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

#include <RNA_ChemicalShiftPotential.hh>

Inheritance diagram for core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential:

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, Real >	reference_shifts_
std::map< std::string, Real >	alphas_
std::map< std::string, Real >	accuracy_weights_
std::map< std::string, bool >	neighbor_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

(

)

c-tor

References cs_verbose_mode_, H5_prime_mode_, import_exp_chemical_shift_data(), include_magnetic_anisotropy_effect_, include_ring_current_effect_, larmord_beta_, larmord_distance_cutoff_, load_larmord_neighbor_atoms(), load_larmord_parameters(), load_larmord_reference_shifts(), load_larmord_weights(), nuchemics_mode_, path_to_parameter_files_, string_list(), and core::scoring::TR().

Member Function Documentation

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::assert_is_calc_chem_shift_atom ( ChemicalShiftData const &  CS_data ) const

private

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::scoring::rna::chemical_shift::csca, core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, nuchemics_mode_, core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::scoring::rna::chemical_shift::ChemicalShiftData::realatomdata_index, core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, and rna_cs_params_.

Referenced by import_exp_chemical_shift_data().

bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data ( core::conformation::Residue const &  rsd, Size const  atomno  ) const

private

References core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), EXP_chem_shift_data_list_, core::scoring::rna::chemical_shift::remove_whitespaces(), core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, and core::conformation::Residue::seqpos().

Referenced by eval_atom_derivative().

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

LarmorD Derivative.

References atom_has_exp_chemical_shift_data(), core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::chemical::rna::chi1_torsion_atom_index(), EXP_chem_shift_data_list_, get_deriv_for_chemical_shift(), get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_neighbor_atom(), get_ring_current_deriv_for_src_base(), core::chemical::name_from_aa(), core::conformation::Residue::natoms(), nuchemics_mode_, core::scoring::rna::chemical_shift::remove_whitespaces(), core::pose::Pose::residue(), core::scoring::rna_chem_shift, core::id::AtomID::rsd(), core::pose::Pose::size(), and core::scoring::TR().

Referenced by core::energy_methods::RNA_ChemicalShiftEnergy::eval_atom_derivative().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy	(	pose::Pose const &	pose,
		EnergyMap &	totals
	)		const

References get_chemical_shift_energy(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::scoring::rna_chem_shift, core::pose::Pose::size(), and update_calc_chem_shift_list().

Referenced by core::energy_methods::RNA_ChemicalShiftEnergy::finalize_total_energy().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_accuracy_weight

(

std::string const &

key

)

const

References accuracy_weights_.

Referenced by import_exp_chemical_shift_data().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_alpha

(

std::string const &

key

)

const

References alphas_.

Referenced by get_calc_chem_shift_value_larmord(), and get_deriv_for_chemical_shift().

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

References core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::scoring::rna::chemical_shift::ChemicalShiftData::exp_shift, H5_prime_mode_, core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, and core::scoring::TR().

Referenced by get_chemical_shift_energy(), get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_ring_current_deriv_for_src_base(), and import_exp_chemical_shift_data().

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

References core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::accuracy_weight, core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), cs_verbose_mode_, core::scoring::rna::chemical_shift::ChemicalShiftData::exp_shift, get_alpha(), get_neighbor_atom(), larmord_beta_, larmord_distance_cutoff_, core::chemical::name_from_aa(), core::conformation::Residue::natoms(), core::scoring::rna::chemical_shift::ChemicalShiftData::ref_shift, core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, core::pose::Pose::residue(), core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by update_calc_chem_shift_list().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics ( ChemicalShiftData const &  CS_data, pose::Pose const &  pose  ) const

private

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, cs_verbose_mode_, core::scoring::rna::chemical_shift::dround(), core::scoring::rna::chemical_shift::ChemicalShiftData::exp_shift, 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::magnetic_anisotropy_effect(), core::chemical::name_from_aa(), core::scoring::rna::chemical_shift::oshi, 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(), core::scoring::rna::chemical_shift::ring_current_effect(), rna_cs_params_, core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, core::pose::Pose::size(), core::scoring::rna::chemical_shift::suga, core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_ring_current_deriv_for_src_base(), and update_calc_chem_shift_list().

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

References EXP_chem_shift_data_list_, and get_best_exp_to_calc_chem_shift_mapping().

Referenced by finalize_total_energy().

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

References core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::accuracy_weight, core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, cs_verbose_mode_, core::scoring::rna::chemical_shift::ChemicalShiftData::exp_shift, get_alpha(), larmord_beta_, larmord_distance_cutoff_, core::chemical::name_from_aa(), core::conformation::Residue::natoms(), core::scoring::rna::chemical_shift::ChemicalShiftData::ref_shift, core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by eval_atom_derivative().

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

Derivative at the magnetic_anisotropy_src_atom (right how only base heavy-atoms) due to the magnetic_anistropy_effect. Include contribution from all CS_data atoms (non-polar protons).

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_, 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_realatomdata_index(), 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().

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

References core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, EXP_chem_shift_data_list_, core::scoring::rna::chemical_shift::remove_whitespaces(), and core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num.

Referenced by get_deriv_for_chemical_shift_data_atom().

bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_neighbor_atom

(

std::string const &

key

)

const

References neighbor_atoms_.

Referenced by eval_atom_derivative(), and get_calc_chem_shift_value_larmord().

Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_realatomdata_index ( std::string const &  in_atom_name, chemical::AA const  res_aa  ) const

private

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size(), core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), core::scoring::rna::chemical_shift::remove_whitespaces(), and rna_cs_params_.

Referenced by get_magnetic_anisotropy_deriv_for_src_atom(), import_exp_chemical_shift_data(), and Is_magnetic_anisotropy_source_atom().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_reference_shift

(

std::string const &

key

)

const

References reference_shifts_.

Referenced by import_exp_chemical_shift_data().

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

Derivative due to the ring_current effect of the source base. Include contribution from all CS_data atoms (non-polar protons). Note, there are 1 or 2 ring centers per base. This function should be called once for each residue only at the first_base_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_, get_best_exp_to_calc_chem_shift_mapping(), get_calc_chem_shift_value_nuchemics(), core::scoring::rna::chemical_shift::get_ring_current_deriv(), core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), include_ring_current_effect_, core::chemical::name_from_aa(), nuchemics_mode_, core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::num_rings(), 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().

Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points

(

)

const

References total_exp_chemical_shift_data_points_.

Referenced by protocols::rna::denovo::RNA_DeNovoProtocol::add_chem_shift_info(), and protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::add_chem_shift_info().

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

References assert_is_calc_chem_shift_atom(), EXP_chem_shift_data_list_, core::scoring::rna::chemical_shift::filter_chem_shift_data_list(), get_accuracy_weight(), get_best_exp_to_calc_chem_shift_mapping(), get_realatomdata_index(), get_reference_shift(), core::scoring::rna::chemical_shift::get_res_aa_from_BASE_name(), core::scoring::rna::chemical_shift::get_rosetta_hatom_name(), core::scoring::rna::chemical_shift::is_polar_hydrogen(), core::chemical::name_from_aa(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::scoring::rna::chemical_shift::remove_whitespaces(), core::scoring::rna::chemical_shift::string_to_int(), core::scoring::rna::chemical_shift::string_to_real(), total_exp_chemical_shift_data_points_, core::scoring::TR(), and verbose_.

Referenced by RNA_ChemicalShiftPotential().

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

References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), core::scoring::rna::chemical_shift::dround(), get_realatomdata_index(), core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(), core::scoring::rna::chemical_shift::maca, core::scoring::rna::chemical_shift::remove_whitespaces(), and rna_cs_params_.

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms

(

std::string const &

filename

)

References core::scoring::rna::chemical_shift::add_whitespaces(), neighbor_atoms_, and core::scoring::rna::chemical_shift::remove_whitespaces().

Referenced by RNA_ChemicalShiftPotential().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters

(

std::string const &

filename

)

References core::scoring::rna::chemical_shift::add_whitespaces(), alphas_, and core::scoring::rna::chemical_shift::remove_whitespaces().

Referenced by RNA_ChemicalShiftPotential().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_reference_shifts

(

std::string const &

filename

)

References reference_shifts_, and core::scoring::rna::chemical_shift::remove_whitespaces().

Referenced by RNA_ChemicalShiftPotential().

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_weights

(

std::string const &

filename

)

References accuracy_weights_, and core::scoring::rna::chemical_shift::remove_whitespaces().

Referenced by RNA_ChemicalShiftPotential().

utility::vector1< std::string > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::string_list ( std::string const &  string_one ) const

private

Referenced by RNA_ChemicalShiftPotential(), and string_list().

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

References core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, EXP_chem_shift_data_list_, get_calc_chem_shift_value_larmord(), get_calc_chem_shift_value_nuchemics(), and nuchemics_mode_.

Referenced by finalize_total_energy().

Member Data Documentation

std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::accuracy_weights_

private

Referenced by get_accuracy_weight(), and load_larmord_weights().

std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::alphas_

private

Referenced by get_alpha(), and load_larmord_parameters().

bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::cs_verbose_mode_

private

Referenced by get_calc_chem_shift_value_larmord(), get_calc_chem_shift_value_nuchemics(), get_deriv_for_chemical_shift(), and RNA_ChemicalShiftPotential().

utility::vector1< utility::vector1 < ChemicalShiftData > > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::EXP_chem_shift_data_list_

private

Referenced by atom_has_exp_chemical_shift_data(), eval_atom_derivative(), get_chemical_shift_energy(), get_magnetic_anisotropy_deriv_for_src_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_matching_CS_data_entry(), get_ring_current_deriv_for_src_base(), import_exp_chemical_shift_data(), and update_calc_chem_shift_list().

std::string core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::H5_prime_mode_

private

Referenced by get_best_exp_to_calc_chem_shift_mapping(), and RNA_ChemicalShiftPotential().

bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::include_magnetic_anisotropy_effect_

private

Referenced by get_calc_chem_shift_value_nuchemics(), get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_atom(), get_magnetic_anisotropy_deriv_for_src_base(), and RNA_ChemicalShiftPotential().

bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::include_ring_current_effect_

private

Referenced by get_calc_chem_shift_value_nuchemics(), get_deriv_for_chemical_shift_data_atom(), get_ring_current_deriv_for_src_base(), and RNA_ChemicalShiftPotential().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::larmord_beta_

private

Referenced by get_calc_chem_shift_value_larmord(), get_deriv_for_chemical_shift(), and RNA_ChemicalShiftPotential().

Real core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::larmord_distance_cutoff_

private

Referenced by get_calc_chem_shift_value_larmord(), get_deriv_for_chemical_shift(), and RNA_ChemicalShiftPotential().

std::map< std::string, bool > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::neighbor_atoms_

private

Referenced by get_neighbor_atom(), and load_larmord_neighbor_atoms().

bool core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::nuchemics_mode_

private

Referenced by assert_is_calc_chem_shift_atom(), eval_atom_derivative(), get_deriv_for_chemical_shift_data_atom(), get_ring_current_deriv_for_src_base(), RNA_ChemicalShiftPotential(), and update_calc_chem_shift_list().

std::string core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::path_to_parameter_files_

private

Referenced by RNA_ChemicalShiftPotential().

std::map< std::string, Real > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::reference_shifts_

private

Referenced by get_reference_shift(), and load_larmord_reference_shifts().

RNA_CS_parameters const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::rna_cs_params_

private

Referenced by assert_is_calc_chem_shift_atom(), get_calc_chem_shift_value_nuchemics(), get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_realatomdata_index(), get_ring_current_deriv_for_src_base(), and Is_magnetic_anisotropy_source_atom().

core::Size core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::total_exp_chemical_shift_data_points_

private

Referenced by get_total_exp_chemical_shift_data_points(), and import_exp_chemical_shift_data().

bool const core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::verbose_

private

Referenced by import_exp_chemical_shift_data().

---

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

• src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh
• src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc