TranslatorSet.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/chemical/ChemicalManager.cc
/// @brief  Chemical manager class
/// @author Oliver Lange (olange@u.washington.edu)

#include <core/coarse/TranslatorSet.hh>

// Package headers
#include <core/coarse/Translator.hh>

// Project headers
#include <core/chemical/ResidueTypeSet.hh>
// AUTO-REMOVED #include <core/conformation/Conformation.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>

#include <basic/Tracer.hh>

//Auto Headers
#include <core/conformation/Residue.hh>
#include <core/kinematics/Jump.hh>

using basic::T;
using basic::Error;
using basic::Warning;

namespace core {
namespace coarse {

static basic::Tracer TR("core.coarse.TranslatorSet");

using namespace chemical;

TranslatorSet::TranslatorSet(
  const RuleSet &rules,
  ResidueTypeSetCAP residue_set,
  ResidueTypeSetAP coarse_set)
: residue_set_(residue_set),
  coarse_residue_set_(coarse_set)
{
  using namespace std;
  TR.Error << "constructing TranslatorSet..." << "\n";
  for ( ResidueTypeSet::const_residue_iterator it=residue_set_->all_residues_begin(),
        eit=residue_set_->all_residues_end();
        it!=eit;
         ++it )
    {
      const ResidueType& res = *(it->second);
      T("coarse.setup") << "in loop " << res.name() << " " << res.name3() << "  aa: " << res.aa() <<  "\n";
      if ( coarse_residue_set_->has_name( res.name() ) ) {
  TranslatorOP cmap_ptr =
    new Translator( rules,ResidueTypeCOP( res ),
      ResidueTypeAP( const_cast<ResidueType&> (coarse_residue_set_->name_map( res.name() )) )
    ); //the non-const object is only needed in the construction of Translator (fix_geometry)
  //, a CAP is stored for later...
  cmap_ptr->pretty_print(cout);
  coarse_maps_.insert(TranslatorMap::value_type(it->first,cmap_ptr));
      } else {
  Warning() << res.name() << " not found in coarse_residue set... ignored..." << "\n";
      }
    }
}

void
TranslatorSet::pretty_print( std::ostream &os ) const
{
  for ( const_iterator it=begin(), eit=end(); it!=eit; ++it ) {
    it->second->pretty_print(os);
    os << std::endl;
  }
}

TranslatorCOP const&
TranslatorSet::default_for_aa( chemical::AA aa ) const
{
  chemical::ResidueTypeCOPs types=residue_set_->aa_map(aa);
  if (types.size() > 1) {
    Warning() << "WARNING: coarse/Translator.cc: using the first residue in the set with AA "
        << aa << "\n" << "do not know if that is the best choice. Might be good to add " <<
      "knowledge about the 'default' residue_type to the residueset " << "\n";
  };
  return (coarse_maps_[types.front()->name()]);
}

void
 TranslatorSet::coarsify( pose::Pose &pose_out, pose::Pose const &pose_in ) const
{
  pose_out.clear();
  for (uint seqpos = 1;seqpos<=pose_in.total_residue();seqpos++) {
    pose_out.append_residue_by_bond( *coarsify(pose_in.residue(seqpos)) );
  };
  pose_out.fold_tree( kinematics::FoldTree( pose_out.total_residue() ) );
}


conformation::ResidueOP TranslatorSet::coarsify(const conformation::Residue& fine_rsd) const {
  assert( has(fine_rsd.name()) ); // silly check
  return coarse_maps_[fine_rsd.name()]->coarsify(fine_rsd);
}

bool TranslatorSet::has(TranslatorSet::ResName name) const {
  return ( coarse_maps_.find(name) != coarse_maps_.end() );
}



}
}