setup.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
/// @brief
/// @author

#include <core/scoring/dna/setup.hh>
#include <core/scoring/dna/base_geometry.hh>
#include <core/scoring/dna/BasePartner.hh>

#include <core/conformation/Residue.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/Tracer.hh>

#include <utility/vector1.hh>



namespace core {
namespace scoring {
namespace dna {

static basic::Tracer TR("core.scoring.dna.setup");

void
set_base_partner(
  pose::Pose & pose
)
{
  //using core::pose::datacache::CacheableDataType::BASE_PARTNER;
  utility::vector1< Size > partner;
  find_basepairs( pose, partner );
  pose.data().set( core::pose::datacache::CacheableDataType::BASE_PARTNER, new BasePartner( partner ) );
}

void
find_basepairs(
  pose::Pose const & pose,
  //utility::vector1< std::pair< int, int > > & pairs,
  utility::vector1< Size > & partner
)
{
  using conformation::Residue;
  using namespace chemical;

  Real const max_d( 4.0 );
  Size const nres( pose.total_residue() );

  //pairs.clear();
  partner.clear();
  partner.resize( nres, 0 );

  std::map< AA, AA > base_partner;
  base_partner[ na_ade ] = na_thy;
  base_partner[ na_thy ] = na_ade;
  base_partner[ na_gua ] = na_cyt;
  base_partner[ na_cyt ] = na_gua;

  std::map< AA, std::string > hbond_atom;
  hbond_atom[ na_ade ] = "N1";
  hbond_atom[ na_thy ] = "N3";
  hbond_atom[ na_gua ] = "N1";
  hbond_atom[ na_cyt ] = "N3";

  for ( Size i=1; i<= nres; ++i ) {
    Residue const & i_rsd( pose.residue(i) );
    AA const & i_aa( i_rsd.aa() );
    if ( i_rsd.is_DNA() ) {
      // hbond atom, base y-axis
      Vector const & i_xyz( i_rsd.xyz( hbond_atom[ i_aa ] ) );
      Vector const i_axis( get_y_axis( i_rsd, 1 /*strand*/ ) );

      Real best(1000.0);
      for ( Size j=1; j<= nres; ++j ) {
        if ( j==i ) continue;
        Residue const & j_rsd( pose.residue( j ) );
        AA const & j_aa( j_rsd.aa() );
        if ( j_aa == base_partner[ i_aa ] ) {
          Vector const & j_xyz( j_rsd.xyz( hbond_atom[ j_aa ] ) );
          Real d( i_xyz.distance( j_xyz ) );
          if ( d<max_d ) {
            Vector const j_axis( get_y_axis( j_rsd, 2 /*strand*/ ) );
            Vector const u( ( i_xyz - j_xyz ).normalized() );
            Real const dot1( dot( i_axis, j_axis ) );
            Real const dot2( dot( i_axis, u ) );
            Real const dot3( dot( j_axis, u ) );
            d -= dot1+dot2+dot3;
            if ( d<best && dot1 > 0.75 && dot2 > 0.75 && dot3 > 0.75 ) {
              best = d;
              partner[i] = j;
            }
          }
        }
      }
    }
  }

  for ( Size i=1; i<= nres; ++i ) {
    if ( !partner[i] ) continue;

    if ( partner[ partner[i] ] != i ) {
      partner[i] = 0;
      continue;
    }

    if ( i < partner[i] ) {
      //pairs.push_back( std::make_pair( i, partner[i] ) );
      TR(basic::t_debug) << "found basepair: " << i << ' ' << partner[i] << std::endl;
    }
  }
}





} // namespace dna
}} // scoring core