InsertChunkMover.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.
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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
/// @brief Align a random jump to template
/// @detailed
/// @author Yifan Song

#ifndef INCLUDED_protocols_hybridization_InsertChunkMover_hh
#define INCLUDED_protocols_hybridization_InsertChunkMover_hh

#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.hh>
#include <core/util/kinematics_util.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>

#include <protocols/moves/Mover.hh>

#include <numeric/xyz.functions.hh>

#include <basic/Tracer.hh>

#include <set>

namespace protocols {
namespace hybridization {

using namespace core;

class InsertChunkMover: public protocols::moves::Mover
{

public:

  InsertChunkMover();
  ~InsertChunkMover();

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

  bool success() {
      return success_;
  }

  void set_template(core::pose::PoseCOP template_pose, core::Size template_id,
            std::map <core::Size, core::Size> const & sequence_alignment);

  void set_aligned_chunk(core::pose::Pose const & pose, Size const jump_number, bool anchor_insert_only_in);

  bool get_local_sequence_mapping(core::pose::Pose & pose,
                  int registry_shift = 0,
                  Size MAX_TRIAL = 100 );

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

  void set_registry_shift(int registry_shift);

  Size trial_counter(Size ires);

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

  std::string get_name() const;

private:
  core::pose::PoseCOP template_pose_;
  core::Size template_id_;
  std::map <core::Size, core::Size> sequence_alignment_;
  int registry_shift_;
  bool anchor_insert_only_;

  Size jump_number_; // the jump to be realigned
  Size seqpos_start_; // start and end seqpose of the chunk, downstream of the jump
  Size seqpos_stop_;
  Size seqpos_aligned_start_; // start and end seqpose of the aligned piece
  Size seqpos_aligned_stop_;

  bool success_;

  // parameters of the protocol
  bool align_to_ss_only_; // only use the secondary structure portion to align to the template
  bool copy_ss_torsion_only_; // only copy the secondary structure information from the template

  char secstruct_;

  std::map <core::Size, core::Size> sequence_alignment_local_; // with registry shift of the aligned chunk
  core::id::AtomID_Map< core::id::AtomID > atom_map_; // atom map for superposition
  utility::vector1 <Size> align_trial_counter_;

};

} // hybridization
} // protocols

#endif