GenBornEnergy.hh

Go to the documentation of this file.

// -*- 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/GenBornEnergy.hh
/// @brief  Statistically derived rotamer pair potential class declaration
/// @author Phil Bradley


#ifndef INCLUDED_core_scoring_methods_GenBornEnergy_hh
#define INCLUDED_core_scoring_methods_GenBornEnergy_hh

// Unit Headers
#include <core/scoring/methods/GenBornEnergy.fwd.hh>

// Package headers
#include <core/scoring/methods/EnergyMethodOptions.fwd.hh>
#include <core/scoring/methods/ContextDependentLRTwoBodyEnergy.hh>
#include <core/scoring/GenBornPotential.fwd.hh>
#include <core/scoring/EnergyMap.fwd.hh>
#include <core/kinematics/DomainMap.fwd.hh>

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

#include <utility/vector1.hh>


// Utility headers
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
/**

   This is a reimplementation of Jim Havranek's original rosetta++ Gen Born code.
   source files: rosetta++/gb_elec*

**/
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////


namespace core {
namespace scoring {
namespace methods {

///
class GenBornEnergy : public ContextDependentLRTwoBodyEnergy  {
public:
  typedef ContextDependentLRTwoBodyEnergy  parent;
public:

  /// for use by ScoringManager
  GenBornEnergy( EnergyMethodOptions const & options );

  ///
  GenBornEnergy( GenBornEnergy const & src );


  LongRangeEnergyType long_range_type() const
  {
    return gen_born_lr;
  }

  virtual
  bool
  defines_residue_pair_energy(
    pose::Pose const & pose,
    Size res1,
    Size res2
  ) const;

  /// clone
  virtual
  EnergyMethodOP
  clone() const;

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

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

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

  virtual
  void
  prepare_rotamers_for_packing(
    pose::Pose const & pose,
    conformation::RotamerSetBase & set
  ) const;

  virtual
  void
  update_residue_for_packing(
    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;

  virtual
  void
  evaluate_rotamer_intrares_energies(
    conformation::RotamerSetBase const & set,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    utility::vector1< core::PackerEnergy > & energies
  ) const;

  virtual
  void
  evaluate_rotamer_intrares_energy_maps(
    conformation::RotamerSetBase const & set,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    utility::vector1< EnergyMap > & emaps
  ) const;

  /// @brief Batch computation of rotamer pair energies.  Need not be overriden in
  /// derived class -- by default, iterates over all pairs of rotamers,
  /// and calls derived class's residue_pair_energy method.  Since short range rotamer pairs
  /// may not need calculation, the default method looks at blocks of residue type pairs
  /// and only calls the residue_pair_energy method if the rotamer pairs are within range
  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 Batch computation of rotamer/background energies.  Need not be overriden
  /// in derived class -- by default, iterates over all rotamers in the set, and calls
  /// derived class's residue_pair_energy method for each one against the background rotamer
  /// Since short range rotamer pairs may not need calculation, the default method
  /// looks at blocks of residue type pairs and only calls the residue_pair_energy method
  /// if the rotamer pairs are within range
  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;

  /// @brief Batch computation of rotamer/background energies.  Need not be overriden
  /// in derived class -- by default, iterates over all rotamers in the set, and calls
  /// derived class's residue_pair_energy method for each one against the background rotamer
  /// Since short range rotamer pairs may not need calculation, the default method
  /// looks at blocks of residue type pairs and only calls the residue_pair_energy method
  /// if the rotamer pairs are within range
  virtual
  void
  evaluate_rotamer_background_energy_maps(
    conformation::RotamerSetBase const & set,
    conformation::Residue const & residue,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap const & weights,
    utility::vector1< EnergyMap > & emaps
  ) 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
//  Distance
//  atomic_interaction_cutoff() const;

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

  virtual
  bool
  defines_intrares_energy( EnergyMap const & /*weights*/ ) const;

  virtual
  void
  eval_intrares_energy(
    conformation::Residue const & rsd,
    pose::Pose const & pose,
    ScoreFunction const & sfxn,
    EnergyMap & emap
  ) const;

  /// this is our own special function
  Real
  packing_interaction_cutoff() const
  {
    return 5.5; // MAGIC NUMBER!!
  }

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

private:

  // const-ref to scoring database
  GenBornPotential const & potential_;

  ///
  bool const exclude_DNA_DNA_;
virtual
core::Size version() const;

};


}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH