core::io::nmr Namespace Reference

Classes
class	AtomSelection
class	ParaIon
class	ParamagneticDatabaseHandler
class	SpinlabelDatabaseEntry
class	SpinlabelDatabaseHandler

Typedefs
typedef utility::pointer::shared_ptr< AtomSelection >	AtomSelectionOP
typedef utility::pointer::shared_ptr< AtomSelection const >	AtomSelectionCOP
typedef utility::pointer::weak_ptr< AtomSelection >	AtomSelectionAP
typedef utility::pointer::weak_ptr< AtomSelection const >	AtomSelectionCAP
typedef utility::pointer::shared_ptr< ParaIon >	ParaIonOP
typedef utility::pointer::shared_ptr< ParaIon const >	ParaIonCOP
typedef utility::pointer::weak_ptr< ParaIon >	ParaIonAP
typedef utility::pointer::weak_ptr< ParaIon const >	ParaIonCAP
typedef utility::pointer::shared_ptr< ParamagneticDatabaseHandler >	ParamagneticDatabaseHandlerOP
typedef utility::pointer::shared_ptr< ParamagneticDatabaseHandler const >	ParamagneticDatabaseHandlerCOP
typedef utility::pointer::shared_ptr< SpinlabelDatabaseHandler >	SpinlabelDatabaseHandlerOP
typedef utility::pointer::shared_ptr< SpinlabelDatabaseHandler const >	SpinlabelDatabaseHandlerCOP
typedef utility::pointer::shared_ptr< SpinlabelDatabaseEntry >	SpinlabelDatabaseEntryOP
typedef utility::pointer::shared_ptr< SpinlabelDatabaseEntry const >	SpinlabelDatabaseEntryCOP

Functions
bool	operator< (AtomSelection const &lhs, AtomSelection const &rhs)
bool	operator> (AtomSelection const &lhs, AtomSelection const &rhs)
bool	operator<= (AtomSelection const &lhs, AtomSelection const &rhs)
bool	operator>= (AtomSelection const &lhs, AtomSelection const &rhs)
bool	operator== (AtomSelection const &lhs, AtomSelection const &rhs)
bool	operator!= (AtomSelection const &lhs, AtomSelection const &rhs)
static basic::Tracer	TR ("core.io.nmr.ParamagneticDatabaseHandler")
std::map< std::string, ParaIon >	read_in_database_file (std::string const &filename)
	Some utility function to read in database file. More...
static basic::Tracer	TR ("core.io.nmr.SpinlabelDatabaseHandler")
void	read_in_database_file (std::string const &filename, SpinlabelDatabaseHandler::SpinlabelDatabaseMap &table)
	Some utility function to read in database file. More...
static basic::Tracer	TR ("core.io.nmr.util")
void	read_atom_selection_from_string (std::string const &str, AtomSelection &atom)
	reads residue number, atom name and chain ID for one spin stores it in an AtomSelection object More...
Size	read_selection_group_from_string (std::string const &str, utility::vector1< AtomSelection > &group, Size offset)
	read residue number, atom name and chain ID for multiple spins within a selection and store them in a vector of AtomSelection objects More...
void	read_pcs_datafile (std::string const &filename, utility::vector1< utility::vector1< AtomSelection > > &spins, utility::vector1< Real > &values, utility::vector1< Real > &errors)
	reads complete pcs data file More...
void	read_rdc_datafile (std::string const &filename, utility::vector1< utility::vector1< AtomSelection > > &spinsA, utility::vector1< utility::vector1< AtomSelection > > &spinsB, utility::vector1< Real > &values, utility::vector1< Real > &errors)
	reads complete rdc data file More...
void	read_pre_datafile (std::string const &filename, utility::vector1< utility::vector1< AtomSelection > > &spins, utility::vector1< Real > &values, utility::vector1< Real > &errors)
	reads complete pre data file More...
void	read_key_value_pair_from_line (std::string const &line, std::string const &key, std::map< std::string, std::string > &key_value_map, Size line_number)
	utility function to read in key-value pairs from the NMR data main input file More...
std::string	strip_brackets (std::string const &str)
	strip brackets from string of dataset list More...
utility::vector1< std::string >	read_pcs_dataset_params_list (std::string const &str)
	convert PCS dataset string and get vector of items [ file, lanthanide, weight, single value weighting, averaging type, computation type, xM, yM, zM, Xax, Xrh, alpha, beta, gamma ] More...
utility::vector1< std::string >	read_rdc_dataset_params_list (std::string const &str)
	convert RDC dataset string and get vector of items [ file, weight, single value weighting ] More...
utility::vector1< std::string >	read_pre_dataset_params_list (std::string const &str)
	convert PRE dataset string and get vector of items [ file, weight, single value weighting, rate type, B0 ] More...
utility::vector1< Real >	read_rdc_tensor_values_from_string (std::string const &str)
	convert RDC tensor values from string More...
utility::vector1< std::string >	read_gridsearch_values_from_string (std::string const &str)
	read gridsearch values from string [ atom1, atom2, distance center-atom1, stepsize, inner radius, outer radius ] More...

Typedef Documentation

AtomSelectionAP

typedef utility::pointer::weak_ptr< AtomSelection > core::io::nmr::AtomSelectionAP

AtomSelectionCAP

typedef utility::pointer::weak_ptr< AtomSelection const > core::io::nmr::AtomSelectionCAP

AtomSelectionCOP

typedef utility::pointer::shared_ptr< AtomSelection const > core::io::nmr::AtomSelectionCOP

AtomSelectionOP

typedef utility::pointer::shared_ptr< AtomSelection > core::io::nmr::AtomSelectionOP

ParaIonAP

typedef utility::pointer::weak_ptr< ParaIon > core::io::nmr::ParaIonAP

ParaIonCAP

typedef utility::pointer::weak_ptr< ParaIon const > core::io::nmr::ParaIonCAP

ParaIonCOP

typedef utility::pointer::shared_ptr< ParaIon const > core::io::nmr::ParaIonCOP

ParaIonOP

typedef utility::pointer::shared_ptr< ParaIon > core::io::nmr::ParaIonOP

ParamagneticDatabaseHandlerCOP

typedef utility::pointer::shared_ptr< ParamagneticDatabaseHandler const > core::io::nmr::ParamagneticDatabaseHandlerCOP

ParamagneticDatabaseHandlerOP

typedef utility::pointer::shared_ptr< ParamagneticDatabaseHandler > core::io::nmr::ParamagneticDatabaseHandlerOP

SpinlabelDatabaseEntryCOP

typedef utility::pointer::shared_ptr< SpinlabelDatabaseEntry const > core::io::nmr::SpinlabelDatabaseEntryCOP

SpinlabelDatabaseEntryOP

typedef utility::pointer::shared_ptr< SpinlabelDatabaseEntry > core::io::nmr::SpinlabelDatabaseEntryOP

SpinlabelDatabaseHandlerCOP

typedef utility::pointer::shared_ptr< SpinlabelDatabaseHandler const > core::io::nmr::SpinlabelDatabaseHandlerCOP

SpinlabelDatabaseHandlerOP

typedef utility::pointer::shared_ptr< SpinlabelDatabaseHandler > core::io::nmr::SpinlabelDatabaseHandlerOP

Function Documentation

operator!=()

bool core::io::nmr::operator!=	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

operator<()

bool core::io::nmr::operator<	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

operator<=()

bool core::io::nmr::operator<=	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

operator==()

bool core::io::nmr::operator==	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

operator>()

bool core::io::nmr::operator>	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

operator>=()

bool core::io::nmr::operator>=	(	AtomSelection const &	lhs,
		AtomSelection const &	rhs
	)

read_atom_selection_from_string()

void core::io::nmr::read_atom_selection_from_string	(	std::string const &	str,
		AtomSelection &	atom
	)

reads residue number, atom name and chain ID for one spin stores it in an AtomSelection object

References core::io::nmr::AtomSelection::set_atom(), core::io::nmr::AtomSelection::set_chain(), core::io::nmr::AtomSelection::set_rsd(), and protocols::kinmatch::str().

Referenced by read_selection_group_from_string().

read_gridsearch_values_from_string()

utility::vector1< std::string > core::io::nmr::read_gridsearch_values_from_string

(

std::string const &

str

)

read gridsearch values from string [ atom1, atom2, distance center-atom1, stepsize, inner radius, outer radius ]

References protocols::kinmatch::str(), and strip_brackets().

Referenced by core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), and core::scoring::nmr::pre::PREData::init_pre_data_from_file().

read_in_database_file() [1/2]

std::map< std::string, ParaIon > core::io::nmr::read_in_database_file

(

std::string const &

filename

)

Some utility function to read in database file.

References protocols::abinitio::filename(), protocols::features::L, core::chemical::element::S, and TR().

Referenced by core::io::nmr::SpinlabelDatabaseHandler::SpinlabelDatabaseHandler().

read_in_database_file() [2/2]

void core::io::nmr::read_in_database_file	(	std::string const &	filename,
		SpinlabelDatabaseHandler::SpinlabelDatabaseMap &	table
	)

Some utility function to read in database file.

References protocols::abinitio::filename(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_distance_potential_histogram(), core::io::nmr::SpinlabelDatabaseEntry::set_path_to_ensemble_conformers(), and TR().

read_key_value_pair_from_line()

void core::io::nmr::read_key_value_pair_from_line	(	std::string const &	line,
		std::string const &	key,
		std::map< std::string, std::string > &	key_value_map,
		Size	line_number
	)

utility function to read in key-value pairs from the NMR data main input file

References TR().

Referenced by core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), core::scoring::nmr::pre::PREData::init_pre_data_from_file(), and core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file().

read_pcs_datafile()

void core::io::nmr::read_pcs_datafile	(	std::string const &	filename,
		utility::vector1< utility::vector1< AtomSelection > > &	spins,
		utility::vector1< Real > &	values,
		utility::vector1< Real > &	errors
	)

reads complete pcs data file

each line contains an AtomSelection or a vector of AtomSelections for equivalent spins on equivalent subunits, the measured pcs value and its error

each line contains an AtomSelection for a protein spin, the measured pcs value and its error

References protocols::abinitio::filename(), core::conformation::membrane::in, read_selection_group_from_string(), and TR().

Referenced by core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), protocols::qsar::scoring_grid::PCSSingleGrid::init_pcs_values_from_file(), and read_pre_datafile().

read_pcs_dataset_params_list()

utility::vector1< std::string > core::io::nmr::read_pcs_dataset_params_list

(

std::string const &

str

)

convert PCS dataset string and get vector of items [ file, lanthanide, weight, single value weighting, averaging type, computation type, xM, yM, zM, Xax, Xrh, alpha, beta, gamma ]

References protocols::kinmatch::str(), and strip_brackets().

Referenced by core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), and protocols::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file().

read_pre_datafile()

void core::io::nmr::read_pre_datafile	(	std::string const &	filename,
		utility::vector1< utility::vector1< AtomSelection > > &	spins,
		utility::vector1< Real > &	values,
		utility::vector1< Real > &	errors
	)

reads complete pre data file

each line contains an AtomSelection for a protein spin, the measured pre value and its error

References protocols::abinitio::filename(), and read_pcs_datafile().

Referenced by core::scoring::nmr::pre::PRESingleSet::init_from_filedata().

read_pre_dataset_params_list()

utility::vector1< std::string > core::io::nmr::read_pre_dataset_params_list

(

std::string const &

str

)

convert PRE dataset string and get vector of items [ file, weight, single value weighting, rate type, B0 ]

References protocols::kinmatch::str(), and strip_brackets().

Referenced by core::scoring::nmr::pre::PREData::init_pre_data_from_file().

read_rdc_datafile()

void core::io::nmr::read_rdc_datafile	(	std::string const &	filename,
		utility::vector1< utility::vector1< AtomSelection > > &	spinsA,
		utility::vector1< utility::vector1< AtomSelection > > &	spinsB,
		utility::vector1< Real > &	values,
		utility::vector1< Real > &	errors
	)

reads complete rdc data file

each line contains two AtomSelections of the interacting protein spins, the measured rdc value and its error

References protocols::abinitio::filename(), core::conformation::membrane::in, read_selection_group_from_string(), and TR().

Referenced by core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata().

read_rdc_dataset_params_list()

utility::vector1< std::string > core::io::nmr::read_rdc_dataset_params_list

(

std::string const &

str

)

convert RDC dataset string and get vector of items [ file, weight, single value weighting ]

References protocols::kinmatch::str(), and strip_brackets().

Referenced by core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file().

read_rdc_tensor_values_from_string()

utility::vector1< Real > core::io::nmr::read_rdc_tensor_values_from_string

(

std::string const &

str

)

convert RDC tensor values from string

References protocols::kinmatch::str(), and strip_brackets().

Referenced by core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file().

read_selection_group_from_string()

Size core::io::nmr::read_selection_group_from_string	(	std::string const &	str,
		utility::vector1< AtomSelection > &	group,
		Size	offset
	)

read residue number, atom name and chain ID for multiple spins within a selection and store them in a vector of AtomSelection objects

References core::sequence::end, core::io::nmr::AtomSelection::get_atom(), read_atom_selection_from_string(), protocols::loops::start, protocols::kinmatch::str(), and TR().

Referenced by read_pcs_datafile(), and read_rdc_datafile().

strip_brackets()

std::string core::io::nmr::strip_brackets

(

std::string const &

str

)

strip brackets from string of dataset list

References core::sequence::end, and protocols::kinmatch::str().

Referenced by read_gridsearch_values_from_string(), read_pcs_dataset_params_list(), read_pre_dataset_params_list(), read_rdc_dataset_params_list(), and read_rdc_tensor_values_from_string().

TR() [1/3]

static basic::Tracer core::io::nmr::TR ( "core.io.nmr.ParamagneticDatabaseHandler"  )

static

Referenced by read_in_database_file(), read_key_value_pair_from_line(), read_pcs_datafile(), read_rdc_datafile(), read_selection_group_from_string(), and core::io::nmr::AtomSelection::show().

TR() [2/3]

static basic::Tracer core::io::nmr::TR ( "core.io.nmr.SpinlabelDatabaseHandler"  )

static

TR() [3/3]

static basic::Tracer core::io::nmr::TR ( "core.io.nmr.util"  )

static