From 103e7472c3efc837d22fe6696add3c4c5d31dff7 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <niklaus.johner@unibas.ch>
Date: Fri, 21 Nov 2014 14:11:48 +0100
Subject: [PATCH] Fixed bug in TopologyCreator
Multiple periodic dihedrals and impropers for a single set of atoms
were not terated properly when read from a BuildingBlock.
---
modules/mol/mm/src/topology_creator.cc | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 71401b50b..d21526c24 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -652,6 +652,7 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
if(settings->add_dihedrals){
//handle dihedrals
+ std::set<Index<4> > dihedrals_to_delete;
for(uint i = 0; i < top->GetNumResidues(); ++i){
interaction_list = building_blocks[i]->GetDihedrals();
for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
@@ -681,7 +682,8 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
ss << "defines dihedral, that doesn't exist!";
throw ost::Error(ss.str());
}
- dihedrals.erase(dihedral_index);
+
+ dihedrals_to_delete.insert(dihedral_index);
//only periodic dihedrals are supported...
parameters = (*j)->GetParam();
top->AddPeriodicDihedral(one,two,three,four,
@@ -689,6 +691,11 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
}
}
}
+
+ for(std::set<Index<4> >::iterator i = dihedrals_to_delete.begin();
+ i != dihedrals_to_delete.end(); ++i){
+ dihedrals.erase(*i);
+ }
//add pointers of dihedrals definitions, that are not already parametrized
//in the building blocks
@@ -726,6 +733,7 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
if(settings->add_impropers){
//handle impropers
+ std::set<Index<4> > impropers_to_delete;
for(uint i = 0; i < building_blocks.size(); ++i){
interaction_list = building_blocks[i]->GetImpropers();
for(std::vector<MMInteractionPtr>::iterator j = interaction_list.begin();
@@ -740,7 +748,7 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
uint three = top->GetAtomIndex(i, interaction_atom_names[2]);
uint four = top->GetAtomIndex(i, interaction_atom_names[3]);
Index<4> improper_index(one,two,three,four);
- impropers.erase(improper_index);
+ impropers_to_delete.insert(improper_index);
parameters = (*j)->GetParam();
switch((*j)->GetFuncType()){
case PeriodicImproper:{
@@ -760,6 +768,12 @@ TopologyPtr TopologyCreator::Create(const ost::mol::EntityHandle& handle,
}
}
}
+
+ for(std::set<Index<4> >::iterator i = impropers_to_delete.begin();
+ i != impropers_to_delete.end(); ++i){
+ impropers.erase(*i);
+ }
+
//add pointers of improper definitions, that are not already parametrized
//in the building blocks
--
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