test_class.declarator: builder
test_class.original_string: DefaultChemObjectBuilder builder;
test_class.type: DefaultChemObjectBuilder
test_class.var_name: builder
test_class.file: descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtilsTest.java
test_class.identifier: ChiIndexUtilsTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testDeltaVSulphurSO2() {
          IAtom s = builder.newInstance(IAtom.class, "S");
          IAtom o1 = builder.newInstance(IAtom.class, "O");
          IAtom o2 = builder.newInstance(IAtom.class, "O");
          IBond b1 = builder.newInstance(IBond.class, s, o1);
          IBond b2 = builder.newInstance(IBond.class, s, o2);
          b1.setOrder(IBond.Order.DOUBLE);
          b2.setOrder(IBond.Order.DOUBLE);
  
          IAtomContainer m = builder.newInstance(IAtomContainer.class);
          m.addAtom(s);
          m.addAtom(o1);
          m.addBond(b1);
          m.addAtom(o2);
          m.addBond(b2);
  
          double deltav = ChiIndexUtils.deltavSulphur(s, m);
          Assert.assertEquals(2.67, deltav, 0.01);
      }
test_case.class_method_signature: ChiIndexUtilsTest.testDeltaVSulphurSO2()
test_case.full_signature: @Test public void testDeltaVSulphurSO2()
test_case.identifier: testDeltaVSulphurSO2
test_case.invocations: newInstance newInstance newInstance newInstance newInstance setOrder setOrder newInstance addAtom addAtom addBond addAtom addBond deltavSulphur assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testDeltaVSulphurSO2()
focal_class.file: descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java
focal_class.identifier: ChiIndexUtils
focal_class.class_method_signature: ChiIndexUtils.getFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries)
focal_class.full_signature: public static List<List<Integer>> getFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries)
focal_class.identifier: getFragments
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer, QueryAtomContainer[] queries)
focal_class.return: List<List<Integer>>
focal_class.signature: List<List<Integer>> getFragments(IAtomContainer atomContainer, QueryAtomContainer[] queries)
focal_class.class_method_signature: ChiIndexUtils.evalSimpleIndex(IAtomContainer atomContainer, List<List<Integer>> fragLists)
focal_class.full_signature: public static double evalSimpleIndex(IAtomContainer atomContainer, List<List<Integer>> fragLists)
focal_class.identifier: evalSimpleIndex
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer, List<List<Integer>> fragLists)
focal_class.return: double
focal_class.signature: double evalSimpleIndex(IAtomContainer atomContainer, List<List<Integer>> fragLists)
focal_class.class_method_signature: ChiIndexUtils.evalValenceIndex(IAtomContainer atomContainer, List<List<Integer>> fragList)
focal_class.full_signature: public static double evalValenceIndex(IAtomContainer atomContainer, List<List<Integer>> fragList)
focal_class.identifier: evalValenceIndex
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer atomContainer, List<List<Integer>> fragList)
focal_class.return: double
focal_class.signature: double evalValenceIndex(IAtomContainer atomContainer, List<List<Integer>> fragList)
focal_class.class_method_signature: ChiIndexUtils.getValenceElectronCount(IAtom atom)
focal_class.full_signature: private static int getValenceElectronCount(IAtom atom)
focal_class.identifier: getValenceElectronCount
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: int
focal_class.signature: int getValenceElectronCount(IAtom atom)
focal_class.class_method_signature: ChiIndexUtils.deltavSulphur(IAtom atom, IAtomContainer atomContainer)
focal_class.full_signature: protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer)
focal_class.identifier: deltavSulphur
focal_class.modifiers: protected static
focal_class.parameters: (IAtom atom, IAtomContainer atomContainer)
focal_class.return: double
focal_class.signature: double deltavSulphur(IAtom atom, IAtomContainer atomContainer)
focal_class.class_method_signature: ChiIndexUtils.deltavPhosphorous(IAtom atom, IAtomContainer atomContainer)
focal_class.full_signature: private static double deltavPhosphorous(IAtom atom, IAtomContainer atomContainer)
focal_class.identifier: deltavPhosphorous
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom, IAtomContainer atomContainer)
focal_class.return: double
focal_class.signature: double deltavPhosphorous(IAtom atom, IAtomContainer atomContainer)
focal_class.class_method_signature: ChiIndexUtils.getUniqueBondSubgraphs(List<List<RMap>> subgraphs, IAtomContainer ac)
focal_class.full_signature: private static List<List<Integer>> getUniqueBondSubgraphs(List<List<RMap>> subgraphs, IAtomContainer ac)
focal_class.identifier: getUniqueBondSubgraphs
focal_class.modifiers: private static
focal_class.parameters: (List<List<RMap>> subgraphs, IAtomContainer ac)
focal_class.return: List<List<Integer>>
focal_class.signature: List<List<Integer>> getUniqueBondSubgraphs(List<List<RMap>> subgraphs, IAtomContainer ac)
focal_method.body: protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer) {
          if (atom.getAtomicNumber() != IElement.S) return -1;
  
          // check whether it's a S in S-S
          List<IAtom> connected = atomContainer.getConnectedAtomsList(atom);
          for (IAtom connectedAtom : connected) {
              if (connectedAtom.getAtomicNumber() == IElement.S
                      && atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.SINGLE) return .89;
          }
  
          int count = 0;
          for (IAtom connectedAtom : connected) {
              if (connectedAtom.getAtomicNumber() == IElement.O
                      && atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.DOUBLE) count++;
          }
          if (count == 1)
              return 1.33; // check whether it's a S in -SO-
          else if (count == 2) return 2.67; // check whether it's a S in -SO2-
  
          return -1;
      }
focal_method.class_method_signature: ChiIndexUtils.deltavSulphur(IAtom atom, IAtomContainer atomContainer)
focal_method.full_signature: protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer)
focal_method.identifier: deltavSulphur
focal_method.invocations: getAtomicNumber getConnectedAtomsList getAtomicNumber getOrder getBond getAtomicNumber getOrder getBond
focal_method.modifiers: protected static
focal_method.parameters: (IAtom atom, IAtomContainer atomContainer)
focal_method.return: double
focal_method.signature: double deltavSulphur(IAtom atom, IAtomContainer atomContainer)