def test_create_database_3() -> None:
"""Test the backwards compatiblity of pre-``0.3`` databases."""
shutil.copytree(DB_PATH_OLD3, DB_PATH_NEW3)
db = Database(DB_PATH_NEW3)
with db.hdf5('r', libver='latest') as f:
pdb = PDBContainer.from_hdf5(f['ligand'])
mol_list = pdb.to_molecules()
mol_list_ref = []
files = ('C3H7O1.pdb', 'C2H5O1.pdb', 'C1H3O1.pdb')
for _path in files:
path = str(DB_PATH_NEW3 / _path)
mol_list_ref.append(readpdb(path))
# Compare molecules
for mol1, mol2 in zip(mol_list, mol_list_ref):
msg = f'{mol1.get_formula()} & {mol2.get_formula()}'
np.testing.assert_allclose(mol1,
mol2,
rtol=0,
atol=10**-2,
err_msg=msg)
np.testing.assert_array_equal(mol1.bond_matrix(),
mol2.bond_matrix(),
err_msg=msg)
with db.hdf5('r', libver='latest') as f:
group = f['ligand']
pdb.validate_hdf5(group)
def test_call() -> None:
"""Tests for :meth:`MolDissociater.__call__`."""
mol_iterator = dissociate_ligand(MOL, lig_count=2, core_index=CORE_IDX)
filename = str(PATH / '{}.pdb')
for mol in mol_iterator:
name = mol.properties.core_topology
mol_ref = readpdb(filename.format(name))
xyz = mol.as_array()
ref = mol_ref.as_array()
np.testing.assert_allclose(xyz, ref)
def recreate_molecule(self) -> Molecule:
"""Create a |Molecule| instance from ``"$JN.pdb"``."""
pdb_file = self['$JN.pdb']
try:
return readpdb(self['$JN.pdb'])
except AttributeError as ex:
# readpdb() will pass None to from_rdmol(), resulting in an AttributeError down the line
raise FileError(
f"Failed to parse the content of ...{os.sep}{pdb_file!r}"
) from ex
def _prepare_pdb(self, stream):
"""Fill :attr:`MatchJob.pdb` with a string-representation of the .pdb file."""
conitions = {'filename' in self.settings.input, bool(self.molecule)}
if not any(conitions):
raise JobError("Ambiguous input: either `molecule` or "
"`settings.input.filename` must be specified")
if all(conitions):
raise JobError(
"Ambiguous input: `molecule` and "
"`settings.input.filename` cannot be both specified")
if self.molecule:
writepdb(self.molecule, stream)
else:
filename = self.settings.input.pop('filename')
writepdb(readpdb(filename), stream)
self.pdb: str = stream.getvalue()
def test_call_no_core() -> None:
"""Tests for :meth:`MolDissociater.__call__` where `core == lig`."""
lig_idx = [148, 190, 224, 294]
dissociate = MolDissociater(MOL, lig_idx, ligand_count=1)
pair1 = dissociate.get_pairs_closest(LIG_IDX, n_pairs=1)
pair2 = dissociate.get_pairs_closest(LIG_IDX, n_pairs=2)
dissociate.ligand_count = 2
pair3 = dissociate.get_pairs_closest(LIG_IDX, n_pairs=1)
pair4 = dissociate.get_pairs_closest(LIG_IDX, n_pairs=2)
pairs = (pair1, pair2, pair3, pair4)
for i, pair in enumerate(pairs, 1):
ref = np.load(PATH / f'call_no_core_{i}.npy')
np.testing.assert_array_equal(pair, ref)
mol_iterator = dissociate_ligand(MOL, lig_count=1, core_index=lig_idx)
filename = str(PATH / '{}.pdb')
for mol in mol_iterator:
name = mol.properties.core_topology
mol_ref = readpdb(filename.format(name))
xyz = mol.as_array()
ref = mol_ref.as_array()
np.testing.assert_allclose(xyz, ref)
"""Tests for :mod:`nanoCAT.bde.guess_core_dist`."""
from pathlib import Path
from scm.plams import readpdb, Molecule
from assertionlib import assertion
from nanoCAT.bde.guess_core_dist import guess_core_core_dist
PATH = Path('tests') / 'test_files'
with open(PATH / 'mol.pdb', 'r') as f:
MOL: Molecule = readpdb(f)
def test_guess_core_core_dist() -> None:
"""Tests for :func:`nanoCAT.bde.guess_core_dist.guess_core_core_dist`."""
dist = guess_core_core_dist(MOL, 'Cd')
ref = 5.175623211939212
assertion.allclose(dist, ref)
:annotation: : pathlib.Path = ...
.. autodata:: HDF5_READ
:annotation: : pathlib.Path = ...
"""
from typing import Tuple
from pathlib import Path
from scm.plams import readpdb, Molecule
from .pdb_array import PDBContainer
from .data import PDB_TUPLE
__all__ = ['MOL_TUPLE', 'MOL', 'PDB', 'HDF5_TMP', 'HDF5_READ']
#: A tuple of PLAMS Molecules.
MOL_TUPLE: Tuple[Molecule, ...] = tuple(readpdb(f) for f in PDB_TUPLE)
#: A PLAMS Molecule.
MOL: Molecule = MOL_TUPLE[0]
#: A PDBContainer.
PDB: PDBContainer = PDBContainer.from_molecules(MOL_TUPLE)
#: A path to a temporary (to-be created) hdf5 file.
HDF5_TMP = Path('tests') / 'test_files' / '.structures.hdf5'
#: A path to a read-only hdf5 file.
HDF5_READ = Path('tests') / 'test_files' / 'database' / 'structures.hdf5'