PDBSilentStruct.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:
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//
// (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/io/silent/PDBSilentStruct.hh
///
/// @brief Representation of rosetta++ protein silent-file structures.
/// @author James Thompson

#ifndef INCLUDED_core_import_pose_PDBSilentStruct_hh
#define INCLUDED_core_import_pose_PDBSilentStruct_hh

// mini headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/pdb/file_data.hh>
// AUTO-REMOVED #include <core/io/silent/SilentFileData.fwd.hh>


#include <core/chemical/ResidueTypeSet.fwd.hh>

#include <utility/pointer/ReferenceCount.hh>

// C++ Headers
#include <string>

#include <utility/vector1.hh>


namespace core {
namespace import_pose {

class PDBSilentStruct : public core::io::silent::SilentStruct {

public:

  /// @brief Constructors.
  PDBSilentStruct() {
    decoy_tag( "empty_tag" );
  }

  PDBSilentStruct(
    core::pose::Pose const & pose,
    std::string tag = "empty_tag"
  );

  virtual core::io::silent::SilentStructOP clone() const {
    return new PDBSilentStruct( *this );
  }

  // destructor
  ~PDBSilentStruct() {}

  using core::io::silent::SilentStruct::print_header;

  virtual void print_header( std::ostream & out );

  /// @brief Test if this PDBSilentStruct is equal to the given PDBSilentStruct in terms of conformation.
  /// Doesn't check energies.
  PDBSilentStruct & operator= (
    PDBSilentStruct const & src
  );

  /// @brief Tells this PDBSilentStruct object to initialize itself from the given set of lines. Lines should
  /// be of the format
  virtual bool init_from_lines(
    utility::vector1< std::string > const & lines,
    core::io::silent::SilentFileData & container
  );

  /// @brief Configure the conformation of the given Pose with the conformational data within this PDBSilentStruct.
  /// Calls pose.clear() and rebuilds Pose from scratch using FA_STANDARD residue types.
  virtual void fill_pose(
    core::pose::Pose & pose
  ) const;

  /// @brief Configure the conformation of the given Pose with the
  /// conformational data within this PDBSilentStruct. Calls pose.clear() and
  /// rebuilds Pose from scratch using the / user-specified residue types.
  virtual void fill_pose(
    core::pose::Pose & pose,
    core::chemical::ResidueTypeSet const & residue_set
  ) const;

  /// @brief opposite of fill_pose
  virtual void fill_struct(
    core::pose::Pose const & pose,
    std::string tag = "empty_tag"
  );

  /// @brief Prints the conformation information within this PDBSilentStruct
  /// to the given std::ostream.
  virtual void print_conformation( std::ostream & output ) const;

  /// @brief data getters/setters
  core::io::pdb::FileData
  file_data() const {
    return fd_;
  }

  void file_data( core::io::pdb::FileData new_fd ) {
    fd_ = new_fd;
  }

  std::string get_pdb_lines() const {
    return pdb_lines_;
  }

  /// @brief returns the positions of the CA atoms in this PDBSilentStruct.
  /// Useful for RMS calculations.
  virtual ObjexxFCL::FArray2D< Real > get_CA_xyz() const;

  /// @brief calculates the RMSD between the C-alpha atoms of a Pose built from the torsions in this
  /// PDBSilentStruct and the C-alpha atoms from this PDBSilentStruct.
  virtual Real get_debug_rmsd();

protected:
  mutable core::io::pdb::FileData fd_;
  std::string pdb_lines_; // a concatenated version of all the lines in the pdb file
}; // class PDBSilentStruct

} // namespace import_pose
} // namespace core

#endif