StepWiseRNA_AnalyticalLoopCloseSampler.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 res 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 StepWiseRNA_AnalyticalLoopCloseSampler.hh
/// @brief Alternative SWA sampling using Analytical Loop Closure
/// @author Fang-Chieh Chou


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_AnalyticalLoopCloseSampler_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_AnalyticalLoopCloseSampler_HH

#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_BaseCentroidScreener.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_FloatingBase_Sampler_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.fwd.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>


namespace protocols {
namespace swa {
namespace rna {

//  typedef std::map< std::string, core::pose::PoseOP > PoseList;

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

  //constructor!
  StepWiseRNA_AnalyticalLoopCloseSampler ( StepWiseRNA_JobParametersCOP & job_parameters_ );

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

  /// @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 "StepWiseRNA_AnalyticalLoopCloseSampler";
  }

  void
  set_centroid_screen ( bool const setting ) {
    centroid_screen_ = setting;
  }

  void
  set_base_pairing_only_screen ( bool const setting ) {
    base_pairing_only_screen_ = setting;
  }

  void
  set_VDW_atr_rep_screen ( bool const setting ) {
    VDW_atr_rep_screen_ = setting;
  }


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

  void
  set_output_filename ( std::string const & output_filename );

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

  void
  set_fast ( bool const & setting );

  void
  set_medium_fast ( bool const & setting );

  void
  set_native_rmsd_screen ( bool const & setting );

  void
  set_native_screen_rmsd_cutoff ( core::Real const & setting ) {
    native_screen_rmsd_cutoff_ = setting ;
  }

  void
  set_verbose ( bool const & setting );

  void
  set_o2star_screen ( bool const & setting );

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

  // Undefined, commenting out to fix PyRosetta build  void set_allow_bulge_at_chainbreak ( bool const & setting );

  utility::vector1< pose_data_struct2 > &
  get_pose_data_list();

  core::io::silent::SilentFileDataOP & silent_file_data();

  void output_pose_data_list ( std::string const final_sampler_output_silent_file ) const;

  void set_num_pose_kept ( core::Size const & num_pose_kept );

  void
  set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP & screener );

  void
  set_distinguish_pucker ( bool const & setting ) {
    distinguish_pucker_ = setting ;
  }

  void
  set_finer_sampling_at_chain_closure ( bool const & setting ) {
    finer_sampling_at_chain_closure_ = setting;
  }

  void
  set_PBP_clustering_at_chain_closure ( bool const & setting ) {
    PBP_clustering_at_chain_closure_ = setting;
  }

  void
  set_user_input_VDW_bin_screener ( StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener );

  void
  set_allow_syn_pyrimidine( bool const & setting ) { 
    allow_syn_pyrimidine_ =setting;
  }

  void
  set_extra_syn_chi_rotamer ( bool const & setting ) {
    extra_syn_chi_rotamer_ = setting;
  }

  void
  set_extra_anti_chi_rotamer ( bool const & setting ) {
    extra_anti_chi_rotamer_ = setting;
  }

  void
  set_use_phenix_geo ( bool const & setting ) {
    use_phenix_geo_ = setting;
  }
private:

  void
  initialize_scorefunctions();

  void
  standard_sampling ( core::pose::Pose & pose, utility::vector1< pose_data_struct2 > & pose_data_list );

  void
  copy_suite_torsion ( core::pose::Pose & pose, core::pose::Pose const & ref_pose, core::Size const & suite_num );

  void
  get_base_atr_rep_score ( core::pose::Pose const & pose, core::Real & base_atr_score, core::Real & base_rep_score );

  bool
  Full_atom_van_der_Waals_screening_REPLICATE (
    core::pose::Pose & current_pose_screen,
    core::Real const & base_rep_score,
    core::Real const &  base_atr_score,
    core::Real & delta_rep_score,
    core::Real & delta_atr_score,
    core::Size const & gap_size,
    bool const & Is_internal );


  bool
  Full_atom_van_der_Waals_screening (
    core::pose::Pose & current_pose_screen,
    core::Real const & base_rep_score,
    core::Real const &  base_atr_score,
    core::Real & delta_rep_score,
    core::Real & delta_atr_score,
    core::Size const & gap_size,
    bool const & Is_internal );

  void
  initialize_o2star_packer_task ( core::pose::Pose const & pose );

  void
  sample_o2star_hydrogen ( core::pose::Pose & pose , core::pose::Pose & pose_with_original_HO2star_torsion );

  core::Real
  Pose_selection_by_full_score ( utility::vector1< pose_data_struct2 >& pose_data_list, core::pose::Pose & current_pose, std::string const & tag );


  void
  Update_pose_data_list ( std::string const & tag, utility::vector1< pose_data_struct2 > & pose_data_list, core::pose::Pose const & current_pose, core::Real const & current_score ) const;

  void
  cluster_pose_data_list ( utility::vector1< pose_data_struct2 > & pose_data_list );

  std::string
  create_tag ( std::string const prestring, StepWiseRNA_RotamerGenerator_WrapperOP const & rotamer_generator ) const;

  std::string //silly function to convert to real to string
  create_torsion_value_string ( core::Real const & torsion_value ) const;

  std::string
  create_rotamer_string ( core::pose::Pose const & pose ) const;

  /////////////////////////////////////function related to sampling/setup virtual sugar /////////////////////////////////////////////////////////////////


  ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


private:

  StepWiseRNA_JobParametersCOP job_parameters_; //need to use the full_to_sub map...should convert to const style.. Parin Feb 28, 2010

  core::io::silent::SilentFileDataOP sfd_;
  utility::vector1< pose_data_struct2 > pose_data_list_;

  core::scoring::ScoreFunctionOP scorefxn_;
  core::scoring::ScoreFunctionOP atr_rep_screening_scorefxn_;
  core::scoring::ScoreFunctionOP sampling_scorefxn_;
  core::scoring::ScoreFunctionOP o2star_pack_scorefxn_;
  core::scoring::ScoreFunctionOP chainbreak_scorefxn_;

  utility::vector1 < core::Size > working_rmsd_res_;

  SillyCountStruct count_data_;
  std::string silent_file_;
  std::string output_filename_;
  core::Real const bin_size_; /*ALWAYS 20!!!*/
  core::Real const rep_cutoff_;
  core::Size num_pose_kept_;
  core::Size const multiplier_;
  core::Real cluster_rmsd_;
  bool verbose_;
  bool native_rmsd_screen_;
  core::Real native_screen_rmsd_cutoff_;

  bool o2star_screen_;
  core::pack::task::PackerTaskOP o2star_pack_task_;
  bool fast_;
  bool medium_fast_;

  StepWiseRNA_BaseCentroidScreenerOP base_centroid_screener_;

  bool centroid_screen_;
  bool base_pairing_only_screen_;
  bool VDW_atr_rep_screen_;
  bool distinguish_pucker_;
  core::Real current_score_cutoff_;
  bool finer_sampling_at_chain_closure_;
  bool PBP_clustering_at_chain_closure_;
  bool extra_anti_chi_rotamer_;
  bool extra_syn_chi_rotamer_;
  bool allow_syn_pyrimidine_;
  bool use_phenix_geo_;

  StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_;


};

}
} //swa
} // protocols

#endif