def load_pdb_pocket(self, pdb, pdb_dir="/data/databases/pdb/"):
utils = PDBs(pdb_dir)
if not os.path.exists(utils.pdb_pockets_path(pdb)):
utils.update_pdb(pdb)
fpocket = FPocket(utils.pdb_path(pdb))
result = fpocket.hunt_pockets()
mkdir(os.path.dirname(utils.pdb_pockets_path(pdb)))
result.save(utils.pdb_pockets_path(pdb))
with open(utils.pdb_pockets_path(pdb)) as h:
result = json.load(h)
self.pdb_data[pdb]["pockets"] = result
return self.pdb_data[pdb]["pockets"]
def handle(self, *args, **options):
tmp = os.path.abspath(options['tmp'])
if not os.path.exists(tmp):
os.makedirs(tmp)
qs = PDB.objects.filter(code=options["pdb"]) if options["pdb"] else PDB.objects.all()
total = qs.count()
utils = PDBs(options["pdbs_dir"])
with tqdm(qs, total=total) as pbar:
for pdb in pbar:
pbar.set_description(pdb.code)
try:
fpocket2sql = FPocket2SQL()
fpocket2sql.create_or_get_pocket_properties()
fpocket2sql.load_pdb(pdb.code)
fpocket2sql.run_fpocket(options['tmp'],pdb_path=utils.pdb_path(pdb.code),
pockets_path=utils.pdb_pockets_path(pdb.code),
force=options["force"])
fpocket2sql.load_pockets()
# res.delete_dir()
except IOError as ex:
traceback.print_exc()
self.stderr.write("error processing pockets from %s: %s" % (pdb.code, str(ex)))
except Exception as ex:
traceback.print_exc()
raise CommandError(ex)
def handle(self, *args, **options):
if options["verbose"] == 1:
import logging
logging.basicConfig(level=logging.DEBUG)
pdbs = PDBs(options["pdbs_dir"])
pdbs.url_pdb_entries = options["entries_url"]
if not os.path.exists(options["entries_path"]):
pdbs.download_pdb_entries()
pdbio = PDBIO(options['pdbs_dir'] + "/", options['entries_path'],
options['tmp'])
pdbio.init()
try:
pdbs.update_pdb(options['code'])
pdbio.process_pdb(options['code'],
force=options['force'],
pocket_path=pdbs.pdb_pockets_path(
options['code']),
pdb_path=pdbs.pdb_path(options['code']))
except IOError as ex:
traceback.print_exc()
self.stderr.write("error processing pockets from %s: %s" %
(options['code'], str(ex)))
except Exception as ex:
traceback.print_exc()
raise CommandError(ex)