From 3cb6b129c7a3b545ff7dfe07643eafc4a1425765 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 14 May 2025 09:47:40 +0200
Subject: [PATCH] bugfix in deprecated DRMSD implementation
Penalties for missing residues also included values for distances
within the same residue => the penalty logic did not consider
the specified sequence separation.
---
modules/mol/alg/src/distance_rmsd_test.cc | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/src/distance_rmsd_test.cc b/modules/mol/alg/src/distance_rmsd_test.cc
index 6bb500e36..95d09e062 100644
--- a/modules/mol/alg/src/distance_rmsd_test.cc
+++ b/modules/mol/alg/src/distance_rmsd_test.cc
@@ -129,8 +129,17 @@ void fill_values(const GlobalRDMap& glob_dist_list,
rnum_one = i->first;
res_positions_one = positions.find(rnum_one);
if(res_positions_one == positions.end()){
- //this residue is missing, so we give it the full penalty
- drmsd_values[rnum_one] = std::make_pair(i->second.size()*squared_cap_distance,i->second.size());
+ // this residue is missing, count how many interactions there are
+ // towards residues that fulfill sequence separation threshold
+ int n = 0;
+ for(ResidueRDMap::const_iterator j = i->second.begin(); j != i->second.end(); ++j){
+ //check sequence separation
+ rnum_two = j->first.second.GetResNum();
+ if(std::abs(rnum_one.GetNum() - rnum_two.GetNum()) > sequence_separation){
+ ++n;
+ }
+ }
+ drmsd_values[rnum_one] = std::make_pair(n*squared_cap_distance,n);
continue;
}
--
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