WatsonCrickRotamerCouplings.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.

#include <protocols/dna/WatsonCrickRotamerCouplings.hh>
#include <protocols/dna/WatsonCrickRotamerCouplingsCreator.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <protocols/dna/DnaChains.hh>
#include <protocols/dna/util.hh> // find_basepairs

#include <core/conformation/ResidueMatcher.hh> // WatsonCrickResidueMatcher
#include <core/chemical/ResidueType.hh>
// AUTO-REMOVED #include <basic/options/option.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>

#include <basic/Tracer.hh>

// option key includes
// AUTO-REMOVED #include <basic/options/keys/dna.OptionKeys.gen.hh>

#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <basic/options/keys/OptionKeys.hh>

#ifdef WIN32
  #include <utility/tag/Tag.hh>
#endif


namespace protocols {
namespace dna {

using namespace core;
  using namespace chemical;
  using namespace conformation;
  using namespace basic::options;
  using namespace pack;
    using namespace rotamer_set;
    using namespace task;
      using namespace operation;

using basic::t_info;
using basic::t_debug;
using basic::t_trace;
static basic::Tracer TR("protocols.dna.WatsonCrickRotamerCouplings",t_info);

TaskOperationOP WatsonCrickRotamerCouplingsCreator::create_task_operation() const
{
  return new WatsonCrickRotamerCouplings;
}

WatsonCrickRotamerCouplings::~WatsonCrickRotamerCouplings() {}

TaskOperationOP WatsonCrickRotamerCouplings::clone() const
{
  return new WatsonCrickRotamerCouplings( *this );
}

void
WatsonCrickRotamerCouplings::parse_tag( TagPtr /*tag*/ )
{}

void
WatsonCrickRotamerCouplings::apply(
  Pose const & pose,
  PackerTask & ptask
) const
{
  // find DNA chains
  DnaChains dna_chains;
  find_basepairs( pose, dna_chains );
  Size const nres( pose.total_residue() );
  // setup residue couplings
  RotamerCouplingsOP couplings( new RotamerCouplings );
  couplings->resize( nres );
  for ( DnaPositions::const_iterator it( dna_chains.begin() ); it != dna_chains.end(); ++it ) {
    //mjo commenting out 'resid' because it is unused and causes a warning
    //Size const resid( it->first );
    DnaPosition const & dnapos( it->second );
    if ( ! dnapos.paired() ) continue;
    Size top( dnapos.top() );
    Size bot( dnapos.bottom() );
    TR << "base pair " << pose.pdb_info()->chain(top) << "." << pose.pdb_info()->number(top) << "."
      << dna_full_name3( pose.residue_type(top).name3() ) << " - " << pose.pdb_info()->chain(bot)
      << "." << pose.pdb_info()->number(bot) << "." << dna_full_name3( pose.residue_type(bot).name3() )
      << std::endl;
    (*couplings)[ top ].first = bot;
    (*couplings)[ top ].second = new conformation::WatsonCrickResidueMatcher();
    (*couplings)[ bot ].first = top;
    (*couplings)[ bot ].second = new conformation::WatsonCrickResidueMatcher();
  }
  ptask.rotamer_couplings( couplings );
}

} // namespace dna
} // namespace protocols