RNA_CS_Util.cc

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// (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/chemical_shift/RNA_CS_Util.cc
/// @brief
/// @author Parin Sripakdeevong (sripakpa@stanford.edu)


#include <core/scoring/rna/chemical_shift/RNA_CS_Util.hh>

#include <ObjexxFCL/format.hh>
#include <core/chemical/AA.hh>

#include <numeric/xyzMatrix.hh>

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

using namespace core;

namespace core {
namespace scoring {
namespace rna {
namespace chemical_shift {


numeric::xyzMatrix< core::Real > const
get_rna_base_coordinate_system_from_CS_params( core::conformation::Residue const & rsd, RNA_CS_residue_parameters const & rna_cs_rsd_params){ //x and y coordinate different from 'standard' get_rna_base_coordinate_system;

  using namespace chemical;
  Size res_type = rsd.aa();

  if( rsd.is_RNA()==false ) utility_exit_with_message("rsd.is_RNA()==false!");

  if( rsd.aa()!= rna_cs_rsd_params.aa() ) utility_exit_with_message("rsd.aa()!= rna_cs_rsd_params.aa()!");

  //RNA_CS_residue_parameters const & rna_cs_rsd_params=rna_cs_params.get_RNA_CS_residue_parameters(rsd.aa());


    numeric::xyzVector<core::Real> xf_xyz(0.0, 0.0, 0.0);
    numeric::xyzVector<core::Real> yf_xyz(0.0, 0.0, 0.0);
    numeric::xyzVector<core::Real> xt_xyz(0.0, 0.0, 0.0);
    numeric::xyzVector<core::Real> yt_xyz(0.0, 0.0, 0.0);

  Size xf_count = 0;
  Size yf_count = 0;

  Size xt_count = 0;
  Size yt_count = 0;

  Size const maxatoms=rna_cs_rsd_params.get_atomnames_size();

  for (Size count = 1; count < maxatoms; count++)
  {

    Size const atom_index=rsd.atom_index(rna_cs_rsd_params.get_atomname(count));

    numeric::xyzVector<core::Real> const & atom_xyz=rsd.xyz(atom_index);

    if(dround(rna_cs_rsd_params.atom_data(count, xdir))==1){
      xf_count++;
      xf_xyz += atom_xyz;
    }else if(dround(rna_cs_rsd_params.atom_data(count, xdir))==2){
      xt_count++;
      xt_xyz += atom_xyz;
    }

    if(dround(rna_cs_rsd_params.atom_data(count, ydir))==1){
      yf_count++;
      yf_xyz += atom_xyz;
    }else if(dround(rna_cs_rsd_params.atom_data(count, ydir))==2){
      yt_count++;
      yt_xyz += atom_xyz;
    }
             
  }

  if(xf_count!=1 && xf_count!=2) utility_exit_with_message("xf_count!=1 && xf_count!=2");

  if(xt_count!=1 && xt_count!=2) utility_exit_with_message("xt_count!=1 && xt_count!=2");

  if(yf_count!=1 && yf_count!=2) utility_exit_with_message("yf_count!=1 && yf_count!=2");

  if(yt_count!=1 && yt_count!=2) utility_exit_with_message("yt_count!=1 && yt_count!=2");

  //Feb 21, 2012: UMM THIS FOLLOWS DEFINITION GIVEN IN NUCHEMICS..BUT x_base_coor and y_base_coor might not be completely perpendicular!

  numeric::xyzVector<core::Real> x_base_coor = ( (xt_xyz / xt_count) - (xf_xyz / xf_count) );

  x_base_coor.normalize();


    numeric::xyzVector<core::Real> y_base_coor = ( (yt_xyz / yt_count) - (yf_xyz / yf_count) );

    y_base_coor.normalize();

  numeric::xyzVector<core::Real> z_base_coor = cross(x_base_coor, y_base_coor);

  z_base_coor.normalize(); //necessary since x_base_coor and y_base_corr are not completely orthogonal!


  numeric::xyzMatrix< core::Real > const M=numeric::xyzMatrix< core::Real >::cols( x_base_coor, y_base_coor, z_base_coor );

  return M;

}


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



} // chemical_shift
} // rna
} // scoring
} // core