RNA_Mg_Energy.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_Mg_Energy.hh
/// @brief  Statistically derived Mg(2+) binding potential for RNA.
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_Mg_Energy_hh
#define INCLUDED_core_scoring_rna_RNA_Mg_Energy_hh

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

// Package headers
#include <core/conformation/Residue.fwd.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/rna/RNA_ScoringInfo.hh>
#include <core/scoring/rna/Gaussian_parameter.hh>
#include <core/scoring/hbonds/HBondOptions.fwd.hh>

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

#include <utility/vector1.hh>


// AUTO-REMOVED #include <map>

// Utility headers


namespace core {
namespace scoring {
namespace rna {

///
class RNA_Mg_Energy : public methods::ContextIndependentTwoBodyEnergy  {
public:
  typedef methods::ContextIndependentTwoBodyEnergy  parent;

public:

  ///
  RNA_Mg_Energy();

  /// 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
  Distance
  atomic_interaction_cutoff() const;

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

private:

  Size
  get_vdw_atom_number(
     utility::vector1< utility::vector1< Size > > const & atom_numbers_for_vdw_calculation,
     Size const & pos1,
     Size const & i ) const;

  Size
  get_vdw_atom_number(
                      char const which_nucleotide,
                      Size const & i ) const;

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

private:

  //Helper functions just to get things set up.
  void
  setup_info_for_mg_calculation( pose::Pose & pose ) const;

  void
  residue_pair_energy_one_way(
                              conformation::Residue const & rsd1, // The RNA residue
                              conformation::Residue const & rsd2, // The Mg(2+)
                              pose::Pose const & pose,
                              EnergyMap & emap
                              ) const;
  Real
  get_gaussian_potential_score(
                               Gaussian_parameter const & mg_potential_gaussian_parameter,
                               Vector const & pos1,
                               Vector const & pos2 ) const;

  Real
  get_gaussian_score(
                     Gaussian_parameter const & mg_potential_gaussian_parameter,
                     Real const d) const;

  Real
  get_cos_theta( core::conformation::Residue const & rsd1,
             Size const i, Vector const & i_xyz, Vector const & j_xyz ) const;

  virtual
  core::Size version() const;

  RNA_Mg_KnowledgeBasedPotentialOP rna_mg_knowledge_based_potential_;
  core::scoring::hbonds::HBondOptionsOP hbond_options_;

  bool const verbose_;

};


}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH