sap

Bindings for core::pack::guidance_scoreterms::sap namespace

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.BlockParam

Bases: pybind11_builtins.pybind11_object

property full_block
property max_sasa_score
property no_block
class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric

Bases: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric

A per-residue metric that will calculate SASA for each residue given in a selector.

static add_schema(complex_schema: utility::tag::XMLSchemaComplexTypeGenerator) None

Add options to the schema from this base class.

C++: core::simple_metrics::PerResidueRealMetric::add_schema(class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>) –> void

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None

  3. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None

  4. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None

  5. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose as a score.

labeled as out_label

Score is added to the SimpleMetricData cache in the pose

A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

C++: core::simple_metrics::PerResidueRealMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, ot: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::operator=(const class core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric &) –> class core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double

  2. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> pyrosetta.rosetta.std.map_unsigned_long_double

  3. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> pyrosetta.rosetta.std.map_unsigned_long_double

  4. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double

  5. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool, use_ref_pose_for_cache: bool) -> pyrosetta.rosetta.std.map_unsigned_long_double

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums

using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

C++: core::simple_metrics::PerResidueRealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool, bool) const –> class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

calculate(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.map_unsigned_long_double
Calculate the metric.

This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::calculate(const class core::pose::Pose &) const –> class std::map<unsigned long, double, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, double> > >

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

get_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Output data name will be prefix+custom_type+type+suffix

C++: core::simple_metrics::SimpleMetric::get_custom_type() const –> std::string

get_final_sm_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

C++: core::simple_metrics::SimpleMetric::get_final_sm_type() const –> std::string

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the submetric names that this Metric will calculate

C++: core::simple_metrics::PerResidueRealMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_selector(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) core::select::residue_selector::ResidueSelector

Get the set residue selector of this class.

C++: core::simple_metrics::PerResidueRealMetric::get_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

metric(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric) str

Name of the metric

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric) str

Name of the class

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_per_residue_tag(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

C++: core::simple_metrics::SimpleMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_output_as_pdb_nums(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, output_as_pdb_nums: bool) None
Set to output in PDB numbering instead of Rosetta during the Apply function,

which adds the data to pose as extra scores.

C++: core::simple_metrics::PerResidueRealMetric::set_output_as_pdb_nums(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric, selector: core::select::residue_selector::ResidueSelector) None

Set a ResidueSelector for which we will calculate values over.

C++: core::simple_metrics::PerResidueRealMetric::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sap_calculate_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::set_sap_calculate_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_sasa_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::set_sasa_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_score_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::set_score_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

simple_metric_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

C++: core::simple_metrics::SimpleMetric::simple_metric_type() const –> std::string

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator::operator=(const class core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator &) –> class core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator) str

Return a string that will be used to instantiate the particular SimpleMetric

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.RotamerRotamerHasher

C++: core::pack::guidance_scoreterms::sap::RotamerRotamerHasher::operator=(const struct core::pack::guidance_scoreterms::sap::RotamerRotamerHasher &) –> struct core::pack::guidance_scoreterms::sap::RotamerRotamerHasher &

property hasher
class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint

Bases: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint, other: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint

C++: core::pack::guidance_scoreterms::sap::SapConstraint::operator=(const class core::pack::guidance_scoreterms::sap::SapConstraint &) –> class core::pack::guidance_scoreterms::sap::SapConstraint &

atom(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) pyrosetta.rosetta.core.id.AtomID

Implemented because the base class requires it; not used by a sequence constraint.

Always returns AtomID(0,0).

C++: core::scoring::aa_composition_energy::SequenceConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

Clone operator

C++: core::pack::guidance_scoreterms::sap::SapConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func) -> float

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_const_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint) core::pack::guidance_scoreterms::sap::SapConstraintOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraint::get_const_options() const –> class std::shared_ptr<const class core::pack::guidance_scoreterms::sap::SapConstraintOptions>

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

get_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint) core::pack::guidance_scoreterms::sap::SapConstraintOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraint::get_options() –> class std::shared_ptr<class core::pack::guidance_scoreterms::sap::SapConstraintOptions>

natoms(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint) int

Implemented because the base class requires it; not used by a sequence constraint.

Always returns zero.

C++: core::scoring::aa_composition_energy::SequenceConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) None
Reads the definition of a Constraint from the given std::istream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint, : pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::guidance_scoreterms::sap::SapConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns

an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

same_type_as_me(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: core::pack::guidance_scoreterms::sap::SapConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream) None
This method is intended to show the value of the Constraint function

evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

C++: core::scoring::constraints::Constraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None
Prints the definition of a Constraint to the given std::ostream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

  2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Returns a unique string identified for this constraint. Used in several

places, including the ConstraintIO class.

C++: core::scoring::constraints::Constraint::type() const –> std::string

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy

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

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergy::operator=(const class core::pack::guidance_scoreterms::sap::SapConstraintEnergy &) –> class core::pack::guidance_scoreterms::sap::SapConstraintEnergy &

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.

  1. calculate_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, current_rotamer_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

  2. calculate_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, current_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.

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergy::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

clean_up_residuearrayannealableenergy_after_packing(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy, pose: pyrosetta.rosetta.core.pose.Pose) None

Clear the cached data from the pose after packing.

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

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy) 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::sap::SapConstraintEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy) None

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergy::commit_considered_substitution() –> void

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.sap.SapConstraintEnergy, pose: pyrosetta.rosetta.core.pose.Pose) None

Re-enable this energy after minimization.

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

finalize_total_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy, 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::pack::guidance_scoreterms::sap::SapConstraintEnergy::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.sap.SapConstraintEnergy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) None
SapConstraintEnergy is context-independent and thus indicates that no context graphs need to be maintained by

class Energies.

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergy::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.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

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

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) bool
Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

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

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.pack.guidance_scoreterms.sap.SapConstraintEnergy, 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::sap::SapConstraintEnergy::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.sap.SapConstraintEnergy, 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::pack::guidance_scoreterms::sap::SapConstraintEnergy::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None
if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

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

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

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

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

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

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

  6. Annealing

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

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

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

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) None
if an energy method needs to cache something in the pose (e.g. in pose.energies()),

before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

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

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None
Do any setup work before scoring, caching any slow-to-compute data that will be used during

energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

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

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

show additional information of the energy method

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

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) None
If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

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

version(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy) int

SapConstraintEnergy is version 1.0 right now.

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergy::version() const –> unsigned long

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator

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

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator

C++: core::pack::guidance_scoreterms::sap::SapConstraintEnergyCreator::operator=(const class core::pack::guidance_scoreterms::sap::SapConstraintEnergyCreator &) –> class core::pack::guidance_scoreterms::sap::SapConstraintEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergyCreator, options: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new SapConstraintEnergy.

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

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper

Bases: pybind11_builtins.pybind11_object

calculate_energy(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper, resvect: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, substitution_position: int) float

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::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) –> double

commit_considered_substitution(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper) None

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::commit_considered_substitution() –> void

current_score(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper) float

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::current_score() const –> double

get_per_atom_sap(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.id.AtomID_Map_double_t

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::get_per_atom_sap(const class core::pose::Pose &) const –> class core::id::AtomID_Map<double>

init_with_pose(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper, pose: pyrosetta.rosetta.core.pose.Pose, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::init_with_pose(const class core::pose::Pose &, const class core::pack::rotamer_set::RotamerSets &) –> class core::pack::rotamer_set::RotamerSets

options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper) core::pack::guidance_scoreterms::sap::SapConstraintOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::options() const –> class std::shared_ptr<const class core::pack::guidance_scoreterms::sap::SapConstraintOptions>

report(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper) None

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::report() –> void

report_final_score(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper, actual_sap: float) None

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::report_final_score(double) const –> void

set_accurate_sasa_and_recalc(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: core::pack::guidance_scoreterms::sap::SapConstraintHelper::set_accurate_sasa_and_recalc(const class core::pose::Pose &) –> double

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::operator=(const class core::pack::guidance_scoreterms::sap::SapConstraintOptions &) –> class core::pack::guidance_scoreterms::sap::SapConstraintOptions &

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::clone() const –> class std::shared_ptr<class core::pack::guidance_scoreterms::sap::SapConstraintOptions>

fast(*args, **kwargs)

Overloaded function.

  1. fast(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, fast: bool) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::fast(bool) –> void

  1. fast(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> bool

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::fast() const –> bool

full_accuracy_when_scoring(*args, **kwargs)

Overloaded function.

  1. full_accuracy_when_scoring(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, full_accuracy: bool) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::full_accuracy_when_scoring(bool) –> void

  1. full_accuracy_when_scoring(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> bool

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::full_accuracy_when_scoring() const –> bool

lightning(*args, **kwargs)

Overloaded function.

  1. lightning(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, lightning: bool) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::lightning(bool) –> void

  1. lightning(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> bool

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::lightning() const –> bool

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, name: str) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::name(const std::string &) –> void

  1. name(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> str

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::name() const –> std::string

packing_correction(*args, **kwargs)

Overloaded function.

  1. packing_correction(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, adjustment: float) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::packing_correction(double) –> void

  1. packing_correction(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> float

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::packing_correction() const –> double

penalty_per_sap(*args, **kwargs)

Overloaded function.

  1. penalty_per_sap(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, penalty: float) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::penalty_per_sap(double) –> void

  1. penalty_per_sap(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> float

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::penalty_per_sap() const –> double

sanity_check(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sanity_check() const –> void

sap_calculate_selector(*args, **kwargs)

Overloaded function.

  1. sap_calculate_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_calculate_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

  1. sap_calculate_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_calculate_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

sap_goal(*args, **kwargs)

Overloaded function.

  1. sap_goal(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, goal: float) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_goal(double) –> void

  1. sap_goal(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> float

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_goal() const –> double

sap_lb_goal(*args, **kwargs)

Overloaded function.

  1. sap_lb_goal(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, lb_goal: float) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_lb_goal(double) –> void

  1. sap_lb_goal(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> float

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_lb_goal() const –> double

sap_parameter_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sap_parameter_options() –> class core::pack::guidance_scoreterms::sap::SapParameterOptions &

sasa_selector(*args, **kwargs)

Overloaded function.

  1. sasa_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sasa_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

  1. sasa_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::sasa_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

score_selector(*args, **kwargs)

Overloaded function.

  1. score_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::score_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

  1. score_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::score_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

transform_sap_to_score(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, score: float, approximate: bool) float

C++: core::pack::guidance_scoreterms::sap::SapConstraintOptions::transform_sap_to_score(double, bool) const –> double

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase

Bases: pyrosetta.rosetta.utility.SingletonBase_core_pack_guidance_scoreterms_sap_SapDatabase_t

atomtype_to_block_param(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase) std::unordered_map<std::string, core::pack::guidance_scoreterms::sap::BlockParam, std::hash<std::string>, std::equal_to<std::string>, std::allocator<std::pair<std::string const, core::pack::guidance_scoreterms::sap::BlockParam> > >

C++: core::pack::guidance_scoreterms::sap::SapDatabase::atomtype_to_block_param() const –> class std::shared_ptr<const class std::unordered_map<std::string, struct core::pack::guidance_scoreterms::sap::BlockParam, struct std::hash<std::string>, struct std::equal_to<std::string >, class std::allocator<struct std::pair<const std::string, struct core::pack::guidance_scoreterms::sap::BlockParam> > > >

static get_instance() core::pack::guidance_scoreterms::sap::SapDatabase

C++: utility::SingletonBase<core::pack::guidance_scoreterms::sap::SapDatabase>::get_instance() –> class core::pack::guidance_scoreterms::sap::SapDatabase *

get_name1_name3(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase, res: pyrosetta.rosetta.core.conformation.Residue, warn: bool) Tuple[str, str]

C++: core::pack::guidance_scoreterms::sap::SapDatabase::get_name1_name3(const class core::conformation::Residue &, bool) const –> struct std::pair<char, std::string >

hydrophobic_weight(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase, aa: str) float

C++: core::pack::guidance_scoreterms::sap::SapDatabase::hydrophobic_weight(char) const –> double

max_sasa(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase, aa: str) float

C++: core::pack::guidance_scoreterms::sap::SapDatabase::max_sasa(char) const –> double

symm_debug(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase) bool

C++: core::pack::guidance_scoreterms::sap::SapDatabase::symm_debug() const –> bool

symm_debug_force_map(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase) bool

C++: core::pack::guidance_scoreterms::sap::SapDatabase::symm_debug_force_map() const –> bool

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint

Bases: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint

add_constraint(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, weight: float, name: str) None

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::add_constraint(double, const std::string &) –> void

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, other: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::operator=(const class core::pack::guidance_scoreterms::sap::SapMathConstraint &) –> class core::pack::guidance_scoreterms::sap::SapMathConstraint &

atom(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) pyrosetta.rosetta.core.id.AtomID

Implemented because the base class requires it; not used by a sequence constraint.

Always returns AtomID(0,0).

C++: core::scoring::aa_composition_energy::SequenceConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : numeric::random::RandomGenerator) int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint) pyrosetta.rosetta.core.scoring.constraints.Constraint

Clone operator

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float

  2. dist(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func) -> float

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : pyrosetta.rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.numeric.xyzVector_double_t, : pyrosetta.rosetta.core.scoring.EMapVector) None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

lower_bound(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, lower: float) None

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::lower_bound(double) –> void

natoms(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint) int

Implemented because the base class requires it; not used by a sequence constraint.

Always returns zero.

C++: core::scoring::aa_composition_energy::SequenceConstraint::natoms() const –> unsigned long

penalty_per_unit(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, penalty: float) None

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::penalty_per_unit(double) –> void

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) None
This method is totally redundant with read_def YAY

DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(std::istream &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) None
initialize this Constraint from the given std::istream. It’s amazing

that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(std::istream &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) None
Reads the definition of a Constraint from the given std::istream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(std::istream &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, : pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) pyrosetta.rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns

an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

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

same_type_as_me(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) bool

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float

  2. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float

  3. score(self: pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.EMapVector, : pyrosetta.rosetta.core.scoring.EMapVector) -> None

Implemented because the base class requires it; not used by a sequence constraint.

C++: core::scoring::aa_composition_energy::SequenceConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream) None
This method is intended to show the value of the Constraint function

evaluated over some reasonable range of values. For example, a constraint between pairs of atoms might show the values of the Constraint function between 4 and 12 angstroms.

C++: core::scoring::constraints::Constraint::show(std::ostream &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) None
Prints the definition of a Constraint to the given std::ostream,

using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(std::ostream &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int

  2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int

Prints the violations of this constraint to the given

std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(std::ostream &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Convenience function, returns the results of show() as a string.

Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) str
Returns a unique string identified for this constraint. Used in several

places, including the ConstraintIO class.

C++: core::scoring::constraints::Constraint::type() const –> std::string

upper_bound(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint, upper: float) None

C++: core::pack::guidance_scoreterms::sap::SapMathConstraint::upper_bound(double) –> void

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions

C++: core::pack::guidance_scoreterms::sap::SapParameterOptions::operator=(const class core::pack::guidance_scoreterms::sap::SapParameterOptions &) –> class core::pack::guidance_scoreterms::sap::SapParameterOptions &

property hydrop_adder
property hydrop_lys_arg_setting
class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric

Bases: pyrosetta.rosetta.core.simple_metrics.RealMetric

A metric to report the SapScore of a pose

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> None

  3. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str) -> None

  4. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, suffix: str, override_existing_data: bool) -> None

  5. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  6. apply(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, out_label: str, pose: pyrosetta.rosetta.core.pose.Pose, override_existing_data: bool) -> None

Calculate the metric and add it to the pose as a score.

labeled as out_label.

Score is added to the SimpleMetricData cache

Data is output into the final score file, but can be accessed if needed through the cache.

C++: core::simple_metrics::RealMetric::apply(const std::string &, class core::pose::Pose &, bool) const –> void

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, ot: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::operator=(const class core::pack::guidance_scoreterms::sap::SapScoreMetric &) –> class core::pack::guidance_scoreterms::sap::SapScoreMetric &

cached_calculate(*args, **kwargs)

Overloaded function.

  1. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool) -> float

  2. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str) -> float

  3. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str) -> float

  4. cached_calculate(self: pyrosetta.rosetta.core.simple_metrics.RealMetric, pose: pyrosetta.rosetta.core.pose.Pose, use_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> float

Grab the data from the pose if it exists or calculate the metric

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice,

for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

C++: core::simple_metrics::RealMetric::cached_calculate(const class core::pose::Pose &, bool, std::string, std::string, bool) const –> double

calculate(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, pose: pyrosetta.rosetta.core.pose.Pose) float
Calculate the metric.

Returns the total score from the scorefunction or the total score of each residue in the residue selector.

If a comparison pose is given,

will calculate the delta between them (pose - comparison_pose).

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::calculate(const class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::clone() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

static complex_type_generator_for_simple_metric(: utility::tag::XMLSchemaDefinition) utility::tag::XMLSchemaComplexTypeGenerator

C++: core::simple_metrics::SimpleMetric::complex_type_generator_for_simple_metric(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

get_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Output data name will be prefix+custom_type+type+suffix

C++: core::simple_metrics::SimpleMetric::get_custom_type() const –> std::string

get_final_sm_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

Get the final name of this metric including its simple_metric_type_ name and any set custom type.

C++: core::simple_metrics::SimpleMetric::get_final_sm_type() const –> std::string

get_metric_names(self: pyrosetta.rosetta.core.simple_metrics.RealMetric) pyrosetta.rosetta.utility.vector1_std_string

Get the metric name(s) that this Metric will calculate

C++: core::simple_metrics::RealMetric::get_metric_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

metric(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric) str

Name of the metric

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::metric() const –> std::string

name(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric) str

Name of the class

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::name() const –> std::string

static name_static() str

Name of the class for creator.

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::name_static() –> std::string

parse_base_tag(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, tag: utility::tag::Tag) None

Parse the base class tag. Keep required interface for parse_my_tag.

C++: core::simple_metrics::SimpleMetric::parse_base_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_my_tag(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, tag: utility::tag::Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

called by parse_my_tag – should not be used directly

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

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

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

C++: core::simple_metrics::SimpleMetric::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

sap_parameter_options(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::sap_parameter_options() –> class core::pack::guidance_scoreterms::sap::SapParameterOptions &

set_custom_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric, custom_type: str) None

C++: core::simple_metrics::SimpleMetric::set_custom_type(const std::string &) –> void

set_sap_calculate_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::set_sap_calculate_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_sasa_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::set_sasa_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

set_score_selector(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

C++: core::pack::guidance_scoreterms::sap::SapScoreMetric::set_score_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &) –> void

simple_metric_type(self: pyrosetta.rosetta.core.simple_metrics.SimpleMetric) str

C++: core::simple_metrics::SimpleMetric::simple_metric_type() const –> std::string

class pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator

Bases: pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator

assign(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator, : pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator

C++: core::pack::guidance_scoreterms::sap::SapScoreMetricCreator::operator=(const class core::pack::guidance_scoreterms::sap::SapScoreMetricCreator &) –> class core::pack::guidance_scoreterms::sap::SapScoreMetricCreator &

create_simple_metric(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator) pyrosetta.rosetta.core.simple_metrics.SimpleMetric

Instantiate a particular SimpleMetric

C++: core::pack::guidance_scoreterms::sap::SapScoreMetricCreator::create_simple_metric() const –> class std::shared_ptr<class core::simple_metrics::SimpleMetric>

keyname(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator) str

Return a string that will be used to instantiate the particular SimpleMetric

C++: core::pack::guidance_scoreterms::sap::SapScoreMetricCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::pack::guidance_scoreterms::sap::SapScoreMetricCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.calculate_per_atom_sap(*args, **kwargs)

Overloaded function.

  1. calculate_per_atom_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> pyrosetta.rosetta.core.id.AtomID_Map_double_t

  2. calculate_per_atom_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_parameter_options: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions) -> pyrosetta.rosetta.core.id.AtomID_Map_double_t

C++: core::pack::guidance_scoreterms::sap::calculate_per_atom_sap(const class core::pose::Pose &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class core::pack::guidance_scoreterms::sap::SapParameterOptions &) –> class core::id::AtomID_Map<double>

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.calculate_per_res_sap(*args, **kwargs)

Overloaded function.

  1. calculate_per_res_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> pyrosetta.rosetta.utility.vector1_double

  2. calculate_per_res_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_parameter_options: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions) -> pyrosetta.rosetta.utility.vector1_double

C++: core::pack::guidance_scoreterms::sap::calculate_per_res_sap(const class core::pose::Pose &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class core::pack::guidance_scoreterms::sap::SapParameterOptions &) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.calculate_sap(*args, **kwargs)

Overloaded function.

  1. calculate_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> float

  2. calculate_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_parameter_options: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions) -> float

C++: core::pack::guidance_scoreterms::sap::calculate_sap(const class core::pose::Pose &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class core::pack::guidance_scoreterms::sap::SapParameterOptions &) –> double

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.calculate_slow_approx_sap(*args, **kwargs)

Overloaded function.

  1. calculate_slow_approx_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> float

  2. calculate_slow_approx_sap(pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_parameter_options: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapParameterOptions) -> float

C++: core::pack::guidance_scoreterms::sap::calculate_slow_approx_sap(const class core::pose::Pose &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class core::pack::guidance_scoreterms::sap::SapParameterOptions &) –> double

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.common_setup(options: pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions, pose: pyrosetta.rosetta.core.pose.Pose, score_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sap_calculate_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sasa_sel: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, res_vector: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintHelper

C++: core::pack::guidance_scoreterms::sap::common_setup(const class std::shared_ptr<class core::pack::guidance_scoreterms::sap::SapConstraintOptions> &, const class core::pose::Pose &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> &, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> class std::shared_ptr<class core::pack::guidance_scoreterms::sap::SapConstraintHelper>

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.rotamer_sets_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, res_vector: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: core::pack::guidance_scoreterms::sap::rotamer_sets_from_pose(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>

pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.sap_atom_sasa(pose: pyrosetta.rosetta.core.pose.Pose, sasa_sub: pyrosetta.rosetta.utility.vector1_bool) pyrosetta.rosetta.core.id.AtomID_Map_double_t

C++: core::pack::guidance_scoreterms::sap::sap_atom_sasa(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class core::id::AtomID_Map<double>