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/RadicalSiteHrDeltaReactionTest.java
test_class.identifier: RadicalSiteHrDeltaReactionTest
test_class.superclass: extends ReactionProcessTest
test_case.body: @Test
      public void testManuallyCentreActive() throws Exception {
          IReactionProcess type = new RadicalSiteHrDeltaReaction();
          IAtomContainerSet setOfReactants = getExampleReactants();
          IAtomContainer molecule = setOfReactants.getAtomContainer(0);
  
          molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getAtom(7).setFlag(CDKConstants.REACTIVE_CENTER, true);
          molecule.getBond(6).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);
          IReactionSet setOfReactions = type.initiate(setOfReactants, null);
  
          Assert.assertEquals(1, setOfReactions.getReactionCount());
          Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
  
          IAtomContainer product = setOfReactions.getReaction(0).getProducts().getAtomContainer(0);
          IAtomContainer molecule2 = getExpectedProducts().getAtomContainer(0);
  
          assertEquals(molecule2, product);
      }
test_case.class_method_signature: RadicalSiteHrDeltaReactionTest.testManuallyCentreActive()
test_case.full_signature: @Test public void testManuallyCentreActive()
test_case.identifier: testManuallyCentreActive
test_case.invocations: getExampleReactants getAtomContainer setFlag getAtom setFlag getAtom setFlag getAtom setFlag getBond setParameter add setParameterList initiate assertEquals getReactionCount assertEquals getProductCount getReaction getAtomContainer getProducts getReaction getAtomContainer getExpectedProducts assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testManuallyCentreActive()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(RadicalSiteHrDeltaReaction.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(RadicalSiteHrDeltaReaction.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java
focal_class.identifier: RadicalSiteHrDeltaReaction
focal_class.interfaces: implements IReactionProcess
focal_class.class_method_signature: RadicalSiteHrDeltaReaction.RadicalSiteHrDeltaReaction()
focal_class.full_signature: public  RadicalSiteHrDeltaReaction()
focal_class.identifier: RadicalSiteHrDeltaReaction
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  RadicalSiteHrDeltaReaction()
focal_class.class_method_signature: RadicalSiteHrDeltaReaction.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: RadicalSiteHrDeltaReaction.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: RadicalSiteHrDeltaReaction.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: RadicalSiteHrDeltaReaction");
  
          if (reactants.getAtomContainerCount() != 1) {
              throw new CDKException("RadicalSiteHrDeltaReaction only expects one reactant");
          }
          if (agents != null) {
              throw new CDKException("RadicalSiteHrDeltaReaction don't expects agents");
          }
  
          IReactionSet setOfReactions = reactants.getBuilder().newInstance(IReactionSet.class);
          IAtomContainer reactant = reactants.getAtomContainer(0);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactant);
          Aromaticity.cdkLegacy().apply(reactant);
          AllRingsFinder arf = new AllRingsFinder();
          IRingSet ringSet = arf.findAllRings(reactant);
          for (int ir = 0; ir < ringSet.getAtomContainerCount(); ir++) {
              IRing ring = (IRing) ringSet.getAtomContainer(ir);
              for (int jr = 0; jr < ring.getAtomCount(); jr++) {
                  IAtom aring = ring.getAtom(jr);
                  aring.setFlag(CDKConstants.ISINRING, true);
              }
          }
          /*
           * 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);
  
          HOSECodeGenerator hcg = new HOSECodeGenerator();
          Iterator<IAtom> atomis = reactant.atoms().iterator();
          while (atomis.hasNext()) {
              IAtom atomi = atomis.next();
              if (atomi.getFlag(CDKConstants.REACTIVE_CENTER) && reactant.getConnectedSingleElectronsCount(atomi) == 1) {
  
                  hcg.getSpheres(reactant, atomi, 5, true);
                  Iterator<IAtom> atomls = hcg.getNodesInSphere(5).iterator();
                  while (atomls.hasNext()) {
                      IAtom atoml = atomls.next();
                      if (atoml != null && atoml.getFlag(CDKConstants.REACTIVE_CENTER)
                              && !atoml.getFlag(CDKConstants.ISINRING)
                              && (atoml.getFormalCharge() == CDKConstants.UNSET ? 0 : atoml.getFormalCharge()) == 0
                              && !atoml.getSymbol().equals("H") && reactant.getMaximumBondOrder(atoml) == IBond.Order.SINGLE) {
  
                          Iterator<IAtom> atomhs = reactant.getConnectedAtomsList(atoml).iterator();
                          while (atomhs.hasNext()) {
                              IAtom atomh = atomhs.next();
                              if (reactant.getBond(atomh, atoml).getFlag(CDKConstants.REACTIVE_CENTER)
                                      && atomh.getFlag(CDKConstants.REACTIVE_CENTER) && atomh.getSymbol().equals("H")) {
  
                                  ArrayList<IAtom> atomList = new ArrayList<IAtom>();
                                  atomList.add(atomh);
                                  atomList.add(atomi);
                                  atomList.add(atoml);
                                  ArrayList<IBond> bondList = new ArrayList<IBond>();
                                  bondList.add(reactant.getBond(atomh, atoml));
  
                                  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: RadicalSiteHrDeltaReaction.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 percieveAtomTypesAndConfigureAtoms apply cdkLegacy findAllRings getAtomContainerCount getAtomContainer getAtomCount getAtom setFlag getParameterClass isSetParameter setActiveCenters iterator atoms hasNext next getFlag getConnectedSingleElectronsCount getSpheres iterator getNodesInSphere hasNext next getFlag getFlag getFormalCharge getFormalCharge equals getSymbol getMaximumBondOrder iterator getConnectedAtomsList hasNext next getFlag getBond getFlag equals getSymbol add add add add getBond 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)