def __init__(self, ref_file, alt_files, simple_selection):
self.selection = SelectionParser(simple_selection)
self.ref_struct = PDBParser(PERMISSIVE=True).get_structure(
'ref', ref_file)[0]
assert self.ref_struct, self.logger.error(
"Can't parse the ref file %s".format(ref_file))
if self.selection.generic_numbers != [] or self.selection.helices != []:
if not check_gn(self.ref_struct):
gn_assigner = GenericNumbering(structure=self.ref_struct)
self.ref_struct = gn_assigner.assign_generic_numbers()
self.alt_structs = []
for alt_id, alt_file in enumerate(alt_files):
try:
tmp_struct = PDBParser(PERMISSIVE=True).get_structure(
alt_id, alt_file)[0]
if self.selection.generic_numbers != [] or self.selection.helices != []:
if not check_gn(tmp_struct):
gn_assigner = GenericNumbering(structure=tmp_struct)
self.alt_structs.append(
gn_assigner.assign_generic_numbers())
self.alt_structs[-1].id = alt_id
else:
self.alt_structs.append(tmp_struct)
except Exception as e:
logger.warning("Can't parse the file {!s}\n{!s}".format(
alt_id, e))
self.selector = CASelector(self.selection, self.ref_struct,
self.alt_structs)
def post(self, request):
root, ext = os.path.splitext(request.FILES['pdb_file'].name)
generic_numbering = GenericNumbering(
StringIO(request.FILES['pdb_file'].file.read().decode(
'UTF-8', "ignore")))
out_struct = generic_numbering.assign_generic_numbers()
out_stream = StringIO()
io = PDBIO()
io.set_structure(out_struct)
io.save(out_stream)
print(len(out_stream.getvalue()))
# filename="{}_GPCRdb.pdb".format(root)
return Response(out_stream.getvalue())
def __init__(self, pdb_file=None, pdb_filename=None):
#pdb_file can be either a name/path or a handle to an open file
self.pdb_file = pdb_file
self.pdb_filename = pdb_filename
self.pdb_seq = {}
self.blast = BlastSearch()
self.pdb_struct = self.parse_pdb()
if not check_gn(self.pdb_struct):
gn_assigner = GenericNumbering(structure=self.pdb_struct)
self.pdb_struct = gn_assigner.assign_generic_numbers()
self.target = Protein.objects.get(pk=gn_assigner.prot_id_list[0])
else:
self.target = Protein.objects.get(pk=self.identify_receptor())
