test_class.declarator: lpcheck = new LonePairElectronChecker()
test_class.modifier: private final
test_class.original_string: private final LonePairElectronChecker lpcheck = new LonePairElectronChecker();
test_class.type: LonePairElectronChecker
test_class.var_name: lpcheck
test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private
test_class.original_string: private IChemObjectBuilder            builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.file: base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java
test_class.identifier: RearrangementLonePairReactionTest
test_class.superclass: extends ReactionProcessTest
test_case.body: @Test
      public void testFluorobenzene() throws Exception {
  
          IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
          molecule.addAtom(builder.newInstance(IAtom.class, "F"));
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(0, 1, IBond.Order.SINGLE);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(1, 2, IBond.Order.DOUBLE);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(2, 3, IBond.Order.SINGLE);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(3, 4, IBond.Order.DOUBLE);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(4, 5, IBond.Order.SINGLE);
          molecule.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule.addBond(5, 6, IBond.Order.DOUBLE);
          molecule.addBond(6, 1, IBond.Order.SINGLE);
  
          addExplicitHydrogens(molecule);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
  
          lpcheck.saturate(molecule);
  
          IReactionProcess type = new RearrangementLonePairReaction();
  
          IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class);
          setOfReactants.addAtomContainer(molecule);
          /* 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);
          Assert.assertEquals(1, setOfReactions.getReactionCount());
          Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
          IAtomContainer product1 = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
  
          IAtomContainer molecule1 = builder.newInstance(IAtomContainer.class);
          molecule1.addAtom(builder.newInstance(IAtom.class, "F"));
          molecule1.getAtom(0).setFormalCharge(1);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.addBond(0, 1, IBond.Order.DOUBLE);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.getAtom(2).setFormalCharge(-1);
          molecule1.addBond(1, 2, IBond.Order.SINGLE);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.addBond(2, 3, IBond.Order.SINGLE);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.addBond(3, 4, IBond.Order.DOUBLE);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.addBond(4, 5, IBond.Order.SINGLE);
          molecule1.addAtom(builder.newInstance(IAtom.class, "C"));
          molecule1.addBond(5, 6, IBond.Order.DOUBLE);
          molecule1.addBond(6, 1, IBond.Order.SINGLE);
          addExplicitHydrogens(molecule1);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule1);
          lpcheck.saturate(molecule1);
  
          assertEquals(molecule1, product1);
      }
test_case.class_method_signature: RearrangementLonePairReactionTest.testFluorobenzene()
test_case.full_signature: @Test public void testFluorobenzene()
test_case.identifier: testFluorobenzene
test_case.invocations: newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate newInstance getInstance addAtomContainer setParameter add setParameterList initiate assertEquals getReactionCount assertEquals getProductCount getReaction getAtomContainer getProducts getReaction newInstance addAtom newInstance setFormalCharge getAtom addAtom newInstance addBond addAtom newInstance setFormalCharge getAtom addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testFluorobenzene()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(RearrangementLonePairReaction.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(RearrangementLonePairReaction.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementLonePairReaction.java
focal_class.identifier: RearrangementLonePairReaction
focal_class.interfaces: implements IReactionProcess
focal_class.class_method_signature: RearrangementLonePairReaction.RearrangementLonePairReaction()
focal_class.full_signature: public  RearrangementLonePairReaction()
focal_class.identifier: RearrangementLonePairReaction
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  RearrangementLonePairReaction()
focal_class.class_method_signature: RearrangementLonePairReaction.getSpecification()
focal_class.full_signature: @Override public ReactionSpecification getSpecification()
focal_class.identifier: getSpecification
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: ReactionSpecification
focal_class.signature: ReactionSpecification getSpecification()
focal_class.class_method_signature: RearrangementLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
focal_class.full_signature: @Override public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
focal_class.identifier: initiate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainerSet reactants, IAtomContainerSet agents)
focal_class.return: IReactionSet
focal_class.signature: IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
focal_class.class_method_signature: RearrangementLonePairReaction.setActiveCenters(IAtomContainer reactant)
focal_class.full_signature: private void setActiveCenters(IAtomContainer reactant)
focal_class.identifier: setActiveCenters
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer reactant)
focal_class.return: void
focal_class.signature: void setActiveCenters(IAtomContainer reactant)
focal_class.superclass: extends ReactionEngine
focal_method.body: @Override
      public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException {
  
          logger.debug("initiate reaction: RearrangementLonePairReaction");
  
          if (reactants.getAtomContainerCount() != 1) {
              throw new CDKException("RearrangementLonePairReaction only expects one reactant");
          }
          if (agents != null) {
              throw new CDKException("RearrangementLonePairReaction don't expects agents");
          }
  
          IReactionSet setOfReactions = reactants.getBuilder().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> atomis = reactant.atoms().iterator();
          while (atomis.hasNext()) {
              IAtom atomi = atomis.next();
              if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
                      && (atomi.getFormalCharge() == CDKConstants.UNSET ? 0 : atomi.getFormalCharge()) == 0
                      && reactant.getConnectedLonePairsCount(atomi) > 0) {
  
                  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.getOther(atomi);
                          if (atomj.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.getOther(atomj);
  
                                      if (atomk.getFlag(CDKConstants.REACTIVE_CENTER)
                                              && reactant.getConnectedSingleElectronsCount(atomk) == 0
                                              && (atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : 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);
  
                                          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;
  
      }
focal_method.class_method_signature: RearrangementLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
focal_method.full_signature: @Override public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
focal_method.identifier: initiate
focal_method.invocations: debug getAtomContainerCount newInstance getBuilder getAtomContainer getParameterClass isSetParameter setActiveCenters iterator atoms hasNext next getFlag getFormalCharge getFormalCharge getConnectedLonePairsCount iterator getConnectedBondsList hasNext next getFlag getOrder getOther getFlag getFormalCharge getFormalCharge getConnectedSingleElectronsCount iterator getConnectedBondsList hasNext next equals getFlag getOrder getOther getFlag getConnectedSingleElectronsCount getFormalCharge getFormalCharge add add add add add newInstance getBuilder addAtomContainer initiate addReaction
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainerSet reactants, IAtomContainerSet agents)
focal_method.return: IReactionSet
focal_method.signature: IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)