SwapSegment.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 protocols/seeded_abinitio/SwapSegment.hh
/// @author Eva-Maria Strauch (evas01@u.washington.edu)

#ifndef INCLUDED_protocols_seeded_abinitio_SwapSegment_hh
#define INCLUDED_protocols_seeded_abinitio_SwapSegment_hh

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>

namespace protocols {
namespace seeded_abinitio {

class SwapSegment : public protocols::moves::Mover {
 public:
  typedef core::pose::Pose Pose;

  SwapSegment();

  void apply( core::pose::Pose & pose );

  virtual std::string get_name() const;
  virtual protocols::moves::MoverOP clone() const;
  virtual protocols::moves::MoverOP fresh_instance() const;

  void parse_my_tag( utility::tag::TagPtr const tag,
                     protocols::moves::DataMap &,
                     protocols::filters::Filters_map const &,
                     protocols::moves::Movers_map const &,
                     core::pose::Pose const & );


  virtual ~SwapSegment();

 private:
  void copying_side_chains(
      core::pose::Pose & pose,
      core::pose::PoseOP & swap_segment,
      protocols::loops::Loops & seeds);

  void swap_segment(
      core::pose::Pose & pose,
      core::pose::PoseOP & swap_segment,
      protocols::loops::Loops & seeds);

  void swap_chain(
                core::pose::Pose & pose,
                core::pose::PoseOP & target_chain,
                core::Size chain_to_swap);

  bool copy_sidechains_;

  bool swap_segment_;

  core::Size swap_chain_;

  ///input pdb that contains the segments that should be swapped
  core::pose::PoseOP seeds_pdb_;

  ///check for the segments
  bool seeds_presence_;

  protocols::loops::Loops all_seeds_;

  ///chain that contains the seed in the seed_pdb
  core::Size from_chain_;

  ///chain in which the segments should be swapped/side chain replaced
  core::Size to_chain_;

  core::scoring::ScoreFunctionOP scorefxn_;

  ///switch to determine what numbering needs to be used since
  ///parse time is different from computing time and if the pose has changed, numbering will be off
  bool previously_grown_;
};

}
}

#endif