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rstoolbox

Python Toolbox For Rosetta Silent Files Processing

https://github.com/jaumebonet/rosettasilenttoolbox

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    6 of 10 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.1%) to scientific vocabulary

Keywords

data-analysis data-visualization protein-design protein-sequence science
Last synced: 9 months ago · JSON representation

Repository

Python Toolbox For Rosetta Silent Files Processing

Basic Info
Statistics
  • Stars: 10
  • Watchers: 3
  • Forks: 9
  • Open Issues: 19
  • Releases: 0
Topics
data-analysis data-visualization protein-design protein-sequence science
Created almost 9 years ago · Last pushed almost 5 years ago
Metadata Files
Readme Contributing License Code of conduct

README.rst 

RosettaSilentToolbox
====================

.. image:: https://travis-ci.org/jaumebonet/RosettaSilentToolbox.svg?branch=master
    :target: https://travis-ci.org/jaumebonet/RosettaSilentToolbox
    :alt: Build Status

.. image:: https://coveralls.io/repos/github/jaumebonet/RosettaSilentToolbox/badge.svg?branch=master
    :target: https://coveralls.io/github/jaumebonet/RosettaSilentToolbox?branch=master
    :alt: Coverage Status

.. image:: https://codecov.io/gh/jaumebonet/RosettaSilentToolbox/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/jaumebonet/RosettaSilentToolbox
    :alt: codecov

.. image:: https://img.shields.io/pypi/pyversions/rstoolbox.svg
    :target: https://pypi.org/project/rstoolbox/
    :alt: Python Versions

.. image:: https://api.codacy.com/project/badge/Grade/8e2823ea80984efc8b764f9d8d26ecf6
    :target: https://www.codacy.com/app/jaumebonet/RosettaSilentToolbox?utm_source=github.com&utm_medium=referral&utm_content=jaumebonet/RosettaSilentToolbox&utm_campaign=Badge_Grade
    :alt: Codacy Badge

The ``rstoolbox`` is a python library aimed to the analysis and management of big populations of protein or nucleotide decoys.

.. image:: https://img.shields.io/badge/bioRxiv%20preprint-doi.org/10.1101/428045-blue.svg
    :target: https://doi.org/10.1101/428045
    :alt: bioRxiv

.. image:: https://img.shields.io/badge/BMC%20Bioinformatics-doi.org/10.1186/s12859--019--2796--3-green.svg
    :target: https://doi.org/10.1186/s12859-019-2796-3
    :alt: BMC Bioinformatics

Although inspired by the output of the protein design tool **ROSETTA**, the library aims to be of a wider applicability, and can be
easily set up to retrieve data from other design tools.

It is particularly aimed towards two distinct user profiles:

1. Protein designers comfortable with light scripting to process their data. Ideally, used to work with **Ipython**, for which this library has a particular affinity.
2. Developers that develop new protein design tools/protocols/approaches and wish to benchmark their innovations with previously existing methods.

See a working example notebook at:

.. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/jaumebonet/RosettaSilentToolbox/fd7b663?filepath=notebook
    :alt: Binder

Despite its name, the library **does not require a local installation of ROSETTA**, files can be imported from whatever cluster service the user has access to. That said, some functions can or need to exploit **ROSETTA**. Those functions are few and their requirements are
clearly highlighted on their `documentation `_.

Start using the ``rstoolbox`` is as easy as installing it via pip:

.. code-block:: bash

    pip install rstoolbox


A complete `documentation `_ with detailed explanation for each function is available.

Owner

  • Name: Jaume Bonet
  • Login: jaumebonet
  • Kind: user
  • Location: Lausanne, Switzerland

Computational biologist in the making.

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 346
  • Total Committers: 10
  • Avg Commits per committer: 34.6
  • Development Distribution Score (DDS): 0.182
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jaume Bonet j****t@g****m 283
zanderharteveld z****d@e****h 25
dependabot[bot] s****t@d****m 18
bud-graziano g****b@g****m 6
dependabot-preview[bot] 2****] 5
Zander h****l@t****h 3
Fabian Sesterhenn f****n@e****h 3
zanderharteveld z****d@v****h 1
Fabian Sesterhenn s****e@t****h 1
Zander h****l@t****h 1
Committer Domains (Top 20 + Academic)
epfl.ch: 2 tsf-484-wpa-2-154.epfl.ch: 1 tsf-428-wpa-7-084.epfl.ch: 1 vpn-251-155.epfl.ch: 1 tsf-484-wpa-4-157.epfl.ch: 1 dependabot.com: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 7
  • Total pull requests: 93
  • Average time to close issues: 4 days
  • Average time to close pull requests: 2 months
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 0.29
  • Average comments per pull request: 1.08
  • Merged pull requests: 6
  • Bot issues: 1
  • Bot pull requests: 89
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jaumebonet (2)
  • longlongman (1)
  • FloLangenfeld (1)
  • Chokerino (1)
  • guyujun (1)
  • dependabot-preview[bot] (1)
Pull Request Authors
  • dependabot-preview[bot] (89)
  • jaumebonet (2)
  • FloLangenfeld (2)
  • zanderharteveld (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels
dependencies (89) security (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 23 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 9
  • Total maintainers: 1
pypi.org: rstoolbox

management and analysis of design populations

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 23 Last month
  • Docker Downloads: 0
Rankings
Docker downloads count: 4.5%
Dependent packages count: 10.0%
Forks count: 10.9%
Average: 15.5%
Stargazers count: 18.5%
Dependent repos count: 21.7%
Downloads: 27.5%
Maintainers (1)
Jaume.Bonet
Last synced: 10 months ago

Dependencies

ci/requirements_devel.txt pypi
  • Ipython ==5.8.0 development
  • Ipython ==7.7.0 development
  • codacy-coverage * development
  • coverage >=4.0.3 development
  • coveralls * development
  • pytest >=3.5 development
  • pytest-cov >=2.5 development
  • pytest-mpl >=0.9 development
  • python-coveralls * development
  • sphinx >=1.7 development
  • sphinx-argparse >=0.2.2 development
  • sphinx_bootstrap_theme >=0.6 development
  • tox >=3.0 development
ci/requirements_test.txt pypi
  • distro ==1.4.0 test
  • libconfig ==0.9.2 test
  • matplotlib ==2.2.3 test
  • matplotlib ==3.0.3 test
  • networkx ==2.3 test
  • networkx ==2.2 test
  • pandas ==0.24.2 test
  • pandas ==0.25.0 test
  • pyyaml ==5.1.2 test
  • seaborn ==0.9.0 test
  • six ==1.12.0 test