def retrieve_pdb_file(self, pdb_code, obsolete=False, pdir=None, file_format=None, overwrite=False):
"""Fetch PDB structure file from PDB server, and store it locally.
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.
NOTE. The default download format has changed from PDB to PDBx/mmCif
@param pdb_code: 4-symbols structure Id from PDB (e.g. 3J92).
@type pdb_code: string
@param file_format:
File format. Available options:
* "mmCif" (default, PDBx/mmCif file),
* "pdb" (format PDB),
* "xml" (PDBML/XML format),
* "mmtf" (highly compressed),
* "bundle" (PDB formatted archive for large structure}
@type file_format: string
@param overwrite: if set to True, existing structure files will be overwritten. Default: False
@type overwrite: bool
@param obsolete:
Has a meaning only for obsolete structures. If True, download the obsolete structure
to 'obsolete' folder, otherwise download won't be performed.
This option doesn't work for mmtf format as obsoleted structures aren't stored in mmtf.
Also doesn't have meaning when parameter pdir is specified.
Note: make sure that you are about to download the really obsolete structure.
Trying to download non-obsolete structure into obsolete folder will not work
and you face the "structure doesn't exists" error.
Default: False
@type obsolete: bool
@param pdir: put the file in this directory (default: create a PDB-style directory tree)
@type pdir: string
@return: filename
@rtype: string
"""
file_format = self._print_default_format_warning(file_format) # Deprecation warning
# Get the compressed PDB structure
code = pdb_code.lower()
archive = {'pdb': 'pdb%s.ent.gz', 'mmCif': '%s.cif.gz', 'xml': '%s.xml.gz', 'mmtf': '%s',
'bundle': '%s-pdb-bundle.tar.gz'}
archive_fn = archive[file_format] % code
if file_format not in archive.keys():
raise("Specified file_format %s doesn't exists or is not supported. Maybe a typo. "
"Please, use one of the following: mmCif, pdb, xml, mmtf, bundle" % file_format)
if file_format in ('pdb', 'mmCif', 'xml'):
pdb_dir = "divided" if not obsolete else "obsolete"
file_type = "pdb" if file_format == "pdb" else "mmCIF" if file_format == "mmCif" else "XML"
url = (self.pdb_server + '/pub/pdb/data/structures/%s/%s/%s/%s' % (pdb_dir, file_type, code[1:3], archive_fn))
elif file_format == 'bundle':
url = (self.pdb_server + '/pub/pdb/compatible/pdb_bundle/%s/%s/%s' % (code[1:3], code, archive_fn))
else:
url = ('http://mmtf.rcsb.org/v1.0/full/%s' % code)
# 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 = {'pdb': 'pdb%s.ent', 'mmCif': '%s.cif', 'xml': '%s.xml',
'mmtf': '%s.mmtf', 'bundle': '%s-pdb-bundle.tar'}
final_file = os.path.join(path, final[file_format] % code)
# Skip download if the file already exists
if not 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)
try:
_urlcleanup()
_urlretrieve(url, filename)
except IOError:
print("Desired structure doesn't exists")
else:
with gzip.open(filename, 'rb') as gz:
with open(final_file, 'wb') as out:
out.writelines(gz)
os.remove(filename)
return final_file
def retrieve_pdb_file(self,
pdb_code,
obsolete=False,
pdir=None,
file_format=None,
overwrite=False):
"""Fetch PDB structure file from PDB server, and store it locally.
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.
NOTE. The default download format has changed from PDB to PDBx/mmCif
:param pdb_code: 4-symbols structure Id from PDB (e.g. 3J92).
:type pdb_code: string
:param file_format:
File format. Available options:
* "mmCif" (default, PDBx/mmCif file),
* "pdb" (format PDB),
* "xml" (PDBML/XML format),
* "mmtf" (highly compressed),
* "bundle" (PDB formatted archive for large structure}
:type file_format: string
:param overwrite: if set to True, existing structure files will be overwritten. Default: False
:type overwrite: bool
:param obsolete:
Has a meaning only for obsolete structures. If True, download the obsolete structure
to 'obsolete' folder, otherwise download won't be performed.
This option doesn't work for mmtf format as obsoleted structures aren't stored in mmtf.
Also doesn't have meaning when parameter pdir is specified.
Note: make sure that you are about to download the really obsolete structure.
Trying to download non-obsolete structure into obsolete folder will not work
and you face the "structure doesn't exists" error.
Default: False
:type obsolete: bool
:param pdir: put the file in this directory (default: create a PDB-style directory tree)
:type pdir: string
:return: filename
:rtype: string
"""
file_format = self._print_default_format_warning(
file_format) # Deprecation warning
# Get the compressed PDB structure
code = pdb_code.lower()
archive = {
"pdb": "pdb%s.ent.gz",
"mmCif": "%s.cif.gz",
"xml": "%s.xml.gz",
"mmtf": "%s",
"bundle": "%s-pdb-bundle.tar.gz"
}
archive_fn = archive[file_format] % code
if file_format not in archive.keys():
raise (
"Specified file_format %s doesn't exists or is not supported. Maybe a typo. "
"Please, use one of the following: mmCif, pdb, xml, mmtf, bundle"
% file_format)
if file_format in ("pdb", "mmCif", "xml"):
pdb_dir = "divided" if not obsolete else "obsolete"
file_type = "pdb" if file_format == "pdb" else "mmCIF" if file_format == "mmCif" else "XML"
url = (self.pdb_server + "/pub/pdb/data/structures/%s/%s/%s/%s" %
(pdb_dir, file_type, code[1:3], archive_fn))
elif file_format == "bundle":
url = (self.pdb_server +
"/pub/pdb/compatible/pdb_bundle/%s/%s/%s" %
(code[1:3], code, archive_fn))
else:
url = ("http://mmtf.rcsb.org/v1.0/full/%s" % code)
# 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 = {
"pdb": "pdb%s.ent",
"mmCif": "%s.cif",
"xml": "%s.xml",
"mmtf": "%s.mmtf",
"bundle": "%s-pdb-bundle.tar"
}
final_file = os.path.join(path, final[file_format] % code)
# Skip download if the file already exists
if not overwrite:
if os.path.exists(final_file):
if self._verbose:
print("Structure exists: '%s' " % final_file)
return final_file
# Retrieve the file
if self._verbose:
print("Downloading PDB structure '%s'..." % pdb_code)
try:
_urlcleanup()
_urlretrieve(url, filename)
except IOError:
print("Desired structure doesn't exists")
else:
with gzip.open(filename, "rb") as gz:
with open(final_file, "wb") as out:
out.writelines(gz)
os.remove(filename)
return final_file
def retrieve_pdb_file(
self,
pdb_code,
obsolete=False,
pdir=None,
file_format=None,
overwrite=False,
biounit=False):
"""
Replacement for Bio.PDB.PDBList.retrieve_pdb_file to support
MMB PDB API. Defaults to Biopython super() if standard server is used.
"""
if self.pdb_server != 'mmb':
return super().retrieve_pdb_file(
pdb_code, obsolete, pdir, file_format, overwrite
)
self._verbose = True
code = pdb_code.lower()
if file_format in ('pdb', 'mmCif', 'xml'):
if file_format == 'mmCif':
file_format = 'cif'
if not biounit:
url = (URL_PREFIX + '/%s.%s' % (code, file_format))
else:
file_format = 'pdb'
url = (URL_PREFIX + '/%s_bn%s.pdb' % (code, biounit))
else:
print('Error: MMB Server: File format', file_format, 'not supported')
sys.exit(1)
#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)
if biounit:
final = {
'pdb': '%s_%s.pdb',
'mmCif': '%s_%s.cif',
'cif': '%s_%s.cif',
'xml': '%s_%s.xml'
}
final_file = os.path.join(path, final[file_format] % (code, biounit))
else:
final = {
'pdb': '%s.pdb',
'mmCif': '%s.cif',
'cif': '%s.cif',
'xml': '%s.xml'
}
final_file = os.path.join(path, final[file_format] % code)
# Skip download if the file already exists
if not overwrite:
if os.path.exists(final_file):
if self._verbose:
print("Structure exists: '%s' " % final_file)
return final_file
# Retrieve the file
if self._verbose:
if biounit:
print("Downloading PDB structure '%s.%s'..." % (pdb_code, biounit))
else:
print("Downloading PDB structure '%s'..." % pdb_code)
try:
_urlcleanup()
_urlretrieve(url, final_file)
except IOError:
print("Desired structure doesn't exists")
return final_file