From c766aaabfd21f40402961daccfbb0a036e8da390 Mon Sep 17 00:00:00 2001 From: hyunp2 <42776897+hyunp2@users.noreply.github.com> Date: Tue, 26 Sep 2023 13:20:14 -0500 Subject: [PATCH] Update 2_generate_frag_sdf.py --- 2_generate_frag_sdf.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/2_generate_frag_sdf.py b/2_generate_frag_sdf.py index c30b9c8c..069e3fe8 100644 --- a/2_generate_frag_sdf.py +++ b/2_generate_frag_sdf.py @@ -39,13 +39,13 @@ 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) - sdf_path = os.path.join(args.sdf_dir, f'{args.template}_{pid}.sdf') - out_mol_path = os.path.join(args.out_dir, f'{args.template}_mol_{pid}.sdf') - out_frag_path = os.path.join(args.out_dir, f'{args.template}_frag_{pid}.sdf') - out_link_path = os.path.join(args.out_dir, f'{args.template}_link_{pid}.sdf') - out_table_path = os.path.join(args.out_dir, f'{args.template}_table_{pid}.csv') + sdf_path = os.path.join(OUT_DIR, f'{args.template}.sdf') + out_mol_path = os.path.join(OUT_DIR, f'{args.template}_mol.sdf') + out_frag_path = os.path.join(args.out_dir, f'{args.template}_frag.sdf') + out_link_path = os.path.join(args.out_dir, f'{args.template}_link.sdf') + out_table_path = os.path.join(args.out_dir, f'{args.template}_table.csv') prep.run(table_path={INPUT_SMILES}, sdf_path={OUTPUT_TEMPLATE} --out-dir {OUT_DIR} --template {OUTPUT_TEMPLATE} --cores {CORES}) - prep.run(table_path={INPUT_SMILES}, sdf_path={OUTPUT_TEMPLATE}, out_mol_path, out_frag_path, out_link_path, out_table_path,) + prep.run(table_path={INPUT_SMILES}, sdf_path={OUTPUT_TEMPLATE}, out_mol_path=out_mol_path, out_frag_path=out_frag_path, out_link_path=out_link_path, out_table_path=out_table_path) # filter and merge print(f'Filtering and merging ...')