aa_composition_energy

Bindings for core::scoring::aa_composition_energy namespace

class pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy

Bases: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy, pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy

AACompositionEnergy, an energy function to penalize stretches of the same residue, derived from base class for EnergyMethods, which are meaningful only on entire structures. These EnergyMethods do all of their work in the “finalize_total_energy” section of score function evaluation.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, options: core::scoring::methods::EnergyMethodOptions) -> None
  2. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, arg0: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> None
__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, : pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy

C++: core::scoring::aa_composition_energy::AACompositionEnergy::operator=(const class core::scoring::aa_composition_energy::AACompositionEnergy &) –> class core::scoring::aa_composition_energy::AACompositionEnergy &

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

calculate_energy(*args, **kwargs)

Overloaded function.

  1. calculate_energy(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> float

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

Called directly by the ResidueArrayAnnealingEvaluator during packer runs.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::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 –> double

  1. calculate_energy(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, setup_helpers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_aa_composition_energy_AACompositionEnergySetup_t, masks: pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> float

Calculate the total energy given a vector of const owning pointers to residues, vectors of AACompositionEnergySetup objects, and vectors of masks.

Called by finalize_total_energy() and during packer runs. Requires that setup_residuearrayannealablenergy_for_packing() be called first.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::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<class std::shared_ptr<const class core::scoring::aa_composition_energy::AACompositionEnergySetup>, class std::allocator<class std::shared_ptr<const class core::scoring::aa_composition_energy::AACompositionEnergySetup> > > &, const class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > > &) const –> double

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod
Clone: create a copy of this object, and return an owning pointer
to the copy.

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

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

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

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: ObjexxFCL::FArray1D<int>, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None
Evaluate the XYZ derivative for an atom in the pose.

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

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

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

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

called at the end of derivatives evaluation

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

finalize_total_energy(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

Actually calculate the total energy

Called by the scoring machinery.

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

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None
AACompositionEnergy is context-independent and thus indicates that no context graphs need to be maintained by
class Energies.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

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

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

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

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

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None
If an energy method needs to cache data in a packing::RotamerSet object before
rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

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

report(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) → None

Get a summary of all loaded data.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::report() const –> void

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

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

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

Returns the score types that this energy method computes.

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

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None
Called immediately before atom- and DOF-derivatives are calculated
allowing the derived class a chance to prepare for future calls.

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → None
Called at the beginning of atom tree minimization, this method
allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

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

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None
if an energy method needs to cache data in the Energies object,
before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

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

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None
if an energy method needs to cache something in the pose (e.g. in pose.energies()),
before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None
Do any setup work before scoring, caching any slow-to-compute data that will be used during
energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

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

setup_residuearrayannealableenergy_for_packing(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

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

C++: core::scoring::aa_composition_energy::AACompositionEnergy::setup_residuearrayannealableenergy_for_packing(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

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

show additional information of the energy method

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.core.pose.Pose, resid: int) → None
If the pose changes in the middle of a packing (as happens in rotamer trials) and if
an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

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

version(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) → int

AACompositionEnergy is version 1.0 right now.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::version() const –> unsigned long

class pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup

Bases: pybind11_builtins.pybind11_object

AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method that stores all of its setup data.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> None
  2. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, arg0: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> None
__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, : pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::operator=(const class core::scoring::aa_composition_energy::AACompositionEnergySetup &) –> class core::scoring::aa_composition_energy::AACompositionEnergySetup &

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup
Clone: create a copy of this object, and return an owning pointer
to the copy.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::clone() const –> class std::shared_ptr<class core::scoring::aa_composition_energy::AACompositionEnergySetup>

expected_by_properties_absolute(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → int

Get the expected absolute number of residues for a given set of properties, by property set index.

Warning! For speed, there’s no check that the index is in range!

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_absolute(const unsigned long) const –> long

expected_by_properties_fraction(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → float

Get the expected fractional number of residues for a given set of properties, by property set index.

Warning! For speed, there’s no check that the index is in range!

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_fraction(const unsigned long) const –> double

fract_property_penalty(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_fract: float, property_set_index: int) → float

Look up the penalty for a property set of internal index property_set_index, given a fractional content given by fract.

This version is for fractional property penalties.

The measured fractional content of amino acids matching this property set in the pose or pose subset minus the expected.

The index of this property set.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::fract_property_penalty(const double, const unsigned long) const –> double

get_tailfunction_from_name(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, name: str) → pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction

Get tail function enum from name.

This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_from_name(const class std::basic_string<char> &) const –> enum core::scoring::aa_composition_energy::TailFunction

get_tailfunction_name(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, tf: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → str

Get tail function name from enum.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_name(const enum core::scoring::aa_composition_energy::TailFunction) const –> std::string

initialize_from_file(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filename: str) → None

Initialize from a .comp file.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file(const class std::basic_string<char> &) –> void

initialize_from_file_contents(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filecontents: str) → None

Initialize from a string in the format of a .comp file.

Allows external code to initialize object without having it read directly from disk.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file_contents(const class std::basic_string<char> &) –> void

n_property_sets(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → int

Get the number of sets of properties that we’ll be counting.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::n_property_sets() const –> unsigned long

property_penalty(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_expected: int, property_set_index: int) → float
Look up the penalty for a property set of internal index property_set_index, given a deviation from
the desired count given by delta_expected.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::property_penalty(const long, const unsigned long) const –> double

property_set_indices_matching_residue(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, indices_out: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Get the indices of all of the property sets corresponding to the current residue.

Returns empty vector if none of the property sets that we’re counting corresponds to the current residue.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::property_set_indices_matching_residue(const class core::chemical::ResidueType &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

report(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → str

Get a summary of the data stored in this object

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::report() const –> std::string

reset(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → None

Reset all data in this data storage object.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::reset() –> void

use_fract_expected_values_any(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → bool

Determine whether ANY of the property sets of this helper object use fractional expected values.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_expected_values_any() const –> bool

use_fract_ranges(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index: int) → bool

Look up whether we’re using absolute (return false) or fractional (return true) penalty ranges.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges(const unsigned long) const –> bool

use_fract_ranges_any(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) → bool

Determine whether ANY of the property sets of this helper object use fractional ranges.

C++: core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges_any() const –> bool

class pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet

Bases: pybind11_builtins.pybind11_object

AACompositionPropertiesSet, a helper class that stores: - names of residue types that WILL be counted (TYPE) - names of residue types that WILL NOT be counted (NOT_TYPE) - properties that MUST be present in order for a residue to be counted (PROPERTIES). - properties, any of which is sufficient for a residue to be counted (OR_PROPERTIES). - properties that MUST NOT be present in order for a residue to be counted (NOT_PROPERTIES).

The logic is as follows: a residue is counted if and only if [any TYPE matches] OR [ (no NOT_TYPE matches) AND ( {all PROPERTIES match} OR {any OR_PROPERTIES match} OR {no TYPEs defined AND no PROPERTIES defined AND no OR_PROPERTIES defined } ) AND ( no NOT_PROPERTIES match) ]

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> None
  2. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, included_type_strings: pyrosetta.rosetta.utility.vector1_std_string, excluded_type_strings: pyrosetta.rosetta.utility.vector1_std_string, included_properties_strings: pyrosetta.rosetta.utility.vector1_std_string, or_properties_strings: pyrosetta.rosetta.utility.vector1_std_string, excluded_properties_strings: pyrosetta.rosetta.utility.vector1_std_string) -> None
  3. __init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, arg0: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> None
__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, : pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::operator=(const class core::scoring::aa_composition_energy::AACompositionPropertiesSet &) –> class core::scoring::aa_composition_energy::AACompositionPropertiesSet &

clone(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) → pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet
Clone: create a copy of this object, and return an owning pointer
to the copy.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::clone() const –> class std::shared_ptr<class core::scoring::aa_composition_energy::AACompositionPropertiesSet>

one_line_report(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) → str

Generate a one-line summary of the properties stored in this AACompositionPropertySet

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::one_line_report() const –> std::string

parse_excluded_properites(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None

Take a list of excluded property strings and parse it.

Populates the excluded_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_properites(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

parse_excluded_types(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist: pyrosetta.rosetta.utility.vector1_std_string) → None
Take a list of excluded type strings and add it to the list of excluded types, checking that

none of the types has already been added.

Populates the excluded_types_ vector based on the types named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

parse_included_properites(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_properites(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

parse_included_types(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist: pyrosetta.rosetta.utility.vector1_std_string) → None
Take a list of included type strings and add it to the list of included types, checking that

none of the types has already been added.

Populates the included_types_ vector based on the types named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

parse_or_properties(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist: pyrosetta.rosetta.utility.vector1_std_string) → None

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_or_properties(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

properties_match_this(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Check whether the properties of a residue type match those of this set.

This checks: 1. Whether the residue name matches an exlcuded name -> return false. 2. Whether the residue name matches an included name -> return true. 3. Whether the residue properties match an excluded property -> return false. 4. Whether all three of the included_types and or_properties and included_property lists are empty -> return true. 5. Whether any or_property is matched -> return true. 6. Whether there exist any proprties to match -> if not, return false. 7. Whether any properties are not matched -> return false. Returns true

C++: core::scoring::aa_composition_energy::AACompositionPropertiesSet::properties_match_this(const class core::chemical::ResidueType &) const –> bool

class pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction

Bases: pybind11_builtins.pybind11_object

The different types of behaviour for the penalty values past the defined range.

When values are added to this enum, they should also be added to the AACompositionEnergySetup::get_tailfunction_name() function.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

  1. __eq__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) -> bool
  2. __eq__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: int) -> bool
__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → tuple
__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → int
__init__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: int) → None
__init_subclass__()

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → int
__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

  1. __ne__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) -> bool
  2. __ne__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: int) -> bool
__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction) → str
__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.TailFunction, arg0: tuple) → None
__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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