From bd89422654f2af297ccce699297393ff92e96a4a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 3 Jul 2024 10:02:45 +0200
Subject: [PATCH] bugfix: avoid setting n_ter/c_ter generic properties in
TopologyCreator
This may cause trouble for downstream applications when called on the same
entity several times. The result may be a generic property that marks a
terminal residue which is not terminal anymore because the entity has been
updated. This leads to a crash in the parameterization stage.
---
modules/mol/mm/src/topology_creator.cc | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 00ba0738d..9f0222b9c 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -88,7 +88,8 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
//this should be enough for most needs
ost::mol::ResidueHandle next,prev;
- bool n_ter,c_ter;
+ bool n_ter, c_ter;
+ std::set<unsigned long> n_ter_residues, c_ter_residues;
ost::mol::AtomHandle peptide_n,peptide_c,nucleotide_p,nucleotide_o;
for(ost::mol::ResidueHandleList::iterator i = res_list.begin();
@@ -133,8 +134,8 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
- if(n_ter) i->SetBoolProp("n_ter",true);
- if(c_ter) i->SetBoolProp("c_ter",true);
+ if(n_ter) n_ter_residues.insert(i->GetHashCode());
+ if(c_ter) c_ter_residues.insert(i->GetHashCode());
}
@@ -181,7 +182,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
//check for n terminus
- if(i->HasProp("n_ter")){
+ if(n_ter_residues.find(i->GetHashCode()) != n_ter_residues.end()){
String exception_name = "";
if(settings->termini_exceptions->HasException(*i)){
exception_name = settings->termini_exceptions->GetException(*i);
@@ -193,7 +194,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
block->RemoveInteractionsToPrev();
}
}
- if(i->HasProp("c_ter")){
+ if(c_ter_residues.find(i->GetHashCode()) != c_ter_residues.end()){
String exception_name = "";
if(settings->termini_exceptions->HasException(*i)){
exception_name = settings->termini_exceptions->GetException(*i);
--
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