def handle(self, *args, **options):
print("Working on file {}".format(options['pdb_file']))
frag_sp = FragmentSuperpose(options['pdb_file'])
superposed_fragments = frag_sp.superpose_fragments(use_similar=True)
if superposed_fragments == []:
print("No fragments were aligned.")
else:
print("{} fragments were aligned.".format(
len(superposed_fragments)))
io = PDBIO()
zipf = zipfile.ZipFile(options['pdb_file'].replace('.pdb', '.zip'),
'a', zipfile.ZIP_DEFLATED)
for fragment, pdb_data in superposed_fragments:
io.set_structure(pdb_data)
tmp = StringIO()
io.save(tmp)
zipf.writestr(
"all_fragments/{!s}".format(fragment.generate_filename()),
tmp.getvalue())
zipf.close()
