RNA_SugarCloseEnergy.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_SugarCloseEnergy.hh
/// @brief  Statistically derived rotamer pair potential class declaration
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_SugarCloseEnergy_HH
#define INCLUDED_core_scoring_rna_RNA_SugarCloseEnergy_HH

// Unit headers
#include <core/scoring/rna/RNA_SugarCloseEnergy.fwd.hh>

// Package headers
#include <core/scoring/methods/ContextIndependentOneBodyEnergy.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/HarmonicFunc.fwd.hh>
#include <core/scoring/constraints/FadeFunc.hh>

// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/id/DOF_ID.fwd.hh>

#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace rna {

///
class RNA_SugarCloseEnergy : public core::scoring::methods::ContextIndependentOneBodyEnergy  {
public:
  typedef core::scoring::methods::ContextIndependentOneBodyEnergy  parent;

public:

  /// @brief ctor
  RNA_SugarCloseEnergy();

  /// @brief dtor
  virtual ~RNA_SugarCloseEnergy();

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

  /////////////////////////////////////////////////////////////////////////////
  // methods for ContextIndependentOneBodyEnergies
  /////////////////////////////////////////////////////////////////////////////

  ///
  virtual
  void
  residue_energy(
    conformation::Residue const & rsd,
    EnergyMap & emap
  ) const;


  ///
  virtual
  void
  residue_energy(
    conformation::Residue const & rsd,
    pose::Pose const &,
    EnergyMap & emap
  ) const;


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

  ///
///////////////////////////////////////////////////////////////////////////////
  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;


  /// @brief RNA_SugarCloseEnergy is context independent; indicates that no
  /// context graphs are required
  virtual
  void indicate_required_context_graphs( utility::vector1< bool > & ) const;

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

  void
  add_sugar_ring_closure_constraints( conformation::Residue const & rsd, constraints::ConstraintSet & cst_set ) const;

  // data
private:

  // Ribose closure
  Real const scale_rna_torsion_tether_;
  Real const scale_rna_torsion_sd_;
  Distance const o4star_c1star_bond_length_;
  Distance const o4star_c1star_sd_;
  constraints::HarmonicFuncOP o4star_c1star_dist_harm_func_;

  Real const angle_sd_;
  Real const o4star_c1star_c2star_bond_angle_;
  constraints::HarmonicFuncOP o4star_c1star_c2star_angle_harm_func_;
  Real const o4star_c1star_first_base_bond_angle_;
  constraints::HarmonicFuncOP o4star_c1star_first_base_angle_harm_func_;
  Real const c4star_o4star_c1star_bond_angle_;
  constraints::HarmonicFuncOP c4star_o4star_c1star_angle_harm_func_;

  //phenix-based constraint
  bool const use_phenix_sugar_close_;
  Distance const o4star_c1star_bond_north_;
  Distance const o4star_c1star_bond_south_;
  Distance const bond_sd_;
  Real const o4star_c1star_c2star_angle_north_;
  Real const o4star_c1star_c2star_angle_south_;
  Real const o4star_c1star_n1_9_angle_north_;
  Real const o4star_c1star_n1_9_angle_south_;
  Real const c4star_o4star_c1star_angle_north_;
  Real const c4star_o4star_c1star_angle_south_;
  Real const angle_sd1_, angle_sd2_;
  core::scoring::constraints::FuncOP fade_delta_north_, fade_delta_south_;

  mutable constraints::ConstraintSetOP rna_sugar_close_constraints_;

  virtual
  core::Size version() const;


};

} // rna
} // scoring
} // core


#endif // INCLUDED_core_scoring_EtableEnergy_HH