Script adapted and developed to plot the molecular similarity in a chemical space grid.
This script has been adapted from iwatobipen, according to the papper written by Atsushi Yoshimori et.al.
I strongly advise to check iwatobipen github and blog if you are interested on chemical space, chemical similarity and other cheminformatics topics.
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pandas - a Python package that provides fast, flexible, and expressive data structures designed to make working with "relational" or "labeled" data both easy and intuitive.
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NumPy - the fundamental package for array computing with Python
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RDKit - Open source toolkit for cheminformatics
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scikit-learn - Machine Learning in Python.
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Matplotlib - a comprehensive library for creating static, animated, and interactive visualizations in Python.
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seaborn - a Python data visualization library based on matplotlib.
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SciPy.org - a Python-based ecosystem of open-source software for mathematics, science, and engineering.
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pyLAPJV - Linear Assignment Problem solver using Jonker-Volgenant algorithm.
Libraries were used in a Miniconda3 environment using python 3.6.13, with exception of pyLAPJV.
Miniconda3: Installation
pandas:
conda install -c anaconda pandas
numpy
conda install -c anaconda numpy
RDKit
conda install -c rdkit rdkit
scikit-learn
conda install -c anaconda scikit-learn
Matplotlib
conda install -c conda-forge matplotlib
seaborn
conda install -c anaconda seaborn
SciPy.org
conda install -c anaconda scipy
pyLAPJV (pip install)
pip3 install lapjv
- Download the code and unzip it on the desirable directory
To run use the following command:
python chemical_space.py
This script has been elaborated using as references the following articles and codes:
The dataset used as example was made publically available by the Government of India as a part of their Drug Discovery Hackathon and is found at the following link:
- Author: Brenda Ferrari (brendaferrari)
Social preview original photo by Brenda Ferrari (brendaferrari)