FullAtomRNA_Fragments.hh

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//Auto using namespaces
//Auto using namespaces end
// -*- 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.
/// @author Rhiju Das

#ifndef INCLUDED_protocols_rna_FullAtomRNA_Fragments_HH
#define INCLUDED_protocols_rna_FullAtomRNA_Fragments_HH

#include <protocols/rna/FullAtomRNA_Fragments.fwd.hh>
// AUTO-REMOVED #include <protocols/toolbox/AllowInsert.hh>
#include <protocols/rna/RNA_Fragments.hh>

// ObjexxFCL Headers
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray3D.hh>

#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <protocols/rna/RNA_MatchType.hh>
#include <utility/pointer/ReferenceCount.hh>

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

#include <utility/vector1.hh>


//Auto using namespaces
namespace ObjexxFCL { } using namespace ObjexxFCL; // AUTO USING NS


/////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////
// 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 rna{

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class TorsionSet {
  public:
    TorsionSet & operator =( TorsionSet const & src );
    TorsionSet( core::Size const size );

    //make this private?
    FArray2D <core::Real>   torsions;  // dimensions: (NUM_RNA_TORSIONS, SRange(0, size) );
    FArray1D <std::string> torsion_source_name;  // dimensions: ( SRange(0, size) );
    FArray1D <char>   secstruct;

     FArray3D <core::Real>   non_main_chain_sugar_coords;
     bool  non_main_chain_sugar_coords_defined;

     inline
     core::Size get_size() const { return size_; }

   private:
     core::Size size_;

  };


  class FullAtomRNA_Fragments; // defined below.

  /////////////////////////////////////////////////////////////////////////////////////////////////
  /////////////////////////////////////////////////////////////////////////////////////////////////
  class FragmentLibrary : public utility::pointer::ReferenceCount  {
  public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~FragmentLibrary();

    //constructor!
    //FragmentLibrary();

    //destructor -- necessary?
    //~FragmentLibrary();

    core::Real get_fragment_torsion(
                                    core::Size const num_torsion,
                                    Size const which_frag,
                                    core::Size const offset );

    TorsionSet const get_fragment_torsion_set( core::Size const which_frag );

    void  add_torsion( TorsionSet const torsion_set );

    void  add_torsion(
          FullAtomRNA_Fragments const & vall,
          core::Size const position,
          core::Size const size
                      );

    core::Size get_align_depth();

  private:
    std::vector< TorsionSet > align_torsions_;

  };

  /////////////////////////////////////////////////////////////////////////////////////////////////
  typedef utility::pointer::owning_ptr< FragmentLibrary > FragmentLibraryOP;
  typedef std::pair< std::string, std::string > SequenceSecStructPair;
  typedef std::map< SequenceSecStructPair, FragmentLibraryOP >  FragmentLibraryPointerMap;

  /////////////////////////////////////////////////////////////////////////////////////////////////
  class FullAtomRNA_Fragments : public RNA_Fragments {
  public:
    //Constructor -- needs vall_torsions_file to get started.
    // RNA_Fragments();
    FullAtomRNA_Fragments( std::string const & filename );

    ~FullAtomRNA_Fragments(){}

    //Probably the only thing that will actually get called publicly:
    virtual void
    apply_random_fragment(
          core::pose::Pose & pose,
          core::Size const position,
          core::Size const size,
          core::Size const type,
        toolbox::AllowInsertOP allow_insert );

    virtual bool
    is_fullatom();

    void read_vall_torsions( std::string const filename );


    core::Real
    torsions( core::Size const & i, core::Size const & j ) const { return vall_torsions_( i, j ); }

    std::string
    name( core::Size const & i ) const { return vall_name_( i ); }

    char
    secstruct( core::Size const & i ) const { return vall_secstruct_( i ); }

    bool
    non_main_chain_sugar_coords_defined() const { return vall_non_main_chain_sugar_coords_defined_; }

    core::Real
    non_main_chain_sugar_coords( core::Size const & i, core::Size const & j, core::Size const & k ) const{ return vall_non_main_chain_sugar_coords_( i, j, k);}

  private:

    void
    pick_random_fragment(
          TorsionSet & torsion_set,
          std::string const RNA_string,
          std::string const RNA_secstruct_string,
          core::Size const type = MATCH_YR );

    void
    pick_random_fragment(
          TorsionSet & torsion_set,
          core::pose::Pose & pose,
          core::Size const position,
          core::Size const size,
          core::Size const type = MATCH_YR );

    void
    insert_fragment(
                    core::pose::Pose & pose,
                    Size const position,
                    protocols::rna::TorsionSet const & torsion_set,
                  toolbox::AllowInsertOP allow_insert );

  private:

    // Probably should make following "vall" stuff a different object
    // and, come on, these could be a vector to save memory!
    FArray2D <core::Real> vall_torsions_;
    FArray3D <core::Real> vall_non_main_chain_sugar_coords_;
    FArray1D <char>  vall_sequence_;
    FArray1D <bool>  vall_is_chainbreak_;
    FArray2D <bool>  vall_edge_is_base_pairing_;
    FArray1D <bool>  vall_makes_canonical_base_pair_;
    FArray1D <char>  vall_secstruct_;
    FArray1D <std::string>  vall_name_;
    core::Size vall_size_;
    bool vall_non_main_chain_sugar_coords_defined_;

    // Need to hold on to some fragment libraries. These
    // will be picked on the fly when the code requires them.
    //   Indexed by sequence, e.g., AAA, AGA, GUA ... or even RYR ...  or even NNN (totally generic!)
    FragmentLibraryPointerMap fragment_library_pointer_map;

    void pick_fragment_library( SequenceSecStructPair const & key );

    void pick_random_fragment( FArray1D <core::Real> & RNA_torsions, std::string const RNA_string );

  };

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


}
}

#endif