Update 1_fragmentation.py

globus-labs · Sep 18, 2023 · 8fb0882 · 8fb0882
1 parent 2f16896
commit 8fb0882
Showing 1 changed file with 3 additions and 1 deletion.
diff --git 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)