test_class.declarator: standAlone = false
test_class.original_string: boolean standAlone = false;
test_class.type: boolean
test_class.var_name: standAlone
test_class.file: legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSTest.java
test_class.identifier: CDKMCSTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetOverlaps_IAtomContainer_IAtomContainer() throws Exception {
          String file1 = "data/mdl/5SD.mol";
          String file2 = "data/mdl/ADN.mol";
          IAtomContainer mol1 = new AtomContainer();
          IAtomContainer mol2 = new AtomContainer();
  
          InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(file1);
          new MDLV2000Reader(ins1, Mode.STRICT).read(mol1);
          InputStream ins2 = this.getClass().getClassLoader().getResourceAsStream(file2);
          new MDLV2000Reader(ins2, Mode.STRICT).read(mol2);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
          CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol1.getBuilder());
          adder.addImplicitHydrogens(mol1);
          Aromaticity.cdkLegacy().apply(mol1);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
          adder = CDKHydrogenAdder.getInstance(mol2.getBuilder());
          adder.addImplicitHydrogens(mol2);
          Aromaticity.cdkLegacy().apply(mol2);
  
          List<IAtomContainer> list = CDKMCS.getOverlaps(mol1, mol2, true);
          Assert.assertEquals(1, list.size());
          Assert.assertEquals(11, (list.get(0)).getAtomCount());
  
          list = CDKMCS.getOverlaps(mol2, mol1, true);
          Assert.assertEquals(1, list.size());
          Assert.assertEquals(11, (list.get(0)).getAtomCount());
      }
test_case.class_method_signature: CDKMCSTest.testGetOverlaps_IAtomContainer_IAtomContainer()
test_case.full_signature: @Test public void testGetOverlaps_IAtomContainer_IAtomContainer()
test_case.identifier: testGetOverlaps_IAtomContainer_IAtomContainer
test_case.invocations: getResourceAsStream getClassLoader getClass read getResourceAsStream getClassLoader getClass read percieveAtomTypesAndConfigureAtoms getInstance getBuilder addImplicitHydrogens apply cdkLegacy percieveAtomTypesAndConfigureAtoms getInstance getBuilder addImplicitHydrogens apply cdkLegacy getOverlaps assertEquals size assertEquals getAtomCount get getOverlaps assertEquals size assertEquals getAtomCount get
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetOverlaps_IAtomContainer_IAtomContainer()
focal_class.declarator: ID1         = 0
focal_class.modifier: final static
focal_class.original_string: final static int           ID1         = 0;
focal_class.type: int
focal_class.var_name: ID1
focal_class.declarator: ID2         = 1
focal_class.modifier: final static
focal_class.original_string: final static int           ID2         = 1;
focal_class.type: int
focal_class.var_name: ID2
focal_class.declarator: timeManager = null
focal_class.modifier: private static
focal_class.original_string: private static TimeManager timeManager = null;
focal_class.type: TimeManager
focal_class.var_name: timeManager
focal_class.file: legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java
focal_class.identifier: CDKMCS
focal_class.class_method_signature: CDKMCS.isIsomorph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.full_signature: public static boolean isIsomorph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.identifier: isIsomorph
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.return: boolean
focal_class.signature: boolean isIsomorph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getIsomorphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<CDKRMap> getIsomorphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getIsomorphMap
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> getIsomorphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getIsomorphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<CDKRMap> getIsomorphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getIsomorphAtomsMap
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> getIsomorphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<List<CDKRMap>> getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getIsomorphMaps
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getSubgraphMaps
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<CDKRMap> getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getSubgraphMap
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<List<CDKRMap>> getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getSubgraphAtomsMaps
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getSubgraphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<CDKRMap> getSubgraphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getSubgraphAtomsMap
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> getSubgraphAtomsMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.isSubgraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.full_signature: public static boolean isSubgraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.identifier: isSubgraph
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.return: boolean
focal_class.signature: boolean isSubgraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.identifier: getOverlaps
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.getBitSet(IAtomContainer atomContainer)
focal_class.full_signature: public static BitSet getBitSet(IAtomContainer atomContainer)
focal_class.identifier: getBitSet
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: BitSet
focal_class.signature: BitSet getBitSet(IAtomContainer atomContainer)
focal_class.class_method_signature: CDKMCS.buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.full_signature: public static CDKRGraph buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.identifier: buildRGraph
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.return: CDKRGraph
focal_class.signature: CDKRGraph buildRGraph(IAtomContainer sourceGraph, IAtomContainer targetGraph, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.search(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap,
              boolean shouldMatchBonds)
focal_class.full_signature: public static List<List<CDKRMap>> search(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap,
              boolean shouldMatchBonds)
focal_class.identifier: search
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap,
              boolean shouldMatchBonds)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> search(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              BitSet sourceBitSet, BitSet targetBitSet, boolean findAllStructure, boolean findAllMap,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.project(List<CDKRMap> rMapList, IAtomContainer graph, int key)
focal_class.full_signature: public static IAtomContainer project(List<CDKRMap> rMapList, IAtomContainer graph, int key)
focal_class.identifier: project
focal_class.modifiers: public static
focal_class.parameters: (List<CDKRMap> rMapList, IAtomContainer graph, int key)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer project(List<CDKRMap> rMapList, IAtomContainer graph, int key)
focal_class.class_method_signature: CDKMCS.projectList(List<List<CDKRMap>> rMapsList, IAtomContainer graph, int key)
focal_class.full_signature: public static ArrayList<IAtomContainer> projectList(List<List<CDKRMap>> rMapsList, IAtomContainer graph, int key)
focal_class.identifier: projectList
focal_class.modifiers: public static
focal_class.parameters: (List<List<CDKRMap>> rMapsList, IAtomContainer graph, int key)
focal_class.return: ArrayList<IAtomContainer>
focal_class.signature: ArrayList<IAtomContainer> projectList(List<List<CDKRMap>> rMapsList, IAtomContainer graph, int key)
focal_class.class_method_signature: CDKMCS.getMaximum(ArrayList<IAtomContainer> graphList, boolean shouldMatchBonds)
focal_class.full_signature: private static List<IAtomContainer> getMaximum(ArrayList<IAtomContainer> graphList, boolean shouldMatchBonds)
focal_class.identifier: getMaximum
focal_class.modifiers: private static
focal_class.parameters: (ArrayList<IAtomContainer> graphList, boolean shouldMatchBonds)
focal_class.return: List<IAtomContainer>
focal_class.signature: List<IAtomContainer> getMaximum(ArrayList<IAtomContainer> graphList, boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph)
focal_class.full_signature: public static List<CDKRMap> checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph)
focal_class.identifier: checkSingleAtomCases
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> checkSingleAtomCases(IAtomContainer sourceGraph, IAtomContainer targetGraph)
focal_class.class_method_signature: CDKMCS.makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.full_signature: public static List<List<CDKRMap>> makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.identifier: makeAtomsMapsOfBondsMaps
focal_class.modifiers: public static
focal_class.parameters: (List<List<CDKRMap>> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.return: List<List<CDKRMap>>
focal_class.signature: List<List<CDKRMap>> makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.class_method_signature: CDKMCS.makeAtomsMapOfBondsMap(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.full_signature: public static List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.identifier: makeAtomsMapOfBondsMap
focal_class.modifiers: public static
focal_class.parameters: (List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.return: List<CDKRMap>
focal_class.signature: List<CDKRMap> makeAtomsMapOfBondsMap(List<CDKRMap> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph)
focal_class.class_method_signature: CDKMCS.nodeConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2,
              boolean shouldMatchBonds)
focal_class.full_signature: private static void nodeConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2,
              boolean shouldMatchBonds)
focal_class.identifier: nodeConstructor
focal_class.modifiers: private static
focal_class.parameters: (CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2,
              boolean shouldMatchBonds)
focal_class.return: void
focal_class.signature: void nodeConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2,
              boolean shouldMatchBonds)
focal_class.full_signature: private static boolean isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2,
              boolean shouldMatchBonds)
focal_class.identifier: isMatchFeasible
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2,
              boolean shouldMatchBonds)
focal_class.return: boolean
focal_class.signature: boolean isMatchFeasible(IAtomContainer ac1, IBond bondA1, IAtomContainer ac2, IBond bondA2,
              boolean shouldMatchBonds)
focal_class.class_method_signature: CDKMCS.arcConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2)
focal_class.full_signature: private static void arcConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2)
focal_class.identifier: arcConstructor
focal_class.modifiers: private static
focal_class.parameters: (CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2)
focal_class.return: void
focal_class.signature: void arcConstructor(CDKRGraph graph, IAtomContainer ac1, IAtomContainer ac2)
focal_class.class_method_signature: CDKMCS.hasCommonAtom(IBond bondA, IBond bondB)
focal_class.full_signature: private static boolean hasCommonAtom(IBond bondA, IBond bondB)
focal_class.identifier: hasCommonAtom
focal_class.modifiers: private static
focal_class.parameters: (IBond bondA, IBond bondB)
focal_class.return: boolean
focal_class.signature: boolean hasCommonAtom(IBond bondA, IBond bondB)
focal_class.class_method_signature: CDKMCS.getCommonSymbol(IBond bondA, IBond bondB)
focal_class.full_signature: private static String getCommonSymbol(IBond bondA, IBond bondB)
focal_class.identifier: getCommonSymbol
focal_class.modifiers: private static
focal_class.parameters: (IBond bondA, IBond bondB)
focal_class.return: String
focal_class.signature: String getCommonSymbol(IBond bondA, IBond bondB)
focal_class.class_method_signature: CDKMCS.queryAdjacency(IBond bondA1, IBond bondB1, IBond bondA2, IBond bondB2)
focal_class.full_signature: private static boolean queryAdjacency(IBond bondA1, IBond bondB1, IBond bondA2, IBond bondB2)
focal_class.identifier: queryAdjacency
focal_class.modifiers: private static
focal_class.parameters: (IBond bondA1, IBond bondB1, IBond bondA2, IBond bondB2)
focal_class.return: boolean
focal_class.signature: boolean queryAdjacency(IBond bondA1, IBond bondB1, IBond bondA2, IBond bondB2)
focal_class.class_method_signature: CDKMCS.queryAdjacencyAndOrder(IBond bond1, IBond bond2, IBond queryBond1, IBond queryBond2)
focal_class.full_signature: private static boolean queryAdjacencyAndOrder(IBond bond1, IBond bond2, IBond queryBond1, IBond queryBond2)
focal_class.identifier: queryAdjacencyAndOrder
focal_class.modifiers: private static
focal_class.parameters: (IBond bond1, IBond bond2, IBond queryBond1, IBond queryBond2)
focal_class.return: boolean
focal_class.signature: boolean queryAdjacencyAndOrder(IBond bond1, IBond bond2, IBond queryBond1, IBond queryBond2)
focal_class.class_method_signature: CDKMCS.testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
focal_class.full_signature: private static boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
focal_class.identifier: testSubgraphHeuristics
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer ac1, IAtomContainer ac2)
focal_class.return: boolean
focal_class.signature: boolean testSubgraphHeuristics(IAtomContainer ac1, IAtomContainer ac2)
focal_class.class_method_signature: CDKMCS.getTimeout()
focal_class.full_signature: protected synchronized static double getTimeout()
focal_class.identifier: getTimeout
focal_class.modifiers: protected synchronized static
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getTimeout()
focal_class.class_method_signature: CDKMCS.getTimeManager()
focal_class.full_signature: protected synchronized static TimeManager getTimeManager()
focal_class.identifier: getTimeManager
focal_class.modifiers: protected synchronized static
focal_class.parameters: ()
focal_class.return: TimeManager
focal_class.signature: TimeManager getTimeManager()
focal_class.class_method_signature: CDKMCS.setTimeManager(TimeManager aTimeManager)
focal_class.full_signature: protected synchronized static void setTimeManager(TimeManager aTimeManager)
focal_class.identifier: setTimeManager
focal_class.modifiers: protected synchronized static
focal_class.parameters: (TimeManager aTimeManager)
focal_class.return: void
focal_class.signature: void setTimeManager(TimeManager aTimeManager)
focal_class.class_method_signature: CDKMCS.isTimeOut()
focal_class.full_signature: public synchronized static boolean isTimeOut()
focal_class.identifier: isTimeOut
focal_class.modifiers: public synchronized static
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isTimeOut()
focal_method.body: public static List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          List<List<CDKRMap>> rMapsList = search(sourceGraph, targetGraph, new BitSet(), new BitSet(), true, false,
                  shouldMatchBonds);
  
          // projection on G1
          ArrayList<IAtomContainer> graphList = projectList(rMapsList, sourceGraph, ID1);
  
          // reduction of set of solution (isomorphism and substructure
          // with different 'mappings'
  
          return getMaximum(graphList, shouldMatchBonds);
      }
focal_method.class_method_signature: CDKMCS.getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.full_signature: public static List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.identifier: getOverlaps
focal_method.invocations: search projectList getMaximum
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.return: List<IAtomContainer>
focal_method.signature: List<IAtomContainer> getOverlaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)