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28 Mar 2024: if i and i % 10000 == 0: print('%d hits from %6d.' % (ct, i)) if not self.settings.test(e): continue try: mol = e.molecule except RuntimeError: continue donors = [a for a

28 Mar 2024: The pharmacophore query will be generated from a subset of 13 CDK2 inhibitors taken from the AZ test set, a benchmarking data set for pharmacophore programs.

28 Mar 2024: We can use the CavityDatabase API to construct a test database:. >>>

28 Mar 2024: from ccdc.utilities import _test_output_dir >>> tempdir = _test_output_dir(). Let us also get a testosterone molecule out of the CSD. >>> ... With any of these substructures, a test may be made that a particular atom matches an atom of the substructure,

28 Mar 2024: API tests are dependent on a specific CSD version being present, that may not match what the user has, may be skipped. ... There is a new method, ccdc.search.Search.Settings.test() which will determine whether anor ccdc.molecule.Molecule satisfies the

28 Mar 2024: We can test for containment in a ring:. >>> print(cemguy.atom('C1') in rings[0]) True >>> print(cemguy.bond('C6', 'C1') in rings[0]) True.

28 Mar 2024: tests', 'csp', 'testdata',. 'Axitinib_00001.CIF') >>> p=Prediction.from_cif(cif_file) >>> len(p.molecule.atoms) 46 >>> p.classification_energy_relative 0.0 >>> p.optimisation_energy_model 'Force Field' >>>

28 Mar 2024: We can't use a location relative to this file as it may have been installed to a location that is entirely separate from the test files. ''' ... is not present.''' try: _get_csd_dir_content() except RuntimeError as e: return pytest.mark.skip("Test

28 Mar 2024: of this conformation in the CSD.""" self.identifier = hit.identifier self.count = 1 self.mol = hit.molecule self.atoms = hit.match_atoms() def matches(self, hit, tolerance): """Test whether a hit ... 1) (0, 2)" # A pair of planes --plane-angle "PLANE1

28 Mar 2024: os.path.dirname(os.path.abspath(__file__)), '.', '.', 'tests',. 'csp', 'testdata', 'csd_landscape_generator', 'HXACAN_shapes.sqlite'). code:: python >>> landscape_generator.settings.nstructures=3 >>> landscape = list(landscape_generator.generate(mol)