def test_determine_b_group_calpha_true():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1a1q.pdb"
pdb_id = "1a1q"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["calpha_only"], True)
def test_determine_b_group_nucleic_None():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1av1.pdb"
pdb_id = "1av1"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["nucleic_b"], None)
def test_determine_b_group_protein_2ADP():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/3zzt.pdb"
pdb_id = "3zzt"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "residue_2ADP")
def test_determine_b_group_calpha_true_3():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1efg.pdb"
pdb_id = "1efg"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "overall")
eq_(result["calpha_only"], True)
def test_determine_b_group_protein_no_b_factors():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1mcb.pdb"
pdb_id = "1mcb"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "no_b-factors")
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], None)
def test_determine_b_group_nucleic_individual():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/100d.pdb"
pdb_id = "100d"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], None)
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], "individual")
def test_determine_b_group_nucleic_2ADP():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1hlz.pdb"
pdb_id = "1hlz"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "residue_1ADP")
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], "residue_2ADP")
def test_determine_b_group_protein_overall():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/1etu.pdb"
pdb_id = "1etu"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "overall")
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], None)
def test_determine_b_group_too_short():
"""Tests that b_group is correctly determined."""
pdb_file_path = "pdbb/tests/pdb/files/438d.pdb"
pdb_id = "438d"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], None)
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], None)
eq_(result["phos_only"], False)
def test_determine_b_group_protein_overall_4():
"""Tests that b_group is correctly determined.
1av1 has the same B-factor for large stretches
of residues; overall is probably the best term.
"""
pdb_file_path = "pdbb/tests/pdb/files/1av1.pdb"
pdb_id = "1av1"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "overall")
def test_determine_b_group_protein_overall_3():
"""Tests that b_group is correctly determined.
1c2y has the same B-factor everywhere,
except for some THR and LEU atoms end-of-side-chain
overall is probably the best term.
"""
pdb_file_path = "pdbb/tests/pdb/files/1c2y.pdb"
pdb_id = "1c2y"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "overall")
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], None)
def test_determine_b_group_protein_overall_2():
"""Tests that b_group is correctly determined.
1az2 is has 16.67 for all N CA and C atoms
and 20.54 for O and side-chain atoms.
overall is probably the best term.
"""
pdb_file_path = "pdbb/tests/pdb/files/1az2.pdb"
pdb_id = "1az2"
structure = get_structure(pdb_file_path, pdb_id)
result = determine_b_group(structure)
eq_(result["protein_b"], "overall")
eq_(result["calpha_only"], False)
eq_(result["nucleic_b"], None)
def create_bdb_entry(pdb_file_path, pdb_id, verbose=False):
"""Create a bdb entry.
Return True when a bdb has been created successfully.
"""
_log.debug("Creating bdb entry...")
# Parse the given pdb file into a dict...
pdb_records = parse_pdb_file(pdb_file_path)
# and a Biopython structure
structure = get_structure(pdb_file_path, pdb_id, verbose)
bdbd = {"pdb_id": pdb_id}
expdta = check_exp_methods(pdb_records, pdb_id)
bdbd.update(expdta)
created_bdb_file = False
if expdta["expdta_useful"]:
refi_data = get_refi_data(pdb_records, structure, pdb_id)
bdbd.update(refi_data)
# Info about B-factor group type
b_group = determine_b_group(structure)
bdbd.update(b_group)
# skttles outliers
skttls = {"skttls_tot": None, "skttls_95th": None, "skttls_99th": None}
bdbd.update(skttls)
if refi_data["is_bdb_includable"]:
bdb_file_dir = pyconfig.get("BDB_FILE_DIR_PATH")
bdb_file_path = os.path.join(bdb_file_dir, pdb_id + ".bdb")
if refi_data["req_tlsanl"]:
if run_tlsanl(pdb_file_path=pdb_file_path,
xyzout=bdb_file_path,
pdb_id=pdb_id,
log_out_dir=bdb_file_dir):
created_bdb_file = True
tlsanl_log = os.path.join(bdb_file_dir,
pyconfig.get("TLSANL_LOG"))
skttls = parse_skttls_summ(tlsanl_log=tlsanl_log)
bdbd.update(skttls)
elif refi_data["b_msqav"]:
if write_multiplied_8pipi(pdb_file_path=pdb_file_path,
xyzout=bdb_file_path,
pdb_id=pdb_id,
verbose=verbose):
created_bdb_file = True
elif refi_data["assume_iso"]:
shutil.copy(pdb_file_path, bdb_file_path)
created_bdb_file = True
else:
message = "Unexpected bdb status"
write_whynot(pdb_id, message)
_log.error("{}.".format(message))
# Write the bdb metadata to a json file
try:
with open(
os.path.join(pyconfig.get("BDB_FILE_DIR_PATH"),
pdb_id + ".json"), "w") as f:
json.dump(bdbd,
f,
sort_keys=True,
indent=4,
default=date_handler)
except IOError as ex:
_log.error(ex)
return False
return created_bdb_file