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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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