cenrot

Bindings for core::pack::dunbrack::cenrot namespace

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy

Bases: ContextIndependentOneBodyEnergy

assign(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, : pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy) → pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::operator=(const class core::pack::dunbrack::cenrot::CenRotDunEnergy &) –> class core::pack::dunbrack::cenrot::CenRotDunEnergy &

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

clone(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, p: pyrosetta.rosetta.core.pose.Pose) → bool

Yes. The DunbrackEnergy defines derivatives

for phi/psi and the chi dihedrals.

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::defines_dof_derivatives(const class core::pose::Pose &) const –> bool

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

defines_score_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, : pyrosetta.rosetta.core.conformation.Residue) → bool

During minimization, energy methods are allowed to decide that they say nothing

about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return “true” for all residues.

C++: core::scoring::methods::OneBodyEnergy::defines_score_for_residue(const class core::conformation::Residue &) 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_dof_derivative(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, dof_id: pyrosetta.rosetta.core.id.DOF_ID, tor_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

Deprecated.

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

eval_residue_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector, atom_derivs: pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair) → None

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, const class core::scoring::EMapVector &, class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &) const –> void

eval_residue_dof_derivative(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: pyrosetta.rosetta.core.id.TorsionID, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector) → float

Evaluate the phi/psi and chi dihedral derivatives

for the input residue.

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &) const –> double

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.pack.dunbrack.cenrot.CenRotDunEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) 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.pack.dunbrack.cenrot.CenRotDunEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

Returns the ci_1b element of the EnergyMethodType enumeration; this

method should NOT be overridden by derived classes.

C++: core::scoring::methods::ContextIndependentOneBodyEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, : pyrosetta.rosetta.core.pose.Pose) → bool

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

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_derivatives_for_residue_opportunity(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_minimization(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, pose: core::pose::Pose) → bool

Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so.

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

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

residue_energy(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

residue_energy_ext(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, min_data: core::scoring::ResSingleMinimizationData, pose: core::pose::Pose, emap: core::scoring::EMapVector) → None

Evaluate the one-body energies for a particular residue, in the context of a

given Pose, and with the help of a piece of cached data for minimization, increment those one body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns “true”. Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::residue_energy_ext(const class core::conformation::Residue &, const class core::scoring::ResSingleMinimizationData &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

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_derivatives_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None

Do any setup work necessary before evaluating the derivatives for this residue

C++: core::scoring::methods::OneBodyEnergy::setup_for_derivatives_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &, class basic::datacache::BasicDataCache &) 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_minimizing_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase, : pyrosetta.rosetta.basic.datacache.BasicDataCache, : core::scoring::ResSingleMinimizationData) → None

Called at the beginning of minimization, allowing this energy method to cache data

pertinent for a single residue in the the ResSingleMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. The Pose merely serves as context, and the input residue is not required to be a member of the Pose.

C++: core::scoring::methods::OneBodyEnergy::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class basic::datacache::BasicDataCache &, class core::scoring::ResSingleMinimizationData &) 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.pack.dunbrack.cenrot.CenRotDunEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::dunbrack::cenrot::CenRotDunEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(*args, **kwargs)

Overloaded function.

1. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) -> None

2. setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, min_data: core::scoring::ResSingleMinimizationData) -> None

Do any setup work should the coordinates of this residue, who is still guaranteed to be

of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed

C++: core::scoring::methods::OneBodyEnergy::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::ResSingleMinimizationData &) 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

use_extended_residue_energy_interface(self: pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy) → bool

Rely on the extended version of the residue_energy function during score-function

evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return ‘true’ for the extended version. The default method implemented in this class returns ‘false’

C++: core::scoring::methods::OneBodyEnergy::use_extended_residue_energy_interface() const –> bool

version(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → int

Return the version of the energy method

C++: core::scoring::methods::EnergyMethod::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator, : pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator) → pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator

C++: core::pack::dunbrack::cenrot::CenRotDunEnergyCreator::operator=(const class core::pack::dunbrack::cenrot::CenRotDunEnergyCreator &) –> class core::pack::dunbrack::cenrot::CenRotDunEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new CenRotDunEnergy

C++: core::pack::dunbrack::cenrot::CenRotDunEnergyCreator::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.pack.dunbrack.cenrot.CenRotDunEnergyCreator) → 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::pack::dunbrack::cenrot::CenRotDunEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary

Bases: SingletonBase_core_pack_dunbrack_cenrot_CenrotLibrary_t

Stores and handles loading of centroid rotamers for the canonical amino acids.

get_cenrot_library_by_aa(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenrotLibrary, aa: pyrosetta.rosetta.core.chemical.AA) → core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary

C++: core::pack::dunbrack::cenrot::CenrotLibrary::get_cenrot_library_by_aa(const enum core::chemical::AA &) const –> class std::shared_ptr<const class core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary>

static get_instance() → core::pack::dunbrack::cenrot::CenrotLibrary

C++: utility::SingletonBase<core::pack::dunbrack::cenrot::CenrotLibrary>::get_instance() –> class core::pack::dunbrack::cenrot::CenrotLibrary *

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData

Bases: pybind11_object

Simple class storing all the data for one centroid-rotamer well

angle(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::angle() const –> double

assign_best_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) → None

generate the best rot (mean of the well)

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::assign_best_rotamer(class utility::fixedsizearray1<double, 3> &) const –> void

assign_random_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, RG: pyrosetta.rosetta.numeric.random.RandomGenerator) → None

generate a random rot inside the well

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::assign_random_rotamer(class utility::fixedsizearray1<double, 3> &, class numeric::random::RandomGenerator &) const –> void

cal_delta_internal_coordinates(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, rsd: pyrosetta.rosetta.core.conformation.Residue, delta_d: float, delta_a: float, delta_w: float) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(const class core::conformation::Residue &, double &, double &, double &) const –> double

cal_delta_internal_coordinates_squared(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, rsd: pyrosetta.rosetta.core.conformation.Residue, d_sq: float, a_sq: float, w_sq: float) → float

return the value of angle (in rad)

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates_squared(const class core::conformation::Residue &, double &, double &, double &) const –> double

cal_distance(*args, **kwargs)

Overloaded function.

1. cal_distance(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> float

2. cal_distance(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, use_xyz: bool) -> float

DOF3 sample: (dis, ange, dih)

calculate the distance between this rot and given CEN

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance(const class utility::fixedsizearray1<double, 3> &, bool) const –> double

cal_distance_squared(*args, **kwargs)

Overloaded function.

1. cal_distance_squared(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> float

2. cal_distance_squared(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, sample: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, use_xyz: bool) -> float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(const class utility::fixedsizearray1<double, 3> &, bool) const –> double

3. cal_distance_squared(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, rsd: pyrosetta.rosetta.core.conformation.Residue) -> float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(const class core::conformation::Residue &) const –> double

dihedral(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::dihedral() const –> double

distance(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::distance() const –> double

energy(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::energy() const –> double

norm_factor(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::norm_factor() const –> double

private_data_to_public_array(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::private_data_to_public_array() –> void

prob(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::prob() const –> double

public_array_to_private_data(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::public_array_to_private_data() –> void

sd_ang(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_ang() const –> double

sd_dih(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dih() const –> double

sd_dis(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData) → float

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dis() const –> double

set_angle(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, a: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_angle(double) –> void

set_dihedral(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, w: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_dihedral(double) –> void

set_distance(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, d: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_distance(double) –> void

set_prob(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, p: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_prob(double) –> void

set_sd_ang(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, s: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_ang(double) –> void

set_sd_dih(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, s: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_dih(double) –> void

set_sd_dis(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData, s: float) → None

C++: core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_dis(double) –> void

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary

Bases: SingleResidueRotamerLibrary

aa(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary) → pyrosetta.rosetta.core.chemical.AA

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::aa() const –> enum core::chemical::AA

assign_random_rotamer_with_bias(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, RG: pyrosetta.rosetta.numeric.random.RandomGenerator, new_chi_angles: pyrosetta.rosetta.utility.vector1_double, perturb_from_rotamer_center: bool) → None

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::assign_random_rotamer_with_bias(const class core::conformation::Residue &, const class core::pose::Pose &, class numeric::random::RandomGenerator &, class utility::vector1<double, class std::allocator<double> > &, bool) const –> void

atoms_w_dof_derivatives(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.set_core_id_PartialAtomID_t

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::atoms_w_dof_derivatives(const class core::conformation::Residue &, const class core::pose::Pose &) const –> class std::set<class core::id::PartialAtomID, struct std::less<class core::id::PartialAtomID>, class std::allocator<class core::id::PartialAtomID> >

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool) → float

Returns the energy of the lowest-energy rotamer accessible to the given residue

(based on e.g. its current phi and psi values). If curr_rotamer_only is true, then consider only the idealized version of the residue’s current rotamer (local optimum); otherwise, consider all rotamers (global optimum).

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool) const –> double

bump_check(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

bump_filter(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, packer_neighbor_graph: utility::graph::Graph) → None

Filter a RotamerVector by “bump energy” of a rotamer:

All rotamers with bump energies over a certain threshold will be discarded Exception: if all rotamers are over the threshold, one rotamer (with the lowest bump energy) will be reserved. The vector “rotamers” will be modified “in-place”

C++: core::pack::rotamers::SingleResidueRotamerLibrary::bump_filter(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> void

compute_proton_chi_samplings(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, rlt: core::pack::task::ResidueLevelTask, buried: bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Return a vector (indexed by proton_chi number) of vectors of dihedral values

to use in proton chi sampling

C++: core::pack::rotamers::SingleResidueRotamerLibrary::compute_proton_chi_samplings(const class core::chemical::ResidueType &, const class core::pack::task::ResidueLevelTask &, bool) const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

current_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → int

Adds the current rotamer to rotamer vector, if the Rotlib supports it

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::current_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> unsigned long

emergency_rotamer(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → None

Generate an “emergency rotamer” if we don’t have any

This is in this class mainly because of historical behavior of certain rotamer libraries not supporting current rotamers

C++: core::pack::rotamers::SingleResidueRotamerLibrary::emergency_rotamer(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> void

eval_rotameric_energy_bb_dof_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, tor_id: pyrosetta.rosetta.core.id.TorsionID) → float

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv(const class core::conformation::Residue &, const class core::id::TorsionID &) const –> double

eval_rotameric_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, dis_ang_dih: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, eval_deriv: bool) → float

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv(const class core::conformation::Residue &, class utility::fixedsizearray1<double, 5> &, bool) const –> double

expand_proton_chis(*args, **kwargs)

Overloaded function.

1. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

2. expand_proton_chis(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, max_rotamers: int) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t

Given a vector of vectors of dihedrals to sample on proton chis,

Will create the ChiSet vector combinitorially on those chi values (Note: The ChiSets are only valid/defined over the proton chis.)

C++: core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, const class core::chemical::ResidueType &, unsigned long) const –> class utility::vector1<class std::shared_ptr<class core::pack::dunbrack::ChiSet>, class std::allocator<class std::shared_ptr<class core::pack::dunbrack::ChiSet> > >

fill_rotamer_vector(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue, extra_chi_steps: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried: bool, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &, const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &, bool, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) const –> void

get_closest_rotamer(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, nrot: int, dis: float) → pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_closest_rotamer(const class core::conformation::Residue &, unsigned long &, double &) const –> const class core::pack::dunbrack::cenrot::CentroidRotamerSampleData &

get_rotamer_samples(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::get_rotamer_samples(const class core::conformation::Residue &) const –> const class utility::vector1<class core::pack::dunbrack::cenrot::CentroidRotamerSampleData, class std::allocator<class core::pack::dunbrack::cenrot::CentroidRotamerSampleData> >

read_from_file(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool) → str

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(class utility::io::izstream &, bool) –> std::string

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tenergy: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → float

Virtual functions required by the base classes

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, struct core::pack::rotamers::TorsionEnergy &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, tor_id: pyrosetta.rosetta.core.id.TorsionID, tderiv: pyrosetta.rosetta.core.pack.rotamers.TorsionEnergy) → None

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::id::TorsionID &, struct core::pack::rotamers::TorsionEnergy &) const –> void

virtual_sidechain(self: pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid: int, pose: pyrosetta.rosetta.core.pose.Pose, task: core::pack::task::PackerTask, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, existing_residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t

Add a virtualized sidechain to the rotamer vector if

settings call for it.

C++: core::pack::rotamers::SingleResidueRotamerLibrary::virtual_sidechain(const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::conformation::Residue &) const –> class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > >

write_to_file(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary, out: pyrosetta.rosetta.utility.io.ozstream) → None

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::write_to_file(class utility::io::ozstream &) const –> void

class pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator

Bases: SingleResidueRotamerLibraryCreator

assign(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator, : pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator) → pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::operator=(const class core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator &) –> class core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator &

create(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator, : pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::create(const class core::chemical::ResidueType &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

keyname(self: pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibraryCreator) → str

C++: core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::keyname() const –> std::string