RNA_LoopCloseSampler.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 RNA_LoopCloseSampler
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_rna_RNA_LoopCloseSampler_HH
#define INCLUDED_protocols_swa_rna_RNA_LoopCloseSampler_HH

#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <utility/vector1.hh>
#include <protocols/moves/Mover.hh>
#include <string>
#include <map>

using namespace core;

namespace protocols {
namespace swa {
namespace rna {

/////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////
class RNA_LoopCloseSampler: public protocols::moves::Mover {
public:

  //constructor!
  RNA_LoopCloseSampler ( Size const moving_suite, Size const chainbreak_suite );

  //destructor -- necessary?
  ~RNA_LoopCloseSampler();

  /// @brief Apply the minimizer to one pose
  virtual void apply ( core::pose::Pose & pose_to_visualize );

  /// @brief Each derived class must specify its name.  The class name.
  virtual std::string get_name() const {
    return "RNA_LoopCloseSampler";
  }
  utility::vector1< utility::vector1< Real > >  all_torsion_info() {
    return all_torsion_info_;
  }
  Size n_construct() {
    return n_construct_;
  }
  void fill_pose ( pose::Pose & pose, Size construct_number );
  void clear_all();

  void set_bin_size ( Size const setting ) {
    bin_size_ = setting;
  }

  void set_epsilon_range ( Real const setting ) {
    epsilon_range_ = setting;
  }

  void set_rep_cutoff ( Real const rep_cutoff ) {
    rep_cutoff_ = rep_cutoff;
  }
  void set_torsion_range ( Real const torsion_range ) {
    torsion_range_ = torsion_range;
  }
  void set_torsion_increment ( Real const torsion_increment ) {
    torsion_increment_ = torsion_increment;
  }

  void set_just_output_score ( bool const setting ) {
    just_output_score_ = setting;
  }
  void set_sample_only ( bool const setting ) {
    sample_only_ = setting;
  }

  void set_sample_native_torsion ( bool const setting ) {
    sample_native_torsion_ = setting;
  }

  void set_rbs_new_pair ( utility::vector1< Real > const & rbs_new_pair ) {
    rbs_new_pair_ = rbs_new_pair;
  }

  void set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn );
  // Undefined, commenting out to fix PyRosetta build  Size get_n_construct();


private:

  bool
  torsion_angles_within_cutoffs ( pose::Pose const & pose,
                                  Size const moving_suite,
                                  Size const chainbreak_suite);

  void initialize_rep_scorefxn();

  Real
  initialize_fa_rep ( pose::Pose const & pose,
                      utility::vector1< Size > const & moving_suites,
                      scoring::ScoreFunctionOP rep_scorefxn );

  bool
  check_clash ( pose::Pose & pose,
                Real const & fa_rep_score_baseline,
                Real const & rep_cutoff_,
                scoring::ScoreFunctionOP rep_scorefxn );

private:

  Size const moving_suite_, chainbreak_suite_;

  core::scoring::ScoreFunctionOP scorefxn_, rep_scorefxn_;
  Size bin_size_, n_construct_;
  Real rep_cutoff_, torsion_range_, torsion_increment_, epsilon_range_;
  bool just_output_score_, sample_only_, sample_native_torsion_;
  utility::vector1< Real > rbs_new_pair_;

  utility::vector1< Real > torsion_info_;
  utility::vector1< utility::vector1< Real > > all_torsion_info_;
};

}
} //swa
} // protocols

#endif