Sheet.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// Copyright in the Rosetta software belongs to the developers and their institutions.
// For more information, see www.rosettacommons.org.

/// @file ./src/protocols/fldsgn/topology/Sheet.hh
/// @brief
/// @author Nobuyasu Koga ( nobuyasu@u.washington.edu )

#ifndef INCLUDED_protocols_fldsgn_topology_Sheet_hh
#define INCLUDED_protocols_fldsgn_topology_Sheet_hh

// unit headers
#include <core/pose/Pose.fwd.hh>
#include <protocols/fldsgn/topology/Sheet.fwd.hh>

// project headers
#include <core/types.hh>
#include <protocols/fldsgn/topology/StrandPairing.hh>
#include <protocols/fldsgn/topology/SS_Info2.fwd.hh>

// utility headers
#include <utility/pointer/ReferenceCount.hh>

// C++ headers
#include <map>

#include <utility/vector1.hh>
#include <numeric/xyzVector.hh>


namespace protocols {
namespace fldsgn {
namespace topology {

class Sheet : public utility::pointer::ReferenceCount {
public:


  typedef core::Size Size;
  typedef core::Real Real;
  typedef core::Vector Vector;
  typedef core::pose::Pose Pose;
  typedef utility::vector1< Size > VecSize;
  typedef utility::vector1< int > VecInt;
  typedef utility::vector1< Real > VecReal;
  typedef protocols::fldsgn::topology::SS_Info2_COP SS_Info2_COP;


public:// construct/destruct


  /// @brief default constructor
  Sheet();

  /// @brief value constructor
  Sheet( VecSize const & order_strands, VecInt const & orient_strands, bool is_barrel );

  /// @brief copy constructor
  Sheet( Sheet const & s );

  /// @brief default destructor
  virtual ~Sheet();

  /// @brief clone this object
  SheetOP clone() {
    return new Sheet( *this );
  }

  /// @brief return strand pairing
  friend
  std::ostream & operator<<( std::ostream & out, const Sheet &s );


public:


  /// @brief intialize this class
  void initialize();


public: //accessors


  /// @brief the number strands inclued in
  Size num_strands() const {  return num_strands_;  }

  /// @brief is this barrel ?
  bool is_barrel() const { return is_barrel_; }

  VecSize order_strands() const { return order_strands_; }

  Size order_strand( Size const s ) const { return order_strands_[ s ]; }

  VecInt orient_strands() const { return orient_strands_; }

  int orient_strand( Size const s ) const { return orient_strands_[ s ]; }

  Size strand_order( Size const s ) { return strand_order_[ s ];  }

  VecInt ca_cb_orients() const { return ca_cb_orients_; }

  int ca_cb_orient( Size const s ) const { return ca_cb_orients_[ s ]; }


public:

  /// @brief
  int
  which_side( Vector const vec ) const;

  /// @brief calc surface areas only with beta-sheet
  utility::vector1< Real >
  calc_sasa_bothsides( Pose const & pose, SS_Info2_COP const ssinfo, Real pore_radius=1.5 );

  /// @brief calc geometry of sheet, sheet_plane_, sheet_center_, ca_cb_orients_
  void
  calc_geometry( SS_Info2_COP const ssinfo );


public: //

  bool is_member( Size const s );

private:  // data

  /// @brief
  Size num_strands_;

  /// @brief
  bool is_barrel_;

  /// @brief order of strand in sheet -> id of strand
  VecSize order_strands_;

  /// @brief order of strand in sheet -> id of strand
  VecInt orient_strands_;

  /// @brief id of strand -> order of strand in sheet
  std::map< Size, Size > strand_order_;

  /// @brief vector defining sheet plane
  Vector sheet_plane_;

  /// @brief "center" of sheet
  Vector sheet_center_;

  VecInt ca_cb_orients_;

  /// @brief geometries was calculated or not
  bool is_geometry_initialized_;

};


class SheetSet : public utility::pointer::ReferenceCount {
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~SheetSet();


  typedef core::Size Size;
  typedef core::Real Real;
  typedef utility::vector1< int > VecInt;
  typedef utility::vector1< Size > VecSize;
  typedef utility::vector1< Real > VecReal;
  typedef protocols::fldsgn::topology::StrandPairingSet StrandPairingSet;
  typedef protocols::fldsgn::topology::StrandPairingSetCOP StrandPairingSetCOP;
  typedef protocols::fldsgn::topology::SS_Info2_COP SS_Info2_COP;


public:// construct/destruct


  /// @brief default constructor
  SheetSet();

  /// @brief value constructor
  SheetSet( Sheets const & sheets );

  /// @brief value constructor
  SheetSet( SS_Info2_COP const ssinfo, StrandPairingSetCOP const spairset );

  /// @brief copy constructor
  SheetSet( SheetSet const & s );

  /// @brief return strand pairing
  friend
  std::ostream & operator<<( std::ostream & out, const SheetSet &s );


public:


  void initialize( SS_Info2_COP const ssinfo, StrandPairingSetCOP const spairset );


public: // mutators


  /// @brief
  void push_back( SheetOP const sop );

  /// @brief
  void clear();


public: // accessors


  /// @brief
  SheetOP sheet( Size const s ) const;

  /// @brief
  inline Sheets sheets() const { return sheets_; }

  /// @brief return number of sheets
  inline Size num_sheets() const { return sheets_.size(); }

  /// @brief return number of sheets
  inline Size size() const { return sheets_.size(); }

  /// @brief return the id of sheet that a given strand belongs to.
  Size which_sheet( Size const s ) const;

  /// @brief return strand pairing set
  StrandPairingSet spairset() const;

public:


  /// @brief
  void calc_geometry( SS_Info2_COP const ssinfo );


private://


  /// @brief
  void set_sheet_number() const;


private:  // data


  /// @brief sheet number given a strand
  mutable std::map< Size, Size > sheet_number_;

  /// @brief
  Sheets sheets_;

  /// @brief
  StrandPairingSet spairset_;


};

} // namespace topology
} // namespace fldsgn
} // namespace protocol

#endif