jump_selector

Bindings for core::select::jump_selector namespace

class pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

The AndJumpSelector combines the output of multiple JumpSelectors using AND logic, i.e., only jumps selected by ALL contained JumpSelectors will be selected. JumpSelecters can be pulled in from a DataMap, from subtags (for JumpSelectors known to the JumpSelectorFactory) or programmatically through %add_jump_selector.

add_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector, selector: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) None

adds a JumpSelector

C++: core::select::jump_selector::AndJumpSelector::add_jump_selector(class std::shared_ptr<const class core::select::jump_selector::JumpSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

apply_and_to_subset(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector, 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::jump_selector::AndJumpSelector::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.jump_selector.AndJumpSelector, : pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector) pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector

C++: core::select::jump_selector::AndJumpSelector::operator=(const class core::select::jump_selector::AndJumpSelector &) –> class core::select::jump_selector::AndJumpSelector &

static class_name() str

C++: core::select::jump_selector::AndJumpSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::AndJumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector) str

C++: core::select::jump_selector::AndJumpSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector) int

C++: core::select::jump_selector::AndJumpSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

class pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator

C++: core::select::jump_selector::AndJumpSelectorCreator::operator=(const class core::select::jump_selector::AndJumpSelectorCreator &) –> class core::select::jump_selector::AndJumpSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::AndJumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator) str

C++: core::select::jump_selector::AndJumpSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::AndJumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

The InterchainJumpSelector returns a JumpSubset, i.e. a utility::vector1< bool > containing ‘true’ for jump where the take-off residue is on a different chain from the landing residue.

apply(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

assign(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector, : pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector) pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector

C++: core::select::jump_selector::InterchainJumpSelector::operator=(const class core::select::jump_selector::InterchainJumpSelector &) –> class core::select::jump_selector::InterchainJumpSelector &

static class_name() str

C++: core::select::jump_selector::InterchainJumpSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::InterchainJumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector) str

C++: core::select::jump_selector::InterchainJumpSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

class pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator

C++: core::select::jump_selector::InterchainJumpSelectorCreator::operator=(const class core::select::jump_selector::InterchainJumpSelectorCreator &) –> class core::select::jump_selector::InterchainJumpSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::InterchainJumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator) str

C++: core::select::jump_selector::InterchainJumpSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::InterchainJumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.JumpForResidue

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

apply(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue, : pyrosetta.rosetta.core.select.jump_selector.JumpForResidue) pyrosetta.rosetta.core.select.jump_selector.JumpForResidue

C++: core::select::jump_selector::JumpForResidue::operator=(const class core::select::jump_selector::JumpForResidue &) –> class core::select::jump_selector::JumpForResidue &

static class_name() str

C++: core::select::jump_selector::JumpForResidue::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::JumpForResidue::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue) str

C++: core::select::jump_selector::JumpForResidue::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

set_allow_multiple_results(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue, setting: bool) None

If false, we will assert that every residue passed in is built by the same jump

C++: core::select::jump_selector::JumpForResidue::set_allow_multiple_results(const bool) –> void

set_residue_selector(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidue, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None

We will select the jumps that build the residues selected by this residue selector

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

class pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator, : pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator) pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator

C++: core::select::jump_selector::JumpForResidueCreator::operator=(const class core::select::jump_selector::JumpForResidueCreator &) –> class core::select::jump_selector::JumpForResidueCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::JumpForResidueCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator) str

C++: core::select::jump_selector::JumpForResidueCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::JumpForResidueCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

The JumpIndexSelector returns a JumpSubset, i.e. a utility::vector1< bool > containing ‘true’ for jump 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.jump_selector.JumpIndexSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector, : pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector) pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector

C++: core::select::jump_selector::JumpIndexSelector::operator=(const class core::select::jump_selector::JumpIndexSelector &) –> class core::select::jump_selector::JumpIndexSelector &

static class_name() str

C++: core::select::jump_selector::JumpIndexSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::JumpIndexSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector) str

C++: core::select::jump_selector::JumpIndexSelector::get_name() const –> std::string

jump(*args, **kwargs)

Overloaded function.

  1. jump(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector) -> int

C++: core::select::jump_selector::JumpIndexSelector::jump() const –> int

  1. jump(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector, jump: int) -> None

C++: core::select::jump_selector::JumpIndexSelector::jump(int) –> void

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

class pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator

C++: core::select::jump_selector::JumpIndexSelectorCreator::operator=(const class core::select::jump_selector::JumpIndexSelectorCreator &) –> class core::select::jump_selector::JumpIndexSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::JumpIndexSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator) str

C++: core::select::jump_selector::JumpIndexSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::JumpIndexSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Bases: pybind11_builtins.pybind11_object

apply(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool
Return a JumpSubset indicating a selection of Jumps from the input

Pose; the JumpSubset is an array of booleans of length pose.num_jump() where a value of “true” for position i indicates that jump i is a part of the selected subset – and a value of “false” would indicate that it is not.

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

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, : pyrosetta.rosetta.core.select.jump_selector.JumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::JumpSelector::operator=(const class core::select::jump_selector::JumpSelector &) –> class core::select::jump_selector::JumpSelector &

clone(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

All JumpSelectors must implement a clone() operator. This must create a copy of the object and return a JumpSelectorOP to the newly-created object.

C++: core::select::jump_selector::JumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) str

C++: core::select::jump_selector::JumpSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, 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::jump_selector::JumpSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

class pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

C++: core::select::jump_selector::JumpSelectorCreator::operator=(const class core::select::jump_selector::JumpSelectorCreator &) –> class core::select::jump_selector::JumpSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Instantiate a particular JumpSelector

C++: core::select::jump_selector::JumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator) str
Return a string that will be used to instantiate the particular JumpSelector

from an XML file – the name for the tag. E.g. “Neighborhood” for the NeighborhoodJumpSelector

C++: core::select::jump_selector::JumpSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator, : utility::tag::XMLSchemaDefinition) None
Define the structure of the XML file for the JumpSelector that this

%JumpSelectorCreator instantiates using the XML Schema language.

C++: core::select::jump_selector::JumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_core_select_jump_selector_JumpSelectorFactory_t

creator_map(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t

Read access to the map of creator names to creators – for unit testing purposes only

C++: core::select::jump_selector::JumpSelectorFactory::creator_map() const –> const class std::map<std::string, class std::shared_ptr<class core::select::jump_selector::JumpSelectorCreator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::select::jump_selector::JumpSelectorCreator> > > > &

define_jump_selector_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory, xsd: utility::tag::XMLSchemaDefinition) None
The %JumpSelectorFactory is the point of entry for the definition of the XML Schemas

for every JumpSelector that may be instantiated from a file. It is responsible for defining an xs:group named “jump_selector” listing each of the jump-selector-complex types that may be initialized using the %JumpSelectorFactory and to iterate across each of the JumpSelectorCreators it contains asking them for the XML schema of the JumpSelector they are responsible for creating.

C++: core::select::jump_selector::JumpSelectorFactory::define_jump_selector_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

factory_register(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory, creator: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator) None

C++: core::select::jump_selector::JumpSelectorFactory::factory_register(class std::shared_ptr<class core::select::jump_selector::JumpSelectorCreator>) –> void

static get_instance() core::select::jump_selector::JumpSelectorFactory

C++: utility::SingletonBase<core::select::jump_selector::JumpSelectorFactory>::get_instance() –> class core::select::jump_selector::JumpSelectorFactory *

has_type(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory, : str) bool

C++: core::select::jump_selector::JumpSelectorFactory::has_type(const std::string &) const –> bool

static jump_selector_xml_schema_group_name() str

C++: core::select::jump_selector::JumpSelectorFactory::jump_selector_xml_schema_group_name() –> std::string

new_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory, selector_name: str, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::JumpSelectorFactory::new_jump_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::jump_selector::JumpSelector>

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory, selector_name: str, xsd: utility::tag::XMLSchemaDefinition) None

Get the XML schema for a given jump selector.

Throws an error if the jump selector is unknown to Rosetta.

Vikram K. Mulligan (vmullig.edu)

C++: core::select::jump_selector::JumpSelectorFactory::provide_xml_schema(const std::string &, class utility::tag::XMLSchemaDefinition &) const –> void

set_throw_on_double_registration(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory) None
Should the Factory throw an exception or call utility::exit when it encounters the

second of two JumpSelctorCreators 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::jump_selector::JumpSelectorFactory::set_throw_on_double_registration() –> void

class pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

The NotJumpSelector negates the input of one loaded JumpSelector, i.e., it is a logical NOT - it selects all unselected jumps and deselects the selected ones. True becomes false, false becomes true. The JumpSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for JumpSelectors known to the JumpSelectorFactory or programmatically using set_jump_selector. Note that since most JumpSelectors clear the input JumpSubset, NOT can be thought of as simply selecting the opposite of the passed in selector.

apply(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

assign(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector, : pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector) pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector

C++: core::select::jump_selector::NotJumpSelector::operator=(const class core::select::jump_selector::NotJumpSelector &) –> class core::select::jump_selector::NotJumpSelector &

static class_name() str

C++: core::select::jump_selector::NotJumpSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::NotJumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector) str

C++: core::select::jump_selector::NotJumpSelector::get_name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

set_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector, selector: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) None

sets a JumpSelector

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

class pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator

C++: core::select::jump_selector::NotJumpSelectorCreator::operator=(const class core::select::jump_selector::NotJumpSelectorCreator &) –> class core::select::jump_selector::NotJumpSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::NotJumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator) str

C++: core::select::jump_selector::NotJumpSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::NotJumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelector

The OrJumpSelector combines the output of multiple JumpSelectors using OR logic, i.e., jumps selected by ANY of the contained JumpSelectors will be selected. JumpSelectors can be pulled in from a DataMap, from subtags (for JumpSelectors known to the JumpSelectorFactory) or programmatically through %add_jump_selector.

add_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector, selector: pyrosetta.rosetta.core.select.jump_selector.JumpSelector) None

adds a JumpSelector

C++: core::select::jump_selector::OrJumpSelector::add_jump_selector(class std::shared_ptr<const class core::select::jump_selector::JumpSelector>) –> void

apply(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_bool

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

apply_or_to_subset(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector, 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::jump_selector::OrJumpSelector::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.jump_selector.OrJumpSelector, : pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector) pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector

C++: core::select::jump_selector::OrJumpSelector::operator=(const class core::select::jump_selector::OrJumpSelector &) –> class core::select::jump_selector::OrJumpSelector &

static class_name() str

C++: core::select::jump_selector::OrJumpSelector::class_name() –> std::string

clone(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

Clone operator.

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

C++: core::select::jump_selector::OrJumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

get_name(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector) str

C++: core::select::jump_selector::OrJumpSelector::get_name() const –> std::string

num_selectors(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector) int

C++: core::select::jump_selector::OrJumpSelector::num_selectors() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

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

class pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator

Bases: pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator

assign(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator, : pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator

C++: core::select::jump_selector::OrJumpSelectorCreator::operator=(const class core::select::jump_selector::OrJumpSelectorCreator &) –> class core::select::jump_selector::OrJumpSelectorCreator &

create_jump_selector(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

C++: core::select::jump_selector::OrJumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>

keyname(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator) str

C++: core::select::jump_selector::OrJumpSelectorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator, : utility::tag::XMLSchemaDefinition) None

C++: core::select::jump_selector::OrJumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.core.select.jump_selector.attributes_for_parse_jump_selector(*args, **kwargs)

Overloaded function.

  1. attributes_for_parse_jump_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

  2. attributes_for_parse_jump_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None

  3. attributes_for_parse_jump_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_jump_selector

C++: core::select::jump_selector::attributes_for_parse_jump_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.jump_selector.attributes_for_parse_jump_selector_default_option_name(*args, **kwargs)

Overloaded function.

  1. attributes_for_parse_jump_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

  2. attributes_for_parse_jump_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, documentation_string: str) -> None

Companion function for parse_jump_selector

This assumes the default jump selector option name (“jump_selector”).

C++: core::select::jump_selector::attributes_for_parse_jump_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.jump_selector.attributes_for_parse_jump_selector_when_required(*args, **kwargs)

Overloaded function.

  1. attributes_for_parse_jump_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

  2. attributes_for_parse_jump_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None

  3. attributes_for_parse_jump_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str, documentation_string: str) -> None

Companion function for parse_jump_selector to be used when it is unacceptible

for the parse_jump_selector function to return a null pointer

C++: core::select::jump_selector::attributes_for_parse_jump_selector_when_required(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.jump_selector.complex_type_name_for_jump_selector(js_type: str) str
Used to name the xs:complexType for a jump selector that is

created with the “js_type” tag-name. Does so by prepending “js_” and appending “Type” to the “js_type”. E.g., “js_AndType” would be the name given to the complexType to describe the format of the AndJumpSelector.

C++: core::select::jump_selector::complex_type_name_for_jump_selector(const std::string &) –> std::string

pyrosetta.rosetta.core.select.jump_selector.get_jump_selector(selector_name: str, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.core.select.jump_selector.JumpSelector

returns a jump selector given a selector’s name and datamap

Looks for selector in the datamap

Returns a const ptr to the selector

utility::excn::EXCN_Msg_Exception if selector is not found in datamap

C++: core::select::jump_selector::get_jump_selector(const std::string &, const class basic::datacache::DataMap &) –> class std::shared_ptr<const class core::select::jump_selector::JumpSelector>

pyrosetta.rosetta.core.select.jump_selector.parse_jump_selector(*args, **kwargs)

Overloaded function.

  1. parse_jump_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.jump_selector.JumpSelector

  2. parse_jump_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, option_name: str) -> pyrosetta.rosetta.core.select.jump_selector.JumpSelector

returns a jump selector given a tag and datamap

Looks for “jump_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_jump_selector()

C++: core::select::jump_selector::parse_jump_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::jump_selector::JumpSelector>

pyrosetta.rosetta.core.select.jump_selector.xsd_type_definition_w_attributes(xsd: utility::tag::XMLSchemaDefinition, js_type: str, js_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None
Define the XML schema definition for a JumpSelector that

contains no other JumpSelectors but may contain some number of attributes (aka options).

C++: core::select::jump_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.jump_selector.xsd_type_definition_w_attributes_and_optional_subselector(xsd: utility::tag::XMLSchemaDefinition, js_type: str, js_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None
Define the XML schema definition for a JumpSelector that

contains a single JumpSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::jump_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.jump_selector.xsd_type_definition_w_attributes_and_optional_subselectors(*args, **kwargs)

Overloaded function.

  1. xsd_type_definition_w_attributes_and_optional_subselectors(xsd: utility::tag::XMLSchemaDefinition, js_type: str, js_description: str, attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None

Define the XML schema definition for a JumpSelector that

contains more than one JumpSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::jump_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

  1. xsd_type_definition_w_attributes_and_optional_subselectors(xsd: utility::tag::XMLSchemaDefinition, js_type: str, js_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 JumpSelector that

contains more than one JumpSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

C++: core::select::jump_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