def to_file_mmtf(item,
atom_indices='all',
structure_indices='all',
output_filename=None,
check=True):
if check:
from molsysmt.tools.mmtf_MMTFDecoder.is_mmtf_MMTFDecoder import _checking_form
_checking_form(item, check=check)
if output_filename is None:
raise ValueError
from molsysmt.tools.mmtf_MMTFDecoder import extract
from mmtf.api.default_api import write_mmtf, MMTFDecoder
tmp_item = extract(item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
write_mmtf(output_filename, tmp_item, MMTFDecoder.pass_data_on)
tmp_item = output_filename
return tmp_item
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 to_file_mmtf(item,
atom_indices='all',
structure_indices='all',
output_filename=None,
check=True):
if check:
digest_item(item, 'mmtf.MMTFDecoder')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from . import extract
from mmtf.api.default_api import write_mmtf, MMTFDecoder
tmp_item = extract(item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
write_mmtf(output_filename, tmp_item, MMTFDecoder.pass_data_on)
tmp_item = output_filename
return tmp_item
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 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)