ProtPlot.jl

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Protein ribbon plots implemented in Julia using Makie

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# <img width="25%" src="./docs/src/assets/logo.png" align="right" /> ProtPlot

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ProtPlot is a Julia package for rendering 3D protein ribbon and other miscellaneous protein-related plots using [Makie.jl](https://github.com/MakieOrg/Makie.jl).

## Examples

Ribbon plots are constructed from vectors of protein backbones represented as `3x3xL` arrays.
For convenience, argument conversion methods are defined, and the ribbon constructors can take:
- a `3x3xL` array of residue backbone atom coordinates (N, Ca, C), or a vector of these for each chain.
- a `BioStructures.MolecularStructure` or `BioStructures.Chain`.
- a PDB file path.

```julia
using GLMakie # use the GLMakie backend
using ProtPlot

# Create and display a ribbon plot in an interactive window
ribbon_scene("test/data/1ASS.pdb", backgroundcolor=:black, colormap=:jet)
```
![plain gradient](https://raw.githubusercontent.com/MurrellGroup/ProtPlot.jl/main/docs/src/assets/1ASS.png)

## Customizing colors

Use the `colors` keyword argument to customize colors at the residue level. This argument should be a vector of vectors, where each vector contains either:

- values between 0 and 1, representing the colors of each residue in their respective chains according to the `colormap`.
- a list of [`Colorant`s](https://github.com/JuliaGraphics/ColorTypes.jl?tab=readme-ov-file#colortypes), one per residue. For example, `RGBA(1, 0, 0, 0.5)` for a 50% transparent red. Load the `ColorTypes` or `Colors` package to create such `Colorant`s.

```julia
# Load protein data from a PDB file
chains = readpdb("test/data/1ASS.pdb")

colors = rand.(length.(chains))

ribbon_scene(chains, colors=colors, colormap=:hsv)
```
![random colors](https://raw.githubusercontent.com/MurrellGroup/ProtPlot.jl/main/docs/src/assets/1ASS-color.png)

Chains can be colored by chain using something like:

```julia
colormap = [:royalblue, :violet, :limegreen, :chocolate1]
colors = [fill(i-1, l) / (length(colormap)-1) for (i, l) in enumerate(length.(struc))]
ribbon!(scene, chains; colors, colormap)
```

and then you might get something like:

## Camera controls

Makie allows programmatic control over the [camera](https://docs.makie.org/stable/explanations/cameras/index.html).
Use the `camcontrols` keyword to control the initial view in a `ribbon_scene` call:

```julia
ribbon_scene("test/data/1ASS.pdb", camcontrols=(; lookat=Vec3f(30, 0, 60), eyeposition=Vec3f(160, -75, 0), upvector=Vec3f(0, 0, 1)))
```
![camera](https://raw.githubusercontent.com/MurrellGroup/ProtPlot.jl/main/docs/src/assets/1ASS-camera.png)

## See also
- [BioMakie.jl](https://github.com/BioJulia/BioMakie.jl) (designed for more interactivity)

ProtPlot.jl

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