[Rdkit-discuss] Solved! (was, Re: Fwd: Jupyter renders only from the outermost level?)

[Peter S. S. <sh...@gm...>]

In an earlier thread, I reported that I could not get Jupyter to render
except from the outermost level of the notebook. For instance, the
following code would not render Benzene:

----------
from rdkit import Chem
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG, display

m = Chem.MolFromSmiles("c1ccccc1")

def render_mol(m):
    rdDepictor.Compute2DCoords(m)
    drawer = rdMolDraw2D.MolDraw2DSVG(400, 200)
    drawer.DrawMolecule(m)
    drawer.FinishDrawing()
    svg = drawer.GetDrawingText().replace('svg:','')
    SVG(svg)

render_mol(m)
----------

Googling around for something else, I accidentally found out how to make
this work. Namely, replace the last line in render_mol() with:

    display(SVG(svg))

In other words, use the IPython.display.display function. This function
will render to the screen from anywhere in your notebook code. You'll note
I have imported it in the above excerpt.

The suggestion at the time was to use MolsToGridImage(), which is a great
facility, but it might not always be what you want. So I was happy to find
this.

-P.