RNA_LoopCloser.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 loopRNA_minimizer.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_rna_RNA_LoopCloser_hh
#define INCLUDED_protocols_rna_RNA_LoopCloser_hh

#include <protocols/moves/Mover.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

#include <core/types.hh>

//// C++ headers
// AUTO-REMOVED #include <cstdlib>
#include <string>

#include <utility/vector1.hh>



namespace protocols {
namespace rna {

/// @brief The RNA de novo structure modeling protocol
class RNA_LoopCloser: public protocols::moves::Mover {
public:
  /// @brief Construct the protocol object
  RNA_LoopCloser();

  /// @brief Clone this object
  virtual protocols::moves::MoverOP clone() const {
    return new RNA_LoopCloser(*this);
  }

  /// @brief Apply the loop-rebuild protocol to the input pose
  using protocols::moves::Mover::apply;
  void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

  /// @brief Apply the loop-rebuild protocol to the input pose
  void apply( core::pose::Pose & pose, std::map< Size, Size > const & connections );

  /// @brief Apply the loop-rebuild protocol to the input pose
  core::Real apply( core::pose::Pose & pose, std::map< Size, Size > const & connections, Size const & cutpoint );

  /// @brief Apply the loop-rebuild protocol to the input pose
  core::Real apply( core::pose::Pose & pose, Size const & cutpoint );

  //Need get/set functions for options.

  void fast_scan( bool const & setting ) { fast_scan_ = setting; }

  //  void
  //  close_loops_carefully(
  //     core::pose::Pose & pose,
  //     std::map< Size, Size > const & connections,
  //     Size const close_loops_rounds );

  void
  close_loops_carefully(
     core::pose::Pose & pose,
     std::map< Size, Size > const & connections );

  //  void
  //  close_loops_carefully_one_round( core::pose::Pose & pose, core::scoring::ScoreFunctionOP const & scorefxn );

  bool
  check_closure( core::pose::Pose & pose, core::Real ccd_tolerance = 0.0 /* 0.0 means use absolute_ccd_tolerance_*/ );

private:

  bool
  passes_fast_scan( core::pose::Pose & pose, Size const i ) const;

  // Returns final coordinate error.
  core::Real
  rna_ccd_close( core::pose::Pose & pose, std::map< Size, Size > const & connections, Size const & cutpoint ) const;

  core::Real
  get_dist_err( core::pose::Pose & pose,
                Size const cutpoint
                ) const;

  core::Real
  get_chainbreak_xyz( core::pose::Pose & pose,
                      Size const cutpoint,
                      utility::vector1< core::Vector > & upstream_xyzs,
                      utility::vector1< core::Vector > & downstream_xyzs
                      ) const;

  core::Real
  get_gap_distance( core::pose::Pose & pose,
                Size const cutpoint
                ) const;


  utility::vector1< Size >
  get_extra_cutpoints( core::pose::Pose const & pose ) const;

  void
  setup_variants_at_extra_cutpoints( core::pose::Pose & pose, utility::vector1< Size > const & extra_cutpoints ) const;

  void
  remove_variants_at_extra_cutpoints( core::pose::Pose & pose, utility::vector1< Size > const & extra_cutpoints ) const;

  void
  local_minimize_at_chainbreaks( core::pose::Pose & pose, core::scoring::ScoreFunctionOP & scorefxn ) const;

  void
  tight_minimize( core::pose::Pose & pose ) const;

 private:
  //Make these options:
  bool verbose_;
  Size NUM_ROUNDS_;
  bool check_tolerance_;
  core::Real ccd_tolerance_;
  core::Real absolute_ccd_tolerance_;
  core::Real attempt_closure_cutoff_;
  core::Real gap_distance_cutoff_;
  bool fast_scan_;
}; // class RNA_LoopCloser



} //rna
} // protocols

#endif