@Test
public void unionMolecules() throws IOException, CDKException {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol1 = sp.parseSmiles("OOC1=CC=CC=C1");
IAtomContainer mol2 = sp.parseSmiles("c1ccc(cc1)c2ccccc2");
int i = 0;
for (IAtom atom1 : mol1.atoms()) {
atom1.setID(String.valueOf((i++)));
}
int j = 0;
for (IAtom atom2 : mol2.atoms()) {
atom2.setID(String.valueOf((j++)));
}
MoleculeSanityCheck.aromatizeMolecule(mol1);
MoleculeSanityCheck.aromatizeMolecule(mol2);
Isomorphism isomorphism = new Isomorphism(mol1, mol2, Algorithm.DEFAULT, true, false, false);
isomorphism.setChemFilters(false, false, false);
int combinations = 1;
List<String> acSet = new ArrayList<String>();
if (isomorphism.getFirstAtomMapping() != null) {
for (AtomAtomMapping mapping : isomorphism.getAllAtomMapping()) {
IAtomContainer union = new AtomContainer();
for (IAtom atom : mol1.atoms()) {
union.addAtom(atom);
}
for (IBond bond : mol1.bonds()) {
union.addBond(bond);
}
for (IBond bond : mol2.bonds()) {
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
if (!mapping.getMappingsByAtoms().containsValue(a1)
&& !mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a1)) {
union.addAtom(a1);
}
if (!union.contains(a2)) {
union.addAtom(a2);
}
union.addBond(bond);
} else if (mapping.getMappingsByAtoms().containsValue(a1)
&& !mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a2)) {
union.addAtom(a2);
}
union.addBond(
new Bond(
a2,
getKey(a1, mapping.getMappingsByAtoms()),
bond.getOrder(),
bond.getStereo()));
} else if (!mapping.getMappingsByAtoms().containsValue(a1)
&& mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a1)) {
union.addAtom(a1);
}
union.addBond(
new Bond(
a1,
getKey(a2, mapping.getMappingsByAtoms()),
bond.getOrder(),
bond.getStereo()));
}
}
/*check if this combination is chemically valid*/
if (isChemicallyValid(union)) {
String molSMILES = getSMILES(union).toString();
if (!acSet.contains(molSMILES)) {
acSet.add(molSMILES);
}
}
}
}
// for (String container : acSet) {
// System.out.println("\n-------------" + " Combination " + combinations++ +
// "--------------------");
// System.out.println("Query SMILES " + getSMILES(mol1).toString() + ", count " +
// mol1.getAtomCount());
// System.out.println("Target SMILES " + getSMILES(mol2).toString() + ", count " +
// mol2.getAtomCount());
// System.out.println("Union SMILES " + container + ", count " +
// sp.parseSmiles(container).getAtomCount());
// }
}
