biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/J/adapter/readers/quantum/AdfReader.js

A BioJS 2.0 component to view protein structures

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", "$.Lst", "J.api.JmolAdapter", "J.quantum.SlaterData", "JU.Logger"], function () {
c$ = 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$, "checkLine", 
function () {
if (this.line.indexOf ("Irreducible Representations, including subspecies") >= 0) {
this.readSymmetries ();
return true;
}if (this.line.indexOf ("S F O s  ***  (Symmetrized Fragment Orbitals)  ***") >= 0) {
this.readSlaterBasis ();
return true;
}if (this.line.indexOf (" Coordinates (Cartesian, in Input Orientation)") >= 0 || this.line.indexOf ("G E O M E T R Y  ***") >= 0) {
if (!this.doGetModel (++this.modelNumber, null)) return this.checkLastModel ();
this.readCoordinates ();
return true;
}if (this.line.indexOf (" ======  Eigenvectors (rows) in BAS representation") >= 0) {
if (this.doReadMolecularOrbitals) this.readMolecularOrbitals (J.adapter.smarter.AtomSetCollectionReader.getTokensStr (this.symLine)[1]);
return true;
}if (!this.doProcessLines) return true;
if (this.line.indexOf ("Energy:") >= 0) {
var tokens = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (this.line.substring (this.line.indexOf ("Energy:")));
this.energy = tokens[1];
return true;
}if (this.line.indexOf ("Vibrations") >= 0) {
this.readFrequencies ();
return true;
}if (this.line.indexOf (" === ") >= 0) {
this.symLine = this.line;
return true;
}if (this.line.indexOf (" ======  Eigenvectors (rows) in BAS representation") >= 0) {
this.readMolecularOrbitals (J.adapter.smarter.AtomSetCollectionReader.getTokensStr (this.symLine)[1]);
return true;
}return true;
});
Clazz.defineMethod (c$, "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];
if (J.api.JmolAdapter.getElementNumber (symbol) < 1) this.nXX++;
 else this.addAtomXYZSymName (tokens, pt0, symbol, null);
}
});
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 = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (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.parseIntStr (this.rd ().substring (15));
sd.nBF = this.parseIntStr (this.rd ().substring (75));
var funcList = "";
while (this.rd () != null && this.line.length > 1) funcList += this.line;

var tokens = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (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 = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (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 = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (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 = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (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].iAtom += iAtom0;

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 ();
};
});