core::select::jump_selector Namespace Reference

Classes
class	AndJumpSelector
	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. More...
class	AndJumpSelectorCreator
class	InterchainJumpSelector
	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. More...
class	InterchainJumpSelectorCreator
class	JumpIndexSelector
	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. More...
class	JumpIndexSelectorCreator
class	JumpSelector
class	JumpSelectorCreator
class	JumpSelectorFactory
class	JumpSelectorRegistrator
	This templated class will register an instance of an JumpSelectorCreator (class T) with the JumpSelectorFactory. It will ensure that no JumpSelector creator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	NotJumpSelector
	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. More...
class	NotJumpSelectorCreator
class	OrJumpSelector
	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. More...
class	OrJumpSelectorCreator

Typedefs
typedef utility::pointer::shared_ptr < AndJumpSelector >	AndJumpSelectorOP
typedef utility::pointer::shared_ptr < AndJumpSelector const >	AndJumpSelectorCOP
typedef utility::pointer::shared_ptr < InterchainJumpSelector >	InterchainJumpSelectorOP
typedef utility::pointer::shared_ptr < InterchainJumpSelector const >	InterchainJumpSelectorCOP
typedef utility::pointer::shared_ptr < JumpIndexSelector >	JumpIndexSelectorOP
typedef utility::pointer::shared_ptr < JumpIndexSelector const >	JumpIndexSelectorCOP
typedef utility::vector1< bool >	JumpSubset
typedef utility::pointer::shared_ptr < JumpSubset >	JumpSubsetOP
typedef utility::pointer::shared_ptr < JumpSubset const >	JumpSubsetCOP
typedef utility::pointer::weak_ptr < JumpSubset >	JumpSubsetAP
typedef utility::pointer::weak_ptr < JumpSubset const >	JumpSubsetCAP
typedef utility::pointer::shared_ptr < JumpSelector >	JumpSelectorOP
typedef utility::pointer::shared_ptr < JumpSelector const >	JumpSelectorCOP
typedef utility::pointer::weak_ptr < JumpSelector >	JumpSelectorAP
typedef utility::pointer::weak_ptr < JumpSelector const >	JumpSelectorCAP
typedef utility::pointer::shared_ptr < JumpSelectorCreator >	JumpSelectorCreatorOP
typedef utility::pointer::shared_ptr < JumpSelectorCreator const >	JumpSelectorCreatorCOP
typedef utility::pointer::shared_ptr < NotJumpSelector >	NotJumpSelectorOP
typedef utility::pointer::shared_ptr < NotJumpSelector const >	NotJumpSelectorCOP
typedef utility::pointer::shared_ptr < OrJumpSelector >	OrJumpSelectorOP
typedef utility::pointer::shared_ptr < OrJumpSelector const >	OrJumpSelectorCOP

Functions
static basic::Tracer	TR ("core.select.jump_selector.JumpIndexSelector")
std::string	complex_type_name_for_jump_selector (std::string const &js_type)
	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. More...
void	xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &js_type, std::string const &js_description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a JumpSelector that contains no other JumpSelectors but may contain some number of attributes (aka options). More...
void	xsd_type_definition_w_attributes_and_optional_subselector (utility::tag::XMLSchemaDefinition &xsd, std::string const &js_type, std::string const &js_description, utility::tag::AttributeList const &attributes)
	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). More...
void	xsd_type_definition_w_attributes_and_optional_subselectors (utility::tag::XMLSchemaDefinition &xsd, std::string const &js_type, std::string const &js_description, utility::tag::AttributeList const &attributes)
	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). More...
void	xsd_type_definition_w_attributes_and_optional_subselectors (utility::tag::XMLSchemaDefinition &xsd, std::string const &js_type, std::string const &js_description, core::Size min_occurrence, core::Size max_occurrence, utility::tag::AttributeList const &attributes)
	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). More...
JumpSelectorCOP	parse_jump_selector (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &option_name="jump_selector")
	returns a jump selector given a tag and datamap More...
void	attributes_for_parse_jump_selector_default_option_name (utility::tag::AttributeList &attlist, std::string const &documentation_string)
	Companion function for parse_jump_selector. More...
void	attributes_for_parse_jump_selector (utility::tag::AttributeList &attlist, std::string const &option_name="jump_selector", std::string const &documentation_string="")
	Companion function for parse_jump_selector. More...
void	attributes_for_parse_jump_selector_when_required (utility::tag::AttributeList &attlist, std::string const &option_name="jump_selector", std::string const &documentation_string="")
	Companion function for parse_jump_selector to be used when it is unacceptible for the parse_jump_selector function to return a null pointer. More...
JumpSelectorCOP	get_jump_selector (std::string const &selector_name, basic::datacache::DataMap const &data)
	returns a jump selector given a selector's name and datamap More...

Typedef Documentation

typedef utility::pointer::shared_ptr< AndJumpSelector const > core::select::jump_selector::AndJumpSelectorCOP

typedef utility::pointer::shared_ptr< AndJumpSelector > core::select::jump_selector::AndJumpSelectorOP

typedef utility::pointer::shared_ptr< InterchainJumpSelector const > core::select::jump_selector::InterchainJumpSelectorCOP

typedef utility::pointer::shared_ptr< InterchainJumpSelector > core::select::jump_selector::InterchainJumpSelectorOP

typedef utility::pointer::shared_ptr< JumpIndexSelector const > core::select::jump_selector::JumpIndexSelectorCOP

typedef utility::pointer::shared_ptr< JumpIndexSelector > core::select::jump_selector::JumpIndexSelectorOP

typedef utility::pointer::weak_ptr< JumpSelector > core::select::jump_selector::JumpSelectorAP

typedef utility::pointer::weak_ptr< JumpSelector const > core::select::jump_selector::JumpSelectorCAP

typedef utility::pointer::shared_ptr< JumpSelector const > core::select::jump_selector::JumpSelectorCOP

typedef utility::pointer::shared_ptr< JumpSelectorCreator const > core::select::jump_selector::JumpSelectorCreatorCOP

typedef utility::pointer::shared_ptr< JumpSelectorCreator > core::select::jump_selector::JumpSelectorCreatorOP

typedef utility::pointer::shared_ptr< JumpSelector > core::select::jump_selector::JumpSelectorOP

typedef utility::vector1< bool > core::select::jump_selector::JumpSubset

typedef utility::pointer::weak_ptr< JumpSubset > core::select::jump_selector::JumpSubsetAP

typedef utility::pointer::weak_ptr< JumpSubset const > core::select::jump_selector::JumpSubsetCAP

typedef utility::pointer::shared_ptr< JumpSubset const > core::select::jump_selector::JumpSubsetCOP

typedef utility::pointer::shared_ptr< JumpSubset > core::select::jump_selector::JumpSubsetOP

typedef utility::pointer::shared_ptr< NotJumpSelector const > core::select::jump_selector::NotJumpSelectorCOP

typedef utility::pointer::shared_ptr< NotJumpSelector > core::select::jump_selector::NotJumpSelectorOP

typedef utility::pointer::shared_ptr< OrJumpSelector const > core::select::jump_selector::OrJumpSelectorCOP

typedef utility::pointer::shared_ptr< OrJumpSelector > core::select::jump_selector::OrJumpSelectorOP

Function Documentation

void core::select::jump_selector::attributes_for_parse_jump_selector	(	utility::tag::AttributeList &	attlist,
		std::string const &	option_name,
		std::string const &	documentation_string
	)

Companion function for parse_jump_selector.

Referenced by attributes_for_parse_jump_selector_default_option_name().

void core::select::jump_selector::attributes_for_parse_jump_selector_default_option_name	(	utility::tag::AttributeList &	attlist,
		std::string const &	documentation_string
	)

Companion function for parse_jump_selector.

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

References attributes_for_parse_jump_selector().

void core::select::jump_selector::attributes_for_parse_jump_selector_when_required	(	utility::tag::AttributeList &	attlist,
		std::string const &	option_name,
		std::string const &	documentation_string
	)

Companion function for parse_jump_selector to be used when it is unacceptible for the parse_jump_selector function to return a null pointer.

Referenced by core::select::movemap::MoveMapFactory::provide_xml_schema().

std::string core::select::jump_selector::complex_type_name_for_jump_selector

(

std::string const &

js_type

)

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.

Referenced by core::select::jump_selector::JumpSelectorFactory::define_jump_selector_xml_schema(), xsd_type_definition_w_attributes(), xsd_type_definition_w_attributes_and_optional_subselector(), and xsd_type_definition_w_attributes_and_optional_subselectors().

JumpSelectorCOP core::select::jump_selector::get_jump_selector	(	std::string const &	selector_name,
		basic::datacache::DataMap const &	data
	)

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

Looks for selector in the datamap Returns a const ptr to the selector

Exceptions

utility::excn::EXCN_Msg_Exception

if selector is not found in datamap

References TR().

Referenced by parse_jump_selector().

JumpSelectorCOP core::select::jump_selector::parse_jump_selector	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const &	option_name = "jump_selector"
	)

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()

References get_jump_selector().

Referenced by core::select::movemap::MoveMapFactory::parse_my_tag().

static basic::Tracer core::select::jump_selector::TR ( "core.select.jump_selector.JumpIndexSelector"  )

static

Referenced by core::select::jump_selector::JumpIndexSelector::apply(), and get_jump_selector().

void core::select::jump_selector::xsd_type_definition_w_attributes	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	js_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

Define the XML schema definition for a JumpSelector that contains no other JumpSelectors but may contain some number of attributes (aka options).

References complex_type_name_for_jump_selector().

Referenced by core::select::jump_selector::InterchainJumpSelector::provide_xml_schema(), and core::select::jump_selector::JumpIndexSelector::provide_xml_schema().

void core::select::jump_selector::xsd_type_definition_w_attributes_and_optional_subselector	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	js_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

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).

References complex_type_name_for_jump_selector(), and core::select::jump_selector::JumpSelectorFactory::jump_selector_xml_schema_group_name().

Referenced by core::select::jump_selector::NotJumpSelector::provide_xml_schema(), and core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema().

void core::select::jump_selector::xsd_type_definition_w_attributes_and_optional_subselectors	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	js_type,
		std::string const &	description,
		utility::tag::AttributeList const &	attributes
	)

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).

References complex_type_name_for_jump_selector(), and core::select::jump_selector::JumpSelectorFactory::jump_selector_xml_schema_group_name().

Referenced by core::select::jump_selector::OrJumpSelector::provide_xml_schema(), and core::select::jump_selector::AndJumpSelector::provide_xml_schema().

void core::select::jump_selector::xsd_type_definition_w_attributes_and_optional_subselectors	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	js_type,
		std::string const &	description,
		core::Size	min_occurrence,
		core::Size	max_occurrence,
		utility::tag::AttributeList const &	attributes
	)

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).

References complex_type_name_for_jump_selector(), and core::select::jump_selector::JumpSelectorFactory::jump_selector_xml_schema_group_name().