CombineChainsMover.cc

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/// @file   protocols/domain_assembly/CombineChainsMover.cc
/// @brief  Takes a multichain pose and returns a single-chain one
/// @author Dominik Gront

#include <protocols/domain_assembly/CombineChainsMover.hh>

#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.hh>


#include <core/sequence/Sequence.hh>
#include <core/sequence/SequenceAlignment.hh>

#include <protocols/comparative_modeling/ThreadingMover.hh>

// AUTO-REMOVED #include <basic/options/option_macros.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

#include <core/types.hh>

#include <core/pose/annotated_sequence.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace domain_assembly {

void CombineChainsMover::apply( core::pose::Pose & pose ) {

  using namespace basic::options;
  using namespace basic::options::OptionKeys;

  core::sequence::SequenceAlignment aln;
  core::sequence::SequenceOP seq = new core::sequence::Sequence( pose.sequence(), "this comment here is really irrelevant..." );

  core::pose::Pose extended_pose;
        core::chemical::ResidueTypeSetCAP rsd_set = core::chemical::ChemicalManager::get_instance()->residue_type_set(
                  option[ in::file::residue_type_set ]() );
  core::pose::make_pose_from_sequence(extended_pose, pose.sequence(), *rsd_set);

  aln.add_sequence(seq);
  aln.add_sequence(seq);
  protocols::comparative_modeling::ThreadingMover mover( aln, pose );
  mover.randomize_loop_coords( false );
  mover.build_loops( false );
  mover.apply( extended_pose );


  extended_pose.dump_pdb("out.pdb");

  pose = extended_pose;
} // apply


}//namespace domain_assembly
}//namespace protocols