RNA_ChemicalShiftPotential.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   core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh
/// @brief  The real workhorse behind RNA_ChemicalShiftEnergy.cc
/// @author Parin Sripakdeevong (sripakpa@stanford.edu)


#ifndef INCLUDED_core_scoring_rna_chemical_shift_RNA_ChemicalShiftPotential_HH
#define INCLUDED_core_scoring_rna_chemical_shift_RNA_ChemicalShiftPotential_HH



// Project headers
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <numeric/xyzVector.hh>

#include <utility/pointer/ReferenceCount.hh>
///////////////////////////////////
#include <core/chemical/AA.hh>
#include <core/scoring/rna/chemical_shift/RNA_CS_Parameters.hh>

#include <core/scoring/EnergyMap.fwd.hh>

// Utility headers


namespace core {
namespace scoring {
namespace rna {
namespace chemical_shift {


/////////////////////////////////////////////////////////////////////////////
class ChemicalShiftData : public utility::pointer::ReferenceCount{

  public:

    ChemicalShiftData(core::Size const in_seq_num, 
                     chemical::AA const in_res_aa,
                     std::string const in_atom_name, 
                     core::Size const in_realatomdata_index,
                     core::Real const in_exp_shift, 
                     std::string const in_data_line):
      seq_num( in_seq_num ),
      res_aa( in_res_aa ),
      atom_name( in_atom_name ),
      realatomdata_index( in_realatomdata_index ),
      exp_shift( in_exp_shift ), 
      //Feb 28, 2012: Warning exp_shift this might be switch due to ambiguity of geminal atoms (H5'/H5'' and etcs) or be a duplicate.
      //Always use get_best_exp_to_calc_chem_shift_mapping() to get best mapping to specific calc_chem_shift to get actual exp_shift!
      data_line( in_data_line)
    {
    }

    ~ChemicalShiftData(){};

  public:

    core::Size seq_num;
    chemical::AA res_aa;
    std::string atom_name;
    core::Size realatomdata_index; //For accessing  realatomdata in RNA_CS_Parameters 
    core::Real exp_shift;
    std::string data_line;

};


class RNA_ChemicalShiftPotential : public utility::pointer::ReferenceCount{

  public:

    RNA_ChemicalShiftPotential();

    Size
    get_total_exp_chemical_shift_data_points() const;
    

  private:

    Size
    get_realatomdata_index(std::string const & in_atom_name, chemical::AA const res_aa) const;

    void
    assert_is_calc_chem_shift_atom(ChemicalShiftData const & CS_data) const;

    bool
    Is_magnetic_anisotropy_source_atom(core::conformation::Residue const & rsd, Size const atomno) const;

    bool
    atom_has_exp_chemical_shift_data(core::conformation::Residue const & rsd, Size const atomno) const;

    utility::vector1 < ChemicalShiftData > const & 
    get_matching_CS_data_entry(Size const seq_num, std::string const in_atom_name) const;

    utility::vector1< std::string > 
    string_list(std::string const string_one) const;

    utility::vector1< std::string > 
    string_list(std::string const string_one, std::string const string_two) const;

    

    void
    import_exp_chemical_shift_data(std::string exp_CS_data_filename, 
                                 utility::vector1 < core::Size > include_res_list,
                                 utility::vector1 < utility::vector1< std::string > > const & proton_entry_list);

    void
    get_best_exp_to_calc_chem_shift_mapping(utility::vector1 < ChemicalShiftData > const & EXP_chem_shift_data_entry, 
                                          utility::vector1 < Real > const & calc_chem_shift_entry, 
                                          utility::vector1 < Real > & actual_exp_chem_shift_entry,
                                          utility::vector1 < bool > & do_include_CS_data) const; 

    core::Real
    get_calc_chem_shift_value(ChemicalShiftData const & CS_data, pose::Pose const & pose) const;

    void
    update_calc_chem_shift_list(pose::Pose const & pose, utility::vector1 < utility::vector1 < Real > > & cal_chem_shift_list) const;

    core::Real
    get_chemical_shift_energy(utility::vector1 < utility::vector1 < Real > > const & calc_chem_shift_list) const;

    void
    get_deriv_for_chemical_shift_data_atom( pose::Pose const & pose,
                                          conformation::Residue const & CS_data_rsd,
                                          Size const CS_data_atomno,
                                          Vector & f1,
                                          Vector & f2) const;

    void
    get_ring_current_deriv_for_src_base(  pose::Pose const & pose,
                                        conformation::Residue const & rc_source_rsd,
                                        Size const chi1_torsion_atomnno,
                                        Vector & f1,
                                        Vector & f2) const;

    void
    get_magnetic_anisotropy_deriv_for_src_base( pose::Pose const & pose,
                                              conformation::Residue const & ma_source_rsd,
                                              Size const chi1_torsion_atomnno,
                                              Vector & f1,
                                              Vector & f2) const;

    void
    get_magnetic_anisotropy_deriv_for_src_atom( pose::Pose const & pose,
                                              conformation::Residue const & ma_source_rsd,
                                              Size const ma_source_atomno,
                                              Vector & f1,
                                              Vector & f2) const; 




  public:

  /////////////////////////////////////////////////////////////////////////////
  // scoring
  /////////////////////////////////////////////////////////////////////////////

    void
    finalize_total_energy( pose::Pose const & pose, EnergyMap & totals) const;

    /////////////////////////////////
    void
    eval_atom_derivative(
      id::AtomID const & atom_id,
      pose::Pose const & pose,
      kinematics::DomainMap const & domain_map,
      EnergyMap const & weights,
      Vector & F1,
      Vector & F2 ) const;

    void
    indicate_required_context_graphs(
      utility::vector1< bool > & /*context_graphs_required*/
    ) const {}

  private:

    RNA_CS_parameters const rna_cs_params_;
    std::string H5_prime_mode_;
    bool const verbose_;
    bool const include_ring_current_effect_;
    bool const include_magnetic_anisotropy_effect_;
    utility::vector1 < utility::vector1 < ChemicalShiftData > > EXP_chem_shift_data_list_;
    core::Size total_exp_chemical_shift_data_points_;


};


} // chemical_shift
} // rna
} // scoring
} // core

#endif // INCLUDED_core_scoring_methods_RG_Energy_RNA_HH