From 879363a16c09eeaab3f0151f74c50f3587198d5b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Sat, 31 Jan 2015 16:50:07 +0100
Subject: [PATCH] make it possible the merge topologies with corresponding
entities, but also the raw topologies
---
modules/mol/mm/pymod/export_topology.cc | 17 +-
modules/mol/mm/src/topology.cc | 201 ++++++++++++++----------
modules/mol/mm/src/topology.hh | 11 ++
3 files changed, 142 insertions(+), 87 deletions(-)
diff --git a/modules/mol/mm/pymod/export_topology.cc b/modules/mol/mm/pymod/export_topology.cc
index eb7a16fcb..05198b22d 100644
--- a/modules/mol/mm/pymod/export_topology.cc
+++ b/modules/mol/mm/pymod/export_topology.cc
@@ -299,6 +299,14 @@ namespace{
return VecToList<uint>(return_vec);
}
+ void MergeTop(ost::mol::mm::TopologyPtr top, ost::mol::mm::TopologyPtr other){
+ top->Merge(other);
+ }
+
+ void MergeTopEnt(ost::mol::mm::TopologyPtr top, ost::mol::EntityHandle& ent,
+ ost::mol::mm::TopologyPtr other, ost::mol::EntityHandle& other_ent){
+ top->Merge(ent,other,other_ent);
+ }
}
void export_Topology()
@@ -313,6 +321,7 @@ void export_Topology()
.def("__init__",make_constructor(&WrapTopologyConstructor))
.def("Save",&ost::mol::mm::Topology::Save)
.def("Load",&ost::mol::mm::Topology::Load).staticmethod("Load")
+
//interaction adding functions
.def("AddHarmonicBond",&ost::mol::mm::Topology::AddHarmonicBond)
.def("AddHarmonicAngle",&ost::mol::mm::Topology::AddHarmonicAngle)
@@ -329,6 +338,7 @@ void export_Topology()
.def("ResetExclusions",&ost::mol::mm::Topology::ResetExclusions)
.def("AddHarmonicPositionRestraint",&ost::mol::mm::Topology::AddHarmonicPositionRestraint,(arg("index"),arg("ref_position"),arg("k"),arg("x_scale")=1.0,arg("y_scale")=1.0,arg("z_scale")=1.0))
.def("AddHarmonicDistanceRestraint",&ost::mol::mm::Topology::AddHarmonicDistanceRestraint)
+
//single atom parameter getter and setter functions
.def("SetSigmas",&WrapSetSigmas)
.def("SetSigma",&ost::mol::mm::Topology::SetSigma)
@@ -352,11 +362,13 @@ void export_Topology()
.def("GetMass",&ost::mol::mm::Topology::GetMass)
.def("GetOBCScaling",&ost::mol::mm::Topology::GetOBCScaling)
.def("GetGBSARadius",&ost::mol::mm::Topology::GetGBSARadius)
+
//getter and setter functions for nonbonded fudge parameters
.def("SetFudgeLJ",&ost::mol::mm::Topology::SetFudgeLJ)
.def("SetFudgeQQ",&ost::mol::mm::Topology::SetFudgeQQ)
.def("GetFudgeLJ",&ost::mol::mm::Topology::GetFudgeLJ)
.def("GetFudgeQQ",&ost::mol::mm::Topology::GetFudgeQQ)
+
//getter functions for interaction parameters
.def("GetHarmonicBondParameters",&WrapGetHarmonicBondParam)
.def("GetHarmonicAngleParameters",&WrapGetHarmonicAngleParam)
@@ -369,6 +381,7 @@ void export_Topology()
.def("GetDistanceConstraintParameters",&WrapGetDistanceConstraintParam)
.def("GetHarmonicPositionRestraintParameters",&WrapGetHarmonicPositionRestraintParam)
.def("GetHarmonicDistanceRestraintParameters",&WrapGetHarmonicDistanceRestraintParam)
+
//setter functions for interaction parameters
.def("SetHarmonicBondParameters",&ost::mol::mm::Topology::SetHarmonicBondParameters)
.def("SetHarmonicAngleParameters",&ost::mol::mm::Topology::SetHarmonicAngleParameters)
@@ -381,6 +394,7 @@ void export_Topology()
.def("SetDistanceConstraintParameters",&ost::mol::mm::Topology::SetDistanceConstraintParameters)
.def("SetHarmonicPositionRestraintParameters",&ost::mol::mm::Topology::SetHarmonicPositionRestraintParameters)
.def("SetHarmonicDistanceRestraintParameters",&ost::mol::mm::Topology::SetHarmonicDistanceRestraintParameters)
+
//functions to find interactions certain atoms are involved in
.def("GetHarmonicBondIndices",&GetHarmonicBondIndices)
.def("GetHarmonicBondIndices",&GetHarmonicBondIndicesSingleIndex)
@@ -418,7 +432,8 @@ void export_Topology()
.def("GetNumHarmonicPositionRestraints",&ost::mol::mm::Topology::GetNumHarmonicPositionRestraints)
.def("GetNumHarmonicDistanceRestraints",&ost::mol::mm::Topology::GetNumHarmonicDistanceRestraints)
- .def("Merge",&ost::mol::mm::Topology::Merge)
+ .def("Merge",&MergeTop)
+ .def("Merge",&MergeTopEnt)
;
boost::python::register_ptr_to_python<ost::mol::mm::TopologyPtr>();
diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc
index d5b238b84..99dc19c47 100644
--- a/modules/mol/mm/src/topology.cc
+++ b/modules/mol/mm/src/topology.cc
@@ -911,99 +911,23 @@ std::vector<uint> Topology::GetHarmonicDistanceRestraintIndices(uint atom_index)
void Topology::Merge(ost::mol::EntityHandle& ent, TopologyPtr other,
const ost::mol::EntityHandle& other_ent){
- //check whether the particle numbers match
- if(num_particles_ != static_cast<uint>(ent.GetAtomCount())){
- throw ost::Error("Num Particles is not consistent with num atoms of provided ent!");
- }
-
- if(other->GetNumParticles() != static_cast<uint>(other_ent.GetAtomCount())){
- throw ost::Error("Num Particles is not consistent with num atoms of provided other_ent!");
- }
-
- //check whether there is chain from the new entity is already present in the actual entity
- ost::mol::ChainHandleList other_chains = other_ent.GetChainList();
- for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
- e = other_chains.end(); i != e; ++i){
- if(ent.FindChain(i->GetName()).IsValid()){
- std::stringstream ss;
- ss << "Chain with name \"" << i->GetName() << "\" from other topology";
- ss << "is already present in destination topology!";
- throw ost::Error(ss.str());
- }
- }
- //check whether the fudge parameters are consistent
- if(other->fudge_lj_ != fudge_lj_ || other->fudge_qq_ != fudge_qq_){
- throw ost::Error("Expect the fudge parameters of source topology to consistent with the fudge parameters from the destination topology!");
- }
-
- if(!charges_.empty()){
- if(other->charges_.empty()){
- throw ost::Error("Cannot merge topology without charges into a topology with defined charges!");
- }
- }
+ this->CheckEntToAdd(ent,other,other_ent);
+ this->CheckTopToAdd(other);
+ this->MergeEnt(ent, other_ent);
+ this->MergeTop(other);
+}
- if(!sigmas_.empty()){
- if(other->sigmas_.empty()){
- throw ost::Error("Cannot merge topology without lj sigmas into a topology with defined sigmas!");
- }
- }
+void Topology::Merge(TopologyPtr other){
- if(!epsilons_.empty()){
- if(other->epsilons_.empty()){
- throw ost::Error("Cannot merge topology without lj epsilons into a topology with defined epsilons!");
- }
- }
+ this->CheckTopToAdd(other);
+ this->MergeTop(other);
+}
- if(!gbsa_radii_.empty()){
- if(other->gbsa_radii_.empty()){
- throw ost::Error("Cannot merge topology without gbsa radii into a topology with defined radii!");
- }
- }
-
- if(!obc_scaling_.empty()){
- if(other->obc_scaling_.empty()){
- throw ost::Error("Cannot merge topology without obc scaling into a topology with defined scaling!");
- }
- }
+void Topology::MergeTop(TopologyPtr other){
uint old_num_particles = num_particles_;
num_particles_ = num_particles_ + other->GetNumParticles();
- //mapper of hashcode from source atom to index in added_atom list
- std::map<long,int> index_mapper;
- ost::mol::AtomHandleList added_atoms;
-
-
- //let's create an editor to copy over all chains, residues and atoms
- //from the other topologies entity
- ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
- for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
- e = other_chains.end(); i != e; ++i){
- ost::mol::ResidueHandleList res_list = i->GetResidueList();
- ost::mol::ChainHandle added_chain = ed.InsertChain(i->GetName());
-
- for(ost::mol::ResidueHandleList::iterator j = res_list.begin();
- j != res_list.end(); ++j){
- ost::mol::AtomHandleList atom_list = j->GetAtomList();
- ost::mol::ResidueHandle added_residue = ed.AppendResidue(added_chain,*j);
-
- for(ost::mol::AtomHandleList::iterator k = atom_list.begin();
- k != atom_list.end(); ++k){
- index_mapper[k->GetHashCode()] = added_atoms.size();
- added_atoms.push_back(ed.InsertAtom(added_residue,*k));
- }
- }
- }
-
- //let's rebuild the connectivity
- ost::mol::BondHandleList bond_list = other_ent.GetBondList();
- for(ost::mol::BondHandleList::iterator i = bond_list.begin();
- i != bond_list.end(); ++i){
- ed.Connect(added_atoms[index_mapper[i->GetFirst().GetHashCode()]],
- added_atoms[index_mapper[i->GetSecond().GetHashCode()]]);
- }
- ed.UpdateICS();
-
//let's map over masses
atom_masses_.resize(old_num_particles + other->GetNumParticles());
memcpy(&atom_masses_[old_num_particles],&other->atom_masses_[0],other->GetNumParticles() * sizeof(Real));
@@ -1200,6 +1124,111 @@ void Topology::Merge(ost::mol::EntityHandle& ent, TopologyPtr other,
old_num_particles + (*i)[1]));
}
+
+
+}
+
+void Topology::MergeEnt(ost::mol::EntityHandle& ent, const ost::mol::EntityHandle& other_ent){
+
+ //mapper of hashcode from source atom to index in added_atom list
+ std::map<long,int> index_mapper;
+ ost::mol::AtomHandleList added_atoms;
+
+ ost::mol::ChainHandleList other_chains = other_ent.GetChainList();
+
+ //let's create an editor to copy over all chains, residues and atoms
+ //from the other topologies entity
+ ost::mol::XCSEditor ed = ent.EditXCS(ost::mol::BUFFERED_EDIT);
+ for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
+ e = other_chains.end(); i != e; ++i){
+ ost::mol::ResidueHandleList res_list = i->GetResidueList();
+ ost::mol::ChainHandle added_chain = ed.InsertChain(i->GetName());
+
+ for(ost::mol::ResidueHandleList::iterator j = res_list.begin();
+ j != res_list.end(); ++j){
+ ost::mol::AtomHandleList atom_list = j->GetAtomList();
+ ost::mol::ResidueHandle added_residue = ed.AppendResidue(added_chain,*j);
+
+ for(ost::mol::AtomHandleList::iterator k = atom_list.begin();
+ k != atom_list.end(); ++k){
+ index_mapper[k->GetHashCode()] = added_atoms.size();
+ added_atoms.push_back(ed.InsertAtom(added_residue,*k));
+ }
+ }
+ }
+
+ //let's rebuild the connectivity
+ ost::mol::BondHandleList bond_list = other_ent.GetBondList();
+ for(ost::mol::BondHandleList::iterator i = bond_list.begin();
+ i != bond_list.end(); ++i){
+ ed.Connect(added_atoms[index_mapper[i->GetFirst().GetHashCode()]],
+ added_atoms[index_mapper[i->GetSecond().GetHashCode()]]);
+ }
+ ed.UpdateICS();
+}
+
+
+void Topology::CheckTopToAdd(TopologyPtr other){
+
+ if(other->fudge_lj_ != fudge_lj_ || other->fudge_qq_ != fudge_qq_){
+ throw ost::Error("Expect the fudge parameters of source topology to consistent with the fudge parameters from the destination topology!");
+ }
+
+ if(!charges_.empty()){
+ if(other->charges_.empty()){
+ throw ost::Error("Cannot merge topology without charges into a topology with defined charges!");
+ }
+ }
+
+ if(!sigmas_.empty()){
+ if(other->sigmas_.empty()){
+ throw ost::Error("Cannot merge topology without lj sigmas into a topology with defined sigmas!");
+ }
+ }
+
+ if(!epsilons_.empty()){
+ if(other->epsilons_.empty()){
+ throw ost::Error("Cannot merge topology without lj epsilons into a topology with defined epsilons!");
+ }
+ }
+
+ if(!gbsa_radii_.empty()){
+ if(other->gbsa_radii_.empty()){
+ throw ost::Error("Cannot merge topology without gbsa radii into a topology with defined radii!");
+ }
+ }
+
+ if(!obc_scaling_.empty()){
+ if(other->obc_scaling_.empty()){
+ throw ost::Error("Cannot merge topology without obc scaling into a topology with defined scaling!");
+ }
+ }
+}
+
+void Topology::CheckEntToAdd(ost::mol::EntityHandle& ent, TopologyPtr other,
+ const ost::mol::EntityHandle& other_ent){
+
+ //check whether the particle numbers match
+ if(num_particles_ != static_cast<uint>(ent.GetAtomCount())){
+ throw ost::Error("Num Particles is not consistent with num atoms of provided ent!");
+ }
+
+ if(other->GetNumParticles() != static_cast<uint>(other_ent.GetAtomCount())){
+ throw ost::Error("Num Particles is not consistent with num atoms of provided other_ent!");
+ }
+
+ //check whether there is a chain from the new entity is already
+ //present in the actual entity
+ ost::mol::ChainHandleList other_chains = other_ent.GetChainList();
+ for(ost::mol::ChainHandleList::iterator i = other_chains.begin(),
+ e = other_chains.end(); i != e; ++i){
+ if(ent.FindChain(i->GetName()).IsValid()){
+ std::stringstream ss;
+ ss << "Chain with name \"" << i->GetName() << "\" from other topology";
+ ss << "is already present in destination topology!";
+ throw ost::Error(ss.str());
+ }
+ }
}
}}}//ns
diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh
index 5298a6007..0c9b800d9 100644
--- a/modules/mol/mm/src/topology.hh
+++ b/modules/mol/mm/src/topology.hh
@@ -356,6 +356,8 @@ public:
void Merge(ost::mol::EntityHandle& ent, TopologyPtr other, const ost::mol::EntityHandle& other_ent);
+ void Merge(TopologyPtr other);
+
template <typename DS>
void Serialize(DS& ds){
@@ -665,6 +667,15 @@ public:
private:
+ void MergeTop(TopologyPtr other);
+
+ void MergeEnt(ost::mol::EntityHandle& ent, const ost::mol::EntityHandle& other_ent);
+
+ void CheckTopToAdd(TopologyPtr other);
+
+ void CheckEntToAdd(ost::mol::EntityHandle& ent, TopologyPtr other,
+ const ost::mol::EntityHandle& other_ent);
+
uint num_particles_;
//fudge parameters for lj 1,4 pairs
--
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