RNA_DataBackboneEnergy.hh

Go to the documentation of this file.

// -*- 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_DataBackboneEnergy.hh
/// @brief  Statistically derived rotamer pair potential class declaration
/// @author Phil Bradley
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_DataBackboneEnergy_hh
#define INCLUDED_core_scoring_rna_RNA_DataBackboneEnergy_hh

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

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

#include <core/scoring/constraints/Func.fwd.hh>

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

// Utility headers
// AUTO-REMOVED #include <numeric/xyzVector.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace rna {

///

typedef numeric::xyzVector< core::Real > Vector;

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

  ///
  RNA_DataBackboneEnergy();


  /// 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
  setup_for_packing( pose::Pose & pose, utility::vector1< bool > const &, utility::vector1< bool > 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 & scorefxn,
                       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 {}

  void
  initialize_atom_numbers_sugar();

  //Vector
  //  get_mean_sugar_pos( core::conformation::Residue const & rsd ) const;

  Real
  get_sugar_env_score( core::conformation::Residue const & rsd_buried, core::conformation::Residue const & rsd_other ) const;

  bool
  check_sugar_atom( Size const & n ) const;

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

private:

  Real const dist_cutoff_;
  Real const dist_fade_;
  Real const well_depth_burial_;
  Real const well_depth_exposed_;
  utility::vector1< Size > atom_numbers_sugar_;
  utility::vector1< Size > atom_numbers_sugar_coarse_;
  constraints::FuncOP burial_function_;
virtual
core::Size version() const;

};


}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH