LayerOperations.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 protocols/toolbox/LayerOperations.hh
/// @brief select residues depending on layer: core, boundary, and surface
/// and the layer are defined by accessible surface area of each residue, like nobu's just more general
/// @author Eva

#ifndef INCLUDED_protocols_toolbox_LayerOperations_hh
#define INCLUDED_protocols_toolbox_LayerOperations_hh

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/chemical/AA.hh>
#include <core/id/AtomID_Map.hh>
#include <core/chemical/AtomType.hh>

#include <core/scoring/sasa.hh>
//#include <protocols/toolbox/LayerOperations.fwd.hh>
#include <map>
#include <utility/vector1.hh>

//package headers
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/types.hh>


// Utility Headers
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.hh>

namespace protocols {
namespace toolbox {
namespace task_operations{

class LayerOperations : public core::pack::task::operation::TaskOperation {
public:
  typedef core::Size Size;
  //typedef core::Real Real;
  typedef std::string String;
  //typedef core::chemical::AA AA;
  typedef core::pose::Pose Pose;
  typedef core::Real Real;
  //typedef core::pose::Pose Pose;
  typedef core::pack::task::PackerTask PackerTask;
  typedef core::pack::task::operation::TaskOperation TaskOperation;
  typedef core::pack::task::operation::TaskOperationOP TaskOperationOP;
  typedef TaskOperation parent;
  typedef utility::tag::TagPtr TagPtr;

public: // constructor/destructor

  /// @brief default constructor
  LayerOperations();

  /// @brief value constructor
  LayerOperations( bool const pick_core, bool const pick_boundary, bool const pick_surface );

  /// @brief value constructor
  /// @detail selected layer can be given by string, for example, core_surface or core_boundary_surface
  LayerOperations( String const pick );

  /// @brief destructor
  ~LayerOperations();
    
    /// @brief make clone
  virtual TaskOperationOP clone() const;

public:

  void initialize( Real burial, Real surface );

public:  // mutator

  /// @brief
  void
  set_design_layer( bool const pick_core, bool const pick_boundary, bool const pick_surface )
  {
    pick_core_ = pick_core;
    pick_boundary_ = pick_boundary;
    pick_surface_ = pick_surface;
  }

  /// @brief set pore radius for colculating asa
  void pore_radius( Real const ps ){
    pore_radius_ = ps;
  }

  /// @brief accessible surface for evaluating residues are in surface or not
  void sasa_surface( Real const r, String const ss="" );

  /// @brief accessible surface for evaluating residues are in core or not
  void sasa_core( Real const r, String const ss="" );

  /// @brief accessible surface for evaluating residues are in core or not
  void make_rasmol_format_file( bool const b ){
    make_rasmol_format_file_ = b;
  }

  /// @brief
  //void exclude_aatypes_for_selection( utility::vector1< AA > const & aas );

  /// @brief
  //void restrict_aatypes_for_selection( utility::vector1< AA > const & aas );

public:  // accessor

  /// @brief accessbile surface are of each residue
  Real rsd_sasa( Size const i ) const;

  /// @brief return defined layer for each residue
  String layer( Size const i ) const;

  /// @brief selected residues on boundary
  utility::vector1< Size > const & selected_boundary_residues() const;

  /// @brief selected residues in core
  utility::vector1< Size > const & selected_core_residues() const;

  /// @brief selected residues on surface
  utility::vector1< Size > const & selected_surface_residues() const;


public: // main operation


  /// @brief apply
  utility::vector1< Size > const
  compute( Pose const & pose );

private: // helper functions

  /// @brief
  LayerOperations(LayerOperations const &);

  /// @brief
  utility::vector1< Real > const
  calc_rsd_sasa( Pose const & pose ) const;

protected:

  /// @brief design/repack core ?
  bool pick_core_;

  /// @brief design/repack boundary ?
  bool pick_boundary_;

  /// @brief design surface ?
  bool pick_surface_;

  /// @brief pore radius for calculating asa( accessible surface area )
  Real pore_radius_;

  /// @brief asa pore radius for calculating asa
  std::map< char, Real > burial_;

  /// @brief pore radius for calculating asa
  std::map< char, Real > surface_;

  /// @brief amino acid types excluded for selection
  //utility::vector1< AA > excluded_aatypes_for_selection_;

  /// @brief amino acid types restricted for selection
  //utility::vector1< AA > restricted_aatypes_for_selection_;

  /// @brief selected residues in core
  utility::vector1< Size > selected_core_residues_;

  /// @brief selected residues at boundary
  utility::vector1< Size > selected_boundary_residues_;

  /// @brief selected residues on surface
  utility::vector1< Size > selected_surface_residues_;

  /// @brief create rasmol format script for selected residues; red: surface, blue: core, green: boundary
  bool make_rasmol_format_file_;

  /// @brief asa for each residue
  utility::vector1< Real > rsd_sasa_;

  /// @brief
  utility::vector1< String > rsd_layer_;

  /// @brief design selection?
  bool design_;

  /// @brief repack the rest of the protein?
  bool repack_rest_;

  /// @brief which chain to pick
  core::Size chain_;
  
  /// @brief take chains apart, as defined by user specified jump number
  core::Size jump_;

};

}
} 
} // protocols

#endif