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: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java
test_class.identifier: SigmaElectronegativityDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testCompareIonized() throws ClassNotFoundException, CDKException, java.lang.Exception {
  
          IAtomContainer molA = builder.newInstance(IAtomContainer.class);
          molA.addAtom(builder.newInstance(IAtom.class, "C"));
          molA.addAtom(builder.newInstance(IAtom.class, "C"));
          molA.addBond(0, 1, IBond.Order.SINGLE);
          molA.addAtom(builder.newInstance(IAtom.class, "C"));
          molA.addBond(1, 2, IBond.Order.SINGLE);
          molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
          molA.addBond(2, 3, IBond.Order.SINGLE);
  
          addExplicitHydrogens(molA);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
          lpcheck.saturate(molA);
  
          double resultA = ((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
  
          IAtomContainer molB = builder.newInstance(IAtomContainer.class);
          molB.addAtom(builder.newInstance(IAtom.class, "C"));
          molB.addAtom(builder.newInstance(IAtom.class, "C"));
          molB.addBond(0, 1, IBond.Order.SINGLE);
          molB.addAtom(builder.newInstance(IAtom.class, "C"));
          molB.addBond(1, 2, IBond.Order.SINGLE);
          molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
          molB.getAtom(3).setFormalCharge(1);
          molB.addSingleElectron(3);
          molB.addLonePair(3);
          molB.addLonePair(3);
          molB.addBond(2, 3, IBond.Order.SINGLE);
  
          addExplicitHydrogens(molB);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
          lpcheck.saturate(molB);
  
          Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
          Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
          Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
  
          double resultB = ((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
  
          Assert.assertEquals(resultA, resultB, 0.00001);
      }
test_case.class_method_signature: SigmaElectronegativityDescriptorTest.testCompareIonized()
test_case.full_signature: @Test public void testCompareIonized()
test_case.identifier: testCompareIonized
test_case.invocations: newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate doubleValue getValue calculate getAtom newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance setFormalCharge getAtom addSingleElectron addLonePair addLonePair addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate assertEquals getFormalCharge getAtom assertEquals getSingleElectronCount assertEquals getLonePairCount doubleValue getValue calculate getAtom assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCompareIonized()
focal_class.declarator: maxIterations   = 0
focal_class.modifier: private
focal_class.original_string: private int                   maxIterations   = 0;
focal_class.type: int
focal_class.var_name: maxIterations
focal_class.declarator: NAMES = {"elecSigmA"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] NAMES = {"elecSigmA"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: electronegativity
focal_class.modifier: private
focal_class.original_string: private Electronegativity     electronegativity;
focal_class.type: Electronegativity
focal_class.var_name: electronegativity
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java
focal_class.identifier: SigmaElectronegativityDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: SigmaElectronegativityDescriptor.SigmaElectronegativityDescriptor()
focal_class.full_signature: public  SigmaElectronegativityDescriptor()
focal_class.identifier: SigmaElectronegativityDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  SigmaElectronegativityDescriptor()
focal_class.class_method_signature: SigmaElectronegativityDescriptor.getSpecification()
focal_class.full_signature: @Override public DescriptorSpecification getSpecification()
focal_class.identifier: getSpecification
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: DescriptorSpecification
focal_class.signature: DescriptorSpecification getSpecification()
focal_class.class_method_signature: SigmaElectronegativityDescriptor.setParameters(Object[] params)
focal_class.full_signature: @Override public void setParameters(Object[] params)
focal_class.identifier: setParameters
focal_class.modifiers: @Override public
focal_class.parameters: (Object[] params)
focal_class.return: void
focal_class.signature: void setParameters(Object[] params)
focal_class.class_method_signature: SigmaElectronegativityDescriptor.getParameters()
focal_class.full_signature: @Override public Object[] getParameters()
focal_class.identifier: getParameters
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: Object[]
focal_class.signature: Object[] getParameters()
focal_class.class_method_signature: SigmaElectronegativityDescriptor.getDescriptorNames()
focal_class.full_signature: @Override public String[] getDescriptorNames()
focal_class.identifier: getDescriptorNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getDescriptorNames()
focal_class.class_method_signature: SigmaElectronegativityDescriptor.calculate(IAtom atom, IAtomContainer ac)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer ac)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom, IAtomContainer ac)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer ac)
focal_class.class_method_signature: SigmaElectronegativityDescriptor.getParameterNames()
focal_class.full_signature: @Override public String[] getParameterNames()
focal_class.identifier: getParameterNames
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getParameterNames()
focal_class.class_method_signature: SigmaElectronegativityDescriptor.getParameterType(String name)
focal_class.full_signature: @Override public Object getParameterType(String name)
focal_class.identifier: getParameterType
focal_class.modifiers: @Override public
focal_class.parameters: (String name)
focal_class.return: Object
focal_class.signature: Object getParameterType(String name)
focal_class.superclass: extends AbstractAtomicDescriptor
focal_method.body: @Override
      public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
  
          IAtomContainer clone;
          IAtom localAtom;
          try {
              clone = (IAtomContainer) ac.clone();
              localAtom = clone.getAtom(ac.indexOf(atom));
              AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(clone);
          } catch (CDKException e) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                      Double.NaN), NAMES, e);
          } catch (CloneNotSupportedException e) {
              return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(
                      Double.NaN), NAMES, e);
          }
  
          if (maxIterations != -1 && maxIterations != 0) electronegativity.setMaxIterations(maxIterations);
  
          double result = electronegativity.calculateSigmaElectronegativity(clone, localAtom);
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result),
                                     NAMES);
      }
focal_method.class_method_signature: SigmaElectronegativityDescriptor.calculate(IAtom atom, IAtomContainer ac)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer ac)
focal_method.identifier: calculate
focal_method.invocations: clone getAtom indexOf percieveAtomTypesAndConfigureAtoms getSpecification getParameterNames getParameters getSpecification getParameterNames getParameters setMaxIterations calculateSigmaElectronegativity getSpecification getParameterNames getParameters
focal_method.modifiers: @Override public
focal_method.parameters: (IAtom atom, IAtomContainer ac)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtom atom, IAtomContainer ac)