Generating Chemdraw 2d Figures from MOL file or Smiles file. Download SAMPL1_Dataset from https://github.com/leelasd/SAMPL1/blob/master/SAMPL1_Dataset.csv.

Fig_from_smiles.py

## installing dependencies
## conda install boost
## conda install rdkit
## Download SAMPL1 database file from leelasd/SAMPL1 github repo
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import AllChem,Draw
import pandas as pd
df=pd.read_csv('SAMPL1_Dataset.csv')
mols = [Chem.MolFromSmiles(smi) for smi in df.SMILES]
for m,name in zip(mols,df.NAME):
        tmp=AllChem.Compute2DCoords(m)
        Draw.MolToFile(m,'SAMPL1/'+name+'.png',size=(300,300),fitImage=True)

Dependencies include

• Matplotlib
• Pandas
• RDkit

It produces output like this