StepWiseRNA_CombineLongLoopFilterer.hh

Go to the documentation of this file.

// -*- 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 StepWiseRNA_CombineLongLoopFilterer.hh
/// @brief
/// @detailed
///
/// @author Parin Sripakdeevong (sripakpa@stanford.edu)
/// @author Rhiju Das (rhiju@stanford.edu)


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_CombineLongLoopFilterer_hh
#define INCLUDED_protocols_swa_rna_StepWiseRNA_CombineLongLoopFilterer_hh

#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <protocols/moves/Mover.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>

#include <string>
#include <map>


namespace protocols {
namespace swa {
namespace rna {

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

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class Combine_Tags_Info{

    public:

    Combine_Tags_Info():
      side_one_tag( "" ),
      side_two_tag( "" ),
      //combine_score( 999999999999.99 ) //Feb 12, 2012 This might lead to server-test error at R47200
      combine_score( 999999.9) //Feb 12, 2012
    {
    }

    ~Combine_Tags_Info(){};

    public:

      std::string side_one_tag;
      std::string side_two_tag;
      core::Real combine_score;
  };


  class Filterer_Count{

    public:

      Filterer_Count():
        total_count( 0 ),
        score_cut_count( 0 ),
        chain_closable_screen( 0 ),
        filter_for_previous_contact( 0 ),
        filter_for_previous_clash( 0 ),
        filter_for_moving_res_contact( 0 )
      {
      }

      ~Filterer_Count(){};

    public:

      core::Size total_count;
      core::Size score_cut_count;
      core::Size chain_closable_screen;
      core::Size filter_for_previous_contact;
      core::Size filter_for_previous_clash;
      core::Size filter_for_moving_res_contact;
  };


  class StepWiseRNA_CombineLongLoopFilterer: public utility::pointer::ReferenceCount {
  public:

    //constructor!
    StepWiseRNA_CombineLongLoopFilterer( StepWiseRNA_JobParametersCOP const & job_parameters, bool const combine_helical_silent_file);

    //destructor -- necessary?
    virtual ~StepWiseRNA_CombineLongLoopFilterer();

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


    void
    set_silent_files_in( utility::vector1< std::string > const & setting){ silent_files_in_= setting; } //Only called if COPY_DOF is true

    void
    set_parin_favorite_output( bool const setting){ parin_favorite_output_=setting; }

    void
    filter();

    void
    set_output_filename(std::string const setting){output_filename_=setting;}

    //void
    //set_score_diff_cut(core::Real const setting){score_diff_cut_=setting;}

    void
    set_filter_for_previous_contact(core::Real const setting){filter_for_previous_contact_=setting;}

    void
    set_filter_for_previous_clash(core::Real const setting){filter_for_previous_clash_=setting;}

    void
    set_undercount_ribose_rotamers( bool const setting){ undercount_ribose_rotamers_=setting;}

    void set_max_decoys( core::Size const & setting ){ max_decoys_ = setting; }

    private:

    void
    figure_out_appended_and_prepended_res_list();

    void
    figure_out_last_appended_and_last_prepended_res();


    utility::vector1< pose_data_struct2 >
    convert_silent_file_to_pose_data_list( core::import_pose::pose_stream::SilentFilePoseInputStreamOP & silent_file_stream, core::Size const pose_list_id);


    bool
    previously_builded_res_VDW_filter(pose_data_struct2 const & side_ONE_pose_data ,
                                    pose_data_struct2 const & side_TWO_pose_data ,
                                    core::Real const overlap_dist_cutoff,
                                    core::Size const num_atom_contacts_cutoff);

    bool
    previously_builded_res_contact_filter(pose_data_struct2 const & side_ONE_pose_data , pose_data_struct2 const & side_TWO_pose_data );

    bool
    previously_builded_res_clash_filter(pose_data_struct2 const & side_ONE_pose_data , pose_data_struct2 const & side_TWO_pose_data );

    bool
    moving_res_contact_filter(pose_data_struct2 const & side_ONE_pose_data , pose_data_struct2 const & side_TWO_pose_data );

    void
    align_all_pose( utility::vector1< pose_data_struct2 > const & side_ONE_pose_data_list,
                   utility::vector1< pose_data_struct2 > const & side_TWO_pose_data_list);


    void
    do_some_filtering();

    bool
    pass_all_filters(pose_data_struct2 const & side_ONE_pose_data, pose_data_struct2 const & side_TWO_pose_data );

    void
    setup_silent_file_stream();

    void
    figure_out_NUM_pose_list();

    void
    setup_tag_to_source_map();

//    bool
//    score_sort_citeria(Combine_Tags_Info tag_info_1, Combine_Tags_Info tag_info_2);

    void
    sort_Combine_Tags_Info(utility::vector1< Combine_Tags_Info > & combine_tags_info_list);


    std::string
    get_parent_tag(utility::vector1<std::string> const & tag_token) const;

    bool
    Is_virt_sample_ribose_tag(std::string const & tag, utility::vector1<std::string> const & tag_token) const;

    bool
    Is_sibling_ribose_rotamer_pose(std::string const & curr_tag, std::string const & prev_tag, std::map< std::string , std::string > const & tag_to_source_map) const;


  private:

//    utility::vector1< utility::vector1< Size > > input_res_vectors_;

    Filterer_Count filterer_count_;

    core::chemical::ResidueTypeSetCAP rsd_set_;
    utility::vector1< std::string > silent_files_in_;
    core::import_pose::pose_stream::SilentFilePoseInputStreamOP silent_file_stream_ONE_;
    core::import_pose::pose_stream::SilentFilePoseInputStreamOP silent_file_stream_TWO_;
    StepWiseRNA_JobParametersCOP const job_parameters_;
    bool verbose_;
    bool parin_favorite_output_;
    bool filter_for_previous_contact_;
    bool filter_for_previous_clash_;
    bool undercount_ribose_rotamers_;
    bool const filter_for_chain_closable_;
    bool const filter_for_moving_res_contact_;
    bool const moving_res_to_base_contact_only_;

    core::Size total_input_struct_pair_;
    core::Size pass_screen_struct_pair_;
    core::Size input_pose_ONE_last_appended_res_;
    core::Size input_pose_TWO_last_prepended_res_;
    utility::vector1<core::Size> input_pose_ONE_appended_res_list_;
    utility::vector1<core::Size> input_pose_TWO_prepended_res_list_;

    std::map< core::Size, core::Size > full_to_input_res_map_ONE_;
    std::map< core::Size, core::Size > full_to_input_res_map_TWO_;
    std::string output_filename_;
    core::Real best_combine_score_;
    core::Real worst_combine_score_;
    //core::Real score_diff_cut_;
    core::Real const contact_dist_cutoff_;
    core::Real const clash_dist_cutoff_;
    core::Size const num_contact_cutoff_;
    core::Size const num_clash_cutoff_;

    core::Size const max_pose_data_list_size_;
    core::Size side_ONE_NUM_pose_list_;
    core::Size side_TWO_NUM_pose_list_;
    core::Size side_ONE_pose_list_id_;
    core::Size side_TWO_pose_list_id_;
    core::Real moving_res_contact_dist_cutoff_;
    utility::vector1< Combine_Tags_Info > filterered_combine_tag_info_list_;

    Size max_decoys_;
    bool combine_helical_silent_file_;

    std::map< std::string , std::string > tag_to_source_map_ONE_;
    std::map< std::string , std::string > tag_to_source_map_TWO_;


  };

}
} //swa
} // protocols

#endif