ProteinChains

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

BackboneGeometry(;
    N_Ca_length = 1.46,
    Ca_C_length = 1.52,
    C_N_length = 1.33,

    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.

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.

ProteinChain{T<:Real}

Represents a protein chain with a basic set of fields from which some other properties might be derived.

ProteinStructure{T} <: AbstractVector{ProteinChain{T}}

Fields

• name::String: Usually just the base name of the original file.
• chains::Vector{ProteinChain{T}}: a collection of ProteinChains.
• atoms::Vector{Atom{T}}: free atoms from the structure that were not part of any protein residue.

ProteinStructureStore <: AbstractDict{InlineStrings.String31,ProteinStructure}

A JLD2-based store for protein structures implementing the AbstractDict interface, allowing for dictionary operations on the stored structures.

Keys are stored as InlineStrings.String31 objects to reduce references. This means keys are limited to 31 bytes.

A ProteinStructureStore gets closed automatically when there no longer exists a program-accessible reference to it.

Examples

julia> store = ProteinStructureStore("store.pss")
ProteinStructureStore with 0 entries

julia> store["3HFM"] = pdb"3HFM"
[ Info: Downloading file from PDB: 3HFM
3-element ProteinStructure "3HFM.cif":
 215-residue ProteinChain{Float64} (H)
 214-residue ProteinChain{Float64} (L)
 129-residue ProteinChain{Float64} (Y)

julia> store
ProteinStructureStore with 1 entry

julia> keys(store)
Set{InlineStrings.String31} with 1 element:
  InlineStrings.String31("3HFM")

julia> delete!(store, "3HFM")
ProteinStructureStore with 0 entries

ProteinStructureStore(f::Function, filename, mode="a+")

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.

deserialize(filename::AbstractString)

Deserialize ProteinStructure objects from a JLD2 file. Returns a Vector{ProteinStructure} of all structures stored in the file.

mapmmcif(mmcifdict, field1 => field2, field3 => field4, ...)

julia> import BioStructures

julia> filename = BioStructures.downloadpdb("3HFM", format=BioStructures.MMCIFFormat);
[ Info: Downloading file from PDB: 3HFM

julia> mmcifdict = BioStructures.MMCIFDict(filename);

julia> mapmmcif(mmcifdict,
           "_atom_site.auth_asym_id"   => "_atom_site.label_entity_id",
           "_entity_src_gen.entity_id" => "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id")
Dict{String, String} with 3 entries:
  "Y" => "9031"
  "L" => "10090"
  "H" => "10090"

pdbentry(pdbid::AbstractString; format=MMCIFFormat, kws...)

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-element ProteinStructure "1EYE.cif":
 256-residue ProteinChain{Float64} (A)

julia> pdb"1EYE" # string macro for convenience
[ Info: File exists: 1EYE
1-element ProteinStructure "1EYE.cif":
 256-residue ProteinChain{Float64} (A)

julia> pdb"1EYE"A # string suffix to get a specific chain
[ Info: File exists: 1EYE
256-residue ProteinChain{Float64} (A)

julia> pdb"1EYE"1 # integer suffix to specify "ba_number" keyword
[ Info: Downloading file from PDB: 1EYE
2-element ProteinStructure "1EYE_ba1.cif":
 256-residue ProteinChain{Float64} (A)
 256-residue ProteinChain{Float64} (A-2)

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.

serialize(filename::AbstractString, structures::AbstractVector{<:ProteinStructure})

Serialize a vector of ProteinStructure objects to a JLD2 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.