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All Projects → jgreener64 → Bio3DView.jl

jgreener64 / Bio3DView.jl

Licence: other
A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

Programming Languages

julia
2034 projects

Labels

bioinformaticsstructural-biologyprotein-structurejupyter-notebookplutoijuliastructural-bioinformatics

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Bio3DView.jl

Build status codecov

Bio3DView.jl provides a viewer for molecular structures in Julia. It is a wrapper round the excellent 3Dmol.js package [1]. When used from the REPL or a file, the viewer shows in a popup using Blink.jl. When used from IJulia running in a Jupyter notebook or JupyterLab, or from Pluto.jl, the viewer shows in the output cell. You can also use Bio3DView.jl to generate standalone HTML, e.g. for use in a web page.

[1] Nicholas Rego and David Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics (2015) 31(8): 1322-1324 - link

Contributions and bug reports are welcome.

Installation

Julia v1.0 or later is required. Install Bio3DView from the package mode of the Julia REPL (press ]):

add Bio3DView

Bio3DView uses Requires.jl to minimise dependencies so you will also need to install either Blink, IJulia or Pluto to make this package useful, though you can generate HTML without them. If you are using Blink, you will need to run using Blink before the Bio3DView functions work. To view structural objects from BioStructures.jl you will need to have BioStructures.jl installed.

Usage

See the tutorial notebook.

Citation

If you use Bio3DView, please cite the BioStructures paper where it is mentioned:

Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14):4206-4207 (2020) - link - PDF

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