/** * Get the resonance structures from an IMolecule. * * @param molecule The IMolecule to analyze * @return The different resonance structures */ @TestMethod("testGetStructures_IMolecule") public IMoleculeSet getStructures(IMolecule molecule) { int countStructure = 0; IMoleculeSet setOfMol = molecule.getBuilder().newMoleculeSet(); setOfMol.addMolecule(molecule); for (int i = 0; i < setOfMol.getMoleculeCount(); i++) { IMolecule mol = setOfMol.getMolecule(i); for (IReactionProcess aReactionsList : reactionsList) { IReactionProcess reaction = aReactionsList; IMoleculeSet setOfReactants = molecule.getBuilder().newMoleculeSet(); setOfReactants.addMolecule(mol); try { IReactionSet setOfReactions = reaction.initiate(setOfReactants, null); if (setOfReactions.getReactionCount() != 0) for (int k = 0; k < setOfReactions.getReactionCount(); k++) for (int j = 0; j < setOfReactions.getReaction(k).getProducts().getAtomContainerCount(); j++) { IMolecule product = setOfReactions.getReaction(k).getProducts().getMolecule(j); if (!existAC(setOfMol, product)) { setOfMol.addMolecule(product); countStructure++; if (countStructure > maxStructures) return setOfMol; } } } catch (CDKException e) { e.printStackTrace(); } } } return setOfMol; }
/** * Test for SF bug #1309731. * * @cdk.bug 1309731 */ @Test public void testModelBuilder3D_keepChemObjectIDs() throws Exception { ModelBuilder3D mb3d = ModelBuilder3D.getInstance(); IMolecule methanol = new org.openscience.cdk.Molecule(); IChemObjectBuilder builder = methanol.getBuilder(); IAtom carbon1 = builder.newInstance(IAtom.class, "C"); carbon1.setID("carbon1"); methanol.addAtom(carbon1); for (int i = 0; i < 3; i++) { IAtom hydrogen = builder.newInstance(IAtom.class, "H"); methanol.addAtom(hydrogen); methanol.addBond(builder.newInstance(IBond.class, carbon1, hydrogen, IBond.Order.SINGLE)); } IAtom oxygen1 = builder.newInstance(IAtom.class, "O"); oxygen1.setID("oxygen1"); methanol.addAtom(oxygen1); methanol.addBond(builder.newInstance(IBond.class, carbon1, oxygen1, IBond.Order.SINGLE)); IAtom hydrogen = builder.newInstance(IAtom.class, "H"); methanol.addAtom(hydrogen); methanol.addBond(builder.newInstance(IBond.class, hydrogen, oxygen1, IBond.Order.SINGLE)); Assert.assertEquals(6, methanol.getAtomCount()); Assert.assertEquals(5, methanol.getBondCount()); mb3d.generate3DCoordinates(methanol, false); checkAverageBondLength(methanol); Assert.assertEquals("carbon1", carbon1.getID()); Assert.assertEquals("oxygen1", oxygen1.getID()); }
/** * Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class * tools.HydrogenAdder. * * @param reactants reactants of the reaction * @param agents agents of the reaction (Must be in this case null) * @exception CDKException Description of the Exception */ @TestMethod("testInitiate_IMoleculeSet_IMoleculeSet") public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException { logger.debug("initiate reaction: HeterolyticCleavagePBReaction"); if (reactants.getMoleculeCount() != 1) { throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant"); } if (agents != null) { throw new CDKException("HeterolyticCleavagePBReaction don't expects agents"); } IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class); IMolecule reactant = reactants.getMolecule(0); /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/ IParameterReact ipr = super.getParameterClass(SetReactionCenter.class); if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant); Iterator<IBond> bondis = reactant.bonds().iterator(); while (bondis.hasNext()) { IBond bondi = bondis.next(); IAtom atom1 = bondi.getAtom(0); IAtom atom2 = bondi.getAtom(1); if (bondi.getFlag(CDKConstants.REACTIVE_CENTER) && bondi.getOrder() != IBond.Order.SINGLE && atom1.getFlag(CDKConstants.REACTIVE_CENTER) && atom2.getFlag(CDKConstants.REACTIVE_CENTER) && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0 && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0 && reactant.getConnectedSingleElectronsCount(atom1) == 0 && reactant.getConnectedSingleElectronsCount(atom2) == 0) { /**/ for (int j = 0; j < 2; j++) { ArrayList<IAtom> atomList = new ArrayList<IAtom>(); if (j == 0) { atomList.add(atom1); atomList.add(atom2); } else { atomList.add(atom2); atomList.add(atom1); } ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class); moleculeSet.addMolecule(reactant); IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if (reaction == null) continue; else setOfReactions.addReaction(reaction); } } } return setOfReactions; }
/** * Initiate process. * * @param reactants reactants of the reaction. * @param agents agents of the reaction (Must be in this case null). * @exception CDKException Description of the Exception */ @TestMethod("testInitiate_IMoleculeSet_IMoleculeSet") public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException { logger.debug("initiate reaction: RadicalChargeSiteInitiationReaction"); if (reactants.getMoleculeCount() != 1) { throw new CDKException("RadicalChargeSiteInitiationReaction only expects one reactant"); } if (agents != null) { throw new CDKException("RadicalChargeSiteInitiationReaction don't expects agents"); } IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newReactionSet(); IMolecule reactant = reactants.getMolecule(0); /* if the parameter hasActiveCenter is not fixed yet, set the active centers*/ IParameterReact ipr = super.getParameterClass(SetReactionCenter.class); if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant); Iterator<IAtom> atoms = reactants.getMolecule(0).atoms().iterator(); while (atoms.hasNext()) { IAtom atomi = atoms.next(); if (atomi.getFlag(CDKConstants.REACTIVE_CENTER) && reactant.getConnectedSingleElectronsCount(atomi) == 1 && atomi.getFormalCharge() == 1) { Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator(); while (bondis.hasNext()) { IBond bondi = bondis.next(); if (bondi.getFlag(CDKConstants.REACTIVE_CENTER) && bondi.getOrder() == IBond.Order.SINGLE) { IAtom atomj = bondi.getConnectedAtom(atomi); if (atomj.getFlag(CDKConstants.REACTIVE_CENTER) && atomj.getFormalCharge() == 0) { Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator(); while (bondjs.hasNext()) { IBond bondj = bondjs.next(); if (bondj.equals(bondi)) continue; if (bondj.getFlag(CDKConstants.REACTIVE_CENTER) && bondj.getOrder() == IBond.Order.SINGLE) { IAtom atomk = bondj.getConnectedAtom(atomj); if (atomk.getFlag(CDKConstants.REACTIVE_CENTER) && atomk.getSymbol().equals("C") && atomk.getFormalCharge() == 0) { ArrayList<IAtom> atomList = new ArrayList<IAtom>(); atomList.add(atomi); atomList.add(atomj); atomList.add(atomk); ArrayList<IBond> bondList = new ArrayList<IBond>(); bondList.add(bondi); bondList.add(bondj); IMoleculeSet moleculeSet = reactant.getBuilder().newMoleculeSet(); moleculeSet.addMolecule(reactant); IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if (reaction == null) continue; else setOfReactions.addReaction(reaction); } } } } } } } } return setOfReactions; }
/** * 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; }