Major Tracking Issue

[zachcp]

High-level issues here. Update as progress is made.

Visualization

• AtomCollection --> Cartoon
• AtomCollection --> Ribbon
• Update to Bevy 0.15 which simplifies Mesh creation ( begun )
• UI. Something in the style of molstar. Prob some big bevy changes. would be nice to consolidate on single, canoncial UI.
• UI: Be able to move/alreadt global params.
  • bevy_cobweb_ui uses a JSON tree for UI. Looks similar enough to MVSJ.
  • bevy_animation_graph looks a bit like molecular nodes.....
• Explore possible rerun plugin.
• Port of cellscape. h/t to bioicons. Started in Initial Stab at a CellScape implementation #19
• New Bevy 0.15 has a remote protocol. E.g. Great for control / manipulation
• Factor out pymol deps to its own crate Pymol Refactor #75

Protein Utilities

• more file IO. PDB/mmcif are great for now but it would lie nice to have more coverage. biotite.
• multiple structures? maybe via
• Selections. a.la pymol, prody, molstar, biotite-filters
  • started here Create Selection API #14
  • added more iterators through Residues here Implement initial Selections; Add CDD Data; Init Tests #15
• Structural Featurizer:
  • begun work in Initialize Protein-->Tensor Functions #20
• Port ligand-mpnn.
  • initial CLI in Initial Featurization CLI #24
  • refactor and consolidation efforts More LMPNN #25
  • see blog post on work as of 11/05
  • get model loading code in place. Load Protein MPNN PyTorch Model #48
  • get core scoring function in place Full Protein -> Logits scoring! Woohoo. #53
  • Get Device passes in from outside so we can use Metal Begin Refactoring LigandMPNN CLI Call to use Metal #56
  • Ligand MPNN Test Suite. Tracking Issue Here: LigandMPNN Test Suite Compatibility #58
• Port ESM-Cambrian
  • initial attempt here ESM-C Part I #66
  • load model / layers ESMC Init Part II #67
• Port Amplify
  • Get Amplify 150M loading. Amplify to Rust/Candle #30
  • Create Tokenizer Amplify Tokenizer #31
  • Implement forward fn Amplify Forward Functions #32
  • ensure roudntrips and write Fns to get attention map Refactored Amplify model and Outputs #45
  • CLI For PDB / fasta to tokens.
  • Tokens to Embeddings.
  • Replicate a set software proteins in python / PyTorch and Rust/Candle.
  • Add Metal Support to AMPLIFY AMPLIFY + Metal #69
  • Run AMPLIFY on WASM
• MolviewSpec:
  • Factor out MSVJ to its own crate. Factor out Molview spec #12
  • Ferritin as MolviewSpec Renderer. Tracking at Ferritin As MolViewSpec Renderer #18

General

• Wasm: Example with WASM compilation
• Bevy: Embrace the ECS system. Figure out how to make selections work as ECS elements - e.g. auto update on the fly.
• Docs: update docs Documentation Update #9
• Docs: start a devlog. Started in Initial Blogpost #17
• Docs: per-crate docs Core API Cleanup and Docs Update #34
• Factor our file conversion code Refactor PDB and PSE Conversion code #13