rna

Bindings for core::scoring::rna namespace

class pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW, : pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW) pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW

C++: core::scoring::rna::RNA_AtomVDW::operator=(const class core::scoring::rna::RNA_AtomVDW &) –> class core::scoring::rna::RNA_AtomVDW &

bump_parameter(self: pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW, atom1: int, atom2: int, rsd1: pyrosetta.rosetta.core.chemical.ResidueType, rsd2: pyrosetta.rosetta.core.chemical.ResidueType) float

C++: core::scoring::rna::RNA_AtomVDW::bump_parameter(const unsigned long, const unsigned long, const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) const –> double

bump_parameter_rnp(self: pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW, atom_RNA: int, atom_protein: int, rna_type: pyrosetta.rosetta.core.chemical.ResidueType) float

C++: core::scoring::rna::RNA_AtomVDW::bump_parameter_rnp(const unsigned long, const unsigned long, const class core::chemical::ResidueType &) const –> double

initialize_rnp_vdw_parameters(self: pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW) None

C++: core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters() –> void

vdw_atom_list(self: pyrosetta.rosetta.core.scoring.rna.RNA_AtomVDW, rt: pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.utility.vector1_std_string

C++: core::scoring::rna::RNA_AtomVDW::vdw_atom_list(const class core::chemical::ResidueType &) const –> const class utility::vector1<std::string, class std::allocator<std::string > >

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!

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.

  1. 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

  1. 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_EnergyMethodOptions

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, : pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions

C++: core::scoring::rna::RNA_EnergyMethodOptions::operator=(const class core::scoring::rna::RNA_EnergyMethodOptions &) –> class core::scoring::rna::RNA_EnergyMethodOptions &

initialize_from_options(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) None

C++: core::scoring::rna::RNA_EnergyMethodOptions::initialize_from_options() –> void

rna_base_pair_xy_filename(*args, **kwargs)

Overloaded function.

  1. rna_base_pair_xy_filename(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) -> str

Parameter for changing rna_base_pair_xy file name.

C++: core::scoring::rna::RNA_EnergyMethodOptions::rna_base_pair_xy_filename() const –> std::string

  1. rna_base_pair_xy_filename(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, setting: str) -> None

C++: core::scoring::rna::RNA_EnergyMethodOptions::rna_base_pair_xy_filename(const std::string &) –> void

show(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::rna::RNA_EnergyMethodOptions::show(std::ostream &) const –> void

suiteness_bonus(*args, **kwargs)

Overloaded function.

  1. suiteness_bonus(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) -> str

Parameter for changing suiteness_bonus directory name.

C++: core::scoring::rna::RNA_EnergyMethodOptions::suiteness_bonus() const –> std::string

  1. suiteness_bonus(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, setting: str) -> None

C++: core::scoring::rna::RNA_EnergyMethodOptions::suiteness_bonus(const std::string &) –> void

syn_G_potential_bonus(*args, **kwargs)

Overloaded function.

  1. syn_G_potential_bonus(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) -> float

Parameter for adjusting syn-G potential level in RNA_TorsionPotential.

C++: core::scoring::rna::RNA_EnergyMethodOptions::syn_G_potential_bonus() const –> double

  1. syn_G_potential_bonus(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, setting: float) -> None

C++: core::scoring::rna::RNA_EnergyMethodOptions::syn_G_potential_bonus(double) –> void

torsion_potential(*args, **kwargs)

Overloaded function.

  1. torsion_potential(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions) -> str

Parameter for changing torsion_potential directory name.

C++: core::scoring::rna::RNA_EnergyMethodOptions::torsion_potential() const –> std::string

  1. torsion_potential(self: pyrosetta.rosetta.core.scoring.rna.RNA_EnergyMethodOptions, setting: str) -> None

C++: core::scoring::rna::RNA_EnergyMethodOptions::torsion_potential(const std::string &) –> void

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

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

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

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) None
Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

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, : 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: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: 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, : core::pose::Pose, : 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_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) None
Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

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

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, total_energy: 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.

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

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

  3. 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

  4. 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

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) bool
Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?

Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) bool
Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?

NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

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, : 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, : 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

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: 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: core::pose::Pose, sfxn: 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, : core::pose::Pose, : core::scoring::ScoreFunction, : 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, : 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_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) None
if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : 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: core::pose::Pose, sfxn: 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, : core::pose::Pose, : bool) None

show additional information of the energy method

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : 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_LowResolutionPotentialCreator

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

assign(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator, : pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator) pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator

C++: core::scoring::rna::RNA_LowResolutionPotentialCreator::operator=(const class core::scoring::rna::RNA_LowResolutionPotentialCreator &) –> class core::scoring::rna::RNA_LowResolutionPotentialCreator &

create_energy_method(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new RNA_LowResolutionPotential

C++: core::scoring::rna::RNA_LowResolutionPotentialCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotentialCreator) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType
Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: core::scoring::rna::RNA_LowResolutionPotentialCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.scoring.rna.RNA_Motif

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motif, : pyrosetta.rosetta.core.scoring.rna.RNA_Motif) pyrosetta.rosetta.core.scoring.rna.RNA_Motif

C++: core::scoring::rna::RNA_Motif::operator=(const class core::scoring::rna::RNA_Motif &) –> class core::scoring::rna::RNA_Motif &

residues(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motif) pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::scoring::rna::RNA_Motif::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_residues(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motif, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::scoring::rna::RNA_Motif::set_residues(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_type(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motif, setting: pyrosetta.rosetta.core.scoring.rna.RNA_MotifType) None

C++: core::scoring::rna::RNA_Motif::set_type(const enum core::scoring::rna::RNA_MotifType &) –> void

type(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motif) pyrosetta.rosetta.core.scoring.rna.RNA_MotifType

C++: core::scoring::rna::RNA_Motif::type() const –> enum core::scoring::rna::RNA_MotifType

class pyrosetta.rosetta.core.scoring.rna.RNA_MotifType

Bases: pybind11_builtins.pybind11_object

Members:

U_TURN

UA_HANDLE

T_LOOP

INTERCALATED_T_LOOP

LOOP_E_SUBMOTIF

BULGED_G

GNRA_TETRALOOP

STRICT_WC_STACKED_PAIR

WC_STACKED_PAIR

A_MINOR

PLATFORM

TL_RECEPTOR

TETRALOOP_TL_RECEPTOR

Z_TURN

TANDEM_GA_SHEARED

TANDEM_GA_WATSON_CRICK

GA_MINOR

DOUBLE_T_LOOP

A_MINOR = <RNA_MotifType.A_MINOR: 9>
BULGED_G = <RNA_MotifType.BULGED_G: 5>
DOUBLE_T_LOOP = <RNA_MotifType.DOUBLE_T_LOOP: 17>
GA_MINOR = <RNA_MotifType.GA_MINOR: 16>
GNRA_TETRALOOP = <RNA_MotifType.GNRA_TETRALOOP: 6>
INTERCALATED_T_LOOP = <RNA_MotifType.INTERCALATED_T_LOOP: 3>
LOOP_E_SUBMOTIF = <RNA_MotifType.LOOP_E_SUBMOTIF: 4>
PLATFORM = <RNA_MotifType.PLATFORM: 10>
STRICT_WC_STACKED_PAIR = <RNA_MotifType.STRICT_WC_STACKED_PAIR: 7>
TANDEM_GA_SHEARED = <RNA_MotifType.TANDEM_GA_SHEARED: 14>
TANDEM_GA_WATSON_CRICK = <RNA_MotifType.TANDEM_GA_WATSON_CRICK: 15>
TETRALOOP_TL_RECEPTOR = <RNA_MotifType.TETRALOOP_TL_RECEPTOR: 12>
TL_RECEPTOR = <RNA_MotifType.TL_RECEPTOR: 11>
T_LOOP = <RNA_MotifType.T_LOOP: 2>
UA_HANDLE = <RNA_MotifType.UA_HANDLE: 1>
U_TURN = <RNA_MotifType.U_TURN: 0>
WC_STACKED_PAIR = <RNA_MotifType.WC_STACKED_PAIR: 8>
Z_TURN = <RNA_MotifType.Z_TURN: 13>
property name
class pyrosetta.rosetta.core.scoring.rna.RNA_Motifs

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs, : pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) pyrosetta.rosetta.core.scoring.rna.RNA_Motifs

C++: core::scoring::rna::RNA_Motifs::operator=(const class core::scoring::rna::RNA_Motifs &) –> class core::scoring::rna::RNA_Motifs &

get_motifs(*args, **kwargs)

Overloaded function.

  1. get_motifs(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) -> pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif

C++: core::scoring::rna::RNA_Motifs::get_motifs() const –> const class utility::vector1<class core::scoring::rna::RNA_Motif, class std::allocator<class core::scoring::rna::RNA_Motif> > &

  1. get_motifs(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs, type: pyrosetta.rosetta.core.scoring.rna.RNA_MotifType) -> pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif

C++: core::scoring::rna::RNA_Motifs::get_motifs(const enum core::scoring::rna::RNA_MotifType &) const –> const class utility::vector1<class core::scoring::rna::RNA_Motif, class std::allocator<class core::scoring::rna::RNA_Motif> > &

push_back(self: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs, rna_motif: pyrosetta.rosetta.core.scoring.rna.RNA_Motif) None

C++: core::scoring::rna::RNA_Motifs::push_back(const class core::scoring::rna::RNA_Motif &) –> void

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.

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 std::string &) –> 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 std::string &) –> 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.RNA_SuitePotential

Bases: pybind11_builtins.pybind11_object

class pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential

Bases: pybind11_builtins.pybind11_object

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential, 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_TorsionPotential::eval_atom_derivative(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_intrares_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &) –> double

intrares_side_chain_score(self: pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential) float

C++: core::scoring::rna::RNA_TorsionPotential::intrares_side_chain_score() const –> double

residue_pair_energy(self: pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: core::scoring::rna::RNA_TorsionPotential::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) const –> double

set_verbose(self: pyrosetta.rosetta.core.scoring.rna.RNA_TorsionPotential, setting: bool) None

C++: core::scoring::rna::RNA_TorsionPotential::set_verbose(const bool) –> void

class pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential

Bases: pybind11_builtins.pybind11_object

calc_rnp_pair_dist_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential, protein_rsd: pyrosetta.rosetta.core.conformation.Residue, RNA_rsd: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

convert_aa_to_index(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential, c: str) int

C++: core::scoring::rna::RNP_LowResPairDistPotential::convert_aa_to_index(const char) const –> unsigned long

evaluate_rnp_pair_dist_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, rnp_pair_dist_score: float) None

C++: core::scoring::rna::RNP_LowResPairDistPotential::evaluate_rnp_pair_dist_score(const class core::conformation::Residue &, const class core::conformation::Residue &, double &) const –> void

initialize_rnp_pair_dist(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResPairDistPotential) None

C++: core::scoring::rna::RNP_LowResPairDistPotential::initialize_rnp_pair_dist() –> void

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

Bases: pybind11_builtins.pybind11_object

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

class pyrosetta.rosetta.core.scoring.rna.RNP_LowResStackData

Bases: pybind11_builtins.pybind11_object

evaluate_rnp_stack_xy_score(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResStackData, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, x: float, y: float, rnp_stack_score: float) None

C++: core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(const class core::conformation::Residue &, const class core::conformation::Residue &, const double &, const double &, double &) const –> void

initialize_rnp_stack_xy(self: pyrosetta.rosetta.core.scoring.rna.RNP_LowResStackData) None

C++: core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy() –> void

class pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential

Bases: pybind11_builtins.pybind11_object

eval_score(self: pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: core::scoring::rna::TNA_SuitePotential::eval_score(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &) const –> bool

get_deriv(self: pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential) pyrosetta.rosetta.utility.fixedsizearray1_double_4_t

C++: core::scoring::rna::TNA_SuitePotential::get_deriv() const –> class utility::fixedsizearray1<double, 4>

get_score(self: pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential) float

C++: core::scoring::rna::TNA_SuitePotential::get_score() const –> double

get_torsion_ids(self: pyrosetta.rosetta.core.scoring.rna.TNA_SuitePotential) pyrosetta.rosetta.utility.vector1_core_id_TorsionID

C++: core::scoring::rna::TNA_SuitePotential::get_torsion_ids() const –> class utility::vector1<class core::id::TorsionID, class std::allocator<class core::id::TorsionID> >

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.

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

  2. 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. Used to be inlined – since this function is long, this is probably to no one’s advantage.

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_motifs_to_pymol(out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, rna_motifs: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) None

sets up .pml file that will color motifs.

C++: core::scoring::rna::output_motifs_to_pymol(std::ostream &, const class core::pose::Pose &, const class core::scoring::rna::RNA_Motifs &) –> void

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(*args, **kwargs)

Overloaded function.

  1. output_rna_motifs(out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, motifs: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) -> None

  2. output_rna_motifs(out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, motifs: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs, output_WC_stacked_pair: bool) -> None

C++: core::scoring::rna::output_rna_motifs(std::ostream &, const class core::pose::Pose &, const class core::scoring::rna::RNA_Motifs &, const bool) –> void

pyrosetta.rosetta.core.scoring.rna.output_rna_motifs_detailed(pose: pyrosetta.rosetta.core.pose.Pose, motifs: pyrosetta.rosetta.core.scoring.rna.RNA_Motifs) None

C++: core::scoring::rna::output_rna_motifs_detailed(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.

  1. protein_atom_name_to_num(name: str) -> int

C++: core::scoring::rna::protein_atom_name_to_num(const std::string &) –> unsigned long

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

C++: core::scoring::rna::protein_atom_name_to_num(const std::string &, const std::string &) –> 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