From 5c100f2c22174cff547b318356592f7848c350e6 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Mon, 9 Sep 2024 13:19:06 +0000 Subject: [PATCH] build based on 738d3e6 --- dev/.documenter-siteinfo.json | 2 +- dev/index.html | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index b219403..ef95c73 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T12:52:22","documenter_version":"1.7.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T13:19:04","documenter_version":"1.7.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index c793a14..0871065 100644 --- a/dev/index.html +++ b/dev/index.html @@ -3,7 +3,7 @@ 3×3 IdealResidue{Float64}: -1.06447 -0.199174 1.26364 0.646303 -0.529648 -0.116655 - 0.0 0.0 0.0source
ProteinChains.BackboneGeometry — Type
BackboneGeometry(;
+  0.0        0.0        0.0
source
ProteinChains.BackboneGeometry — Type
BackboneGeometry(;
     N_Ca_length = 1.46,
     Ca_C_length = 1.52,
     C_N_length = 1.33,
@@ -11,9 +11,9 @@
     N_Ca_C_angle = 1.94,
     Ca_C_N_angle = 2.03,
     C_N_Ca_angle = 2.13,
-)

Define the idealized bond lengths and bond angles of a protein backbone.

source
ProteinChains.IdealResidue — Type
IdealResidue{T<:AbstractFloat} <: AbstractMatrix{T}
+)

Define the idealized bond lengths and bond angles of a protein backbone.

source
ProteinChains.IdealResidue — Type
IdealResidue{T<:AbstractFloat} <: AbstractMatrix{T}
 
-IdealResidue{T}(backbone_geometry=DEFAULT_BACKBONE_GEOMETRY; template=nothing) where T

A 3x3 matrix representing the idealized geometry of a protein residue, with columns representing the N, Ca, and C atom positions of a residue positioned at the origin.

source
ProteinChains.ProteinChain — Type
ProteinChain{T<:AbstractFloat}

Examples

julia> structure = pdb"1EYE";
+IdealResidue{T}(backbone_geometry=DEFAULT_BACKBONE_GEOMETRY; template=nothing) where T

A 3x3 matrix representing the idealized geometry of a protein residue, with columns representing the N, Ca, and C atom positions of a residue positioned at the origin.

source
ProteinChains.ProteinChain — Type
ProteinChain{T<:AbstractFloat}

Examples

julia> structure = pdb"1EYE";
 [ Info: Downloading file from PDB: 1EYE
 
 julia> structure[1]
@@ -25,11 +25,11 @@
     atoms::Vector{Vector{ProteinChains.Atom{Float64}}} = <field value exceeds max length>
   2 properties:
     numbering::Vector{Int64} = [5, 6, 7, 8, 9, 10, 11, 12, 13, 14  …  265, 266, 267, 268, 269, 270, 271, 272, 273, 274]
-    modelnum::Int64 = 1
source
ProteinChains.ProteinStructure — Type
ProteinStructure{T<:AbstractFloat} <: AbstractVector{ProteinChain{T}}

Examples

julia> pdb"1EYE"
+    modelnum::Int64 = 1
source
ProteinChains.ProteinStructure — Type
ProteinStructure{T<:AbstractFloat} <: AbstractVector{ProteinChain{T}}

Examples

julia> pdb"1EYE"
 1-chain ProteinStructure "1EYE.cif" with 2 dynamic properties:
   2 fields:
     name::String = "1EYE.cif"
     chains::Vector{ProteinChain{Float64}} = <field value exceeds max length>
   2 properties:
     ids::Vector{String} = ["A"]
-    lengths::Vector{Int64} = [253]
source
ProteinChains.append_residue — Method
append_residue(Backbone::Backbone, torsion_angles::Vector{<:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)

Create a new backbone by appending 3 new torsion angles (ψ, ω, ϕ) at the end, using bond lengths and bond angles specified in BackboneGeometry.

source
ProteinChains.prepend_residue — Method
append_residue(Backbone::Backbone, torsion_angles::Vector{<:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)

Create a new backbone by prepending 3 new torsion angles (ψ, ω, ϕ) at the beginning, using bond lengths and bond angles specified in the BackboneGeometry.

Note

The torsion angle order is the same as it would be when appending. The order is not reversed.

source
ProteinChains.renumber! — Method
renumber!(structure::ProteinStructure, mmcif_dict::BioStructures.MMCIFDict)

Renumber the residues in a ProteinStructure object according to the numbering aligned to a reference sequence in the MMCIF file.

source
+ lengths::Vector{Int64} = [253]source
ProteinChains.append_residue — Method
append_residue(Backbone::Backbone, torsion_angles::Vector{<:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)

Create a new backbone by appending 3 new torsion angles (ψ, ω, ϕ) at the end, using bond lengths and bond angles specified in BackboneGeometry.

source
ProteinChains.prepend_residue — Method
append_residue(Backbone::Backbone, torsion_angles::Vector{<:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)

Create a new backbone by prepending 3 new torsion angles (ψ, ω, ϕ) at the beginning, using bond lengths and bond angles specified in the BackboneGeometry.

Note

The torsion angle order is the same as it would be when appending. The order is not reversed.

source
ProteinChains.renumber! — Method
renumber!(structure::ProteinStructure, mmcif_dict::BioStructures.MMCIFDict)

Renumber the residues in a ProteinStructure object according to the numbering aligned to a reference sequence in the MMCIF file.

source