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 testPuParsing() throws InvalidSmilesException {
          SmilesParser p = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = p.parseSmiles("[Pu]");
          Assert.assertEquals("Pu", mol.getAtom(0).getSymbol());
      }
test_case.class_method_signature: SmilesParserTest.testPuParsing()
test_case.full_signature: @Test public void testPuParsing()
test_case.identifier: testPuParsing
test_case.invocations: getInstance parseSmiles assertEquals getSymbol getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testPuParsing()
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)