RNA_AnalyticLoopCloser.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_swa_rna_RNA_AnalyticLoopCloser_HH
#define INCLUDED_protocols_swa_rna_RNA_AnalyticLoopCloser_HH

#include <protocols/moves/Mover.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <ObjexxFCL/FArray1D.hh>

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

// AUTO-REMOVED #include <vector>
using namespace core;

namespace protocols {
namespace swa {
namespace rna {

/// @brief The RNA de novo structure modeling protocol
class RNA_AnalyticLoopCloser: public protocols::moves::Mover {
public:
  /// @brief Construct the protocol object
  RNA_AnalyticLoopCloser ( Size const moving_suite, Size const chainbreak_suite );

  /// @brief Clone this object
  virtual protocols::moves::MoverOP clone() const;

  /// @brief Each derived class must specify its name.  The class name.
  virtual std::string get_name() const {
    return "RNA_AnalyticLoopCloser";
  }

  /// @brief Apply the loop-rebuild protocol to the input pose
  virtual
  void apply ( pose::Pose & pose );

  void
  choose_best_solution_based_on_score_function ( scoring::ScoreFunctionOP scorefxn );

  void
  choose_least_perturb_solution();

  // Undefined, commenting out to fix PyRosetta build  void choose_random_solution();

  void
  get_all_solutions ( pose::Pose & pose,
                      utility::vector1< pose::PoseOP > & pose_list );

  Size nsol() {
    return nsol_;
  }

  void
  fill_solution ( pose::Pose & pose,
                  Size const n ) const;

  utility::vector1< Real >
  get_torsions ( Size const n );

  utility::vector1< utility::vector1< Real > >
  get_torsions_for_all_solutions();

private:

  bool
  close_at_cutpoint ( pose::Pose & pose );

  void
  figure_out_dof_ids_and_offsets ( pose::Pose const & pose,
                                   utility::vector1<Real> const & dt_ang );

  void
  figure_out_offset (
    pose::Pose const & pose,
    id::DOF_ID const & dof_id,
    Real const & original_torsion_value,
    utility::vector1< Real > & offset_save );

  void
  apply_solutions ( pose::Pose & pose );


  void
  output_chainTORS ( utility::vector1< Real > const & dt_ang,
                     utility::vector1< Real > const & db_ang,
                     utility::vector1< Real > const & db_len ) const;

  void
  fill_chainTORS (
    pose::Pose const & pose,
    utility::vector1< id::NamedAtomID> const & atom_ids,
    utility::vector1<utility::vector1<Real> > & atoms,
    utility::vector1<Real> & dt_ang,
    utility::vector1<Real> & db_ang,
    utility::vector1<Real> & db_len ) const;


private:

  Size const moving_suite_;
  Size const chainbreak_suite_;

  bool const verbose_;
  int nsol_;

  scoring::ScoreFunctionOP scorefxn_;

  utility::vector1< id::NamedAtomID > atom_ids_;
  utility::vector1< Real > offset_save_;
  utility::vector1< id::DOF_ID > dof_ids_;

  utility::vector1<utility::vector1<Real> > t_ang_, b_ang_, b_len_;

  bool choose_least_perturb_solution_;
  bool choose_best_solution_;
  bool choose_random_solution_;
  bool save_all_solutions_;

}; // class RNA_AnalyticLoopCloser


} //rna
} //swa
} // protocols

#endif