From 28ad9cd0c6bbd61788726db84f4d21101dd6b64a Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Fri, 8 Mar 2013 16:54:47 +0100
Subject: [PATCH] Bonds included in filtered structure

---
 modules/mol/alg/src/filter_clashes.cc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index dc450498e..b7a22ba13 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -502,6 +502,7 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
   }
   std::cout << "Average Z-Score angle widths: " << std::fixed << std::setprecision(5) << avg_zscore_angles << std::endl;
   std::cout << "Angles outside of tolerance range: " << bad_angle_count << " out of " << angle_count << std::endl;
+  filtered.AddAllInclusiveBonds();
   return filtered;
 }
 
@@ -608,6 +609,7 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
   }
   std::cout << bad_distance_count << " non-bonded short-range distances shorter than tolerance distance" << std::endl;
   std::cout << "Distances shorter than tolerance are on average shorter by: " << std::fixed << std::setprecision(5) << average_offset << std::endl;
+  filtered.AddAllInclusiveBonds();
   return filtered;
 }
 
-- 
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