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: @Test
      public void testGetPaulingElectronegativities() throws Exception {
          InductivePartialCharges ipc = new InductivePartialCharges();
          double[] eneg = ipc.getPaulingElectronegativities(mol, true);
          long[] expected = {};
          Assert.assertEquals("Error in C electronegativity", 2.20, eneg[0], 0.01);
          Assert.assertEquals("Error in Cl electronegativity", 3.28, eneg[1], 0.01);
          Assert.assertEquals("Error in Br electronegativity", 3.13, eneg[2], 0.01);
          Assert.assertEquals("Error in H electronegativity", 2.10, eneg[3], 0.01);
          Assert.assertEquals("Error in O electronegativity", 3.20, eneg[4], 0.01);
      }
test_case.class_method_signature: InductivePartialChargesTest.testGetPaulingElectronegativities()
test_case.full_signature: @Test public void testGetPaulingElectronegativities()
test_case.identifier: testGetPaulingElectronegativities
test_case.invocations: getPaulingElectronegativities assertEquals assertEquals assertEquals assertEquals assertEquals
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testGetPaulingElectronegativities()
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[] getPaulingElectronegativities(IAtomContainer ac, boolean modified) throws CDKException {
          double[] paulingElectronegativities = new double[ac.getAtomCount()];
          IElement element = null;
          String symbol = null;
          int atomicNumber = 0;
          try {
              ifac = Isotopes.getInstance();
              for (int i = 0; i < ac.getAtomCount(); i++) {
                  IAtom atom = ac.getAtom(i);
                  symbol = ac.getAtom(i).getSymbol();
                  element = ifac.getElement(symbol);
                  atomicNumber = element.getAtomicNumber();
                  if (modified) {
                      if (symbol.equals("Cl")) {
                          paulingElectronegativities[i] = 3.28;
                      } else if (symbol.equals("Br")) {
                          paulingElectronegativities[i] = 3.13;
                      } else if (symbol.equals("I")) {
                          paulingElectronegativities[i] = 2.93;
                      } else if (symbol.equals("H")) {
                          paulingElectronegativities[i] = 2.10;
                      } else if (symbol.equals("C")) {
                          if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
                              // Csp3
                              paulingElectronegativities[i] = 2.20;
                          } else if (ac.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
                              paulingElectronegativities[i] = 2.31;
                          } else {
                              paulingElectronegativities[i] = 3.15;
                          }
                      } else if (symbol.equals("O")) {
                          if (ac.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
                              // Osp3
                              paulingElectronegativities[i] = 3.20;
                          } else if (ac.getMaximumBondOrder(atom) != IBond.Order.SINGLE) {
                              paulingElectronegativities[i] = 4.34;
                          }
                      } else if (symbol.equals("Si")) {
                          paulingElectronegativities[i] = 1.99;
                      } else if (symbol.equals("S")) {
                          paulingElectronegativities[i] = 2.74;
                      } else if (symbol.equals("N")) {
                          paulingElectronegativities[i] = 2.59;
                      } else {
                          paulingElectronegativities[i] = pauling[atomicNumber];
                      }
                  } else {
                      paulingElectronegativities[i] = pauling[atomicNumber];
                  }
              }
              return paulingElectronegativities;
          } catch (Exception ex1) {
              logger.debug(ex1);
              throw new CDKException("Problems with IsotopeFactory due to " + ex1.toString(), ex1);
          }
      }
focal_method.class_method_signature: InductivePartialCharges.getPaulingElectronegativities(IAtomContainer ac, boolean modified)
focal_method.full_signature: public double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified)
focal_method.identifier: getPaulingElectronegativities
focal_method.invocations: getAtomCount getInstance getAtomCount getAtom getSymbol getAtom getElement getAtomicNumber equals equals equals equals equals getMaximumBondOrder getMaximumBondOrder equals getMaximumBondOrder getMaximumBondOrder equals equals equals debug toString
focal_method.modifiers: public
focal_method.parameters: (IAtomContainer ac, boolean modified)
focal_method.return: double[]
focal_method.signature: double[] getPaulingElectronegativities(IAtomContainer ac, boolean modified)