fix(ferritin-core): 9 API correctness and performance fixes

- default_distance_range: return Option<(f32,f32)> instead of panicking on unknown atom pair
- vdw_radius: remove duplicate Bondi-1964 table; Element::atomic_radius() is the single source
- intern feature: delete dead-code intern.rs and feature flag
- atom_order: cache in OnceLock<HashMap<&str, usize>> — eliminates per-call heap allocation
- Segmentation::from_offsets: validate monotonicity to prevent silent corrupt state
- BondOrder: add AromaticSingle/AromaticDouble variants (CCD codes 5/6 were silently mislabeled)
- OrderedSet::iter: replace Box<dyn Iterator> with zero-alloc OrderedSetIter enum
- AminoAcid enum: replace three parallel match tables with a typed enum + thin wrappers
- AtomsTable.element: change Vec<String> to Vec<Element> — fixes silent Carbon fallback on round-trip

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

Author: zachcp

.beads/interactions.jsonl

@@ -79,3 +79,13 @@
 {"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."}}
+{"id":"int-104f7be4c5e009c36095058e933c76d5","kind":"field_change","created_at":"2026-06-29T12:21:53.97428Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-4tl","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"All non-deferred phases complete: P-1 through P5a landed (data/ primitives, Model/Hierarchy/Conformation, Trajectory, IO model-splitting, AtomCollection adapter, Unit view). Deferred items filed as ferritin-229 (P5b: SymmetryOperator) and ferritin-h04 (P5c: selection DSL). Dead-code cleanup and atom37/AA-index consolidation into ferritin-core::info done on feat/ferritin-4tl-resume branch."}}
+{"id":"int-24dc181a89e17c90f5a220e3207601c0","kind":"field_change","created_at":"2026-06-29T12:32:45.300326Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-2l3","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-d8dec6f9ef080285d72116751f4c6b25","kind":"field_change","created_at":"2026-06-29T12:32:45.898357Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-ynd","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-a95e52a60f1455154d910213b7439f0b","kind":"field_change","created_at":"2026-06-29T12:32:46.483357Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-0ao","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-9ebdecd1092aeabf68eeeea545cf771d","kind":"field_change","created_at":"2026-06-30T01:41:10.346296Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-nd0","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-811db0f32604800bad59179531e2fe40","kind":"field_change","created_at":"2026-06-30T01:41:11.372553Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-d0k","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-b5de508208c77bda02883a90b099db1b","kind":"field_change","created_at":"2026-06-30T01:41:12.195374Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-70w","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-dbcd26bd3705ca83f13be9ba1eac2220","kind":"field_change","created_at":"2026-06-30T01:43:46.503278Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-4iv","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-291e15638b84b558373f9b674ec0f2e9","kind":"field_change","created_at":"2026-06-30T01:43:47.220266Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-0eg","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}
+{"id":"int-a854d1eb6633ae97335602f7eea255b1","kind":"field_change","created_at":"2026-06-30T01:49:00.285368Z","actor":"Zachary Charlop-Powers","issue_id":"ferritin-h6y","extra":{"field":"status","new_value":"closed","old_value":"in_progress","reason":"Closed"}}

crates/ferritin-core/Cargo.toml

@@ -6,10 +6,6 @@ authors.workspace = true
 license.workspace = true
 description.workspace = true
 
-[features]
-default = []
-intern = []
-
 [dependencies]
 anyhow.workspace = true
 itertools.workspace = true

crates/ferritin-core/src/atomcollection.rs

@@ -367,7 +367,7 @@ impl AtomCollection {
 
         let atoms = AtomsTable {
             atom_name: self.atom_names.clone(),
-            element: self.elements.iter().map(|e| e.symbol().to_string()).collect(),
+            element: self.elements.clone(),
             alt_loc: vec![None; n_atoms],
             formal_charge: vec![None; n_atoms],
         };
@@ -492,12 +492,7 @@ impl From<&Model> for AtomCollection {
             chain_ids.push(hierarchy.chains.auth_asym_id[chain_idx].clone());
         }
 
-        let elements: Vec<Element> = hierarchy
-            .atoms
-            .element
-            .iter()
-            .map(|s| Element::from_symbol(s).unwrap_or(Element::C))
-            .collect();
+        let elements = hierarchy.atoms.element.clone();
 
         let atom_names = hierarchy.atoms.atom_name.clone();
 

crates/ferritin-core/src/bonds.rs

@@ -45,6 +45,8 @@ pub enum BondOrder {
     Double = 2,
     Triple = 3,
     Quadruple = 4,
+    AromaticSingle = 5,
+    AromaticDouble = 6,
 }
 
 impl From<i32> for BondOrder {
@@ -54,7 +56,10 @@ impl From<i32> for BondOrder {
             1 => BondOrder::Single,
             2 => BondOrder::Double,
             3 => BondOrder::Triple,
-            _ => BondOrder::Quadruple,
+            4 => BondOrder::Quadruple,
+            5 => BondOrder::AromaticSingle,
+            6 => BondOrder::AromaticDouble,
+            _ => BondOrder::Unset,
         }
     }
 }

crates/ferritin-core/src/data/intern.rs

@@ -1,9 +1,5 @@
-pub mod intern;
 pub mod ordered_set;
 pub mod segmentation;
 
 pub use ordered_set::OrderedSet;
 pub use segmentation::Segmentation;
-
-#[cfg(feature = "intern")]
-pub use intern::{InternedId, Interner};

crates/ferritin-core/src/data/mod.rs

@@ -5,6 +5,22 @@
 
 use std::sync::Arc;
 
+/// Allocation-free iterator over an [`OrderedSet`].
+pub enum OrderedSetIter<'a> {
+    Interval(std::ops::Range<u32>),
+    Sorted(std::iter::Copied<std::slice::Iter<'a, u32>>),
+}
+
+impl<'a> Iterator for OrderedSetIter<'a> {
+    type Item = u32;
+    fn next(&mut self) -> Option<u32> {
+        match self {
+            OrderedSetIter::Interval(r) => r.next(),
+            OrderedSetIter::Sorted(it) => it.next(),
+        }
+    }
+}
+
 /// Ordered set of indices — either a contiguous interval or sorted array.
 ///
 /// The `Interval` variant provides O(1) membership tests for contiguous ranges.
@@ -77,19 +93,10 @@ impl OrderedSet {
     }
 
     /// Iterate over the elements of this set in ascending order.
-    pub fn iter(&self) -> impl Iterator<Item = u32> + '_ {
+    pub fn iter(&self) -> OrderedSetIter<'_> {
         match self {
-            OrderedSet::Interval { start, end } => {
-                // Use a box to unify the two iterator types
-                let iter: Box<dyn Iterator<Item = u32> + '_> =
-                    Box::new(*start..*end);
-                iter
-            }
-            OrderedSet::Sorted(v) => {
-                let iter: Box<dyn Iterator<Item = u32> + '_> =
-                    Box::new(v.iter().copied());
-                iter
-            }
+            OrderedSet::Interval { start, end } => OrderedSetIter::Interval(*start..*end),
+            OrderedSet::Sorted(v) => OrderedSetIter::Sorted(v.iter().copied()),
         }
     }
 

crates/ferritin-core/src/data/ordered_set.rs

@@ -22,6 +22,14 @@ impl Segmentation {
     /// Panics if `offsets` is empty (needs at least the sentinel `[0]`).
     pub fn from_offsets(offsets: Vec<u32>) -> Self {
         assert!(!offsets.is_empty(), "offsets must have at least one element");
+        for window in offsets.windows(2) {
+            assert!(
+                window[0] <= window[1],
+                "offsets must be monotonically non-decreasing; found {} > {}",
+                window[0],
+                window[1]
+            );
+        }
         Self { offsets }
     }
 
@@ -176,4 +184,10 @@ mod tests {
         let ranges: Vec<Range<usize>> = seg.iter().collect();
         assert_eq!(ranges, vec![0..3, 3..5, 5..6]);
     }
+
+    #[test]
+    #[should_panic(expected = "monotonically non-decreasing")]
+    fn test_segmentation_from_offsets_non_monotonic_panics() {
+        Segmentation::from_offsets(vec![0, 10, 5, 15]);
+    }
 }