From 8fb088229714d3e731d5297a0246840d8a95e251 Mon Sep 17 00:00:00 2001 From: hyunp2 <42776897+hyunp2@users.noreply.github.com> Date: Mon, 18 Sep 2023 10:45:27 -0500 Subject: [PATCH] Update 1_fragmentation.py --- 1_fragmentation.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/1_fragmentation.py b/1_fragmentation.py index 9c260de6..4afc694d 100644 --- a/1_fragmentation.py +++ b/1_fragmentation.py @@ -5,6 +5,7 @@ import pandas as pd import rdkit.Chem.AllChem as Chem from rdkit.Chem import AllChem +from utils.prepare_data_from_sdf import prepare_sdf def fragmentation(): # data cleaning @@ -101,4 +102,5 @@ def fragmentation(): if not os.path.isfile(f'data/fragments_smi/frag_{node_name}.txt'): # generate fragment SMILES print('Generating SMILES ... ') - subprocess.run(f'python utils/prepare_data_from_sdf.py --sdf_path data/conformers/conformers_{node_name}.sdf --output_path data/fragments_smi/frag_{node_name}.txt --verbose',shell=True) + prepare_sdf() + # subprocess.run(f'python utils/prepare_data_from_sdf.py --sdf_path data/conformers/conformers_{node_name}.sdf --output_path data/fragments_smi/frag_{node_name}.txt --verbose',shell=True)