test_class.declarator: mol
test_class.modifier: private static
test_class.original_string: private static IAtomContainer mol;
test_class.type: IAtomContainer
test_class.var_name: mol
test_class.file: tool/charges/src/test/java/org/openscience/cdk/charges/InductivePartialChargesTest.java
test_class.identifier: InductivePartialChargesTest
test_class.superclass: extends CDKTestCase
test_case.body: @Ignore
      @Test
      public void testGetAtomicSoftness() throws Exception {
          InductivePartialCharges ipc = new InductivePartialCharges();
          double softness = ipc.getAtomicSoftnessCore(mol, 0);
          Assert.fail("Not validated - need known values");
      }
test_case.class_method_signature: InductivePartialChargesTest.testGetAtomicSoftness()
test_case.full_signature: @Ignore @Test public void testGetAtomicSoftness()
test_case.identifier: testGetAtomicSoftness
test_case.invocations: getAtomicSoftnessCore fail
test_case.modifiers: @Ignore @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetAtomicSoftness()
focal_class.declarator: pauling
focal_class.modifier: private static
focal_class.original_string: private static double[]     pauling;
focal_class.type: double[]
focal_class.var_name: pauling
focal_class.declarator: ifac    = null
focal_class.modifier: private
focal_class.original_string: private IsotopeFactory      ifac    = null;
focal_class.type: IsotopeFactory
focal_class.var_name: ifac
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.declarator: logger  = LoggingToolFactory.createLoggingTool(InductivePartialCharges.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger  = LoggingToolFactory.createLoggingTool(InductivePartialCharges.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java
focal_class.identifier: InductivePartialCharges
focal_class.interfaces: implements IChargeCalculator
focal_class.class_method_signature: InductivePartialCharges.InductivePartialCharges()
focal_class.full_signature: public  InductivePartialCharges()
focal_class.identifier: InductivePartialCharges
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  InductivePartialCharges()
focal_class.class_method_signature: InductivePartialCharges.assignInductivePartialCharges(IAtomContainer ac)
focal_class.full_signature: public IAtomContainer assignInductivePartialCharges(IAtomContainer ac)
focal_class.identifier: assignInductivePartialCharges
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer assignInductivePartialCharges(IAtomContainer ac)
focal_class.class_method_signature: InductivePartialCharges.calculateCharges(IAtomContainer container)
focal_class.full_signature: @Override public void calculateCharges(IAtomContainer container)
focal_class.identifier: calculateCharges
focal_class.modifiers: @Override public
focal_class.parameters: (IAtomContainer container)
focal_class.return: void
focal_class.signature: void calculateCharges(IAtomContainer container)
focal_class.class_method_signature: InductivePartialCharges.getPaulingElectronegativities(IAtomContainer ac, boolean modified)
focal_class.full_signature: public double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified)
focal_class.identifier: getPaulingElectronegativities
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, boolean modified)
focal_class.return: double[]
focal_class.signature: double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified)
focal_class.class_method_signature: InductivePartialCharges.getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
focal_class.full_signature: public double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
focal_class.identifier: getAtomicSoftnessCore
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, int atomPosition)
focal_class.return: double
focal_class.signature: double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
focal_class.class_method_signature: InductivePartialCharges.getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, double[] ElEn, int as)
focal_class.full_signature: private double getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, double[] ElEn, int as)
focal_class.identifier: getAtomicChargeIncrement
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac, int atomPosition, double[] ElEn, int as)
focal_class.return: double
focal_class.signature: double getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, double[] ElEn, int as)
focal_class.class_method_signature: InductivePartialCharges.getCovalentRadius(String symbol, IBond.Order maxBondOrder)
focal_class.full_signature: private double getCovalentRadius(String symbol, IBond.Order maxBondOrder)
focal_class.identifier: getCovalentRadius
focal_class.modifiers: private
focal_class.parameters: (String symbol, IBond.Order maxBondOrder)
focal_class.return: double
focal_class.signature: double getCovalentRadius(String symbol, IBond.Order maxBondOrder)
focal_class.class_method_signature: InductivePartialCharges.calculateSquaredDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.full_signature: private double calculateSquaredDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_class.identifier: calculateSquaredDistanceBetweenTwoAtoms
focal_class.modifiers: private
focal_class.parameters: (IAtom atom1, IAtom atom2)
focal_class.return: double
focal_class.signature: double calculateSquaredDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2)
focal_method.body: public double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition) throws CDKException {
          if (factory == null) {
              factory = AtomTypeFactory
                      .getInstance("org/openscience/cdk/config/data/jmol_atomtypes.txt", ac.getBuilder());
          }
          IAtom target = null;
          double core = 0;
          double radiusTarget = 0;
          target = ac.getAtom(atomPosition);
          double partial = 0;
          double radius = 0;
          String symbol = null;
          IAtomType type = null;
          try {
              symbol = ac.getAtom(atomPosition).getSymbol();
              type = factory.getAtomType(symbol);
              if (getCovalentRadius(symbol, ac.getMaximumBondOrder(target)) > 0) {
                  radiusTarget = getCovalentRadius(symbol, ac.getMaximumBondOrder(target));
              } else {
                  radiusTarget = type.getCovalentRadius();
              }
  
          } catch (Exception ex1) {
              logger.debug(ex1);
              throw new CDKException("Problems with AtomTypeFactory due to " + ex1.getMessage(), ex1);
          }
  
          Iterator<IAtom> atoms = ac.atoms().iterator();
          while (atoms.hasNext()) {
              IAtom atom = atoms.next();
              if (!target.equals(atom)) {
                  symbol = atom.getSymbol();
                  partial = 0;
                  try {
                      type = factory.getAtomType(symbol);
                  } catch (Exception ex1) {
                      logger.debug(ex1);
                      throw new CDKException("Problems with AtomTypeFactory due to " + ex1.getMessage(), ex1);
                  }
                  if (getCovalentRadius(symbol, ac.getMaximumBondOrder(atom)) > 0) {
                      radius = getCovalentRadius(symbol, ac.getMaximumBondOrder(atom));
                  } else {
                      radius = type.getCovalentRadius();
                  }
                  partial += radius * radius;
                  partial += (radiusTarget * radiusTarget);
                  partial = partial / (calculateSquaredDistanceBetweenTwoAtoms(target, atom));
                  core += partial;
              }
          }
          core = 2 * core;
          core = 0.172 * core;
          return core;
      }
focal_method.class_method_signature: InductivePartialCharges.getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
focal_method.full_signature: public double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)
focal_method.identifier: getAtomicSoftnessCore
focal_method.invocations: getInstance getBuilder getAtom getSymbol getAtom getAtomType getCovalentRadius getMaximumBondOrder getCovalentRadius getMaximumBondOrder getCovalentRadius debug getMessage iterator atoms hasNext next equals getSymbol getAtomType debug getMessage getCovalentRadius getMaximumBondOrder getCovalentRadius getMaximumBondOrder getCovalentRadius calculateSquaredDistanceBetweenTwoAtoms
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer ac, int atomPosition)
focal_method.return: double
focal_method.signature: double getAtomicSoftnessCore(IAtomContainer ac, int atomPosition)