PDBOutput.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.

/// @author ashworth

#ifndef INCLUDED_protocols_dna_PDBOutput_hh
#define INCLUDED_protocols_dna_PDBOutput_hh

#include <protocols/dna/PDBOutput.fwd.hh>
#include <protocols/jd2/PDBJobOutputter.hh> // base class
#include <protocols/jd2/Job.fwd.hh>

//#include <protocols/dna/typedefs.hh> // Strings

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

#include <utility/vector1.hh>

#include <string>
#include <list>
#include <iosfwd>
#include <map>

namespace protocols {
namespace dna {

class PDBOutput : public jd2::PDBJobOutputter {
public:
  typedef std::list< std::string > Strings; // needs to match typedef in jd2/Job.hh
  typedef std::map< std::string, Strings > StringsMap;
  typedef jd2::JobCOP JobCOP;
  typedef core::pose::Pose Pose;
  typedef core::pose::PoseOP PoseOP;
  typedef core::pose::PoseCOP PoseCOP;
  typedef core::scoring::ScoreFunction ScoreFunction;
  typedef core::scoring::ScoreFunctionCOP ScoreFunctionOP;
  typedef core::scoring::ScoreFunctionCOP ScoreFunctionCOP;
  typedef core::pack::task::PackerTaskCOP PackerTaskCOP;
  typedef core::conformation::Residue Residue;
  typedef utility::io::ozstream ozstream;

public:
  PDBOutput();
  virtual ~PDBOutput();
  ///@brief JobDistributor calls this method
  virtual void final_pose( JobCOP, Pose const & );
  ///@brief functor for non-JobDistributor usage
  void operator() ( Pose const &, std::string const & );

  void enabled( bool value ) const { enabled_ = value; }
  bool enabled() const { return enabled_; }

  virtual void starting_pose( Pose const & );
  virtual void reference_pose( Pose const & );
  PoseCOP reference_pose() const;

  void score_function( ScoreFunction const & sf );
  ScoreFunctionCOP score_function() const;

  void add_info( std::string const &, Strings const &, bool append = true );
  bool remove_info( std::string const & );

  void designed_residue( core::Size, bool value = true );
  void note_designed_residues( PackerTaskCOP );
  bool residues_are_different( Residue const &, Residue const & ) const;

private: // methods
  void get_residue_indices_to_output();
  void output_pdb( ozstream & );
  void output_info( ozstream & );
  void output_score_info( ozstream & );
  void output_hbond_info( ozstream & );
  void output_buried_unsatisfied_hbonds( ozstream & );
  void output_design_tags( ozstream & ) const;

private: // data
  PoseOP pose_copy_; // to allow rescoring (nonconst)
  PoseCOP reference_pose_;
  ScoreFunctionOP score_function_;
  core::Real chi_diff_threshold_, mainchain_torsion_diff_threshold_;
  mutable bool enabled_;
  StringsMap info_map_; // deprecated in favor of jd2 framework (extract_data_from_Job)
  utility::vector1< core::Size > res_indices_to_output_;
  utility::vector1< bool > designed_residues_;
};

void make_subdirs( std::string const & );

} // namespace dna
} // namespace protocols

#endif