DnaChains.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 DnaChains.cc
/// @author ashworth

#include <protocols/dna/DnaChains.hh>

#include <core/chemical/ResidueType.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>

#include <ObjexxFCL/format.hh> // I()

#include <utility/vector1.hh>


using utility::vector1;

namespace protocols {
namespace dna {

using namespace ObjexxFCL::fmt;
using namespace core;

DnaChains::DnaChains() : utility::pointer::ReferenceCount() {}

DnaChains::~DnaChains(){}

DnaChains::DnaChains( DnaChains const & other )
  : utility::pointer::ReferenceCount()
{
  positions_ = other.positions();
}

DnaChainsOP DnaChains::clone() const
{
  return new DnaChains( *this );
}

bool
DnaChains::contains( Size index ) const
{
  if ( is_top(index) ) {
    runtime_assert( (*this)[ index ].top() == index );
    return true;
  }
  // bottom strand check
  for ( DnaPositions::const_iterator pos( positions_.begin() );
        pos != positions_.end(); ++pos ) {
    if ( index == pos->second.bottom() ) return true;
  }
  return false;
}

void
DnaChains::print(
  pose::Pose const & pose,
  std::ostream & os
) const
{
  os << "There are " << positions_.size() << " dna positions:" << '\n';
  for ( DnaPositions::const_iterator iter( positions_.begin() );
        iter != positions_.end(); ++iter ) {

    Size const top_i( iter->first );
    DnaPosition const & pos( iter->second );
    runtime_assert( top_i == pos.top() );
    os << I( 4, top_i );
    if ( pose.pdb_info() ) {
      os << " (pdb " << pose.pdb_info()->chain( top_i ) << " "
      << I( 4, pose.pdb_info()->number( top_i ) ) << ")";
    }
    os << pose.residue_type( top_i ).name3();
    if ( pos.paired() ) {
      Size const bot_i( pos.bottom() );
      os << "  <=>" << pose.residue_type( bot_i ).name3() << "  " << I( 4, bot_i );
      if ( pose.pdb_info() ) {
        os << " (pdb " << pose.pdb_info()->chain( bot_i ) << " "
          << I( 4, pose.pdb_info()->number( bot_i ) ) << ")";
      }
    }
    else os << " (unpaired)";
    os << '\n';
  }
  os << std::endl;
}

} // namespace dna
} // namespace protocols