ProLint2: Lipid-Protein Interaction Analysis.
Project description
ProLint v2: an optimized tool for the analysis of lipid protein interactions.
Overview
ProLint2 calculates distance-based lipid-protein interactions from molecular dynamics trajectories of membrane protein systems.
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 documentation.
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.
Copyright
Copyright (c) 2022, Daniel P. Ramirez & Besian I. Sejdiu
Acknowledgements
The respository structure of ProLint2 is based on the Computational Molecular Science Python Cookiecutter version 1.6.
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