test_class.file: legacy/src/test/java/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java
test_class.identifier: SMARTSQueryToolTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void setAromaticity() throws Exception {
          SMARTSQueryTool sqt = new SMARTSQueryTool("[a]", DefaultChemObjectBuilder.getInstance());
  
          IAtomContainer furan = smiles("O1C=CC=C1");
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(furan);
  
          sqt.setAromaticity(new Aromaticity(ElectronDonation.cdk(), Cycles.mcb()));
          assertTrue(sqt.matches(furan, true));
  
          sqt.setAromaticity(new Aromaticity(ElectronDonation.piBonds(), Cycles.mcb()));
          assertFalse(sqt.matches(furan, true));
      }
test_case.class_method_signature: SMARTSQueryToolTest.setAromaticity()
test_case.full_signature: @Test public void setAromaticity()
test_case.identifier: setAromaticity
test_case.invocations: getInstance smiles percieveAtomTypesAndConfigureAtoms setAromaticity cdk mcb assertTrue matches setAromaticity piBonds mcb assertFalse matches
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void setAromaticity()
focal_class.declarator: logger        = LoggingToolFactory.createLoggingTool(SMARTSQueryTool.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger        = LoggingToolFactory.createLoggingTool(SMARTSQueryTool.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: smarts
focal_class.modifier: private
focal_class.original_string: private String              smarts;
focal_class.type: String
focal_class.var_name: smarts
focal_class.declarator: atomContainer = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer      atomContainer = null;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.declarator: query         = null
focal_class.modifier: private
focal_class.original_string: private QueryAtomContainer  query         = null;
focal_class.type: QueryAtomContainer
focal_class.var_name: query
focal_class.declarator: mappings
focal_class.modifier: private
focal_class.original_string: private List<int[]>         mappings;
focal_class.type: List<int[]>
focal_class.var_name: mappings
focal_class.declarator: ringSet         = RingSet.EssentialRings
focal_class.modifier: private
focal_class.original_string: private RingSet                  ringSet         = RingSet.EssentialRings;
focal_class.type: RingSet
focal_class.var_name: ringSet
focal_class.declarator: builder
focal_class.modifier: private final
focal_class.original_string: private final IChemObjectBuilder builder;
focal_class.type: IChemObjectBuilder
focal_class.var_name: builder
focal_class.declarator: aromaticity     = new Aromaticity(ElectronDonation.daylight(),
                                                               Cycles.allOrVertexShort())
focal_class.modifier: private
focal_class.original_string: private Aromaticity              aromaticity     = new Aromaticity(ElectronDonation.daylight(),
                                                               Cycles.allOrVertexShort());
focal_class.type: Aromaticity
focal_class.var_name: aromaticity
focal_class.declarator: skipAromaticity = false
focal_class.modifier: private
focal_class.original_string: private boolean                  skipAromaticity = false;
focal_class.type: boolean
focal_class.var_name: skipAromaticity
focal_class.declarator: MAX_ENTRIES     = 20
focal_class.modifier: private
focal_class.original_string: private int                      MAX_ENTRIES     = 20;
focal_class.type: int
focal_class.var_name: MAX_ENTRIES
focal_class.declarator: cache           = new LinkedHashMap<String, QueryAtomContainer>(MAX_ENTRIES + 1,
                                                               .75F, true) {
  
                                                           @Override
                                                           public boolean removeEldestEntry(Map.Entry eldest) {
                                                               return size() > MAX_ENTRIES;
                                                           }
                                                       }
focal_class.original_string: Map<String, QueryAtomContainer>  cache           = new LinkedHashMap<String, QueryAtomContainer>(MAX_ENTRIES + 1,
                                                               .75F, true) {
  
                                                           @Override
                                                           public boolean removeEldestEntry(Map.Entry eldest) {
                                                               return size() > MAX_ENTRIES;
                                                           }
                                                       };
focal_class.type: Map<String, QueryAtomContainer>
focal_class.var_name: cache
focal_class.file: legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
focal_class.identifier: SMARTSQueryTool
focal_class.class_method_signature: SMARTSQueryTool.SMARTSQueryTool(String smarts, IChemObjectBuilder builder)
focal_class.full_signature: public  SMARTSQueryTool(String smarts, IChemObjectBuilder builder)
focal_class.identifier: SMARTSQueryTool
focal_class.modifiers: public
focal_class.parameters: (String smarts, IChemObjectBuilder builder)
focal_class.signature:  SMARTSQueryTool(String smarts, IChemObjectBuilder builder)
focal_class.class_method_signature: SMARTSQueryTool.setQueryCacheSize(int maxEntries)
focal_class.full_signature: public void setQueryCacheSize(int maxEntries)
focal_class.identifier: setQueryCacheSize
focal_class.modifiers: public
focal_class.parameters: (int maxEntries)
focal_class.return: void
focal_class.signature: void setQueryCacheSize(int maxEntries)
focal_class.class_method_signature: SMARTSQueryTool.useSmallestSetOfSmallestRings()
focal_class.full_signature: public void useSmallestSetOfSmallestRings()
focal_class.identifier: useSmallestSetOfSmallestRings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void useSmallestSetOfSmallestRings()
focal_class.class_method_signature: SMARTSQueryTool.useRelevantRings()
focal_class.full_signature: public void useRelevantRings()
focal_class.identifier: useRelevantRings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void useRelevantRings()
focal_class.class_method_signature: SMARTSQueryTool.useEssentialRings()
focal_class.full_signature: public void useEssentialRings()
focal_class.identifier: useEssentialRings
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void useEssentialRings()
focal_class.class_method_signature: SMARTSQueryTool.setAromaticity(Aromaticity aromaticity)
focal_class.full_signature: public void setAromaticity(Aromaticity aromaticity)
focal_class.identifier: setAromaticity
focal_class.modifiers: public
focal_class.parameters: (Aromaticity aromaticity)
focal_class.return: void
focal_class.signature: void setAromaticity(Aromaticity aromaticity)
focal_class.class_method_signature: SMARTSQueryTool.getSmarts()
focal_class.full_signature: public String getSmarts()
focal_class.identifier: getSmarts
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getSmarts()
focal_class.class_method_signature: SMARTSQueryTool.setSmarts(String smarts)
focal_class.full_signature: public void setSmarts(String smarts)
focal_class.identifier: setSmarts
focal_class.modifiers: public
focal_class.parameters: (String smarts)
focal_class.return: void
focal_class.signature: void setSmarts(String smarts)
focal_class.class_method_signature: SMARTSQueryTool.matches(IAtomContainer atomContainer)
focal_class.full_signature: public boolean matches(IAtomContainer atomContainer)
focal_class.identifier: matches
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: boolean
focal_class.signature: boolean matches(IAtomContainer atomContainer)
focal_class.class_method_signature: SMARTSQueryTool.matches(IAtomContainer atomContainer, boolean forceInitialization)
focal_class.full_signature: public boolean matches(IAtomContainer atomContainer, boolean forceInitialization)
focal_class.identifier: matches
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, boolean forceInitialization)
focal_class.return: boolean
focal_class.signature: boolean matches(IAtomContainer atomContainer, boolean forceInitialization)
focal_class.class_method_signature: SMARTSQueryTool.countMatches()
focal_class.full_signature: public int countMatches()
focal_class.identifier: countMatches
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int countMatches()
focal_class.class_method_signature: SMARTSQueryTool.getMatchingAtoms()
focal_class.full_signature: public List<List<Integer>> getMatchingAtoms()
focal_class.identifier: getMatchingAtoms
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<Integer>>
focal_class.signature: List<List<Integer>> getMatchingAtoms()
focal_class.class_method_signature: SMARTSQueryTool.getUniqueMatchingAtoms()
focal_class.full_signature: public List<List<Integer>> getUniqueMatchingAtoms()
focal_class.identifier: getUniqueMatchingAtoms
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<List<Integer>>
focal_class.signature: List<List<Integer>> getUniqueMatchingAtoms()
focal_class.class_method_signature: SMARTSQueryTool.initializeMolecule()
focal_class.full_signature: private void initializeMolecule()
focal_class.identifier: initializeMolecule
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void initializeMolecule()
focal_class.class_method_signature: SMARTSQueryTool.initializeQuery()
focal_class.full_signature: private void initializeQuery()
focal_class.identifier: initializeQuery
focal_class.modifiers: private
focal_class.parameters: ()
focal_class.return: void
focal_class.signature: void initializeQuery()
focal_class.class_method_signature: SMARTSQueryTool.matchedAtoms(List<List<RMap>> bondMapping, IAtomContainer atomContainer)
focal_class.full_signature: private List<Set<Integer>> matchedAtoms(List<List<RMap>> bondMapping, IAtomContainer atomContainer)
focal_class.identifier: matchedAtoms
focal_class.modifiers: private
focal_class.parameters: (List<List<RMap>> bondMapping, IAtomContainer atomContainer)
focal_class.return: List<Set<Integer>>
focal_class.signature: List<Set<Integer>> matchedAtoms(List<List<RMap>> bondMapping, IAtomContainer atomContainer)
focal_method.body: public void setAromaticity(Aromaticity aromaticity) {
          this.aromaticity = checkNotNull(aromaticity, "aromaticity was not provided");
      }
focal_method.class_method_signature: SMARTSQueryTool.setAromaticity(Aromaticity aromaticity)
focal_method.full_signature: public void setAromaticity(Aromaticity aromaticity)
focal_method.identifier: setAromaticity
focal_method.invocations: checkNotNull
focal_method.modifiers: public
focal_method.parameters: (Aromaticity aromaticity)
focal_method.return: void
focal_method.signature: void setAromaticity(Aromaticity aromaticity)