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: tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java
test_class.identifier: GasteigerPEPEPartialChargesTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testAssignrPiMarsilliFactors_IAtomContainerSet() throws Exception {
          GasteigerPEPEPartialCharges peoe = new GasteigerPEPEPartialCharges();
  
          IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
          molecule.addAtom(new Atom("C"));
          molecule.addAtom(new Atom("F"));
          molecule.addBond(0, 1, IBond.Order.SINGLE);
  
          addExplicitHydrogens(molecule);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
          lpcheck.saturate(molecule);
          for (Iterator<IAtom> it = molecule.atoms().iterator(); it.hasNext();)
              it.next().setCharge(0.0);
  
          IAtomContainerSet set = builder.newInstance(IAtomContainerSet.class);
          set.addAtomContainer(molecule);
          set.addAtomContainer(molecule);
  
          addExplicitHydrogens(molecule);
          AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
          lpcheck.saturate(molecule);
  
          Assert.assertNotNull(peoe.assignrPiMarsilliFactors(set));
  
      }
test_case.class_method_signature: GasteigerPEPEPartialChargesTest.testAssignrPiMarsilliFactors_IAtomContainerSet()
test_case.full_signature: @Test public void testAssignrPiMarsilliFactors_IAtomContainerSet()
test_case.identifier: testAssignrPiMarsilliFactors_IAtomContainerSet
test_case.invocations: newInstance addAtom addAtom addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate iterator atoms hasNext setCharge next newInstance addAtomContainer addAtomContainer addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate assertNotNull assignrPiMarsilliFactors
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testAssignrPiMarsilliFactors_IAtomContainerSet()
focal_class.declarator: MX_ITERATIONS = 8
focal_class.modifier: private
focal_class.original_string: private int                 MX_ITERATIONS = 8;
focal_class.type: int
focal_class.var_name: MX_ITERATIONS
focal_class.declarator: MX_RESON      = 50
focal_class.modifier: private
focal_class.original_string: private int                 MX_RESON      = 50;
focal_class.type: int
focal_class.var_name: MX_RESON
focal_class.declarator: STEP_SIZE     = 5
focal_class.modifier: private
focal_class.original_string: private int                 STEP_SIZE     = 5;
focal_class.type: int
focal_class.var_name: STEP_SIZE
focal_class.declarator: factory
focal_class.modifier: private
focal_class.original_string: private AtomTypeFactory     factory;
focal_class.type: AtomTypeFactory
focal_class.var_name: factory
focal_class.declarator: ISCHANGEDFC   = 0x1
focal_class.modifier: private static
focal_class.original_string: private static int          ISCHANGEDFC   = 0x1;
focal_class.type: int
focal_class.var_name: ISCHANGEDFC
focal_class.declarator: fE            = 1.1
focal_class.modifier: private
focal_class.original_string: private double              fE            = 1.1;
focal_class.type: double
focal_class.var_name: fE
focal_class.declarator: fS            = 0.37
focal_class.modifier: private
focal_class.original_string: private double              fS            = 0.37;
focal_class.type: double
focal_class.var_name: fS
focal_class.declarator: logger        = LoggingToolFactory.createLoggingTool(GasteigerPEPEPartialCharges.class)
focal_class.modifier: private static
focal_class.original_string: private static ILoggingTool logger        = LoggingToolFactory.createLoggingTool(GasteigerPEPEPartialCharges.class);
focal_class.type: ILoggingTool
focal_class.var_name: logger
focal_class.file: tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
focal_class.identifier: GasteigerPEPEPartialCharges
focal_class.interfaces: implements IChargeCalculator
focal_class.class_method_signature: GasteigerPEPEPartialCharges.GasteigerPEPEPartialCharges()
focal_class.full_signature: public  GasteigerPEPEPartialCharges()
focal_class.identifier: GasteigerPEPEPartialCharges
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  GasteigerPEPEPartialCharges()
focal_class.class_method_signature: GasteigerPEPEPartialCharges.setMaxGasteigerIters(int iters)
focal_class.full_signature: public void setMaxGasteigerIters(int iters)
focal_class.identifier: setMaxGasteigerIters
focal_class.modifiers: public
focal_class.parameters: (int iters)
focal_class.return: void
focal_class.signature: void setMaxGasteigerIters(int iters)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.setMaxResoStruc(int numbReson)
focal_class.full_signature: public void setMaxResoStruc(int numbReson)
focal_class.identifier: setMaxResoStruc
focal_class.modifiers: public
focal_class.parameters: (int numbReson)
focal_class.return: void
focal_class.signature: void setMaxResoStruc(int numbReson)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getMaxGasteigerIters()
focal_class.full_signature: public int getMaxGasteigerIters()
focal_class.identifier: getMaxGasteigerIters
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getMaxGasteigerIters()
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getMaxResoStruc()
focal_class.full_signature: public int getMaxResoStruc()
focal_class.identifier: getMaxResoStruc
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getMaxResoStruc()
focal_class.class_method_signature: GasteigerPEPEPartialCharges.assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.full_signature: public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.identifier: assignGasteigerPiPartialCharges
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, boolean setCharge)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.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: GasteigerPEPEPartialCharges.removingFlagsAromaticity(IAtomContainer ac)
focal_class.full_signature: private IAtomContainer removingFlagsAromaticity(IAtomContainer ac)
focal_class.identifier: removingFlagsAromaticity
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer removingFlagsAromaticity(IAtomContainer ac)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.setFlags(IAtomContainer container, IAtomContainer ac, boolean b)
focal_class.full_signature: private IAtomContainer setFlags(IAtomContainer container, IAtomContainer ac, boolean b)
focal_class.identifier: setFlags
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, IAtomContainer ac, boolean b)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer setFlags(IAtomContainer container, IAtomContainer ac, boolean b)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.setAntiFlags(IAtomContainer container, IAtomContainer ac, int number, boolean b)
focal_class.full_signature: private IAtomContainer setAntiFlags(IAtomContainer container, IAtomContainer ac, int number, boolean b)
focal_class.identifier: setAntiFlags
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer container, IAtomContainer ac, int number, boolean b)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer setAntiFlags(IAtomContainer container, IAtomContainer ac, int number, boolean b)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getHyperconjugationInteractions(IAtomContainer ac, IAtomContainerSet iSet)
focal_class.full_signature: private IAtomContainerSet getHyperconjugationInteractions(IAtomContainer ac, IAtomContainerSet iSet)
focal_class.identifier: getHyperconjugationInteractions
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac, IAtomContainerSet iSet)
focal_class.return: IAtomContainerSet
focal_class.signature: IAtomContainerSet getHyperconjugationInteractions(IAtomContainer ac, IAtomContainerSet iSet)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getElectrostaticPotentialN(IAtomContainer ac, int atom1, double[] ds)
focal_class.full_signature: private double getElectrostaticPotentialN(IAtomContainer ac, int atom1, double[] ds)
focal_class.identifier: getElectrostaticPotentialN
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac, int atom1, double[] ds)
focal_class.return: double
focal_class.signature: double getElectrostaticPotentialN(IAtomContainer ac, int atom1, double[] ds)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getTopologicalFactors(IAtomContainer atomContainer, IAtomContainer ac)
focal_class.full_signature: private double getTopologicalFactors(IAtomContainer atomContainer, IAtomContainer ac)
focal_class.identifier: getTopologicalFactors
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer atomContainer, IAtomContainer ac)
focal_class.return: double
focal_class.signature: double getTopologicalFactors(IAtomContainer atomContainer, IAtomContainer ac)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.getStepSize()
focal_class.full_signature: public int getStepSize()
focal_class.identifier: getStepSize
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: int
focal_class.signature: int getStepSize()
focal_class.class_method_signature: GasteigerPEPEPartialCharges.setStepSize(int step)
focal_class.full_signature: public void setStepSize(int step)
focal_class.identifier: setStepSize
focal_class.modifiers: public
focal_class.parameters: (int step)
focal_class.return: void
focal_class.signature: void setStepSize(int step)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.assignPiFactors(IAtomContainerSet setAc)
focal_class.full_signature: private double[][] assignPiFactors(IAtomContainerSet setAc)
focal_class.identifier: assignPiFactors
focal_class.modifiers: private
focal_class.parameters: (IAtomContainerSet setAc)
focal_class.return: double[][]
focal_class.signature: double[][] assignPiFactors(IAtomContainerSet setAc)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)
focal_class.full_signature: public double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)
focal_class.identifier: assignrPiMarsilliFactors
focal_class.modifiers: public
focal_class.parameters: (IAtomContainerSet setAc)
focal_class.return: double[][]
focal_class.signature: double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)
focal_class.class_method_signature: GasteigerPEPEPartialCharges.cleanFlagReactiveCenter(IAtomContainer ac)
focal_class.full_signature: private void cleanFlagReactiveCenter(IAtomContainer ac)
focal_class.identifier: cleanFlagReactiveCenter
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac)
focal_class.return: void
focal_class.signature: void cleanFlagReactiveCenter(IAtomContainer ac)
focal_method.body: public double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc) {
          //a,b,c,denom,chi,q
          double[][] gasteigerFactors = new double[setAc.getAtomContainerCount()][(setAc.getAtomContainer(0)
                  .getAtomCount() * (STEP_SIZE + 1))];
          String AtomSymbol = "";
          double[] factors = new double[]{0.0, 0.0, 0.0};
          for (int k = 1; k < setAc.getAtomContainerCount(); k++) {
              IAtomContainer ac = setAc.getAtomContainer(k);
  
              for (int i = 0; i < ac.getAtomCount(); i++) {
                  factors[0] = 0.0;
                  factors[1] = 0.0;
                  factors[2] = 0.0;
                  AtomSymbol = ac.getAtom(i).getSymbol();
                  if (AtomSymbol.equals("H")) {
                      factors[0] = 0.0;
                      factors[1] = 0.0;
                      factors[2] = 0.0;
                  } else if (AtomSymbol.equals("C")) {
                      factors[0] = 5.98;/* 5.98-5.60 */
                      factors[1] = 7.93;/* 7.93-8.93 */
                      factors[2] = 1.94;
                  } else if (AtomSymbol.equals("O")) {
                      if (ac.getMaximumBondOrder(ac.getAtom(i)) != IBond.Order.SINGLE) {
                          factors[0] = 11.2;/* 11.2-10.0 */
                          factors[1] = 13.24;/* 13.24-13.86 */
                          factors[2] = 9.68;
                      } else {
                          factors[0] = 7.91;
                          factors[1] = 14.76;
                          factors[2] = 6.85;
                      }
                  } else if (AtomSymbol.equals("N")) {
                      if (ac.getMaximumBondOrder(ac.getAtom(i)) != IBond.Order.SINGLE) {
  
                          factors[0] = 8.95;/* 7.95 */
                          factors[1] = 9.73;/* 9.73 */
                          factors[2] = 2.67;/* 2.67 */
                      } else {
                          factors[0] = 4.54;
                          factors[1] = 11.86;
                          factors[2] = 7.32;
                      }
                  } else if (AtomSymbol.equals("P")) {// <--No correct
                      if (ac.getMaximumBondOrder(ac.getAtom(i)) != IBond.Order.SINGLE) {
                          factors[0] = 10.73;// <--No correct
                          factors[1] = 11.16;// <--No correct
                          factors[2] = 6.81;// <--No correct
                      } else {
                          factors[0] = 9.60;// <--No correct
                          factors[1] = 13.32;// <--No correct
                          factors[2] = 2.72;// <--No correct
                      }
                  } else if (AtomSymbol.equals("S")) {
                      if (ac.getMaximumBondOrder(ac.getAtom(i)) != IBond.Order.SINGLE) {
  
                          factors[0] = 7.73;
                          factors[1] = 8.16;
                          factors[2] = 1.81;
                      } else {
                          factors[0] = 6.60;
                          factors[1] = 10.32;
                          factors[2] = 3.72;
                      }
                  } else if (AtomSymbol.equals("F")) {
                      factors[0] = 7.14/* 7.34 */;
                      factors[1] = 13.86;
                      factors[2] = 5.68;
                  } else if (AtomSymbol.equals("Cl")) {
                      factors[0] = 6.51;/* 6.50 */
                      factors[1] = 11.02;
                      factors[2] = 4.52;
                  } else if (AtomSymbol.equals("Br")) {
                      factors[0] = 5.20;
                      factors[1] = 9.68;
                      factors[2] = 4.48;
                  } else if (AtomSymbol.equals("I")) {
                      factors[0] = 4.95;
                      factors[1] = 8.81;
                      factors[2] = 3.86;
                  }
  
                  gasteigerFactors[k][STEP_SIZE * i + i] = factors[0];
                  gasteigerFactors[k][STEP_SIZE * i + i + 1] = factors[1];
                  gasteigerFactors[k][STEP_SIZE * i + i + 2] = factors[2];
                  gasteigerFactors[k][STEP_SIZE * i + i + 5] = ac.getAtom(i).getCharge();
  
                  if (factors[0] == 0 && factors[1] == 0 && factors[2] == 0) {
                      gasteigerFactors[k][STEP_SIZE * i + i + 3] = 1;
                  } else {
                      gasteigerFactors[k][STEP_SIZE * i + i + 3] = factors[0] + factors[1] + factors[2];
                  }
              }
          }
  
          return gasteigerFactors;
      }
focal_method.class_method_signature: GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)
focal_method.full_signature: public double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)
focal_method.identifier: assignrPiMarsilliFactors
focal_method.invocations: getAtomContainerCount getAtomCount getAtomContainer getAtomContainerCount getAtomContainer getAtomCount getSymbol getAtom equals equals equals getMaximumBondOrder getAtom equals getMaximumBondOrder getAtom equals getMaximumBondOrder getAtom equals getMaximumBondOrder getAtom equals equals equals equals getCharge getAtom
focal_method.modifiers: public
focal_method.parameters: (IAtomContainerSet setAc)
focal_method.return: double[][]
focal_method.signature: double[][] assignrPiMarsilliFactors(IAtomContainerSet setAc)