MotifLibrary.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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 MotifLibrary.hh
/// @brief class declaration for sets of interaction motifs between residues
/// @author havranek, sthyme (sthyme@gmail.com)

#ifndef INCLUDED_protocols_motifs_MotifLibrary_hh
#define INCLUDED_protocols_motifs_MotifLibrary_hh

// Unit Headers
#include <protocols/motifs/MotifLibrary.fwd.hh>

// Package Headers
#include <protocols/motifs/Motif.fwd.hh>

// Project Headers
#include <core/types.hh>

// Utility Headers
#include <utility/file/FileName.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

// C++ Headers
#include <iosfwd>

//Auto Headers
namespace protocols {
namespace motifs {

class MotifLibrary : public utility::pointer::ReferenceCount
{

public:

  typedef utility::vector1< utility::file::FileName > const FileNames;

  // Constructor
  MotifLibrary();

  // Destructor
  virtual ~MotifLibrary();

  // Constructor for loading motifs from motif PDBs
  MotifLibrary(
    utility::vector1< utility::file::FileName > const & motif_filenames
  );

  // Constructor for loading motifs from a file with coordinates
  MotifLibrary(
    std::istream & motif_info
  );

  // Add motif to library
  void
  add_to_library(
    Motif const & new_motif
  );

  // Constructor for loading motifs from a file with coordinates for ligands
MotifLibrary(
  std::istream & motif_info, core::Size ligand_marker
  );

  // Add ligand motif from a PDB file
  void
  add_ligand_from_file(
    std::string const & motif_filename
  );

  // Add motif from a PDB file
  void
  add_from_file(
    std::string const & motif_filename
  );

  // Number of motifs
  core::Size
  nmotifs();

  // Iterators
  MotifCOPs::const_iterator begin() { return library_.begin(); }
  MotifCOPs::const_iterator end() { return library_.end(); }

  MotifCOPs::const_iterator begin() const { return library_.begin(); }
  MotifCOPs::const_iterator end() const { return library_.end(); }

  // Accessors
  MotifCOPs const & library() const { return library_; }

  // Overloaded operator for output
  friend std::ostream & operator <<(
    std::ostream & os,
    MotifLibrary const & mot_lib
  );

private:
  MotifCOPs library_;

};

} // namespace motifs
} // namespace protocols

#endif // INCLUDED_protocols_motifs_MotifLibrary