Add torsion edges to aspirin reference data and update ToyReferenceData structure to include them in the toy pipeline

data/toy/aspirin_reference.json

@@ -339,5 +339,34 @@
       "length_angstrom": 1.417065754107979
     }
   ],
-  "torsion_edges": []
+  "torsion_edges": [
+    {
+      "bond_index": 2,
+      "atom_left": 1,
+      "atom_right": 3,
+      "rotating_side": [
+        0,
+        2
+      ]
+    },
+    {
+      "bond_index": 3,
+      "atom_left": 3,
+      "atom_right": 4,
+      "rotating_side": [
+        0,
+        1,
+        2
+      ]
+    },
+    {
+      "bond_index": 9,
+      "atom_left": 10,
+      "atom_right": 9,
+      "rotating_side": [
+        11,
+        12
+      ]
+    }
+  ]
 }

examples/toy_pipeline.rs

@@ -8,7 +8,7 @@ use riemann_flow_gnn::{
     api::{OneSampleToyBatch, OneSampleToyPipeline},
     conformer::LigandConformer,
     geometry::PoseState,
-    graph::{Atom, Bond, LigandGraph},
+    graph::{Atom, Bond, LigandGraph, TorsionEdge},
     viz::{export_simulation_video, plot_static_png},
 };
 use serde::Deserialize;
@@ -48,6 +48,15 @@ struct ToyReferenceData {
     atoms: Vec<ToyAtom>,
     bonds: Vec<ToyBond>,
     coords_angstrom: Vec<[f32; 3]>,
+    torsion_edges: Vec<TorsionEdgeJson>,
+}
+
+#[derive(Debug, Deserialize)]
+struct TorsionEdgeJson {
+    bond_index: usize,
+    atom_left: usize,
+    atom_right: usize,
+    rotating_side: Vec<usize>,
 }
 
 fn load_toy_reference(path: &str) -> Result<(LigandGraph, LigandConformer), Box<dyn std::error::Error>> {
@@ -76,7 +85,17 @@ fn load_toy_reference(path: &str) -> Result<(LigandGraph, LigandConformer), Box<
             is_rotatable: b.is_rotatable,
         })
         .collect::<Vec<_>>();
-    let graph = LigandGraph::new(atoms, bonds, vec![]);
+    let torsion_edges = parsed
+        .torsion_edges
+        .into_iter()
+        .map(|t| TorsionEdge {
+            bond_index: t.bond_index,
+            atom_left: t.atom_left,
+            atom_right: t.atom_right,
+            rotating_side: t.rotating_side,
+        })
+        .collect::<Vec<_>>();
+    let graph = LigandGraph::new(atoms, bonds, torsion_edges);
     let reference = LigandConformer::new(graph.clone(), parsed.coords_angstrom)?;
     Ok((graph, reference))
 }