RNA_LJ_BaseEnergy.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file   core/scoring/rna/RNA_LJ_BaseEnergy.hh
/// @brief  van der waals over aromatics
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_LJ_BaseEnergy_hh
#define INCLUDED_core_scoring_rna_RNA_LJ_BaseEnergy_hh

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

// Package headers
#include <core/conformation/Atom.fwd.hh>
#include <core/scoring/methods/ContextIndependentTwoBodyEnergy.hh>
#include <core/scoring/etable/Etable.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

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

// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>

#include <utility/vector1.hh>
#include <ObjexxFCL/FArray3D.fwd.hh>


namespace core {
namespace scoring {
namespace rna {

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

public:

  RNA_LJ_BaseEnergy( etable::Etable const & etable_in );

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

  RNA_LJ_BaseEnergy( RNA_LJ_BaseEnergy const & src );

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

  /// called during gradient-based minimization inside dfunc
  /**
     F1 and F2 are not zeroed -- contributions from this atom are
     just summed in
  **/
  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;


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

  virtual
  bool
  defines_intrares_energy( EnergyMap const & /*weights*/ ) const { return false; }

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

  virtual
  Distance
  atomic_interaction_cutoff() const;


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

  Real
  eval_atom_energy(
    id::AtomID const & id,
    pose::Pose const & pose
  ) const;

private:

  void
  eval_lj(
  conformation::Atom const & atom1,
  conformation::Atom const & atom2,
  Real const & d2,
  Real & fa_atr_score,
  Real & fa_rep_score,
  Real & deriv_atr,
  Real & deriv_rep
  ) const;

  virtual
  void
  finalize_total_energy(
    pose::Pose & pose,
    ScoreFunction const &,
    EnergyMap &// totals
  ) const;

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

private:
  etable::Etable const & etable_; // shouldn't this be a pointer? Reference count information is (dangerously) lost when
  //a reference is taken, instead of a smart pointer.  There's the potential for a dangling reference with this.


  /// these guys are taken from the etable
  ObjexxFCL::FArray3D< Real > const & ljatr_;
  ObjexxFCL::FArray3D< Real > const & ljrep_;

  ObjexxFCL::FArray3D< Real > const & dljatr_;
  ObjexxFCL::FArray3D< Real > const & dljrep_;

  Real const safe_max_dis2_;
  Real const get_bins_per_A2_;

  bool const verbose_;
virtual
core::Size version() const;

};

}
}
}

#endif // INCLUDED_core_scoring_methods_RNA_LJ_BaseEnergy_HH