2_generate_frag_sdf.py

import os
from glob import glob
import shutil
import subprocess
from subprocess import PIPE

nodes = ['CuCu']
# change to the line below to reproduce paper result
# nodes = [i.split('_')[1].split('.sdf')[0] for i in os.listdir('data/conformers') if 'conformers' in i]

# create necessary folders
os.makedirs(f'data/sdf',exist_ok=True)

for node in nodes:
    print(f'Now on node {node}')
    TARGET_DIR = f'data/sdf/{node}/'
    INPUT_SMILES=f'data/fragments_smi/frag_{node}.txt'
    OUTPUT_TEMPLATE=f'hMOF'
    OUT_DIR=f'data/fragments_all/{node}/'
    CORES='18'
    
    # generate sdf of molecular fragments
    print('Generating molecule sdf files...')
    os.makedirs(TARGET_DIR,exist_ok=True)
    subprocess.run([f'python -W ignore utils/rdkit_conf_parallel.py {INPUT_SMILES} {OUTPUT_TEMPLATE} --cores {CORES}'],shell=True,stdout=PIPE,stderr=PIPE)
    for sdf in glob('*.sdf'):
        shutil.move(sdf,TARGET_DIR) 
    
    # generate sdf for fragment and connection atom
    print(f'Generating fragment and connection atom sdf files...')
    os.makedirs(OUT_DIR,exist_ok=True)
    subprocess.run(f'python -W ignore utils/prepare_dataset_parallel.py --table {INPUT_SMILES} --sdf-dir {TARGET_DIR} --out-dir {OUT_DIR} --template {OUTPUT_TEMPLATE} --cores {CORES}',shell=True)

    # filter and merge
    print(f'Filtering and merging ...')
    subprocess.run(f'python -W ignore utils/filter_and_merge.py --in-dir {OUT_DIR} --out-dir {OUT_DIR} --template {OUTPUT_TEMPLATE} --number-of-files {CORES}',shell=True)