def thorough_exercise():
"""
This exercises all currently available options, so makes 64 requests.
Took 20 minutes, therefore disabled from the general testing.
"""
lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
n_good = 0
for po in [True, False]:
for do in [True, False]:
for sbr in [True, False]:
for xro in [True, False]:
for d_max in [None, 3.0]:
for d_min in [None, 1.0]:
print("ARGUMENTS:", po, do, sbr, xro, d_max, d_min)
homologs = rcsb_web_services.sequence_search(
lysozyme,
xray_only=xro,
d_max=d_max,
d_min=d_min,
protein_only=po,
data_only=do,
sort_by_resolution=sbr)
if len(homologs) > 200:
n_good += 1
print("GOOD:", n_good)
print(n_good)
assert n_good == 64
def exercise():
lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
assert (len(homologs) > 500)
atp_binding = rcsb_web_services.chemical_id_search("ATP",
protein_only=True)
assert (len(atp_binding) > 650)
report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
# print (report)
report = rcsb_web_services.get_high_resolution_and_residue_count_for_structures(
atp_binding)
assert (len(report) == len(atp_binding)) and (len(report[0]) == 3)
# print (report)
ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
# print (ligand_info)
assert ligand_info == [
['1MRU', 'A', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'],
['1MRU', 'B', 'MG', 24.305, 'Mg', 'MAGNESIUM ION', '[Mg++]'],
[
'1MRU', 'A', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S',
'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER',
'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O'
],
[
'1MRU', 'B', 'AGS', 523.247, 'C10 H16 N5 O12 P3 S',
'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER',
'Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O'
]
]
def exercise () :
from mmtbx.wwpdb import rcsb_web_services
lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
assert (len(homologs) > 500)
atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True)
assert (len(atp_binding) > 650)
report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
assert (len(ligand_info) == 4)
print "OK"
def exercise () :
from mmtbx.wwpdb import rcsb_web_services
lysozyme = """KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL"""
homologs = rcsb_web_services.sequence_search(lysozyme, d_max=2.0)
assert (len(homologs) > 500)
atp_binding = rcsb_web_services.chemical_id_search("ATP", protein_only=True)
assert (len(atp_binding) > 650)
report = rcsb_web_services.get_high_resolution_for_structures(atp_binding)
assert (len(report) == len(atp_binding)) and (len(report[0]) == 2)
ligand_info = rcsb_web_services.get_ligand_info_for_structures(['1mru'])
assert (len(ligand_info) == 4)
assert (ligand_info[1][-1] == u'[Mg+2]')
print "OK"
def fetch_similar_pdb_ids(
sequence,
min_identity=0.95,
min_resolution=3.0,
xray_only=True,
data_only=False,
expect=0.0000001,
sort_by_resolution=True,
ligands=None,
log=None):
"""
Finds closely related structures in the RCSB database, optionally limited to
structures with specific ligands.
"""
if (log is None) : log = null_out()
from mmtbx.wwpdb import rcsb_web_services
allowed_set = None
if (ligands is not None) and (len(ligands) > 0):
for lig_str in ligands :
resnames = lig_str.replace(" ", ",").split(",")
for resname in resnames :
ids = rcsb_web_services.chemical_id_search(
resname=resname,
d_max=min_resolution,
xray_only=xray_only,
data_only=data_only)
if (allowed_set is None) : allowed_set = set([])
allowed_set.update([ pdb_id.lower() for pdb_id in ids ])
matching_ids = rcsb_web_services.sequence_search(
sequence=sequence,
min_identity=min_identity,
expect=expect,
xray_only=xray_only,
data_only=data_only,
d_max=min_resolution,
sort_by_resolution=sort_by_resolution,
log=log)
filtered = []
for pdb_id in matching_ids :
pdb_id = pdb_id.lower()
if (allowed_set is not None) and (not pdb_id in allowed_set):
continue
filtered.append(pdb_id)
return filtered
def fetch_similar_pdb_ids (
sequence,
min_identity=0.95,
min_resolution=3.0,
xray_only=True,
data_only=False,
expect=0.0000001,
sort_by_resolution=True,
ligands=None,
log=None) :
"""
Finds closely related structures in the RCSB database, optionally limited to
structures with specific ligands.
"""
if (log is None) : log = null_out()
from mmtbx.wwpdb import rcsb_web_services
allowed_set = None
if (ligands is not None) and (len(ligands) > 0) :
for lig_str in ligands :
resnames = lig_str.replace(" ", ",").split(",")
for resname in resnames :
ids = rcsb_web_services.chemical_id_search(
resname=resname,
d_max=min_resolution,
xray_only=xray_only,
data_only=data_only)
if (allowed_set is None) : allowed_set = set([])
allowed_set.update([ pdb_id.lower() for pdb_id in ids ])
matching_ids = rcsb_web_services.sequence_search(
sequence=sequence,
min_identity=min_identity,
expect=expect,
xray_only=xray_only,
data_only=data_only,
d_max=min_resolution,
sort_by_resolution=sort_by_resolution,
log=log)
filtered = []
for pdb_id in matching_ids :
pdb_id = pdb_id.lower()
if (allowed_set is not None) and (not pdb_id in allowed_set) :
continue
filtered.append(pdb_id)
return filtered
