boolean setupCalculations() {
Vector calc;
DistanceCalc distanceCalc = new DistanceCalc();
calc = calculations[CALC_DISTANCE] = new Vector();
for (int i = 0; i < bondCount; i++) {
MinBond bond = bonds[i];
double bondOrder = bond.atomIndexes[2];
if (bond.isAromatic) bondOrder = 1.5;
if (bond.isAmide) bondOrder = 1.41;
distanceCalc.setData(calc, bond.atomIndexes[0], bond.atomIndexes[1], bondOrder);
}
calc = calculations[CALC_ANGLE] = new Vector();
AngleCalc angleCalc = new AngleCalc();
for (int i = angles.length; --i >= 0; ) angleCalc.setData(calc, i);
calc = calculations[CALC_TORSION] = new Vector();
TorsionCalc torsionCalc = new TorsionCalc();
for (int i = torsions.length; --i >= 0; ) torsionCalc.setData(calc, i);
calc = calculations[CALC_OOP] = new Vector();
// set up the special atom arrays
OOPCalc oopCalc = new OOPCalc();
int elemNo;
for (int i = 0; i < atomCount; i++) {
MinAtom a = atoms[i];
if (a.nBonds == 3 && isInvertible(elemNo = a.atom.getElementNumber()))
oopCalc.setData(calc, i, elemNo);
}
pairSearch(calculations[CALC_VDW] = new Vector(), new VDWCalc());
return true;
}
double compute(int iType, Object[] dataIn) {
switch (iType) {
case CALC_DISTANCE:
return bondCalc.compute(dataIn);
case CALC_ANGLE:
return angleCalc.compute(dataIn);
case CALC_TORSION:
return torsionCalc.compute(dataIn);
case CALC_OOP:
return oopCalc.compute(dataIn);
case CALC_VDW:
return vdwCalc.compute(dataIn);
case CALC_ES:
return esCalc.compute(dataIn);
}
return 0.0;
}