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BiochemicalAlgorithms

The Biochemical Algorithms Library in Julia

https://github.com/hildebrandtlab/biochemicalalgorithms.jl

Science Score: 44.0%

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
  • ○
    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

The Biochemical Algorithms Library in Julia

Basic Info
  • Host: GitHub
  • Owner: hildebrandtlab
  • License: mit
  • Language: Julia
  • Default Branch: develop
  • Size: 9.01 MB
Statistics
  • Stars: 19
  • Watchers: 4
  • Forks: 11
  • Open Issues: 14
  • Releases: 21
Created about 4 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

BiochemicalAlgorithms

Stable Dev Build Status

BiochemicalAlgorithms.jl is a redesign of the popular Biochemical Algorithms Library (BALL), the largest open source C++-framework of its kind. We focused on three main design goals: efficiency, ease of use and rapid application development (RAD). Our library provides functionality for file I/O, molecular modeling, molecular mechanics methods, and molecular visualization, and hence can serve as a foundation for developing applications within the Julia ecosystem.

Installation

To install BiochemicalAlgorithms, open a Julia REPL, switch to the package mode by pressing ], and type

julia pkg> add BiochemicalAlgorithms

Usage

Here is a simple impression of what you can do with BiochemicalAlgorithms.jl. Central to every application is a System, which is filled with structures by reading in atom coordinates from PDB or PubChem JSON files. The system is preprocessed by the FragmentDB performing three steps: name normalization, reconstruction of missing atoms, and the construction of atomic bonds. The energy of the structure is evaluated using Amber forcefield. With the help of BiochemicalVisualization.jl the structure can be visualized as a ball-and-stick model.

```julia using BiochemicalAlgorithms

Read PDB file from the BiochemicalAlgorithms.jl repository

sys = loadpdb(balldata_path("../test/data/AlaAla.pdb"))

println("Number of atoms: ", natoms(sys)) println("Number of bonds: ", nbonds(sys))

Prepare molecule

fdb = FragmentDB() normalizenames!(sys, fdb) reconstructfragments!(sys, fdb) build_bonds!(sys, fdb) println("Number of bonds: ", nbonds(sys))

Create Amber force field and compute the energy of the system

amber = AmberFF(sys) compute_energy!(amber) println(amber.energy) ```

Documentation

If the previous section whetted your appetite, have a look at our tutorials to get started.

Contributing

You have ideas for improvements, criticism, or ran into problems? You are looking for a feature that you know from BALL? Feedback and contributions are very welcome. Check out our guidelines and use our issue tracker or contact us via e-mail.

Owner

  • Name: hildebrandtlab
  • Login: hildebrandtlab
  • Kind: organization

Citation (CITATION.bib) 

@misc{BiochemicalAlgorithms.jl,
	author  = {Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de> and contributors},
	title   = {BiochemicalAlgorithms.jl},
	url     = {https://github.com/hildebrandtlab/BiochemicalAlgorithms.jl},
	version = {v0.1.0},
	year    = {2022},
	month   = {4}
}

GitHub Events

Total
  • Create event: 90
  • Commit comment event: 27
  • Issues event: 36
  • Release event: 11
  • Watch event: 6
  • Delete event: 66
  • Issue comment event: 18
  • Push event: 298
  • Pull request review comment event: 45
  • Pull request review event: 16
  • Pull request event: 86
Last Year
  • Create event: 90
  • Commit comment event: 27
  • Issues event: 36
  • Release event: 11
  • Watch event: 6
  • Delete event: 66
  • Issue comment event: 18
  • Push event: 298
  • Pull request review comment event: 45
  • Pull request review event: 16
  • Pull request event: 86

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 19
  • Total pull requests: 45
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 8 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 0.37
  • Average comments per pull request: 0.07
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 15
Past Year
  • Issues: 14
  • Pull requests: 33
  • Average time to close issues: 8 days
  • Average time to close pull requests: 4 days
  • Issue authors: 4
  • Pull request authors: 4
  • Average comments per issue: 0.29
  • Average comments per pull request: 0.06
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 8
View more stats
Top Authors
Issue Authors
  • tkemmer (25)
  • jeleclaire (5)
  • anmabu (1)
  • anhi (1)
  • JuliaTagBot (1)
Pull Request Authors
  • tkemmer (56)
  • github-actions[bot] (16)
  • jeleclaire (10)
  • anhi (2)
  • jgreener64 (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
bug (24) enhancement (2) question (2) consistency (2)
Pull Request Labels
bug (22) enhancement (13) release (9) dependencies (7) documentation (5) breaking change (3) consistency (3) blocked (1) github_actions (1)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 4 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 21
juliahub.com: BiochemicalAlgorithms

The Biochemical Algorithms Library in Julia

  • Versions: 21
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4 Total
Rankings
Dependent repos count: 3.2%
Downloads: 3.8%
Average: 7.8%
Dependent packages count: 16.3%
Last synced: 10 months ago

Dependencies

.github/workflows/CI.yml actions
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  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/julia-runtest v1 composite
  • julia-actions/setup-julia v1 composite
.github/workflows/Cleanup.yml actions
  • Mattraks/delete-workflow-runs v2 composite
.github/workflows/DCO.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite
.github/workflows/CompatHelper.yml actions