nmr¶

Bindings for core::io::nmr namespace

class pyrosetta.rosetta.core.io.nmr.AtomSelection¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.nmr.AtomSelection, rhs: pyrosetta.rosetta.core.io.nmr.AtomSelection) → pyrosetta.rosetta.core.io.nmr.AtomSelection¶

copy assignment

C++: core::io::nmr::AtomSelection::operator=(const class core::io::nmr::AtomSelection &) –> class core::io::nmr::AtomSelection &

get_atom(self: pyrosetta.rosetta.core.io.nmr.AtomSelection) → str¶: C++: core::io::nmr::AtomSelection::get_atom() const –> std::string

get_chain(self: pyrosetta.rosetta.core.io.nmr.AtomSelection) → str¶: C++: core::io::nmr::AtomSelection::get_chain() const –> const char &

get_rsd(self: pyrosetta.rosetta.core.io.nmr.AtomSelection) → int¶: C++: core::io::nmr::AtomSelection::get_rsd() const –> unsigned long

set_atom(self: pyrosetta.rosetta.core.io.nmr.AtomSelection, atom: str) → None¶: C++: core::io::nmr::AtomSelection::set_atom(const std::string &) –> void

set_chain(self: pyrosetta.rosetta.core.io.nmr.AtomSelection, chain: str) → None¶: C++: core::io::nmr::AtomSelection::set_chain(const char &) –> void

set_rsd(self: pyrosetta.rosetta.core.io.nmr.AtomSelection, residue: int) → None¶: C++: core::io::nmr::AtomSelection::set_rsd(const unsigned long) –> void

show(self: pyrosetta.rosetta.core.io.nmr.AtomSelection, TR: pyrosetta.rosetta.std.ostream) → None¶: C++: core::io::nmr::AtomSelection::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.io.nmr.ParaIon¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.nmr.ParaIon, src: pyrosetta.rosetta.core.io.nmr.ParaIon) → pyrosetta.rosetta.core.io.nmr.ParaIon¶

assignment operator

C++: core::io::nmr::ParaIon::operator=(const class core::io::nmr::ParaIon &) –> class core::io::nmr::ParaIon &

calc_gJ(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → None¶

calculate Lande g-factor

C++: core::io::nmr::ParaIon::calc_gJ() –> void

get_J(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_J() const –> double

get_L(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_L() const –> double

get_S(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_S() const –> double

get_charge(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_charge() const –> double

get_gJ(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_gJ() const –> double

get_ion_label(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → str¶

Setters and Getters

C++: core::io::nmr::ParaIon::get_ion_label() const –> std::string

get_tau_e(self: pyrosetta.rosetta.core.io.nmr.ParaIon) → float¶: C++: core::io::nmr::ParaIon::get_tau_e() const –> double

set_J(self: pyrosetta.rosetta.core.io.nmr.ParaIon, j: float) → None¶: C++: core::io::nmr::ParaIon::set_J(double) –> void

set_L(self: pyrosetta.rosetta.core.io.nmr.ParaIon, l: float) → None¶: C++: core::io::nmr::ParaIon::set_L(double) –> void

set_S(self: pyrosetta.rosetta.core.io.nmr.ParaIon, s: float) → None¶: C++: core::io::nmr::ParaIon::set_S(double) –> void

set_charge(self: pyrosetta.rosetta.core.io.nmr.ParaIon, charge: float) → None¶: C++: core::io::nmr::ParaIon::set_charge(double) –> void

set_gJ(self: pyrosetta.rosetta.core.io.nmr.ParaIon, gj: float) → None¶: C++: core::io::nmr::ParaIon::set_gJ(double) –> void

set_ion_label(self: pyrosetta.rosetta.core.io.nmr.ParaIon, label: str) → None¶: C++: core::io::nmr::ParaIon::set_ion_label(const std::string &) –> void

set_tau_e(self: pyrosetta.rosetta.core.io.nmr.ParaIon, te: float) → None¶: C++: core::io::nmr::ParaIon::set_tau_e(double) –> void

show(self: pyrosetta.rosetta.core.io.nmr.ParaIon, out: pyrosetta.rosetta.std.ostream) → None¶

output ParaIon data

C++: core::io::nmr::ParaIon::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler¶

Bases: SingletonBase_core_io_nmr_ParamagneticDatabaseHandler_t

static get_instance() → core::io::nmr::ParamagneticDatabaseHandler¶: C++: utility::SingletonBase<core::io::nmr::ParamagneticDatabaseHandler>::get_instance() –> class core::io::nmr::ParamagneticDatabaseHandler *

get_ion_data(self: pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler, ion: str) → pyrosetta.rosetta.core.io.nmr.ParaIon¶

return data for one paramagnetic ion

C++: core::io::nmr::ParamagneticDatabaseHandler::get_ion_data(const std::string &) –> class core::io::nmr::ParaIon

get_ion_data_table(self: pyrosetta.rosetta.core.io.nmr.ParamagneticDatabaseHandler) → pyrosetta.rosetta.std.map_std_string_core_io_nmr_ParaIon¶

return map with paramagnetic ion data

C++: core::io::nmr::ParamagneticDatabaseHandler::get_ion_data_table() const –> const class std::map<std::string, class core::io::nmr::ParaIon, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::io::nmr::ParaIon> > > &

class pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry, : pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry¶: C++: core::io::nmr::SpinlabelDatabaseEntry::operator=(const class core::io::nmr::SpinlabelDatabaseEntry &) –> class core::io::nmr::SpinlabelDatabaseEntry &

distance_potential_histogram(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::distance_potential_histogram() const –> const std::string &

ensemble_conformers(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::ensemble_conformers() const –> const std::string &

fullname(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::fullname() const –> const std::string &

one_letter_code(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::one_letter_code() const –> const char &

radical_atom(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::radical_atom() const –> const std::string &

set_path_to_distance_potential_histogram(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry, filename: str) → None¶: C++: core::io::nmr::SpinlabelDatabaseEntry::set_path_to_distance_potential_histogram(const std::string &) –> void

set_path_to_ensemble_conformers(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry, filename: str) → None¶: C++: core::io::nmr::SpinlabelDatabaseEntry::set_path_to_ensemble_conformers(const std::string &) –> void

three_letter_code(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry) → str¶: C++: core::io::nmr::SpinlabelDatabaseEntry::three_letter_code() const –> const std::string &

class pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler¶

Bases: SingletonBase_core_io_nmr_SpinlabelDatabaseHandler_t

static get_instance() → core::io::nmr::SpinlabelDatabaseHandler¶: C++: utility::SingletonBase<core::io::nmr::SpinlabelDatabaseHandler>::get_instance() –> class core::io::nmr::SpinlabelDatabaseHandler *

get_spinlabel_data(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler, spinlabel: str) → pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry¶

return data for spinlabel

C++: core::io::nmr::SpinlabelDatabaseHandler::get_spinlabel_data(const std::string &) const –> const class core::io::nmr::SpinlabelDatabaseEntry &

get_spinlabel_data_table(self: pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseHandler) → pyrosetta.rosetta.std.map_std_string_core_io_nmr_SpinlabelDatabaseEntry¶

return map with spinlabel database entries

C++: core::io::nmr::SpinlabelDatabaseHandler::get_spinlabel_data_table() const –> const class std::map<std::string, class core::io::nmr::SpinlabelDatabaseEntry, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::io::nmr::SpinlabelDatabaseEntry> > > &

pyrosetta.rosetta.core.io.nmr.read_atom_selection_from_string(str: str, atom: pyrosetta.rosetta.core.io.nmr.AtomSelection) → None¶

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

C++: core::io::nmr::read_atom_selection_from_string(const std::string &, class core::io::nmr::AtomSelection &) –> void

pyrosetta.rosetta.core.io.nmr.read_gridsearch_values_from_string(str: str) → pyrosetta.rosetta.utility.vector1_std_string¶

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

C++: core::io::nmr::read_gridsearch_values_from_string(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.io.nmr.read_in_database_file(*args, **kwargs)¶

Overloaded function.

read_in_database_file(filename: str) -> pyrosetta.rosetta.std.map_std_string_core_io_nmr_ParaIon

Some utility function to read in database file

C++: core::io::nmr::read_in_database_file(const std::string &) –> class std::map<std::string, class core::io::nmr::ParaIon, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::io::nmr::ParaIon> > >

read_in_database_file(filename: str, table: pyrosetta.rosetta.std.map_std_string_core_io_nmr_SpinlabelDatabaseEntry) -> None

Some utility function to read in database file

C++: core::io::nmr::read_in_database_file(const std::string &, class std::map<std::string, class core::io::nmr::SpinlabelDatabaseEntry, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::io::nmr::SpinlabelDatabaseEntry> > > &) –> void

pyrosetta.rosetta.core.io.nmr.read_key_value_pair_from_line(line: str, key: str, key_value_map: pyrosetta.rosetta.std.map_std_string_std_string, line_number: int) → None¶

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

C++: core::io::nmr::read_key_value_pair_from_line(const std::string &, const std::string &, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &, unsigned long) –> void

pyrosetta.rosetta.core.io.nmr.read_pcs_dataset_params_list(str: str) → pyrosetta.rosetta.utility.vector1_std_string¶

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 ]

C++: core::io::nmr::read_pcs_dataset_params_list(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.io.nmr.read_pre_dataset_params_list(str: str) → pyrosetta.rosetta.utility.vector1_std_string¶

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

C++: core::io::nmr::read_pre_dataset_params_list(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.io.nmr.read_rdc_dataset_params_list(str: str) → pyrosetta.rosetta.utility.vector1_std_string¶

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

C++: core::io::nmr::read_rdc_dataset_params_list(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.io.nmr.read_rdc_tensor_values_from_string(str: str) → pyrosetta.rosetta.utility.vector1_double¶

convert RDC tensor values from string

C++: core::io::nmr::read_rdc_tensor_values_from_string(const std::string &) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.io.nmr.strip_brackets(str: str) → str¶

strip brackets from string of dataset list

C++: core::io::nmr::strip_brackets(const std::string &) –> std::string