test_class.file: storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIToStructureTest.java
test_class.identifier: InChIToStructureTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void r_penta_2_3_diene() throws Exception {
          InChIToStructure parser = new InChIToStructure("InChI=1S/C5H8/c1-3-5-4-2/h3-4H,1-2H3/t5-/m0/s1",
                  SilentChemObjectBuilder.getInstance());
          IAtomContainer container = parser.getAtomContainer();
  
          Iterator<IStereoElement> ses = container.stereoElements().iterator();
          org.hamcrest.MatcherAssert.assertThat(container, is(instanceOf(SilentChemObjectBuilder.getInstance().newAtomContainer().getClass())));
          assertTrue(ses.hasNext());
          IStereoElement se = ses.next();
          assertThat(se, is(instanceOf(ExtendedTetrahedral.class)));
          ExtendedTetrahedral element = (ExtendedTetrahedral) se;
          assertThat(element.peripherals(),
                  is(new IAtom[]{container.getAtom(5), container.getAtom(0), container.getAtom(1), container.getAtom(6)}));
          assertThat(element.focus(), is(container.getAtom(4)));
          assertThat(element.winding(), is(ITetrahedralChirality.Stereo.ANTI_CLOCKWISE));
      }
test_case.class_method_signature: InChIToStructureTest.r_penta_2_3_diene()
test_case.full_signature: @Test public void r_penta_2_3_diene()
test_case.identifier: r_penta_2_3_diene
test_case.invocations: getInstance getAtomContainer iterator stereoElements assertThat is instanceOf getClass newAtomContainer getInstance assertTrue hasNext next assertThat is instanceOf assertThat peripherals is getAtom getAtom getAtom getAtom assertThat focus is getAtom assertThat winding is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void r_penta_2_3_diene()
focal_class.declarator: input
focal_class.modifier: protected
focal_class.original_string: protected JniInchiInputInchi      input;
focal_class.type: JniInchiInputInchi
focal_class.var_name: input
focal_class.declarator: output
focal_class.modifier: protected
focal_class.original_string: protected JniInchiOutputStructure output;
focal_class.type: JniInchiOutputStructure
focal_class.var_name: output
focal_class.declarator: molecule
focal_class.modifier: protected
focal_class.original_string: protected IAtomContainer          molecule;
focal_class.type: IAtomContainer
focal_class.var_name: molecule
focal_class.declarator: ISOTOPIC_SHIFT_FLAG = 10000
focal_class.modifier: private static final
focal_class.original_string: private static final int          ISOTOPIC_SHIFT_FLAG = 10000;
focal_class.type: int
focal_class.var_name: ISOTOPIC_SHIFT_FLAG
focal_class.file: storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java
focal_class.identifier: InChIToStructure
focal_class.class_method_signature: InChIToStructure.InChIToStructure(String inchi, IChemObjectBuilder builder)
focal_class.full_signature: protected  InChIToStructure(String inchi, IChemObjectBuilder builder)
focal_class.identifier: InChIToStructure
focal_class.modifiers: protected
focal_class.parameters: (String inchi, IChemObjectBuilder builder)
focal_class.signature:  InChIToStructure(String inchi, IChemObjectBuilder builder)
focal_class.class_method_signature: InChIToStructure.InChIToStructure(String inchi, IChemObjectBuilder builder, String options)
focal_class.full_signature: protected  InChIToStructure(String inchi, IChemObjectBuilder builder, String options)
focal_class.identifier: InChIToStructure
focal_class.modifiers: protected
focal_class.parameters: (String inchi, IChemObjectBuilder builder, String options)
focal_class.signature:  InChIToStructure(String inchi, IChemObjectBuilder builder, String options)
focal_class.class_method_signature: InChIToStructure.InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
focal_class.full_signature: protected  InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
focal_class.identifier: InChIToStructure
focal_class.modifiers: protected
focal_class.parameters: (String inchi, IChemObjectBuilder builder, List<String> options)
focal_class.signature:  InChIToStructure(String inchi, IChemObjectBuilder builder, List<String> options)
focal_class.class_method_signature: InChIToStructure.generateAtomContainerFromInchi(IChemObjectBuilder builder)
focal_class.full_signature: protected void generateAtomContainerFromInchi(IChemObjectBuilder builder)
focal_class.identifier: generateAtomContainerFromInchi
focal_class.modifiers: protected
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void generateAtomContainerFromInchi(IChemObjectBuilder builder)
focal_class.class_method_signature: InChIToStructure.findOtherSinglyBonded(IAtomContainer container, IAtom atom, IAtom exclude)
focal_class.full_signature: private static IAtom findOtherSinglyBonded(IAtomContainer container, IAtom atom, IAtom exclude)
focal_class.identifier: findOtherSinglyBonded
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, IAtom atom, IAtom exclude)
focal_class.return: IAtom
focal_class.signature: IAtom findOtherSinglyBonded(IAtomContainer container, IAtom atom, IAtom exclude)
focal_class.class_method_signature: InChIToStructure.getAtomContainer()
focal_class.full_signature: public IAtomContainer getAtomContainer()
focal_class.identifier: getAtomContainer
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer getAtomContainer()
focal_class.class_method_signature: InChIToStructure.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: InChIToStructure.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: InChIToStructure.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_class.class_method_signature: InChIToStructure.getWarningFlags()
focal_class.full_signature: public long[][] getWarningFlags()
focal_class.identifier: getWarningFlags
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: long[][]
focal_class.signature: long[][] getWarningFlags()
focal_method.body: public IAtomContainer getAtomContainer() {
          return (molecule);
      }
focal_method.class_method_signature: InChIToStructure.getAtomContainer()
focal_method.full_signature: public IAtomContainer getAtomContainer()
focal_method.identifier: getAtomContainer
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.return: IAtomContainer
focal_method.signature: IAtomContainer getAtomContainer()