StepWiseRNA_Classes.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_Classes.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_rna_StepWiseRNA_Classes_HH
#define INCLUDED_protocols_swa_rna_StepWiseRNA_Classes_HH


#include <core/pose/Pose.fwd.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <core/id/TorsionID.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 <protocols/moves/GreenPacker.fwd.hh>
#include <string>
#include <map>
#include <utility/exit.hh> //April 29, 2011


#define O3I_C5IPLUS2_MAX_DIST 11.4226  //See ~/minirosetta/04_2010_Early_RUN/test/Apr_9_calculate_theortical_RNA_distance_O3i_C5iplus2/140_220 for detail.
#define O3I_C5I_PLUS_ONE_MAX_DIST 3.968000 //see data below the function get_C4_C3_distance_range() in StepWiseRNA_Classes.hh
#define O3I_O3I_PLUS_ONE_MAX_DIST 7.45583 //see ~/minirosetta/test/Sept_19_calculate_MAX_O3_O3_distance/trail_1_range_0_360_bin_size_5/output.txt
#define C5I_C5I_PLUS_ONE_MAX_DIST 7.71355 //see ~/minirosetta/test/Sept_19_calculate_MAX_C5_C5_distance/trail_3_0_torsion_range_360_5_degree_bin/output.txt


//using namespace core;
typedef  numeric::xyzMatrix< core::Real > Matrix;

namespace protocols {
namespace swa {
namespace rna {

enum PuckerState{ ALL, NORTH, SOUTH };
enum BaseState{ BOTH, ANTI, SYN, NONE }; //April 29, 2011 USED TO BE //enum BaseState{ BOTH, ANTI, NONE };



class Jump_point{

    public:

    Jump_point():
    five_prime_seq_num( 0 ),
    five_prime_atom("O3*"),
    three_prime_seq_num( 0 ),
    three_prime_atom("P"),
    cut_point( 0 )
  {
  }

  ~Jump_point(){};

  public:

  core::Size five_prime_seq_num;
  std::string five_prime_atom;
  core::Size three_prime_seq_num;
  std::string three_prime_atom;
  core::Size cut_point; //Choose the residue five_prime of the actual cutpoint position

};

// Why don't we just keep this in a "regular" kinematics::Stub?
/*
struct base_stub{
  numeric::xyzVector<core::Real> centroid;
  Matrix base_coordinate_matrix;
};
*/


struct pose_data_struct2{
  core::Real score;
  core::pose::PoseOP pose_OP;
  std::string tag;
};

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

struct Torsion_Info{
  core::id::TorsionID id;
  core::Real value;
};

/*
class Torsion_Info{
  public:
   Torsion_Info():
      value(0.0)
    {
    }

    ~Torsion_Info(){};

  core::id::TorsionID id;
  core::Real value;

};
*/



struct output_data_struct {

  core::Real rmsd_wrt_correct_minimized;
  core::Real rmsd_wrt_minimized;
  core::Real rmsd;
  core::Real loop_rmsd_wrt_correct_minimized;
  core::Real loop_rmsd_wrt_minimized;
  core::Real loop_rmsd;
  core::Real diff_torsions;
  core::Real current_score;
  core::Real O3_C5_distance;
};

class InternalWorkingResidueParameter{

public:

  InternalWorkingResidueParameter():
    fake_working_moving_suite( 0 ),
    possible_working_res_1( 0 ),
    possible_working_res_2( 0 )
    {
  }

  ~InternalWorkingResidueParameter(){};

  public:

    core::Size fake_working_moving_suite;
    core::Size possible_working_res_1;
    core::Size possible_working_res_2;
};





class SillyCountStruct{

public:

  SillyCountStruct():
    output_pose_count( 0 ),
    good_bin_rep_count( 0 ),
    good_rep_rotamer_count( 0 ),
    good_atr_rotamer_count( 0 ),
    good_angle_count( 0 ),
    good_distance_count( 0 ),
    chain_break_screening_count( 0 ),
    chain_closable_count( 0 ),
    Near_Native_Rotamer_Count( 0 ),
    base_pairing_count( 0 ),
    base_stack_count( 0 ),
    strict_base_pairing_count( 0 ),
    pass_base_centroid_screen( 0 ),
    both_count( 0 ),
    tot_rotamer_count( 0 ),
    fine_rmsd_count( 0 ),
    rmsd_count( 0 ),
    non_clash_ribose( 0 ),
    fast_full_atom_VDW_replusion_screen( 0 ),
    in_range_CCD_torsion( 0 ),
    total_bin( 0 ),
    bulge_at_chain_closure_count( 0 ),
    before_chain_break_grid_index_screening( 0 ),
    chain_break_grid_index_screening( 0 ),
    residues_contact_screen( 0 ),
    test_count_one( 0 ),
    test_count_two( 0 )
    {
  }


  ~SillyCountStruct(){};

public:

  core::Size output_pose_count;
  core::Size good_bin_rep_count;
  core::Size good_rep_rotamer_count;
  core::Size good_atr_rotamer_count;
  core::Size good_angle_count;
  core::Size good_distance_count;
  core::Size chain_break_screening_count;
  core::Size chain_closable_count;
  core::Size Near_Native_Rotamer_Count;
  core::Size base_pairing_count;
  core::Size base_stack_count;
  core::Size strict_base_pairing_count;
  core::Size pass_base_centroid_screen;
  core::Size both_count;
  core::Size tot_rotamer_count;
  core::Size fine_rmsd_count;
  core::Size rmsd_count;
  core::Size non_clash_ribose;
  core::Size fast_full_atom_VDW_replusion_screen;
  core::Size in_range_CCD_torsion;
  core::Size total_bin;
  core::Size bulge_at_chain_closure_count;
  core::Size before_chain_break_grid_index_screening;
  core::Size chain_break_grid_index_screening;
  core::Size residues_contact_screen;
  core::Size test_count_one;
  core::Size test_count_two;
};

////////////////////////////////////////////////////////////
}
}
}

#endif