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
def run(args, out=sys.stdout):
if (len(args) == 0) or ("--help" in args):
raise Usage("""mmtbx.find_residue_in_pdb RESNAME [options]
Use the RCSB web services to retrieve a list of PDB structures containing the
specified chemical ID.
Full parameters:
%s
""" % master_phil.as_str(prefix=" "))
sources = []
def process_unknown(arg):
if (1 <= len(arg) <= 3) and (arg.isalnum()):
return libtbx.phil.parse("resname=%s" % arg)
cai = libtbx.phil.command_line.argument_interpreter(
master_phil=master_phil)
working_phil = cai.process_and_fetch(args=args,
custom_processor=process_unknown)
params = working_phil.extract()
if (params.resname is None):
raise Sorry("No residue ID specified.")
from mmtbx.wwpdb import rcsb_web_services
pdb_ids = rcsb_web_services.chemical_id_search(
resname=params.resname,
d_max=params.d_max,
polymeric_type=params.polymeric_type,
xray_only=params.xray_only,
data_only=params.data_only,
identity_cutoff=params.identity_cutoff)
pdb_ids = [id.lower() for id in pdb_ids]
if (len(pdb_ids) == 0):
raise Sorry("No structures found matching the specified criteria.")
else:
if (not params.quiet):
print >> out, "%d PDB IDs retrieved:" % len(pdb_ids)
i = 0
while (i < len(pdb_ids)):
print >> out, " %s" % " ".join(pdb_ids[i:i + 16])
i += 16
else:
print >> out, "%d PDB IDs matching" % len(pdb_ids)
def run (args, out=sys.stdout) :
if (len(args) == 0) or ("--help" in args) :
raise Usage("""mmtbx.find_residue_in_pdb RESNAME [options]
Use the RCSB web services to retrieve a list of PDB structures containing the
specified chemical ID.
Full parameters:
%s
""" % master_phil.as_str(prefix=" "))
sources = []
def process_unknown (arg) :
if (1 <= len(arg) <= 3) and (arg.isalnum()) :
return libtbx.phil.parse("resname=%s" % arg)
cai = libtbx.phil.command_line.argument_interpreter(master_phil=master_phil)
working_phil = cai.process_and_fetch(args=args,
custom_processor=process_unknown)
params = working_phil.extract()
if (params.resname is None) :
raise Sorry("No residue ID specified.")
from mmtbx.wwpdb import rcsb_web_services
pdb_ids = rcsb_web_services.chemical_id_search(
resname=params.resname,
d_max=params.d_max,
polymeric_type=params.polymeric_type,
xray_only=params.xray_only,
data_only=params.data_only,
identity_cutoff=params.identity_cutoff)
pdb_ids = [ id.lower() for id in pdb_ids ]
if (len(pdb_ids) == 0) :
raise Sorry("No structures found matching the specified criteria.")
else :
if (not params.quiet) :
print >> out, "%d PDB IDs retrieved:" % len(pdb_ids)
i = 0
while (i < len(pdb_ids)) :
print >> out, " %s" % " ".join(pdb_ids[i:i+16])
i += 16
else :
print >> out, "%d PDB IDs matching" % len(pdb_ids)
def exercise_2():
fes_binding = rcsb_web_services.chemical_id_search("FES", xray_only=False)
assert len(fes_binding) > 765, len(fes_binding)
