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 &

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

provide_xml_schema(xsd: pyrosetta.rosetta.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.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 &

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

provide_xml_schema(xsd: pyrosetta.rosetta.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.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 &

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

2. 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

provide_xml_schema(xsd: pyrosetta.rosetta.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.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 &

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

provide_xml_schema(xsd: pyrosetta.rosetta.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.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 &

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: core::select::jump_selector::OrJumpSelector::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, 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 class std::basic_string<char> &) –> class std::shared_ptr<const class core::select::jump_selector::JumpSelector>

pyrosetta.rosetta.core.select.jump_selector.xsd_type_definition_w_attributes(xsd: pyrosetta.rosetta.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 class std::basic_string<char> &, const class std::basic_string<char> &, 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: pyrosetta.rosetta.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 class std::basic_string<char> &, const class std::basic_string<char> &, 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: pyrosetta.rosetta.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 class std::basic_string<char> &, const class std::basic_string<char> &, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

2. xsd_type_definition_w_attributes_and_optional_subselectors(xsd: pyrosetta.rosetta.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 class std::basic_string<char> &, const class std::basic_string<char> &, unsigned long, unsigned long, const class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void