GrowPeptides.hh

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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 protocols/seeded_abinitio/GrowPeptides.cc
/// @author Eva-Maria Strauch (evas01@u.washington.edu)

#ifndef INCLUDED_protocols_seeded_abinitio_GrowPeptides_hh
#define INCLUDED_protocols_seeded_abinitio_GrowPeptides_hh

#include <core/pose/Pose.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <utility/string_util.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <utility/vector1.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <set>

namespace protocols {
namespace seeded_abinitio {

class GrowPeptides : public protocols::moves::Mover
{
public:
  GrowPeptides();

  virtual ~GrowPeptides();
  void apply( core::pose::Pose & pose );
  virtual std::string get_name() const;
  virtual protocols::moves::MoverOP clone() const;
  virtual protocols::moves::MoverOP fresh_instance() const;

  void parse_my_tag(      utility::tag::TagPtr const tag,
                protocols::moves::DataMap &,
                protocols::filters::Filters_map const &,
                protocols::moves::Movers_map const &,
                core::pose::Pose const & );

  // Undefined, commenting out to fix PyRosetta build   void add_chainbreakterm( bool ac );

  // Undefined, commenting out to fix PyRosetta build   bool add_chainbreakterm();

  bool ddg();

private: ///functions

  void append_residues_nterminally (
                    core::Size seq_register,
                    core::Size res_pos,
                    core::Size stop,
                    std::string & nat_seq ,
                    core::pose::Pose & target_seeds
                    );

  void append_residues_cterminally (
                    core::Size seq_register,
                    core::Size res_pos,
                    core::Size stop,
                    std::string & nat_seq ,
                    core::pose::Pose & target_seeds
                     );

  void grow_from_seeds(
                  core::pose::Pose curr_pose, //the pose that gets changed
                  std::string sequence,
                  protocols::loops::Loops & seeds,
                  utility::vector1< Size > cutpoints//,
                  );


  void grow_from_verteces(
                   core::pose::Pose & curr_pose,
                   std::string sequence,
                   protocols::loops::Loops & seeds,
                   std::set< core::Size > vertex_set
                  );

  void setup_cached_observers( core::pose::Pose & pose );

    private: /// data

      core::Size extend_nterm;
      core::Size extend_cterm;
      std::string nsequence_;
      std::string csequence_;
      std::string seq_;
      bool all_ala_N;
      bool all_ala_C;
      //bool add_chainbreakterm_;

      bool ddg_;
      /// template pose to derrive a sequence from
      core::pose::PoseOP template_pdb_;
      bool template_presence;
      bool anchor_specified_;
      utility::vector1< core::Size > anchors_;
      core::scoring::ScoreFunctionOP scorefxn_;
      bool output_centroid;
      /// vector of sequence pieces
      utility::vector1< std::string > sequence_chunks_;
      protocols::loops::Loops all_seeds_;
      bool fetch_foldtree;
      ///foldtree after growing out peptide pieces
      core::kinematics::FoldTreeOP seed_foldtree_;
      /// pointer for the current pose
      core::pose::PoseOP curr_pose_;
      std::set< core::Size > verteces_;
      //bool add_chainbreakterm_;

    };
  }//end seeded_abinitio
}//end protocols

#endif