From 367555b964238d9da1ed6d3a66d7ef491b441a7a Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Sun, 24 Nov 2024 22:05:59 +0000 Subject: [PATCH] build based on 903c7ab --- dev/.documenter-siteinfo.json | 2 +- dev/index.html | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index ce93e07..6867a79 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-18T18:59:53","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-24T22:05:55","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index dafcc86..94ce190 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,5 +1,5 @@ -Home · ProteinChains.jl
GitHub

ProteinChains

Documentation for ProteinChains.

ProteinChains.IndexableProperty — Type
IndexableProperty
+Home · ProteinChains.jl
GitHub
ProteinChains
Documentation for ProteinChains.
ProteinChains.IndexableProperty — Type
IndexableProperty
 
 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;
 
@@ -9,7 +9,7 @@
 false
 
 julia> chain.y[:,1:10] == chain[1:10].y
-true
source
ProteinChains.ProteinChain — Type
ProteinChain{T<:Real}
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 add 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.
  • ins_codes::String: Insertion codes for each residue.
  • numbering::Vector{Int32}: Residue numbering (author).
  • properties::ProteinChains.NamedProperties: Named properties associated with the chain.
See also addproperties!, StandardProperty, 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 residue.
  • chains::Vector{ProteinChain{T}}: a collection of ProteinChains.
  • properties::NamedProperties: arbitrary properties.
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
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ProteinChains.ProteinChain — Type
ProteinChain{T<:Real}
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 add 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.
  • ins_codes::String: Insertion codes for each residue.
  • numbering::Vector{Int32}: Residue numbering (author).
  • properties::ProteinChains.NamedProperties: Named properties associated with the chain.
See also addproperties!, StandardProperty, 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 residue.
  • chains::Vector{ProteinChain{T}}: a collection of ProteinChains.
  • properties::NamedProperties: arbitrary properties.
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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"
@@ -27,10 +27,10 @@
   "3HFM"
 
 julia> delete!(store, "3HFM")
-ProteinStructureStore with 0 entries
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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)
Structure attributes
The ProteinStructureStore type allows for storing metadata about each structure in the file, that can be lazily read from the file without loading the structure into memory using readattribute. These attributes are only written to the file when the structure is written, and are not preserved in memory after the structure has been read.
  • T: type of the coordinates in the structure.
  • n_residues: vector of number of residues per model in the structure.
  • n_chains: vector of number of chains per model in the structure.
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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)
Structure attributes
The ProteinStructureStore type allows for storing metadata about each structure in the file, that can be lazily read from the file without loading the structure into memory using readattribute. These attributes are only written to the file when the structure is written, and are not preserved in memory after the structure has been read.
  • T: type of the coordinates in the structure.
  • n_residues: vector of number of residues per model in the structure.
  • n_chains: vector of number of chains per model in the structure.
source
ProteinChains.addproperties! — Method
addproperties!(chain::ProteinChain, properties::NamedTuple)
-addproperties!(chain::ProteinChain; properties...)
Creates a new ProteinChain instance with the added properties. Indexing of property values can be specified with a wrapper type, such as IndexableProperty.    
See also removeproperties!, IndexableProperty.
source
ProteinChains.deleteproperty — Method
deleteproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol)
Delete a property from a chain in a structure. Chains are indexed from 1 to length(store, name).
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ProteinChains.deserialize — Method
deserialize(filename::AbstractString)
Deserialize ProteinStructure objects from an HDF5 file. Returns a Vector{ProteinStructure} of all structures stored in the file.
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ProteinChains.addproperties! — Method
addproperties!(chain::ProteinChain, properties::NamedTuple)
+addproperties!(chain::ProteinChain; properties...)
Creates a new ProteinChain instance with the added properties. Indexing of property values can be specified with a wrapper type, such as IndexableProperty.    
See also removeproperties!, IndexableProperty.
source
ProteinChains.deleteproperty — Method
deleteproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol)
Delete a property from a chain in a structure. Chains are indexed from 1 to length(store, name).
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
@@ -43,7 +43,7 @@
 Dict{String, String} with 3 entries:
   "Y" => "9031"
   "L" => "10090"
-  "H" => "10090"
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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)
@@ -61,4 +61,4 @@
 [ 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)
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ProteinChains.readattribute — Method
readattribute(store::ProteinStructureStore, name::AbstractString, attribute::AbstractString)
Read metadata about a structure without loading the structure into memory.
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ProteinChains.readproperty — Method
readproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol)
Read a property from a chain in a structure. Chains are indexed from 1 to length(store, name).
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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
ProteinChains.writeattribute — Method
writeattribute(store::ProteinStructureStore, name::AbstractString, attribute::AbstractString, value)
Write metadata about a structure.
source
ProteinChains.writeproperty — Method
writeproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol, value)
Write a property to a chain in a structure. Chains are indexed from 1 to length(store, name).
source

+ 256-residue ProteinChain{Float64, @NamedTuple{}} (A-2)
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ProteinChains.readattribute — Method
readattribute(store::ProteinStructureStore, name::AbstractString, attribute::AbstractString)

Read metadata about a structure without loading the structure into memory.

source
ProteinChains.readproperty — Method
readproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol)

Read a property from a chain in a structure. Chains are indexed from 1 to length(store, name).

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
ProteinChains.writeattribute — Method
writeattribute(store::ProteinStructureStore, name::AbstractString, attribute::AbstractString, value)

Write metadata about a structure.

source
ProteinChains.writeproperty — Method
writeproperty(store::ProteinStructureStore, name::AbstractString, index::Integer, property::Symbol, value)

Write a property to a chain in a structure. Chains are indexed from 1 to length(store, name).

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