test_class.file: tool/charges/src/test/java/org/openscience/cdk/charges/PolarizabilityTest.java
test_class.identifier: PolarizabilityTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom() throws Exception {
          Polarizability pol = new Polarizability();
          SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
          IAtomContainer mol = sp.parseSmiles("NCCN(C)(C)");
          double result = pol.getPolarizabilitiyFactorForAtom(mol, mol.getAtom(0));
          Assert.assertFalse(Double.isNaN(result));
          result = pol.getPolarizabilitiyFactorForAtom(mol, mol.getAtom(3));
          Assert.assertFalse(Double.isNaN(result));
      }
test_case.class_method_signature: PolarizabilityTest.testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom()
test_case.full_signature: @Test public void testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom()
test_case.identifier: testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom
test_case.invocations: getInstance parseSmiles getPolarizabilitiyFactorForAtom getAtom assertFalse isNaN getPolarizabilitiyFactorForAtom getAtom assertFalse isNaN
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetPolarizabilitiyFactorForAtom_IAtomContainer_IAtom()
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(Polarizability.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(Polarizability.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: tool/charges/src/main/java/org/openscience/cdk/charges/Polarizability.java
focal_class.identifier: Polarizability
focal_class.class_method_signature: Polarizability.Polarizability()
focal_class.full_signature: public  Polarizability()
focal_class.identifier: Polarizability
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Polarizability()
focal_class.class_method_signature: Polarizability.addExplicitHydrogens(IAtomContainer container)
focal_class.full_signature: private void addExplicitHydrogens(IAtomContainer container)
focal_class.identifier: addExplicitHydrogens
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void addExplicitHydrogens(IAtomContainer container)
focal_class.class_method_signature: Polarizability.getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
focal_class.full_signature: public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
focal_class.identifier: getPolarizabilitiyFactorForAtom
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom)
focal_class.return: double
focal_class.signature: double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
focal_class.class_method_signature: Polarizability.calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
focal_class.full_signature: public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
focal_class.identifier: calculateKJMeanMolecularPolarizability
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: double
focal_class.signature: double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer)
focal_class.class_method_signature: Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              int influenceSphereCutOff, boolean addExplicitH)
focal_class.full_signature: public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              int influenceSphereCutOff, boolean addExplicitH)
focal_class.identifier: calculateGHEffectiveAtomPolarizability
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom,
              int influenceSphereCutOff, boolean addExplicitH)
focal_class.return: double
focal_class.signature: double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              int influenceSphereCutOff, boolean addExplicitH)
focal_class.class_method_signature: Polarizability.calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              boolean addExplicitH, int[][] distanceMatrix)
focal_class.full_signature: public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              boolean addExplicitH, int[][] distanceMatrix)
focal_class.identifier: calculateGHEffectiveAtomPolarizability
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom,
              boolean addExplicitH, int[][] distanceMatrix)
focal_class.return: double
focal_class.signature: double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer, IAtom atom,
              boolean addExplicitH, int[][] distanceMatrix)
focal_class.class_method_signature: Polarizability.calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
focal_class.full_signature: public double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
focal_class.identifier: calculateBondPolarizability
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer atomContainer, IBond bond)
focal_class.return: double
focal_class.signature: double calculateBondPolarizability(IAtomContainer atomContainer, IBond bond)
focal_class.class_method_signature: Polarizability.getKJPolarizabilityFactor(IAtomContainer atomContainer, IAtom atom)
focal_class.full_signature: private double getKJPolarizabilityFactor(IAtomContainer atomContainer, IAtom atom)
focal_class.identifier: getKJPolarizabilityFactor
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom)
focal_class.return: double
focal_class.signature: double getKJPolarizabilityFactor(IAtomContainer atomContainer, IAtom atom)
focal_class.class_method_signature: Polarizability.getNumberOfHydrogen(IAtomContainer atomContainer, IAtom atom)
focal_class.full_signature: private int getNumberOfHydrogen(IAtomContainer atomContainer, IAtom atom)
focal_class.identifier: getNumberOfHydrogen
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, IAtom atom)
focal_class.return: int
focal_class.signature: int getNumberOfHydrogen(IAtomContainer atomContainer, IAtom atom)
focal_method.body: public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom) {
          IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer);
          addExplicitHydrogens(acH);
          return getKJPolarizabilityFactor(acH, atom);
      }
focal_method.class_method_signature: Polarizability.getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
focal_method.full_signature: public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)
focal_method.identifier: getPolarizabilitiyFactorForAtom
focal_method.invocations: newInstance getBuilder addExplicitHydrogens getKJPolarizabilityFactor
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer atomContainer, IAtom atom)
focal_method.return: double
focal_method.signature: double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom)