StepWiseRNA_Clusterer.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 StepWiseRNA_Clusterer.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das, Parin Sripakdeevong


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_Clusterer_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_Clusterer_HH

#include <core/pose/Pose.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>
#include <core/types.hh>
#include <core/io/silent/SilentStruct.fwd.hh>

#include <protocols/swa/rna/StepWiseRNA_PoseSetup.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>

#include <map>

namespace protocols {
namespace swa {
namespace rna {

  class SlicedPoseJobParameters: public utility::pointer::ReferenceCount{

    public:
  
       SlicedPoseJobParameters():
        verbose_(true),
        Is_setup_(false)
      {
      }

      virtual ~SlicedPoseJobParameters(); // auto-removing definition from header{};

      void 
      setup(protocols::swa::rna::StepWiseRNA_JobParametersCOP & job_parameters);

      core::pose::Pose
      create_sliced_pose(core::pose::Pose const & working_pose);

    public:
      utility::vector1< core::Size > sliced_pose_best_alignment; //check
      utility::vector1 < core::Size > sliced_pose_rmsd_res_list; 
      std::map< core::Size, core::Size > sliced_pose_full_to_sub;
      std::map< core::Size, bool > sliced_pose_Is_prepend_map;
      



    private:
      utility::vector1< bool > Is_sliced_res_;
      utility::vector1 < core::Size > working_to_sliced_res_map_; 
      utility::vector1 < core::Size > sliced_to_working_res_map_; 
      utility::vector1< std::pair< core::Size, core::Size > > delete_res_range_list_;
      bool verbose_;
      bool Is_setup_;

  };

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class Cluster_Member{

    public:

    Cluster_Member():
    ID( 0 ),
    RMSD( 0.0 ),
    score(9999.99)
    {
    }

    ~Cluster_Member(){};

    public:

    core::Size ID;
    core::Real RMSD;
    core::Real score;

  };


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

  class StepWiseRNA_Clusterer: public utility::pointer::ReferenceCount {
  public:

    //constructor!
    StepWiseRNA_Clusterer( utility::vector1< std::string > const & silent_files_in );

    StepWiseRNA_Clusterer( std::string const & silent_file_in );

    StepWiseRNA_Clusterer(  core::io::silent::SilentFileDataOP & sfd );

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

    /// @brief Filter a list of poses by score.

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

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

    void set_perform_score_diff_cut( bool const & setting ){ perform_score_diff_cut_ = setting; }

    void set_cluster_radius( core::Real const & setting ){ whole_struct_cluster_radius_ = setting; }

    void set_suite_cluster_radius( core::Real const & setting ){ suite_cluster_radius_ = setting; }

    void set_loop_cluster_radius( core::Real const & setting ){ loop_cluster_radius_ = setting; }

    void set_rename_tags( core::Real const & setting ){ rename_tags_ = setting; }

    void set_distinguish_pucker( core::Real const & setting ){ distinguish_pucker_ = setting; }

    void set_add_lead_zero_to_tag( core::Real const & setting ){ add_lead_zero_to_tag_ = setting; }

    void set_job_parameters( protocols::swa::rna::StepWiseRNA_JobParametersCOP & job_parameters);

    void set_job_parameters_exist( bool const job_parameters_exist);

    void set_quick_alignment( bool const & setting){ quick_alignment_ = setting;}

    void set_align_only_over_base_atoms( bool const & setting){ align_only_over_base_atoms_ = setting; }
  
    void set_optimize_memory_usage(  bool const & setting){ optimize_memory_usage_ = setting;}

    void set_keep_pose_in_memory(  bool const & setting){ keep_pose_in_memory_ = setting;}

    void set_two_stage_clustering(  bool const & setting){ two_stage_clustering_ = setting;}

    void set_verbose(  bool const & setting){ verbose_ = setting;}


    void cluster();

    void
    output_silent_file( std::string const & silent_file );

    void
    recalculate_rmsd_and_output_silent_file(std::string const & silent_file, 
                                            protocols::swa::rna::StepWiseRNA_PoseSetupOP & stepwise_rna_pose_setup,
                                          bool const write_score_only);

    void
    get_best_neighboring_shift_RMSD_and_output_silent_file( std::string const & silent_file );

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

    void
    set_skip_clustering( bool const & setting){skip_clustering_= setting; }

    void
    set_filter_virtual_res_list( utility::vector1 < core::Size > const & setting){ filter_virtual_res_list_=setting; }

    void
    set_perform_VDW_rep_screen( bool const & setting){perform_VDW_rep_screen_= setting; }

    void
    set_perform_filters( bool const & setting){perform_filters_= setting; }

    void
    set_min_num_south_ribose_filter( Size const & setting){min_num_south_ribose_filter_= setting; }

    void
    set_VDW_rep_screen_info( utility::vector1< std::string > const & setting ){ VDW_rep_screen_info_=setting; }

    void
    set_user_input_VDW_bin_screener(protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener){ user_input_VDW_bin_screener_= user_input_VDW_bin_screener; }

    void
    set_full_length_loop_rmsd_clustering(bool const & setting){full_length_loop_rmsd_clustering_= setting; }

    void
    set_ignore_FARFAR_no_auto_bulge_tag(bool const & setting){ignore_FARFAR_no_auto_bulge_tag_=setting; }

    void
    set_ignore_FARFAR_no_auto_bulge_parent_tag(bool const & setting){ignore_FARFAR_no_auto_bulge_parent_tag_=setting; }

    void
    set_ignore_unmatched_virtual_res(bool const & setting){ignore_unmatched_virtual_res_=setting; }

    void
    set_output_pdb( bool const setting){ output_pdb_=setting;}

  private:

    void
    initialize_parameters_and_input();

    void
    create_silent_file_and_tag_list();

    void
    do_some_clustering();

    void
    two_stage_clustering();

    void
    create_large_cluster_centers_member_list();


    bool 
    Is_old_individual_suite_cluster(core::pose::Pose const & current_pose, 
                                    core::pose::Pose const & cluster_center_pose,
                                    utility::vector1 < core::Size > const & rmsd_res_list,
                                  std::map< core::Size, core::Size > const & full_to_sub,
                                  std::map< core::Size, bool > const & Is_prepend_map,
                                  core::Real const & cluster_radius) const;


    core::pose::PoseOP
    get_poseOP(Size const n);

    void
    setup_fail_triangle_inequailty_list(core::pose::Pose & current_pose, std::string const & tag, utility::vector1< bool > & fail_triangle_inequality_list);


    bool 
    Is_new_cluster_center_with_job_parameters(core::pose::PoseOP const & pose_op, std::string const & tag);

    bool
    check_for_closeness_without_job_parameters( core::pose::PoseOP const & pose_op );


    bool
    check_for_closeness( core::pose::PoseOP const & pose_op , std::string const & tag );

    utility::vector1< core::Size > const &
    get_act_alignment_res()  const;

    utility::vector1 < core::Size > const &
    get_act_rmsd_res_list()  const;

    std::map< core::Size, core::Size > const &
    get_act_full_to_sub()  const;

    std::map< core::Size, bool > const &
    get_act_Is_prepend_map() const;

    void
    initialize_quick_alignment_pose();

    void
    initialize_max_memory_pose_num();

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

    void
    initialize_VDW_rep_screener();

    void
    create_tags_map();

    bool
    pass_FARFAR_no_auto_bulge_filter(core::io::silent::SilentStructOP const & silent_struct) const;


  private:

    utility::vector1< std::string > silent_files_;
    core::import_pose::pose_stream::SilentFilePoseInputStreamOP input_;

    utility::vector1< core::pose::PoseOP > pose_output_list_;
    utility::vector1< std::string > tag_output_list_;
    utility::vector1< core::io::silent::SilentStructOP > silent_struct_output_list_;

    Size max_decoys_;
    core::Real score_diff_cut_;
    bool perform_score_diff_cut_;

    core::Real whole_struct_cluster_radius_;
    core::Real suite_cluster_radius_;
    core::Real loop_cluster_radius_;

    bool rename_tags_;
    protocols::swa::rna::StepWiseRNA_JobParametersCOP job_parameters_;
    bool job_parameters_exist_;
    bool distinguish_pucker_;
    bool add_lead_zero_to_tag_;
    bool quick_alignment_;
    bool align_only_over_base_atoms_;
    bool optimize_memory_usage_;
    SlicedPoseJobParameters sliced_pose_job_params_;

    bool verbose_;
    bool keep_pose_in_memory_;
    bool keep_pose_in_memory_hydrid_;
    Size max_memory_pose_num_;

    bool two_stage_clustering_;
    bool use_triangle_inequality_;
    core::pose::Pose first_pose_;
    utility::vector1< utility::vector1< Cluster_Member > > cluster_centers_neighbor_list_;
    utility::vector1< core::pose::PoseOP > large_cluster_pose_list_;
    utility::vector1< core::Size> all_pose_to_output_pose_ID_map_;
    bool PBP_clustering_at_chain_closure_;

    bool quick_alignment_pose_is_intialized_;
    core::pose::Pose quick_alignment_pose_;
    std::string quick_alignment_tag_;
    bool skip_clustering_;

    protocols::swa::rna::StepWiseRNA_VDW_Bin_ScreenerOP user_input_VDW_bin_screener_;
    bool perform_VDW_rep_screen_;
    bool perform_filters_;
    Size min_num_south_ribose_filter_;
    utility::vector1< std::string > VDW_rep_screen_info_;
    bool full_length_loop_rmsd_clustering_;

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

    std::map< std::string, bool > current_tags_map_;
    std::map< std::string, bool > parent_tags_map_;

    bool ignore_FARFAR_no_auto_bulge_parent_tag_;
    bool ignore_FARFAR_no_auto_bulge_tag_;
    bool ignore_unmatched_virtual_res_;
    bool output_pdb_;
    core::chemical::ResidueTypeSetCAP rsd_set_;

  };

} //rna
} //swa
} // protocols

#endif