Embed interactive plot in jupyter notebook with panel #chemoinformatics #RDKit #memo #panel

As you know Jupyter notebook is very useful tool for data scientist. It can analyze scientific data with nice view. And there are lots of packages for data visualization. And I often use matplotlib and seaborn for my task. However few days ago, I found an interesting package named Panel which is high level app and dashbording app for python. I posted another package dash before but I’ve never used panel. So I tried to use panel with rdkit.

Panel can install via conda from pyviz channel or pip. I installed panel by using conda.

After installed panel I tested it.

At first I tried to visualize rdkit mol object. Import packages and molecules.

import numpy as np
import pandas as pd
import os
import panel as pn
from rdkit import Chem
from rdkit import RDPaths
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
import matplotlib.pyplot as plt

sdf = os.path.join(RDPaths.RDDocsDir, 'Book/data/cdk2.sdf')
mols = [m for m in Chem.SDMolSupplier(sdf)]
for m in mols:

Then made IntSlider to set index of molecule which would like to render. Following example uses depends decorator for making interactive view.

slider = pn.widgets.IntSlider(start=0, end=len(mols), step=1, value=0)
def callback(value):
    return Draw.MolToImage(mols[value])
row = pn.Column(slider, callback)

Now molecule was rendered with slider widget.

It seems work well, next I tried to add range slider to draw molecules. Code is almost same as above.

rangeslider = pn.widgets.IntRangeSlider(start=0, end=len(mols), step=1)
def callback(value):
    return Draw.MolsToGridImage(mols[value[0]: value[1]], molsPerRow=5)
pn.Column(rangeslider, callback)

IntRangeSlider returns tuple of user defined value. So I could select range which would like to render on the notebook.

Next example, I tried to make interactive scatter plot of molecular properties.

To do it, I calculated molecular descriptors with rdkit Descriptors class.

from rdkit.Chem import Descriptors
from collections import defaultdict
dlist = Descriptors._descList
desc_dec = defaultdict(list)
for mol in mols:
    for k, f  in dlist:
df = pd.DataFrame(desc_dec)

Following example used Select widget to select x and y axis and FloatSlider for setting alpha of scatter plot.

from matplotlib.figure import Figure, FigureCanvasBase
columns = df.columns.to_list()
x = pn.widgets.Select(options=columns, name='x_', value='MolWt')
y = pn.widgets.Select(options=columns, name='y_', value='qed')
alpha = pn.widgets.FloatSlider(name='alpha', value=0.5)

@pn.depends(x.param.value, y.param.value, alpha.param.value)
def get_plot(x_v, y_v, a):
    with plt.xkcd():
        fig = Figure()
        ax = fig.subplots()
        ax.scatter(df[x_v], df[y_v], c='blue', alpha = a)
        #fig = df.plot.scatter(x_v, x_v)
        return fig
pn.Column(pn.Row(x, y, alpha), get_plot)

I updated matplotlib version to 3.1.3. From version 3.1.2 matplotlib can make plot with xkcd taste. ;) It’s easy to do it just make plot in with plt.xkcd() line.

Now the scatter plot can interactively select axis and alpha params. I would like to know how to get index of each point and get the value. If I can it I could render molecule when I mouse over the point.

I uploaded today’s code my repo.


Interactive plot can’t see from githubrepo or nbvier so if reader has interest the package I recommend to try it your own PC. ;)

Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: