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OpenCADD-KLIFS

OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database - Published in JOSS (2022)

https://github.com/volkamerlab/opencadd

Science Score: 95.0%

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
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    3 of 9 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

molecule
Last synced: 6 months ago · JSON representation

Repository

A Python library for structural cheminformatics

Basic Info
Statistics
  • Stars: 102
  • Watchers: 2
  • Forks: 20
  • Open Issues: 31
  • Releases: 7
Created about 6 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Code of conduct

README.md

OpenCADD

GH Actions Status codecov Documentation Status Conda Version License

DOI DOI

OpenCADD

A Python library for structural cheminformatics.

Overview

Some modules of this library are still in early stages of development as indicated below.

  • databases.klifs: utilities to query the KLIFS database, offline or online.
  • :construction: io: read and write molecules from/to files.
  • :construction: structure.pocket: identification and analysis of protein (sub)pockets.
  • :construction: structure.superposition (formerly superposer): superimpose macromolecules using sequence and structural information.

Documentation

The documentation is available here.

Citation

If you are using the OpenCADD-KLIFS module, please cite our JOSS publication:

@article{Sydow2022, doi = {10.21105/joss.03951}, url = {https://doi.org/10.21105/joss.03951}, year = {2022}, publisher = {The Open Journal}, volume = {7}, number = {70}, pages = {3951}, author = {Dominique Sydow and Jaime Rodríguez-Guerra and Andrea Volkamer}, title = {OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database}, journal = {Journal of Open Source Software} }

If you are using other modules of the OpenCADD package, please cite our Zenodo entry.

License

opencadd is free software and is licensed under the MIT license. Copyright (c) 2020, Volkamer Lab

Authors

opencadd is the cumulative work of several members of the Volkamer Lab, as well as contributions from students that have participated in our lab. In no particular order:

  • Jaime Rodríguez-Guerra, PhD
  • Dominique Sydow
  • Dennis Köser, Annie Pham, Enes Kurnaz, Julian Pipart (structural superposition, 2020)

Acknowledgements

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

Owner

  • Name: Volkamer Lab
  • Login: volkamerlab
  • Kind: organization
  • Location: Berlin, Germany

JOSS Publication

OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database
Published
February 17, 2022
DOI
Volume 7, Issue 70, Page 3951
Authors
Dominique Sydow ORCID
_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
Jaime Rodríguez-Guerra ORCID
_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
Andrea Volkamer ORCID
_In Silico_ Toxicology and Structural Bioinformatics, Institute of Physiology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
Editor
Richard Gowers ORCID
Tags
KLIFS kinase
View PDF Review Thread Software Archive

GitHub Events

Total
  • Issues event: 1
  • Watch event: 9
  • Delete event: 3
  • Issue comment event: 6
  • Push event: 9
  • Pull request review event: 5
  • Pull request review comment event: 3
  • Pull request event: 6
  • Fork event: 2
  • Create event: 2
Last Year
  • Issues event: 1
  • Watch event: 9
  • Delete event: 3
  • Issue comment event: 6
  • Push event: 9
  • Pull request review event: 5
  • Pull request review comment event: 3
  • Pull request event: 6
  • Fork event: 2
  • Create event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 857
  • Total Committers: 9
  • Avg Commits per committer: 95.222
  • Development Distribution Score (DDS): 0.26
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Unknown d****w@p****e 634
Jaime RGP j****e@g****m 107
pipaj97 6****7 64
Dennis Köser d****r@g****m 23
Enes e****i@g****m 17
Annie Pham a****m@z****e 9
Daniel S. Katz d****z@i****g 1
Armin Ariamajd a****m@f****e 1
dominiquesydow d****w@c****e 1
Committer Domains (Top 20 + Academic)
charite.de: 1 fu-berlin.de: 1 ieee.org: 1 zedat.fu-berlin.de: 1 posteo.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 52
  • Total pull requests: 65
  • Average time to close issues: 2 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 15
  • Total pull request authors: 8
  • Average comments per issue: 1.67
  • Average comments per pull request: 1.68
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 17 days
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dominiquesydow (23)
  • jaimergp (9)
  • ojeda-e (3)
  • andrewtarzia (3)
  • schallerdavid (2)
  • pipaj97 (2)
  • noahharrison64 (2)
  • njbamboo (1)
  • AndreaVolkamer (1)
  • ljmartin (1)
  • Carlbullish (1)
  • mcs07 (1)
  • yanz-24 (1)
  • kabu00002 (1)
  • seymasoyler (1)
Pull Request Authors
  • dominiquesydow (45)
  • pipaj97 (10)
  • AAriam (6)
  • Armin-Ariamajd (1)
  • jaimergp (1)
  • schallerdavid (1)
  • Allend95 (1)
  • danielskatz (1)
Top Labels
Issue Labels
module-structure-superposition (11) joss-review (7) module-databases-klifs (7) enhancement (6) documentation (2) module-io (2) module-structure-pocket (2) module-structure (1)
Pull Request Labels
module-databases-klifs (13) enhancement (10) module-structure-superposition (9) documentation (5) joss-review (4) module-io (2) module-structure-pocket (1) module-utils (1) not-continued (1) module-compounds-standardization (1)

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 1
    (may contain duplicates)
  • Total versions: 14
proxy.golang.org: github.com/volkamerlab/opencadd
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
conda-forge.org: opencadd

A Python library for structural cheminformatics

  • Versions: 7
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent packages count: 19.6%
Dependent repos count: 24.3%
Average: 30.2%
Stargazers count: 36.8%
Forks count: 40.2%
Last synced: 6 months ago

Dependencies

.github/workflows/ci.yaml actions
  • actions/checkout v3 composite
  • codecov/codecov-action v1 composite
  • conda-incubator/setup-miniconda v2 composite
.github/workflows/docs.yaml actions
  • actions/checkout v3 composite
  • conda-incubator/setup-miniconda v2 composite
setup.py pypi