Science Score: 44.0%
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Repository
A Julia package to read and write MMTF files
Basic Info
Statistics
- Stars: 9
- Watchers: 13
- Forks: 4
- Open Issues: 0
- Releases: 3
Topics
Metadata Files
README.md
MMTF.jl
Latest Release:
Development Status:
Description
The Macromolecular Transmission Format (MMTF) is a compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis. MMTF.jl lets you encode and decode MMTF files.
Note that as of July 2024 MMTF files are not available to download from the RCSB PDB and the BinaryCIF format is preferred.
Installation
Install MMTF.jl from the Julia REPL:
julia
julia> using Pkg
julia> Pkg.add("MMTF")
To start using the package:
julia
julia> using MMTF
Usage
To download and parse a MMTF file as Julia Dict from RCSB database.
julia
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
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
julia> writemmtf(MMTFdict, "path/to/write/MMTF/file", gzip=false)
gzip::Bool - if set to true, writes a compressed MMTF file.
See BioStructures.jl for how to read MMTF files into a hierarchical data structure and convert them to PDB/mmCIF files.
Citation
If you use MMTF.jl, please cite the BioStructures.jl paper where it is mentioned:
Greener JG, Selvaraj J and Ward BJ. BioStructures.jl: read, write and manipulate macromolecular structures in Julia, Bioinformatics 36(14):4206-4207 (2020) - link - PDF
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.
Owner
- Name: BioJulia
- Login: BioJulia
- Kind: organization
- Website: https://biojulia.dev
- Repositories: 79
- Profile: https://github.com/BioJulia
Bioinformatics and Computational Biology in Julia
Citation (CITATION.bib)
@article{BioStructures.jl-2020,
author="Greener, J G and Selvaraj, J and Ward, B J",
title="{BioStructures.jl: read, write and manipulate macromolecular structures in Julia}",
journal="Bioinformatics",
year="2020",
volume="36",
number="14",
pages="4206--4207",
doi="10.1093/bioinformatics/btaa502",
}
GitHub Events
Total
Last Year
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Joe Greener | j****r@h****k | 15 |
| Joel S | j****r@g****m | 5 |
| Seth Axen | s****n@g****m | 5 |
| Ben J. Ward | w****0@g****m | 4 |
| Joel S | j****r@o****m | 4 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 0
- Total pull requests: 5
- Average time to close issues: N/A
- Average time to close pull requests: 17 days
- Total issue authors: 0
- Total pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 3.2
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
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- joelselvaraj (3)
- sethaxen (1)
- SabrinaJaye (1)
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- actions/cache v1 composite
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- codecov/codecov-action v1 composite
- julia-actions/julia-buildpkg v1 composite
- julia-actions/julia-processcoverage v1 composite
- julia-actions/julia-runtest v1 composite
- julia-actions/setup-julia v1 composite