test_class.declarator: smiles = new SmilesParser(SilentChemObjectBuilder.getInstance())
test_class.modifier: static
test_class.original_string: static SmilesParser   smiles = new SmilesParser(SilentChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: smiles
test_class.declarator: molecule
test_class.modifier: static
test_class.original_string: static IAtomContainer molecule;
test_class.type: IAtomContainer
test_class.var_name: molecule
test_class.declarator: ligands
test_class.modifier: static
test_class.original_string: static ILigand[]      ligands;
test_class.type: ILigand[]
test_class.var_name: ligands
test_class.file: descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPToolTest.java
test_class.identifier: CIPToolTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testDefineLigancyFourChirality() {
          LigancyFourChirality chirality = CIPTool.defineLigancyFourChirality(molecule, 1, 0, 2, 3, 4,
                  Stereo.ANTI_CLOCKWISE);
          Assert.assertEquals(molecule.getAtom(1), chirality.getChiralAtom());
          Assert.assertEquals(Stereo.ANTI_CLOCKWISE, chirality.getStereo());
          ILigand[] ligands = chirality.getLigands();
          Assert.assertEquals(molecule, ligands[0].getAtomContainer());
          Assert.assertEquals(molecule.getAtom(0), ligands[0].getLigandAtom());
          Assert.assertEquals(molecule.getAtom(1), ligands[0].getCentralAtom());
          Assert.assertEquals(molecule, ligands[1].getAtomContainer());
          Assert.assertEquals(molecule.getAtom(2), ligands[1].getLigandAtom());
          Assert.assertEquals(molecule.getAtom(1), ligands[1].getCentralAtom());
          Assert.assertEquals(molecule, ligands[2].getAtomContainer());
          Assert.assertEquals(molecule.getAtom(3), ligands[2].getLigandAtom());
          Assert.assertEquals(molecule.getAtom(1), ligands[2].getCentralAtom());
          Assert.assertEquals(molecule, ligands[3].getAtomContainer());
          Assert.assertEquals(molecule.getAtom(4), ligands[3].getLigandAtom());
          Assert.assertEquals(molecule.getAtom(1), ligands[3].getCentralAtom());
      }
test_case.class_method_signature: CIPToolTest.testDefineLigancyFourChirality()
test_case.full_signature: @Test public void testDefineLigancyFourChirality()
test_case.identifier: testDefineLigancyFourChirality
test_case.invocations: defineLigancyFourChirality assertEquals getAtom getChiralAtom assertEquals getStereo getLigands assertEquals getAtomContainer assertEquals getAtom getLigandAtom assertEquals getAtom getCentralAtom assertEquals getAtomContainer assertEquals getAtom getLigandAtom assertEquals getAtom getCentralAtom assertEquals getAtomContainer assertEquals getAtom getLigandAtom assertEquals getAtom getCentralAtom assertEquals getAtomContainer assertEquals getAtom getLigandAtom assertEquals getAtom getCentralAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testDefineLigancyFourChirality()
focal_class.declarator: HYDROGEN = -1
focal_class.modifier: public static final
focal_class.original_string: public static final int      HYDROGEN = -1;
focal_class.type: int
focal_class.var_name: HYDROGEN
focal_class.declarator: cipRule  = new CIPLigandRule()
focal_class.modifier: private static
focal_class.original_string: private static CIPLigandRule cipRule  = new CIPLigandRule();
focal_class.type: CIPLigandRule
focal_class.var_name: cipRule
focal_class.file: descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java
focal_class.identifier: CIPTool
focal_class.class_method_signature: CIPTool.getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (LigancyFourChirality stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(LigancyFourChirality stereoCenter)
focal_class.class_method_signature: CIPTool.label(IAtomContainer container)
focal_class.full_signature: public static void label(IAtomContainer container)
focal_class.identifier: label
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void label(IAtomContainer container)
focal_class.class_method_signature: CIPTool.getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(IAtomContainer container, ITetrahedralChirality stereoCenter)
focal_class.class_method_signature: CIPTool.getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.full_signature: public static CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.identifier: getCIPChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.return: CIP_CHIRALITY
focal_class.signature: CIP_CHIRALITY getCIPChirality(IAtomContainer container, IDoubleBondStereochemistry stereoCenter)
focal_class.class_method_signature: CIPTool.getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.full_signature: private static ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.identifier: getLigands
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] getLigands(IAtom atom, IAtomContainer container, IAtom exclude)
focal_class.class_method_signature: CIPTool.checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.full_signature: public static boolean checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.identifier: checkIfAllLigandsAreDifferent
focal_class.modifiers: public static
focal_class.parameters: (ILigand[] ligands)
focal_class.return: boolean
focal_class.signature: boolean checkIfAllLigandsAreDifferent(ILigand[] ligands)
focal_class.class_method_signature: CIPTool.order(ILigand[] ligands)
focal_class.full_signature: public static ILigand[] order(ILigand[] ligands)
focal_class.identifier: order
focal_class.modifiers: public static
focal_class.parameters: (ILigand[] ligands)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] order(ILigand[] ligands)
focal_class.class_method_signature: CIPTool.permParity(final ILigand[] ligands)
focal_class.full_signature: private static int permParity(final ILigand[] ligands)
focal_class.identifier: permParity
focal_class.modifiers: private static
focal_class.parameters: (final ILigand[] ligands)
focal_class.return: int
focal_class.signature: int permParity(final ILigand[] ligands)
focal_class.class_method_signature: CIPTool.defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.full_signature: public static LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.identifier: defineLigancyFourChirality
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.return: LigancyFourChirality
focal_class.signature: LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_class.class_method_signature: CIPTool.defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.full_signature: public static ILigand defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.identifier: defineLigand
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.return: ILigand
focal_class.signature: ILigand defineLigand(IAtomContainer container, VisitedAtoms visitedAtoms, int chiralAtom,
              int ligandAtom)
focal_class.class_method_signature: CIPTool.getLigandLigands(ILigand ligand)
focal_class.full_signature: public static ILigand[] getLigandLigands(ILigand ligand)
focal_class.identifier: getLigandLigands
focal_class.modifiers: public static
focal_class.parameters: (ILigand ligand)
focal_class.return: ILigand[]
focal_class.signature: ILigand[] getLigandLigands(ILigand ligand)
focal_class.class_method_signature: CIPTool.getDuplication(Order order)
focal_class.full_signature: private static int getDuplication(Order order)
focal_class.identifier: getDuplication
focal_class.modifiers: private static
focal_class.parameters: (Order order)
focal_class.return: int
focal_class.signature: int getDuplication(Order order)
focal_method.body: public static LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo) {
          int[] atomIndices = {ligand1, ligand2, ligand3, ligand4};
          VisitedAtoms visitedAtoms = new VisitedAtoms();
          ILigand[] ligands = new ILigand[4];
          for (int i = 0; i < 4; i++) {
              ligands[i] = defineLigand(container, visitedAtoms, chiralAtom, atomIndices[i]);
          }
          return new LigancyFourChirality(container.getAtom(chiralAtom), ligands, stereo);
      }
focal_method.class_method_signature: CIPTool.defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_method.full_signature: public static LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_method.identifier: defineLigancyFourChirality
focal_method.invocations: defineLigand getAtom
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)
focal_method.return: LigancyFourChirality
focal_method.signature: LigancyFourChirality defineLigancyFourChirality(IAtomContainer container, int chiralAtom,
              int ligand1, int ligand2, int ligand3, int ligand4, Stereo stereo)