CloseFold.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/CloseFold.cc
/// @author Eva-Maria Strauch (evas01@u.washington.edu)

#ifndef INCLUDED_protocols_seeded_abinitio_CloseFold_hh
#define INCLUDED_protocols_seeded_abinitio_CloseFold_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 <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <utility/vector1.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/Frame.hh>

#include <boost/unordered/unordered_map.hpp>

namespace protocols {
  namespace seeded_abinitio {
    
    class CloseFold : public protocols::moves::Mover
    {

    public:
      CloseFold();
      
      virtual ~CloseFold();
      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 & );
      
      
    private: ///functions
      
      protocols::loops::LoopsOP find_loops (  core::pose::Pose & pose, 
                          std::string secstr, 
                          core::Size offset,
                          protocols::loops::Loops seeds );
    
      bool is_cut( utility::vector1<Size> & cut_points, Size residue);
      
      bool chainbreakweights();
      
      void add_chainbreakweights( bool acbw );
      
      bool use_cutpoints();
      
      void use_cutpoints( bool uc );
      
      core::Size trials();
      
      void set_trials( core::Size trials_quick_ccd );

      void initialize_fragments();
      
//      core::scoring::ScoreFunction cen_scorefxn();
//      core::scoring::ScoreFunction fa_scorefxn();

    private: /// data
      
      /// fragment set used for ccd
      core::fragment::FragSetOP fragments_;

      ///position-indexable list of Frames, populating library
      ///void initialize_library();
      
      ///index-based access to the data contained in the FragSet
      boost::unordered_map<core::Size, core::fragment::Frame> library_;
      //FrameMap library_;

      void fast_loopclose( core::pose::Pose &pose, protocols::loops::LoopsOP const loops, bool kic );

      void quick_closure( core::pose::Pose &pose, protocols::loops::LoopsOP const loops );  

      core::pose::PoseOP template_pdb_;
      
      std::string secstructure_;
      
      utility::vector1< core::Size > chains_;
      
      //gather all loops for specified chains or just the ones that have a cutpoint
      bool use_cutpoints_;
      
      ///residues specifying the seeds
      utility::vector1< std::pair < std::string,std::string > > seed_vector_;

      //protocols::loops::Loops seeds_;
      //utility::vector1< core::Size > seed_vector_;

      protocols::loops::LoopsOP loops_;
        
      ///add cutpoint variants for closure
      bool chainbreakweights_;
      
      ///option for quick ccd protocol, how many attempts
      core::Size trials_;
      
      ///options for fast_ccd protocol
      bool idealize_;
      
      ///should kinematic loop mover be used after the fast ccd
      bool kic_;  
      bool ccd_;
      core::scoring::ScoreFunctionOP cen_scorefxn_;

      core::scoring::ScoreFunctionOP fa_scorefxn_;    
    };
  }//end seeded_abinitio
}//end protocols

#endif