CarbonHBondPotential.hh

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// 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
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/// @file   core/scoring/carbon_hbonds/CarbonHBondPotential.hh
/// @brief  Statistically derived rotamer pair potential class declaration
/// @author Phil Bradley


#ifndef INCLUDED_core_scoring_carbon_hbonds_CarbonHBondPotential_hh
#define INCLUDED_core_scoring_carbon_hbonds_CarbonHBondPotential_hh

// Unit Headers
#include <core/scoring/carbon_hbonds/CarbonHBondPotential.fwd.hh>

// Package headers

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

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

#include <ObjexxFCL/FArray1D.hh>
// AUTO-REMOVED #include <ObjexxFCL/FArray2D.hh>

// AUTO-REMOVED #include <map>

#include <utility/vector1_bool.hh>



namespace core {
namespace scoring {
namespace carbon_hbonds {

class CarbonHBondPotential : public utility::pointer::ReferenceCount {

public:

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

  /// @brief Calculate chbond energies for non-rna atom pairs.
  Real get_potential(
    Size const & atom_type,
    Vector const & H_A_vector, //vector of hydrogen to acceptor
    Vector const & D_H_vector, //vector of donor hv atom to hydrogen
    Vector const & B_A_vector, //vector of acceptor's base atom to acceptor
    bool calculate_deriv, // early exit if this is false
    Vector & deriv_vector
  ) const;

  /// @brief Calculate the rna-specific chbond energies.  The derivative vector returned is the
  /// force vector on the acceptor atom.  Multiply by -1 to get the force vector on the donor atom
  Real
  get_potential_RNA(
    Vector const & r_H_A,
    Vector const & z_i /*unit vector pointing from donor to its connected hydrogen*/,
    bool const & update_deriv,
    Vector & deriv
  ) const;

  ///@brief second declaration to allow skipping deriv; gcc 4.1.3 does not like setting default parameters for a pass-by-reference parameter
  Real get_potential(
    Size const & atom_type,
    Vector const & H_A_vector, //vector of hydrogen to acceptor
    Vector const & D_H_vector, //vector of donor hv atom to hydrogen
    Vector const & B_A_vector  //vector of acceptor's base atom to acceptor
  ) const;

  Real max_dis() const {
    return max_dist_;
  }

private: //data

  void
  read_potential();

  //Which atoms to loop over during VDW check?
  Real bin_width_;
  Real max_dist_;
  Real const aroC_scale_factor_;

  Size const num_carbon_donor_atoms_;
  Size const num_bins_;
  utility::vector1<  ObjexxFCL::FArray1D <Real>  > carbon_hbond_parameter_;
  //  ObjexxFCL::FArray2D < Real > carbon_hbond_deriv_ /*(5, 45)*/;

  utility::vector1< std::string > carbon_donors_;
  ObjexxFCL::FArray1D < Size > standard_atomtype_to_carbon_donor_index_;

  Real const rna_cos_theta_cutoff_;
  Real const rna_cos_theta_fade_zone_;
  Real const rna_ch_o_bond_distance_;

  };

}
}
}

#endif // INCLUDED_core_scoring_ScoreFunction_HH