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https://github.com/prolint/prolint2

Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories.

https://github.com/prolint/prolint2

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.4%) to scientific vocabulary

Keywords

lipid-protein-interactions membrane-proteins molecular-dynamics python-library
Last synced: 6 months ago · JSON representation

Repository

Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories.

Basic Info
Statistics
  • Stars: 7
  • Watchers: 2
  • Forks: 3
  • Open Issues: 3
  • Releases: 18
Topics
lipid-protein-interactions membrane-proteins molecular-dynamics python-library
Created almost 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

ProLint v2: an optimized tool for the analysis of lipid protein interactions.

PyPI LICENSE GitHub Actions Build Status codecov docs

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:

bash conda create -n prolint2 python=3.8 conda activate prolint2

Then you can install prolint2 via pip:

bash pip install prolint2

Basic examples:

Using the Prolint2's API:

```python 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:

bash 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.

Owner

  • Name: ProLint
  • Login: ProLint
  • Kind: organization

Automated analysis and visualization of lipid-protein interactions.

GitHub Events

Total
  • Release event: 2
  • Delete event: 5
  • Push event: 8
  • Pull request event: 6
  • Fork event: 1
  • Create event: 3
Last Year
  • Release event: 2
  • Delete event: 5
  • Push event: 8
  • Pull request event: 6
  • Fork event: 1
  • Create event: 3

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 345
  • Total Committers: 3
  • Avg Commits per committer: 115.0
  • Development Distribution Score (DDS): 0.475
Top Committers
Name Email Commits
Daniel Pastor Ramirez d****e@u****a 181
Besian Sejdiu b****u@g****m 163
HK 6****0@u****m 1
Committer Domains (Top 20 + Academic)
ucalgary.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 43
  • Total pull requests: 57
  • Average time to close issues: 2 months
  • Average time to close pull requests: 12 days
  • Total issue authors: 7
  • Total pull request authors: 3
  • Average comments per issue: 0.4
  • Average comments per pull request: 0.42
  • Merged pull requests: 45
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • danielpastor97 (24)
  • bisejdiu (13)
  • amiel-ab (2)
  • Nancyarvin (1)
  • chelsea-brown (1)
  • yggrdrasil (1)
  • AngusSMacDonald (1)
Pull Request Authors
  • danielpastor97 (39)
  • bisejdiu (17)
  • flop20 (1)
Top Labels
Issue Labels
enhancement (26) documentation (1) bug (1)
Pull Request Labels
enhancement (14) bug (5)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 171 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 17
  • Total maintainers: 1
pypi.org: prolint2

ProLint2: Lipid-Protein Interaction Analysis.

  • Versions: 17
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 171 Last month
Rankings
Dependent packages count: 6.6%
Downloads: 12.8%
Average: 19.3%
Forks count: 23.2%
Stargazers count: 23.3%
Dependent repos count: 30.6%
Maintainers (1)
danielpastor97
Last synced: 6 months ago

Dependencies

.github/workflows/CI.yaml actions
  • actions/checkout v1 composite
  • codecov/codecov-action v2 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/release.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
setup.py pypi
  • bottle *
  • mdanalysis *