cosmetic changes to qa module

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<>())

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) {

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_;
 }; 
 
 }}

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:

modules/qa/src/packing_potential.hh

@@ -84,7 +84,7 @@ public:
   /// 
   /// See documentation for PackingStatistics::Extract()
   Real GetTotalEnergy(const mol::EntityView& view, 
-                        const mol::EntityViewList& views);
+                      const mol::EntityViewList& views);
 
   int GetEnergyCounts();
   
@@ -109,7 +109,7 @@ private:
   // used to calculate total energy...
   mol::EntityView        view_;
   mol::EntityViewList    views_;  
-  Real                 energy_;
+  Real                   energy_;
   int                    energy_counts_;
 };
 

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;