feat(ferritin-bevy): interactive protein viewer with orbit camera, cartoon, and color fixes (#161)

* feat(ferritin-bevy): migrate Structure from AtomCollection to Model

Add `load_model` to ferritin-core (CIF-backed, returns the new
Arc<AtomicHierarchy>-based Model from ferritin-4tl). Update
ferritin-bevy's Structure to hold Model instead of AtomCollection,
replacing all AtomCollection API calls with their Model equivalents
(residues_aminoacid, atoms, hierarchy.bonds SoA, coord()).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* feat(ferritin-bevy): absorb ferritin-structure-mesh, port StructurePlugin to Model

Move StructurePlugin/StructureSettings/LoadProteinEvent into ferritin-bevy
(updated to load_model), port ToRerun conversions behind rerun feature,
update all 4 bevy examples to import from ferritin-bevy, and delete the
now-redundant ferritin-structure-mesh crate from the workspace.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix(ferritin-bevy): use load_model in StructurePlugin, drop AtomCollection

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* feat(ferritin-examples): add interactive protein viewer with bevy_feathers UI

Adds bevy_interactive_viewer example that lets the user switch between
all five RenderOptions (Wireframe, Cartoon, BallAndStick, Solid, Putty)
and four ColorScheme presets via a feathers-themed bottom control panel.

Updated from the worktree prototype to use the ferritin-bevy APIs
introduced in this branch (load_model, Model instead of AtomCollection).

- Add bevy_feathers = "0.19.0" dependency
- New example: crates/ferritin-examples/examples/bevy/interactive_viewer.rs
  - FeathersPlugins + dark theme for panel background theming
  - ViewerState resource drives mesh rebuild via resource_changed condition
  - ButtonAction component on each button drives state mutations
  - Standard Bevy Interaction system for hover/press feedback

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix: add fix bevy example

* chore(beads): close 4 bevy_interactive_viewer issues

Close ferritin-0iy, ferritin-pvg, ferritin-hn9, ferritin-jbs —
all implemented in the preceding commit.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: zachcp

.beads/interactions.jsonl

@@ -73,3 +73,9 @@
 {"id":"int-525992e0ab84cb661e5c4edec13ab0d0","kind":"field_change","created_at":"2026-06-28T22:20:10.292716Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-pya","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
 {"id":"int-9fae29a206e20cef13219abad3ad80dd","kind":"field_change","created_at":"2026-06-28T22:20:10.880608Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-1ti","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
 {"id":"int-3872aafcd715ed80bb645d4fa090c323","kind":"field_change","created_at":"2026-06-28T22:20:11.462779Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-lgr","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-1e9f87c42f380859cd05a5de0951ab07","kind":"field_change","created_at":"2026-06-28T23:11:05.476258Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-d8w","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-c3562b01287d93334f13aaf3f826dc5c","kind":"field_change","created_at":"2026-06-28T23:51:59.678168Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-myf","extra":{"field":"status","new_value":"closed","old_value":"open","reason":"Closed"}}
+{"id":"int-e3a2d07cb3f7060cb416fd15f3799477","kind":"field_change","created_at":"2026-06-29T11:44:59.611308Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-0iy","extra":{"field":"status","new_value":"closed","old_value":"open","reason":"Added Structure::centroid(); rebuild_protein() now applies Transform::from_translation(-centroid) on mesh spawn."}}
+{"id":"int-2d686c6a90c0dc2c2b0b90f6113830a6","kind":"field_change","created_at":"2026-06-29T11:45:00.208583Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-pvg","extra":{"field":"status","new_value":"closed","old_value":"open","reason":"Bevy 0.19 auto-enables VERTEX_COLORS shader when mesh has ATTRIBUTE_COLOR. Confirmed vertex colors already set in mesh; build+tests pass."}}
+{"id":"int-2c133f49a4748c2f22624fb9adfa3755","kind":"field_change","created_at":"2026-06-29T11:45:00.799531Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-hn9","extra":{"field":"status","new_value":"closed","old_value":"open","reason":"Rewrote render_cartoon() to use generate_cartoon_mesh() with per-curve-point SS assignment. Added vertex colors (salmon/periwinkle/green) to cartoon mesh. Removed broken generate_alpha_helix_mesh / generate_beta_sheet_mesh."}}
+{"id":"int-628cc6166189d5ab997b6c8c15c5fe66","kind":"field_change","created_at":"2026-06-29T11:45:01.383696Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-jbs","extra":{"field":"status","new_value":"closed","old_value":"open","reason":"Added OrbitCamera component + orbit_camera system to interactive_viewer.rs. Left-drag=orbit, right-drag=pan, scroll=zoom."}}

Cargo.lock

@@ -8,7 +8,6 @@ members = [
     # "crates/ferritin-molviewspec",
     "crates/ferritin-plms",
     # "crates/ferritin-pymol",
-    "crates/ferritin-structure-mesh",
     "crates/ferritin-test-data",
     # "crates/ferritin-wasm-examples/ligandmpnn",
     # "crates/ferritin-wasm-examples/ligandmpnn-wasm",

Cargo.toml

@@ -6,11 +6,16 @@ authors.workspace = true
 license.workspace = true
 description.workspace = true
 
+[features]
+rerun = ["dep:rerun"]
+
 [dependencies]
 anyhow.workspace = true
 bevy = { workspace = true, default-features = true }
 bon.workspace = true
 ferritin-core = { path = "../ferritin-core" }
+itertools.workspace = true
+rerun = { workspace = true, optional = true }
 
 [dev-dependencies]
 ferritin-test-data = { path = "../ferritin-test-data" }

crates/ferritin-bevy/Cargo.toml

@@ -1,7 +1,14 @@
 //! Bevy-based protein structure rendering for ferritin.
 
 pub mod colors;
+pub mod plugin;
 pub mod structure;
 
 pub use colors::ColorScheme;
+pub use plugin::{LoadProteinEvent, StructurePlugin, StructureSettings};
 pub use structure::{RenderOptions, Structure};
+
+#[cfg(feature = "rerun")]
+pub mod conversions;
+#[cfg(feature = "rerun")]
+pub use conversions::ToRerun;

…rritin-structure-mesh/src/conversions.rs crates/ferritin-bevy/src/conversions.rscrates/ferritin-structure-mesh/src/conversions.rs renamed to crates/ferritin-bevy/src/conversions.rs crates/ferritin-structure-mesh/src/conversions.rs renamed to crates/ferritin-bevy/src/conversions.rs

@@ -4,7 +4,7 @@
 //!
 use super::{ColorScheme, RenderOptions, Structure};
 use bevy::prelude::*;
-use ferritin_core::{AtomCollection, load_structure};
+use ferritin_core::load_model;
 use std::path::Path;
 use std::path::PathBuf;
 
@@ -74,15 +74,10 @@ fn load_initial_proteins(
             continue;
         }
 
-        // Todo: revisit this portion about the right default visuals later on
-        // by default lets only keep the amino acids.
-        let mut ac: AtomCollection = load_structure(file_path).unwrap();
-
-        // add the bonds back in as they are removed during the collection process above.
-        ac.connect_via_residue_names();
+        let model = load_model(file_path).unwrap();
 
         let structure = Structure::builder()
-            .pdb(ac)
+            .pdb(model)
             .rendertype(settings.render_type.clone())
             .color_scheme(settings.color_scheme.clone())
             .material(settings.material.clone())