RNA_CentroidInfo.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/methods/RNA_BaseBasePotential.cc
/// @brief  Statistically derived rotamer pair potential class implementation
/// @author Phil Bradley
/// @author Andrew Leaver-Fay


// Unit headers
#include <core/scoring/rna/RNA_CentroidInfo.hh>
// AUTO-REMOVED #include <core/scoring/rna/RNA_CentroidInfo.fwd.hh>

// Package headers

// Project headers
#include <core/chemical/AA.hh>
// AUTO-REMOVED #include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/pose/Pose.hh>

// Utility headers
#include <numeric/xyzMatrix.hh>

#include <utility/vector1.hh>
#include <core/scoring/rna/RNA_Util.hh>


// C++

///////////////////////////////////////////////////////
// Keep track of some base geometry that is
// useful for RNA scoring.
///////////////////////////////////////////////////////

namespace core {
namespace scoring {
namespace rna {

/// @details Copy constructors must copy all data, not just some...
RNA_CentroidInfo::RNA_CentroidInfo( RNA_CentroidInfo const & src ) :
  CacheableData()
{
  base_centroids_ = src.base_centroids_;
  base_stubs_ = src.base_stubs_;
  calculated_ = src.calculated_;
}

typedef  numeric::xyzMatrix< Real > Matrix;


///////////////////////////////////////////////////////////////////////////////
Vector
RNA_CentroidInfo::get_base_centroid( conformation::Residue const & rsd ) const
{
  bool const verbose = false;

  return get_rna_base_centroid( rsd, verbose);  
}


kinematics::Stub
RNA_CentroidInfo::get_base_coordinate_system( conformation::Residue const & rsd, Vector const & centroid ) const
{
  return kinematics::Stub(get_rna_base_coordinate_system(rsd, centroid), centroid );
}

//////////////////////////////////////////////////////////////////////////////////////
void
RNA_CentroidInfo::initialize_base_centroids_and_stubs( pose::Pose const & pose )
{

  base_centroids_.clear();
  base_stubs_.clear();

  for (Size i = 1; i <= pose.total_residue(); i++ ){
    conformation::Residue const & res_i  ( pose.residue(i) );

    Vector centroid_i( 0.0  );
    kinematics::Stub stub_i;

    if ( res_i.is_RNA() ) {
      centroid_i = get_base_centroid( res_i );
      stub_i     = get_base_coordinate_system(res_i, centroid_i );
    }

    base_centroids_.push_back( centroid_i );
    base_stubs_.push_back( stub_i );

  }

}

//////////////////////////////////////////////////////////////////////////////////////
void
RNA_CentroidInfo::update( pose::Pose const & pose )
{
  initialize_base_centroids_and_stubs( pose );
}


}
}
}