Clazz.declarePackage("J.quantum");
Clazz.load(["J.quantum.MepCalculation"], "J.quantum.MlpCalculation", ["JU.Logger"], function(){
var c$ = Clazz.declareType(J.quantum, "MlpCalculation", J.quantum.MepCalculation);
Clazz.makeConstructor(c$, 
function(){
Clazz.superConstructor(this, J.quantum.MlpCalculation);
this.distanceMode = 3;
});
Clazz.overrideMethod(c$, "assignPotentials", 
function(atoms, potentials, bsAromatic, bsCarbonyl, bsIgnore, data){
this.getAtomicPotentials(data, "atomicLipophilicity.txt");
for (var i = 0; i < atoms.length; i++) {
var f = Math.abs(atoms[i].getFormalCharge());
if (f == 0) {
if (bsIgnore != null && bsIgnore.get(i)) {
f = NaN;
} else {
f = this.getTabulatedPotential(atoms[i]);
if (Float.isNaN(f)) switch (atoms[i].getElementNumber()) {
case 6:
f = (bsAromatic.get(i) ? 0.31 : bsCarbonyl.get(i) ? -0.54 : 0.45);
break;
case 7:
f = (bsAromatic.get(i) ? -0.6 : bsCarbonyl.get(i) ? -0.44 : -1.0);
break;
case 8:
f = (bsCarbonyl.get(i) ? -0.9 : -0.17);
break;
default:
f = NaN;
}
}}if (JU.Logger.debugging) JU.Logger.debug(atoms[i].getInfo() + " " + f);
potentials[i] = f;
}
}, "~A,~A,JU.BS,JU.BS,JU.BS,~S");
});
;//5.0.1-v2 Tue Jul 23 17:25:20 CDT 2024
