MMTF.jl

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Description

The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis

Installation

Install MMTF.jl from the Julia REPL:

julia> using Pkg
julia> add("MMTF")

To start using the package:

julia> using MMTF

Usage

To download and parse a MMTF file as Julia Dict from RCSB database.

julia> MMTFdict = fetchmmtf("4HHB")
Dict{String,Any} with 39 entries:
  "chainNameList" => String["A", "B", "C", "D", "A", "B", "B", "C", "D", "D", "A", "B", "C", "D"]
  "bondAtomList"  => Int32[7, 2, 15, 9, 21, 17, 28, 23, 33, 30  …  4337, 4331, 4342, 4339, 4352, 4344, 4361, 4354, 4373, 4363]
  "numGroups"     => 801
  "bFactorList"   => Float32[49.05, 43.14, 24.8, 37.68, 72.12, 61.79, 80.12, 26.44, 26.32, 32.96  …  43.37, 43.46, 41.77, 43.68, 45.36, 41.53, 36.25, …
  "groupIdList"   => Int32[1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
  "structureId"   => "4HHB"
  "unitCell"      => Any[63.15, 83.59, 53.8, 90.0, 99.34, 90.0]
  "numAtoms"      => 4779
  "groupList"     => Any[Dict{Any,Any}(Pair{Any,Any}("groupName", "VAL"),Pair{Any,Any}("bondAtomList", Any[1, 0, 2, 1, 3, 2, 4, 1, 5, 4, 6, 4]),Pair{A…
  "numChains"     => 14
  "groupTypeList" => Int32[0, 11, 22, 13, 9, 7, 1, 21, 10, 0  …  3, 3, 3, 3, 3, 3, 3, 3, 3, 3]
  ⋮               => ⋮

pdbid::AbstractString - PDB ID of the structure.

To parse an existing MMTF file as Julia Dict.

julia> MMTFDict = parsemmtf("path/to/MMTF/file", gzip=false)

gzip::Bool - if set to true, parses a compressed MMTF file.

To write a valid MMTF Julia Dict as MMTF file

julia> writemmtf(MMTFdict, "path/to/write/MMTF/file", gzip=false)

gzip::Bool - if set to true, writes a compressed MMTF file.

Contributing and Questions

We appreciate contributions from users including reporting bugs, fixing issues, improving performance and adding new features.

If you have a question about contributing or using this package, our Gitter chat room would be the best starting place to communicate with other users and developers. You are encouraged to use the Bio category of the Julia discourse site for technical questions.