Remove Protein submodule and Zygote extension, torsional -> torsion

MurrellGroup · Sep 1, 2024 · 0cf7f2b · 0cf7f2b
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diff --git a/Project.toml b/Project.toml
@@ -1,35 +1,25 @@
 name = "Backboner"
 uuid = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
 authors = ["Anton Oresten <anton.oresten42@gmail.com>"]
-version = "0.11.4"
+version = "0.12.0"
 
 [deps]
-BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Rotations = "6038ab10-8711-5258-84ad-4b1120ba62dc"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
-[weakdeps]
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
-[extensions]
-ZygoteIdealizationExt = ["Zygote"]
-
 [compat]
-BioStructures = "4"
 LinearAlgebra = "1"
 NNlib = "0.9"
 PrecompileTools = "1"
 Rotations = "1"
 StaticArrays = "1"
-Zygote = "0.6"
 julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Test", "Zygote"]
+test = ["Test"]
diff --git a/README.md b/README.md
@@ -10,10 +10,10 @@ This package offers types and functions for working with molecular *backbones*,
 
 Backbones can be represented with different types:
 - `Backbone`: a type containing a 3xN matrix of coordinates
-- `ChainedBonds`: a type that holds vectors of bond lengths, bond angles, and dihedral angles
+- `ChainedBonds`: a type that holds vectors of bond lengths, bond angles, and torsion angles
 - `Frames`: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)
 
-The `Protein` submodule contains utilities for working specifically with proteins. A protein can be loaded from a PDB file using the `Backboner.Protein.readpdb` function, which returns a `Vector{Backboner.Protein.Chain}`. Conversely, a `Vector{Backboner.Protein.Chain}` instance can be written to a PDB file using the `writepdb` function.
+Most functions are implemented especially with differentiability in mind, and can be used in combination with automatic differentiation packages like [Zygote.jl](https://github.com/FluxML/Zygote.jl).
 
 ## Installation
 
@@ -26,48 +26,25 @@ add Backboner
 ## Example usage
 
 ```julia
-julia> using Backboner, Backboner.Protein
-
-julia> chains = readpdb("test/data/1ZAK.pdb")
-2-element Vector{Chain}:
- Chain A with 220 residues
- Chain B with 220 residues
-
-julia> backbone = chains[1].backbone
-660-element Backbone{Float64, Matrix{Float64}}:
- [22.346, 17.547, 23.294]
- [22.901, 18.031, 21.993]
- [23.227, 16.793, 21.163]
- [24.115, 16.923, 20.175]
- [24.478, 15.779, 19.336]
- ⋮
- [21.480, 14.668, 4.974]
- [22.041, 14.866, 3.569]
- [21.808, 13.861, 2.734]
- [22.263, 13.862, 1.355]
- [21.085, 14.233, 0.446]
+julia> using Backboner
+
+julia> backbone = Backbone(rand(Float32, 3, 9))
+10-element Backbone{Float32, Matrix{Float32}}:
+ [0.48967552, 0.91008425, 0.5339774]
+ [0.2951318, 0.38963223, 0.8952989]
+ [0.83763623, 0.5279301, 0.3407849]
+ [0.88848716, 0.643387, 0.76827604]
+ [0.697279, 0.63588345, 0.0889622]
+ [0.08590478, 0.6086006, 0.6478121]
+ [0.06308746, 0.6704904, 0.55852276]
+ [0.46147835, 0.56259614, 0.7884294]
+ [0.9694153, 0.052023113, 0.08127427]
 
 julia> ChainedBonds(backbone)
-ChainedBonds{Float64, Vector{Float64}} with 659 bonds, 658 angles, and 657 dihedrals
+ChainedBonds{Float32, Vector{Float32}} with 8 bond lengths, 7 bond angles, and 6 torsion angles
 
 julia> is_knotted(backbone)
 false
-
-julia> import Zygote # unlock the `idealize` method for backbones
-
-julia> idealize(backbone, Float64[1.46, 1.52, 1.33], Float64[1.94, 2.04, 2.13])
-660-element Backbone{Float64, Matrix{Float64}}:
- [22.348574, 17.582397, 23.289886]
- [22.90583, 17.977451, 21.999538]
- [23.216103, 16.762234, 21.140835]
- [24.204561, 16.88515, 20.259508]
- [24.52946, 15.827013, 19.307465]
- ⋮
- [21.501173, 14.705252, 4.9825864]
- [22.007494, 14.864742, 3.5582967]
- [21.822643, 13.836198, 2.7356021]
- [22.24875, 13.874594, 1.3396943]
- [21.091076, 14.233609, 0.42247167]
 ```
 
 [^1]: In some contexts, the term *backbone* may be used more loosely, and allow for atoms that are not part of the main continuous chain of atoms. This package does not support storing e.g. oxygen and beta-carbon atoms in the matrix of coordinates, as they are not part of the continuous chain of atoms.
diff --git a/docs/make.jl b/docs/make.jl
@@ -10,8 +10,7 @@ makedocs(;
     doctest = false,
     pages = [
         "Overview" => "index.md",
-        "Backboner API" => "backboner.md",
-        "Protein API" => "protein.md",
+        "API Reference" => "API.md",
     ],
     authors = "Anton Oresten",
     checkdocs = :all,

diff --git a/docs/src/backboner.md → docs/src/API.md b/docs/src/backboner.md → docs/src/API.md
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -13,12 +13,14 @@ end
 [![Build Status](https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml?query=branch%3Amain)
 [![Coverage](https://codecov.io/gh/MurrellGroup/Backboner.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/MurrellGroup/Backboner.jl)
 
-Backboner is a Julia package that offers a set of types and functions for working with molecular *backbones*: defined here as continuous chains of bonded atoms.[^1] The package provides a few different types for representing backbones:
+This package offers types and functions for working with molecular *backbones*, defined here as continuous chains of bonded atoms.[^1]
+
+Backbones can be represented with different types:
 - `Backbone`: a type containing a 3xN matrix of coordinates
-- `ChainedBonds`: a type that holds vectors of bond lengths, bond angles, and dihedral angles
+- `ChainedBonds`: a type that holds vectors of bond lengths, bond angles, and torsion angles
 - `Frames`: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)
 
-The `Protein` submodule contains functions and types for working specifically with proteins. A protein can be loaded from a PDB file using the `Backboner.Protein.readpdb` function, which returns a `Vector{Backboner.Protein.Chain}`. Conversely, a `Vector{Backboner.Protein.Chain}` instance can be written to a PDB file using the `writepdb` function.
+Most functions are implemented especially with differentiability in mind, and can be used in combination with automatic differentiation packages like [Zygote.jl](https://github.com/FluxML/Zygote.jl).
 
 [View the source code on GitHub](https://github.com/MurrellGroup/Backboner.jl) (licensed under MIT).
 
@@ -33,48 +35,25 @@ add Backboner
 ## Example usage
 
 ```julia
-julia> using Backboner, Backboner.Protein
-
-julia> chains = readpdb("test/data/1ZAK.pdb")
-2-element Vector{Chain}:
- Chain A with 220 residues
- Chain B with 220 residues
-
-julia> backbone = chains[1].backbone
-660-element Backbone{Float64, Matrix{Float64}}:
- [22.346, 17.547, 23.294]
- [22.901, 18.031, 21.993]
- [23.227, 16.793, 21.163]
- [24.115, 16.923, 20.175]
- [24.478, 15.779, 19.336]
- ⋮
- [21.48, 14.668, 4.974]
- [22.041, 14.866, 3.569]
- [21.808, 13.861, 2.734]
- [22.263, 13.862, 1.355]
- [21.085, 14.233, 0.446]
+julia> using Backboner
+
+julia> backbone = Backbone(rand(Float32, 3, 9))
+10-element Backbone{Float32, Matrix{Float32}}:
+ [0.48967552, 0.91008425, 0.5339774]
+ [0.2951318, 0.38963223, 0.8952989]
+ [0.83763623, 0.5279301, 0.3407849]
+ [0.88848716, 0.643387, 0.76827604]
+ [0.697279, 0.63588345, 0.0889622]
+ [0.08590478, 0.6086006, 0.6478121]
+ [0.06308746, 0.6704904, 0.55852276]
+ [0.46147835, 0.56259614, 0.7884294]
+ [0.9694153, 0.052023113, 0.08127427]
 
 julia> ChainedBonds(backbone)
-ChainedBonds{Float64, Vector{Float64}} with 659 bonds, 658 angles, and 657 dihedrals
+ChainedBonds{Float32, Vector{Float32}} with 8 bond lengths, 7 bond angles, and 6 torsion angles
 
 julia> is_knotted(backbone)
 false
-
-julia> import Zygote # unlock the `idealize` method for backbones
-
-julia> idealize(backbone, Float64[1.46, 1.52, 1.33], Float64[1.94, 2.04, 2.13])
-660-element Backbone{Float64, Matrix{Float64}}:
- [22.348574, 17.582397, 23.289886]
- [22.90583, 17.977451, 21.999538]
- [23.216103, 16.762234, 21.140835]
- [24.204561, 16.88515, 20.259508]
- [24.52946, 15.827013, 19.307465]
- ⋮
- [21.501173, 14.705252, 4.9825864]
- [22.007494, 14.864742, 3.5582967]
- [21.822643, 13.836198, 2.7356021]
- [22.24875, 13.874594, 1.3396943]
- [21.091076, 14.233609, 0.42247167]
 ```
 
 [^1]: In some contexts, the term *backbone* may be used more loosely, and allow for atoms that are not part of the main continuous chain of atoms. This package does not support storing e.g. oxygen and beta-carbon atoms in the matrix of coordinates, as they are not part of the continuous chain of atoms.
diff --git a/docs/src/protein.md b/docs/src/protein.md
diff --git a/ext/ZygoteIdealizationExt.jl b/ext/ZygoteIdealizationExt.jl
diff --git a/src/Backboner.jl b/src/Backboner.jl
@@ -8,22 +8,16 @@ export prepend_bonds!, prepend_bonds
 export get_bond_vectors
 export get_bond_lengths
 export get_bond_angles
-export get_torsional_angles
+export get_torsion_angles
 
 export Frames
 
 export is_knotted
 
-export idealize
-
-export Protein
-
 include("backbone.jl")
 include("bonds.jl")
 include("frames.jl")
 include("knots.jl")
-include("idealization.jl")
-include("protein/protein.jl")
 
 using PrecompileTools
 
@@ -33,8 +27,9 @@ using PrecompileTools
     bonds = ChainedBonds(backbone)
     Backbone(bonds)
 
-    frames = Frames(backbone, Protein.STANDARD_TRIANGLE_ANGSTROM)
-    Backbone(frames, Protein.STANDARD_TRIANGLE_ANGSTROM)
+    standard = randn(3,3)
+    frames = Frames(backbone, standard)
+    Backbone(frames, standard)
 
     is_knotted(backbone)
 end