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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< boolJumpSubset
 
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< JumpIndexSelector const > core::select::jump_selector::JumpIndexSelectorCOP
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< 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_Exceptionif 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
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().