def __init__(self, residue_selectors=(TrueResidueSelector(), TrueResidueSelector()), atom_selectors=(('N', 'CA', 'C'), ('N', 'CA', 'C')), minimum_sequence_distance=1, maximum_neighborhood_distance=20.0, hash_function_kwargs={ 'cart_resl': 1.0, 'ori_resl': 15.0, 'cart_bound': 512.0 }, hash_table_kwargs={ 'key_type': np.dtype('i8'), 'value_type': np.dtype('i8'), 'filename': None }): print(hash_table_kwargs['filename']) self.hash_function = xbin.XformBinner(**hash_function_kwargs) self.hash_table = gp.MultiDict(**hash_table_kwargs) self.residue_selectors = residue_selectors self.atom_selectors = atom_selectors self.minimum_sequence_distance = minimum_sequence_distance self.maximum_neighborhood_distance = maximum_neighborhood_distance
def test_getpy_very_big_multidict_u8_S16(): key_type = np.dtype('u8') value_type = np.dtype('S16') gp_dict = gp.MultiDict(key_type, value_type) values = np.array([np.random.bytes(16) for i in range(10**5)], dtype=value_type) for i in range(10**2): keys = np.random.randint(10**15, size=10**5, dtype=key_type) gp_dict[keys] = values
def test_getpy_big_multidict_u8_u8_lookup(): key_type = np.dtype('u8') value_type = np.dtype('u8') gp_dict = gp.MultiDict(key_type, value_type) keys = np.random.randint(10**5, size=10**5, dtype=key_type) values = np.random.randint(10**15, size=10**5, dtype=value_type) gp_dict[keys] = values for i in range(10**2): values = gp_dict[keys]
import xbin from rdkit import Chem chi_resolution = 30.0 assert 360.0 / chi_resolution < 256.0 hash_function_kwargs = { 'cart_resl': 1.0, 'ori_resl': 15.0, 'cart_bound': 512.0 } hash_function = xbin.XformBinner(**hash_function_kwargs) hash_table_kwargs = {'key_type': np.dtype('i8'), 'value_type': np.dtype('i4')} hash_table = gp.MultiDict(**hash_table_kwargs) for pdb in tqdm.tqdm( glob.glob('/home/apmoyer/stapler/data/native_disulfide/*.pdb')): mol = Chem.MolFromPDBFile(pdb) xyz = np.array([ mol.GetConformer(0).GetAtomPosition(0), # N1 mol.GetConformer(0).GetAtomPosition(1), # CA1 mol.GetConformer(0).GetAtomPosition(2), # C1 mol.GetConformer(0).GetAtomPosition(4), # CB1 mol.GetConformer(0).GetAtomPosition(5), # SG1 mol.GetConformer(0).GetAtomPosition(11), # SG2 mol.GetConformer(0).GetAtomPosition(10), # CB2 mol.GetConformer(0).GetAtomPosition(7), # CA2 mol.GetConformer(0).GetAtomPosition(6), # N2