diff --git a/core/src/tetrahedral_polytope.hh b/core/src/tetrahedral_polytope.hh
index bb12cab98c8cae3017d46c748b94cdbe44a3b6ec..c1cf892fe3b7cfdaf687ca82e23de7d356f720aa 100644
--- a/core/src/tetrahedral_polytope.hh
+++ b/core/src/tetrahedral_polytope.hh
@@ -8,10 +8,10 @@
namespace promod3{ namespace core{
-// Tetrahedral polytope for rapid collision detection.
-// Initialize with a position and a collision distance (radius)
+// Tetrahedral polytope for collision detection.
+// Initialize it with a position and a collision distance (radius)
// The Overlap function guarantees to return true if two polytopes are closer
-// than the sum of their radii but the it might already return true if they're
+// than the sum of their radii but it might already return true if they're
// a bit further away...
struct TetrahedralPolytope{
diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index 06b44e96c60de4599d5dad64c01367fc6e84c936..be9f5c7558e9e14d9f90c0507a0766933ed5daaa 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -55,7 +55,7 @@ for i,r in enumerate(prot.residues):
r, rotamer_ids[i], i, library,
torsion_angles[i][0], torsion_angles[i][1])
- frame.SetFrameEnergy(rot_group)
+ rot_group.SetFrameEnergy(frame)
# remove super unlikely rotamer in rotamer group
# e.g. those who clash with the frame
rot_group.ApplySelfEnergyThresh()
diff --git a/sidechain/pymod/_reconstruct_sidechains.py b/sidechain/pymod/_reconstruct_sidechains.py
index 3c15dd49e454f887561aa3bea4af40b9d284819b..d402500c1f650893e0c4ce4ed8345a335b7cead4 100644
--- a/sidechain/pymod/_reconstruct_sidechains.py
+++ b/sidechain/pymod/_reconstruct_sidechains.py
@@ -289,7 +289,7 @@ def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
except:
continue
# keep best ones
- frame.SetFrameEnergy(rot_group)
+ rot_group.SetFrameEnergy(frame)
rot_group.ApplySelfEnergyThresh()
rotamer_groups.append(rot_group)
residues_with_rotamer_group.append(i)
@@ -324,7 +324,7 @@ def _GetDisulfidBridges(frame_residues, cystein_indices, res_list, rotamer_libra
rot_group = _GetRotamerGroup(r.handle, sidechain.CYD, i, rotamer_library,
rotamer_constructor, phi_angles[i],
psi_angles[i], use_frm, bbdep)
- frame.AddFrameEnergy(rot_group)
+ rot_group.AddFrameEnergy(frame)
cystein_rotamers.append(rot_group)
# get CYS with disulfid bonds and the chosen rotamers
diff --git a/sidechain/pymod/export_frame.cc b/sidechain/pymod/export_frame.cc
index 7cff9995e8fafd06688b2d39adcbb66391ec0274..f9b1e1389164bb150f1d46555c5e41220e8f781d 100644
--- a/sidechain/pymod/export_frame.cc
+++ b/sidechain/pymod/export_frame.cc
@@ -32,32 +32,12 @@ ParticlePtr WrapGetItem(FrameResiduePtr p, uint index){
return ret_particle;
}
-void SetFrameEnergyOne(FramePtr frame, RRMRotamerGroupPtr p){
- frame->SetFrameEnergy(p);
-}
-
-void SetFrameEnergyTwo(FramePtr frame, FRMRotamerGroupPtr p){
- frame->SetFrameEnergy(p);
-}
-
-void AddFrameEnergyOne(FramePtr frame, RRMRotamerGroupPtr p){
- frame->AddFrameEnergy(p);
-}
-
-void AddFrameEnergyTwo(FramePtr frame, FRMRotamerGroupPtr p){
- frame->AddFrameEnergy(p);
-}
-
}
void export_Frame()
{
class_<Frame, boost::noncopyable>("Frame", no_init)
.def("__init__",make_constructor(&WrapFrameInit))
- .def("SetFrameEnergy",&SetFrameEnergyOne,(arg("rrm_rotamer_group")))
- .def("SetFrameEnergy",&SetFrameEnergyTwo,(arg("frm_rotamer_group")))
- .def("AddFrameEnergy",&AddFrameEnergyOne,(arg("rrm_rotamer_group")))
- .def("AddFrameEnergy",&AddFrameEnergyTwo,(arg("frm_rotamer_group")))
;
register_ptr_to_python<FramePtr>();
diff --git a/sidechain/pymod/export_rotamer.cc b/sidechain/pymod/export_rotamer.cc
index 4d88fa70e6eca5304cbc105fd2f1867db969efe1..da649f0e9defd2ab150c9235c8f879110f0f8de2 100644
--- a/sidechain/pymod/export_rotamer.cc
+++ b/sidechain/pymod/export_rotamer.cc
@@ -194,6 +194,8 @@ void export_Rotamer()
.def("ApplyOnResidue", WrapRRMGApplyOnResAA,
(arg("index"), arg("all_atom"), arg("res_idx")))
.def("Merge",&RRMRotamerGroup::Merge,(arg("other")))
+ .def("SetFrameEnergy",&RRMRotamerGroup::SetFrameEnergy,(arg("frame")))
+ .def("AddFrameEnergy",&RRMRotamerGroup::AddFrameEnergy,(arg("frame")))
.def("ApplySelfEnergyThresh", &RRMRotamerGroup::ApplySelfEnergyThresh,
(arg("thresh")=30))
;
@@ -211,6 +213,8 @@ void export_Rotamer()
.def("ApplyOnResidue", WrapFRMGApplyOnResAA,
(arg("index"), arg("all_atom"), arg("res_idx")))
.def("Merge",&FRMRotamerGroup::Merge,(arg("other")))
+ .def("SetFrameEnergy",&FRMRotamerGroup::SetFrameEnergy,(arg("frame")))
+ .def("AddFrameEnergy",&FRMRotamerGroup::AddFrameEnergy,(arg("frame")))
.def("ApplySelfEnergyThresh", &FRMRotamerGroup::ApplySelfEnergyThresh,
(arg("thresh")=30))
;
diff --git a/sidechain/src/frame.cc b/sidechain/src/frame.cc
index 57d798e26ec1111caa2d4a0f2e0b3df3d09af7c1..52a526216e00f2e666177976d2972409b7b60595 100644
--- a/sidechain/src/frame.cc
+++ b/sidechain/src/frame.cc
@@ -1,38 +1,6 @@
#include <promod3/sidechain/frame.hh>
#include <promod3/core/runtime_profiling.hh>
-
-namespace{
-
-Real LogSumExp(double* values, int n){
-
- double min = std::numeric_limits<double>::max();
- double max = -std::numeric_limits<double>::max();
-
- for(int i = 0; i < n; ++i){
- min = std::min(min, values[i]);
- max = std::max(max, values[i]);
- }
-
- double range = max - min;
-
- if(range > 100){
- // The log sum exp function (LSE) is bound by
- // max(x1, x2, ..., xn) <= LSE(x1, x2, ..., xn) <=
- // max(x1, x2, ..., xn) + log(n)
- // the maximum value is therefore a rather good approximation
- // this gets returned if the range get's too large because
- // even the LSE trick implemented below gets numerical problems...
- return max;
- }
- else{
- double a = (max + min) / 2;
- double sum = 0.0;
- for(int i = 0; i < n; ++i) sum += std::exp(values[i]-a);
- return std::log(sum) + a;
- }
-}
-
-}
+#include <ost/mol/xcs_editor.hh>
namespace promod3{ namespace sidechain{
@@ -87,136 +55,4 @@ Frame::Frame(const std::vector<FrameResiduePtr>& frame_residues):
collision_tree_.ResetTree(particle_positions, collision_distances);
}
-void Frame::SetFrameEnergy(RRMRotamerGroupPtr p) const{
-
- for(RRMRotamerGroup::iterator i = p->begin(); i != p->end(); ++i){
- (*i)->SetFrameEnergy(0.0);
- }
- this->AddFrameEnergy(p);
-}
-
-void Frame::AddFrameEnergy(RRMRotamerGroupPtr p) const{
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "Frame::AddFrameEnergy", 2);
-
- overlapping_particles_.clear();
- collision_tree_.OverlappingPolytopes(p->GetCollisionTree(),
- overlapping_particles_);
-
- const std::vector<int>& p_rotamer_indices = p->GetRotamerIndices();
- const std::vector<Particle*>& p_particles = p->GetParticles();
- uint p_residue_index = p->GetResidueIndex();
-
- Real frame_energies[p->size()];
- memset(frame_energies,0,p->size()*sizeof(Real));
- Real energy;
-
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles_.begin(),
- e = overlapping_particles_.end(); i != e; ++i){
-
- if(residue_indices_[i->first] == p_residue_index) continue;
-
- energy = frame_particles_[i->first]->PairwiseEnergy(p_particles[i->second]);
- frame_energies[p_rotamer_indices[i->second]] += energy;
- }
-
- Real* e_ptr = frame_energies;
- for(RRMRotamerGroup::iterator i = p->begin(), e = p->end(); i != e; ++i){
- (*i)->AddFrameEnergy(*e_ptr);
- ++e_ptr;
- }
-}
-
-void Frame::SetFrameEnergy(FRMRotamerGroupPtr p) const{
-
- for(FRMRotamerGroup::iterator i = p->begin(); i != p->end(); ++i){
- (*i)->SetFrameEnergy(0);
- for(uint j = 0, e = (*i)->subrotamer_size(); j < e; ++j){
- (*i)->SetFrameEnergy(0,j);
- }
- }
- this->AddFrameEnergy(p);
-}
-
-void Frame::AddFrameEnergy(FRMRotamerGroupPtr p) const{
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "Frame::AddFrameEnergy", 2);
-
- overlapping_particles_.clear();
- collision_tree_.OverlappingPolytopes(p->GetCollisionTree(),
- overlapping_particles_);
-
- const std::vector<int>& p_rotamer_indices = p->GetRotamerIndices();
- const std::vector<FRMRotamer::subrotamer_association_iterator>& p_ass_ind_b = p->GetSubrotamerAssociationIndB();
- const std::vector<FRMRotamer::subrotamer_association_iterator>& p_ass_ind_e = p->GetSubrotamerAssociationIndE();
- const std::vector<Particle*>& p_particles = p->GetParticles();
- uint p_residue_index = p->GetResidueIndex();
-
-
- //reserve the memory
- Real** frame_energies = new Real*[p->size()];
- int counter = 0;
- int subrotamer_size;
- int max_subrotamer_size = 0;
- for(FRMRotamerGroup::iterator i = p->begin(); i != p->end(); ++i){
- subrotamer_size = (*i)->subrotamer_size();
- frame_energies[counter] = new Real[subrotamer_size];
- //set the subrotamer frame energies to the already existing
- //energies
- for(int j = 0; j < subrotamer_size; ++j){
- frame_energies[counter][j] = (*i)->GetFrameEnergy(j);
- }
- max_subrotamer_size = std::max(max_subrotamer_size,subrotamer_size);
- ++counter;
- }
-
- Real energy;
- Real* e_ptr;
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles_.begin(),
- e = overlapping_particles_.end(); i != e ; ++i){
-
-
- if(residue_indices_[i->first] == p_residue_index){
- continue;
- }
-
- energy = frame_particles_[i->first]->PairwiseEnergy(p_particles[i->second]);
- if(energy == 0) continue;
-
- e_ptr = frame_energies[p_rotamer_indices[i->second]];
-
- for(FRMRotamer::subrotamer_association_iterator j = p_ass_ind_b[i->second];
- j != p_ass_ind_e[i->second]; ++j){
- e_ptr[*j] += energy;
- }
- }
-
- double exp_buffer[max_subrotamer_size];
- counter = 0;
- Real T;
- Real one_over_T;
- int actual_subrotamer_size;
-
- for(FRMRotamerGroup::iterator i = p->begin(), e = p->end(); i != e; ++i){
- actual_subrotamer_size = (*i)->subrotamer_size();
- e_ptr = frame_energies[counter];
- T = (*i)->GetTemperature();
- one_over_T = 1.0/T;
- for(int j = 0; j < actual_subrotamer_size; ++j){
- (*i)->SetFrameEnergy(e_ptr[j],j);
- exp_buffer[j] = -e_ptr[j]*one_over_T;
-
- }
- (*i)->SetFrameEnergy(-T*LogSumExp(exp_buffer,actual_subrotamer_size));
- ++counter;
- }
-
- for(uint i = 0; i < p->size(); ++i){
- delete [] frame_energies[i];
- }
- delete [] frame_energies;
-}
-
}}//ns
diff --git a/sidechain/src/frame.hh b/sidechain/src/frame.hh
index aca991606b7614e7f144388481eb0f11ea50e825..abd444060c4a4eb4073a9f579e597be297cfacd2 100644
--- a/sidechain/src/frame.hh
+++ b/sidechain/src/frame.hh
@@ -9,7 +9,8 @@
#include <promod3/core/tetrahedral_polytope.hh>
#include <promod3/sidechain/particle.hh>
#include <promod3/core/message.hh>
-#include <promod3/sidechain/rotamer_group.hh>
+
+#include <ost/mol/residue_handle.hh>
#include <boost/shared_ptr.hpp>
@@ -58,25 +59,24 @@ public:
Frame(const std::vector<FrameResiduePtr>& frame_residues);
- void SetFrameEnergy(RRMRotamerGroupPtr p) const;
-
- void SetFrameEnergy(FRMRotamerGroupPtr p) const;
-
- void AddFrameEnergy(RRMRotamerGroupPtr p) const;
-
- void AddFrameEnergy(FRMRotamerGroupPtr p) const;
+ const std::vector<uint>& GetResidueIndices() const {
+ return residue_indices_;
+ }
const promod3::core::TetrahedralPolytopeTree& GetCollisionTree() const {
return collision_tree_;
}
+ const std::vector<Particle*>& GetParticles() const {
+ return frame_particles_;
+ }
+
private:
std::vector<Particle*> frame_particles_;
std::vector<FrameResiduePtr> frame_residues_;
std::vector<uint> residue_indices_;
promod3::core::TetrahedralPolytopeTree collision_tree_;
- mutable std::vector<std::pair<int,int> > overlapping_particles_;
};
diff --git a/sidechain/src/rotamer_group.cc b/sidechain/src/rotamer_group.cc
index e4038ba2698b495ff668a64fba174f3f7714f871..a106aa5b63efe533df6c896bddb86f75ca06d6d5 100644
--- a/sidechain/src/rotamer_group.cc
+++ b/sidechain/src/rotamer_group.cc
@@ -72,6 +72,41 @@ void RRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
rotamers_[rotamer_index]->ApplyOnResidue(all_atom, res_idx);
}
+void RRMRotamerGroup::SetFrameEnergy(FramePtr frame) {
+
+ for(iterator i = this->begin(); i != this->end(); ++i){
+ (*i)->SetFrameEnergy(0.0);
+ }
+ this->AddFrameEnergy(frame);
+}
+
+void RRMRotamerGroup::AddFrameEnergy(FramePtr frame) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RRMRotamerGroup::AddFrameEnergy", 2);
+
+ std::vector<std::pair<int, int> > overlapping_particles;
+ collision_tree_.OverlappingPolytopes(frame->GetCollisionTree(),
+ overlapping_particles);
+
+ const std::vector<uint>& frame_residue_indices = frame->GetResidueIndices();
+ const std::vector<Particle*>& frame_particles = frame->GetParticles();
+ std::vector<Real> frame_energies(this->size(), 0.0);
+ Real energy;
+
+ for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
+ e = overlapping_particles.end(); i != e; ++i){
+ if(frame_residue_indices[i->second] != residue_index_){
+ energy = particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
+ frame_energies[rotamer_indices_[i->first]] += energy;
+ }
+ }
+
+ for(uint i = 0; i < this->size(); ++i){
+ rotamers_[i]->AddFrameEnergy(frame_energies[i]);
+ }
+}
+
Real* RRMRotamerGroup::CalculatePairwiseEnergies(RRMRotamerGroupPtr other,
Real threshold) {
@@ -91,19 +126,21 @@ Real* RRMRotamerGroup::CalculatePairwiseEnergies(RRMRotamerGroupPtr other,
int this_size = this->size();
int other_size = other->size();
Real* data = new Real[this_size * other_size];
- memset(data,0,this_size*other_size*sizeof(Real));
+ memset(data, 0, this_size*other_size*sizeof(Real));
Real energy;
for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
e = overlapping_particles.end(); i!= e; ++i){
energy = particles_[i->first]->PairwiseEnergy(other->particles_[i->second]);
- if(energy == 0) continue;
- data[rotamer_indices_[i->first]*other_size+other->rotamer_indices_[i->second]] += energy;
+ if(energy != Real(0.0)){
+ data[rotamer_indices_[i->first]*other_size +
+ other->rotamer_indices_[i->second]] += energy;
+ }
}
Real max_e = 0.0;
for(int i = 0; i < this_size*other_size; ++i){
- max_e = (max_e<data[i])?data[i]:max_e;
+ max_e = (max_e < data[i]) ? data[i] : max_e;
}
if(max_e < threshold){
@@ -234,6 +271,92 @@ void FRMRotamerGroup::Merge(const FRMRotamerGroupPtr other){
this->Init();
}
+void FRMRotamerGroup::SetFrameEnergy(FramePtr frame){
+
+ for(iterator i = this->begin(); i != this->end(); ++i){
+ (*i)->SetFrameEnergy(0);
+ for(uint j = 0, e = (*i)->subrotamer_size(); j < e; ++j){
+ (*i)->SetFrameEnergy(0,j);
+ }
+ }
+ this->AddFrameEnergy(frame);
+}
+
+void FRMRotamerGroup::AddFrameEnergy(FramePtr frame){
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "FRMRotamerGroup::AddFrameEnergy", 2);
+
+ std::vector<std::pair<int, int> > overlapping_particles;
+ collision_tree_.OverlappingPolytopes(frame->GetCollisionTree(),
+ overlapping_particles);
+
+ const std::vector<uint>& frame_residue_indices = frame->GetResidueIndices();
+ const std::vector<Particle*>& frame_particles = frame->GetParticles();
+
+ //reserve the memory
+ Real** frame_energies = new Real*[this->size()];
+ int counter = 0;
+ int subrotamer_size;
+ int max_subrotamer_size = 0;
+ for(iterator i = this->begin(); i != this->end(); ++i){
+ subrotamer_size = (*i)->subrotamer_size();
+ frame_energies[counter] = new Real[subrotamer_size];
+ //set the subrotamer frame energies to the already existing
+ //energies
+ for(int j = 0; j < subrotamer_size; ++j){
+ frame_energies[counter][j] = (*i)->GetFrameEnergy(j);
+ }
+ max_subrotamer_size = std::max(max_subrotamer_size, subrotamer_size);
+ ++counter;
+ }
+
+ Real energy;
+ Real* e_ptr;
+ for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
+ e = overlapping_particles.end(); i != e ; ++i){
+
+ if(frame_residue_indices[i->second] != residue_index_){
+ energy = particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
+
+ if(energy != Real(0.0)){
+
+ e_ptr = frame_energies[rotamer_indices_[i->first]];
+
+ for(FRMRotamer::subrotamer_association_iterator j = ass_ind_b_[i->first];
+ j != ass_ind_e_[i->first]; ++j){
+ e_ptr[*j] += energy;
+ }
+ }
+ }
+ }
+
+ std::vector<double> exp_buffer(max_subrotamer_size, 0.0);
+ counter = 0;
+ Real T;
+ Real one_over_T;
+ int actual_subrotamer_size;
+
+ for(iterator i = this->begin(), e = this->end(); i != e; ++i){
+ actual_subrotamer_size = (*i)->subrotamer_size();
+ e_ptr = frame_energies[counter];
+ T = (*i)->GetTemperature();
+ one_over_T = 1.0/T;
+ for(int j = 0; j < actual_subrotamer_size; ++j){
+ (*i)->SetFrameEnergy(e_ptr[j],j);
+ exp_buffer[j] = -e_ptr[j]*one_over_T;
+ }
+ (*i)->SetFrameEnergy(-T*LogSumExp(&exp_buffer[0], actual_subrotamer_size));
+ ++counter;
+ }
+
+ for(uint i = 0; i < this->size(); ++i){
+ delete [] frame_energies[i];
+ }
+ delete [] frame_energies;
+
+}
+
Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
Real threshold) {
@@ -294,24 +417,25 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
energy = particles_[i->first]->PairwiseEnergy(other->particles_[i->second]);
- if(energy == 0.0) continue;
+ if(energy != Real(0.0)){
- r_index_j = other->rotamer_indices_[i->second];
+ r_index_j = other->rotamer_indices_[i->second];
- other_subrotamer_size = other_subrotamer_sizes[r_index_j];
+ other_subrotamer_size = other_subrotamer_sizes[r_index_j];
- j_b = ass_ind_b_[i->first];
- j_e = ass_ind_e_[i->first];
- temp_it = other->ass_ind_b_[i->second];
- k_e = other->ass_ind_e_[i->second];
+ j_b = ass_ind_b_[i->first];
+ j_e = ass_ind_e_[i->first];
+ temp_it = other->ass_ind_b_[i->second];
+ k_e = other->ass_ind_e_[i->second];
- e_ptr = subrotamer_energies[rotamer_indices_[i->first]*other_size+r_index_j];
+ e_ptr = subrotamer_energies[rotamer_indices_[i->first]*other_size+r_index_j];
- for(;j_b != j_e; ++j_b){
- k_b = temp_it;
- temp = (*j_b)*other_subrotamer_size;
- for(;k_b != k_e; ++k_b){
- e_ptr[temp+(*k_b)] += energy;
+ for(;j_b != j_e; ++j_b){
+ k_b = temp_it;
+ temp = (*j_b)*other_subrotamer_size;
+ for(;k_b != k_e; ++k_b){
+ e_ptr[temp+(*k_b)] += energy;
+ }
}
}
}
@@ -332,7 +456,7 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
return NULL;
}
- double exponent_buffer[max_subrotamer_combinations];
+ std::vector<double> exp_buffer(max_subrotamer_combinations, 0.0);
Real* energy_ptr;
Real* data_ptr = &data[0];
double* double_ptr;
@@ -370,7 +494,7 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
energy_ptr = subrotamer_energies[temp+j];
T = 0.5 * (T_i + j_temperatures[j]);
one_over_T = 1.0/T;
- double_ptr = &exponent_buffer[0];
+ double_ptr = &exp_buffer[0];
b = other_subrotamer_sizes[j];
for(int k = 0; k < a; ++k){
@@ -382,7 +506,7 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
}
}
- *data_ptr = -T*LogSumExp(exponent_buffer,a*b) - i_frame_energy - j_frame_energies[j];
+ *data_ptr = -T*LogSumExp(&exp_buffer[0], a*b) - i_frame_energy - j_frame_energies[j];
++data_ptr;
Real_ptr+=b;
}
diff --git a/sidechain/src/rotamer_group.hh b/sidechain/src/rotamer_group.hh
index 2a48f9b56fecf7c552d73fc6fdcae3f7fe3a9cd8..5163b4dd09f907d93d3485579a22c35014dd1abe 100644
--- a/sidechain/src/rotamer_group.hh
+++ b/sidechain/src/rotamer_group.hh
@@ -9,6 +9,7 @@
#include <promod3/core/tetrahedral_polytope.hh>
#include <promod3/sidechain/rotamer.hh>
+#include <promod3/sidechain/frame.hh>
#include <promod3/core/message.hh>
#include <ost/mol/residue_handle.hh>
@@ -37,6 +38,10 @@ public:
void ApplyOnResidue(uint rotamer_index, loop::AllAtomPositions& all_atom,
uint res_idx) const;
+ void SetFrameEnergy(FramePtr p);
+
+ void AddFrameEnergy(FramePtr p);
+
Real* CalculatePairwiseEnergies(RRMRotamerGroupPtr other, Real threshold);
Real GetMaxP() const;
@@ -70,8 +75,8 @@ public:
const_iterator begin() const { return rotamers_.begin(); }
const_iterator end() const { return rotamers_.end(); }
- const std::vector<int>& GetRotamerIndices() { return rotamer_indices_; }
- const std::vector<Particle*>& GetParticles() { return particles_; }
+ //const std::vector<int>& GetRotamerIndices() { return rotamer_indices_; }
+ //const std::vector<Particle*>& GetParticles() { return particles_; }
const std::vector<RRMRotamerPtr>& GetRotamers() { return rotamers_; }
private:
@@ -103,6 +108,10 @@ public:
void ApplyOnResidue(uint rotamer_index, loop::AllAtomPositions& all_atom,
uint res_idx) const;
+ void SetFrameEnergy(FramePtr p);
+
+ void AddFrameEnergy(FramePtr p);
+
Real* CalculatePairwiseEnergies(FRMRotamerGroupPtr other, Real threshold);
Real GetMaxP() const;
@@ -136,13 +145,7 @@ public:
const_iterator begin() const { return rotamers_.begin(); }
const_iterator end() const { return rotamers_.end(); }
- const std::vector<int>& GetRotamerIndices() { return rotamer_indices_; }
- const std::vector<Particle*>& GetParticles() { return particles_; }
const std::vector<FRMRotamerPtr>& GetRotamers() { return rotamers_; }
- const std::vector<FRMRotamer::subrotamer_association_iterator>&
- GetSubrotamerAssociationIndB() { return ass_ind_b_; }
- const std::vector<FRMRotamer::subrotamer_association_iterator>&
- GetSubrotamerAssociationIndE() { return ass_ind_e_; }
private:
diff --git a/sidechain/src/sidechain_reconstructor.cc b/sidechain/src/sidechain_reconstructor.cc
index 7a8f72579506eb8511142178d1449e656c94e6f0..eb91586567f8e638d7c9baff82a2b708921ea5a2 100644
--- a/sidechain/src/sidechain_reconstructor.cc
+++ b/sidechain/src/sidechain_reconstructor.cc
@@ -155,12 +155,12 @@ template<typename RotamerGroup> void SidechainReconstructor::BuildDisulfids_(
loop::AllAtomPositions& out_pos = *(res->env_pos->all_pos);
// collect rotamers and assign frame energies with what we know so far
- Frame frame(frame_residues);
+ FramePtr frame(new Frame(frame_residues));
std::vector<RotamerGroupPtr> cys_rotamer_groups(cys_indices.size());
for (uint i = 0; i < cys_indices.size(); ++i) {
const uint res_idx = res_indices[cys_indices[i]];
env_->GetCydRotamerGroup(cys_rotamer_groups[i], res_idx);
- if (cys_rotamer_groups[i]) frame.SetFrameEnergy(cys_rotamer_groups[i]);
+ if (cys_rotamer_groups[i]) cys_rotamer_groups[i]->SetFrameEnergy(frame);
}
// look for bridges (cys_rotamers[i] only non-null if bridge found)
@@ -307,9 +307,9 @@ void SidechainReconstructor::SolveSystem_(
CollectRotamerGroups_(res, rotamer_groups, has_sidechain);
// set frame energies in rotamers (note: internal energies are precomputed)
- Frame frame(frame_residues);
+ FramePtr frame(new Frame(frame_residues));
for (uint i = 0; i < rotamer_groups.size(); ++i) {
- frame.SetFrameEnergy(rotamer_groups[i]);
+ rotamer_groups[i]->SetFrameEnergy(frame);
rotamer_groups[i]->ApplySelfEnergyThresh();
}