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#!/usr/bin/python
# -*- coding:utf-8 -*-
import os
import argparse
from data.mmap_dataset import create_mmap
from data.format import VOCAB
from data.converter.pdb_to_list_blocks import pdb_to_list_blocks
from data.converter.blocks_interface import blocks_interface, blocks_cb_interface
from utils.logger import print_log
def parse():
parser = argparse.ArgumentParser(description='Process protein-peptide complexes')
parser.add_argument('--index', type=str, default=None, help='Index file of the dataset')
parser.add_argument('--out_dir', type=str, required=True, help='Output Directory')
parser.add_argument('--pocket_th', type=float, default=10.0,
help='Threshold for determining binding site')
return parser.parse_args()
def process_iterator(items, pocket_th):
for cnt, pdb_id in enumerate(items):
summary = items[pdb_id]
rec_chain, lig_chain = summary['rec_chain'], summary['pep_chain']
non_standard = 0
rec_blocks, lig_blocks = pdb_to_list_blocks(summary['pdb_path'], selected_chains=[rec_chain, lig_chain])
_, (_, pep_if_idx) = blocks_interface(rec_blocks, lig_blocks, 6.0) # 6A for atomic interaction
if len(pep_if_idx) == 0:
continue
try:
_, (pocket_idx, _) = blocks_cb_interface(rec_blocks, lig_blocks, pocket_th) # 10A for pocket size based on CB
except KeyError:
print_log(f'{pdb_id} missing backbone atoms')
continue # missing both CB and backbone atoms
rec_num_units = sum([len(block) for block in rec_blocks])
lig_num_units = sum([len(block) for block in lig_blocks])
data = ([block.to_tuple() for block in rec_blocks], [block.to_tuple() for block in lig_blocks])
rec_seq = ''.join([VOCAB.abrv_to_symbol(block.abrv) for block in rec_blocks])
lig_seq = ''.join([VOCAB.abrv_to_symbol(block.abrv) for block in lig_blocks])
# if '?' in [rec_seq[i] for i in pocket_idx] or '?' in lig_seq:
if '?' in lig_seq:
non_standard = 1 # has non-standard amino acids
yield pdb_id, data, [
len(rec_blocks), len(lig_blocks), rec_num_units, lig_num_units,
rec_chain, lig_chain, rec_seq, lig_seq, non_standard,
','.join([str(idx) for idx in pocket_idx]),
], cnt
def main(args):
if not os.path.exists(args.out_dir):
os.makedirs(args.out_dir)
# 1. get index file
with open(args.index, 'r') as fin:
lines = fin.readlines()
indexes = {}
root_dir = os.path.dirname(args.index)
for line in lines:
line = line.strip().split('\t')
pdb_id = line[0]
indexes[pdb_id] = {
'rec_chain': line[1],
'pep_chain': line[2],
'pdb_path': os.path.join(root_dir, 'pdbs', pdb_id + '.pdb')
}
# 3. process pdb files into our format (mmap)
create_mmap(
process_iterator(indexes, args.pocket_th),
args.out_dir, len(indexes))
print_log('Finished!')
if __name__ == '__main__':
main(parse()) |