RNA_AtomVDW.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.
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// (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   core/scoring/rna/RNA_AtomVDW.hh
/// @brief  Information on which atoms to use for computing clashes
/// @author Rhiju Das


#ifndef INCLUDED_core_scoring_rna_RNA_AtomVDW_hh
#define INCLUDED_core_scoring_rna_RNA_AtomVDW_hh

// Unit Headers
#include <core/scoring/rna/RNA_AtomVDW.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/AA.hh>

// Package headers

// Project headers
#include <core/types.hh>

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

// AUTO-REMOVED #include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray4D.hh>

#include <map>

#include <utility/vector1.fwd.hh>



namespace core {
namespace scoring {
namespace rna {


class RNA_AtomVDW : public utility::pointer::ReferenceCount {

public:

  /// @brief ctor, reads data file
  RNA_AtomVDW();

  ///
  utility::vector1 < std::string > const
  vdw_atom_list( char const which_nucleotide ) const;

  Real
  bump_parameter( Size const atom1, Size const atom2,
                  char const which_nucleotide1, char const which_nucleotide2 ) const;

private: //data

  //Which atoms to loop over during VDW check?
  typedef std::map< char, utility::vector1< std::string > >  AtomList;
  AtomList rna_vdw_atom_;

  //Radii for VDW calculations...
  // I originally had this as a crazy map,
  // but it was really slow... now its an FArray,
  // with a helper function to convert a,c,g,u to indices 1,2,3,4.
  ObjexxFCL::FArray4D <Real> rna_vdw_parameter_;


  };

}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH