moldbprep

Prepare, standardize and merge molecule databases for virtual screening.

Install

Clone this repository

Open a new terminal and clone this repository

cd ~
git clone https://github.com/schallerdavid/moldbprep

Install dependencies

PyRod is written in python 3.8 and uses molvs (>=0.1.1, is shipped with RDKit and Pandas), RDKit and Pandas which can be easily installed using conda:

conda create -n moldbprep -c conda-forge molvs python=3.8

Create alias for your bash

echo 'alias moldbprep="python3 ~/moldbprep/moldbprep.py"' >> ~/.bashrc

Run examples

Load conda environment

Activate conda environment.

source activate moldbprep

Run standardization of sample dbs.

moldbprep -i /home/david/moldbprep/moldbprep/data/db1.sdf,/home/david/moldbprep/moldbprep/data/db2.sdf,/home/david/moldbprep/moldbprep/data/db3.sdf -o /home/david/Documents/moldbprep -p 4

Run tests

Activate conda environment.

source activate moldbprep

Install pytest

conda install pytest

Run tests

cd moldbprep
pytest

Copyright

Copyright (c) 2020, David Schaller

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.