test_class.file: descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java
test_class.identifier: InductiveAtomicSoftnessDescriptorTest
test_class.superclass: extends AtomicDescriptorTest
test_case.body: @Test
      public void testInductiveAtomicSoftnessDescriptor() throws ClassNotFoundException, CDKException,
              java.lang.Exception {
          double[] testResult = {0.78};
  
          Point3d c_coord = new Point3d(1.392, 0.0, 0.0);
          Point3d f_coord = new Point3d(0.0, 0.0, 0.0);
          Point3d h1_coord = new Point3d(1.7439615035767404, 1.0558845107302222, 0.0);
          Point3d h2_coord = new Point3d(1.7439615035767404, -0.5279422553651107, 0.914422809754875);
          Point3d h3_coord = new Point3d(1.7439615035767402, -0.5279422553651113, -0.9144228097548747);
  
          IAtomContainer mol = new AtomContainer(); // molecule is CF
  
          Atom c = new Atom("C");
          mol.addAtom(c);
          c.setPoint3d(c_coord);
  
          Atom f = new Atom("F");
          mol.addAtom(f);
          f.setPoint3d(f_coord);
  
          Atom h1 = new Atom("H");
          mol.addAtom(h1);
          h1.setPoint3d(h1_coord);
  
          Atom h2 = new Atom("H");
          mol.addAtom(h2);
          h2.setPoint3d(h2_coord);
  
          Atom h3 = new Atom("H");
          mol.addAtom(h3);
          h3.setPoint3d(h3_coord);
  
          mol.addBond(0, 1, IBond.Order.SINGLE); // 1
          mol.addBond(0, 2, IBond.Order.SINGLE); // 1
          mol.addBond(0, 3, IBond.Order.SINGLE); // 1
          mol.addBond(0, 4, IBond.Order.SINGLE); // 1
  
          IAtomicDescriptor descriptor = new InductiveAtomicSoftnessDescriptor();
  
          double retval = ((DoubleResult) descriptor.calculate(mol.getAtom(0), mol).getValue()).doubleValue();
          Assert.assertEquals(testResult[0], retval, 0.1);
  
          // F: expected is 0.32, calculated is 0.35
          // difference depends on different starting values (3D distances and small differences
          // in electronegativity values
  
          // H: expected is 0.28, calculated is 0.28
      }
test_case.class_method_signature: InductiveAtomicSoftnessDescriptorTest.testInductiveAtomicSoftnessDescriptor()
test_case.full_signature: @Test public void testInductiveAtomicSoftnessDescriptor()
test_case.identifier: testInductiveAtomicSoftnessDescriptor
test_case.invocations: addAtom setPoint3d addAtom setPoint3d addAtom setPoint3d addAtom setPoint3d addAtom setPoint3d addBond addBond addBond addBond doubleValue getValue calculate getAtom assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testInductiveAtomicSoftnessDescriptor()
focal_class.declarator: NAMES   = {"indAtomSoftness"}
focal_class.modifier: private static final
focal_class.original_string: private static final String[] NAMES   = {"indAtomSoftness"};
focal_class.type: String[]
focal_class.var_name: NAMES
focal_class.declarator: logger  = LoggingToolFactory
                                                    .createLoggingTool(InductiveAtomicSoftnessDescriptor.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool   logger  = LoggingToolFactory
                                                    .createLoggingTool(InductiveAtomicSoftnessDescriptor.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.declarator: factory = null
focal_class.modifier: private
focal_class.original_string: private AtomTypeFactory       factory = null;
focal_class.type: AtomTypeFactory
focal_class.var_name: factory
focal_class.file: descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java
focal_class.identifier: InductiveAtomicSoftnessDescriptor
focal_class.interfaces: implements IAtomicDescriptor
focal_class.class_method_signature: InductiveAtomicSoftnessDescriptor.InductiveAtomicSoftnessDescriptor()
focal_class.full_signature: public  InductiveAtomicSoftnessDescriptor()
focal_class.identifier: InductiveAtomicSoftnessDescriptor
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  InductiveAtomicSoftnessDescriptor()
focal_class.class_method_signature: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.calculateSquareDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.full_signature: private double calculateSquareDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.identifier: calculateSquareDistanceBetweenTwoAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: double
focal_class.signature: double calculateSquareDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.class_method_signature: InductiveAtomicSoftnessDescriptor.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: InductiveAtomicSoftnessDescriptor.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: public InductiveAtomicSoftnessDescriptor() throws IOException, ClassNotFoundException {}
focal_method.class_method_signature: InductiveAtomicSoftnessDescriptor.InductiveAtomicSoftnessDescriptor()
focal_method.full_signature: public  InductiveAtomicSoftnessDescriptor()
focal_method.identifier: InductiveAtomicSoftnessDescriptor
focal_method.modifiers: public
focal_method.parameters: ()
focal_method.signature:  InductiveAtomicSoftnessDescriptor()