From 32f7a32c2b2aca78100894c345c5a6afd0b70591 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 20 Mar 2015 08:36:35 +0100
Subject: [PATCH] rely on atom naming to identify hydrogen atoms when settings
hydrogen constraints
check for first char equals H
---
modules/mol/mm/src/topology_creator.cc | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc
index a278b0581..2f46a885e 100644
--- a/modules/mol/mm/src/topology_creator.cc
+++ b/modules/mol/mm/src/topology_creator.cc
@@ -224,7 +224,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
std::vector<Real> atom_charges;
std::vector<String> atom_names;
std::vector<Real> atom_masses;
- std::vector<String> atom_elements;
std::vector<String> residue_names_of_atoms;
ost::mol::AtomHandleList bonded_atoms;
std::vector<uint> temp;
@@ -236,7 +235,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
i!=atom_list.end();++i){
residue_index = residue_indices[i->GetResidue().GetHashCode()];
residue_names_of_atoms.push_back(i->GetResidue().GetName());
- atom_elements.push_back(i->GetElement());
atom_types.push_back(building_blocks[residue_index]->GetType(i->GetName()));
atom_charges.push_back(building_blocks[residue_index]->GetCharge(i->GetName()));
atom_masses.push_back(ff->GetMass(atom_types.back()));
@@ -462,8 +460,7 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent,
continue;
}
if(settings->constrain_hbonds){
- //if(atom_elements[(*i)[0]] == "H" || atom_elements[(*i)[1]] == "H"){
- if(atom_masses[(*i)[0]] < 1.1 || atom_masses[(*i)[1]] < 1.1){
+ if(atom_names[(*i)[0]][0] == 'H' || atom_names[(*i)[1]][0] == 'H'){
if(distance_constraints.find(*i) != distance_constraints.end()) continue;
distance_constraints.insert(*i);
Real distance;
--
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