test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private
test_class.original_string: private IChemObjectBuilder      builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
test_class.declarator: lpcheck = new LonePairElectronChecker()
test_class.modifier: private
test_class.original_string: private LonePairElectronChecker lpcheck = new LonePairElectronChecker();
test_class.type: LonePairElectronChecker
test_class.var_name: lpcheck
test_class.file: tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java
test_class.identifier: ElectronegativityTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testCalculateSigmaElectronegativity_IAtomContainer_IAtom() throws Exception {
          double[] testResult = {11.308338, 8.7184094, 7.5289848, 7.5289848, 7.5289848};
          Electronegativity pe = new Electronegativity();
  
          IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
          molecule.addAtom(new Atom("F"));
          molecule.addAtom(new Atom("C"));
          molecule.addBond(0, 1, IBond.Order.SINGLE);
  
          addExplicitHydrogens(molecule);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
          lpcheck.saturate(molecule);
  
          for (int i = 0; i < molecule.getAtomCount(); i++)
              Assert.assertEquals(testResult[i], pe.calculateSigmaElectronegativity(molecule, molecule.getAtom(i)), 0.001);
  
      }
test_case.class_method_signature: ElectronegativityTest.testCalculateSigmaElectronegativity_IAtomContainer_IAtom()
test_case.full_signature: @Test public void testCalculateSigmaElectronegativity_IAtomContainer_IAtom()
test_case.identifier: testCalculateSigmaElectronegativity_IAtomContainer_IAtom
test_case.invocations: newInstance addAtom addAtom addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate getAtomCount assertEquals calculateSigmaElectronegativity getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCalculateSigmaElectronegativity_IAtomContainer_IAtom()
focal_class.declarator: peoe  = null
focal_class.modifier: private
focal_class.original_string: private GasteigerMarsiliPartialCharges peoe  = null;
focal_class.type: GasteigerMarsiliPartialCharges
focal_class.var_name: peoe
focal_class.declarator: maxI  = 6
focal_class.modifier: private
focal_class.original_string: private int                            maxI  = 6;
focal_class.type: int
focal_class.var_name: maxI
focal_class.declarator: maxRS = 50
focal_class.modifier: private
focal_class.original_string: private int                            maxRS = 50;
focal_class.type: int
focal_class.var_name: maxRS
focal_class.declarator: molSigma
focal_class.modifier: private
focal_class.original_string: private IAtomContainer                 molSigma;
focal_class.type: IAtomContainer
focal_class.var_name: molSigma
focal_class.declarator: acOldS
focal_class.modifier: private
focal_class.original_string: private IAtomContainer                 acOldS;
focal_class.type: IAtomContainer
focal_class.var_name: acOldS
focal_class.declarator: marsiliFactors
focal_class.modifier: private
focal_class.original_string: private double[]                       marsiliFactors;
focal_class.type: double[]
focal_class.var_name: marsiliFactors
focal_class.declarator: logger = LoggingToolFactory.createLoggingTool(Electronegativity.class)
focal_class.modifier: private final
focal_class.original_string: private final ILoggingTool logger = LoggingToolFactory.createLoggingTool(Electronegativity.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: tool/charges/src/main/java/org/openscience/cdk/charges/Electronegativity.java
focal_class.identifier: Electronegativity
focal_class.class_method_signature: Electronegativity.Electronegativity()
focal_class.full_signature: public  Electronegativity()
focal_class.identifier: Electronegativity
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  Electronegativity()
focal_class.class_method_signature: Electronegativity.Electronegativity(int maxIterations, int maxResonStruc)
focal_class.full_signature: public  Electronegativity(int maxIterations, int maxResonStruc)
focal_class.identifier: Electronegativity
focal_class.modifiers: public
focal_class.parameters: (int maxIterations, int maxResonStruc)
focal_class.signature:  Electronegativity(int maxIterations, int maxResonStruc)
focal_class.class_method_signature: Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)
focal_class.full_signature: public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)
focal_class.identifier: calculateSigmaElectronegativity
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, IAtom atom)
focal_class.return: double
focal_class.signature: double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)
focal_class.class_method_signature: Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
focal_class.full_signature: public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
focal_class.identifier: calculateSigmaElectronegativity
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
focal_class.return: double
focal_class.signature: double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom, int maxIterations, int maxResonStruc)
focal_class.class_method_signature: Electronegativity.setMaxIterations(int maxIterations)
focal_class.full_signature: public void setMaxIterations(int maxIterations)
focal_class.identifier: setMaxIterations
focal_class.modifiers: public
focal_class.parameters: (int maxIterations)
focal_class.return: void
focal_class.signature: void setMaxIterations(int maxIterations)
focal_class.class_method_signature: Electronegativity.setMaxResonStruc(int maxResonStruc)
focal_class.full_signature: public void setMaxResonStruc(int maxResonStruc)
focal_class.identifier: setMaxResonStruc
focal_class.modifiers: public
focal_class.parameters: (int maxResonStruc)
focal_class.return: void
focal_class.signature: void setMaxResonStruc(int maxResonStruc)
focal_class.class_method_signature: Electronegativity.getMaxIterations()
focal_class.full_signature: public int getMaxIterations()
focal_class.identifier: getMaxIterations
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getMaxIterations()
focal_class.class_method_signature: Electronegativity.getMaxResonStruc()
focal_class.full_signature: public int getMaxResonStruc()
focal_class.identifier: getMaxResonStruc
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getMaxResonStruc()
focal_method.body: public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom) {
  
          return calculateSigmaElectronegativity(ac, atom, maxI, maxRS);
      }
focal_method.class_method_signature: Electronegativity.calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)
focal_method.full_signature: public double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)
focal_method.identifier: calculateSigmaElectronegativity
focal_method.invocations: calculateSigmaElectronegativity
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer ac, IAtom atom)
focal_method.return: double
focal_method.signature: double calculateSigmaElectronegativity(IAtomContainer ac, IAtom atom)