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core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential Class Reference

#include <RNA_ChemicalShiftPotential.hh>

Inheritance diagram for core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential:
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Public Member Functions

 RNA_ChemicalShiftPotential ()
 c-tor More...
 
Size get_total_exp_chemical_shift_data_points () const
 
void finalize_total_energy (pose::Pose const &pose, EnergyMap &totals) const
 
void load_larmord_parameters (std::string const &filename)
 
void load_larmord_weights (std::string const &filename)
 
void load_larmord_reference_shifts (std::string const &filename)
 
void load_larmord_neighbor_atoms (std::string const &filename)
 
bool get_neighbor_atom (std::string const &key) const
 
Real get_accuracy_weight (std::string const &key) const
 
Real get_reference_shift (std::string const &key) const
 
Real get_alpha (std::string const &key) 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
 LarmorD Derivative. More...
 
void indicate_required_context_graphs (utility::vector1< bool > &) const
 

Private Member Functions

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 const &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_nuchemics (ChemicalShiftData const &CS_data, pose::Pose const &pose) const
 
core::Real get_calc_chem_shift_value_larmord (ChemicalShiftData const &CS_data, pose::Pose const &pose) 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 (id::AtomID const &atom_id, ChemicalShiftData const &CS_data, pose::Pose const &pose, Vector &f1, Vector &f2, utility::vector1< std::string > atom_names, std::string atom_name_in, std::string atom_name_whitespace_in, bool is_source_atom, bool is_neighbor_atom) 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
 

Private Attributes

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_
 
bool nuchemics_mode_
 
bool cs_verbose_mode_
 
utility::vector1
< utility::vector1
< ChemicalShiftData > > 
EXP_chem_shift_data_list_
 
core::Size total_exp_chemical_shift_data_points_
 
std::map< std::string, Realreference_shifts_
 
std::map< std::string, Realalphas_
 
std::map< std::string, Realaccuracy_weights_
 
std::map< std::string, boolneighbor_atoms_
 
std::string path_to_parameter_files_
 
Real larmord_distance_cutoff_
 
Real larmord_beta_
 

Constructor & Destructor Documentation

core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::RNA_ChemicalShiftPotential ( )

Member Function Documentation

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::assert_is_calc_chem_shift_atom ( ChemicalShiftData const &  CS_data) const
private
bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data ( core::conformation::Residue const &  rsd,
Size const  atomno 
) const
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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 core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy ( pose::Pose const &  pose,
EnergyMap totals 
) const
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_accuracy_weight ( std::string const &  key) const
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_alpha ( std::string const &  key) const
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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
private
core::Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value ( ChemicalShiftData const &  CS_data,
pose::Pose const &  pose 
) const
private
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord ( ChemicalShiftData const &  CS_data,
pose::Pose const &  pose 
) const
private
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics ( ChemicalShiftData const &  CS_data,
pose::Pose const &  pose 
) const
private
core::Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_chemical_shift_energy ( utility::vector1< utility::vector1< Real > > const &  calc_chem_shift_list) const
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift ( id::AtomID const &  atom_id,
ChemicalShiftData const &  CS_data,
pose::Pose const &  pose,
Vector f1,
Vector f2,
utility::vector1< std::string >  atom_names,
std::string  atom_name_in,
std::string  atom_name_whitespace_in,
bool  is_source_atom,
bool  is_neighbor_atom 
) const
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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
private

Derivative of the specified CS_data atom (non-polar proton). Both ring current and magnetic_anisotropy effects. This function should be called once for each CS_data atom!

References core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::accuracy_weight, core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), core::scoring::rna::chemical_shift::dround(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomname(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size(), get_best_exp_to_calc_chem_shift_mapping(), get_calc_chem_shift_value_nuchemics(), core::scoring::rna::chemical_shift::get_delta_magnetic_anisotropy_deriv(), get_matching_CS_data_entry(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), include_magnetic_anisotropy_effect_, include_ring_current_effect_, core::scoring::rna::chemical_shift::maca, nuchemics_mode_, core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::num_rings(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::scoring::rna::chemical_shift::ChemicalShiftData::realatomdata_index, core::scoring::rna::chemical_shift::remove_whitespaces(), core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, core::pose::Pose::residue(), rna_cs_params_, core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, core::conformation::Residue::seqpos(), core::pose::Pose::size(), core::scoring::rna::chemical_shift::suga, core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by eval_atom_derivative().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base ( pose::Pose const &  pose,
conformation::Residue const &  ma_source_rsd,
Size const  chi1_torsion_atomno,
Vector f1,
Vector f2 
) const
private

Derivative due to the manisotropy effect of the source base. Include contribution from all CS_data atoms (non-polar protons). This function should be called once for each residue only at the chi1_torsion_atomno.

References core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::accuracy_weight, core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), core::scoring::rna::chemical_shift::dround(), EXP_chem_shift_data_list_, core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomname(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size(), get_best_exp_to_calc_chem_shift_mapping(), get_calc_chem_shift_value_nuchemics(), core::scoring::rna::chemical_shift::get_delta_magnetic_anisotropy_deriv(), core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), include_magnetic_anisotropy_effect_, core::scoring::rna::chemical_shift::maca, core::chemical::name_from_aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::realatomdata_index, core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, core::pose::Pose::residue(), rna_cs_params_, core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, core::conformation::Residue::seqpos(), core::scoring::rna::chemical_shift::suga, core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by eval_atom_derivative().

utility::vector1< ChemicalShiftData > const & core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_matching_CS_data_entry ( Size const  seq_num,
std::string const &  in_atom_name 
) const
private
bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_neighbor_atom ( std::string const &  key) const
Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_realatomdata_index ( std::string const &  in_atom_name,
chemical::AA const  res_aa 
) const
private
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_reference_shift ( std::string const &  key) const
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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
private
Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points ( ) const
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data ( std::string const &  exp_CS_data_filename,
utility::vector1< core::Size > &  include_res_list,
utility::vector1< utility::vector1< std::string > > const &  proton_entry_list 
)
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::indicate_required_context_graphs ( utility::vector1< bool > &  ) const
inline
bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom ( core::conformation::Residue const &  rsd,
Size const  atomno 
) const
private
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms ( std::string const &  filename)
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters ( std::string const &  filename)
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_reference_shifts ( std::string const &  filename)
void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_weights ( std::string const &  filename)
utility::vector1< std::string > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::string_list ( std::string const &  string_one) const
private
utility::vector1< std::string > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::string_list ( std::string const &  string_one,
std::string const &  string_two 
) const
private

References string_list().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::update_calc_chem_shift_list ( pose::Pose const &  pose,
utility::vector1< utility::vector1< Real > > &  cal_chem_shift_list 
) const
private

Member Data Documentation

std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::accuracy_weights_
private
std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::alphas_
private
bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::cs_verbose_mode_
private
utility::vector1< utility::vector1 < ChemicalShiftData > > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::EXP_chem_shift_data_list_
private
std::string core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::H5_prime_mode_
private
bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::include_magnetic_anisotropy_effect_
private
bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::include_ring_current_effect_
private
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::larmord_beta_
private
Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::larmord_distance_cutoff_
private
std::map< std::string, bool > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::neighbor_atoms_
private
bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::nuchemics_mode_
private
std::string core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::path_to_parameter_files_
private
std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::reference_shifts_
private
RNA_CS_parameters const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::rna_cs_params_
private
core::Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::total_exp_chemical_shift_data_points_
private
bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::verbose_
private

The documentation for this class was generated from the following files: