RNA_FullAtomStackingEnergy.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/scoring/rna/RNA_FullAtomStacking.hh
/// @brief  Statistically derived rotamer pair potential class declaration
/// @author Phil Bradley
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_FullAtomStackingEnergy_HH
#define INCLUDED_core_scoring_rna_RNA_FullAtomStackingEnergy_HH

// Unit Headers
#include <core/scoring/rna/RNA_FullAtomStackingEnergy.fwd.hh>

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

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

//Auto Headers
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.fwd.hh>



namespace core {
namespace scoring {
namespace rna {

typedef  numeric::xyzMatrix< Real > Matrix;

///

class RNA_FullAtomStackingEnergy : public methods::ContextIndependentTwoBodyEnergy  {
public:
  typedef methods::ContextIndependentTwoBodyEnergy  parent;

public:

  ///
  RNA_FullAtomStackingEnergy();


  /// clone
  virtual
  methods::EnergyMethodOP
  clone() const;

  /////////////////////////////////////////////////////////////////////////////
  // scoring
  /////////////////////////////////////////////////////////////////////////////

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

  virtual
  void
  setup_for_derivatives( pose::Pose & pose, ScoreFunction const & ) 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 {}


  virtual
  void
  eval_atom_derivative(
    id::AtomID const & atom_id,
    pose::Pose const & pose,
    kinematics::DomainMap const & domain_map,
    ScoreFunction const &,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;

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

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

  virtual
  Distance
  atomic_interaction_cutoff() const;

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


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

private:

  //  Real
  //  get_fa_stack_score( Distance const dist, Real const cos_kappa ) const;

  Real
  get_fa_stack_score( Vector const r_vec, Matrix const M_i ) const;

  Vector
  get_fa_stack_deriv( Vector const r_vec, Matrix const M_i ) const;

  Real
  residue_pair_energy_one_way(
                              conformation::Residue const & rsd1,
                              conformation::Residue const & rsd2,
                              pose::Pose const & pose,
                              Real & score_aro
                              ) const;

  bool
  check_base_base_OK(
     conformation::Residue const & rsd1,
     conformation::Residue const & rsd2,
     Size const & m, Size const & n ) const;

  bool
  is_aro(
         conformation::Residue const & rsd1,
         Size const & m ) const;

  virtual
  core::Size version() const;

  Real const prefactor_;
  Distance const full_stack_cutoff_;
  Distance const dist_cutoff_;
  Real const dist_cutoff2_;
  bool const base_base_only_;

};


}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH