StepWiseScreener.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 SWA_Screener.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_StepWiseScreener_hh
#define INCLUDED_protocols_swa_StepWiseScreener_hh

#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>
#include <protocols/swa/MainChainTorsionSet.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <core/scoring/Ramachandran.hh>
#include <string>
#include <map>

//Auto Headers


namespace protocols {
namespace swa {

typedef std::map< std::string, core::pose::PoseOP > PoseList;
typedef std::map< core::Size, core::Size > ResMap;
/////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////
class StepWiseScreener: public protocols::moves::Mover {
public:

  //constructor!
  StepWiseScreener(
    utility::vector1< Size > const & moving_residues
  );

  //destructor -- necessary? -- YES destructors are necessary.
  ~StepWiseScreener();

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

  void
  set_silent_file( std::string const & setting );

  void
  set_rmsd_cutoff( core::Real const & setting );

  void
  set_n_sample( core::Size const & setting );

  void
  set_nstruct_centroid( core::Size const & setting );

  void
  set_filter_native_big_bins( bool const & setting );

  void
  set_centroid_screen( bool const & setting );

  void
  set_ghost_loops( bool const & setting );

  void
  set_apply_vdw_cut( bool const & setting );

  void
  set_centroid_scorefxn( core::scoring::ScoreFunctionOP const & scorefxn );

  void
  set_centroid_score_diff_cut( core::Real const & setting );

  utility::vector1< MainChainTorsionSetList > const & main_chain_torsion_set_lists() const;

private:

  void
  filter_main_chain_torsion_sets();

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

  void
  initialize_ghost_pose(
    core::pose::PoseOP & ghost_pose,
    std::string const & desired_sequence,
    core::pose::Pose const & template_pose,
    ResMap const & ghost_map,
    core::kinematics::FoldTree f
  );

  void
  copy_coords( core::pose::Pose & pose, core::pose::Pose const & template_pose, ResMap const & ghost_map ) const;

  core::kinematics::FoldTree
  figure_out_fold_tree( ResMap const & ghost_map ) const;

  void
  sample_residues_recursively(
    Size const which_res,
    Size & count,
    core::pose::Pose & pose
  );

  void
  filter_and_output(
    core::pose::Pose & pose,
    std::string const & tag
  );

  void
  get_main_chain_torsion_set_list(
    core::Size const & n,
    core::pose::Pose const & pose,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );

  void
  get_main_chain_torsion_set_list_coarse(
    core::Size const & n,
    core::pose::Pose const & pose,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );

  void
  get_main_chain_torsion_set_list_full(
    core::Size const & n, core::pose::Pose const & pose, core::Real const & best_energy_cutoff,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );


  void
  get_main_chain_torsion_set_list_n_terminus(
    core::Size const & n, core::pose::Pose const & pose, core::Real const & best_energy_cutoff,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );


  void
  get_main_chain_torsion_set_list_c_terminus(
    core::Size const & n,
    core::pose::Pose const & pose,
    core::Real const & best_energy_cutoff,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );


  void
  get_main_chain_torsion_set_list_sample_phi_only(
    core::Size const & n,
    core::pose::Pose const & pose,
    core::Real const & best_energy_cutoff,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );


  void
  get_main_chain_torsion_set_list_sample_psi_only(
    core::Size const & n, core::pose::Pose const & pose, core::Real const & best_energy_cutoff,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );

  void
  filter_native_BIG_BINS(
    core::Size const & n,
    MainChainTorsionSetList & main_chain_torsion_set_list
  );

private:

  core::Size
  get_big_bin( core::Real const phi, core::Real const psi ) const;

  void
  output_centroid_silent_struct(
                                core::pose::Pose const & pose, core::pose::PoseCOP const & native_pose_op,
                                std::string const silent_file, std::string const & tag );

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


private:

  utility::vector1< Size > moving_residues_;
  core::Size n_sample_;
  core::Real rmsd_cutoff_;

  core::scoring::ScoreFunctionOP centroid_scorefxn_;
  std::string silent_file_;
  bool filter_native_big_bins_;
  bool centroid_screen_;
  core::Real centroid_score_ref_;
  core::Real centroid_score_diff_cut_;

  bool apply_vdw_cut_;
  core::Real centroid_vdw_ref_;

  Size nstruct_centroid_;

  core::scoring::Ramachandran ramachandran_;

  MainChainTorsionSetList main_chain_torsion_set_for_moving_residues_;
  utility::vector1< MainChainTorsionSetList > main_chain_torsion_sets_for_moving_residues_;
  utility::vector1< core::Real > centroid_scores_;

  bool ghost_loops_;
  ResMap ghost_map_;
  core::pose::PoseOP ghost_pose_, ghost_native_pose_;

};

} //swa
} // protocols

#endif