chemical_shift¶

Bindings for core::scoring::rna::chemical_shift namespace

class pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData¶

Bases: pybind11_object

property accuracy_weight¶

assign(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData, : pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData) → pyrosetta.rosetta.core.scoring.rna.chemical_shift.ChemicalShiftData¶: C++: core::scoring::rna::chemical_shift::ChemicalShiftData::operator=(const class core::scoring::rna::chemical_shift::ChemicalShiftData &) –> class core::scoring::rna::chemical_shift::ChemicalShiftData &

property atom_name¶

property data_line¶

property exp_shift¶

property realatomdata_index¶

property ref_shift¶

property res_aa¶

property seq_num¶

class pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters¶

Bases: pybind11_object

get_RNA_CS_residue_parameters(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_parameters, res_aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters¶: C++: core::scoring::rna::chemical_shift::RNA_CS_parameters::get_RNA_CS_residue_parameters(const enum core::chemical::AA) const –> const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &

class pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters¶

Bases: pybind11_object

aa(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → pyrosetta.rosetta.core.chemical.AA¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::aa() const –> enum core::chemical::AA

atom_data(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, atom: int, item: pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::atom_data(const unsigned long, const enum core::scoring::rna::chemical_shift::atomitem) const –> double

base_name(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → str¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::base_name() const –> const std::string

get_atomname(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, count: int) → str¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomname(const unsigned long) const –> const std::string

get_atomnames_size(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → int¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::get_atomnames_size() const –> unsigned long

magentic_anisotropy_q_coeff(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_q_coeff() const –> double

magentic_anisotropy_r_coeff(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::magentic_anisotropy_r_coeff() const –> double

num_rings(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → int¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::num_rings() const –> unsigned long

ring_current_coeff(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_current_coeff() const –> double

ring_height(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, ring_ID: int) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_height(const unsigned long) const –> double

ring_intensity(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, ring_ID: int) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_intensity(const unsigned long) const –> double

ring_radius(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, ring_ID: int) → float¶: C++: core::scoring::rna::chemical_shift::RNA_CS_residue_parameters::ring_radius(const unsigned long) const –> double

class pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential¶

Bases: pybind11_object

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, weights: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, pose: pyrosetta.rosetta.core.pose.Pose, totals: core::scoring::EMapVector) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::finalize_total_energy(const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

get_accuracy_weight(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, key: str) → float¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_accuracy_weight(const std::string &) const –> double

get_alpha(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, key: str) → float¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_alpha(const std::string &) const –> double

get_neighbor_atom(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, key: str) → bool¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_neighbor_atom(const std::string &) const –> bool

get_reference_shift(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, key: str) → float¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_reference_shift(const std::string &) const –> double

get_total_exp_chemical_shift_data_points(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential) → int¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points() const –> unsigned long

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, : pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

load_larmord_neighbor_atoms(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, filename: str) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_neighbor_atoms(const std::string &) –> void

load_larmord_parameters(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, filename: str) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_parameters(const std::string &) –> void

load_larmord_reference_shifts(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, filename: str) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_reference_shifts(const std::string &) –> void

load_larmord_weights(self: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential, filename: str) → None¶: C++: core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::load_larmord_weights(const std::string &) –> void

class pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem¶

Bases: pybind11_object

Members:

oshi

xdir

ydir

zdir

csca

suga

rcl1

rcl2

rcl3

maca

maqx

maqw

maqy

maqz

marx

mary

marz

chco

chrg

last_atomdesc

chco = <atomitem.chco: 18>¶

chrg = <atomitem.chrg: 19>¶

csca = <atomitem.csca: 5>¶

last_atomdesc = <atomitem.last_atomdesc: 20>¶

maca = <atomitem.maca: 10>¶

maqw = <atomitem.maqw: 12>¶

maqx = <atomitem.maqx: 11>¶

maqy = <atomitem.maqy: 13>¶

maqz = <atomitem.maqz: 14>¶

marx = <atomitem.marx: 15>¶

mary = <atomitem.mary: 16>¶

marz = <atomitem.marz: 17>¶

property name¶

oshi = <atomitem.oshi: 1>¶

rcl1 = <atomitem.rcl1: 7>¶

rcl2 = <atomitem.rcl2: 8>¶

rcl3 = <atomitem.rcl3: 9>¶

suga = <atomitem.suga: 6>¶

property value¶

xdir = <atomitem.xdir: 2>¶

ydir = <atomitem.ydir: 3>¶

zdir = <atomitem.zdir: 4>¶

pyrosetta.rosetta.core.scoring.rna.chemical_shift.dround(var: float) → int¶: C++: core::scoring::rna::chemical_shift::dround(double) –> unsigned long

pyrosetta.rosetta.core.scoring.rna.chemical_shift.get_delta_magnetic_anisotropy_deriv(CS_data_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, source_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, base_coordinate_matrix: pyrosetta.rosetta.numeric.xyzMatrix_double_t, source_rsd_CS_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, realatomdata_index: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::scoring::rna::chemical_shift::get_delta_magnetic_anisotropy_deriv(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzMatrix<double> &, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &, const unsigned long) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.rna.chemical_shift.get_ring_current_deriv(CS_data_atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, source_rsd: pyrosetta.rosetta.core.conformation.Residue, source_ring_ID: int, source_rsd_CS_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::scoring::rna::chemical_shift::get_ring_current_deriv(const class numeric::xyzVector<double> &, const class core::conformation::Residue &, const unsigned long, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.rna.chemical_shift.get_rna_base_coordinate_system_from_CS_params(rsd: pyrosetta.rosetta.core.conformation.Residue, rna_cs_rsd_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → pyrosetta.rosetta.numeric.xyzMatrix_double_t¶: C++: core::scoring::rna::chemical_shift::get_rna_base_coordinate_system_from_CS_params(const class core::conformation::Residue &, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &) –> const class numeric::xyzMatrix<double>

pyrosetta.rosetta.core.scoring.rna.chemical_shift.magnetic_anisotropy_effect(atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, source_rsd: pyrosetta.rosetta.core.conformation.Residue, source_rsd_CS_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → float¶: C++: core::scoring::rna::chemical_shift::magnetic_anisotropy_effect(const class numeric::xyzVector<double> &, const class core::conformation::Residue &, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &) –> double

pyrosetta.rosetta.core.scoring.rna.chemical_shift.ring_current_effect(atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, source_rsd: pyrosetta.rosetta.core.conformation.Residue, rna_cs_rsd_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters) → float¶: C++: core::scoring::rna::chemical_shift::ring_current_effect(const class numeric::xyzVector<double> &, const class core::conformation::Residue &, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &) –> double

pyrosetta.rosetta.core.scoring.rna.chemical_shift.ring_pos(rsd: pyrosetta.rosetta.core.conformation.Residue, rna_cs_rsd_params: pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters, ring_ID: int) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::scoring::rna::chemical_shift::ring_pos(const class core::conformation::Residue &, const class core::scoring::rna::chemical_shift::RNA_CS_residue_parameters &, const unsigned long) –> class numeric::xyzVector<double>