SurfaceEnergies.hh

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// vi: set ts=2 noet:
//
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/// @file   core/scoring/solid_surface/SurfaceEnergies.hh
/// @brief  SurfaceEnergies class
/// @author Andrew Leaver-Fay (aleaverfay@gmail.com)
/// @author Mike Pacella (mpacella@gmail.com)


#ifndef INCLUDED_core_scoring_solid_surface_SurfaceEnergies_hh
#define INCLUDED_core_scoring_solid_surface_SurfaceEnergies_hh

// Package Headers
#include <core/scoring/solid_surface/SurfaceEnergies.fwd.hh>

// Project Headers
#include <core/scoring/Energies.hh>
#include <core/conformation/find_neighbors.fwd.hh>

// Numeric Headers
//#include <numeric/geometry/BoundingBox.hh>

namespace core {
namespace scoring {
namespace solid_surface {

  /// A derived class from class Energies for efficiently representing the
  /// interactions between a protein and a fixed surface

class SurfaceEnergies : public Energies
{
public:
  typedef Energies parent;

public:
  /// ctor -- ensure correct initial state
  SurfaceEnergies();

  // Explicit copy ctor to avoid #include .hh's
  SurfaceEnergies( SurfaceEnergies const & src );

  // Explicit assignmnet operator to avoid #include .hh's
  virtual Energies const & operator = ( Energies const & rhs );

  ///@details determine whether my type is the same as another Conformation's
  virtual
  bool
  same_type_as_me( Energies const & other, bool recurse = true ) const;

  /// dtor
  virtual
  ~SurfaceEnergies();

  virtual
  EnergiesOP
  clone() const;

  /// @brief The SurfaceEnergies object needs to know how many residues are in its pose;
  /// it also has to be told which residues are considered part of the surface and which
  /// residues are not part of the surface.
  void
  set_total_residue( Size total_residue );

  /// @brief Wipe away all the information in the SurfacEnergies object describing which
  /// residues are considered part of the surface and which residues are not part of the
  /// surface.  (Afterwards, all residues are going to be considered part of the surface).
  void
  reset_surface_residue_information();
  
  /// @brief Tell the SurfacEnergies that the following residues are considered not
  /// part of the surface.
  void
  set_residue_range_not_surface( Size seqpos_begin, Size seqpos_end );

  /// @brief Does the SurfaceEnergies object consider a particular residue to be part of the surface?
  bool
  residue_is_surface( Size seqpos ) const;
  
  
  /////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////
  // private methods
  /////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////

private:

  /// @brief Create a point graph representing the xyz coordinates of the "neighbor
  /// atoms."  (Each residue_type indicates one of its atoms to be used for
  /// neighbor detection -- e.g. CB for most amino acids, CA for GLY.)  The point
  /// graph will then be used in a call to find_neighbors to add upper-edges to
  /// neighboring residues.
  virtual
  void fill_point_graph( pose::Pose const & pose, conformation::PointGraphOP pg ) const;

  /// @brief Create a new surface grid, bounding box and dimension for the surface residues.
  /// This might get called if the range on the score function changes or if the surface 
  /// moves.  (NOTE: currently not prepared to handle the case where the surface moves!)
  //void
  //prepare_surface_grid( conformation::PointGraphOP pg, Real neighbor_cutoff ) const;

  /// @brief Wipe everything held in the surface grid, ensuring that in the next score function
  /// evaluation, a new grid will be computed.
  //void
  //reset_surface_grid() const;

private:
  Size total_residue_; // The total number of residues in the pose. NOTE: if this disagrees with parent::size(), we're in trouble 
  utility::vector1< std::pair< Size, Size > > non_surface_ranges_; // The residue beginning and ending indices which are considered not part of the surface
  utility::vector1< bool > is_surface_; // The residues considered part of the surface


  // Data for representing the surface that's used in neighbor detection
  mutable Real neighbor_cutoff_;
  //mutable std::map< core::conformation::CubeKey, utility::vector1< Size > > surface_grid_;
  //mutable numeric::geometry::BoundingBox< numeric::xyzVector< Real > > surf_bb_;
  //mutable core::conformation::CubeKey surf_dim_;
  
};


} // namespace solid_surface
} // namespace scoring
} // namespace core


#endif // INCLUDED_core_scoring_solid_surface_Energies_HH