Using RDKit and Ipython notebook is useful for interactive coding.
User can check molecules directly in notebook
It can not only one molecule but also list of molecules. If user want to draw molecules as grid image, MolsToGridImage method is good choice.
Also the method highlight atoms.
Example is following.
from rdkit import Chem from rdkit.Chem import rdBase from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole from rdkit import RDConfig import os sdf = Chem.SDMolSupplier( os.path.join(RDConfig.RDDocsDir, 'Book/data/cdk2.sdf')) mols = [ m for m in sdf ] core = Chem.MolFromSmiles( 'c1ncc2nc[nH]c2n1' ) img = Draw.MolsToGridImage( mols, molsPerRow=3, highlightAtomLists=[ mol.GetSubstructMatch(core) for mol in mols], useSVG=True ) img
User can set Highlight atoms for each molecules. I think it’s very flexible for development.