ProClosureEnergy.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file   core/scoring/methods/ProClosureEnergy.hh
/// @brief  Proline ring closure energy method class declaration
/// @author Andrew Leaver-Fay


#ifndef INCLUDED_core_scoring_methods_ProClosureEnergy_hh
#define INCLUDED_core_scoring_methods_ProClosureEnergy_hh

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

// Package headers
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/MinimizationData.fwd.hh>

#include <core/kinematics/DomainMap.fwd.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace methods {

///
class ProClosureEnergy : public ContextIndependentTwoBodyEnergy  {
public:
  typedef ContextIndependentTwoBodyEnergy  parent;

public:

  /// ctor
  ProClosureEnergy();

  // dstor
  ~ProClosureEnergy();

  /// clone
  virtual
  EnergyMethodOP
  clone() const;

  /////////////////////////////////////////////////////////////////////////////
  // methods for ContextIndependentTwoBodyEnergies
  /////////////////////////////////////////////////////////////////////////////

  /// @brief Pro-closure terms only apply between bonded residues where i+1 is
  /// proline -- skip residue pairs that don't apply during minimization.
  virtual
  bool
  defines_score_for_residue_pair(
    conformation::Residue const & res1,
    conformation::Residue const & res2,
    bool res_moving_wrt_eachother
  ) const;

  /// @brief Evaluate the interaction between a given residue pair
  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

  bool
  minimize_in_whole_structure_context( pose::Pose const & ) const { return false; }

  /// @brief Evaluate the derivative for the input residue pair.
  /// This will only be called if rsd1 and rsd2 are bonded and one of them is a proline
  /// because ProClosureEnergy defines the "defines_score_for_residue_pair" method.
  /*virtual
  void
  eval_atom_derivative_for_residue_pair(
    Size const atom_index,
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    ResSingleMinimizationData const & minsingle_data1,
    ResSingleMinimizationData const & minsingle_data2,
    ResPairMinimizationData const & min_data,
    pose::Pose const & pose, // provides context
    kinematics::DomainMap const & domain_map,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;*/

  virtual
  void
  eval_residue_pair_derivatives(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    ResSingleMinimizationData const &,
    ResSingleMinimizationData const &,
    ResPairMinimizationData const &,
    pose::Pose const &,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & r1_atom_derivs,
    utility::vector1< DerivVectorPair > & r2_atom_derivs
  ) const;

  /// @brief Non-virtual interface; takes only the needed parameters.
  /*void
  eval_atom_derivative_for_residue_pair2(
    Size const atom_index,
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;*/

  /// @brief Penalize the pucker-up residue type if its chi1 is positive;
  /// penalize the pucker-down residue type if its chi1 is negative.  Only
  /// applies this penalty when the other_residue is the next polymeric residue
  /// after pro_residue (i+1), unless pro_residue is an upper_term,
  /// in which case it applies the penalty for pro_residue's previous polymeric
  /// residue.
  virtual
  void
  bump_energy_full(
    conformation::Residue const & pro_residue,
    conformation::Residue const & other_residue,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
  ) const;

  /// @brief Penalize the pucker-up residue type if its chi1 is positive;
  /// penalize the pucker-down residue type if its chi1 is negative.  Only
  /// applies this penalty when the other_residue is the next polymeric residue
  /// after pro_residue (i+1), unless pro_residue is an upper_term,
  /// in which case it applies the penalty for pro_residue's previous polymeric
  /// residue.
  virtual
  void
  bump_energy_backbone(
    conformation::Residue const & pro_residue,
    conformation::Residue const & other_residue,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
  ) const;


  virtual
  bool
  defines_intrares_energy( EnergyMap const & weights ) const;

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const & rsd,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;


  /// @brief Returns false if res is not a proline.
  bool
  defines_intrares_energy_for_residue(
    conformation::Residue const & res
  ) const;

  /// @brief This should only be handed a proline.
  virtual
  void
  eval_intrares_derivatives(
    conformation::Residue const & rsd,
    ResSingleMinimizationData const & min_data,
    pose::Pose const & pose,
    EnergyMap const & weights,
    utility::vector1< DerivVectorPair > & atom_derivs
  ) const;

  /// @brief ProClosure Energy is context independent and thus
  /// indicates that no context graphs need to
  /// be maintained by class Energies
  virtual
  void indicate_required_context_graphs(
    utility::vector1< bool > & /*context_graphs_required*/
  ) const;

  virtual
  Distance
  atomic_interaction_cutoff() const
  { return 4.0; }

private:

  /// @brief measure in radians the chi4 between two residues;
  /// upper_residue must be a proline chi4 is wrapped to be in
  /// the range [-pi_over_2, 3/2*pi )
  Real
  measure_chi4(
    conformation::Residue const & lower_residue,
    conformation::Residue const & upper_residue
  ) const;

  Real
  chi4E(
    Real chi4
  ) const;

  Real
  dchi4E_dchi4(
    Real chi4
  ) const;

  // data
private:
  Real const n_nv_dist_sd_; // coorinate variation stdev

  Real const trans_chi4_mean_;
  Real const trans_chi4_sd_;
  Real const cis_chi4_mean_;
  Real const cis_chi4_sd_;

  std::string const bbN_;
  std::string const scNV_;
  std::string const scCD_;
  std::string const bbC_;
  std::string const bbO_;
virtual
core::Size version() const;

};

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


#endif // INCLUDED_core_scoring_EtableEnergy_HH