/** * Get the container which the bond is found on resonance from a IMolecule. It is based on looking * if the order of the bond changes. Return null is any is found. * * @param molecule The IMolecule to analyze * @param bond The IBond * @return The container with the bond */ @TestMethod("testGetContainer_IMolecule_IBond") public IAtomContainer getContainer(IMolecule molecule, IBond bond) { IAtomContainerSet setOfCont = getContainers(molecule); if (setOfCont == null) return null; for (IAtomContainer container : setOfCont.atomContainers()) { if (container.contains(bond)) return container; } return null; }
/** * Get the container which is found resonance from a IMolecule. It is based on looking if the * order of the bond changes. * * @param molecule The IMolecule to analyze * @return The different containers */ @TestMethod("testGetContainers_IMolecule") public IAtomContainerSet getContainers(IMolecule molecule) { IAtomContainerSet setOfCont = molecule.getBuilder().newAtomContainerSet(); IMoleculeSet setOfMol = getStructures(molecule); if (setOfMol.getMoleculeCount() == 0) return setOfCont; /*extraction of all bonds which has been produced a changes of order*/ List<IBond> bondList = new ArrayList<IBond>(); for (int i = 1; i < setOfMol.getMoleculeCount(); i++) { IMolecule mol = setOfMol.getMolecule(i); for (int j = 0; j < mol.getBondCount(); j++) { IBond bond = molecule.getBond(j); if (!mol.getBond(j).getOrder().equals(bond.getOrder())) { if (!bondList.contains(bond)) bondList.add(bond); } } } if (bondList.size() == 0) return null; int[] flagBelonging = new int[bondList.size()]; for (int i = 0; i < flagBelonging.length; i++) flagBelonging[i] = 0; int[] position = new int[bondList.size()]; int maxGroup = 1; /*Analysis if the bond are linked together*/ List<IBond> newBondList = new ArrayList<IBond>(); newBondList.add(bondList.get(0)); int pos = 0; for (int i = 0; i < newBondList.size(); i++) { if (i == 0) flagBelonging[i] = maxGroup; else { if (flagBelonging[position[i]] == 0) { maxGroup++; flagBelonging[position[i]] = maxGroup; } } IBond bondA = newBondList.get(i); for (int ato = 0; ato < 2; ato++) { IAtom atomA1 = bondA.getAtom(ato); List<IBond> bondA1s = molecule.getConnectedBondsList(atomA1); for (int j = 0; j < bondA1s.size(); j++) { IBond bondB = bondA1s.get(j); if (!newBondList.contains(bondB)) for (int k = 0; k < bondList.size(); k++) if (bondList.get(k).equals(bondB)) if (flagBelonging[k] == 0) { flagBelonging[k] = maxGroup; pos++; newBondList.add(bondB); position[pos] = k; } } } // if it is final size and not all are added if (newBondList.size() - 1 == i) for (int k = 0; k < bondList.size(); k++) if (!newBondList.contains(bondList.get(k))) { newBondList.add(bondList.get(k)); position[i + 1] = k; break; } } /*creating containers according groups*/ for (int i = 0; i < maxGroup; i++) { IAtomContainer container = molecule.getBuilder().newAtomContainer(); for (int j = 0; j < bondList.size(); j++) { if (flagBelonging[j] != i + 1) continue; IBond bond = bondList.get(j); IAtom atomA1 = bond.getAtom(0); IAtom atomA2 = bond.getAtom(1); if (!container.contains(atomA1)) container.addAtom(atomA1); if (!container.contains(atomA2)) container.addAtom(atomA2); container.addBond(bond); } setOfCont.addAtomContainer(container); } return setOfCont; }