core::scoring::rna::chemical_shift Namespace Reference

Classes
class	ChemicalShiftData
class	RNA_ChemicalShiftPotential
class	RNA_CS_parameters
class	RNA_CS_residue_parameters

Typedefs
typedef utility::pointer::shared_ptr < RNA_ChemicalShiftPotential >	RNA_ChemicalShiftPotentialOP
typedef utility::pointer::shared_ptr < RNA_ChemicalShiftPotential const >	RNA_ChemicalShiftPotentialCOP

Enumerations
enum	atomitem {   oshi = 1, xdir, ydir, zdir,   csca, suga, rcl1, rcl2,   rcl3, maca, maqx, maqw,   maqy, maqz, marx, mary,   marz, chco, chrg, last_atomdesc }

Functions
chemical::AA	get_res_aa_from_BASE_name (std::string const &BASE_name, std::string const &text_line)
std::string	remove_whitespaces (std::string const &in_atom_name)
std::string	add_whitespaces (std::string const &in_atom_name)
bool	is_polar_hydrogen (std::string const &input_atom_name)
std::string	get_rosetta_hatom_name (std::string const &input_atom_name, std::string const &text_line, utility::vector1< std::string > const &flat_proton_entry_list)
void	print_chemical_shift_data (std::string const &prestring, ChemicalShiftData const &CS_data, bool const print_data_line)
core::Size	string_to_int (std::string const &input_string)
core::Real	string_to_real (std::string const &input_string)
bool	Contain_seq_num (Size const &seq_num, utility::vector1< core::Size > const &residue_list)
utility::vector1 < ChemicalShiftData >	filter_chem_shift_data_list (utility::vector1< ChemicalShiftData > const &flat_EXP_chem_shift_data_list, core::Size const seq_num, utility::vector1< std::string > const &proton_entry)
Real	delta_magnetic_anisotropy (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, numeric::xyzVector< core::Real > const &source_atom_xyz, numeric::xyzMatrix< core::Real > const &base_coordinate_matrix, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const realatomdata_index)
	The magnetic_anisotropy contribution of heavy-base atom at src_xyz to the chemqical_shift at CS_data_atom_xyz. More...
numeric::xyzVector< core::Real >	get_delta_magnetic_anisotropy_deriv (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, numeric::xyzVector< core::Real > const &source_atom_xyz, numeric::xyzMatrix< core::Real > const &base_coordinate_matrix, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const realatomdata_index)
Real	magnetic_anisotropy_effect (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &source_rsd_CS_params)
	The magnetic_anisotropy contribution of source_rsd to the chemical_shift at atom_xyz. More...
numeric::xyzVector< core::Real >	ring_pos (conformation::Residue const &rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params, Size const ring_ID)
static Real	dellintk_dm (Real const m)
static Real	dellinte_dm (Real const m)
static Real	ellintk (Real const m)
static Real	ellinte (Real const m)
void	get_rho_and_z (numeric::xyzVector< core::Real > const &atom_xyz, numeric::xyzVector< core::Real > const &ring_center, numeric::xyzVector< core::Real > const &base_z_axis, Real &rho, Real &z)
Real	delta_ring_current_term (Real const rho, Real const z, Real const ring_radius, Real const ring_z_offset)
void	get_ring_current_term_derivatives (Real const rho, Real const z, Real const ring_radius, Real const ring_z_offset, Real &dterm_drho, Real &dterm_dz)
Real	delta_ring_current (numeric::xyzVector< core::Real > const &atom_xyz, numeric::xyzVector< core::Real > const &molecular_ring_center, numeric::xyzVector< core::Real > const &base_z_axis, RNA_CS_residue_parameters const &source_rsd_CS_params, Size const ring_ID)
Real	ring_current_effect (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params)
	The ring_current contribution of source_rsd to the chemical_shift at atom_xyz. More...
Real	ring_current_effect_individual_ring (numeric::xyzVector< core::Real > const &atom_xyz, conformation::Residue const &source_rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params, Size const source_ring_ID)
numeric::xyzVector< core::Real >	get_ring_current_deriv (numeric::xyzVector< core::Real > const &CS_data_atom_xyz, conformation::Residue const &source_rsd, core::Size const source_ring_ID, RNA_CS_residue_parameters const &source_rsd_CS_params)
numeric::xyzMatrix< core::Real > const	get_rna_base_coordinate_system_from_CS_params (core::conformation::Residue const &rsd, RNA_CS_residue_parameters const &rna_cs_rsd_params)
core::Size	dround (core::Real var)

Typedef Documentation

typedef utility::pointer::shared_ptr< RNA_ChemicalShiftPotential const > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotentialCOP

typedef utility::pointer::shared_ptr< RNA_ChemicalShiftPotential > core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotentialOP

Enumeration Type Documentation

enum core::scoring::rna::chemical_shift::atomitem

Enumerator
oshi
xdir
ydir
zdir
csca
suga
rcl1
rcl2
rcl3
maca
maqx
maqw
maqy
maqz
marx
mary
marz
chco
chrg
last_atomdesc

Function Documentation

std::string core::scoring::rna::chemical_shift::add_whitespaces

(

std::string const &

in_atom_name

)

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms(), and core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters().

bool core::scoring::rna::chemical_shift::Contain_seq_num	(	Size const &	seq_num,
		utility::vector1< core::Size > const &	residue_list
	)

static Real core::scoring::rna::chemical_shift::dellinte_dm ( Real const  m )

static

Referenced by get_ring_current_term_derivatives().

static Real core::scoring::rna::chemical_shift::dellintk_dm ( Real const  m )

static

Referenced by get_ring_current_term_derivatives().

Real core::scoring::rna::chemical_shift::delta_magnetic_anisotropy	(	numeric::xyzVector< core::Real > const &	CS_data_atom_xyz,
		numeric::xyzVector< core::Real > const &	source_atom_xyz,
		numeric::xyzMatrix< core::Real > const &	base_coordinate_matrix,
		RNA_CS_residue_parameters const &	source_rsd_CS_params,
		Size const	realatomdata_index
	)

The magnetic_anisotropy contribution of heavy-base atom at src_xyz to the chemqical_shift at CS_data_atom_xyz.

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_q_coeff(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_r_coeff(), maqw, maqx, maqy, maqz, marx, mary, and marz.

Referenced by magnetic_anisotropy_effect().

Real core::scoring::rna::chemical_shift::delta_ring_current	(	numeric::xyzVector< core::Real > const &	atom_xyz,
		numeric::xyzVector< core::Real > const &	molecular_ring_center,
		numeric::xyzVector< core::Real > const &	base_z_axis,
		RNA_CS_residue_parameters const &	source_rsd_CS_params,
		Size const	ring_ID
	)

References delta_ring_current_term(), get_rho_and_z(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_current_coeff(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_height(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_intensity(), and core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_radius().

Referenced by ring_current_effect(), and ring_current_effect_individual_ring().

Real core::scoring::rna::chemical_shift::delta_ring_current_term	(	Real const	rho,
		Real const	z,
		Real const	ring_radius,
		Real const	ring_z_offset
	)

References ellinte(), and ellintk().

Referenced by delta_ring_current().

core::Size core::scoring::rna::chemical_shift::dround ( core::Real  var )

inline

Referenced by protocols::mpi_refinement::MPI_Refinement::add_structure_to_library_single_replace(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), magnetic_anisotropy_effect(), and ring_pos().

static Real core::scoring::rna::chemical_shift::ellinte ( Real const  m )

static

Referenced by delta_ring_current_term(), and get_ring_current_term_derivatives().

static Real core::scoring::rna::chemical_shift::ellintk ( Real const  m )

static

Referenced by delta_ring_current_term(), and get_ring_current_term_derivatives().

utility::vector1< ChemicalShiftData > core::scoring::rna::chemical_shift::filter_chem_shift_data_list	(	utility::vector1< ChemicalShiftData > const &	flat_EXP_chem_shift_data_list,
		core::Size const	seq_num,
		utility::vector1< std::string > const &	proton_entry
	)

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

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().

numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::get_delta_magnetic_anisotropy_deriv	(	numeric::xyzVector< core::Real > const &	CS_data_atom_xyz,
		numeric::xyzVector< core::Real > const &	source_atom_xyz,
		numeric::xyzMatrix< core::Real > const &	base_coordinate_matrix,
		RNA_CS_residue_parameters const &	source_rsd_CS_params,
		Size const	realatomdata_index
	)

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_q_coeff(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_r_coeff(), maqw, maqx, maqy, maqz, marx, mary, and marz.

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), and core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base().

chemical::AA core::scoring::rna::chemical_shift::get_res_aa_from_BASE_name	(	std::string const &	BASE_name,
		std::string const &	text_line
	)

References core::chemical::aa_unk, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, and core::chemical::na_ura.

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().

void core::scoring::rna::chemical_shift::get_rho_and_z	(	numeric::xyzVector< core::Real > const &	atom_xyz,
		numeric::xyzVector< core::Real > const &	ring_center,
		numeric::xyzVector< core::Real > const &	base_z_axis,
		Real &	rho,
		Real &	z
	)

Referenced by delta_ring_current(), and get_ring_current_deriv().

numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::get_ring_current_deriv	(	numeric::xyzVector< core::Real > const &	CS_data_atom_xyz,
		conformation::Residue const &	source_rsd,
		core::Size const	source_ring_ID,
		RNA_CS_residue_parameters const &	source_rsd_CS_params
	)

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), get_rho_and_z(), get_ring_current_term_derivatives(), get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_current_coeff(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_height(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_intensity(), ring_pos(), and core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_radius().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), and core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base().

void core::scoring::rna::chemical_shift::get_ring_current_term_derivatives	(	Real const	rho,
		Real const	z,
		Real const	ring_radius,
		Real const	ring_z_offset,
		Real &	dterm_drho,
		Real &	dterm_dz
	)

References dellinte_dm(), dellintk_dm(), ellinte(), and ellintk().

Referenced by get_ring_current_deriv().

numeric::xyzMatrix< core::Real > const core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params	(	core::conformation::Residue const &	rsd,
		RNA_CS_residue_parameters const &	rna_cs_rsd_params
	)

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), dround(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomname(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size(), core::conformation::Residue::is_RNA(), xdir, core::conformation::Residue::xyz(), and ydir.

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), get_ring_current_deriv(), magnetic_anisotropy_effect(), ring_current_effect(), and ring_current_effect_individual_ring().

std::string core::scoring::rna::chemical_shift::get_rosetta_hatom_name	(	std::string const &	input_atom_name,
		std::string const &	text_line,
		utility::vector1< std::string > const &	flat_proton_entry_list
	)

References core::scoring::TR().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().

bool core::scoring::rna::chemical_shift::is_polar_hydrogen

(

std::string const &

input_atom_name

)

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), and core::scoring::etable::MembEtable::precalc_etable_coefficients().

core::Real core::scoring::rna::chemical_shift::magnetic_anisotropy_effect	(	numeric::xyzVector< core::Real > const &	atom_xyz,
		conformation::Residue const &	source_rsd,
		RNA_CS_residue_parameters const &	source_rsd_CS_params
	)

The magnetic_anisotropy contribution of source_rsd to the chemical_shift at atom_xyz.

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), delta_magnetic_anisotropy(), 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_rna_base_coordinate_system_from_CS_params(), maca, and core::conformation::Residue::xyz().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics().

void core::scoring::rna::chemical_shift::print_chemical_shift_data	(	std::string const &	prestring,
		ChemicalShiftData const &	CS_data,
		bool const	print_data_line
	)

References core::scoring::rna::chemical_shift::ChemicalShiftData::atom_name, core::scoring::rna::chemical_shift::ChemicalShiftData::data_line, core::scoring::rna::chemical_shift::ChemicalShiftData::exp_shift, core::chemical::name_from_aa(), core::scoring::rna::chemical_shift::ChemicalShiftData::realatomdata_index, core::scoring::rna::chemical_shift::ChemicalShiftData::res_aa, core::scoring::rna::chemical_shift::ChemicalShiftData::seq_num, and core::scoring::TR().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::assert_is_calc_chem_shift_atom(), filter_chem_shift_data_list(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_best_exp_to_calc_chem_shift_mapping(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), and core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().

std::string core::scoring::rna::chemical_shift::remove_whitespaces

(

std::string const &

in_atom_name

)

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::atom_has_exp_chemical_shift_data(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift_data_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_matching_CS_data_entry(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_realatomdata_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::Is_magnetic_anisotropy_source_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_reference_shifts(), and core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_weights().

core::Real core::scoring::rna::chemical_shift::ring_current_effect	(	numeric::xyzVector< core::Real > const &	atom_xyz,
		conformation::Residue const &	source_rsd,
		RNA_CS_residue_parameters const &	rna_cs_rsd_params
	)

The ring_current contribution of source_rsd to the chemical_shift at atom_xyz.

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), delta_ring_current(), get_rna_base_coordinate_system_from_CS_params(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::num_rings(), and ring_pos().

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics().

Real core::scoring::rna::chemical_shift::ring_current_effect_individual_ring	(	numeric::xyzVector< core::Real > const &	atom_xyz,
		conformation::Residue const &	source_rsd,
		RNA_CS_residue_parameters const &	rna_cs_rsd_params,
		Size const	source_ring_ID
	)

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), delta_ring_current(), get_rna_base_coordinate_system_from_CS_params(), and ring_pos().

numeric::xyzVector< core::Real > core::scoring::rna::chemical_shift::ring_pos	(	conformation::Residue const &	rsd,
		RNA_CS_residue_parameters const &	rna_cs_rsd_params,
		Size const	ring_ID
	)

References core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa(), core::conformation::Residue::aa(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(), core::conformation::Residue::atom_index(), dround(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomname(), core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size(), rcl1, rcl2, and core::conformation::Residue::xyz().

Referenced by get_ring_current_deriv(), ring_current_effect(), and ring_current_effect_individual_ring().

core::Size core::scoring::rna::chemical_shift::string_to_int

(

std::string const &

input_string

)

References core::conformation::membrane::in, and core::conformation::membrane::out.

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().

core::Real core::scoring::rna::chemical_shift::string_to_real

(

std::string const &

input_string

)

References core::conformation::membrane::in, and core::conformation::membrane::out.

Referenced by core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data().