test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibTurboHandlerTest.java
test_class.identifier: VFlibTurboHandlerTest
test_class.superclass: extends AbstractSubGraphTest
test_case.body: @Test
      public void testGetFirstMapping() throws InvalidSmilesException {
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer target = sp.parseSmiles("C\\C=C/Nc1cccc(c1)N(O)\\C=C\\C\\C=C\\C=C/C");
          IAtomContainer queryac = sp.parseSmiles("Nc1ccccc1");
  
          VFlibSubStructureHandler smsd1 = new VFlibSubStructureHandler();
          MolHandler mol1 = new MolHandler(queryac, true, true);
          MolHandler mol2 = new MolHandler(target, true, true);
          smsd1.set(mol1, mol2);
          smsd1.isSubgraph(true);
  
          assertEquals(7, smsd1.getFirstMapping().size());
      }
test_case.class_method_signature: VFlibTurboHandlerTest.testGetFirstMapping()
test_case.full_signature: @Test public void testGetFirstMapping()
test_case.identifier: testGetFirstMapping
test_case.invocations: getInstance parseSmiles parseSmiles set isSubgraph assertEquals size getFirstMapping
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetFirstMapping()
focal_class.declarator: allAtomMCS     = null
focal_class.modifier: private
focal_class.original_string: private              List<Map<IAtom, IAtom>>     allAtomMCS     = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: allAtomMCS
focal_class.declarator: atomsMCS       = null
focal_class.modifier: private
focal_class.original_string: private              Map<IAtom, IAtom>           atomsMCS       = null;
focal_class.type: Map<IAtom, IAtom>
focal_class.var_name: atomsMCS
focal_class.declarator: allAtomMCSCopy = null
focal_class.modifier: private
focal_class.original_string: private              List<Map<IAtom, IAtom>>     allAtomMCSCopy = null;
focal_class.type: List<Map<IAtom, IAtom>>
focal_class.var_name: allAtomMCSCopy
focal_class.declarator: firstMCS       = null
focal_class.modifier: private
focal_class.original_string: private              Map<Integer, Integer>       firstMCS       = null;
focal_class.type: Map<Integer, Integer>
focal_class.var_name: firstMCS
focal_class.declarator: allMCS         = null
focal_class.modifier: private
focal_class.original_string: private              List<Map<Integer, Integer>> allMCS         = null;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: allMCS
focal_class.declarator: allMCSCopy     = null
focal_class.modifier: private
focal_class.original_string: private              List<Map<Integer, Integer>> allMCSCopy     = null;
focal_class.type: List<Map<Integer, Integer>>
focal_class.var_name: allMCSCopy
focal_class.declarator: queryMol       = null
focal_class.modifier: private
focal_class.original_string: private              IQueryAtomContainer         queryMol       = null;
focal_class.type: IQueryAtomContainer
focal_class.var_name: queryMol
focal_class.declarator: mol1           = null
focal_class.modifier: private
focal_class.original_string: private              IAtomContainer              mol1           = null;
focal_class.type: IAtomContainer
focal_class.var_name: mol1
focal_class.declarator: mol2           = null
focal_class.modifier: private
focal_class.original_string: private              IAtomContainer              mol2           = null;
focal_class.type: IAtomContainer
focal_class.var_name: mol2
focal_class.declarator: vfLibSolutions = null
focal_class.modifier: private
focal_class.original_string: private              Map<INode, IAtom>           vfLibSolutions = null;
focal_class.type: Map<INode, IAtom>
focal_class.var_name: vfLibSolutions
focal_class.declarator: vfMCSSize      = -1
focal_class.modifier: private
focal_class.original_string: private              int                         vfMCSSize      = -1;
focal_class.type: int
focal_class.var_name: vfMCSSize
focal_class.declarator: bondMatchFlag  = false
focal_class.modifier: private
focal_class.original_string: private              boolean                     bondMatchFlag  = false;
focal_class.type: boolean
focal_class.var_name: bondMatchFlag
focal_class.declarator: LOGGER         = LoggingToolFactory
              .createLoggingTool(VFlibTurboHandler.class)
focal_class.modifier: private final static
focal_class.original_string: private final static ILoggingTool                LOGGER         = LoggingToolFactory
              .createLoggingTool(VFlibTurboHandler.class);
focal_class.type: ILoggingTool
focal_class.var_name: LOGGER
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibTurboHandler.java
focal_class.identifier: VFlibTurboHandler
focal_class.interfaces: implements IMCSBase
focal_class.class_method_signature: VFlibTurboHandler.VFlibTurboHandler()
focal_class.full_signature: public  VFlibTurboHandler()
focal_class.identifier: VFlibTurboHandler
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  VFlibTurboHandler()
focal_class.class_method_signature: VFlibTurboHandler.setFirstMappings()
focal_class.full_signature: private void setFirstMappings()
focal_class.identifier: setFirstMappings
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void setFirstMappings()
focal_class.class_method_signature: VFlibTurboHandler.mcgregorFlag()
focal_class.full_signature: private boolean mcgregorFlag()
focal_class.identifier: mcgregorFlag
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean mcgregorFlag()
focal_class.class_method_signature: VFlibTurboHandler.set(MolHandler reactant, MolHandler product)
focal_class.full_signature: @Override public void set(MolHandler reactant, MolHandler product)
focal_class.identifier: set
focal_class.modifiers: @Override public
focal_class.parameters: (MolHandler reactant, MolHandler product)
focal_class.return: void
focal_class.signature: void set(MolHandler reactant, MolHandler product)
focal_class.class_method_signature: VFlibTurboHandler.set(IQueryAtomContainer source, IAtomContainer target)
focal_class.full_signature: @Override public void set(IQueryAtomContainer source, IAtomContainer target)
focal_class.identifier: set
focal_class.modifiers: @Override public
focal_class.parameters: (IQueryAtomContainer source, IAtomContainer target)
focal_class.return: void
focal_class.signature: void set(IQueryAtomContainer source, IAtomContainer target)
focal_class.class_method_signature: VFlibTurboHandler.hasMap(Map<Integer, Integer> map, List<Map<Integer, Integer>> mapGlobal)
focal_class.full_signature: private boolean hasMap(Map<Integer, Integer> map, List<Map<Integer, Integer>> mapGlobal)
focal_class.identifier: hasMap
focal_class.modifiers: private
focal_class.parameters: (Map<Integer, Integer> map, List<Map<Integer, Integer>> mapGlobal)
focal_class.return: boolean
focal_class.signature: boolean hasMap(Map<Integer, Integer> map, List<Map<Integer, Integer>> mapGlobal)
focal_class.class_method_signature: VFlibTurboHandler.getAllAtomMapping()
focal_class.full_signature: @Override public List<Map<IAtom, IAtom>> getAllAtomMapping()
focal_class.identifier: getAllAtomMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Map<IAtom, IAtom>>
focal_class.signature: List<Map<IAtom, IAtom>> getAllAtomMapping()
focal_class.class_method_signature: VFlibTurboHandler.getAllMapping()
focal_class.full_signature: @Override public List<Map<Integer, Integer>> getAllMapping()
focal_class.identifier: getAllMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: List<Map<Integer, Integer>>
focal_class.signature: List<Map<Integer, Integer>> getAllMapping()
focal_class.class_method_signature: VFlibTurboHandler.getFirstAtomMapping()
focal_class.full_signature: @Override public Map<IAtom, IAtom> getFirstAtomMapping()
focal_class.identifier: getFirstAtomMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<IAtom, IAtom>
focal_class.signature: Map<IAtom, IAtom> getFirstAtomMapping()
focal_class.class_method_signature: VFlibTurboHandler.getFirstMapping()
focal_class.full_signature: @Override public Map<Integer, Integer> getFirstMapping()
focal_class.identifier: getFirstMapping
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Map<Integer, Integer>
focal_class.signature: Map<Integer, Integer> getFirstMapping()
focal_class.class_method_signature: VFlibTurboHandler.checkCommonAtomCount(IAtomContainer reactantMolecule, IAtomContainer productMolecule)
focal_class.full_signature: private int checkCommonAtomCount(IAtomContainer reactantMolecule, IAtomContainer productMolecule)
focal_class.identifier: checkCommonAtomCount
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer reactantMolecule, IAtomContainer productMolecule)
focal_class.return: int
focal_class.signature: int checkCommonAtomCount(IAtomContainer reactantMolecule, IAtomContainer productMolecule)
focal_class.class_method_signature: VFlibTurboHandler.searchVFMappings()
focal_class.full_signature: private void searchVFMappings()
focal_class.identifier: searchVFMappings
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void searchVFMappings()
focal_class.class_method_signature: VFlibTurboHandler.searchMcGregorMapping()
focal_class.full_signature: private void searchMcGregorMapping()
focal_class.identifier: searchMcGregorMapping
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void searchMcGregorMapping()
focal_class.class_method_signature: VFlibTurboHandler.setVFMappings(boolean ronp, IQuery query)
focal_class.full_signature: private void setVFMappings(boolean ronp, IQuery query)
focal_class.identifier: setVFMappings
focal_class.modifiers: private
focal_class.parameters: (boolean ronp, IQuery query)
focal_class.return: void
focal_class.signature: void setVFMappings(boolean ronp, IQuery query)
focal_class.class_method_signature: VFlibTurboHandler.setMcGregorMappings(List<List<Integer>> mappings)
focal_class.full_signature: private void setMcGregorMappings(List<List<Integer>> mappings)
focal_class.identifier: setMcGregorMappings
focal_class.modifiers: private
focal_class.parameters: (List<List<Integer>> mappings)
focal_class.return: void
focal_class.signature: void setMcGregorMappings(List<List<Integer>> mappings)
focal_class.class_method_signature: VFlibTurboHandler.isSubgraph(boolean shouldMatchBonds)
focal_class.full_signature: @Override public boolean isSubgraph(boolean shouldMatchBonds)
focal_class.identifier: isSubgraph
focal_class.modifiers: @Override public
focal_class.parameters: (boolean shouldMatchBonds)
focal_class.return: boolean
focal_class.signature: boolean isSubgraph(boolean shouldMatchBonds)
focal_class.class_method_signature: VFlibTurboHandler.isBondMatchFlag()
focal_class.full_signature: public boolean isBondMatchFlag()
focal_class.identifier: isBondMatchFlag
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isBondMatchFlag()
focal_class.class_method_signature: VFlibTurboHandler.setBondMatchFlag(boolean shouldMatchBonds)
focal_class.full_signature: public void setBondMatchFlag(boolean shouldMatchBonds)
focal_class.identifier: setBondMatchFlag
focal_class.modifiers: public
focal_class.parameters: (boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void setBondMatchFlag(boolean shouldMatchBonds)
focal_class.class_method_signature: VFlibTurboHandler.getReactantMol()
focal_class.full_signature: private IAtomContainer getReactantMol()
focal_class.identifier: getReactantMol
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getReactantMol()
focal_class.class_method_signature: VFlibTurboHandler.getProductMol()
focal_class.full_signature: private IAtomContainer getProductMol()
focal_class.identifier: getProductMol
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getProductMol()
focal_class.superclass: extends AbstractSubGraph
focal_method.body: @Override
      public Map<Integer, Integer> getFirstMapping() {
          return Collections.unmodifiableMap(firstMCS);
      }
focal_method.class_method_signature: VFlibTurboHandler.getFirstMapping()
focal_method.full_signature: @Override public Map<Integer, Integer> getFirstMapping()
focal_method.identifier: getFirstMapping
focal_method.invocations: unmodifiableMap
focal_method.modifiers: @Override public
focal_method.parameters: ()
focal_method.return: Map<Integer, Integer>
focal_method.signature: Map<Integer, Integer> getFirstMapping()