File size: 2,625 Bytes
4947683 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 | #!/usr/bin/python
# -*- coding:utf-8 -*-
import os
import gzip
import shutil
import argparse
import numpy as np
from utils.logger import print_log
from data.format import VOCAB
from data.converter.pdb_to_list_blocks import pdb_to_list_blocks
from data.converter.blocks_to_data import blocks_to_data
from data.mmap_dataset import create_mmap
def parse():
parser = argparse.ArgumentParser(description='Process PDB to monomers')
parser.add_argument('--pdb_dir', type=str, required=True,
help='Directory of pdb database')
parser.add_argument('--out_dir', type=str, required=True,
help='Output directory')
return parser.parse_args()
def process_iterator(data_dir):
tmp_dir = './tmp'
if not os.path.exists(tmp_dir):
os.makedirs(tmp_dir)
for category in os.listdir(data_dir):
category_dir = os.path.join(data_dir, category)
for pdb_file in os.listdir(category_dir):
path = os.path.join(category_dir, pdb_file)
tmp_file = os.path.join(tmp_dir, f'{pdb_file}.decompressed')
try:
# uncompress the file to the tmp file
with gzip.open(path, 'rb') as fin:
with open(tmp_file, 'wb') as fout:
shutil.copyfileobj(fin, fout)
list_blocks, chains = pdb_to_list_blocks(tmp_file, return_chain_ids=True)
except Exception as e:
print_log(f'Parsing {pdb_file} failed: {e}', level='WARN')
continue
for blocks, chain in zip(list_blocks, chains):
item_id = chain + '_' + pdb_file
# data = blocks_to_data(blocks)
num_blocks = len(blocks)
num_units = sum([len(block.units) for block in blocks])
seq = ''.join([block.symbol for block in blocks])
data = blocks_to_data(blocks)
for key in data:
if isinstance(data[key], np.ndarray):
data[key] = data[key].tolist()
# id, data, properties, whether this entry is finished for producing data
yield item_id, data, [num_blocks, num_units, chain, seq]
if os.path.exists(tmp_file):
os.remove(tmp_file)
shutil.rmtree(tmp_dir)
def main(args):
print_log(f'Processing data from directory: {args.pdb_dir}.')
create_mmap(
process_iterator(args.pdb_dir),
args.out_dir)
print_log('Finished!')
if __name__ == '__main__':
main(parse()) |