test_class.declarator: sp = new SmilesParser(SilentChemObjectBuilder.getInstance())
test_class.modifier: private static
test_class.original_string: private static SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: sp
test_class.file: storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java
test_class.identifier: SmilesParserTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testFormalNeighborBount() throws Exception {
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("Oc1ccc(O)cc1");
          atomtype(mol);
          Assert.assertEquals("O.sp3", mol.getAtom(0).getAtomTypeName());
          Assert.assertEquals(2, mol.getAtom(0).getFormalNeighbourCount().intValue());
          Assert.assertEquals("C.sp2", mol.getAtom(1).getAtomTypeName());
          Assert.assertEquals(3, mol.getAtom(1).getFormalNeighbourCount().intValue());
          IAtomContainer clone = (IAtomContainer) mol.clone();
          Assert.assertEquals("O.sp3", clone.getAtom(0).getAtomTypeName());
          Assert.assertEquals(2, clone.getAtom(0).getFormalNeighbourCount().intValue());
          Assert.assertEquals("C.sp2", clone.getAtom(1).getAtomTypeName());
          Assert.assertEquals(3, clone.getAtom(1).getFormalNeighbourCount().intValue());
      }
test_case.class_method_signature: SmilesParserTest.testFormalNeighborBount()
test_case.full_signature: @Test public void testFormalNeighborBount()
test_case.identifier: testFormalNeighborBount
test_case.invocations: getInstance parseSmiles atomtype assertEquals getAtomTypeName getAtom assertEquals intValue getFormalNeighbourCount getAtom assertEquals getAtomTypeName getAtom assertEquals intValue getFormalNeighbourCount getAtom clone assertEquals getAtomTypeName getAtom assertEquals intValue getFormalNeighbourCount getAtom assertEquals getAtomTypeName getAtom assertEquals intValue getFormalNeighbourCount getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testFormalNeighborBount()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(SmilesParser.class)
focal_class.modifier: private
focal_class.original_string: private ILoggingTool logger = LoggingToolFactory.createLoggingTool(SmilesParser.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
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: beamToCDK
focal_class.modifier: private final
focal_class.original_string: private final BeamToCDK          beamToCDK;
focal_class.type: BeamToCDK
focal_class.var_name: beamToCDK
focal_class.declarator: kekulise = true
focal_class.modifier: private
focal_class.original_string: private boolean                  kekulise = true;
focal_class.type: boolean
focal_class.var_name: kekulise
focal_class.declarator: strict = false
focal_class.modifier: private
focal_class.original_string: private boolean                  strict = false;
focal_class.type: boolean
focal_class.var_name: strict
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
focal_class.identifier: SmilesParser
focal_class.class_method_signature: SmilesParser.SmilesParser(final IChemObjectBuilder builder)
focal_class.full_signature: public  SmilesParser(final IChemObjectBuilder builder)
focal_class.identifier: SmilesParser
focal_class.modifiers: public
focal_class.parameters: (final IChemObjectBuilder builder)
focal_class.signature:  SmilesParser(final IChemObjectBuilder builder)
focal_class.class_method_signature: SmilesParser.setStrict(boolean strict)
focal_class.full_signature: public void setStrict(boolean strict)
focal_class.identifier: setStrict
focal_class.modifiers: public
focal_class.parameters: (boolean strict)
focal_class.return: void
focal_class.signature: void setStrict(boolean strict)
focal_class.class_method_signature: SmilesParser.parseReactionSmiles(String smiles)
focal_class.full_signature: public IReaction parseReactionSmiles(String smiles)
focal_class.identifier: parseReactionSmiles
focal_class.modifiers: public
focal_class.parameters: (String smiles)
focal_class.return: IReaction
focal_class.signature: IReaction parseReactionSmiles(String smiles)
focal_class.class_method_signature: SmilesParser.parseSmiles(String smiles)
focal_class.full_signature: public IAtomContainer parseSmiles(String smiles)
focal_class.identifier: parseSmiles
focal_class.modifiers: public
focal_class.parameters: (String smiles)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer parseSmiles(String smiles)
focal_class.class_method_signature: SmilesParser.parseSmiles(String smiles, boolean isRxnPart)
focal_class.full_signature: private IAtomContainer parseSmiles(String smiles, boolean isRxnPart)
focal_class.identifier: parseSmiles
focal_class.modifiers: private
focal_class.parameters: (String smiles, boolean isRxnPart)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer parseSmiles(String smiles, boolean isRxnPart)
focal_class.class_method_signature: SmilesParser.parseIntSafe(String val)
focal_class.full_signature: private int parseIntSafe(String val)
focal_class.identifier: parseIntSafe
focal_class.modifiers: private
focal_class.parameters: (String val)
focal_class.return: int
focal_class.signature: int parseIntSafe(String val)
focal_class.class_method_signature: SmilesParser.parseMolCXSMILES(String title, IAtomContainer mol)
focal_class.full_signature: private void parseMolCXSMILES(String title, IAtomContainer mol)
focal_class.identifier: parseMolCXSMILES
focal_class.modifiers: private
focal_class.parameters: (String title, IAtomContainer mol)
focal_class.return: void
focal_class.signature: void parseMolCXSMILES(String title, IAtomContainer mol)
focal_class.class_method_signature: SmilesParser.parseRxnCXSMILES(String title, IReaction rxn)
focal_class.full_signature: private void parseRxnCXSMILES(String title, IReaction rxn)
focal_class.identifier: parseRxnCXSMILES
focal_class.modifiers: private
focal_class.parameters: (String title, IReaction rxn)
focal_class.return: void
focal_class.signature: void parseRxnCXSMILES(String title, IReaction rxn)
focal_class.class_method_signature: SmilesParser.handleFragmentGrouping(IReaction rxn, CxSmilesState cxstate)
focal_class.full_signature: private void handleFragmentGrouping(IReaction rxn, CxSmilesState cxstate)
focal_class.identifier: handleFragmentGrouping
focal_class.modifiers: private
focal_class.parameters: (IReaction rxn, CxSmilesState cxstate)
focal_class.return: void
focal_class.signature: void handleFragmentGrouping(IReaction rxn, CxSmilesState cxstate)
focal_class.class_method_signature: SmilesParser.assignCxSmilesInfo(IChemObjectBuilder bldr,
                                      IChemObject chemObj,
                                      List<IAtom> atoms,
                                      Map<IAtom, IAtomContainer> atomToMol,
                                      CxSmilesState cxstate)
focal_class.full_signature: private void assignCxSmilesInfo(IChemObjectBuilder bldr,
                                      IChemObject chemObj,
                                      List<IAtom> atoms,
                                      Map<IAtom, IAtomContainer> atomToMol,
                                      CxSmilesState cxstate)
focal_class.identifier: assignCxSmilesInfo
focal_class.modifiers: private
focal_class.parameters: (IChemObjectBuilder bldr,
                                      IChemObject chemObj,
                                      List<IAtom> atoms,
                                      Map<IAtom, IAtomContainer> atomToMol,
                                      CxSmilesState cxstate)
focal_class.return: void
focal_class.signature: void assignCxSmilesInfo(IChemObjectBuilder bldr,
                                      IChemObject chemObj,
                                      List<IAtom> atoms,
                                      Map<IAtom, IAtomContainer> atomToMol,
                                      CxSmilesState cxstate)
focal_class.class_method_signature: SmilesParser.setPreservingAromaticity(boolean preservingAromaticity)
focal_class.full_signature: @Deprecated public void setPreservingAromaticity(boolean preservingAromaticity)
focal_class.identifier: setPreservingAromaticity
focal_class.modifiers: @Deprecated public
focal_class.parameters: (boolean preservingAromaticity)
focal_class.return: void
focal_class.signature: void setPreservingAromaticity(boolean preservingAromaticity)
focal_class.class_method_signature: SmilesParser.isPreservingAromaticity()
focal_class.full_signature: @Deprecated public boolean isPreservingAromaticity()
focal_class.identifier: isPreservingAromaticity
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: boolean
focal_class.signature: boolean isPreservingAromaticity()
focal_class.class_method_signature: SmilesParser.kekulise(boolean kekulise)
focal_class.full_signature: public void kekulise(boolean kekulise)
focal_class.identifier: kekulise
focal_class.modifiers: public
focal_class.parameters: (boolean kekulise)
focal_class.return: void
focal_class.signature: void kekulise(boolean kekulise)
focal_method.body: public IAtomContainer parseSmiles(String smiles) throws InvalidSmilesException {
          return parseSmiles(smiles, false);
      }
focal_method.class_method_signature: SmilesParser.parseSmiles(String smiles)
focal_method.full_signature: public IAtomContainer parseSmiles(String smiles)
focal_method.identifier: parseSmiles
focal_method.invocations: parseSmiles
focal_method.modifiers: public
focal_method.parameters: (String smiles)
focal_method.return: IAtomContainer
focal_method.signature: IAtomContainer parseSmiles(String smiles)