SelectResiduesByLayer.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
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/// @file protocols/toolbox/SelectResiduesByLayer.hh
/// @brief select residues depending on layer: core, boundary, and surface
/// and the layer are defined by accessible sufrace area of each residue
/// @author Nobuyasu Koga ( nobuyasu@uw.edu )

#ifndef INCLUDED_protocols_toolbox_SelectResiduesByLayer_hh
#define INCLUDED_protocols_toolbox_SelectResiduesByLayer_hh

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/chemical/AA.hh>
#include <protocols/toolbox/SelectResiduesByLayer.fwd.hh>

#include <map>
// AUTO-REMOVED #include <fstream>
// AUTO-REMOVED #include <string>
#include <utility/vector1.hh>

#include <utility/pointer/ReferenceCount.hh>


namespace protocols {
namespace toolbox {

class SelectResiduesByLayer : public utility::pointer::ReferenceCount {
public:


  typedef core::Size Size;
  typedef core::Real Real;
  typedef std::string String;
  typedef core::chemical::AA AA;
  typedef core::pose::Pose Pose;


public: // constructor/destructor


  /// @brief default constructor
  SelectResiduesByLayer();

  /// @brief value constructor
  SelectResiduesByLayer( 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
  SelectResiduesByLayer( String const pick );

  /// @brief destructor
  virtual ~SelectResiduesByLayer();


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, String secstruct="" );


private: // helper functions


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

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


protected:


  /// @brief design core ?
  bool pick_core_;

  /// @brief design 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 output in rasmol format


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

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


};


} // flxbb
} // protocols

#endif