DNA_BasePotential.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.
// (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.

/// @file
/// @brief
/// @author

#ifndef INCLUDED_core_scoring_dna_DNA_BasePotential_hh
#define INCLUDED_core_scoring_dna_DNA_BasePotential_hh

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/kinematics/Stub.fwd.hh>
// AUTO-REMOVED #include <core/pose/Pose.fwd.hh>

#include <utility/vector1.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
// AUTO-REMOVED #include <numeric/xyzVector.hh>
#include <numeric/xyzMatrix.fwd.hh>

#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/FArray4D.hh>

namespace core {
namespace scoring {
namespace dna {


class DNA_BasePotential : public utility::pointer::ReferenceCount {
public:
  ///@brief Automatically generated virtual destructor for class deriving directly from ReferenceCount
  virtual ~DNA_BasePotential();
  typedef numeric::xyzMatrix< Real > Matrix;
  typedef utility::vector1< Real > Params;
  typedef conformation::Residue Residue;
  typedef ObjexxFCL::FArray3D< Real > FArray3D_Real;
  typedef ObjexxFCL::FArray4D< Real > FArray4D_Real;

public:
  /// ctor
  DNA_BasePotential();

  ///
  Real
  base_step_score(
    Residue const & rsd1,
    Residue const & rsd2
  ) const;

  ///
  Real
  base_pair_score(
    Residue const & rsd1,
    Residue const & rsd2
  ) const;

  ///
  void
  eval_base_step_derivative(
    Residue const & rsd1,
    Residue const & rsd2,
    Vector & F1,
    Vector & F2,
    Real const external_sign_factor // should probably be +1 or -1
  ) const;

  ///
  void
  eval_base_pair_derivative(
    Residue const & rsd1,
    Residue const & rsd2,
    Vector & F1,
    Vector & F2,
    Real const sign_factor // need to think about this, see logic in pose_dna
  ) const;

  void
  eval_base_pair_Z_scores(
    Residue const & rsd1,
    Residue const & rsd2,
    utility::vector1< Real > & z_scores
  ) const;

  void
  eval_base_step_Z_scores(
    Residue const & rsd1,
    Residue const & rsd2,
    utility::vector1< Real > & z_scores
  ) const;


private:

  enum InteractionType {
    BP_type = 1,
    BS_type
  };


  inline
  Real
  mean( InteractionType const & t, std::string const & bases, int const p ) const
  {
    int i1(0),i2(0);
    get_array_indices( t, bases, i1, i2 );
    return mean_( p, i1, i2 );
  }

  inline
  Real
  stddev( InteractionType const & t, std::string const & bases, int const p ) const
  {
    int i1(0),i2(0);
    get_array_indices( t, bases, i1, i2 );
    return stddev_( p, i1, i2 );
  }

  inline
  Real
  stiffness( InteractionType const & t, std::string const & bases, int const p1, int const p2 ) const
  {
    int i1(0),i2(0);
    get_array_indices( t, bases, i1, i2 );
    return stiffness_( p1, p2, i1, i2 );
  }

  /// "A","C","T","G"
  inline
  std::string
  base_string( Residue const & rsd ) const;

private:

  /// i1 = 1,2
  /// i2 = 1,16
  void
  get_array_indices( InteractionType const & t, std::string const & bases, int & i1, int & i2 ) const;

  ///
  void
  load_score_tables();

  ///
  void
  set_mean_and_stddev(
    InteractionType const & type,
    std::string const & bases,
    int const index,
    Real mean,
    Real stddev
  );

  ///
  void
  set_stiffness(
    InteractionType const & type,
    std::string const & bases,
    int const index1,
    int const index2,
    Real const val
  );

  ///
  Real
  base_score(
    InteractionType const & type,
    std::string const & bases,
    utility::vector1< Real > const & params
  ) const;

private:

  FArray3D_Real      mean_; //(    6, 2, 16 );
  FArray3D_Real    stddev_; //(    6, 2, 16 );
  FArray4D_Real stiffness_; //( 6, 6, 2, 16 );

};



} // namespace dna
} // scoring
} // core

#endif