biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/J/adapter/readers/xtal/ShelxReader.js

A BioJS 2.0 component to view protein structures

Clazz.declarePackage ("J.adapter.readers.xtal");
Clazz.load (["J.adapter.smarter.AtomSetCollectionReader"], "J.adapter.readers.xtal.ShelxReader", ["java.lang.Float", "JU.AU", "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$, "processSupportedRecord", 
 function (recordIndex) {
switch (recordIndex) {
case 0:
case 8:
break;
case 1:
this.cell ();
this.setSymmetryOperator ("x,y,z");
break;
case 2:
this.setSpaceGroupName (J.adapter.smarter.AtomSetCollectionReader.parseTrimmedAt (this.line, 4));
break;
case 3:
this.parseSfacRecord ();
break;
case 4:
this.parseLattRecord ();
break;
case 5:
this.parseSymmRecord ();
break;
case 6:
this.isCmdf = true;
break;
case 7:
this.isCmdf = true;
this.processCmdfAtoms ();
break;
}
}, "~N");
Clazz.defineMethod (c$, "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$, "parseSfacRecord", 
 function () {
var allElementSymbols = true;
for (var i = this.tokens.length; allElementSymbols && --i >= 1; ) {
var token = this.tokens[i];
allElementSymbols = J.adapter.smarter.Atom.isValidElementSymbolNoCaseSecondChar (token);
}
var sfacTokens = J.adapter.smarter.AtomSetCollectionReader.getTokensStr (this.line.substring (4));
if (allElementSymbols) this.parseSfacElementSymbols (sfacTokens);
 else this.parseSfacCoefficients (sfacTokens);
});
Clazz.defineMethod (c$, "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");
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", ["TITL", "CELL", "SPGR", "SFAC", "LATT", "SYMM", "NOTE", "ATOM", "END"]);
});