test_class.declarator: forceFieldConfigurator = new ForceFieldConfigurator()
test_class.original_string: ForceFieldConfigurator forceFieldConfigurator = new ForceFieldConfigurator();
test_class.type: ForceFieldConfigurator
test_class.var_name: forceFieldConfigurator
test_class.file: tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java
test_class.identifier: ForceFieldConfiguratorTest
test_case.body: @Test
      public void testSetMMFF94Parameters() throws Exception {
          forceFieldConfigurator.setMMFF94Parameters(DefaultChemObjectBuilder.getInstance());
          assertNotNull(forceFieldConfigurator.getParameterSet());
          List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes();
          IAtomType atomtype4 = atomtypeList.get(4);
          assertEquals("CO2M", atomtype4.getAtomTypeName());
          assertEquals(6, (int) atomtype4.getAtomicNumber());
          assertEquals(3, (int) atomtype4.getFormalNeighbourCount());
          assertEquals(12, (int) atomtype4.getMassNumber());
  
      }
test_case.class_method_signature: ForceFieldConfiguratorTest.testSetMMFF94Parameters()
test_case.full_signature: @Test public void testSetMMFF94Parameters()
test_case.identifier: testSetMMFF94Parameters
test_case.invocations: setMMFF94Parameters getInstance assertNotNull getParameterSet getAtomTypes get assertEquals getAtomTypeName assertEquals getAtomicNumber assertEquals getFormalNeighbourCount assertEquals getMassNumber
test_case.modifiers: @Test public
test_case.parameters: ()
test_case.return: void
test_case.signature: void testSetMMFF94Parameters()
focal_class.declarator: ffName       = "mmff94"
focal_class.modifier: private
focal_class.original_string: private String                        ffName       = "mmff94";
focal_class.type: String
focal_class.var_name: ffName
focal_class.declarator: atomTypes
focal_class.modifier: private
focal_class.original_string: private List<IAtomType>               atomTypes;
focal_class.type: List<IAtomType>
focal_class.var_name: atomTypes
focal_class.declarator: parameterSet = null
focal_class.modifier: private
focal_class.original_string: private Map<String, Object>           parameterSet = null;
focal_class.type: Map<String, Object>
focal_class.var_name: parameterSet
focal_class.declarator: mm2          = null
focal_class.modifier: private
focal_class.original_string: private MM2BasedParameterSetReader    mm2          = null;
focal_class.type: MM2BasedParameterSetReader
focal_class.var_name: mm2
focal_class.declarator: mmff94       = null
focal_class.modifier: private
focal_class.original_string: private MMFF94BasedParameterSetReader mmff94       = null;
focal_class.type: MMFF94BasedParameterSetReader
focal_class.var_name: mmff94
focal_class.declarator: ins          = null
focal_class.modifier: private
focal_class.original_string: private InputStream                   ins          = null;
focal_class.type: InputStream
focal_class.var_name: ins
focal_class.declarator: fftypes      = {"mm2", "mmff94"}
focal_class.modifier: private
focal_class.original_string: private String[]                      fftypes      = {"mm2", "mmff94"};
focal_class.type: String[]
focal_class.var_name: fftypes
focal_class.file: tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
focal_class.identifier: ForceFieldConfigurator
focal_class.class_method_signature: ForceFieldConfigurator.ForceFieldConfigurator()
focal_class.full_signature: public  ForceFieldConfigurator()
focal_class.identifier: ForceFieldConfigurator
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.signature:  ForceFieldConfigurator()
focal_class.class_method_signature: ForceFieldConfigurator.setInputStream(InputStream ins)
focal_class.full_signature: public void setInputStream(InputStream ins)
focal_class.identifier: setInputStream
focal_class.modifiers: public
focal_class.parameters: (InputStream ins)
focal_class.return: void
focal_class.signature: void setInputStream(InputStream ins)
focal_class.class_method_signature: ForceFieldConfigurator.getFfTypes()
focal_class.full_signature: public String[] getFfTypes()
focal_class.identifier: getFfTypes
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: String[]
focal_class.signature: String[] getFfTypes()
focal_class.class_method_signature: ForceFieldConfigurator.checkForceFieldType(String ffname)
focal_class.full_signature: public boolean checkForceFieldType(String ffname)
focal_class.identifier: checkForceFieldType
focal_class.modifiers: public
focal_class.parameters: (String ffname)
focal_class.return: boolean
focal_class.signature: boolean checkForceFieldType(String ffname)
focal_class.class_method_signature: ForceFieldConfigurator.setForceFieldConfigurator(String ffname, IChemObjectBuilder builder)
focal_class.full_signature: public void setForceFieldConfigurator(String ffname, IChemObjectBuilder builder)
focal_class.identifier: setForceFieldConfigurator
focal_class.modifiers: public
focal_class.parameters: (String ffname, IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void setForceFieldConfigurator(String ffname, IChemObjectBuilder builder)
focal_class.class_method_signature: ForceFieldConfigurator.setAtomTypes(List<IAtomType> atomtypes)
focal_class.full_signature: public void setAtomTypes(List<IAtomType> atomtypes)
focal_class.identifier: setAtomTypes
focal_class.modifiers: public
focal_class.parameters: (List<IAtomType> atomtypes)
focal_class.return: void
focal_class.signature: void setAtomTypes(List<IAtomType> atomtypes)
focal_class.class_method_signature: ForceFieldConfigurator.setParameters(Map<String, Object> parameterset)
focal_class.full_signature: public void setParameters(Map<String, Object> parameterset)
focal_class.identifier: setParameters
focal_class.modifiers: public
focal_class.parameters: (Map<String, Object> parameterset)
focal_class.return: void
focal_class.signature: void setParameters(Map<String, Object> parameterset)
focal_class.class_method_signature: ForceFieldConfigurator.setMM2Parameters(IChemObjectBuilder builder)
focal_class.full_signature: public void setMM2Parameters(IChemObjectBuilder builder)
focal_class.identifier: setMM2Parameters
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void setMM2Parameters(IChemObjectBuilder builder)
focal_class.class_method_signature: ForceFieldConfigurator.setMMFF94Parameters(IChemObjectBuilder builder)
focal_class.full_signature: public void setMMFF94Parameters(IChemObjectBuilder builder)
focal_class.identifier: setMMFF94Parameters
focal_class.modifiers: public
focal_class.parameters: (IChemObjectBuilder builder)
focal_class.return: void
focal_class.signature: void setMMFF94Parameters(IChemObjectBuilder builder)
focal_class.class_method_signature: ForceFieldConfigurator.getAtomTypes()
focal_class.full_signature: public List<IAtomType> getAtomTypes()
focal_class.identifier: getAtomTypes
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: List<IAtomType>
focal_class.signature: List<IAtomType> getAtomTypes()
focal_class.class_method_signature: ForceFieldConfigurator.getParameterSet()
focal_class.full_signature: public Map<String, Object> getParameterSet()
focal_class.identifier: getParameterSet
focal_class.modifiers: public
focal_class.parameters: ()
focal_class.return: Map<String, Object>
focal_class.signature: Map<String, Object> getParameterSet()
focal_class.class_method_signature: ForceFieldConfigurator.getAtomType(String ID)
focal_class.full_signature: private IAtomType getAtomType(String ID)
focal_class.identifier: getAtomType
focal_class.modifiers: private
focal_class.parameters: (String ID)
focal_class.return: IAtomType
focal_class.signature: IAtomType getAtomType(String ID)
focal_class.class_method_signature: ForceFieldConfigurator.assignAtomTyps(IAtomContainer molecule)
focal_class.full_signature: public IRingSet assignAtomTyps(IAtomContainer molecule)
focal_class.identifier: assignAtomTyps
focal_class.modifiers: public
focal_class.parameters: (IAtomContainer molecule)
focal_class.return: IRingSet
focal_class.signature: IRingSet assignAtomTyps(IAtomContainer molecule)
focal_class.class_method_signature: ForceFieldConfigurator.isHeteroRingSystem(IAtomContainer ac)
focal_class.full_signature: private boolean isHeteroRingSystem(IAtomContainer ac)
focal_class.identifier: isHeteroRingSystem
focal_class.modifiers: private
focal_class.parameters: (IAtomContainer ac)
focal_class.return: boolean
focal_class.signature: boolean isHeteroRingSystem(IAtomContainer ac)
focal_class.class_method_signature: ForceFieldConfigurator.setAtom(IAtom atom, String ID)
focal_class.full_signature: private IAtom setAtom(IAtom atom, String ID)
focal_class.identifier: setAtom
focal_class.modifiers: private
focal_class.parameters: (IAtom atom, String ID)
focal_class.return: IAtom
focal_class.signature: IAtom setAtom(IAtom atom, String ID)
focal_class.class_method_signature: ForceFieldConfigurator.configureAtom(IAtom atom, String hoseCode, boolean _boolean)
focal_class.full_signature: public IAtom configureAtom(IAtom atom, String hoseCode, boolean _boolean)
focal_class.identifier: configureAtom
focal_class.modifiers: public
focal_class.parameters: (IAtom atom, String hoseCode, boolean _boolean)
focal_class.return: IAtom
focal_class.signature: IAtom configureAtom(IAtom atom, String hoseCode, boolean _boolean)
focal_class.class_method_signature: ForceFieldConfigurator.configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing)
focal_class.full_signature: public IAtom configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing)
focal_class.identifier: configureMM2BasedAtom
focal_class.modifiers: public
focal_class.parameters: (IAtom atom, String hoseCode, boolean hetRing)
focal_class.return: IAtom
focal_class.signature: IAtom configureMM2BasedAtom(IAtom atom, String hoseCode, boolean hetRing)
focal_class.class_method_signature: ForceFieldConfigurator.removeAromaticityFlagsFromHoseCode(String hoseCode)
focal_class.full_signature: public String removeAromaticityFlagsFromHoseCode(String hoseCode)
focal_class.identifier: removeAromaticityFlagsFromHoseCode
focal_class.modifiers: public
focal_class.parameters: (String hoseCode)
focal_class.return: String
focal_class.signature: String removeAromaticityFlagsFromHoseCode(String hoseCode)
focal_class.class_method_signature: ForceFieldConfigurator.configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing)
focal_class.full_signature: public IAtom configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing)
focal_class.identifier: configureMMFF94BasedAtom
focal_class.modifiers: public
focal_class.parameters: (IAtom atom, String hoseCode, boolean isInHetRing)
focal_class.return: IAtom
focal_class.signature: IAtom configureMMFF94BasedAtom(IAtom atom, String hoseCode, boolean isInHetRing)
focal_method.body: public void setMMFF94Parameters(IChemObjectBuilder builder) throws Exception {
          if (mmff94 == null) mmff94 = new MMFF94BasedParameterSetReader();
          mmff94.readParameterSets(builder);
          parameterSet = mmff94.getParamterSet();
          atomTypes = mmff94.getAtomTypes();
      }
focal_method.class_method_signature: ForceFieldConfigurator.setMMFF94Parameters(IChemObjectBuilder builder)
focal_method.full_signature: public void setMMFF94Parameters(IChemObjectBuilder builder)
focal_method.identifier: setMMFF94Parameters
focal_method.invocations: readParameterSets getParamterSet getAtomTypes
focal_method.modifiers: public
focal_method.parameters: (IChemObjectBuilder builder)
focal_method.return: void
focal_method.signature: void setMMFF94Parameters(IChemObjectBuilder builder)