test_class.file: storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
test_class.identifier: SmilesGeneratorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testSFBug1089770_2() throws Exception {
          String filename = "data/mdl/bug1089770-2.mol";
          InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
          MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
          IAtomContainer mol1 = reader.read(new AtomContainer());
          SmilesGenerator sg = new SmilesGenerator();
          String moleculeSmile = sg.create(mol1);
          //logger.debug(filename + " -> " + moleculeSmile);
          Assert.assertEquals("C=1\\CC/C=C\\CC/C1", moleculeSmile);
      }
test_case.class_method_signature: SmilesGeneratorTest.testSFBug1089770_2()
test_case.full_signature: @Test public void testSFBug1089770_2()
test_case.identifier: testSFBug1089770_2
test_case.invocations: getResourceAsStream getClassLoader getClass read create assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testSFBug1089770_2()
focal_class.declarator: flavour
focal_class.modifier: private final
focal_class.original_string: private final int       flavour;
focal_class.type: int
focal_class.var_name: flavour
focal_class.file: storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
focal_class.identifier: SmilesGenerator
focal_class.class_method_signature: SmilesGenerator.SmilesGenerator()
focal_class.full_signature: @Deprecated public  SmilesGenerator()
focal_class.identifier: SmilesGenerator
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.signature:  SmilesGenerator()
focal_class.class_method_signature: SmilesGenerator.SmilesGenerator(int flavour)
focal_class.full_signature: public  SmilesGenerator(int flavour)
focal_class.identifier: SmilesGenerator
focal_class.modifiers: public
focal_class.parameters: (int flavour)
focal_class.signature:  SmilesGenerator(int flavour)
focal_class.class_method_signature: SmilesGenerator.aromatic()
focal_class.full_signature: public SmilesGenerator aromatic()
focal_class.identifier: aromatic
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator aromatic()
focal_class.class_method_signature: SmilesGenerator.withAtomClasses()
focal_class.full_signature: @Deprecated public SmilesGenerator withAtomClasses()
focal_class.identifier: withAtomClasses
focal_class.modifiers: @Deprecated public
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator withAtomClasses()
focal_class.class_method_signature: SmilesGenerator.generic()
focal_class.full_signature: public static SmilesGenerator generic()
focal_class.identifier: generic
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator generic()
focal_class.class_method_signature: SmilesGenerator.isomeric()
focal_class.full_signature: public static SmilesGenerator isomeric()
focal_class.identifier: isomeric
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator isomeric()
focal_class.class_method_signature: SmilesGenerator.unique()
focal_class.full_signature: public static SmilesGenerator unique()
focal_class.identifier: unique
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator unique()
focal_class.class_method_signature: SmilesGenerator.absolute()
focal_class.full_signature: public static SmilesGenerator absolute()
focal_class.identifier: absolute
focal_class.modifiers: public static
focal_class.parameters: ()
focal_class.return: SmilesGenerator
focal_class.signature: SmilesGenerator absolute()
focal_class.class_method_signature: SmilesGenerator.createSMILES(IAtomContainer molecule)
focal_class.full_signature: @Deprecated public String createSMILES(IAtomContainer molecule)
focal_class.identifier: createSMILES
focal_class.modifiers: @Deprecated public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: String
focal_class.signature: String createSMILES(IAtomContainer molecule)
focal_class.class_method_signature: SmilesGenerator.createSMILES(IReaction reaction)
focal_class.full_signature: @Deprecated public String createSMILES(IReaction reaction)
focal_class.identifier: createSMILES
focal_class.modifiers: @Deprecated public
focal_class.parameters: (IReaction reaction)
focal_class.return: String
focal_class.signature: String createSMILES(IReaction reaction)
focal_class.class_method_signature: SmilesGenerator.create(IAtomContainer molecule)
focal_class.full_signature: public String create(IAtomContainer molecule)
focal_class.identifier: create
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: String
focal_class.signature: String create(IAtomContainer molecule)
focal_class.class_method_signature: SmilesGenerator.create(IAtomContainer molecule, int[] order)
focal_class.full_signature: public String create(IAtomContainer molecule, int[] order)
focal_class.identifier: create
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule, int[] order)
focal_class.return: String
focal_class.signature: String create(IAtomContainer molecule, int[] order)
focal_class.class_method_signature: SmilesGenerator.create(IAtomContainer molecule, int flavour, int[] order)
focal_class.full_signature: public static String create(IAtomContainer molecule, int flavour, int[] order)
focal_class.identifier: create
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer molecule, int flavour, int[] order)
focal_class.return: String
focal_class.signature: String create(IAtomContainer molecule, int flavour, int[] order)
focal_class.class_method_signature: SmilesGenerator.createReactionSMILES(IReaction reaction)
focal_class.full_signature: @Deprecated public String createReactionSMILES(IReaction reaction)
focal_class.identifier: createReactionSMILES
focal_class.modifiers: @Deprecated public
focal_class.parameters: (IReaction reaction)
focal_class.return: String
focal_class.signature: String createReactionSMILES(IReaction reaction)
focal_class.class_method_signature: SmilesGenerator.create(IReaction reaction)
focal_class.full_signature: public String create(IReaction reaction)
focal_class.identifier: create
focal_class.modifiers: public
focal_class.parameters: (IReaction reaction)
focal_class.return: String
focal_class.signature: String create(IReaction reaction)
focal_class.class_method_signature: SmilesGenerator.safeAddSgroups(List<Sgroup> sgroups, IAtomContainer mol)
focal_class.full_signature: private void safeAddSgroups(List<Sgroup> sgroups, IAtomContainer mol)
focal_class.identifier: safeAddSgroups
focal_class.modifiers: private
focal_class.parameters: (List<Sgroup> sgroups, IAtomContainer mol)
focal_class.return: void
focal_class.signature: void safeAddSgroups(List<Sgroup> sgroups, IAtomContainer mol)
focal_class.class_method_signature: SmilesGenerator.create(IReaction reaction, int[] ordering)
focal_class.full_signature: public String create(IReaction reaction, int[] ordering)
focal_class.identifier: create
focal_class.modifiers: public
focal_class.parameters: (IReaction reaction, int[] ordering)
focal_class.return: String
focal_class.signature: String create(IReaction reaction, int[] ordering)
focal_class.class_method_signature: SmilesGenerator.setUseAromaticityFlag(boolean useAromaticityFlag)
focal_class.full_signature: @Deprecated public void setUseAromaticityFlag(boolean useAromaticityFlag)
focal_class.identifier: setUseAromaticityFlag
focal_class.modifiers: @Deprecated public
focal_class.parameters: (boolean useAromaticityFlag)
focal_class.return: void
focal_class.signature: void setUseAromaticityFlag(boolean useAromaticityFlag)
focal_class.class_method_signature: SmilesGenerator.labels(int flavour, final IAtomContainer molecule)
focal_class.full_signature: private static int[] labels(int flavour, final IAtomContainer molecule)
focal_class.identifier: labels
focal_class.modifiers: private static
focal_class.parameters: (int flavour, final IAtomContainer molecule)
focal_class.return: int[]
focal_class.signature: int[] labels(int flavour, final IAtomContainer molecule)
focal_class.class_method_signature: SmilesGenerator.inchiNumbers(IAtomContainer container)
focal_class.full_signature: private static long[] inchiNumbers(IAtomContainer container)
focal_class.identifier: inchiNumbers
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container)
focal_class.return: long[]
focal_class.signature: long[] inchiNumbers(IAtomContainer container)
focal_class.class_method_signature: SmilesGenerator.getRgrps(IAtomContainer container, Elements reversed)
focal_class.full_signature: private static List<IAtom> getRgrps(IAtomContainer container, Elements reversed)
focal_class.identifier: getRgrps
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, Elements reversed)
focal_class.return: List<IAtom>
focal_class.signature: List<IAtom> getRgrps(IAtomContainer container, Elements reversed)
focal_class.class_method_signature: SmilesGenerator.ensureNotNull(Integer x)
focal_class.full_signature: private static Integer ensureNotNull(Integer x)
focal_class.identifier: ensureNotNull
focal_class.modifiers: private static
focal_class.parameters: (Integer x)
focal_class.return: Integer
focal_class.signature: Integer ensureNotNull(Integer x)
focal_class.class_method_signature: SmilesGenerator.toAtomIdxs(Collection<IAtom> atoms, Map<IAtom, Integer> atomidx)
focal_class.full_signature: private static List<Integer> toAtomIdxs(Collection<IAtom> atoms, Map<IAtom, Integer> atomidx)
focal_class.identifier: toAtomIdxs
focal_class.modifiers: private static
focal_class.parameters: (Collection<IAtom> atoms, Map<IAtom, Integer> atomidx)
focal_class.return: List<Integer>
focal_class.signature: List<Integer> toAtomIdxs(Collection<IAtom> atoms, Map<IAtom, Integer> atomidx)
focal_class.class_method_signature: SmilesGenerator.getCxSmilesState(int flavour, IAtomContainer mol)
focal_class.full_signature: private static CxSmilesState getCxSmilesState(int flavour, IAtomContainer mol)
focal_class.identifier: getCxSmilesState
focal_class.modifiers: private static
focal_class.parameters: (int flavour, IAtomContainer mol)
focal_class.return: CxSmilesState
focal_class.signature: CxSmilesState getCxSmilesState(int flavour, IAtomContainer mol)
focal_class.class_method_signature: SmilesGenerator.getSgroupPolymerKey(Sgroup sgroup)
focal_class.full_signature: private static String getSgroupPolymerKey(Sgroup sgroup)
focal_class.identifier: getSgroupPolymerKey
focal_class.modifiers: private static
focal_class.parameters: (Sgroup sgroup)
focal_class.return: String
focal_class.signature: String getSgroupPolymerKey(Sgroup sgroup)
focal_class.class_method_signature: SmilesGenerator.createComparator(final IAtomContainer mol,
                                                       final int flavor)
focal_class.full_signature: public static Comparator<IAtom> createComparator(final IAtomContainer mol,
                                                       final int flavor)
focal_class.identifier: createComparator
focal_class.modifiers: public static
focal_class.parameters: (final IAtomContainer mol,
                                                       final int flavor)
focal_class.return: Comparator<IAtom>
focal_class.signature: Comparator<IAtom> createComparator(final IAtomContainer mol,
                                                       final int flavor)
focal_method.body: public String create(IAtomContainer molecule) throws CDKException {
          return create(molecule, new int[molecule.getAtomCount()]);
      }
focal_method.class_method_signature: SmilesGenerator.create(IAtomContainer molecule)
focal_method.full_signature: public String create(IAtomContainer molecule)
focal_method.identifier: create
focal_method.invocations: create getAtomCount
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer molecule)
focal_method.return: String
focal_method.signature: String create(IAtomContainer molecule)