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 testSFBug1708336() throws Exception {
          IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
          IAtomContainer atomContainer = builder.newInstance(IAtomContainer.class);
          atomContainer.addAtom(builder.newInstance(IAtom.class, "C"));
          atomContainer.addAtom(builder.newInstance(IAtom.class, "C"));
          atomContainer.addAtom(builder.newInstance(IAtom.class, "N"));
          atomContainer.addBond(0, 1, IBond.Order.SINGLE);
          atomContainer.addBond(1, 2, IBond.Order.SINGLE);
          IQueryAtomContainer query = new QueryAtomContainer(DefaultChemObjectBuilder.getInstance());
          IQueryAtom a1 = new SymbolQueryAtom(DefaultChemObjectBuilder.getInstance());
          a1.setSymbol("C");
  
          AnyAtom a2 = new AnyAtom(DefaultChemObjectBuilder.getInstance());
  
          IBond b1 = new OrderQueryBond(a1, a2, IBond.Order.SINGLE, DefaultChemObjectBuilder.getInstance());
  
          IQueryAtom a3 = new SymbolQueryAtom(DefaultChemObjectBuilder.getInstance());
          a3.setSymbol("C");
  
          IBond b2 = new OrderQueryBond(a2, a3, IBond.Order.SINGLE, DefaultChemObjectBuilder.getInstance());
          query.addAtom(a1);
          query.addAtom(a2);
          query.addAtom(a3);
  
          query.addBond(b1);
          query.addBond(b2);
  
          List<List<CDKRMap>> list = CDKMCS.getSubgraphMaps(atomContainer, query, true);
  
          Assert.assertTrue(list.isEmpty());
      }
test_case.class_method_signature: CDKMCSTest.testSFBug1708336()
test_case.full_signature: @Test public void testSFBug1708336()
test_case.identifier: testSFBug1708336
test_case.invocations: getInstance newInstance addAtom newInstance addAtom newInstance addAtom newInstance addBond addBond getInstance getInstance setSymbol getInstance getInstance getInstance setSymbol getInstance addAtom addAtom addAtom addBond addBond getSubgraphMaps assertTrue isEmpty
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testSFBug1708336()
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<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          return search(sourceGraph, targetGraph, new BitSet(), getBitSet(targetGraph), true, true, shouldMatchBonds);
      }
focal_method.class_method_signature: CDKMCS.getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.full_signature: public static List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.identifier: getSubgraphMaps
focal_method.invocations: search getBitSet
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)
focal_method.return: List<List<CDKRMap>>
focal_method.signature: List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds)