LK_CosThetaEnergy.hh

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// vi: set ts=2 noet:
//
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/// @file   core/scoring/methods/LK_CosThetaEnergy.hh
/// @brief  LK Solvation using hemisphere culling class declaration
/// @author David Baker
/// @author Andrew Leaver-Fay


#ifndef INCLUDED_core_scoring_methods_LK_CosThetaEnergy_hh
#define INCLUDED_core_scoring_methods_LK_CosThetaEnergy_hh

// Unit Headers
#include <core/scoring/methods/LK_CosThetaEnergy.fwd.hh>

// Package headers
#include <core/conformation/Atom.fwd.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/etable/Etable.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>

#include <utility/vector1.hh>
#include <ObjexxFCL/FArray3D.fwd.hh>


namespace core {
namespace scoring {
namespace methods {

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

public:

  LK_CosThetaEnergy( etable::Etable const & etable_in );


  /// clone
  virtual
  EnergyMethodOP
  clone() const;

  LK_CosThetaEnergy( LK_CosThetaEnergy const & src );

  virtual
  void
  setup_for_derivatives(
    pose::Pose & pose,
    ScoreFunction const & scfxn
  ) const;


  void
  eval_atom_derivative_intra_RNA( //Called by eval_atom_derivative, specific case for RNA intra_res. Parin Sripakdeevong June 27, 2011.
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    kinematics::DomainMap const & domain_map,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) 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
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) 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 & ,
    EnergyMap & emap
  ) const;


  virtual
  Distance
  atomic_interaction_cutoff() const;


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


  virtual
  void
  finalize_total_energy(
    pose::Pose & pose,
    ScoreFunction const &,
    EnergyMap &// totals
  ) const;

private:

  Vector
  get_base_vector( conformation::Residue const & rsd1, Size const i, pose::Pose const & pose ) const;

  void
  get_residue_energy_RNA_intra(
    conformation::Residue const & rsd,
    pose::Pose const & pose,
    Real & lk_polar_intra_RNA_score,
    Real & lk_nonpolar_intra_RNA_score,
    Real & lk_costheta_intra_RNA_score
  ) const;

  void
  get_residue_pair_energy_one_way(
     conformation::Residue const & rsd1,
     conformation::Residue const & rsd2,
     pose::Pose const & pose,
     Real & lk_polar_score,
     Real & lk_nonpolar_score,
     Real & lk_costheta_score  ) const;

  Real
  eval_lk(
  conformation::Atom const & atom1,
  conformation::Atom const & atom2,
  Real const & d2,
  Real & deriv ) const;

  void
  distribute_pseudo_base_atom_derivatives( pose::Pose const & pose ) const;


/////////////////////////////////////////////////////////////////////////////
// data
/////////////////////////////////////////////////////////////////////////////

private:
  etable::Etable const & etable_; // shouldn't this be a pointer? Reference count information is (dangerously) lost when
  //a reference is taken, instead of a smart pointer.  There's the potential for a dangling reference with this.


  /// these guys are taken from the etable
  ObjexxFCL::FArray3D< Real > const & solv1_;
  ObjexxFCL::FArray3D< Real > const & solv2_;

  ObjexxFCL::FArray3D< Real > const & dsolv1_;

  Real const safe_max_dis2_;
  Real const get_bins_per_A2_;

  bool const verbose_;

  /// Used soley when calculating derivatives
  /// Could/should be moved into the Pose's cachable data.
  mutable utility::vector1< utility::vector1< Size > >   nneighbs_;
  mutable utility::vector1< utility::vector1< Vector > > orientation_vectors_;
  mutable utility::vector1< utility::vector1< Vector > > base_pseudo_atom_centers_;
  mutable utility::vector1< utility::vector1< std::pair< Vector, Vector > > > atom_f1_f2s_;
  mutable utility::vector1< utility::vector1< std::pair< Vector, Vector > > > base_pseudo_atom_f1_f2s_;
  mutable Real lk_costheta_weight_; // hold this while calculating derivatives.
virtual
core::Size version() const;
};

}
}
}

#endif // INCLUDED_core_scoring_methods_LK_CosThetaEnergy_HH