def mmtf_fetch(pdb, cache_dir='cath/mmtf/'):
""" Retrieve mmtf record from PDB with local caching """
mmtf_file = cache_dir + pdb + '.mmtf.gz'
url = 'http://mmtf.rcsb.org/v1.0/full/' + pdb + '.mmtf.gz'
mmtf_file = download_cached(url, mmtf_file)
mmtf_record = mmtf.parse_gzip(mmtf_file)
return mmtf_record
def get_structure_gzip(file_path):
"""Get a structrue from a gzipped file - given a file path.
:param file_path: the input file path
:return the structure
"""
decoder = parse_gzip(file_path)
return get_from_decoded(decoder)
def get_structure(file_path):
"""Get a structure from a file - given a file path.
:param file_path: the input file path
:return: the structure
"""
try:
decoder = parse(file_path)
except Exception:
decoder = parse_gzip(file_path)
return get_from_decoded(decoder)
def _parse_mmtf(fn):
if fn.endswith('gz'):
return mmtf.parse_gzip(fn)
else:
return mmtf.parse(fn)
def setUp(self):
top = mmtf.parse_gzip(MMTF_gz)
self.u = mda.Universe(top)
def test_round_trip(self):
data_in = parse_gzip("mmtf/tests/testdatastore/4CUP.mmtf.gz")
write_mmtf("test.mmtf", data_in, MMTFDecoder.pass_data_on)
data_rt = parse("test.mmtf")
self.check_equal(data_in, data_rt)
def test_gz_decoder(self):
decoded = parse_gzip("mmtf/tests/testdatastore/4CUP.mmtf.gz")
def u(self):
top = mmtf.parse_gzip(MMTF_gz)
return mda.Universe(top)
def u(self):
top = mmtf.parse_gzip(MMTF_gz)
return mda.Universe(top)
def _parse_mmtf(fn):
if fn.endswith('gz'):
return mmtf.parse_gzip(fn)
else:
return mmtf.parse(fn)