brendaferrari / interactive_plot

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

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)