f ts

Author: alongd

arc/checks/ts.py

@@ -574,7 +574,10 @@ def _perceive_irc_fragments(xyz: dict,
     n_atoms = len(symbols)
 
     dmat = xyz_to_dmat(xyz)
-    bonds = get_bonds_from_dmat(dmat=dmat, elements=symbols)
+    # Use n_fragments=0 to disable the heavy-atom bridging heuristic in
+    # get_bonds_from_dmat, which would collapse genuinely multi-fragment
+    # IRC endpoints (e.g., loose complexes) into a single component.
+    bonds = get_bonds_from_dmat(dmat=dmat, elements=symbols, n_fragments=0)
 
     # Find connected components via DFS
     adj = {i: set() for i in range(n_atoms)}
@@ -614,7 +617,10 @@ def _perceive_irc_fragments(xyz: dict,
 
     # For multi-fragment systems, search over charge splits that sum to the total charge.
     # Prefer splits that minimize the total absolute charge (e.g., 0,0 over +1,-1).
-    # Derive per-fragment charge bounds from total charge to handle |charge| > 2.
+    # Cap at 4 fragments to keep the combinatorial search bounded;
+    # more fragments likely indicates over-fragmentation from bond perception.
+    if n_frags > 4:
+        return None
     max_abs_charge = max(2, abs(charge) + 1)
     charge_range = range(-max_abs_charge, max_abs_charge + 1)
     best_mols = None