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modelcif

Python package for handling ModelCIF mmCIF and BinaryCIF files

https://github.com/ihmwg/python-modelcif

Science Score: 67.0%

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

  • ✓
    CITATION.cff file
    Found 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
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Python package for handling ModelCIF mmCIF and BinaryCIF files

Basic Info
  • Host: GitHub
  • Owner: ihmwg
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 2.03 MB
Statistics
  • Stars: 13
  • Watchers: 4
  • Forks: 1
  • Open Issues: 0
  • Releases: 14
Created about 4 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License Citation

README.md

DOI docs conda package pypi package Linux Build Status Windows Build Status codecov

This is a Python package to assist in handling mmCIF and BinaryCIF files compliant with the ModelCIF extension. It works with Python 3.6 or later.

Please see the documentation or some worked examples for more details.

Installation with conda or pip

If you are using Anaconda Python, install with

conda install -c conda-forge modelcif

On a Fedora or RedHat Enterprise Linux box, install with

dnf copr enable salilab/salilab; dnf install python3-modelcif

Alternatively, install with pip:

pip install modelcif

Installation from source code

To build and install from a clone of the GitHub repository, first build and install version 2.6 or later of the python-ihm module. Then run:

python setup.py build python setup.py install

If you want to read or write BinaryCIF files, you will also need the Python msgpack package.

Testing

There are a number of testcases in the test directory. Each one can be run like a normal Python script to test the library. They can also be all run at once using nose or pytest.

Owner

  • Name: IHM Working Group
  • Login: ihmwg
  • Kind: organization

Development of an mmCIF extension dictionary to handle integrative/hybrid models

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Webb"
  given-names: "Benjamin"
title: "python-modelcif"
url: "https://github.com/ihmwg/python-modelcif"
preferred-citation:
  type: article
  authors:
  - family-names: "Vallat"
    given-names: "Brinda"
  - family-names: "Tauriello"
    given-names: "Gerardo"
  - family-names: "Bienert"
    given-names: "Stefan"
  - family-names: "Haas"
    given-names: "Juergen"
  - family-names: "Webb"
    given-names: "Benjamin M."
  - family-names: "Žídek"
    given-names: "Augustin"
  - family-names: "Zheng"
    given-names: "Wei"
  - family-names: "Peisach"
    given-names: "Ezra"
  - family-names: "Piehl"
    given-names: "Dennis W."
  - family-names: "Anischanka"
    given-names: "Ivan"
  - family-names: "Sillitoe"
    given-names: "Ian"
  - family-names: "Tolchard"
    given-names: "James"
  - family-names: "Varadi"
    given-names: "Mihaly"
  - family-names: "Baker"
    given-names: "David"
  - family-names: "Orengo"
    given-names: "Christine"
  - family-names: "Zhang"
    given-names: "Yang"
  - family-names: "Hoch"
    given-names: "Jeffrey C."
  - family-names: "Kurisu"
    given-names: "Genji"
  - family-names: "Patwardhan"
    given-names: "Ardan"
  - family-names: "Velankar"
    given-names: "Sameer"
  - family-names: "Burley"
    given-names: "Stephen K."
  - family-names: "Sali"
    given-names: "Andrej"
  - family-names: "Schwede"
    given-names: "Torsten"
  - family-names: "Berman"
    given-names: "Helen M."
  - family-names: "Westbrook"
    given-names: "John D."
  doi: "10.1016/j.jmb.2023.168021"
  journal: "J Mol Biol"
  month: 7
  start: 168021
  title: "ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models"
  volume: 435
  issue: 14
  year: 2023

GitHub Events

Total
  • Create event: 3
  • Issues event: 16
  • Release event: 3
  • Watch event: 4
  • Issue comment event: 7
  • Push event: 33
Last Year
  • Create event: 3
  • Issues event: 16
  • Release event: 3
  • Watch event: 4
  • Issue comment event: 7
  • Push event: 33

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 1,192
  • Total Committers: 5
  • Avg Commits per committer: 238.4
  • Development Distribution Score (DDS): 0.02
Past Year
  • Commits: 58
  • Committers: 2
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.069
Top Committers
Name Email Commits
Ben Webb b****n@s****g 1,168
B13nch3n b****1@t****e 12
hankec c****e@h****e 8
Rodrigo V Honorato r****o@u****l 3
Christian A. Hanke 3****e@u****m 1
Committer Domains (Top 20 + Academic)
uu.nl: 1 hhu.de: 1 theb-si.de: 1 salilab.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 42
  • Total pull requests: 10
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 1.64
  • Average comments per pull request: 0.9
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 17
  • Pull requests: 0
  • Average time to close issues: 14 days
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gtauriello (18)
  • benmwebb (13)
  • bienchen (9)
  • aozalevsky (2)
Pull Request Authors
  • bienchen (10)
Top Labels
Issue Labels
enhancement (12) bug (6) AlphaFold (2) ModelArchive (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 46,377 last-month
  • Total dependent packages: 1
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 19
  • Total maintainers: 1
pypi.org: modelcif

Package for handling ModelCIF mmCIF and BinaryCIF files

  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 5
  • Downloads: 46,377 Last month
Rankings
Dependent repos count: 6.8%
Downloads: 7.3%
Dependent packages count: 7.4%
Average: 12.9%
Stargazers count: 20.4%
Forks count: 22.8%
Maintainers (1)
benmwebb
Last synced: 6 months ago
conda-forge.org: modelcif

This is a Python package to assist in handling mmCIF (http://mmcif.wwpdb.org/) and BinaryCIF (https://github.com/molstar/BinaryCIF) files compliant with the ModelCIF extension (https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/). It works with Python 3.6 or later. Please see the documentation at https://python-modelcif.readthedocs.org/ or some worked examples at https://github.com/ihmwg/python-modelcif/tree/main/examples for more details.

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 50.2%
Dependent packages count: 51.2%
Forks count: 57.4%
Stargazers count: 58.4%
Last synced: 6 months ago

Dependencies

.github/workflows/codeql-analysis.yml actions
  • actions/checkout v2 composite
  • github/codeql-action/analyze v1 composite
  • github/codeql-action/init v1 composite
.github/workflows/linter.yml actions
  • actions/checkout v2 composite
  • docker://github/super-linter v2.1.0 composite
.github/workflows/testpy.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1 composite
docs/requirements.txt pypi
  • ihm >=0.27
requirements.txt pypi
  • ihm >=0.34
setup.py pypi
  • ihm >=0.34