RNA_TorsionPotential.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_TorsionPotential.hh
/// @brief  RNA_TorsionPotential potential class delcaration
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)

#ifndef INCLUDED_core_scoring_rna_RNA_TorsionPotential_HH
#define INCLUDED_core_scoring_rna_RNA_TorsionPotential_HH

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

// Project Headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/Func.fwd.hh>
#include <core/scoring/constraints/SumFunc.fwd.hh>
#include <core/scoring/constraints/SumFunc.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>


#include <core/conformation/Residue.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <utility/vector1.hh>
#include <string>


namespace core {
namespace scoring {
namespace rna {

class RNA_TorsionPotential : public utility::pointer::ReferenceCount
{

public:
  RNA_TorsionPotential();
  virtual ~RNA_TorsionPotential() ; // auto-removing definition from header{}


  //  void update_constraints( pose::Pose & pose ) const;
  Real
  eval_intrares_energy(
                       core::conformation::Residue const & rsd,
                       pose::Pose const & pose
                       ) const;


  Real
  residue_pair_energy(
                      core::conformation::Residue const & rsd1,
                      core::conformation::Residue const & rsd2,
                      pose::Pose const & pose ) const;

  void
  eval_atom_derivative(
    id::AtomID const & id,
    pose::Pose const & pose,
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;


  //Real
  //  compute_torsion_potential( Size const & torsion_number, Real const & value, Real const & delta , Real const & next_alpha ) const;

private:

  bool
  check_intra_residue( id::TorsionID const & torsion_id, pose::Pose const & pose, Size const seqpos ) const;

  void
  init_potentials_from_rna_torsion_database_files();

  void
  initialize_potential_from_file( core::scoring::constraints::FuncOP & func,
                                  std::string const & filename );

  void
  init_fade_functions();

  bool
  Should_score_torsion( core::pose::Pose const & pose, core::id::TorsionID const & torsion_id) const;

  bool
  get_f1_f2( core::id::TorsionID const & torsion_id,
           core::pose::Pose const & pose, core::id::AtomID const & id, Vector & f1, Vector & f2 ) const;

  void
  Output_boolean(std::string const & tag, bool boolean) const;

  bool
  Is_cutpoint_closed_atom(core::conformation::Residue const & rsd, core::id::AtomID const & id) const;

  void
  print_torsion_info(core::pose::Pose const & pose, id::TorsionID const & torsion_id) const;

  bool
  Is_cutpoint_closed_torsion( core::pose::Pose const & pose, core::id::TorsionID const & torsion_id) const;

  std::string path_to_torsion_files_;

  // alpha, beta, gamma, delta, epsilon, zeta
  bool const rna_tight_torsions_;
  Real const delta_fade_;
  Real const alpha_fade_;

  core::scoring::constraints::FuncOP alpha_potential_, beta_potential_, gamma_potential_, delta_north_potential_,
  delta_south_potential_, epsilon_north_potential_, epsilon_south_potential_, zeta_alpha_sc_minus_potential_,
  zeta_alpha_sc_plus_potential_, zeta_alpha_ap_potential_, nu2_north_potential_, nu2_south_potential_,
  nu1_north_potential_, nu1_south_potential_, chi_north_potential_others_, chi_south_potential_others_,
  chi_north_potential_guanosine_, chi_south_potential_guanosine_, chi_purine_north_potential_, chi_purine_south_potential_,
  chi_pyrimidine_north_potential_, chi_pyrimidine_south_potential_, o2h_north_potential_, o2h_south_potential_;

  core::scoring::constraints::FuncOP fade_delta_north_, fade_delta_south_;
  core::scoring::constraints::FuncOP fade_alpha_sc_minus_, fade_alpha_sc_plus_;
  core::scoring::constraints::SumFuncOP fade_alpha_ap_;

  bool const skip_chainbreak_torsions_;
  bool const verbose_;
  bool use_new_potential_;
  bool const use_2prime_OH_potential_;

};

}
}
}

#endif