test_class.declarator: sp      = new SmilesParser(DefaultChemObjectBuilder.getInstance())
test_class.modifier: private
test_class.original_string: private SmilesParser            sp      = new SmilesParser(DefaultChemObjectBuilder.getInstance());
test_class.type: SmilesParser
test_class.var_name: sp
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: legacy/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java
test_class.identifier: IPMolecularLearningDescriptorTest
test_class.superclass: extends MolecularDescriptorTest
test_case.body: @Test
      @Category(SlowTest.class)
      public void testIPDescriptor_2() throws Exception {
  
          IAtomContainer mol = sp.parseSmiles("COCCCC=O");
  
          addExplicitHydrogens(mol);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
          lpcheck.saturate(mol);
  
          IPMolecularLearningDescriptor descriptor = new IPMolecularLearningDescriptor();
          DoubleArrayResult dar = ((DoubleArrayResult) (descriptor).calculatePlus(mol).getValue());
  
          double resultAccordingNIST = 9.37;
  
          Assert.assertEquals(2, dar.length());
          Assert.assertEquals(resultAccordingNIST, dar.get(0), 0.3);
      }
test_case.class_method_signature: IPMolecularLearningDescriptorTest.testIPDescriptor_2()
test_case.full_signature: @Test @Category(SlowTest.class) public void testIPDescriptor_2()
test_case.identifier: testIPDescriptor_2
test_case.invocations: parseSmiles addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate getValue calculatePlus assertEquals length assertEquals get
test_case.modifiers: @Test @Category(SlowTest.class) public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testIPDescriptor_2()
focal_class.declarator: addlp = true
focal_class.modifier: private
focal_class.original_string: private boolean               addlp = true;
focal_class.type: boolean
focal_class.var_name: addlp
focal_class.declarator: names = {"MolIP"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] names = {"MolIP"};
focal_class.type: String[]
focal_class.var_name: names
focal_class.file: legacy/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptor.java
focal_class.identifier: IPMolecularLearningDescriptor
focal_class.interfaces: implements IMolecularDescriptor
focal_class.class_method_signature: IPMolecularLearningDescriptor.IPMolecularLearningDescriptor()
focal_class.full_signature: public  IPMolecularLearningDescriptor()
focal_class.identifier: IPMolecularLearningDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  IPMolecularLearningDescriptor()
focal_class.class_method_signature: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.calculate(IAtomContainer atomContainer)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtomContainer atomContainer)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer atomContainer)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtomContainer atomContainer)
focal_class.class_method_signature: IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
focal_class.full_signature: public DescriptorValue calculatePlus(IAtomContainer container)
focal_class.identifier: calculatePlus
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer container)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculatePlus(IAtomContainer container)
focal_class.class_method_signature: IPMolecularLearningDescriptor.arrangingEnergy(ArrayList<Double> array)
focal_class.full_signature: private DoubleArrayResult arrangingEnergy(ArrayList<Double> array)
focal_class.identifier: arrangingEnergy
focal_class.modifiers: private
focal_class.parameters: (ArrayList<Double> array)
focal_class.return: DoubleArrayResult
focal_class.signature: DoubleArrayResult arrangingEnergy(ArrayList<Double> array)
focal_class.class_method_signature: IPMolecularLearningDescriptor.getDescriptorResultType()
focal_class.full_signature: @Override public IDescriptorResult getDescriptorResultType()
focal_class.identifier: getDescriptorResultType
focal_class.modifiers: @Override public
focal_class.parameters: ()
focal_class.return: IDescriptorResult
focal_class.signature: IDescriptorResult getDescriptorResultType()
focal_class.class_method_signature: IPMolecularLearningDescriptor.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: IPMolecularLearningDescriptor.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 AbstractMolecularDescriptor
focal_method.body: public DescriptorValue calculatePlus(IAtomContainer container) throws CDKException {
  
          ArrayList<Double> dar = new ArrayList<Double>();
          for (Iterator<IAtom> itA = container.atoms().iterator(); itA.hasNext();) {
              IAtom atom = itA.next();
              double value = IonizationPotentialTool.predictIP(container, atom);
              if (value != 0) dar.add(value);
          }
          for (Iterator<IBond> itB = container.bonds().iterator(); itB.hasNext();) {
              IBond bond = itB.next();
              if (bond.getOrder() == IBond.Order.DOUBLE & bond.getBegin().getSymbol().equals("C")
                      & bond.getEnd().getSymbol().equals("C")) {
                  double value = IonizationPotentialTool.predictIP(container, bond);
                  if (value != 0) dar.add(value);
  
              }
          }
  
          DoubleArrayResult results = arrangingEnergy(dar);
  
          return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), results,
                  getDescriptorNames(), null);
  
      }
focal_method.class_method_signature: IPMolecularLearningDescriptor.calculatePlus(IAtomContainer container)
focal_method.full_signature: public DescriptorValue calculatePlus(IAtomContainer container)
focal_method.identifier: calculatePlus
focal_method.invocations: iterator atoms hasNext next predictIP add iterator bonds hasNext next getOrder equals getSymbol getBegin equals getSymbol getEnd predictIP add arrangingEnergy getSpecification getParameterNames getParameters getDescriptorNames
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer container)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculatePlus(IAtomContainer container)