Welcome to the ProLint2’s documentation!#

Last updated: Oct 14, 2023

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Overview#

ProLint2 is an efficient and user-friendly framework for the automated analysis and interactive visualization of distance-based lipid-protein interactions from molecular dynamics simulations.

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Table of contents#

Installation#

To install prolint2 we recommend creating a new conda environment as follows:

conda create -n prolint2 python=3.8
conda activate prolint2

Then you can install prolint2 via pip:

pip install prolint2

Basic examples#

Using the Prolint2’s API:

from prolint2 import Universe
from prolint2.sampledata import GIRKDataSample
GIRK = GIRKDataSample()

u = Universe(GIRK.coordinates, GIRK.trajectory)

contacts = u.compute_contacts(cutoff=7) # cutoff in Angstroms

Using the Prolint2’s command-line interface:

prolint2 coordinates.gro trajectory.xtc -c 7

You can find more details on how to use prolint2 in the usage page.

How to contribute?#

If you find a bug in the source code, you can help us by submitting an issue here. Even better, you can submit a Pull Request with a fix.

We really appreciate your feedback!

License#

Source code included in this project is available under the MIT License.

Acknowledgements#

The respository structure of ProLint2 is based on the Computational Molecular Science Python Cookiecutter version 1.6.