mol_from_smiles_list.py

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
import string

filename_smiles = "/Users/jan/Desktop/diels_alder.smiles"

molecules = []
names = []

with open(filename_smiles, "r") as file:
    for line in file:
        if len(line.split()) == 4:
            name, smiles, energy, filenames = line.split()
            name = name + " " + energy
        else:
            name, smiles = line.split()
        smiles = string.replace(smiles,".[H][H]","",3)
        mol = Chem.MolFromSmiles(smiles)
        names.append(name)
        molecules.append(mol)

print len(molecules)
img = Draw.MolsToGridImage(molecules,molsPerRow=5,legends=[x for x in names],subImgSize=(200,200))
img