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Searched refs:mol3 (Results 1 – 25 of 76) sorted by relevance

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/dports/science/py-pymol/pymol-open-source-2.4.0/test/inp/
H A DC0800matrices.pml25 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
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/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Dspacegrouptest.cpp378 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()
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/dports/science/avogadrolibs/avogadrolibs-1.94.0/tests/core/
H A Dspacegrouptest.cpp378 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()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/
H A DStabilizationPlusChargeDescriptorTest.java172 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()
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/dports/science/cdk/cdk-cdk-2.3/descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/
H A DMACCSFingerprinterTest.java67 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Docs/Book/C++Examples/
H A Dexample4.cpp33 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()
H A Dexample8.cpp17 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()
H A Dexample14.cpp45 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()
H A Dexample12.cpp46 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()
H A Dexample3.cpp27 std::shared_ptr<RDKit::ROMol> mol3(RDKit::SmilesToMol("n1ccccc1")); in main() local
28 std::cout << RDKit::MolToSmiles(*mol3) << std::endl; in main()
/dports/science/cdk/cdk-cdk-2.3/base/testdata/src/test/resources/data/mdl/
H A Diterconftest.sdf1234 mol3
1299 mol3
1364 mol3
1429 mol3
1494 mol3
1559 mol3
1624 mol3
1689 mol3
1754 mol3
1819 mol3
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/
H A Dcptest.cpp128 RWMol mol3(mol2); in testGithub2144()
129 TEST_ASSERT(mol2.getNumBonds() == mol3.getNumBonds()) in testGithub2144()
130 TEST_ASSERT(mol2.getNumAtoms() == mol3.getNumAtoms()) in testGithub2144()
H A Dtest-valgrind.cpp70 RDKit::RWMol mol3; in testCopyConstructor() local
71 mol3 = mol2; in testCopyConstructor()
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/
H A DDumper.t16 my $mol3 = Chemistry::Mol->read("t/test1.pl");
20 is_deeply($mol, $mol3, 'deep compare');
/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/
H A DDumper.t16 my $mol3 = Chemistry::Mol->read("t/test1.pl");
20 is_deeply($mol, $mol3, 'deep compare');
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_nylon/
H A Din.tiny_nylon.unstabilized28 molecule mol3 rxn1_stp2_unreacted.data_template
37 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
H A Din.tiny_nylon.stabilized28 molecule mol3 rxn1_stp2_unreacted.data_template
37 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
H A Din.tiny_nylon.stabilized_variable_probability32 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
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/ChemTransforms/
H A DtestChemTransforms.cpp1250 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()
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/dports/science/py-pyscf/pyscf-2.0.1/examples/mcscf/
H A D14-project_init_guess.py63 mol3 = gto.M( variable
67 mf = scf.RHF(mol3)
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/nylon,6-6_melt/
H A Din.large_nylon_melt27 molecule mol3 rxn1_stp2_unreacted.data_template
36 react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_epoxy/
H A Din.tiny_epoxy.stabilized26 molecule mol3 rxn1_stp2_post.data_template
37 react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map &
/dports/science/lammps/lammps-stable_29Sep2021/examples/PACKAGES/reaction/tiny_polystyrene/
H A Din.tiny_polystyrene.stabilized33 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 &
/dports/science/quantum-espresso/q-e-qe-6.7.0/CPV/examples/example02/
H A Drun_example210 cat > h2o-mol3.in << EOF
272 $FPMD_COMMAND < h2o-mol3.in > h2o-mol3.out
/dports/science/py-pyscf/pyscf-2.0.1/pyscf/gto/
H A Dmole.py682 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
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