RNA_FittedTorsionInfo.cc

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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   core/scoring/rna/RNA_FittedTorsionInfo.cc
/// @brief  Statistically derived torsion information for RNA
/// @author Rhiju Das


// Unit headers
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>

#include <utility/vector1.hh>


// Package headers


// Project headers

// Utility headers

// C++

///////////////////////////////////////////////////////
// Keep track of information from, e.g., chemical
// accessibility experiments -- useful for scoring.
///////////////////////////////////////////////////////

namespace core {
namespace scoring {
namespace rna {


  RNA_FittedTorsionInfo::RNA_FittedTorsionInfo():
    rna_tight_torsions_( true ),
    DELTA_CUTOFF_( 115.0 ),
    //// Following are torsions that are optimized to minimize rna_torsion + sugar_close.
    ////  [ Due to frustration, impossible to satisfy ideal bond lengths+angles for arbitrary delta. ]
    ideal_delta_north_( 85.4184 ),
    ideal_nu2_north_( 37.3643 ),
    ideal_nu1_north_( 92.2042 ),
    ideal_delta_south_( 152.467 ),
    ideal_nu2_south_( -38.085 ),
    ideal_nu1_south_( 150.133 )
  {
    init_rna_torsion_gaussian_parameters();
  }

  RNA_FittedTorsionInfo::~RNA_FittedTorsionInfo(){}

  ///////////////////////////////////////////////////////////////////////////////////////
  void
  RNA_FittedTorsionInfo::init_rna_torsion_gaussian_parameters()
  {
    // These numbers refer to amplitude, mean, and width of fitted Gaussians.

    ////////////////////////////////////////////////////////////////////////////
    // Parameters for alpha,beta,gamma,delta, etc. torsion constraints...
    ////////////////////////////////////////////////////////////////////////////
    // "Tight torsion" means use the width of the major peak in the torsion
    // histogram to determine how strong the harmonic constraint will be. Otherwise, be less restrictive,
    // and use width of the minor fatter peak that lies under the sharp peak.

    if ( rna_tight_torsions_ ) {
      gaussian_parameter_set_alpha_.push_back( Gaussian_parameter(222.03, -64.11,  9.64) );
    } else {
      gaussian_parameter_set_alpha_.push_back( Gaussian_parameter(13.12, -73.74,  35.97) );
    }
    gaussian_parameter_set_alpha_.push_back( Gaussian_parameter(10.51, 66.01,  18.09) );
    gaussian_parameter_set_alpha_.push_back( Gaussian_parameter(18.40, 161.80,  18.12) );

    if ( rna_tight_torsions_ ) {
      gaussian_parameter_set_beta_.push_back( Gaussian_parameter(181.33, 176.33,  11.54) );
    } else {
      gaussian_parameter_set_beta_.push_back( Gaussian_parameter(32.30, 174.52,  43.56) );
    }

    if ( rna_tight_torsions_ ) {
      gaussian_parameter_set_gamma_.push_back( Gaussian_parameter(366.90, 53.08,  6.64) );
    } else {
      gaussian_parameter_set_gamma_.push_back( Gaussian_parameter(18.26, 56.59,  20.57) );
    }
    gaussian_parameter_set_gamma_.push_back( Gaussian_parameter(21.61, 178.19,  13.61) );
    gaussian_parameter_set_gamma_.push_back( Gaussian_parameter(3.98, -64.02,  17.76) );

    gaussian_parameter_set_delta_north_.push_back( Gaussian_parameter(687.92, 82.90,  3.99) );
    gaussian_parameter_set_delta_south_.push_back( Gaussian_parameter(53.18, 145.25,  6.35) );

    gaussian_parameter_set_epsilon_north_.push_back( Gaussian_parameter(178.08, -150.17,  14.64) );
    gaussian_parameter_set_epsilon_north_.push_back( Gaussian_parameter(2.52, 68.28,  32.29) );

    gaussian_parameter_set_epsilon_south_.push_back( Gaussian_parameter(11.95, -98.45, 26.80) );
    gaussian_parameter_set_epsilon_south_.push_back( Gaussian_parameter( 0.58, 159.70, 103.86) );

    if ( rna_tight_torsions_ ) {
      gaussian_parameter_set_zeta_alpha_sc_minus_.push_back( Gaussian_parameter( 143.97, -71.45, 7.91) );
    } else {
      gaussian_parameter_set_zeta_alpha_sc_minus_.push_back( Gaussian_parameter( 78.74, -68.60, 16.19) );
    }
    //  gaussian_parameter_set_zeta_alpha_sc_minus_.push_back( Gaussian_parameter(  2.43, 178.84, 114.82) );
    gaussian_parameter_set_zeta_alpha_sc_minus_.push_back( Gaussian_parameter(  2.43, 178.84, 40.00) );

    gaussian_parameter_set_zeta_alpha_sc_plus_.push_back( Gaussian_parameter(2.08, -137.28,  63.12) );
    gaussian_parameter_set_zeta_alpha_sc_plus_.push_back( Gaussian_parameter(3.37, 87.07,  32.69) );

    gaussian_parameter_set_zeta_alpha_ap_.push_back( Gaussian_parameter(13.65, -69.74,  15.28) );
    gaussian_parameter_set_zeta_alpha_ap_.push_back( Gaussian_parameter(2.69, 63.03,  33.61) );

    //These need to be flipped by -180.0, due to change in chi def. from r++ to mini.
    //  gaussian_parameter_set_chi_north_.push_back( Gaussian_parameter(228.92, -100.57, 11.43) );
    //  gaussian_parameter_set_chi_north_.push_back( Gaussian_parameter( 1.07, 129.24, 26.11) );
    gaussian_parameter_set_chi_north_.push_back( Gaussian_parameter(228.92, 79.43, 11.43) );
    gaussian_parameter_set_chi_north_.push_back( Gaussian_parameter( 1.07, -50.76, 26.11) );

    //  gaussian_parameter_set_chi_south_.push_back( Gaussian_parameter(12.53, -63.40, 25.23) );
    //  gaussian_parameter_set_chi_south_.push_back( Gaussian_parameter( 0.64, 130.09, 28.10) );
    gaussian_parameter_set_chi_south_.push_back( Gaussian_parameter(12.53, 116.60, 25.23) );
    gaussian_parameter_set_chi_south_.push_back( Gaussian_parameter( 0.64, -49.91, 28.10) );

    gaussian_parameter_set_nu2_north_.push_back( Gaussian_parameter(1148.01, 38.82, -2.77) );
    gaussian_parameter_set_nu2_south_.push_back( Gaussian_parameter(173.15, -37.22, 3.00) );

    gaussian_parameter_set_nu1_north_.push_back( Gaussian_parameter(631.56, 95.34,  4.20) );
    gaussian_parameter_set_nu1_south_.push_back( Gaussian_parameter(57.04, 155.51,  6.00) );

  }



}
}
}