I found interesting topics in rdkit discuss. How to draw molecule with atom index.
Greg developer of RDKit answered tips to do it. It can use molAtomMapNumber.
https://sourceforge.net/p/rdkit/mailman/message/31663468/
I didn’t know that!
I tried that in my PC. RDKit can draw molecule easily using IPythonConsole.
from rdkit import Chem from rdkit.Chem import Draw from rdkit.Chem.Draw import IPythonConsole IPythonConsole.ipython_useSVG = True def mol_with_atom_index( mol ): atoms = mol.GetNumAtoms() for idx in range( atoms ): mol.GetAtomWithIdx( idx ).SetProp( 'molAtomMapNumber', str( mol.GetAtomWithIdx( idx ).GetIdx() ) ) return mol
Test in a kinase inhibitor
mol = Chem.MolFromSmiles( "C1CC2=C3C(=CC=C2)C(=CN3C1)[C@H]4[C@@H](C(=O)NC4=O)C5=CNC6=CC=CC=C65" )
Draw molecule.
#Default mol #With index mol_with_atom_index(mol)
https://github.com/iwatobipen/chemo_info/blob/master/rdkit_notebook/drawmol_with%2Bidx.ipynb
