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28 Mar 2024: For speed of running this test we will scale the search to 10% of the normal run, set the number of docking poses to 5, set the results directory to a

28 Mar 2024: 0: # match the atoms to the molecule atoms_to_test = [] for j in range(molecule_subset.natoms()): # To replicate the comparison using numpy.allclose() we use, # for all atom pairs: # ... y()) and abs(at.coordinates.z - o.z()) <= 1.e-8 1.e-5 abs(o.z()): #

28 Mar 2024: It is a good way to access the CSD if using the _csd_required annotation on tests, as that way the CSD isn't loaded until the test has been checked

28 Mar 2024: organometallic = False for entry in EntryReader('CSD'): # filter out entries that don't match the search parameters if not settings.test(entry): continue # filter out entries that don't have a

28 Mar 2024: docs] def test(self, argument): '''Test that the argument satisfies the requirements of the settings instance. ... RuntimeError, TypeError): return False return CSDSQLDatabaseLib.test_molecule_settings_constraints( self._settings, argument._molecule ).

28 Mar 2024: self._atom.element().atomic_weight() @property def is_cyclic(self): '''Test whether the atom is part of a ring system. >>> ... False @property def is_acceptor(self): '''Test whether or not the atom is a hydrogen bond acceptor. >>>

28 Mar 2024: def _check_missing_h(self, mol): if not self.settings.reject_missing_hydrogen: return True test_mol = mol.copy() test_mol.add_hydrogens(mode='missing', add_sites=False) return ... atoms) == len(test_mol.atoms). ############################################

28 Mar 2024: solubility_tests() except AttributeError: solubility_measurements = [] solubility_data = [] for solubility_measurement in solubility_measurements: sol = SolubilityMeasurement( solubility_measurement.solubility(), solubility_measurement.temperature(),

28 Mar 2024: Navigation. ». Index. A. B. C. ccdc.cavity. ccdc.conformer. ccdc.crystal. ccdc.csp.csd_landscape_generator. ccdc.csp.database. ccdc.csp.prediction. ccdc.descriptors. ccdc.diagram. ccdc.docking. ccdc.interaction. ccdc.molecule. ccdc.morphology.

28 Mar 2024: Navigation. ». Source code for ccdc.pharmacophore. # # This code is Copyright (C) 2015 The Cambridge Crystallographic Data Centre # (CCDC) of 12 Union Road, Cambridge CB2 1EZ, UK and a proprietary work of CCDC. # This code may not be used,