| /dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/fraggle/ |
| H A D | cxn_tversky.py | 53 mol = MolHandler(smi).getMolecule()
80 mol = MolHandler(info[2]).getMolecule()
97 mol = MolHandler(dbsmi).getMolecule()
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/src/tools/ |
| H A D | csg_gmxtopol.cc | 91 if (ic->getMolecule() != cg.getId()) { in WriteInteractions()
108 err += to_string(ic->getMolecule() + 1) + ":" + ic->getGroup(); in WriteInteractions()
117 out << to_string(ic->getMolecule() + 1); in WriteInteractions()
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/src/tools/ |
| H A D | csg_gmxtopol.cc | 91 if (ic->getMolecule() != cg.getId()) { in WriteInteractions()
108 err += to_string(ic->getMolecule() + 1) + ":" + ic->getGroup(); in WriteInteractions()
117 out << to_string(ic->getMolecule() + 1); in WriteInteractions()
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| /dports/science/xtb/xtb-6.4.1/TESTSUITE/ |
| H A D | gfnff.f90 | 269 use xtb_test_molstock, only : getMolecule
314 call getMolecule(mol, mindless(iMol))
346 use xtb_test_molstock, only : getMolecule
396 call getMolecule(mol, mindless(iMol))
430 use xtb_test_molstock, only : getMolecule
474 call getMolecule(mol, trim(molecules(iMol)))
509 use xtb_test_molstock, only : getMolecule
546 call getMolecule(mol, 'pdb-4qxx')
582 use xtb_test_molstock, only : getMolecule
621 call getMolecule(mol, 'bug332')
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| H A D | gfn2.f90 | 500 use xtb_test_molstock, only : getMolecule
550 call getMolecule(mol, mindless(iMol))
583 use xtb_test_molstock, only : getMolecule
638 call getMolecule(mol, mindless(iMol))
673 use xtb_test_molstock, only : getMolecule
713 call getMolecule(mol, 'feco5')
750 use xtb_test_molstock, only : getMolecule
804 call getMolecule(mol, mindless(iMol))
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| /dports/science/jdftx/jdftx-1.6.0/fluid1D/fluid/ |
| H A D | Fex_TM_ScalarEOS.h | 51 const Molecule* getMolecule() const { return &molecule; } in getMolecule() function
64 const Molecule* getMolecule() const { return &molecule; } in getMolecule() function
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| H A D | Fex_H2O_ScalarEOS.cpp | 58 std::vector<double> ljWeights = getMolecule()->getLJweights(); in compute()
76 std::vector<double> ljWeights = getMolecule()->getLJweights(); in computeUniform()
90 std::vector<double> ljWeights = getMolecule()->getLJweights(); in directCorrelations()
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| H A D | Fex_TM_ScalarEOS.cpp | 40 std::vector<double> ljWeights = getMolecule()->getLJweights(); in compute()
58 std::vector<double> ljWeights = getMolecule()->getLJweights(); in computeUniform()
72 std::vector<double> ljWeights = getMolecule()->getLJweights(); in directCorrelations()
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| H A D | Fex.h | 40 virtual const Molecule* getMolecule() const=0;
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| H A D | Fex_H2O_BondedVoids.h | 33 const Molecule* getMolecule() const { return &molecule; } in getMolecule() function
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| H A D | Fex_H2O_FittedCorrelations.h | 32 const Molecule* getMolecule() const { return &molecule; } in getMolecule() function
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| H A D | Fex_H2O_ScalarEOS.h | 31 const Molecule* getMolecule() const { return &molecule; } in getMolecule() function
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| H A D | IdealGas.cpp | 24 : nIndep(nIndep), molecule(fex->getMolecule()), in IdealGas()
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/ |
| H A D | Isomorphism.java | 207 int rBondCount = mol1.getMolecule().getBondCount(); in mcsBuilder()
208 int pBondCount = mol2.getMolecule().getBondCount(); in mcsBuilder()
210 int rAtomCount = mol1.getMolecule().getAtomCount(); in mcsBuilder()
211 int pAtomCount = mol2.getMolecule().getAtomCount(); in mcsBuilder()
220 … setAllBondMaps(makeBondMapsOfAtomMaps(mol1.getMolecule(), mol2.getMolecule(), allAtomMCS)); in mcsBuilder()
712 return queryMol == null ? rMol.getMolecule() : queryMol; in getReactantMolecule()
719 return pAC == null ? pMol.getMolecule() : pAC; in getProductMolecule()
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/src/tests/ |
| H A D | test_lammpsdatareader.cc | 81 auto mol = top.getMolecule(0); in BOOST_AUTO_TEST_CASE()
144 auto mol = top.getMolecule(0); in BOOST_AUTO_TEST_CASE()
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| H A D | test_interaction.cc | 59 BOOST_CHECK_EQUAL(bond1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
80 BOOST_CHECK_EQUAL(angle1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
100 BOOST_CHECK_EQUAL(dihedral1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/src/tests/ |
| H A D | test_lammpsdatareader.cc | 81 auto mol = top.getMolecule(0); in BOOST_AUTO_TEST_CASE()
144 auto mol = top.getMolecule(0); in BOOST_AUTO_TEST_CASE()
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| H A D | test_interaction.cc | 59 BOOST_CHECK_EQUAL(bond1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
80 BOOST_CHECK_EQUAL(angle1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
100 BOOST_CHECK_EQUAL(dihedral1.getMolecule(), 1); in BOOST_AUTO_TEST_CASE()
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| /dports/science/coordgenlibs/coordgenlibs-3.0.0/ |
| H A D | sketcherMinimizerBond.cpp | 196 size_t totalAtomsNumber = getStartAtom()->getMolecule()->getAtoms().size(); in flip()
203 getStartAtom()->getMolecule()->getBonds(); in flip()
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| /dports/science/openbabel/openbabel-3.1.1/external/coordgen-master/coordgen/ |
| H A D | sketcherMinimizerBond.cpp | 196 size_t totalAtomsNumber = getStartAtom()->getMolecule()->getAtoms().size(); in flip()
203 getStartAtom()->getMolecule()->getBonds(); in flip()
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/ |
| H A D | MCSPlusHandler.java | 78 this.source = source.getMolecule(); in set()
79 this.target = target.getMolecule(); in set()
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/include/votca/csg/ |
| H A D | moleculeitem.h | 36 Molecule *getMolecule() const {
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| /dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/include/votca/csg/ |
| H A D | moleculeitem.h | 36 Molecule *getMolecule() const {
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| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/ |
| H A D | moleculemodelitem.h | 52 const Molecule* getMolecule();
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| /dports/science/cdk/cdk-cdk-2.3/legacy/src/main/java/org/openscience/cdk/smsd/algorithm/single/ |
| H A D | SingleMappingHandler.java | 85 this.source = source.getMolecule(); in set()
86 this.target = target.getMolecule(); in set()
|