RNA_FullAtomVDW_BasePhosphate.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_FullAtomVDW_BasePhosphate.hh
/// @brief  FullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide
/// @author Parin Sripakdeevong (sripakpa@stanford.edu), Rhiju Das (rhiju@stanford.edu)


#ifndef INCLUDED_core_scoring_rna_RNA_FullAtomVDW_BasePhosphate_hh
#define INCLUDED_core_scoring_rna_RNA_FullAtomVDW_BasePhosphate_hh

// Unit headers
#include <core/scoring/rna/RNA_FullAtomVDW_BasePhosphate.fwd.hh>
#include <core/scoring/etable/EtableEnergy.hh>
// Package headers
#include <core/scoring/methods/ContextIndependentOneBodyEnergy.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>

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

namespace core {
namespace scoring {
namespace rna {

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

public:

  /// @brief ctor
  RNA_FullAtomVDW_BasePhosphate( etable::TableLookupEtableEnergy const & etable_energy_in, etable::Etable const & etable_in);

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

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

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

  void
  residue_fast_pair_energy_attached_H( //copy from atom_pair_energy_inline.hh
    core::conformation::Residue const & res1,
    int const atomno1,
    core::conformation::Residue const & res2,
    Size const atomno2,
    Size const at1hbegin, //at1hbegin and at1hend define a range of hydrogen atom indices -- those h's bound to at1
    Size const at1hend,
    Size const at2hbegin,
    Size const at2hend,
    EnergyMap & emap
  ) const;

  ///
  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
  eval_atom_derivative(
    id::AtomID const & id,
    pose::Pose const & pose,
    kinematics::DomainMap const &, // domain_map,
    ScoreFunction const & /*sfxn*/, // needed for non-nblist minimization
    EnergyMap const & weights,
    Vector & F1,
    Vector & F2
  ) const;

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


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

/*
  virtual
  void
  setup_for_packing( pose::Pose & pose, pack::task::PackerTask const & ) const;
*/


private:

  etable::TableLookupEtableEnergy const etable_energy_;
  etable::Etable const & etable_; // shouldn't this be a pointer? Reference count information is (dangerously) lost when

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

  virtual
  core::Size version() const;

/*

  ///
///////////////////////////////////////////////////////////////////////////////




*/

};

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


#endif // INCLUDED_core_scoring_EtableEnergy_HH