Show HN: Open-source protein and ligand viewer

https://github.com/David-OConnor/daedalus

17•the__alchemist•2d ago

I just published an open-source protein and ligand viewer. Goal: fast and easy-to-use. Long-term: It's a platform for docking and molecular dynamics. The basic functionality for viewing and inspecting work. I'm currently working on Coot-like electron-density viewing.

I'm gradually splitting it into standalone libs, published to crates.io. Some are up already, others are integrated, and will be split off when sufficiently mature and decoupled.

Uses parallel execution when able, through thread pools (Rayon), CPU SIMD and Cuda.

The default control scheme is non-standard, unless you play video games...

Any feedback and critique appreciated!

Comments

landl0rd•5h ago

This looks really nice, but what's the plugin/extension story? Part of the reason PyMol is popular is bc it's easy to write plugins in Python, which ngl is much closer to what a lot of researchers are comfortable with. This looks way better and I'd love something faster for quick-and-dirty work than PyVol but extensibility is king :)

Thanks for the work on this! It's badly needed.

gilleain•4h ago

Looks good. Colour scheme looks a but wacky in the screenshots. Hopefully CPK or other standards are in your backlog :)

(For some reason Rasmol used to have 'hotpink' as a colour option)

bionhoward•3h ago

Is this “scriptable” in rust? I have a lot of Pymol scripts I’d love to rewrite in rust

colingauvin•2h ago

I'm a structural biologist working for a small biotech. Very interested in alternatives to PyMOL and ChimeraX. Took it for a small spin, right away I'm unable to move with the mouse using the free cam. Also was unable to open a .pdb file that I had locally (fetching from RCSB worked though). Really cool work thus far though.

what type of docking are you planning to support? Autodock? Or something from scratch?

landl0rd•2h ago

Second this question; would be really cool if we had solid support for some of the qvina2/qvina-w/gpuvina implementations too along with stuff like haddock for affinity-based protein-protein.

P.S. putting this here since I can't edit prior comment; fails to build on mac. It looks like you may have local updated versions of dependency crates (bio_apis) not pushed to gh since I see things like missing `rcsb::load_validation_2fo_fc_cif`, `f32x8` (I assume this is SIMD?), derive(Debug) on ReqError, etc. even with your forked versions of the crates.

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