CoarseRNA_Fragments.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:
//  CVS information:
//  $Revision: 1.1.2.1 $
//  $Date: 2005/11/07 21:05:35 $
//  $Author: rhiju $
// (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.

#ifndef INCLUDED_protocols_coarse_rna_CoarseRNA_Fragments_HH
#define INCLUDED_protocols_coarse_rna_CoarseRNA_Fragments_HH

#include <protocols/rna/RNA_Fragments.hh>
#include <protocols/toolbox/AllowInsert.fwd.hh>
// AUTO-REMOVED #include <protocols/rna/RNA_MatchType.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/MiniPose.hh>
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.hh>

// C++ Headers
#include <string>
#include <map>
#include <vector>


/////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////
// Goal: to make a fragment object that can choose fragments
// "on the fly" for RNA ab inito folding.
//
// After reading in a set of torsions from, e.g., the ribosome crystal structure,
//  should be able to generate fragments of size 1, 2, or 3, with
//  exact sequence matches, partial Y/R matches, or ignoring sequence.
//
namespace protocols{
namespace coarse_rna{

  typedef std::pair< std::string, std::string > SequenceSecStructPair;

  class SourcePositions : public utility::pointer::ReferenceCount{

  public:

    SourcePositions(){}
    virtual ~SourcePositions();
    core::Size size() const { return source_positions_.size(); }
    void push_back( core::Size const & value ){ source_positions_.push_back( value ); }
    core::Size operator[]( core::Size num ){ return source_positions_[ num ]; }

  private:

    utility::vector1< core::Size > source_positions_;

  };

  typedef utility::pointer::owning_ptr< SourcePositions > SourcePositionsOP;


  /////////////////////////////////////////////////////////////////////////////////////////////////
  class CoarseRNA_Fragments : public protocols::rna::RNA_Fragments {
  public:

    //Constructor -- needs vall_torsions_file to get started.
    // CoarseRNA_Fragments();
    CoarseRNA_Fragments( std::string const & filename );
    virtual ~CoarseRNA_Fragments();

    virtual void
    apply_random_fragment(
          core::pose::Pose & pose,
          core::Size const position,
          core::Size const size,
          core::Size const type,
          protocols::toolbox::AllowInsertOP allow_insert );

    virtual bool
    is_fullatom();

  private:

    void
    insert_fragment(
                    core::pose::Pose & pose,
                    Size const & insert_res,
                    Size const & source_res,
                    Size const & frag_size,
                    protocols::toolbox::AllowInsertOP allow_insert );

    void
    find_source_positions( SequenceSecStructPair const & key );

    Size
    pick_random_fragment(
                         std::string const RNA_string,
                         std::string const RNA_secstruct_string,
                         Size const type /* = MATCH_YR */);

    Size
    pick_random_fragment(
                         core::pose::Pose & pose,
                         Size const position,
                         Size const size,
                         Size const type );

    void
    initialize_frag_source_pose();

    std::string frag_source_secstruct_;

    std::string const frag_source_file_;
    core::pose::MiniPoseOP frag_source_pose_;
    std::map< SequenceSecStructPair, SourcePositionsOP > source_positions_map_;

    std::map< std::string, Size > coarse_rna_name_to_num_;
  };

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////


}
}

#endif