test_class.file: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topolTest.java
test_class.identifier: RDFProtonDescriptor_GHR_topolTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testReturnsNaNForNonHydrogen() throws Exception {
          IAtomContainer mol = new AtomContainer();
          IAtom atom = new Atom("O");
          mol.addAtom(atom);
          DescriptorValue dv = descriptor.calculate(atom, mol);
          IDescriptorResult result = dv.getValue();
          Assert.assertNotNull(result);
          Assert.assertTrue(result instanceof DoubleArrayResult);
          DoubleArrayResult dResult = (DoubleArrayResult) result;
          for (int i = 0; i < result.length(); i++) {
              Assert.assertEquals(Double.NaN, dResult.get(i), 0.000001);
          }
      }
test_case.class_method_signature: RDFProtonDescriptor_GHR_topolTest.testReturnsNaNForNonHydrogen()
test_case.full_signature: @Test public void testReturnsNaNForNonHydrogen()
test_case.identifier: testReturnsNaNForNonHydrogen
test_case.invocations: addAtom calculate getValue assertNotNull assertTrue length assertEquals get
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testReturnsNaNForNonHydrogen()
focal_class.declarator: checkAromaticity      = false
focal_class.modifier: private
focal_class.original_string: private boolean                   checkAromaticity      = false;
focal_class.type: boolean
focal_class.var_name: checkAromaticity
focal_class.declarator: acold                 = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainer            acold                 = null;
focal_class.type: IAtomContainer
focal_class.var_name: acold
focal_class.declarator: varRingSet            = null
focal_class.modifier: private
focal_class.original_string: private IRingSet                  varRingSet            = null;
focal_class.type: IRingSet
focal_class.var_name: varRingSet
focal_class.declarator: varAtomContainerSet   = null
focal_class.modifier: private
focal_class.original_string: private IAtomContainerSet         varAtomContainerSet   = null;
focal_class.type: IAtomContainerSet
focal_class.var_name: varAtomContainerSet
focal_class.declarator: LOGGER                = LoggingToolFactory
                                                                      .createLoggingTool(RDFProtonDescriptor_GHR_topol.class)
focal_class.modifier: private final static
focal_class.original_string: private final static ILoggingTool LOGGER                = LoggingToolFactory
                                                                      .createLoggingTool(RDFProtonDescriptor_GHR_topol.class);
focal_class.type: ILoggingTool
focal_class.var_name: LOGGER
focal_class.declarator: ghr_topol_desc_length = 15
focal_class.modifier: private final
focal_class.original_string: private final int                 ghr_topol_desc_length = 15;
focal_class.type: int
focal_class.var_name: ghr_topol_desc_length
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
focal_class.identifier: RDFProtonDescriptor_GHR_topol
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.RDFProtonDescriptor_GHR_topol()
focal_class.full_signature: public  RDFProtonDescriptor_GHR_topol()
focal_class.identifier: RDFProtonDescriptor_GHR_topol
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  RDFProtonDescriptor_GHR_topol()
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.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: RDFProtonDescriptor_GHR_topol.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: RDFProtonDescriptor_GHR_topol.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: RDFProtonDescriptor_GHR_topol.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: RDFProtonDescriptor_GHR_topol.getDummyDescriptorValue(Exception e)
focal_class.full_signature: private DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.identifier: getDummyDescriptorValue
focal_class.modifiers: private
focal_class.parameters: (Exception e)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue getDummyDescriptorValue(Exception e)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
focal_class.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer varAtomContainerSet)
focal_class.identifier: calculate
focal_class.modifiers: @Override public
focal_class.parameters: (IAtom atom, IAtomContainer varAtomContainerSet)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer varAtomContainerSet)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
focal_class.full_signature: public DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
focal_class.identifier: calculate
focal_class.modifiers: public
focal_class.parameters: (IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
focal_class.return: DescriptorValue
focal_class.signature: DescriptorValue calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.getIfBondIsNotRotatable(IAtomContainer mol, IBond bond, IAtomContainer detected)
focal_class.full_signature: private boolean getIfBondIsNotRotatable(IAtomContainer mol, IBond bond, IAtomContainer detected)
focal_class.identifier: getIfBondIsNotRotatable
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, IBond bond, IAtomContainer detected)
focal_class.return: boolean
focal_class.signature: boolean getIfBondIsNotRotatable(IAtomContainer mol, IBond bond, IAtomContainer detected)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.getIfACarbonIsDoubleBondedToAnOxygen(IAtomContainer mol, IAtom carbonAtom)
focal_class.full_signature: private boolean getIfACarbonIsDoubleBondedToAnOxygen(IAtomContainer mol, IAtom carbonAtom)
focal_class.identifier: getIfACarbonIsDoubleBondedToAnOxygen
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, IAtom carbonAtom)
focal_class.return: boolean
focal_class.signature: boolean getIfACarbonIsDoubleBondedToAnOxygen(IAtomContainer mol, IAtom carbonAtom)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.calculateAngleBetweenTwoLines(Vector3d a, Vector3d b, Vector3d c, Vector3d d)
focal_class.full_signature: private double calculateAngleBetweenTwoLines(Vector3d a, Vector3d b, Vector3d c, Vector3d d)
focal_class.identifier: calculateAngleBetweenTwoLines
focal_class.modifiers: private
focal_class.parameters: (Vector3d a, Vector3d b, Vector3d c, Vector3d d)
focal_class.return: double
focal_class.signature: double calculateAngleBetweenTwoLines(Vector3d a, Vector3d b, Vector3d c, Vector3d d)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.checkAndStore(int bondToStore, IBond.Order bondOrder, ArrayList<Integer> singleVec,
              ArrayList<Integer> doubleVec, ArrayList<Integer> cycloexVec, int a1, ArrayList<Integer> atomVec,
              int sphere, boolean isBondInCycloex)
focal_class.full_signature: private void checkAndStore(int bondToStore, IBond.Order bondOrder, ArrayList<Integer> singleVec,
              ArrayList<Integer> doubleVec, ArrayList<Integer> cycloexVec, int a1, ArrayList<Integer> atomVec,
              int sphere, boolean isBondInCycloex)
focal_class.identifier: checkAndStore
focal_class.modifiers: private
focal_class.parameters: (int bondToStore, IBond.Order bondOrder, ArrayList<Integer> singleVec,
              ArrayList<Integer> doubleVec, ArrayList<Integer> cycloexVec, int a1, ArrayList<Integer> atomVec,
              int sphere, boolean isBondInCycloex)
focal_class.return: void
focal_class.signature: void checkAndStore(int bondToStore, IBond.Order bondOrder, ArrayList<Integer> singleVec,
              ArrayList<Integer> doubleVec, ArrayList<Integer> cycloexVec, int a1, ArrayList<Integer> atomVec,
              int sphere, boolean isBondInCycloex)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.calculateDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.full_signature: private double calculateDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.identifier: calculateDistanceBetweenTwoAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: double
focal_class.signature: double calculateDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bond)
focal_class.full_signature: private int getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bond)
focal_class.identifier: getNearestBondtoAGivenAtom
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer mol, IAtom atom, IBond bond)
focal_class.return: int
focal_class.signature: int getNearestBondtoAGivenAtom(IAtomContainer mol, IAtom atom, IBond bond)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond)
focal_class.full_signature: private double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond)
focal_class.identifier: calculateDistanceBetweenAtomAndBond
focal_class.modifiers: private
focal_class.parameters: (IAtom proton, IBond theBond)
focal_class.return: double[]
focal_class.signature: double[] calculateDistanceBetweenAtomAndBond(IAtom proton, IBond theBond)
focal_class.class_method_signature: RDFProtonDescriptor_GHR_topol.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: RDFProtonDescriptor_GHR_topol.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 varAtomContainerSet) {
          return (calculate(atom, varAtomContainerSet, null));
      }
focal_method.class_method_signature: RDFProtonDescriptor_GHR_topol.calculate(IAtom atom, IAtomContainer varAtomContainerSet)
focal_method.full_signature: @Override public DescriptorValue calculate(IAtom atom, IAtomContainer varAtomContainerSet)
focal_method.identifier: calculate
focal_method.invocations: calculate
focal_method.modifiers: @Override public
focal_method.parameters: (IAtom atom, IAtomContainer varAtomContainerSet)
focal_method.return: DescriptorValue
focal_method.signature: DescriptorValue calculate(IAtom atom, IAtomContainer varAtomContainerSet)