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GEMMI

GEMMI: A library for structural biology - Published in JOSS (2022)

https://github.com/project-gemmi/gemmi

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 3 DOI reference(s) in README and JOSS metadata
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 22 committers (9.1%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

ccp4 cif crystallography mmcif molecular-structures mtz pdb-files protein-structure structural-biology
Last synced: 6 months ago · JSON representation

Repository

macromolecular crystallography library and utilities

Basic Info
Statistics
  • Stars: 283
  • Watchers: 20
  • Forks: 50
  • Open Issues: 14
  • Releases: 22
Topics
ccp4 cif crystallography mmcif molecular-structures mtz pdb-files protein-structure structural-biology
Created about 9 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

CI Build status

GEMMI can help if you work with:

  • macromolecular models (from mmCIF, PDB and mmJSON files),
  • refinement restraints (CIF files) and small molecule models,
  • crystallographic reflections (from MTZ and SF-mmCIF files),
  • electron and other density maps (MRC/CCP4 files),
  • crystallographic symmetries,
  • or if you just read and write CIF/STAR files (where C=Crystallographic).

GEMMI is a C++ library (currently, C++14) accompanied by:

  • command-line tools,
  • Python bindings,
  • Fortran 2003+ interface (in progress),
  • partial WebAssembly bindings,
  • online tools and little data viz projects.

Documentation: http://gemmi.readthedocs.io/en/latest/

GEMMI is an open-source project of CCP4 and Global Phasing Ltd, two major providers of software for macromolecular crystallography.

Citing: JOSS paper.

License: MPLv2, or (at your option) LGPLv3. © 2017-2024 Global Phasing Ltd.

Owner

  • Name: GEMMI
  • Login: project-gemmi
  • Kind: organization

Macromolecular Crystallography / Structural Bioinformatics

JOSS Publication

GEMMI: A library for structural biology
Published
May 04, 2022
DOI
Volume 7, Issue 73, Page 4200
Authors
Marcin Wojdyr ORCID
Global Phasing Ltd., Cambridge, UK
Editor
Kelly Rowland ORCID
Tags
structural biology crystallography CIF
View PDF Review Thread Software Archive

Papers & Mentions

Total mentions: 1

Are the St John's wort Hyp-1 superstructures different?
Last synced: 4 months ago

GitHub Events

Total
  • Create event: 3
  • Commit comment event: 1
  • Release event: 3
  • Issues event: 51
  • Watch event: 53
  • Issue comment event: 88
  • Push event: 158
  • Pull request review comment event: 11
  • Pull request review event: 11
  • Pull request event: 13
  • Fork event: 6
Last Year
  • Create event: 3
  • Commit comment event: 1
  • Release event: 3
  • Issues event: 51
  • Watch event: 53
  • Issue comment event: 88
  • Push event: 158
  • Pull request review comment event: 11
  • Pull request review event: 11
  • Pull request event: 13
  • Fork event: 6

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 4,556
  • Total Committers: 22
  • Avg Commits per committer: 207.091
  • Development Distribution Score (DDS): 0.047
Past Year
  • Commits: 434
  • Committers: 8
  • Avg Commits per committer: 54.25
  • Development Distribution Score (DDS): 0.039
Top Committers
Name Email Commits
Marcin Wojdyr w****r@g****m 4,340
keitaroyam k****m 175
ClAuS Flensburg c****s@g****m 9
Sergei Izmailov s****v@g****m 5
Jack Greisman J****n@g****m 4
Clemens Vonrhein v****n@g****m 4
Paul Bond p****d 3
Dmitriy Marin d****n@i****r 2
Keitaro Yamashita k****m@u****m 1
rimmartin r****r@f****m 1
Alexander Korsunsky a****y@l****e 1
Alexander Shtyrov 6****5 1
ConorFWild 4****d 1
Dominik Tichy t****1@g****m 1
FX Coudert f****t@g****m 1
Kale Kundert k****e@t****t 1
Markus Gerstel m****l@d****k 1
Martin Malý 4****M 1
Matt Swain m****n@m****m 1
Milot Mirdita m****t@m****e 1
Tomáš Raček t****m@k****t 1
richard r****s@g****m 1
Committer Domains (Top 20 + Academic)
globalphasing.com: 2 krab1k.net: 1 mirdita.de: 1 me.com: 1 diamond.ac.uk: 1 thekunderts.net: 1 liu.se: 1 frodo.quantumbioinc.com: 1 users.noreply.gitlab.com: 1 inria.fr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 151
  • Total pull requests: 60
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 17 days
  • Total issue authors: 89
  • Total pull request authors: 17
  • Average comments per issue: 3.28
  • Average comments per pull request: 2.12
  • Merged pull requests: 50
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 40
  • Pull requests: 14
  • Average time to close issues: 8 days
  • Average time to close pull requests: 20 days
  • Issue authors: 30
  • Pull request authors: 7
  • Average comments per issue: 1.58
  • Average comments per pull request: 2.36
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rimmartin (14)
  • CV-GPhL (7)
  • yurivict (5)
  • zhangfq-chemistry (5)
  • dominiquesydow (4)
  • merkys (4)
  • biochem-fan (4)
  • jasondbiggs (3)
  • kmdalton (3)
  • cycle20 (3)
  • jrobsontull (3)
  • isohelio (2)
  • danny305 (2)
  • lpravda (2)
  • aliaksei-chareshneu (2)
Pull Request Authors
  • keitaroyam (31)
  • githubgphl (5)
  • CV-GPhL (4)
  • MartinMalyMM (4)
  • rimmartin (3)
  • paulsbond (2)
  • milot-mirdita (2)
  • akors (2)
  • ConorFWild (2)
  • as2875 (2)
  • kalekundert (2)
  • jrobsontull (2)
  • Dialpuri (1)
  • MergunFrimen (1)
  • richardjgowers (1)
Top Labels
Issue Labels
low-priority (2)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • npm 1 last-month
    • pypi 130,810 last-month
  • Total docker downloads: 47
  • Total dependent packages: 51
    (may contain duplicates)
  • Total dependent repositories: 40
    (may contain duplicates)
  • Total versions: 88
  • Total maintainers: 1
pypi.org: gemmi

library for structural biology

  • Versions: 53
  • Dependent Packages: 44
  • Dependent Repositories: 37
  • Downloads: 130,810 Last month
  • Docker Downloads: 38
Rankings
Dependent packages count: 0.4%
Dependent repos count: 2.4%
Average: 2.5%
Downloads: 2.5%
Docker downloads count: 4.6%
Maintainers (1)
wojdyr
Last synced: 6 months ago
npmjs.org: mtz

MTZ reflection data to density map (structural biology)

  • Versions: 1
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 1 Last month
  • Docker Downloads: 9
Rankings
Stargazers count: 5.3%
Forks count: 5.5%
Dependent packages count: 9.5%
Average: 17.8%
Dependent repos count: 25.3%
Downloads: 43.6%
Maintainers (1)
wojdyr
Last synced: 6 months ago
conda-forge.org: gemmi
  • Versions: 34
  • Dependent Packages: 5
  • Dependent Repositories: 3
Rankings
Dependent packages count: 10.4%
Dependent repos count: 17.9%
Average: 21.9%
Stargazers count: 28.7%
Forks count: 30.6%
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • sphinx >=2.4.4
  • sphinx_rtd_theme >=1.0.0
.github/workflows/ci.yml actions
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  • actions/upload-artifact v3 composite
.github/workflows/codeql.yml actions
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  • github/codeql-action/analyze v2 composite
  • github/codeql-action/autobuild v2 composite
  • github/codeql-action/init v2 composite
.github/workflows/wheels.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • actions/upload-artifact v2 composite
  • pypa/cibuildwheel v1.12.0 composite
.github/workflows/wheels2.yml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • pypa/cibuildwheel v2.11.3 composite