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/RearrangementRadicalReactionTest.java
test_class.identifier: RearrangementRadicalReactionTest
test_class.superclass: extends ReactionProcessTest
test_case.body: @Test
      public void testCDKConstants_REACTIVE_CENTER() throws Exception {
          IReactionProcess type = new RearrangementRadicalReaction();
  
          IAtomContainerSet setOfReactants = getExampleReactants();
          IAtomContainer molecule = setOfReactants.getAtomContainer(0);
  
          /* manually put the reactive center */
          molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getAtom(2).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getBond(1).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(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.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
          Assert.assertTrue(reactant.getAtom(2).getFlag(CDKConstants.REACTIVE_CENTER));
          Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
          Assert.assertTrue(reactant.getBond(0).getFlag(CDKConstants.REACTIVE_CENTER));
          Assert.assertTrue(molecule.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
          Assert.assertTrue(reactant.getBond(1).getFlag(CDKConstants.REACTIVE_CENTER));
      }
test_case.class_method_signature: RearrangementRadicalReactionTest.testCDKConstants_REACTIVE_CENTER()
test_case.full_signature: @Test public void testCDKConstants_REACTIVE_CENTER()
test_case.identifier: testCDKConstants_REACTIVE_CENTER
test_case.invocations: getExampleReactants getAtomContainer setFlag getAtom setFlag getAtom setFlag getAtom setFlag getBond setFlag getBond setParameter add setParameterList initiate getAtomContainer getReactants getReaction assertTrue getFlag getAtom assertTrue getFlag getAtom assertTrue getFlag getAtom assertTrue getFlag getAtom assertTrue getFlag getAtom assertTrue getFlag getAtom assertTrue getFlag getBond assertTrue getFlag getBond assertTrue getFlag getBond assertTrue getFlag getBond
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCDKConstants_REACTIVE_CENTER()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(RearrangementRadicalReaction.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(RearrangementRadicalReaction.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementRadicalReaction.java
focal_class.identifier: RearrangementRadicalReaction
focal_class.interfaces: implements IReactionProcess
focal_class.class_method_signature: RearrangementRadicalReaction.RearrangementRadicalReaction()
focal_class.full_signature: public  RearrangementRadicalReaction()
focal_class.identifier: RearrangementRadicalReaction
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  RearrangementRadicalReaction()
focal_class.class_method_signature: RearrangementRadicalReaction.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: RearrangementRadicalReaction.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: RearrangementRadicalReaction.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: 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 = 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> 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.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)
                                              && (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;
  
      }
focal_method.class_method_signature: RearrangementRadicalReaction.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 getAtomContainer hasNext next getFlag getConnectedSingleElectronsCount iterator getConnectedBondsList hasNext next getFlag getOrder getOther getFlag getFormalCharge getFormalCharge getConnectedSingleElectronsCount iterator getConnectedBondsList hasNext next equals getFlag getOrder getOther getFlag getFormalCharge getFormalCharge getConnectedSingleElectronsCount 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)