def test_chemical_composition(self):
""" Test crystals.PDBParser returns the same chemical composition as BIO.PDB.PDBParser implementation,
i.e. the same elements in the right proportions. """
with catch_warnings():
filterwarnings(
"ignore", category=biopdb.PDBExceptions.PDBConstructionWarning)
with tempfile.TemporaryDirectory() as temp_dir:
for protein_id in self.test_ids:
with self.subTest(f"Protein ID: {protein_id}"):
with PDBParser(protein_id,
download_dir=temp_dir) as parser:
fname = self.pdb_list.retrieve_pdb_file(
protein_id, pdir=temp_dir, file_format="pdb")
# Note: Bio.PDB atoms store element as uppercase strings. Thus, they must be changed to titlecase
crystals_chemical_composition = Counter(
[atm.element for atm in parser.atoms()])
biopdb_chemical_composition = Counter([
atm.element.title()
for atm in self.biopdb_parser.get_structure(
protein_id, fname).get_atoms()
])
self.assertDictEqual(
biopdb_chemical_composition,
crystals_chemical_composition,
)
def test_symmetry_operators(self):
""" Test that the non-translation part of the symmetry_operators is an invertible
matrix of determinant 1 | -1 """
with tempfile.TemporaryDirectory() as temp_dir:
with PDBParser("1fbb", download_dir=temp_dir) as parser:
for sym_op in parser.symmetry_operators():
t = sym_op[:3, :3]
self.assertAlmostEqual(abs(np.linalg.det(t)), 1, places=5)
def test_pdb_parser_symmetry_operators():
"""Test that the non-translation part of the symmetry_operators is an invertible
matrix of determinant 1 | -1"""
with tempfile.TemporaryDirectory() as temp_dir:
with PDBParser("1fbb", download_dir=temp_dir) as parser:
for sym_op in parser.symmetry_operators():
t = sym_op[:3, :3]
assert round(abs(abs(np.linalg.det(t)) - 1), 5) == 0
def test_residues(self):
""" Test the parsing of residues for 1fbb """
with tempfile.TemporaryDirectory() as temp_dir:
with PDBParser("1fbb", download_dir=temp_dir) as parser:
residues = list(parser.residues())
atoms = list(parser.atoms())
# Flatten residues into a list of atoms
residue_atoms = list(chain.from_iterable(residues))
self.assertEqual(len(residue_atoms), len(atoms))
def test_atomic_positions(self):
""" Test crystals.PDBParser returns atoms in the same position as the BIO.PDB.PDBParser implementation """
with catch_warnings():
filterwarnings(
"ignore", category=biopdb.PDBExceptions.PDBConstructionWarning
)
with tempfile.TemporaryDirectory() as temp_dir:
for protein_id in ("1fbb", "1fat", "1gzx"):
with self.subTest(f"Protein ID: {protein_id}"):
with PDBParser(protein_id, download_dir=temp_dir) as parser:
fname = self.pdb_list.retrieve_pdb_file(
protein_id, pdir=temp_dir, file_format="pdb"
)
biopdb_atoms = self.biopdb_parser.get_structure(
protein_id, fname
).get_atoms()
crystals_atoms = parser.atoms()
# To compare atom positions, we build "generic" atoms (just tuples (elem, coords))
# Note: Bio.PDB atoms store element as uppercase strings. Thus, they must be changed to titlecase
# Since numpy arrays are unhashable, they are converted to tuples
# crystals.PDBParser returns atoms in fractional coordinates, so we must also do the same with Bio.PDB atoms
bio_pdb_generic_atoms = set()
for atm in biopdb_atoms:
coords = np.round(
frac_coords(
atm.coord_fractional, parser.lattice_vectors()
),
3,
)
elem = atm.element.title()
bio_pdb_generic_atoms.add(
GenericAtom(elem, tuple(coords))
)
crystals_generic_atoms = set()
for atm in crystals_atoms:
coords = np.round(atm.coords_fractional, 3)
crystals_generic_atoms.add(
GenericAtom(atm.element, tuple(coords))
)
self.assertEqual(
bio_pdb_generic_atoms, crystals_generic_atoms
)
def test_chemical_composition(protein_id):
"""Test crystals.PDBParser returns the same chemical composition as BIO.PDB.PDBParser implementation,
i.e. the same elements in the right proportions."""
pdb_list = biopdb.PDBList(verbose=False, obsolete_pdb=gettempdir())
biopdb_parser = biopdb.PDBParser()
with catch_warnings():
filterwarnings("ignore",
category=biopdb.PDBExceptions.PDBConstructionWarning)
with tempfile.TemporaryDirectory() as temp_dir:
with PDBParser(protein_id, download_dir=temp_dir) as parser:
fname = pdb_list.retrieve_pdb_file(protein_id,
pdir=temp_dir,
file_format="pdb")
# Note: Bio.PDB atoms store element as uppercase strings. Thus, they must be changed to titlecase
crystals_chemical_composition = Counter(
[atm.element for atm in parser.atoms()])
biopdb_chemical_composition = Counter([
atm.element.title() for atm in biopdb_parser.get_structure(
protein_id, fname).get_atoms()
])
assert biopdb_chemical_composition == crystals_chemical_composition
def test_default_download_dir(self):
""" Test that the file is saved in the correct temporary directory by default """
filename = PDBParser.download_pdb_file("1fbb")
self.assertTrue(filename.exists())
self.assertEqual(filename.parent, STRUCTURE_CACHE)
def test_fractional_atoms(self):
""" Test the PDBParser returns fractional atomic coordinates. """
with tempfile.TemporaryDirectory() as temp_dir:
with PDBParser("1fbb", download_dir=temp_dir) as parser:
for atm in parser.atoms():
pass # TODO: find a test for this.
def test_pdb_parser_default_download_dir():
"""Test that the file is saved in the correct temporary directory by default"""
filename = PDBParser.download_pdb_file("1fbb")
assert filename.exists()
assert filename.parent == STRUCTURE_CACHE
