HybridizeFoldtreeDynamic.hh

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// 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
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/// @file protocols/hybridization/HybridizeFoldtreeDynamic.hh
/// @author Yifan Song

#ifndef INCLUDED_protocols_hybridization_HybridizeFoldtreeDynamic_hh
#define INCLUDED_protocols_hybridization_HybridizeFoldtreeDynamic_hh

// Unit headers
#include <protocols/hybridization/HybridizeFoldtreeDynamic.fwd.hh>

// C/C++ headers
#include <string>

// Project headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/loops/Loops.hh>

#include <utility/vector1.hh>

#include <set>

namespace protocols {
namespace hybridization {

class HybridizeFoldtreeDynamic {
public:
  HybridizeFoldtreeDynamic( );

  // initialize pose ... add VRT if needed
  void initialize(
        core::pose::Pose & pose,
        protocols::loops::Loops const & core_chunks,
        utility::vector1< std::pair< core::Size, core::Size > > const & strand_pairs,
        std::set<core::Size> const & strand_pair_library_positions
  );
  void reset( core::pose::Pose & pose );

  utility::vector1 < core::Size > get_anchors() { return anchor_positions_; }

private:
  // HELPER FUNCTIONS

  // stochastically selects an anchor position
  core::Size choose_anchor_position(const protocols::loops::Loop& chunk) const;

  // update pose fold tree with new chunks .. assume vrt already added
  void update(core::pose::Pose & pose);

  // set the core chunks ... where anchors must lie and cuts are forbidden
  void set_core_chunks(const protocols::loops::Loops & chunks);

  // fold tree
  //void jumps_and_cuts_from_pose( core::pose::Pose & pose, utility::vector1< std::pair<int, int > > & jumps, utility::vector1< int > & cuts);
  void jumps_and_cuts_from_foldtree( core::kinematics::FoldTree & foldtree, utility::vector1< std::pair<core::Size, core::Size > > & jumps, utility::vector1< core::Size > & cuts);

  // cutpoints selection logic
  utility::vector1 < core::Size > decide_cuts(core::pose::Pose & pose, core::Size n_residues);

  // anchor selection logic
  void choose_anchors();

  void make_complete_chunks(
    utility::vector1 < core::Size > cut_positions,
    core::Size n_residues);

  // straind pairings

  // gets core chunks that are strand paired to a specific chunk
  void get_pair_core_chunks( core::Size const chunk_index, utility::vector1<core::Size> & pair_chunks, utility::vector1<std::pair<core::Size, core::Size> > & pair_chunks_pairs );

  // gets a core chunk that covers a specific position
  void get_core_chunk_index_from_position( core::Size const position, core::Size & index );

  void add_overlapping_pair_chunks(
    core::Size const index,
    utility::vector1<core::Size> & cuts,
    utility::vector1<std::pair<core::Size, core::Size> > & jumps,
    std::set<core::Size> & rooted_chunk_indices );

  void remove_cut( core::Size const cut, utility::vector1<core::Size> & cuts );

private:
  // DATA

  // segment the entire pose, defining cutpoints
  protocols::loops::Loops chunks_last_;
  protocols::loops::Loops chunks_;

  // segment pose into "core regions" where anchors may lie
  protocols::loops::Loops core_chunks_last_;
  protocols::loops::Loops core_chunks_;

  utility::vector1 < core::Size > anchor_positions_last_;
  utility::vector1 < core::Size > anchor_positions_;

  /// index of the virtual residue we added to the pose in set_up()
  int virtual_res_;
  core::Size num_nonvirt_residues_;
  core::Size num_protein_residues_;

  // backup original info
  core::kinematics::FoldTree initial_asymm_foldtree_;
  core::kinematics::FoldTree saved_ft_;
  core::Size saved_n_residue_;

  // strand pairings
  utility::vector1< std::pair< core::Size, core::Size > > strand_pairs_; // res pos of strand pairs
  std::set<core::Size> strand_pair_library_positions_; // strand pair positions that are from the pairing library (not from a pdb template)
  std::set<core::Size> template_core_chunk_indices_; // core_chunks_ indices of chunks from templates (not from pairing library)
  std::set<core::Size> rooted_chunk_indices_; // chunk indices that have a jump to the root of the star fold tree

};

}  //  namespace hybridization
}  //  namespace protocols

#endif  // INCLUDED_protocols_hybridization_HybridizeFoldtreeDynamic_hh