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/GasteigerMarsiliPartialChargesTest.java
test_class.identifier: GasteigerMarsiliPartialChargesTest
test_class.superclass: extends CDKTestCase
test_case.body: @Test
      public void testCalculateCharges_IAtomContainer() throws Exception {
          double[] testResult = {0.07915, -0.25264, 0.05783, 0.05783, 0.05783};
  
          GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
  
          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);
  
          peoe.calculateCharges(molecule);
          for (int i = 0; i < molecule.getAtomCount(); i++) {
              //logger.debug("Charge for atom:"+i+" S:"+mol.getAtomAt(i).getSymbol()+" Charge:"+mol.getAtomAt(i).getCharge());
              Assert.assertEquals(testResult[i], molecule.getAtom(i).getCharge(), 0.01);
          }
      }
test_case.class_method_signature: GasteigerMarsiliPartialChargesTest.testCalculateCharges_IAtomContainer()
test_case.full_signature: @Test public void testCalculateCharges_IAtomContainer()
test_case.identifier: testCalculateCharges_IAtomContainer
test_case.invocations: newInstance addAtom addAtom addBond addExplicitHydrogens percieveAtomTypesAndConfigureAtoms saturate calculateCharges getAtomCount assertEquals getCharge getAtom
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testCalculateCharges_IAtomContainer()
focal_class.declarator: DEOC_HYDROGEN = 20.02
focal_class.modifier: private
focal_class.original_string: private double DEOC_HYDROGEN = 20.02;
focal_class.type: double
focal_class.var_name: DEOC_HYDROGEN
focal_class.declarator: MX_DAMP       = 0.5
focal_class.modifier: private
focal_class.original_string: private double MX_DAMP       = 0.5;
focal_class.type: double
focal_class.var_name: MX_DAMP
focal_class.declarator: MX_ITERATIONS = 20
focal_class.modifier: private
focal_class.original_string: private double MX_ITERATIONS = 20;
focal_class.type: double
focal_class.var_name: MX_ITERATIONS
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.file: tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
focal_class.identifier: GasteigerMarsiliPartialCharges
focal_class.interfaces: implements IChargeCalculator
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.GasteigerMarsiliPartialCharges()
focal_class.full_signature: public  GasteigerMarsiliPartialCharges()
focal_class.identifier: GasteigerMarsiliPartialCharges
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  GasteigerMarsiliPartialCharges()
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.setChiCatHydrogen(double chiCat)
focal_class.full_signature: public void setChiCatHydrogen(double chiCat)
focal_class.identifier: setChiCatHydrogen
focal_class.modifiers: public
focal_class.parameters: (double chiCat)
focal_class.return: void
focal_class.signature: void setChiCatHydrogen(double chiCat)
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.setMaxGasteigerDamp(double damp)
focal_class.full_signature: public void setMaxGasteigerDamp(double damp)
focal_class.identifier: setMaxGasteigerDamp
focal_class.modifiers: public
focal_class.parameters: (double damp)
focal_class.return: void
focal_class.signature: void setMaxGasteigerDamp(double damp)
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.setMaxGasteigerIters(double iters)
focal_class.full_signature: public void setMaxGasteigerIters(double iters)
focal_class.identifier: setMaxGasteigerIters
focal_class.modifiers: public
focal_class.parameters: (double iters)
focal_class.return: void
focal_class.signature: void setMaxGasteigerIters(double iters)
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.getChiCatHydrogen()
focal_class.full_signature: public double getChiCatHydrogen()
focal_class.identifier: getChiCatHydrogen
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getChiCatHydrogen()
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.getMaxGasteigerDamp()
focal_class.full_signature: public double getMaxGasteigerDamp()
focal_class.identifier: getMaxGasteigerDamp
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getMaxGasteigerDamp()
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.getMaxGasteigerIters()
focal_class.full_signature: public double getMaxGasteigerIters()
focal_class.identifier: getMaxGasteigerIters
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: double
focal_class.signature: double getMaxGasteigerIters()
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.full_signature: public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.identifier: assignGasteigerMarsiliSigmaPartialCharges
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac, boolean setCharge)
focal_class.return: IAtomContainer
focal_class.signature: IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge)
focal_class.class_method_signature: GasteigerMarsiliPartialCharges.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: GasteigerMarsiliPartialCharges.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: GasteigerMarsiliPartialCharges.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: GasteigerMarsiliPartialCharges.assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
focal_class.full_signature: public double[] assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
focal_class.identifier: assignGasteigerSigmaMarsiliFactors
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer ac)
focal_class.return: double[]
focal_class.signature: double[] assignGasteigerSigmaMarsiliFactors(IAtomContainer ac)
focal_method.body: @Override
      public void calculateCharges(IAtomContainer container) throws CDKException {
          try {
              this.assignGasteigerMarsiliSigmaPartialCharges(container, true);
          } catch (Exception exception) {
              throw new CDKException("Could not calculate Gasteiger-Marsili sigma charges: " + exception.getMessage(),
                      exception);
          }
      }
focal_method.class_method_signature: GasteigerMarsiliPartialCharges.calculateCharges(IAtomContainer container)
focal_method.full_signature: @Override public void calculateCharges(IAtomContainer container)
focal_method.identifier: calculateCharges
focal_method.invocations: assignGasteigerMarsiliSigmaPartialCharges getMessage
focal_method.modifiers: @Override public
focal_method.parameters: (IAtomContainer container)
focal_method.return: void
focal_method.signature: void calculateCharges(IAtomContainer container)