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rnaimehaom/convert_molecules.py

Forked from leelasd/convert_molecules.py
Created December 17, 2021 20:36
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Convert Smiles code to 3D and save to SDF
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convert_molecules.py
import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
df = pd.read_csv('SMILES.csv')
mols = [Chem.MolFromSmiles(smi) for smi in df.SMILES]
hmols = [Chem.AddHs(m) for m in mols]
for mol in hmols:
AllChem.EmbedMolecule(mol,AllChem.ETKDG())
print(AllChem.UFFOptimizeMolecule(mol,1000))
smiles = list(df.SMILES)
sid = list(df.SOURCE_ID)
libs = df[df.columns[0]]
writer = Chem.SDWriter('TEST.sdf')
for n in range(len(libs)):
hmols[n].SetProp("_Library","%s"%libs[n])
hmols[n].SetProp("_Name","%s"%sid[n])
hmols[n].SetProp("_SourceID","%s"%sid[n])
hmols[n].SetProp("_SMILES","%s"%smiles[n])
writer.write(hmols[n])
writer.close()
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