private boolean unMappedAtomsEqualsIndexI(
int setNumB,
List<Integer> i_bond_setB,
int newMappingSize,
int atomIndex,
int counter,
List<Integer> new_Mapping,
Integer indexI,
Integer indexJ,
Integer order) {
boolean normal_bond = true;
for (int c = 0; c < newMappingSize; c++) {
if (new_Mapping.get(c * 2 + 1).equals(indexJ)) {
setBondNeighbors(indexI, indexJ, order);
if (cTab2Copy.get(atomIndex * 4 + 3).compareToIgnoreCase("X") == 0) {
step1(atomIndex, counter);
McGregorChecks.changeCharBonds(
indexJ, signArray[counter], setNumB, i_bond_setB, cTab2Copy);
int cor_atom =
McGregorChecks.searchCorrespondingAtom(newMappingSize, indexJ, 2, new_Mapping);
McGregorChecks.changeCharBonds(
cor_atom, signArray[counter], newNeighborNumA, newINeighborsA, newCNeighborsA);
counter++;
} else {
step2(atomIndex);
}
normal_bond = false;
neighborBondNumB++;
}
}
return normal_bond;
}
private boolean unMappedAtomsEqualsIndexJ(
IAtomContainer target,
int mappingSize,
int atomIndex,
int counter,
List<Integer> mapped_atoms,
Integer indexI,
Integer indexJ,
Integer order) {
boolean normal_bond = true;
for (int c = 0; c < mappingSize; c++) {
if (mapped_atoms.get(c * 2 + 1).equals(indexI)) {
setBondNeighbors(indexI, indexJ, order);
if (cTab2Copy.get(atomIndex * 4 + 2).compareToIgnoreCase("X") == 0) {
step3(atomIndex, counter);
McGregorChecks.changeCharBonds(
indexI, signArray[counter], target.getBondCount(), target, cTab2Copy);
int cor_atom =
McGregorChecks.searchCorrespondingAtom(mappingSize, indexI, 2, mapped_atoms);
McGregorChecks.changeCharBonds(
cor_atom, signArray[counter], newNeighborNumA, newINeighborsA, newCNeighborsA);
// changeCharBonds(cor_atom, signArray[counter],
// query.getBondCount(), query, cTab1Copy);
counter++;
} else {
step4(atomIndex);
}
normal_bond = false;
neighborBondNumB++;
}
}
return normal_bond;
}
