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biobox

a toolbox for the manipulation, modelling and analysis of molecular structures

https://github.com/Degiacomi-Lab/biobox

Science Score: 36.0%

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
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 9 committers (55.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary

Keywords from Contributors

molecular-dynamics molecular-modeling protein-structure
Last synced: 10 months ago · JSON representation

Repository

a toolbox for the manipulation, modelling and analysis of molecular structures

Basic Info
  • Host: GitHub
  • Owner: Degiacomi-Lab
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 2.56 MB
Statistics
  • Stars: 27
  • Watchers: 5
  • Forks: 7
  • Open Issues: 0
  • Releases: 7
Created over 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

Biobox provides a collection of data structures and methods for loading, manipulating and analyzing atomistic and pseudoatomistic structures.

Biobox main features: * importing of PDB, PQR and GRO files, possibly containing multiple conformations (e.g. multi-PDB, gro trajectory) * generation of coarse grain shapes composed of specific arrangements of pseudo-atoms * loading and manipulation of density maps, including their transformation into a solid object upon isovalue definition * assemblies of any points arrangement can be produced (i.e. densities converted in solid and geometric shapes can be equally treated).

Allowed operations on structures incude: * generation of assemblies according to custom symmetries * rototranslation and alignment on principal axes * on ensembles: RMSD, RMSF, PCA and clustering * calculation of CCS, SAXS, SASA, convex hull, s2 (for molecules), mass and volume estimation (for densities) * atomselect for molecules and assemblies of molecules * shortest solvent accessible path between atoms on molecule (using lazy Theta* or A*) * density map simulation.

INSTALLATION AND REQUIREMENTS

The best way to install Biobox is via Anaconda conda install biobox -c conda-forge

Biobox can be also installed via pip pip install biobox

Biobox can otherwise be installed manually typing the followin command in the Biobox folder: python setup.py build_ext --inplace followed by python setup.py install. Please make sure the folder where Biobox is located is in your PYTHONPATH.

Biobox requires Python3.x and the following packages: * numpy * scipy * pandas * scikit-learn * cython

Optional external software: * CCS calculation relies on a call to IMPACT (requires definition of IMPACTPATH environment variable) * SAXS simulations rely on a call to crysol, from ATSAS suite (requires definition of ATSASPATH environment variable)

USAGE

Documentation: * Biobox's API is available at https://Degiacomi-Lab.github.io/biobox/

Tutorial: * A Jupyter notebook presenting Biobox's main functionalities is available at https://github.com/Degiacomi-Lab/bioboxnotebook * The notebook can be run directly in a browser via Binder: https://mybinder.org/v2/gh/degiacom/bioboxnotebook/HEAD

CITATION

When using Biobox in your work, please cite: L. S. P. Rudden, S. C. Musson, J. L. P. Benesch, M. T. Degiacomi (2021). Biobox: a toolbox for biomolecular modelling, Bioinformatics

Owner

  • Name: Degiacomi Research Group
  • Login: Degiacomi-Lab
  • Kind: organization
  • Email: matteo.t.degiacomi@durham.ac.uk
  • Location: United Kingdom

GitHub Events

Total
  • Watch event: 3
  • Push event: 1
Last Year
  • Watch event: 3
  • Push event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 130
  • Total Committers: 9
  • Avg Commits per committer: 14.444
  • Development Distribution Score (DDS): 0.562
Past Year
  • Commits: 8
  • Committers: 3
  • Avg Commits per committer: 2.667
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Matteo Degiacomi m****i@g****m 57
Lucas Rudden l****1@b****m 31
DEGIACOMI x****5@d****k 13
SCM s****n@d****k 10
Degiacomi Research Group d****m 8
Lucas Rudden l****n@e****h 5
ccwmca c****a@g****m 2
dclw29 d****9@d****k 2
Lucas Rudden l****n@e****h 2
Committer Domains (Top 20 + Academic)
durham.ac.uk: 3 epfl.ch: 2 btinternet.com: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Total issue authors: 0
  • Total pull request authors: 4
  • Average comments per issue: 0
  • Average comments per pull request: 0.17
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
Pull Request Authors
  • SCMusson (2)
  • dclw29 (2)
  • degiacom (1)
  • ymohit (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 1
conda-forge.org: biobox

Biobox provides a collection of data structures and methods for loading, manipulating, and analyzing atomistic and pseudoatomistic structures.

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 39.7%
Forks count: 47.7%
Stargazers count: 48.3%
Last synced: 11 months ago