Merge pull request #1922 from ghutchis/dont-wrap-bonds

Remove bonds before wrapping atoms to the unit cell
OpenChemistry · Jan 7, 2025 · 857517c · 857517c
2 parents 2df9224 + ca3eb41
commit 857517c
Showing 1 changed file with 7 additions and 0 deletions.
diff --git 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;
 }