.rd ());
for (var i = 0; i < nThisLine; i++) {
mos[i].put ("energy", Float.$valueOf (JU.PT.fVal (tokens[i])));
}
this.rd ();
break;
case 2:
var haveSymmetry = (this.line.length > 0 || this.rd () != null);
tokens = this.getTokens ();
for (var i = 0; i < nThisLine; i++) mos[i].put ("occupancy", Float.$valueOf (tokens[i].charAt (0) == '-' ? 2.0 : this.parseFloatStr (tokens[i])));
this.rd ();
if (!haveSymmetry) return;
}
if (this.line.length > 0) {
tokens = this.getTokens ();
for (var i = 0; i < nThisLine; i++) mos[i].put ("symmetry", tokens[i]);
}}, "~N,~A,~A,~N");
Clazz.defineMethod (c$, "addMOData",
function (nColumns, data, mos) {
for (var i = 0; i < nColumns; i++) {
var coefs = Clazz.newFloatArray (data[i].size (), 0);
for (var j = coefs.length; --j >= 0; ) coefs[j] = this.parseFloatStr (data[i].get (j));
mos[i].put ("coefficients", coefs);
this.setMO (mos[i]);
}
}, "~N,~A,~A");
Clazz.defineMethod (c$, "setMOData",
function (clearOrbitals) {
if (this.shells != null && this.gaussians != null && (this.allowNoOrbitals || this.orbitals.size () != 0)) {
this.moData.put ("calculationType", this.calculationType);
this.moData.put ("energyUnits", this.energyUnits);
this.moData.put ("shells", this.shells);
this.moData.put ("gaussians", this.gaussians);
this.moData.put ("mos", this.orbitals);
this.finalizeMOData (this.lastMoData = this.moData);
}if (clearOrbitals) {
this.clearOrbitals ();
}}, "~B");
Clazz.defineMethod (c$, "readSecondOrderData",
function () {
this.readLines (5);
if (this.lastMoData == null || this.moTypes == null) return;
var ht = new java.util.Hashtable ();
for (var i = this.moTypes.size (); --i >= 0; ) ht.put (JU.PT.rep (this.moTypes.get (i).substring (10), " ", ""), Integer.$valueOf (i + this.iMo0));
var strSecondOrderData = new JU.Lst ();
while (this.rd () != null && this.line.indexOf ("NBO") < 0) {
if (this.line.length < 5 || this.line.charAt (4) != '.') continue;
strSecondOrderData.addLast ( Clazz.newArray (-1, [JU.PT.rep (this.line.substring (5, 27).trim (), " ", ""), JU.PT.rep (this.line.substring (32, 54).trim (), " ", ""), this.line.substring (55, 62).trim (), this.line.substring (71).trim ()]));
}
var secondOrderData = Clazz.newFloatArray (strSecondOrderData.size (), 4, 0);
this.lastMoData.put ("secondOrderData", secondOrderData);
this.lastMoData = null;
var IMO;
for (var i = strSecondOrderData.size (); --i >= 0; ) {
var a = strSecondOrderData.get (i);
IMO = ht.get (a[0]);
if (IMO != null) secondOrderData[i][0] = IMO.intValue ();
IMO = ht.get (a[1]);
if (IMO != null) secondOrderData[i][1] = IMO.intValue ();
secondOrderData[i][2] = this.parseFloatStr (a[2]);
secondOrderData[i][3] = this.parseFloatStr (a[3]);
}
});
Clazz.defineStatics (c$,
"P_LIST", "(PX) (PY) (PZ)",
"DS_LIST", "(D5) (D2) (D3) (D4) (D1)",
"DC_LIST", "(D1) (D4) (D6) (D2) (D3) (D5)",
"FS_LIST", "(F1) (F2) (F3) (F4) (F5) (F6) (F7)",
"FC_LIST", "(F1) (F2) (F10) (F4) (F2) (F3) (F6) (F9) (F8) (F5)");
});

372
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MopacSlaterReader", "JU.BS"], "J.adapter.readers.quantum.MoldenReader", ["java.lang.Exception", "$.Float", "java.util.Arrays", "$.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.loadGeometries = false;
this.loadVibrations = false;
this.vibOnly = false;
this.optOnly = false;
this.doSort = true;
this.orbitalType = "";
this.modelAtomCount = 0;
this.bsAtomOK = null;
this.bsBadIndex = null;
this.nSPDF = null;
this.haveEnergy = true;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "MoldenReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.prepareFields (c$, function () {
this.bsAtomOK = new JU.BS ();
this.bsBadIndex = new JU.BS ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.vibOnly = this.checkFilterKey ("VIBONLY");
this.optOnly = this.checkFilterKey ("OPTONLY");
this.doSort = !this.checkFilterKey ("NOSORT");
this.loadGeometries = !this.vibOnly && this.desiredVibrationNumber < 0 && !this.checkFilterKey ("NOOPT");
this.loadVibrations = !this.optOnly && this.desiredModelNumber < 0 && !this.checkFilterKey ("NOVIB");
if (this.checkFilterKey ("ALPHA")) this.filter = "alpha";
else if (this.checkFilterKey ("BETA")) this.filter = "beta";
else this.filter = this.getFilter ("SYM=");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (!this.line.contains ("[")) return true;
this.line = this.line.toUpperCase ().trim ();
if (!this.line.startsWith ("[")) return true;
JU.Logger.info (this.line);
if (this.line.indexOf ("[ATOMS]") == 0) {
this.readAtoms ();
this.modelAtomCount = this.asc.atomSetAtomCounts[0];
if (this.asc.atomSetCount == 1 && this.moData != null) this.finalizeMOData (this.moData);
return false;
}if (this.line.indexOf ("[GTO]") == 0) return this.readGaussianBasis ();
if (this.line.indexOf ("[STO]") == 0) return this.readSlaterBasis ();
if (this.line.indexOf ("[MO]") == 0) return (!this.doReadMolecularOrbitals || this.readMolecularOrbitals ());
if (this.line.indexOf ("[FREQ]") == 0) return (!this.loadVibrations || this.readFreqsAndModes ());
if (this.line.indexOf ("[GEOCONV]") == 0) return (!this.loadGeometries || this.readGeometryOptimization ());
if (this.checkOrbitalType (this.line)) return true;
if (this.checkSymmetry ()) return false;
return true;
});
Clazz.defineMethod (c$, "checkSymmetry",
function () {
if (this.line.startsWith ("[SPACEGROUP]")) {
this.setSpaceGroupName (this.rd ());
this.rd ();
return true;
}if (this.line.startsWith ("[OPERATORS]")) {
while (this.rd () != null && this.line.indexOf ("[") < 0) if (this.line.length > 0) {
JU.Logger.info ("adding operator " + this.line);
this.setSymmetryOperator (this.line);
}
return true;
}if (this.line.startsWith ("[CELL]")) {
this.rd ();
JU.Logger.info ("setting cell dimensions " + this.line);
this.next[0] = 0;
for (var i = 0; i < 6; i++) this.setUnitCellItem (i, this.parseFloat ());
this.rd ();
return true;
}if (this.line.startsWith ("[CELLAXES]")) {
var f = Clazz.newFloatArray (9, 0);
this.fillFloatArray (null, 0, f);
this.addExplicitLatticeVector (0, f, 0);
this.addExplicitLatticeVector (1, f, 3);
this.addExplicitLatticeVector (2, f, 6);
return true;
}return false;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (!this.bsBadIndex.isEmpty ()) try {
var ilast = 0;
var atoms = this.asc.atoms;
var nAtoms = this.asc.ac;
this.bsAtomOK.set (nAtoms);
var n = this.shells.size ();
for (var i = 0; i < n; i++) {
var iatom = this.shells.get (i)[0];
if (iatom != 2147483647) {
ilast = atoms[iatom - 1].elementNumber;
continue;
}for (var j = this.bsAtomOK.nextClearBit (0); j >= 0; j = this.bsAtomOK.nextClearBit (j + 1)) {
if (atoms[j].elementNumber == ilast) {
this.shells.get (i)[0] = j + 1;
JU.Logger.info ("MoldenReader assigning shells starting with " + i + " for ** to atom " + (j + 1) + " z " + ilast);
for (; ++i < n && !this.bsBadIndex.get (i) && this.shells.get (i)[0] == 2147483647; ) this.shells.get (i)[0] = j + 1;
i--;
this.bsAtomOK.set (j);
break;
}}
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
JU.Logger.error ("Molden reader could not assign shells -- abandoning MOs");
this.asc.setCurrentModelInfo ("moData", null);
} else {
throw e;
}
}
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "readAtoms",
function () {
var coordUnit = JU.PT.getTokens (this.line.$replace (']', ' '))[1];
var isFractional = (coordUnit.indexOf ("FRACTIONAL") >= 0);
var isAU = (!isFractional && coordUnit.indexOf ("ANGS") < 0);
if (isAU && coordUnit.indexOf ("AU") < 0) JU.Logger.error ("Molden atom line does not indicate units ANGS, AU, or FRACTIONAL -- AU assumed: " + this.line);
this.setFractionalCoordinates (isFractional);
var f = (isAU ? 0.5291772 : 1);
while (this.rd () != null && this.line.indexOf ('[') < 0) {
var tokens = this.getTokens ();
if (tokens.length < 6) continue;
var atom = this.setAtomCoordScaled (null, tokens, 3, f);
atom.atomName = tokens[0];
atom.elementNumber = this.parseIntStr (tokens[2]);
}
});
Clazz.defineMethod (c$, "readSlaterBasis",
function () {
this.nCoef = 0;
while (this.rd () != null && this.line.indexOf ("[") < 0) {
var tokens = this.getTokens ();
if (tokens.length < 7) continue;
this.addSlater (this.parseIntStr (tokens[0]), this.parseIntStr (tokens[1]), this.parseIntStr (tokens[2]), this.parseIntStr (tokens[3]), this.parseIntStr (tokens[4]), this.parseFloatStr (tokens[5]), this.parseFloatStr (tokens[6]));
this.nCoef++;
}
this.setSlaters (false, false);
return false;
});
Clazz.defineMethod (c$, "readGaussianBasis",
function () {
this.shells = new JU.Lst ();
var gdata = new JU.Lst ();
var atomIndex = 0;
var gaussianPtr = 0;
this.nCoef = 0;
this.nSPDF = Clazz.newIntArray (12, 0);
this.discardLinesUntilNonBlank ();
while (this.line != null && !((this.line = this.line.trim ()).length == 0 || this.line.charAt (0) == '[')) {
var tokens = this.getTokens ();
atomIndex = this.parseIntStr (tokens[0]) - 1;
if (atomIndex == 2147483647) {
this.bsBadIndex.set (this.shells.size ());
} else {
this.bsAtomOK.set (atomIndex);
}while (this.rd () != null && (this.line = this.line.trim ()).length > 0 && this.line.charAt (0) != '[') {
tokens = this.getTokens ();
var shellLabel = tokens[0].toUpperCase ();
var type = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (shellLabel);
var nPrimitives = this.parseIntStr (tokens[1]);
var slater = Clazz.newIntArray (4, 0);
this.nSPDF[type]++;
slater[0] = atomIndex + 1;
slater[1] = type;
slater[2] = gaussianPtr + 1;
slater[3] = nPrimitives;
var n = this.getDfCoefMaps ()[type].length;
this.nCoef += n;
for (var ip = nPrimitives; --ip >= 0; ) {
var primTokens = JU.PT.getTokens (this.rd ());
var nTokens = primTokens.length;
var orbData = Clazz.newFloatArray (nTokens, 0);
for (var d = 0; d < nTokens; d++) orbData[d] = this.parseFloatStr (primTokens[d]);
gdata.addLast (orbData);
gaussianPtr++;
}
this.shells.addLast (slater);
}
if (this.line.length > 0 && this.line.charAt (0) == '[') break;
this.rd ();
}
var garray = JU.AU.newFloat2 (gaussianPtr);
for (var i = 0; i < gaussianPtr; i++) {
garray[i] = gdata.get (i);
}
this.moData.put ("shells", this.shells);
this.moData.put ("gaussians", garray);
JU.Logger.info (this.shells.size () + " slater shells read");
JU.Logger.info (garray.length + " gaussian primitives read");
JU.Logger.info (this.nCoef + " MO coefficients expected for orbital type " + this.orbitalType);
this.asc.setCurrentModelInfo ("moData", this.moData);
return false;
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function () {
while (this.checkOrbitalType (this.rd ())) {
}
this.fixOrbitalType ();
var tokens = this.getMoTokens (this.line);
while (tokens != null && tokens.length > 0 && tokens[0].indexOf ('[') < 0) {
var mo = new java.util.Hashtable ();
var data = new JU.Lst ();
var energy = NaN;
var occupancy = NaN;
var symmetry = null;
var key;
while (this.parseIntStr (key = tokens[0]) == -2147483648) {
if (key.startsWith ("Ene")) {
energy = this.parseFloatStr (tokens[1]);
} else if (key.startsWith ("Occup")) {
occupancy = this.parseFloatStr (tokens[1]);
} else if (key.startsWith ("Sym")) {
symmetry = tokens[1];
} else if (key.startsWith ("Spin")) {
this.alphaBeta = tokens[1].toLowerCase ();
}tokens = this.getMoTokens (null);
}
var pt = 0;
while (tokens != null && tokens.length > 0 && this.parseIntStr (tokens[0]) != -2147483648) {
if (tokens.length != 2) throw new Exception ("invalid MO coefficient specification");
var i = this.parseIntStr (tokens[0]);
while (i > ++pt) data.addLast ("0");
data.addLast (tokens[1]);
tokens = this.getMoTokens (null);
}
if (this.orbitalType.equals ("") && data.size () < this.nCoef) {
JU.Logger.info ("too few orbital coefficients for 6D");
this.checkOrbitalType ("[5D]");
}while (++pt <= this.nCoef) {
data.addLast ("0");
}
var coefs = Clazz.newFloatArray (this.nCoef, 0);
for (var i = data.size (); --i >= 0; ) coefs[i] = this.parseFloatStr (data.get (i));
var l = this.line;
this.line = "" + symmetry;
if (this.filterMO ()) {
mo.put ("coefficients", coefs);
if (Float.isNaN (energy)) {
this.haveEnergy = false;
} else {
mo.put ("energy", Float.$valueOf (energy));
}if (!Float.isNaN (occupancy)) mo.put ("occupancy", Float.$valueOf (occupancy));
if (symmetry != null) mo.put ("symmetry", symmetry);
if (this.alphaBeta.length > 0) mo.put ("type", this.alphaBeta);
this.setMO (mo);
if (this.debugging) {
JU.Logger.debug (coefs.length + " coefficients in MO " + this.orbitals.size ());
}}this.line = l;
}
if (this.debugging) JU.Logger.debug ("read " + this.orbitals.size () + " MOs");
this.setMOs ("eV");
if (this.haveEnergy && this.doSort) this.sortMOs ();
return false;
});
Clazz.defineMethod (c$, "sortMOs",
function () {
var list = this.orbitals.toArray ( new Array (this.orbitals.size ()));
java.util.Arrays.sort (list, Clazz.innerTypeInstance (J.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter, this, null));
this.orbitals.clear ();
for (var i = 0; i < list.length; i++) this.orbitals.addLast (list[i]);
});
Clazz.defineMethod (c$, "getMoTokens",
function (line) {
return (line == null && (line = this.rd ()) == null ? null : JU.PT.getTokens (line.$replace ('=', ' ')));
}, "~S");
Clazz.defineMethod (c$, "checkOrbitalType",
function (line) {
if (line.length > 3 && "5D 6D 7F 10 9G 15 11 21".indexOf (line.substring (1, 3)) >= 0) {
if (this.orbitalType.indexOf (line) >= 0) return true;
if (line.indexOf ("G") >= 0 || line.indexOf ("H") >= 0 || line.indexOf ("I") >= 0) this.appendLoadNote ("Unsupported orbital type ignored: " + line);
this.orbitalType += line;
JU.Logger.info ("Orbital type set to " + this.orbitalType);
this.fixOrbitalType ();
return true;
}return false;
}, "~S");
Clazz.defineMethod (c$, "fixOrbitalType",
function () {
if (this.orbitalType.contains ("5D")) {
this.fixSlaterTypes (4, 3);
this.fixSlaterTypes (6, 5);
this.fixSlaterTypes (8, 7);
this.fixSlaterTypes (10, 9);
}if (this.orbitalType.contains ("10F")) {
this.fixSlaterTypes (5, 6);
this.fixSlaterTypes (7, 8);
this.fixSlaterTypes (9, 10);
}if (this.orbitalType.contains ("15G")) {
this.fixSlaterTypes (7, 8);
this.fixSlaterTypes (9, 10);
}});
Clazz.defineMethod (c$, "readFreqsAndModes",
function () {
var tokens;
var frequencies = new JU.Lst ();
while (this.rd () != null && this.line.indexOf ('[') < 0) {
var f = this.getTokens ()[0];
frequencies.addLast (f);
}
var nFreqs = frequencies.size ();
this.skipTo ("[FR-COORD]");
if (!this.vibOnly) this.readAtomSet ("frequency base geometry", true, true);
this.skipTo ("[FR-NORM-COORD]");
var haveVib = false;
for (var nFreq = 0; nFreq < nFreqs; nFreq++) {
this.skipTo ("vibration");
this.doGetVibration (++this.vibrationNumber);
if (haveVib) this.asc.cloneLastAtomSet ();
haveVib = true;
this.asc.setAtomSetFrequency (null, null, "" + JU.PT.dVal (frequencies.get (nFreq)), null);
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0; i < this.modelAtomCount; i++) {
tokens = JU.PT.getTokens (this.rd ());
this.asc.addVibrationVector (i + i0, this.parseFloatStr (tokens[0]) * 0.5291772, this.parseFloatStr (tokens[1]) * 0.5291772, this.parseFloatStr (tokens[2]) * 0.5291772);
}
}
return true;
});
Clazz.defineMethod (c$, "readGeometryOptimization",
function () {
var energies = new JU.Lst ();
this.rd ();
while (this.rd () != null && this.line.indexOf ("force") < 0) energies.addLast ("" + JU.PT.dVal (this.line.trim ()));
this.skipTo ("[GEOMETRIES] XYZ");
var nGeom = energies.size ();
var firstModel = (this.optOnly || this.desiredModelNumber >= 0 ? 0 : 1);
this.modelNumber = firstModel;
var haveModel = false;
if (this.desiredModelNumber == 0 || this.desiredModelNumber == nGeom) this.desiredModelNumber = nGeom;
else if (this.asc.atomSetCount > 0) this.finalizeMOData (this.moData);
for (var i = 0; i < nGeom; i++) {
this.readLines (2);
if (this.doGetModel (++this.modelNumber, null)) {
this.readAtomSet ("Step " + (this.modelNumber - firstModel) + "/" + nGeom + ": " + energies.get (i), false, !this.optOnly || haveModel);
haveModel = true;
} else {
this.readLines (this.modelAtomCount);
}}
return true;
});
Clazz.defineMethod (c$, "skipTo",
function (key) {
key = key.toUpperCase ();
if (this.line == null || !this.line.toUpperCase ().contains (key)) while (this.rd () != null && this.line.toUpperCase ().indexOf (key) < 0) {
}
}, "~S");
Clazz.defineMethod (c$, "readAtomSet",
function (atomSetName, isBohr, asClone) {
if (asClone && this.desiredModelNumber < 0) this.asc.cloneFirstAtomSet (0);
var f = (isBohr ? 0.5291772 : 1);
this.asc.setAtomSetName (atomSetName);
if (this.asc.ac == 0) {
while (this.rd () != null && this.line.indexOf ('[') < 0) {
var tokens = this.getTokens ();
if (tokens.length == 4) this.setAtomCoordScaled (null, tokens, 1, f).atomName = tokens[0];
}
this.modelAtomCount = this.asc.getLastAtomSetAtomCount ();
return;
}var atoms = this.asc.atoms;
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0; i < this.modelAtomCount; i++) this.setAtomCoordScaled (atoms[i + i0], JU.PT.getTokens (this.rd ()), 1, f);
}, "~S,~B,~B");
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MopacSlaterReader"], "J.adapter.readers.quantum.MopacGraphfReader", ["java.lang.Float", "java.util.Hashtable", "JU.AU", "$.Lst"], function () {
c$ = Clazz.decorateAsClass (function () {
this.ac = 0;
this.nCoefficients = 0;
this.invMatrix = null;
this.isNewFormat = false;
this.orbitalData = null;
this.orbitalInfo = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "MopacGraphfReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.alphaBeta = "alpha";
});
Clazz.overrideMethod (c$, "checkLine",
function () {
this.readAtoms ();
if (this.doReadMolecularOrbitals) {
this.readSlaterBasis ();
this.readMolecularOrbitals (false);
if (this.readKeywords ()) this.readMolecularOrbitals (true);
}this.continuing = false;
return false;
});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.asc.newAtomSet ();
this.ac = this.parseIntStr (this.line);
this.atomicNumbers = Clazz.newIntArray (this.ac, 0);
for (var i = 0; i < this.ac; i++) {
this.rd ();
this.atomicNumbers[i] = this.parseIntRange (this.line, 0, 4);
var atom = this.asc.addNewAtom ();
this.setAtomCoordXYZ (atom, this.parseFloatRange (this.line, 4, 17), this.parseFloatRange (this.line, 17, 29), this.parseFloatRange (this.line, 29, 41));
if (this.line.length > 41) atom.partialCharge = this.parseFloatStr (this.line.substring (41));
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.atomicNumbers[i]);
}
});
Clazz.defineMethod (c$, "readSlaterBasis",
function () {
this.nCoefficients = 0;
var values = Clazz.newFloatArray (3, 0);
for (var iAtom = 0; iAtom < this.ac; iAtom++) {
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.rd (), values, 3);
var atomicNumber = this.atomicNumbers[iAtom];
var zeta;
if ((zeta = values[0]) != 0) {
this.createSphericalSlaterByType (iAtom, atomicNumber, "S", zeta, 1);
}if ((zeta = values[1]) != 0) {
this.createSphericalSlaterByType (iAtom, atomicNumber, "Px", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Py", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Pz", zeta, 1);
}if ((zeta = values[2]) != 0) {
this.createSphericalSlaterByType (iAtom, atomicNumber, "Dx2-y2", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Dxz", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Dz2", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Dyz", zeta, 1);
this.createSphericalSlaterByType (iAtom, atomicNumber, "Dxy", zeta, 1);
}}
this.nCoefficients = this.slaters.size ();
this.setSlaters (true, false);
});
Clazz.defineMethod (c$, "readMolecularOrbitals",
function (isBeta) {
if (isBeta) this.alphaBeta = "beta";
var list = null;
if (this.rd () == null) return;
this.isNewFormat = (this.line.indexOf ("ORBITAL") >= 0);
if (this.isNewFormat) {
this.orbitalData = new JU.Lst ();
if (this.line.length > 10) this.orbitalInfo = new JU.Lst ();
} else {
list = Clazz.newFloatArray (this.nCoefficients, this.nCoefficients, 0);
}for (var iMo = 0; iMo < this.nCoefficients; iMo++) {
if (iMo != 0) this.rd ();
var data;
if (this.isNewFormat) {
if (this.line == null || this.line.indexOf ("ORBITAL") < 0 || this.line.indexOf ("ORBITAL_LIST") >= 0) break;
this.orbitalData.addLast (data = Clazz.newFloatArray (this.nCoefficients, 0));
if (this.orbitalInfo != null) this.orbitalInfo.addLast (this.line);
this.rd ();
} else {
data = list[iMo];
}this.fillFloatArray (this.line, 15, data);
}
if (this.invMatrix == null) {
if (this.isNewFormat && this.line.indexOf ("MATRIX") < 0) this.rd ();
this.invMatrix = JU.AU.newFloat2 (this.nCoefficients);
for (var iMo = 0; iMo < this.nCoefficients; iMo++) this.fillFloatArray (null, 15, this.invMatrix[iMo] = Clazz.newFloatArray (iMo + 1, 0));
}this.nOrbitals = (this.orbitalData == null ? this.nCoefficients : this.orbitalData.size ());
if (this.orbitalData != null) {
list = JU.AU.newFloat2 (this.nOrbitals);
for (var i = this.nOrbitals; --i >= 0; ) list[i] = this.orbitalData.get (i);
}var list2 = Clazz.newFloatArray (this.nOrbitals, this.nCoefficients, 0);
for (var i = 0; i < this.nOrbitals; i++) for (var j = 0; j < this.nCoefficients; j++) {
for (var k = 0; k < this.nCoefficients; k++) list2[i][j] += (list[i][k] * (k >= j ? this.invMatrix[k][j] : this.invMatrix[j][k]));
if (Math.abs (list2[i][j]) < 1.0E-4) list2[i][j] = 0;
}
if (this.isNewFormat && this.orbitalInfo == null && this.line != null && this.line.indexOf ("ORBITAL_LIST") < 0) this.rd ();
var values = Clazz.newFloatArray (2, 0);
for (var iMo = 0; iMo < this.nOrbitals; iMo++) {
var mo = new java.util.Hashtable ();
if (this.orbitalInfo != null) {
this.line = this.orbitalInfo.get (iMo);
var tokens = this.getTokens ();
mo.put ("energy", Float.$valueOf (this.parseFloatStr (tokens[3])));
mo.put ("occupancy", Float.$valueOf (this.parseFloatStr (tokens[1])));
} else if (this.rd () != null) {
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.line, values, 2);
mo.put ("energy", Float.$valueOf (values[0]));
mo.put ("occupancy", Float.$valueOf (values[1]));
}mo.put ("coefficients", list2[iMo]);
if (isBeta) mo.put ("type", "beta");
this.line = "\n";
if (this.filterMO ()) this.setMO (mo);
}
this.setMOs ("eV");
}, "~B");
Clazz.defineMethod (c$, "readKeywords",
function () {
if (this.rd () == null || this.line.indexOf (" Keywords:") < 0) return false;
this.moData.put ("calculationType", this.calculationType = this.line.substring (11).trim ());
var isUHF = (this.line.indexOf ("UHF") >= 0);
if (isUHF) {
for (var i = this.orbitals.size (); --i >= 0; ) {
this.orbitals.get (i).put ("type", "alpha");
}
}return isUHF;
});
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.SlaterReader"], "J.adapter.readers.quantum.MopacSlaterReader", null, function () {
c$ = Clazz.decorateAsClass (function () {
this.atomicNumbers = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "MopacSlaterReader", J.adapter.readers.quantum.SlaterReader);
Clazz.defineMethod (c$, "createSphericalSlaterByType",
function (iAtom, atomicNumber, type, zeta, coef) {
var pt = "S Px Py Pz Dx2-y2Dxz Dz2 Dyz Dxy".indexOf (type);
switch (pt) {
case 0:
this.addSlater (iAtom + 1, 0, 0, 0, J.adapter.readers.quantum.MopacSlaterReader.getNPQs (atomicNumber) - 1, zeta, coef);
return;
case 2:
case 5:
case 8:
this.addSlater (iAtom + 1, pt == 2 ? 1 : 0, pt == 5 ? 1 : 0, pt == 8 ? 1 : 0, J.adapter.readers.quantum.MopacSlaterReader.getNPQp (atomicNumber) - 2, zeta, coef);
return;
}
pt = (pt >> 2) * 3 - 9;
this.addSlater (iAtom + 1, J.adapter.readers.quantum.MopacSlaterReader.sphericalDValues[pt++], J.adapter.readers.quantum.MopacSlaterReader.sphericalDValues[pt++], J.adapter.readers.quantum.MopacSlaterReader.sphericalDValues[pt++], J.adapter.readers.quantum.MopacSlaterReader.getNPQd (atomicNumber) - 3, zeta, coef);
}, "~N,~N,~S,~N,~N");
Clazz.defineMethod (c$, "scaleSlater",
function (ex, ey, ez, er, zeta) {
if (ex >= 0 && ey >= 0) {
return Clazz.superCall (this, J.adapter.readers.quantum.MopacSlaterReader, "scaleSlater", [ex, ey, ez, er, zeta]);
}var el = Math.abs (ex + ey + ez);
if (el == 3) {
return 0;
}return J.adapter.readers.quantum.SlaterReader.getSlaterConstDSpherical (el + er + 1, Math.abs (zeta), ex, ey);
}, "~N,~N,~N,~N,~N");
c$.getNPQ = Clazz.defineMethod (c$, "getNPQ",
function (atomicNumber) {
return (atomicNumber < J.adapter.readers.quantum.MopacSlaterReader.principalQuantumNumber.length ? J.adapter.readers.quantum.MopacSlaterReader.principalQuantumNumber[atomicNumber] : 0);
}, "~N");
c$.getNPQs = Clazz.defineMethod (c$, "getNPQs",
function (atomicNumber) {
var n = J.adapter.readers.quantum.MopacSlaterReader.getNPQ (atomicNumber);
switch (atomicNumber) {
case 10:
case 18:
case 36:
case 54:
case 86:
return n + 1;
default:
return n;
}
}, "~N");
c$.getNPQp = Clazz.defineMethod (c$, "getNPQp",
function (atomicNumber) {
var n = J.adapter.readers.quantum.MopacSlaterReader.getNPQ (atomicNumber);
switch (atomicNumber) {
case 2:
return n + 1;
default:
return n;
}
}, "~N");
c$.getNPQd = Clazz.defineMethod (c$, "getNPQd",
function (atomicNumber) {
return (atomicNumber < J.adapter.readers.quantum.MopacSlaterReader.npqd.length ? J.adapter.readers.quantum.MopacSlaterReader.npqd[atomicNumber] : 0);
}, "~N");
Clazz.defineStatics (c$,
"MIN_COEF", 0.0001,
"sphericalDValues", Clazz.newIntArray (-1, [0, -2, 0, 1, 0, 1, -2, 0, 0, 0, 1, 1, 1, 1, 0]),
"principalQuantumNumber", Clazz.newIntArray (-1, [0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6]),
"npqd", Clazz.newIntArray (-1, [0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 3, 3, 3, 3, 3, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 7]));
});

392
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (null, "J.adapter.readers.quantum.NBOParser", ["java.util.Hashtable", "JU.Lst", "$.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.vwr = null;
this.haveBeta = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "NBOParser");
Clazz.makeConstructor (c$,
function () {
});
Clazz.defineMethod (c$, "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)")) break;
if (org.contains ("*") || org.contains ("(cr)")) 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, "-");
if (names.length == 3) {
System.out.println ("NBOParser 3-center bonnd " + org + " ignored for Kekule structure");
continue;
}var ia = J.adapter.readers.quantum.NBOParser.getAtomIndex (names[0]);
var ib = J.adapter.readers.quantum.NBOParser.getAtomIndex (names[1]);
matrix[ia][ib]++;
}
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.charCodeAt (i)) < 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, bsAtoms, 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");
});

403
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/quantum/NWChemReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader", "java.util.Hashtable"], "J.adapter.readers.quantum.NWChemReader", ["java.lang.Character", "$.Float", "JU.AU", "$.BS", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.SmarterJmolAdapter", "J.api.JmolAdapter", "JU.Elements", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.taskNumber = 1;
this.equivalentAtomSets = 0;
this.energyKey = "";
this.energyValue = "";
this.converged = false;
this.haveEnergy = false;
this.haveAt = false;
this.inInput = false;
this.atomTypes = null;
this.htMOs = null;
this.nBasisFunctions = 0;
this.moCount = 0;
this.purging = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "NWChemReader", J.adapter.readers.quantum.MOReader);
Clazz.prepareFields (c$, function () {
this.htMOs = new java.util.Hashtable ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.calculationType = "(NWCHEM)";
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.trim ().startsWith ("NWChem")) {
this.inInput = (this.line.indexOf ("NWChem Input Module") >= 0);
if (this.inInput) {
this.checkMOs ();
}}if (this.line.startsWith (" Step")) {
this.init ();
return true;
}if (this.line.indexOf (" wavefunction = ") >= 0) {
this.calculationType = this.line.substring (this.line.indexOf ("=") + 1).trim () + "(NWCHEM)";
this.moData.put ("calculationType", this.calculationType);
return true;
}if (this.line.indexOf ("Total") >= 0) {
this.readTotal ();
return true;
}if (this.line.indexOf ("@") >= 0) {
this.readAtSign ();
return true;
}if (this.line.startsWith (" Task times")) {
this.init ();
this.taskNumber++;
return true;
}if (this.line.startsWith (" Optimization converged")) {
this.converged = true;
return true;
}if (this.line.startsWith (" Symmetry information")) {
this.readSymmetry ();
return true;
}if (this.line.indexOf ("Output coordinates in ") >= 0) {
var thisLine = this.line;
if (!this.htMOs.isEmpty ()) this.checkMOs ();
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.equivalentAtomSets++;
this.readAtoms (thisLine);
return true;
}if (this.line.indexOf ("Vibrational analysis") >= 0) {
this.readFrequencies ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.startsWith (" Mulliken analysis of the total density")) {
if (this.equivalentAtomSets != 0) this.readPartialCharges ();
return true;
}if (this.line.contains ("Basis \"ao basis\"") && this.doReadMolecularOrbitals) {
return this.readBasis ();
}if (this.line.contains ("Molecular Orbital Analysis")) {
if (this.equivalentAtomSets != 0) this.readMOs ();
return true;
}return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.checkMOs ();
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "init",
function () {
this.haveEnergy = false;
this.haveAt = false;
this.converged = false;
this.inInput = false;
this.equivalentAtomSets = 0;
});
Clazz.defineMethod (c$, "setEnergies",
function (key, value, nAtomSets) {
this.energyKey = key;
this.energyValue = value;
this.setProps (this.energyKey, this.energyValue, this.equivalentAtomSets);
this.setNames (this.energyKey + " = " + this.energyValue, null, this.equivalentAtomSets);
this.asc.setAtomSetEnergy (value, this.parseFloatStr (value));
this.haveEnergy = true;
}, "~S,~S,~N");
Clazz.defineMethod (c$, "setEnergy",
function (key, value) {
this.energyKey = key;
this.energyValue = value;
this.asc.setAtomSetModelProperty (this.energyKey, this.energyValue);
this.asc.setAtomSetName (this.energyKey + " = " + this.energyValue);
this.haveEnergy = true;
}, "~S,~S");
Clazz.defineMethod (c$, "readSymmetry",
function () {
var tokens = JU.PT.getTokens (this.readLines (3));
this.setProps ("Symmetry group name", tokens[tokens.length - 1], this.equivalentAtomSets);
});
Clazz.defineMethod (c$, "readTotal",
function () {
var tokens = this.getTokens ();
try {
if (tokens[2].startsWith ("energy")) {
if (!this.haveAt) this.setEnergies ("E(" + tokens[1] + ")", tokens[tokens.length - 1], this.equivalentAtomSets);
}} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
});
Clazz.defineMethod (c$, "readAtSign",
function () {
if (this.line.charAt (2) == 'S') {
if (this.readLines (2) == null) return;
}var tokens = this.getTokens ();
if (!this.haveEnergy) {
this.setEnergies ("E", tokens[2], this.equivalentAtomSets);
} else {
this.setEnergies (this.energyKey, this.energyValue, this.equivalentAtomSets);
}this.setProps ("Step", tokens[1], this.equivalentAtomSets);
this.haveAt = true;
});
Clazz.defineMethod (c$, "setProps",
function (key, value, n) {
for (var i = this.asc.iSet; --n >= 0 && i >= 0; --i) this.asc.setAtomSetModelPropertyForSet (key, value, i);
}, "~S,~S,~N");
Clazz.defineMethod (c$, "setNames",
function (atomSetName, namedSets, n) {
for (var i = this.asc.iSet; --n >= 0 && i >= 0; --i) if (namedSets == null || !namedSets.get (i)) this.asc.setModelInfoForSet ("name", atomSetName, i);
}, "~S,JU.BS,~N");
Clazz.defineMethod (c$, "readAtoms",
function (thisLine) {
var scale = (thisLine.indexOf ("angstroms") < 0 ? 0.5291772 : 1);
this.readLines (3);
var tokens;
this.haveEnergy = false;
this.asc.newAtomSet ();
this.asc.setAtomSetModelProperty (".PATH", "Task " + this.taskNumber + (this.inInput ? J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Input" : J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Geometry"));
this.atomTypes = new JU.Lst ();
while (this.rd () != null && this.line.length > 0) {
tokens = this.getTokens ();
if (tokens.length < 6) break;
var name = this.fixTag (tokens[1]);
this.setAtomCoordScaled (null, tokens, 3, scale).atomName = name;
this.atomTypes.addLast (name);
}
if (this.converged) {
this.setEnergy (this.energyKey, this.energyValue);
this.asc.setAtomSetModelProperty ("Step", "converged");
} else if (this.inInput) {
this.asc.setAtomSetName ("Input");
}}, "~S");
Clazz.defineMethod (c$, "readFrequencies",
function () {
var firstFrequencyAtomSetIndex = this.asc.atomSetCount;
var firstVibrationNumber = this.vibrationNumber;
var path = "Task " + this.taskNumber + J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR + "Frequencies";
this.discardLinesUntilContains ("Atom information");
this.readLines (2);
this.asc.newAtomSet ();
var tokens;
while (this.rd () != null && this.line.indexOf ("---") < 0) {
tokens = this.getTokens ();
this.setAtomCoordScaled (null, tokens, 2, 0.5291772).atomName = this.fixTag (tokens[0]);
}
this.discardLinesUntilContains ("(Projected Frequencies expressed in cm-1)");
this.readLines (3);
var firstTime = true;
var bsIgnore = new JU.BS ();
while (this.rd () != null && this.line.indexOf ("P.Frequency") >= 0) {
tokens = JU.PT.getTokensAt (this.line, 12);
var frequencyCount = tokens.length;
var iAtom0 = this.asc.ac;
var ac = this.asc.getLastAtomSetAtomCount ();
if (firstTime) iAtom0 -= ac;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = (tokens[i].equals ("0.00") || !this.doGetVibration (++this.vibrationNumber));
if (ignore[i]) {
bsIgnore.set (this.vibrationNumber);
continue;
}if (!firstTime) this.asc.cloneLastAtomSet ();
firstTime = false;
this.asc.setAtomSetFrequency (path, null, tokens[i], null);
}
this.readLines (1);
this.fillFrequencyData (iAtom0, ac, ac, ignore, false, 0, 0, null, 0);
this.readLines (3);
}
try {
this.discardLinesUntilContains ("Infra Red Intensities");
this.readLines (2);
var idx = firstFrequencyAtomSetIndex;
for (var i = firstVibrationNumber; i < this.vibrationNumber; ++i) {
if (this.rd () == null) return;
if (bsIgnore.get (i)) continue;
tokens = this.getTokens ();
var iset = this.asc.iSet;
this.asc.iSet = idx++;
this.asc.setAtomSetModelProperty ("IRIntensity", tokens[3] + " au");
this.asc.iSet = iset;
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
System.out.println ("nwchem infra red issue" + e);
} else {
throw e;
}
}
});
Clazz.defineMethod (c$, "readPartialCharges",
function () {
var tokens;
this.readLines (4);
var ac = this.asc.ac;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var atoms = this.asc.atoms;
for (var i = i0; i < ac; ++i) {
while (atoms[i].elementNumber == 0) ++i;
do {
if (this.rd () == null || this.line.length < 3) return;
tokens = this.getTokens ();
} while (tokens[0].indexOf (".") >= 0);
atoms[i].partialCharge = this.parseIntStr (tokens[2]) - this.parseFloatStr (tokens[3]);
}
});
Clazz.defineMethod (c$, "fixTag",
function (tag) {
if (tag.equalsIgnoreCase ("bq")) return "X";
if (tag.toLowerCase ().startsWith ("bq")) tag = tag.substring (2) + "-Bq";
return "" + Character.toUpperCase (tag.charAt (0)) + (tag.length == 1 ? "" : "" + Character.toLowerCase (tag.charAt (1)));
}, "~S");
Clazz.defineMethod (c$, "readBasis",
function () {
this.gaussianCount = 0;
this.shellCount = 0;
this.nBasisFunctions = 0;
var isD6F10 = (this.line.indexOf ("cartesian") >= 0);
if (isD6F10) {
this.getDFMap ("DC", J.adapter.readers.quantum.NWChemReader.$DC_LIST, 4, "DXX DYY DZZ DXY DXZ DYZ", 3);
this.getDFMap ("FC", J.adapter.readers.quantum.NWChemReader.$FC_LIST, 6, "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ", 3);
} else {
this.getDFMap ("DS", J.adapter.readers.quantum.NWChemReader.$DS_LIST, 3, "d0 d1+ d1- d2+ d2-", 2);
this.getDFMap ("FS", J.adapter.readers.quantum.NWChemReader.$FS_LIST, 5, "f0 f1+ f1- f2+ f2- f3+ f3-", 2);
}this.shells = new JU.Lst ();
var atomInfo = new java.util.Hashtable ();
var atomSym = null;
var atomData = null;
var shellData = null;
while (this.line != null) {
var nBlankLines = 0;
while (this.line.length < 3 || this.line.charAt (2) == ' ') {
shellData = new JU.Lst ();
this.rd ();
if (this.line.length < 3) nBlankLines++;
}
if (nBlankLines >= 2) break;
if (this.parseIntStr (this.line) == -2147483648) {
atomSym = this.getTokens ()[0];
if (atomSym.length > 2) atomSym = J.api.JmolAdapter.getElementSymbol (JU.Elements.elementNumberFromName (atomSym));
atomData = new JU.Lst ();
atomInfo.put (atomSym, atomData);
this.rd ();
this.rd ();
continue;
}while (this.line != null && this.line.length > 3) {
var tokens = this.getTokens ();
var o = Clazz.newArray (-1, [tokens[1], Clazz.newFloatArray (-1, [this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3])])]);
shellData.addLast (o);
this.rd ();
}
atomData.addLast (shellData);
}
var nD = (isD6F10 ? 6 : 5);
var nF = (isD6F10 ? 10 : 7);
var gdata = new JU.Lst ();
for (var i = 0; i < this.atomTypes.size (); i++) {
atomData = atomInfo.get (this.atomTypes.get (i));
var nShells = atomData.size ();
for (var ishell = 0; ishell < nShells; ishell++) {
this.shellCount++;
shellData = atomData.get (ishell);
var nGaussians = shellData.size ();
var type = shellData.get (0)[0];
switch (type.charAt (0)) {
case 'S':
this.nBasisFunctions += 1;
break;
case 'P':
this.nBasisFunctions += 3;
break;
case 'D':
this.nBasisFunctions += nD;
break;
case 'F':
this.nBasisFunctions += nF;
break;
}
var slater = Clazz.newIntArray (4, 0);
slater[0] = i + 1;
slater[1] = (isD6F10 ? J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (type) : J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagIDSpherical (type));
slater[2] = this.gaussianCount + 1;
slater[3] = nGaussians;
this.shells.addLast (slater);
for (var ifunc = 0; ifunc < nGaussians; ifunc++) gdata.addLast (shellData.get (ifunc)[1]);
this.gaussianCount += nGaussians;
}
}
this.gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) this.gaussians[i] = gdata.get (i);
JU.Logger.info (this.gaussianCount + " Gaussians read");
return true;
});
Clazz.defineMethod (c$, "readMOs",
function () {
var lines = new JU.Lst ();
this.htMOs.put (this.line, lines);
lines.addLast (this.line);
var nblank = 0;
while (nblank != 2 && this.rd () != null) {
lines.addLast (this.line);
if (this.line.length < 2) nblank++;
else nblank = 0;
}
return true;
});
Clazz.defineMethod (c$, "checkMOs",
function () {
if (this.shells == null) return;
for (var entry, $entry = this.htMOs.entrySet ().iterator (); $entry.hasNext () && ((entry = $entry.next ()) || true);) {
this.line = entry.getKey ();
this.alphaBeta = this.line.substring (0, this.line.indexOf ("Final")).trim () + " ";
var moCount = 0;
if (!this.filterMO ()) continue;
var list = entry.getValue ();
var n = list.size ();
JU.Logger.info (this.line);
for (var i = 3; i < n; i++) {
while (i < n && ((this.line = list.get (i)).length < 2 || this.line.charAt (1) != 'V')) i++;
if (i == n) break;
this.line = this.line.$replace ('=', ' ');
var tokens = this.getTokens ();
var occupancy = this.parseFloatStr (tokens[3]);
var energy = this.parseFloatStr (tokens[5]);
var symmetry = (tokens.length > 7 ? tokens[7] : null);
var mo = new java.util.Hashtable ();
mo.put ("occupancy", Float.$valueOf (occupancy));
mo.put ("energy", Float.$valueOf (energy));
if (symmetry != null) mo.put ("symmetry", symmetry);
var coefs = null;
this.setMO (mo);
mo.put ("type", this.alphaBeta + (++moCount));
coefs = Clazz.newFloatArray (this.nBasisFunctions, 0);
mo.put ("coefficients", coefs);
i += 3;
while ((this.line = list.get (++i)) != null && this.line.length > 3) {
tokens = this.getTokens ();
coefs[this.parseIntStr (tokens[0]) - 1] = this.parseFloatStr (tokens[1]);
var pt = Clazz.doubleToInt (tokens.length / 2);
if (pt == 5 || pt == 6) coefs[this.parseIntStr (tokens[pt]) - 1] = this.parseFloatStr (tokens[pt + 1]);
}
}
}
this.energyUnits = "a.u.";
this.setMOData (true);
this.htMOs.clear ();
});
Clazz.overrideMethod (c$, "rd",
function () {
this.RL ();
if (!this.purging && this.line != null && this.line.startsWith ("--")) {
this.purging = true;
this.discardLinesUntilStartsWith ("*");
this.rd ();
this.purging = false;
this.RL ();
}return this.line;
});
Clazz.defineStatics (c$,
"$DS_LIST", "d2- d1- d0 d1+ d2+",
"$FS_LIST", "f3- f2- f1- f0 f1+ f2+ f3+",
"$DC_LIST", "DXX DXY DXZ DYY DYZ DZZ",
"$FC_LIST", "XXX XXY XXZ XYY XYZ XZZ YYY YYZ YZZ ZZZ");
});

202
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader", "java.util.Hashtable", "JU.Lst"], "J.adapter.readers.quantum.PsiReader", ["java.lang.Float", "JU.AU", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.api.JmolAdapter", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.atomNames = null;
this.shellsByUniqueAtom = null;
this.uniqueAtomMap = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "PsiReader", J.adapter.readers.quantum.MOReader);
Clazz.prepareFields (c$, function () {
this.atomNames = new JU.Lst ();
this.shellsByUniqueAtom = new JU.Lst ();
this.uniqueAtomMap = new java.util.Hashtable ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("-Geometry after Center-of-Mass shift and reorientation (a.u.):") >= 0) {
this.readAtoms (true);
this.doProcessLines = true;
return true;
}if (this.line.indexOf ("-Unique atoms in the canonical coordinate system (a.u.):") >= 0) {
this.readUniqueAtoms ();
this.doProcessLines = true;
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("New Cartesian Geometry in a.u.") >= 0) {
this.readAtoms (false);
return true;
}if (this.line.startsWith (" label = ")) {
this.moData.put ("calculationType", this.calculationType = this.line.substring (17).trim ());
return true;
}if (this.line.startsWith ("molecular orbitals for ")) {
this.moData.put ("energyUnits", "");
return true;
}if (this.line.startsWith (" -BASIS SETS:")) {
this.readBasis ();
return true;
}if (this.line.indexOf ("Molecular Orbital Coefficients") >= 0) {
if (this.filterMO ()) this.readPsiMolecularOrbitals ();
return true;
}if (this.line.indexOf ("SCF total energy =") >= 0) {
this.readSCFDone ();
return true;
}if (this.line.indexOf ("Normal Modes") >= 0) {
this.readFrequencies ();
return true;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "readSCFDone",
function () {
this.asc.setAtomSetName (this.line);
});
Clazz.defineMethod (c$, "readAtoms",
function (isInitial) {
if (isInitial) {
this.asc.newAtomSet ();
this.asc.setAtomSetName ("");
this.discardLinesUntilContains ("----");
}var atomPt = 0;
while (this.rd () != null && this.line.length > 0) {
var tokens = this.getTokens ();
var atom = (isInitial ? this.asc.addNewAtom () : this.asc.atoms[atomPt++]);
if (isInitial) {
this.atomNames.addLast (tokens[0]);
if (tokens[0].length <= 2) atom.elementNumber = J.api.JmolAdapter.getElementNumber (tokens[0]);
} else {
atom.elementNumber = this.parseIntStr (tokens[0]);
}if (atom.elementNumber < 0) atom.elementNumber = 0;
this.setAtomCoordScaled (atom, tokens, 1, 0.5291772);
}
}, "~B");
Clazz.defineMethod (c$, "readBasis",
function () {
var gdata = new JU.Lst ();
this.gaussianCount = 0;
this.shellCount = 0;
var tokens;
var slater = null;
var slatersByUniqueAtom = null;
this.rd ();
while (this.rd () != null && this.line.startsWith (" -Basis set on")) {
slatersByUniqueAtom = new JU.Lst ();
var nGaussians = 0;
while (this.rd () != null && !this.line.startsWith (" )")) {
this.line = this.line.$replace ('(', ' ').$replace (')', ' ');
tokens = this.getTokens ();
var ipt = 0;
switch (tokens.length) {
case 3:
if (slater != null) {
slatersByUniqueAtom.addLast (slater);
}ipt = 1;
slater = Clazz.newIntArray (3, 0);
slater[0] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (tokens[0]);
slater[1] = this.gaussianCount;
this.shellCount++;
break;
case 2:
break;
}
nGaussians++;
gdata.addLast ( Clazz.newArray (-1, [tokens[ipt], tokens[ipt + 1]]));
slater[2] = nGaussians;
}
if (slater != null) {
slatersByUniqueAtom.addLast (slater);
}this.shellsByUniqueAtom.addLast (slatersByUniqueAtom);
this.gaussianCount += nGaussians;
this.rd ();
}
var garray = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0; i < this.gaussianCount; i++) {
tokens = gdata.get (i);
garray[i] = Clazz.newFloatArray (tokens.length, 0);
for (var j = 0; j < tokens.length; j++) garray[i][j] = this.parseFloatStr (tokens[j]);
}
this.moData.put ("gaussians", garray);
if (this.debugging) {
JU.Logger.debug (this.shellCount + " slater shells read");
JU.Logger.debug (this.gaussianCount + " gaussian primitives read");
}});
Clazz.defineMethod (c$, "readUniqueAtoms",
function () {
var sdata = new JU.Lst ();
this.discardLinesUntilContains ("----");
var n = 0;
while (this.rd () != null && this.line.length > 0) {
var tokens = this.getTokens ();
this.uniqueAtomMap.put (tokens[0], Integer.$valueOf (n++));
}
var ac = this.atomNames.size ();
for (var i = 0; i < ac; i++) {
var atomType = this.atomNames.get (i);
var iUnique = this.uniqueAtomMap.get (atomType).intValue ();
var slaters = this.shellsByUniqueAtom.get (iUnique);
if (slaters == null) {
JU.Logger.error ("slater for atom " + i + " atomType " + atomType + " was not found in listing. Ignoring molecular orbitals");
return;
}for (var j = 0; j < slaters.size (); j++) {
var slater = slaters.get (j);
sdata.addLast ( Clazz.newIntArray (-1, [i + 1, slater[0], slater[1], slater[2]]));
}
}
this.moData.put ("shells", sdata);
});
Clazz.defineMethod (c$, "readPsiMolecularOrbitals",
function () {
var mos = JU.AU.createArrayOfHashtable (5);
var data = JU.AU.createArrayOfArrayList (5);
var nThisLine = 0;
while (this.rd () != null && this.line.toUpperCase ().indexOf ("DENS") < 0) {
var tokens = this.getTokens ();
var ptData = (this.line.charAt (5) == ' ' ? 2 : 4);
if (this.line.indexOf (" ") == 0) {
this.addMOData (nThisLine, data, mos);
nThisLine = tokens.length;
tokens = JU.PT.getTokens (this.rd ());
for (var i = 0; i < nThisLine; i++) {
mos[i] = new java.util.Hashtable ();
data[i] = new JU.Lst ();
mos[i].put ("symmetry", tokens[i]);
}
tokens = J.adapter.smarter.AtomSetCollectionReader.getStrings (this.rd ().substring (21), nThisLine, 10);
for (var i = 0; i < nThisLine; i++) {
mos[i].put ("energy", Float.$valueOf (JU.PT.fVal (tokens[i])));
}
continue;
}try {
for (var i = 0; i < nThisLine; i++) {
data[i].addLast (tokens[i + ptData]);
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
JU.Logger.error ("Error reading Psi3 file molecular orbitals at line: " + this.line);
break;
} else {
throw e;
}
}
}
this.addMOData (nThisLine, data, mos);
this.moData.put ("mos", this.orbitals);
this.finalizeMOData (this.moData);
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
this.rd ();
var ac = this.asc.getLastAtomSetAtomCount ();
var tokens;
while (this.rd () != null && this.line.indexOf ("Frequency") >= 0) {
tokens = this.getTokens ();
var iAtom0 = this.asc.ac;
var ignore = Clazz.newBooleanArray (1, false);
if (!this.doGetVibration (++this.vibrationNumber)) continue;
this.asc.cloneLastAtomSet ();
this.asc.setAtomSetFrequency (null, null, tokens[1], null);
this.readLines (2);
this.fillFrequencyData (iAtom0, ac, ac, ignore, true, 0, 0, null, 0);
this.rd ();
}
});
});

235
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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MoldenReader"], "J.adapter.readers.quantum.QCJSONReader", ["java.lang.Double", "$.Float", "java.util.Arrays", "$.Hashtable", "JU.AU", "$.Lst", "$.SB", "J.adapter.readers.quantum.BasisFunctionReader", "J.api.JmolAdapter", "JU.Logger", "org.qcschema.QCSchemaUnits"], function () {
c$ = Clazz.decorateAsClass (function () {
this.job = null;
this.jobCount = 0;
this.modelCount = 0;
this.$haveEnergy = true;
this.lastBasisID = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "QCJSONReader", J.adapter.readers.quantum.MoldenReader);
Clazz.defineMethod (c$, "initializeReader",
function () {
Clazz.superCall (this, J.adapter.readers.quantum.QCJSONReader, "initializeReader", []);
var sb = new JU.SB ();
try {
while (this.rd () != null) sb.append (this.line);
var json = this.vwr.parseJSONArray (sb.toString ());
JU.Logger.info (json.get (0).toString ());
this.jobCount = json.size () - 2;
for (var i = 0; i < this.jobCount; i++) this.processJob (json.get (i + 2));
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
e.printStackTrace ();
} else {
throw e;
}
}
this.continuing = false;
});
Clazz.defineMethod (c$, "processJob",
function (job) {
this.job = job;
this.readSteps ();
}, "java.util.Map");
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "readSteps",
function () {
var steps = org.qcschema.QCSchemaUnits.getList (this.job, "steps");
var nSteps = steps.size ();
for (var iStep = 0; iStep < nSteps; iStep++) {
if (!this.doGetModel (++this.modelCount, null)) {
if (!this.checkLastModel ()) return;
continue;
}this.asc.newAtomSet ();
var step = steps.get (iStep);
var topology = J.adapter.readers.quantum.QCJSONReader.getMapSafely (step, "topology");
var atoms = J.adapter.readers.quantum.QCJSONReader.getMapSafely (topology, "atoms");
var symbols = org.qcschema.QCSchemaUnits.getStringArray (atoms, "symbol");
var atomNumbers = org.qcschema.QCSchemaUnits.getIntArray (atoms, "atom_number");
var atom_names = org.qcschema.QCSchemaUnits.getStringArray (atoms, "atom_names");
var coords = org.qcschema.QCSchemaUnits.getDoubleArray (atoms, "coords");
this.modelAtomCount = Clazz.doubleToInt (coords.length / 3);
var f = org.qcschema.QCSchemaUnits.getConversionFactor (atoms, "coords", "angstroms");
var isFractional = (f == 0);
this.setFractionalCoordinates (isFractional);
if (isFractional) {
f = org.qcschema.QCSchemaUnits.getConversionFactor (atoms, "unit_cell", "angstroms");
var cell = org.qcschema.QCSchemaUnits.getDoubleArray (atoms, "unit_cell");
if (cell == null) {
JU.Logger.error ("topology.unit_cell is missing even though atoms are listed as fractional");
} else {
for (var i = 0; i < 6; i++) {
switch (i) {
case 3:
f = 1;
default:
this.setUnitCellItem (i, (cell[i] * f));
break;
}
}
}}for (var i = 0, pt = 0; i < this.modelAtomCount; i++) {
var atom = this.asc.addNewAtom ();
this.setAtomCoordXYZ (atom, (coords[pt++] * f), (coords[pt++] * f), (coords[pt++] * f));
var sym = (symbols == null ? J.api.JmolAdapter.getElementSymbol (atomNumbers[i]) : symbols[i]);
atom.atomName = (atom_names == null ? sym : atom_names[i]);
atom.elementNumber = (atomNumbers == null ? J.api.JmolAdapter.getElementNumber (sym) : atomNumbers[i]);
}
if (this.doReadMolecularOrbitals) {
this.readMolecularOrbitals (J.adapter.readers.quantum.QCJSONReader.getMapSafely (step, "molecular_orbitals"));
this.clearOrbitals ();
}this.applySymmetryAndSetTrajectory ();
if (this.loadVibrations) {
this.readFreqsAndModes (org.qcschema.QCSchemaUnits.getList (step, "vibrations"));
}}
});
Clazz.defineMethod (c$, "readFreqsAndModes",
function (vibrations) {
var $private = Clazz.checkPrivateMethod (arguments);
if ($private != null) {
return $private.apply (this, arguments);
}
if (vibrations != null) {
var n = vibrations.size ();
for (var i = 0; i < n; i++) {
var vib = vibrations.get (i);
var freq = org.qcschema.QCSchemaUnits.getDouble (vib, "frequency", "cm-1");
var vectors = org.qcschema.QCSchemaUnits.getDoubleArray (vib, "vectors");
if (i > 0) this.asc.cloneLastAtomSet ();
this.asc.setAtomSetFrequency (null, null, "" + freq, "cm-1");
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var j = 0, pt = 0; j < this.modelAtomCount; j++) {
this.asc.addVibrationVector (j + i0, (vectors[pt++] * 0.5291772), (vectors[pt++] * 0.5291772), (vectors[pt++] * 0.5291772));
}
}
}return true;
}, "java.util.ArrayList");
Clazz.defineMethod (c$, "readMolecularOrbitals",
function (molecular_orbitals) {
var $private = Clazz.checkPrivateMethod (arguments);
if ($private != null) {
return $private.apply (this, arguments);
}
if (molecular_orbitals == null) return false;
var moBasisID = molecular_orbitals.get ("basis_id").toString ();
if (!this.readBasis (moBasisID)) return false;
var isNormalized = molecular_orbitals.get ("__jmol_normalized");
if (isNormalized != null && isNormalized.booleanValue ()) this.moData.put ("isNormalized", isNormalized);
this.calculationType = molecular_orbitals.get ("__jmol_calculation_type");
if (this.calculationType == null) this.calculationType = "?";
this.moData.put ("calculationType", this.calculationType);
var mos = org.qcschema.QCSchemaUnits.getList (molecular_orbitals, "orbitals");
var n = mos.size ();
for (var i = 0; i < n; i++) {
var thisMO = mos.get (i);
var energy = org.qcschema.QCSchemaUnits.getDouble (thisMO, "energy", "ev");
var occupancy = org.qcschema.QCSchemaUnits.getDouble (thisMO, "occupancy", null);
var symmetry = thisMO.get ("symmetry");
var spin = thisMO.get ("type");
if (spin != null) {
if (spin.indexOf ("beta") >= 0) this.alphaBeta = "beta";
else if (spin.indexOf ("alpha") >= 0) this.alphaBeta = "alpha";
}var coefs = this.toFloatArray (org.qcschema.QCSchemaUnits.getDoubleArray (thisMO, "coefficients"));
this.line = "" + symmetry;
if (this.filterMO ()) {
var mo = new java.util.Hashtable ();
mo.put ("coefficients", coefs);
if (Double.isNaN (energy)) {
this.$haveEnergy = false;
} else {
mo.put ("energy", Float.$valueOf (energy));
}if (!Double.isNaN (occupancy)) mo.put ("occupancy", Float.$valueOf (occupancy));
if (symmetry != null) mo.put ("symmetry", symmetry);
if (this.alphaBeta.length > 0) mo.put ("type", this.alphaBeta);
this.setMO (mo);
if (this.debugging) {
JU.Logger.debug (coefs.length + " coefficients in MO " + this.orbitals.size ());
}}}
if (this.debugging) JU.Logger.debug ("read " + this.orbitals.size () + " MOs");
var units = org.qcschema.QCSchemaUnits.getList (molecular_orbitals, "orbitals_energy_units");
var sunits = (units == null ? null : units.get (0).toString ());
this.setMOs (sunits == null || sunits.equals ("?") ? "?" : sunits);
if (this.$haveEnergy && this.doSort) this.sortMOs ();
return false;
}, "java.util.Map");
Clazz.defineMethod (c$, "toFloatArray",
function (da) {
var fa = Clazz.newFloatArray (da.length, 0);
for (var j = da.length; --j >= 0; ) fa[j] = da[j];
return fa;
}, "~A");
Clazz.defineMethod (c$, "readBasis",
function (moBasisID) {
var moBasisData = J.adapter.readers.quantum.QCJSONReader.getMapSafely (this.job, "mo_bases");
var moBasis = J.adapter.readers.quantum.QCJSONReader.getMapSafely (moBasisData, moBasisID);
if (moBasis == null) {
JU.Logger.error ("No job.mo_bases entry for " + moBasisID);
return false;
}if (moBasisID === this.lastBasisID) return true;
this.lastBasisID = moBasisID;
var listG = org.qcschema.QCSchemaUnits.getList (moBasis, "gaussians");
var listS = org.qcschema.QCSchemaUnits.getList (moBasis, "shells");
if (listG == null && listS == null) {
listG = listS = org.qcschema.QCSchemaUnits.getList (moBasis, "slaters");
}if ((listG == null) != (listS == null)) {
JU.Logger.error ("gaussians/shells or slaters missing");
return false;
}if (listG === listS) {
this.readSlaterBasis (listS);
} else {
this.readGaussianBasis (listG, listS);
}return true;
}, "~S");
Clazz.defineMethod (c$, "readSlaterBasis",
function (listS) {
this.nCoef = listS.size ();
for (var i = 0; i < this.nCoef; i++) {
var a = org.qcschema.QCSchemaUnits.getDoubleArray (listS.get (i), null);
this.addSlater (Clazz.doubleToInt (a[0]), Clazz.doubleToInt (a[1]), Clazz.doubleToInt (a[2]), Clazz.doubleToInt (a[3]), Clazz.doubleToInt (a[4]), a[5], a[6]);
}
this.setSlaters (false, false);
return true;
}, "java.util.ArrayList");
Clazz.defineMethod (c$, "readGaussianBasis",
function (listG, listS) {
var $private = Clazz.checkPrivateMethod (arguments);
if ($private != null) {
return $private.apply (this, arguments);
}
this.shells = new JU.Lst ();
for (var i = 0; i < listS.size (); i++) this.shells.addLast (org.qcschema.QCSchemaUnits.getIntArray (listS.get (i), null));
var gaussianPtr = listG.size ();
var garray = JU.AU.newFloat2 (gaussianPtr);
for (var i = 0; i < gaussianPtr; i++) garray[i] = this.toFloatArray (org.qcschema.QCSchemaUnits.getDoubleArray (listG.get (i), null));
this.moData.put ("shells", this.shells);
this.moData.put ("gaussians", garray);
JU.Logger.info (this.shells.size () + " slater shells read");
JU.Logger.info (garray.length + " gaussian primitives read");
this.asc.setCurrentModelInfo ("moData", this.moData);
return false;
}, "java.util.ArrayList,java.util.ArrayList");
Clazz.defineMethod (c$, "sortMOs",
function () {
var $private = Clazz.checkPrivateMethod (arguments);
if ($private != null) {
return $private.apply (this, arguments);
}
var list = this.orbitals.toArray ( new Array (this.orbitals.size ()));
java.util.Arrays.sort (list, Clazz.innerTypeInstance (J.adapter.readers.quantum.BasisFunctionReader.MOEnergySorter, this, null));
this.orbitals.clear ();
for (var i = 0; i < list.length; i++) this.orbitals.addLast (list[i]);
});
c$.getMapSafely = Clazz.defineMethod (c$, "getMapSafely",
function (map, key) {
return (map == null ? null : map.get (key));
}, "java.util.Map,~S");
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MOReader"], "J.adapter.readers.quantum.QchemReader", ["java.lang.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.api.JmolAdapter", "J.quantum.QS", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.calculationNumber = 1;
this.isFirstJob = true;
this.alphas = null;
this.betas = null;
this.nBasis = 0;
this.dFixed = false;
this.fFixed = false;
this.dList = "";
this.fList = "";
this.dSpherical = false;
this.fSpherical = false;
if (!Clazz.isClassDefined ("J.adapter.readers.quantum.QchemReader.MOInfo")) {
J.adapter.readers.quantum.QchemReader.$QchemReader$MOInfo$ ();
}
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "QchemReader", J.adapter.readers.quantum.MOReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.energyUnits = "au";
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("Standard Nuclear Orientation") >= 0) {
this.readAtoms ();
this.moData = null;
return true;
}if (this.line.indexOf ("Total energy") >= 0 || this.line.indexOf ("total energy") >= 0 || this.line.indexOf ("Energy is") >= 0) {
if (this.line.indexOf ("Excitation") == -1) this.readEnergy ();
return true;
}if (this.line.indexOf ("Requested basis set is") >= 0) {
this.readCalculationType ();
return true;
}if (this.line.indexOf ("VIBRATIONAL FREQUENCIES") >= 0) {
this.readFrequencies ();
return true;
}if (this.line.indexOf ("Mulliken Net Atomic Charges") >= 0) {
this.readPartialCharges ();
return true;
}if (this.line.startsWith ("Job ") || this.line.startsWith ("Running Job")) {
if (this.isFirstJob && this.line.startsWith ("Running")) this.calculationNumber = 0;
this.calculationNumber++;
this.isFirstJob = false;
this.moData = null;
return true;
}if (this.line.indexOf ("Basis set in general basis input format") >= 0) {
if (this.moData == null) {
this.readBasis ();
}return true;
}if (this.moData == null) return true;
if (this.line.indexOf ("Orbital Energies (a.u.) and Symmetries") >= 0) {
this.readESym (true);
return true;
}if (this.line.indexOf ("Orbital Energies (a.u.)") >= 0) {
this.readESym (false);
return true;
}if (this.line.indexOf ("MOLECULAR ORBITAL COEFFICIENTS") >= 0) {
if (this.filterMO ()) this.readQchemMolecularOrbitals ();
return true;
}return this.checkNboLine ();
});
Clazz.defineMethod (c$, "readCalculationType",
function () {
this.calculationType = this.line.substring (this.line.indexOf ("set is") + 6).trim ();
});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.asc.newAtomSet ();
this.setMOData (true);
this.dFixed = this.fFixed = false;
this.readLines (2);
var tokens;
while (this.rd () != null && !this.line.startsWith (" --")) {
tokens = this.getTokens ();
if (tokens.length < 5) continue;
var symbol = tokens[1];
if (J.api.JmolAdapter.getElementNumber (symbol) > 0) this.addAtomXYZSymName (tokens, 2, symbol, null);
}
this.asc.setAtomSetModelProperty (".PATH", "Job " + this.calculationNumber);
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
while (this.rd () != null && this.line.indexOf ("STANDARD") < 0) {
if (!this.line.startsWith (" Frequency:")) this.discardLinesUntilStartsWith (" Frequency:");
var frequencies = this.getTokens ();
var frequencyCount = frequencies.length - 1;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
var ac = this.asc.getLastAtomSetAtomCount ();
var iAtom0 = this.asc.ac;
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneLastAtomSet ();
this.asc.setAtomSetFrequency ("Job " + this.calculationNumber, null, frequencies[i + 1], null);
}
this.discardLinesUntilStartsWith (" X");
this.fillFrequencyData (iAtom0, ac, ac, ignore, true, 0, 0, null, 0);
this.discardLinesUntilBlank ();
}
});
Clazz.defineMethod (c$, "readPartialCharges",
function () {
this.readLines (3);
var atoms = this.asc.atoms;
var ac = this.asc.getLastAtomSetAtomCount ();
for (var i = 0; i < ac && this.rd () != null; ++i) atoms[i].partialCharge = this.parseFloatStr (this.getTokens ()[2]);
});
Clazz.defineMethod (c$, "readEnergy",
function () {
var ac = this.asc.getLastAtomSetAtomCount ();
var tokens = this.getTokens ();
var energyKey = "E(" + tokens[0] + ")";
var energyString = tokens[tokens.length - 1];
this.asc.setAtomSetEnergy (energyString, this.parseFloatStr (energyString));
this.asc.setAtomSetName (energyKey + " = " + energyString);
this.asc.setModelInfoForSet ("name", energyKey + " " + energyString, ac);
});
Clazz.defineMethod (c$, "readBasis",
function () {
this.moData = new java.util.Hashtable ();
var ac = 1;
var shellCount = 0;
var gaussianCount = 0;
this.shells = new JU.Lst ();
var gdata = new JU.Lst ();
var tokens;
this.discardLinesUntilStartsWith ("$basis");
this.rd ();
while (this.rd () != null) {
if (this.line.startsWith ("****")) {
ac++;
if (this.rd () != null && this.line.startsWith ("$end")) break;
continue;
}shellCount++;
var slater = Clazz.newIntArray (4, 0);
tokens = this.getTokens ();
slater[0] = ac;
slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (tokens[0]);
slater[2] = gaussianCount + 1;
var nGaussians = this.parseIntStr (tokens[1]);
slater[3] = nGaussians;
this.shells.addLast (slater);
gaussianCount += nGaussians;
for (var i = 0; i < nGaussians; i++) {
gdata.addLast (JU.PT.getTokens (this.rd ()));
}
}
this.gaussians = JU.AU.newFloat2 (gaussianCount);
for (var i = 0; i < gaussianCount; i++) {
tokens = gdata.get (i);
this.gaussians[i] = Clazz.newFloatArray (tokens.length, 0);
for (var j = 0; j < tokens.length; j++) this.gaussians[i][j] = this.parseFloatStr (tokens[j]);
}
if (this.debugging) {
JU.Logger.debug (shellCount + " slater shells read");
JU.Logger.debug (gaussianCount + " gaussian primitives read");
}this.discardLinesUntilStartsWith (" There are");
tokens = this.getTokens ();
this.nBasis = this.parseIntStr (tokens[5]);
});
Clazz.defineMethod (c$, "readESym",
function (haveSym) {
this.alphas = new Array (this.nBasis);
this.betas = new Array (this.nBasis);
var moInfos;
var ne = 0;
var readBetas = false;
this.discardLinesUntilStartsWith (" Alpha");
var tokens = this.getTokens ();
moInfos = this.alphas;
for (var e = 0; e < 2; e++) {
var nMO = 0;
while (this.rd () != null) {
if (this.line.startsWith (" -- ")) {
ne = 0;
if (this.line.indexOf ("Vacant") < 0) {
if (this.line.indexOf ("Occupied") > 0) ne = 1;
}this.rd ();
}if (this.line.startsWith (" -------")) {
e = 2;
break;
}var nOrbs = this.getTokens ().length;
if (nOrbs == 0 || this.line.startsWith (" Warning")) {
this.discardLinesUntilStartsWith (" Beta");
readBetas = true;
moInfos = this.betas;
break;
}if (haveSym) tokens = JU.PT.getTokens (this.rd ());
for (var i = 0, j = 0; i < nOrbs; i++, j += 2) {
var info = Clazz.innerTypeInstance (J.adapter.readers.quantum.QchemReader.MOInfo, this, null);
info.ne = ne;
if (haveSym) info.moSymmetry = tokens[j] + tokens[j + 1] + " ";
moInfos[nMO] = info;
nMO++;
}
}
}
if (!readBetas) this.betas = this.alphas;
}, "~B");
Clazz.defineMethod (c$, "readQchemMolecularOrbitals",
function () {
var orbitalType = this.getTokens ()[0];
this.alphaBeta = "A";
this.readMOs (orbitalType.equals ("RESTRICTED"), this.alphas);
if (orbitalType.equals ("ALPHA")) {
this.discardLinesUntilContains ("BETA");
this.alphaBeta = "B";
this.readMOs (false, this.betas);
}var isOK = true;
if (this.dList.length > 0) {
if (this.dSpherical) isOK = this.getDFMap ("DS", this.dList, 3, J.adapter.readers.quantum.QchemReader.$DS_LIST, 2);
else isOK = this.getDFMap ("DC", this.dList, 4, J.adapter.readers.quantum.QchemReader.$DC_LIST, 3);
if (!isOK) {
JU.Logger.error ("atomic orbital order is unrecognized -- skipping reading of MOs. dList=" + this.dList);
this.shells = null;
}}if (this.fList.length > 0) {
if (this.fSpherical) isOK = this.getDFMap ("FS", this.fList, 5, J.adapter.readers.quantum.QchemReader.$FS_LIST, 2);
else isOK = this.getDFMap ("FC", this.fList, 6, J.adapter.readers.quantum.QchemReader.$FC_LIST, 3);
if (!isOK) {
JU.Logger.error ("atomic orbital order is unrecognized -- skipping reading of MOs. fList=" + this.fList);
this.shells = null;
}}this.setMOData (this.shells == null);
this.shells = null;
});
Clazz.defineMethod (c$, "readMOs",
function (restricted, moInfos) {
var mos = JU.AU.createArrayOfHashtable (6);
var mocoef = JU.AU.newFloat2 (6);
var moid = Clazz.newIntArray (6, 0);
var tokens;
var energy;
var nMOs = 0;
while (this.rd ().length > 2) {
tokens = this.getTokens ();
var nMO = tokens.length;
energy = JU.PT.getTokens (this.rd ().substring (13));
for (var i = 0; i < nMO; i++) {
moid[i] = this.parseIntStr (tokens[i]) - 1;
mocoef[i] = Clazz.newFloatArray (this.nBasis, 0);
mos[i] = new java.util.Hashtable ();
}
for (var i = 0, pt = 0; i < this.nBasis; i++) {
tokens = JU.PT.getTokens (this.rd ());
var s = this.line.substring (12, 17).trim ();
var ch = s.charAt (0);
switch (ch) {
case 'd':
s = s.substring (s.length - 3).toUpperCase ();
if (s.startsWith ("D ")) {
if (!this.dFixed) this.fixSlaterTypes (4, 3);
s = "D" + s.charAt (2);
this.dSpherical = true;
}if (this.dList.indexOf (s) < 0) this.dList += s + " ";
this.dFixed = true;
break;
case 'f':
s = s.substring (s.length - 3).toUpperCase ();
if (s.startsWith ("F ")) {
if (!this.fFixed) this.fixSlaterTypes (6, 5);
s = "F" + s.charAt (2);
this.fSpherical = true;
}if (this.fList.indexOf (s) < 0) this.fList += s + " ";
this.fFixed = true;
break;
default:
if (!J.quantum.QS.isQuantumBasisSupported (ch)) continue;
break;
}
for (var j = tokens.length - nMO, k = 0; k < nMO; j++, k++) mocoef[k][pt] = this.parseFloatStr (tokens[j]);
pt++;
}
for (var i = 0; i < nMO; i++) {
var moInfo = moInfos[moid[i]];
mos[i].put ("energy", Float.$valueOf (JU.PT.fVal (energy[i])));
mos[i].put ("coefficients", mocoef[i]);
var label = this.alphaBeta;
var ne = moInfo.ne;
if (restricted) ne = this.alphas[moid[i]].ne + this.betas[moid[i]].ne;
mos[i].put ("occupancy", Float.$valueOf (ne));
switch (ne) {
case 2:
label = "AB";
break;
case 1:
break;
case 0:
if (restricted) label = "V";
else label = "V" + label;
break;
}
mos[i].put ("symmetry", moInfo.moSymmetry + label + "(" + (moid[i] + 1) + ")");
this.orbitals.addLast (mos[i]);
}
nMOs += nMO;
}
return nMOs;
}, "~B,~A");
c$.$QchemReader$MOInfo$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
this.ne = 0;
this.moSymmetry = "";
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum.QchemReader, "MOInfo");
c$ = Clazz.p0p ();
};
c$.$DC_LIST = c$.prototype.$DC_LIST = "DXX DYY DZZ DXY DXZ DYZ";
Clazz.defineStatics (c$,
"$DS_LIST", "D3 D4 D2 D5 D1");
c$.$FC_LIST = c$.prototype.$FC_LIST = "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ";
Clazz.defineStatics (c$,
"$FS_LIST", "F4 F5 F3 F6 F2 F7 F1");
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.BasisFunctionReader", "JU.Lst"], "J.adapter.readers.quantum.SlaterReader", ["java.util.Arrays", "J.quantum.SlaterData", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.slaters = null;
this.slaterArray = null;
if (!Clazz.isClassDefined ("J.adapter.readers.quantum.SlaterReader.SlaterSorter")) {
J.adapter.readers.quantum.SlaterReader.$SlaterReader$SlaterSorter$ ();
}
if (!Clazz.isClassDefined ("J.adapter.readers.quantum.SlaterReader.OrbitalSorter")) {
J.adapter.readers.quantum.SlaterReader.$SlaterReader$OrbitalSorter$ ();
}
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum, "SlaterReader", J.adapter.readers.quantum.BasisFunctionReader);
Clazz.prepareFields (c$, function () {
this.slaters = new JU.Lst ();
});
Clazz.defineMethod (c$, "addSlater",
function (iAtom, a, b, c, d, zeta, coef) {
this.slaters.addLast ( new J.quantum.SlaterData (iAtom, a, b, c, d, zeta, coef));
}, "~N,~N,~N,~N,~N,~N,~N");
Clazz.defineMethod (c$, "addSlater",
function (sd, n) {
sd.index = n;
this.slaters.addLast (sd);
}, "J.quantum.SlaterData,~N");
Clazz.defineMethod (c$, "setSlaters",
function (doScale, doSort) {
if (this.slaterArray == null) {
var nSlaters = this.slaters.size ();
this.slaterArray = new Array (nSlaters);
for (var i = 0; i < this.slaterArray.length; i++) this.slaterArray[i] = this.slaters.get (i);
}if (doScale) for (var i = 0; i < this.slaterArray.length; i++) {
var sd = this.slaterArray[i];
sd.coef *= this.scaleSlater (sd.x, sd.y, sd.z, sd.r, sd.zeta);
if (this.debugging) {
JU.Logger.debug ("SlaterReader " + i + ": " + sd.atomNo + " " + sd.x + " " + sd.y + " " + sd.z + " " + sd.r + " " + sd.zeta + " " + sd.coef);
}}
if (doSort) {
java.util.Arrays.sort (this.slaterArray, Clazz.innerTypeInstance (J.adapter.readers.quantum.SlaterReader.SlaterSorter, this, null));
var pointers = Clazz.newIntArray (this.slaterArray.length, 0);
for (var i = 0; i < this.slaterArray.length; i++) pointers[i] = this.slaterArray[i].index;
this.sortOrbitalCoefficients (pointers);
}this.moData.put ("slaters", this.slaterArray);
this.asc.setCurrentModelInfo ("moData", this.moData);
}, "~B,~B");
Clazz.defineMethod (c$, "setMOs",
function (units) {
this.moData.put ("mos", this.orbitals);
this.moData.put ("energyUnits", units);
this.finalizeMOData (this.moData);
}, "~S");
Clazz.defineMethod (c$, "sortOrbitalCoefficients",
function (pointers) {
for (var i = this.orbitals.size (); --i >= 0; ) {
var mo = this.orbitals.get (i);
var coefs = mo.get ("coefficients");
var sorted = Clazz.newFloatArray (pointers.length, 0);
for (var j = 0; j < pointers.length; j++) {
var k = pointers[j];
if (k < coefs.length) sorted[j] = coefs[k];
}
mo.put ("coefficients", sorted);
}
}, "~A");
Clazz.defineMethod (c$, "sortOrbitals",
function () {
var array = this.orbitals.toArray ( new Array (0));
java.util.Arrays.sort (array, Clazz.innerTypeInstance (J.adapter.readers.quantum.SlaterReader.OrbitalSorter, this, null));
this.orbitals.clear ();
for (var i = 0; i < array.length; i++) this.orbitals.addLast (array[i]);
});
Clazz.defineMethod (c$, "scaleSlater",
function (ex, ey, ez, er, zeta) {
var el = ex + ey + ez;
switch (el) {
case 0:
case 1:
ez = -1;
break;
}
return J.adapter.readers.quantum.SlaterReader.getSlaterConstCartesian (el + er + 1, Math.abs (zeta), el, ex, ey, ez);
}, "~N,~N,~N,~N,~N");
c$.fact = Clazz.defineMethod (c$, "fact",
function (f, zeta, n) {
return Math.pow (2 * zeta, n + 0.5) * Math.sqrt (f * 0.07957747154594767 / J.adapter.readers.quantum.SlaterReader.fact1[n]);
}, "~N,~N,~N");
c$.getSlaterConstCartesian = Clazz.defineMethod (c$, "getSlaterConstCartesian",
function (n, zeta, el, ex, ey, ez) {
return J.adapter.readers.quantum.SlaterReader.fact (ez < 0 ? J.adapter.readers.quantum.SlaterReader.dfact2[el + 1] : J.adapter.readers.quantum.SlaterReader.dfact2[el + 1] / J.adapter.readers.quantum.SlaterReader.dfact2[ex] / J.adapter.readers.quantum.SlaterReader.dfact2[ey] / J.adapter.readers.quantum.SlaterReader.dfact2[ez], zeta, n);
}, "~N,~N,~N,~N,~N,~N");
c$.getSlaterConstDSpherical = Clazz.defineMethod (c$, "getSlaterConstDSpherical",
function (n, zeta, ex, ey) {
return J.adapter.readers.quantum.SlaterReader.fact (Clazz.doubleToInt (15 / (ex < 0 ? 12 : ey < 0 ? 4 : 1)), zeta, n);
}, "~N,~N,~N,~N");
c$.$SlaterReader$SlaterSorter$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum.SlaterReader, "SlaterSorter", null, java.util.Comparator);
Clazz.overrideMethod (c$, "compare",
function (a, b) {
return (a.atomNo < b.atomNo ? -1 : a.atomNo > b.atomNo ? 1 : 0);
}, "J.quantum.SlaterData,J.quantum.SlaterData");
c$ = Clazz.p0p ();
};
c$.$SlaterReader$OrbitalSorter$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
Clazz.instantialize (this, arguments);
}, J.adapter.readers.quantum.SlaterReader, "OrbitalSorter", null, java.util.Comparator);
Clazz.overrideMethod (c$, "compare",
function (a, b) {
var c = (a.get ("energy")).floatValue ();
var d = (b.get ("energy")).floatValue ();
return (c < d ? -1 : d < c ? 1 : 0);
}, "java.util.Map,java.util.Map");
c$ = Clazz.p0p ();
};
Clazz.defineStatics (c$,
"_1_4pi", 0.07957747154594767,
"fact1", Clazz.newDoubleArray (-1, [1.0, 2.0, 24.0, 720.0, 40320.0, 362880.0, 87178291200.0]),
"dfact2", Clazz.newDoubleArray (-1, [1, 1, 3, 15, 105]));
});

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Clazz.declarePackage ("J.adapter.readers.quantum");
Clazz.load (["J.adapter.readers.quantum.MopacSlaterReader"], "J.adapter.readers.quantum.WebMOReader", ["java.lang.Boolean", "$.Exception", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.BasisFunctionReader", "J.adapter.smarter.Bond", "JU.Logger"], function () {
c$ = Clazz.declareType (J.adapter.readers.quantum, "WebMOReader", J.adapter.readers.quantum.MopacSlaterReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.equals ("[HEADER]")) {
this.readHeader ();
return true;
}if (this.line.equals ("[ATOMS]")) {
this.readAtoms ();
return false;
}if (this.line.equals ("[BONDS]")) {
this.readBonds ();
return false;
}if (!this.doReadMolecularOrbitals) return true;
if (this.line.equals ("[AO_ORDER]")) {
this.readAtomicOrbitalOrder ();
return false;
}if (this.line.equals ("[GTO]")) {
this.readGaussianBasis ();
return false;
}if (this.line.equals ("[STO]")) {
this.readSlaterBasis ();
return false;
}if (this.line.indexOf ("[MO") == 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.readMolecularOrbital ();
return false;
}return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderASCR ();
if (this.nOrbitals > 0) this.setMOs ("eV");
if (this.debugging) JU.Logger.debug (this.orbitals.size () + " molecular orbitals read");
});
Clazz.defineMethod (c$, "readHeader",
function () {
this.moData.put ("isNormalized", Boolean.TRUE);
while (this.rd () != null && this.line.length > 0) {
this.moData.put ("calculationType", "?");
var tokens = this.getTokens ();
tokens[0] = tokens[0].substring (0, 1).toLowerCase () + tokens[0].substring (1, tokens[0].length);
var str = "";
for (var i = 1; i < tokens.length; i++) str += (i == 1 ? "" : " ") + tokens[i].toLowerCase ();
this.moData.put (tokens[0], str);
}
});
Clazz.defineMethod (c$, "readAtoms",
function () {
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length == 0) continue;
var sym = tokens[0];
var atNo = this.parseIntStr (sym);
this.setAtomCoordScaled (null, tokens, 1, 0.5291772).elementSymbol = (atNo == -2147483648 ? sym : J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (atNo));
}
});
Clazz.defineMethod (c$, "readBonds",
function () {
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length == 0) continue;
var atomIndex1 = this.parseIntStr (tokens[0]);
var atomIndex2 = this.parseIntStr (tokens[1]);
var order = this.parseIntStr (tokens[2]);
this.asc.addBond ( new J.adapter.smarter.Bond (atomIndex1 - 1, atomIndex2 - 1, order));
}
});
Clazz.defineMethod (c$, "readAtomicOrbitalOrder",
function () {
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length == 0) continue;
var data = this.line.substring (9).trim ().toLowerCase ();
var isOK = false;
switch (tokens.length - 1) {
case 3:
case 4:
isOK = true;
break;
case 5:
isOK = (tokens[0].equals ("DOrbitals") && this.getDFMap ("DS", data, 3, J.adapter.readers.quantum.WebMOReader.DS_LIST, 99));
break;
case 6:
isOK = (tokens[0].equals ("DOrbitals") && this.getDFMap ("DC", data, 4, J.adapter.readers.quantum.WebMOReader.DC_LIST, 2));
break;
case 7:
isOK = (tokens[0].equals ("FOrbitals") && this.getDFMap ("FS", data, 5, J.adapter.readers.quantum.WebMOReader.FS_LIST, 99));
break;
case 10:
isOK = (tokens[0].equals ("FOrbitals") && this.getDFMap ("FC", data, 6, J.adapter.readers.quantum.WebMOReader.FC_LIST, 3));
break;
}
if (!isOK) {
JU.Logger.error ("atomic orbital order is unrecognized -- skipping reading of MOs due to line: " + this.line);
this.orbitals = null;
}}
});
Clazz.defineMethod (c$, "getLine",
function () {
return (this.rd () != null && (this.line.length == 0 || this.line.charAt (0) != '['));
});
Clazz.defineMethod (c$, "readGaussianBasis",
function () {
var sdata = new JU.Lst ();
var gdata = new JU.Lst ();
var atomNo = 1;
var gaussianPtr = 0;
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length == 0) continue;
if (tokens.length != 1) throw new Exception ("Error reading GTOs: missing atom index");
var slater = Clazz.newIntArray (4, 0);
atomNo = this.parseIntStr (tokens[0]);
tokens = JU.PT.getTokens (this.rd ());
var nGaussians = this.parseIntStr (tokens[1]);
slater[0] = atomNo;
slater[1] = J.adapter.readers.quantum.BasisFunctionReader.getQuantumShellTagID (tokens[0]);
slater[2] = gaussianPtr + 1;
slater[3] = nGaussians;
for (var i = 0; i < nGaussians; i++) {
var strData = JU.PT.getTokens (this.rd ());
var nData = strData.length;
var data = Clazz.newFloatArray (nData, 0);
for (var d = 0; d < nData; d++) {
data[d] = this.parseFloatStr (strData[d]);
}
gdata.addLast (data);
gaussianPtr++;
}
sdata.addLast (slater);
}
var garray = JU.AU.newFloat2 (gaussianPtr);
for (var i = 0; i < gaussianPtr; i++) {
garray[i] = gdata.get (i);
}
this.moData.put ("shells", sdata);
this.moData.put ("gaussians", garray);
if (this.debugging) {
JU.Logger.debug (sdata.size () + " slater shells read");
JU.Logger.debug (garray.length + " gaussian primitives read");
}this.asc.setCurrentModelInfo ("moData", this.moData);
});
Clazz.defineMethod (c$, "readSlaterBasis",
function () {
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length < 7) continue;
this.addSlater (this.parseIntStr (tokens[0]), this.parseIntStr (tokens[1]), this.parseIntStr (tokens[2]), this.parseIntStr (tokens[3]), this.parseIntStr (tokens[4]), this.parseFloatStr (tokens[5]), this.parseFloatStr (tokens[6]));
}
this.setSlaters (false, false);
});
Clazz.defineMethod (c$, "readMolecularOrbital",
function () {
if (this.orbitals == null) {
JU.Logger.error ("MOLECULAR ORBITALS SKIPPED");
while (this.getLine ()) {
}
return;
}var mo = new java.util.Hashtable ();
var data = new JU.Lst ();
var energy = this.parseFloatStr (this.rd ());
var occupancy = this.parseFloatStr (this.rd ());
while (this.getLine ()) {
var tokens = this.getTokens ();
if (tokens.length == 0) {
continue;
}data.addLast (tokens[1]);
}
var coefs = Clazz.newFloatArray (data.size (), 0);
for (var i = data.size (); --i >= 0; ) {
coefs[i] = this.parseFloatStr (data.get (i));
}
mo.put ("energy", Float.$valueOf (energy));
mo.put ("occupancy", Float.$valueOf (occupancy));
mo.put ("coefficients", coefs);
this.orbitals.addLast (mo);
this.nOrbitals++;
if (occupancy > 0) this.moData.put ("HOMO", Integer.$valueOf (this.nOrbitals));
});
Clazz.defineStatics (c$,
"DS_LIST", "NOT IMPLEMENTED IN THIS READER",
"DC_LIST", "xx yy zz xy xz yz",
"FS_LIST", "NOT IMPLEMENTED IN THIS READER",
"FC_LIST", "xxx yyy zzz yyx xxy xxz zzx zzy yyz xyz");
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.AlchemyReader", ["java.lang.Character", "JU.PT", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.decorateAsClass (function () {
this.isM3D = false;
this.ac = 0;
this.bondCount = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "AlchemyReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.asc.newAtomSet ();
this.rd ();
if (this.line.indexOf ("ATOMS") < 0) {
this.isM3D = true;
this.rd ();
}var tokens = this.getTokens ();
this.ac = this.parseIntStr (tokens[0]);
this.bondCount = this.parseIntStr (tokens[this.isM3D ? 1 : 2]);
this.readAtoms ();
this.readBonds ();
this.continuing = false;
});
Clazz.defineMethod (c$, "readAtoms",
function () {
var pt = (this.isM3D ? 3 : 2);
for (var i = this.ac; --i >= 0; ) {
var tokens = JU.PT.getTokens (this.rd ());
var atom = new J.adapter.smarter.Atom ();
atom.atomSerial = this.parseIntStr (tokens[0]);
var name = tokens[1];
if (!this.isM3D) {
atom.atomName = name;
atom.elementSymbol = name.substring (0, 1);
var c1 = name.charAt (0);
var c2 = ' ';
var nChar = (name.length == 2 && (J.adapter.smarter.Atom.isValidSym2 (c1, c2 = Character.toLowerCase (name.charAt (1))) || name.equals ("Du")) ? 2 : 1);
name = (nChar == 1 ? "" + c1 : "" + c1 + c2);
}atom.elementSymbol = name;
this.setAtomCoordTokens (atom, tokens, pt);
atom.partialCharge = (tokens.length >= 6 ? this.parseFloatStr (tokens[pt + 3]) : 0);
this.asc.addAtomWithMappedSerialNumber (atom);
}
});
Clazz.defineMethod (c$, "readBonds",
function () {
for (var i = this.bondCount; --i >= 0; ) {
var tokens = JU.PT.getTokens (this.rd ());
var atomSerial1 = tokens[1];
var atomSerial2 = tokens[2];
var sOrder = (tokens.length < 4 ? "1" : tokens[3].toUpperCase ());
var order = 0;
switch (sOrder.charAt (0)) {
default:
case '1':
case 'S':
order = 1;
break;
case '2':
case 'D':
order = 2;
break;
case '3':
case 'T':
order = 3;
break;
case 'A':
order = 515;
break;
case 'H':
order = 2048;
break;
}
this.asc.addNewBondFromNames (atomSerial1, atomSerial2, order);
}
});
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.AmpacReader", ["JU.P3"], function () {
c$ = Clazz.decorateAsClass (function () {
this.ac = 0;
this.freqAtom0 = -1;
this.partialCharges = null;
this.atomPositions = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "AmpacReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("CARTESIAN COORDINATES") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.readCoordinates ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("NET ATOMIC CHARGES") >= 0) {
this.readPartialCharges ();
return true;
}if (this.line.indexOf ("VIBRATIONAL FREQUENCIES") >= 0) {
this.readFrequencies ();
return true;
}return true;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
var haveFreq = (this.freqAtom0 >= 0);
if (haveFreq) {
this.atomPositions = new Array (this.ac);
} else {
this.asc.newAtomSet ();
}this.rd ();
this.ac = 0;
while (this.rd () != null) {
var tokens = this.getTokens ();
if (tokens.length < 5) break;
if (haveFreq) {
this.atomPositions[this.ac] = JU.P3.new3 (this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[4]));
} else {
this.addAtomXYZSymName (tokens, 2, tokens[1], null);
}this.ac++;
}
if (haveFreq) this.setPositions ();
});
Clazz.defineMethod (c$, "setPositions",
function () {
var maxAtom = this.asc.ac;
var atoms = this.asc.atoms;
for (var i = this.freqAtom0; i < maxAtom; i++) {
atoms[i].setT (this.atomPositions[i % this.ac]);
atoms[i].partialCharge = this.partialCharges[i % this.ac];
}
});
Clazz.defineMethod (c$, "readPartialCharges",
function () {
this.rd ();
this.partialCharges = Clazz.newFloatArray (this.ac, 0);
var tokens;
for (var i = 0; i < this.ac; i++) {
if (this.rd () == null || (tokens = this.getTokens ()).length < 4) break;
this.partialCharges[i] = this.parseFloatStr (tokens[2]);
}
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
while (this.rd () != null && this.line.indexOf ("FREQ :") < 0) {
}
while (this.line != null && this.line.indexOf ("FREQ :") >= 0) {
var frequencies = this.getTokens ();
while (this.rd () != null && this.line.indexOf ("IR I") < 0) {
}
var iAtom0 = this.asc.ac;
if (this.vibrationNumber == 0) this.freqAtom0 = iAtom0;
var frequencyCount = frequencies.length - 2;
var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
this.asc.cloneLastAtomSet ();
this.asc.setAtomSetName (frequencies[i + 2] + " cm^-1");
this.asc.setAtomSetModelProperty ("Frequency", frequencies[i + 2] + " cm^-1");
this.asc.setAtomSetModelProperty (".PATH", "Frequencies");
}
this.fillFrequencyData (iAtom0, this.ac, this.ac, ignore, false, 8, 9, null, 0);
this.rd ();
this.rd ();
}
});
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/simple/CubeReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.CubeReader", ["JU.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.ac = 0;
this.isAngstroms = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "CubeReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.asc.newAtomSet ();
this.readTitleLines ();
this.readAtomCountAndOrigin ();
this.readLines (3);
this.readAtoms ();
this.applySymmetryAndSetTrajectory ();
this.continuing = false;
});
Clazz.defineMethod (c$, "readTitleLines",
function () {
if (this.rd ().indexOf ("#JVXL") == 0) while (this.rd ().indexOf ("#") == 0) {
}
this.checkCurrentLineForScript ();
var name = this.line.trim ();
this.rd ();
this.checkCurrentLineForScript ();
this.asc.setAtomSetName (name + " - " + this.line.trim ());
});
Clazz.defineMethod (c$, "readAtomCountAndOrigin",
function () {
this.rd ();
this.isAngstroms = (this.line.indexOf ("ANGSTROMS") >= 0);
var tokens = this.getTokens ();
if (tokens[0].charAt (0) == '+') tokens[0] = tokens[0].substring (1);
this.ac = Math.abs (this.parseIntStr (tokens[0]));
});
Clazz.defineMethod (c$, "readAtoms",
function () {
var f = (this.isAngstroms ? 1 : 0.5291772);
for (var i = 0; i < this.ac; ++i) {
var tokens = JU.PT.getTokens (this.rd ());
this.setAtomCoordScaled (null, tokens, 2, f).elementNumber = this.parseIntStr (tokens[0]);
}
});
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.FoldingXyzReader", ["java.util.Hashtable", "JU.PT", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.declareType (J.adapter.readers.simple, "FoldingXyzReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (this.asc.bondCount > 0) this.asc.setNoAutoBond ();
this.isTrajectory = false;
this.finalizeReaderASCR ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var next = Clazz.newIntArray (-1, [0]);
var token = JU.PT.parseTokenNext (this.line, next);
if (token == null) return true;
var addAtoms = this.doGetModel (++this.modelNumber, null);
var modelAtomCount = this.parseIntStr (token);
if (addAtoms) {
this.asc.newAtomSet ();
var tokens = this.getTokens ();
this.asc.setAtomSetName (tokens.length == 2 ? "Protein " + tokens[1] : this.line.substring (next[0]).trim ());
}var readLine = this.readAtoms (modelAtomCount + 1, addAtoms);
this.continuing = !addAtoms || !this.isLastModel (this.modelNumber);
return readLine;
});
Clazz.defineMethod (c$, "readAtoms",
function (ac, addAtoms) {
var htBondCounts = new java.util.Hashtable ();
var bonds = new Array (ac);
var haveAtomTypes = true;
var checking = true;
var lastAtom = null;
var readNextLine = true;
for (var i = 0; i < ac; i++) {
this.discardLinesUntilNonBlank ();
if (this.line == null) break;
var tokens = this.getTokens ();
var sIndex = tokens[0];
if (sIndex.equals (lastAtom)) {
readNextLine = false;
break;
}lastAtom = sIndex;
if (!addAtoms) continue;
var atom = new J.adapter.smarter.Atom ();
atom.atomName = tokens[1];
atom.elementSymbol = this.getElement (tokens[1]);
atom.atomSerial = this.parseIntStr (sIndex);
if (!this.filterAtom (atom, i)) continue;
this.setAtomCoordTokens (atom, tokens, 2);
this.asc.addAtomWithMappedSerialNumber (atom);
var n = tokens.length - 5;
bonds[i] = new Array (n + 1);
bonds[i][n] = sIndex;
for (var j = 0; j < n; j++) {
var t = tokens[j + 5];
var i2 = this.parseIntStr (t);
bonds[i][j] = t;
if (checking) {
if (n == 0 || t.equals (sIndex) || i2 <= 0 || i2 > ac) {
haveAtomTypes = (n > 0);
checking = false;
} else {
var count = htBondCounts.get (t);
if (count == null) htBondCounts.put (t, count = Clazz.newIntArray (1, 0));
if (++count[0] > 10) haveAtomTypes = !(checking = false);
}}}
}
if (addAtoms) {
this.makeBonds (bonds, !checking && haveAtomTypes);
this.applySymmetryAndSetTrajectory ();
}return readNextLine;
}, "~N,~B");
Clazz.defineMethod (c$, "makeBonds",
function (bonds, haveAtomTypes) {
for (var i = bonds.length; --i >= 0; ) {
var b = bonds[i];
if (b == null) continue;
var a1 = this.asc.getAtomFromName (b[b.length - 1]);
var b0 = 0;
if (haveAtomTypes) a1.atomName += "\0" + b[b0++];
for (var j = b.length - 1; --j >= b0; ) {
var a2 = this.asc.getAtomFromName (b[j]);
if (a1.index < a2.index) this.asc.addNewBondWithOrderA (a1, a2, 1);
}
}
}, "~A,~B");
Clazz.defineMethod (c$, "getElement",
function (name) {
var n = name.length;
switch (n) {
case 1:
break;
default:
var c1 = name.charAt (0);
var c2 = name.charAt (1);
n = (J.adapter.smarter.Atom.isValidSym2 (c1, c2) || c1 == 'C' && c2 == 'L' ? 2 : 1);
}
return name.substring (0, n);
}, "~S");
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/simple/GhemicalMMReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.GhemicalMMReader", ["java.lang.Exception", "JU.PT"], function () {
c$ = Clazz.declareType (J.adapter.readers.simple, "GhemicalMMReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.startsWith ("!Header")) {
this.processHeader ();
return true;
}if (this.line.startsWith ("!Info")) {
this.processInfo ();
return true;
}if (this.line.startsWith ("!Atoms")) {
this.processAtoms ();
return true;
}if (this.line.startsWith ("!Bonds")) {
this.processBonds ();
return true;
}if (this.line.startsWith ("!Coord")) {
this.processCoord ();
return true;
}if (this.line.startsWith ("!Charges")) {
this.processCharges ();
return true;
}return true;
});
Clazz.defineMethod (c$, "processHeader",
function () {
});
Clazz.defineMethod (c$, "processInfo",
function () {
});
Clazz.defineMethod (c$, "processAtoms",
function () {
var ac = this.parseIntAt (this.line, 6);
for (var i = 0; i < ac; ++i) {
if (this.asc.ac != i) throw new Exception ("GhemicalMMReader error #1");
this.rd ();
var atomIndex = this.parseIntStr (this.line);
if (atomIndex != i) throw new Exception ("bad atom index in !Atomsexpected: " + i + " saw:" + atomIndex);
var elementNumber = this.parseInt ();
var atom = this.asc.addNewAtom ();
atom.elementNumber = elementNumber;
}
});
Clazz.defineMethod (c$, "processBonds",
function () {
var bondCount = this.parseIntAt (this.line, 6);
for (var i = 0; i < bondCount; ++i) {
this.rd ();
var atomIndex1 = this.parseIntStr (this.line);
var atomIndex2 = this.parseInt ();
var orderCode = this.parseToken ();
var order = 0;
switch (orderCode.charAt (0)) {
case 'C':
order = 515;
break;
case 'T':
order = 3;
break;
case 'D':
order = 2;
break;
case 'S':
default:
order = 1;
}
this.asc.addNewBondWithOrder (atomIndex1, atomIndex2, order);
}
});
Clazz.defineMethod (c$, "processCoord",
function () {
var atoms = this.asc.atoms;
var ac = this.asc.ac;
for (var i = 0; i < ac; ++i) this.setAtomCoordScaled (atoms[i], JU.PT.getTokens (this.rd ()), 1, 10);
});
Clazz.defineMethod (c$, "processCharges",
function () {
var atoms = this.asc.atoms;
var ac = this.asc.ac;
for (var i = 0; i < ac; ++i) {
this.rd ();
var atomIndex = this.parseIntStr (this.line);
if (atomIndex != i) throw new Exception ("bad atom index in !Chargesexpected: " + i + " saw:" + atomIndex);
atoms[i].partialCharge = this.parseFloat ();
}
});
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.HyperChemReader", ["java.lang.Exception"], function () {
c$ = Clazz.decorateAsClass (function () {
this.atomIndex = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "HyperChemReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.length == 0 || this.line.charAt (0) == ';') return true;
if (this.line.startsWith ("mol ")) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.processMol ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.startsWith ("atom ")) {
this.processAtom ();
return true;
}if (this.line.startsWith ("endmol ")) {
this.applySymmetryAndSetTrajectory ();
return true;
}return true;
});
Clazz.defineMethod (c$, "processMol",
function () {
this.asc.newAtomSet ();
var molName = this.getMolName ();
this.asc.setAtomSetName (molName);
this.atomIndex = 0;
this.baseAtomIndex = this.asc.ac;
});
Clazz.defineMethod (c$, "getMolName",
function () {
this.parseTokenStr (this.line);
this.parseToken ();
return this.parseToken ();
});
Clazz.defineMethod (c$, "processAtom",
function () {
var fileAtomNumber = this.parseIntAt (this.line, 5);
if (fileAtomNumber - 1 != this.atomIndex) {
throw new Exception ("bad atom number sequence ... expected:" + (this.atomIndex + 1) + " found:" + fileAtomNumber);
}var atom = this.asc.addNewAtom ();
this.parseToken ();
atom.elementSymbol = this.parseToken ();
this.parseToken ();
this.parseToken ();
atom.partialCharge = this.parseFloat ();
this.setAtomCoordXYZ (atom, this.parseFloat (), this.parseFloat (), this.parseFloat ());
var bondCount = this.parseInt ();
for (var i = 0; i < bondCount; ++i) {
var otherAtomNumber = this.parseInt ();
var bondTypeToken = this.parseToken ();
if (otherAtomNumber > this.atomIndex) continue;
var bondOrder;
switch (bondTypeToken.charAt (0)) {
case 's':
bondOrder = 1;
break;
case 'd':
bondOrder = 2;
break;
case 't':
bondOrder = 3;
break;
case 'a':
bondOrder = 515;
break;
default:
throw new Exception ("unrecognized bond type:" + bondTypeToken + " atom #" + fileAtomNumber);
}
this.asc.addNewBondWithOrder (this.baseAtomIndex + this.atomIndex, this.baseAtomIndex + otherAtomNumber - 1, bondOrder);
}
++this.atomIndex;
});
});

320
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/simple/InputReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "java.util.Hashtable", "JU.Lst", "$.P3", "$.P4", "$.V3"], "J.adapter.readers.simple.InputReader", ["java.lang.Exception", "$.Float", "JU.Measure", "$.PT", "$.Quat", "J.adapter.smarter.Atom", "$.Bond", "J.api.JmolAdapter", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.ac = 0;
this.vAtoms = null;
this.atomMap = null;
this.tokens = null;
this.isJmolZformat = false;
this.lineBuffer = null;
this.symbolicMap = null;
this.isMopac = false;
this.isHeader = true;
this.firstLine = true;
this.pt0 = null;
this.v1 = null;
this.v2 = null;
this.plane1 = null;
this.plane2 = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "InputReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.vAtoms = new JU.Lst ();
this.atomMap = new java.util.Hashtable ();
this.lineBuffer = new JU.Lst ();
this.symbolicMap = new java.util.Hashtable ();
this.pt0 = new JU.P3 ();
this.v1 = new JU.V3 ();
this.v2 = new JU.V3 ();
this.plane1 = new JU.P4 ();
this.plane2 = new JU.P4 ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.firstLine) {
this.firstLine = false;
var tokens = this.getTokens ();
if (tokens.length == 3 && this.parseIntStr (tokens[0]) > 0 && this.parseIntStr (tokens[1]) > 0 && this.parseIntStr (tokens[2]) > 0) {
this.readConFile ();
return this.continuing = false;
}}this.cleanLine ();
if (this.line.length <= 2) this.isHeader = false;
if (this.line.startsWith ("#") || this.line.startsWith ("*") || this.isMopac && this.isHeader) {
if (this.line.startsWith ("#ZMATRIX")) this.isJmolZformat = this.line.toUpperCase ().indexOf ("GAUSSIAN") < 0 && !(this.isMopac = (this.line.toUpperCase ().indexOf ("MOPAC") >= 0));
this.checkCurrentLineForScript ();
return true;
}if (this.line.indexOf ("#") >= 0) this.line = this.line.substring (0, this.line.indexOf ("#"));
if (this.line.indexOf (":") >= 0) return true;
if (this.line.contains ("$molecule")) {
this.rd ();
return this.readBlock ("$end");
}if (this.line.startsWith ("$")) return true;
if (this.line.contains ("%mem")) {
this.discardLinesUntilBlank ();
this.discardLinesUntilBlank ();
this.rd ();
return this.readBlock (null);
}if (this.line.contains ("ATOMS cartesian")) {
return this.readBlock ("END");
}if (this.line.contains ("geometry units angstroms")) {
return this.readBlock ("end");
}if (this.line.contains ("&zmat")) {
return this.readBlock ("&");
}if (this.line.contains ("%coords")) {
this.discardLinesUntilContains ("coords");
return this.readBlock ("end");
}if (this.line.contains ("GEOM=PQS")) {
return this.readBlock ("BASIS");
}if (this.line.contains ("geometry={")) {
this.readLines (2);
return this.readBlock ("}");
}this.tokens = this.getTokens ();
if (this.tokens.length > 10) return this.readVFI ();
switch (this.tokens.length) {
case 1:
if (this.tokens[0].indexOf ("=") < 0) {
this.lineBuffer.clear ();
break;
}this.tokens = JU.PT.split (this.tokens[0], "=");
case 2:
if (this.parseIntStr (this.line) > 0 && this.parseInt () >= 0) {
this.readCFI ();
return (this.continuing = false);
}this.getSymbolic ();
return true;
case 10:
if (this.tokens[0].equals ("0")) return (this.continuing = false);
if (this.tokens[1].indexOf (".") < 0) return true;
if (this.lineBuffer.size () > 0 && this.lineBuffer.get (this.lineBuffer.size () - 1).length < 8) this.lineBuffer.clear ();
break;
}
this.lineBuffer.addLast (this.tokens);
return true;
});
Clazz.defineMethod (c$, "readConFile",
function () {
this.rd ();
var map = new java.util.Hashtable ();
var lstTokens = new JU.Lst ();
var n = 0;
while (this.rd () != null && this.line.length > 40) {
n++;
var tokens = this.getTokens ();
lstTokens.addLast (tokens);
map.put (tokens[1], this.addAtomXYZSymName (tokens, 2, tokens[0], null));
}
for (var i = 0; i < n; i++) {
var tokens = lstTokens.get (i);
var a = map.get (tokens[1]);
for (var j = 6; j < tokens.length; j++) this.asc.addBond ( new J.adapter.smarter.Bond (a.index, map.get (tokens[j]).index, 1));
}
});
Clazz.defineMethod (c$, "readCFI",
function () {
this.tokens = this.getTokens ();
var nAtoms = Clazz.floatToInt (this.getValue (0));
var nBonds = Clazz.floatToInt (this.getValue (1));
var map = new java.util.Hashtable ();
for (var i = 0; i < nAtoms; i++) {
this.tokens = JU.PT.getTokens (this.rd ());
if (this.tokens[1].equals ("0") || this.tokens[1].equals ("2")) continue;
var a = this.addAtomXYZSymName (this.tokens, 2, null, null);
a.elementNumber = Clazz.floatToShort (this.getValue (1));
map.put (this.tokens[0], a);
}
var bonds = this.fillFloatArray (null, 0, Clazz.newFloatArray (nBonds * 2, 0));
var orders = this.fillFloatArray (null, 0, Clazz.newFloatArray (nBonds, 0));
for (var i = 0, pt = 0; i < nBonds; i++) this.asc.addBond ( new J.adapter.smarter.Bond (map.get ("" + Clazz.floatToInt (bonds[pt++])).index, map.get ("" + Clazz.floatToInt (bonds[pt++])).index, Clazz.floatToInt (orders[i])));
});
Clazz.defineMethod (c$, "readVFI",
function () {
var map = new java.util.Hashtable ();
var bonds = new JU.Lst ();
while (this.tokens != null && this.tokens.length > 0) {
for (var i = this.tokens.length; --i >= 11; ) bonds.addLast ( Clazz.newArray (-1, [this.tokens[3], this.tokens[i]]));
var id = this.tokens[3];
this.tokens = (this.tokens[2].equals ("0") ? Clazz.newArray (-1, [this.tokens[4]]) : this.tokens[1].equals ("0") ? Clazz.newArray (-1, [this.tokens[4], this.tokens[2], this.tokens[5]]) : this.tokens[0].equals ("0") ? Clazz.newArray (-1, [this.tokens[4], this.tokens[2], this.tokens[5], this.tokens[1], this.tokens[7]]) : Clazz.newArray (-1, [this.tokens[4], this.tokens[2], this.tokens[5], this.tokens[1], this.tokens[7], this.tokens[0], this.tokens[9]]));
var atom = this.getAtom ();
map.put (id, atom);
this.tokens = JU.PT.getTokens (this.rd ());
}
for (var i = bonds.size (); --i >= 0; ) {
var b = bonds.get (i);
this.asc.addBond ( new J.adapter.smarter.Bond (map.get (b[0]).index, map.get (b[1]).index, 1));
}
return (this.continuing = false);
});
Clazz.defineMethod (c$, "readBlock",
function (strEnd) {
this.lineBuffer.clear ();
while (this.rd () != null && this.cleanLine () != null && (strEnd == null ? this.line.length > 0 : this.line.indexOf (strEnd) < 0)) this.lineBuffer.addLast (this.getTokens ());
return (this.continuing = false);
}, "~S");
Clazz.defineMethod (c$, "cleanLine",
function () {
this.line = this.line.$replace (',', ' ');
var pt1;
var pt2;
while ((pt1 = this.line.indexOf ('(')) >= 0 && (pt2 = this.line.indexOf ('(', pt1)) >= 0) this.line = this.line.substring (0, pt1) + " " + this.line.substring (pt2 + 1);
return (this.line = this.line.trim ());
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
var firstLine = 0;
for (var i = firstLine; i < this.lineBuffer.size (); i++) if ((this.tokens = this.lineBuffer.get (i)).length > 0) this.getAtom ();
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "getSymbolic",
function () {
if (this.symbolicMap.containsKey (this.tokens[0])) return;
var f = this.parseFloatStr (this.tokens[1]);
this.symbolicMap.put (this.tokens[0], Float.$valueOf (f));
JU.Logger.info ("symbolic " + this.tokens[0] + " = " + f);
});
Clazz.defineMethod (c$, "getAtom",
function () {
var atom = new J.adapter.smarter.Atom ();
var element = this.tokens[0];
var i = element.length;
while (--i >= 0 && JU.PT.isDigit (element.charAt (i))) {
}
if (++i == 0) element = J.api.JmolAdapter.getElementSymbol (this.parseIntStr (element));
if (i == 0 || i == element.length) {
atom.atomName = element + (this.ac + 1);
} else {
atom.atomName = element;
element = element.substring (0, i);
}if (this.isMopac && i != this.tokens[0].length) element = this.tokens[0].substring (i) + element;
this.parseAtomTokens (atom, element);
return atom;
});
Clazz.defineMethod (c$, "parseAtomTokens",
function (atom, element) {
this.setElementAndIsotope (atom, element);
if (this.tokens.length > 5 && this.tokens[1].indexOf (".") >= 0) {
var t = this.tokens;
var l = t.length;
this.tokens = (t[l - 3].equals ("0") ? Clazz.newArray (-1, [t[0]]) : t[l - 2].equals ("0") ? Clazz.newArray (-1, [t[0], t[l - 3], t[1]]) : t[l - 1].equals ("0") ? Clazz.newArray (-1, [t[0], t[l - 3], t[1], t[l - 2], t[3]]) : Clazz.newArray (-1, [t[0], t[l - 3], t[1], t[l - 2], t[3], t[l - 1], t[5]]));
}var ia = this.getAtomIndex (1);
var bondOrder = 0;
switch (this.tokens.length) {
case 8:
case 6:
atom = this.getAtomGeneral (atom, ia, bondOrder = Clazz.floatToInt (this.getValue (this.tokens.length - 1)));
break;
case 5:
if (this.tokens[1].equals ("0")) {
atom.set (this.getValue (2), this.getValue (3), this.getValue (4));
break;
}case 7:
atom = this.getAtomGeneral (atom, ia, 0);
break;
case 4:
if (this.getAtomIndex (1) < 0) {
atom.set (this.getValue (1), this.getValue (2), this.getValue (3));
break;
}bondOrder = Clazz.floatToInt (this.getValue (3));
case 3:
if (this.ac != 1 || (ia = this.getAtomIndex (1)) != 0) {
atom = null;
} else {
atom.set (this.getValue (2), 0, 0);
}break;
case 1:
if (this.ac != 0) atom = null;
else atom.set (0, 0, 0);
break;
default:
atom = null;
}
if (atom == null) throw new Exception ("bad Z-Matrix line");
this.vAtoms.addLast (atom);
this.atomMap.put (atom.atomName, Integer.$valueOf (this.ac++));
if (element.startsWith ("X") && J.api.JmolAdapter.getElementNumber (element) < 1) {
JU.Logger.info ("#dummy atom ignored: atom " + this.ac + " - " + atom.atomName);
} else {
this.asc.addAtom (atom);
this.setAtomCoord (atom);
JU.Logger.info (atom.atomName + " " + atom.x + " " + atom.y + " " + atom.z);
if (bondOrder < 0 || this.isJmolZformat && bondOrder > 0) this.asc.addBond ( new J.adapter.smarter.Bond (atom.index, this.vAtoms.get (ia).index, Math.abs (bondOrder)));
}}, "J.adapter.smarter.Atom,~S");
Clazz.defineMethod (c$, "getAtomGeneral",
function (atom, ia, bondOrder) {
var ib;
var ic;
if (this.tokens.length < 7 && this.ac != 2 || (ib = this.getAtomIndex (3)) < 0 || (ic = (this.tokens.length < 7 ? -2 : this.getAtomIndex (5))) == -1) {
return null;
}var d = this.getValue (2);
var theta1 = this.getValue (4);
var theta2 = (this.tokens.length < 7 ? 3.4028235E38 : this.getValue (6));
if (this.tokens.length == 8 && !this.isJmolZformat && !this.isMopac && bondOrder == 1) d = -Math.abs (d);
return atom = this.setAtom (atom, ia, ib, ic, d, theta1, theta2);
}, "J.adapter.smarter.Atom,~N,~N");
Clazz.defineMethod (c$, "getSymbolic",
function (key) {
var isNeg = key.startsWith ("-");
var F = this.symbolicMap.get (isNeg ? key.substring (1) : key);
if (F == null) return NaN;
var f = F.floatValue ();
return (isNeg ? -f : f);
}, "~S");
Clazz.defineMethod (c$, "getValue",
function (i) {
var f = this.getSymbolic (this.tokens[i]);
if (Float.isNaN (f)) {
f = this.parseFloatStr (this.tokens[i]);
if (Float.isNaN (f)) throw new Exception ("Bad Z-matrix value: " + this.tokens[i]);
}return f;
}, "~N");
Clazz.defineMethod (c$, "getAtomIndex",
function (i) {
var name;
if (i >= this.tokens.length || (name = this.tokens[i]).indexOf (".") >= 0 || !JU.PT.isLetterOrDigit (name.charAt (0))) return -1;
var ia = this.parseIntStr (name);
if (ia <= 0 || name.length != ("" + ia).length) {
var I = this.atomMap.get (name);
if (I == null) {
for (i = this.vAtoms.size (); --i >= 0; ) {
var atom = this.vAtoms.get (i);
if (atom.atomName.startsWith (name) && atom.atomName.length > name.length && JU.PT.isDigit (atom.atomName.charAt (name.length))) {
I = this.atomMap.get (atom.atomName);
break;
}}
}if (I == null) ia = -1;
else ia = I.intValue ();
} else {
ia--;
}return ia;
}, "~N");
Clazz.defineMethod (c$, "setAtom",
function (atom, ia, ib, ic, d, theta1, theta2) {
if (Float.isNaN (theta1) || Float.isNaN (theta2)) return null;
this.pt0.setT (this.vAtoms.get (ia));
this.v1.sub2 (this.vAtoms.get (ib), this.pt0);
this.v1.normalize ();
if (theta2 == 3.4028235E38) {
this.v2.set (0, 0, 1);
(JU.Quat.newVA (this.v2, theta1)).transform2 (this.v1, this.v2);
} else if (d >= 0) {
this.v2.sub2 (this.vAtoms.get (ic), this.pt0);
this.v2.cross (this.v1, this.v2);
(JU.Quat.newVA (this.v2, theta1)).transform2 (this.v1, this.v2);
(JU.Quat.newVA (this.v1, -theta2)).transform2 (this.v2, this.v2);
} else {
JU.Measure.getPlaneThroughPoint (this.setAtom (atom, ia, ib, ic, -d, theta1, 0), this.v1, this.plane1);
JU.Measure.getPlaneThroughPoint (this.setAtom (atom, ia, ic, ib, -d, theta2, 0), this.v1, this.plane2);
var list = JU.Measure.getIntersectionPP (this.plane1, this.plane2);
if (list.size () == 0) return null;
this.pt0.setT (list.get (0));
d = Math.sqrt (d * d - this.pt0.distanceSquared (this.vAtoms.get (ia))) * Math.signum (theta1) * Math.signum (theta2);
this.v2.setT (list.get (1));
}atom.scaleAdd2 (d, this.v2, this.pt0);
return atom;
}, "J.adapter.smarter.Atom,~N,~N,~N,~N,~N,~N");
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.JSONReader", ["JU.P3", "$.PT", "J.adapter.smarter.Bond", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.scale = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "JSONReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.asc.setCollectionName ("JSON");
this.asc.newAtomSet ();
var s = "";
while (this.rd () != null) s += this.line;
s = JU.PT.replaceAllCharacters (s, "\" ", "").$replace (',', ':');
if (s.contains ("_is2D:true")) this.set2D ();
if (s.contains ("_scale:")) this.getScaling (this.getSection (s, "_scale", false));
s = JU.PT.replaceAllCharacters (s, "}", "").$replace (',', ':');
this.readAtoms (this.getSection (s, "a", true));
this.readBonds (this.getSection (s, "b", true));
this.continuing = false;
});
Clazz.defineMethod (c$, "getScaling",
function (s) {
var xyz = JU.PT.split (s[0], ":");
this.scale = JU.P3.new3 (1, 1, 1);
for (var j = 0; j < xyz.length; j += 2) if (xyz[j].length == 1) switch (xyz[j].charAt (0)) {
case 'x':
this.scale.x = this.parseFloatStr (xyz[j + 1]);
break;
case 'y':
this.scale.y = this.parseFloatStr (xyz[j + 1]);
break;
case 'z':
this.scale.z = this.parseFloatStr (xyz[j + 1]);
break;
}
JU.Logger.info ("scale set to " + this.scale);
}, "~A");
Clazz.defineMethod (c$, "getSection",
function (json, key, isArray) {
var a = JU.PT.split (json, key + ":" + (isArray ? "[" : "") + "{");
if (a.length < 2) return a;
var data = a[1];
data = data.substring (0, data.indexOf ((isArray ? "]" : "}"))) + ":";
return JU.PT.split (data, "{");
}, "~S,~S,~B");
Clazz.defineMethod (c$, "readAtoms",
function (atoms) {
for (var i = 0; i < atoms.length; ++i) {
var lxyz = JU.PT.split (atoms[i], ":");
var atom = this.asc.addNewAtom ();
var x = 0;
var y = 0;
var z = 0;
var l = "C";
for (var j = 0; j < lxyz.length; j += 2) if (lxyz[j].length == 1) switch (lxyz[j].charAt (0)) {
case 'x':
x = this.parseFloatStr (lxyz[j + 1]);
break;
case 'y':
y = this.parseFloatStr (lxyz[j + 1]);
break;
case 'z':
z = this.parseFloatStr (lxyz[j + 1]);
break;
case 'l':
l = lxyz[j + 1];
break;
}
if (this.scale != null) {
x /= this.scale.x;
y /= this.scale.y;
z /= this.scale.z;
}this.setAtomCoordXYZ (atom, x, y, z);
atom.elementSymbol = l;
}
}, "~A");
Clazz.defineMethod (c$, "readBonds",
function (bonds) {
for (var i = 0; i < bonds.length; ++i) {
var beo = JU.PT.split (bonds[i], ":");
var b = 0;
var e = 0;
var order = 1;
for (var j = 0; j < beo.length; j += 2) if (beo[j].length == 1) switch (beo[j].charAt (0)) {
case 'b':
b = this.parseIntStr (beo[j + 1]);
break;
case 'e':
e = this.parseIntStr (beo[j + 1]);
break;
case 'o':
var o = Clazz.floatToInt (this.parseFloatStr (beo[j + 1]) * 2);
switch (o) {
case 0:
continue;
case 2:
case 4:
case 6:
case 8:
order = Clazz.doubleToInt (o / 2);
break;
case 1:
order = 33;
break;
case 3:
order = 66;
break;
case 5:
order = 97;
break;
default:
order = 1;
break;
}
break;
}
this.asc.addBond ( new J.adapter.smarter.Bond (b, e, order));
}
}, "~A");
});

58
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/simple/JmeReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.JmeReader", ["JU.PT", "J.adapter.smarter.Bond"], function () {
c$ = Clazz.declareType (J.adapter.readers.simple, "JmeReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.asc.setCollectionName ("JME");
this.asc.newAtomSet ();
this.line = this.rd ().$replace ('\t', ' ');
this.checkCurrentLineForScript ();
this.addJmolScript ("jmeString='" + this.line + "'");
var ac = this.parseInt ();
var bondCount = this.parseInt ();
this.readAtoms (ac);
this.readBonds (bondCount);
this.set2D ();
this.continuing = false;
});
Clazz.defineMethod (c$, "readAtoms",
function (ac) {
for (var i = 0; i < ac; ++i) {
var strAtom = this.parseToken ();
var atom = this.asc.addNewAtom ();
this.setAtomCoordXYZ (atom, this.parseFloat (), this.parseFloat (), 0);
var indexColon = strAtom.indexOf (':');
var elementSymbol = (indexColon > 0 ? strAtom.substring (0, indexColon) : strAtom);
if (elementSymbol.indexOf ("+") >= 0) {
elementSymbol = JU.PT.trim (elementSymbol, "+");
atom.formalCharge = 1;
} else if (elementSymbol.indexOf ("-") >= 0) {
elementSymbol = JU.PT.trim (elementSymbol, "-");
atom.formalCharge = -1;
}atom.elementSymbol = elementSymbol;
}
}, "~N");
Clazz.defineMethod (c$, "readBonds",
function (bondCount) {
for (var i = 0; i < bondCount; ++i) {
var atomIndex1 = this.parseInt () - 1;
var atomIndex2 = this.parseInt () - 1;
var order = this.parseInt ();
switch (order) {
default:
continue;
case 1:
case 2:
case 3:
break;
case -1:
order = 1025;
break;
case -2:
order = 1041;
break;
}
this.asc.addBond ( new J.adapter.smarter.Bond (atomIndex1, atomIndex2, order));
}
}, "~N");
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.readers.simple.InputReader"], "J.adapter.readers.simple.MopacArchiveReader", ["java.lang.Float", "JU.P3", "J.adapter.smarter.Atom", "J.api.JmolAdapter"], function () {
c$ = Clazz.decorateAsClass (function () {
this.energyWithUnits = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "MopacArchiveReader", J.adapter.readers.simple.InputReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.asc.newAtomSet ();
if (!this.checkFilterKey ("NOCENTER")) this.doCentralize = true;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.indexOf ("=") == 34) return this.getMyValue ();
if (this.line.indexOf ("FINAL GEOMETRY OBTAINED") >= 0) return this.readCoordinates ();
return true;
});
Clazz.defineMethod (c$, "getMyValue",
function () {
if (this.line.substring (0, 10).trim ().length != 0) return true;
var key = this.line.substring (0, 34).trim ().$replace (' ', '_');
var value = this.line.substring (35).trim ();
this.asc.setCurrentModelInfo (key, value);
if (this.line.indexOf ("TOTAL ENERGY") >= 0) {
var tokens = this.getTokens ();
this.energyWithUnits = " (" + tokens[3] + " " + tokens[4] + ")";
this.asc.setAtomSetEnergy (tokens[3], this.parseFloatStr (tokens[3]));
}return true;
});
Clazz.defineMethod (c$, "readCoordinates",
function () {
this.rd ();
this.line = this.rd ().trim ();
this.asc.setAtomSetName (this.line + (this.energyWithUnits == null ? "" : this.energyWithUnits));
this.rd ();
var atom = null;
var sym = null;
this.setFractionalCoordinates (false);
while (this.rd () != null && this.line.length >= 50) {
this.vAtoms.addLast (atom = new J.adapter.smarter.Atom ());
atom.x = this.parseFloatRange (this.line, 5, 18);
atom.y = this.parseFloatRange (this.line, 21, 34);
atom.z = this.parseFloatRange (this.line, 37, 50);
if (this.line.length > 58 && this.line.charAt (58) != ' ') {
switch (this.ac) {
case 0:
break;
case 1:
atom.sub (this.vAtoms.get (0));
break;
case 2:
this.setAtom (atom, 0, 1, 0, atom.x, atom.y, 3.4028235E38);
break;
default:
this.setAtom (atom, this.parseIntRange (this.line, 54, 59) - 1, this.parseIntRange (this.line, 60, 65) - 1, this.parseIntRange (this.line, 66, 71) - 1, atom.x, atom.y, atom.z);
}
}sym = this.line.substring (1, 3).trim ();
atom.elementSymbol = sym;
if (!sym.equals ("Tv")) {
this.ac++;
if (this.line.length >= 84) atom.partialCharge = this.parseFloatRange (this.line, 76, 84);
if (J.api.JmolAdapter.getElementNumber (sym) != 0) this.asc.addAtom (atom);
this.setAtomCoord (atom);
}}
if (sym.equals ("Tv")) {
this.setSpaceGroupName ("P1");
var nTv = this.vAtoms.size () - this.ac;
for (var i = nTv; i < 3; i++) this.vAtoms.addLast ( new J.adapter.smarter.Atom ());
var xyz = Clazz.newFloatArray (9, 0);
for (var i = 0; i < 3; i++) {
var j = i * 3;
atom = this.vAtoms.get (this.ac + i);
if (!Float.isNaN (atom.x)) {
xyz[j] = atom.x;
xyz[j + 1] = atom.y;
xyz[j + 2] = atom.z;
}this.addExplicitLatticeVector (i, xyz, j);
}
for (var i = this.ac; --i >= 0; ) this.setAtomCoord (this.vAtoms.get (i));
var ptMax = JU.P3.new3 (-3.4028235E38, -3.4028235E38, -3.4028235E38);
var ptMin = JU.P3.new3 (3.4028235E38, 3.4028235E38, 3.4028235E38);
if (this.doCentralize) {
for (var i = this.ac; --i >= 0; ) {
atom = this.vAtoms.get (i);
ptMax.x = Math.max (ptMax.x, atom.x);
ptMax.y = Math.max (ptMax.y, atom.y);
ptMax.z = Math.max (ptMax.z, atom.z);
ptMin.x = Math.min (ptMin.x, atom.x);
ptMin.y = Math.min (ptMin.y, atom.y);
ptMin.z = Math.min (ptMin.z, atom.z);
}
var ptCenter = new JU.P3 ();
switch (nTv) {
case 3:
ptCenter.x = 0.5;
case 2:
ptCenter.y = 0.5;
case 1:
ptCenter.z = 0.5;
}
ptCenter.scaleAdd2 (-0.5, ptMin, ptCenter);
ptCenter.scaleAdd2 (-0.5, ptMax, ptCenter);
for (var i = this.ac; --i >= 0; ) this.vAtoms.get (i).add (ptCenter);
}this.doCentralize = false;
}return true;
});
});

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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.simple.MopacReader", ["java.lang.Exception", "$.Float", "JU.BS", "$.PT", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.chargesFound = false;
this.haveHeader = false;
this.mopacVersion = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.simple, "MopacReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
while (this.mopacVersion == 0) {
this.discardLinesUntilContains ("MOPAC");
if (this.line.indexOf ("2009") >= 0) this.mopacVersion = 2009;
else if (this.line.indexOf ("6.") >= 0) this.mopacVersion = 6;
else if (this.line.indexOf ("7.") >= 0) this.mopacVersion = 7;
else if (this.line.indexOf ("93") >= 0) this.mopacVersion = 93;
else if (this.line.indexOf ("2002") >= 0) this.mopacVersion = 2002;
else if (this.line.indexOf ("MOPAC2") >= 0) this.mopacVersion = JU.PT.parseInt (this.line.substring (this.line.indexOf ("MOPAC2") + 5));
}
JU.Logger.info ("MOPAC version " + this.mopacVersion);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (!this.haveHeader) {
if (this.line.trim ().equals ("CARTESIAN COORDINATES")) {
this.processCoordinates ();
this.asc.setAtomSetName ("Input Structure");
return true;
}this.haveHeader = this.line.startsWith (" ---");
return true;
}if (this.line.indexOf ("TOTAL ENERGY") >= 0) {
this.processTotalEnergy ();
return true;
}if (this.line.indexOf ("ATOMIC CHARGES") >= 0) {
this.processAtomicCharges ();
return true;
}if (this.line.trim ().equals ("CARTESIAN COORDINATES")) {
this.processCoordinates ();
return true;
}if (this.line.indexOf ("ORIENTATION OF MOLECULE IN FORCE") >= 0) {
this.processCoordinates ();
this.asc.setAtomSetName ("Orientation in Force Field");
return true;
}if (this.line.indexOf ("NORMAL COORDINATE ANALYSIS") >= 0) {
this.readFrequencies ();
return true;
}return true;
});
Clazz.defineMethod (c$, "processTotalEnergy",
function () {
});
Clazz.defineMethod (c$, "processAtomicCharges",
function () {
this.readLines (2);
this.asc.newAtomSet ();
this.baseAtomIndex = this.asc.ac;
var expectedAtomNumber = 0;
while (this.rd () != null) {
var atomNumber = this.parseIntStr (this.line);
if (atomNumber == -2147483648) break;
++expectedAtomNumber;
if (atomNumber != expectedAtomNumber) throw new Exception ("unexpected atom number in atomic charges");
var atom = this.asc.addNewAtom ();
atom.elementSymbol = this.parseToken ();
atom.partialCharge = this.parseFloat ();
}
this.chargesFound = true;
});
Clazz.defineMethod (c$, "processCoordinates",
function () {
if (!this.chargesFound) {
this.asc.newAtomSet ();
this.baseAtomIndex = this.asc.ac;
} else {
this.chargesFound = false;
}var atoms = this.asc.atoms;
var atomNumber;
while (this.rd ().trim ().length == 0 || this.line.indexOf ("ATOM") >= 0) {
}
while (this.line != null) {
var tokens = this.getTokens ();
if (tokens.length == 0 || (atomNumber = this.parseIntStr (tokens[0])) == -2147483648) break;
var atom = atoms[this.baseAtomIndex + atomNumber - 1];
if (atom == null) atom = this.asc.addNewAtom ();
atom.atomSerial = atomNumber;
this.setAtomCoordTokens (atom, tokens, 2);
var elementSymbol = tokens[1];
var atno = this.parseIntStr (elementSymbol);
if (atno != -2147483648) elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (atno);
atom.elementSymbol = elementSymbol;
this.rd ();
}
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
var bsOK = new JU.BS ();
var n0 = this.asc.iSet + 1;
var tokens;
var done = false;
while (!done && this.rd () != null && this.line.indexOf ("DESCRIPTION") < 0 && this.line.indexOf ("MASS-WEIGHTED") < 0) if (this.line.toUpperCase ().indexOf ("ROOT") >= 0) {
this.discardLinesUntilNonBlank ();
tokens = this.getTokens ();
if (Float.isNaN (JU.PT.parseFloatStrict (tokens[tokens.length - 1]))) {
this.discardLinesUntilNonBlank ();
tokens = this.getTokens ();
}var frequencyCount = tokens.length;
this.rd ();
var iAtom0 = this.asc.ac;
var ac = this.asc.getLastAtomSetAtomCount ();
var ignore = Clazz.newBooleanArray (frequencyCount, false);
var freq1 = JU.PT.parseFloatStrict (tokens[0]);
var ignoreNegative = (freq1 < 0);
for (var i = 0; i < frequencyCount; ++i) {
ignore[i] = done || (done = (!ignoreNegative && JU.PT.parseFloatStrict (tokens[i]) < 1)) || !this.doGetVibration (++this.vibrationNumber);
if (ignore[i]) continue;
bsOK.set (this.vibrationNumber - 1);
this.asc.cloneLastAtomSet ();
}
this.fillFrequencyData (iAtom0, ac, ac, ignore, false, 0, 0, null, 2);
}
var info = new Array (this.vibrationNumber);
if (this.line.indexOf ("DESCRIPTION") < 0) this.discardLinesUntilContains ("DESCRIPTION");
while (this.discardLinesUntilContains ("VIBRATION") != null) {
tokens = this.getTokens ();
var freqNo = this.parseIntStr (tokens[1]);
tokens[0] = JU.PT.getTokens (this.rd ())[1];
if (tokens[2].equals ("ATOM")) tokens[2] = null;
info[freqNo - 1] = tokens;
if (freqNo == this.vibrationNumber) break;
}
for (var i = this.vibrationNumber - 1; --i >= 0; ) if (info[i] == null) info[i] = info[i + 1];
for (var i = 0, n = n0; i < this.vibrationNumber; i++) {
if (!bsOK.get (i)) continue;
this.asc.iSet = n++;
this.asc.setAtomSetFrequency (null, info[i][2], info[i][0], null);
}
});
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/simple/TinkerReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.simple");
Clazz.load (["J.adapter.readers.simple.FoldingXyzReader"], "J.adapter.readers.simple.TinkerReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.simple, "TinkerReader", J.adapter.readers.simple.FoldingXyzReader);
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/spartan/OdysseyReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (["J.adapter.readers.spartan.SpartanInputReader"], "J.adapter.readers.spartan.OdysseyReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.spartan, "OdysseyReader", J.adapter.readers.spartan.SpartanInputReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
var title = this.readInputRecords ();
this.asc.setAtomSetName (title == null ? "Odyssey file" : title);
this.continuing = false;
});
});

450
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/spartan/SpartanArchive.js Normal file
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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (null, "J.adapter.readers.spartan.SpartanArchive", ["java.lang.Boolean", "$.Float", "java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "$.V3", "J.adapter.smarter.AtomSetCollectionReader", "$.Bond", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.modelCount = 0;
this.modelAtomCount = 0;
this.ac = 0;
this.bondData = null;
this.moCount = 0;
this.coefCount = 0;
this.shellCount = 0;
this.gaussianCount = 0;
this.endCheck = null;
this.isSMOL = false;
this.r = null;
this.line = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.spartan, "SpartanArchive");
Clazz.makeConstructor (c$,
function (r, bondData, endCheck, smolAtomCount) {
this.initialize (r, bondData);
this.modelAtomCount = smolAtomCount;
this.endCheck = endCheck;
this.isSMOL = (endCheck != null);
}, "J.adapter.readers.quantum.BasisFunctionReader,~S,~S,~N");
Clazz.defineMethod (c$, "initialize",
function (r, bondData) {
this.r = r;
r.moData.put ("isNormalized", Boolean.TRUE);
r.moData.put ("energyUnits", "");
this.bondData = bondData;
}, "J.adapter.readers.quantum.BasisFunctionReader,~S");
Clazz.defineMethod (c$, "readArchive",
function (infoLine, haveGeometryLine, ac0, doAddAtoms) {
this.modelAtomCount = this.setInfo (infoLine);
this.line = (haveGeometryLine ? "GEOMETRY" : "");
var haveMOData = false;
var skipping = false;
while (this.line != null) {
if (this.line.equals ("GEOMETRY")) {
if (!this.isSMOL && !this.r.doGetModel (++this.modelCount, null)) {
this.readLine ();
skipping = true;
continue;
}skipping = false;
this.readAtoms (ac0, doAddAtoms);
if (doAddAtoms && this.bondData.length > 0) this.addBonds (this.bondData, ac0);
} else if (this.line.indexOf ("BASIS") == 0) {
if (this.r.doReadMolecularOrbitals) {
this.readBasis ();
} else {
this.r.discardLinesUntilContains ("ENERGY");
this.line = this.r.line;
continue;
}} else if (this.line.indexOf ("WAVEFUNC") == 0 || this.line.indexOf ("BETA") == 0) {
if (this.r.doReadMolecularOrbitals && !skipping) {
this.readMolecularOrbital ();
haveMOData = true;
} else {
this.r.discardLinesUntilContains ("GEOM");
this.line = this.r.line;
}} else if (this.line.indexOf ("ENERGY") == 0 && !skipping) {
this.readEnergy ();
} else if (this.line.equals ("ENDARCHIVE") || this.isSMOL && this.line.indexOf (this.endCheck) == 0) {
break;
}this.readLine ();
}
if (haveMOData) this.r.finalizeMOData (this.r.moData);
return this.modelAtomCount;
}, "~S,~B,~N,~B");
Clazz.defineMethod (c$, "readEnergy",
function () {
var tokens = JU.PT.getTokens (this.readLine ());
var value = this.parseFloat (tokens[0]);
this.r.asc.setCurrentModelInfo ("energy", Float.$valueOf (value));
if (this.isSMOL) (this.r).setEnergy (value);
this.r.asc.setAtomSetEnergy (tokens[0], value);
});
Clazz.defineMethod (c$, "setInfo",
function (info) {
var tokens = JU.PT.getTokens (info);
if (JU.Logger.debugging) {
JU.Logger.debug ("reading Spartan archive info :" + info);
}this.modelAtomCount = this.parseInt (tokens[0]);
this.coefCount = this.parseInt (tokens[1]);
this.shellCount = this.parseInt (tokens[2]);
this.gaussianCount = this.parseInt (tokens[3]);
this.moCount = this.parseInt (tokens[6]);
this.r.calculationType = tokens[9];
var s = this.r.moData.get ("calculationType");
if (s == null) s = this.r.calculationType;
else if (s.indexOf (this.r.calculationType) < 0) s = this.r.calculationType + s;
this.r.moData.put ("calculationType", this.r.calculationType = s);
return this.modelAtomCount;
}, "~S");
Clazz.defineMethod (c$, "readAtoms",
function (ac0, doAddAtoms) {
for (var i = 0; i < this.modelAtomCount; i++) {
var tokens = JU.PT.getTokens (this.readLine ());
var atom = (doAddAtoms ? this.r.asc.addNewAtom () : this.r.asc.atoms[ac0 - this.modelAtomCount + i]);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.parseInt (tokens[0]));
this.r.setAtomCoordScaled (atom, tokens, 1, 0.5291772);
}
if (doAddAtoms && JU.Logger.debugging) {
JU.Logger.debug (this.r.asc.ac + " atoms read");
}}, "~N,~B");
Clazz.defineMethod (c$, "addBonds",
function (data, ac0) {
var tokens = JU.PT.getTokens (data);
for (var i = this.modelAtomCount; i < tokens.length; ) {
var sourceIndex = this.parseInt (tokens[i++]) - 1 + ac0;
var targetIndex = this.parseInt (tokens[i++]) - 1 + ac0;
var bondOrder = this.parseInt (tokens[i++]);
if (bondOrder > 0) {
this.r.asc.addBond ( new J.adapter.smarter.Bond (sourceIndex, targetIndex, bondOrder < 4 ? bondOrder : bondOrder == 5 ? 515 : 1));
}}
var bondCount = this.r.asc.bondCount;
if (JU.Logger.debugging) {
JU.Logger.debug (bondCount + " bonds read");
}}, "~S,~N");
Clazz.defineMethod (c$, "readBasis",
function () {
var shells = new JU.Lst ();
var gaussians = JU.AU.newFloat2 (this.gaussianCount);
var typeArray = Clazz.newIntArray (this.gaussianCount, 0);
for (var i = 0; i < this.shellCount; i++) {
var tokens = JU.PT.getTokens (this.readLine ());
var isSpherical = (tokens[4].charAt (0) == '1');
var slater = Clazz.newIntArray (4, 0);
slater[0] = this.parseInt (tokens[3]);
var iBasis = this.parseInt (tokens[0]);
switch (iBasis) {
case 0:
iBasis = 0;
break;
case 1:
iBasis = (isSpherical ? 1 : 2);
break;
case 2:
iBasis = (isSpherical ? 3 : 4);
break;
case 3:
iBasis = (isSpherical ? 5 : 6);
break;
}
slater[1] = iBasis;
slater[2] = this.parseInt (tokens[2]);
var gaussianPtr = slater[2] - 1;
var nGaussians = slater[3] = this.parseInt (tokens[1]);
for (var j = 0; j < nGaussians; j++) typeArray[gaussianPtr + j] = iBasis;
shells.addLast (slater);
}
for (var i = 0; i < this.gaussianCount; i++) {
var alpha = this.parseFloat (this.readLine ());
var tokens = JU.PT.getTokens (this.readLine ());
var nData = tokens.length;
var data = Clazz.newFloatArray (nData + 1, 0);
data[0] = alpha;
switch (typeArray[i]) {
case 0:
data[1] = this.parseFloat (tokens[0]);
break;
case 1:
data[1] = this.parseFloat (tokens[1]);
break;
case 2:
data[1] = this.parseFloat (tokens[0]);
data[2] = this.parseFloat (tokens[1]);
if (data[1] == 0) {
data[1] = data[2];
typeArray[i] = 2;
}break;
case 4:
case 3:
data[1] = this.parseFloat (tokens[2]);
break;
case 6:
case 5:
data[1] = this.parseFloat (tokens[3]);
break;
}
gaussians[i] = data;
}
var nCoeff = 0;
for (var i = 0; i < this.shellCount; i++) {
var slater = shells.get (i);
switch (typeArray[slater[2] - 1]) {
case 0:
nCoeff++;
break;
case 1:
slater[1] = 1;
nCoeff += 3;
break;
case 2:
nCoeff += 4;
break;
case 3:
nCoeff += 5;
break;
case 4:
nCoeff += 6;
break;
case 5:
nCoeff += 7;
break;
case 6:
nCoeff += 10;
break;
}
}
var isD5F7 = (nCoeff < this.coefCount);
if (isD5F7) for (var i = 0; i < this.shellCount; i++) {
var slater = shells.get (i);
switch (typeArray[i]) {
case 4:
slater[1] = 3;
break;
case 6:
slater[1] = 5;
break;
}
}
this.r.moData.put ("shells", shells);
this.r.moData.put ("gaussians", gaussians);
if (JU.Logger.debugging) {
JU.Logger.debug (shells.size () + " slater shells read");
JU.Logger.debug (gaussians.length + " gaussian primitives read");
}});
Clazz.defineMethod (c$, "readMolecularOrbital",
function () {
var tokenPt = 0;
this.r.orbitals = new JU.Lst ();
var tokens = JU.PT.getTokens ("");
var energies = Clazz.newFloatArray (this.moCount, 0);
var coefficients = Clazz.newFloatArray (this.moCount, this.coefCount, 0);
for (var i = 0; i < this.moCount; i++) {
if (tokenPt == tokens.length) {
tokens = JU.PT.getTokens (this.readLine ());
tokenPt = 0;
}energies[i] = this.parseFloat (tokens[tokenPt++]);
}
for (var i = 0; i < this.moCount; i++) {
for (var j = 0; j < this.coefCount; j++) {
if (tokenPt == tokens.length) {
tokens = JU.PT.getTokens (this.readLine ());
tokenPt = 0;
}coefficients[i][j] = this.parseFloat (tokens[tokenPt++]);
}
}
for (var i = 0; i < this.moCount; i++) {
var mo = new java.util.Hashtable ();
mo.put ("energy", Float.$valueOf (energies[i]));
mo.put ("coefficients", coefficients[i]);
this.r.setMO (mo);
}
if (JU.Logger.debugging) {
JU.Logger.debug (this.r.orbitals.size () + " molecular orbitals read");
}this.r.moData.put ("mos", this.r.orbitals);
});
Clazz.defineMethod (c$, "readProperties",
function () {
if (JU.Logger.debugging) JU.Logger.debug ("Reading PROPARC properties records...");
while (this.readLine () != null && !this.line.startsWith ("ENDPROPARC") && !this.line.startsWith ("END Directory Entry ")) {
if (this.line.startsWith ("PROP")) this.readProperty ();
else if (this.line.startsWith ("DIPOLE")) this.readDipole ();
else if (this.line.startsWith ("VIBFREQ")) this.readVibFreqs ();
}
this.setVibrationsFromProperties ();
});
Clazz.defineMethod (c$, "readDipole",
function () {
this.setDipole (JU.PT.getTokens (this.readLine ()));
});
Clazz.defineMethod (c$, "setDipole",
function (tokens) {
if (tokens.length != 3) return;
var dipole = JU.V3.new3 (this.parseFloat (tokens[0]), this.parseFloat (tokens[1]), this.parseFloat (tokens[2]));
this.r.asc.setCurrentModelInfo ("dipole", dipole);
}, "~A");
Clazz.defineMethod (c$, "readProperty",
function () {
var tokens = JU.PT.getTokens (this.line);
if (tokens.length == 0) return;
var isString = (tokens[1].startsWith ("STRING"));
var keyName = tokens[2];
var isDipole = (keyName.equals ("DIPOLE_VEC"));
var value = new Clazz._O ();
var vector = new JU.Lst ();
if (tokens[3].equals ("=")) {
if (isString) {
value = this.getQuotedString (tokens[4].substring (0, 1));
} else {
value = Float.$valueOf (this.parseFloat (tokens[4]));
}} else if (tokens[tokens.length - 1].equals ("BEGIN")) {
var nValues = this.parseInt (tokens[tokens.length - 2]);
if (nValues == 0) nValues = 1;
var isArray = (tokens.length == 6);
var atomInfo = new JU.Lst ();
var ipt = 0;
while (this.readLine () != null && !this.line.substring (0, 3).equals ("END")) {
if (isString) {
value = this.getQuotedString ("\"");
vector.addLast (value);
} else {
var tokens2 = JU.PT.getTokens (this.line);
if (isDipole) this.setDipole (tokens2);
for (var i = 0; i < tokens2.length; i++, ipt++) {
if (isArray) {
atomInfo.addLast (Float.$valueOf (this.parseFloat (tokens2[i])));
if ((ipt + 1) % nValues == 0) {
vector.addLast (atomInfo);
atomInfo = new JU.Lst ();
}} else {
value = Float.$valueOf (this.parseFloat (tokens2[i]));
vector.addLast (value);
}}
}}
value = null;
} else {
if (JU.Logger.debugging) {
JU.Logger.debug (" Skipping property line " + this.line);
}}if (value != null) this.r.asc.setInfo (keyName, value);
if (vector.size () != 0) this.r.asc.setInfo (keyName, vector);
});
Clazz.defineMethod (c$, "readVibFreqs",
function () {
this.readLine ();
var label = "";
var frequencyCount = this.parseInt (this.line);
var vibrations = new JU.Lst ();
var freqs = new JU.Lst ();
if (JU.Logger.debugging) {
JU.Logger.debug ("reading VIBFREQ vibration records: frequencyCount = " + frequencyCount);
}var ignore = Clazz.newBooleanArray (frequencyCount, false);
for (var i = 0; i < frequencyCount; ++i) {
var ac0 = this.r.asc.ac;
ignore[i] = !this.r.doGetVibration (i + 1);
if (!ignore[i] && this.r.desiredVibrationNumber <= 0) {
this.r.asc.cloneLastAtomSet ();
this.addBonds (this.bondData, ac0);
}this.readLine ();
var info = new java.util.Hashtable ();
var freq = this.parseFloat (this.line);
info.put ("freq", Float.$valueOf (freq));
if (this.line.length > 15 && !(label = this.line.substring (15, this.line.length)).equals ("???")) info.put ("label", label);
freqs.addLast (info);
if (!ignore[i]) {
this.r.asc.setAtomSetFrequency (null, label, "" + freq, null);
}}
this.r.asc.setInfo ("VibFreqs", freqs);
var ac = this.r.asc.atomSetAtomCounts[0];
var vib = new JU.Lst ();
var vibatom = new JU.Lst ();
var ifreq = 0;
var iatom = ac;
var nValues = 3;
var atomInfo = Clazz.newFloatArray (3, 0);
while (this.readLine () != null) {
var tokens2 = JU.PT.getTokens (this.line);
for (var i = 0; i < tokens2.length; i++) {
var f = this.parseFloat (tokens2[i]);
atomInfo[i % nValues] = f;
vibatom.addLast (Float.$valueOf (f));
if ((i + 1) % nValues == 0) {
if (!ignore[ifreq]) {
this.r.asc.addVibrationVector (iatom, atomInfo[0], atomInfo[1], atomInfo[2]);
vib.addLast (vibatom);
vibatom = new JU.Lst ();
}++iatom;
}}
if (iatom % ac == 0) {
if (!ignore[ifreq]) {
vibrations.addLast (vib);
}vib = new JU.Lst ();
if (++ifreq == frequencyCount) {
break;
}}}
this.r.asc.setInfo ("vibration", vibrations);
});
Clazz.defineMethod (c$, "setVibrationsFromProperties",
function () {
var freq_modes = this.r.asc.atomSetInfo.get ("FREQ_MODES");
if (freq_modes == null) {
return;
}var freq_lab = this.r.asc.atomSetInfo.get ("FREQ_LAB");
var freq_val = this.r.asc.atomSetInfo.get ("FREQ_VAL");
var frequencyCount = freq_val.size ();
var vibrations = new JU.Lst ();
var freqs = new JU.Lst ();
if (JU.Logger.debugging) {
JU.Logger.debug ("reading PROP VALUE:VIB FREQ_MODE vibration records: frequencyCount = " + frequencyCount);
}var v;
for (var i = 0; i < frequencyCount; ++i) {
var ac0 = this.r.asc.ac;
this.r.asc.cloneLastAtomSet ();
this.addBonds (this.bondData, ac0);
var info = new java.util.Hashtable ();
info.put ("freq", (v = freq_val.get (i)));
var freq = v.floatValue ();
var label = freq_lab.get (i);
if (!label.equals ("???")) {
info.put ("label", label);
}freqs.addLast (info);
this.r.asc.setAtomSetName (label + " " + freq + " cm^-1");
this.r.asc.setAtomSetModelProperty ("Frequency", freq + " cm^-1");
this.r.asc.setAtomSetModelProperty (".PATH", "Frequencies");
}
this.r.asc.setInfo ("VibFreqs", freqs);
var ac = this.r.asc.atomSetAtomCounts[0];
var iatom = ac;
for (var i = 0; i < frequencyCount; i++) {
if (!this.r.doGetVibration (i + 1)) continue;
var ipt = 0;
var vib = new JU.Lst ();
var mode = freq_modes.get (i);
for (var ia = 0; ia < ac; ia++, iatom++) {
var vibatom = new JU.Lst ();
var vx = (v = mode.get (ipt++)).floatValue ();
vibatom.addLast (v);
var vy = (v = mode.get (ipt++)).floatValue ();
vibatom.addLast (v);
var vz = (v = mode.get (ipt++)).floatValue ();
vibatom.addLast (v);
this.r.asc.addVibrationVector (iatom, vx, vy, vz);
vib.addLast (vibatom);
}
vibrations.addLast (vib);
}
this.r.asc.setInfo ("vibration", vibrations);
});
Clazz.defineMethod (c$, "getQuotedString",
function (strQuote) {
var i = this.line.indexOf (strQuote);
var j = this.line.lastIndexOf (strQuote);
return (j == i ? "" : this.line.substring (i + 1, j));
}, "~S");
Clazz.defineMethod (c$, "parseInt",
function (info) {
return this.r.parseIntStr (info);
}, "~S");
Clazz.defineMethod (c$, "parseFloat",
function (info) {
return this.r.parseFloatStr (info);
}, "~S");
Clazz.defineMethod (c$, "readLine",
function () {
return (this.line = this.r.rd ());
});
});

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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (["J.adapter.readers.quantum.BasisFunctionReader"], "J.adapter.readers.spartan.SpartanInputReader", ["JU.PT", "J.adapter.smarter.Bond", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.modelAtomCount = 0;
this.bondData = "";
this.constraints = "";
Clazz.instantialize (this, arguments);
}, J.adapter.readers.spartan, "SpartanInputReader", J.adapter.readers.quantum.BasisFunctionReader);
Clazz.defineMethod (c$, "readInputRecords",
function () {
var ac0 = this.asc.ac;
var modelName = this.readInputHeader ();
while (this.rd () != null) {
var tokens = this.getTokens ();
if (tokens.length == 2 && this.parseIntStr (tokens[0]) != -2147483648 && this.parseIntStr (tokens[1]) >= 0) break;
}
if (this.line == null) return null;
this.readInputAtoms ();
this.discardLinesUntilContains ("ATOMLABELS");
if (this.line != null) this.readAtomNames ();
if (this.modelAtomCount > 1) {
this.discardLinesUntilContains ("HESSIAN");
if (this.line != null) this.readBonds (ac0);
if (this.line != null && this.line.indexOf ("BEGINCONSTRAINTS") >= 0) this.readConstraints ();
}while (this.line != null && this.line.indexOf ("END ") < 0 && this.line.indexOf ("MOLSTATE") < 0) this.rd ();
if (this.line != null && this.line.indexOf ("MOLSTATE") >= 0) this.readTransform ();
return modelName;
});
Clazz.defineMethod (c$, "readConstraints",
function () {
this.constraints = "";
while (this.rd () != null && this.line.indexOf ("END") < 0) this.constraints += (this.constraints === "" ? "" : "\n") + this.line;
this.rd ();
if (this.constraints.length == 0) return;
this.asc.setCurrentModelInfo ("constraints", this.constraints);
this.asc.setAtomSetModelProperty (".PATH", "EnergyProfile");
this.asc.setAtomSetModelProperty ("Constraint", this.constraints);
});
Clazz.defineMethod (c$, "readTransform",
function () {
this.rd ();
var tokens = JU.PT.getTokens (this.rd () + " " + this.rd ());
this.setTransform (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[4]), this.parseFloatStr (tokens[5]), this.parseFloatStr (tokens[6]), this.parseFloatStr (tokens[8]), this.parseFloatStr (tokens[9]), this.parseFloatStr (tokens[10]));
});
Clazz.defineMethod (c$, "readInputHeader",
function () {
while (this.rd () != null && !this.line.startsWith (" ")) {
}
this.rd ();
return this.line.substring (0, (this.line + ";").indexOf (";")).trim ();
});
Clazz.defineMethod (c$, "readInputAtoms",
function () {
this.modelAtomCount = 0;
while (this.rd () != null && !this.line.startsWith ("ENDCART")) {
var tokens = this.getTokens ();
this.addAtomXYZSymName (tokens, 1, J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.parseIntStr (tokens[0])), null);
this.modelAtomCount++;
}
if (this.debugging) JU.Logger.debug (this.asc.ac + " atoms read");
});
Clazz.defineMethod (c$, "readAtomNames",
function () {
var atom0 = this.asc.ac - this.modelAtomCount;
for (var i = 0; i < this.modelAtomCount; i++) {
this.line = this.rd ().trim ();
var name = this.line.substring (1, this.line.length - 1);
this.asc.atoms[atom0 + i].atomName = name;
}
});
Clazz.defineMethod (c$, "readBonds",
function (ac0) {
var nAtoms = this.modelAtomCount;
this.bondData = "";
while (this.rd () != null && !this.line.startsWith ("ENDHESS")) {
var tokens = this.getTokens ();
this.bondData += this.line + " ";
if (nAtoms == 0) {
var sourceIndex = this.parseIntStr (tokens[0]) - 1 + ac0;
var targetIndex = this.parseIntStr (tokens[1]) - 1 + ac0;
var bondOrder = this.parseIntStr (tokens[2]);
if (bondOrder > 0) {
this.asc.addBond ( new J.adapter.smarter.Bond (sourceIndex, targetIndex, bondOrder < 4 ? bondOrder : bondOrder == 5 ? 515 : 1));
}} else {
nAtoms -= tokens.length;
}}
this.rd ();
if (this.debugging) JU.Logger.debug (this.asc.bondCount + " bonds read");
}, "~N");
});

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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (["J.adapter.readers.quantum.BasisFunctionReader"], "J.adapter.readers.spartan.SpartanReader", ["java.lang.Float", "java.util.Hashtable", "J.adapter.readers.spartan.SpartanArchive"], function () {
c$ = Clazz.declareType (J.adapter.readers.spartan, "SpartanReader", J.adapter.readers.quantum.BasisFunctionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
var cartesianHeader = "Cartesian Coordinates (Ang";
if (this.isSpartanArchive (cartesianHeader)) {
this.moData = new java.util.Hashtable ();
var spartanArchive = new J.adapter.readers.spartan.SpartanArchive (this, "", null, 0);
var ac = spartanArchive.readArchive (this.line, true, 0, true);
if (ac > 0) this.asc.setAtomSetName ("Spartan file");
} else if (this.line.indexOf (cartesianHeader) >= 0) {
this.readAtoms ();
this.discardLinesUntilContains ("Vibrational Frequencies");
if (this.line != null) this.readFrequencies ();
}this.continuing = false;
});
Clazz.defineMethod (c$, "isSpartanArchive",
function (strNotArchive) {
var lastLine = "";
while (this.rd () != null) {
if (this.line.equals ("GEOMETRY")) {
this.line = lastLine;
return true;
}if (this.line.indexOf (strNotArchive) >= 0) return false;
lastLine = this.line;
}
return false;
}, "~S");
Clazz.defineMethod (c$, "readAtoms",
function () {
this.discardLinesUntilBlank ();
while (this.rd () != null && (this.parseIntRange (this.line, 0, 3)) > 0) {
var atom = this.asc.addNewAtom ();
atom.elementSymbol = this.parseTokenRange (this.line, 4, 6);
atom.atomName = this.parseTokenRange (this.line, 7, 13);
this.setAtomCoordXYZ (atom, this.parseFloatRange (this.line, 17, 30), this.parseFloatRange (this.line, 31, 44), this.parseFloatRange (this.line, 45, 58));
}
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
var ac = this.asc.atomSetAtomCounts[0];
while (true) {
this.discardLinesUntilNonBlank ();
var lineBaseFreqCount = this.vibrationNumber;
this.next[0] = 16;
var lineFreqCount;
var ignore = Clazz.newBooleanArray (3, false);
for (lineFreqCount = 0; lineFreqCount < 3; ++lineFreqCount) {
var frequency = this.parseFloat ();
if (Float.isNaN (frequency)) break;
ignore[lineFreqCount] = !this.doGetVibration (++this.vibrationNumber);
if (!ignore[lineFreqCount]) {
if (this.vibrationNumber > 1) this.asc.cloneFirstAtomSet (0);
this.asc.setAtomSetFrequency (null, null, "" + frequency, null);
}}
if (lineFreqCount == 0) return;
this.readLines (2);
for (var i = 0; i < ac; ++i) {
this.rd ();
for (var j = 0; j < lineFreqCount; ++j) {
var ichCoords = j * 23 + 10;
var x = this.parseFloatRange (this.line, ichCoords, ichCoords + 7);
var y = this.parseFloatRange (this.line, ichCoords + 7, ichCoords + 14);
var z = this.parseFloatRange (this.line, ichCoords + 14, ichCoords + 21);
if (!ignore[j]) this.asc.addVibrationVector (i + (lineBaseFreqCount + j) * ac, x, y, z);
}
}
}
});
});

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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (["J.adapter.readers.spartan.SpartanInputReader"], "J.adapter.readers.spartan.SpartanSmolReader", ["java.lang.Boolean", "java.util.Hashtable", "JU.BC", "$.PT", "$.SB", "J.adapter.readers.spartan.SpartanArchive", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.iHaveModelStatement = false;
this.isCompoundDocument = false;
this.inputOnly = false;
this.espCharges = false;
this.natCharges = false;
this.isInputFirst = false;
this.iHaveNewDir = false;
this.title = null;
this.spartanArchive = null;
this.titles = null;
this.haveCharges = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.spartan, "SpartanSmolReader", J.adapter.readers.spartan.SpartanInputReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.isCompoundDocument = (this.rd ().indexOf ("Compound Document File Directory") >= 0);
this.inputOnly = this.checkFilterKey ("INPUT");
this.natCharges = this.checkFilterKey ("NATCHAR");
this.espCharges = !this.natCharges && !this.checkFilterKey ("MULLIKEN");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var pt = 3;
var isNewDir = (this.isCompoundDocument && this.line.startsWith ("NEW Directory M") && !this.line.startsWith ("NEW Directory Molecules"));
if (isNewDir) this.iHaveNewDir = true;
var isMolecule = (!this.iHaveNewDir && !isNewDir && this.isCompoundDocument && this.line.equals ("BEGIN Directory Entry Molecule"));
var isMacDir = (!this.isCompoundDocument && (pt = this.line.indexOf ("#JMOL_MODEL")) >= 0);
if (isNewDir || isMolecule || isMacDir) {
if (this.modelNumber > 0 && !this.isInputFirst) this.applySymmetryAndSetTrajectory ();
this.iHaveModelStatement = true;
var modelNo = (isMolecule ? 0 : this.parseIntAt (this.line, pt + 12));
this.modelNumber = (this.bsModels == null && modelNo != -2147483648 && modelNo != 0 ? modelNo : this.modelNumber + 1);
this.bondData = "";
if (!this.doGetModel (this.modelNumber, null)) {
if (this.isInputFirst) {
this.asc.removeCurrentAtomSet ();
this.discardLinesUntilContains ("BEGIN Directory Entry Input");
} else if (isNewDir) {
this.discardLinesUntilContains ("NEW Directory M");
} else if (isMolecule) {
this.discardLinesUntilContains ("BEGIN Directory Entry M");
} else {
this.discardLinesUntilContains ("#JMOL_MODEL");
}this.checkLastModel ();
return false;
}if (!this.isInputFirst) {
this.makeNewAtomSet ();
}this.moData = new java.util.Hashtable ();
this.moData.put ("isNormalized", Boolean.TRUE);
var isOK = false;
if (modelNo == -2147483648 || this.titles == null) {
modelNo = this.modelNumber;
this.title = "Model " + modelNo;
} else {
isOK = true;
this.title = this.titles.get ("Title" + modelNo);
this.title = "Profile " + modelNo + (this.title == null ? "" : ": " + this.title);
}if (this.constraints == null && (isOK || !this.isInputFirst)) this.asc.setAtomSetName (this.title);
this.setModelPDB (false);
this.asc.setCurrentAtomSetNumber (modelNo);
if (isMolecule) this.readMyTransform ();
return true;
}if (this.iHaveModelStatement && !this.doProcessLines) return true;
if ((this.line.indexOf ("BEGIN") == 0)) {
var lcline = this.line.toLowerCase ();
if (lcline.endsWith ("input")) {
if (!this.iHaveModelStatement) this.isInputFirst = true;
if (this.isInputFirst) {
this.makeNewAtomSet ();
}this.bondData = "";
this.title = this.readInputRecords ();
if (this.asc.errorMessage != null) {
this.continuing = false;
return false;
}if (this.title != null && this.constraints == null) this.asc.setAtomSetName (this.title);
this.setCharges ();
if (this.inputOnly) {
this.continuing = false;
return false;
}} else if (lcline.endsWith ("_output")) {
return true;
} else if (lcline.endsWith ("output")) {
this.readOutput ();
return false;
} else if (lcline.endsWith ("molecule") || lcline.endsWith ("molecule:asbinarystring")) {
this.readMyTransform ();
return false;
} else if (lcline.endsWith ("proparc") || lcline.endsWith ("propertyarchive")) {
this.readProperties ();
return false;
} else if (lcline.endsWith ("archive")) {
this.asc.setAtomSetName (this.readArchive ());
return false;
}return true;
}if (this.line.indexOf ("5D shell") >= 0) this.moData.put ("calculationType", this.calculationType = this.line);
return true;
});
Clazz.defineMethod (c$, "makeNewAtomSet",
function () {
if (this.asc.ac == 0) this.asc.removeCurrentAtomSet ();
this.asc.newAtomSet ();
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.finalizeReaderASCR ();
if (this.asc.ac > 0 && this.spartanArchive != null && this.asc.bondCount == 0 && this.bondData != null) this.spartanArchive.addBonds (this.bondData, 0);
if (this.moData != null) {
var n = this.asc.atomSetInfo.get ("HOMO_N");
if (n != null) {
var i = n.intValue ();
this.moData.put ("HOMO", Integer.$valueOf (i));
}}});
Clazz.defineMethod (c$, "readMyTransform",
function () {
var mat;
var binaryCodes = this.rd ();
var tokens = JU.PT.getTokens (binaryCodes.trim ());
if (tokens.length < 16) return;
var bytes = Clazz.newByteArray (tokens.length, 0);
for (var i = 0; i < tokens.length; i++) bytes[i] = JU.PT.parseIntRadix (tokens[i], 16);
mat = Clazz.newFloatArray (16, 0);
for (var i = 16, j = bytes.length - 8; --i >= 0; j -= 8) mat[i] = JU.BC.bytesToDoubleToFloat (bytes, j, false);
this.setTransform (mat[0], mat[1], mat[2], mat[4], mat[5], mat[6], mat[8], mat[9], mat[10]);
});
Clazz.defineMethod (c$, "readOutput",
function () {
this.titles = new java.util.Hashtable ();
var header = new JU.SB ();
var pt;
while (this.rd () != null && !this.line.startsWith ("END ")) {
header.append (this.line).append ("\n");
if ((pt = this.line.indexOf (")")) > 0) this.titles.put ("Title" + this.parseIntRange (this.line, 0, pt), (this.line.substring (pt + 1).trim ()));
}
this.asc.setInfo ("fileHeader", header.toString ());
});
Clazz.defineMethod (c$, "readArchive",
function () {
this.spartanArchive = new J.adapter.readers.spartan.SpartanArchive (this, this.bondData, "END Directory Entry ", 0);
var modelName = this.readArchiveHeader ();
if (modelName != null) this.modelAtomCount = this.spartanArchive.readArchive (this.line, false, this.asc.ac, false);
return (this.constraints == null ? modelName : null);
});
Clazz.defineMethod (c$, "setCharges",
function () {
if (this.haveCharges || this.asc.ac == 0) return;
this.haveCharges = (this.espCharges && this.asc.setAtomSetCollectionPartialCharges ("ESPCHARGES") || this.natCharges && this.asc.setAtomSetCollectionPartialCharges ("NATCHARGES") || this.asc.setAtomSetCollectionPartialCharges ("MULCHARGES") || this.asc.setAtomSetCollectionPartialCharges ("Q1_CHARGES") || this.asc.setAtomSetCollectionPartialCharges ("ESPCHARGES"));
});
Clazz.defineMethod (c$, "readProperties",
function () {
if (this.modelAtomCount == 0) {
this.rd ();
return;
}if (this.spartanArchive == null) this.spartanArchive = new J.adapter.readers.spartan.SpartanArchive (this, this.bondData, "END Directory Entry ", this.modelAtomCount);
this.spartanArchive.readProperties ();
this.rd ();
this.setCharges ();
});
Clazz.defineMethod (c$, "readArchiveHeader",
function () {
var modelInfo = this.rd ();
if (this.debugging) JU.Logger.debug (modelInfo);
if (modelInfo.indexOf ("Error:") == 0) return null;
this.asc.setCollectionName (modelInfo);
this.asc.setAtomSetName (modelInfo);
var modelName = this.rd ();
if (this.debugging) JU.Logger.debug (modelName);
this.rd ();
return modelName;
});
Clazz.defineMethod (c$, "setEnergy",
function (value) {
this.asc.setAtomSetName (this.constraints + (this.constraints.length == 0 ? "" : " ") + "Energy=" + value + " KJ");
}, "~N");
Clazz.defineStatics (c$,
"endCheck", "END Directory Entry ");
});

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Clazz.declarePackage ("J.adapter.readers.spartan");
Clazz.load (null, "J.adapter.readers.spartan.SpartanUtil", ["java.io.BufferedInputStream", "java.util.Hashtable", "$.StringTokenizer", "JU.Lst", "$.PT", "$.Rdr", "$.SB", "J.api.Interface", "JU.Escape", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.fm = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.spartan, "SpartanUtil");
Clazz.makeConstructor (c$,
function () {
});
Clazz.defineMethod (c$, "set",
function (fm) {
this.fm = fm;
return this;
}, "JV.FileManager");
Clazz.defineMethod (c$, "getFileList",
function (name, isTypeCheckOnly) {
var pt = name.lastIndexOf (".spardir");
var info = null;
if (name.endsWith (".spardir.zip")) {
info = Clazz.newArray (-1, ["SpartanSmol", "Directory Entry ", name + "|output"]);
} else {
name = name.$replace ('\\', '/');
if (!name.endsWith (".spardir") && name.indexOf (".spardir/") < 0) return null;
info = (name.lastIndexOf ("/") > pt ? Clazz.newArray (-1, ["SpartanSmol", "Directory Entry ", name + "/input", name + "/archive", name + "/parchive", name + "/Molecule:asBinaryString", name + "/proparc"]) : Clazz.newArray (-1, ["SpartanSmol", "Directory Entry ", name + "/output"]));
}if (isTypeCheckOnly) return info;
var name00 = name;
var header = info[1];
var outputFileName = info[2];
var fileData = new java.util.Hashtable ();
if (info.length == 3) {
outputFileName = this.spartanGetObjectAsSections (outputFileName, header, fileData);
fileData.put ("OUTPUT", outputFileName);
info = this.spartanFileList (name, fileData.get (outputFileName));
if (info.length == 3) {
outputFileName = this.spartanGetObjectAsSections (info[2], header, fileData);
fileData.put ("OUTPUT", outputFileName);
info = this.spartanFileList (info[1], fileData.get (outputFileName));
}}var sb = new JU.SB ();
var s;
if (fileData.get ("OUTPUT") != null) {
sb.append (fileData.get (fileData.get ("OUTPUT")));
}for (var i = 2; i < info.length; i++) {
name = info[i];
name = this.spartanGetObjectAsSections (name, header, fileData);
JU.Logger.info ("reading " + name);
s = fileData.get (name);
sb.append (s);
}
s = sb.toString ();
if (this.fm.spardirCache == null) this.fm.spardirCache = new java.util.Hashtable ();
this.fm.spardirCache.put (name00.$replace ('\\', '/'), s.getBytes ());
return JU.Rdr.getBR (s);
}, "~S,~B");
Clazz.defineMethod (c$, "getData",
function (is, zipDirectory) {
var data = new JU.SB ();
data.append ("Zip File Directory: ").append ("\n").append (JU.Escape.eAS (zipDirectory, true)).append ("\n");
var fileData = new java.util.Hashtable ();
this.fm.vwr.getJzt ().getAllZipData (is, Clazz.newArray (-1, []), "", "Molecule", "__MACOSX", fileData);
var prefix = "|";
var outputData = fileData.get (prefix + "output");
if (outputData == null) outputData = fileData.get ((prefix = "|" + zipDirectory[1]) + "output");
data.append (outputData);
var files = this.getSpartanFileList (prefix, this.getSpartanDirs (outputData));
for (var i = 2; i < files.length; i++) {
var name = files[i];
if (fileData.containsKey (name)) data.append (fileData.get (name));
else data.append (name + "\n");
}
return data;
}, "java.io.InputStream,~A");
Clazz.defineMethod (c$, "spartanFileList",
function (name, outputFileData) {
var dirNums = this.getSpartanDirs (outputFileData);
if (dirNums.length == 0) {
if (name.endsWith (".spardir")) return this.getSpartanFileList (name, Clazz.newArray (-1, ["M0001"]));
if (name.endsWith (".spardir.zip")) {
if (outputFileData.indexOf (".zip|output") >= 0) {
var sname = name.$replace ('\\', '/');
var pt = name.lastIndexOf (".spardir");
pt = sname.lastIndexOf ("/");
sname = name + "|" + JU.PT.rep (name.substring (pt + 1, name.length - 4), "DROP_", "");
return Clazz.newArray (-1, ["SpartanSmol", sname, sname + "/output"]);
}}}return this.getSpartanFileList (name, dirNums);
}, "~S,~S");
Clazz.defineMethod (c$, "getSpartanDirs",
function (outputFileData) {
if (outputFileData == null) return Clazz.newArray (-1, []);
var v = new JU.Lst ();
var token;
var lastToken = "";
if (outputFileData.startsWith ("java.io.FileNotFoundException") || outputFileData.startsWith ("FILE NOT FOUND") || outputFileData.indexOf ("<html") >= 0) return new Array (0);
try {
var tokens = new java.util.StringTokenizer (outputFileData, " \t\r\n");
while (tokens.hasMoreTokens ()) {
if ((token = tokens.nextToken ()).equals (")")) v.addLast (lastToken);
else if (token.equals ("Start-") && tokens.nextToken ().equals ("Molecule")) v.addLast (JU.PT.split (tokens.nextToken (), "\"")[1]);
else if (token.equals ("Molecules")) {
var n = JU.PT.parseInt (lastToken);
for (var i = 1; i <= n; i++) {
var s = "0000" + i;
v.addLast ("M" + s.substring (s.length - 4));
}
}lastToken = token;
}
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
return (v.size () == 0 ? Clazz.newArray (-1, ["M0001"]) : v.toArray ( new Array (v.size ())));
}, "~S");
Clazz.defineMethod (c$, "getSpartanFileList",
function (name, dirNums) {
var files = new Array (2 + dirNums.length * 6);
files[0] = "SpartanSmol";
files[1] = "Directory Entry ";
var pt = 2;
name = name.$replace ('\\', '/');
if (name.endsWith ("/")) name = name.substring (0, name.length - 1);
var sep = (name.equals ("|") ? "" : name.endsWith (".zip") ? "|" : "/");
for (var i = 0; i < dirNums.length; i++) {
var path = name + sep;
var s = dirNums[i];
path += (JU.PT.isDigit (s.charAt (0)) ? "Profile." + s : s) + "/";
files[pt++] = path + "#JMOL_MODEL " + dirNums[i];
files[pt++] = path + "input";
files[pt++] = path + "archive";
files[pt++] = path + "parchive";
files[pt++] = path + "Molecule:asBinaryString";
files[pt++] = path + "proparc";
}
return files;
}, "~S,~A");
Clazz.defineMethod (c$, "spartanGetObjectAsSections",
function (name, header, fileData) {
if (name == null) return null;
var subFileList = null;
var asBinaryString = false;
var path = name.$replace ('\\', '/');
if (name.indexOf (":asBinaryString") >= 0) {
asBinaryString = true;
name = name.substring (0, name.indexOf (":asBinaryString"));
}var sb = null;
if (fileData.containsKey (path)) return path;
if (path.indexOf ("#JMOL_MODEL ") >= 0) {
fileData.put (path, path + "\n");
return path;
}var fullName = name;
if (name.indexOf ("|") >= 0) {
subFileList = JU.PT.split (name, "|");
name = subFileList[0];
}var bis = null;
try {
var t = this.fm.getBufferedInputStreamOrErrorMessageFromName (name, fullName, false, false, null, false, true);
if (Clazz.instanceOf (t, String)) {
fileData.put (path, t + "\n");
return path;
}name = name.$replace ('\\', '/');
bis = t;
if (JU.Rdr.isCompoundDocumentS (bis)) {
var doc = J.api.Interface.getInterface ("JU.CompoundDocument", this.fm.vwr, "file");
doc.setDocStream (this.fm.vwr.getJzt (), bis);
doc.getAllDataMapped (name, "Molecule", fileData);
} else if (JU.Rdr.isZipS (bis)) {
this.fm.vwr.getJzt ().getAllZipData (bis, subFileList, name, "Molecule", "__MACOSX", fileData);
} else if (asBinaryString) {
var bd = J.api.Interface.getInterface ("JU.BinaryDocument", this.fm.vwr, "file");
bd.setStream (bis, false);
sb = new JU.SB ();
if (header != null) sb.append ("BEGIN Directory Entry " + path + "\n");
try {
while (true) sb.append (Integer.toHexString (bd.readByte () & 0xFF)).appendC (' ');
} catch (e1) {
if (Clazz.exceptionOf (e1, Exception)) {
sb.appendC ('\n');
} else {
throw e1;
}
}
if (header != null) sb.append ("\nEND Directory Entry " + path + "\n");
fileData.put (path, sb.toString ());
} else {
var br = JU.Rdr.getBufferedReader (JU.Rdr.isGzipS (bis) ? new java.io.BufferedInputStream (this.fm.vwr.getJzt ().newGZIPInputStream (bis)) : bis, null);
var line;
sb = new JU.SB ();
if (header != null) sb.append ("BEGIN Directory Entry " + path + "\n");
while ((line = br.readLine ()) != null) {
sb.append (line);
sb.appendC ('\n');
}
br.close ();
if (header != null) sb.append ("\nEND Directory Entry " + path + "\n");
fileData.put (path, sb.toString ());
}} catch (ioe) {
if (Clazz.exceptionOf (ioe, Exception)) {
fileData.put (path, ioe.toString ());
} else {
throw ioe;
}
}
if (bis != null) try {
bis.close ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
if (!fileData.containsKey (path)) fileData.put (path, "FILE NOT FOUND: " + path + "\n");
return path;
}, "~S,~S,java.util.Map");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlArgusReader", ["java.lang.Float", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.decorateAsClass (function () {
this.atomName1 = null;
this.atomName2 = null;
this.bondOrder = 0;
this.elementContext = 0;
this.trans = null;
this.ptTrans = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlArgusReader", J.adapter.readers.xml.XmlReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlArgusReader, []);
});
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
for (var i = J.adapter.readers.xml.XmlArgusReader.keepCharsList.length; --i >= 0; ) if (J.adapter.readers.xml.XmlArgusReader.keepCharsList[i].equals (localName)) {
this.setKeepChars (true);
break;
}
if ("molecule".equals (localName)) {
this.asc.newAtomSet ();
return;
}if ("atom".equals (localName)) {
this.elementContext = 2;
this.atom = new J.adapter.smarter.Atom ();
return;
}if ("bond".equals (localName)) {
this.elementContext = 3;
this.atomName1 = null;
this.atomName2 = null;
this.bondOrder = this.parseBondToken (this.atts.get ("order"));
return;
}if ("transformmat".equals (localName)) {
this.elementContext = 4;
this.trans = Clazz.newFloatArray (16, 0);
return;
}}, "~S,~S");
Clazz.defineMethod (c$, "parseBondToken",
function (str) {
var floatOrder = this.parseFloatStr (str);
if (Float.isNaN (floatOrder) && str.length >= 1) {
str = str.toUpperCase ();
switch (str.charAt (0)) {
case 'S':
return 1;
case 'D':
return 2;
case 'T':
return 3;
case 'A':
return 515;
}
return this.parseIntStr (str);
}if (floatOrder == 1.5) return 515;
if (floatOrder == 2) return 2;
if (floatOrder == 3) return 3;
return 1;
}, "~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
var n = this.chars.length ();
if (n > 0 && this.chars.charAt (n - 1) == '\n') this.chars.setLength (n - 1);
if ("molecule".equals (localName)) {
this.elementContext = 0;
return;
}if ("atom".equals (localName)) {
if (this.atom.elementSymbol != null && !Float.isNaN (this.atom.z)) {
this.parent.setAtomCoord (this.atom);
this.asc.addAtomWithMappedName (this.atom);
}this.atom = null;
this.elementContext = 0;
return;
}if ("bond".equals (localName)) {
if (this.atomName2 != null) this.asc.addNewBondFromNames (this.atomName1, this.atomName2, this.bondOrder);
this.elementContext = 0;
return;
}if ("transformmat".equals (localName)) {
this.elementContext = 0;
this.parent.setTransform (this.trans[0], this.trans[1], this.trans[2], this.trans[4], this.trans[5], this.trans[6], this.trans[8], this.trans[9], this.trans[10]);
return;
}if (this.elementContext == 1) {
if ("name".equals (localName)) {
this.asc.setAtomSetName (this.chars.toString ());
this.setKeepChars (false);
}return;
}if (this.atom != null && this.elementContext == 2) {
if ("x".equals (localName)) {
this.atom.x = this.parseFloatStr (this.chars.toString ());
} else if ("y".equals (localName)) {
this.atom.y = this.parseFloatStr (this.chars.toString ());
return;
} else if ("z".equals (localName)) {
this.atom.z = this.parseFloatStr (this.chars.toString ());
return;
} else if ("atsym".equals (localName)) {
this.atom.elementSymbol = this.chars.toString ();
return;
} else if ("formalchg".equals (localName)) {
this.atom.formalCharge = this.parseIntStr (this.chars.toString ());
} else if ("atomkey".equals (localName)) {
this.atom.atomName = this.chars.toString ();
}this.setKeepChars (false);
return;
}if (this.elementContext == 3) {
if ("atomkey".equals (localName)) {
if (this.atomName1 == null) this.atomName1 = this.chars.toString ();
else this.atomName2 = this.chars.toString ();
this.setKeepChars (false);
}return;
}if (this.elementContext == 4) {
this.trans[this.ptTrans++] = this.parseFloatStr (this.chars.toString ());
this.setKeepChars (false);
return;
}}, "~S");
Clazz.defineStatics (c$,
"keepCharsList", Clazz.newArray (-1, ["name", "x", "y", "z", "formalchg", "atomkey", "atsym", "e00", "e01", "e02", "e03", "e10", "e11", "e12", "e13", "e20", "e21", "e22", "e23", "e30", "e31", "e32", "e33"]),
"UNSET", 0,
"MOLECULE", 1,
"ATOM", 2,
"BOND", 3,
"TRANSFORMMAT", 4);
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader", "JU.Lst"], "J.adapter.readers.xml.XmlChem3dReader", ["java.lang.Boolean", "$.Float", "java.util.Hashtable", "JU.PT", "J.adapter.smarter.Atom", "J.api.Interface", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.orbitals = null;
this.moData = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlChem3dReader", J.adapter.readers.xml.XmlReader);
Clazz.prepareFields (c$, function () {
this.orbitals = new JU.Lst ();
});
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlChem3dReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
this.processXml2 (parent, saxReader);
this.finalizeMOData (this.moData);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
var tokens;
if ("model".equals (localName)) {
this.asc.newAtomSet ();
return;
}if ("atom".equals (localName)) {
this.atom = new J.adapter.smarter.Atom ();
this.atom.atomName = this.atts.get ("id");
this.atom.elementSymbol = this.atts.get ("symbol");
if (this.atts.containsKey ("cartcoords")) {
var xyz = this.atts.get ("cartcoords");
tokens = JU.PT.getTokens (xyz);
this.atom.set (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]));
}return;
}if ("bond".equals (localName)) {
var atom1 = this.atts.get ("bondatom1");
var atom2 = this.atts.get ("bondatom2");
var order = 1;
if (this.atts.containsKey ("bondorder")) order = this.parseIntStr (this.atts.get ("bondorder"));
this.asc.addNewBondFromNames (atom1, atom2, order);
return;
}if ("electronicstructurecalculation".equals (localName)) {
tokens = JU.PT.getTokens (this.atts.get ("calcpartialcharges"));
var tokens2 = JU.PT.getTokens (this.atts.get ("calcatoms"));
for (var i = this.parseIntStr (tokens[0]); --i >= 0; ) this.asc.mapPartialCharge (tokens2[i + 1], this.parseFloatStr (tokens[i + 1]));
}if ("griddata".equals (localName)) {
var nPointsX = this.parseIntStr (this.atts.get ("griddatxdim"));
var nPointsY = this.parseIntStr (this.atts.get ("griddatydim"));
var nPointsZ = this.parseIntStr (this.atts.get ("griddatzdim"));
var xStep = this.parseFloatStr (this.atts.get ("griddatxsize")) / (nPointsX);
var yStep = this.parseFloatStr (this.atts.get ("griddatysize")) / (nPointsY);
var zStep = this.parseFloatStr (this.atts.get ("griddatzsize")) / (nPointsZ);
tokens = JU.PT.getTokens (this.atts.get ("griddatorigin"));
var ox = this.parseFloatStr (tokens[0]);
var oy = this.parseFloatStr (tokens[1]);
var oz = this.parseFloatStr (tokens[2]);
tokens = JU.PT.getTokens (this.atts.get ("griddatdata"));
var pt = 1;
var voxelData = Clazz.newFloatArray (nPointsX, nPointsY, nPointsZ, 0);
var sum = 0;
for (var z = 0; z < nPointsZ; z++) for (var y = 0; y < nPointsY; y++) for (var x = 0; x < nPointsX; x++) {
var f = this.parseFloatStr (tokens[pt++]);
voxelData[x][y][z] = f;
sum += f * f;
}
sum = (1 / Math.sqrt (sum));
for (var z = 0; z < nPointsZ; z++) for (var y = 0; y < nPointsY; y++) for (var x = 0; x < nPointsX; x++) {
voxelData[x][y][z] *= sum;
}
var vd = J.api.Interface.getOption ("jvxl.data.VolumeData", this.vwr, "file");
vd.setVoxelCounts (nPointsX, nPointsY, nPointsZ);
vd.setVolumetricVector (0, xStep, 0, 0);
vd.setVolumetricVector (1, 0, yStep, 0);
vd.setVolumetricVector (2, 0, 0, zStep);
vd.setVolumetricOrigin (ox, oy, oz);
vd.setVoxelDataAsArray (voxelData);
if (this.moData == null) {
this.moData = new java.util.Hashtable ();
this.moData.put ("defaultCutoff", Float.$valueOf (0.01));
this.moData.put ("haveVolumeData", Boolean.TRUE);
this.moData.put ("calculationType", "Chem3D");
this.orbitals = new JU.Lst ();
this.moData.put ("mos", this.orbitals);
}var mo = new java.util.Hashtable ();
mo.put ("volumeData", vd);
this.orbitals.addLast (mo);
JU.Logger.info ("Chem3D molecular orbital data displayable using ISOSURFACE MO " + this.orbitals.size ());
return;
}}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if ("atom".equals (localName)) {
if (this.atom.elementSymbol != null && !Float.isNaN (this.atom.z)) {
this.parent.setAtomCoord (this.atom);
this.asc.addAtomWithMappedName (this.atom);
}this.atom = null;
return;
}this.setKeepChars (false);
}, "~S");
});

592
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xml/XmlCmlReader.js Normal file
View File

@@ -0,0 +1,592 @@
Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlCmlReader", ["java.lang.Float", "$.IndexOutOfBoundsException", "java.util.Hashtable", "$.Properties", "$.StringTokenizer", "JU.BS", "$.Lst", "$.PT", "J.adapter.smarter.Atom", "$.Bond", "J.api.JmolAdapter", "JU.BSUtil", "$.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.scalarDictRef = null;
this.scalarDictValue = null;
this.scalarTitle = null;
this.cellParameterType = null;
this.checkedSerial = false;
this.isSerial = false;
this.moleculeNesting = 0;
this.latticeVectorPtr = 0;
this.embeddedCrystal = false;
this.atomIdNames = null;
this.tokens = null;
this.aaLen = 0;
this.atomArray = null;
this.bondCount = 0;
this.bondArray = null;
this.tokenCount = 0;
this.moduleNestingLevel = 0;
this.haveMolecule = false;
this.localSpaceGroupName = null;
this.processing = true;
this.state = 0;
this.atomIndex0 = 0;
this.joinList = null;
this.mapRtoA = null;
this.deleteAtoms = null;
this.moleculeID = null;
this.htModelAtomMap = null;
this.optimize2d = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlCmlReader", J.adapter.readers.xml.XmlReader);
Clazz.prepareFields (c$, function () {
this.tokens = new Array (16);
this.atomArray = new Array (100);
this.bondArray = new Array (100);
});
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlCmlReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
this.optimize2d = parent.checkFilterKey ("2D");
this.processXml2 (parent, saxReader);
if (this.optimize2d) this.set2D ();
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (name, nodeName) {
if (!this.processing) return;
this.processStart2 (name);
}, "~S,~S");
Clazz.defineMethod (c$, "processStart2",
function (name) {
name = name.toLowerCase ();
var val;
switch (this.state) {
case 0:
if (name.equals ("molecule")) {
this.moleculeID = this.atts.get ("id");
this.state = 6;
this.haveMolecule = true;
if (this.moleculeNesting == 0) this.createNewAtomSet ();
this.moleculeNesting++;
} else if (name.equals ("crystal")) {
this.state = 2;
} else if (name.equals ("symmetry")) {
this.state = 17;
if ((val = this.atts.get ("spacegroup")) != null) {
this.localSpaceGroupName = val;
} else {
this.localSpaceGroupName = "P1";
this.parent.clearUnitCell ();
}} else if (name.equals ("module")) {
this.moduleNestingLevel++;
} else if (name.equals ("latticevector")) {
this.state = 18;
this.setKeepChars (true);
}break;
case 2:
this.checkedSerial = true;
this.isSerial = false;
if (name.equals ("scalar")) {
this.state = 3;
this.setKeepChars (true);
this.scalarTitle = this.atts.get ("title");
this.getDictRefValue ();
} else if (name.equals ("symmetry")) {
this.state = 4;
if ((val = this.atts.get ("spacegroup")) != null) {
this.localSpaceGroupName = val;
for (var i = 0; i < this.localSpaceGroupName.length; i++) if (this.localSpaceGroupName.charAt (i) == '_') this.localSpaceGroupName = this.localSpaceGroupName.substring (0, i) + this.localSpaceGroupName.substring ((i--) + 1);
}} else if (name.equals ("cellparameter")) {
if ((val = this.atts.get ("parametertype")) != null) {
this.cellParameterType = val;
this.setKeepChars (true);
}}break;
case 18:
this.setKeepChars (true);
break;
case 17:
case 3:
case 4:
if (name.equals ("transform3")) {
this.state = 5;
this.setKeepChars (true);
}break;
case 5:
case 6:
if (name.equals ("fragmentlist")) {
this.joinList = new JU.Lst ();
this.mapRtoA = new java.util.Hashtable ();
if (this.deleteAtoms == null) this.deleteAtoms = new JU.BS ();
} else if (name.equals ("crystal")) {
this.state = 2;
this.embeddedCrystal = true;
} else if (name.equals ("molecule")) {
this.state = 6;
this.moleculeNesting++;
} else if (name.equals ("join")) {
var order = -1;
this.tokenCount = 0;
if ((val = this.atts.get ("atomrefs2")) != null) {
this.breakOutTokens (val);
if ((val = this.atts.get ("order")) != null) order = this.parseBondToken (val);
if (this.tokenCount == 2 && order > 0) this.joinList.addLast ( Clazz.newArray (-1, [this.tokens[0], this.tokens[1], "" + order]));
}} else if (name.equals ("bondarray")) {
this.state = 10;
this.bondCount = 0;
if ((val = this.atts.get ("order")) != null) {
this.breakOutBondTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].order = this.parseBondToken (this.tokens[i]);
}if ((val = this.atts.get ("atomref1")) != null) {
this.breakOutBondTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].atomIndex1 = this.getAtomIndex (this.tokens[i]);
}if ((val = this.atts.get ("atomref2")) != null) {
this.breakOutBondTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.bondArray[i].atomIndex2 = this.getAtomIndex (this.tokens[i]);
}} else if (name.equals ("atomarray")) {
this.state = 7;
this.aaLen = 0;
var coords3D = false;
if ((val = this.atts.get ("atomid")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].atomName = this.tokens[i];
}var is3d = (!this.optimize2d && (val = this.atts.get ("x3")) != null);
if (is3d) {
is3d = true;
coords3D = true;
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].x = this.parseFloatStr (this.tokens[i]);
if ((val = this.atts.get ("y3")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].y = this.parseFloatStr (this.tokens[i]);
}if ((val = this.atts.get ("z3")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].z = this.parseFloatStr (this.tokens[i]);
}} else {
if ((val = this.atts.get ("x2")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].x = this.parseFloatStr (this.tokens[i]);
}if ((val = this.atts.get ("y2")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].y = this.parseFloatStr (this.tokens[i]);
}}if ((val = this.atts.get ("elementtype")) != null) {
this.breakOutAtomTokens (val);
for (var i = this.tokenCount; --i >= 0; ) this.atomArray[i].elementSymbol = this.tokens[i];
}for (var i = this.aaLen; --i >= 0; ) {
var atom = this.atomArray[i];
if (!coords3D) atom.z = 0;
this.addAtom (atom);
}
} else if (name.equals ("formula")) {
this.state = 13;
} else if (name.equals ("association")) {
this.state = 19;
}break;
case 10:
if (name.equals ("bond")) {
this.state = 11;
var order = -1;
this.tokenCount = 0;
if ((val = this.atts.get ("atomrefs2")) != null) this.breakOutTokens (val);
if ((val = this.atts.get ("order")) != null) order = this.parseBondToken (val);
if (this.tokenCount == 2 && order > 0) {
this.addNewBond (this.tokens[0], this.tokens[1], order);
}}break;
case 7:
if (name.equals ("atom")) {
this.state = 8;
this.atom = new J.adapter.smarter.Atom ();
this.parent.setFractionalCoordinates (false);
var id = this.atts.get ("id");
if ((val = this.atts.get ("name")) != null) this.atom.atomName = val;
else if ((val = this.atts.get ("title")) != null) this.atom.atomName = val;
else if ((val = this.atts.get ("label")) != null) this.atom.atomName = val;
else this.atom.atomName = id;
if (!this.checkedSerial) {
this.isSerial = (id != null && id.length > 1 && id.startsWith ("a") && JU.PT.parseInt (id.substring (1)) != -2147483648);
this.checkedSerial = true;
}if (this.isSerial) this.atom.atomSerial = JU.PT.parseInt (id.substring (1));
if ((val = this.atts.get ("xfract")) != null && (this.parent.iHaveUnitCell || !this.atts.containsKey ("x3"))) {
this.parent.setFractionalCoordinates (true);
this.atom.set (this.parseFloatStr (val), this.parseFloatStr (this.atts.get ("yfract")), this.parseFloatStr (this.atts.get ("zfract")));
} else if ((val = this.atts.get ("x3")) != null) {
this.atom.set (this.parseFloatStr (val), this.parseFloatStr (this.atts.get ("y3")), this.parseFloatStr (this.atts.get ("z3")));
} else if ((val = this.atts.get ("x2")) != null) {
this.atom.set (this.parseFloatStr (val), this.parseFloatStr (this.atts.get ("y2")), 0);
}if ((val = this.atts.get ("elementtype")) != null) {
var sym = val;
if ((val = this.atts.get ("isotope")) != null) this.atom.elementNumber = ((this.parseIntStr (val) << 7) + J.api.JmolAdapter.getElementNumber (sym));
this.atom.elementSymbol = sym;
}if ((val = this.atts.get ("formalcharge")) != null) this.atom.formalCharge = this.parseIntStr (val);
}break;
case 11:
if ((val = this.atts.get ("builtin")) != null) {
this.setKeepChars (true);
this.state = 15;
this.scalarDictValue = val;
} else if (name.equals ("bondstereo")) {
this.state = 12;
}break;
case 12:
this.setKeepChars (true);
this.state = 12;
break;
case 8:
if (name.equals ("scalar")) {
this.state = 9;
this.setKeepChars (true);
this.scalarTitle = this.atts.get ("title");
this.getDictRefValue ();
} else if ((val = this.atts.get ("builtin")) != null) {
this.setKeepChars (true);
this.state = 14;
this.scalarDictValue = val;
}break;
case 9:
break;
case 13:
break;
case 14:
break;
case 15:
break;
}
}, "~S");
Clazz.defineMethod (c$, "getAtomIndex",
function (label) {
return this.asc.getAtomIndex (this.isSerial ? label.substring (1) : label);
}, "~S");
Clazz.overrideMethod (c$, "processEndElement",
function (name) {
if (!this.processing) return;
this.processEnd2 (name);
}, "~S");
Clazz.defineMethod (c$, "processEnd2",
function (name) {
name = name.toLowerCase ();
switch (this.state) {
case 0:
if (name.equals ("module")) {
if (--this.moduleNestingLevel == 0) {
if (this.parent.iHaveUnitCell) this.applySymmetryAndSetTrajectory ();
this.setAtomNames ();
}}break;
case 19:
if (name.equals ("association")) this.state = 6;
break;
case 2:
if (name.equals ("crystal")) {
if (this.embeddedCrystal) {
this.state = 6;
this.embeddedCrystal = false;
} else {
this.state = 0;
}} else if (name.equals ("cellparameter") && this.keepChars) {
var tokens = JU.PT.getTokens (this.chars.toString ());
this.setKeepChars (false);
if (tokens.length != 3 || this.cellParameterType == null) {
} else if (this.cellParameterType.equals ("length")) {
for (var i = 0; i < 3; i++) this.parent.setUnitCellItem (i, this.parseFloatStr (tokens[i]));
break;
} else if (this.cellParameterType.equals ("angle")) {
for (var i = 0; i < 3; i++) this.parent.setUnitCellItem (i + 3, this.parseFloatStr (tokens[i]));
break;
}JU.Logger.error ("bad cellParameter information: parameterType=" + this.cellParameterType + " data=" + this.chars);
this.parent.setFractionalCoordinates (false);
}break;
case 3:
if (name.equals ("scalar")) {
this.state = 2;
if (this.scalarTitle != null) this.checkUnitCellItem (J.adapter.readers.xml.XmlCmlReader.unitCellParamTags, this.scalarTitle);
else if (this.scalarDictRef != null) this.checkUnitCellItem (J.api.JmolAdapter.cellParamNames, (this.scalarDictValue.startsWith ("_") ? this.scalarDictValue : "_" + this.scalarDictValue));
}this.setKeepChars (false);
this.scalarTitle = null;
this.scalarDictRef = null;
break;
case 5:
if (name.equals ("transform3")) {
this.setKeepChars (false);
this.state = 4;
}break;
case 18:
var values = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.chars.toString (), null, 3);
this.parent.addExplicitLatticeVector (this.latticeVectorPtr, values, 0);
this.latticeVectorPtr = (this.latticeVectorPtr + 1) % 3;
this.setKeepChars (false);
this.state = 0;
break;
case 4:
case 17:
if (name.equals ("symmetry")) this.state = (this.state == 4 ? 2 : 0);
if (this.moduleNestingLevel == 0 && this.parent.iHaveUnitCell && !this.embeddedCrystal) this.applySymmetryAndSetTrajectory ();
break;
case 6:
if (name.equals ("fragmentlist")) {
for (var i = this.joinList.size (); --i >= 0; ) {
var join = this.joinList.get (i);
var r1 = this.asc.getAtomFromName (this.fixSerialName (join[0]));
var r2 = this.asc.getAtomFromName (this.fixSerialName (join[1]));
if (r1 != null && r2 != null) {
this.deleteAtoms.set (r1.index);
this.deleteAtoms.set (r2.index);
this.addNewBond (this.mapRtoA.get (r1), this.mapRtoA.get (r2), this.parseIntStr (join[2]));
}}
this.joinList = null;
this.mapRtoA = null;
}if (name.equals ("molecule")) {
if (--this.moleculeNesting == 0) {
this.applySymmetryAndSetTrajectory ();
this.setAtomNames ();
this.state = 0;
} else {
this.state = 6;
}}break;
case 10:
if (name.equals ("bondarray")) {
this.state = 6;
for (var i = 0; i < this.bondCount; ++i) this.addBond (this.bondArray[i]);
this.parent.applySymmetryToBonds = true;
}break;
case 7:
if (name.equals ("atomarray")) {
this.state = 6;
}break;
case 11:
if (name.equals ("bond")) {
this.state = 10;
}break;
case 8:
if (name.equals ("atom")) {
this.state = 7;
this.addAtom (this.atom);
this.atom = null;
}break;
case 9:
if (name.equals ("scalar")) {
this.state = 8;
if ("jmol:charge".equals (this.scalarDictRef)) {
this.atom.partialCharge = this.parseFloatStr (this.chars.toString ());
} else if (this.scalarDictRef != null && "_atom_site_label".equals (this.scalarDictValue)) {
if (this.atomIdNames == null) this.atomIdNames = new java.util.Properties ();
this.atomIdNames.put (this.atom.atomName, this.chars.toString ());
}}this.setKeepChars (false);
this.scalarTitle = null;
this.scalarDictRef = null;
break;
case 14:
this.state = 8;
if (this.scalarDictValue.equals ("x3")) this.atom.x = this.parseFloatStr (this.chars.toString ());
else if (this.scalarDictValue.equals ("y3")) this.atom.y = this.parseFloatStr (this.chars.toString ());
else if (this.scalarDictValue.equals ("z3")) this.atom.z = this.parseFloatStr (this.chars.toString ());
else if (this.scalarDictValue.equals ("elementType")) this.atom.elementSymbol = this.chars.toString ();
this.setKeepChars (false);
break;
case 12:
var stereo = this.chars.toString ();
if (this.bond.order == 1) this.bond.order = (stereo.equals ("H") ? 1041 : 1025);
this.setKeepChars (false);
this.state = 11;
break;
case 15:
this.state = 11;
if (this.scalarDictValue.equals ("atomRef")) {
if (this.tokenCount == 0) this.tokens = new Array (2);
if (this.tokenCount < 2) this.tokens[this.tokenCount++] = this.chars.toString ();
} else if (this.scalarDictValue.equals ("order")) {
var order = this.parseBondToken (this.chars.toString ());
if (order > 0 && this.tokenCount == 2) this.addNewBond (this.tokens[0], this.tokens[1], order);
}this.setKeepChars (false);
break;
case 13:
this.state = 6;
break;
}
}, "~S");
Clazz.defineMethod (c$, "addBond",
function (bond) {
var a1 = this.asc.atoms[bond.atomIndex1];
var a2 = this.asc.atoms[bond.atomIndex2];
if (this.joinList != null && !this.checkBondToR (a1.atomName, a2.atomName)) this.asc.addBond (bond);
}, "J.adapter.smarter.Bond");
Clazz.defineMethod (c$, "checkBondToR",
function (a1name, a2name) {
var a1 = this.asc.getAtomFromName (a1name);
var a2 = this.asc.getAtomFromName (a2name);
if (a1 == null || a2 == null) return true;
if ("R".equals (a1.elementSymbol)) {
this.mapRtoA.put (a1, a2.atomName);
return true;
} else if ("R".equals (a2.elementSymbol)) {
this.mapRtoA.put (a2, a1.atomName);
return true;
}return false;
}, "~S,~S");
Clazz.defineMethod (c$, "setAtomNames",
function () {
if (this.atomIdNames == null) return;
var s;
var atoms = this.asc.atoms;
for (var i = this.atomIndex0; i < this.asc.ac; i++) if ((s = this.atomIdNames.getProperty (atoms[i].atomName)) != null) atoms[i].atomName = s;
this.atomIdNames = null;
this.atomIndex0 = this.asc.ac;
});
Clazz.defineMethod (c$, "addNewBond",
function (a1, a2, order) {
if (a1 == null || a2 == null) return;
this.parent.applySymmetryToBonds = true;
a1 = this.fixSerialName (a1);
a2 = this.fixSerialName (a2);
if (this.joinList == null || !this.checkBondToR (a1, a2)) {
this.asc.addNewBondFromNames (a1, a2, order);
this.bond = this.asc.bonds[this.asc.bondCount - 1];
}}, "~S,~S,~N");
Clazz.defineMethod (c$, "fixSerialName",
function (a) {
return (this.isSerial ? a.substring (1) : a);
}, "~S");
Clazz.defineMethod (c$, "getDictRefValue",
function () {
this.scalarDictRef = this.atts.get ("dictref");
if (this.scalarDictRef != null) {
var iColon = this.scalarDictRef.indexOf (":");
this.scalarDictValue = this.scalarDictRef.substring (iColon + 1);
}});
Clazz.defineMethod (c$, "checkUnitCellItem",
function (tags, value) {
for (var i = tags.length; --i >= 0; ) if (value.equals (tags[i])) {
this.parent.setUnitCellItem (i, this.parseFloatStr (this.chars.toString ()));
return;
}
}, "~A,~S");
Clazz.defineMethod (c$, "addAtom",
function (atom) {
if ((atom.elementSymbol == null && atom.elementNumber < 0) || Float.isNaN (atom.z)) return;
this.parent.setAtomCoord (atom);
if (this.htModelAtomMap != null) this.htModelAtomMap.put (this.moleculeID + atom.atomName, atom);
if (this.isSerial) this.asc.addAtomWithMappedSerialNumber (atom);
else this.asc.addAtomWithMappedName (atom);
}, "J.adapter.smarter.Atom");
Clazz.defineMethod (c$, "parseBondToken",
function (str) {
var floatOrder = this.parseFloatStr (str);
if (Float.isNaN (floatOrder) && str.length >= 1) {
str = str.toUpperCase ();
switch (str.charAt (0)) {
case 'S':
return 1;
case 'D':
return 2;
case 'T':
return 3;
case 'A':
return 515;
case 'P':
return 66;
}
return this.parseIntStr (str);
}if (floatOrder == 1.5) return 515;
if (floatOrder == 2) return 2;
if (floatOrder == 3) return 3;
return 1;
}, "~S");
Clazz.defineMethod (c$, "breakOutTokens",
function (str) {
var st = new java.util.StringTokenizer (str);
this.tokenCount = st.countTokens ();
if (this.tokenCount > this.tokens.length) this.tokens = new Array (this.tokenCount);
for (var i = 0; i < this.tokenCount; ++i) {
try {
this.tokens[i] = st.nextToken ();
} catch (nsee) {
if (Clazz.exceptionOf (nsee, java.util.NoSuchElementException)) {
this.tokens[i] = null;
} else {
throw nsee;
}
}
}
}, "~S");
Clazz.defineMethod (c$, "breakOutAtomTokens",
function (str) {
this.breakOutTokens (str);
this.checkAtomArrayLength (this.tokenCount);
}, "~S");
Clazz.defineMethod (c$, "checkAtomArrayLength",
function (newAtomCount) {
if (this.aaLen == 0) {
if (newAtomCount > this.atomArray.length) this.atomArray = new Array (newAtomCount);
for (var i = newAtomCount; --i >= 0; ) this.atomArray[i] = new J.adapter.smarter.Atom ();
this.aaLen = newAtomCount;
} else if (newAtomCount != this.aaLen) {
throw new IndexOutOfBoundsException ("bad atom attribute length");
}}, "~N");
Clazz.defineMethod (c$, "breakOutBondTokens",
function (str) {
this.breakOutTokens (str);
this.checkBondArrayLength (this.tokenCount);
}, "~S");
Clazz.defineMethod (c$, "checkBondArrayLength",
function (newBondCount) {
if (this.bondCount == 0) {
if (newBondCount > this.bondArray.length) this.bondArray = new Array (newBondCount);
for (var i = newBondCount; --i >= 0; ) this.bondArray[i] = new J.adapter.smarter.Bond (-1, -1, 1);
this.bondCount = newBondCount;
} else if (newBondCount != this.bondCount) {
throw new IndexOutOfBoundsException ("bad bond attribute length");
}}, "~N");
Clazz.defineMethod (c$, "createNewAtomSet",
function () {
this.asc.newAtomSet ();
var val;
if (this.htModelAtomMap != null) this.htModelAtomMap.put ("" + this.asc.iSet, "" + this.moleculeID);
var collectionName = ((val = this.atts.get ("title")) != null || (val = this.atts.get ("id")) != null ? val : null);
if (collectionName != null) {
this.asc.setAtomSetName (collectionName);
}});
Clazz.defineMethod (c$, "applySymmetryAndSetTrajectory",
function () {
if (this.moduleNestingLevel > 0 || !this.haveMolecule || this.localSpaceGroupName == null) return;
this.parent.setSpaceGroupName (this.localSpaceGroupName);
this.parent.iHaveSymmetryOperators = this.iHaveSymmetryOperators;
this.parent.applySymmetryAndSetTrajectory ();
});
Clazz.overrideMethod (c$, "endDocument",
function () {
if (this.deleteAtoms != null) {
var bs = (this.asc.bsAtoms == null ? this.asc.bsAtoms = JU.BSUtil.newBitSet2 (0, this.asc.ac) : this.asc.bsAtoms);
bs.andNot (this.deleteAtoms);
}});
Clazz.defineStatics (c$,
"START", 0,
"CML", 1,
"CRYSTAL", 2,
"CRYSTAL_SCALAR", 3,
"CRYSTAL_SYMMETRY", 4,
"CRYSTAL_SYMMETRY_TRANSFORM3", 5,
"MOLECULE", 6,
"MOLECULE_ATOM_ARRAY", 7,
"MOLECULE_ATOM", 8,
"MOLECULE_ATOM_SCALAR", 9,
"MOLECULE_BOND_ARRAY", 10,
"MOLECULE_BOND", 11,
"MOLECULE_BOND_STEREO", 12,
"MOLECULE_FORMULA", 13,
"MOLECULE_ATOM_BUILTIN", 14,
"MOLECULE_BOND_BUILTIN", 15,
"MODULE", 16,
"SYMMETRY", 17,
"LATTICE_VECTOR", 18,
"ASSOCIATION", 19,
"unitCellParamTags", Clazz.newArray (-1, ["a", "b", "c", "alpha", "beta", "gamma"]));
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["org.xml.sax.helpers.DefaultHandler"], "J.adapter.readers.xml.XmlHandler", ["JU.Logger", "org.xml.sax.InputSource"], function () {
c$ = Clazz.decorateAsClass (function () {
this.xmlReader = null;
this.debugContext = "";
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlHandler", org.xml.sax.helpers.DefaultHandler);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlHandler, []);
});
Clazz.defineMethod (c$, "parseXML",
function (xmlReader, saxReaderObj, reader) {
this.xmlReader = xmlReader;
var saxReader = saxReaderObj;
saxReader.setFeature ("http://xml.org/sax/features/validation", false);
saxReader.setFeature ("http://xml.org/sax/features/namespaces", true);
saxReader.setEntityResolver (this);
saxReader.setContentHandler (this);
saxReader.setErrorHandler (this);
var is = new org.xml.sax.InputSource (reader);
is.setSystemId ("foo");
saxReader.parse (is);
}, "J.adapter.readers.xml.XmlReader,~O,java.io.BufferedReader");
Clazz.overrideMethod (c$, "startDocument",
function () {
});
Clazz.overrideMethod (c$, "endDocument",
function () {
this.xmlReader.endDocument ();
});
Clazz.overrideMethod (c$, "startElement",
function (namespaceURI, localName, nodeName, attributes) {
this.xmlReader.atts.clear ();
for (var i = attributes.getLength (); --i >= 0; ) this.xmlReader.atts.put (attributes.getLocalName (i).toLowerCase (), attributes.getValue (i));
if (JU.Logger.debugging) {
this.debugContext += " " + localName;
JU.Logger.debug ("start " + this.debugContext);
}this.xmlReader.processStartElement (localName.toLowerCase (), nodeName.toLowerCase ());
}, "~S,~S,~S,org.xml.sax.Attributes");
Clazz.overrideMethod (c$, "endElement",
function (uri, localName, qName) {
if (JU.Logger.debugging) {
if (JU.Logger.debugging) {
JU.Logger.debug ("end " + this.debugContext);
}this.debugContext = this.debugContext.substring (0, this.debugContext.lastIndexOf (" "));
}this.xmlReader.processEndElement (localName.toLowerCase ());
}, "~S,~S,~S");
Clazz.overrideMethod (c$, "characters",
function (ch, start, length) {
if (this.xmlReader.keepChars) this.xmlReader.chars.appendCB (ch, start, length);
}, "~A,~N,~N");
Clazz.defineMethod (c$, "resolveEntity",
function (name, publicId, baseURI, systemId) {
if (JU.Logger.debugging) {
JU.Logger.debug ("Not resolving this:\n name: " + name + "\n systemID: " + systemId + "\n publicID: " + publicId + "\n baseURI: " + baseURI);
}return null;
}, "~S,~S,~S,~S");
Clazz.overrideMethod (c$, "error",
function (exception) {
JU.Logger.error ("SAX ERROR:" + exception.getMessage ());
}, "org.xml.sax.SAXParseException");
Clazz.overrideMethod (c$, "fatalError",
function (exception) {
JU.Logger.error ("SAX FATAL:" + exception.getMessage ());
}, "org.xml.sax.SAXParseException");
Clazz.overrideMethod (c$, "warning",
function (exception) {
JU.Logger.warn ("SAX WARNING:" + exception.getMessage ());
}, "org.xml.sax.SAXParseException");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlCmlReader"], "J.adapter.readers.xml.XmlMOReader", ["java.util.Hashtable", "JU.AU", "$.Lst", "$.PT", "J.adapter.readers.quantum.MOReader", "J.adapter.smarter.Resolver", "J.quantum.QS", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.moReader = null;
this.skipMOs = false;
this.htSlaterIDs = null;
this.basisData = null;
this.basisId = null;
this.isSpherical = false;
this.minL = 0;
this.maxL = 0;
this.basisIds = null;
this.basisAtoms = null;
this.orbOcc = 0;
this.orbEnergy = 0;
this.gaussianCount = 0;
this.slaterCount = 0;
this.coefCount = 0;
this.groupCount = 0;
this.lstGaussians = null;
this.moCount = 0;
this.calcType = null;
this.iModelMO = 0;
this.dclist = null;
this.dslist = null;
this.fclist = null;
this.fslist = null;
this.iHaveCoefMaps = false;
this.maxContraction = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlMOReader", J.adapter.readers.xml.XmlCmlReader);
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
this.htModelAtomMap = new java.util.Hashtable ();
this.processXml2 (parent, saxReader);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.defineMethod (c$, "processStartMO",
function (localName) {
if (!this.parent.doReadMolecularOrbitals) return false;
if (localName.equals ("molecule")) {
var method = this.atts.get ("method");
if (method != null) this.calcType = method + "(" + this.atts.get ("basis") + ")";
return true;
}if (localName.equals ("basisset")) {
this.iModelMO = this.asc.iSet;
this.lstGaussians = new JU.Lst ();
this.htSlaterIDs = new java.util.Hashtable ();
this.coefCount = this.groupCount = this.gaussianCount = this.slaterCount = 0;
if (this.moReader == null && !this.skipMOs) {
var rdr = J.adapter.smarter.Resolver.getReader ("MO", this.parent.htParams);
if ((Clazz.instanceOf (rdr, String))) {
this.skipMOs = true;
} else {
this.moReader = rdr;
this.moReader.asc = this.asc;
if (this.iHaveCoefMaps) {
var m = this.moReader.getDfCoefMaps ();
if (this.dclist != null) J.quantum.QS.createDFMap (m[4], this.dclist, "DXX DYY DZZ DXY DXZ DYZ", 2);
if (this.dslist != null) J.quantum.QS.createDFMap (m[3], this.dslist, "d0 d1+ d1- d2+ d2-", 2);
if (this.fclist != null) J.quantum.QS.createDFMap (m[6], this.fclist, "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ", 2);
if (this.fslist != null) J.quantum.QS.createDFMap (m[5], this.fslist, "f0 f1+ f1- f2+ f2- f3+ f3-", 2);
}}}if (this.moReader != null) this.moReader.calculationType = this.calcType;
return true;
}if (this.moReader != null) {
if (localName.equals ("basisgroup")) {
this.groupCount++;
this.basisId = this.atts.get ("id");
this.isSpherical = "spherical".equalsIgnoreCase (this.atts.get ("angular"));
this.minL = JU.PT.parseInt (this.atts.get ("minl"));
this.maxL = JU.PT.parseInt (this.atts.get ("maxl"));
var nContractions = JU.PT.parseInt (this.atts.get ("contractions"));
var n = nContractions * (this.isSpherical ? this.minL * 2 + 1 : Clazz.doubleToInt (this.minL * (this.minL + 3) / 2) + 1);
this.htModelAtomMap.put (this.basisId + "_count", Integer.$valueOf (n));
return true;
}if (localName.equals ("basisexponents") || localName.equals ("basiscontraction")) {
this.setKeepChars (true);
return true;
}if (localName.equals ("orbital") && this.gaussianCount > 0) {
this.orbOcc = JU.PT.parseFloat (this.atts.get ("occupation"));
this.orbEnergy = JU.PT.parseFloat (this.atts.get ("energy"));
this.setKeepChars (true);
return true;
}}return false;
}, "~S");
Clazz.defineMethod (c$, "processEndMO",
function (localName) {
if (this.moReader != null) {
if (localName.equals ("basisexponents")) {
this.basisData = new JU.Lst ();
this.basisData.addLast (JU.PT.parseFloatArray (this.chars.toString ()));
this.setKeepChars (false);
return true;
}if (localName.equals ("basiscontraction")) {
var data = JU.PT.parseFloatArray (this.chars.toString ());
this.basisData.addLast (data);
if (this.basisData.size () > this.maxContraction) this.maxContraction = this.basisData.size ();
this.setKeepChars (false);
return true;
}if (localName.equals ("basisgroup")) {
var otype;
switch (this.minL) {
case 0:
otype = (this.maxL == 1 ? "L" : "S");
break;
case 1:
otype = "P";
break;
default:
otype = (this.minL <= 7 ? "SPDFGHI".substring (this.minL, this.minL + 1) : "?");
if (this.isSpherical) otype = (2 * (this.minL) + 1) + otype;
}
this.lstGaussians.addLast (this.basisData);
var nPrimitives = this.basisData.get (0).length;
for (var i = 1, n = this.basisData.size (); i < n; i++) {
this.htSlaterIDs.put (this.basisId + "_" + i, Clazz.newIntArray (-1, [-1, this.moReader.getQuantumShellTagID (otype), this.gaussianCount + 1, nPrimitives]));
this.gaussianCount += nPrimitives;
}
return true;
}if (localName.equals ("basisset")) {
this.buildSlaters ();
return true;
}if (localName.equals ("orbital")) {
if (this.gaussianCount == 0) return true;
var coef = JU.PT.parseFloatArray (this.chars.toString ());
if (this.moCount == 0) {
if (coef.length != this.coefCount) {
JU.Logger.error ("Number of orbital coefficients (" + coef.length + ") does not agree with expected number (" + this.coefCount + ")");
this.moReader = null;
return this.skipMOs = true;
}JU.Logger.info (this.coefCount + " coefficients found");
}this.moReader.addCoef ( new java.util.Hashtable (), coef, null, this.orbEnergy, this.orbOcc, this.moCount++);
this.setKeepChars (false);
return true;
}if (localName.equals ("orbitals")) {
this.moReader.setMOData (true);
JU.Logger.info ("XmlMOReader created\n " + this.gaussianCount + " gaussians\n " + this.slaterCount + " slaters\n " + this.groupCount + " groups\n " + this.coefCount + " orbital coefficients\n " + this.moCount + " orbitals");
return true;
}if (this.state == 19) {
if (localName.equals ("bases")) {
this.basisIds = this.getXlink (this.atts.get ("href"), "basisGroup", false);
} else if (localName.equals ("atoms")) {
this.basisAtoms = this.getXlink (this.atts.get ("href"), "atom", true);
} else if (localName.equals ("association")) {
this.state = 6;
for (var i = this.basisAtoms.length; --i >= 0; ) {
var a = this.htModelAtomMap.get (this.basisAtoms[i]);
if (a == null) {
JU.Logger.error ("XmlMOReader atom not found; orbitals skipped: " + a);
this.moReader = null;
return this.skipMOs = true;
}this.htModelAtomMap.put (this.basisAtoms[i] + "_basis", this.basisIds);
}
this.slaterCount += this.basisIds.length * this.basisAtoms.length;
}return true;
}}return false;
}, "~S");
Clazz.defineMethod (c$, "buildSlaters",
function () {
var gaussians = JU.AU.newFloat2 (this.gaussianCount);
for (var i = 0, p = 0, n = this.lstGaussians.size (); i < n; i++) {
this.basisData = this.lstGaussians.get (i);
var exp = this.basisData.get (0);
for (var ii = 1, nn = this.basisData.size (); ii < nn; ii++) {
var coef = this.basisData.get (ii);
for (var j = 0; j < exp.length; j++) gaussians[p++] = Clazz.newFloatArray (-1, [exp[j], coef[j], 0]);
}
}
this.moReader.gaussians = gaussians;
var slaters = new JU.Lst ();
var modelID = this.htModelAtomMap.get ("" + this.iModelMO);
var i0 = this.asc.getAtomSetAtomIndex (this.iModelMO);
for (var i = 0, n = this.asc.getAtomSetAtomCount (this.iModelMO); i < n; i++) {
var ids = this.htModelAtomMap.get (modelID + this.asc.atoms[i0 + i].atomName + "_basis");
if (ids == null) continue;
for (var k = 0; k < ids.length; k++) {
var key = ids[k] + "_count";
this.coefCount += (this.htModelAtomMap.get (key)).intValue ();
for (var kk = 1; kk < this.maxContraction; kk++) {
var slater = this.htSlaterIDs.get (ids[k] + "_" + kk);
if (slater == null) break;
slater = JU.AU.arrayCopyI (slater, -1);
this.moReader.shells = slaters;
slater[0] = i + 1;
slaters.addLast (slater);
}
}
}
});
Clazz.defineMethod (c$, "getXlink",
function (href, key, addMoleculeID) {
var p = href.indexOf (key + "[") + 1;
var tokens = JU.PT.split (href.substring (p), "'");
var data = new Array (Clazz.doubleToInt (tokens.length / 2));
var molID = (addMoleculeID ? JU.PT.getQuotedAttribute (href.substring (0, p).$replace ('\'', '"'), "molecule[@id") : "");
for (var i = 1, pt = 0; i < tokens.length; i += 2) data[pt++] = molID + tokens[i];
return data;
}, "~S,~S,~B");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlMagResReader", ["JU.Logger"], function () {
c$ = Clazz.declareType (J.adapter.readers.xml, "XmlMagResReader", J.adapter.readers.xml.XmlReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlMagResReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
parent.doProcessLines = true;
this.processXml2 (parent, saxReader);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
if (this.debugging) JU.Logger.debug ("xmlmagres: start " + localName);
if (!this.parent.continuing) return;
if ("calculation".equals (localName)) {
this.setKeepChars (true);
return;
}if ("atoms".equals (localName)) {
this.setKeepChars (true);
return;
}}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if (this.debugging) JU.Logger.debug ("xmlmagres: end " + localName);
while (true) {
if ("calculation".equals (localName)) {
break;
}if (!this.parent.doProcessLines) break;
if ("atoms".equals (localName)) {
break;
}return;
}
this.setKeepChars (false);
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlMOReader"], "J.adapter.readers.xml.XmlMolproReader", ["JU.PT"], function () {
c$ = Clazz.declareType (J.adapter.readers.xml, "XmlMolproReader", J.adapter.readers.xml.XmlMOReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlMolproReader, []);
this.dslist = "d0 d2- d1+ d2+ d1-";
this.fclist = "XXX YYY ZZZ XXY XXZ XYY YYZ XZZ YZZ XYZ";
this.fslist = "f1+ f1- f0 f3+ f2- f3- f2+";
this.iHaveCoefMaps = true;
});
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
if (!this.processing) return;
this.processStart2 (localName);
if (!this.processStartMO (localName)) {
if (localName.equals ("normalcoordinate")) {
this.setKeepChars (false);
if (!this.parent.doGetVibration (++this.vibrationNumber)) return;
try {
this.asc.cloneLastAtomSet ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
System.out.println ("" + e);
this.asc.errorMessage = "Error processing normalCoordinate: " + e.getMessage ();
this.vibrationNumber = 0;
return;
} else {
throw e;
}
}
if (this.atts.containsKey ("wavenumber")) {
var wavenumber = this.atts.get ("wavenumber");
var units = "cm^-1";
if (this.atts.containsKey ("units")) {
units = this.atts.get ("units");
if (units.startsWith ("inverseCent")) units = "cm^-1";
}this.asc.setAtomSetFrequency (null, null, wavenumber, units);
this.setKeepChars (true);
}return;
}if (localName.equals ("vibrations")) {
this.vibrationNumber = 0;
return;
}}}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if (!this.processEndMO (localName)) {
if (localName.equals ("normalcoordinate")) {
if (!this.keepChars) return;
var ac = this.asc.getLastAtomSetAtomCount ();
var baseAtomIndex = this.asc.getLastAtomSetAtomIndex ();
this.tokens = JU.PT.getTokens (this.chars.toString ());
for (var offset = this.tokens.length - ac * 3, i = 0; i < ac; i++) {
this.asc.addVibrationVector (i + baseAtomIndex, this.parseFloatStr (this.tokens[offset++]), this.parseFloatStr (this.tokens[offset++]), this.parseFloatStr (this.tokens[offset++]));
}
this.setKeepChars (false);
}}this.processEnd2 (localName);
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlOdysseyReader", ["java.lang.Float", "JU.P3", "$.PT", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.decorateAsClass (function () {
this.modelName = null;
this.formula = null;
this.phase = null;
this.formalCharge = -2147483648;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlOdysseyReader", J.adapter.readers.xml.XmlReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlOdysseyReader, []);
});
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
if ("structure".equals (localName)) {
this.asc.newAtomSet ();
return;
}if ("atom".equals (localName)) {
var id = this.atts.get ("id");
(this.atom = new J.adapter.smarter.Atom ()).atomName = this.atts.get (this.atts.containsKey ("label") ? "label" : "id");
if (id != null && this.stateScriptVersionInt >= 140400) this.asc.atomSymbolicMap.put (id, this.atom);
if (this.atts.containsKey ("xyz")) {
var xyz = this.atts.get ("xyz");
var tokens = JU.PT.getTokens (xyz);
this.atom.set (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]));
}if (this.atts.containsKey ("element")) {
this.atom.elementSymbol = this.atts.get ("element");
}return;
}if ("bond".equals (localName)) {
var atom1 = this.atts.get ("a");
var atom2 = this.atts.get ("b");
var order = 1;
if (this.atts.containsKey ("order")) order = this.parseBondToken (this.atts.get ("order"));
this.asc.addNewBondFromNames (atom1, atom2, order);
return;
}if ("group".equals (localName)) {
var charge = this.atts.get ("charge");
if (charge != null && charge.indexOf (".") < 0) {
this.formalCharge = JU.PT.parseInt (charge);
}return;
}if ("member".equals (localName) && this.formalCharge != -2147483648) {
var atom = this.asc.getAtomFromName (this.atts.get ("entity"));
if (atom != null) atom.formalCharge = this.formalCharge;
return;
}if ("boundary".equals (localName)) {
var boxDim = JU.PT.getTokens (this.atts.get ("box"));
var x = this.parseFloatStr (boxDim[0]);
var y = this.parseFloatStr (boxDim[1]);
var z = this.parseFloatStr (boxDim[2]);
this.parent.setUnitCellItem (0, x);
this.parent.setUnitCellItem (1, y);
this.parent.setUnitCellItem (2, z);
this.parent.setUnitCellItem (3, 90);
this.parent.setUnitCellItem (4, 90);
this.parent.setUnitCellItem (5, 90);
var pt = JU.P3.new3 (-x / 2, -y / 2, -z / 2);
var atoms = this.asc.atoms;
for (var i = this.asc.ac; --i >= 0; ) {
atoms[i].sub (pt);
this.parent.setAtomCoord (atoms[i]);
}
if (this.parent.latticeCells[0] == 0) this.parent.latticeCells[0] = this.parent.latticeCells[1] = this.parent.latticeCells[2] = 1;
return;
}if ("odyssey_simulation".equals (localName)) {
if (this.modelName != null && this.phase != null) this.modelName += " - " + this.phase;
if (this.modelName != null) this.asc.setAtomSetName (this.modelName);
if (this.formula != null) this.asc.setCurrentModelInfo ("formula", this.formula);
}if ("title".equals (localName) || "formula".equals (localName) || "phase".equals (localName)) this.setKeepChars (true);
}, "~S,~S");
Clazz.defineMethod (c$, "parseBondToken",
function (str) {
if (str.length >= 1) {
switch (str.charAt (0)) {
case 's':
return 1;
case 'd':
return 2;
case 't':
return 3;
case 'a':
return 515;
}
return this.parseIntStr (str);
}return 1;
}, "~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if ("atom".equals (localName)) {
if (this.atom.elementSymbol != null && !Float.isNaN (this.atom.z)) {
this.asc.addAtomWithMappedName (this.atom);
}this.atom = null;
return;
}if ("group".equals (localName)) {
this.formalCharge = -2147483648;
} else if ("title".equals (localName)) {
this.modelName = this.chars.toString ();
} else if ("formula".equals (localName)) {
this.formula = this.chars.toString ();
} else if ("phase".equals (localName)) {
this.phase = this.chars.toString ();
}this.setKeepChars (false);
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlQEReader", ["JU.PT", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.a = 0;
this.b = 0;
this.c = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlQEReader", J.adapter.readers.xml.XmlReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlQEReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
parent.doProcessLines = true;
this.processXml2 (parent, saxReader);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
if (this.debugging) JU.Logger.debug ("xmlqe: start " + localName);
if (!this.parent.continuing) return;
if ("number_of_atoms".equals (localName) || "cell_dimensions".equals (localName) || "at".equals (localName)) {
this.setKeepChars (true);
return;
}if (localName.startsWith ("atom.")) {
this.parent.setAtomCoordScaled (null, JU.PT.getTokens (this.atts.get ("tau")), 0, 0.5291772).elementSymbol = this.atts.get ("species").trim ();
}if ("structure".equals (localName)) {
if (!this.parent.doGetModel (++this.parent.modelNumber, null)) {
this.parent.checkLastModel ();
return;
}this.parent.setFractionalCoordinates (true);
this.asc.doFixPeriodic = true;
this.asc.newAtomSet ();
return;
}if (!this.parent.doProcessLines) return;
}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if (this.debugging) JU.Logger.debug ("xmlqe: end " + localName);
while (true) {
if (!this.parent.doProcessLines) break;
if ("cell_dimensions".equals (localName)) {
this.parent.setFractionalCoordinates (true);
var data = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.chars.toString (), null, 6);
this.a = data[0];
this.b = (data[1] == 0 ? this.a : data[1]);
this.c = (data[2] == 0 ? this.a : data[2]);
break;
}if ("at".equals (localName)) {
var m = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.chars.toString (), null, 9);
for (var i = 0; i < 9; i += 3) {
m[i] *= this.a;
m[i + 1] *= this.b;
m[i + 2] *= this.c;
}
this.parent.addExplicitLatticeVector (0, m, 0);
this.parent.addExplicitLatticeVector (1, m, 3);
this.parent.addExplicitLatticeVector (2, m, 6);
break;
}if ("geometry_info".equals (localName)) {
try {
this.parent.applySymmetryAndSetTrajectory ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
break;
}return;
}
this.setKeepChars (false);
}, "~S");
});

205
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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "JU.SB"], "J.adapter.readers.xml.XmlReader", ["java.io.BufferedInputStream", "java.util.Hashtable", "JU.Rdr", "J.adapter.smarter.AtomSetCollection", "$.Resolver", "J.api.Interface", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.atom = null;
this.bond = null;
this.parent = null;
this.atts = null;
this.keepChars = false;
this.chars = null;
this.domObj = null;
this.attribs = null;
this.attArgs = null;
this.nullObj = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.chars = JU.SB.newN (2000);
this.domObj = new Array (1);
this.nullObj = new Array (0);
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.initCML ();
});
Clazz.defineMethod (c$, "initCML",
function () {
this.atts = new java.util.Hashtable ();
this.setMyError (this.parseXML ());
this.continuing = false;
});
Clazz.defineMethod (c$, "setMyError",
function (err) {
if (err != null && (this.asc == null || this.asc.errorMessage == null)) {
this.asc = new J.adapter.smarter.AtomSetCollection ("xml", this, null, null);
this.asc.errorMessage = err;
}}, "~S");
Clazz.defineMethod (c$, "parseXML",
function () {
var saxReader = null;
{
}return this.selectReaderAndGo (saxReader);
});
Clazz.defineMethod (c$, "selectReaderAndGo",
function (saxReader) {
this.asc = new J.adapter.smarter.AtomSetCollection (this.readerName, this, null, null);
var className = null;
var thisReader = null;
var pt = this.readerName.indexOf ("(");
var name = (pt < 0 ? this.readerName : this.readerName.substring (0, pt));
className = J.adapter.smarter.Resolver.getReaderClassBase (name);
if ((thisReader = this.getInterface (className)) == null) return "File reader was not found: " + className;
try {
thisReader.processXml (this, saxReader);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
return "Error reading XML: " + ((this.parent == null ? this.vwr : this.parent.vwr).isJS ? e : e.getMessage ());
} else {
throw e;
}
}
return null;
}, "~O");
Clazz.defineMethod (c$, "processXml",
function (parent, saxReader) {
this.processXml2 (parent, saxReader);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.defineMethod (c$, "processXml2",
function (parent, saxReader) {
this.parent = parent;
this.asc = parent.asc;
this.reader = parent.reader;
this.atts = parent.atts;
if (saxReader == null) {
this.attribs = new Array (1);
this.attArgs = new Array (1);
this.domObj = new Array (1);
var o = "";
var data = null;
{
o = this.reader.lock.lock; if (o.$in) data = o.$in.buf;
}if (Clazz.instanceOf (o, java.io.BufferedInputStream)) o = JU.Rdr.StreamToUTF8String (JU.Rdr.getBIS (data));
{
this.domObj[0] = this.createDomNodeJS("xmlReader",o);
this.walkDOMTree(); this.createDomNodeJS("xmlReader",null);
}} else {
(J.api.Interface.getOption ("adapter.readers.xml.XmlHandler", this.vwr, "file")).parseXML (this, saxReader, this.reader);
}}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.defineMethod (c$, "createDomNodeJS",
function (id, data) {
var applet = this.parent.vwr.html5Applet;
{
// id = applet._id + "_" + id;
// var d = document.getElementById(id);
// if (d)
// document.body.removeChild(d);
if (!data)
return;
if (data.indexOf("<?") == 0)
data = data.substring(data.indexOf("<", 1));
if (data.indexOf("/>") >= 0) {
var D = data.split("/>");
for (var i = D.length - 1; --i >= 0;) {
var s = D[i];
var pt = s.lastIndexOf("<") + 1;
var pt2 = pt;
var len = s.length;
var name = "";
while (++pt2 < len) {
if (" \t\n\r".indexOf(s.charAt(pt2))>= 0) {
var name = s.substring(pt, pt2);
D[i] = s + "></"+name+">";
break;
}
}
}
data = D.join('');
}
var d = document.createElement("_xml");
d.innerHTML = data;
return d;
}}, "~S,~O");
Clazz.overrideMethod (c$, "applySymmetryAndSetTrajectory",
function () {
try {
if (this.parent == null) this.applySymTrajASCR ();
else this.parent.applySymmetryAndSetTrajectory ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
System.out.println ((this.parent == null ? this : this.parent).vwr.isJS ? e : e.getMessage ());
JU.Logger.error ("applySymmetry failed: " + e);
} else {
throw e;
}
}
});
Clazz.overrideMethod (c$, "processDOM",
function (DOMNode) {
this.domObj = Clazz.newArray (-1, [DOMNode]);
this.setMyError (this.selectReaderAndGo (null));
}, "~O");
Clazz.defineMethod (c$, "processStartElement",
function (localName, nodeName) {
}, "~S,~S");
Clazz.defineMethod (c$, "setKeepChars",
function (TF) {
this.keepChars = TF;
this.chars.setLength (0);
}, "~B");
Clazz.defineMethod (c$, "processEndElement",
function (localName) {
}, "~S");
Clazz.defineMethod (c$, "walkDOMTree",
function () {
var localName;
{
localName = "nodeName";
}var nodeName = (this.jsObjectGetMember (this.domObj, localName));
localName = this.fixLocal (nodeName);
if (localName == null) return;
if (localName.equals ("#text")) {
if (this.keepChars) this.chars.append (this.jsObjectGetMember (this.domObj, "data"));
return;
}localName = localName.toLowerCase ();
nodeName = nodeName.toLowerCase ();
this.attribs[0] = this.jsObjectGetMember (this.domObj, "attributes");
this.getDOMAttributesA (this.attribs);
this.processStartElement (localName, nodeName);
var haveChildren;
{
haveChildren = this.domObj[0].hasChildNodes;
}if (haveChildren) {
var nextNode = this.jsObjectGetMember (this.domObj, "firstChild");
while (nextNode != null) {
this.domObj[0] = nextNode;
this.walkDOMTree ();
this.domObj[0] = nextNode;
nextNode = this.jsObjectGetMember (this.domObj, "nextSibling");
}
}this.processEndElement (localName);
});
Clazz.defineMethod (c$, "fixLocal",
function (name) {
{
var pt = (name== null ? -1 : name.indexOf(":")); return (pt >=
0 ? name.substring(pt+1) : name);
}}, "~S");
Clazz.defineMethod (c$, "getDOMAttributesA",
function (attributes) {
this.atts.clear ();
if (attributes == null) return;
{
var nodes = attributes[0]; for (var i = nodes.length; --i >=
0;) { var key = this.fixLocal(nodes[i].name);
this.atts.put(key.toLowerCase(), nodes[i].value); }
return;
}}, "~A");
Clazz.defineMethod (c$, "jsObjectGetMember",
function (jsObject, name) {
{
return jsObject[0][name];
}}, "~A,~S");
Clazz.defineMethod (c$, "endDocument",
function () {
});
});

159
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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader"], "J.adapter.readers.xml.XmlVaspReader", ["java.lang.Double", "JU.PT", "$.SB", "$.V3", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.data = null;
this.name = null;
this.ac = 0;
this.iAtom = 0;
this.isE_wo_entrp = false;
this.isE_fr_energy = false;
this.enthalpy = null;
this.gibbsEnergy = null;
this.haveUnitCell = false;
this.atomNames = null;
this.atomSyms = null;
this.atomName = null;
this.atomSym = null;
this.a = 0;
this.b = 0;
this.c = 0;
this.alpha = 0;
this.beta = 0;
this.gamma = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlVaspReader", J.adapter.readers.xml.XmlReader);
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlVaspReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
parent.doProcessLines = true;
this.processXml2 (parent, saxReader);
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
if (this.debugging) JU.Logger.debug ("xmlvasp: start " + localName);
if (!this.parent.continuing) return;
if ("calculation".equals (localName)) {
this.enthalpy = null;
this.gibbsEnergy = null;
return;
}if ("i".equals (localName)) {
var s = this.atts.get ("name");
if (s.charAt (0) != 'e') return;
this.isE_wo_entrp = s.equals ("e_wo_entrp");
this.isE_fr_energy = s.equals ("e_fr_energy");
this.setKeepChars (this.isE_wo_entrp || this.isE_fr_energy);
return;
}if ("structure".equals (localName)) {
if (!this.parent.doGetModel (++this.parent.modelNumber, null)) {
this.parent.checkLastModel ();
return;
}this.parent.setFractionalCoordinates (true);
this.asc.doFixPeriodic = true;
this.asc.newAtomSet ();
if (this.enthalpy != null) {
this.asc.setCurrentModelInfo ("enthalpy", Double.$valueOf (JU.PT.dVal (this.enthalpy)));
}if (this.gibbsEnergy != null) {
this.asc.setAtomSetEnergy ("" + this.gibbsEnergy, this.parseFloatStr (this.gibbsEnergy));
this.asc.setCurrentModelInfo ("gibbsEnergy", Double.$valueOf (JU.PT.dVal (this.gibbsEnergy)));
}if (this.enthalpy != null && this.gibbsEnergy != null) this.asc.setAtomSetName ("Enthalpy = " + this.enthalpy + " eV Gibbs Energy = " + this.gibbsEnergy + " eV");
return;
}if (!this.parent.doProcessLines) return;
if ("v".equals (localName)) {
this.setKeepChars (this.data != null);
return;
}if ("c".equals (localName)) {
this.setKeepChars (this.iAtom < this.ac);
return;
}if ("varray".equals (localName)) {
this.name = this.atts.get ("name");
if (this.name != null && JU.PT.isOneOf (this.name, ";basis;positions;forces;")) this.data = new JU.SB ();
return;
}if ("atoms".equals (localName)) {
this.setKeepChars (true);
return;
}}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if (this.debugging) JU.Logger.debug ("xmlvasp: end " + localName);
while (true) {
if (!this.parent.doProcessLines) break;
if (this.isE_wo_entrp) {
this.isE_wo_entrp = false;
this.enthalpy = this.chars.toString ().trim ();
break;
}if (this.isE_fr_energy) {
this.isE_fr_energy = false;
this.gibbsEnergy = this.chars.toString ().trim ();
break;
}if ("v".equals (localName) && this.data != null) {
this.data.append (this.chars.toString ());
break;
}if ("c".equals (localName)) {
if (this.iAtom < this.ac) {
if (this.atomName == null) {
this.atomName = this.atomSym = this.chars.toString ().trim ();
} else {
this.atomNames[this.iAtom++] = this.atomName + this.chars.toString ().trim ();
this.atomName = null;
}}break;
}if ("atoms".equals (localName)) {
this.ac = this.parseIntStr (this.chars.toString ());
this.atomNames = new Array (this.ac);
this.atomSyms = new Array (this.ac);
this.iAtom = 0;
break;
}if ("varray".equals (localName) && this.data != null) {
if (this.name == null) {
} else if ("basis".equals (this.name) && !this.haveUnitCell) {
this.haveUnitCell = true;
var ijk = J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.data.toString (), null, 9);
var va = JU.V3.new3 (ijk[0], ijk[1], ijk[2]);
var vb = JU.V3.new3 (ijk[3], ijk[4], ijk[5]);
var vc = JU.V3.new3 (ijk[6], ijk[7], ijk[8]);
this.a = va.length ();
this.b = vb.length ();
this.c = vc.length ();
va.normalize ();
vb.normalize ();
vc.normalize ();
this.alpha = (Math.acos (vb.dot (vc)) * 180 / 3.141592653589793);
this.beta = (Math.acos (va.dot (vc)) * 180 / 3.141592653589793);
this.gamma = (Math.acos (va.dot (vb)) * 180 / 3.141592653589793);
} else if ("positions".equals (this.name)) {
this.parent.setUnitCell (this.a, this.b, this.c, this.alpha, this.beta, this.gamma);
var fdata = Clazz.newFloatArray (this.ac * 3, 0);
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.data.toString (), fdata, this.ac * 3);
var fpt = 0;
for (var i = 0; i < this.ac; i++) {
var atom = this.asc.addNewAtom ();
this.parent.setAtomCoordXYZ (atom, fdata[fpt++], fdata[fpt++], fdata[fpt++]);
atom.elementSymbol = this.atomSyms[i];
atom.atomName = this.atomNames[i];
}
} else if ("forces".equals (this.name)) {
var fdata = Clazz.newFloatArray (this.ac * 3, 0);
J.adapter.smarter.AtomSetCollectionReader.getTokensFloat (this.data.toString (), fdata, this.ac * 3);
var fpt = 0;
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0; i < this.ac; i++) this.asc.addVibrationVector (i0 + i, fdata[fpt++], fdata[fpt++], fdata[fpt++]);
}this.data = null;
break;
}if ("structure".equals (localName)) {
try {
this.parent.applySymmetryAndSetTrajectory ();
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
} else {
throw e;
}
}
break;
}return;
}
this.setKeepChars (false);
}, "~S");
});

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Clazz.declarePackage ("J.adapter.readers.xml");
Clazz.load (["J.adapter.readers.xml.XmlReader", "JU.BS"], "J.adapter.readers.xml.XmlXsdReader", ["java.lang.Float", "JU.PT", "J.adapter.smarter.Atom"], function () {
c$ = Clazz.decorateAsClass (function () {
this.bsBackbone = null;
this.iChain = -1;
this.iGroup = 0;
this.iAtom = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xml, "XmlXsdReader", J.adapter.readers.xml.XmlReader);
Clazz.prepareFields (c$, function () {
this.bsBackbone = new JU.BS ();
});
Clazz.makeConstructor (c$,
function () {
Clazz.superConstructor (this, J.adapter.readers.xml.XmlXsdReader, []);
});
Clazz.overrideMethod (c$, "processXml",
function (parent, saxReader) {
parent.htParams.put ("backboneAtoms", this.bsBackbone);
this.processXml2 (parent, saxReader);
this.asc.atomSymbolicMap.clear ();
}, "J.adapter.readers.xml.XmlReader,~O");
Clazz.overrideMethod (c$, "processStartElement",
function (localName, nodeName) {
var tokens;
if ("molecule".equals (localName)) {
this.asc.newAtomSet ();
this.asc.setAtomSetName (this.atts.get ("name"));
return;
}if ("linearchain".equals (localName)) {
this.iGroup = 0;
this.iChain++;
}if ("repeatunit".equals (localName)) {
this.iGroup++;
}if ("atom3d".equals (localName)) {
this.atom = new J.adapter.smarter.Atom ();
this.atom.elementSymbol = this.atts.get ("components");
this.atom.atomName = this.atts.get ("id");
this.atom.atomSerial = ++this.iAtom;
if (this.iChain >= 0) this.parent.setChainID (this.atom, "" + String.fromCharCode ((this.iChain - 1) % 26 + 65));
this.atom.group3 = "UNK";
if (this.iGroup == 0) this.iGroup = 1;
this.atom.sequenceNumber = this.iGroup;
var xyz = this.atts.get ("xyz");
if (xyz != null) {
tokens = JU.PT.getTokens (xyz.$replace (',', ' '));
this.atom.set (this.parseFloatStr (tokens[0]), this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]));
}var isBackbone = "1".equals (this.atts.get ("isbackboneatom"));
if (isBackbone) this.bsBackbone.set (this.iAtom);
return;
}if ("bond".equals (localName)) {
var atoms = JU.PT.split (this.atts.get ("connects"), ",");
var order = 1;
if (this.atts.containsKey ("type")) {
var type = this.atts.get ("type");
if (type.equals ("Double")) order = 2;
else if (type.equals ("Triple")) order = 3;
}this.asc.addNewBondFromNames (atoms[0], atoms[1], order);
return;
}}, "~S,~S");
Clazz.overrideMethod (c$, "processEndElement",
function (localName) {
if ("atom3d".equalsIgnoreCase (localName)) {
if (this.atom.elementSymbol != null && !Float.isNaN (this.atom.z)) {
this.parent.setAtomCoord (this.atom);
this.asc.addAtomWithMappedName (this.atom);
}this.atom = null;
return;
}this.setKeepChars (false);
}, "~S");
});

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CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/AbinitReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.AbinitReader", null, function () {
c$ = Clazz.decorateAsClass (function () {
this.znucl = null;
this.inputOnly = false;
this.nAtom = 0;
this.nType = 0;
this.typeArray = null;
this.cellLattice = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "AbinitReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setSpaceGroupName ("P1");
this.doApplySymmetry = true;
this.setFractionalCoordinates (false);
this.inputOnly = this.checkFilterKey ("INPUT");
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains ("natom")) {
this.readNoatom ();
} else if (this.line.contains ("ntypat") || this.line.contains ("ntype")) {
this.readNotypes ();
} else if (this.line.contains ("typat") || this.line.contains ("type")) {
this.readTypesequence ();
} else if (this.line.contains ("Pseudopotential")) {
this.readAtomSpecies ();
} else if (this.line.contains ("Symmetries :")) {
this.readSpaceGroup ();
} else if (this.line.contains ("Real(R)+Recip(G)")) {
this.readIntiallattice ();
if (this.inputOnly) this.continuing = false;
} else if (this.line.contains ("xcart")) {
this.readAtoms ();
}return true;
});
Clazz.defineMethod (c$, "readNoatom",
function () {
var tokens = this.getTokens ();
if (tokens.length <= 2) this.nAtom = this.parseIntStr (tokens[1]);
});
Clazz.defineMethod (c$, "readNotypes",
function () {
var tokens = this.getTokens ();
if (tokens.length <= 2) this.nType = this.parseIntStr (tokens[1]);
});
Clazz.defineMethod (c$, "readTypesequence",
function () {
this.fillFloatArray (this.line.substring (12), 0, this.typeArray = Clazz.newFloatArray (this.nAtom, 0));
});
Clazz.defineMethod (c$, "readAtomSpecies",
function () {
this.znucl = Clazz.newFloatArray (this.nType, 0);
for (var i = 0; i < this.nType; i++) {
this.discardLinesUntilContains ("zion");
var tokens = this.getTokens ();
this.znucl[i] = this.parseFloatStr (tokens[tokens[0] === "-" ? 1 : 0]);
}
});
Clazz.defineMethod (c$, "readSpaceGroup",
function () {
});
Clazz.defineMethod (c$, "readIntiallattice",
function () {
var f = 0;
this.cellLattice = Clazz.newFloatArray (9, 0);
for (var i = 0; i < 9; i++) {
if (i % 3 == 0) {
this.line = this.rd ().substring (6);
f = this.parseFloatStr (this.line);
}this.cellLattice[i] = f * 0.5291772;
f = this.parseFloat ();
}
this.applySymmetry ();
});
Clazz.defineMethod (c$, "applySymmetry",
function () {
if (this.cellLattice == null) return;
this.setSpaceGroupName ("P1");
for (var i = 0; i < 3; i++) this.addExplicitLatticeVector (i, this.cellLattice, i * 3);
var atoms = this.asc.atoms;
var i0 = this.asc.getAtomSetAtomIndex (this.asc.iSet);
if (!this.iHaveFractionalCoordinates) for (var i = this.asc.ac; --i >= i0; ) this.setAtomCoord (atoms[i]);
this.applySymmetryAndSetTrajectory ();
});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.asc.newAtomSet ();
this.iHaveFractionalCoordinates = false;
var i0 = this.asc.ac;
this.line = this.line.substring (12);
while (this.line != null && !this.line.contains ("x")) {
var atom = this.asc.addNewAtom ();
this.setAtomCoordScaled (atom, this.getTokens (), 0, 0.5291772);
this.rd ();
}
this.discardLinesUntilContains ("z");
if (this.znucl == null) this.fillFloatArray (this.line.substring (12), 0, this.znucl = Clazz.newFloatArray (this.nType, 0));
var atoms = this.asc.atoms;
for (var i = 0; i < this.nAtom; i++) atoms[i + i0].elementNumber = Clazz.floatToShort (this.znucl[Clazz.floatToInt (this.typeArray[i]) - 1]);
this.applySymmetry ();
});
});

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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.AimsReader", ["JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.globalDoApplySymmetry = false;
this.isFractional = false;
this.nLatticeVectors = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "AimsReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.globalDoApplySymmetry = this.doApplySymmetry;
this.doApplySymmetry = true;
this.isFractional = true;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var tokens = this.getTokens ();
if (tokens.length == 0) return true;
if (tokens[0].equals ("lattice_vector")) {
this.readLatticeVector (tokens);
return true;
}if (tokens[0].equals ("atom")) {
this.readAtom (tokens, false);
return true;
}if (tokens[0].equals ("atom_frac")) {
this.readAtom (tokens, true);
return true;
}if (tokens[0].equals ("multipole")) {
this.readMultipole (tokens);
return true;
}return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.doApplySymmetry = this.globalDoApplySymmetry;
if (this.nLatticeVectors == 1 || this.nLatticeVectors == 2) {
JU.Logger.warn ("ignoring translation symmetry for more or less than 3 dimensions(which is currently neither supported by FHI-aims");
}this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "readLatticeVector",
function (tokens) {
if (tokens.length < 4) {
JU.Logger.warn ("cannot read line with FHI-aims lattice vector: " + this.line);
} else if (this.nLatticeVectors == 3) {
JU.Logger.warn ("more than 3 FHI-aims lattice vectors found with line: " + this.line);
} else {
this.addExplicitLatticeVector (this.nLatticeVectors++, Clazz.newFloatArray (-1, [this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3])]), 0);
this.setFractionalCoordinates (this.nLatticeVectors == 3);
}}, "~A");
Clazz.defineMethod (c$, "readAtom",
function (tokens, isFractional) {
if (tokens.length < 5) {
JU.Logger.warn ("cannot read line with FHI-aims line: " + this.line);
return;
}if (this.isFractional != isFractional) this.setFractionalCoordinates (this.isFractional = isFractional);
this.addAtomXYZSymName (tokens, 1, tokens[4], null);
}, "~A,~B");
Clazz.defineMethod (c$, "readMultipole",
function (tokens) {
if (tokens.length < 6) {
JU.Logger.warn ("cannot read line with FHI-aims atom data: " + this.line);
return;
}var order = this.parseIntStr (tokens[4]);
if (order > 0) {
JU.Logger.warn ("multipole line ignored since only monopoles are currently supported: " + this.line);
return;
}if (this.isFractional) this.setFractionalCoordinates (this.isFractional = false);
this.addAtomXYZSymName (tokens, 1, null, null).partialCharge = this.parseFloatStr (tokens[5]);
}, "~A");
});

161
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.BilbaoReader", ["java.lang.Float", "JU.PT", "$.SB", "$.V3", "JU.Vibration"], function () {
c$ = Clazz.decorateAsClass (function () {
this.getHigh = false;
this.getSym = false;
this.normDispl = false;
this.doDisplace = false;
this.kvec = null;
this.i0 = 0;
this.nAtoms = 0;
this.isBCSfile = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "BilbaoReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.normDispl = !this.checkFilterKey ("NONORM");
this.doDisplace = this.isTrajectory;
this.getSym = true;
this.getHigh = this.checkFilterKey ("HIGH") && !this.doDisplace;
this.asc.vibScale = 1;
this.appendLoadNote ("Bilbao Crystallographic Server\ncryst@wm.lc.ehu.es");
if (this.rd ().indexOf ("<") < 0) {
this.readBilbaoDataFile ();
this.continuing = false;
}});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains (">Bilbao Crystallographic Server<")) {
this.line = this.line.substring (this.line.lastIndexOf (">") + 1).trim ();
if (this.line.length > 0) this.appendLoadNote (this.line + "\n");
} else if (this.line.contains ("High symmetry structure<")) {
if (this.getHigh) this.readBilbaoFormat ("high symmetry", NaN);
} else if (this.line.contains ("Low symmetry structure<")) {
if (!this.doDisplace) this.readBilbaoFormat ("low symmetry", NaN);
} else if (this.line.contains ("structure in the subgroup basis<")) {
if (!this.doDisplace) this.readBilbaoFormat ("high symmetry in the subgroup basis", NaN);
} else if (this.line.contains ("Low symmetry structure after the origin shift<")) {
this.readBilbaoFormat ("low symmetry after origin shift", NaN);
} else if (this.line.contains ("<h3>Irrep:")) {
this.readVirtual ();
}return true;
});
Clazz.defineMethod (c$, "readBilbaoDataFile",
function () {
this.isBCSfile = true;
this.checkComment ();
while (this.line != null) {
this.readBilbaoFormat (null, NaN);
if (this.rdLine () == null || this.line.indexOf ("##disp-par##") < 0) {
this.applySymmetryAndSetTrajectory ();
} else {
this.readDisplacements (1);
this.rdLine ();
}}
});
Clazz.defineMethod (c$, "checkComment",
function () {
if (!this.line.startsWith ("#") || this.line.indexOf ("disp-par") >= 0) return false;
if (this.isBCSfile) {
this.appendLoadNote (this.line);
if (this.line.startsWith ("# Title:")) this.asc.setAtomSetName (this.line.substring (8).trim ());
}return true;
});
Clazz.defineMethod (c$, "readBilbaoFormat",
function (title, fAmp) {
this.setFractionalCoordinates (true);
if (!this.doGetModel (++this.modelNumber, title)) return;
this.asc.newAtomSet ();
if (this.line.startsWith ("Bilbao Crys:")) {
title = this.line.substring (13).trim ();
this.rdLine ();
}this.setTitle (title);
var ptPre = this.line.indexOf ("<pre>");
if (ptPre >= 0) this.line = this.line.substring (ptPre + 5);
var intTableNo = this.parseIntStr (this.line);
if (intTableNo == 0) {
this.setSpaceGroupName ("bilbao:" + this.line.substring (2));
} else {
while (intTableNo < 0 && this.rdLine () != null) intTableNo = this.parseIntStr (this.line);
this.setSpaceGroupName ("bilbao:" + intTableNo);
}var data = Clazz.newFloatArray (6, 0);
this.fillFloatArray (null, 0, data);
for (var i = 0; i < 6; i++) this.setUnitCellItem (i, data[i]);
this.i0 = this.asc.ac;
this.nAtoms = this.parseIntStr (this.rdLine ());
for (var i = this.nAtoms; --i >= 0; ) {
var tokens = JU.PT.getTokens (this.rdLine ());
if (!this.getSym && tokens[1].contains ("_")) continue;
if (tokens.length == 3) this.addAtomXYZSymName (tokens, 0, "Be", "Be1");
else this.addAtomXYZSymName (tokens, 3, tokens[0], tokens[0] + tokens[1]);
}
if (Float.isNaN (fAmp)) {
if (ptPre >= 0) this.applySymmetryAndSetTrajectory ();
return;
}this.line = null;
this.readDisplacements (fAmp);
}, "~S,~N");
Clazz.defineMethod (c$, "readDisplacements",
function (fAmp) {
for (var i = 0; i < this.nAtoms; i++) {
if (this.line == null) this.rdLine ();
var tokens = JU.PT.split (this.line, "x|x");
if (this.getSym || !tokens[0].contains ("_")) this.asc.atoms[this.i0 + i].vib = JU.V3.new3 (this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[2]), this.parseFloatStr (tokens[3]));
this.line = null;
}
this.applySymmetryAndSetTrajectory ();
for (var i = this.asc.ac; --i >= this.i0; ) {
var a = this.asc.atoms[i];
if (a.vib != null) {
var v = new JU.Vibration ();
v.setT (a.vib);
a.vib = v;
this.asc.getSymmetry ().toCartesian (v, true);
v.scale (1 / fAmp);
}}
this.appendLoadNote ((this.asc.ac - this.i0) + " displacements");
}, "~N");
Clazz.defineMethod (c$, "setTitle",
function (title) {
if (title != null) {
this.asc.setAtomSetName (title);
this.appendLoadNote (title);
}}, "~S");
Clazz.defineMethod (c$, "rdLine",
function () {
while (this.rd () != null && (this.line.length == 0 || this.checkComment ())) {
}
return this.line;
});
Clazz.defineMethod (c$, "readVirtual",
function () {
if (this.line.contains ("<h3>K-vector:")) this.kvec = this.line.substring (this.line.indexOf ("("), this.line.indexOf (")") + 1);
var s = this.getLinesUntil ("\"BCS\"");
var pt = s.indexOf ("The amplitude");
pt = s.indexOf ("=", pt);
var amp = s.substring (pt + 2, s.indexOf (" ", pt + 2));
var fAmp = (this.normDispl ? this.parseFloatStr (amp) : 1);
var irrep = this.getAttr (s, "irrep");
if (irrep.indexOf (":") >= 0) irrep = irrep.substring (0, irrep.indexOf (":"));
this.line = this.line.substring (this.line.indexOf ("value=") + 7);
this.readBilbaoFormat (this.kvec + " " + irrep + " (" + amp + " Ang.)", fAmp);
});
Clazz.defineMethod (c$, "getAttr",
function (s, key) {
var pt = s.indexOf ("value", s.indexOf ("\"" + key + "\""));
s = JU.PT.getQuotedStringAt (s, pt);
s = JU.PT.rep (s, "<i>", "");
s = JU.PT.rep (s, "</i>", "");
return s.trim ();
}, "~S,~S");
Clazz.defineMethod (c$, "getLinesUntil",
function (key) {
var sb = new JU.SB ();
do {
sb.append (this.line);
} while (!this.rd ().contains (key));
return sb.toString ();
}, "~S");
});

523
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.CastepReader", ["java.lang.Double", "$.Float", "JU.DF", "$.Lst", "$.M4", "$.P3", "$.PT", "$.V3", "J.adapter.smarter.Atom", "JU.Escape", "$.Logger", "$.Tensor"], function () {
c$ = Clazz.decorateAsClass (function () {
this.tokens = null;
this.isPhonon = false;
this.isTS = false;
this.isOutput = false;
this.isCell = false;
this.a = 0;
this.b = 0;
this.c = 0;
this.alpha = 0;
this.beta = 0;
this.gamma = 0;
this.abc = null;
this.ac = 0;
this.atomPts = null;
this.havePhonons = false;
this.lastQPt = null;
this.qpt2 = 0;
this.desiredQpt = null;
this.desiredQ = null;
this.chargeType = "MULL";
this.isAllQ = false;
this.haveCharges = false;
this.tsType = null;
this.matSupercell = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "CastepReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.abc = new Array (3);
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
if (this.filter != null) {
this.chargeType = this.getFilter ("CHARGE=");
if (this.chargeType != null && this.chargeType.length > 4) this.chargeType = this.chargeType.substring (0, 4);
this.filter = this.filter.$replace ('(', '{').$replace (')', '}');
this.filter = JU.PT.rep (this.filter, " ", " ");
this.isAllQ = this.checkFilterKey ("Q=ALL");
this.tsType = this.getFilter ("TSTYPE=");
if (!this.isAllQ && this.filter.indexOf ("{") >= 0) this.setDesiredQpt (this.filter.substring (this.filter.indexOf ("{")));
this.filter = JU.PT.rep (this.filter, "-PT", "");
}this.continuing = this.readFileData ();
});
Clazz.defineMethod (c$, "setDesiredQpt",
function (s) {
this.desiredQpt = new JU.V3 ();
this.desiredQ = "";
var num = 1;
var denom = 1;
var ipt = 0;
var xyz = 0;
var useSpace = (s.indexOf (',') < 0);
for (var i = 0; i < s.length; i++) {
var c = s.charAt (i);
switch (c) {
case '{':
ipt = i + 1;
num = 1;
denom = 1;
break;
case '/':
num = this.parseFloatStr (s.substring (ipt, i));
ipt = i + 1;
denom = 0;
break;
case ',':
case ' ':
case '}':
if (c == '}') this.desiredQ = s.substring (0, i + 1);
else if ((c == ' ') != useSpace) break;
if (denom == 0) {
denom = this.parseFloatStr (s.substring (ipt, i));
} else {
num = this.parseFloatStr (s.substring (ipt, i));
}num /= denom;
switch (xyz++) {
case 0:
this.desiredQpt.x = num;
break;
case 1:
this.desiredQpt.y = num;
break;
case 2:
this.desiredQpt.z = num;
break;
}
denom = 1;
if (c == '}') i = s.length;
ipt = i + 1;
break;
}
}
JU.Logger.info ("Looking for q-pt=" + this.desiredQpt);
}, "~S");
Clazz.defineMethod (c$, "readFileData",
function () {
while (this.tokenizeCastepCell () > 0) if (this.tokens.length >= 2 && this.tokens[0].equalsIgnoreCase ("%BLOCK")) {
JU.Logger.info (this.line);
if (this.tokens[1].equalsIgnoreCase ("LATTICE_ABC")) {
this.readLatticeAbc ();
continue;
}if (this.tokens[1].equalsIgnoreCase ("LATTICE_CART")) {
this.readLatticeCart ();
continue;
}if (this.tokens[1].equalsIgnoreCase ("POSITIONS_FRAC")) {
this.setFractionalCoordinates (true);
this.readPositionsFrac ();
continue;
}if (this.tokens[1].equalsIgnoreCase ("POSITIONS_ABS")) {
this.setFractionalCoordinates (false);
this.readPositionsAbs ();
continue;
}}
if (this.isPhonon || this.isOutput || this.isTS) {
if (this.isPhonon) {
this.isTrajectory = (this.desiredVibrationNumber <= 0);
this.asc.allowMultiple = false;
}return true;
}return false;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.isOutput) {
if (this.line.contains ("Real Lattice(A)")) {
this.readOutputUnitCell ();
} else if (this.line.contains ("Fractional coordinates of atoms")) {
if (this.doGetModel (++this.modelNumber, null)) {
this.readOutputAtoms ();
}} else if (this.doProcessLines && (this.line.contains ("Atomic Populations (Mulliken)") || this.line.contains ("Hirshfield Charge (e)"))) {
this.readOutputCharges ();
} else if (this.doProcessLines && this.line.contains ("Born Effective Charges")) {
this.readOutputBornChargeTensors ();
} else if (this.line.contains ("Final energy ")) {
this.readEnergy (3, null);
} else if (this.line.contains ("Dispersion corrected final energy*")) {
this.readEnergy (5, null);
} else if (this.line.contains ("Total energy corrected")) {
this.readEnergy (8, null);
}return true;
}if (this.line.contains ("<-- E")) {
this.readPhononTrajectories ();
return true;
}if (this.line.indexOf ("Unit cell vectors") == 1) {
this.readPhononUnitCell ();
return true;
}if (this.line.indexOf ("Fractional Co-ordinates") >= 0) {
this.readPhononFractionalCoord ();
return true;
}if (this.line.indexOf ("q-pt") >= 0) {
this.readPhononFrequencies ();
return true;
}return true;
});
Clazz.defineMethod (c$, "readOutputUnitCell",
function () {
this.applySymmetryAndSetTrajectory ();
this.asc.newAtomSetClear (false);
this.setFractionalCoordinates (true);
this.abc = this.read3Vectors (false);
this.setLatticeVectors ();
});
Clazz.defineMethod (c$, "readOutputAtoms",
function () {
this.readLines (2);
while (this.rd ().indexOf ("xxx") < 0) {
var atom = new J.adapter.smarter.Atom ();
this.tokens = this.getTokens ();
atom.elementSymbol = this.tokens[1];
atom.atomName = this.tokens[1] + this.tokens[2];
this.asc.addAtomWithMappedName (atom);
this.setAtomCoordTokens (atom, this.tokens, 3);
}
});
Clazz.defineMethod (c$, "readEnergy",
function (pt, prefix) {
if (this.isTrajectory) this.applySymmetryAndSetTrajectory ();
this.tokens = this.getTokens ();
try {
var energy = Double.$valueOf (Double.parseDouble (this.tokens[pt]));
this.asc.setAtomSetName (prefix + "Energy = " + energy + " eV");
this.asc.setAtomSetEnergy ("" + energy, energy.floatValue ());
this.asc.setCurrentModelInfo ("Energy", energy);
} catch (e) {
if (Clazz.exceptionOf (e, Exception)) {
this.appendLoadNote ("CASTEP Energy could not be read: " + this.line);
} else {
throw e;
}
}
}, "~N,~S");
Clazz.defineMethod (c$, "readPhononTrajectories",
function () {
if (!this.isTS) this.isTrajectory = (this.desiredVibrationNumber <= 0);
if (this.isTrajectory) this.asc.setTrajectory ();
this.doApplySymmetry = true;
while (this.line != null && this.line.contains ("<-- E")) {
var skip = (this.isTS && this.tsType != null && this.prevline.indexOf (this.tsType) < 0);
if (!skip) {
this.asc.newAtomSetClear (false);
if (this.isTS) this.readEnergy (0, JU.PT.getTokens (this.prevline + " -")[0] + " ");
this.discardLinesUntilContains ("<-- h");
this.setSpaceGroupName ("P1");
this.abc = this.read3Vectors (true);
this.setLatticeVectors ();
this.setFractionalCoordinates (false);
this.discardLinesUntilContains ("<-- R");
while (this.line != null && this.line.contains ("<-- R")) {
this.tokens = this.getTokens ();
this.setAtomCoordScaled (null, this.tokens, 2, 0.5291772).elementSymbol = this.tokens[0];
this.rd ();
}
this.applySymmetryAndSetTrajectory ();
}this.discardLinesUntilContains ("<-- E");
}
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (this.isPhonon || this.isOutput || this.isTS) {
this.isTrajectory = false;
} else {
this.doApplySymmetry = true;
this.setLatticeVectors ();
var nAtoms = this.asc.ac;
for (var i = 0; i < nAtoms; i++) this.setAtomCoord (this.asc.atoms[i]);
}this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "setLatticeVectors",
function () {
if (this.abc[0] == null) {
this.setUnitCell (this.a, this.b, this.c, this.alpha, this.beta, this.gamma);
return;
}var lv = Clazz.newFloatArray (3, 0);
for (var i = 0; i < 3; i++) {
lv[0] = this.abc[i].x;
lv[1] = this.abc[i].y;
lv[2] = this.abc[i].z;
this.addExplicitLatticeVector (i, lv, 0);
}
});
Clazz.defineMethod (c$, "readLatticeAbc",
function () {
if (this.tokenizeCastepCell () == 0) return;
var factor = this.readLengthUnit (this.tokens[0]);
if (this.tokens.length >= 3) {
this.a = this.parseFloatStr (this.tokens[0]) * factor;
this.b = this.parseFloatStr (this.tokens[1]) * factor;
this.c = this.parseFloatStr (this.tokens[2]) * factor;
} else {
JU.Logger.warn ("error reading a,b,c in %BLOCK LATTICE_ABC in CASTEP .cell file");
return;
}if (this.tokenizeCastepCell () == 0) return;
if (this.tokens.length >= 3) {
this.alpha = this.parseFloatStr (this.tokens[0]);
this.beta = this.parseFloatStr (this.tokens[1]);
this.gamma = this.parseFloatStr (this.tokens[2]);
} else {
JU.Logger.warn ("error reading alpha,beta,gamma in %BLOCK LATTICE_ABC in CASTEP .cell file");
}});
Clazz.defineMethod (c$, "readLatticeCart",
function () {
if (this.tokenizeCastepCell () == 0) return;
var factor = this.readLengthUnit (this.tokens[0]);
var x;
var y;
var z;
for (var i = 0; i < 3; i++) {
if (this.tokens.length >= 3) {
x = this.parseFloatStr (this.tokens[0]) * factor;
y = this.parseFloatStr (this.tokens[1]) * factor;
z = this.parseFloatStr (this.tokens[2]) * factor;
this.abc[i] = JU.V3.new3 (x, y, z);
} else {
JU.Logger.warn ("error reading coordinates of lattice vector " + Integer.toString (i + 1) + " in %BLOCK LATTICE_CART in CASTEP .cell file");
return;
}if (this.tokenizeCastepCell () == 0) return;
}
this.a = this.abc[0].length ();
this.b = this.abc[1].length ();
this.c = this.abc[2].length ();
this.alpha = (this.abc[1].angle (this.abc[2]) * 57.29578);
this.beta = (this.abc[2].angle (this.abc[0]) * 57.29578);
this.gamma = (this.abc[0].angle (this.abc[1]) * 57.29578);
});
Clazz.defineMethod (c$, "readPositionsFrac",
function () {
if (this.tokenizeCastepCell () == 0) return;
this.readAtomData (1.0);
});
Clazz.defineMethod (c$, "readPositionsAbs",
function () {
if (this.tokenizeCastepCell () == 0) return;
var factor = this.readLengthUnit (this.tokens[0]);
this.readAtomData (factor);
});
Clazz.defineMethod (c$, "readLengthUnit",
function (units) {
var factor = 1.0;
for (var i = 0; i < J.adapter.readers.xtal.CastepReader.lengthUnitIds.length; i++) if (units.equalsIgnoreCase (J.adapter.readers.xtal.CastepReader.lengthUnitIds[i])) {
factor = J.adapter.readers.xtal.CastepReader.lengthUnitFactors[i];
this.tokenizeCastepCell ();
break;
}
return factor;
}, "~S");
Clazz.defineMethod (c$, "readAtomData",
function (factor) {
do {
if (this.tokens.length >= 4) {
var atom = this.asc.addNewAtom ();
var pt = this.tokens[0].indexOf (":");
if (pt >= 0) {
atom.elementSymbol = this.tokens[0].substring (0, pt);
atom.atomName = this.tokens[0];
} else {
atom.elementSymbol = this.tokens[0];
}atom.set (this.parseFloatStr (this.tokens[1]), this.parseFloatStr (this.tokens[2]), this.parseFloatStr (this.tokens[3]));
atom.scale (factor);
} else {
JU.Logger.warn ("cannot read line with CASTEP atom data: " + this.line);
}} while (this.tokenizeCastepCell () > 0 && !this.tokens[0].equalsIgnoreCase ("%ENDBLOCK"));
}, "~N");
Clazz.defineMethod (c$, "tokenizeCastepCell",
function () {
while (this.rd () != null) {
if ((this.line = this.line.trim ()).length == 0 || this.line.startsWith ("#") || this.line.startsWith ("!")) continue;
if (!this.isCell) {
if (this.line.startsWith ("%")) {
this.isCell = true;
break;
}if (this.line.startsWith ("LST")) {
this.isTS = true;
JU.Logger.info ("reading CASTEP .ts file");
return -1;
}if (this.line.startsWith ("BEGIN header")) {
this.isPhonon = true;
JU.Logger.info ("reading CASTEP .phonon file");
return -1;
}if (this.line.contains ("CASTEP")) {
this.isOutput = true;
JU.Logger.info ("reading CASTEP .castep file");
return -1;
}}break;
}
return (this.line == null ? 0 : (this.tokens = this.getTokens ()).length);
});
Clazz.defineMethod (c$, "readOutputBornChargeTensors",
function () {
if (this.rd ().indexOf ("--------") < 0) return;
var atoms = this.asc.atoms;
this.appendLoadNote ("Ellipsoids: Born Charge Tensors");
while (this.rd ().indexOf ('=') < 0) this.getTensor (atoms[this.readOutputAtomIndex ()], this.line.substring (12));
});
Clazz.defineMethod (c$, "readOutputAtomIndex",
function () {
this.tokens = this.getTokens ();
return this.asc.getAtomIndex (this.tokens[0] + this.tokens[1]);
});
Clazz.defineMethod (c$, "getTensor",
function (atom, line0) {
var data = Clazz.newFloatArray (9, 0);
var a = Clazz.newDoubleArray (3, 3, 0);
this.fillFloatArray (line0, 0, data);
JU.Logger.info ("tensor " + atom.atomName + "\t" + JU.Escape.eAF (data));
for (var p = 0, i = 0; i < 3; i++) for (var j = 0; j < 3; j++) a[i][j] = data[p++];
atom.addTensor (( new JU.Tensor ()).setFromAsymmetricTensor (a, "charge", atom.atomName + " " + line0), null, false);
if (!this.haveCharges) this.appendLoadNote ("Ellipsoids set \"charge\": Born Effective Charges");
this.haveCharges = true;
}, "J.adapter.smarter.Atom,~S");
Clazz.defineMethod (c$, "readOutputCharges",
function () {
if (this.line.toUpperCase ().indexOf (this.chargeType) < 0) return;
JU.Logger.info ("reading charges: " + this.line);
this.readLines (2);
var haveSpin = (this.line.indexOf ("Spin") >= 0);
this.rd ();
var atoms = this.asc.atoms;
var spins = (haveSpin ? Clazz.newFloatArray (atoms.length, 0) : null);
if (spins != null) for (var i = 0; i < spins.length; i++) spins[i] = 0;
while (this.rd () != null && this.line.indexOf ('=') < 0) {
var index = this.readOutputAtomIndex ();
var charge = this.parseFloatStr (this.tokens[haveSpin ? this.tokens.length - 2 : this.tokens.length - 1]);
atoms[index].partialCharge = charge;
if (haveSpin) spins[index] = this.parseFloatStr (this.tokens[this.tokens.length - 1]);
}
if (haveSpin) this.asc.setAtomProperties ("spin", spins, -1, false);
});
Clazz.defineMethod (c$, "readPhononUnitCell",
function () {
this.abc = this.read3Vectors (this.line.indexOf ("bohr") >= 0);
this.setSpaceGroupName ("P1");
this.setLatticeVectors ();
});
Clazz.defineMethod (c$, "readPhononFractionalCoord",
function () {
this.setFractionalCoordinates (true);
while (this.rd () != null && this.line.indexOf ("END") < 0) {
this.tokens = this.getTokens ();
this.addAtomXYZSymName (this.tokens, 1, this.tokens[4], null).bfactor = this.parseFloatStr (this.tokens[5]);
}
this.ac = this.asc.ac;
this.atomPts = new Array (this.ac);
var atoms = this.asc.atoms;
for (var i = 0; i < this.ac; i++) this.atomPts[i] = JU.P3.newP (atoms[i]);
});
Clazz.defineMethod (c$, "readPhononFrequencies",
function () {
this.tokens = this.getTokens ();
var v = new JU.V3 ();
var qvec = JU.V3.new3 (this.parseFloatStr (this.tokens[2]), this.parseFloatStr (this.tokens[3]), this.parseFloatStr (this.tokens[4]));
var fcoord = this.getFractionalCoord (qvec);
var qtoks = "{" + this.tokens[2] + " " + this.tokens[3] + " " + this.tokens[4] + "}";
if (fcoord == null) fcoord = qtoks;
else fcoord = "{" + fcoord + "}";
var isOK = this.isAllQ;
var isSecond = (this.tokens[1].equals (this.lastQPt));
this.qpt2 = (isSecond ? this.qpt2 + 1 : 1);
this.lastQPt = this.tokens[1];
if (!isOK && this.checkFilterKey ("Q=")) {
if (this.desiredQpt != null) {
v.sub2 (this.desiredQpt, qvec);
if (v.length () < 0.001) fcoord = this.desiredQ;
}isOK = (this.checkFilterKey ("Q=" + fcoord + "." + this.qpt2 + ";") || this.checkFilterKey ("Q=" + this.lastQPt + "." + this.qpt2 + ";") || !isSecond && this.checkFilterKey ("Q=" + fcoord + ";") || !isSecond && this.checkFilterKey ("Q=" + this.lastQPt + ";"));
if (!isOK) return;
}var isGammaPoint = (qvec.length () == 0);
var nx = 1;
var ny = 1;
var nz = 1;
if (this.ptSupercell != null && !isOK && !isSecond) {
this.matSupercell = new JU.M4 ();
this.matSupercell.m00 = this.ptSupercell.x;
this.matSupercell.m11 = this.ptSupercell.y;
this.matSupercell.m22 = this.ptSupercell.z;
this.matSupercell.m33 = 1;
JU.Logger.info ("Using supercell \n" + this.matSupercell);
nx = this.ptSupercell.x;
ny = this.ptSupercell.y;
nz = this.ptSupercell.z;
var dx = (qvec.x == 0 ? 1 : qvec.x) * nx;
var dy = (qvec.y == 0 ? 1 : qvec.y) * ny;
var dz = (qvec.z == 0 ? 1 : qvec.z) * nz;
if ((nx != 1 || ny != 1 || nz != 1) && isGammaPoint || !J.adapter.readers.xtal.CastepReader.isInt (dx) || !J.adapter.readers.xtal.CastepReader.isInt (dy) || !J.adapter.readers.xtal.CastepReader.isInt (dz)) return;
isOK = true;
}if (this.ptSupercell == null || !this.havePhonons) this.appendLoadNote (this.line);
if (!isOK && isSecond) return;
if (!isOK && (this.ptSupercell == null) == !isGammaPoint) return;
if (this.havePhonons && !this.isAllQ) return;
this.havePhonons = true;
var qname = "q=" + this.lastQPt + " " + fcoord;
this.applySymmetryAndSetTrajectory ();
if (isGammaPoint) qvec = null;
var freqs = new JU.Lst ();
while (this.rd () != null && this.line.indexOf ("Phonon") < 0) {
this.tokens = this.getTokens ();
freqs.addLast (Float.$valueOf (this.parseFloatStr (this.tokens[1])));
}
this.rd ();
var frequencyCount = freqs.size ();
var data = Clazz.newFloatArray (8, 0);
var t = new JU.V3 ();
this.asc.setCollectionName (qname);
for (var i = 0; i < frequencyCount; i++) {
if (!this.doGetVibration (++this.vibrationNumber)) {
for (var j = 0; j < this.ac; j++) this.rd ();
continue;
}if (this.desiredVibrationNumber <= 0) {
if (!this.isTrajectory) {
this.cloneLastAtomSet (this.ac, this.atomPts);
this.applySymmetryAndSetTrajectory ();
}}this.symmetry = this.asc.getSymmetry ();
var iatom = this.asc.getLastAtomSetAtomIndex ();
var freq = freqs.get (i).floatValue ();
var atoms = this.asc.atoms;
var aCount = this.asc.ac;
for (var j = 0; j < this.ac; j++) {
this.fillFloatArray (null, 0, data);
for (var k = iatom++; k < aCount; k++) if (atoms[k].atomSite == j) {
t.sub2 (atoms[k], atoms[atoms[k].atomSite]);
if (this.matSupercell != null) this.matSupercell.rotTrans (t);
this.setPhononVector (data, atoms[k], t, qvec, v);
this.asc.addVibrationVectorWithSymmetry (k, v.x, v.y, v.z, true);
}
}
if (this.isTrajectory) this.asc.setTrajectory ();
this.asc.setAtomSetFrequency (null, null, "" + freq, null);
this.asc.setAtomSetName (JU.DF.formatDecimal (freq, 2) + " cm-1 " + qname);
}
});
Clazz.defineMethod (c$, "getFractionalCoord",
function (qvec) {
return (this.symmetry != null && J.adapter.readers.xtal.CastepReader.isInt (qvec.x * 12) && J.adapter.readers.xtal.CastepReader.isInt (qvec.y * 12) && J.adapter.readers.xtal.CastepReader.isInt (qvec.z * 12) ? this.symmetry.fcoord (qvec) : null);
}, "JU.V3");
c$.isInt = Clazz.defineMethod (c$, "isInt",
function (f) {
return (Math.abs (f - Math.round (f)) < 0.001);
}, "~N");
Clazz.defineMethod (c$, "setPhononVector",
function (data, atom, rTrans, qvec, v) {
if (qvec == null) {
v.set (data[2], data[4], data[6]);
} else {
var phase = qvec.dot (rTrans);
var cosph = Math.cos (6.283185307179586 * phase);
var sinph = Math.sin (6.283185307179586 * phase);
v.x = (cosph * data[2] - sinph * data[3]);
v.y = (cosph * data[4] - sinph * data[5]);
v.z = (cosph * data[6] - sinph * data[7]);
}v.scale (Math.sqrt (1 / atom.bfactor));
}, "~A,J.adapter.smarter.Atom,JU.V3,JU.V3,JU.V3");
Clazz.defineStatics (c$,
"RAD_TO_DEG", (57.29577951308232),
"lengthUnitIds", Clazz.newArray (-1, ["bohr", "m", "cm", "nm", "ang", "a0"]),
"lengthUnitFactors", Clazz.newFloatArray (-1, [0.5291772, 1E10, 1E8, 1E1, 1.0, 0.5291772]),
"TWOPI", 6.283185307179586);
});

165
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/CgdReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "JU.V3"], "J.adapter.readers.xtal.CgdReader", ["java.lang.Character", "java.util.Hashtable", "JU.Lst", "$.M3", "$.P3", "$.PT", "J.adapter.smarter.Bond", "JU.Logger"], function () {
c$ = 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$, "initializeReader",
function () {
this.setFractionalCoordinates (true);
this.asc.setNoAutoBond ();
this.asc.vibScale = 1;
this.forceSymmetry (!this.checkFilterKey ("NOPACK"));
this.noBondSym = this.checkFilterKey ("NOBONDSYM");
});
Clazz.overrideMethod (c$, "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");
Clazz.defineStatics (c$,
"SG_ALIASES", ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;");
c$.vecs = c$.prototype.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)]);
});

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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "JU.P3"], "J.adapter.readers.xtal.CrystalReader", ["java.lang.Character", "$.Double", "java.util.Arrays", "JU.BS", "$.DF", "$.Lst", "$.M3", "$.PT", "$.Quat", "$.SB", "$.V3", "JU.Logger", "$.Tensor"], function () {
c$ = Clazz.decorateAsClass (function () {
this.isVersion3 = false;
this.$isPrimitive = false;
this.isPolymer = false;
this.isSlab = false;
this.$isMolecular = false;
this.haveCharges = false;
this.inputOnly = false;
this.isLongMode = false;
this.getLastConventional = false;
this.havePrimitiveMapping = false;
this.isProperties = false;
this.ac = 0;
this.atomIndexLast = 0;
this.atomFrag = null;
this.primitiveToIndex = null;
this.nuclearCharges = null;
this.vCoords = null;
this.energy = null;
this.ptOriginShift = null;
this.primitiveToCryst = null;
this.directLatticeVectors = null;
this.spaceGroupName = null;
this.primitiveVolume = 0;
this.primitiveDensity = 0;
this.vPrimitiveMapping = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "CrystalReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.ptOriginShift = new JU.P3 ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.doProcessLines = false;
this.inputOnly = this.checkFilterKey ("INPUT");
this.$isPrimitive = !this.inputOnly && !this.checkFilterKey ("CONV");
this.addVibrations = new Boolean (this.addVibrations & !this.inputOnly).valueOf ();
this.getLastConventional = (!this.$isPrimitive && this.desiredModelNumber == 0);
this.setFractionalCoordinates (this.readHeader ());
this.asc.checkLatticeOnly = true;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.startsWith (" LATTICE PARAMETER")) {
var isConvLattice = (this.line.indexOf ("- CONVENTIONAL") >= 0);
if (isConvLattice) {
if (this.$isPrimitive) return true;
this.readLatticeParams (true);
} else if (!this.$isPrimitive && !this.havePrimitiveMapping && !this.getLastConventional) {
this.readLines (3);
this.readPrimitiveMapping ();
if (this.setPrimitiveMapping ()) return true;
}this.readLatticeParams (true);
if (!this.$isPrimitive) {
this.discardLinesUntilContains (" TRANSFORMATION");
this.readTransformationMatrix ();
this.discardLinesUntilContains (" CRYSTALLOGRAPHIC");
this.readLatticeParams (false);
this.discardLinesUntilContains (" CRYSTALLOGRAPHIC");
this.readCoordLines ();
if (!this.getLastConventional) {
if (this.doGetModel (++this.modelNumber, null)) {
this.createAtomsFromCoordLines ();
} else {
this.vCoords = null;
this.checkLastModel ();
}}}return true;
}if (!this.$isPrimitive) {
if (this.line.startsWith (" SHIFT OF THE ORIGIN")) return this.readShift ();
if (this.line.startsWith (" INPUT COORDINATES")) {
this.readCoordLines ();
if (this.inputOnly) this.continuing = false;
return true;
}}if (this.line.startsWith (" DIRECT LATTICE VECTOR")) return this.setDirect ();
if (this.line.indexOf ("DIMENSIONALITY OF THE SYSTEM") >= 0) {
if (this.line.indexOf ("2") >= 0) this.isSlab = true;
if (this.line.indexOf ("1") >= 0) this.isPolymer = true;
return true;
}if (this.addVibrations && this.line.startsWith (" FREQUENCIES COMPUTED ON A FRAGMENT")) return this.readFreqFragments ();
if (this.line.indexOf ("CONSTRUCTION OF A NANOTUBE FROM A SLAB") >= 0) {
this.isPolymer = true;
this.isSlab = false;
return true;
}if (this.line.indexOf ("* CLUSTER CALCULATION") >= 0) {
this.$isMolecular = true;
this.isSlab = false;
this.isPolymer = false;
return true;
}if (((this.$isPrimitive || this.$isMolecular) && this.line.startsWith (" ATOMS IN THE ASYMMETRIC UNIT")) || this.isProperties && this.line.startsWith (" ATOM N.AT.")) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
return this.readAtoms ();
}if (this.line.startsWith (" * SUPERCELL OPTION")) {
this.discardLinesUntilContains ("GENERATED");
return true;
}if (!this.doProcessLines) return true;
if (this.line.startsWith (" TOTAL ENERGY(")) {
this.line = JU.PT.rep (this.line, "( ", "(");
var tokens = this.getTokens ();
this.energy = Double.$valueOf (Double.parseDouble (tokens[2]));
this.setEnergy ();
this.rd ();
if (this.line.startsWith (" ********")) this.discardLinesUntilContains ("SYMMETRY ALLOWED");
else if (this.line.startsWith (" TTTTTTTT")) this.discardLinesUntilContains2 ("PREDICTED ENERGY CHANGE", "HHHHHHH");
return true;
}if (this.line.startsWith (" TYPE OF CALCULATION")) {
this.calculationType = this.line.substring (this.line.indexOf (":") + 1).trim ();
return true;
}if (this.line.startsWith (" MULLIKEN POPULATION ANALYSIS")) return this.readPartialCharges ();
if (this.line.startsWith (" TOTAL ATOMIC CHARGES")) return this.readTotalAtomicCharges ();
if (this.addVibrations && this.line.contains (this.isVersion3 ? "EIGENVALUES (EV) OF THE MASS" : "EIGENVALUES (EIGV) OF THE MASS") || this.line.indexOf ("LONGITUDINAL OPTICAL (LO)") >= 0) {
this.createAtomsFromCoordLines ();
this.isLongMode = (this.line.indexOf ("LONGITUDINAL OPTICAL (LO)") >= 0);
return this.readFrequencies ();
}if (this.line.startsWith (" MAX GRADIENT")) return this.readGradient ();
if (this.line.startsWith (" ATOMIC SPINS SET")) return this.readData ("spin", 3);
if (this.line.startsWith (" TOTAL ATOMIC SPINS :")) return this.readData ("magneticMoment", 1);
if (this.line.startsWith (" BORN CHARGE TENSOR.")) return this.readBornChargeTensors ();
if (!this.isProperties) return true;
if (this.line.startsWith (" DEFINITION OF TRACELESS")) return this.getQuadrupoleTensors ();
if (this.line.startsWith (" MULTIPOLE ANALYSIS BY ATOMS")) {
this.appendLoadNote ("Multipole Analysis");
return true;
}return true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.createAtomsFromCoordLines ();
if (this.energy != null) this.setEnergy ();
this.finalizeReaderASCR ();
});
Clazz.defineMethod (c$, "setDirect",
function () {
var isBohr = (this.line.indexOf ("(BOHR") >= 0);
this.directLatticeVectors = this.read3Vectors (isBohr);
var a = new JU.V3 ();
var b = new JU.V3 ();
if (this.$isPrimitive) {
a = this.directLatticeVectors[0];
b = this.directLatticeVectors[1];
} else {
if (this.primitiveToCryst == null) return true;
var mp = new JU.M3 ();
mp.setColumnV (0, this.directLatticeVectors[0]);
mp.setColumnV (1, this.directLatticeVectors[1]);
mp.setColumnV (2, this.directLatticeVectors[2]);
mp.mul (this.primitiveToCryst);
a = new JU.V3 ();
b = new JU.V3 ();
mp.getColumnV (0, a);
mp.getColumnV (1, b);
}this.matUnitCellOrientation = JU.Quat.getQuaternionFrame ( new JU.P3 (), a, b).getMatrix ();
JU.Logger.info ("oriented unit cell is in model " + this.asc.atomSetCount);
return !this.isProperties;
});
Clazz.defineMethod (c$, "readTransformationMatrix",
function () {
this.primitiveToCryst = JU.M3.newA9 (this.fillFloatArray (null, 0, Clazz.newFloatArray (9, 0)));
});
Clazz.defineMethod (c$, "readShift",
function () {
var tokens = this.getTokens ();
var pt = tokens.length - 3;
this.ptOriginShift.set (JU.PT.parseFloatFraction (tokens[pt++]), JU.PT.parseFloatFraction (tokens[pt++]), JU.PT.parseFloatFraction (tokens[pt]));
return true;
});
Clazz.defineMethod (c$, "setPrimitiveVolumeAndDensity",
function () {
if (this.primitiveVolume != 0) this.asc.setAtomSetModelProperty ("volumePrimitive", JU.DF.formatDecimal (this.primitiveVolume, 3));
if (this.primitiveDensity != 0) this.asc.setAtomSetModelProperty ("densityPrimitive", JU.DF.formatDecimal (this.primitiveDensity, 3));
});
Clazz.defineMethod (c$, "readHeader",
function () {
this.discardLinesUntilContains ("*******************************************************************************");
this.readLines (2);
this.isVersion3 = (this.line.indexOf ("CRYSTAL03") >= 0);
this.discardLinesUntilContains ("EEEEEEEEEE");
var name;
if (this.rd ().length == 0) {
name = this.readLines (2).trim ();
} else {
name = this.line.trim ();
this.rd ();
}var type = this.rd ().trim ();
var pt = type.indexOf ("- PROPERTIES");
if (pt >= 0) {
this.isProperties = true;
type = type.substring (0, pt).trim ();
}if (type.indexOf ("EXTERNAL FILE") >= 0) {
type = this.rd ().trim ();
this.isPolymer = (type.equals ("1D - POLYMER"));
this.isSlab = (type.equals ("2D - SLAB"));
} else {
this.isPolymer = (type.equals ("POLYMER CALCULATION"));
this.isSlab = (type.equals ("SLAB CALCULATION"));
}this.asc.setCollectionName (name + (!this.isProperties && this.desiredModelNumber == 0 ? " (optimized)" : ""));
this.asc.setInfo ("symmetryType", type);
if ((this.isPolymer || this.isSlab) && !this.$isPrimitive) {
JU.Logger.error ("Cannot use FILTER \"conventional\" with POLYMER or SLAB");
this.$isPrimitive = true;
}this.asc.setInfo ("unitCellType", (this.$isPrimitive ? "primitive" : "conventional"));
if (type.indexOf ("MOLECULAR") >= 0) {
this.$isMolecular = this.doProcessLines = true;
this.rd ();
this.asc.setInfo ("molecularCalculationPointGroup", this.line.substring (this.line.indexOf (" OR ") + 4).trim ());
return false;
}this.spaceGroupName = "P1";
if (!this.$isPrimitive) {
this.discardLinesUntilContains2 ("SPACE GROUP", "****");
pt = this.line.indexOf (":");
if (pt >= 0) this.spaceGroupName = this.line.substring (pt + 1).trim ();
}this.doApplySymmetry = this.isProperties;
return !this.isProperties;
});
Clazz.defineMethod (c$, "readLatticeParams",
function (isNewSet) {
var f = (this.line.indexOf ("(BOHR") >= 0 ? 0.5291772 : 1);
if (isNewSet) this.newAtomSet ();
if (this.isPolymer && !this.$isPrimitive) {
this.setUnitCell (this.parseFloatStr (this.line.substring (this.line.indexOf ("CELL") + 4)) * f, -1, -1, 90, 90, 90);
} else {
while (this.rd ().indexOf ("GAMMA") < 0) if (this.line.indexOf ("VOLUME=") >= 0) {
this.primitiveVolume = this.parseFloatStr (this.line.substring (43));
this.primitiveDensity = this.parseFloatStr (this.line.substring (66));
}
var tokens = JU.PT.getTokens (this.rd ());
if (this.isSlab) {
if (this.$isPrimitive) this.setUnitCell (this.parseFloatStr (tokens[0]) * f, this.parseFloatStr (tokens[1]) * f, -1, this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[4]), this.parseFloatStr (tokens[5]));
else this.setUnitCell (this.parseFloatStr (tokens[0]) * f, this.parseFloatStr (tokens[1]) * f, -1, 90, 90, this.parseFloatStr (tokens[2]));
} else if (this.isPolymer) {
this.setUnitCell (this.parseFloatStr (tokens[0]) * f, -1, -1, this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[4]), this.parseFloatStr (tokens[5]));
} else {
this.setUnitCell (this.parseFloatStr (tokens[0]) * f, this.parseFloatStr (tokens[1]) * f, this.parseFloatStr (tokens[2]) * f, this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[4]), this.parseFloatStr (tokens[5]));
}}}, "~B");
Clazz.defineMethod (c$, "readPrimitiveMapping",
function () {
if (this.havePrimitiveMapping) return;
this.vPrimitiveMapping = new JU.Lst ();
while (this.rd () != null && this.line.indexOf ("NUMBER") < 0) this.vPrimitiveMapping.addLast (this.line);
});
Clazz.defineMethod (c$, "setPrimitiveMapping",
function () {
if (this.vCoords == null || this.vPrimitiveMapping == null || this.havePrimitiveMapping) return false;
this.havePrimitiveMapping = true;
var bsInputAtomsIgnore = new JU.BS ();
var n = this.vCoords.size ();
var indexToPrimitive = Clazz.newIntArray (n, 0);
this.primitiveToIndex = Clazz.newIntArray (n, 0);
for (var i = 0; i < n; i++) indexToPrimitive[i] = -1;
var nPrim = 0;
for (var iLine = 0; iLine < this.vPrimitiveMapping.size (); iLine++) {
this.line = this.vPrimitiveMapping.get (iLine);
if (this.line.indexOf (" NOT IRREDUCIBLE") >= 0) {
bsInputAtomsIgnore.set (this.parseIntRange (this.line, 21, 25) - 1);
continue;
}while (this.rd () != null && this.line.indexOf ("NUMBER") < 0) {
if (this.line.length < 2 || this.line.indexOf ("ATOM") >= 0) continue;
var iAtom = this.parseIntRange (this.line, 4, 8) - 1;
if (indexToPrimitive[iAtom] < 0) {
indexToPrimitive[iAtom] = nPrim++;
}}
}
if (bsInputAtomsIgnore.nextSetBit (0) >= 0) for (var i = n; --i >= 0; ) if (bsInputAtomsIgnore.get (i)) this.vCoords.removeItemAt (i);
this.ac = this.vCoords.size ();
JU.Logger.info (nPrim + " primitive atoms and " + this.ac + " conventionalAtoms");
this.primitiveToIndex = Clazz.newIntArray (nPrim, 0);
for (var i = 0; i < nPrim; i++) this.primitiveToIndex[i] = -1;
for (var i = this.ac; --i >= 0; ) {
var iPrim = indexToPrimitive[this.parseIntStr (this.vCoords.get (i).substring (0, 4)) - 1];
if (iPrim >= 0) this.primitiveToIndex[iPrim] = i;
}
this.vPrimitiveMapping = null;
return true;
});
Clazz.defineMethod (c$, "readAtoms",
function () {
if (this.$isMolecular) this.newAtomSet ();
this.vCoords = null;
while (this.rd () != null && this.line.indexOf ("*") < 0) {
if (this.line.indexOf ("X(ANGSTROM") >= 0) {
this.setFractionalCoordinates (false);
this.$isMolecular = true;
}}
var i = this.atomIndexLast;
var doNormalizePrimitive = false;
this.atomIndexLast = this.asc.ac;
while (this.rd () != null && this.line.length > 0 && this.line.indexOf (this.$isPrimitive ? "*" : "=") < 0) {
var atom = this.asc.addNewAtom ();
var tokens = this.getTokens ();
var pt = (this.isProperties ? 1 : 2);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (this.getAtomicNumber (tokens[pt++]));
atom.atomName = J.adapter.readers.xtal.CrystalReader.fixAtomName (tokens[pt++]);
if (this.isProperties) pt++;
var x = this.parseFloatStr (tokens[pt++]);
var y = this.parseFloatStr (tokens[pt++]);
var z = this.parseFloatStr (tokens[pt]);
if (this.haveCharges) atom.partialCharge = this.asc.atoms[i++].partialCharge;
if (this.iHaveFractionalCoordinates && !this.isProperties) {
if (x < 0 && (this.isPolymer || this.isSlab || doNormalizePrimitive)) x += 1;
if (y < 0 && (this.isSlab || doNormalizePrimitive)) y += 1;
if (z < 0 && doNormalizePrimitive) z += 1;
}this.setAtomCoordXYZ (atom, x, y, z);
}
this.ac = this.asc.ac - this.atomIndexLast;
return true;
});
c$.fixAtomName = Clazz.defineMethod (c$, "fixAtomName",
function (s) {
return (s.length > 1 && JU.PT.isLetter (s.charAt (1)) ? s.substring (0, 1) + Character.toLowerCase (s.charAt (1)) + s.substring (2) : s);
}, "~S");
Clazz.defineMethod (c$, "getAtomicNumber",
function (token) {
return this.parseIntStr (token) % 100;
}, "~S");
Clazz.defineMethod (c$, "readCoordLines",
function () {
this.rd ();
this.rd ();
this.vCoords = new JU.Lst ();
while (this.rd () != null && this.line.length > 0) this.vCoords.addLast (this.line);
});
Clazz.defineMethod (c$, "createAtomsFromCoordLines",
function () {
if (this.vCoords == null) return;
this.ac = this.vCoords.size ();
for (var i = 0; i < this.ac; i++) {
var atom = this.asc.addNewAtom ();
var tokens = JU.PT.getTokens (this.vCoords.get (i));
atom.atomSerial = this.parseIntStr (tokens[0]);
var atomicNumber;
var offset;
if (tokens.length == 7) {
atomicNumber = this.getAtomicNumber (tokens[2]);
offset = 2;
} else {
atomicNumber = this.getAtomicNumber (tokens[1]);
offset = 0;
}var x = this.parseFloatStr (tokens[2 + offset]) + this.ptOriginShift.x;
var y = this.parseFloatStr (tokens[3 + offset]) + this.ptOriginShift.y;
var z = this.parseFloatStr (tokens[4 + offset]) + this.ptOriginShift.z;
this.setAtomCoordXYZ (atom, x, y, z);
atom.elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (atomicNumber);
}
this.vCoords = null;
this.setPrimitiveVolumeAndDensity ();
});
Clazz.defineMethod (c$, "newAtomSet",
function () {
if (this.ac > 0 && this.asc.ac > 0) {
this.applySymmetryAndSetTrajectory ();
this.asc.newAtomSet ();
}if (this.spaceGroupName != null) this.setSpaceGroupName (this.spaceGroupName);
this.ac = 0;
});
Clazz.defineMethod (c$, "setEnergy",
function () {
this.asc.setAtomSetEnergy ("" + this.energy, this.energy.floatValue ());
this.asc.setCurrentModelInfo ("Energy", this.energy);
this.asc.setInfo ("Energy", this.energy);
this.asc.setAtomSetName ("Energy = " + this.energy + " Hartree");
});
Clazz.defineMethod (c$, "readPartialCharges",
function () {
if (this.haveCharges || this.asc.ac == 0) return true;
this.haveCharges = true;
this.readLines (3);
var atoms = this.asc.atoms;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var iPrim = 0;
while (this.rd () != null && this.line.length > 3) if (this.line.charAt (3) != ' ') {
var iConv = this.getAtomIndexFromPrimitiveIndex (iPrim);
if (iConv >= 0) atoms[i0 + iConv].partialCharge = this.parseFloatRange (this.line, 9, 11) - this.parseFloatRange (this.line, 12, 18);
iPrim++;
}
return true;
});
Clazz.defineMethod (c$, "readTotalAtomicCharges",
function () {
var data = new JU.SB ();
while (this.rd () != null && this.line.indexOf ("T") < 0) data.append (this.line);
var tokens = JU.PT.getTokens (data.toString ());
var charges = Clazz.newFloatArray (tokens.length, 0);
if (this.nuclearCharges == null) this.nuclearCharges = charges;
if (this.asc.ac == 0) return true;
var atoms = this.asc.atoms;
var i0 = this.asc.getLastAtomSetAtomIndex ();
for (var i = 0; i < charges.length; i++) {
var iConv = this.getAtomIndexFromPrimitiveIndex (i);
if (iConv >= 0) {
charges[i] = this.parseFloatStr (tokens[i]);
atoms[i0 + iConv].partialCharge = this.nuclearCharges[i] - charges[i];
}}
return true;
});
Clazz.defineMethod (c$, "getAtomIndexFromPrimitiveIndex",
function (iPrim) {
return (this.primitiveToIndex == null ? iPrim : this.primitiveToIndex[iPrim]);
}, "~N");
Clazz.defineMethod (c$, "readFreqFragments",
function () {
var numAtomsFrag = this.parseIntRange (this.line, 39, 44);
if (numAtomsFrag < 0) return true;
this.atomFrag = Clazz.newIntArray (numAtomsFrag, 0);
var Sfrag = "";
while (this.rd () != null && this.line.indexOf ("(") >= 0) Sfrag += this.line;
Sfrag = JU.PT.rep (Sfrag, "(", " ");
Sfrag = JU.PT.rep (Sfrag, ")", " ");
var tokens = JU.PT.getTokens (Sfrag);
for (var i = 0, pos = 0; i < numAtomsFrag; i++, pos += 3) this.atomFrag[i] = this.getAtomIndexFromPrimitiveIndex (this.parseIntStr (tokens[pos]) - 1);
java.util.Arrays.sort (this.atomFrag);
return true;
});
Clazz.defineMethod (c$, "readFrequencies",
function () {
this.energy = null;
this.discardLinesUntilContains ("MODES");
var haveIntensities = (this.line.indexOf ("INTENS") >= 0);
this.rd ();
var vData = new JU.Lst ();
var freqAtomCount = this.ac;
while (this.rd () != null && this.line.length > 0) {
var i0 = this.parseIntRange (this.line, 1, 5);
var i1 = this.parseIntRange (this.line, 6, 10);
var irrep = (this.isLongMode ? this.line.substring (48, 51) : this.line.substring (49, 52)).trim ();
var intens = (!haveIntensities ? "not available" : (this.isLongMode ? this.line.substring (53, 61) : this.line.substring (59, 69).$replace (')', ' ')).trim ());
var irActivity = (this.isLongMode ? "A" : this.line.substring (55, 58).trim ());
var ramanActivity = (this.isLongMode ? "I" : this.line.substring (71, 73).trim ());
var data = Clazz.newArray (-1, [irrep, intens, irActivity, ramanActivity]);
for (var i = i0; i <= i1; i++) vData.addLast (data);
}
this.discardLinesUntilContains (this.isLongMode ? "LO MODES FOR IRREP" : this.isVersion3 ? "THE CORRESPONDING MODES" : "NORMAL MODES NORMALIZED TO CLASSICAL AMPLITUDES");
this.rd ();
var lastAtomCount = -1;
while (this.rd () != null && this.line.startsWith (" FREQ(CM**-1)")) {
var tokens = JU.PT.getTokens (this.line.substring (15));
var frequencies = Clazz.newFloatArray (tokens.length, 0);
var frequencyCount = frequencies.length;
for (var i = 0; i < frequencyCount; i++) {
frequencies[i] = this.parseFloatStr (tokens[i]);
if (this.debugging) JU.Logger.debug ((this.vibrationNumber + i) + " frequency=" + frequencies[i]);
}
var ignore = Clazz.newBooleanArray (frequencyCount, false);
var iAtom0 = 0;
var nData = vData.size ();
for (var i = 0; i < frequencyCount; i++) {
tokens = vData.get (this.vibrationNumber % nData);
ignore[i] = (!this.doGetVibration (++this.vibrationNumber) || tokens == null);
if (ignore[i]) continue;
this.applySymmetryAndSetTrajectory ();
lastAtomCount = this.cloneLastAtomSet (this.ac, null);
if (i == 0) iAtom0 = this.asc.getLastAtomSetAtomIndex ();
this.setFreqValue (frequencies[i], tokens);
}
this.rd ();
this.fillFrequencyData (iAtom0, freqAtomCount, lastAtomCount, ignore, false, 14, 10, this.atomFrag, 0);
this.rd ();
}
return true;
});
Clazz.defineMethod (c$, "setFreqValue",
function (freq, data) {
var activity = "IR: " + data[2] + ", Ram.: " + data[3];
this.asc.setAtomSetFrequency (null, activity, "" + freq, null);
this.asc.setAtomSetModelProperty ("IRintensity", data[1] + " km/Mole");
this.asc.setAtomSetModelProperty ("vibrationalSymmetry", data[0]);
this.asc.setAtomSetModelProperty ("IRactivity", data[2]);
this.asc.setAtomSetModelProperty ("Ramanactivity", data[3]);
this.asc.setAtomSetName ((this.isLongMode ? "LO " : "") + data[0] + " " + JU.DF.formatDecimal (freq, 2) + " cm-1 (" + JU.DF.formatDecimal (JU.PT.fVal (data[1]), 0) + " km/Mole), " + activity);
}, "~N,~A");
Clazz.defineMethod (c$, "readGradient",
function () {
var key = null;
while (this.line != null) {
var tokens = this.getTokens ();
if (this.line.indexOf ("MAX GRAD") >= 0) key = "maxGradient";
else if (this.line.indexOf ("RMS GRAD") >= 0) key = "rmsGradient";
else if (this.line.indexOf ("MAX DISP") >= 0) key = "maxDisplacement";
else if (this.line.indexOf ("RMS DISP") >= 0) key = "rmsDisplacement";
else break;
if (this.asc.ac > 0) this.asc.setAtomSetModelProperty (key, tokens[2]);
this.rd ();
}
return true;
});
Clazz.defineMethod (c$, "readData",
function (name, nfields) {
this.createAtomsFromCoordLines ();
var f = Clazz.newFloatArray (this.ac, 0);
for (var i = 0; i < this.ac; i++) f[i] = 0;
var data = "";
while (this.rd () != null && (this.line.length < 4 || JU.PT.isDigit (this.line.charAt (3)))) data += this.line;
data = JU.PT.rep (data, "-", " -");
var tokens = JU.PT.getTokens (data);
for (var i = 0, pt = nfields - 1; i < this.ac; i++, pt += nfields) {
var iConv = this.getAtomIndexFromPrimitiveIndex (i);
if (iConv >= 0) f[iConv] = this.parseFloatStr (tokens[pt]);
}
this.asc.setAtomProperties (name, f, -1, false);
return true;
}, "~S,~N");
Clazz.defineMethod (c$, "getQuadrupoleTensors",
function () {
this.readLines (6);
var atoms = this.asc.atoms;
while (this.rd () != null && this.line.startsWith (" *** ATOM")) {
var tokens = this.getTokens ();
var index = this.parseIntStr (tokens[3]) - 1;
tokens = JU.PT.getTokens (this.readLines (3));
var vectors = new Array (3);
for (var i = 0; i < 3; i++) {
vectors[i] = JU.V3.newV (this.directLatticeVectors[i]);
vectors[i].normalize ();
}
atoms[index].addTensor ( new JU.Tensor ().setFromEigenVectors (vectors, Clazz.newFloatArray (-1, [this.parseFloatStr (tokens[1]), this.parseFloatStr (tokens[3]), this.parseFloatStr (tokens[5])]), "quadrupole", atoms[index].atomName, null), null, false);
this.rd ();
}
this.appendLoadNote ("Ellipsoids set \"quadrupole\": Quadrupole tensors");
return true;
});
Clazz.defineMethod (c$, "readBornChargeTensors",
function () {
this.createAtomsFromCoordLines ();
this.rd ();
var atoms = this.asc.atoms;
while (this.rd ().startsWith (" ATOM")) {
var index = this.parseIntAt (this.line, 5) - 1;
var atom = atoms[index];
this.readLines (2);
var a = Clazz.newDoubleArray (3, 3, 0);
for (var i = 0; i < 3; i++) {
var tokens = JU.PT.getTokens (this.rd ());
for (var j = 0; j < 3; j++) a[i][j] = this.parseFloatStr (tokens[j + 1]);
}
atom.addTensor ( new JU.Tensor ().setFromAsymmetricTensor (a, "charge", atom.elementSymbol + (index + 1)), null, false);
this.rd ();
}
this.appendLoadNote ("Ellipsoids set \"charge\": Born charge tensors");
return false;
});
});

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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.DmolReader", ["java.lang.Double", "JU.DF", "$.PT", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.unitCellData = null;
this.totE = null;
this.geomOpt = false;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "DmolReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains ("** GEOMETRY OPTIMIZATION IN DELOCALIZED COORDINATES **")) {
this.geomOpt = true;
} else if (this.line.contains ("INCOOR, atomic coordinates")) {
this.geomOpt = false;
} else if (!this.geomOpt ? this.line.contains ("$cell vectors") : this.line.contains ("Lattice:")) {
this.readCellParam ();
} else if (!this.geomOpt ? this.line.contains ("$coordinates") : this.line.contains ("Input Coordinates")) {
this.readCoord ();
} else if (this.line.contains (" Total Energy")) {
this.readEnergy ();
} else if (this.line.contains ("Frequencies (cm-1)")) {
this.readFreq ();
}return true;
});
Clazz.defineMethod (c$, "readCellParam",
function () {
this.unitCellData = Clazz.newFloatArray (9, 0);
for (var n = 0, i = 0; n < 3; n++) {
var tokens = JU.PT.getTokens (this.rd ());
this.unitCellData[i++] = this.parseFloatStr (!this.geomOpt ? tokens[0] : tokens[4]) * 0.5291772;
this.unitCellData[i++] = this.parseFloatStr (!this.geomOpt ? tokens[1] : tokens[5]) * 0.5291772;
this.unitCellData[i++] = this.parseFloatStr (!this.geomOpt ? tokens[2] : tokens[6]) * 0.5291772;
}
});
Clazz.defineMethod (c$, "newAtomSet",
function () {
this.applySymmetryAndSetTrajectory ();
this.asc.newAtomSet ();
if (this.totE != null) this.setEnergy ();
this.doApplySymmetry = true;
if (this.unitCellData != null) {
this.addExplicitLatticeVector (0, this.unitCellData, 0);
this.addExplicitLatticeVector (1, this.unitCellData, 3);
this.addExplicitLatticeVector (2, this.unitCellData, 6);
this.setSpaceGroupName ("P1");
}this.setFractionalCoordinates (false);
});
Clazz.defineMethod (c$, "readCoord",
function () {
this.newAtomSet ();
if (this.geomOpt) this.readLines (2);
while (this.rd () != null && !this.geomOpt ? !this.line.contains ("$end") : !this.line.contains ("-----")) {
var tokens = this.getTokens ();
var atom = this.asc.addNewAtom ();
atom.atomName = !this.geomOpt ? tokens[0] : tokens[1];
var factor = (!this.geomOpt ? 0.5291772 : 1.00);
var x = this.parseFloatStr (!this.geomOpt ? tokens[1] : tokens[2]) * factor;
var y = this.parseFloatStr (!this.geomOpt ? tokens[2] : tokens[3]) * factor;
var z = this.parseFloatStr (!this.geomOpt ? tokens[3] : tokens[4]) * factor;
atom.set (x, y, z);
this.setAtomCoord (atom);
}
});
Clazz.defineMethod (c$, "readEnergy",
function () {
this.rd ();
if (this.line.contains ("Ef")) this.totE = Double.$valueOf (Double.parseDouble (JU.PT.getTokens (this.line.substring (this.line.indexOf ("Ef") + 1, this.line.indexOf ("Ha")))[1]));
});
Clazz.defineMethod (c$, "setEnergy",
function () {
this.asc.setAtomSetEnergy ("" + this.totE, this.totE.floatValue ());
this.asc.setInfo ("Energy", this.totE);
this.asc.setAtomSetName ("E = " + this.totE + " Hartree");
});
Clazz.defineMethod (c$, "readFreq",
function () {
var lastAtomCount = 0;
var ac = this.asc.getLastAtomSetAtomCount ();
while (this.rd () != null && this.line.charAt (1) == ' ') {
var tokens = this.getTokens ();
var frequencyCount = Clazz.doubleToInt (tokens.length / 2);
var frequencies = Clazz.newFloatArray (frequencyCount, 0);
for (var i = 1, n = 0; i < tokens.length; i += 2, n++) {
frequencies[n] = this.parseFloatStr (tokens[i]);
if (this.debugging) JU.Logger.debug ((this.vibrationNumber + n) + " frequency=" + frequencies[n]);
}
var ignore = Clazz.newBooleanArray (frequencyCount, false);
var iAtom0 = 0;
for (var i = 0; i < frequencyCount; i++) {
ignore[i] = (!this.doGetVibration (++this.vibrationNumber));
if (ignore[i]) continue;
this.applySymmetryAndSetTrajectory ();
lastAtomCount = this.cloneLastAtomSet (ac, null);
if (i == 0) iAtom0 = this.asc.getLastAtomSetAtomIndex ();
this.asc.setAtomSetFrequency (null, null, String.valueOf (frequencies[i]), null);
this.asc.setAtomSetName (JU.DF.formatDecimal (frequencies[i], 2) + " cm-1");
}
this.rd ();
this.fillFrequencyData (iAtom0, ac, lastAtomCount, ignore, false, 5, 13, null, 0);
this.readLines (2);
}
});
});

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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.EspressoReader", ["java.lang.Double", "JU.PT"], function () {
c$ = Clazz.decorateAsClass (function () {
this.cellParams = null;
this.totEnergy = null;
this.endFlag = false;
this.aPar = 0;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "EspressoReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setSpaceGroupName ("P1");
this.doApplySymmetry = true;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains ("lattice parameter (a_0)") || this.line.contains ("lattice parameter (alat)")) {
this.readAparam ();
} else if (this.line.contains ("crystal axes:")) {
this.readCellParam (false);
} else if (this.line.contains ("CELL_PARAMETERS (")) {
this.readCellParam (true);
} else if (this.line.contains ("Cartesian axes")) {
this.discardLinesUntilContains ("positions (");
if (this.doGetModel (++this.modelNumber, null)) this.readAtoms ();
} else if (this.line.contains ("POSITIONS (")) {
if (this.doGetModel (++this.modelNumber, null)) this.readAtoms ();
} else if (this.line.contains ("! total energy")) {
this.readEnergy ();
} else if (this.line.contains ("A final scf")) {
this.endFlag = true;
}return true;
});
Clazz.defineMethod (c$, "readAparam",
function () {
this.aPar = this.parseFloatStr (this.getTokens ()[4]) * 0.5291772;
});
Clazz.defineMethod (c$, "readCellParam",
function (andAPar) {
var i0 = (andAPar ? 0 : 3);
if (this.line.contains ("bohr")) this.aPar = 0.5291772;
if (andAPar && this.line.contains ("=")) this.aPar = this.parseFloatStr (this.line.substring (this.line.indexOf ("=") + 1)) * 0.5291772;
this.cellParams = Clazz.newFloatArray (9, 0);
for (var n = 0, i = 0; n < 3; n++) {
var tokens = JU.PT.getTokens (this.rd ());
this.cellParams[i++] = this.parseFloatStr (tokens[i0]) * this.aPar;
this.cellParams[i++] = this.parseFloatStr (tokens[i0 + 1]) * this.aPar;
this.cellParams[i++] = this.parseFloatStr (tokens[i0 + 2]) * this.aPar;
}
}, "~B");
Clazz.defineMethod (c$, "newAtomSet",
function () {
this.asc.newAtomSet ();
if (this.totEnergy != null) this.setEnergy ();
});
Clazz.defineMethod (c$, "setCellParams",
function () {
if (this.cellParams != null) {
this.addExplicitLatticeVector (0, this.cellParams, 0);
this.addExplicitLatticeVector (1, this.cellParams, 3);
this.addExplicitLatticeVector (2, this.cellParams, 6);
this.setSpaceGroupName ("P1");
}});
Clazz.defineMethod (c$, "readAtoms",
function () {
this.newAtomSet ();
var isAlat = (this.line.contains ("alat") || this.line.contains ("a_0"));
var firstStr = (this.line.contains ("site n."));
var isFractional = this.line.contains ("crystal");
var isBohr = this.line.contains ("bohr");
var isAngstrom = this.line.contains ("angstrom");
if (isAlat || isFractional || isAngstrom) this.setCellParams ();
this.setFractionalCoordinates (isFractional);
while (this.rd () != null && this.line.length > 45) {
var tokens = this.getTokens ();
var atom = this.asc.addNewAtom ();
atom.atomName = tokens[(isBohr || tokens.length == 4 || !firstStr ? 0 : 1)];
var i1 = (isBohr || tokens.length == 4 || !firstStr ? 1 : tokens.length - 4);
var x = this.parseFloatStr (tokens[i1++]);
var y = this.parseFloatStr (tokens[i1++]);
var z = this.parseFloatStr (tokens[i1++]);
atom.set (x, y, z);
if (isBohr) {
atom.scale (0.5291772);
} else if (isAlat) {
atom.scale (this.aPar);
}this.setAtomCoord (atom);
}
this.applySymmetryAndSetTrajectory ();
if (this.endFlag) this.discardLinesUntilContains ("Harris-Foulkes estimate");
});
Clazz.defineMethod (c$, "readEnergy",
function () {
this.totEnergy = Double.$valueOf (Double.parseDouble (JU.PT.getTokens (this.line.substring (this.line.indexOf ("=") + 1))[0]));
});
Clazz.defineMethod (c$, "setEnergy",
function () {
this.asc.setAtomSetEnergy ("" + this.totEnergy, this.totEnergy.floatValue ());
this.asc.setInfo ("Energy", this.totEnergy);
this.asc.setAtomSetName ("E = " + this.totEnergy + " Ry");
});
});

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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.GulpReader", ["java.lang.Double", "$.Float", "java.util.Hashtable", "JU.PT", "$.V3"], function () {
c$ = Clazz.decorateAsClass (function () {
this.isSlab = false;
this.isPolymer = false;
this.$isPrimitive = false;
this.sep = "-------";
this.coordinatesArePrimitive = false;
this.atomCharges = null;
this.bTest = false;
this.a = 0;
this.b = 0;
this.c = 0;
this.alpha = 0;
this.beta = 0;
this.gamma = 0;
this.primitiveData = null;
this.totEnergy = null;
this.energyUnits = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "GulpReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.$isPrimitive = !this.checkFilterKey ("CONV");
this.coordinatesArePrimitive = true;
this.setFractionalCoordinates (this.readDimensionality ());
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (this.atomCharges == null) return;
var atoms = this.asc.atoms;
var f;
for (var i = this.asc.ac; --i >= 0; ) if ((f = this.atomCharges.get (atoms[i].atomName)) != null || (f = this.atomCharges.get (atoms[i].getElementSymbol ())) != null) atoms[i].partialCharge = f.floatValue ();
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains ("Space group ")) {
this.readSpaceGroup ();
return true;
}if (this.isSlab ? this.line.contains ("Surface cell parameters") : this.isPolymer ? this.line.contains ("Polymer cell parameter") : (this.bTest = this.line.contains ("Cartesian lattice vectors")) || this.line.contains ("Cell parameters (Angstroms/Degrees)") || this.line.contains ("Primitive cell parameters")) {
this.readCellParameters (this.bTest);
return true;
}if (this.line.contains ("Monopole - monopole (total)")) {
this.readEnergy ();
return true;
}if (this.line.contains ("Fractional coordinates of asymmetric unit :") || (this.bTest = this.line.contains ("Final asymmetric unit coordinates")) || (this.bTest = this.line.contains ("Final fractional coordinates ")) || this.line.contains ("Mixed fractional/Cartesian coordinates") || this.line.contains ("Cartesian coordinates of cluster ") || this.line.contains ("Final cartesian coordinates of atoms :") && this.isMolecular) {
if (this.doGetModel (++this.modelNumber, null)) this.readAtomicPos (!this.bTest);
return true;
}if (this.line.contains ("Species output for all configurations")) {
this.readPartialCharges ();
return true;
}if (!this.doProcessLines) return true;
if (this.line.contains ("Final cell parameters and derivatives")) {
this.readFinalCell ();
return true;
}return true;
});
Clazz.defineMethod (c$, "readDimensionality",
function () {
this.discardLinesUntilContains ("Dimensionality");
var tokens = this.getTokens ();
switch (this.parseIntStr (tokens[2])) {
case 0:
this.isMolecular = true;
this.$isPrimitive = false;
return false;
case 1:
this.isPolymer = true;
this.$isPrimitive = false;
break;
case 2:
this.isSlab = true;
this.$isPrimitive = false;
break;
}
return true;
});
Clazz.defineMethod (c$, "readSpaceGroup",
function () {
this.sgName = this.line.substring (this.line.indexOf (":") + 1).trim ();
});
c$.parameterIndex = Clazz.defineMethod (c$, "parameterIndex",
function (key) {
for (var i = J.adapter.readers.xtal.GulpReader.tags.length; --i >= 0; ) if (J.adapter.readers.xtal.GulpReader.tags[i].equals (key)) return i;
return -1;
}, "~S");
Clazz.defineMethod (c$, "setParameter",
function (key, value) {
switch (J.adapter.readers.xtal.GulpReader.parameterIndex (key)) {
case 0:
this.a = value;
break;
case 1:
this.b = value;
break;
case 2:
this.c = value;
break;
case 3:
this.alpha = value;
break;
case 4:
this.beta = value;
break;
case 5:
this.gamma = value;
break;
}
}, "~S,~N");
Clazz.defineMethod (c$, "newAtomSet",
function (doSetUnitCell) {
this.asc.newAtomSet ();
if (doSetUnitCell) {
this.setModelParameters (this.coordinatesArePrimitive);
if (this.totEnergy != null) this.setEnergy ();
}}, "~B");
Clazz.defineMethod (c$, "setModelParameters",
function (isPrimitive) {
if (this.sgName != null) this.setSpaceGroupName (isPrimitive ? "P1" : this.sgName);
if (isPrimitive && this.primitiveData != null) {
this.addExplicitLatticeVector (0, this.primitiveData, 0);
this.addExplicitLatticeVector (1, this.primitiveData, 3);
this.addExplicitLatticeVector (2, this.primitiveData, 6);
} else if (this.a != 0) {
if (this.isSlab) {
this.c = -1;
this.beta = this.gamma = 90;
} else if (this.isPolymer) {
this.b = this.c = -1;
this.alpha = this.beta = this.gamma = 90;
}this.setUnitCell (this.a, this.b, this.c, this.alpha, this.beta, this.gamma);
}}, "~B");
Clazz.defineMethod (c$, "readCellParameters",
function (isLatticeVectors) {
if (isLatticeVectors) {
this.rd ();
this.primitiveData = this.fillFloatArray (null, 0, Clazz.newFloatArray (9, 0));
this.a = 0;
return;
}var i0 = (this.line.indexOf ("Full cell") < 0 ? 0 : 4);
this.coordinatesArePrimitive = (i0 == 0);
this.rd ();
while (this.rd () != null && this.line.contains ("=")) {
var tokens = JU.PT.getTokens (this.line.$replace ('=', ' '));
for (var i = i0; i < i0 + 4; i += 2) if (tokens.length > i + 1) this.setParameter (tokens[i], this.parseFloatStr (tokens[i + 1]));
}
}, "~B");
Clazz.defineMethod (c$, "readFinalCell",
function () {
this.discardLinesUntilContains (this.sep);
var tokens;
while (this.rd () != null && (tokens = this.getTokens ()).length >= 2) this.setParameter (tokens[0], this.parseFloatStr (tokens[1]));
if (this.primitiveData != null) {
this.scalePrimitiveData (0, this.a);
this.scalePrimitiveData (3, this.b);
this.scalePrimitiveData (6, this.c);
if (!this.coordinatesArePrimitive) while (this.rd () != null && this.line.indexOf ("Final") < 0) if (this.line.indexOf ("Non-primitive lattice parameters") > 0) {
this.rd ();
for (var i = 0; i < 2; i++) {
tokens = JU.PT.getTokens (this.rd ().$replace ('=', ' '));
this.setParameter (tokens[0], this.parseFloatStr (tokens[1]));
this.setParameter (tokens[2], this.parseFloatStr (tokens[3]));
this.setParameter (tokens[4], this.parseFloatStr (tokens[5]));
}
break;
}
}this.setModelParameters (this.coordinatesArePrimitive);
this.applySymmetryAndSetTrajectory ();
if (this.totEnergy != null) this.setEnergy ();
});
Clazz.defineMethod (c$, "scalePrimitiveData",
function (i, value) {
var v = JU.V3.new3 (this.primitiveData[i], this.primitiveData[i + 1], this.primitiveData[i + 2]);
v.normalize ();
v.scale (value);
this.primitiveData[i++] = v.x;
this.primitiveData[i++] = v.y;
this.primitiveData[i++] = v.z;
}, "~N,~N");
Clazz.overrideMethod (c$, "applySymmetryAndSetTrajectory",
function () {
if (this.coordinatesArePrimitive && this.iHaveUnitCell && this.doCheckUnitCell && this.primitiveData != null && !this.$isPrimitive) {
this.setModelParameters (false);
var symFull = this.symmetry;
this.setModelParameters (true);
var atoms = this.asc.atoms;
var i0 = this.asc.getLastAtomSetAtomIndex ();
var i1 = this.asc.ac;
for (var i = i0; i < i1; i++) {
var atom = atoms[i];
this.symmetry.toCartesian (atom, true);
symFull.toFractional (atom, true);
if (this.fixJavaFloat) JU.PT.fixPtFloats (atom, 100000.0);
}
this.setModelParameters (false);
}this.applySymTrajASCR ();
});
Clazz.defineMethod (c$, "readAtomicPos",
function (finalizeSymmetry) {
this.newAtomSet (finalizeSymmetry);
this.discardLinesUntilContains (this.sep);
this.discardLinesUntilContains (this.sep);
while (this.rd () != null) {
if (this.line.indexOf (this.sep) >= 0 && this.rd ().indexOf ("Region") < 0) break;
if (this.line.indexOf ("Region") >= 0) {
this.rd ();
continue;
}this.line = this.line.$replace ('*', ' ');
var tokens = this.getTokens ();
if (tokens[2].equals ("c")) this.addAtomXYZSymName (tokens, 3, null, tokens[1]);
}
if (finalizeSymmetry) this.applySymmetryAndSetTrajectory ();
}, "~B");
Clazz.defineMethod (c$, "readPartialCharges",
function () {
this.atomCharges = new java.util.Hashtable ();
this.discardLinesUntilContains (this.sep);
this.discardLinesUntilContains (this.sep);
var tokens;
while ((tokens = JU.PT.getTokens (this.rd ())).length > 5) {
var species = tokens[0];
var charge = this.atomCharges.get (species);
var f = (charge == null ? 0 : charge.floatValue ());
this.atomCharges.put (species, Float.$valueOf ((f + this.parseFloatStr (tokens[4]))));
}
});
Clazz.defineMethod (c$, "readEnergy",
function () {
if (this.line.indexOf ("=") < 0) this.discardLinesUntilContains ("=");
var tokens = JU.PT.getTokens (this.line.substring (this.line.indexOf ("=")));
this.totEnergy = Double.$valueOf (Double.parseDouble (tokens[1]));
this.energyUnits = tokens[2];
this.discardLinesUntilContains (this.sep);
});
Clazz.defineMethod (c$, "setEnergy",
function () {
this.asc.setAtomSetEnergy ("" + this.totEnergy, this.totEnergy.floatValue ());
this.asc.setInfo ("Energy", this.totEnergy);
this.asc.setAtomSetName ("E = " + this.totEnergy + " " + this.energyUnits);
this.totEnergy = null;
});
Clazz.defineStatics (c$,
"tags", Clazz.newArray (-1, ["a", "b", "c", "alpha", "beta", "gamma"]));
});

575
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.JanaReader", ["java.lang.Boolean", "$.Exception", "$.Float", "java.util.Hashtable", "JU.A4", "$.BS", "$.Lst", "$.Matrix", "$.P3", "$.PT", "$.Quat", "$.Rdr", "$.V3", "J.adapter.smarter.Atom", "J.api.Interface", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.lattvecs = null;
this.thisSub = 0;
this.modAxes = null;
this.modDim = 0;
this.haveM40Data = false;
this.qicount = 0;
this.molName = null;
this.molAtoms = null;
this.molTtypes = null;
this.modelMolecule = null;
this.molHasTLS = false;
this.matR = null;
this.rho = null;
this.firstPosition = false;
this.vR = null;
this.v0Cart = null;
this.isLegendre = false;
this.floats = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "JanaReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.floats = Clazz.newFloatArray (6, 0);
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.modAxes = this.getFilter ("MODAXES=");
this.setFractionalCoordinates (true);
this.asc.newAtomSet ();
this.asc.setCurrentModelInfo ("autoBondUsingOccupation", Boolean.TRUE);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.length < 3) return true;
JU.Logger.info (this.line);
this.parseTokenStr (this.line);
switch ("tit cell ndim qi lat sym spg end wma".indexOf (this.line.substring (0, 3))) {
case 0:
this.asc.setAtomSetName (this.line.substring (5).trim ());
break;
case 5:
this.cell ();
this.setSymmetryOperator ("x,y,z");
break;
case 10:
this.ndim ();
break;
case 20:
if (this.lattvecs == null) this.lattvecs = new JU.Lst ();
if (!this.ms.addLatticeVector (this.lattvecs, this.line.substring (8))) this.appendLoadNote (this.line + " not supported");
break;
case 30:
this.setSpaceGroupName (this.getTokens ()[1]);
break;
case 25:
this.symmetry ();
break;
case 15:
this.qi ();
break;
case 35:
while (this.rd () != null) {
if (this.line.startsWith ("command") || this.parseIntStr (this.line) >= 0) {
this.readM40Data (true);
break;
}}
this.continuing = false;
break;
case 40:
var n = 3 + this.modDim;
var m;
if (this.thisSub++ == 0) {
m = JU.Matrix.identity (n, n);
this.ms.addSubsystem ("" + this.thisSub++, m);
}m = new JU.Matrix (null, n, n);
var a = m.getArray ();
var data = Clazz.newFloatArray (n * n, 0);
this.fillFloatArray (null, 0, data);
for (var i = 0, pt = 0; i < n; i++) for (var j = 0; j < n; j++, pt++) a[i][j] = data[pt];
this.ms.addSubsystem ("" + this.thisSub, m);
}
return true;
});
Clazz.overrideMethod (c$, "doPreSymmetry",
function () {
if (this.ms != null) this.ms.setModulation (false, null);
if (this.vibsFractional) this.asc.getXSymmetry ().scaleFractionalVibs ();
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
if (!this.haveM40Data) this.readM40Data (false);
if (this.lattvecs != null && this.lattvecs.size () > 0) this.asc.getSymmetry ().addLatticeVectors (this.lattvecs);
this.applySymmetryAndSetTrajectory ();
this.finalizeReaderASCR ();
});
Clazz.overrideMethod (c$, "finalizeSubclassSymmetry",
function (haveSymmetry) {
this.adjustM40Occupancies ();
if (this.ms != null && haveSymmetry) {
this.ms.setModulation (true, this.asc.getXSymmetry ().getBaseSymmetry ());
this.ms.finalizeModulation ();
}}, "~B");
Clazz.defineMethod (c$, "cell",
function () {
for (var ipt = 0; ipt < 6; ipt++) this.setUnitCellItem (ipt, this.parseFloat ());
});
Clazz.defineMethod (c$, "ndim",
function () {
this.ms = J.api.Interface.getOption ("adapter.readers.cif.MSRdr", this.vwr, "file");
this.modDim = this.ms.initialize (this, (this.parseIntStr (this.getTokens ()[1]) - 3));
});
Clazz.defineMethod (c$, "qi",
function () {
var pt = Clazz.newDoubleArray (this.modDim, 0);
pt[this.qicount] = 1;
var a = Clazz.newDoubleArray (-1, [this.parseFloat (), this.parseFloat (), this.parseFloat ()]);
this.parseTokenStr (this.rd ());
for (var i = 0; i < 3; i++) a[i] += this.parseFloat ();
this.ms.addModulation (null, "W_" + (++this.qicount), a, -1);
this.ms.addModulation (null, "F_" + this.qicount + "_coefs_", pt, -1);
});
Clazz.defineMethod (c$, "symmetry",
function () {
this.setSymmetryOperator (JU.PT.rep (this.line.substring (9).trim (), " ", ","));
});
Clazz.defineMethod (c$, "readM40Data",
function (haveReader) {
if (haveReader) {
this.parseM40Floats ();
} else {
var m40File = this.filePath;
var ipt = m40File.lastIndexOf (".");
if (ipt < 0) return;
m40File = m40File.substring (0, ipt + 2) + "40";
var id = m40File.substring (0, ipt);
this.reader.close ();
this.reader = JU.Rdr.getBR (this.vwr.getLigandModel (id, m40File, "_file", "----"));
if (this.out != null) this.out.append ("******************************* M40 DATA *******************************\n");
this.readM40Floats ();
}this.haveM40Data = true;
if (this.line.startsWith ("command")) this.readM40WaveVectors ();
var nFree = 0;
var nGroups = 0;
var isAxial = false;
var newSub = (this.thisSub == 0 ? null : new JU.BS ());
var iSub = (this.thisSub == 0 ? 1 : this.thisSub);
for (var i = 0, n = 0, pt = 0; i < iSub; i++, pt += 10) {
nFree = this.getInt (pt, pt + 5);
nGroups = this.getInt (pt + 5, pt + 10);
isAxial = (this.getInt (pt + 15, pt + 20) == 1);
if (nGroups != 0 && i > 0) {
throw new Exception ("Jmol cannot read rigid body M40 files for composites");
}if (newSub != null) newSub.set (n = n + nFree);
}
iSub = (newSub == null ? 0 : 1);
var nAtoms = -1;
var refAtomName = null;
this.rho = null;
if (nGroups > 0) {
JU.Logger.info ("JanaReader found " + nFree + " free atoms and " + nGroups + " groups");
this.molName = null;
this.molAtoms = new JU.Lst ();
this.molTtypes = new JU.Lst ();
}while (this.skipToNextAtom () != null) {
nAtoms++;
var atom = new J.adapter.smarter.Atom ();
JU.Logger.info (this.line);
var name = this.line.substring (0, 9).trim ();
atom.atomName = name;
var isRefAtom = name.equals (refAtomName);
atom.foccupancy = this.floats[2];
var isJanaMolecule = Float.isNaN (atom.foccupancy);
if (isJanaMolecule) {
var pointGroup = this.getStr (12, 18);
if (pointGroup.length > 0 && !pointGroup.equals ("1")) {
throw new Exception ("Jmol cannot process M40 files with molecule positions based on point-group symmetry.");
}refAtomName = null;
if (Float.isNaN (this.floats[4])) refAtomName = this.getStr (28, 37);
else this.rho = JU.P3.new3 (this.floats[3], this.floats[4], this.floats[5]);
this.molName = name;
this.molAtoms.clear ();
this.molTtypes.clear ();
this.molHasTLS = false;
this.firstPosition = true;
this.modelMolecule = new JU.Lst ();
continue;
}var isExcluded = false;
var posName = (name.startsWith ("pos#") ? name : null);
if (posName == null) {
if (!this.filterAtom (atom, 0)) {
if (!isRefAtom) continue;
isExcluded = true;
}this.setAtomCoordXYZ (atom, this.floats[3], this.floats[4], this.floats[5]);
if (isRefAtom) {
this.rho = JU.P3.newP (atom);
if (isExcluded) continue;
}this.asc.addAtom (atom);
if (iSub > 0) {
if (newSub.get (nAtoms)) iSub++;
atom.altLoc = ("" + iSub).charAt (0);
}this.readAtomRecord (atom, null, null, false);
if (this.molAtoms != null) this.molAtoms.addLast (atom);
} else {
if (this.molAtoms.size () == 0) continue;
this.processPosition (posName, atom, isAxial);
}}
}, "~B");
Clazz.defineMethod (c$, "getInt",
function (col1, col2) {
var n = this.line.length;
return (n > col1 ? this.parseIntStr (this.getStr (col1, col2)) : 0);
}, "~N,~N");
Clazz.defineMethod (c$, "getStr",
function (col1, col2) {
var n = this.line.length;
return (n > col1 ? this.line.substring (col1, Math.min (n, col2)).trim () : "");
}, "~N,~N");
Clazz.defineMethod (c$, "getFlag",
function (i) {
return (this.getInt (i, i + 1) > 0);
}, "~N");
Clazz.defineMethod (c$, "skipToNextAtom",
function () {
while (this.readM40Floats () != null && (this.line.length == 0 || this.line.charAt (0) == ' ' || this.line.charAt (0) == '-')) {
}
return this.line;
});
Clazz.defineMethod (c$, "readM40WaveVectors",
function () {
while (!this.readM40Floats ().contains ("end")) if (this.line.startsWith ("wave")) {
var tokens = this.getTokens ();
var pt = Clazz.newDoubleArray (this.modDim, 0);
for (var i = 0; i < this.modDim; i++) pt[i] = this.parseFloatStr (tokens[i + 2]);
this.ms.addModulation (null, "F_" + this.parseIntStr (tokens[1]) + "_coefs_", pt, -1);
}
this.readM40Floats ();
});
Clazz.defineMethod (c$, "processPosition",
function (posName, pos, isAxial) {
pos.atomName = this.molName + "_" + posName;
var isImproper = (this.getInt (9, 11) == -1);
var systType = this.getInt (13, 14);
var rm = (systType == 0 ? null : new JU.P3 ());
var rp = (systType == 0 ? null : new JU.P3 ());
if (systType != 0) {
throw new Exception ("Jmol can only read rigid body groups with basic crystallographic settings.");
}var rotData = this.readAtomRecord (pos, rm, rp, true);
var name = pos.atomName;
var n = this.molAtoms.size ();
JU.Logger.info (name + " Molecular group " + this.molName + " has " + n + " atoms");
var ext = "_" + posName.substring (4);
var vTrans = JU.V3.new3 (pos.anisoBorU[3], pos.anisoBorU[4], pos.anisoBorU[5]);
var phi = JU.Quat.newAA (JU.A4.newVA (JU.V3.new3 (0, 0, 1), (pos.anisoBorU[0] / 180 * 3.141592653589793)));
var chi = JU.Quat.newAA (JU.A4.newVA (isAxial ? JU.V3.new3 (0, 1, 0) : JU.V3.new3 (1, 0, 0), (pos.anisoBorU[1] / 180 * 3.141592653589793)));
var psi = JU.Quat.newAA (JU.A4.newVA (isAxial ? JU.V3.new3 (1, 0, 0) : JU.V3.new3 (0, 0, 1), (pos.anisoBorU[2] / 180 * 3.141592653589793)));
this.matR = phi.mulQ (chi).mulQ (psi).getMatrix ();
if (isImproper) this.matR.scale (-1);
var script = "";
for (var i = 0; i < n; i++) {
var a = this.molAtoms.get (i);
var newName = a.atomName;
script += ", " + newName;
if (this.firstPosition) {
newName += ext;
this.modelMolecule.addLast (JU.P3.newP (a));
} else {
a = this.asc.newCloneAtom (a);
newName = newName.substring (0, newName.lastIndexOf ("_")) + ext;
}a.atomName = newName;
var v0 = JU.V3.newVsub (this.modelMolecule.get (i), this.rho);
this.getSymmetry ().toCartesian (this.v0Cart = JU.V3.newV (v0), true);
this.vR = JU.V3.newV (v0);
this.cartesianProduct (this.vR, null);
a.setT (this.rho);
a.add (vTrans);
a.add (this.vR);
this.copyModulations (";" + pos.atomName, ";" + newName);
if (rotData != null) this.setRigidBodyRotations (";" + newName, rotData);
}
this.firstPosition = false;
script = "@" + this.molName + ext + script.substring (1);
this.addJmolScript (script);
this.appendLoadNote (script);
}, "~S,J.adapter.smarter.Atom,~B");
Clazz.defineMethod (c$, "cartesianProduct",
function (vA, vB) {
this.symmetry.toCartesian (vA, true);
if (vB == null) this.matR.rotate2 (vA, vA);
else vA.cross (vA, vB);
this.symmetry.toFractional (vA, true);
}, "JU.T3,JU.T3");
Clazz.defineMethod (c$, "readAtomRecord",
function (atom, rm, rp, isPos) {
var label = ";" + atom.atomName;
var tType = (isPos ? -1 : this.getInt (13, 14));
if (!isPos && this.molTtypes != null) this.molTtypes.addLast (Integer.$valueOf (tType));
var haveSpecialOcc = this.getFlag (60);
var haveSpecialDisp = this.getFlag (61);
var haveSpecialUij = this.getFlag (62);
var nOcc = this.getInt (65, 68);
var nDisp = this.getInt (68, 71);
var nUij = this.getInt (71, 74);
if (rm != null) {
this.readM40Floats ();
rm.set (this.floats[0], this.floats[1], this.floats[2]);
rp.set (this.floats[3], this.floats[4], this.floats[5]);
}if (tType > 2) this.readM40Floats ();
this.readM40Floats ();
switch (tType) {
case 6:
case 5:
case 4:
case 3:
this.readLines (tType - 1);
this.appendLoadNote ("Skipping temperature factors with order > 2");
case 2:
case -1:
for (var j = 0; j < 6; j++) this.asc.setU (atom, j, this.floats[j]);
break;
case 1:
if (this.floats[0] != 0) this.asc.setU (atom, 7, this.floats[0]);
break;
case 0:
this.molHasTLS = true;
this.appendLoadNote ("Jmol cannot process molecular TLS parameters");
break;
}
if (this.modDim == 0) return null;
if (isPos && this.molHasTLS) this.readLines (4);
var pt;
var o_0 = (nOcc > 0 && !haveSpecialOcc ? this.parseFloatStr (this.rd ()) : 1);
if (o_0 != 1) this.ms.addModulation (null, "J_O#0" + label, Clazz.newDoubleArray (-1, [atom.foccupancy, o_0, 0]), -1);
atom.foccupancy *= o_0;
var wv = 0;
var a1;
var a2;
this.isLegendre = false;
for (var j = 0; j < nOcc; j++) {
if (haveSpecialOcc) {
var data = this.readM40FloatLines (2, 1);
a2 = data[0][0];
a1 = data[1][0];
} else {
wv = j + 1;
this.readM40Floats ();
a1 = this.floats[0];
a2 = this.floats[1];
}pt = Clazz.newDoubleArray (-1, [a1, a2, 0]);
if (a1 != 0 || a2 != 0) this.ms.addModulation (null, "O_" + wv + "#0" + label, pt, -1);
}
for (var j = 0; j < nDisp; j++) {
if (haveSpecialDisp) {
this.readM40Floats ();
var c = this.floats[3];
var w = this.floats[4];
for (var k = 0; k < 3; k++) if (this.floats[k] != 0) this.ms.addModulation (null, "D_S#" + J.adapter.readers.xtal.JanaReader.XYZ[k] + label, Clazz.newDoubleArray (-1, [c, w, this.floats[k]]), -1);
} else {
this.addSinCos (j, "D_", label, isPos);
}}
var rotData = (isPos && nDisp > 0 ? this.readM40FloatLines (nDisp, 6) : null);
if (!isPos) {
if (this.isLegendre) nUij *= 2;
for (var j = 0; j < nUij; j++) {
if (tType == 1) {
this.addSinCos (j, "U_", label, false);
} else {
if (haveSpecialUij) {
JU.Logger.error ("JanaReader -- not interpreting SpecialUij flag: " + this.line);
} else if (this.isLegendre) {
var data = this.readM40FloatLines (1, 6);
var order = j + 1;
var coeff = 0;
for (var k = 0, p = 0; k < 6; k++, p += 3) {
if ((coeff = data[0][k]) != 0) this.ms.addModulation (null, "U_L" + order + "#" + "U11U22U33U12U13U23UISO".substring (p, p + 3) + label, Clazz.newDoubleArray (-1, [coeff, order, 0]), -1);
}
} else {
var data = this.readM40FloatLines (2, 6);
for (var k = 0, p = 0; k < 6; k++, p += 3) {
var csin = data[1][k];
var ccos = data[0][k];
this.ms.addModulation (null, "U_" + (j + 1) + "#" + "U11U22U33U12U13U23UISO".substring (p, p + 3) + label, Clazz.newDoubleArray (-1, [csin, ccos, 0]), -1);
}
}}}
}return rotData;
}, "J.adapter.smarter.Atom,JU.P3,JU.P3,~B");
Clazz.defineMethod (c$, "addSinCos",
function (j, key, label, isPos) {
this.readM40Floats ();
if (this.isLegendre) {
for (var i = 0; i < 2; i++) {
var order = (j * 2 + i + 1);
for (var k = 0; k < 3; ++k) {
var coeff = this.floats[3 * i + k];
if (coeff == 0) {
continue;
}var axis = J.adapter.readers.xtal.JanaReader.XYZ[k % 3];
if (this.modAxes != null && this.modAxes.indexOf (axis.toUpperCase ()) < 0) continue;
var id = key + "L#" + axis + order + label;
this.ms.addModulation (null, id, Clazz.newDoubleArray (-1, [coeff, order, 0]), -1);
}
}
return;
}this.ensureFourier (j);
for (var k = 0; k < 3; ++k) {
var csin = this.floats[k];
var ccos = this.floats[k + 3];
if (csin == 0 && ccos == 0) {
if (!isPos) continue;
csin = 1e-10;
}var axis = J.adapter.readers.xtal.JanaReader.XYZ[k % 3];
if (this.modAxes != null && this.modAxes.indexOf (axis.toUpperCase ()) < 0) continue;
var id = key + (j + 1) + "#" + axis + label;
this.ms.addModulation (null, id, Clazz.newDoubleArray (-1, [csin, ccos, 0]), -1);
}
}, "~N,~S,~S,~B");
Clazz.defineMethod (c$, "ensureFourier",
function (j) {
var pt;
if (j > 0 && this.ms.getMod ("F_" + (++j) + "_coefs_") == null && (pt = this.ms.getMod ("F_1_coefs_")) != null) {
var p = Clazz.newDoubleArray (this.modDim, 0);
for (var i = this.modDim; --i >= 0; ) p[i] = pt[i] * j;
this.ms.addModulation (null, "F_" + j + "_coefs_", p, -1);
}}, "~N");
Clazz.defineMethod (c$, "readM40Floats",
function () {
if ((this.line = this.rd ()) == null || this.line.indexOf ("-------") >= 0) return (this.line = null);
if (this.debugging) JU.Logger.debug (this.line);
this.parseM40Floats ();
return this.line;
});
Clazz.defineMethod (c$, "parseM40Floats",
function () {
var ptLast = this.line.length - 9;
for (var i = 0, pt = 0; i < 6; i++, pt += 9) {
this.floats[i] = (pt <= ptLast ? this.parseFloatStr (this.line.substring (pt, pt + 9)) : NaN);
}
});
Clazz.defineMethod (c$, "readM40FloatLines",
function (nLines, nFloats) {
var data = Clazz.newFloatArray (nLines, nFloats, 0);
for (var i = 0; i < nLines; i++) {
this.readM40Floats ();
if (this.line.indexOf ("Legendre") == 19) this.isLegendre = true;
for (var j = 0; j < nFloats; j++) data[i][j] = this.floats[j];
}
return data;
}, "~N,~N");
Clazz.defineMethod (c$, "adjustM40Occupancies",
function () {
var htSiteMult = new java.util.Hashtable ();
var atoms = this.asc.atoms;
var symmetry = this.asc.getSymmetry ();
for (var i = this.asc.ac; --i >= 0; ) {
var a = atoms[i];
var ii = htSiteMult.get (a.atomName);
if (ii == null) htSiteMult.put (a.atomName, ii = Integer.$valueOf (symmetry.getSiteMultiplicity (a)));
a.foccupancy *= ii.intValue ();
}
});
Clazz.defineMethod (c$, "copyModulations",
function (label, newLabel) {
var mapTemp = new java.util.Hashtable ();
for (var e, $e = this.ms.getModulationMap ().entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
var key = e.getKey ();
if (!key.contains (label)) continue;
key = JU.PT.rep (key, label, newLabel);
var val = e.getValue ();
switch (key.charAt (0)) {
case 'O':
this.setRigidBodyPhase (key, val = Clazz.newDoubleArray (-1, [val[0], val[1], 0]));
break;
case 'D':
break;
case 'U':
continue;
}
mapTemp.put (key, val);
}
for (var e, $e = mapTemp.entrySet ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) this.ms.addModulation (null, e.getKey (), e.getValue (), -1);
}, "~S,~S");
Clazz.defineMethod (c$, "setRigidBodyPhase",
function (key, v) {
var isCenter = false;
switch (this.ms.getModType (key)) {
case 'o':
case 'f':
case 'u':
break;
case 'c':
case 's':
isCenter = true;
break;
}
var nqDotD = 0;
var n = -1;
var qcoefs = this.ms.getQCoefs (key);
for (var i = this.modDim; --i >= 0; ) {
if (qcoefs[i] != 0) {
n = qcoefs[i];
var q = this.ms.getMod ("W_" + (i + 1));
nqDotD = n * (q[0] * this.vR.x + q[1] * this.vR.y + q[2] * this.vR.z);
break;
}}
if (isCenter) {
v[0] += nqDotD;
} else {
var sA = v[0];
var cA = v[1];
var sX = Math.sin (2 * 3.141592653589793 * nqDotD);
var cX = Math.cos (2 * 3.141592653589793 * nqDotD);
v[0] = sA * cX + cA * sX;
v[1] = -sA * sX + cA * cX;
}return v;
}, "~S,~A");
Clazz.defineMethod (c$, "setRigidBodyRotations",
function (label, params) {
var n = params.length;
for (var i = 0; i < n; i++) {
this.ensureFourier (i);
var key = "D_" + (i + 1);
var data = params[i];
var vsin = JU.V3.new3 (data[0], data[1], data[2]);
var vcos = JU.V3.new3 (data[3], data[4], data[5]);
this.cartesianProduct (vcos, this.v0Cart);
this.cartesianProduct (vsin, this.v0Cart);
var keyx = key + "#x" + label;
var keyy = key + "#y" + label;
var keyz = key + "#z" + label;
var vx = this.combineModulation (keyx, vsin.x, vcos.x);
var vy = this.combineModulation (keyy, vsin.y, vcos.y);
var vz = this.combineModulation (keyz, vsin.z, vcos.z);
vsin.set (vx[0], vy[0], vz[0]);
vcos.set (vx[1], vy[1], vz[1]);
this.cartesianProduct (vsin, null);
this.cartesianProduct (vcos, null);
this.setMolecularModulation (keyx, vsin.x, vcos.x);
this.setMolecularModulation (keyy, vsin.y, vcos.y);
this.setMolecularModulation (keyz, vsin.z, vcos.z);
}
}, "~S,~A");
Clazz.defineMethod (c$, "combineModulation",
function (key, csin, ccos) {
var v = this.ms.getMod (key);
return Clazz.newDoubleArray (-1, [v[0] + csin, v[1] + ccos, 0]);
}, "~S,~N,~N");
Clazz.defineMethod (c$, "setMolecularModulation",
function (key, csin, ccos) {
this.ms.addModulation (null, key, this.setRigidBodyPhase (key, Clazz.newDoubleArray (-1, [csin, ccos, 0])), -1);
}, "~S,~N,~N");
Clazz.defineStatics (c$,
"records", "tit cell ndim qi lat sym spg end wma",
"TITLE", 0,
"CELL", 5,
"NDIM", 10,
"QI", 15,
"LATT", 20,
"SYM", 25,
"SPG", 30,
"END", 35,
"WMATRIX", 40,
"U_LIST", "U11U22U33U12U13U23UISO",
"XYZ", Clazz.newArray (-1, ["x", "y", "z"]));
});

184
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/MagresReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader", "java.util.Hashtable", "JU.Lst", "$.SB"], "J.adapter.readers.xtal.MagresReader", ["java.lang.Double", "JU.PT", "J.adapter.smarter.Atom", "JU.Escape", "$.Logger", "$.Tensor"], function () {
c$ = Clazz.decorateAsClass (function () {
this.currentBlock = -1;
this.cellParams = null;
this.magresUnits = null;
this.interactionTensors = null;
this.header = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "MagresReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.magresUnits = new java.util.Hashtable ();
this.interactionTensors = new JU.Lst ();
this.header = new JU.SB ();
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setFractionalCoordinates (false);
this.ignoreFileSpaceGroupName = true;
});
Clazz.overrideMethod (c$, "finalizeSubclassReader",
function () {
this.asc.setInfo ("fileHeader", this.header.toString ());
this.finalizeReaderASCR ();
if (this.interactionTensors.size () > 0) this.asc.setCurrentModelInfo ("interactionTensors", this.interactionTensors);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (!this.trimLine ()) return true;
switch (this.checkBlock ()) {
case 0:
this.header.append (this.line).append ("\n");
this.appendLoadNote (this.line);
break;
case 1:
if (this.cellParams == null && this.line.startsWith ("lattice")) return this.readCellParams ();
if (this.line.startsWith ("symmetry")) return this.readSymmetry ();
if (this.line.startsWith ("units")) return this.setUnits (false);
if (this.line.startsWith ("atom")) return this.readAtom ();
break;
case 2:
if (this.line.startsWith ("units")) return this.setUnits (true);
return this.readTensor ();
}
return true;
});
Clazz.defineMethod (c$, "trimLine",
function () {
var pt = this.line.indexOf ("#");
if (pt >= 0) this.line = this.line.substring (0, pt);
this.line = this.line.trim ();
return (this.line.length > 0);
});
Clazz.defineMethod (c$, "checkBlock",
function () {
if (!(this.line.startsWith ("<") && this.line.endsWith (">")) && !(this.line.startsWith ("[") && this.line.endsWith ("]"))) return this.currentBlock;
this.line = JU.PT.rep (this.line, "<", "[");
this.line = JU.PT.rep (this.line, ">", "]");
switch (Clazz.doubleToInt (("...............[calculation]..[/calculation].[atoms]........[/atoms].......[magres].......[/magres]......").indexOf (this.line + ".") / 15)) {
case 0:
JU.Logger.info ("block indicator ignored: " + this.line);
break;
case 1:
if (this.currentBlock == -1) this.currentBlock = 0;
break;
case 2:
if (this.currentBlock == 0) this.currentBlock = -1;
break;
case 3:
if (this.currentBlock == -1) {
this.currentBlock = 1;
this.asc.newAtomSet ();
this.magresUnits = new java.util.Hashtable ();
}break;
case 4:
if (this.currentBlock == 1) this.currentBlock = -1;
break;
case 5:
if (this.currentBlock == -1) {
this.currentBlock = 2;
this.magresUnits = new java.util.Hashtable ();
this.asc.setCurrentModelInfo ("magresUnits", this.magresUnits);
}break;
case 6:
if (this.currentBlock == 2) this.currentBlock = -1;
break;
}
return -2;
});
Clazz.defineMethod (c$, "setUnits",
function (isMagresBlock) {
var tokens = this.getTokens ();
var id = tokens[1];
if (isMagresBlock) this.appendLoadNote ("Ellipsoid set " + JU.PT.esc (id) + ": " + (id.startsWith ("ms") ? "Magnetic Shielding" : id.startsWith ("efg") ? "Electric Field Gradient" : id.startsWith ("isc") ? "J-Coupling" : "?"));
this.magresUnits.put (id, tokens[2]);
return true;
}, "~B");
Clazz.defineMethod (c$, "readSymmetry",
function () {
this.setSymmetryOperator (this.getTokens ()[1]);
return true;
});
Clazz.defineMethod (c$, "readCellParams",
function () {
var tokens = this.getTokens ();
this.cellParams = Clazz.newFloatArray (9, 0);
for (var i = 0; i < 9; i++) this.cellParams[i] = this.parseFloatStr (tokens[i + 1]);
this.addExplicitLatticeVector (0, this.cellParams, 0);
this.addExplicitLatticeVector (1, this.cellParams, 3);
this.addExplicitLatticeVector (2, this.cellParams, 6);
this.setSpaceGroupName ("P1");
return true;
});
Clazz.defineMethod (c$, "readAtom",
function () {
var units = this.magresUnits.get ("atom");
if (units == null) return true;
var f = (units.startsWith ("A") ? 1 : 0.5291772);
var tokens = this.getTokens ();
var atom = new J.adapter.smarter.Atom ();
var pt = 1;
atom.elementSymbol = tokens[pt++];
atom.atomName = J.adapter.readers.xtal.MagresReader.getAtomName (tokens[pt++], tokens[pt++]);
this.asc.addAtomWithMappedName (atom);
var x = this.parseFloatStr (tokens[pt++]) * f;
var y = this.parseFloatStr (tokens[pt++]) * f;
var z = this.parseFloatStr (tokens[pt++]) * f;
atom.set (x, y, z);
this.setAtomCoord (atom);
return true;
});
c$.getAtomName = Clazz.defineMethod (c$, "getAtomName",
function (name, index) {
return name + "_" + index;
}, "~S,~S");
Clazz.defineMethod (c$, "readTensor",
function () {
var tokens = this.getTokens ();
var type = tokens[0];
var units = this.magresUnits.get (type);
if (units == null) {
JU.Logger.warn (type + " ignored; no units defined; line: " + this.line);
return true;
}var isIsc = type.startsWith ("isc");
if (tokens.length == 10) {
this.magresUnits.remove (type);
var data = Clazz.newFloatArray (9, 0);
for (var i = 0; i < 9; ) data[i] = this.parseFloatStr (tokens[++i]);
JU.Logger.info ("Magres reader creating magres_" + type + ": " + JU.Escape.eAF (data));
this.asc.setCurrentModelInfo ("magres_" + type, data);
}var atomName1 = J.adapter.readers.xtal.MagresReader.getAtomName (tokens[1], tokens[2]);
var pt = 3;
var atomName2 = (isIsc ? J.adapter.readers.xtal.MagresReader.getAtomName (tokens[pt++], tokens[pt++]) : null);
if (atomName1.equals (atomName2)) {
JU.Logger.warn (type + " ignored; atom1 == atom2 for " + atomName1 + " line: " + this.line);
return true;
}var id = atomName1;
if (atomName2 != null) id += "//" + atomName2;
var a = Clazz.newDoubleArray (3, 3, 0);
for (var i = 0; i < 3; i++) for (var j = 0; j < 3; j++) a[i][j] = Double.$valueOf (tokens[pt++]).doubleValue ();
var a1 = this.asc.getAtomFromName (atomName1);
if (a1 == null) return true;
var a2 = null;
var t = new JU.Tensor ().setFromAsymmetricTensor (a, type, id);
if (atomName2 == null) {
a1.addTensor (t, null, false);
} else {
a2 = this.asc.getAtomFromName (atomName2);
if (a2 == null) return true;
this.interactionTensors.addLast (t);
}t.setAtomIndexes (a1.index, (a2 == null ? -1 : a2.index));
return true;
});
Clazz.defineStatics (c$,
"BLOCK_NEW", -2,
"BLOCK_NONE", -1,
"BLOCK_CALC", 0,
"BLOCK_ATOMS", 1,
"BLOCK_MAGRES", 2);
});

183
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/ShelxReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.ShelxReader", ["java.lang.Float", "JU.AU", "$.PT", "J.adapter.smarter.Atom", "JU.Logger"], function () {
c$ = Clazz.decorateAsClass (function () {
this.sfacElementSymbols = null;
this.isCmdf = false;
this.tokens = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "ShelxReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.setFractionalCoordinates (true);
});
Clazz.overrideMethod (c$, "checkLine",
function () {
var lineLength;
while ((lineLength = (this.line = this.line.trim ()).length) > 0 && this.line.charAt (lineLength - 1) == '=') this.line = this.line.substring (0, lineLength - 1) + this.rd ();
this.tokens = this.getTokens ();
if (this.tokens.length == 0) return true;
var command = this.tokens[0].toUpperCase ();
if (command.equals ("TITL")) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.sfacElementSymbols = null;
this.applySymmetryAndSetTrajectory ();
this.setFractionalCoordinates (true);
this.asc.newAtomSet ();
this.asc.setAtomSetName (this.line.substring (4).trim ());
return true;
}if (!this.doProcessLines || lineLength < 3) return true;
if (";ZERR;DISP;UNIT;LAUE;REM;MORE;TIME;HKLF;OMIT;SHEL;BASF;TWIN;EXTI;SWAT;HOPE;MERG;SPEC;RESI;MOVE;ANIS;AFIX;HFIX;FRAG;FEND;EXYZ;EXTI;EADP;EQIV;CONN;PART;BIND;FREE;DFIX;DANG;BUMP;SAME;SADI;CHIV;FLAT;DELU;SIMU;DEFS;ISOR;NCSY;SUMP;L.S.;CGLS;BLOC;DAMP;STIR;WGHT;FVAR;BOND;CONF;MPLA;RTAB;HTAB;LIST;ACTA;SIZE;TEMP;WPDB;FMAP;GRID;PLAN;MOLE;".indexOf (";" + command + ";") >= 0) return true;
for (var i = J.adapter.readers.xtal.ShelxReader.supportedRecordTypes.length; --i >= 0; ) if (command.equals (J.adapter.readers.xtal.ShelxReader.supportedRecordTypes[i])) {
this.processSupportedRecord (i);
return true;
}
if (!this.isCmdf) this.assumeAtomRecord ();
return true;
});
Clazz.defineMethod (c$, "processSupportedRecord",
function (recordIndex) {
switch (recordIndex) {
case 0:
case 8:
break;
case 1:
this.cell ();
this.setSymmetryOperator ("x,y,z");
break;
case 2:
this.setSpaceGroupName (JU.PT.parseTrimmedAt (this.line, 4));
break;
case 3:
this.parseSfacRecord ();
break;
case 4:
this.parseLattRecord ();
break;
case 5:
this.parseSymmRecord ();
break;
case 6:
this.isCmdf = true;
break;
case 7:
this.isCmdf = true;
this.processCmdfAtoms ();
break;
}
}, "~N");
Clazz.defineMethod (c$, "parseLattRecord",
function () {
this.asc.getXSymmetry ().setLatticeParameter (this.parseIntStr (this.tokens[1]));
});
Clazz.defineMethod (c$, "parseSymmRecord",
function () {
this.setSymmetryOperator (this.line.substring (4).trim ());
});
Clazz.defineMethod (c$, "cell",
function () {
var ioff = this.tokens.length - 6;
if (ioff == 2) this.asc.setInfo ("wavelength", Float.$valueOf (this.parseFloatStr (this.tokens[1])));
for (var ipt = 0; ipt < 6; ipt++) this.setUnitCellItem (ipt, this.parseFloatStr (this.tokens[ipt + ioff]));
});
Clazz.defineMethod (c$, "parseSfacRecord",
function () {
var allElementSymbols = true;
for (var i = this.tokens.length; allElementSymbols && --i >= 1; ) {
var token = this.tokens[i];
allElementSymbols = J.adapter.readers.xtal.ShelxReader.isValidElementSymbolNoCaseSecondChar (token);
}
var sfacTokens = JU.PT.getTokens (this.line.substring (4));
if (allElementSymbols) this.parseSfacElementSymbols (sfacTokens);
else this.parseSfacCoefficients (sfacTokens);
});
Clazz.defineMethod (c$, "parseSfacElementSymbols",
function (sfacTokens) {
if (this.sfacElementSymbols == null) {
this.sfacElementSymbols = sfacTokens;
} else {
var oldCount = this.sfacElementSymbols.length;
var tokenCount = sfacTokens.length;
this.sfacElementSymbols = JU.AU.arrayCopyS (this.sfacElementSymbols, oldCount + tokenCount);
for (var i = tokenCount; --i >= 0; ) this.sfacElementSymbols[oldCount + i] = sfacTokens[i];
}}, "~A");
Clazz.defineMethod (c$, "parseSfacCoefficients",
function (sfacTokens) {
var a1 = this.parseFloatStr (sfacTokens[1]);
var a2 = this.parseFloatStr (sfacTokens[3]);
var a3 = this.parseFloatStr (sfacTokens[5]);
var a4 = this.parseFloatStr (sfacTokens[7]);
var c = this.parseFloatStr (sfacTokens[9]);
var z = Math.round (a1 + a2 + a3 + a4 + c);
var elementSymbol = J.adapter.smarter.AtomSetCollectionReader.getElementSymbol (z);
var oldCount = 0;
if (this.sfacElementSymbols == null) {
this.sfacElementSymbols = new Array (1);
} else {
oldCount = this.sfacElementSymbols.length;
this.sfacElementSymbols = JU.AU.arrayCopyS (this.sfacElementSymbols, oldCount + 1);
this.sfacElementSymbols[oldCount] = elementSymbol;
}this.sfacElementSymbols[oldCount] = elementSymbol;
}, "~A");
Clazz.defineMethod (c$, "assumeAtomRecord",
function () {
var atomName = this.tokens[0];
var elementIndex = this.parseIntStr (this.tokens[1]);
var x = this.parseFloatStr (this.tokens[2]);
var y = this.parseFloatStr (this.tokens[3]);
var z = this.parseFloatStr (this.tokens[4]);
if (Float.isNaN (x) || Float.isNaN (y) || Float.isNaN (z)) {
JU.Logger.error ("skipping line " + this.line);
return;
}elementIndex--;
var atom = this.asc.addNewAtom ();
atom.atomName = atomName;
if (this.sfacElementSymbols != null && elementIndex >= 0 && elementIndex < this.sfacElementSymbols.length) atom.elementSymbol = this.sfacElementSymbols[elementIndex];
this.setAtomCoordXYZ (atom, x, y, z);
if (this.tokens.length == 12) {
var data = Clazz.newFloatArray (8, 0);
data[0] = this.parseFloatStr (this.tokens[6]);
data[1] = this.parseFloatStr (this.tokens[7]);
data[2] = this.parseFloatStr (this.tokens[8]);
data[3] = this.parseFloatStr (this.tokens[11]);
data[4] = this.parseFloatStr (this.tokens[10]);
data[5] = this.parseFloatStr (this.tokens[9]);
for (var i = 0; i < 6; i++) if (Float.isNaN (data[i])) {
JU.Logger.error ("Bad anisotropic Uij data: " + this.line);
return;
}
this.asc.setAnisoBorU (atom, data, 8);
}});
Clazz.defineMethod (c$, "processCmdfAtoms",
function () {
while (this.rd () != null && this.line.length > 10) {
this.tokens = this.getTokens ();
this.addAtomXYZSymName (this.tokens, 2, this.getSymbol (this.tokens[0]), this.tokens[1]);
}
});
Clazz.defineMethod (c$, "getSymbol",
function (sym) {
if (sym == null) return "Xx";
var len = sym.length;
if (len < 2) return sym;
var ch1 = sym.charAt (1);
if (ch1 >= 'a' && ch1 <= 'z') return sym.substring (0, 2);
return "" + sym.charAt (0);
}, "~S");
c$.isValidElementSymbolNoCaseSecondChar = Clazz.defineMethod (c$, "isValidElementSymbolNoCaseSecondChar",
function (str) {
if (str == null) return false;
var length = str.length;
if (length == 0) return false;
var chFirst = str.charAt (0);
if (length == 1) return J.adapter.smarter.Atom.isValidSym1 (chFirst);
if (length > 2) return false;
var chSecond = str.charAt (1);
return J.adapter.smarter.Atom.isValidSymNoCase (chFirst, chSecond);
}, "~S");
Clazz.defineStatics (c$,
"unsupportedRecordTypes", ";ZERR;DISP;UNIT;LAUE;REM;MORE;TIME;HKLF;OMIT;SHEL;BASF;TWIN;EXTI;SWAT;HOPE;MERG;SPEC;RESI;MOVE;ANIS;AFIX;HFIX;FRAG;FEND;EXYZ;EXTI;EADP;EQIV;CONN;PART;BIND;FREE;DFIX;DANG;BUMP;SAME;SADI;CHIV;FLAT;DELU;SIMU;DEFS;ISOR;NCSY;SUMP;L.S.;CGLS;BLOC;DAMP;STIR;WGHT;FVAR;BOND;CONF;MPLA;RTAB;HTAB;LIST;ACTA;SIZE;TEMP;WPDB;FMAP;GRID;PLAN;MOLE;",
"supportedRecordTypes", Clazz.newArray (-1, ["TITL", "CELL", "SPGR", "SFAC", "LATT", "SYMM", "NOTE", "ATOM", "END"]));
});

81
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/SiestaReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.SiestaReader", ["java.lang.Double"], function () {
c$ = Clazz.decorateAsClass (function () {
this.noAtoms = 0;
this.unitCellData = null;
Clazz.instantialize (this, arguments);
}, J.adapter.readers.xtal, "SiestaReader", J.adapter.smarter.AtomSetCollectionReader);
Clazz.prepareFields (c$, function () {
this.unitCellData = Clazz.newFloatArray (9, 0);
});
Clazz.overrideMethod (c$, "initializeReader",
function () {
this.doApplySymmetry = true;
});
Clazz.overrideMethod (c$, "checkLine",
function () {
if (this.line.contains ("%block LatticeVectors")) {
if (this.doGetModel (++this.modelNumber, null)) this.readCellThenAtomsCartesian ();
return true;
} else if (this.line.contains ("outcoor: Atomic coordinates")) {
if (this.doGetModel (++this.modelNumber, null)) this.readAtomsCartGeomThenCell ();
return true;
}return true;
});
Clazz.defineMethod (c$, "setCell",
function () {
this.fillFloatArray (null, 0, this.unitCellData);
this.addExplicitLatticeVector (0, this.unitCellData, 0);
this.addExplicitLatticeVector (1, this.unitCellData, 3);
this.addExplicitLatticeVector (2, this.unitCellData, 6);
});
Clazz.defineMethod (c$, "readCellThenAtomsCartesian",
function () {
this.newAtomSet ();
this.setCell ();
this.discardLinesUntilContains ("AtomicCoordinatesFormat Ang");
this.rd ();
this.setFractionalCoordinates (false);
while (this.rd () != null && this.line.indexOf ("%endblock Atomic") < 0) {
var tokens = this.getTokens ();
this.addAtomXYZSymName (tokens, 0, null, tokens[4]);
}
this.noAtoms = this.asc.ac;
});
Clazz.defineMethod (c$, "newAtomSet",
function () {
this.applySymmetryAndSetTrajectory ();
this.asc.newAtomSet ();
this.setSpaceGroupName ("P1");
this.setFractionalCoordinates (false);
});
Clazz.defineMethod (c$, "readAtomsCartGeomThenCell",
function () {
this.readLines (1);
this.newAtomSet ();
var atom0 = this.asc.ac;
for (var i = 0; i < this.noAtoms; i++) {
var tokens = this.getTokens ();
var atom = this.asc.addNewAtom ();
atom.atomName = tokens[4];
var x = this.parseFloatStr (tokens[0]);
var y = this.parseFloatStr (tokens[1]);
var z = this.parseFloatStr (tokens[2]);
atom.set (x, y, z);
this.rd ();
}
this.discardLinesUntilContains ("outcell: Unit cell vectors");
this.setCell ();
var atoms = this.asc.atoms;
var ac = this.asc.ac;
for (var i = atom0; i < ac; i++) this.setAtomCoord (atoms[i]);
this.discardLinesUntilContains ("siesta: E_KS(eV) = ");
var tokens = this.getTokens ();
var energy = Double.$valueOf (Double.parseDouble (tokens[3]));
this.asc.setAtomSetEnergy ("" + energy, energy.floatValue ());
this.asc.setCurrentModelInfo ("Energy", energy);
this.asc.setInfo ("Energy", energy);
this.asc.setAtomSetName ("Energy = " + energy + " eV");
});
});

4
CTF/Smol/wordpress.old/wp-content/plugins/jsmol2wp/j2s/J/adapter/readers/xtal/VaspChgcarReader.js Normal file
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Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.readers.xtal.VaspPoscarReader"], "J.adapter.readers.xtal.VaspChgcarReader", null, function () {
c$ = Clazz.declareType (J.adapter.readers.xtal, "VaspChgcarReader", J.adapter.readers.xtal.VaspPoscarReader);
});

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