From 9f7eec7d3fa7377fb352f9e1e26c3897037258de Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Wed, 6 Mar 2024 01:02:49 +0000 Subject: [PATCH] build based on cfec4bf --- dev/.documenter-siteinfo.json | 2 +- dev/backboner/index.html | 4 ++-- dev/protein/index.html | 28 ++++++++++++++-------------- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index b4a280a..84ceccf 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T01:02:16","documenter_version":"1.3.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T01:02:46","documenter_version":"1.3.0"}} \ No newline at end of file diff --git a/dev/backboner/index.html b/dev/backboner/index.html index d82545c..5b17944 100644 --- a/dev/backboner/index.html +++ b/dev/backboner/index.html @@ -21,11 +21,11 @@ 3×12 Backbone{Float64, Matrix{Float64}}: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0source
Backboner.ChainedBonds — Type
ChainedBonds{T <: Real, V <: AbstractVector{T}}

A lazy way to store a backbone as a series of bond lengths, angles, and dihedrals. It can be instantiated from a Backbone or a matrix of bond vectors. It can also be used to instantiate a Backbone using the Backbone(bonds::ChainedBonds) constructor.

Examples

julia> backbone = Protein.readpdb("test/data/1ZAK.pdb")["A"].backbone
+ 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
source
Backboner.ChainedBonds — Type
ChainedBonds{T <: Real, V <: AbstractVector{T}}

A lazy way to store a backbone as a series of bond lengths, angles, and dihedrals. It can be instantiated from a Backbone or a matrix of bond vectors. It can also be used to instantiate a Backbone using the Backbone(bonds::ChainedBonds) constructor.

Examples

julia> backbone = Protein.readpdb("test/data/1ZAK.pdb")["A"].backbone
 3×660 Backbone{Float32, Matrix{Float32}}:
  22.346  22.901  23.227  24.115  24.478  25.289  26.091  26.814  …  23.137  22.572  21.48   22.041  21.808  22.263  21.085
  17.547  18.031  16.793  16.923  15.779  14.65   14.958  13.827     13.041  14.235  14.668  14.866  13.861  13.862  14.233
  23.294  21.993  21.163  20.175  19.336  20.009  21.056  21.652      5.676   5.844   4.974   3.569   2.734   1.355   0.446
 
 julia> bonds = ChainedBonds(backbone)
-ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedrals
source
Backboner.Frame — Type
Frame{T <: Real}
source
Backboner.Frames — Type
Frames{T <: Real} <: AbstractVector{Tuple{QuatRotation{T}, Vector{T}}}

The Frames type is designed to efficiently store and manipulate the rotation and translation of a set of frames.

source
Backboner.append_bonds — Method
append_bonds(backbone, lengths, angles, dihedrals)
source
Backboner.idealize — Function
Note

Zygote must be imported in order to activate the ZygoteIdealizationExt extension, which defines the idealize(::Backbone) method.

source
Backboner.is_knotted — Function
is_knotted(backbone::Backbone)

Check if a backbone is knotted.

source
+ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedralssource
Backboner.Frame — Type
Frame{T <: Real}
source
Backboner.Frames — Type
Frames{T <: Real} <: AbstractVector{Tuple{QuatRotation{T}, Vector{T}}}

The Frames type is designed to efficiently store and manipulate the rotation and translation of a set of frames.

source
Backboner.append_bonds — Method
append_bonds(backbone, lengths, angles, dihedrals)
source
Backboner.idealize — Function
Note

Zygote must be imported in order to activate the ZygoteIdealizationExt extension, which defines the idealize(::Backbone) method.

source
Backboner.is_knotted — Function
is_knotted(backbone::Backbone)

Check if a backbone is knotted.

source
diff --git a/dev/protein/index.html b/dev/protein/index.html index a7b022d..adc8493 100644 --- a/dev/protein/index.html +++ b/dev/protein/index.html @@ -1,20 +1,20 @@ -Protein API · Backboner.jl
GitHub

Protein API

These following functions need to be imported explicitly with using Backboner.Protein

Backboner.Protein.Chain — Type
Chain <: AbstractVector{Residue}

A Chain represents a chain of a protein, and is a vector of Residues, which are instantiated from indexing the chain.

Fields

  • id::AbstractString: A string identifier (usually a single letter).
  • backbone::Backbone: A backbone with a length divisible by 3, to ensure 3 atoms per residue (N, Ca, C).
  • modelnum::Int: The model number of the chain.
  • resnums::Vector{Int}: storing the residue numbers.
  • aavector::Vector{Char}: storing the amino acid sequence.
  • ssvector::Vector{Char}: storing the secondary structure.
source
Backboner.Protein.alphacarbon_angles — Method
alphacarbon_angles(chain::Chain)
-alphacarbon_angles(bonds::ChainedBonds)

Calculate the angles at the alphacarbon atoms (N-Ca-C angles) of a chains backbone, or take directly from a precalculated ChainedBonds instance.

source
Backboner.Protein.alphacarbon_carbonyl_distances — Method
alphacarbon_carbonyl_distances(chain::Chain)
+Protein API · Backboner.jl
GitHub
Protein API
These following functions need to be imported explicitly with using Backboner.Protein
Backboner.Protein.Chain — Type
Chain <: AbstractVector{Residue}
A Chain represents a chain of a protein, and is a vector of Residues, which are instantiated from indexing the chain.
Fields
  • id::AbstractString: A string identifier (usually a single letter).
  • backbone::Backbone: A backbone with a length divisible by 3, to ensure 3 atoms per residue (N, Ca, C).
  • modelnum::Int: The model number of the chain.
  • resnums::Vector{Int}: storing the residue numbers.
  • aavector::Vector{Char}: storing the amino acid sequence.
  • ssvector::Vector{Char}: storing the secondary structure.
source
Backboner.Protein.alphacarbon_angles — Method
alphacarbon_angles(chain::Chain)
+alphacarbon_angles(bonds::ChainedBonds)
Calculate the angles at the alphacarbon atoms (N-Ca-C angles) of a chains backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.alphacarbon_carbonyl_distances — Method
alphacarbon_carbonyl_distances(chain::Chain)
 alphacarbon_carbonyl_distances(backbone::Backbone)
-alphacarbon_carbonyl_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous alpha-carbon and carbonyl atoms in a chain. Returns a vector of distances of length length(chain).
source
Backboner.Protein.carbonyl_angles — Method
carbonyl_angles(chain::Chain)
-carbonyl_angles(bonds::ChainedBonds)
Calculate the angles at the carbonyl atoms (Ca-C-N angles) of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.carbonyl_nitrogen_distances — Method
carbonyl_nitrogen_distances(chain::Chain)
+alphacarbon_carbonyl_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous alpha-carbon and carbonyl atoms in a chain. Returns a vector of distances of length length(chain).
source
Backboner.Protein.carbonyl_angles — Method
carbonyl_angles(chain::Chain)
+carbonyl_angles(bonds::ChainedBonds)
Calculate the angles at the carbonyl atoms (Ca-C-N angles) of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.carbonyl_nitrogen_distances — Method
carbonyl_nitrogen_distances(chain::Chain)
 carbonyl_nitrogen_distances(backbone::Backbone)
-carbonyl_nitrogen_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous carbonyl and nitrogen atoms in a chain. Returns a vector of distances of length length(chain) - 1.
source
Backboner.Protein.nitrogen_alphacarbon_distances — Method
nitrogen_alphacarbon_distances(chain::Chain)
+carbonyl_nitrogen_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous carbonyl and nitrogen atoms in a chain. Returns a vector of distances of length length(chain) - 1.
source
Backboner.Protein.nitrogen_alphacarbon_distances — Method
nitrogen_alphacarbon_distances(chain::Chain)
 nitrogen_alphacarbon_distances(backbone::Backbone)
-nitrogen_alphacarbon_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous nitrogen and alpha-carbon atoms in a chain. Returns a vector of distances of length length(chain).
source
Backboner.Protein.nitrogen_angles — Method
nitrogen_angles(chain::Chain)
+nitrogen_alphacarbon_distances(bonds::ChainedBonds)
Calculate the distances between all pairs of contiguous nitrogen and alpha-carbon atoms in a chain. Returns a vector of distances of length length(chain).
source
Backboner.Protein.nitrogen_angles — Method
nitrogen_angles(chain::Chain)
 nitrogen_angles(backbone::Backbone)
-nitrogen_angles(bonds::ChainedBonds)
Calculate the angles at the nitrogen atoms (C-N-Ca angles) of a chains backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.omega_angles — Method
omega_angles(chain::Chain)
+nitrogen_angles(bonds::ChainedBonds)
Calculate the angles at the nitrogen atoms (C-N-Ca angles) of a chains backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.omega_angles — Method
omega_angles(chain::Chain)
 omega_angles(backbone::Backbone)
-omega_angles(bonds::ChainedBonds)
Calculate the omega (Ω) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.oxygen_coords — Method
oxygen_coords(chain::Chain)
+omega_angles(bonds::ChainedBonds)
Calculate the omega (Ω) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.oxygen_coords — Method
oxygen_coords(chain::Chain)
 oxygen_coords(backbone::Backbone)
Add oxygen atoms to the backbone of a protein, turning the coordinate array from size 3x3xL to 3x4xL-1, where L is the length of the backbone.
Example
julia> chains = readpdb("test/data/1ZAK.pdb")
 2-element Vector{Chain}:
  Chain A with 220 residues
@@ -24,8 +24,8 @@
 3×220 Matrix{Float32}:
  22.6697  25.1719  24.7761  25.8559  …  24.7911   22.7649   22.6578   21.24
  15.7257  13.505   13.5151  11.478      15.0888   12.2361   15.8825   14.2933
- 21.4295  19.5663  22.8638  25.3283      7.95346   4.81901   3.24164  -0.742424        
Note
The oxygen_coords function finds the oxygen atoms to the backbone using idealized geometry, and oxygens atom will on average deviate 0.05 Å from original PDB positions. Moreover, the last oxygen atom is essentially given a random (although deterministic) orientation, as that information is lost when the backbone is reduced to 3 atoms, and there's no next nitrogen atom to compare with.
source
Backboner.Protein.phi_angles — Method
phi_angles(chain::Chain)
+ 21.4295  19.5663  22.8638  25.3283      7.95346   4.81901   3.24164  -0.742424        
Note
The oxygen_coords function finds the oxygen atoms to the backbone using idealized geometry, and oxygens atom will on average deviate 0.05 Å from original PDB positions. Moreover, the last oxygen atom is essentially given a random (although deterministic) orientation, as that information is lost when the backbone is reduced to 3 atoms, and there's no next nitrogen atom to compare with.
source
Backboner.Protein.phi_angles — Method
phi_angles(chain::Chain)
 phi_angles(backbone::Backbone)
-phi_angles(bonds::ChainedBonds)
Calculate the phi (φ) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.psi_angles — Method
psi_angles(chain::Chain)
+phi_angles(bonds::ChainedBonds)
Calculate the phi (φ) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.psi_angles — Method
psi_angles(chain::Chain)
 psi_angles(backbone::Backbone)
-psi_angles(bonds::ChainedBonds)
Calculate the psi (ψ) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.
source
Backboner.Protein.readpdb — Method
readpdb(pdbfile::String)
Loads a protein (represented as a Vector{Protein.Chain}) from a PDB file. Assumes that each residue starts with three atoms: N, CA, C.
source
Backboner.Protein.writepdb — Function
writepdb(protein::Vector{Protein.Chain}, filename)
Write a protein (represented as a Vector{Protein.Chain}s) to a PDB file.
source

+psi_angles(bonds::ChainedBonds)

Calculate the psi (ψ) angles of a chain's backbone, or take directly from a precalculated ChainedBonds instance.

source
Backboner.Protein.readpdb — Method
readpdb(pdbfile::String)

Loads a protein (represented as a Vector{Protein.Chain}) from a PDB file. Assumes that each residue starts with three atoms: N, CA, C.

source
Backboner.Protein.writepdb — Function
writepdb(protein::Vector{Protein.Chain}, filename)

Write a protein (represented as a Vector{Protein.Chain}s) to a PDB file.

source