| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/config/atomtypes/ |
| H A D | OWLAtomTypeHandlerTest.java | 48 Assert.assertNull(handler.getAtomTypes()); in testGetAtomTypes()
56 Assert.assertNull(handler.getAtomTypes()); in testStartDocument()
|
| H A D | AtomTypeHandlerTest.java | 49 Assert.assertNull(handler.getAtomTypes()); in testGetAtomTypes()
57 Assert.assertNull(handler.getAtomTypes()); in testStartDocument()
|
| /dports/science/cdk/cdk-cdk-2.3/base/valencycheck/src/main/java/org/openscience/cdk/tools/ |
| H A D | SaturationChecker.java | 88 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in hasPerfectConfiguration()
163 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in isSaturated()
196 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in isOverSaturated()
227 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in getCurrentMaxBondOrder()
378 … IAtomType[] atomTypes1 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(atom.getSymbol()); in newSaturate()
379 … IAtomType[] atomTypes2 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(partner.getSymbol()); in newSaturate()
448 atomTypes1 = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in saturate()
460 … atomTypes2 = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(partner.getSymbol()); in saturate()
492 … atomTypes2 = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(partner.getSymbol()); in saturate()
619 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in calculateNumberOfImplicitHydrogens()
|
| H A D | SmilesValencyChecker.java | 169 … IAtomType[] atomTypes1 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(atom.getSymbol()); in saturateByIncreasingBondOrder()
170 … IAtomType[] atomTypes2 = getAtomTypeFactory(bond.getBuilder()).getAtomTypes(partner.getSymbol()); in saturateByIncreasingBondOrder()
274 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in calculateNumberOfImplicitHydrogens()
316 … IAtomType[] atomTypes = getAtomTypeFactory(atom.getBuilder()).getAtomTypes(atom.getSymbol()); in isSaturated()
|
| /dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/ |
| H A D | ForceFieldConfiguratorTest.java | 74 List<IAtomType> mmff94AtomTypes = forceFieldConfigurator.getAtomTypes(); in testSetForceFieldConfigurator_String()
83 List<IAtomType> mm2AtomTypes = forceFieldConfigurator.getAtomTypes(); in testSetForceFieldConfigurator_String()
96 List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes(); in testSetMM2Parameters()
107 List<IAtomType> atomtypeList = forceFieldConfigurator.getAtomTypes(); in testSetMMFF94Parameters()
|
| H A D | MMFF94BasedParameterSetReaderTest.java | 56 List<IAtomType> atomtypes = mmff94bpsr.getAtomTypes(); in testreadParameterSets()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/JavaWrappers/ |
| H A D | ForceField.i | 98 boost::tie(types,foundAll)=RDKit::UFF::getAtomTypes(mol); in UFFHasAllMoleculeParams()
113 return RDKit::UFF::getAtomTypes(mol, paramData);
|
| /dports/science/jmol/jmol-14.32.7/src/org/jmol/adapter/readers/more/ |
| H A D | MdTopReader.java | 82 getAtomTypes(); in checkLine()
213 private void getAtomTypes() throws Exception { in getAtomTypes() method in MdTopReader
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ForceFieldHelpers/UFF/ |
| H A D | AtomTyper.h | 30 RDKIT_FORCEFIELDHELPERS_EXPORT std::pair<AtomicParamVect, bool> getAtomTypes(
|
| H A D | testUFFHelpers.cpp | 151 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testUFFTyper2()
160 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2); in testUFFTyper2()
225 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testUFFBuilder1()
270 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testUFFBuilder1()
302 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testUFFBuilder1()
331 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2); in testUFFBuilder1()
483 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testUFFBuilder2()
941 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testSFIssue1653802()
1050 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol2); in testMissingParams()
1386 boost::tie(types, foundAll) = UFF::getAtomTypes(*mol); in testGitHubIssue613()
|
| H A D | AtomTyper.cpp | 393 std::pair<AtomicParamVect, bool> getAtomTypes(const ROMol &mol, in getAtomTypes() function
|
| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/ |
| H A D | AtomTypeFactory.java | 280 public IAtomType[] getAtomTypes(String symbol) { in getAtomTypes() method in AtomTypeFactory
326 IAtomType[] types = getAtomTypes(atom.getSymbol()); in configure()
|
| /dports/science/cdk/cdk-cdk-2.3/tool/structgen/src/main/java/org/openscience/cdk/atomtype/ |
| H A D | StructGenAtomTypeGuesser.java | 85 IAtomType[] types = factory.getAtomTypes(atom.getSymbol()); in possibleAtomTypes()
|
| H A D | StructGenMatcher.java | 92 IAtomType[] types = factory.getAtomTypes(atom.getSymbol()); in findMatchingAtomType()
|
| /dports/science/cdk/cdk-cdk-2.3/base/core/src/main/java/org/openscience/cdk/config/atomtypes/ |
| H A D | OWLAtomTypeReader.java | 116 isotopes = handler.getAtomTypes(); in readAtomTypes()
|
| H A D | AtomTypeReader.java | 130 isotopes = handler.getAtomTypes(); in readAtomTypes()
|
| H A D | OWLAtomTypeHandler.java | 70 public List<IAtomType> getAtomTypes() { in getAtomTypes() method in OWLAtomTypeHandler
|
| H A D | AtomTypeHandler.java | 84 public List<IAtomType> getAtomTypes() { in getAtomTypes() method in AtomTypeHandler
|
| /dports/science/jmol/jmol-14.32.7/src/org/jmol/minimize/forcefield/ |
| H A D | ForceFieldUFF.java | 77 if (ffParams == null || atomTypes == null && (atomTypes = getAtomTypes()) == null) in setModel()
272 private Lst<String[]> getAtomTypes() throws JmolAsyncException { in getAtomTypes() method in ForceFieldUFF
|
| /dports/science/cdk/cdk-cdk-2.3/misc/extra/src/main/java/org/openscience/cdk/validate/ |
| H A D | BasicValidator.java | 229 IAtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol()); in validateMaxBondOrder()
299 IAtomType[] atomTypes = structgenATF.getAtomTypes(atom.getSymbol()); in validateBondOrderSum()
|
| /dports/science/cdk/cdk-cdk-2.3/tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ |
| H A D | ForceFieldConfigurator.java | 193 atomTypes = mm2.getAtomTypes(); in setMM2Parameters()
200 atomTypes = mmff94.getAtomTypes(); in setMMFF94Parameters()
208 public List<IAtomType> getAtomTypes() { in getAtomTypes() method in ForceFieldConfigurator
|
| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/atomtype/ |
| H A D | MM2AtomTypeMatcher.java | 126 return factory.getAtomTypes("DU")[0]; in findMatchingAtomType()
|
| H A D | MMFF94AtomTypeMatcher.java | 123 return factory.getAtomTypes("DU")[0]; in findMatchingAtomType()
|
| /dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ForceFieldHelpers/Wrap/ |
| H A D | rdForceFields.cpp | 102 boost::tie(types, foundAll) = UFF::getAtomTypes(mol); in UFFHasAllMoleculeParams()
|
| /dports/science/cdk/cdk-cdk-2.3/base/test-core/src/test/java/org/openscience/cdk/config/ |
| H A D | AtomTypeFactoryTest.java | 133 IAtomType[] atomTypes = atf.getAtomTypes("C"); in testGetAtomTypes_String()
|