def to_mmtf_MMTFDecoder(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
try:
is_string_pdb_id(item)
except:
raise WrongFormError('string:pdb_id')
try:
atom_indices = digest_atom_indices(atom_indices)
except:
raise WrongAtomIndicesError()
try:
structure_indices = digest_structure_indices(structure_indices)
except:
raise WrongStructureIndicesError()
from mmtf import fetch
from ..mmtf_MMTFDecoder import extract as extract_mmtf_MMTFDecoder
tmp_item = item.split(':')[-1]
tmp_item = fetch(tmp_item)
tmp_item = extract_mmtf_MMTFDecoder(tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False)
return tmp_item
def get_structure_from_url(pdb_id):
"""Get a structure from a URL - given a PDB id.
:param pdb_id: the input PDB id
:return: the structure
"""
decoder = fetch(pdb_id)
return get_from_decoded(decoder)
def round_trip(self,pdb_id):
if _internet_on(BASE_URL):
data_in = fetch(pdb_id)
write_mmtf(pdb_id+".mmtf", data_in, MMTFDecoder.pass_data_on)
data_rt = parse(pdb_id+".mmtf")
self.check_equal(data_in, data_rt)
else:
print("Warning - cannot connect to "+BASE_URL)
def from_id(cls, pdb_id):
"""
Initialize structure by PDB ID (fetches
structure from RCSB servers)
Parameters
----------
pdb_id : str
PDB identifier (e.g. 1hzx)
Returns
-------
PDB
initialized PDB structure
"""
try:
return cls(fetch(pdb_id))
except HTTPError as e:
raise ResourceError(
"Could not fetch MMTF data for {}".format(pdb_id)
) from e
def fetch_mmtf(pdb_id):
"""Create a Universe from the RCSB Protein Data Bank using mmtf format
Parameters
----------
pdb_id : string
PDB code of the desired data, eg '4UCP'
Returns
-------
MDAnalysis Universe of the corresponding PDB system
See Also
--------
mmtf.fetch : Function for fetching raw mmtf data
.. versionadded:: 0.16.0
"""
return Universe(mmtf.fetch(pdb_id))
def fetch_mmtf(pdb_id):
"""Create a Universe from the RCSB Protein Data Bank using mmtf format
Parameters
----------
pdb_id : string
PDB code of the desired data, eg '4UCP'
Returns
-------
Universe
MDAnalysis Universe of the corresponding PDB system
See Also
--------
mmtf.fetch : Function for fetching raw mmtf data
.. versionadded:: 0.16.0
"""
return Universe(mmtf.fetch(pdb_id))
with open(input_args.pdb_id_list, 'r') as fh:
pdb_ids = fh.readlines()
except IOError:
print '\nYou did not give me an acceptable PDB ID file.\n'
sys.exit()
# dump a .csv every 20 trials just in case
index = 0
# for each line (PDB ID) in the given file
for pdb_id in pdb_ids:
# check pdb_id
pdb_id = pdb_id.strip()
# fetch the MMTF data of this pdb
try:
pdb_data = fetch(pdb_id)
except:
print '***** %s was not able to be downloaded' % pdb_id
continue
## for each group in the entity_list of this pdb
# check the description for each group of the pdb
# has -L- or -D- as sugars should have these
for ii in range(len(pdb_data.entity_list)):
# reset data holders
has_D = False
has_L = False
# pull out description and make it all lowercase
description = pdb_data.entity_list[ii]['description'].lower()
# only look at types that are not classified as polymers
def from_pdbid(cls, pdbid):
import mmtf
return cls(mmtf.fetch(pdbid))
from mmtf import fetch
# Get the data for 4CUP
decoded_data = fetch("4CUP")
# Print the number of chains
print("PDB Code: " + str(decoded_data.structure_id) + " has " +
str(decoded_data.num_chains) + " chains")
print(
"Group name:" + str(decoded_data.group_list[0]["groupName"]) +
"has the following atomic charges: " +
",".join([str(x) for x in decoded_data.group_list[0]["formalChargeList"]]))
print("PDB Code:" + str(decoded_data.structure_id) + " has " +
str(len(decoded_data.bio_assembly)) + " bioassemblies")
def test_fetch(self):
if _internet_on(BASE_URL):
decoded = fetch("4CUP")
else:
print("Warning - cannot connect to "+BASE_URL)
def test_fetch(self):
decoded = fetch("4CUP")
def round_trip(self,pdb_id):
data_in = fetch(pdb_id)
write_mmtf(pdb_id+".mmtf", data_in, MMTFDecoder.pass_data_on)
data_rt = parse(pdb_id+".mmtf")
self.check_equal(data_in, data_rt)
def test_fetch(self):
decoded = fetch("4CUP")
