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.

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.

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_energy(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, 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.

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 unsigned long) const –> double

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

clean_up_residuearrayannealableenergy_after_packing(self: pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Allows the ResidueArrayAnnealableEnergy to clean up cached data, either within the EnergyMethod or in the pose, after

a packer run.

Base class version does nothing; may be overridden by derived classes.

C++: core::scoring::annealing::ResidueArrayAnnealableEnergy::clean_up_residuearrayannealableenergy_after_packing(class core::pose::Pose &) –> void

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>

commit_considered_substitution(self: pyrosetta.rosetta.core.scoring.annealing.ResidueArrayAnnealableEnergy) → None¶

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

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::annealing::ResidueArrayAnnealableEnergy::commit_considered_substitution() –> void

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_after_minimizing(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

Re-enable this energy after minimization.

C++: core::scoring::aa_composition_energy::AACompositionEnergy::finalize_after_minimizing(class core::pose::Pose &) 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> > &

set_up_residuearrayannealableenergy_for_packing(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, rotamersets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, 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::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: 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.aa_composition_energy.AACompositionEnergy, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase) → None¶

Disable this energy during minimization.

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

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

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

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

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

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

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

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

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

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

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

show additional information of the energy method

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

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

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

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

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.

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) ]

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.

Members:

tf_linear

tf_quadratic

tf_constant

tf_unknown

tf_end_of_list