NMerPSSMEnergy.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/NMerPSSMEnergy.hh
/// @brief  PSSM energy method declaration
/// @author Chris King (dr.chris.king@gmail.com)


#ifndef INCLUDED_core_scoring_methods_NMerPSSMEnergy_hh
#define INCLUDED_core_scoring_methods_NMerPSSMEnergy_hh

// Unit headers
#include <core/scoring/methods/NMerPSSMEnergy.fwd.hh>

// Package headers
#include <core/scoring/methods/ContextIndependentOneBodyEnergy.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Project headers
#include <core/chemical/AA.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/id/DOF_ID.fwd.hh>

#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <map>

// Utility headers


namespace core {
namespace scoring {
namespace methods {

class NMerPSSMEnergy : public ContextIndependentOneBodyEnergy
{
public:
  typedef ContextIndependentOneBodyEnergy parent;

public:

  ///
  NMerPSSMEnergy();

  ///
  NMerPSSMEnergy( utility::vector1< std::map< core::chemical::AA, utility::vector1< core::Real > > > const & all_nmer_pssms_in );

  ///
  virtual ~NMerPSSMEnergy();

  virtual
  EnergyMethodOP
  clone() const;

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

  ///
  virtual
  void
  residue_energy(
    conformation::Residue const & rsd,
    pose::Pose const & pose,
    EnergyMap & emap
  ) const;

  bool
  minimize_in_whole_structure_context( pose::Pose const & ) const { return false; }

  ///
  virtual
  Real
  eval_dof_derivative(
    id::DOF_ID const & dof_id,
    id::TorsionID const & tor_id,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights
  ) const;

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

  void read_nmer_pssm_list( std::string const );
  void read_nmer_pssm( std::string const );
  void nmer_length( core::Size const );
  void gate_pssm_scores( bool const );
  void nmer_pssm_scorecut( core::Real const );

private:
  utility::vector1< std::map< core::chemical::AA, utility::vector1< core::Real > > > all_nmer_pssms_;
  core::Size nmer_length_;
  core::Size nmer_cterm_;
  bool gate_pssm_scores_;
  core::Real nmer_pssm_scorecut_;

  void read_nmer_pssms_from_options();
  void initialize_from_options();
  virtual
  core::Size version() const;
};

} // methods
} // scoring
} // core


#endif