Data Preparation for HOLO4K about deeppocket HOT 3 CLOSED

import os
from Bio.PDB import PDBParser, PDBIO, Select, Polypeptide
f=open('holo4k.txt','r')
dir='/scratch/rishal/pbsp/data/'
parser = PDBParser()

class LigSelect(Select):
    def __init__(self,ligand):
        self.ligand=ligand
    def accept_residue(self, residue):
        if residue.get_resname() == ligand and not Polypeptide.is_aa(residue,standard=True):
            return 1
        else:
            return 0
for line in f:
    ligand_num=-1
    if not os.path.exists(os.path.join(dir,line.split()[0].split('.pdb')[0].replace('holo4k','holo4k/Dataset'))):
        print(line)
        continue
    for ligand in line.split()[1].split(','):
        ligand_num+=1
        structure = parser.get_structure("protein", os.path.join(dir,line.split()[0]))
        io = PDBIO()
        io.set_structure(structure)
        io.save(os.path.join(dir,line.split()[0].split('.pdb')[0].replace('holo4k','holo4k/Dataset'),'ligand_new'+str(ligand_num)+'.pdb'),LigSelect(ligand))