SS_Info.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   core/scoring/ScoringManager.hh
/// @brief  Scoring manager class header
/// @author Andrew Leaver-Fay (leaverfa@email.unc.edu)


#ifndef INCLUDED_core_scoring_SS_Info_hh
#define INCLUDED_core_scoring_SS_Info_hh

/// Unit headers
#include <core/scoring/SS_Info.fwd.hh>

/// Package headers
#include <core/types.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <basic/datacache/CacheableData.hh>

/// Utility headers
// AUTO-REMOVED #include <utility/vector1.hh>

/// Numeric headers
#include <numeric/xyzVector.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>

// C++ headers
#include <string>
#include <iosfwd>

#include <utility/vector1.hh>


namespace core {
namespace scoring {

//////////////////////////////////////////////////////////////////////////////////////////////////////
class BB_Pos {

public:


  void
  resize( int const nres );

  void
  take_coordinates_from_pose( pose::Pose const & pose );

  /// @details accessor for N's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
  Vector const &
  N( int const i ) const
  {
    return N_[i];
  }

  /// @details accessor for CA's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
  Vector const &
  CA( int const i ) const
  {
    return CA_[i];
  }

  /// @details accessor for CB's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
  Vector const &
  CB( int const i ) const
  {
    return CB_[i];
  }


  /// @details accessor for C's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
  Vector const &
  C( int const i ) const
  {
    return C_[i];
  }

  /// @details accessor for O's coordinate on residue i, requires take_coordinates_from_pose have been recently called.
  Vector const &
  O( int const i ) const
  {
    return O_[i];
  }


private:

  bool bbindices_up_to_date( pose::Pose const & pose ) const;
  void update_indices( pose::Pose const & pose );

private: // DATA
  utility::vector1< Vector > N_;
  utility::vector1< Vector > CA_;
  utility::vector1< Vector > CB_;
  utility::vector1< Vector > C_;
  utility::vector1< Vector > O_;

  /// Residue types must match those of the pose for the indices
  /// to match.
  utility::vector1< chemical::ResidueType const * > residue_types_;
  utility::vector1< Size > N_index_;
  utility::vector1< Size > CA_index_;
  utility::vector1< Size > CB_index_;
  utility::vector1< Size > C_index_;
  utility::vector1< Size > O_index_;

};



//////////////////////////////////////////////////////////////////////////////////////////////////////

struct Strands {

  typedef ObjexxFCL::FArray1D< int > FArray1D_int;
  typedef ObjexxFCL::FArray2D< int > FArray2D_int;

  /// @brief default constructor
  Strands();

  /// @brief total residue constructor
  Strands(
    int const & total_residue
  );

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

  /// @brief default destructor
  ~Strands();

  ///
  void
  resize( Size const nres );

  void clear();

  /// @brief copy assignment
  Strands const &
  operator =( Strands const & s );

  friend
  std::ostream &
  operator<< ( std::ostream & out, Strands const & s );

  /// @brief number of strand dimers
  int total_SS_dimer;

  /// @brief residue number of strand dimer i
  FArray1D_int SS_resnum;

  /// @brief number of strands
  int total_strands;

  /// @brief strand number containing SS_dimer i
  FArray1D_int SS_strand;

  /// @brief dimer number starting with position i
  FArray1D_int SS_dimer;

  /// @brief residue number of first non-E res
  FArray2D_int SS_strand_end;

  /// @brief two neighbors, used for determining sheets
  mutable FArray2D_int dimer_neighbor; // hack to allow updating in sspair

  /// @brief strand-strand score array, resized for each calculation:
  // need to re-add this logic if it turns out to be useful
  //ObjexxFCL::FArray2D< Real > strand_strand_score;

};

//////////////////////////////////////////////////////////////////////////////////////////////////////


struct Helices {

  typedef ObjexxFCL::FArray1D< int > FArray1D_int;
  typedef ObjexxFCL::FArray2D< int > FArray2D_int;

  /// @brief default constructor
  Helices();

  /// @brief total residue constructor
  Helices(
    int const & total_residue
  );

  ///
  void
  resize( int const nres );

  /// @brief copy constructor
  Helices(
    Helices const & h
  );

  /// @brief default destructor
  ~Helices();

  /// @brief copy assignment
  Helices const &
  operator = ( Helices const & h );

  friend
  std::ostream &
  operator<< ( std::ostream & out, Helices const & s );

  /// @brief number of helices
  int total_helices;

/// PRIVATE: !

  // variables
  int total_HH_dimer;
  FArray1D_int HH_resnum;
  FArray2D_int HH_helix_end;
};


//////////////////////////////////////////////////////////////////////////////////////////////////////
class SS_Info : public basic::datacache::CacheableData {
public:

  basic::datacache::CacheableDataOP
  clone() const
  {
    return new SS_Info( *this );
  }

  void
  resize( int const nres )
  {
    bb_pos_.resize( nres );
    strands_.resize( nres );
    helices_.resize( nres );
  }

  ///
  inline
  BB_Pos const &
  bb_pos() const
  {
    return bb_pos_;
  }

  ///
  inline
  BB_Pos &
  bb_pos()
  {
    return bb_pos_;
  }

  ///
  inline
  Strands const &
  strands() const
  {
    return strands_;
  }

  ///
  inline
  Strands &
  strands()
  {
    return strands_;
  }

  ///
  inline
  Helices const &
  helices() const
  {
    return helices_;
  }

  ///
  inline
  Helices &
  helices()
  {
    return helices_;
  }

private:

  BB_Pos bb_pos_;

  Strands strands_;

  Helices helices_;

};

} // ns scoring
} // ns core

#endif