#include <RNA_ChemicalShiftPotential.hh>

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	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 > &) 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 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

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_

utility::vector1 < utility::vector1 < ChemicalShiftData > >	EXP_chem_shift_data_list_

core::Size	total_exp_chemical_shift_data_points_

Constructor & Destructor Documentation

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

c-tor

References H5_prime_mode_, import_exp_chemical_shift_data(), include_magnetic_anisotropy_effect_, include_ring_current_effect_, basic::options::option, basic::options::OptionKeys::score::rna_chemical_shift_exp_data, basic::options::OptionKeys::score::rna_chemical_shift_H5_prime_mode, basic::options::OptionKeys::score::rna_chemical_shift_include_res, string_list(), core::scoring::TR, user, and utility_exit_with_message.

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::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, 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, rna_cs_params_, and utility_exit_with_message.

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, core::conformation::Residue::seqpos(), and utility_exit_with_message.

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

References atom_has_exp_chemical_shift_data(), core::id::AtomID::atomno(), core::chemical::rna::chi1_torsion_atom_index(), get_deriv_for_chemical_shift_data_atom(), get_magnetic_anisotropy_deriv_for_src_base(), get_ring_current_deriv_for_src_base(), core::chemical::name_from_aa(), core::pose::Pose::residue(), core::scoring::rna_chem_shift, and core::id::AtomID::rsd().

Referenced by core::scoring::rna::chemical_shift::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::total_residue(), and update_calc_chem_shift_list().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy::finalize_total_energy().

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 utility_exit_with_message.

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().

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

private

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_, get_best_exp_to_calc_chem_shift_mapping(), and utility_exit_with_message.

Referenced by finalize_total_energy().

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!

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).

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.

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(), core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, and utility_exit_with_message.

Referenced by get_deriv_for_chemical_shift_data_atom().

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(), rna_cs_params_, and utility_exit_with_message.

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

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::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::conformation::Residue::atom_name(), cross(), core::scoring::rna::chemical_shift::dround(), EXP_chem_shift_data_list_, get_best_exp_to_calc_chem_shift_mapping(), get_calc_chem_shift_value(), 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(), 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, 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_, and utility_exit_with_message.

void core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::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
	)

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

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_.

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 EXP_chem_shift_data_list_, get_calc_chem_shift_value(), core::io::serialization::size(), and utility_exit_with_message.

Referenced by finalize_total_energy().

Member Data Documentation

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(), 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(), 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(), get_deriv_for_chemical_shift_data_atom(), get_ring_current_deriv_for_src_base(), and RNA_ChemicalShiftPotential().

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(), 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:

symlinks/rosetta/src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.hh
symlinks/rosetta/src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation