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()
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()
def post (self, request, *args, **kwargs):
frag_sp = FragmentSuperpose(StringIO(request.FILES['pdb_file'].file.read().decode('UTF-8', 'ignore')),request.FILES['pdb_file'].name)
superposed_fragments = []
superposed_fragments_repr = []
if request.POST['similarity'] == 'identical':
if request.POST['representative'] == 'any':
superposed_fragments = frag_sp.superpose_fragments()
else:
superposed_fragments_repr = frag_sp.superpose_fragments(representative=True, state=request.POST['state'])
superposed_fragments = frag_sp.superpose_fragments()
else:
if request.POST['representative'] == 'any':
superposed_fragments = frag_sp.superpose_fragments(use_similar=True)
else:
superposed_fragments_repr = frag_sp.superpose_fragments(representative=True, use_similar=True, state=request.POST['state'])
superposed_fragments = frag_sp.superpose_fragments(use_similar=True)
if superposed_fragments == []:
self.message = "No fragments were aligned."
else:
io = PDBIO()
out_stream = BytesIO()
zipf = zipfile.ZipFile(out_stream, 'a')
for fragment, pdb_data in superposed_fragments:
io.set_structure(pdb_data)
tmp = StringIO()
io.save(tmp)
if request.POST['representative'] == 'any':
zipf.writestr(fragment.generate_filename(), tmp.getvalue())
else:
zipf.writestr("all_fragments//{!s}".format(fragment.generate_filename()), tmp.getvalue())
if superposed_fragments_repr != []:
for fragment, pdb_data in superposed_fragments_repr:
io.set_structure(pdb_data)
tmp = StringIO()
io.save(tmp)
zipf.writestr("representative_fragments//{!s}".format(fragment.generate_filename()), tmp.getvalue())
zipf.close()
if len(out_stream.getvalue()) > 0:
request.session['outfile'] = { 'interacting_moiety_residue_fragments.zip' : out_stream, }
self.outfile = 'interacting_moiety_residue_fragments.zip'
self.success = True
self.zip = 'zip'
self.message = '{:n} fragments were superposed.'.format(len(superposed_fragments))
context = super(FragmentSuperpositionResults, self).get_context_data(**kwargs)
attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
for a in attributes:
if not(a[0].startswith('__') and a[0].endswith('__')):
context[a[0]] = a[1]
return render(request, self.template_name, context)
