def get_seqres_file(self, savefile='pdb_seqres.txt'):
"""Retrieves a (big) file containing all the sequences of PDB entries
and writes it to a file.
"""
print("Retrieving sequence file (takes about 15 MB).")
url = self.pdb_server + '/pub/pdb/derived_data/pdb_seqres.txt'
_urlretrieve(url, savefile)
def get_seqres_file(self, savefile='pdb_seqres.txt'):
"""Retrieves a (big) file containing all the sequences of PDB entries
and writes it to a file.
"""
print("Retrieving sequence file (takes about 15 MB).")
url = self.pdb_server + '/pub/pdb/derived_data/pdb_seqres.txt'
_urlretrieve(url, savefile)
def retrieve_pdb_file(self, pdb_code, obsolete=False, pdir=None):
""" Retrieves a PDB structure file from the PDB server and
stores it in a local file tree.
The PDB structure's file name is returned as a single string.
If obsolete == True, the file will be saved in a special file tree.
@param pdir: put the file in this directory (default: create a PDB-style directory tree)
@type pdir: string
@return: filename
@rtype: string
"""
# Get the compressed PDB structure
code = pdb_code.lower()
archive_fn = "pdb%s.ent.gz" % code
pdb_dir = "divided" if not obsolete else "obsolete"
url = (self.pdb_server +
'/pub/pdb/data/structures/%s/pdb/%s/%s' %
(pdb_dir, code[1:3], archive_fn))
# Where does the final PDB file get saved?
if pdir is None:
path = self.local_pdb if not obsolete else self.obsolete_pdb
if not self.flat_tree: # Put in PDB-style directory tree
path = os.path.join(path, code[1:3])
else: # Put in specified directory
path = pdir
if not os.access(path, os.F_OK):
os.makedirs(path)
filename = os.path.join(path, archive_fn)
final_file = os.path.join(path, "pdb%s.ent" % code) # (decompressed)
# Skip download if the file already exists
if not self.overwrite:
if os.path.exists(final_file):
print("Structure exists: '%s' " % final_file)
return final_file
# Retrieve the file
print("Downloading PDB structure '%s'..." % pdb_code)
_urlretrieve(url, filename)
# Uncompress the archive, delete when done
#Can't use context manager with gzip.open until Python 2.7
gz = gzip.open(filename, 'rb')
with open(final_file, 'wb') as out:
out.writelines(gz)
gz.close()
os.remove(filename)
return final_file
def retrieve_pdb_file(self, pdb_code, obsolete=False, pdir=None):
""" Retrieves a PDB structure file from the PDB server and
stores it in a local file tree.
The PDB structure's file name is returned as a single string.
If obsolete == True, the file will be saved in a special file tree.
@param pdir: put the file in this directory (default: create a PDB-style directory tree)
@type pdir: string
@return: filename
@rtype: string
"""
# Get the compressed PDB structure
code = pdb_code.lower()
archive_fn = "pdb%s.ent.gz" % code
pdb_dir = "divided" if not obsolete else "obsolete"
url = (self.pdb_server + '/pub/pdb/data/structures/%s/pdb/%s/%s' %
(pdb_dir, code[1:3], archive_fn))
# Where does the final PDB file get saved?
if pdir is None:
path = self.local_pdb if not obsolete else self.obsolete_pdb
if not self.flat_tree: # Put in PDB-style directory tree
path = os.path.join(path, code[1:3])
else: # Put in specified directory
path = pdir
if not os.access(path, os.F_OK):
os.makedirs(path)
filename = os.path.join(path, archive_fn)
final_file = os.path.join(path, "pdb%s.ent" % code) # (decompressed)
# Skip download if the file already exists
if not self.overwrite:
if os.path.exists(final_file):
print("Structure exists: '%s' " % final_file)
return final_file
# Retrieve the file
print("Downloading PDB structure '%s'..." % pdb_code)
_urlretrieve(url, filename)
# Uncompress the archive, delete when done
#Can't use context manager with gzip.open until Python 2.7
gz = gzip.open(filename, 'rb')
with open(final_file, 'wb') as out:
out.writelines(gz)
gz.close()
os.remove(filename)
return final_file
