PeptideBondEnergy.hh

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/// @file   core/scoring/methods/PeptideBondEnergy.hh
/// @brief  scoring method that defines ideal bond lengths between
/// carbonyl carbon of residue N and nitrogen of residue N+1.
/// @author James Thompson

#ifndef INCLUDED_core_scoring_methods_PeptideBondEnergy_hh
#define INCLUDED_core_scoring_methods_PeptideBondEnergy_hh

// Unit headers
#include <core/scoring/methods/PeptideBondEnergy.fwd.hh>

// Package headers
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
// AUTO-REMOVED #include <core/scoring/methods/WholeStructureEnergy.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/DomainMap.fwd.hh>
#include <core/id/AtomID.fwd.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace methods {

/// @brief PeptideBondEnergy class iterates across all residues in finalize()
/// and determines the penalty between residues i and i+1 by the distance
/// the C-N bond. Evantually I'd also like to add bond angle constraints as
/// well, but that's handled by OmegaTether at the moment.
//class PeptideBondEnergy : public WholeStructureEnergy  {
class PeptideBondEnergy : public ContextIndependentTwoBodyEnergy  {
public:
  typedef ContextIndependentTwoBodyEnergy  parent;

public:

  PeptideBondEnergy();

  /// clone
  virtual
  EnergyMethodOP
  clone() const
  {
    return new PeptideBondEnergy;
  }

  /// called at the end of energy evaluation
  //virtual
  //void
  //finalize_total_energy(
  //  pose::Pose & pose,
  //  ScoreFunction const &,
  //  EnergyMap & totals
  //) const;

  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) const;

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const &,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
  ) const {}

  /// called during gradient-based minimization inside dfunc
  /**
     F1 and F2 are not zeroed -- contributions from this atom are
     just summed in
  **/
  virtual
  void
  eval_atom_derivative(
    id::AtomID const & id,
    pose::Pose const & pose,
    kinematics::DomainMap const & domain_map,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;

  virtual
  void
  indicate_required_context_graphs( utility::vector1< bool > & ) const;

  virtual
  bool
  defines_intrares_energy( EnergyMap const & /*weights*/ ) const {
    return false;
  }

  virtual
  Distance
  atomic_interaction_cutoff() const;
virtual
core::Size version() const;

private:

};

} // methods
} // scoring
} // core


#endif