biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/JM/FF/ForceField.js

A BioJS 2.0 component to view protein structures

Clazz.declarePackage ("JM.FF");
Clazz.load (null, "JM.FF.ForceField", ["java.lang.Float", "J.io.JmolBinary", "JM.Util", "JU.Logger", "$.Txt", "JV.Viewer"], function () {
c$ = Clazz.decorateAsClass (function () {
this.name = null;
this.calc = null;
this.criterion = 0;
this.e0 = 0;
this.dE = 0;
this.currentStep = 0;
this.stepMax = 0;
this.coordSaved = null;
this.minAtomCount = 0;
this.minBondCount = 0;
this.minAtoms = null;
this.minBonds = null;
this.minAngles = null;
this.minTorsions = null;
this.minPositions = null;
this.bsFixed = null;
this.minimizer = null;
Clazz.instantialize (this, arguments);
}, JM.FF, "ForceField");
Clazz.defineMethod (c$, "setModelFields", 
function () {
this.minAtoms = this.minimizer.minAtoms;
this.minBonds = this.minimizer.minBonds;
this.minAngles = this.minimizer.minAngles;
this.minTorsions = this.minimizer.minTorsions;
this.bsFixed = this.minimizer.bsMinFixed;
this.minAtomCount = this.minAtoms.length;
this.minBondCount = this.minBonds.length;
});
Clazz.defineMethod (c$, "setConstraints", 
function (m) {
this.bsFixed = m.bsMinFixed;
this.calc.setConstraints (m.constraints);
this.coordSaved = null;
}, "JM.Minimizer");
Clazz.defineMethod (c$, "steepestDescentInitialize", 
function (stepMax, criterion) {
this.stepMax = stepMax;
this.criterion = criterion / this.toUserUnits (1);
this.currentStep = 0;
this.clearForces ();
this.calc.setLoggingEnabled (true);
this.calc.setLoggingEnabled (stepMax == 0 || JU.Logger.isActiveLevel (6));
var s = this.name + " " + this.calc.getDebugHeader (-1) + "Jmol Minimization Version " + JV.Viewer.getJmolVersion () + "\n";
this.calc.appendLogData (s);
JU.Logger.info (s);
this.calc.getConstraintList ();
if (this.calc.loggingEnabled) this.calc.appendLogData (this.calc.getAtomList ("S T E E P E S T   D E S C E N T"));
this.dE = 0;
this.calc.setPreliminary (stepMax > 0);
this.e0 = this.energyFull (false, false);
s = JU.Txt.sprintf (" Initial " + this.name + " E = %10.3f " + this.minimizer.units + " criterion = %8.6f max steps = " + stepMax, "ff", [Float.$valueOf (this.toUserUnits (this.e0)), Float.$valueOf (this.toUserUnits (criterion))]);
this.minimizer.report (s, false);
this.calc.appendLogData (s);
}, "~N,~N");
Clazz.defineMethod (c$, "clearForces", 
 function () {
for (var i = 0; i < this.minAtomCount; i++) this.minAtoms[i].force[0] = this.minAtoms[i].force[1] = this.minAtoms[i].force[2] = 0;

});
Clazz.defineMethod (c$, "steepestDescentTakeNSteps", 
function (n) {
if (this.stepMax == 0) return false;
var isPreliminary = true;
for (var iStep = 1; iStep <= n; iStep++) {
this.currentStep++;
this.calc.setSilent (true);
for (var i = 0; i < this.minAtomCount; i++) if (this.bsFixed == null || !this.bsFixed.get (i)) this.setForcesUsingNumericalDerivative (this.minAtoms[i], 1);

this.linearSearch ();
this.calc.setSilent (false);
if (this.calc.loggingEnabled) this.calc.appendLogData (this.calc.getAtomList ("S T E P    " + this.currentStep));
var e1 = this.energyFull (false, false);
this.dE = e1 - this.e0;
var done = JM.Util.isNear3 (e1, this.e0, this.criterion);
if (done || this.currentStep % 10 == 0 || this.stepMax <= this.currentStep) {
var s = JU.Txt.sprintf (this.name + " Step %-4d E = %10.6f    dE = %8.6f ", "Fi", [[e1, (this.dE), this.criterion], Integer.$valueOf (this.currentStep)]);
this.minimizer.report (s, false);
this.calc.appendLogData (s);
}this.e0 = e1;
if (done || this.stepMax <= this.currentStep) {
if (this.calc.loggingEnabled) this.calc.appendLogData (this.calc.getAtomList ("F I N A L  G E O M E T R Y"));
if (done) {
var s = JU.Txt.formatStringF ("\n    " + this.name + " STEEPEST DESCENT HAS CONVERGED: E = %8.5f " + this.minimizer.units + " after " + this.currentStep + " steps", "f", this.toUserUnits (e1));
this.calc.appendLogData (s);
this.minimizer.report (s, true);
JU.Logger.info (s);
}return false;
}if (isPreliminary && this.getNormalizedDE () >= 2) {
this.calc.setPreliminary (isPreliminary = false);
this.e0 = this.energyFull (false, false);
}}
return true;
}, "~N");
Clazz.defineMethod (c$, "getEnergies", 
 function (terms, gradients) {
if ((terms & 1) != 0) return this.energyFull (gradients, true);
var e = 0.0;
if ((terms & 2) != 0) e += this.energyBond (gradients);
if ((terms & 4) != 0) e += this.energyAngle (gradients);
if ((terms & 8) != 0) e += this.energyStretchBend (gradients);
if ((terms & 32) != 0) e += this.energyOOP (gradients);
if ((terms & 16) != 0) e += this.energyTorsion (gradients);
if ((terms & 64) != 0) e += this.energyVDW (gradients);
if ((terms & 128) != 0) e += this.energyES (gradients);
return e;
}, "~N,~B");
Clazz.defineMethod (c$, "setForcesUsingNumericalDerivative", 
 function (atom, terms) {
var delta = 1.0e-5;
atom.force[0] = -this.getDE (atom, terms, 0, delta);
atom.force[1] = -this.getDE (atom, terms, 1, delta);
atom.force[2] = -this.getDE (atom, terms, 2, delta);
return;
}, "JM.MinAtom,~N");
Clazz.defineMethod (c$, "getDE", 
 function (atom, terms, i, delta) {
atom.coord[i] += delta;
var e = this.getEnergies (terms, false);
atom.coord[i] -= delta;
return (e - this.e0) / delta;
}, "JM.MinAtom,~N,~N,~N");
Clazz.defineMethod (c$, "energyFull", 
function (gradients, isSilent) {
var energy;
if (gradients) this.clearForces ();
energy = this.energyBond (gradients) + this.energyAngle (gradients) + this.energyTorsion (gradients) + this.energyStretchBend (gradients) + this.energyOOP (gradients) + this.energyVDW (gradients) + this.energyES (gradients);
if (!isSilent && this.calc.loggingEnabled) this.calc.appendLogData (JU.Txt.sprintf ("\nTOTAL %s ENERGY = %8.3f %s/mol\n", "sfs", [this.name, Float.$valueOf (this.toUserUnits (energy)), this.minimizer.units]));
return energy;
}, "~B,~B");
Clazz.defineMethod (c$, "energyStretchBend", 
function (gradients) {
return this.calc.energyStretchBend (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyBond", 
function (gradients) {
return this.calc.energyBond (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyAngle", 
function (gradients) {
return this.calc.energyAngle (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyTorsion", 
function (gradients) {
return this.calc.energyTorsion (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyOOP", 
function (gradients) {
return this.calc.energyOOP (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyVDW", 
function (gradients) {
return this.calc.energyVDW (gradients);
}, "~B");
Clazz.defineMethod (c$, "energyES", 
function (gradients) {
return this.calc.energyES (gradients);
}, "~B");
Clazz.defineMethod (c$, "linearSearch", 
 function () {
var step = 0.23;
var trustRadius = 0.3;
var trustRadius2 = trustRadius * trustRadius;
var e1 = this.energyFull (false, true);
for (var iStep = 0; iStep < 10; iStep++) {
this.saveCoordinates ();
for (var i = 0; i < this.minAtomCount; ++i) if (this.bsFixed == null || !this.bsFixed.get (i)) {
var force = this.minAtoms[i].force;
var coord = this.minAtoms[i].coord;
var f2 = (force[0] * force[0] + force[1] * force[1] + force[2] * force[2]);
if (f2 > trustRadius2 / step / step) {
f2 = trustRadius / Math.sqrt (f2) / step;
force[0] *= f2;
force[1] *= f2;
force[2] *= f2;
}for (var j = 0; j < 3; ++j) {
if (JM.Util.isFinite (force[j])) {
var tempStep = force[j] * step;
if (tempStep > trustRadius) coord[j] += trustRadius;
 else if (tempStep < -trustRadius) coord[j] -= trustRadius;
 else coord[j] += tempStep;
}}
}
var e2 = this.energyFull (false, true);
if (JM.Util.isNear3 (e2, e1, 1.0e-3)) break;
if (e2 > e1) {
step *= 0.1;
this.restoreCoordinates ();
} else if (e2 < e1) {
e1 = e2;
step *= 2.15;
if (step > 1.0) step = 1.0;
}}
});
Clazz.defineMethod (c$, "saveCoordinates", 
 function () {
if (this.coordSaved == null) this.coordSaved =  Clazz.newDoubleArray (this.minAtomCount, 3, 0);
for (var i = 0; i < this.minAtomCount; i++) for (var j = 0; j < 3; j++) this.coordSaved[i][j] = this.minAtoms[i].coord[j];


});
Clazz.defineMethod (c$, "restoreCoordinates", 
 function () {
for (var i = 0; i < this.minAtomCount; i++) for (var j = 0; j < 3; j++) this.minAtoms[i].coord[j] = this.coordSaved[i][j];


});
Clazz.defineMethod (c$, "detectExplosion", 
function () {
for (var i = 0; i < this.minAtomCount; i++) {
var atom = this.minAtoms[i];
for (var j = 0; j < 3; j++) if (!JM.Util.isFinite (atom.coord[j])) return true;

}
for (var i = 0; i < this.minBondCount; i++) {
var bond = this.minBonds[i];
if (JM.Util.distance2 (this.minAtoms[bond.data[0]].coord, this.minAtoms[bond.data[1]].coord) > 900.0) return true;
}
return false;
});
Clazz.defineMethod (c$, "getCurrentStep", 
function () {
return this.currentStep;
});
Clazz.defineMethod (c$, "getEnergy", 
function () {
return this.e0;
});
Clazz.defineMethod (c$, "getAtomList", 
function (title) {
return this.calc.getAtomList (title);
}, "~S");
Clazz.defineMethod (c$, "getEnergyDiff", 
function () {
return this.dE;
});
Clazz.defineMethod (c$, "getLogData", 
function () {
return this.calc.getLogData ();
});
Clazz.defineMethod (c$, "getNormalizedDE", 
function () {
return Math.abs (this.dE / this.criterion);
});
Clazz.defineMethod (c$, "toUserUnits", 
function (energy) {
return this.toUnits (energy, this.calc.getUnits ());
}, "~N");
Clazz.defineMethod (c$, "toUnits", 
 function (energy, units) {
return (units.equalsIgnoreCase (this.minimizer.units) ? energy : energy * (this.minimizer.units.equals ("kJ") ? 4.1868 : 0.23884589662749595));
}, "~N,~S");
Clazz.defineMethod (c$, "log", 
function (s) {
this.calc.appendLogData (s);
}, "~S");
Clazz.defineMethod (c$, "getBufferedReader", 
function (resourceName) {
return J.io.JmolBinary.getBufferedReaderForResource (this.minimizer.vwr, this, "JM/FF/", "data/" + resourceName);
}, "~S");
Clazz.defineStatics (c$,
"ENERGY", (1),
"EBOND", (2),
"EANGLE", (4),
"ESTRBND", (8),
"ETORSION", (16),
"EOOP", (32),
"EVDW", (64),
"EELECTROSTATIC", (128),
"ABI_IJ", 3,
"ABI_JK", 4,
"TBI_AB", 4,
"TBI_BC", 5,
"TBI_CD", 6,
"R3", 0,
"R4", 1,
"R5", 2,
"R56", 3);
});