def create_or_get_pocket_properties(self):
self.pocket_props = {
name: Property.objects.get_or_create(name=name,
description=desc)[0]
for name, desc in fpocket_properties_map.items()
}
self.rsfpocker = ResidueSet.objects.get_or_create(name="FPocketPocket",
description="")[0]
import traceback
from Bio.PDB.PDBParser import PDBParser
from tqdm import tqdm
from SNDG import init_log, mkdir
from SNDG.Structure.ChainSplitter import ChainSplitter
from SNDG.Structure.FPocket import FPocket, fpocket_properties_map
from SNDG.Structure.PDBdb import *
from SNDG.Structure.PDBs import PDBs
from SNDG.Structure.QMean import QMean
init_log(rootloglevel=logging.INFO)
_log = logging.getLogger(__name__)
pocket_prop_map = {v: k for k, v in fpocket_properties_map.items()}
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):