RNAHackElecEnergy.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/methods/RNAHackElecEnergy.hh
/// @brief  Electrostatics for RNA
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_hackelec_RNAHackElecEnergy_hh
#define INCLUDED_core_scoring_hackelec_RNAHackElecEnergy_hh

/// Unit Headers
#include <core/scoring/hackelec/RNAHackElecEnergy.fwd.hh>

/// Package Headers
#include <core/scoring/hackelec/HackElecEnergy.hh>

#include <core/scoring/ScoreFunction.fwd.hh>

#include <core/scoring/methods/EnergyMethod.fwd.hh>
#include <core/scoring/methods/EnergyMethodOptions.fwd.hh>

#include <ObjexxFCL/FArray2D.fwd.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace hackelec {

///
class RNAHackElecEnergy : public HackElecEnergy  {
public:
  typedef HackElecEnergy parent;
  typedef ContextIndependentTwoBodyEnergy grandparent;

public:

  ///
  RNAHackElecEnergy( methods::EnergyMethodOptions const & options );

  ///
  RNAHackElecEnergy( RNAHackElecEnergy const & src );


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

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

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

  ///
  virtual
  void
  setup_for_packing( pose::Pose & pose, utility::vector1< bool > const &, utility::vector1< bool > const & ) const;


  /// @brief overrides parent class implementation which would have
  /// created several tries
  virtual
  void
  prepare_rotamers_for_packing(
    pose::Pose const & pose,
    conformation::RotamerSetBase & set ) const;

  /// @brief overrides parent class implementation which would have
  /// updated a trie
  virtual
  void
  update_residue_for_packing( pose::Pose & pose, Size resid ) const;

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

  virtual
  void
  residue_pair_energy(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    pose::Pose const & pose,
    ScoreFunction const &,
    EnergyMap & emap
  ) const;

  /// @brief Returns "true" because this energy method has not been updated to
  /// use the new derivative evaluation machinery.  Note that this class requires
  /// the definition of this method because it's parent class, HackElecEnergy,
  /// HAS been updated to use the new derivative evaluation machinery, and,
  /// if this class did not return "true", it would be asked to evaluate derivatives
  /// in ways it cannot yet evaluate them in.
  bool
  minimize_in_whole_structure_context( pose::Pose const & ) const { return true; }


  /// @brief Jan 10, 2012. Parin Sripakdeevon (sripakpa@stanford.edu)
  /// Returns "false" to overwrite the behavior in the parent class (HackElecEnergy)! 
  virtual
  bool
  use_extended_residue_pair_energy_interface() const { return false; }

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const &,
    pose::Pose const &,
    ScoreFunction const &,
    EnergyMap &
  ) const {}

  //@brief overrides default rotamer/rotamer energy calculation
  // and overrides the parent class trie implementatoin
  virtual
  void
  evaluate_rotamer_pair_energies(
    conformation::RotamerSetBase const & set1,
    conformation::RotamerSetBase const & set2,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    ObjexxFCL::FArray2D< core::PackerEnergy > & energy_table
  ) const;


  //@brief overrides default rotamer/background energy calculation
  // and overrides the parent class trie implementatoin
  virtual
  void
  evaluate_rotamer_background_energies(
    conformation::RotamerSetBase const & set,
    conformation::Residue const & residue,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    utility::vector1< core::PackerEnergy > & energy_vector
  ) 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 indicate_required_context_graphs( utility::vector1< bool > & context_graphs_required ) const;

public:


  Real
  residue_pair_energy_RNA(
    conformation::Residue const & rsd1,
    conformation::Residue const & rsd2,
    EnergyMap & emap
  ) const;

  void
  eval_atom_derivative_RNA(
     conformation::Residue const & rsd1,
     Size const & i,
     conformation::Residue const & rsd2,
     EnergyMap const & weights,
     Vector & F1,
     Vector & F2
  ) const;
virtual
core::Size version() const;

};


}
}
}

#endif