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ihm

Python package for handling IHM mmCIF and BinaryCIF files

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

Science Score: 49.0%

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
  • ✓
    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

Keywords

integrative-modeling python python3
Last synced: 6 months ago · JSON representation

Repository

Python package for handling IHM mmCIF and BinaryCIF files

Basic Info
  • Host: GitHub
  • Owner: ihmwg
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 4.21 MB
Statistics
  • Stars: 18
  • Watchers: 7
  • Forks: 9
  • Open Issues: 14
  • Releases: 60
Topics
integrative-modeling python python3
Created almost 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

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 integrative/hybrid modeling (IHM) extension. It works with Python 3.6 or later.

To handle non-integrative theoretical models (for example, homology models), see the python-modelcif package which supports files compliant with the ModelCIF extension.

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

Installation with conda, Homebrew or pip

If you are using Anaconda Python, install with

conda install -c conda-forge ihm

On a Mac with Homebrew, install with

brew tap salilab/salilab; brew install ihm

On a Fedora or RedHat Enterprise Linux box, install with

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

On an Ubuntu LTS box, install from our PPA with

apt install software-properties-common; add-apt-repository ppa:salilab/ppa; apt install python3-ihm

Alternatively, install with pip:

pip install ihm

(Note that pip builds a C extension module for faster reading of mmCIF and BinaryCIF files. This requires that your system has a C compiler. If you don't have a C compiler available, the library will read files using pure Python instead.)

Installation from source code

To build and install from a clone of the GitHub repository, run

python setup.py build python setup.py install

Note that this will attempt to build a C extension module for faster reading of mmCIF and BinaryCIF files. This requires that your system has a C compiler and SWIG. If either of these components are missing, the library will fall back to reading files using pure Python instead.

If you want to write BinaryCIF files (or to read them without the C extension module), 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. They will also test the C extension module if it is first built with python setup.py build_ext --inplace.

Owner

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

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

GitHub Events

Total
  • Create event: 11
  • Release event: 8
  • Issues event: 34
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 18
  • Push event: 117
  • Pull request event: 1
  • Fork event: 2
Last Year
  • Create event: 11
  • Release event: 8
  • Issues event: 34
  • Watch event: 2
  • Delete event: 2
  • Issue comment event: 18
  • Push event: 117
  • Pull request event: 1
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 1,154
  • Total Committers: 7
  • Avg Commits per committer: 164.857
  • Development Distribution Score (DDS): 0.029
Past Year
  • Commits: 124
  • Committers: 4
  • Avg Commits per committer: 31.0
  • Development Distribution Score (DDS): 0.081
Top Committers
Name Email Commits
Ben Webb b****n@s****g 1,121
B13nch3n b****1@t****e 13
hankec c****e@h****e 8
grandrea 4****a 5
Rodrigo V Honorato r****o@u****l 3
Brinda Vallat b****t@r****g 3
Christian A. Hanke 3****e 1
Committer Domains (Top 20 + Academic)
rcsb.org: 1 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: 133
  • Total pull requests: 23
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 22 days
  • Total issue authors: 11
  • Total pull request authors: 8
  • Average comments per issue: 1.05
  • Average comments per pull request: 1.35
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 23
  • Pull requests: 1
  • Average time to close issues: 5 days
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.83
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • benmwebb (72)
  • brindakv (23)
  • aozalevsky (15)
  • bienchen (7)
  • saijananiganesan (5)
  • mtrellet (3)
  • jkosinski (2)
  • CAHanke (2)
  • danpf (1)
  • rvhonorato (1)
  • shruthivis (1)
Pull Request Authors
  • bienchen (10)
  • CAHanke (6)
  • benmwebb (4)
  • danpf (1)
  • brindakv (1)
  • rvhonorato (1)
  • aozalevsky (1)
  • grandrea (1)
Top Labels
Issue Labels
enhancement (52) bug (31) invalid (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • pypi 48,080 last-month
  • Total dependent packages: 4
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 77
  • Total maintainers: 1
pypi.org: ihm

Package for handling IHM mmCIF and BinaryCIF files

  • Versions: 60
  • Dependent Packages: 2
  • Dependent Repositories: 2
  • Downloads: 48,080 Last month
Rankings
Downloads: 5.7%
Dependent packages count: 7.4%
Average: 10.5%
Dependent repos count: 11.8%
Forks count: 12.6%
Stargazers count: 15.2%
Maintainers (1)
benmwebb
Last synced: 6 months ago
conda-forge.org: ihm

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 integrative/hybrid modeling (IHM) extension (http://mmcif.wwpdb.org/dictionaries/mmcif_ihm.dic/Index/). It works with Python 3.6 or later. Please see the documentation at https://python-ihm.readthedocs.org/ or some worked examples at https://github.com/ihmwg/python-ihm/tree/main/examples for more details.

  • Versions: 17
  • Dependent Packages: 2
  • Dependent Repositories: 1
Rankings
Dependent packages count: 19.6%
Dependent repos count: 24.1%
Average: 37.1%
Forks count: 52.0%
Stargazers count: 52.7%
Last synced: 6 months ago

Dependencies

setup.py pypi
  • msgpack *
.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