CoarseRNA_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_coarse_rna_CoarseRNA_LoopCloser_HH
#define INCLUDED_protocols_coarse_rna_CoarseRNA_LoopCloser_HH

#include <protocols/moves/Mover.hh>
#include <protocols/toolbox/AllowInsert.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/DOF_ID.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>


namespace protocols {
namespace coarse_rna {

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

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

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

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

  bool
  apply_after_jump_change( core::pose::Pose & pose, Size const & jumpno );

  virtual std::string get_name() const;

  void
  choose_best_solution_based_on_score_function( core::scoring::ScoreFunctionOP scorefxn );

  void
  choose_least_perturb_solution();

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

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

  void
  set_allow_insert( protocols::toolbox::AllowInsertOP allow_insert );

  protocols::toolbox::AllowInsertOP  allow_insert();

  Size nsol(){ return nsol_; }

  utility::vector1< core::Size > const & cutpos_list(){ return cutpos_list_; }

  ObjexxFCL::FArray1D< bool > const & partition_definition(){ return partition_definition_; }

private:

  bool
  close_at_all_cutpoints( core::pose::Pose & pose );

  ////////////////////////////////////////////////////////////////////////////////////////////////////////////////
  void
  figure_out_which_cutpoints_were_affected( core::pose::Pose const & pose );

  ////////////////////////////////////////////////////////////////////////////////////////
  bool
  figure_out_pivots( core::pose::Pose const & pose );

  ////////////////////////////////////////////////////////////////////////////////////////
  void
  remove_res( utility::vector1< core::Size > & res_vector,
              Size const & res );

  void
  backtrack( core::kinematics::tree::AtomCOP current_atom,
             utility::vector1< core::Size > & upstream_res,
             utility::vector1< bool > & is_upstream_res,
             core::pose::Pose const & pose );

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

  void
  output_forward_backward_res();

  void
  filter_path( utility::vector1< core::Size > & upstream_res,
               utility::vector1< bool > const & is_filter_res,
               core::pose::Pose const & pose );

  void
  figure_out_pivot_res_and_scratch_res();

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

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


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

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

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

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

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

private:

  bool const a_little_verbose_;
  bool const verbose_;
  core::Size seqpos_moved_;
  core::Size cutpos_;
  utility::vector1< core::Size > cutpos_list_;
  int nsol_;

  protocols::toolbox::AllowInsertOP allow_insert_;
  utility::vector1< core::Size > backward_res_, forward_res_, pivot_res_, scratch_res_, pivot_to_scratch_res_;
  utility::vector1< bool > is_backward_res_, is_forward_res_, is_pivot_res_, is_scratch_res_;
  core::Size which_scratch_res_is_cut_;

  core::scoring::ScoreFunctionOP scorefxn_;

  utility::vector1< core::id::NamedAtomID > atom_ids_;
  utility::vector1< core::Real > offset_save1_, offset_save2_;
  utility::vector1< core::id::DOF_ID > dof_ids1_, dof_ids2_;

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

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

  ObjexxFCL::FArray1D< bool > partition_definition_;

}; // class CoarseRNA_LoopCloser



} //rna
} // protocols

#endif