/** * A unit test suite for JUnit for Ethene. Reaction: O=C-C-H => O(H)-C=C. Automatic looking for * active center. * * @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2 * @return The test suite */ @Test public void testInitiate_IMoleculeSet_IMoleculeSet() throws Exception { IReactionProcess type = new AdductionProtonPBReaction(); IMolecule molecule = getEthene(); IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet(); setOfReactants.addMolecule(molecule); /* initiate */ List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.FALSE); paramList.add(param); type.setParameterList(paramList); IReactionSet setOfReactions = type.initiate(setOfReactants, null); Assert.assertEquals(2, setOfReactions.getReactionCount()); Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount()); IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0); IMolecule molecule2 = getExpected(); IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product); Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2, queryAtom)); }
/** * A unit test suite for JUnit. * * @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2 * @return The test suite */ @Test public void testCDKConstants_REACTIVE_CENTER() throws Exception { IReactionProcess type = new AdductionProtonPBReaction(); IMoleculeSet setOfReactants = builder.newMoleculeSet(); IMolecule molecule = getEthene(); /*manually putting the active center*/ molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true); molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true); setOfReactants.addMolecule(molecule); List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.TRUE); paramList.add(param); type.setParameterList(paramList); /* initiate */ IReactionSet setOfReactions = type.initiate(setOfReactants, null); IMolecule reactant = setOfReactions.getReaction(0).getReactants().getMolecule(0); Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(molecule.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getAtom(1).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER)); }
/** * A unit test suite for JUnit. Reaction: * * @return The test suite */ @Test @Override public void testInitiate_IAtomContainerSet_IAtomContainerSet() throws Exception { IReactionProcess type = new RadicalSiteHrBetaReaction(); IAtomContainerSet setOfReactants = getExampleReactants(); /* initiate */ List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.FALSE); paramList.add(param); type.setParameterList(paramList); IReactionSet setOfReactions = type.initiate(setOfReactants, null); Assert.assertEquals(3, setOfReactions.getReactionCount()); Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount()); IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0); IAtomContainer molecule2 = getExpectedProducts().getAtomContainer(0); IQueryAtomContainer queryAtom = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product); Assert.assertTrue(new UniversalIsomorphismTester().isIsomorph(molecule2, queryAtom)); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testCDKConstants_REACTIVE_CENTER() throws Exception { IReactionProcess type = new RadicalSiteHrBetaReaction(); IAtomContainerSet setOfReactants = getExampleReactants(); IAtomContainer molecule = setOfReactants.getAtomContainer(0); /* manually put the reactive center */ molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER, true); molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true); molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true); molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER, true); List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.TRUE); paramList.add(param); type.setParameterList(paramList); /* initiate */ IReactionSet setOfReactions = type.initiate(setOfReactants, null); IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0); Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(molecule.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER)); Assert.assertTrue(reactant.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER)); }
/** * 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; }
private void callDefaultReactions() { List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.FALSE); paramList.add(param); IReactionProcess type = new SharingLonePairReaction(); try { type.setParameterList(paramList); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); type = new PiBondingMovementReaction(); List<IParameterReact> paramList2 = new ArrayList<IParameterReact>(); IParameterReact param2 = new SetReactionCenter(); param2.setParameter(Boolean.FALSE); paramList2.add(param2); try { type.setParameterList(paramList2); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); type = new RearrangementAnionReaction(); try { type.setParameterList(paramList); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); type = new RearrangementCationReaction(); try { type.setParameterList(paramList); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); type = new RearrangementLonePairReaction(); try { type.setParameterList(paramList); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); type = new RearrangementRadicalReaction(); try { type.setParameterList(paramList); } catch (CDKException e) { e.printStackTrace(); } reactionsList.add(type); }
/** * A unit test suite for JUnit. * * @cdk.inchi InChI=1/C2H4/c1-2/h1-2H2 * @return The test suite */ @Test public void testMapping() throws Exception { IReactionProcess type = new AdductionProtonPBReaction(); IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet(); IMolecule molecule = getEthene(); setOfReactants.addMolecule(molecule); /*automatic looking for active center*/ List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.FALSE); paramList.add(param); type.setParameterList(paramList); /* initiate */ IReactionSet setOfReactions = type.initiate(setOfReactants, null); IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0); Assert.assertEquals(3, setOfReactions.getReaction(0).getMappingCount()); IAtom mappedProductA1 = (IAtom) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getAtom(0)); Assert.assertEquals(mappedProductA1, product.getAtom(0)); mappedProductA1 = (IAtom) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getAtom(1)); Assert.assertEquals(mappedProductA1, product.getAtom(1)); IBond mappedProductB1 = (IBond) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getBond(0)); Assert.assertEquals(mappedProductB1, product.getBond(0)); }
/** * A unit test suite for JUnit. * * @return The test suite */ @Test public void testMapping() throws Exception { IReactionProcess type = new RadicalSiteHrBetaReaction(); IAtomContainerSet setOfReactants = getExampleReactants(); IAtomContainer molecule = setOfReactants.getAtomContainer(0); /* automatic search of the center active */ List<IParameterReact> paramList = new ArrayList<IParameterReact>(); IParameterReact param = new SetReactionCenter(); param.setParameter(Boolean.FALSE); paramList.add(param); type.setParameterList(paramList); /* initiate */ IReactionSet setOfReactions = type.initiate(setOfReactants, null); IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0); Assert.assertEquals(19, setOfReactions.getReaction(0).getMappingCount()); IAtom mappedProductA1 = (IAtom) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getAtom(0)); Assert.assertEquals(mappedProductA1, product.getAtom(0)); IAtom mappedProductA2 = (IAtom) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getAtom(6)); Assert.assertEquals(mappedProductA2, product.getAtom(6)); IAtom mappedProductA3 = (IAtom) ReactionManipulator.getMappedChemObject( setOfReactions.getReaction(0), molecule.getAtom(3)); Assert.assertEquals(mappedProductA3, product.getAtom(3)); }
/** * Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class * tools.HydrogenAdder. * * @exception CDKException Description of the Exception * @param reactants reactants of the reaction. * @param agents agents of the reaction (Must be in this case null). */ @TestMethod("testInitiate_IAtomContainerSet_IAtomContainerSet") public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException { logger.debug("initiate reaction: RearrangementRadicalReaction"); if (reactants.getAtomContainerCount() != 1) { throw new CDKException("RearrangementRadicalReaction only expects one reactant"); } if (agents != null) { throw new CDKException("RearrangementRadicalReaction don't expects agents"); } IReactionSet setOfReactions = DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class); IAtomContainer reactant = reactants.getAtomContainer(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.getAtomContainer(0).atoms().iterator(); while (atoms.hasNext()) { IAtom atomi = atoms.next(); if (atomi.getFlag(CDKConstants.REACTIVE_CENTER) && reactant.getConnectedSingleElectronsCount(atomi) == 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 (atomi.getFlag(CDKConstants.REACTIVE_CENTER) && (atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0 && reactant.getConnectedSingleElectronsCount(atomj) == 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.DOUBLE) { IAtom atomk = bondj.getConnectedAtom(atomj); if (atomk.getFlag(CDKConstants.REACTIVE_CENTER) && (atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge()) == 0 && reactant.getConnectedSingleElectronsCount(atomk) == 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); IAtomContainerSet moleculeSet = reactant.getBuilder().newInstance(IAtomContainerSet.class); moleculeSet.addAtomContainer(reactant); IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList); if (reaction == null) continue; else setOfReactions.addReaction(reaction); } } } } } } } } return setOfReactions; }