buried_unsat_penalty¶

graph

Bindings for core::pack::guidance_scoreterms::buried_unsat_penalty namespace

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty¶

Bases: WholeStructureEnergy, ResidueArrayAnnealableEnergy

BuriedUnsatPenalty, an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors or acceptors.

This class is derived from base class WholeStructureEnergy, which is meaningful only on entire structures. These EnergyMethods do all of their work in the “finalize_total_energy” section of scorefunction evaluation.

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty) → pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty¶: C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty &

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

calculate_energy(*args, **kwargs)¶

Overloaded function.

calculate_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, rotamer_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float
calculate_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, rotamer_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, substitution_position: int) -> float

Calculate the total energy given a vector of const owning pointers to residues.

Called directly by the ResidueArrayAnnealingEvaluator during packer runs.

Outside of the context of the packer, this doesn’t behave as expected (and finalize_total_energy() should be called instead).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_energy(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) const –> double

calculate_penalty_once_almost_from_scratch_using_reference_graph(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, reference_graph: core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph, symm_multiplier: int) → float¶

Given a residue vector, calculate the penalty energy using a reference graph.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_almost_from_scratch_using_reference_graph(const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph &, const unsigned long) const –> double

calculate_penalty_once_from_scratch(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose) → float¶

Given a pose, calculate the penalty energy.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch(const class core::pose::Pose &) const –> double

clean_up_residuearrayannealableenergy_after_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Delete cached data from the pose and from this EnergyMethod after packing.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clean_up_residuearrayannealableenergy_after_packing(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

Clone: create a copy of this object, and return an owning pointer: to the copy.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty) → None¶

What to do when a substitution that was considered is accepted.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::commit_considered_substitution() –> void

compute_penalty(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, unsat_acceptor_count: int, unsat_donor_count: int, unsat_acceptor_and_donor_count: int, oversat_acceptor_count: int, oversat_donor_count: int, oversat_acceptor_and_donor_count: int) → float¶

Given the counts of various unsaturateds, return a penalty value.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::compute_penalty(const unsigned long, const unsigned long, const unsigned long, const unsigned long, const unsigned long, const unsigned long) const –> double

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

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.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Re-enable this scoreterm after a minimization trajectory.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

Actually calculate the total energy

Called by the scoring machinery. The update_residue_neighbors() function of the pose must be called first.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None¶

BuriedUnsatPenalty is context-independent and thus indicates that no context graphs need to be maintained by: class Energies.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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

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.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

provide_pymol_commands_to_show_groups(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor

and donor groups orange. Useful for debugging degree of burial.

To use, pass in a pose. If this graph contains residues corresponding to those in the pose, commands for colouring them will be written out. Calls BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(). Must be called only after set_up_residuearrayannealableenergy_for_packing.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::provide_pymol_commands_to_show_groups(std::ostream &, const class core::pose::Pose &) const –> void

report(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty) → None¶

Get a summary of all loaded data.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::report() 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

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> > &

set_prevent_pruning(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, setting: bool) → None¶

Should the graph setup-for-packing skip the step in which groups that are not packable and not able to hydrogen bond to: a packable residue are pruned? Default false; this function allows this to be set, though.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_prevent_pruning(const bool) –> void

set_up_residuearrayannealableenergy_for_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose, rotamersets: core::pack::rotamer_set::RotamerSets, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Cache data from the pose in this EnergyMethod in anticipation of packing.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::set_up_residuearrayannealableenergy_for_packing(class core::pose::Pose &, const class core::pack::rotamer_set::RotamerSets &, const class core::scoring::ScoreFunction &) –> void

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.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → None¶

Disable this scoreterm during minimization trajectory.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::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:

setup_for_packing() is called for all energy methods
rotamers are built
setup_for_packing_with_rotsets() is called for all energy methods
prepare_rotamers_for_packing() is called for all energy methods
The energy methods are asked to score all rotamers and rotamer pairs
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

version(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty) → int¶

BuriedUnsatPenalty is version 1.0 right now.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator¶

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator, : pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator) → pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator¶: C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator::operator=(const class core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator &) –> class core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator &

create_energy_method(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator, options: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

Instantiate a new BuriedUnsatPenalty.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator::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.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenaltyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Return the set of score types claimed by the EnergyMethod that: this EnergyMethodCreator creates in its create_energy_method() function.

C++: core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenaltyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >