Interactive plot for molecules

Script developed to plot any sort of molecular data with molecular compound images hovering in graph.

Libraries used

• NumPy - the fundamental package for array computing with Python

• RDKit - open source toolkit for cheminformatics.

• bokeh - a Python library for creating interactive visualizations for modern web browsers.

Libraries were used in a Miniconda3 environment using python 3.6.13

Instalation

Miniconda3: Installation

numpy

conda install -c anaconda numpy

RDKit

conda install -c rdkit rdkit

bokeh

conda install -c bokeh bokeh

How to use

• Download the code and unzip it on the desirable directory

First, create the molecule images using:

python images.py

Then, to create the interactive plot use:

python interactive_plot.py

Your output will be stored at interactive_plot.html

Observations

The script at images.py has been elaborated using as references the following link and user:

• How would you convert a large sdf file of chemical compounds into individual files containing molecular images? - Oliver Scott

The script at interactive_plot.py has been elaborated using as references the following link:

• Custom Tooltip

The dataset was retrieved from:

• rdkit github

This script will be updated.

Authorship

• Author: Brenda Ferrari (brendaferrari)

Social preview original photo by Brenda Ferrari (brendaferrari)