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