jump_selector¶
Bindings for core::select::jump_selector namespace
- class pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector¶
Bases:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator¶
Bases:
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
Bases:
JumpSelector
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::apply(const class core::pose::Pose &) const –> class utility::vector1<bool, class std::allocator<bool> >
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::operator=(const class core::select::jump_selector::ExclusivelySharedJumpSelector &) –> class core::select::jump_selector::ExclusivelySharedJumpSelector &
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::class_name() –> std::string
Clone operator.
Copy this object and return an owning pointer to the new object.
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::clone() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::get_name() const –> std::string
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
We will select the jumps that build the residues selected by this residue selector
C++: core::select::jump_selector::ExclusivelySharedJumpSelector::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
Bases:
JumpSelectorCreator
C++: core::select::jump_selector::ExclusivelySharedJumpSelectorCreator::operator=(const class core::select::jump_selector::ExclusivelySharedJumpSelectorCreator &) –> class core::select::jump_selector::ExclusivelySharedJumpSelectorCreator &
C++: core::select::jump_selector::ExclusivelySharedJumpSelectorCreator::create_jump_selector() const –> class std::shared_ptr<class core::select::jump_selector::JumpSelector>
C++: core::select::jump_selector::ExclusivelySharedJumpSelectorCreator::keyname() const –> std::string
C++: core::select::jump_selector::ExclusivelySharedJumpSelectorCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- class pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector¶
Bases:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator¶
Bases:
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
- class pyrosetta.rosetta.core.select.jump_selector.JumpForResidue¶
Bases:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- 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:
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
- class pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector¶
Bases:
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.
jump(self: pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector) -> int
C++: core::select::jump_selector::JumpIndexSelector::jump() const –> int
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator¶
Bases:
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
- class pyrosetta.rosetta.core.select.jump_selector.JumpSelector¶
Bases:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator¶
Bases:
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:
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_std_allocator_std_pair_const_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:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- 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:
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
- class pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector¶
Bases:
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
- selection_jumps(self: pyrosetta.rosetta.core.select.jump_selector.JumpSelector, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Calls apply and returns a vector of the selected jump ids
C++: core::select::jump_selector::JumpSelector::selection_jumps(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator¶
Bases:
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
- pyrosetta.rosetta.core.select.jump_selector.attributes_for_parse_jump_selector(*args, **kwargs)¶
Overloaded function.
attributes_for_parse_jump_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_jump_selector(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
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.
attributes_for_parse_jump_selector_default_option_name(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
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.
attributes_for_parse_jump_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) -> None
attributes_for_parse_jump_selector_when_required(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t, option_name: str) -> None
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.
parse_jump_selector(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) -> pyrosetta.rosetta.core.select.jump_selector.JumpSelector
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.
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
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