test_class.declarator: factory
test_class.modifier: protected static
test_class.original_string: protected static InChIGeneratorFactory factory;
test_class.type: InChIGeneratorFactory
test_class.var_name: factory
test_class.file: storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java
test_class.identifier: InChIGeneratorTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void s_penta_2_3_diene_expl_h() throws Exception {
          IAtomContainer m = new AtomContainer(5, 4, 0, 0);
          m.addAtom(new Atom("CH3"));
          m.addAtom(new Atom("C"));
          m.addAtom(new Atom("C"));
          m.addAtom(new Atom("C"));
          m.addAtom(new Atom("CH3"));
          m.addAtom(new Atom("H"));
          m.addAtom(new Atom("H"));
          m.addBond(0, 1, IBond.Order.SINGLE);
          m.addBond(1, 2, IBond.Order.DOUBLE);
          m.addBond(2, 3, IBond.Order.DOUBLE);
          m.addBond(3, 4, IBond.Order.SINGLE);
          m.addBond(1, 5, IBond.Order.SINGLE);
          m.addBond(3, 6, IBond.Order.SINGLE);
  
          int[][] atoms = new int[][]{{0, 5, 6, 4}, {5, 0, 6, 4}, {5, 0, 4, 6}, {0, 5, 4, 6}, {4, 6, 5, 0}, {4, 6, 0, 5},
                  {6, 4, 0, 5}, {6, 4, 5, 0},};
          Stereo[] stereos = new Stereo[]{Stereo.CLOCKWISE, Stereo.ANTI_CLOCKWISE, Stereo.CLOCKWISE,
                  Stereo.ANTI_CLOCKWISE, Stereo.CLOCKWISE, Stereo.ANTI_CLOCKWISE, Stereo.CLOCKWISE, Stereo.ANTI_CLOCKWISE};
  
          for (int i = 0; i < atoms.length; i++) {
  
              IStereoElement element = new ExtendedTetrahedral(m.getAtom(2), new IAtom[]{m.getAtom(atoms[i][0]),
                      m.getAtom(atoms[i][1]), m.getAtom(atoms[i][2]), m.getAtom(atoms[i][3])}, stereos[i]);
              m.setStereoElements(Collections.singletonList(element));
  
              InChIGenerator generator = getFactory().getInChIGenerator(m);
              assertThat(generator.getInchi(), is("InChI=1S/C5H8/c1-3-5-4-2/h3-4H,1-2H3/t5-/m1/s1"));
  
          }
      }
test_case.class_method_signature: InChIGeneratorTest.s_penta_2_3_diene_expl_h()
test_case.full_signature: @Test public void s_penta_2_3_diene_expl_h()
test_case.identifier: s_penta_2_3_diene_expl_h
test_case.invocations: addAtom addAtom addAtom addAtom addAtom addAtom addAtom addBond addBond addBond addBond addBond addBond getAtom getAtom getAtom getAtom getAtom setStereoElements singletonList getInChIGenerator getFactory assertThat getInchi is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void s_penta_2_3_diene_expl_h()
focal_class.declarator: input
focal_class.modifier: protected
focal_class.original_string: protected JniInchiInput input;
focal_class.type: JniInchiInput
focal_class.var_name: input
focal_class.declarator: output
focal_class.modifier: protected
focal_class.original_string: protected JniInchiOutput output;
focal_class.type: JniInchiOutput
focal_class.var_name: output
focal_class.declarator: auxNone
focal_class.modifier: private final
focal_class.original_string: private final boolean auxNone;
focal_class.type: boolean
focal_class.var_name: auxNone
focal_class.declarator: LOGGER = LoggingToolFactory.createLoggingTool(InChIGenerator.class)
focal_class.modifier: private static final
focal_class.original_string: private static final ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(InChIGenerator.class);
focal_class.type: ILoggingTool
focal_class.var_name: LOGGER
focal_class.declarator: atomContainer
focal_class.modifier: protected
focal_class.original_string: protected IAtomContainer atomContainer;
focal_class.type: IAtomContainer
focal_class.var_name: atomContainer
focal_class.file: storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java
focal_class.identifier: InChIGenerator
focal_class.class_method_signature: InChIGenerator.InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds)
focal_class.full_signature: protected  InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds)
focal_class.identifier: InChIGenerator
focal_class.modifiers: protected
focal_class.parameters: (IAtomContainer atomContainer, boolean ignoreAromaticBonds)
focal_class.signature:  InChIGenerator(IAtomContainer atomContainer, boolean ignoreAromaticBonds)
focal_class.class_method_signature: InChIGenerator.InChIGenerator(IAtomContainer atomContainer, String options, boolean ignoreAromaticBonds)
focal_class.full_signature: protected  InChIGenerator(IAtomContainer atomContainer, String options, boolean ignoreAromaticBonds)
focal_class.identifier: InChIGenerator
focal_class.modifiers: protected
focal_class.parameters: (IAtomContainer atomContainer, String options, boolean ignoreAromaticBonds)
focal_class.signature:  InChIGenerator(IAtomContainer atomContainer, String options, boolean ignoreAromaticBonds)
focal_class.class_method_signature: InChIGenerator.InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> options, boolean ignoreAromaticBonds)
focal_class.full_signature: protected  InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> options, boolean ignoreAromaticBonds)
focal_class.identifier: InChIGenerator
focal_class.modifiers: protected
focal_class.parameters: (IAtomContainer atomContainer, List<INCHI_OPTION> options, boolean ignoreAromaticBonds)
focal_class.signature:  InChIGenerator(IAtomContainer atomContainer, List<INCHI_OPTION> options, boolean ignoreAromaticBonds)
focal_class.class_method_signature: InChIGenerator.generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boolean ignore)
focal_class.full_signature: private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boolean ignore)
focal_class.identifier: generateInchiFromCDKAtomContainer
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, boolean ignore)
focal_class.return: void
focal_class.signature: void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer, boolean ignore)
focal_class.class_method_signature: InChIGenerator.onlySingleBonded(List<IBond> bonds)
focal_class.full_signature: private static List<IBond> onlySingleBonded(List<IBond> bonds)
focal_class.identifier: onlySingleBonded
focal_class.modifiers: private static
focal_class.parameters: (List<IBond> bonds)
focal_class.return: List<IBond>
focal_class.signature: List<IBond> onlySingleBonded(List<IBond> bonds)
focal_class.class_method_signature: InChIGenerator.swap(Object[] objs, int i, int j)
focal_class.full_signature: private static void swap(Object[] objs, int i, int j)
focal_class.identifier: swap
focal_class.modifiers: private static
focal_class.parameters: (Object[] objs, int i, int j)
focal_class.return: void
focal_class.signature: void swap(Object[] objs, int i, int j)
focal_class.class_method_signature: InChIGenerator.getReturnStatus()
focal_class.full_signature: public INCHI_RET getReturnStatus()
focal_class.identifier: getReturnStatus
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: INCHI_RET
focal_class.signature: INCHI_RET getReturnStatus()
focal_class.class_method_signature: InChIGenerator.getInchi()
focal_class.full_signature: public String getInchi()
focal_class.identifier: getInchi
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getInchi()
focal_class.class_method_signature: InChIGenerator.getInchiKey()
focal_class.full_signature: public String getInchiKey()
focal_class.identifier: getInchiKey
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getInchiKey()
focal_class.class_method_signature: InChIGenerator.getAuxInfo()
focal_class.full_signature: public String getAuxInfo()
focal_class.identifier: getAuxInfo
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getAuxInfo()
focal_class.class_method_signature: InChIGenerator.getMessage()
focal_class.full_signature: public String getMessage()
focal_class.identifier: getMessage
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getMessage()
focal_class.class_method_signature: InChIGenerator.getLog()
focal_class.full_signature: public String getLog()
focal_class.identifier: getLog
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String
focal_class.signature: String getLog()
focal_method.body: public String getInchi() {
          return (output.getInchi());
      }
focal_method.class_method_signature: InChIGenerator.getInchi()
focal_method.full_signature: public String getInchi()
focal_method.identifier: getInchi
focal_method.invocations: getInchi
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: String
focal_method.signature: String getInchi()