DirectReadoutPotential.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/scoring/methods/DirectReadoutPotential.hh
/// @brief  1st pass implementation of Kono + Sarai's protein-DNA interaction potential
/// @details  Needs polishing, converting to mini standards in some respects, but still in trial stage.
/// @author Amy Ticoll


#ifndef INCLUDED_core_scoring_dna_DirectReadoutPotential_hh
#define INCLUDED_core_scoring_dna_DirectReadoutPotential_hh

// Unit Headers
#include <core/scoring/dna/DirectReadoutPotential.fwd.hh>

// Package headers

// Project headers
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>

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

#include <string>

namespace core {
namespace scoring {
namespace dna {

/// @brief  1st pass implementation of Kono + Sarai's protein-DNA interaction potential
/// @details  Needs polishing, converting to mini standards in some respects, but still in trial stage.

class DirectReadoutPotential : public utility::pointer::ReferenceCount {

public:
  typedef std::string string;

public:

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

  // get score method
  Real rsd_rsd_energy(conformation::Residue const & rsd1,conformation::Residue const & rsd2) const;

private:
  Real score[9][9][4][20][4];
  int num_pairs[4][20];
  //  int pair_base[80];
  //  int pair_aa[80];
  //  int pair_num[80];

  string A_bins[9][9][4];
  string G_bins[9][9][4];
  string T_bins[9][9][4];
  string C_bins[9][9][4];

  int aas_at_grid;
  const Real wt;
  const Real RT;

  void fill_bins(string (&my_array)[9][9][4], char const base);
  void get_pairs();
  int get_xy_bin(Real coord) const;
  int get_z_bin(Real coord) const;

};

}
}
}

#endif