residue_selector¶

slice_enums

Bindings for core::select::residue_selector namespace

pyrosetta.rosetta.core.select.residue_selector.AND_combine(*args, **kwargs)¶

Overloaded function.

AND_combine(sele1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sele2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

If sele1 is already an AndResidueSelector, add sele2 to it.

If not, return a new AndResidueSelector which combines the two.

If either of the selectors are a nullptr, just return the other.

C++: core::select::residue_selector::AND_combine(class std::shared_ptr<class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<class core::select::residue_selector::ResidueSelector>) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

AND_combine(sele1: pyrosetta.rosetta.utility.vector1_bool, sele2: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.utility.vector1_bool

Combine two residue ssubsets with OR logic

C++: core::select::residue_selector::AND_combine(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >

class pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector¶

Bases: ResidueSelector

The AndResidueSelector combines the output of multiple ResidueSelectors using AND logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through %add_residue_selector.

add_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

adds a ResidueSelector

C++: core::select::residue_selector::AndResidueSelector::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::AndResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_and_to_subset(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, newSubset: pyrosetta.rosetta.utility.vector1_bool, existingSubset: pyrosetta.rosetta.utility.vector1_bool) → None¶

applies newSubset to existingSubset and thereby modifies the latter

C++: core::select::residue_selector::AndResidueSelector::apply_and_to_subset(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector¶: C++: core::select::residue_selector::AndResidueSelector::operator=(const class core::select::residue_selector::AndResidueSelector &) –> class core::select::residue_selector::AndResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::AndResidueSelector::class_name() –> std::string

clear(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → None¶

Clear the contained selectors.

C++: core::select::residue_selector::AndResidueSelector::clear() –> void

clone(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::AndResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → str¶: C++: core::select::residue_selector::AndResidueSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector) → int¶

Get the number of contained selectors.

C++: core::select::residue_selector::AndResidueSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::AndResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::AndResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::AndResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator¶: C++: core::select::residue_selector::AndResidueSelectorCreator::operator=(const class core::select::residue_selector::AndResidueSelectorCreator &) –> class core::select::residue_selector::AndResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::AndResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator) → str¶: C++: core::select::residue_selector::AndResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::AndResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector¶

Bases: ResidueSelector

A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose.

apply(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::AsymmetricUnitSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector, : pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector) → pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector¶: C++: core::select::residue_selector::AsymmetricUnitSelector::operator=(const class core::select::residue_selector::AsymmetricUnitSelector &) –> class core::select::residue_selector::AsymmetricUnitSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::AsymmetricUnitSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::AsymmetricUnitSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::AsymmetricUnitSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::AsymmetricUnitSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::AsymmetricUnitSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator¶: C++: core::select::residue_selector::AsymmetricUnitSelectorCreator::operator=(const class core::select::residue_selector::AsymmetricUnitSelectorCreator &) –> class core::select::residue_selector::AsymmetricUnitSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::AsymmetricUnitSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator) → str¶: C++: core::select::residue_selector::AsymmetricUnitSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::AsymmetricUnitSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.BFactorSelector¶

Bases: ResidueSelector

A residue selector dependent on b-factor values

apply(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::BFactorSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, : pyrosetta.rosetta.core.select.residue_selector.BFactorSelector) → pyrosetta.rosetta.core.select.residue_selector.BFactorSelector¶: C++: core::select::residue_selector::BFactorSelector::operator=(const class core::select::residue_selector::BFactorSelector &) –> class core::select::residue_selector::BFactorSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::BFactorSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::BFactorSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::BFactorSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::BFactorSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

This residue selector is unpublished. It returns AmeyaHarmalkar as its author.

C++: core::select::residue_selector::BFactorSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::BFactorSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_cross_chain_boundaries(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, cross: bool) → None¶: C++: core::select::residue_selector::BFactorSelector::set_cross_chain_boundaries(bool) –> void

set_lower_bfactor_threshold(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, lower_thresh: float) → None¶: C++: core::select::residue_selector::BFactorSelector::set_lower_bfactor_threshold(const double) –> void

set_lower_residues(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, nres: int) → None¶: C++: core::select::residue_selector::BFactorSelector::set_lower_residues(const unsigned long) –> void

set_min_contiguous_res(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, nres: int) → None¶: C++: core::select::residue_selector::BFactorSelector::set_min_contiguous_res(const unsigned long) –> void

set_upper_bfactor_threshold(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, upper_thresh: float) → None¶: C++: core::select::residue_selector::BFactorSelector::set_upper_bfactor_threshold(const double) –> void

set_upper_residues(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelector, nres: int) → None¶: C++: core::select::residue_selector::BFactorSelector::set_upper_residues(const unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator¶: C++: core::select::residue_selector::BFactorSelectorCreator::operator=(const class core::select::residue_selector::BFactorSelectorCreator &) –> class core::select::residue_selector::BFactorSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BFactorSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator) → str¶: C++: core::select::residue_selector::BFactorSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::BFactorSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.BinSelector¶

Bases: ResidueSelector

A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin).

apply(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::BinSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, : pyrosetta.rosetta.core.select.residue_selector.BinSelector) → pyrosetta.rosetta.core.select.residue_selector.BinSelector¶: C++: core::select::residue_selector::BinSelector::operator=(const class core::select::residue_selector::BinSelector &) –> class core::select::residue_selector::BinSelector &

bin_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str¶

Get the name of the bin that the residues that we will select must be in.

C++: core::select::residue_selector::BinSelector::bin_name() const –> const std::string &

bin_params_file_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str¶

Get the name of the bin params file that we’ll be using.

C++: core::select::residue_selector::BinSelector::bin_params_file_name() const –> const std::string &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::BinSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::BinSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::BinSelector::get_name() const –> std::string

initialize_and_check(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → None¶

Load the bin params file and check that settings are consistent.

Must be called before apply() function.

C++: core::select::residue_selector::BinSelector::initialize_and_check() –> void

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::BinSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, allowing automatic evaluation of bad XML.

C++: core::select::residue_selector::BinSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

select_only_alpha_aas(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector) → bool¶

Get whether we’re selecting alpha-amino acids only.

C++: core::select::residue_selector::BinSelector::select_only_alpha_aas() const –> bool

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_bin_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, bin_name_in: str) → None¶

Set the name of the bin that the residues that we will select must be in.

C++: core::select::residue_selector::BinSelector::set_bin_name(const std::string &) –> void

set_bin_params_file_name(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, filename_in: str) → None¶

Set the name of the bin params file that we’ll be using.

C++: core::select::residue_selector::BinSelector::set_bin_params_file_name(const std::string &) –> void

set_select_only_alpha_aas(self: pyrosetta.rosetta.core.select.residue_selector.BinSelector, setting: bool) → None¶

Set whether we’re selecting alpha-amino acids only.

C++: core::select::residue_selector::BinSelector::set_select_only_alpha_aas(const bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator¶: C++: core::select::residue_selector::BinSelectorCreator::operator=(const class core::select::residue_selector::BinSelectorCreator &) –> class core::select::residue_selector::BinSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BinSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator) → str¶: C++: core::select::residue_selector::BinSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::BinSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.BlockSelector¶

Bases: ResidueSelector

selectes a specified continuous block of previously selected residues

apply(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::BlockSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, : pyrosetta.rosetta.core.select.residue_selector.BlockSelector) → pyrosetta.rosetta.core.select.residue_selector.BlockSelector¶: C++: core::select::residue_selector::BlockSelector::operator=(const class core::select::residue_selector::BlockSelector &) –> class core::select::residue_selector::BlockSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::BlockSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::BlockSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::BlockSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::BlockSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::BlockSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_block_number(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, block_number: int) → None¶: C++: core::select::residue_selector::BlockSelector::set_block_number(unsigned long) –> void

set_inverse(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, inverse: bool) → None¶: C++: core::select::residue_selector::BlockSelector::set_inverse(bool) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::BlockSelector::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator¶: C++: core::select::residue_selector::BlockSelectorCreator::operator=(const class core::select::residue_selector::BlockSelectorCreator &) –> class core::select::residue_selector::BlockSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BlockSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator) → str¶: C++: core::select::residue_selector::BlockSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::BlockSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector¶

Bases: ResidueSelector

The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector.

Residues in the input_set are included in the final selection.

apply(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::BondedResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector¶: C++: core::select::residue_selector::BondedResidueSelector::operator=(const class core::select::residue_selector::BondedResidueSelector &) –> class core::select::residue_selector::BondedResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::BondedResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BondedResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → str¶: C++: core::select::residue_selector::BondedResidueSelector::get_name() const –> std::string

input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: core::select::residue_selector::BondedResidueSelector::input_set() const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

input_set_defined(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → bool¶: C++: core::select::residue_selector::BondedResidueSelector::input_set_defined() const –> bool

input_set_selector(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BondedResidueSelector::input_set_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

input_set_selector_defined(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → bool¶: C++: core::select::residue_selector::BondedResidueSelector::input_set_selector_defined() const –> bool

input_set_string(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector) → str¶: C++: core::select::residue_selector::BondedResidueSelector::input_set_string() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datacache: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::BondedResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::BondedResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_input_set(*args, **kwargs)¶

Overloaded function.

set_input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, input_set: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

adds a ResidueSelector

C++: core::select::residue_selector::BondedResidueSelector::set_input_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

set_input_set(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, input_set_str: str) -> None

C++: core::select::residue_selector::BondedResidueSelector::set_input_set(const std::string &) –> void

set_input_set_selector(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector, rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::BondedResidueSelector::set_input_set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator¶: C++: core::select::residue_selector::BondedResidueSelectorCreator::operator=(const class core::select::residue_selector::BondedResidueSelectorCreator &) –> class core::select::residue_selector::BondedResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::BondedResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator) → str¶: C++: core::select::residue_selector::BondedResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::BondedResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset¶

Bases: CacheableData

assign(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset, : pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset) → pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset¶: C++: core::select::residue_selector::CachedResidueSubset::operator=(const class core::select::residue_selector::CachedResidueSubset &) –> class core::select::residue_selector::CachedResidueSubset &

clone(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::select::residue_selector::CachedResidueSubset::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

fresh_instance(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: core::select::residue_selector::CachedResidueSubset::fresh_instance() const –> class std::shared_ptr<class basic::datacache::CacheableData>

static from_pose_datacache(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset¶: C++: core::select::residue_selector::CachedResidueSubset::from_pose_datacache(class core::pose::Pose &) –> class core::select::residue_selector::CachedResidueSubset &

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t¶: C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

get_subset(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset, name: str) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::CachedResidueSubset::get_subset(const std::string &) const –> class std::shared_ptr<const class utility::vector1<bool, class std::allocator<bool> > >

has_subset(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset, name: str) → bool¶: C++: core::select::residue_selector::CachedResidueSubset::has_subset(const std::string &) const –> bool

has_subset_prefix(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset, name: str) → bool¶

used to search for residue subsets with a given prefix

C++: core::select::residue_selector::CachedResidueSubset::has_subset_prefix(const std::string &) const –> bool

set_subset(self: pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset, subset: pyrosetta.rosetta.utility.vector1_bool, name: str) → None¶: C++: core::select::residue_selector::CachedResidueSubset::set_subset(const class std::shared_ptr<const class utility::vector1<bool, class std::allocator<bool> > >, const std::string &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ChainSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ChainSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector, : pyrosetta.rosetta.core.select.residue_selector.ChainSelector) → pyrosetta.rosetta.core.select.residue_selector.ChainSelector¶: C++: core::select::residue_selector::ChainSelector::operator=(const class core::select::residue_selector::ChainSelector &) –> class core::select::residue_selector::ChainSelector &

chain_strings(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::select::residue_selector::ChainSelector::chain_strings() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

static class_name() → str¶: C++: core::select::residue_selector::ChainSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ChainSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector) → str¶: C++: core::select::residue_selector::ChainSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ChainSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ChainSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_chain_strings(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelector, : pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::select::residue_selector::ChainSelector::set_chain_strings(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator¶: C++: core::select::residue_selector::ChainSelectorCreator::operator=(const class core::select::residue_selector::ChainSelectorCreator &) –> class core::select::residue_selector::ChainSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ChainSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator) → str¶: C++: core::select::residue_selector::ChainSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ChainSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector¶

Bases: ResidueSelector

A class that finds the neighboring residues for a particular residue by looking at atom-atom distances

apply(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::CloseContactResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector¶: C++: core::select::residue_selector::CloseContactResidueSelector::operator=(const class core::select::residue_selector::CloseContactResidueSelector &) –> class core::select::residue_selector::CloseContactResidueSelector &

central_residue_group_selector(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::CloseContactResidueSelector::central_residue_group_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::CloseContactResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::CloseContactResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::CloseContactResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::CloseContactResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::CloseContactResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector, contact_threshold: float) -> None

C++: core::select::residue_selector::CloseContactResidueSelector::threshold(double) –> void

threshold(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector) -> float

C++: core::select::residue_selector::CloseContactResidueSelector::threshold() const –> double

class pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator¶: C++: core::select::residue_selector::CloseContactResidueSelectorCreator::operator=(const class core::select::residue_selector::CloseContactResidueSelectorCreator &) –> class core::select::residue_selector::CloseContactResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::CloseContactResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator) → str¶: C++: core::select::residue_selector::CloseContactResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::CloseContactResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector¶

Bases: ResidueSelector

selector that selects all the residues between those selected by another selector that are not interspersed with those selected by a third selector

apply(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::ConfluentSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector, : pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector) → pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector¶: C++: core::select::residue_selector::ConfluentSelector::operator=(const class core::select::residue_selector::ConfluentSelector &) –> class core::select::residue_selector::ConfluentSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::ConfluentSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::ConfluentSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::ConfluentSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::ConfluentSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::ConfluentSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_breaking_selector(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector, breaking_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::ConfluentSelector::set_breaking_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_terminus_selector(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector, terminus_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::ConfluentSelector::set_terminus_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator¶: C++: core::select::residue_selector::ConfluentSelectorCreator::operator=(const class core::select::residue_selector::ConfluentSelectorCreator &) –> class core::select::residue_selector::ConfluentSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ConfluentSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator) → str¶: C++: core::select::residue_selector::ConfluentSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ConfluentSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector¶

Bases: ResidueSelector

Selects residues that are considered ‘error’ region with respect to the density resolution.

Uses weighted sum of density, density-compared-to-neighbors, rama (where applicable) and cart_bonded to compute

apply(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, input_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::DensityFitResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector¶: C++: core::select::residue_selector::DensityFitResidueSelector::operator=(const class core::select::residue_selector::DensityFitResidueSelector &) –> class core::select::residue_selector::DensityFitResidueSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::DensityFitResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::DensityFitResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_den_fit_metric(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector) → core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric¶

Edit the density fit metric used to do the calculation in this class.

C++: core::select::residue_selector::DensityFitResidueSelector::get_den_fit_metric() –> class std::shared_ptr<class core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::DensityFitResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::DensityFitResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_cache_options(*args, **kwargs)¶

Overloaded function.

set_cache_options(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, use_sm_cache: bool) -> None
set_cache_options(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, use_sm_cache: bool, prefix: str) -> None
set_cache_options(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, use_sm_cache: bool, prefix: str, suffix: str) -> None
set_cache_options(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, use_sm_cache: bool, prefix: str, suffix: str, fail_on_missing_cache: bool) -> None

Set up options to use any data already stored in the SM cache through its apply method.

C++: core::select::residue_selector::DensityFitResidueSelector::set_cache_options(bool, const std::string &, const std::string &, bool) –> void

set_den_fit_metric(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, den_fit_metric: core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric) → None¶

Set the density fit metric that will be used to do the calculation in this class.: Clones into this class.

C++: core::select::residue_selector::DensityFitResidueSelector::set_den_fit_metric(class std::shared_ptr<const class core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric>) –> void

set_invert(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, invert: bool) → None¶

Set to invert - IE select BAD density instead of GOOD.

C++: core::select::residue_selector::DensityFitResidueSelector::set_invert(bool) –> void

set_score_cut(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector, score_cut: float) → None¶

Set the scorecut to use. From -3 up. -.5 is default. Anything higher, is deemed ‘good’ for zscore.: This is also the correlation for match_mode. Correlation of 1.0 fits density completely. .7 is a good cutoff.

C++: core::select::residue_selector::DensityFitResidueSelector::set_score_cut(double) –> void

class pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator¶: C++: core::select::residue_selector::DensityFitResidueSelectorCreator::operator=(const class core::select::residue_selector::DensityFitResidueSelectorCreator &) –> class core::select::residue_selector::DensityFitResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::DensityFitResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator) → str¶: C++: core::select::residue_selector::DensityFitResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::DensityFitResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::FalseResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector¶: C++: core::select::residue_selector::FalseResidueSelector::operator=(const class core::select::residue_selector::FalseResidueSelector &) –> class core::select::residue_selector::FalseResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::FalseResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::FalseResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector) → str¶: C++: core::select::residue_selector::FalseResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::FalseResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::FalseResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator¶: C++: core::select::residue_selector::FalseResidueSelectorCreator::operator=(const class core::select::residue_selector::FalseResidueSelectorCreator &) –> class core::select::residue_selector::FalseResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::FalseResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator) → str¶: C++: core::select::residue_selector::FalseResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::FalseResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.FractionSelector¶

Bases: ResidueSelector

Selects only either the first or the last residue selected by a provided ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::FractionSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, : pyrosetta.rosetta.core.select.residue_selector.FractionSelector) → pyrosetta.rosetta.core.select.residue_selector.FractionSelector¶: C++: core::select::residue_selector::FractionSelector::operator=(const class core::select::residue_selector::FractionSelector &) –> class core::select::residue_selector::FractionSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::FractionSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::FractionSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::FractionSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::FractionSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::FractionSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_N(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, N: int) → None¶: C++: core::select::residue_selector::FractionSelector::set_N(unsigned long) –> void

set_first(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, first: bool) → None¶: C++: core::select::residue_selector::FractionSelector::set_first(bool) –> void

set_fraction(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, fraction: float) → None¶: C++: core::select::residue_selector::FractionSelector::set_fraction(double) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::FractionSelector::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator¶: C++: core::select::residue_selector::FractionSelectorCreator::operator=(const class core::select::residue_selector::FractionSelectorCreator &) –> class core::select::residue_selector::FractionSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::FractionSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator) → str¶: C++: core::select::residue_selector::FractionSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::FractionSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector¶

Bases: ResidueSelector

A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree. If no layer is set, will select all glycan residues.

apply(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::GlycanLayerSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector¶: C++: core::select::residue_selector::GlycanLayerSelector::operator=(const class core::select::residue_selector::GlycanLayerSelector &) –> class core::select::residue_selector::GlycanLayerSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanLayerSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanLayerSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanLayerSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanLayerSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanLayerSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_layer(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, start: int, end: int) → None¶

Set the layer we will be returning.

C++: core::select::residue_selector::GlycanLayerSelector::set_layer(unsigned long, unsigned long) –> void

set_layer_as_greater_than_or_equal_to(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, start: int) → None¶

Set the layer as all residues greater than or equal to this number (such as the end of the tree)

C++: core::select::residue_selector::GlycanLayerSelector::set_layer_as_greater_than_or_equal_to(unsigned long) –> void

set_layer_as_less_than_or_equal_to(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector, end: int) → None¶

Set the layer as all residue less or equal to this number (the beginning of the tree).

C++: core::select::residue_selector::GlycanLayerSelector::set_layer_as_less_than_or_equal_to(unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator¶: C++: core::select::residue_selector::GlycanLayerSelectorCreator::operator=(const class core::select::residue_selector::GlycanLayerSelectorCreator &) –> class core::select::residue_selector::GlycanLayerSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::GlycanLayerSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator) → str¶: C++: core::select::residue_selector::GlycanLayerSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::GlycanLayerSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector¶

Bases: ResidueSelector

add_range(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, range: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → None¶

Add a range to the list.

C++: core::select::residue_selector::GlycanPositionSelector::add_range(const class core::select::residue_selector::ResidueRange &) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::GlycanPositionSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector¶: C++: core::select::residue_selector::GlycanPositionSelector::operator=(const class core::select::residue_selector::GlycanPositionSelector &) –> class core::select::residue_selector::GlycanPositionSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanPositionSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanPositionSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanPositionSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanPositionSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanPositionSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_positions(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Set a specific set of positions to select on.

C++: core::select::residue_selector::GlycanPositionSelector::set_positions(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_range(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, ranges: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → None¶

Set the range of glycan positions to select from.

C++: core::select::residue_selector::GlycanPositionSelector::set_range(const class utility::vector1<class core::select::residue_selector::ResidueRange, class std::allocator<class core::select::residue_selector::ResidueRange> > &) –> void

set_select_from_residue_position(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, select_from_residue_position: int) → None¶

Set the position from which to select all outer foliage from, (and includeing) this position.

C++: core::select::residue_selector::GlycanPositionSelector::set_select_from_residue_position(const unsigned long) –> void

set_select_to_residue_position(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector, select_to_residue_position: int) → None¶

Set the position where we will select all glycan residues up to this specific glycan position.

C++: core::select::residue_selector::GlycanPositionSelector::set_select_to_residue_position(const unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator¶: C++: core::select::residue_selector::GlycanPositionSelectorCreator::operator=(const class core::select::residue_selector::GlycanPositionSelectorCreator &) –> class core::select::residue_selector::GlycanPositionSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::GlycanPositionSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator) → str¶: C++: core::select::residue_selector::GlycanPositionSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::GlycanPositionSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector¶

Bases: ResidueSelector

A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc.

apply(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::GlycanResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector¶: C++: core::select::residue_selector::GlycanResidueSelector::operator=(const class core::select::residue_selector::GlycanResidueSelector &) –> class core::select::residue_selector::GlycanResidueSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_include_root(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, include_root: bool) → None¶

Option to include the root(s) we are selecting from.: Default FALSE.

C++: core::select::residue_selector::GlycanResidueSelector::set_include_root(bool) –> void

set_select_from_branch_residue(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residue: int) → None¶

Set the residue to select from. These can be the branch points of the glycans or

carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

C++: core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residue(unsigned long) –> void

set_select_from_branch_residues(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector, root_residues: pyrosetta.rosetta.utility.vector1_bool) → None¶

Set the residue(s) to select from. These can be the branch points of the glycans or

carbohydrate residues from which to select the downstream branch from.

Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out.

Note that the Subset will not include the Root residue by default.

C++: core::select::residue_selector::GlycanResidueSelector::set_select_from_branch_residues(class utility::vector1<bool, class std::allocator<bool> >) –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator¶: C++: core::select::residue_selector::GlycanResidueSelectorCreator::operator=(const class core::select::residue_selector::GlycanResidueSelectorCreator &) –> class core::select::residue_selector::GlycanResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::GlycanResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator) → str¶: C++: core::select::residue_selector::GlycanResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::GlycanResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector¶

Bases: ResidueInSequenceMotifSelector

Find glycosylation sequons in pose

Glycosylation sites are typically recognized by enzymes by means of a recognition sequence, or ‘motif’. This ResidueSelector selects all residues that can be glycosylated using one of a few sequence motifs that are pre-defined and can be selected. For selecting residues in other motifs, use the ResidueInSequenceMotifSelctor, which takes regular expressions as input.

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector, : pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector) → pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector¶: C++: core::select::residue_selector::GlycanSequonsSelector::operator=(const class core::select::residue_selector::GlycanSequonsSelector &) –> class core::select::residue_selector::GlycanSequonsSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanSequonsSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::GlycanSequonsSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::GlycanSequonsSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::GlycanSequonsSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::GlycanSequonsSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator¶: C++: core::select::residue_selector::GlycanSequonsSelectorCreator::operator=(const class core::select::residue_selector::GlycanSequonsSelectorCreator &) –> class core::select::residue_selector::GlycanSequonsSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::GlycanSequonsSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator) → str¶: C++: core::select::residue_selector::GlycanSequonsSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::GlycanSequonsSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector¶

Bases: ResidueSelector

The %InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset.

apply(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, : pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::operator=(const class core::select::residue_selector::InterGroupInterfaceByVectorSelector &) –> class core::select::residue_selector::InterGroupInterfaceByVectorSelector &

cb_dist_cut(*args, **kwargs)¶

Overloaded function.

cb_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut() const –> double

cb_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::cb_dist_cut(double) –> void

static class_name() → str¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) → str¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::get_name() const –> std::string

group1_resstring(*args, **kwargs)¶

Overloaded function.

group1_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring() const –> const std::string &

group1_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: str) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_resstring(const std::string &) –> void

group1_selector(*args, **kwargs)¶

Overloaded function.

group1_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

group1_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

group1_set(*args, **kwargs)¶

Overloaded function.

group1_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

group1_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group1_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

group2_resstring(*args, **kwargs)¶

Overloaded function.

group2_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> str

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring() const –> const std::string &

group2_resstring(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: str) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_resstring(const std::string &) –> void

group2_selector(*args, **kwargs)¶

Overloaded function.

group2_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

group2_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

group2_set(*args, **kwargs)¶

Overloaded function.

group2_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> pyrosetta.rosetta.std.set_unsigned_long_t

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set() const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &

group2_set(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: pyrosetta.rosetta.std.set_unsigned_long_t) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::group2_set(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void

nearby_atom_cut(*args, **kwargs)¶

Overloaded function.

nearby_atom_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut() const –> double

nearby_atom_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::nearby_atom_cut(double) –> void

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

vector_angle_cut(*args, **kwargs)¶

Overloaded function.

vector_angle_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut() const –> double

vector_angle_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_angle_cut(double) –> void

vector_dist_cut(*args, **kwargs)¶

Overloaded function.

vector_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector) -> float

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut() const –> double

vector_dist_cut(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector, setting: float) -> None

C++: core::select::residue_selector::InterGroupInterfaceByVectorSelector::vector_dist_cut(double) –> void

class pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::operator=(const class core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator &) –> class core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator) → str¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::InterGroupInterfaceByVectorSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector¶

Bases: ResidueSelector

The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which lie downstream of a given jump in the FoldTree. The jump is specified by an integer index.

apply(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::JumpDownstreamSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, : pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector¶: C++: core::select::residue_selector::JumpDownstreamSelector::operator=(const class core::select::residue_selector::JumpDownstreamSelector &) –> class core::select::residue_selector::JumpDownstreamSelector &

static class_name() → str¶: C++: core::select::residue_selector::JumpDownstreamSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::JumpDownstreamSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector) → str¶: C++: core::select::residue_selector::JumpDownstreamSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::JumpDownstreamSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::JumpDownstreamSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_jump(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, jump: int) → None¶

sets the string by which residues are selected

C++: core::select::residue_selector::JumpDownstreamSelector::set_jump(int) –> void

set_jump_selector(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector, sele: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) → None¶

this overrides the integer setting if this is not null

C++: core::select::residue_selector::JumpDownstreamSelector::set_jump_selector(class std::shared_ptr<const class core::select::jump_selector::JumpSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator¶: C++: core::select::residue_selector::JumpDownstreamSelectorCreator::operator=(const class core::select::residue_selector::JumpDownstreamSelectorCreator &) –> class core::select::residue_selector::JumpDownstreamSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::JumpDownstreamSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator) → str¶: C++: core::select::residue_selector::JumpDownstreamSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::JumpDownstreamSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector¶

Bases: ResidueSelector

The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index.

apply(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::JumpUpstreamSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, : pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector¶: C++: core::select::residue_selector::JumpUpstreamSelector::operator=(const class core::select::residue_selector::JumpUpstreamSelector &) –> class core::select::residue_selector::JumpUpstreamSelector &

static class_name() → str¶: C++: core::select::residue_selector::JumpUpstreamSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::JumpUpstreamSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector) → str¶: C++: core::select::residue_selector::JumpUpstreamSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::JumpUpstreamSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::JumpUpstreamSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_jump(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector, jump: int) → None¶

sets the string by which residues are selected

C++: core::select::residue_selector::JumpUpstreamSelector::set_jump(int) –> void

class pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator¶: C++: core::select::residue_selector::JumpUpstreamSelectorCreator::operator=(const class core::select::residue_selector::JumpUpstreamSelectorCreator &) –> class core::select::residue_selector::JumpUpstreamSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::JumpUpstreamSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator) → str¶: C++: core::select::residue_selector::JumpUpstreamSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::JumpUpstreamSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.LayerSelector¶

Bases: ResidueSelector

The LayerSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

apply(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

Apply function: generate a ResidueSubset given a Pose.

C++: core::select::residue_selector::LayerSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, : pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → pyrosetta.rosetta.core.select.residue_selector.LayerSelector¶: C++: core::select::residue_selector::LayerSelector::operator=(const class core::select::residue_selector::LayerSelector &) –> class core::select::residue_selector::LayerSelector &

static class_name() → str¶

Get the class name.

C++: core::select::residue_selector::LayerSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::LayerSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → str¶

Get the class name.

Calls class_name().

C++: core::select::residue_selector::LayerSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Parse xml tag setting up this selector.

C++: core::select::residue_selector::LayerSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::LayerSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::LayerSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_angle_exponent(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None¶

Set the sidechain neighbor angle exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_angle_exponent(double) –> void

set_angle_shift_factor(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None¶

Set the sidechain neighbor angle shift value.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_angle_shift_factor(double) –> void

set_asu_only(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, asu_only: bool) → None¶

Set select only the asymmetric unit residues or not.

C++: core::select::residue_selector::LayerSelector::set_asu_only(const bool) –> void

set_ball_radius(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, radius: float) → None¶

Set the radius for the rolling ball algorithm used to determine burial.

C++: core::select::residue_selector::LayerSelector::set_ball_radius(double) –> void

set_cache_selection(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: bool) → None¶

Set whether to cache versus recompute the layer selection whenever it is accessed.

C++: core::select::residue_selector::LayerSelector::set_cache_selection(const bool) –> void

set_cutoffs(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, core: float, surf: float) → None¶

Set the cutoffs for core and surface layers.

Boundary is defined implicitly. This can be a SASA cutoff or a neighbor count, depending on the algorithm.

C++: core::select::residue_selector::LayerSelector::set_cutoffs(double, double) –> void

set_dist_exponent(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None¶

Set the sidechain neighbor distance exponent.

See the core::select::util::SelectResiduesByLayer class for details of the math.

C++: core::select::residue_selector::LayerSelector::set_dist_exponent(double) –> void

set_layers(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, pick_core: bool, pick_boundary: bool, pick_surface: bool) → None¶

Set the layers that this selector will choose.

C++: core::select::residue_selector::LayerSelector::set_layers(bool, bool, bool) –> void

set_sc_neighbor_denominator(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None¶

Set the factor by which sidechain neighbor counts are divided if the sidechain: neighbors method is used to define layers.

C++: core::select::residue_selector::LayerSelector::set_sc_neighbor_denominator(double) –> void

set_sc_neighbor_dist_midpoint(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: float) → None¶

Set the midpoint of the distance falloff if the sidechain neighbors method is used: to define layers.

C++: core::select::residue_selector::LayerSelector::set_sc_neighbor_dist_midpoint(double) –> void

set_use_sc_neighbors(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector, val: bool) → None¶

Set whether the sidechain neighbors algorithm is used to determine burial (as: opposed to the rolling ball algorithm).

C++: core::select::residue_selector::LayerSelector::set_use_sc_neighbors(bool) –> void

use_sc_neighbors(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelector) → bool¶

Get whether the sidechain neighbors algorithm is used to determine burial (as: opposed to the rolling ball algorithm).

C++: core::select::residue_selector::LayerSelector::use_sc_neighbors() const –> bool

class pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator¶: C++: core::select::residue_selector::LayerSelectorCreator::operator=(const class core::select::residue_selector::LayerSelectorCreator &) –> class core::select::residue_selector::LayerSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::LayerSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator) → str¶: C++: core::select::residue_selector::LayerSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::LayerSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector¶

Bases: ResidueSelector

A residue selector that takes arbitrarily many residue selectors and performs and/or/not boolean logic within the “residue_selectors” option.

apply(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::LogicResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector¶: C++: core::select::residue_selector::LogicResidueSelector::operator=(const class core::select::residue_selector::LogicResidueSelector &) –> class core::select::residue_selector::LogicResidueSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::LogicResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::LogicResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::LogicResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::LogicResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::LogicResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::LogicResidueSelector::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator¶: C++: core::select::residue_selector::LogicResidueSelectorCreator::operator=(const class core::select::residue_selector::LogicResidueSelectorCreator &) –> class core::select::residue_selector::LogicResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::LogicResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator) → str¶: C++: core::select::residue_selector::LogicResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::LogicResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector¶

Bases: ResidueSelector

The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this!

Note: Uses the 10 A neighbor graph by default. If neighbor distance is great than this, we use slow-style double for loop.

apply(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::operator=(const class core::select::residue_selector::NeighborhoodResidueSelector &) –> class core::select::residue_selector::NeighborhoodResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::NeighborhoodResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector) → str¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::NeighborhoodResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NeighborhoodResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_atom_names_for_distance_measure(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, atom_names: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Set atom names to be used for selecting instead of using neighbor atoms.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_atom_names_for_distance_measure(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_distance(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, distance: float) → None¶

Set the distance we will be measuring to get neighbors

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_distance(double) –> void

set_focus(*args, **kwargs)¶

Overloaded function.

set_focus(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus_str: str) -> None

Set the focus, which is the residues for which we will be getting neighbors of.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus(const std::string &) –> void

set_focus(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, focus: pyrosetta.rosetta.utility.vector1_bool) -> None

Set the focus, which is the residues for which we will be getting neighbors of.

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

set_focus_selector(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, rs: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set a Residue Selector for the focus

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_focus_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_include_focus_in_subset(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector, include_focus: bool) → None¶

Setting to include the focus in the resulting subset or not. Default is TRUE

C++: core::select::residue_selector::NeighborhoodResidueSelector::set_include_focus_in_subset(bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator¶: C++: core::select::residue_selector::NeighborhoodResidueSelectorCreator::operator=(const class core::select::residue_selector::NeighborhoodResidueSelectorCreator &) –> class core::select::residue_selector::NeighborhoodResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::NeighborhoodResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator) → str¶: C++: core::select::residue_selector::NeighborhoodResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NeighborhoodResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector¶

Bases: ResidueSelector

The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT - it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true. The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector. Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting the opposite of the passed in selector.

apply(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::NotResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector¶: C++: core::select::residue_selector::NotResidueSelector::operator=(const class core::select::residue_selector::NotResidueSelector &) –> class core::select::residue_selector::NotResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::NotResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::NotResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector) → str¶: C++: core::select::residue_selector::NotResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::NotResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::NotResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NotResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

sets a ResidueSelector

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

class pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator¶: C++: core::select::residue_selector::NotResidueSelectorCreator::operator=(const class core::select::residue_selector::NotResidueSelectorCreator &) –> class core::select::residue_selector::NotResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::NotResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator) → str¶: C++: core::select::residue_selector::NotResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NotResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::NumNeighborsSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, : pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) → pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector¶: C++: core::select::residue_selector::NumNeighborsSelector::operator=(const class core::select::residue_selector::NumNeighborsSelector &) –> class core::select::residue_selector::NumNeighborsSelector &

static class_name() → str¶: C++: core::select::residue_selector::NumNeighborsSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::NumNeighborsSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

count_water(*args, **kwargs)¶

Overloaded function.

count_water(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) -> bool

C++: core::select::residue_selector::NumNeighborsSelector::count_water() const –> bool

count_water(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, setting: bool) -> None

C++: core::select::residue_selector::NumNeighborsSelector::count_water(bool) –> void

distance_cutoff(*args, **kwargs)¶

Overloaded function.

distance_cutoff(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) -> float

C++: core::select::residue_selector::NumNeighborsSelector::distance_cutoff() const –> double

distance_cutoff(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, setting: int) -> None

C++: core::select::residue_selector::NumNeighborsSelector::distance_cutoff(unsigned long) –> void

get_name(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) → str¶: C++: core::select::residue_selector::NumNeighborsSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::NumNeighborsSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NumNeighborsSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector) -> int

C++: core::select::residue_selector::NumNeighborsSelector::threshold() const –> unsigned long

threshold(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector, setting: int) -> None

C++: core::select::residue_selector::NumNeighborsSelector::threshold(unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator¶: C++: core::select::residue_selector::NumNeighborsSelectorCreator::operator=(const class core::select::residue_selector::NumNeighborsSelectorCreator &) –> class core::select::residue_selector::NumNeighborsSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::NumNeighborsSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator) → str¶: C++: core::select::residue_selector::NumNeighborsSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::NumNeighborsSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.core.select.residue_selector.OR_combine(*args, **kwargs)¶

Overloaded function.

OR_combine(sele1: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, sele2: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

If sele1 is already an OrResidueSelector, add sele2 to it.

If not, return a new OrResidueSelector which combines the two.

If either of the selectors are a nullptr, just return the other.

C++: core::select::residue_selector::OR_combine(class std::shared_ptr<class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<class core::select::residue_selector::ResidueSelector>) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

OR_combine(sele1: pyrosetta.rosetta.utility.vector1_bool, sele2: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.utility.vector1_bool

Combine two residue subsets with OR logic

C++: core::select::residue_selector::OR_combine(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >

class pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector¶

Bases: ResidueSelector

The OrResidueSelector combines the output of multiple ResidueSelectors using OR logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through %add_residue_selector.

add_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

adds a ResidueSelector

C++: core::select::residue_selector::OrResidueSelector::add_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::OrResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

apply_or_to_subset(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, newSubset: pyrosetta.rosetta.utility.vector1_bool, existingSubset: pyrosetta.rosetta.utility.vector1_bool) → None¶

applies newSubset to existingSubset and thereby modifies the latter

C++: core::select::residue_selector::OrResidueSelector::apply_or_to_subset(const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void

assign(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector¶: C++: core::select::residue_selector::OrResidueSelector::operator=(const class core::select::residue_selector::OrResidueSelector &) –> class core::select::residue_selector::OrResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::OrResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::OrResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → str¶: C++: core::select::residue_selector::OrResidueSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector) → int¶: C++: core::select::residue_selector::OrResidueSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::OrResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::OrResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::OrResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator¶: C++: core::select::residue_selector::OrResidueSelectorCreator::operator=(const class core::select::residue_selector::OrResidueSelectorCreator &) –> class core::select::residue_selector::OrResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::OrResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator) → str¶: C++: core::select::residue_selector::OrResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::OrResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.PhiSelector¶

Bases: ResidueSelector

A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences).

apply(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::PhiSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, : pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → pyrosetta.rosetta.core.select.residue_selector.PhiSelector¶: C++: core::select::residue_selector::PhiSelector::operator=(const class core::select::residue_selector::PhiSelector &) –> class core::select::residue_selector::PhiSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::PhiSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone function.

Copy this object and return owning pointer to the copy (created on the heap).

C++: core::select::residue_selector::PhiSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::PhiSelector::get_name() const –> std::string

ignore_unconnected_upper(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → bool¶

Are we ignoring residues with no upper connection?

Default true.

C++: core::select::residue_selector::PhiSelector::ignore_unconnected_upper() const –> bool

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::PhiSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, allowing automatic evaluation of bad XML.

C++: core::select::residue_selector::PhiSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

select_positive_phi(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector) → bool¶

Are we selecting the residues in the positive phi region?

Default true.

C++: core::select::residue_selector::PhiSelector::select_positive_phi() const –> bool

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_ignore_unconnected_upper(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, setting: bool) → None¶

Set whether we’re ignoring residues with no upper connection.

C++: core::select::residue_selector::PhiSelector::set_ignore_unconnected_upper(const bool) –> void

set_select_positive_phi(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelector, setting: bool) → None¶

Set whether we’re selecting residues in the positive phi region.

C++: core::select::residue_selector::PhiSelector::set_select_positive_phi(const bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator¶: C++: core::select::residue_selector::PhiSelectorCreator::operator=(const class core::select::residue_selector::PhiSelectorCreator &) –> class core::select::residue_selector::PhiSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::PhiSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator) → str¶: C++: core::select::residue_selector::PhiSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::PhiSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector¶

Bases: ResidueSelector

The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are located near the given selected residues in primary sequence space

apply(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, : pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::operator=(const class core::select::residue_selector::PrimarySequenceNeighborhoodSelector &) –> class core::select::residue_selector::PrimarySequenceNeighborhoodSelector &

static class_name() → str¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector) → str¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_cross_chain_boundaries(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, cross: bool) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_cross_chain_boundaries(bool) –> void

set_lower_residues(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres: int) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_lower_residues(const unsigned long) –> void

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_upper_residues(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector, nres: int) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelector::set_upper_residues(const unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator::operator=(const class core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator &) –> class core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator) → str¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector¶

Bases: ResidueSelector

Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling.

apply(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::RandomGlycanFoliageSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, : pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector¶: C++: core::select::residue_selector::RandomGlycanFoliageSelector::operator=(const class core::select::residue_selector::RandomGlycanFoliageSelector &) –> class core::select::residue_selector::RandomGlycanFoliageSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set a selector to set the glycan root and subsequent foliage on.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_subset(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector, subset: pyrosetta.rosetta.utility.vector1_bool) → None¶

Set a subset to select the glycan root and subsequent foliage on.

C++: core::select::residue_selector::RandomGlycanFoliageSelector::set_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

class pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator¶: C++: core::select::residue_selector::RandomGlycanFoliageSelectorCreator::operator=(const class core::select::residue_selector::RandomGlycanFoliageSelectorCreator &) –> class core::select::residue_selector::RandomGlycanFoliageSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::RandomGlycanFoliageSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator) → str¶: C++: core::select::residue_selector::RandomGlycanFoliageSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::RandomGlycanFoliageSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector¶

Bases: ResidueSelector

The RandomResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for N randomly selected residue positions, where N is a user-specified integer.

apply(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::RandomResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector¶: C++: core::select::residue_selector::RandomResidueSelector::operator=(const class core::select::residue_selector::RandomResidueSelector &) –> class core::select::residue_selector::RandomResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::RandomResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::RandomResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector) → str¶: C++: core::select::residue_selector::RandomResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::RandomResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::RandomResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator¶: C++: core::select::residue_selector::RandomResidueSelectorCreator::operator=(const class core::select::residue_selector::RandomResidueSelectorCreator &) –> class core::select::residue_selector::RandomResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::RandomResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator) → str¶: C++: core::select::residue_selector::RandomResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::RandomResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector¶

Bases: ResidueSelector

The ResidueInMembraneSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are either in or out of the membrane. default is in.

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ResidueInMembraneSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector¶: C++: core::select::residue_selector::ResidueInMembraneSelector::operator=(const class core::select::residue_selector::ResidueInMembraneSelector &) –> class core::select::residue_selector::ResidueInMembraneSelector &

static class_name() → str¶: C++: core::select::residue_selector::ResidueInMembraneSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueInMembraneSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector) → str¶: C++: core::select::residue_selector::ResidueInMembraneSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ResidueInMembraneSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueInMembraneSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_select_in_membrane(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector, select_in_membrane: bool) → None¶: C++: core::select::residue_selector::ResidueInMembraneSelector::set_select_in_membrane(const bool &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator¶: C++: core::select::residue_selector::ResidueInMembraneSelectorCreator::operator=(const class core::select::residue_selector::ResidueInMembraneSelectorCreator &) –> class core::select::residue_selector::ResidueInMembraneSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueInMembraneSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator) → str¶: C++: core::select::residue_selector::ResidueInMembraneSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueInMembraneSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector¶

Bases: ResidueSelector

Select residues by motif search

This selector takes a regular expression and a position and then finds all matches of the regular expression and selects the n-th residue in each match, where ‘n’ is the specified position.

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector¶: C++: core::select::residue_selector::ResidueInSequenceMotifSelector::operator=(const class core::select::residue_selector::ResidueInSequenceMotifSelector &) –> class core::select::residue_selector::ResidueInSequenceMotifSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::ResidueInSequenceMotifSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator¶: C++: core::select::residue_selector::ResidueInSequenceMotifSelectorCreator::operator=(const class core::select::residue_selector::ResidueInSequenceMotifSelectorCreator &) –> class core::select::residue_selector::ResidueInSequenceMotifSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueInSequenceMotifSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator) → str¶: C++: core::select::residue_selector::ResidueInSequenceMotifSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueInSequenceMotifSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector¶

Bases: ResidueSelector

The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). It can also take range specifications (e.g. 10A-20A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

append_index(*args, **kwargs)¶

Overloaded function.

append_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_in: int) -> None

Append an additional index (in Rosetta numbering) to the list of indices.

Vikram K. Mulligan (vmullig.edu)

C++: core::select::residue_selector::ResidueIndexSelector::append_index(unsigned long) –> void

append_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_in: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Append additional indexes (in Rosetta numbering) to the list of indices.

C++: core::select::residue_selector::ResidueIndexSelector::append_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ResidueIndexSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector¶: C++: core::select::residue_selector::ResidueIndexSelector::operator=(const class core::select::residue_selector::ResidueIndexSelector &) –> class core::select::residue_selector::ResidueIndexSelector &

static class_name() → str¶: C++: core::select::residue_selector::ResidueIndexSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueIndexSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

error_on_out_of_bounds_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → bool¶

Is this selector set to throw an error if an out-of-range index is selected (e.g. residue: 56 of a 55-residue pose)?

C++: core::select::residue_selector::ResidueIndexSelector::error_on_out_of_bounds_index() const –> bool

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector) → str¶: C++: core::select::residue_selector::ResidueIndexSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ResidueIndexSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueIndexSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_error_on_out_of_bounds_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, setting: bool) → None¶

Set whether this selector set to throws an error if an out-of-range index is selected (e.g. residue: 56 of a 55-residue pose).

C++: core::select::residue_selector::ResidueIndexSelector::set_error_on_out_of_bounds_index(const bool) –> void

set_index(*args, **kwargs)¶

Overloaded function.

set_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index_str: str) -> None

sets the string by which residues are selected

C++: core::select::residue_selector::ResidueIndexSelector::set_index(const std::string &) –> void

set_index(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, index: int) -> None

Set an index using a size

C++: core::select::residue_selector::ResidueIndexSelector::set_index(unsigned long) –> void

set_index_range(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector, start: int, end: int) → None¶

Set a range of indexes. Includes start and end.

C++: core::select::residue_selector::ResidueIndexSelector::set_index_range(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator¶: C++: core::select::residue_selector::ResidueIndexSelectorCreator::operator=(const class core::select::residue_selector::ResidueIndexSelectorCreator &) –> class core::select::residue_selector::ResidueIndexSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueIndexSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator) → str¶: C++: core::select::residue_selector::ResidueIndexSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueIndexSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector¶

Bases: ResidueSelector

The ResidueNameSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally.

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ResidueNameSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector¶: C++: core::select::residue_selector::ResidueNameSelector::operator=(const class core::select::residue_selector::ResidueNameSelector &) –> class core::select::residue_selector::ResidueNameSelector &

static class_name() → str¶: C++: core::select::residue_selector::ResidueNameSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueNameSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector) → str¶: C++: core::select::residue_selector::ResidueNameSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ResidueNameSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueNameSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_residue_name3(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, res_name3_str: str) → None¶

sets the comma-separated string of 3-character residue names to be selected

C++: core::select::residue_selector::ResidueNameSelector::set_residue_name3(const std::string &) –> void

set_residue_names(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector, res_name_str: str) → None¶

sets the comma-separated string of residue names to be selected

C++: core::select::residue_selector::ResidueNameSelector::set_residue_names(const std::string &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator¶: C++: core::select::residue_selector::ResidueNameSelectorCreator::operator=(const class core::select::residue_selector::ResidueNameSelectorCreator &) –> class core::select::residue_selector::ResidueNameSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueNameSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator) → str¶: C++: core::select::residue_selector::ResidueNameSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueNameSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector¶

Bases: ResidueSelector

The ResiduePDBInfoHasLabelSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions with the given label in pose PDB info for that residue.

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, : pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::operator=(const class core::select::residue_selector::ResiduePDBInfoHasLabelSelector &) –> class core::select::residue_selector::ResiduePDBInfoHasLabelSelector &

static class_name() → str¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector) → str¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_label(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector, label_str: str) → None¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelector::set_label(const std::string &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator::operator=(const class core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator &) –> class core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator) → str¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector¶

Bases: ResidueSelector

A residue selector that selects based on set residue properties.

Default is to use AND logic for multiple properties. This can be changed via set_selection_logic.

add_property(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, property: pyrosetta.rosetta.core.chemical.ResidueProperty) → None¶

Add a property to the list for selection

C++: core::select::residue_selector::ResiduePropertySelector::add_property(enum core::chemical::ResidueProperty) –> void

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::ResiduePropertySelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, : pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector) → pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector¶: C++: core::select::residue_selector::ResiduePropertySelector::operator=(const class core::select::residue_selector::ResiduePropertySelector &) –> class core::select::residue_selector::ResiduePropertySelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::ResiduePropertySelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::ResiduePropertySelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::ResiduePropertySelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::ResiduePropertySelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::ResiduePropertySelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_properties(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, properties: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → None¶

Set a list of properties for selection

C++: core::select::residue_selector::ResiduePropertySelector::set_properties(class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> >) –> void

set_property(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, property: pyrosetta.rosetta.core.chemical.ResidueProperty) → None¶

Set a single property for selection

C++: core::select::residue_selector::ResiduePropertySelector::set_property(enum core::chemical::ResidueProperty) –> void

set_selection_logic(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector, logic: pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic) → None¶

Set the logic for multiple sets of properties: Default is AND logic.

C++: core::select::residue_selector::ResiduePropertySelector::set_selection_logic(enum core::select::residue_selector::basic_selection_logic) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator¶: C++: core::select::residue_selector::ResiduePropertySelectorCreator::operator=(const class core::select::residue_selector::ResiduePropertySelectorCreator &) –> class core::select::residue_selector::ResiduePropertySelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResiduePropertySelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator) → str¶: C++: core::select::residue_selector::ResiduePropertySelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResiduePropertySelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueRange¶

Bases: pybind11_object

Class for storing a range of resids

set_start(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange, start_res: int) → None¶

Sets starting residue of the range

C++: core::select::residue_selector::ResidueRange::set_start(const unsigned long) –> void

set_stop(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange, stop_res: int) → None¶

Sets stopping residue of the range

C++: core::select::residue_selector::ResidueRange::set_stop(const unsigned long) –> void

start(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → int¶

Returns the starting residue of the range

C++: core::select::residue_selector::ResidueRange::start() const –> unsigned long

stop(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → int¶

Returns the stopping residue of the range

C++: core::select::residue_selector::ResidueRange::stop() const –> unsigned long

to_string(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRange) → str¶

String representation of the range

C++: core::select::residue_selector::ResidueRange::to_string() const –> std::string

class pyrosetta.rosetta.core.select.residue_selector.ResidueRanges¶

Bases: vector1_core_select_residue_selector_ResidueRange

append(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange, arg0: core::select::residue_selector::ResidueRange) → None¶: adds an element to the end

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRanges, : pyrosetta.rosetta.core.select.residue_selector.ResidueRanges) → pyrosetta.rosetta.core.select.residue_selector.ResidueRanges¶: C++: core::select::residue_selector::ResidueRanges::operator=(const class core::select::residue_selector::ResidueRanges &) –> class core::select::residue_selector::ResidueRanges &

back(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → core::select::residue_selector::ResidueRange¶: access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → None¶: clears the contents

erase(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange, arg0: int) → None¶: erases element at index

extend(othervec)¶

from_subset(self: pyrosetta.rosetta.core.select.residue_selector.ResidueRanges, subset: pyrosetta.rosetta.utility.vector1_bool) → None¶

Clears the ranges and uses the provided ResidueSubset to create new ranges

: residue subset from which contiguous ranges of residues will be derived

ResidueRanges created via this method are guaranteed
to be ordered in ascending order by start resid and contain no duplicates

C++: core::select::residue_selector::ResidueRanges::from_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

front(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → core::select::residue_selector::ResidueRange¶: access the first element

l(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → int¶: returns the maximum possible number of elements

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) -> core::select::residue_selector::ResidueRange

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange, arg0: int) -> core::select::residue_selector::ResidueRange

remove and return item at index

reserve(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange, arg0: int) → None¶: reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange, arg0: int) → None¶: changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange) → int¶: upper index

class pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Bases: pybind11_object

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

Return a ResidueSubset indicating a selection of Residues from the: input Pose; the ResidueSubset is an array of booleans where a value of “true” for position i indicates that residue i is a part of the selected subset – and a value of “false” would indicate that it is not.

C++: core::select::residue_selector::ResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueSelector::operator=(const class core::select::residue_selector::ResidueSelector &) –> class core::select::residue_selector::ResidueSelector &

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

All ResidueSelectors must implement a clone() operator. This must create a copy of the object and return a ResidueSelectorOP to the original object.

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

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → str¶: C++: core::select::residue_selector::ResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, tag: utility::tag::Tag, datacache: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Initialize any data members of this instance from an input tag: and a DataMap object

C++: core::select::residue_selector::ResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator¶: C++: core::select::residue_selector::ResidueSelectorCreator::operator=(const class core::select::residue_selector::ResidueSelectorCreator &) –> class core::select::residue_selector::ResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Instantiate a particular ResidueSelector

C++: core::select::residue_selector::ResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator) → str¶

Return a string that will be used to instantiate the particular ResidueSelector: from an XML file – the name for the tag. E.g. “Neighborhood” for the NeighborhoodResidueSelector

C++: core::select::residue_selector::ResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶

Define the structure of the XML file for the ResidueSelector that this: %ResidueSelectorCreator instantiates using the XML Schema language.

C++: core::select::residue_selector::ResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory¶

Bases: SingletonBase_core_select_residue_selector_ResidueSelectorFactory_t

creator_map(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t¶

Read access to the map of creator names to creators – for unit testing purposes only

C++: core::select::residue_selector::ResidueSelectorFactory::creator_map() const –> const class std::map<std::string, class std::shared_ptr<class core::select::residue_selector::ResidueSelectorCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::select::residue_selector::ResidueSelectorCreator> > > > &

define_residue_selector_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, xsd: utility::tag::XMLSchemaDefinition) → None¶

The %ResidueSelectorFactory is the point of entry for the definition of the XML Schemas: for every ResidueSelector that may be instantiated from a file. It is responsible for defining an xs:group named “residue_selector” listing each of the residue-selector-complex types that may be initialized using the %ResidueSelectorFactory and to iterate across each of the ResidueSelectorCreators it contains asking them for the XML schema of the ResidueSelector they are responsible for creating.

C++: core::select::residue_selector::ResidueSelectorFactory::define_residue_selector_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, creator: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator) → None¶: C++: core::select::residue_selector::ResidueSelectorFactory::factory_register(class std::shared_ptr<class core::select::residue_selector::ResidueSelectorCreator>) –> void

get_citation_humanreadable(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, selector_name: str) → str¶

Get a human-readable listing of the citations for a given residue selector, by selector name.

Returns an empty string if there are no citations.

Vikram K. Mulligan (vmulligan.org).

C++: core::select::residue_selector::ResidueSelectorFactory::get_citation_humanreadable(const std::string &) const –> std::string

static get_instance() → core::select::residue_selector::ResidueSelectorFactory¶: C++: utility::SingletonBase<core::select::residue_selector::ResidueSelectorFactory>::get_instance() –> class core::select::residue_selector::ResidueSelectorFactory *

has_type(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, : str) → bool¶: C++: core::select::residue_selector::ResidueSelectorFactory::has_type(const std::string &) const –> bool

new_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, selector_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueSelectorFactory::new_residue_selector(const std::string &, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory, selector_name: str, xsd: utility::tag::XMLSchemaDefinition) → None¶

Get the XML schema for a given residue selector.

Throws an error if the residue selector is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: core::select::residue_selector::ResidueSelectorFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

static residue_selector_xml_schema_group_name() → str¶: C++: core::select::residue_selector::ResidueSelectorFactory::residue_selector_xml_schema_group_name() –> std::string

set_throw_on_double_registration(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory) → None¶

Should the Factory throw an exception or call utility::exit when it encounters the: second of two ResidueSelectorCreators with the same keyname? It’s default behavior is to call utility::exit, but this method allows you to set it so that it will throw an exception instead (which is unit testable).

C++: core::select::residue_selector::ResidueSelectorFactory::set_throw_on_double_registration() –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector¶

Bases: ResidueSelector

The ResidueSpanSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are within a given span. A span is defined by start and end point, each as either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. (The span is defined based on Rosetta indicies, even if residues are given by PDB numbers.)

apply(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::ResidueSpanSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, : pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector¶: C++: core::select::residue_selector::ResidueSpanSelector::operator=(const class core::select::residue_selector::ResidueSpanSelector &) –> class core::select::residue_selector::ResidueSpanSelector &

static class_name() → str¶: C++: core::select::residue_selector::ResidueSpanSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::ResidueSpanSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector) → str¶: C++: core::select::residue_selector::ResidueSpanSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::ResidueSpanSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueSpanSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_span(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector, start: str, end: str) → None¶: C++: core::select::residue_selector::ResidueSpanSelector::set_span(const std::string &, const std::string &) –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator¶: C++: core::select::residue_selector::ResidueSpanSelectorCreator::operator=(const class core::select::residue_selector::ResidueSpanSelectorCreator &) –> class core::select::residue_selector::ResidueSpanSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ResidueSpanSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator) → str¶: C++: core::select::residue_selector::ResidueSpanSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ResidueSpanSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ResidueVector¶

Bases: vector1_unsigned_long

append(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → None¶: adds an element to the end

assign(self: pyrosetta.rosetta.core.select.residue_selector.ResidueVector, : pyrosetta.rosetta.core.select.residue_selector.ResidueVector) → pyrosetta.rosetta.core.select.residue_selector.ResidueVector¶: C++: core::select::residue_selector::ResidueVector::operator=(const class core::select::residue_selector::ResidueVector &) –> class core::select::residue_selector::ResidueVector &

back(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: clears the contents

count(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → int¶: counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → None¶: erases element at index

extend(othervec)¶

from_subset(self: pyrosetta.rosetta.core.select.residue_selector.ResidueVector, subset: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: core::select::residue_selector::ResidueVector::from_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

front(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: access the first element

l(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: returns the maximum possible number of elements

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) -> int

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → None¶: Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → None¶: reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_unsigned_long, arg0: int) → None¶: changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_unsigned_long) → int¶: upper index

class pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector¶

Bases: ResidueSelector

A simple selector that returns the set subset.: This is to enable simplification of code-based interfaces to residue selectors, so that one may accept only selectors, but using this selector, we can set subsets.
This greatly reduces the c++ interface complexity and: private variable - complexity arising from accepting BOTH ResidueSubsets and ResidueSelectors (Which I’m terribly sick of doing at this point).

apply(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Return the set subset.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, : pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector¶: C++: core::select::residue_selector::ReturnResidueSubsetSelector::operator=(const class core::select::residue_selector::ReturnResidueSubsetSelector &) –> class core::select::residue_selector::ReturnResidueSubsetSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_residue_subset(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector, subset: pyrosetta.rosetta.utility.vector1_bool) → None¶

Set the ResidueSubset, which will be returned at apply-time.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::set_residue_subset(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

subset(self: pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector) → pyrosetta.rosetta.utility.vector1_bool¶

Return an editable reference to the stored residue subset.

Please be careful with this. Use with knowledge.: It is here to speed up some parts instead of creating a new subset at each point in some protocol.

C++: core::select::residue_selector::ReturnResidueSubsetSelector::subset() –> class utility::vector1<bool, class std::allocator<bool> > &

class pyrosetta.rosetta.core.select.residue_selector.SSElementSelector¶

Bases: ResidueSelector

The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: “A,B,C” or “A,B”, “c_term”,”n_term”,”middle”

A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix
A could be positive or negative depending if you’re counting from the n_term(positive) or c_term negative

B = secondary structure type as assigned by DSSP , “H”,”E”,”L” C = S=Start, E=End, M=Middle

you can also select with n_term or c_term. Examples: selection=”3,H,S” to_selection=”4,H,E” Would select from the start of Helix 3 to the end of helix 4.

selection=”-1,H,S” to_selection=”4,L,E” Would select from the start of the last helix and go to the end of the fourth loop. (order is not important) selection=”n_term” to_selection=”3,L,M” Would select from the n_term to the middle of the third loop

class SSElement¶

Bases: pybind11_object

property end_res¶

property start_res¶

property type¶

apply(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

apply.

C++: core::select::residue_selector::SSElementSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector, : pyrosetta.rosetta.core.select.residue_selector.SSElementSelector) → pyrosetta.rosetta.core.select.residue_selector.SSElementSelector¶: C++: core::select::residue_selector::SSElementSelector::operator=(const class core::select::residue_selector::SSElementSelector &) –> class core::select::residue_selector::SSElementSelector &

static class_name() → str¶: C++: core::select::residue_selector::SSElementSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SSElementSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

combine_residue_selections(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector, start_selection_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, end_selection_residues: pyrosetta.rosetta.utility.vector1_unsigned_long, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::SSElementSelector::combine_residue_selections(class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector) → str¶: C++: core::select::residue_selector::SSElementSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶

tag parsing

C++: core::select::residue_selector::SSElementSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SSElementSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator¶: C++: core::select::residue_selector::SSElementSelectorCreator::operator=(const class core::select::residue_selector::SSElementSelectorCreator &) –> class core::select::residue_selector::SSElementSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SSElementSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator) → str¶: C++: core::select::residue_selector::SSElementSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SSElementSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

Return a ResidueSubset indicating a selection of Residues from the input Pose.

C++: core::select::residue_selector::ScoreTermValueBasedSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector, : pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector) → pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector¶: C++: core::select::residue_selector::ScoreTermValueBasedSelector::operator=(const class core::select::residue_selector::ScoreTermValueBasedSelector &) –> class core::select::residue_selector::ScoreTermValueBasedSelector &

static class_name() → str¶: C++: core::select::residue_selector::ScoreTermValueBasedSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Creates a copy of the object and return a pointer to the new object.

C++: core::select::residue_selector::ScoreTermValueBasedSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector) → str¶: C++: core::select::residue_selector::ScoreTermValueBasedSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datacache: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Initialize any data members of this instance from an input tag and a DataMap object

C++: core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(: utility::tag::XMLSchemaDefinition) → None¶

Define the structure of the XML file for this ResidueSelector

C++: core::select::residue_selector::ScoreTermValueBasedSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator¶: C++: core::select::residue_selector::ScoreTermValueBasedSelectorCreator::operator=(const class core::select::residue_selector::ScoreTermValueBasedSelectorCreator &) –> class core::select::residue_selector::ScoreTermValueBasedSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::ScoreTermValueBasedSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator) → str¶: C++: core::select::residue_selector::ScoreTermValueBasedSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::ScoreTermValueBasedSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::SecondaryStructureSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, : pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector) → pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector¶: C++: core::select::residue_selector::SecondaryStructureSelector::operator=(const class core::select::residue_selector::SecondaryStructureSelector &) –> class core::select::residue_selector::SecondaryStructureSelector &

static class_name() → str¶: C++: core::select::residue_selector::SecondaryStructureSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SecondaryStructureSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector) → str¶: C++: core::select::residue_selector::SecondaryStructureSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::SecondaryStructureSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SecondaryStructureSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_include_terminal_loops(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, inc_term: bool) → None¶

if true, one-residue terminal “loops” will be included (default=false)

C++: core::select::residue_selector::SecondaryStructureSelector::set_include_terminal_loops(const bool) –> void

set_minE(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, minEval: int) → None¶

sets the minimal number of consecutive E residues to keep the secondary structure assignation (default=1)

C++: core::select::residue_selector::SecondaryStructureSelector::set_minE(const unsigned long) –> void

set_minH(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, minHval: int) → None¶

sets the minimal number of consecutive H residues to keep the secondary structure assignation (default=1)

C++: core::select::residue_selector::SecondaryStructureSelector::set_minH(const unsigned long) –> void

set_overlap(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, overlapval: int) → None¶

sets number of residues around the given SS elements to select (default=0)

C++: core::select::residue_selector::SecondaryStructureSelector::set_overlap(const unsigned long) –> void

set_pose_secstruct(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, ss: str) → None¶

Override pose secondary structure. The secondary structure set by this: method will always be used if it is non-empty.

C++: core::select::residue_selector::SecondaryStructureSelector::set_pose_secstruct(const std::string &) –> void

set_selected_ss(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, selected: str) → None¶

sets ss characters to select – must be set prior to apply()

C++: core::select::residue_selector::SecondaryStructureSelector::set_selected_ss(const std::string &) –> void

set_use_dssp(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector, use_dssp: bool) → None¶

If set, dssp will be used to determine secondary structure. Has no effect if pose_secstruct_

is set

Determines secondary structure by the following rules:

If pose_secstruct_ is user-specified, use that
If use_dssp_ is true, run DSSP and use DSSP secstruct
If use_dssp_ is false, return pose.secstruct()

C++: core::select::residue_selector::SecondaryStructureSelector::set_use_dssp(const bool) –> void

class pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator¶: C++: core::select::residue_selector::SecondaryStructureSelectorCreator::operator=(const class core::select::residue_selector::SecondaryStructureSelectorCreator &) –> class core::select::residue_selector::SecondaryStructureSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SecondaryStructureSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator) → str¶: C++: core::select::residue_selector::SecondaryStructureSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SecondaryStructureSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser¶

Bases: ASTVisitor

Class to traverse the abstract syntax tree produced by the parsing of a properly-formed string in the Arithmetic expression language. Produces a ResidueSelector tree capable of logically joining together already-defined ResidueSelectors.

add_named_selector(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, name: str, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::SelectorLogicParser::add_named_selector(const std::string &, class std::shared_ptr<class core::select::residue_selector::ResidueSelector>) –> void

assign(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser) → pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser¶: C++: core::select::residue_selector::SelectorLogicParser::operator=(const class core::select::residue_selector::SelectorLogicParser &) –> class core::select::residue_selector::SelectorLogicParser &

create_selector(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SelectorLogicParser::create_selector(const class numeric::expression_parser::ArithmeticASTExpression &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

handle_variable_expression(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Factory method to be implemented by derived classes: which may wish to handle variable expressions in a specific manner

C++: core::select::residue_selector::SelectorLogicParser::handle_variable_expression(const class numeric::expression_parser::ArithmeticASTValue &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

parse_string_to_residue_selector(*args, **kwargs)¶

Overloaded function.

parse_string_to_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, dm: pyrosetta.rosetta.basic.datacache.DataMap, selector_logic_string: str) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::SelectorLogicParser::parse_string_to_residue_selector(const class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

parse_string_to_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, input_string: str, selectors: pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: core::select::residue_selector::SelectorLogicParser::parse_string_to_residue_selector(const std::string &, const class std::map<std::string, class std::shared_ptr<class core::select::residue_selector::ResidueSelector>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::select::residue_selector::ResidueSelector> > > > &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

visit(*args, **kwargs)¶

Overloaded function.

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTExpression &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTAndClause &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTOrClause &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTFunction &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTTerm &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTFactor &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTValue &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTRestTerm &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTRestAndClause &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTRestOrClause &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTRestExpression &) –> void

visit(self: pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser, : pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode) -> None

C++: core::select::residue_selector::SelectorLogicParser::visit(const class numeric::expression_parser::ArithmeticASTNode &) –> void

class pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector¶

Bases: ResidueSelector

The SimpleMetricSelector allows conditional application of a residue selector

apply(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::SimpleMetricSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector, ot: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector) → pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector¶: C++: core::select::residue_selector::SimpleMetricSelector::operator=(const class core::select::residue_selector::SimpleMetricSelector &) –> class core::select::residue_selector::SimpleMetricSelector &

static class_name() → str¶: C++: core::select::residue_selector::SimpleMetricSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SimpleMetricSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector) → str¶: C++: core::select::residue_selector::SimpleMetricSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::SimpleMetricSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SimpleMetricSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_metric(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector, metric: pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric) → None¶: C++: core::select::residue_selector::SimpleMetricSelector::set_metric(const class std::shared_ptr<const class core::simple_metrics::PerResidueRealMetric> &) –> void

class pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator¶: C++: core::select::residue_selector::SimpleMetricSelectorCreator::operator=(const class core::select::residue_selector::SimpleMetricSelectorCreator &) –> class core::select::residue_selector::SimpleMetricSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SimpleMetricSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator) → str¶: C++: core::select::residue_selector::SimpleMetricSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SimpleMetricSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector¶

Bases: ResidueSelector

The SliceResidueSelector allows slicing of the returned values of other residue selectors

apply(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::SliceResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector¶: C++: core::select::residue_selector::SliceResidueSelector::operator=(const class core::select::residue_selector::SliceResidueSelector &) –> class core::select::residue_selector::SliceResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::SliceResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SliceResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector) → str¶: C++: core::select::residue_selector::SliceResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::SliceResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide the citation.

C++: core::select::residue_selector::SliceResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SliceResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_from(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, from: int) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_from(int) –> void

set_indices(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, indices: pyrosetta.rosetta.utility.vector1_int) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_indices(const class utility::vector1<int, class std::allocator<int> > &) –> void

set_out_of_bounds_behavior(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, oob_mode: pyrosetta.rosetta.core.select.residue_selector.slice_enums.OutOfBoundsMode) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_out_of_bounds_behavior(enum core::select::residue_selector::slice_enums::OutOfBoundsMode) –> void

set_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_slice_mode(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, slice_mode: pyrosetta.rosetta.core.select.residue_selector.slice_enums.SliceMode) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_slice_mode(enum core::select::residue_selector::slice_enums::SliceMode) –> void

set_to(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector, to: int) → None¶: C++: core::select::residue_selector::SliceResidueSelector::set_to(int) –> void

class pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator¶: C++: core::select::residue_selector::SliceResidueSelectorCreator::operator=(const class core::select::residue_selector::SliceResidueSelectorCreator &) –> class core::select::residue_selector::SliceResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SliceResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator) → str¶: C++: core::select::residue_selector::SliceResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SliceResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector¶

Bases: ResidueSelector

The SymmetricalResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing ‘true’ for residue positions which are symmetrically generated residues of the input list. (IE Union)

If the Pose is not symmetrical, returns the generated subset from the passed residue selector.

apply(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::SymmetricalResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector¶: C++: core::select::residue_selector::SymmetricalResidueSelector::operator=(const class core::select::residue_selector::SymmetricalResidueSelector &) –> class core::select::residue_selector::SymmetricalResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::SymmetricalResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::SymmetricalResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector) → str¶: C++: core::select::residue_selector::SymmetricalResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SymmetricalResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

set_selector(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶: C++: core::select::residue_selector::SymmetricalResidueSelector::set_selector(const class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

class pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator¶: C++: core::select::residue_selector::SymmetricalResidueSelectorCreator::operator=(const class core::select::residue_selector::SymmetricalResidueSelectorCreator &) –> class core::select::residue_selector::SymmetricalResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::SymmetricalResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator) → str¶: C++: core::select::residue_selector::SymmetricalResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::SymmetricalResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector¶

Bases: ResidueSelector

apply(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶: C++: core::select::residue_selector::TrueResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector¶: C++: core::select::residue_selector::TrueResidueSelector::operator=(const class core::select::residue_selector::TrueResidueSelector &) –> class core::select::residue_selector::TrueResidueSelector &

static class_name() → str¶: C++: core::select::residue_selector::TrueResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy this object and return an owning pointer to the new object.

C++: core::select::residue_selector::TrueResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector) → str¶: C++: core::select::residue_selector::TrueResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector, tag: utility::tag::Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: core::select::residue_selector::TrueResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::TrueResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator¶: C++: core::select::residue_selector::TrueResidueSelectorCreator::operator=(const class core::select::residue_selector::TrueResidueSelectorCreator &) –> class core::select::residue_selector::TrueResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::TrueResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator) → str¶: C++: core::select::residue_selector::TrueResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::TrueResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector¶

Bases: ResidueSelector

a residue selector that wraps is_virtual_residue

apply(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_bool¶

“Apply” function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected (“true”) or not (“false”).

C++: core::select::residue_selector::VirtualResidueSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >

assign(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector, : pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector¶: C++: core::select::residue_selector::VirtualResidueSelector::operator=(const class core::select::residue_selector::VirtualResidueSelector &) –> class core::select::residue_selector::VirtualResidueSelector &

static class_name() → str¶

Get the mover class name.

C++: core::select::residue_selector::VirtualResidueSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Clone operator.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

C++: core::select::residue_selector::VirtualResidueSelector::clone() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

get_name(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector) → str¶

Get the mover class name.

C++: core::select::residue_selector::VirtualResidueSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

XML parse.

Parse RosettaScripts tags and set up this mover.

C++: core::select::residue_selector::VirtualResidueSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, : 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 residue selectors wishing to provide citation information.

C++: core::select::residue_selector::ResidueSelector::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

Provide XSD information, enabling mechanical validation of input XML.

C++: core::select::residue_selector::VirtualResidueSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

selection_positions(self: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Calls apply and returns the Rosetta numbering corresponding to the selected residues

C++: core::select::residue_selector::ResidueSelector::selection_positions(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator¶

Bases: ResidueSelectorCreator

assign(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator, : pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator¶: C++: core::select::residue_selector::VirtualResidueSelectorCreator::operator=(const class core::select::residue_selector::VirtualResidueSelectorCreator &) –> class core::select::residue_selector::VirtualResidueSelectorCreator &

create_residue_selector(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶: C++: core::select::residue_selector::VirtualResidueSelectorCreator::create_residue_selector() const –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

keyname(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator) → str¶: C++: core::select::residue_selector::VirtualResidueSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator, : utility::tag::XMLSchemaDefinition) → None¶: C++: core::select::residue_selector::VirtualResidueSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.core.select.residue_selector.all_L_dssp(pose: pyrosetta.rosetta.core.pose.Pose) → bool¶

Is the DSSP all loop?: A pose unfortunately starts with all L as the DSSP when creating a pose from seq and inserting residues as is done for segments.

C++: core::select::residue_selector::all_L_dssp(const class core::pose::Pose &) –> bool

pyrosetta.rosetta.core.select.residue_selector.all_false_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool¶

Returns True if all the positions in the ResidueSubset are False

C++: core::select::residue_selector::all_false_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.all_true_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool¶

Returns True if all the positions in the ResidueSubset are True

C++: core::select::residue_selector::all_true_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.are_selections_equal(selection1: pyrosetta.rosetta.utility.vector1_bool, selection2: pyrosetta.rosetta.utility.vector1_bool) → bool¶

Evaluate if two ResidueSubsets are equal

C++: core::select::residue_selector::are_selections_equal(const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector(*args, **kwargs)¶

Overloaded function.

attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
attributes_for_parse_residue_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_residue_selector

C++: core::select::residue_selector::attributes_for_parse_residue_selector(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector_default_option_name(*args, **kwargs)¶

Overloaded function.

attributes_for_parse_residue_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_residue_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, documentation_string: str) -> None

Companion function for parse_residue_selector

This assumes the default residue selector option name (“residue_selector”).

C++: core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector_logic_string(*args, **kwargs)¶

Overloaded function.

attributes_for_parse_residue_selector_logic_string(xsd: utility::tag::XMLSchemaDefinition, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_residue_selector_logic_string(xsd: utility::tag::XMLSchemaDefinition, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, selector_logic_attribute_name: str) -> None

Append an (optional) attribute that will be used in the call to parse_residue_selector_logic_string

C++: core::select::residue_selector::attributes_for_parse_residue_selector_logic_string(class utility::tag::XMLSchemaDefinition &, class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &) –> void

pyrosetta.rosetta.core.select.residue_selector.attributes_for_parse_residue_selector_when_required(*args, **kwargs)¶

Overloaded function.

attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
attributes_for_parse_residue_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_residue_selector to be used when it is unacceptible: for the parse_residue_selector function to return a null pointer

C++: core::select::residue_selector::attributes_for_parse_residue_selector_when_required(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &, const std::string &, const std::string &) –> void

class pyrosetta.rosetta.core.select.residue_selector.basic_selection_logic¶

Bases: pybind11_object

Members:

and_logic

or_logic

and_logic = <basic_selection_logic.and_logic: 1>¶

property name¶

or_logic = <basic_selection_logic.or_logic: 2>¶

property value¶

pyrosetta.rosetta.core.select.residue_selector.complex_type_name_for_residue_selector(rs_type: str) → str¶

Used to name the xs:complexType for a residue selector that is: created with the “rs_type” tag-name. Does so by prepending “rs_” and appending “Type” to the “rs_type”. E.g., “rs_AndType” would be the name given to the complexType to describe the format of the AndResidueSelector.

C++: core::select::residue_selector::complex_type_name_for_residue_selector(const std::string &) –> std::string

pyrosetta.rosetta.core.select.residue_selector.count_selected(selection: pyrosetta.rosetta.utility.vector1_bool) → int¶

Returns the number of selected residues in the ResidueSubset

C++: core::select::residue_selector::count_selected(const class utility::vector1<bool, class std::allocator<bool> > &) –> unsigned long

pyrosetta.rosetta.core.select.residue_selector.get_cyclic_pose_residue_mappings_from_selectors(*args, **kwargs)¶

Overloaded function.

get_cyclic_pose_residue_mappings_from_selectors(selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector_ref: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t
get_cyclic_pose_residue_mappings_from_selectors(selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector_ref: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, desymmetrize_selectors: bool) -> pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t

C++: core::select::residue_selector::get_cyclic_pose_residue_mappings_from_selectors(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, const class core::pose::Pose &, const class core::pose::Pose &, bool) –> class std::vector<class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >, class std::allocator<class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > > >

pyrosetta.rosetta.core.select.residue_selector.get_embedded_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

utility::excn::EXCN_Msg_Exception if selector is not embedded ( ! tag->size() > 1)

C++: core::select::residue_selector::get_embedded_residue_selector(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.get_residue_mapping_from_selectors(*args, **kwargs)¶

Overloaded function.

get_residue_mapping_from_selectors(selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector_ref: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_unsigned_long_unsigned_long
get_residue_mapping_from_selectors(selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, selector_ref: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector, pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, desymmetrize_selectors: bool) -> pyrosetta.rosetta.std.map_unsigned_long_unsigned_long

Determine the residue mapping by residue selector and the reference selector.

If both are null, will get a map of all residues. De-symmetrizes both residue selectors

By default, we only get a mapping of the master subunit. IE - ALL residues NOT in the asymmetric unit will be false

C++: core::select::residue_selector::get_residue_mapping_from_selectors(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, const class core::pose::Pose &, const class core::pose::Pose &, bool) –> class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >

pyrosetta.rosetta.core.select.residue_selector.get_residue_selector(selector_name: str, data: pyrosetta.rosetta.basic.datacache.DataMap) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

returns a residue selector given a selector’s name and datamap

Looks for selector in the datamap,
if not found, will attempt to parse logicals using SelectorLogicParser. (AND/OR/NOT separated by spaces). Not gets priority. Returns a const ptr to the selector

utility::excn::EXCN_Msg_Exception if selector is not found in datamap

C++: core::select::residue_selector::get_residue_selector(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.has_any_false_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool¶

Returns True if at least one position in the ResidueSubset is False

C++: core::select::residue_selector::has_any_false_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.has_any_true_selection(selection: pyrosetta.rosetta.utility.vector1_bool) → bool¶

Returns True if at least one position in the ResidueSubset is True

C++: core::select::residue_selector::has_any_true_selection(const class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.select.residue_selector.identify_ss_blocks_vec(subset: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t¶

Will eventually replace standard function.

C++: core::select::residue_selector::identify_ss_blocks_vec(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<class utility::vector1<bool, class std::allocator<bool> >, class std::allocator<class utility::vector1<bool, class std::allocator<bool> > > >

pyrosetta.rosetta.core.select.residue_selector.parse_residue_selector(*args, **kwargs)¶

Overloaded function.

parse_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
parse_residue_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, option_name: str) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns a residue selector given a tag and datamap

Looks for “residue_selector” (or whatever option_name is set to)

option in tag.
If that option isn’t found, returns NULL ptr If that option is found, calls get_residue_selector()

C++: core::select::residue_selector::parse_residue_selector(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.parse_residue_selector_logic_string(*args, **kwargs)¶

Overloaded function.

parse_residue_selector_logic_string(dm: pyrosetta.rosetta.basic.datacache.DataMap, tag: pyrosetta.rosetta.utility.tag.Tag) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
parse_residue_selector_logic_string(dm: pyrosetta.rosetta.basic.datacache.DataMap, tag: pyrosetta.rosetta.utility.tag.Tag, selector_logic_attribute_name: str) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Read a string from the input tag with the indicated attribute name and interpret it: as boolean logical operations on a set of existing ResidueSelectors that are already stored in the DataMap.

C++: core::select::residue_selector::parse_residue_selector_logic_string(const class basic::datacache::DataMap &, const class std::shared_ptr<const class utility::tag::Tag> &, const std::string &) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.residue_selector.regex_usable() → bool¶

test regex support

C++: core::select::residue_selector::regex_usable() –> bool

pyrosetta.rosetta.core.select.residue_selector.represent_residue_selector(*args, **kwargs)¶

Overloaded function.

represent_residue_selector(selection: pyrosetta.rosetta.utility.vector1_bool) -> str
represent_residue_selector(selection: pyrosetta.rosetta.utility.vector1_bool, is_true: str) -> str
represent_residue_selector(selection: pyrosetta.rosetta.utility.vector1_bool, is_true: str, is_false: str) -> str

Returns a string representing the ResidueSubset (- for non selected, * for selected)

C++: core::select::residue_selector::represent_residue_selector(const class utility::vector1<bool, class std::allocator<bool> > &, const std::string &, const std::string &) –> std::string

pyrosetta.rosetta.core.select.residue_selector.selection_positions(selection: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the Rosetta Numbering corresponding to the selected residues

C++: core::select::residue_selector::selection_positions(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.select.residue_selector.unselection_positions(selection: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the Rosetta Numbering corresponding to the unselected residues

C++: core::select::residue_selector::unselection_positions(const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶

Define the XML schema definition for a ResidueSelector that: contains no other ResidueSelectors but may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes_and_optional_subselector(xsd: utility::tag::XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶

Define the XML schema definition for a ResidueSelector that: contains a single ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselector(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.core.select.residue_selector.xsd_type_definition_w_attributes_and_optional_subselectors(*args, **kwargs)¶

Overloaded function.

xsd_type_definition_w_attributes_and_optional_subselectors(xsd: utility::tag::XMLSchemaDefinition, rs_type: str, rs_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

Define the XML schema definition for a ResidueSelector that: contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

xsd_type_definition_w_attributes_and_optional_subselectors(xsd: utility::tag::XMLSchemaDefinition, rs_type: str, rs_description: str, min_occurrence: int, max_occurrence: int, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

Define the XML schema definition for a ResidueSelector that: contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors(class utility::tag::XMLSchemaDefinition &, const std::string &, const std::string &, unsigned long, unsigned long, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void