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Classes | Typedefs | Functions
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, ParaIonread_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< Realread_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

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

Function Documentation

bool core::io::nmr::operator!= ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
bool core::io::nmr::operator< ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
bool core::io::nmr::operator<= ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
bool core::io::nmr::operator== ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
bool core::io::nmr::operator> ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
bool core::io::nmr::operator>= ( AtomSelection const &  lhs,
AtomSelection const &  rhs 
)
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(), and core::io::nmr::AtomSelection::set_rsd().

Referenced by read_selection_group_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 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().

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::features::L, core::chemical::element::S, and TR().

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

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

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 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().

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 read_pcs_datafile().

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

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 strip_brackets().

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

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 core::conformation::membrane::in, read_selection_group_from_string(), and TR().

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

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 strip_brackets().

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

utility::vector1< Real > core::io::nmr::read_rdc_tensor_values_from_string ( std::string const &  str)

convert RDC tensor values from string

References strip_brackets().

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

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, and TR().

Referenced by read_pcs_datafile(), and read_rdc_datafile().

std::string core::io::nmr::strip_brackets ( std::string const &  str)
static basic::Tracer core::io::nmr::TR ( "core.io.nmr.ParamagneticDatabaseHandler"  )
static
static basic::Tracer core::io::nmr::TR ( "core.io.nmr.SpinlabelDatabaseHandler"  )
static
static basic::Tracer core::io::nmr::TR ( "core.io.nmr.util"  )
static