T13

Author: alongd

arc/job/adapters/ts/linear.py

@@ -617,31 +617,34 @@ def interpolate_addition(rxn: 'ARCReaction',
         if ts_xyz is not None:
             ts_xyzs.append(ts_xyz)
 
-    # ----- Strategy 2: fragmentation fallback -----
-    if not ts_xyzs:
-        cut_lists = _find_split_bonds_by_fragmentation(uni_mol, multi_species)
-        for cut in cut_lists:
-            sb_key = frozenset(cut)
-            if sb_key in seen_split_sets:
+    # ----- Strategy 2: fragmentation supplement -----
+    # Always run fragmentation-based search in addition to the template path.
+    # The template's r_label_map can mis-identify the primary fragmentation
+    # (e.g. marking a C-H bond as the split instead of the C-O bond in
+    # 1,3_Insertion_ROR), so fragmentation supplements those results.
+    cut_lists = _find_split_bonds_by_fragmentation(uni_mol, multi_species)
+    for cut in cut_lists:
+        sb_key = frozenset(cut)
+        if sb_key in seen_split_sets:
+            continue
+        seen_split_sets.add(sb_key)
+        ts_xyz = _stretch_bond(uni_xyz, uni_mol, cut, cross_bonds=None,
+                               weight=weight, label=f'rxn={rxn.label}, frag-fallback')
+        if ts_xyz is not None:
+            # If H atoms need to migrate between fragments to match
+            # product compositions, partially displace them now.
+            ts_xyz = _migrate_h_between_fragments(
+                ts_xyz, uni_mol, cut, multi_species, weight)
+            # Revalidate: the migration may have introduced collisions
+            # or other geometry defects not present in the pre-migration guess.
+            is_valid, reason = _validate_ts_guess(
+                ts_xyz, set(), cut, uni_mol,
+                label=f'rxn={rxn.label}, frag-fallback-post-migrate')
+            if not is_valid:
+                logger.debug(f'Linear (rxn={rxn.label}, frag-fallback): '
+                             f'post-migration guess rejected — {reason}.')
                 continue
-            seen_split_sets.add(sb_key)
-            ts_xyz = _stretch_bond(uni_xyz, uni_mol, cut, cross_bonds=None,
-                                   weight=weight, label=f'rxn={rxn.label}, frag-fallback')
-            if ts_xyz is not None:
-                # If H atoms need to migrate between fragments to match
-                # product compositions, partially displace them now.
-                ts_xyz = _migrate_h_between_fragments(
-                    ts_xyz, uni_mol, cut, multi_species, weight)
-                # Revalidate: the migration may have introduced collisions
-                # or other geometry defects not present in the pre-migration guess.
-                is_valid, reason = _validate_ts_guess(
-                    ts_xyz, set(), cut, uni_mol,
-                    label=f'rxn={rxn.label}, frag-fallback-post-migrate')
-                if not is_valid:
-                    logger.debug(f'Linear (rxn={rxn.label}, frag-fallback): '
-                                 f'post-migration guess rejected — {reason}.')
-                    continue
-                ts_xyzs.append(ts_xyz)
+            ts_xyzs.append(ts_xyz)
 
     # Deduplicate near-identical guesses.
     unique: List[dict] = []
@@ -931,16 +934,32 @@ def heavy_formula(f: Dict[str, int]) -> Dict[str, int]:
 
         deficit_heavy_coords = ts_coords[deficit_heavy]
 
-        # Sort H atoms by min distance to any deficit-fragment heavy atom.
-        h_dists = []
+        # Identify split-bond anchor atoms in this fragment.  In
+        # insertion/elimination reactions the migrating H should come from
+        # a *non-anchor* heavy atom to create a proper TS ring (e.g. O on
+        # one C of ethylene and H migrating from the other C).
+        split_anchors_in_frag: Set[int] = set()
+        for a, b in split_bonds:
+            if a in fragments[s_fi]:
+                split_anchors_in_frag.add(a)
+            if b in fragments[s_fi]:
+                split_anchors_in_frag.add(b)
+
+        # Sort H atoms by: (1) prefer H not bonded to a split-bond anchor,
+        # (2) then by min distance to any deficit-fragment heavy atom.
+        h_dists: List[Tuple[int, float, int, bool]] = []
         for h_idx in h_indices:
             dists = np.linalg.norm(deficit_heavy_coords - ts_coords[h_idx], axis=1)
             min_dist = float(dists.min())
             nearest_heavy = deficit_heavy[int(dists.argmin())]
-            h_dists.append((h_idx, min_dist, nearest_heavy))
-        h_dists.sort(key=lambda x: x[1])
-
-        for h_idx, _, nearest_heavy in h_dists[:n_to_move]:
+            on_anchor = any(
+                atom_to_idx[nbr] in split_anchors_in_frag
+                for nbr in uni_mol.atoms[h_idx].bonds.keys()
+            )
+            h_dists.append((h_idx, min_dist, nearest_heavy, on_anchor))
+        h_dists.sort(key=lambda x: (x[3], x[1]))
+
+        for h_idx, _, nearest_heavy, _ in h_dists[:n_to_move]:
             # Find the donor heavy atom: the heavy atom bonded to this H in the
             # source fragment.
             donor_heavy = None