From ca3eb41c2c9c66acab78f2519d3ef232fc578641 Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Tue, 7 Jan 2025 10:48:30 -0500
Subject: [PATCH] Remove bonds before wrapping atoms to the unit cell

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 avogadro/core/crystaltools.cpp | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/avogadro/core/crystaltools.cpp b/avogadro/core/crystaltools.cpp
index 1f6b9c344b..bcf035e751 100644
--- a/avogadro/core/crystaltools.cpp
+++ b/avogadro/core/crystaltools.cpp
@@ -29,9 +29,16 @@ bool CrystalTools::wrapAtomsToUnitCell(Molecule& molecule)
   if (!molecule.unitCell())
     return false;
 
+  // remove any bonds first - otherwise they may wrap
+  // across the unit cell strangely
+  molecule.clearBonds();
+
   std::for_each(molecule.atomPositions3d().begin(),
                 molecule.atomPositions3d().end(),
                 WrapAtomsToCellFunctor(molecule));
+
+  molecule.perceiveBondsSimple();
+  molecule.perceiveBondOrders();
   return true;
 }