diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 6fae98d..c7c6f83 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-23T14:16:43","documenter_version":"1.7.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-10-24T16:11:06","documenter_version":"1.7.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index e2d55f6..d0aa2fd 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,9 +1,9 @@ -Home · ProteinChains.jl
GitHub

ProteinChains

Documentation for ProteinChains.

ProteinChains.STANDARD_RESIDUE_TEMPLATE — Constant
STANDARD_RESIDUE_TEMPLATE

This is a template of a "standard residue", with a very specific and distinct shape, size, and orientation. which needs to be consistent if we want to represent protein structures as sets of residue rotations and translations.

Thus, we can use this residue as a template for aligning other residues with very precise geometry to it.

julia> IdealResidue{Float64}(BackboneGeometry(N_Ca_C_angle = 1.93); template=ProteinChains.STANDARD_RESIDUE_TEMPLATE)
+Home · ProteinChains.jl
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ProteinChains
Documentation for ProteinChains.
ProteinChains.STANDARD_RESIDUE_TEMPLATE — Constant
STANDARD_RESIDUE_TEMPLATE
This is a template of a "standard residue", with a very specific and distinct shape, size, and orientation. which needs to be consistent if we want to represent protein structures as sets of residue rotations and translations.
Thus, we can use this residue as a template for aligning other residues with very precise geometry to it.
julia> IdealResidue{Float64}(BackboneGeometry(N_Ca_C_angle = 1.93); template=ProteinChains.STANDARD_RESIDUE_TEMPLATE)
 3×3 IdealResidue{Float64}:
  -1.06447   -0.199174   1.26364
   0.646303  -0.529648  -0.116655
-  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.IndexableProperty — Type
IndexableProperty <: AbstractProperty
+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.IndexableProperty — Type
IndexableProperty <: AbstractProperty
 
 IndexableProperty(value::AbstractArray)
An AbstractArray property with size (dims..., length(chain)), and residue indexing of the chain being propagated to the last dimension of the array.
julia> chain = pdb"1ASS"A;
 
@@ -23,10 +23,10 @@
 false
 
 julia> chain.y[:,1:10] == chain[1:10].y
-true
source
ProteinChains.PersistentProperty — Type
PersistentProperty(value)
A property of arbitrary type that persists after residue indexing of a chain.
julia> chain = addproperties(pdb"1ASS"A; x=PersistentProperty(1));
+true
source
ProteinChains.PersistentProperty — Type
PersistentProperty(value)
A property of arbitrary type that persists after residue indexing of a chain.
julia> chain = addproperties(pdb"1ASS"A; x=PersistentProperty(1));
 
 julia> chain.x == chain[1:10].x
-true
source
ProteinChains.ProteinChain — Type
ProteinChain{T<:Real,Ps<:NamedProperties}
Represents a protein chain with a basic set of fields from which some other properties might be derived. The addproperties function can be used to instantiate new chains with additional properties.
Fields
  • id::String: Identifier for the protein chain.
  • atoms::Vector{Vector{Atom{T}}}: List of atoms in each residue.
  • sequence::String: Amino acid sequence of the protein.
  • numbering::Vector{Int32}: Residue numbering (author). See renumber for renumbering.
  • properties::Ps: Named properties associated with the chain.
See also addproperties, PersistentProperty, IndexableProperty. ```
source
ProteinChains.ProteinStructure — Type
ProteinStructure{T} <: AbstractVector{ProteinChain{T}}
Fields
  • name::String: Usually just the base name of the original file.
  • atoms::Vector{Atom{T}}: free atoms from the structure that were not part of any protein chain.
  • chains::Vector{<:ProteinChain{T}}: a collection of ProteinChains.
Examples
julia> structure = pdb"1ASS"
source
ProteinChains.ProteinStructureStore — Type
ProteinStructureStore <: AbstractDict{String,ProteinStructure}
A mutable struct representing a store for protein structures using HDF5 file format.
The struct implements the AbstractDict interface, allowing for dictionary-like operations.
A ProteinStructureStore gets closed when there no longer exists a program-accessible reference to it.
Examples
julia> store = ProteinStructureStore("store.h5")
+true
source
ProteinChains.ProteinChain — Type
ProteinChain{T<:Real,Ps<:NamedProperties}
Represents a protein chain with a basic set of fields from which some other properties might be derived. The addproperties function can be used to instantiate new chains with additional properties.
Fields
  • id::String: Identifier for the protein chain.
  • atoms::Vector{Vector{Atom{T}}}: List of atoms in each residue.
  • sequence::String: Amino acid sequence of the protein.
  • numbering::Vector{Int32}: Residue numbering (author). See renumber for renumbering.
  • properties::Ps: Named properties associated with the chain.
See also addproperties, PersistentProperty, IndexableProperty. ```
source
ProteinChains.ProteinStructure — Type
ProteinStructure{T} <: AbstractVector{ProteinChain{T}}
Fields
  • name::String: Usually just the base name of the original file.
  • atoms::Vector{Atom{T}}: free atoms from the structure that were not part of any protein chain.
  • chains::Vector{<:ProteinChain{T}}: a collection of ProteinChains.
Examples
julia> structure = pdb"1ASS"
source
ProteinChains.ProteinStructureStore — Type
ProteinStructureStore <: AbstractDict{String,ProteinStructure}
A mutable struct representing a store for protein structures using HDF5 file format.
The struct implements the AbstractDict interface, allowing for dictionary-like operations.
A ProteinStructureStore gets closed when there no longer exists a program-accessible reference to it.
Examples
julia> store = ProteinStructureStore("store.h5")
 ProteinStructureStore with 0 entries
 
 julia> store["3HFM"] = pdb"3HFM"
@@ -44,8 +44,8 @@
   "3HFM"
 
 julia> delete!(store, "3HFM")
-ProteinStructureStore with 0 entries
source
ProteinChains.ProteinStructureStore — Type
ProteinStructureStore(filename, mode="cw")
Open or create an HDF5 file as a ProteinStructureStore where mode is one of:
  • "r" read only
  • "r+" read and write
  • "cw" read and write, create file if not existing, do not truncate
  • "w" read and write, create a new file (destroys any existing contents)
source
ProteinChains.addproperties — Method
addproperties(chain::ProteinChain, names::Symbol...)
-addproperties(chain::ProteinStructure, names::Symbol...)
Add predefined properties to a chain or chains of a structure.
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.deserialize — Method
deserialize(filename::AbstractString)
Deserialize ProteinStructure objects from an HDF5 file. Returns a Vector{ProteinStructure} of all structures stored in the file.
source
ProteinChains.mapmmcif — Method
mapmmcif(mmcifdict, field1 => field2, field3 => field4, ...)
julia> import BioStructures
+ProteinStructureStore with 0 entries
source
ProteinChains.ProteinStructureStore — Type
ProteinStructureStore(filename, mode="cw")
Open or create an HDF5 file as a ProteinStructureStore where mode is one of:
  • "r" read only
  • "r+" read and write
  • "cw" read and write, create file if not existing, do not truncate
  • "w" read and write, create a new file (destroys any existing contents)
source
ProteinChains.addproperties — Method
addproperties(chain::ProteinChain, names::Symbol...)
+addproperties(chain::ProteinStructure, names::Symbol...)
Add predefined properties to a chain or chains of a structure.
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.deserialize — Method
deserialize(filename::AbstractString)
Deserialize ProteinStructure objects from an HDF5 file. Returns a Vector{ProteinStructure} of all structures stored in the file.
source
ProteinChains.mapmmcif — Method
mapmmcif(mmcifdict, field1 => field2, field3 => field4, ...)
julia> import BioStructures
 
 julia> filename = BioStructures.downloadpdb("3HFM", format=BioStructures.MMCIFFormat);
 [ Info: Downloading file from PDB: 3HFM
@@ -58,7 +58,7 @@
 Dict{String, String} with 3 entries:
   "Y" => "9031"
   "L" => "10090"
-  "H" => "10090"
source
ProteinChains.pdbentry — Method
pdbentry(pdbid::AbstractString; format=MMCIFFormat, kwargs...)
Keyword arguments get propagated to BioStructures.downloadpdb
Downloads are cached in a temporary directory.
Examples
julia> pdbentry("1EYE")
 [ Info: Downloading file from PDB: 1EYE
 1-chain ProteinStructure{Float64} "1EYE.cif"
  256-residue ProteinChain{Float64, @NamedTuple{}} (A)
@@ -76,4 +76,4 @@
 [ Info: Downloading file from PDB: 1EYE
 2-chain ProteinStructure{Float64} "1EYE_ba1.cif"
  256-residue ProteinChain{Float64, @NamedTuple{}} (A)
- 256-residue ProteinChain{Float64, @NamedTuple{}} (A-2)
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)
Return residue numbers from "atomsite.labelseqids".
The ProteinStructure will automatically add a renumbering property if an MMCIFDict is passed (default if the file is an MMCIF).
source
ProteinChains.serialize — Method
serialize(filename::AbstractString, structures::AbstractVector{<:ProteinStructure})
Serialize a vector of ProteinStructure objects to an HDF5 file. This function creates a new ProteinStructureStore and writes each structure in the input vector to it. Each structure is stored using its name as the key.
source

+ 256-residue ProteinChain{Float64, @NamedTuple{}} (A-2)
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)

Return residue numbers from "atomsite.labelseqids".

The ProteinStructure will automatically add a renumbering property if an MMCIFDict is passed (default if the file is an MMCIF).

source
ProteinChains.serialize — Method
serialize(filename::AbstractString, structures::AbstractVector{<:ProteinStructure})

Serialize a vector of ProteinStructure objects to an HDF5 file. This function creates a new ProteinStructureStore and writes each structure in the input vector to it. Each structure is stored using its name as the key.

source