test_class.file: storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java
test_class.identifier: InChINumbersToolsTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void fixedH() throws Exception {
          SmilesParser parser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer atomContainer = parser.parseSmiles("N1C=NC2=CC=CC=C12");
          String auxInfo = InChINumbersTools.auxInfo(atomContainer, INCHI_OPTION.FixedH);
          String expected = "AuxInfo=1/1/" + "N:6,7,5,8,2,4,9,3,1/" + "E:(1,2)(3,4)(6,7)(8,9)/" + "F:7,6,8,5,2,9,4,1,3/"
                  + "rA:9NCNCCCCCC/" + "rB:s1;d2;s3;d4;s5;d6;s7;s1s4d8;/" + "rC:;;;;;;;;;";
          assertThat(auxInfo, is(expected));
      }
test_case.class_method_signature: InChINumbersToolsTest.fixedH()
test_case.full_signature: @Test public void fixedH()
test_case.identifier: fixedH
test_case.invocations: getInstance parseSmiles auxInfo assertThat is
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void fixedH()
focal_class.file: storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java
focal_class.identifier: InChINumbersTools
focal_class.class_method_signature: InChINumbersTools.getNumbers(IAtomContainer atomContainer)
focal_class.full_signature: public static long[] getNumbers(IAtomContainer atomContainer)
focal_class.identifier: getNumbers
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: long[]
focal_class.signature: long[] getNumbers(IAtomContainer atomContainer)
focal_class.class_method_signature: InChINumbersTools.parseAuxInfo(String aux, long[] numbers)
focal_class.full_signature: public static void parseAuxInfo(String aux, long[] numbers)
focal_class.identifier: parseAuxInfo
focal_class.modifiers: public static
focal_class.parameters: (String aux, long[] numbers)
focal_class.return: void
focal_class.signature: void parseAuxInfo(String aux, long[] numbers)
focal_class.class_method_signature: InChINumbersTools.getUSmilesNumbers(IAtomContainer container)
focal_class.full_signature: public static long[] getUSmilesNumbers(IAtomContainer container)
focal_class.identifier: getUSmilesNumbers
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: long[]
focal_class.signature: long[] getUSmilesNumbers(IAtomContainer container)
focal_class.class_method_signature: InChINumbersTools.parseUSmilesNumbers(String aux, IAtomContainer container)
focal_class.full_signature: static long[] parseUSmilesNumbers(String aux, IAtomContainer container)
focal_class.identifier: parseUSmilesNumbers
focal_class.modifiers: static
focal_class.parameters: (String aux, IAtomContainer container)
focal_class.return: long[]
focal_class.signature: long[] parseUSmilesNumbers(String aux, IAtomContainer container)
focal_class.class_method_signature: InChINumbersTools.exch(long[] values, int i, int j)
focal_class.full_signature: private static void exch(long[] values, int i, int j)
focal_class.identifier: exch
focal_class.modifiers: private static
focal_class.parameters: (long[] values, int i, int j)
focal_class.return: void
focal_class.signature: void exch(long[] values, int i, int j)
focal_class.class_method_signature: InChINumbersTools.findPiBondedOxygen(IAtomContainer container, IAtom atom)
focal_class.full_signature: private static IAtom findPiBondedOxygen(IAtomContainer container, IAtom atom)
focal_class.identifier: findPiBondedOxygen
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: IAtom
focal_class.signature: IAtom findPiBondedOxygen(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: InChINumbersTools.auxInfo(IAtomContainer container, INCHI_OPTION... options)
focal_class.full_signature: static String auxInfo(IAtomContainer container, INCHI_OPTION... options)
focal_class.identifier: auxInfo
focal_class.modifiers: static
focal_class.parameters: (IAtomContainer container, INCHI_OPTION... options)
focal_class.return: String
focal_class.signature: String auxInfo(IAtomContainer container, INCHI_OPTION... options)
focal_method.body: static String auxInfo(IAtomContainer container, INCHI_OPTION... options) throws CDKException {
          InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
          boolean org = factory.getIgnoreAromaticBonds();
          factory.setIgnoreAromaticBonds(true);
          InChIGenerator gen = factory.getInChIGenerator(container, Arrays.asList(options));
          factory.setIgnoreAromaticBonds(org); // an option on the singleton so we should reset for others
          if (gen.getReturnStatus() != INCHI_RET.OKAY && gen.getReturnStatus() != INCHI_RET.WARNING)
              throw new CDKException("Could not generate InChI Numbers: " + gen.getMessage());
          return gen.getAuxInfo();
      }
focal_method.class_method_signature: InChINumbersTools.auxInfo(IAtomContainer container, INCHI_OPTION... options)
focal_method.full_signature: static String auxInfo(IAtomContainer container, INCHI_OPTION... options)
focal_method.identifier: auxInfo
focal_method.invocations: getInstance getIgnoreAromaticBonds setIgnoreAromaticBonds getInChIGenerator asList setIgnoreAromaticBonds getReturnStatus getReturnStatus getMessage getAuxInfo
focal_method.modifiers: static
focal_method.parameters: (IAtomContainer container, INCHI_OPTION... options)
focal_method.return: String
focal_method.signature: String auxInfo(IAtomContainer container, INCHI_OPTION... options)