diff --git a/modules/qa/pymod/export_interaction.cc b/modules/qa/pymod/export_interaction.cc
index 6e6e119f0a6b2a2d2a9fad3662b6815516b37935..dfc2636cb3cb84503e7b01864f36fdbfe4c54cbb 100644
--- a/modules/qa/pymod/export_interaction.cc
+++ b/modules/qa/pymod/export_interaction.cc
@@ -237,7 +237,7 @@ void export_Interaction()
.def("SaveToFile", &InteractionStatistics::SaveToFile, args("file_name"))
.def("LoadFromFile", &InteractionStatistics::LoadFromFile).staticmethod("LoadFromFile")
.def("RepairCbetaStatistics", &InteractionStatistics::RepairCbetaStatistics)
- .def("isCbetaStaistics", &InteractionStatistics::isCbetaStaistics)
+ .def("IsCBetaOnly", &InteractionStatistics::IsCBetaOnly)
;
class_<AllAtomPotentialOpts>("AllAtomPotentialOpts", init<>())
diff --git a/modules/qa/src/all_atom_potential.cc b/modules/qa/src/all_atom_potential.cc
index 348880447a93c9f8530bc1a4b65a146f809e2d72..606d74d2aecafa12d05e41e354b5ef863fd5251b 100644
--- a/modules/qa/src/all_atom_potential.cc
+++ b/modules/qa/src/all_atom_potential.cc
@@ -153,36 +153,25 @@ AllAtomPotentialPtr AllAtomPotential::LoadFromFile(const String& filename)
return all_atom_p;
}
-
-float AllAtomPotential::GetTotalEnergy(mol::EntityView view, mol::EntityView target_view)
+float AllAtomPotential::GetTotalEnergy(mol::EntityView view,
+ mol::EntityView target_view)
{
AllAtomPotentialCalculator c(energies_, options_, target_view);
mol::EntityHandle e=view.GetHandle();
view.Apply(c);
- interaction_counts_member_=c.GetEnergyCounts();
+ interaction_counts_=c.GetEnergyCounts();
return c.GetEnergy();
}
-float AllAtomPotential::GetEnergy(atom::ChemType type_a, atom::ChemType type_b, float distance)
-{
- return energies_.Get(type_a, type_b, distance);
-}
-
float AllAtomPotential::GetTotalEnergy(mol::EntityView view)
{
AllAtomPotentialCalculator c(energies_, options_, view);
mol::EntityHandle e=view.GetHandle();
view.Apply(c);
- interaction_counts_member_=c.GetEnergyCounts();
+ interaction_counts_=c.GetEnergyCounts();
return c.GetEnergy();
}
-
-int AllAtomPotential::GetEnergyCounts() const {
- return interaction_counts_member_;
-}
-
-
void AllAtomPotential::SetSequenceSeparation(int seq_sep) {
options_.sequence_sep=seq_sep;
}
@@ -258,7 +247,7 @@ void AllAtomPotential::Fill(const InteractionStatisticsPtr& stats)
// potential is only calculated for Cbeta atoms:
// copy the potential for Calpha (Calphas are selected if
// Cbetas are not present)
- if (stats->isCbetaStaistics() == true) {
+ if (stats->IsCBetaOnly() == true) {
//check if Cbeta (has counts) and not Glycin-Calpha
if (t3 != 0) {
if (i==3) {
diff --git a/modules/qa/src/all_atom_potential.hh b/modules/qa/src/all_atom_potential.hh
index 81beef95d7a1bf50168aa309c8865789035a38bd..5f0e15b4e4691090396088435a17f11d8e6802b1 100644
--- a/modules/qa/src/all_atom_potential.hh
+++ b/modules/qa/src/all_atom_potential.hh
@@ -76,8 +76,11 @@ public:
/// \brief extract energy of a specific interaction
/// (for plotting pseudo Lennard-Jones potential).
- float GetEnergy(atom::ChemType type_a, atom::ChemType type_b, float distance);
-
+ float GetEnergy(atom::ChemType type_a, atom::ChemType type_b,
+ float distance)
+ {
+ return energies_.Get(type_a, type_b, distance);
+ }
/// \brief calculate all-atom interaction between two entities.
/// Two entities need to be provided:
/// the atoms for which the energy should be derived and
@@ -85,7 +88,7 @@ public:
float GetTotalEnergy(mol::EntityView view, mol::EntityView target_view);
/// \brief retrieve total number of interactions (for normalisation)
- int GetEnergyCounts() const;
+ int GetEnergyCounts() const { return interaction_counts_; }
/// \brief set different seqeunce separation than used for training
void SetSequenceSeparation(int seq_sep);
@@ -102,7 +105,7 @@ private:
AllAtomPotentialOpts options_;
AllAtomEnergies energies_;
mol::EntityView target_view_;
- int interaction_counts_member_;
+ int interaction_counts_;
};
}}
diff --git a/modules/qa/src/interaction_statistics.hh b/modules/qa/src/interaction_statistics.hh
index a1e8eeb48e1c2eee1efb969eb74a17987968335f..070346c7d76b4a83701c3b6cdebb862b743adb86 100644
--- a/modules/qa/src/interaction_statistics.hh
+++ b/modules/qa/src/interaction_statistics.hh
@@ -111,7 +111,7 @@ public:
virtual bool VisitResidue(const mol::ResidueHandle& r);
virtual bool VisitAtom(const mol::AtomHandle& a);
- inline bool isCbetaStaistics() {return isCbetaStatisticsFlag_;}
+ inline bool IsCBetaOnly() {return isCbetaStatisticsFlag_;}
private:
diff --git a/modules/qa/src/packing_potential.cc b/modules/qa/src/packing_potential.cc
index e7a473fd3ac496291c2c459da974ae930fec9548..10a7de4aeb20f1642f743915bc3cab7719d7062c 100644
--- a/modules/qa/src/packing_potential.cc
+++ b/modules/qa/src/packing_potential.cc
@@ -187,10 +187,7 @@ bool PackingPotential::VisitAtom(const mol::AtomHandle& atom)
e=views_.end(); i!=e; ++i) {
count+=i->FindWithin(atom.GetPos(), options_.cutoff).size();
}
-
- count=count>options_.max_counts ? options_.max_counts : count;
-
- energy_+=energies_.Get(aa, count/options_.bucket_size);
+ energy_+=this->GetPackingEnergy(aa, count);
energy_counts_++;
return false;
}
diff --git a/modules/qa/src/packing_potential.hh b/modules/qa/src/packing_potential.hh
index dec0054f672319ab71d3ab108a907b18a46b1c9b..6d11d2e6c6ff43535e725c1f4267910edbc4a4cf 100644
--- a/modules/qa/src/packing_potential.hh
+++ b/modules/qa/src/packing_potential.hh
@@ -84,10 +84,17 @@ public:
///
/// See documentation for PackingStatistics::Extract()
Real GetTotalEnergy(const mol::EntityView& view,
- const mol::EntityViewList& views);
+ const mol::EntityViewList& views);
int GetEnergyCounts();
+
+ Real GetPackingEnergy(AminoAcid aa, int count) const
+ {
+ count=count>options_.max_counts ? options_.max_counts : count;
+ return energies_.Get(aa, count/options_.bucket_size);
+ }
+
template <typename DS>
void Serialize(DS& ds);
@@ -109,7 +116,7 @@ private:
// used to calculate total energy...
mol::EntityView view_;
mol::EntityViewList views_;
- Real energy_;
+ Real energy_;
int energy_counts_;
};
diff --git a/modules/qa/src/torsion_potential.cc b/modules/qa/src/torsion_potential.cc
index 651718a4f04bc0d53faf6fadf3dd1ab8eb328e0c..2ecf8c655f24de49220a00be1b09b24d1e14b856 100644
--- a/modules/qa/src/torsion_potential.cc
+++ b/modules/qa/src/torsion_potential.cc
@@ -16,6 +16,7 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
+
#include "torsion_potential.hh"
#include "amino_acids.hh"
@@ -39,10 +40,9 @@ namespace {
class TorsionEnergyCalc : public mol::EntityVisitor {
public:
- TorsionEnergyCalc(TorsionPotential::TorsionEnergies& energies,
+ TorsionEnergyCalc(const TorsionPotentialPtr& pot,
TorsionPotentialOpts opts):
- energies_(energies), energy_(0.0),
- opts_(opts), num_torsions_(0)
+ pot_(pot), energy_(0.0), num_torsions_(0)
{
}
@@ -75,24 +75,16 @@ public:
Real next_phi=next_phit.GetAngle()*180/M_PI - 0.001; if (next_phi<-180) next_phi=-180;
Real next_psi=next_psit.GetAngle()*180/M_PI - 0.001; if (next_psi<-180) next_psi=-180;
+
// calculate position of the amino acid in the alphabet
- int icenter=this->GetAAIndex(ca);
-
- if (icenter >-1) {
- energy_+=energies_.Get(icenter, prev_phi, prev_psi,
- central_phi, central_psi,
- next_phi, next_psi);
- num_torsions_++;
- }
- else {
- LOG_INFO("Amino acid not found in alphabets...");
- }
+ energy_+=pot_->GetTorsionEnergy(ca, prev_phi, prev_psi, central_phi,
+ central_psi, next_phi, next_psi);
+ ++num_torsions_;
return false;
}
Real GetEnergy() const {
return energy_;
- //return num_torsions_==0?0:energy_/num_torsions_;
}
int GetEnergyCounts() const {
@@ -100,29 +92,11 @@ public:
}
private:
- int GetAAIndex(AminoAcid aa)
- {
- return this->GetIndex(aa, opts_.alphabet);
- }
-
-
- int GetIndex(AminoAcid aa, AminoAcidAlphabet& alpha) {
- AminoAcidAlphabet::iterator i=alpha.begin();
- for (int index=0; i!=alpha.end(); ++i, ++index) {
- if ((*i).Contains(aa)) {
- return index;
- }
-
- }
- return -1;
- }
-private:
- TorsionPotential::TorsionEnergies& energies_;
+ TorsionPotentialPtr pot_;
AminoAcid prev_;
AminoAcid center_;
mol::ResidueHandle cr_;
Real energy_;
- TorsionPotentialOpts opts_;
int num_torsions_;
};
@@ -153,6 +127,18 @@ TorsionPotentialOpts::TorsionPotentialOpts():
}
+int TorsionPotential::GetAAIndex(AminoAcid aa) const
+{
+ AminoAcidAlphabet::const_iterator i=options_.alphabet.begin();
+ for (int index=0; i!=options_.alphabet.end(); ++i, ++index) {
+ if ((*i).Contains(aa)) {
+ return index;
+ }
+ }
+ return -1;
+}
+
+
TorsionPotentialPtr TorsionPotential::Create(TorsionStatisticsPtr statistics,
const TorsionPotentialOpts& opts,
bool calculate_average_energy_flag)
@@ -225,7 +211,7 @@ void TorsionPotential::SaveToFile(const String& path)
Real TorsionPotential::GetTotalEnergy(mol::EntityHandle entity)
{
- TorsionEnergyCalc c(energies_, options_);
+ TorsionEnergyCalc c(this->shared_from_this(), options_);
entity.Apply(c);
num_torsions_ = c.GetEnergyCounts();
return c.GetEnergy();
@@ -233,7 +219,7 @@ Real TorsionPotential::GetTotalEnergy(mol::EntityHandle entity)
Real TorsionPotential::GetTotalEnergy(mol::EntityView entity)
{
- TorsionEnergyCalc c(energies_, options_);
+ TorsionEnergyCalc c(this->shared_from_this(), options_);
entity.Apply(c);
num_torsions_ = c.GetEnergyCounts();
return c.GetEnergy();
diff --git a/modules/qa/src/torsion_potential.hh b/modules/qa/src/torsion_potential.hh
index 68faeb24fc2ab71cc4c261edf6d719452dd25201..d0048e84ccce0ada40901e93dd70fea536d57d04 100644
--- a/modules/qa/src/torsion_potential.hh
+++ b/modules/qa/src/torsion_potential.hh
@@ -30,6 +30,7 @@
*/
#include <ost/qa/torsion_statistics.hh>
#include <boost/shared_ptr.hpp>
+#include <boost/enable_shared_from_this.hpp>
#include <vector>
#include <boost/scoped_ptr.hpp>
@@ -67,7 +68,8 @@ typedef boost::shared_ptr<TorsionPotential> TorsionPotentialPtr;
/// \brief Torsion potential
///
/// The torsion potential class is parametrisable by TorsionPotentialOpts.
-class DLLEXPORT_OST_QA TorsionPotential {
+class DLLEXPORT_OST_QA TorsionPotential :
+ public boost::enable_shared_from_this<TorsionPotential> {
public:
/// \brief create new torsion potential with the given torsion statistics
/// and options
@@ -89,6 +91,18 @@ public:
/// \brief retrieve total number of energy local (i.e. valid residues)
int GetEnergyCounts() const;
+
+
+
+ Real GetTorsionEnergy(AminoAcid central_aa, Real prev_phi, Real prev_psi,
+ Real central_phi, Real central_psi,
+ Real next_phi, Real next_psi) const {
+ int icenter=this->GetAAIndex(central_aa);
+ return energies_.Get(icenter, prev_phi, prev_psi,
+ central_phi, central_psi,
+ next_phi, next_psi);
+ }
+
/// \brief save torsion potential
///
@@ -106,6 +120,9 @@ public:
typedef MultiClassifier<float, int, Real, Real,
Real, Real, Real, Real> TorsionEnergies;
private:
+
+ int GetAAIndex(AminoAcid aa) const;
+
void Fill(const TorsionStatisticsPtr& stat,
bool calculate_average_energy_flag);
diff --git a/modules/qa/src/torsion_statistics.hh b/modules/qa/src/torsion_statistics.hh
index 15f20089a5d8e7950621d79c347c612bbd0005d0..74ad15562e4a504ebd20dfa83645a7f67002ce44 100644
--- a/modules/qa/src/torsion_statistics.hh
+++ b/modules/qa/src/torsion_statistics.hh
@@ -70,8 +70,8 @@ public:
Real next_phi_angle, Real next_psi_angle) const;
uint64_t GetCount(Real prev_phi_angle, Real prev_psi_angle,
- Real central_phi_angle, Real central_psi_angle,
- Real next_phi_angle, Real next_psi_angle) const;
+ Real central_phi_angle, Real central_psi_angle,
+ Real next_phi_angle, Real next_psi_angle) const;
uint64_t GetCount(const AminoAcidSet& central_aa) const;