def retrieve(pdb_id, cache_dir = None):
'''Creates a PDBML object by using a cached copy of the files if they exists or by retrieving the files from the RCSB.'''
pdb_contents = None
xml_contents = None
pdb_id = pdb_id.upper()
if cache_dir:
# Check to see whether we have a cached copy of the PDB file
filename = os.path.join(cache_dir, "%s.pdb" % pdb_id)
if os.path.exists(filename):
pdb_contents = read_file(filename)
# Check to see whether we have a cached copy of the XML file
filename = os.path.join(cache_dir, "%s.xml" % pdb_id)
if os.path.exists(filename):
xml_contents = read_file(filename)
# Get any missing files from the RCSB and create cached copies if appropriate
if not pdb_contents:
pdb_contents = rcsb.retrieve_pdb(pdb_id)
if cache_dir:
write_file(os.path.join(cache_dir, "%s.pdb" % pdb_id), pdb_contents)
if not xml_contents:
xml_contents = rcsb.retrieve_xml(pdb_id)
if cache_dir:
write_file(os.path.join(cache_dir, "%s.xml" % pdb_id), xml_contents)
# Return the object
return PDBML_slow(xml_contents, pdb_contents)
def retrieve(cls, pdb_id, cache_dir = None):
'''Creates a PDB object by using a cached copy of the file if it exists or by retrieving the file from the RCSB.'''
# Check to see whether we have a cached copy
pdb_id = pdb_id.upper()
if cache_dir:
filename = os.path.join(cache_dir, "%s.pdb" % pdb_id)
if os.path.exists(filename):
return cls(read_file(filename))
# Get a copy from the RCSB
contents = rcsb.retrieve_pdb(pdb_id)
# Create a cached copy if appropriate
if cache_dir:
write_file(os.path.join(cache_dir, "%s.pdb" % pdb_id), contents)
# Return the object
return cls(contents)