pdbtbx 0.10.0

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

• Douwe Schulte
• Tianyi Shi
• DocKDE

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.

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

v0.10.0 'Enumerated Elements'

• Moved from string based elements to enums see Element, this means that the Atom::set_element, Atom::element, and Term::element have changed
• Deprecated the following functions Atom::atom_number, Atom::atomic_radius, Atom::covalent_bond_radii, and Atom::vanderwaals_radius the radius functions are replaced with Element::atomic_radius which contains all these measures in the struct AtomicRadius
• Added Element::weight and Element::electro_negativity data
• Implemented Extend for all levels in the PDB hierarchy
• Implemented FromIterator for the PDB struct
• Removed requirement for atom_site.pdbx_formal_charge, atom_site.group_PDB, atom_site.occupancy, and atom_site.B_iso_or_equiv for mmCIF files (thanks to #93)
• Added support for SCALE, ORIGX, and MTRIX in mmCIF files (open and save)
• Fixed ignoring some of the auth_* series of mmCIF columns, by giving them precedence over the label_* columns in seq_id and asym_id (thanks to #95)
• Fixed remark-type-number 400 missing from the valid number list (thanks to #96)
• Fixed a small bug in saving MtriX records (thanks to #96)

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 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 to project and access to crates.io if that means the project will live on.