rna¶

Bindings for core::scoring::rna namespace

class pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of RNA centroid information inside the pose.

/ Rhiju move this to its own namespace!

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) -> None
__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, arg0: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

base_centroids(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t¶: C++: core::scoring::rna::RNA_CentroidInfo::base_centroids() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

base_stubs(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) → pyrosetta.rosetta.utility.vector1_core_kinematics_Stub¶: C++: core::scoring::rna::RNA_CentroidInfo::base_stubs() const –> const class utility::vector1<class core::kinematics::Stub, class std::allocator<class core::kinematics::Stub> > &

calculated(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) → bool¶: C++: core::scoring::rna::RNA_CentroidInfo::calculated() –> bool &

clone(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::scoring::rna::RNA_CentroidInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_base_centroid(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.numeric.xyzVector_double_t¶: C++: core::scoring::rna::RNA_CentroidInfo::get_base_centroid(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

get_base_coordinate_system(*args, **kwargs)¶

Overloaded function.

get_base_coordinate_system(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, rsd: pyrosetta.rosetta.core.conformation.Residue, centroid: pyrosetta.rosetta.numeric.xyzVector_double_t) -> pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(const class core::conformation::Residue &, const class numeric::xyzVector<double> &) const –> class core::kinematics::Stub

get_base_coordinate_system(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) -> pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(const class core::conformation::Residue &) const –> class core::kinematics::Stub

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

set_calculated(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, setting: bool) → None¶: C++: core::scoring::rna::RNA_CentroidInfo::set_calculated(const bool &) –> void

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

update(self: pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::RNA_CentroidInfo::update(const class core::pose::Pose &) –> void

class pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential¶

Bases: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) -> None
__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, arg0: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → float¶

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

This method allows the WholeStructureEnergy class to define which edges should be included in the EnergyGraph so that during the finalize() method the Energy class can iterate across the EnergyGraph. This iteration occurrs in the SecondaryStructureEnergy class, where the edges must span 12 angstroms between the centroids. Arguably, the SecondaryStructureEnergy class could use the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph span such long distances.

C++: core::scoring::methods::WholeStructureEnergy::atomic_interaction_cutoff() const –> double

base_backbone_distance_cutoff(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff() const –> double

base_backbone_rho_cutoff(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff() const –> double

base_backbone_z_cutoff(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff() const –> double

check_clear_for_stacking(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose, i: int, sign: int) → bool¶: C++: core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(class core::pose::Pose &, const unsigned long &, const int &) const –> bool

check_for_base_neighbor(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, heavy_atom_j: pyrosetta.rosetta.numeric.xyzVector_double_t, atom_cutoff_weight: float) → bool¶: C++: core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(const class core::conformation::Residue &, const class numeric::xyzVector<double> &, double &) const –> bool

check_forming_base_pair(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose, i: int, j: int) → bool¶: C++: core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(class core::pose::Pose &, const unsigned long &, const unsigned long &) const –> bool

clone(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

clone

C++: core::scoring::rna::RNA_LowResolutionPotential::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose) → bool¶

Should this EnergyMethod have score and derivative evaluation: evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: ObjexxFCL::FArray1D<int>, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_atom_derivative_base_base(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_atom_derivative_rna_backbone_backbone(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(const class core::id::AtomID &, const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_atom_derivative_rna_base_backbone(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(const class core::id::AtomID &, const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_atom_derivative_rna_repulsive(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(const class core::id::AtomID &, const class core::pose::Pose &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_rna_base_pair_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rna_raw_base_base_info: pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, centroid1: pyrosetta.rosetta.numeric.xyzVector_double_t, centroid2: pyrosetta.rosetta.numeric.xyzVector_double_t, stub1: pyrosetta.rosetta.core.kinematics.Stub, stub2: pyrosetta.rosetta.core.kinematics.Stub) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy(class core::pose::rna::RNA_RawBaseBaseInfo &, const class core::conformation::Residue &, const class core::conformation::Residue &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class core::kinematics::Stub &, const class core::kinematics::Stub &) const –> void

finalize(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::finalize(class core::pose::Pose &) const –> void

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, total_energy: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

called by the ScoreFunction at the end of energy evaluation.: The derived class has the opportunity to accumulate a score into the pose’s total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.

C++: core::scoring::methods::EnergyMethod::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

get_base_backbone(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, m: int) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const unsigned long &) const –> double

get_rna_stack_score(*args, **kwargs)¶

Overloaded function.

get_rna_stack_score(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, x: float, y: float, z: float) -> float
get_rna_stack_score(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, x: float, y: float, z: float, deriv_x: float) -> float
get_rna_stack_score(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, x: float, y: float, z: float, deriv_x: float, deriv_y: float) -> float
get_rna_stack_score(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, x: float, y: float, z: float, deriv_x: float, deriv_y: float, deriv_z: float) -> float

C++: core::scoring::rna::RNA_LowResolutionPotential::get_rna_stack_score(const double, const double, const double, double &, double &, double &) const –> double

get_zeta_cutoff(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, res_i: pyrosetta.rosetta.core.conformation.Residue, zeta_hoogsteen_cutoff: float, zeta_sugar_cutoff: float) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff(const class core::conformation::Residue &, double &, double &) const –> void

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType¶: C++: core::scoring::methods::WholeStructureEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose) → bool¶

Should this EnergyMethod have score and derivative evaluation: evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

more_precise_base_pair_classification(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, value: bool) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification(const bool &) –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None¶

If an energy method needs to cache data in a packing::RotamerSet object before: rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not: all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

rna_backbone_backbone_pair_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::rna_backbone_backbone_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

rna_base_backbone_pair_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, centroid1: pyrosetta.rosetta.numeric.xyzVector_double_t, centroid2: pyrosetta.rosetta.numeric.xyzVector_double_t, stub1: pyrosetta.rosetta.core.kinematics.Stub, stub2: pyrosetta.rosetta.core.kinematics.Stub) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class core::kinematics::Stub &, const class core::kinematics::Stub &) const –> double

rna_repulsive_pair_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) → float¶: C++: core::scoring::rna::RNA_LowResolutionPotential::rna_repulsive_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Called immediately before atom- and DOF-derivatives are calculated: allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → None¶

Called at the beginning of atom tree minimization, this method: allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None¶

if an energy method needs to cache data in the Energies object,: before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

if an energy method needs to cache something in the pose (e.g. in pose.energies()),: before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None¶

Do any setup work before scoring, caching any slow-to-compute data that will be used during: energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

C++: core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class basic::datacache::BasicDataCache &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : bool) → None¶

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(class std::basic_ostream<char> &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, resid: int) → None¶

If the pose changes in the middle of a packing (as happens in rotamer trials) and if: an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

update_rna_base_base_interactions(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(class core::pose::Pose &) const –> void

update_rna_base_pair_list(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list(class core::pose::Pose &) const –> void

update_rna_centroid_info(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info(class core::pose::Pose &) const –> void

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

class pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo¶

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of RNA centroid, useful atom, base-base info inside the pose.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) -> None
__init__(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo, arg0: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

atom_numbers_for_mg_calculation(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_mg_calculation() const –> const 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> > > > &

atom_numbers_for_vdw_calculation(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_vdw_calculation() const –> const 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> > > > &

calculated(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → bool¶: C++: core::scoring::rna::RNA_ScoringInfo::calculated() const –> bool

clone(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::scoring::rna::RNA_ScoringInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

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

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

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

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

nonconst_atom_numbers_for_mg_calculation(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_mg_calculation() –> 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> > > > &

nonconst_atom_numbers_for_vdw_calculation(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t¶: C++: core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_vdw_calculation() –> 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> > > > &

nonconst_is_buried(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::scoring::rna::RNA_ScoringInfo::nonconst_is_buried() –> class utility::vector1<bool, class std::allocator<bool> > &

nonconst_is_interface(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::scoring::rna::RNA_ScoringInfo::nonconst_is_interface() –> class utility::vector1<bool, class std::allocator<bool> > &

nonconst_is_magnesium(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::scoring::rna::RNA_ScoringInfo::nonconst_is_magnesium() –> class utility::vector1<bool, class std::allocator<bool> > &

rna_centroid_info(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo¶: C++: core::scoring::rna::RNA_ScoringInfo::rna_centroid_info() –> class core::scoring::rna::RNA_CentroidInfo &

rna_data_info(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.core.pose.rna.RNA_DataInfo¶: C++: core::scoring::rna::RNA_ScoringInfo::rna_data_info() –> class core::pose::rna::RNA_DataInfo &

rna_filtered_base_base_info(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo¶: C++: core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info() –> class core::pose::rna::RNA_FilteredBaseBaseInfo &

rna_raw_base_base_info(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo) → pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo¶: C++: core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info() –> class core::pose::rna::RNA_RawBaseBaseInfo &

set_mg_calculation_annotated_sequence(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo, sequence: str) → None¶: C++: core::scoring::rna::RNA_ScoringInfo::set_mg_calculation_annotated_sequence(const class std::basic_string<char> &) –> void

set_vdw_calculation_annotated_sequence(self: pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo, sequence: str) → None¶: C++: core::scoring::rna::RNA_ScoringInfo::set_vdw_calculation_annotated_sequence(const class std::basic_string<char> &) –> void

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

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

class pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential) -> None
__init__(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential, arg0: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

evaluate_rnp_aa_rna_backbone_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential, protein_rsd: pyrosetta.rosetta.core.conformation.Residue, dist_to_backbone: float) → float¶: C++: core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(const class core::conformation::Residue &, const double &) const –> double

evaluate_rnp_base_pair_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, rnp_bp_score: float) → None¶: C++: core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(const class core::conformation::Residue &, const class core::conformation::Residue &, const double &, const double &, double &) const –> void

evaluate_rnp_pair_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, rsd1_is_interface: bool, rsd1_is_buried: bool, rsd2_is_interface: bool, rsd2_is_buried: bool, d: float, rnp_pair_score: float) → None¶: C++: core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(const class core::conformation::Residue &, const class core::conformation::Residue &, const bool &, const bool &, const bool &, const bool &, const double &, double &) const –> void

initialize_rnp_aa_rna_backbone(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential) → None¶: C++: core::scoring::rna::RNP_LowResPotential::initialize_rnp_aa_rna_backbone() –> void

initialize_rnp_base_pair(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential) → None¶: C++: core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair() –> void

initialize_rnp_pair(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential) → None¶: C++: core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair() –> void

pyrosetta.rosetta.core.scoring.rna.check_rna_loop(pose: pyrosetta.rosetta.core.pose.Pose, n: int, nloop: int) → bool¶: C++: core::scoring::rna::check_rna_loop(const class core::pose::Pose &, const unsigned long &, const unsigned long &) –> bool

pyrosetta.rosetta.core.scoring.rna.check_stack(i: int, j: int, base_stack_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack) → bool¶: C++: core::scoring::rna::check_stack(const unsigned long &, const unsigned long &, const class utility::vector1<class core::pose::rna::BaseStack, class std::allocator<class core::pose::rna::BaseStack> > &) –> bool

pyrosetta.rosetta.core.scoring.rna.check_watson_crick_sequence(*args, **kwargs)¶

Overloaded function.

check_watson_crick_sequence(pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) -> bool
check_watson_crick_sequence(pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int, strict: bool) -> bool

C++: core::scoring::rna::check_watson_crick_sequence(const class core::pose::Pose &, const unsigned long &, const unsigned long &, const bool) –> bool

pyrosetta.rosetta.core.scoring.rna.clear_rna_scoring_info(pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: core::scoring::rna::clear_rna_scoring_info(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.rna.get_fade_correction(z: float, cutoff_lower: float, cutoff_upper: float, fade_zone: float, fade_value: float, fade_deriv: float) → None¶: C++: core::scoring::rna::get_fade_correction(const double, const double, const double, const double, double &, double &) –> void

pyrosetta.rosetta.core.scoring.rna.get_rna_motif_score(pose: pyrosetta.rosetta.core.pose.Pose, potential: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, filtered_base_base_info: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → float¶

wrapper around get_rna_motifs – outputs score.

C++: core::scoring::rna::get_rna_motif_score(const class core::pose::Pose &, const class core::scoring::rna::RNA_LowResolutionPotential &, const class core::pose::rna::RNA_FilteredBaseBaseInfo &) –> double

pyrosetta.rosetta.core.scoring.rna.get_rna_motifs(pose: pyrosetta.rosetta.core.pose.Pose, potential: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential, filtered_base_base_info: pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo) → pyrosetta.rosetta.core.scoring.rna.RNA_Motifs¶

identify RNA motifs inside pose

this version allows user to supply preinstantiated potential

and precalculated filtered_base_base_info for speed.

C++: core::scoring::rna::get_rna_motifs(const class core::pose::Pose &, const class core::scoring::rna::RNA_LowResolutionPotential &, const class core::pose::rna::RNA_FilteredBaseBaseInfo &) –> class core::scoring::rna::RNA_Motifs

pyrosetta.rosetta.core.scoring.rna.nonconst_rna_scoring_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo¶: C++: core::scoring::rna::nonconst_rna_scoring_info_from_pose(class core::pose::Pose &) –> class core::scoring::rna::RNA_ScoringInfo &

pyrosetta.rosetta.core.scoring.rna.output_rna_motif(pose: pyrosetta.rosetta.core.pose.Pose, motif: pyrosetta.rosetta.core.scoring.rna.RNA_Motif) → None¶: C++: core::scoring::rna::output_rna_motif(const class core::pose::Pose &, const class core::scoring::rna::RNA_Motif &) –> void

pyrosetta.rosetta.core.scoring.rna.output_rna_motifs(pose: pyrosetta.rosetta.core.pose.Pose, motifs: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) → None¶: C++: core::scoring::rna::output_rna_motifs(const class core::pose::Pose &, const class core::scoring::rna::RNA_Motifs &) –> void

pyrosetta.rosetta.core.scoring.rna.protein_atom_name_to_num(*args, **kwargs)¶

Overloaded function.

protein_atom_name_to_num(name: str) -> int

C++: core::scoring::rna::protein_atom_name_to_num(const class std::basic_string<char> &) –> unsigned long

protein_atom_name_to_num(name: str, resname: str) -> int

C++: core::scoring::rna::protein_atom_name_to_num(const class std::basic_string<char> &, const class std::basic_string<char> &) –> unsigned long

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

pyrosetta.rosetta.core.scoring.rna.rna_scoring_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo¶: C++: core::scoring::rna::rna_scoring_info_from_pose(const class core::pose::Pose &) –> const class core::scoring::rna::RNA_ScoringInfo &

pyrosetta.rosetta.core.scoring.rna.to_string(type: pyrosetta.rosetta.core.scoring.rna.RNA_MotifType) → str¶: C++: core::scoring::rna::to_string(enum core::scoring::rna::RNA_MotifType) –> std::string