test_class.declarator: lpcheck = new LonePairElectronChecker()
test_class.original_string: LonePairElectronChecker lpcheck = new LonePairElectronChecker();
test_class.type: LonePairElectronChecker
test_class.var_name: lpcheck
test_class.file: legacy/src/test/java/org/openscience/cdk/tools/IonizationPotentialToolTest.java
test_class.identifier: IonizationPotentialToolTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testBenzene() throws Exception {
          String smiles = "c1ccccc1";
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer molecule = sp.parseSmiles(smiles);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
          addExplicitHydrogens(molecule);
          Aromaticity.cdkLegacy().apply(molecule);
          lpcheck.saturate(molecule);
  
          List<Double> carbonIPs = new ArrayList<Double>();
          Iterator<IAtom> atoms = molecule.atoms().iterator();
          while (atoms.hasNext()) {
              IAtom atom = atoms.next();
              if (atom.getSymbol().equals("H")) continue;
              carbonIPs.add(IonizationPotentialTool.predictIP(molecule, atom));
          }
  
          double firstIP = carbonIPs.get(0);
          for (double ip : carbonIPs) {
              Assert.assertEquals(firstIP, ip, 0.0001);
          }
      }
test_case.class_method_signature: IonizationPotentialToolTest.testBenzene()
test_case.full_signature: @Test public void testBenzene()
test_case.identifier: testBenzene
test_case.invocations: getInstance parseSmiles percieveAtomTypesAndConfigureAtoms addExplicitHydrogens apply cdkLegacy saturate iterator atoms hasNext next equals getSymbol add predictIP get assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testBenzene()
focal_class.file: legacy/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java
focal_class.identifier: IonizationPotentialTool
focal_class.class_method_signature: IonizationPotentialTool.predictIP(IAtomContainer container, IAtom atom)
focal_class.full_signature: public static double predictIP(IAtomContainer container, IAtom atom)
focal_class.identifier: predictIP
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: double
focal_class.signature: double predictIP(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: IonizationPotentialTool.predictIP(IAtomContainer container, IBond bond)
focal_class.full_signature: public static double predictIP(IAtomContainer container, IBond bond)
focal_class.identifier: predictIP
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IBond bond)
focal_class.return: double
focal_class.signature: double predictIP(IAtomContainer container, IBond bond)
focal_class.class_method_signature: IonizationPotentialTool.familyHalogen(IAtom atom)
focal_class.full_signature: private static boolean familyHalogen(IAtom atom)
focal_class.identifier: familyHalogen
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean familyHalogen(IAtom atom)
focal_class.class_method_signature: IonizationPotentialTool.familyOxygen(IAtom atom)
focal_class.full_signature: private static boolean familyOxygen(IAtom atom)
focal_class.identifier: familyOxygen
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean familyOxygen(IAtom atom)
focal_class.class_method_signature: IonizationPotentialTool.familyNitrogen(IAtom atom)
focal_class.full_signature: private static boolean familyNitrogen(IAtom atom)
focal_class.identifier: familyNitrogen
focal_class.modifiers: private static
focal_class.parameters: (IAtom atom)
focal_class.return: boolean
focal_class.signature: boolean familyNitrogen(IAtom atom)
focal_class.class_method_signature: IonizationPotentialTool.familyBond(IAtomContainer container, IBond bond)
focal_class.full_signature: private static boolean familyBond(IAtomContainer container, IBond bond)
focal_class.identifier: familyBond
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, IBond bond)
focal_class.return: boolean
focal_class.signature: boolean familyBond(IAtomContainer container, IBond bond)
focal_class.class_method_signature: IonizationPotentialTool.getDoubleBondNumber(IAtomContainer container)
focal_class.full_signature: private static int getDoubleBondNumber(IAtomContainer container)
focal_class.identifier: getDoubleBondNumber
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container)
focal_class.return: int
focal_class.signature: int getDoubleBondNumber(IAtomContainer container)
focal_class.class_method_signature: IonizationPotentialTool.getQSARs(IAtomContainer container, IAtom atom)
focal_class.full_signature: public static double[] getQSARs(IAtomContainer container, IAtom atom)
focal_class.identifier: getQSARs
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: double[]
focal_class.signature: double[] getQSARs(IAtomContainer container, IAtom atom)
focal_class.class_method_signature: IonizationPotentialTool.getQSARs(IAtomContainer container, IBond bond)
focal_class.full_signature: public static double[] getQSARs(IAtomContainer container, IBond bond)
focal_class.identifier: getQSARs
focal_class.modifiers: public static
focal_class.parameters: (IAtomContainer container, IBond bond)
focal_class.return: double[]
focal_class.signature: double[] getQSARs(IAtomContainer container, IBond bond)
focal_class.class_method_signature: IonizationPotentialTool.getDTHalogenF(double[] resultsH)
focal_class.full_signature: private static double getDTHalogenF(double[] resultsH)
focal_class.identifier: getDTHalogenF
focal_class.modifiers: private static
focal_class.parameters: (double[] resultsH)
focal_class.return: double
focal_class.signature: double getDTHalogenF(double[] resultsH)
focal_class.class_method_signature: IonizationPotentialTool.getDTOxygenF(double[] resultsH)
focal_class.full_signature: private static double getDTOxygenF(double[] resultsH)
focal_class.identifier: getDTOxygenF
focal_class.modifiers: private static
focal_class.parameters: (double[] resultsH)
focal_class.return: double
focal_class.signature: double getDTOxygenF(double[] resultsH)
focal_class.class_method_signature: IonizationPotentialTool.getDTNitrogenF(double[] resultsH)
focal_class.full_signature: private static double getDTNitrogenF(double[] resultsH)
focal_class.identifier: getDTNitrogenF
focal_class.modifiers: private static
focal_class.parameters: (double[] resultsH)
focal_class.return: double
focal_class.signature: double getDTNitrogenF(double[] resultsH)
focal_class.class_method_signature: IonizationPotentialTool.getDTBondF(double[] resultsH)
focal_class.full_signature: private static double getDTBondF(double[] resultsH)
focal_class.identifier: getDTBondF
focal_class.modifiers: private static
focal_class.parameters: (double[] resultsH)
focal_class.return: double
focal_class.signature: double getDTBondF(double[] resultsH)
focal_class.class_method_signature: IonizationPotentialTool.initiateIonization(IAtomContainer container, IAtom atom)
focal_class.full_signature: private static IAtomContainer initiateIonization(IAtomContainer container, IAtom atom)
focal_class.identifier: initiateIonization
focal_class.modifiers: private static
focal_class.parameters: (IAtomContainer container, IAtom atom)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer initiateIonization(IAtomContainer container, IAtom atom)
focal_method.body: public static double predictIP(IAtomContainer container, IAtom atom) throws CDKException {
          double value = 0;
  
          // at least one lone pair orbital is necessary to ionize
          if (container.getConnectedLonePairsCount(atom) == 0) return value;
  
          // control if the IAtom belongs in some family
          if (familyHalogen(atom))
              value = getDTHalogenF(getQSARs(container, atom));
          else if (familyOxygen(atom))
              value = getDTOxygenF(getQSARs(container, atom));
          else if (familyNitrogen(atom)) value = getDTNitrogenF(getQSARs(container, atom));
  
          return value;
      }
focal_method.class_method_signature: IonizationPotentialTool.predictIP(IAtomContainer container, IAtom atom)
focal_method.full_signature: public static double predictIP(IAtomContainer container, IAtom atom)
focal_method.identifier: predictIP
focal_method.invocations: getConnectedLonePairsCount familyHalogen getDTHalogenF getQSARs familyOxygen getDTOxygenF getQSARs familyNitrogen getDTNitrogenF getQSARs
focal_method.modifiers: public static
focal_method.parameters: (IAtomContainer container, IAtom atom)
focal_method.return: double
focal_method.signature: double predictIP(IAtomContainer container, IAtom atom)