RNA_ResidueType.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:
//
// (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.
//////////////////////////////////////////////////////////////////////
/// @begin RNA_residueType
///
/// @brief
/// RNA specific properties
///
/// @author Parin Sripakdeevong (sripakpa@stanford.edu)
////////////////////////////////////////////////////////////////////////



#ifndef INCLUDED_core_chemical_rna_RNA_ResidueType_hh
#define INCLUDED_core_chemical_rna_RNA_ResidueType_hh


// Package headers
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/rna/RNA_ResidueType.fwd.hh>

// Numeric headers

// Utility headers
#include <utility/pointer/ReferenceCount.hh>

// C++ headers
#include <utility/vector1.hh>


namespace core {
namespace chemical {
namespace rna {


/////////////////////////////////////Parin S, Dec 23, 2011: RNA stuff//////////////////////////////////////////
class RNA_ResidueType : public utility::pointer::ReferenceCount {


  public:

  RNA_ResidueType();

  virtual ~RNA_ResidueType();

  ///////////////////////////Implemented for fast lookup! Parin Sripakdeevong, June 25th, 2011//////////////////
  private:

  void
  rna_note_chi_controls_atom( core::Size const chi, core::Size const atomno, utility::vector1< core::Size > & last_controlling_chi);


  public:

  void
  update_derived_rna_data(ResidueTypeCOP const residue_type_in);

  void
  rna_update_last_controlling_chi(ResidueTypeCOP const residue_type_in,
                                utility::vector1< core::Size > & last_controlling_chi,
                                utility::vector1< AtomIndices >  &  atoms_last_controlled_by_chi);
  
  ////////////Fast lookup functions///////

  utility::vector1< bool > const &
  Is_virtual_atom_list() const;

  bool
  atom_is_virtual( Size const atomno ) const;

  utility::vector1< bool > const &
  Is_phosphate_atom_list() const;

  /// @brief quick lookup: is the atom with the given index is part of the RNA phosphate or not?
  bool
  atom_is_phosphate( Size const atomno ) const;

  utility::vector1< bool > const &
  Is_RNA_base_atom_list() const;

  bool
  is_RNA_base_atom( Size const atomno ) const;

  AtomIndices const &
  RNA_base_atoms() const;

  Size
  ho2star_index() const;

  Size
  o2star_index() const;

  Size
  p_atom_index() const;

  Size
  o1p_atom_index() const;

  Size
  o2p_atom_index() const;

  Size
  o5star_atom_index() const;

  Size
  o3star_atom_index() const;

  Size
  o4star_atom_index() const;

  Size
  c1star_atom_index() const;

  Size
  c2star_atom_index() const;

  Size
  c4star_atom_index() const;

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

  public:

  //o2star atom
  core::Size o2star_index_;
  core::Size ho2star_index_;

  //Phosphate atoms
  core::Size p_atom_index_;
  core::Size o1p_atom_index_;
  core::Size o2p_atom_index_;
  core::Size o5star_index_;
  core::Size o3star_index_;

  //Ribose atoms
  core::Size o4star_index_;
  core::Size c1star_index_;
  core::Size c2star_index_;
  core::Size c4star_index_;

  AtomIndices base_atom_list_;

  utility::vector1< bool > Is_RNA_base_atom_list_;
  utility::vector1< bool > Is_phosphate_atom_list_;
  //For fast look whether atom is VIRTUAL type.
  utility::vector1< bool > Is_virtual_atom_list_;
  //AtomIndices base_heavy_atoms_;
  //AtomIndices base_hydrogen_atoms_;
  
  ResidueTypeCOP residue_type_; //Pointer to the main ResidueType object that this RNA_ResidueType object belongs to.

}; //RNA_ResidueType



} // rna
} // chemical
} // core

#endif // INCLUDED_core_chemical_rna_RNA_ResidueType_hh