def fetch_pdb_data (
pdb_id,
pdb_dir=None,
sf_dir=None,
log=None,
verbose=False) :
"""
Copy data from local repository if defined and available, or download it
from the PDB, and run cif_as_mtz.
"""
from mmtbx.command_line import fetch_pdb
from mmtbx.command_line import cif_as_mtz
if (log is None) :
if (verbose) : log = sys.stdout
else : log = null_out()
pdb_file = "%s.pdb" % pdb_id
cif_file = "%s-sf.cif" % pdb_id
mtz_file = "%s.mtz" % pdb_id
fetch_pdb.run2(args=[pdb_id], log=log)
assert (os.path.isfile(pdb_file))
fetch_pdb.run2(args=["-x", pdb_id], log=log)
if (not os.path.isfile("%s-sf.cif" % pdb_id)) :
raise Sorry("Structure factors are not available for %s." % pdb_id)
cif_as_mtz.run(args=[
cif_file,
"--symmetry=%s" % pdb_file,
"--merge",
"--output_file_name=%s" % mtz_file])
if (not os.path.isfile(mtz_file)) :
raise RuntimeError("Missing %s!\ncif_as_mtz stderr:\n%s" %
(mtz_file, "\n".join(import_out.stderr_lines)))
return os.path.abspath(pdb_file), os.path.abspath(mtz_file)
def fetch_pdb_data(pdb_id, pdb_dir=None, sf_dir=None, log=None, verbose=False):
"""
Copy data from local repository if defined and available, or download it
from the PDB, and run cif_as_mtz.
"""
from mmtbx.command_line import fetch_pdb
from mmtbx.command_line import cif_as_mtz
if (log is None):
if (verbose): log = sys.stdout
else: log = null_out()
pdb_file = "%s.pdb" % pdb_id
cif_file = "%s-sf.cif" % pdb_id
mtz_file = "%s.mtz" % pdb_id
fetch_pdb.run2(args=[pdb_id], log=log)
assert (os.path.isfile(pdb_file))
fetch_pdb.run2(args=["-x", pdb_id], log=log)
if (not os.path.isfile("%s-sf.cif" % pdb_id)):
raise Sorry("Structure factors are not available for %s." % pdb_id)
cif_as_mtz.run(args=[
cif_file,
"--symmetry=%s" % pdb_file, "--merge",
"--output_file_name=%s" % mtz_file
])
if (not os.path.isfile(mtz_file)):
raise RuntimeError("Missing %s!\ncif_as_mtz stderr:\n%s" %
(mtz_file, "\n".join(import_out.stderr_lines)))
return os.path.abspath(pdb_file), os.path.abspath(mtz_file)
def combine_split_structure(
pdb_file,
pdb_id,
base_dir=None,
log=None):
"""
Assembles complete structures from split PDB files (e.g. ribosomes),
preserving the original file name. Return value is a list of IDs which
were added to the current model (or None).
"""
from mmtbx.command_line import fetch_pdb
from iotbx import pdb
if (log is None) : log = sys.stdout
pdb_in = pdb.input(file_name=pdb_file)
title = pdb_in.title_section()
other_ids = None
for line in title :
if (line.startswith("SPLIT")):
fields = line.strip().lower().split()
other_ids = fields[1:]
assert (len(other_ids) > 0)
if (other_ids is not None):
pdb_files = [pdb_file]
combined_ids = []
for other_id in other_ids :
if (other_id.lower() == pdb_id.lower()):
continue
dest_dir_2 = os.path.join(base_dir, other_id)
if (not os.path.isdir(dest_dir_2)):
dest_dir_2 = os.getcwd()
pdb_file_2 = os.path.join(dest_dir_2, "%s.pdb" % other_id)
if (not os.path.isfile(pdb_file_2)):
fetch_pdb.run2(args=[other_id])
if (not os.path.isfile(pdb_file_2)):
break
pdb_files.append(pdb_file_2)
combined_ids.append(other_id)
if (len(pdb_files) > 1):
pdb_all = os.path.join(base_dir, "%s_new.pdb" % pdb_id)
print >> log, "Joining multi-part structure: %s %s" % (pdb_id,
" ".join(other_ids))
easy_run.call("iotbx.pdb.join_fragment_files %s > %s" %
(" ".join(pdb_files), pdb_all))
os.remove(pdb_file)
os.rename(pdb_all, pdb_file)
return combined_ids
return None
def combine_split_structure (
pdb_file,
pdb_id,
base_dir=None,
log=None) :
"""
Assembles complete structures from split PDB files (e.g. ribosomes),
preserving the original file name. Return value is a list of IDs which
were added to the current model (or None).
"""
from mmtbx.command_line import fetch_pdb
from iotbx import pdb
if (log is None) : log = sys.stdout
pdb_in = pdb.input(file_name=pdb_file)
title = pdb_in.title_section()
other_ids = None
for line in title :
if (line.startswith("SPLIT")) :
fields = line.strip().lower().split()
other_ids = fields[1:]
assert (len(other_ids) > 0)
if (other_ids is not None) :
pdb_files = [pdb_file]
combined_ids = []
for other_id in other_ids :
if (other_id.lower() == pdb_id.lower()) :
continue
dest_dir_2 = os.path.join(base_dir, other_id)
if (not os.path.isdir(dest_dir_2)) :
dest_dir_2 = os.getcwd()
pdb_file_2 = os.path.join(dest_dir_2, "%s.pdb" % other_id)
if (not os.path.isfile(pdb_file_2)) :
fetch_pdb.run2(args=[other_id])
if (not os.path.isfile(pdb_file_2)) :
break
pdb_files.append(pdb_file_2)
combined_ids.append(other_id)
if (len(pdb_files) > 1) :
pdb_all = os.path.join(base_dir, "%s_new.pdb" % pdb_id)
print >> log, "Joining multi-part structure: %s %s" % (pdb_id,
" ".join(other_ids))
easy_run.call("iotbx.pdb.join_fragment_files %s > %s" %
(" ".join(pdb_files), pdb_all))
os.remove(pdb_file)
os.rename(pdb_all, pdb_file)
return combined_ids
return None
def get_pdb_files(pdb_code,pdbcif=False) :
from mmtbx.command_line import fetch_pdb
# note that mtz and pdb cif can't be done simultaneously
if pdbcif : args=["-c", pdb_code]
else : args=["--mtz", pdb_code]
data_files = fetch_pdb.run2(args)
if pdbcif : return {"pdbcif":data_files}
d = {}
for df in data_files :
df_input_file = any_file(df)
if df_input_file.file_type == "hkl" :
if df.endswith('.mtz') : d["hklmtz"] = df
elif df.endswith('.cif') : d["hklcif"] = df
elif df_input_file.file_type == "pdb":
d["pdb"] = df
elif df_input_file.file_type == "seq":
d["seq"] = df
return d
def download_coords(struct):
if not os.path.isfile(struct + ".pdb"):
from mmtbx.command_line.fetch_pdb import run2
run2([struct])
def create_reference_results_from_pdb():
from mmtbx.command_line.fetch_pdb import run2
run2(["1m2a"])
pdb_lines = open("1m2a.pdb").read()
return pdb_lines
