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mmtf-python

The python implementation of the MMTF API, decoder and encoder.

https://github.com/rcsb/mmtf-python

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 14 committers (21.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.2%) to scientific vocabulary

Keywords from Contributors

bioinformatics protein-structure molecular-dynamics computational-chemistry genomics closember molecular-simulation pdb structural-bioinformatics dna
Last synced: 11 months ago · JSON representation

Repository

The python implementation of the MMTF API, decoder and encoder.

Basic Info
  • Host: GitHub
  • Owner: rcsb
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage: http://mmtf.rcsb.org/
  • Size: 12.3 MB
Statistics
  • Stars: 46
  • Watchers: 11
  • Forks: 25
  • Open Issues: 3
  • Releases: 0
Created over 10 years ago · Last pushed about 4 years ago
Metadata Files
Readme Changelog License

README.md

Build Status Version License Changelog

The macromolecular transmission format (MMTF) is a binary encoding of biological structures.

This repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

The MMTF python API is available from pip: pip install mmtf-python

Quick getting started.

1) Get the data for a PDB structure and print the number of chains: ```python from mmtf import fetch

Get the data for 4CUP

decodeddata = fetch("4CUP") print("PDB Code: "+str(decodeddata.structureid)+" has "+str(decodeddata.numchains)+" chains") 2) Show the charge information for the first group: python print("Group name: "+str(decodeddata.group_list[0]["groupName"])+" has the following atomic charges: "+",".join([str(x) for x in decodeddata.grouplist[0]["formalChargeList"]]))

3) Show how many bioassemblies it has: python print("PDB Code: "+str(decodeddata.structureid)+" has "+str(len(decodeddata.bioassembly))+" bioassemblies") ```

Owner

  • Name: RCSB PDB
  • Login: rcsb
  • Kind: organization
  • Location: United States

Github repository of the RCSB Protein Data Bank

GitHub Events

Total
  • Issue comment event: 1
Last Year
  • Issue comment event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 215
  • Total Committers: 14
  • Avg Commits per committer: 15.357
  • Development Distribution Score (DDS): 0.172
Past Year
  • Commits: 8
  • Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
abradle a****y@g****m 178
marshuang80 m****0@g****m 8
Peter Rose p****e@u****u 7
Peter Rose p****d@g****m 6
abradle y****u@e****m 5
Max Linke m****e@g****e 3
yuy079 y****9@u****u 1
Zachary Riedlshah g****t@z****e 1
Danny Farrell d****f@u****u 1
Richard Gowers r****s@g****m 1
richard r****d@n****m 1
dependabot[bot] 4****]@u****m 1
Peter Cock p****k@g****m 1
Jon Wedell j****l@g****m 1
Committer Domains (Top 20 + Academic)
ucsd.edu: 2 nextmovesoftware.com: 1 uw.edu: 1 zacharyrs.me: 1 gmx.de: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 27
  • Total pull requests: 36
  • Average time to close issues: 22 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 14
  • Total pull request authors: 11
  • Average comments per issue: 2.07
  • Average comments per pull request: 0.97
  • Merged pull requests: 35
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • zacharyrs (4)
  • abradle (4)
  • marshuang80 (3)
  • yurivict (3)
  • danpf (2)
  • rathann (2)
  • hainm (2)
  • dkoes (1)
  • pwrose (1)
  • molecules (1)
  • tomnewport (1)
  • dominiquesydow (1)
  • dprada (1)
  • jgreener64 (1)
Pull Request Authors
  • abradle (18)
  • pwrose (6)
  • richardjgowers (2)
  • marshuang80 (2)
  • kain88-de (2)
  • danpf (1)
  • yuy079 (1)
  • zacharyrs (1)
  • jonwedell (1)
  • dependabot[bot] (1)
  • peterjc (1)
Top Labels
Issue Labels
dependencies (1)
Pull Request Labels
dependencies (1)

Packages

  • Total packages: 4
  • Total downloads:
    • pypi 246,877 last-month
  • Total docker downloads: 902
  • Total dependent packages: 13
    (may contain duplicates)
  • Total dependent repositories: 77
    (may contain duplicates)
  • Total versions: 48
  • Total maintainers: 3
pypi.org: mmtf-python

A decoding libary for the PDB mmtf format

  • Versions: 27
  • Dependent Packages: 10
  • Dependent Repositories: 61
  • Downloads: 246,877 Last month
  • Docker Downloads: 902
Rankings
Dependent packages count: 1.1%
Docker downloads count: 1.6%
Dependent repos count: 1.9%
Downloads: 1.9%
Average: 4.0%
Forks count: 7.6%
Stargazers count: 9.7%
Maintainers (2)
abradle marshuang80
Last synced: 12 months ago
proxy.golang.org: github.com/rcsb/mmtf-python
  • Versions: 11
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 4.4%
Stargazers count: 6.1%
Average: 7.7%
Dependent packages count: 9.6%
Dependent repos count: 10.8%
Last synced: 11 months ago
spack.io: py-mmtf-python

The macromolecular transmission format (MMTF) is a binary encoding of biological structures.

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Average: 17.2%
Forks count: 18.5%
Stargazers count: 22.1%
Dependent packages count: 28.1%
Maintainers (1)
adamjstewart
Last synced: 11 months ago
conda-forge.org: mmtf-python

The macromolecular transmission format (MMTF) is a binary encoding of biological structures. This repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.

  • Homepage: http://mmtf.rcsb.org
  • License: Apache-2.0
  • Latest release: 1.1.3
    published about 4 years ago
  • Versions: 9
  • Dependent Packages: 2
  • Dependent Repositories: 16
Rankings
Dependent repos count: 8.8%
Dependent packages count: 19.6%
Average: 25.6%
Forks count: 33.1%
Stargazers count: 41.1%
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • msgpack >=1.0.0
  • nose *
  • numpy *
setup.py pypi
  • msgpack >=1.0.0