def smart_load_dictionary(name=None,
file_path=None,
url=None,
registry_location=cifdic_register_url,
save_local=False,
store_dir=None):
from iotbx import cif
assert [name, file_path, url].count(None) < 3
cif_dic = None
if store_dir is None:
store_dir = libtbx.env.under_dist(module_name='iotbx',
path='cif/dictionaries')
if name is not None and [file_path, url].count(None) == 2:
if file_path is None:
if os.path.isfile(name):
file_path = name
else:
file_path = os.path.join(store_dir, name)
if not os.path.isfile(file_path):
gzip_path = file_path + '.gz'
if os.path.isfile(gzip_path):
if save_local:
gz = smart_open.for_reading(gzip_path)
f = smart_open.for_writing(file_path)
shutil.copyfileobj(gz, f)
gz.close()
f.close()
else:
file_path = gzip_path
if file_path is not None and os.path.isfile(file_path):
file_object = smart_open.for_reading(file_path)
cif_dic = dictionary(cif.reader(file_object=file_object).model())
file_object.close()
else:
if url is None:
url = locate_dictionary(name, registry_location=registry_location)
file_object = urlopen(url)
if save_local:
if name is None:
name = os.path.basename(url)
f = open(os.path.join(store_dir, name), 'wb')
shutil.copyfileobj(file_object, f)
f.close()
cif_dic = dictionary(
cif.reader(file_path=os.path.join(store_dir, name)).model())
else:
cif_dic = dictionary(cif.reader(file_object=file_object).model())
assert cif_dic is not None
return cif_dic
def __init__(self,
file_path=None,
file_object=None,
input_string=None,
cif_object=None,
builder=None,
raise_if_errors=True,
strict=True):
assert [file_path, file_object, input_string].count(None) == 2
self.file_path = file_path
if builder is None:
builder = builders.cif_model_builder(cif_object)
else:
assert cif_object is None
self.builder = builder
if file_path is not None:
file_object = smart_open.for_reading(file_path)
else:
file_path = "memory"
if file_object is not None:
input_string = file_object.read()
# check input_string for binary, and abort if necessary
binary_detector = detect_binary_file()
binary_detector.monitor_initial = min(len(input_string),
binary_detector.monitor_initial)
if binary_detector.is_binary_file(block=input_string):
raise CifParserError("Binary file detected, aborting parsing.")
self.parser = ext.fast_reader(builder, input_string, file_path, strict)
if raise_if_errors and len(self.parser.lexer_errors()):
raise CifParserError(self.parser.lexer_errors()[0])
if raise_if_errors and len(self.parser.parser_errors()):
raise CifParserError(self.parser.parser_errors()[0])
def __init__(self,
file_path=None,
file_object=None,
input_string=None,
cif_object=None,
builder=None,
raise_if_errors=True,
strict=True):
assert [file_path, file_object, input_string].count(None) == 2
self.file_path = file_path
if builder is None:
builder = builders.cif_model_builder(cif_object)
else: assert cif_object is None
self.builder = builder
if file_path is not None:
file_object = smart_open.for_reading(file_path)
else:
file_path = "memory"
if file_object is not None:
input_string = file_object.read()
# check input_string for binary, and abort if necessary
binary_detector = detect_binary_file()
binary_detector.monitor_initial = min(
len(input_string), binary_detector.monitor_initial)
if binary_detector.is_binary_file(block=input_string):
raise CifParserError("Binary file detected, aborting parsing.")
self.parser = ext.fast_reader(builder, input_string, file_path, strict)
if raise_if_errors and len(self.parser.lexer_errors()):
raise CifParserError(self.parser.lexer_errors()[0])
if raise_if_errors and len(self.parser.parser_errors()):
raise CifParserError(self.parser.parser_errors()[0])
def __init__(self, file_object=None, file_name=None):
assert [file_object, file_name].count(None) == 1
if (file_object is None):
from libtbx import smart_open
file_object = smart_open.for_reading(file_name=file_name)
from cctbx.array_family import flex
super(reader, self).__init__(lines=flex.split_lines(file_object.read()))
def __init__(self, file_object=None, file_name=None):
assert [file_object, file_name].count(None) == 1
if (file_object is None):
from libtbx import smart_open
file_object = smart_open.for_reading(file_name=file_name)
from cctbx.array_family import flex
super(reader, self).__init__(lines=flex.split_lines(file_object.read()))
def smart_load_dictionary(name=None, file_path=None, url=None,
registry_location=cifdic_register_url,
save_local=False, store_dir=None):
from iotbx import cif
assert [name, file_path, url].count(None) < 3
cif_dic = None
if store_dir is None:
store_dir = libtbx.env.under_dist(
module_name='iotbx', path='cif/dictionaries')
if name is not None and [file_path, url].count(None) == 2:
if file_path is None:
if os.path.isfile(name):
file_path = name
else:
file_path = os.path.join(store_dir, name)
if not os.path.isfile(file_path):
gzip_path = file_path + '.gz'
if os.path.isfile(gzip_path):
if save_local:
gz = smart_open.for_reading(gzip_path)
f = smart_open.for_writing(file_path)
shutil.copyfileobj(gz, f)
gz.close()
f.close()
else:
file_path = gzip_path
if file_path is not None and os.path.isfile(file_path):
file_object = smart_open.for_reading(file_path)
cif_dic = dictionary(cif.reader(file_object=file_object).model())
file_object.close()
else:
if url is None:
url = locate_dictionary(name, registry_location=registry_location)
file_object = urlopen(url)
if save_local:
if name is None:
name = os.path.basename(url)
f = open(os.path.join(store_dir, name), 'wb')
shutil.copyfileobj(file_object, f)
f.close()
cif_dic = dictionary(cif.reader(
file_path=os.path.join(store_dir, name)).model())
else:
cif_dic = dictionary(cif.reader(
file_object=file_object).model())
assert cif_dic is not None
return cif_dic
def from_msgpack_file(filename):
'''
Read the reflection table from file in msgpack format
'''
from libtbx import smart_open
with smart_open.for_reading(filename, 'rb') as infile:
return reflection_table.from_msgpack(infile.read())
def __init__(self):
"""
Loads pickle with data. Path is temporary in current work dir.
Should be centralized somewhere else upon going to production.
"""
db_dict = {}
pdb_info_file = libtbx.env.find_in_repositories(
relative_path="cctbx_project/iotbx/bioinformatics/pdb_info.csv.gz",
test=os.path.isfile)
csv_file = smart_open.for_reading(file_name=pdb_info_file)
csv_reader = csv.reader(csv_file, delimiter=";")
for row in csv_reader:
db_dict[row[0]] = (row[1], row[2], row[3], row[4], row[5])
self.db_dict = db_dict
def extract_remark_2_and_3_records(file_name, file_lines=None):
result = []
if (file_lines is None):
file_lines = smart_open.for_reading(
file_name=file_name).read().splitlines()
else:
assert (file_name is None)
for rec in file_lines:
if (rec.startswith("REMARK 3 ") or rec.startswith("REMARK 2 ")):
start = True
result.append(rec)
else:
if (rec.startswith("ATOM ") or rec.startswith("HETATM ")):
break
return result
def extract_remark_2_and_3_records(file_name, file_lines=None):
result = []
if (file_lines is None) :
file_lines = smart_open.for_reading(
file_name = file_name).read().splitlines()
else :
assert (file_name is None)
for rec in file_lines:
if(rec.startswith("REMARK 3 ") or rec.startswith("REMARK 2 ")):
start = True
result.append(rec)
else:
if(rec.startswith("ATOM ") or rec.startswith("HETATM ")):
break
return result
def from_pickle(filename):
'''
Read the reflection table from pickle file.
:param filename: The pickle filename
:return: The reflection table
'''
import six.moves.cPickle as pickle
from libtbx import smart_open
with smart_open.for_reading(filename, 'rb') as infile:
result = pickle.load(infile)
assert (isinstance(result, reflection_table))
return result
def from_pickle(filename):
'''
Read the reflection table from pickle file.
:param filename: The pickle filename
:return: The reflection table
'''
import cPickle as pickle
from libtbx import smart_open
with smart_open.for_reading(filename, 'rb') as infile:
result = pickle.load(infile)
assert(isinstance(result, reflection_table))
return result
def run(args):
for f in args:
try:
file_object = smart_open.for_reading(file_name=f)
miller_arrays = iotbx.cif.reader(file_object=file_object).as_miller_arrays()
except KeyboardInterrupt:
raise
except Exception, e:
print "Error extracting miller arrays from file: %s:" % (
show_string(f))
print " ", str(e)
continue
for miller_array in miller_arrays:
miller_array.show_comprehensive_summary()
print
r, _ = op.splitext(op.basename(f))
easy_pickle.dump(file_name=r+'_miller_arrays.pickle', obj=miller_arrays)
def run():
data_dir = '/net/cci/youval/Work/work/MTRIX/Data'
#data_dir = r'c:\Phenix\Dev\Work\work\MTRIX\Data'
os.chdir(data_dir)
file_to_year_dict = {}
files_with_good_MTRIX = set(pickle.load(open(os.path.join(data_dir,'files_with_good_MTRIX'),'r')))
good_MTRIX_pdb_files = pickle.load(open(os.path.join(data_dir,'dict_good_MTRIX_pdb_files'),'r'))
# find the file in LBL pdb mirror folder
for fn in files_with_good_MTRIX:
file_name_with_path = good_MTRIX_pdb_files[fn]
file_lines = smart_open.for_reading(
file_name = file_name_with_path).read().splitlines()
year = get_year(file_lines)
file_to_year_dict[fn] = year
print len(file_to_year_dict)
def extract_from(file_name=None, file=None, monitor_initial=None):
assert [file_name, file].count(None) == 1
if (file is None):
file = smart_open.for_reading(file_name=file_name)
detect_binary = detect_binary_file(monitor_initial=monitor_initial)
line_number = 0
for line in file:
line_number += 1
if (detect_binary is not None):
is_binary = detect_binary.is_binary_file(block=line)
if (is_binary is not None):
if (is_binary): break
detect_binary = None
if (line.startswith("CRYST1")):
return cryst1_interpretation.crystal_symmetry(cryst1_record=line)
crystal_symmetry = cns_pdb_remarks.extract_symmetry(pdb_record=line)
if (crystal_symmetry is not None):
return crystal_symmetry
raise RuntimeError("No CRYST1 record.")
def fetch(id,
data_type="pdb",
format="pdb",
mirror="rcsb",
log=None,
force_download=False,
local_cache=None):
"""
Locate and open a data file for the specified PDB ID and format, either in a
local mirror or online.
:param id: 4-character PDB ID (e.g. '1hbb')
:param data_type: type of content to download: pdb, xray, or fasta
:param format: format of data: cif, pdb, or xml
:param mirror: remote site to use, either rcsb, pdbe, pdbj or pdb-redo
:returns: a filehandle-like object (with read() method)
"""
assert data_type in ["pdb", "xray", "fasta", "seq"]
assert format in ["cif", "pdb", "xml"]
assert mirror in ["rcsb", "pdbe", "pdbj", "pdb-redo"]
validate_pdb_id(id)
if (log is None): log = null_out()
id = id.lower()
if (not force_download):
if (local_cache is not None) and (data_type == "pdb"):
from iotbx.file_reader import guess_file_type
if (local_cache is Auto):
local_cache = os.getcwd()
cache_files = os.listdir(local_cache)
for file_name in cache_files:
if (len(file_name) > 4):
file_id = re.sub("^pdb", "", file_name)[0:4]
if (file_id.lower() == id):
if (guess_file_type(file_name) == "pdb"):
file_name = os.path.join(local_cache, file_name)
print >> log, "Reading from cache directory:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
# try local mirror for PDB and X-ray data files first, if it exists
if (data_type == "pdb") and (format == "pdb") and \
("PDB_MIRROR_PDB" in os.environ) :
subdir = os.path.join(os.environ["PDB_MIRROR_PDB"], id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "pdb%s.ent.gz" % id)
if (os.path.isfile(file_name)):
print >> log, "Reading from local mirror:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
if (data_type == "pdb") and (format == "cif") and \
("PDB_MIRROR_MMCIF" in os.environ) :
subdir = os.path.join(os.environ["PDB_MIRROR_MMCIF"], id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "%s.cif.gz" % id)
if (os.path.isfile(file_name)):
print >> log, "Reading from local mirror:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
if ((data_type == "xray")
and ("PDB_MIRROR_STRUCTURE_FACTORS" in os.environ)):
sf_dir = os.environ["PDB_MIRROR_STRUCTURE_FACTORS"]
subdir = os.path.join(sf_dir, id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "r%ssf.ent.gz" % id)
if (os.path.isfile(file_name)):
print >> log, "Reading from local mirror:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
# No mirror found (or out of date), default to HTTP download
url = None
compressed = False
if (mirror == "rcsb"):
url_base = 'https://files.rcsb.org/download/'
pdb_ext = ".pdb"
sf_prefix = ""
sf_ext = "-sf.cif"
elif (mirror == "pdbe"):
url_base = "https://www.ebi.ac.uk/pdbe-srv/view/files/"
pdb_ext = ".ent"
sf_prefix = "r"
sf_ext = "sf.ent"
elif (mirror == "pdbj"):
url_base = "ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/"
if (data_type == "pdb"):
compressed = True
if (format == "pdb"):
url = url_base + "pdb/%s/pdb%s.ent.gz" % (id[1:3], id)
elif (format == "cif"):
url = url_base + "mmCIF/%s/%s.cif.gz" % (id[1:3], id)
elif (data_type == "xray"):
compressed = True
url = url_base + "structure_factors/%s/r%ssf.ent.gz" % (id[1:3],
id)
elif (data_type in ["fasta", "seq"]):
url = "https://pdbj.org/rest/downloadPDBfile?format=fasta&id=%s" % id
if (url is None) and (data_type != "fasta"):
raise Sorry(
"Can't determine PDBj download URL for this data/format " +
"combination.")
elif mirror == "pdb-redo":
url_base = "https://pdb-redo.eu/db/"
pdb_ext = "_final.pdb"
cif_ext = "_final.cif"
sf_prefix = ""
sf_ext = "_final.mtz"
if (data_type == 'pdb'):
if (format == 'pdb'):
url = url_base + "{id}/{id}{format}".format(id=id,
format=pdb_ext)
elif (format == 'cif'):
url = url_base + "{id}/{id}{format}".format(id=id,
format=cif_ext)
elif (data_type == 'xray'):
url = url_base + "{id}/{id}{format}".format(id=id, format=sf_ext)
if (data_type in ["fasta", "seq"]):
# XXX the RCSB doesn't appear to have a simple URL for FASTA files
if (url is None): # TODO PDBe equivalent doesn't exist?
url = "https://www.rcsb.org/pdb/download/downloadFastaFiles.do?structureIdList=%s&compressionType=uncompressed" % id
try:
data = libtbx.utils.urlopen(url)
except urllib2.HTTPError, e:
if e.getcode() == 404:
raise RuntimeError("Couldn't download sequence for %s." % id)
else:
raise
def fetch (id, data_type="pdb", format="pdb", mirror="rcsb", log=None,
force_download=False,
local_cache=None) :
"""
Locate and open a data file for the specified PDB ID and format, either in a
local mirror or online.
:param id: 4-character PDB ID (e.g. '1hbb')
:param data_type: type of content to download: pdb, xray, or fasta
:param format: format of data: cif, pdb, or xml
:param mirror: remote site to use, either rcsb or pdbe
:returns: a filehandle-like object (with read() method)
"""
assert data_type in ["pdb", "xray", "fasta", "seq"]
assert format in ["cif", "pdb", "xml"]
assert mirror in ["rcsb", "pdbe", "pdbj"]
validate_pdb_id(id)
if (log is None) : log = null_out()
id = id.lower()
if (not force_download) :
if (local_cache is not None) and (data_type == "pdb") :
from iotbx.file_reader import guess_file_type
if (local_cache is Auto) :
local_cache = os.getcwd()
cache_files = os.listdir(local_cache)
for file_name in cache_files :
if (len(file_name) > 4) :
file_id = re.sub("^pdb", "", file_name)[0:4]
if (file_id.lower() == id) :
if (guess_file_type(file_name) == "pdb") :
file_name = os.path.join(local_cache, file_name)
print >> log, "Reading from cache directory:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
# try local mirror for PDB and X-ray data files first, if it exists
if (data_type == "pdb") and ("PDB_MIRROR_PDB" in os.environ) :
subdir = os.path.join(os.environ["PDB_MIRROR_PDB"], id[1:3])
if (os.path.isdir(subdir)) :
file_name = os.path.join(subdir, "pdb%s.ent.gz" % id)
if (os.path.isfile(file_name)) :
print >> log, "Reading from local mirror:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
if ((data_type == "xray") and
("PDB_MIRROR_STRUCTURE_FACTORS" in os.environ)) :
sf_dir = os.environ["PDB_MIRROR_STRUCTURE_FACTORS"]
subdir = os.path.join(sf_dir, id[1:3])
if (os.path.isdir(subdir)) :
file_name = os.path.join(subdir, "r%ssf.ent.gz" % id)
if (os.path.isfile(file_name)) :
print >> log, "Reading from local mirror:"
print >> log, " " + file_name
f = smart_open.for_reading(file_name)
return f
# No mirror found (or out of date), default to HTTP download
url = None
compressed = False
if (mirror == "rcsb") :
url_base = "http://www.rcsb.org/pdb/files/"
pdb_ext = ".pdb"
sf_prefix = ""
sf_ext = "-sf.cif"
elif (mirror == "pdbe") :
url_base = "http://www.ebi.ac.uk/pdbe-srv/view/files/"
pdb_ext = ".ent"
sf_prefix = "r"
sf_ext = "sf.ent"
elif (mirror == "pdbj") :
url_base = "ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/"
if (data_type == "pdb") :
compressed = True
if (format == "pdb") :
url = url_base + "pdb/%s/pdb%s.ent.gz" % (id[1:3], id)
elif (format == "cif") :
url = url_base + "mmCIF/%s/%s.cif.gz" % (id[1:3], id)
elif (data_type == "xray") :
compressed = True
url = url_base + "structure_factors/%s/r%ssf.ent.gz" % (id[1:3], id)
elif (data_type in ["fasta", "seq"]) :
url = "http://pdbj.org/app//downloadFasta4PDBID?pdbid=%s" % id
if (url is None) and (data_type != "fasta") :
raise Sorry("Can't determine PDBj download URL for this data/format "+
"combination.")
if (data_type in ["fasta", "seq"]) :
# XXX the RCSB doesn't appear to have a simple URL for FASTA files
if (url is None) : # TODO PDBe equivalent doesn't exist?
url = "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=FASTA&compression=NO&structureId=%s" % id
try :
data = libtbx.utils.urlopen(url)
except urllib2.HTTPError, e :
if e.getcode() == 404 :
raise RuntimeError("Couldn't download sequence for %s." % id)
else :
raise
def fetch(id,
data_type="pdb",
format="pdb",
mirror="rcsb",
log=None,
force_download=False,
local_cache=None):
"""
Locate and open a data file for the specified PDB ID and format, either in a
local mirror or online.
:param id: 4-character PDB ID (e.g. '1hbb')
:param data_type: type of content to download: pdb, xray, or fasta
:param format: format of data: cif, pdb, or xml (or cif_or_pdb)
:param mirror: remote site to use, either rcsb, pdbe, pdbj or pdb-redo
:returns: a filehandle-like object (with read() method)
"""
assert data_type in ["pdb", "xray", "fasta", "seq"]
assert format in ["cif", "pdb", "xml", "cif_or_pdb"]
assert mirror in ["rcsb", "pdbe", "pdbj", "pdb-redo"]
validate_pdb_id(id)
if (log is None): log = null_out()
id = id.lower()
if (not force_download):
if (local_cache is not None) and (data_type == "pdb"):
from iotbx.file_reader import guess_file_type
if (local_cache is Auto):
local_cache = os.getcwd()
cache_files = os.listdir(local_cache)
for file_name in cache_files:
if (len(file_name) > 4):
file_id = re.sub("^pdb", "", file_name)[0:4]
if (file_id.lower() == id):
if (guess_file_type(file_name) == "pdb"):
file_name = os.path.join(local_cache, file_name)
print("Reading from cache directory:", file=log)
print(" " + file_name, file=log)
f = smart_open.for_reading(file_name)
return f
# try local mirror for PDB and X-ray data files first, if it exists
if (data_type == "pdb") and (format in ["pdb", "cif_or_pdb"]) and \
("PDB_MIRROR_PDB" in os.environ):
subdir = os.path.join(os.environ["PDB_MIRROR_PDB"], id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "pdb%s.ent.gz" % id)
if (os.path.isfile(file_name)):
print("Reading from local mirror:", file=log)
print(" " + file_name, file=log)
f = smart_open.for_reading(file_name)
return f
if (data_type == "pdb") and (format in ["cif", "cif_or_pdb"]) and \
("PDB_MIRROR_MMCIF" in os.environ):
subdir = os.path.join(os.environ["PDB_MIRROR_MMCIF"], id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "%s.cif.gz" % id)
if (os.path.isfile(file_name)):
print("Reading from local mirror:", file=log)
print(" " + file_name, file=log)
f = smart_open.for_reading(file_name)
return f
if ((data_type == "xray")
and ("PDB_MIRROR_STRUCTURE_FACTORS" in os.environ)):
sf_dir = os.environ["PDB_MIRROR_STRUCTURE_FACTORS"]
subdir = os.path.join(sf_dir, id[1:3])
if (os.path.isdir(subdir)):
file_name = os.path.join(subdir, "r%ssf.ent.gz" % id)
if (os.path.isfile(file_name)):
print("Reading from local mirror:", file=log)
print(" " + file_name, file=log)
f = smart_open.for_reading(file_name)
return f
# No mirror found (or out of date), default to HTTP download
url = None
compressed = False
if (mirror == "rcsb"):
url_base = 'https://files.rcsb.org/download/'
pdb_ext = ".pdb"
sf_prefix = ""
sf_ext = "-sf.cif"
elif (mirror == "pdbe"):
url_base = "https://www.ebi.ac.uk/pdbe-srv/view/files/"
pdb_ext = ".ent"
sf_prefix = "r"
sf_ext = "sf.ent"
elif (mirror == "pdbj"):
url_base = "ftp://ftp.pdbj.org/pub/pdb/data/structures/divided/"
if (data_type == "pdb"):
compressed = True
if (format == "pdb"):
url = url_base + "pdb/%s/pdb%s.ent.gz" % (id[1:3], id)
elif (format in ["cif", "cif_or_pdb"]):
url = url_base + "mmCIF/%s/%s.cif.gz" % (id[1:3], id)
elif (data_type == "xray"):
compressed = True
url = url_base + "structure_factors/%s/r%ssf.ent.gz" % (id[1:3],
id)
elif (data_type in ["fasta", "seq"]):
url = "https://pdbj.org/rest/downloadPDBfile?format=fasta&id=%s" % id
if (url is None) and (data_type != "fasta"):
raise Sorry(
"Can't determine PDBj download URL for this data/format " +
"combination.")
elif mirror == "pdb-redo":
url_base = "https://pdb-redo.eu/db/"
pdb_ext = "_final.pdb"
cif_ext = "_final.cif"
sf_prefix = ""
sf_ext = "_final.mtz"
if (data_type == 'pdb'):
if (format == 'pdb'):
url = url_base + "{id}/{id}{format}".format(id=id,
format=pdb_ext)
elif (format in ['cif', 'cif_or_pdb']):
url = url_base + "{id}/{id}{format}".format(id=id,
format=cif_ext)
elif (data_type == 'xray'):
url = url_base + "{id}/{id}{format}".format(id=id, format=sf_ext)
if (data_type in ["fasta", "seq"]):
if (url is None): # TODO PDBe equivalent doesn't exist?
# Seems that this url should be working:
url = "https://www.rcsb.org/fasta/entry/%s" % id
try:
data = libtbx.utils.urlopen(url)
except HTTPError as e:
if e.getcode() == 404:
raise RuntimeError("Couldn't download sequence for %s." % id)
else:
raise
elif data_type == "xray":
if (url is None):
url = url_base + sf_prefix + id + sf_ext
try:
data = libtbx.utils.urlopen(url)
except HTTPError as e:
if e.getcode() == 404:
raise RuntimeError(
"Couldn't download structure factors for %s." % id)
else:
raise
else:
if (url is None):
if format == "pdb":
url = url_base + id + pdb_ext
elif format == "cif_or_pdb":
url = url_base + id + "." + "cif"
else:
url = url_base + id + "." + format
try:
data = libtbx.utils.urlopen(url)
except HTTPError as e:
if e.getcode() == 404:
raise RuntimeError("Couldn't download model for %s." % id)
else:
raise
if (compressed):
try:
import gzip
except ImportError:
raise Sorry(
"gzip module not available - please use an uncompressed " +
"source of PDB data.")
else:
# XXX due to a bug in urllib2, we can't pass the supposedly file-like
# object directly, so we read the data into a StringIO object instead
return gzip.GzipFile(fileobj=StringIO(data.read()))
return data