def process_chain(pdb_path, code, chain_id, pdb_model, props):
chain_pdb_path = cs.make_pdb(pdb_path, code, chain_id, overwrite=True)
qm = QMean.assesment(chain_pdb_path)
residues_qm = qm["residues"]
for k, v in residues_qm.items():
chain, resid, resname = k.split("_")
r = Residue.select().where(
Residue.pdb == pdb_model & Residue.chain == chain
& Residue.resid == int(resid)).first()
for prop, val in v.items():
prop_model = props["qr_" + prop]
if not math.isnan(val):
ResidueProperty(residue=r, property=prop_model,
value=val).save()
del qm["residues"]
for k, v in qm.items():
prop_model = Property.select().where(Property.name == ("q_" +
prop)).first()
ChainProperty(pdb=pdb_model, chain=chain_id, name=k, value=v) #.save()
res = FPocket(chain_pdb_path, chains_dir).hunt_pockets()
for pocket in res.pockets:
rs = ResidueSet(name="ChainPocket%i" % pocket.pocket_num,
pdb=pdb_model)
# rs.save()
for k, v in pocket.properties.items():
prop = "f_" + pocket_prop_map[k]
prop_model = Property.select().where(Property.name == prop).first()
ResidueSetProperty(residue_set=rs, property=prop_model,
value=v) #.save()
res.delete_dir()
def hunt_pockets(pdb):
pocket_data = pdb + ".pocket.json"
if not os.path.exists(pocket_data):
fpo = FPocket(pdb)
result = fpo.hunt_pockets()
result.save(pocket_data)
result.delete_dir()
def process_chain(pdb_path, code, chain_id, pdb_model):
chain_pdb_path = cs.make_pdb(pdb_path, code, chain_id, overwrite=True)
qm = QMean.assesment(chain_pdb_path)
residues_qm = qm["residues"]
for k, v in residues_qm.items():
chain, resid, resname = k.split("_")
r = Residue(pdb=pdb_model,
chain=chain,
resname=resname,
resid=int(resid))
for prop, val in v.items():
if not math.isnan(val):
ResidueProperty(residue=r, name=prop, value=val).save()
del qm["residues"]
for k, v in qm.items():
ChainProperty(pdb=pdb_model, chain=chain.id, name=k, value=v).save()
res = FPocket(chain_pdb_path, chains_dir).hunt_pockets()
for pocket in res.pockets:
rs = ResidueSet(name="ChainPocket%i" % pocket.pocket_num,
pdb=pdb_model)
rs.save()
for k, v in pocket.properties.items():
ResidueSetProperty(residue_set=rs, name=k, value=v).save()
res.delete_dir()
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 run_fpocket(self, tmp="/tmp/pockets/", pdb_path=None):
if not os.path.exists(tmp):
os.makedirs(tmp)
if not pdb_path:
pdb_path = tmp + self.pdb.code + ".pdb"
pockets_path = os.path.abspath(
tmp) + "/" + self.pdb.code + ".pockets.json"
if not os.path.exists(pockets_path):
if not os.path.exists(pdb_path):
with open(pdb_path, "w") as h:
h.write(self.pdb.text)
res = FPocket(pdb_path, tmp).hunt_pockets()
res.save(pockets_path)
with open(pockets_path) as h:
self.res_pockets = json.load(h)
def run_fpocket(self,
tmp="/tmp/pockets/",
pdb_path=None,
pockets_path=None,
force=False):
if not os.path.exists(tmp):
os.makedirs(tmp)
if not pdb_path:
pdb_path = tmp + self.pdb.code + ".pdb"
pockets_path = pockets_path if pockets_path else (
os.path.abspath(tmp) + "/" + self.pdb.code + ".pockets.json")
if force or not os.path.exists(pockets_path):
res = FPocket(pdb_path, tmp).hunt_pockets()
res.save(pockets_path)
else:
_log.debug(f'{pockets_path} already exists')
with open(pockets_path) as h:
self.res_pockets = json.load(h)
def process_domain(domains_dir, chain, dn_start, dn_end, pdb_model):
mkdir(domains_dir)
cs.filter = SelectResidues(chain.id, {
y: 1
for y in [x.id[1] for x in chain.get_residues()][dn_start:dn_end]
})
domain_pdb_path = cs.make_pdb(pdb_path, code, chain.id, overwrite=True)
res = FPocket(domain_pdb_path, domains_dir).hunt_pockets()
for pocket in res.pockets:
rs = ResidueSet(name="DomainPocket%i" % pocket.pocket_num,
pdb=pdb_model)
rs.save()
for k, v in pocket.properties.items():
ResidueSetProperty(residue_set=rs, name=k, value=v).save()
res.delete_dir()
qm = QMean.assesment(domain_pdb_path)
residues_qm = qm["residues"]
del qm["residues"]
for k, v in qm.items():
ChainProperty(pdb=pdb_model, chain=chain.id, name=k, value=v).save()
def complete_pockets(pdb, strdoc, structure, pdbUtils):
pdb_file = pdbUtils.pdb_path(pdb)
pockets_json = pdbUtils.pdb_pockets_path(pdb)
mkdir(os.path.dirname(pockets_json))
if not os.path.exists(pockets_json) or os.path.getsize(pockets_json) < 10:
r = FPocket(pdb_file).hunt_pockets()
r.save(pockets_json)
r.delete_dir()
if os.path.exists(pockets_json):
strdoc.pockets = StructureAnotator.pocket_residue_set(
pockets_json, structure.get_atoms())
from SNDG import init_log
from SNDG.Structure.FPocket import FPocket
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--models_directory", required=True)
parser.add_argument("-l", "--log_path", default=None)
args = parser.parse_args()
assert os.path.exists(args.models_directory), "%s does not exists" % args.models_directory
if not args.log_path:
args.log_path = args.models_directory + "/pocketome.log"
init_log(args.log_path, logging.INFO)
_log = logging.getLogger("pocketome")
with tqdm(glob.glob(args.models_directory + "/*.pdb")) as pbar:
for pdb in pbar:
pbar.set_description(pdb)
try:
pocket_data = pdb + ".json"
if not os.path.exists(pocket_data):
fpo = FPocket(pdb)
result = fpo.hunt_pockets()
result.save(pocket_data)
result.delete_dir()
except Exception as e:
_log.warn(e)