rna¶

Bindings for core::chemical::rna namespace

class pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation¶

Bases: pybind11_object

Members:

ANY_BASE_DOUBLET_ORIENTATION

ANTIPARALLEL

PARALLEL

ANTIPARALLEL = <BaseDoubletOrientation.ANTIPARALLEL: 1>¶

ANY_BASE_DOUBLET_ORIENTATION = <BaseDoubletOrientation.ANY_BASE_DOUBLET_ORIENTATION: 0>¶

PARALLEL = <BaseDoubletOrientation.PARALLEL: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.BaseEdge¶

Bases: pybind11_object

Members:

ANY_BASE_EDGE

WATSON_CRICK

HOOGSTEEN

SUGAR

O2PRIME

PHOSPHATE

ANY_BASE_EDGE = <BaseEdge.ANY_BASE_EDGE: 0>¶

HOOGSTEEN = <BaseEdge.HOOGSTEEN: 2>¶

O2PRIME = <BaseEdge.O2PRIME: 4>¶

PHOSPHATE = <BaseEdge.PHOSPHATE: 5>¶

SUGAR = <BaseEdge.SUGAR: 3>¶

WATSON_CRICK = <BaseEdge.WATSON_CRICK: 1>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.BaseStackWhichSide¶

Bases: pybind11_object

Members:

ANY_BASE_STACK_SIDE

ABOVE

BELOW

ABOVE = <BaseStackWhichSide.ABOVE: 1>¶

ANY_BASE_STACK_SIDE = <BaseStackWhichSide.ANY_BASE_STACK_SIDE: 0>¶

BELOW = <BaseStackWhichSide.BELOW: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.ChiState¶

Bases: pybind11_object

Members:

ANY_CHI

ANTI

SYN

NO_CHI

ANTI = <ChiState.ANTI: 1>¶

ANY_CHI = <ChiState.ANY_CHI: 0>¶

NO_CHI = <ChiState.NO_CHI: 3>¶

SYN = <ChiState.SYN: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.GaussianParameter¶

Bases: pybind11_object

property amplitude¶

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

property center¶

property width¶

class pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation¶

Bases: pybind11_object

Members:

ANY_LW_BASE_DOUBLET_ORIENTATION

CIS

TRANS

ANY_LW_BASE_DOUBLET_ORIENTATION = <LW_BaseDoubletOrientation.ANY_LW_BASE_DOUBLET_ORIENTATION: 0>¶

CIS = <LW_BaseDoubletOrientation.CIS: 1>¶

TRANS = <LW_BaseDoubletOrientation.TRANS: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.PuckerState¶

Bases: pybind11_object

Members:

ANY_PUCKER

NORTH

SOUTH

NO_PUCKER

ANY_PUCKER = <PuckerState.ANY_PUCKER: 0>¶

NORTH = <PuckerState.NORTH: 1>¶

NO_PUCKER = <PuckerState.NO_PUCKER: 3>¶

SOUTH = <PuckerState.SOUTH: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo¶

Bases: pybind11_object

alpha_aform(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::alpha_aform() const –> double

beta_aform(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::beta_aform() const –> double

chi_north_anti(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::chi_north_anti() const –> double

chi_north_syn(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::chi_north_syn() const –> double

chi_south_anti(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::chi_south_anti() const –> double

chi_south_syn(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::chi_south_syn() const –> double

delta_cutoff(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::delta_cutoff() const –> double

delta_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::delta_north() const –> double

delta_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::delta_south() const –> double

epsilon_aform(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::epsilon_aform() const –> double

epsilon_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::epsilon_north() const –> double

epsilon_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::epsilon_south() const –> double

gamma_aform(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gamma_aform() const –> double

gaussian_parameter_set_alpha(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_alpha() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_beta(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_beta() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_chi_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_chi_north() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_chi_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_chi_south() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_delta_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_delta_north() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_delta_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_delta_south() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_epsilon_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_epsilon_north() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_epsilon_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_epsilon_south() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_gamma(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_gamma() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_nu1_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_nu1_north() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_nu1_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_nu1_south() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_nu2_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_nu2_north() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_nu2_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_nu2_south() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_zeta_alpha_ap(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_zeta_alpha_ap() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_zeta_alpha_sc_minus(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_zeta_alpha_sc_minus() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

gaussian_parameter_set_zeta_alpha_sc_plus(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::gaussian_parameter_set_zeta_alpha_sc_plus() const –> class utility::vector1<class core::chemical::rna::GaussianParameter, class std::allocator<class core::chemical::rna::GaussianParameter> >

nu1_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::nu1_north() const –> double

nu1_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::nu1_south() const –> double

nu2_north(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::nu2_north() const –> double

nu2_south(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::nu2_south() const –> double

zeta_aform(self: pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo) → float¶: C++: core::chemical::rna::RNA_FittedTorsionInfo::zeta_aform() const –> double

class pyrosetta.rosetta.core.chemical.rna.RNA_Info¶

Bases: pybind11_object

//////////////////////////////////Parin S, Dec 23, 2011: RNA stuff//////////////////////////////////////////

RNA_base_atoms(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::chemical::rna::RNA_Info::RNA_base_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

atom_is_phosphate(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info, atomno: int) → bool¶

quick lookup: is the atom with the given index is part of the RNA phosphate or not?

C++: core::chemical::rna::RNA_Info::atom_is_phosphate(const unsigned long) const –> bool

atom_is_virtual(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info, atomno: int) → bool¶: C++: core::chemical::rna::RNA_Info::atom_is_virtual(const unsigned long) const –> bool

property base_atom_list_¶

c1prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::c1prime_atom_index() const –> unsigned long

property c1prime_index_¶

c2prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::c2prime_atom_index() const –> unsigned long

property c2prime_index_¶

c3prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::c3prime_atom_index() const –> unsigned long

property c3prime_index_¶

c4prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::c4prime_atom_index() const –> unsigned long

property c4prime_index_¶

c5prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::c5prime_atom_index() const –> unsigned long

property c5prime_index_¶

chi_number_pseudoalpha(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::chi_number_pseudoalpha() const –> unsigned long

property chi_number_pseudoalpha_¶

chi_number_pseudobeta(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::chi_number_pseudobeta() const –> unsigned long

property chi_number_pseudobeta_¶

chi_number_pseudoepsilon(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::chi_number_pseudoepsilon() const –> unsigned long

property chi_number_pseudoepsilon_¶

chi_number_pseudogamma(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::chi_number_pseudogamma() const –> unsigned long

property chi_number_pseudogamma_¶

chi_number_pseudozeta(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::chi_number_pseudozeta() const –> unsigned long

property chi_number_pseudozeta_¶

ho2prime_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::ho2prime_index() const –> unsigned long

property ho2prime_index_¶

is_RNA_base(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::chemical::rna::RNA_Info::is_RNA_base() const –> const class utility::vector1<bool, class std::allocator<bool> > &

property is_RNA_base_¶

is_RNA_base_atom(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info, atomno: int) → bool¶: C++: core::chemical::rna::RNA_Info::is_RNA_base_atom(const unsigned long) const –> bool

is_phosphate(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::chemical::rna::RNA_Info::is_phosphate() const –> const class utility::vector1<bool, class std::allocator<bool> > &

property is_phosphate_¶

is_virtual(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → pyrosetta.rosetta.utility.vector1_bool¶

/////////Fast lookup functions///////

C++: core::chemical::rna::RNA_Info::is_virtual() const –> const class utility::vector1<bool, class std::allocator<bool> > &

property is_virtual_¶

o2prime_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::o2prime_index() const –> unsigned long

property o2prime_index_¶

o3prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::o3prime_atom_index() const –> unsigned long

property o3prime_index_¶

o4prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::o4prime_atom_index() const –> unsigned long

property o4prime_index_¶

o5prime_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::o5prime_atom_index() const –> unsigned long

property o5prime_index_¶

op1_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::op1_atom_index() const –> unsigned long

property op1_atom_index_¶

op2_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::op2_atom_index() const –> unsigned long

property op2_atom_index_¶

p_atom_index(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info) → int¶: C++: core::chemical::rna::RNA_Info::p_atom_index() const –> unsigned long

property p_atom_index_¶

static rna_update_last_controlling_chi(residue_type_in: pyrosetta.rosetta.core.chemical.ResidueType, last_controlling_chi: pyrosetta.rosetta.utility.vector1_unsigned_long, atoms_last_controlled_by_chi: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None¶

This is used for setting up the two passed vectors on the ResidueType.: This can/will be called before this RNA_Info object is complete, so it’s static.

C++: core::chemical::rna::RNA_Info::rna_update_last_controlling_chi(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &) –> void

update_derived_rna_data(self: pyrosetta.rosetta.core.chemical.rna.RNA_Info, residue_type_in: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::rna::RNA_Info::update_derived_rna_data(const class core::chemical::ResidueType &) –> void

class pyrosetta.rosetta.core.chemical.rna.RNA_Torsion¶

Bases: pybind11_object

Members:

ANY_TORSION

ALPHA

BETA

GAMMA

DELTA

EPSILON

ZETA

CHI

NU2

NU1

O2H

ALPHA = <RNA_Torsion.ALPHA: 1>¶

ANY_TORSION = <RNA_Torsion.ANY_TORSION: 0>¶

BETA = <RNA_Torsion.BETA: 2>¶

CHI = <RNA_Torsion.CHI: 7>¶

DELTA = <RNA_Torsion.DELTA: 4>¶

EPSILON = <RNA_Torsion.EPSILON: 5>¶

GAMMA = <RNA_Torsion.GAMMA: 3>¶

NU1 = <RNA_Torsion.NU1: 9>¶

NU2 = <RNA_Torsion.NU2: 8>¶

O2H = <RNA_Torsion.O2H: 10>¶

ZETA = <RNA_Torsion.ZETA: 6>¶

property name¶

property value¶

pyrosetta.rosetta.core.chemical.rna.add_values_from_center(torsions: pyrosetta.rosetta.utility.vector1_double, center: float, max_range: float, bin_size: float) → None¶: C++: core::chemical::rna::add_values_from_center(class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double) –> void

pyrosetta.rosetta.core.chemical.rna.chi1_torsion_atom(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rna::chi1_torsion_atom(const class core::chemical::ResidueType &) –> const std::string

pyrosetta.rosetta.core.chemical.rna.chi1_torsion_atom_index(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::rna::chi1_torsion_atom_index(const class core::chemical::ResidueType &) –> unsigned long

pyrosetta.rosetta.core.chemical.rna.convert_acgu_to_1234(c: str) → int¶: C++: core::chemical::rna::convert_acgu_to_1234(const char) –> unsigned long

pyrosetta.rosetta.core.chemical.rna.default_jump_atom(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rna::default_jump_atom(const class core::chemical::ResidueType &) –> const std::string

pyrosetta.rosetta.core.chemical.rna.first_base_atom(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rna::first_base_atom(const class core::chemical::ResidueType &) –> const std::string

pyrosetta.rosetta.core.chemical.rna.first_base_atom_index(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::rna::first_base_atom_index(const class core::chemical::ResidueType &) –> unsigned long

pyrosetta.rosetta.core.chemical.rna.get_LW_orientation_from_char(o: str) → pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation¶: C++: core::chemical::rna::get_LW_orientation_from_char(const char) –> enum core::chemical::rna::LW_BaseDoubletOrientation

pyrosetta.rosetta.core.chemical.rna.get_LW_orientation_from_num(num: int) → str¶: C++: core::chemical::rna::get_LW_orientation_from_num(const unsigned long) –> char

pyrosetta.rosetta.core.chemical.rna.get_WC_atom(res_type: pyrosetta.rosetta.core.chemical.AA) → str¶: C++: core::chemical::rna::get_WC_atom(const enum core::chemical::AA &) –> std::string

pyrosetta.rosetta.core.chemical.rna.get_base_pair_atoms(rsd_type1: pyrosetta.rosetta.core.chemical.ResidueType, rsd_type2: pyrosetta.rosetta.core.chemical.ResidueType, atom_ids1: pyrosetta.rosetta.utility.vector1_std_string, atom_ids2: pyrosetta.rosetta.utility.vector1_std_string, edge1: pyrosetta.rosetta.core.chemical.rna.BaseEdge, edge2: pyrosetta.rosetta.core.chemical.rna.BaseEdge, orientation: pyrosetta.rosetta.core.chemical.rna.LW_BaseDoubletOrientation) → None¶: C++: core::chemical::rna::get_base_pair_atoms(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &, class utility::vector1<std::string, class std::allocator<std::string > > &, class utility::vector1<std::string, class std::allocator<std::string > > &, const enum core::chemical::rna::BaseEdge, const enum core::chemical::rna::BaseEdge, const enum core::chemical::rna::LW_BaseDoubletOrientation) –> void

pyrosetta.rosetta.core.chemical.rna.get_edge_from_char(e: str) → pyrosetta.rosetta.core.chemical.rna.BaseEdge¶: C++: core::chemical::rna::get_edge_from_char(const char) –> enum core::chemical::rna::BaseEdge

pyrosetta.rosetta.core.chemical.rna.get_edge_from_num(num: int) → str¶: C++: core::chemical::rna::get_edge_from_num(const unsigned long) –> char

pyrosetta.rosetta.core.chemical.rna.get_epsilon_torsions(*args, **kwargs)¶

Overloaded function.

get_epsilon_torsions(delta: float, extra_epsilon: bool, bin_size: float) -> pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::rna::get_epsilon_torsions(const double, const bool, const double) –> class utility::vector1<double, class std::allocator<double> >

get_epsilon_torsions(north_pucker: bool) -> pyrosetta.rosetta.utility.vector1_double
get_epsilon_torsions(north_pucker: bool, extra_epsilon: bool) -> pyrosetta.rosetta.utility.vector1_double
get_epsilon_torsions(north_pucker: bool, extra_epsilon: bool, bin_size: float) -> pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::rna::get_epsilon_torsions(const bool, const bool, const double) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.chemical.rna.get_full_LW_orientation_from_num(num: int) → str¶: C++: core::chemical::rna::get_full_LW_orientation_from_num(const unsigned long) –> std::string

pyrosetta.rosetta.core.chemical.rna.get_full_edge_from_num(num: int) → str¶: C++: core::chemical::rna::get_full_edge_from_num(const unsigned long) –> std::string

pyrosetta.rosetta.core.chemical.rna.get_full_orientation_from_num(num: int) → str¶: C++: core::chemical::rna::get_full_orientation_from_num(const unsigned long) –> std::string

pyrosetta.rosetta.core.chemical.rna.get_full_side_from_num(num: int) → str¶: C++: core::chemical::rna::get_full_side_from_num(const unsigned long) –> std::string

pyrosetta.rosetta.core.chemical.rna.get_full_torsions(*args, **kwargs)¶

Overloaded function.

get_full_torsions() -> pyrosetta.rosetta.utility.vector1_double
get_full_torsions(bin_size: float) -> pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::rna::get_full_torsions(const double) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.chemical.rna.get_orientation_from_char(o: str) → pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation¶: C++: core::chemical::rna::get_orientation_from_char(const char) –> enum core::chemical::rna::BaseDoubletOrientation

pyrosetta.rosetta.core.chemical.rna.get_orientation_from_num(num: int) → str¶: C++: core::chemical::rna::get_orientation_from_num(const unsigned long) –> char

pyrosetta.rosetta.core.chemical.rna.get_residue_base_state(rsd: core::conformation::Residue) → pyrosetta.rosetta.core.chemical.rna.ChiState¶: C++: core::chemical::rna::get_residue_base_state(const class core::conformation::Residue &) –> enum core::chemical::rna::ChiState

pyrosetta.rosetta.core.chemical.rna.get_residue_pucker_state(rsd: core::conformation::Residue) → pyrosetta.rosetta.core.chemical.rna.PuckerState¶: C++: core::chemical::rna::get_residue_pucker_state(const class core::conformation::Residue &) –> enum core::chemical::rna::PuckerState

pyrosetta.rosetta.core.chemical.rna.get_rna_base_centroid(*args, **kwargs)¶

Overloaded function.

get_rna_base_centroid(rsd: core::conformation::Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t
get_rna_base_centroid(rsd: core::conformation::Residue, verbose: bool) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::rna::get_rna_base_centroid(const class core::conformation::Residue &, bool) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.chemical.rna.get_rna_base_coordinate_system(rsd: core::conformation::Residue, centroid: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzMatrix_double_t¶: C++: core::chemical::rna::get_rna_base_coordinate_system(const class core::conformation::Residue &, const class numeric::xyzVector<double> &) –> class numeric::xyzMatrix<double>

pyrosetta.rosetta.core.chemical.rna.get_rna_base_coordinate_system_stub(rsd: core::conformation::Residue) → core::kinematics::Stub¶: C++: core::chemical::rna::get_rna_base_coordinate_system_stub(const class core::conformation::Residue &) –> class core::kinematics::Stub

pyrosetta.rosetta.core.chemical.rna.get_side_from_num(num: int) → str¶: C++: core::chemical::rna::get_side_from_num(const unsigned long) –> char

pyrosetta.rosetta.core.chemical.rna.get_watson_crick_base_pair_atoms(rsd_type1: pyrosetta.rosetta.core.chemical.ResidueType, rsd_type2: pyrosetta.rosetta.core.chemical.ResidueType, atom1: str, atom2: str) → None¶: C++: core::chemical::rna::get_watson_crick_base_pair_atoms(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &, std::string &, std::string &) –> void

pyrosetta.rosetta.core.chemical.rna.is_base_phosphate_atom_pair(rsd_1: core::conformation::Residue, rsd_2: core::conformation::Residue, atomno_1: int, atomno_2: int) → bool¶: C++: core::chemical::rna::is_base_phosphate_atom_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long, const unsigned long) –> bool

pyrosetta.rosetta.core.chemical.rna.possibly_canonical(aa1: pyrosetta.rosetta.core.chemical.AA, aa2: pyrosetta.rosetta.core.chemical.AA) → bool¶: C++: core::chemical::rna::possibly_canonical(const enum core::chemical::AA &, const enum core::chemical::AA &) –> bool

pyrosetta.rosetta.core.chemical.rna.possibly_canonical_strict(aa1: pyrosetta.rosetta.core.chemical.AA, aa2: pyrosetta.rosetta.core.chemical.AA) → bool¶: C++: core::chemical::rna::possibly_canonical_strict(const enum core::chemical::AA &, const enum core::chemical::AA &) –> bool

pyrosetta.rosetta.core.chemical.rna.rna_dna_match(aa1: pyrosetta.rosetta.core.chemical.AA, aa2: pyrosetta.rosetta.core.chemical.AA) → bool¶: C++: core::chemical::rna::rna_dna_match(const enum core::chemical::AA &, const enum core::chemical::AA &) –> bool