/dports/science/py-pymol/pymol-open-source-2.4.0/test/inp/ |
H A D | C0800matrices.pml | 25 load dat/pept.pdb, mol3 33 dump_mat(cmd.get_object_matrix("mol3")) 45 dump_mat(cmd.get_object_matrix("mol3")) 59 dump_mat(cmd.get_object_matrix("mol3")) 64 dele mol3 65 load dat/pept.pdb,mol3 73 dump_mat(cmd.get_object_matrix("mol3")) 78 matrix_transfer mol1, mol3 82 dump_mat(cmd.get_object_matrix("mol3")) 91 matrix_transfer mol2, mol3 [all …]
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | spacegrouptest.cpp | 378 Molecule mol3; in TEST() local 386 mol3.setUnitCell(uc3); in TEST() 400 mol3.addAtom(8).setPosition3d( in TEST() 402 mol3.addAtom(8).setPosition3d( in TEST() 404 mol3.addAtom(8).setPosition3d( in TEST() 406 mol3.addAtom(8).setPosition3d( in TEST() 408 mol3.addAtom(8).setPosition3d( in TEST() 410 mol3.addAtom(8).setPosition3d( in TEST() 412 mol3.addAtom(8).setPosition3d( in TEST() 414 mol3.addAtom(8).setPosition3d( in TEST() [all …]
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/ |
H A D | spacegrouptest.cpp | 378 Molecule mol3; in TEST() local 386 mol3.setUnitCell(uc3); in TEST() 400 mol3.addAtom(8).setPosition3d( in TEST() 402 mol3.addAtom(8).setPosition3d( in TEST() 404 mol3.addAtom(8).setPosition3d( in TEST() 406 mol3.addAtom(8).setPosition3d( in TEST() 408 mol3.addAtom(8).setPosition3d( in TEST() 410 mol3.addAtom(8).setPosition3d( in TEST() 412 mol3.addAtom(8).setPosition3d( in TEST() 414 mol3.addAtom(8).setPosition3d( in TEST() [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ |
H A D | StabilizationPlusChargeDescriptorTest.java | 172 IAtomContainer mol3 = builder.newInstance(IAtomContainer.class); in testStabilizationComparative() local 173 mol3.addAtom(builder.newInstance(IAtom.class, "C")); in testStabilizationComparative() 174 mol3.addAtom(builder.newInstance(IAtom.class, "C")); in testStabilizationComparative() 175 mol3.getAtom(1).setFormalCharge(1); in testStabilizationComparative() 176 mol3.addBond(0, 1, Order.SINGLE); in testStabilizationComparative() 177 mol3.addAtom(builder.newInstance(IAtom.class, "C")); in testStabilizationComparative() 178 mol3.addBond(1, 2, Order.SINGLE); in testStabilizationComparative() 179 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol3); in testStabilizationComparative() 180 addExplicitHydrogens(mol3); in testStabilizationComparative() 181 lpcheck.saturate(mol3); in testStabilizationComparative() [all …]
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ |
H A D | MACCSFingerprinterTest.java | 67 IAtomContainer mol3 = parser.parseSmiles("CCC.CCC"); in testFingerprint() local 71 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol3); in testFingerprint() 74 Aromaticity.cdkLegacy().apply(mol3); in testFingerprint() 78 BitSet bs3 = printer.getBitFingerprint(mol3).asBitSet(); in testFingerprint() 99 IAtomContainer mol3 = parser.parseSmiles("CCCC"); in testfp2() local 103 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol3); in testfp2() 107 Aromaticity.cdkLegacy().apply(mol3); in testfp2() 111 BitSet bs3 = printer.getBitFingerprint(mol3).asBitSet(); in testfp2()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/C++Examples/ |
H A D | example4.cpp | 33 std::shared_ptr<RDKit::ROMol> mol3( RDKit::MolOps::addHs( *mol2 ) ); in main() local 34 RDKit::MMFF::MMFFOptimizeMolecule( *mol3 , 1000 , "MMFF94s" ); in main() 35 std::cout << RDKit::MolToMolBlock( *mol3 ) << std::endl; in main() 37 std::shared_ptr<RDKit::RWMol> mol4( new RDKit::RWMol( *mol3 ) ); in main() 46 std::shared_ptr<RDKit::ROMol> mol5( RDKit::MolOps::removeHs( *mol3 ) ); in main()
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H A D | example8.cpp | 17 std::shared_ptr<RDKit::RWMol> mol3( new RDKit::RWMol( *mol2 ) ); in main() local 18 RDKit::MolOps::removeHs( *mol3 ); in main() 19 std::cout << "Number of atoms : " << mol3->getNumAtoms() << std::endl; in main()
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H A D | example14.cpp | 45 std::shared_ptr<RDKit::ROMol> mol3( mol_supplier.next() ); in main() local 46 if( mol3 && RDKit::SubstructMatch( *mol3 , *patt1 , res ) ) { in main() 47 matches.push_back( mol3 ); in main()
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H A D | example12.cpp | 46 RDKit::ROMol mol3; in main() local 48 RDKit::MolPickler::molFromPickle( pickle_istream , mol3 ); in main() 55 << mol3.getProp<std::string>("_Name") << std::endl; in main()
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H A D | example3.cpp | 27 std::shared_ptr<RDKit::ROMol> mol3(RDKit::SmilesToMol("n1ccccc1")); in main() local 28 std::cout << RDKit::MolToSmiles(*mol3) << std::endl; in main()
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/dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/mdl/ |
H A D | iterconftest.sdf | 1234 mol3 1299 mol3 1364 mol3 1429 mol3 1494 mol3 1559 mol3 1624 mol3 1689 mol3 1754 mol3 1819 mol3 [all …]
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ |
H A D | cptest.cpp | 128 RWMol mol3(mol2); in testGithub2144() 129 TEST_ASSERT(mol2.getNumBonds() == mol3.getNumBonds()) in testGithub2144() 130 TEST_ASSERT(mol2.getNumAtoms() == mol3.getNumAtoms()) in testGithub2144()
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H A D | test-valgrind.cpp | 70 RDKit::RWMol mol3; in testCopyConstructor() local 71 mol3 = mol2; in testCopyConstructor()
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/ |
H A D | Dumper.t | 16 my $mol3 = Chemistry::Mol->read("t/test1.pl"); 20 is_deeply($mol, $mol3, 'deep compare');
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/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/ |
H A D | Dumper.t | 16 my $mol3 = Chemistry::Mol->read("t/test1.pl"); 20 is_deeply($mol, $mol3, 'deep compare');
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/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_nylon/ |
H A D | in.tiny_nylon.unstabilized | 28 molecule mol3 rxn1_stp2_unreacted.data_template 37 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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H A D | in.tiny_nylon.stabilized | 28 molecule mol3 rxn1_stp2_unreacted.data_template 37 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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H A D | in.tiny_nylon.stabilized_variable_probability | 32 molecule mol3 rxn1_stp2_unreacted.data_template 41 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/ |
H A D | testChemTransforms.cpp | 1250 ROMol *mol3 = combineMols(*mol1, *mol2); in testCombineMols() local 1251 TEST_ASSERT(mol3->getNumAtoms() == in testCombineMols() 1253 MolOps::findSSSR(*mol3); in testCombineMols() 1257 delete mol3; in testCombineMols() 1268 ROMol *mol3 = combineMols(*mol1, *mol2); in testCombineMols() local 1269 TEST_ASSERT(mol3->getNumAtoms() == in testCombineMols() 1271 TEST_ASSERT(mol3->getNumConformers() == 1); in testCombineMols() 1279 delete mol3; in testCombineMols() 1281 TEST_ASSERT(mol3->getNumAtoms() == in testCombineMols() 1283 TEST_ASSERT(mol3->getNumConformers() == 1); in testCombineMols() [all …]
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/dports/science/py-pyscf/pyscf-2.0.1/examples/mcscf/ |
H A D | 14-project_init_guess.py | 63 mol3 = gto.M( variable 67 mf = scf.RHF(mol3)
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/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/nylon,6-6_melt/ |
H A D | in.large_nylon_melt | 27 molecule mol3 rxn1_stp2_unreacted.data_template 36 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
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/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_epoxy/ |
H A D | in.tiny_epoxy.stabilized | 26 molecule mol3 rxn1_stp2_post.data_template 37 react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map &
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/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_polystyrene/ |
H A D | in.tiny_polystyrene.stabilized | 33 molecule mol3 chain_plus_styrene_unreacted.data_template 44 react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 &
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/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/example02/ |
H A D | run_example | 210 cat > h2o-mol3.in << EOF 272 $FPMD_COMMAND < h2o-mol3.in > h2o-mol3.out
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/dports/science/py-pyscf/pyscf-2.0.1/pyscf/gto/ |
H A D | mole.py | 682 mol3 = Mole() 683 mol3._built = True 685 mol3._atm, mol3._bas, mol3._env = \ 702 mol3.verbose = mol1.verbose 703 mol3.output = mol1.output 707 mol3.symmetry = False 712 mol3.atom = mol3._atom 713 mol3.unit = 'Bohr' 721 mol3.basis = mol3._basis 722 mol3.ecp = mol3._ecp [all …]
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