test_class.declarator: builder = SilentChemObjectBuilder.getInstance()
test_class.modifier: private final static
test_class.original_string: private final static IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
test_class.type: IChemObjectBuilder
test_class.var_name: builder
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: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptorTest.java
test_class.identifier: StabilizationPlusChargeDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      @Category(SlowTest.class)
      public void testCompareIonized() throws 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);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
          addExplicitHydrogens(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);
  
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
          addExplicitHydrogens(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.assertNotSame(resultA, resultB);
      }
test_case.class_method_signature: StabilizationPlusChargeDescriptorTest.testCompareIonized()
test_case.full_signature: @Test @Category(SlowTest.class) public void testCompareIonized()
test_case.identifier: testCompareIonized
test_case.invocations: newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance addBond percieveAtomTypesAndConfigureAtoms addExplicitHydrogens saturate doubleValue getValue calculate getAtom newInstance addAtom newInstance addAtom newInstance addBond addAtom newInstance addBond addAtom newInstance setFormalCharge getAtom addSingleElectron addLonePair addLonePair addBond percieveAtomTypesAndConfigureAtoms addExplicitHydrogens saturate assertEquals getFormalCharge getAtom assertEquals getSingleElectronCount assertEquals getLonePairCount doubleValue getValue calculate getAtom assertNotSame
test_case.modifiers: @Test @Category(SlowTest.class) public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCompareIonized()
focal_class.declarator: NAMES = {"stabilPlusC"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] NAMES = {"stabilPlusC"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: stabil
focal_class.modifier: private
focal_class.original_string: private StabilizationCharges stabil;
focal_class.type: StabilizationCharges
focal_class.var_name: stabil
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java
focal_class.identifier: StabilizationPlusChargeDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: StabilizationPlusChargeDescriptor.StabilizationPlusChargeDescriptor()
focal_class.full_signature: public  StabilizationPlusChargeDescriptor()
focal_class.identifier: StabilizationPlusChargeDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  StabilizationPlusChargeDescriptor()
focal_class.class_method_signature: StabilizationPlusChargeDescriptor.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: StabilizationPlusChargeDescriptor.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: StabilizationPlusChargeDescriptor.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: StabilizationPlusChargeDescriptor.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: StabilizationPlusChargeDescriptor.calculate(IAtom atom, IAtomContainer container)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom, IAtomContainer container)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_class.class_method_signature: StabilizationPlusChargeDescriptor.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: StabilizationPlusChargeDescriptor.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 container) {
  
          IAtomContainer clone;
          IAtom localAtom;
          try {
              clone = (IAtomContainer) container.clone();
              localAtom = clone.getAtom(container.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);
          }
  
          double result = stabil.calculatePositive(clone, localAtom);
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult(result),
                                     NAMES);
      }
focal_method.class_method_signature: StabilizationPlusChargeDescriptor.calculate(IAtom atom, IAtomContainer container)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer container)
focal_method.identifier: calculate
focal_method.invocations: clone getAtom indexOf percieveAtomTypesAndConfigureAtoms getSpecification getParameterNames getParameters getSpecification getParameterNames getParameters calculatePositive getSpecification getParameterNames getParameters
focal_method.modifiers: @Override public
focal_method.parameters: (IAtom atom, IAtomContainer container)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtom atom, IAtomContainer container)