From b0de58cec3d9363efdce6ee98068da123fdc47f7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 20 Mar 2015 08:50:07 +0100
Subject: [PATCH] check for different names when identifying water for
constraints right new they are: SOL HOH TIP3
---
modules/mol/mm/src/topology_creator.cc | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index 2f46a885e..f2ede5a38 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -442,6 +442,11 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
+ std::set<String> water_res_names;
+ water_res_names.insert("SOL");
+ water_res_names.insert("HOH");
+ water_res_names.insert("TIP3");
+
//add distance constrains given the corresponding settings
if(settings->constrain_bonds || settings->constrain_hbonds || settings->rigid_water){
for(std::set<Index<2> >::iterator i = bonds.begin();
@@ -475,7 +480,8 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
}
}
if(settings->rigid_water){
- if(residue_names_of_atoms[(*i)[0]] == "SOL" && residue_names_of_atoms[(*i)[1]] == "SOL"){
+ if(water_res_names.find(residue_names_of_atoms[(*i)[0]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[1]]) != water_res_names.end()){
if(distance_constraints.find(*i) != distance_constraints.end()) continue;
distance_constraints.insert(*i);
Real distance;
@@ -493,8 +499,9 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
if(settings->rigid_water){
for(std::set<Index<3> >::iterator i = angles.begin();
i != angles.end(); ++i){
- if(residue_names_of_atoms[(*i)[0]] == "SOL" && residue_names_of_atoms[(*i)[0]] == "SOL" &&
- residue_names_of_atoms[(*i)[2]] == "SOL"){
+ if(water_res_names.find(residue_names_of_atoms[(*i)[0]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[1]]) != water_res_names.end() &&
+ water_res_names.find(residue_names_of_atoms[(*i)[2]]) != water_res_names.end()){
//we only have to add the H-H distance constant, the O-H distance is already
//constrained above
Real distance;
--
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