StepWiseRNA_VDW_Bin_Screener.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_VDW_Bin_Screener.hh
/// @brief
/// @detailed
///
/// @author Parin Sripkaddevong


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_VDW_Bin_Screener_hh
#define INCLUDED_protocols_swa_rna_StepWiseRNA_VDW_Bin_Screener_hh



#include <protocols/swa/rna/StepWiseRNA_Classes.hh> /*For PuckerState and Torsion_Info*/
#include <protocols/swa/rna/StepWiseRNA_JobParameters.fwd.hh>

#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <utility/vector1.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <string>
#include <map>
#include <core/chemical/AA.hh>

#include <core/conformation/Residue.hh>
#include <set>





typedef  numeric::xyzMatrix< core::Real > Matrix;

namespace protocols {
namespace swa {
namespace rna {

  struct Atom_Bin{
    int x;
    int y;
    int z;
  };


  class VDW_RepScreeninfo{

    public:

    VDW_RepScreeninfo():
      input_string(""),
      pose_name(""),
      in_root_partition(false),
      import_ID(0)
    {
      VDW_align_res.clear();
      working_align_res.clear();
      full_align_res.clear();
      VDW_ignore_res.clear();
    }

    ~VDW_RepScreeninfo(){};

    public:

    utility::vector1< core::Size > VDW_align_res;
    utility::vector1< core::Size > working_align_res;
    utility::vector1< core::Size > full_align_res;
    utility::vector1< core::Size > VDW_ignore_res;
    core::pose::Pose VDW_pose;
    std::string input_string;
    std::string pose_name;
    bool in_root_partition;
    core::Size import_ID;

  };

  

  class StepWiseRNA_VDW_Bin_Screener: public utility::pointer::ReferenceCount {
 
   public:

    //constructor!
    StepWiseRNA_VDW_Bin_Screener();

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

    void
    FARFAR_setup_using_user_input_VDW_pose(utility::vector1< std::string > const & VDW_rep_screen_pose_info, core::pose::Pose const & const_working_pose);


    void
    setup_using_user_input_VDW_pose(utility::vector1< std::string > const & VDW_rep_screen_pose_info, core::pose::Pose const & const_working_pose, StepWiseRNA_JobParametersCOP const & job_parameters );
  
    void
    setup_using_working_pose(core::pose::Pose const & const_working_pose, StepWiseRNA_JobParametersCOP const & job_parameters );


    void
    update_VDW_screen_bin(core::pose::Pose const & pose, 
                        utility::vector1< core::Size > const & ignore_res_list, 
                        bool const Is_prepend,  //associated with ignore_res_list
                        std::ofstream & outfile_act);

    void
    create_VDW_screen_bin(core::pose::Pose const & pose, 
                        utility::vector1< core::Size > const & ignore_res_list, 
                        bool const Is_prepend,  //associated with ignore_res_list
                         numeric::xyzVector<core::Real> const & reference_xyz, 
                        bool const verbose=false);
    void
    create_VDW_screen_bin(utility::vector1< VDW_RepScreeninfo > const & VDW_rep_screen_info_list,  
                          numeric::xyzVector<core::Real> const & reference_xyz, 
                         bool const verbose);


    void
    create_VDW_screen_bin(utility::vector1< core::pose::Pose> const & pose_list, 
                        utility::vector1< utility::vector1< core::Size > > const & list_of_ignore_res_list, 
                        utility::vector1< bool > const list_of_Is_prepend,  
                         numeric::xyzVector<core::Real> const & reference_xyz, 
                        bool const verbose);



    //fast version
    bool
    VDW_rep_screen(core::pose::Pose const & screening_pose, //Warning..this pose coordinate is not update...use here for VIRTUAL atom screening.
                                           core::Size const & moving_res, 
                                           core::conformation::Residue const & rsd_at_origin, 
                                           core::kinematics::Stub const & moving_res_base_stub); //the actual updated coordiate

    //Slow version (in the sense that position of screening_pose had to be updated before this function is called)..
    bool
    VDW_rep_screen( core::pose::Pose const & screening_pose, core::Size const & moving_res);

    bool
    VDW_rep_screen_with_act_pose(core::pose::Pose const & screening_pose, utility::vector1< core::Size > const & moving_res_list, bool const local_verbose=true);


    bool
    user_inputted_VDW_screen_pose() const;

    void
    reference_xyz_consistency_check( numeric::xyzVector<core::Real> const & inputted_reference_xyz) const;

    void
    set_VDW_rep_alignment_RMSD_CUTOFF( core::Real const & setting){ VDW_rep_alignment_RMSD_CUTOFF_= setting ;}

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

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

    void
    set_physical_pose_clash_dist_cutoff( core::Real const & setting){ physical_pose_clash_dist_cutoff_= setting ;}

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

    private:

    void
    check_VDW_screen_bin_is_setup() const;

    bool
    Is_atom_bin_in_range(Atom_Bin const & atom_pos_bin) const;

    bool
    check_atom_bin_in_range(Atom_Bin const & atom_pos_bin);

    void
    set_reference_xyz(numeric::xyzVector<core::Real> const & reference_xyz);
    
    Atom_Bin
    get_atom_bin(numeric::xyzVector<core::Real> const & atom_pos) const;

    numeric::xyzVector<core::Real> 
    get_atom_pos(Atom_Bin const & atom_bin) const;

    void
    output_atom_bin(std::string const filename) const;


    /*
    void
    delete_matching_res_in_VDW_rep_screen_pose(core::pose::Pose & VDW_rep_screen_pose, 
                                            core::pose::Pose const & working_pose, 
                                            utility::vector1< core::Size > const & VDW_rep_screen_align_res,
                                            utility::vector1< core::Size > const & working_align_res,
                                            std::map< core::Size, core::Size > & full_to_sub,
                                            bool const verbose) const;
    */

    //replacement for delete_matching_res_in_VDW_rep_screen_pose()!
    utility::vector1< core::Size > 
    get_matching_res_in_VDW_rep_screen_pose(core::pose::Pose const & VDW_rep_screen_pose, 
                                          core::pose::Pose const & working_pose, 
                                          utility::vector1< core::Size > const & VDW_rep_screen_align_res,
                                          utility::vector1< core::Size > const & working_align_res,
                                          std::map< core::Size, core::Size > & full_to_sub) const;


    void
    align_VDW_rep_screen_pose(core::pose::Pose & VDW_rep_screen_pose, 
                             core::pose::Pose const & working_pose, 
                             utility::vector1< core::Size > const & VDW_rep_screen_align_res,
                             utility::vector1< core::Size > const & working_align_res,
                             bool const verbose) const;

    void
    create_VDW_rep_screen_pose(VDW_RepScreeninfo & VDW_rep_screen_info, //This function update this class!
                              core::pose::Pose const & working_pose, 
                              std::map< core::Size, core::Size > & full_to_sub,
                              bool const verbose) const;



    private:

      core::Real max_distance_;
      core::Real atom_bin_size_;

      int const bin_min_;
      int const bin_max_;
      int const bin_offset_;
      core::Size const num_clash_atom_cutoff_;
      bool const write_to_file_;
      bool Is_reference_xyz_setup_;
      bool Is_VDW_screen_bin_setup_;
      bool user_inputted_VDW_screen_pose_;

      //Still working...
      utility::vector1< utility::vector1< utility::vector1< bool > > > VDW_screen_bin_;
      numeric::xyzVector<core::Real> reference_xyz_;

      core::Real VDW_rep_alignment_RMSD_CUTOFF_;
      bool tolerate_off_range_atom_bin_;
      int num_atom_pos_bin_out_of_range_message_outputted_;


      bool VDW_rep_screen_with_physical_pose_verbose_;
      core::Real physical_pose_clash_dist_cutoff_;

      utility::vector1< std::string > VDW_rep_ignore_matching_res_;

      bool use_VDW_rep_pose_for_screening_;

      utility::vector1< VDW_RepScreeninfo > VDW_rep_screen_info_list_;
      bool output_pdb_;

  };

}
}
}

#endif