#pdb #protein #crystal #scientific-computing #mmcif

pdbtbx

A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files

27 releases

0.11.0 Sep 1, 2023
0.10.2 May 23, 2023
0.10.1 Dec 4, 2022
0.10.0 Aug 13, 2022
0.6.2 Mar 31, 2021

#252 in Biology

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123 downloads per month
Used in 6 crates

MIT license

525KB
11K SLoC

DOI Compile & Test pdbtbx documentation Crates.io rustc 1.56+

Description

This is a Rust library helping to parse, edit and save crystallographic PDB/mmCIF files. It can read most atomic data from PDB/mmCIF files. Its high level goal is to create a stable, efficient and easy to use interface to PDB/mmCIF files written in pure Rust.

Contributing

As this is a library in active development, feel free to share your thoughts, ideas, hopes, and criticisms. Every comment will be read and discussed so that this library is as useful as possible for all users. Of course we all like a civilised discussion so please follow the community guidelines, but over all please be a civilised human being.

License

MIT

Why

It started as a way to use Rust in a scientific project. But it moved to an open source project because I think that using Rust in scientific computing is be really helpful and a great addition alongside the ubiquitous Python. So by creating it I hope to extend the usability of Rust a little bit more. Since Nature published an article (technology feature) which laid out the benefits of using Rust and showed that Rust is used more and more, I am planning on working more with Rust in scientific projects. And I think that the best way to help Rust move forward (in the scientific community) is by creating more support for scientific projects in Rust.

Contributors

Supported features

As the main goal of this library is to allow access to the atomical data many metadata features of both PDB and mmCIF are unsupported. For both file formats the recent versions (PDB v3.30 and mmcif v5.338) are used, but as both are quite stable file formats the exact version should not matter to end users.

PDB Feature PDB mmCIF Corresponding in mmCIF
HEADER (ID) ✔️ ✔️ entry.id
REMARK ✔️ _pdbx_database_remark.id
ATOM ✔️ ✔️ atom_site
ANISOU ✔️ ✔️ atom_site
SCALE ✔️ ✔️ _atom_sites.Cartn_transf
ORIGX ✔️ ✔️ _database_PDB_matrix.origx
MATRIX ✔️ ✔️ struct_ncs_oper
CRYSTAL ✔️ ✔️ cell + symmetry
MODEL ✔️ ✔️ atom_site
MASTER 〰️ _pdbx_database_PDB_master
SEQRES 〰️ ?
DBREF ✔️ pdbx_dbref
DBREF1/2 ✔️ pdbx_dbref
MODRES ✔️ ?
SEQADV ✔️ ?
Section Keywords Support
Heterogen HET, HETNAM, HETSYN, FORMUL 🔍
Secondary structure HELIX, SHEET 🔍
Connectivity SSBOND, LINK, CISPEP, CONNECT 🔍
Title OBSLTE, TITLE, SPLIT, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, NUMMDL, MDLTYP, AUTHOR, REVDAT, SPRSDE, JRNL, HEADER (other columns)
Misc. SITE
Symbol Description
✔️ Supported
〰️ Partially supported
Support planned (v1.0)
🔍 Support envisioned (>v1.0)
Support not envisioned

The features where support is planned are planned to be included in the 1.0 release. The features where support is envisioned are candidates to be included, but not necessarily in the 1.0 release. The features where support is not planned are thought to be unnecessary for atomic data computations on theses files. If any of these are really needed for your use case, please raise an issue and we can discuss its inclusion. Also if you need a feature that is 'planned' or 'envisioned', feel free to raise an issue to guide development to spots where it can make a real life impact.

Additional crate features

  • The crate leverages the power of the crate Rayon to provide multithreaded iterators over PDB structures.
  • The crate leverages the power of the crate rstar to provide very efficient spatial lookup.
  • The crate has a performant way of selecting atom(s), see Search.
  • The crate has many nice helper methods for common PDB operations (renumbering, sorting, atomic properties lookup).
  • The crate has many ways of iterating over the PDB structure to allow for convenient access and control over the performance.

Latest update

v0.11.0

  • Added support for zipped (.gz) files (Thanks to OWisset)
  • Does not automatically convert chain names to uppercase anymore (Thanks to OWisset)

Also see changelog.

Support and development

When I am actively using this crate in my own projects this crate is actively worked on and extended. I am more than happy to receive and work on PRs and Issues even if the project seems a bit stale. But if anyone finds this project stale and wants to take over moderation and/or main development feel free to reach out and we can discuss. I would be happy to transfer the project and access to crates.io if that means the project will live on.

Dependencies

~5MB
~99K SLoC