RNA_JumpLibrary.hh

Go to the documentation of this file.

// -*- 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_rna_RNA_JumpLibrary_HH
#define INCLUDED_protocols_rna_RNA_JumpLibrary_HH

// AUTO-REMOVED #include <core/pose/Pose.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.fwd.hh>
// C++ Headers
#include <string>
#include <map>

#include <utility/vector1.hh>



namespace protocols {
namespace rna {

  ///////////////////////////////////////////////////////////////////////////////////
  class BasePairType{
  public:
    char aa1;
    char aa2;
    char edge1;
    char edge2;
    char orientation;

    BasePairType( char const aa1_in, char const aa2_in,
                  char const edge1_in, char const edge2_in,
                  char const orientation_in){
      aa1 = aa1_in;   aa2 = aa2_in;
      edge1 = edge1_in;   edge2 = edge2_in;
      orientation = orientation_in;
    }

    friend
    bool operator < (BasePairType const & lhs, BasePairType const & rhs )
    {
      //There must be a more elegant way to do this...
      if( lhs.aa1 < rhs.aa1 ) {
        return true;
      } else if ( lhs.aa1 == rhs.aa1 ) {
        if ( lhs.aa2 < rhs.aa2 ) {
          return true;
        } else if ( lhs.aa2 == rhs.aa2 ) {
          if ( lhs.edge1 < rhs.edge1 ) {
            return true;
          } else if ( lhs.edge1 == rhs.edge1 ) {
            if ( lhs.edge2 < rhs.edge2 ) {
              return true;
            } else {
              if ( lhs.edge2 == rhs.edge2) {
                return ( lhs.orientation < rhs.orientation);
              }
            }
          }
        }
      }
      return false;
    }

  };

  ///////////////////////////////////////////////////////////////////////////////////
  class RNA_PairingTemplate : public utility::pointer::ReferenceCount {

  public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~RNA_PairingTemplate();

    RNA_PairingTemplate( core::kinematics::Jump const j, std::string const atom_name1, std::string const atom_name2 );

    RNA_PairingTemplate( core::kinematics::Jump const j1, core::kinematics::Jump const j2, std::string const atom_name1, std::string const atom_name2 );

    core::kinematics::Jump const &
    jump() const { return jump_forward_; }

    core::kinematics::Jump const &
    jump_forward() const { return jump_forward_; }

    core::kinematics::Jump const &
    jump_backward() const { return jump_backward_; }

    std::string const &
    atom_name1() const {return atom_name1_; }

    std::string const &
    atom_name2() const {return atom_name2_; }

  private:
    core::kinematics::Jump const jump_forward_;
    core::kinematics::Jump const jump_backward_;
    std::string const atom_name1_;
    std::string const atom_name2_;
  };

  typedef utility::pointer::owning_ptr< RNA_PairingTemplate > RNA_PairingTemplateOP;

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

  typedef utility::vector1< RNA_PairingTemplateOP > RNA_PairingTemplateList;
  typedef std::map< BasePairType, RNA_PairingTemplateList > RNA_PairingTemplateMap;

  ///////////////////////////////////////////////////////////////////////////////////
  class RNA_JumpLibrary : public utility::pointer::ReferenceCount {
  public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~RNA_JumpLibrary();
    RNA_JumpLibrary( std::string const filename ){ read_jumps_from_file( filename ); };

    void
    read_jumps_from_file( std::string const & jump_library_filename );

    void
    check_forward_backward(
                           std::string & atom_name,
                           bool const forward,
                           core::kinematics::Jump & j,
                           RNA_PairingTemplateOP const & t) const;

    core::kinematics::Jump
    get_random_base_pair_jump(
                              char const aa1,
                              char const aa2,
                              char const edge1,
                              char const edge2,
                              char const orientation,
                              std::string & atom_name1,
                              std::string & atom_name2,
                              bool & success,
                              bool const forward1 = true,
                              bool const forward2 = true ) const;

  private:

    void
    save_in_jump_library( core::Size const reschar1, core::Size const reschar2,
                          char const edgechar1, char const edgechar2,
                          char const orientation,
                          std::string const & atom_name1,
                          std::string const & atom_name2,
                          core::kinematics::Jump const & jump1,
                          core::kinematics::Jump const & jump2 );


    RNA_PairingTemplateMap rna_pairing_template_map_;

  };

  typedef utility::pointer::owning_ptr< RNA_JumpLibrary > RNA_JumpLibraryOP;

} //rna
} //protocols

#endif