core::select::residue_selector Namespace Reference

Namespaces
	slice_enums

Classes
class	AndResidueSelector
	The AndResidueSelector combines the output of multiple ResidueSelectors using AND logic, i.e., only residues selected by ALL contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector. More...
class	AsymmetricUnitSelector
	A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose. More...
class	AsymmetricUnitSelectorCreator
class	BFactorSelector
	A residue selector dependent on b-factor values. More...
class	BFactorSelectorCreator
class	BinSelector
	A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin). More...
class	BlockSelector
	selectes a specified continuous block of previously selected residues More...
class	BlockSelectorCreator
class	BondedResidueSelector
	The BondedResidueSelector selects residues that are connected to some set of residues (input_set) by a chemical bond. The input_set can be directly set using a set of residue positions or by a ResidueSelector. More...
class	CachedResidueSubset
class	ChainSelector
class	CloseContactResidueSelector
	A class that finds the neighboring residues for a particular residue by looking at atom-atom distances. More...
class	CloseContactResidueSelectorCreator
class	ConfluentSelector
	selector that selects all the residues between those selected by another selector that are not interspersed with those selected by a third selector More...
class	ConfluentSelectorCreator
class	DensityFitResidueSelector
	Selects residues that are considered 'error' region with respect to the density resolution. More...
class	FalseResidueSelector
class	FractionSelector
	Selects only either the first or the last residue selected by a provided ResidueSelector. More...
class	FractionSelectorCreator
class	GlycanLayerSelector
	A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree. If no layer is set, will select all glycan residues. More...
class	GlycanLayerSelectorCreator
class	GlycanPositionSelector
	A Residue Selector for selecting specific parts of arbitrary glycans by 'position'. More...
class	GlycanResidueSelector
	A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc. More...
class	GlycanSequonsSelector
	Find glycosylation sequons in pose @detail Glycosylation sites are typically recognized by enzymes by means of a recognition sequence, or 'motif'. This ResidueSelector selects all residues that can be glycosylated using one of a few sequence motifs that are pre-defined and can be selected. For selecting residues in other motifs, use the ResidueInSequenceMotifSelctor, which takes regular expressions as input. More...
class	InterGroupInterfaceByVectorSelector
	The InterGroupInterfaceByVectorSelector identifies residues at the interface between two groups of residues using two distance cutoffs: the first, shorter cutoff is based on atom-atom distances, the second, longer cutoff is used if the c-alpha/c-beta vector of the residues in the first group point toward the c-alphas of the other group. Each group may be specified either explicitly through a std::set of residue indices, through a string of comma-separated values giving either residue indices or PDB ids (e.g. 13B for residue 13 on chain B) or through a ResidueSelector. Clears the passed ReisueSubset. More...
class	JumpDownstreamSelector
	The JumpDownstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie downstream of a given jump in the FoldTree. The jump is specified by an integer index. More...
class	JumpUpstreamSelector
	The JumpUpstreamSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which lie upstream of a given jump in the FoldTree. The jump is specified by its integer index. More...
class	LayerSelector
	The LayerSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. More...
class	LogicResidueSelector
	A residue selector that takes arbitrarily many residue selectors and performs and/or/not boolean logic within the "residue_selectors" option. More...
class	LogicResidueSelectorCreator
class	NeighborhoodResidueSelector
	The NeighborhoodResidueSelector selects residues neighboring a defined set of residues (the focus). The focus residue set can be obtained from another ResidueSelector, from a set of positions. Focus is included in subset by default. Use include_focus_in_subset to change this! More...
class	NotResidueSelector
	The NotResidueSelector negates the input of one loaded ResidueSelector, i.e., it is a logical NOT - it selects all unselected residues and deselects the selected ones. True becomes false, false becomes true. The ResidueSelector to be negated can be pulled in through RosettaScipt using the selector option, subtags for ResidueSelectors known to the ResidueSelectorFactory or programmatically using set_residue_selector. Note that since most ResidueSelectors clear the input ResidueSubset, NOT can be thought of as simply selecting the opposite of the passed in selector. More...
class	NumNeighborsSelector
class	OrResidueSelector
	The OrResidueSelector combines the output of multiple ResidueSelectors using OR logic, i.e., residues selected by ANY of the contained ResidueSelectors will be selected. ResidueSelecters can be pulled in from a DataMap, from subtags (for ResidueSelectors known to the ResidueSelectorFactory) or programmatically through add_residue_selector. More...
class	PhiSelector
	A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences). More...
class	PrimarySequenceNeighborhoodSelector
	The PrimarySequenceNeighborhoodSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are located near the given selected residues in primary sequence space. More...
class	PrimarySequenceNeighborhoodSelectorCreator
class	RandomGlycanFoliageSelector
	Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling. More...
class	RandomResidueSelector
	The RandomResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for N randomly selected residue positions, where N is a user-specified integer. More...
class	ResidueIndexSelector
	The ResidueIndexSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). It can also take range specifications (e.g. 10A-20A). Detection and mapping from PDB to Rosetta residue numbers is done internally. More...
class	ResidueInMembraneSelector
	The ResidueInMembraneSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are either in or out of the membrane. default is in. More...
class	ResidueInSequenceMotifSelector
	Select residues by motif search @detail This selector takes a regular expression and a position and then finds all matches of the regular expression and selects the n-th residue in each match, where 'n' is the specified position. More...
class	ResidueNameSelector
	The ResidueNameSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which match the given residue index. The index is read as comma-separated list of either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. More...
class	ResiduePDBInfoHasLabelSelector
	The ResiduePDBInfoHasLabelSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions with the given label in pose PDB info for that residue. More...
class	ResiduePropertySelector
	A residue selector that selects based on set residue properties. More...
class	ResiduePropertySelectorCreator
class	ResidueRange
	Class for storing a range of resids. More...
class	ResidueRanges
class	ResidueSelector
class	ResidueSelectorCreator
class	AndResidueSelectorCreator
class	BinSelectorCreator
class	BondedResidueSelectorCreator
class	ChainSelectorCreator
class	DensityFitResidueSelectorCreator
class	InterGroupInterfaceByVectorSelectorCreator
class	GlycanPositionSelectorCreator
class	GlycanResidueSelectorCreator
class	GlycanSequonsSelectorCreator
class	LayerSelectorCreator
class	NotResidueSelectorCreator
class	ResidueIndexSelectorCreator
class	ResidueSpanSelectorCreator
class	ResidueNameSelectorCreator
class	ResidueInMembraneSelectorCreator
class	NeighborhoodResidueSelectorCreator
class	NumNeighborsSelectorCreator
class	OrResidueSelectorCreator
class	PhiSelectorCreator
class	JumpUpstreamSelectorCreator
class	JumpDownstreamSelectorCreator
class	SecondaryStructureSelectorCreator
class	SSElementSelectorCreator
class	TrueResidueSelectorCreator
class	FalseResidueSelectorCreator
class	ResiduePDBInfoHasLabelSelectorCreator
class	RandomResidueSelectorCreator
class	RandomGlycanFoliageSelectorCreator
class	ScoreTermValueBasedSelectorCreator
class	ResidueInSequenceMotifSelectorCreator
class	SliceResidueSelectorCreator
class	SimpleMetricSelectorCreator
class	ResidueSelectorFactory
class	ResidueSelectorRegistrator
	This templated class will register an instance of an ResidueSelectorCreator (class T) with the ResidueSelectorFactory. It will ensure that no ResidueSelector creator is registered twice, and centralizes this registration logic so that thread safety issues can be handled in one place. More...
class	ResidueSpanSelector
	The ResidueSpanSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are within a given span. A span is defined by start and end point, each as either Rosetta indices (e.g. 10) or PDB numbers (e.g. 10A, residue 10 of chain A). Detection and mapping from PDB to Rosetta residue numbers is done internally. (The span is defined based on Rosetta indicies, even if residues are given by PDB numbers.) More...
class	ResidueVector
class	ReturnResidueSubsetSelector
	A simple selector that returns the set subset. This is to enable simplification of code-based interfaces to residue selectors, so that one may accept only selectors, but using this selector, we can set subsets. More...
class	ScoreTermValueBasedSelector
class	SecondaryStructureSelector
class	SelectorLogicParser
	Class to traverse the abstract syntax tree produced by the parsing of a properly-formed string in the Arithmetic expression language. Produces a ResidueSelector tree capable of logically joining together already-defined ResidueSelectors. More...
class	SimpleMetricSelector
	The SimpleMetricSelector allows conditional application of a residue selector. More...
class	SliceResidueSelector
	The SliceResidueSelector allows slicing of the returned values of other residue selectors. More...
class	SSElementSelector
	The SSElementSelector allows you to select objects based on their secondary structure defintion. Language: "A,B,C" or "A,B", "c_term","n_term","middle" A = numerical position of THAT type of secondary structure. So if the secondary structure was Helix-Sheet-Helix. 2,H would refer to the second helix A could be positive or negative depending if you're counting from the n_term(positive) or c_term negative B = secondary structure type as assigned by DSSP , "H","E","L" C = S=Start, E=End, M=Middle. More...
class	SymmetricalResidueSelector
	The SymmetricalResidueSelector returns a ResidueSubset, i.e. a utility::vector1< bool > containing 'true' for residue positions which are symmetrically generated residues of the input list. (IE Union) More...
class	SymmetricalResidueSelectorCreator
class	TrueResidueSelector
class	VirtualResidueSelector
	a residue selector that wraps is_virtual_residue More...
class	VirtualResidueSelectorCreator

Typedefs
typedef utility::pointer::shared_ptr< AndResidueSelector >	AndResidueSelectorOP
typedef utility::pointer::shared_ptr< AndResidueSelector const >	AndResidueSelectorCOP
typedef utility::pointer::shared_ptr< AsymmetricUnitSelector >	AsymmetricUnitSelectorOP
typedef utility::pointer::shared_ptr< AsymmetricUnitSelector const >	AsymmetricUnitSelectorCOP
using	BFactorSelectorOP = utility::pointer::shared_ptr< BFactorSelector >
using	BFactorSelectorCOP = utility::pointer::shared_ptr< BFactorSelector const >
typedef utility::pointer::shared_ptr< BinSelector >	BinSelectorOP
typedef utility::pointer::shared_ptr< BinSelector const >	BinSelectorCOP
using	BlockSelectorOP = utility::pointer::shared_ptr< BlockSelector >
using	BlockSelectorCOP = utility::pointer::shared_ptr< BlockSelector const >
typedef utility::pointer::shared_ptr< BondedResidueSelector >	BondedResidueSelectorOP
typedef utility::pointer::shared_ptr< BondedResidueSelector const >	BondedResidueSelectorCOP
typedef utility::pointer::shared_ptr< CachedResidueSubset >	CachedResidueSubsetOP
typedef utility::pointer::shared_ptr< CachedResidueSubset const >	CachedResidueSubsetCOP
typedef utility::pointer::shared_ptr< ChainSelector >	ChainSelectorOP
typedef utility::pointer::shared_ptr< ChainSelector const >	ChainSelectorCOP
typedef utility::pointer::shared_ptr< CloseContactResidueSelector >	CloseContactResidueSelectorOP
typedef utility::pointer::shared_ptr< CloseContactResidueSelector const >	CloseContactResidueSelectorCOP
using	ConfluentSelectorOP = utility::pointer::shared_ptr< ConfluentSelector >
using	ConfluentSelectorCOP = utility::pointer::shared_ptr< ConfluentSelector const >
typedef utility::pointer::shared_ptr< DensityFitResidueSelector >	DensityFitResidueSelectorOP
typedef utility::pointer::shared_ptr< DensityFitResidueSelector const >	DensityFitResidueSelectorCOP
typedef utility::pointer::shared_ptr< FalseResidueSelector >	FalseResidueSelectorOP
typedef utility::pointer::shared_ptr< FalseResidueSelector const >	FalseResidueSelectorCOP
typedef utility::pointer::shared_ptr< FractionSelector >	FractionSelectorOP
typedef utility::pointer::shared_ptr< FractionSelector const >	FractionSelectorCOP
typedef utility::pointer::shared_ptr< GlycanLayerSelector >	GlycanLayerSelectorOP
typedef utility::pointer::shared_ptr< GlycanLayerSelector const >	GlycanLayerSelectorCOP
typedef utility::pointer::shared_ptr< GlycanPositionSelector >	GlycanPositionSelectorOP
typedef utility::pointer::shared_ptr< GlycanPositionSelector const >	GlycanPositionSelectorCOP
typedef utility::pointer::shared_ptr< GlycanResidueSelector >	GlycanResidueSelectorOP
typedef utility::pointer::shared_ptr< GlycanResidueSelector const >	GlycanResidueSelectorCOP
typedef utility::pointer::shared_ptr< GlycanSequonsSelector >	GlycanSequonsSelectorOP
typedef utility::pointer::shared_ptr< GlycanSequonsSelector const >	GlycanSequonsSelectorCOP
typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelector >	InterGroupInterfaceByVectorSelectorOP
typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelector const >	InterGroupInterfaceByVectorSelectorCOP
typedef utility::pointer::shared_ptr< JumpDownstreamSelector >	JumpDownstreamSelectorOP
typedef utility::pointer::shared_ptr< JumpDownstreamSelector const >	JumpDownstreamSelectorCOP
typedef utility::pointer::shared_ptr< JumpUpstreamSelector >	JumpUpstreamSelectorOP
typedef utility::pointer::shared_ptr< JumpUpstreamSelector const >	JumpUpstreamSelectorCOP
typedef utility::pointer::shared_ptr< LayerSelector >	LayerSelectorOP
typedef utility::pointer::shared_ptr< LayerSelector const >	LayerSelectorCOP
using	LogicResidueSelectorOP = utility::pointer::shared_ptr< LogicResidueSelector >
using	LogicResidueSelectorCOP = utility::pointer::shared_ptr< LogicResidueSelector const >
typedef utility::pointer::shared_ptr< NeighborhoodResidueSelector >	NeighborhoodResidueSelectorOP
typedef utility::pointer::shared_ptr< NeighborhoodResidueSelector const >	NeighborhoodResidueSelectorCOP
typedef utility::pointer::shared_ptr< NotResidueSelector >	NotResidueSelectorOP
typedef utility::pointer::shared_ptr< NotResidueSelector const >	NotResidueSelectorCOP
typedef utility::pointer::shared_ptr< NumNeighborsSelector >	NumNeighborsSelectorOP
typedef utility::pointer::shared_ptr< NumNeighborsSelector const >	NumNeighborsSelectorCOP
typedef utility::pointer::shared_ptr< OrResidueSelector >	OrResidueSelectorOP
typedef utility::pointer::shared_ptr< OrResidueSelector const >	OrResidueSelectorCOP
typedef utility::pointer::shared_ptr< PhiSelector >	PhiSelectorOP
typedef utility::pointer::shared_ptr< PhiSelector const >	PhiSelectorCOP
typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelector >	PrimarySequenceNeighborhoodSelectorOP
typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelector const >	PrimarySequenceNeighborhoodSelectorCOP
typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelector >	RandomGlycanFoliageSelectorOP
typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelector const >	RandomGlycanFoliageSelectorCOP
typedef utility::pointer::shared_ptr< RandomResidueSelector >	RandomResidueSelectorOP
typedef utility::pointer::shared_ptr< RandomResidueSelector const >	RandomResidueSelectorCOP
typedef utility::pointer::shared_ptr< ResidueIndexSelector >	ResidueIndexSelectorOP
typedef utility::pointer::shared_ptr< ResidueIndexSelector const >	ResidueIndexSelectorCOP
typedef utility::pointer::shared_ptr< ResidueInMembraneSelector >	ResidueInMembraneSelectorOP
typedef utility::pointer::shared_ptr< ResidueInMembraneSelector const >	ResidueInMembraneSelectorCOP
typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelector >	ResidueInSequenceMotifSelectorOP
typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelector const >	ResidueInSequenceMotifSelectorCOP
typedef utility::pointer::shared_ptr< ResidueNameSelector >	ResidueNameSelectorOP
typedef utility::pointer::shared_ptr< ResidueNameSelector const >	ResidueNameSelectorCOP
typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelector >	ResiduePDBInfoHasLabelSelectorOP
typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelector const >	ResiduePDBInfoHasLabelSelectorCOP
typedef utility::pointer::shared_ptr< ResiduePropertySelector >	ResiduePropertySelectorOP
typedef utility::pointer::shared_ptr< ResiduePropertySelector const >	ResiduePropertySelectorCOP
typedef utility::pointer::shared_ptr< ResidueRanges >	ResidueRangesOP
typedef utility::pointer::shared_ptr< ResidueRanges const >	ResidueRangesCOP
typedef utility::pointer::weak_ptr< ResidueRanges >	ResidueRangesAP
typedef utility::pointer::weak_ptr< ResidueRanges const >	ResidueRangesCAP
typedef utility::vector1< bool >	ResidueSubset
typedef utility::pointer::shared_ptr< ResidueSubset >	ResidueSubsetOP
typedef utility::pointer::shared_ptr< ResidueSubset const >	ResidueSubsetCOP
typedef utility::pointer::weak_ptr< ResidueSubset >	ResidueSubsetAP
typedef utility::pointer::weak_ptr< ResidueSubset const >	ResidueSubsetCAP
typedef utility::pointer::shared_ptr< ResidueSelector >	ResidueSelectorOP
typedef utility::pointer::shared_ptr< ResidueSelector const >	ResidueSelectorCOP
typedef utility::pointer::weak_ptr< ResidueSelector >	ResidueSelectorAP
typedef utility::pointer::weak_ptr< ResidueSelector const >	ResidueSelectorCAP
typedef utility::pointer::shared_ptr< ResidueSelectorCreator >	ResidueSelectorCreatorOP
typedef utility::pointer::shared_ptr< ResidueSelectorCreator const >	ResidueSelectorCreatorCOP
typedef utility::pointer::shared_ptr< ResidueSpanSelector >	ResidueSpanSelectorOP
typedef utility::pointer::shared_ptr< ResidueSpanSelector const >	ResidueSpanSelectorCOP
typedef utility::pointer::shared_ptr< ResidueVector >	ResidueVectorOP
typedef utility::pointer::shared_ptr< ResidueVector const >	ResidueVectorCOP
typedef utility::pointer::weak_ptr< ResidueVector >	ResidueVectorAP
typedef utility::pointer::weak_ptr< ResidueVector const >	ResidueVectorCAP
typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelector >	ReturnResidueSubsetSelectorOP
typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelector const >	ReturnResidueSubsetSelectorCOP
typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelector >	ScoreTermValueBasedSelectorOP
typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelector const >	ScoreTermValueBasedSelectorCOP
typedef utility::pointer::shared_ptr< SecondaryStructureSelector >	SecondaryStructureSelectorOP
typedef utility::pointer::shared_ptr< SecondaryStructureSelector const >	SecondaryStructureSelectorCOP
typedef utility::pointer::shared_ptr< SelectorLogicParser >	SelectorLogicParserOP
typedef utility::pointer::shared_ptr< SelectorLogicParser const >	SelectorLogicParserCOP
typedef utility::pointer::shared_ptr< SimpleMetricSelector >	SimpleMetricSelectorOP
typedef utility::pointer::shared_ptr< SimpleMetricSelector const >	SimpleMetricSelectorCOP
typedef utility::pointer::shared_ptr< SliceResidueSelector >	SliceResidueSelectorOP
typedef utility::pointer::shared_ptr< SliceResidueSelector const >	SliceResidueSelectorCOP
typedef utility::pointer::shared_ptr< SSElementSelector >	SSElementSelectorOP
typedef utility::pointer::shared_ptr< SSElementSelector const >	SSElementSelectorCOP
typedef utility::pointer::shared_ptr< SymmetricalResidueSelector >	SymmetricalResidueSelectorOP
typedef utility::pointer::shared_ptr< SymmetricalResidueSelector const >	SymmetricalResidueSelectorCOP
typedef utility::pointer::shared_ptr< TrueResidueSelector >	TrueResidueSelectorOP
typedef utility::pointer::shared_ptr< TrueResidueSelector const >	TrueResidueSelectorCOP
typedef utility::pointer::shared_ptr< VirtualResidueSelector >	VirtualResidueSelectorOP
typedef utility::pointer::shared_ptr< VirtualResidueSelector const >	VirtualResidueSelectorCOP

Enumerations
enum	basic_selection_logic { and_logic = 1 , or_logic }

Functions
static basic::Tracer	TR ("core.select.residue_selector.CachedResidueSubset")
static const std::map< std::string, basic_selection_logic >	logic_map ({ { "or_logic", or_logic }, { "and_logic", and_logic } })
void	set_pose_secstruct (std::string const &ss)
bool	has_option (utility::tag::TagCOP const &tag, std::string const &key)
std::map< core::Size, core::Size >	get_residue_mapping_from_selectors (select::residue_selector::ResidueSelectorCOP selector, select::residue_selector::ResidueSelectorCOP selector_ref, core::pose::Pose const &pose, core::pose::Pose const &ref_pose, bool desymmetrize_selectors=true)
	Determine the residue mapping by residue selector and the reference selector. If both are null, will get a map of all residues. De-symmetrizes both residue selectors. More...
std::vector< std::map< core::Size, core::Size > >	get_cyclic_pose_residue_mappings_from_selectors (select::residue_selector::ResidueSelectorCOP residue_selector, select::residue_selector::ResidueSelectorCOP residue_selector_ref, core::pose::Pose const &pose, core::pose::Pose const &ref_pose, bool desymmetrize_selectors)
std::string	complex_type_name_for_residue_selector (std::string const &rs_type)
	Used to name the xs:complexType for a residue selector that is created with the "rs_type" tag-name. Does so by prepending "rs_" and appending "Type" to the "rs_type". E.g., "rs_AndType" would be the name given to the complexType to describe the format of the AndResidueSelector. More...
void	xsd_type_definition_w_attributes (utility::tag::XMLSchemaDefinition &xsd, std::string const &rs_type, std::string const &rs_description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a ResidueSelector that contains no other ResidueSelectors 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 &rs_type, std::string const &rs_description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a ResidueSelector that contains a single ResidueSelector 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 &rs_type, std::string const &rs_description, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a ResidueSelector that contains more than one ResidueSelector 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 &rs_type, std::string const &rs_description, core::Size min_occurrence, core::Size max_occurrence, utility::tag::AttributeList const &attributes)
	Define the XML schema definition for a ResidueSelector that contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options). More...
ResidueSelectorCOP	parse_residue_selector (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const &option_name="residue_selector")
	returns a residue selector given a tag and datamap More...
void	attributes_for_parse_residue_selector_default_option_name (utility::tag::AttributeList &attlist, std::string const &documentation_string)
	Companion function for parse_residue_selector. More...
std::string	parse_residue_selector_xsd_documentation ()
void	attributes_for_parse_residue_selector (utility::tag::AttributeList &attlist, std::string const &option_name="residue_selector", std::string const &documentation_string="")
	Companion function for parse_residue_selector. More...
void	attributes_for_parse_residue_selector_when_required (utility::tag::AttributeList &attlist, std::string const &option_name="residue_selector", std::string const &documentation_string="")
	Companion function for parse_residue_selector to be used when it is unacceptible for the parse_residue_selector function to return a null pointer. More...
ResidueSelectorCOP	get_residue_selector (std::string const &selector_name, basic::datacache::DataMap const &data)
	returns a residue selector given a selector's name and datamap More...
ResidueSelectorOP	get_embedded_residue_selector (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	returns a residue selector embeded in a tag. for example, the Chain selector in the example below: More...
utility::vector1< ResidueSelectorOP >	get_embedded_residue_selectors (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap)
	returns residue selectors embeded in a tag. for example, the Chain selector in the example below: More...
bool	all_false_selection (ResidueSubset const &selection)
	Returns True if all the positions in the ResidueSubset are False. More...
bool	all_true_selection (ResidueSubset const &selection)
	Returns True if all the positions in the ResidueSubset are True. More...
bool	has_any_false_selection (ResidueSubset const &selection)
	Returns True if at least one position in the ResidueSubset is False. More...
bool	has_any_true_selection (ResidueSubset const &selection)
	Returns True if at least one position in the ResidueSubset is True. More...
core::Size	count_selected (ResidueSubset const &selection)
	Returns the number of selected residues in the ResidueSubset. More...
utility::vector1< core::Size >	selection_positions (ResidueSubset const &selection)
	Returns the Rosetta Numbering corresponding to the selected residues. More...
utility::vector1< core::Size >	unselection_positions (ResidueSubset const &selection)
	Returns the Rosetta Numbering corresponding to the unselected residues. More...
bool	are_selections_equal (ResidueSubset const &selection1, ResidueSubset const &selection2)
	Evaluate if two ResidueSubsets are equal. More...
std::string	represent_residue_selector (ResidueSubset const &selection, std::string const &is_true, std::string const &is_false)
	Returns a string representing the ResidueSubset (· for non selected, * for selected) More...
ResidueSelectorOP	OR_combine (ResidueSelectorOP sele1, ResidueSelectorOP sele2)
	If sele1 is already an OrResidueSelector, add sele2 to it. If not, return a new OrResidueSelector which combines the two. More...
ResidueSubset	OR_combine (ResidueSubset const &sele1, ResidueSubset const &sele2)
	Combine two residue subsets with OR logic. More...
ResidueSelectorOP	AND_combine (ResidueSelectorOP sele1, ResidueSelectorOP sele2)
	If sele1 is already an AndResidueSelector, add sele2 to it. If not, return a new AndResidueSelector which combines the two. More...
ResidueSubset	AND_combine (ResidueSubset const &sele1, ResidueSubset const &sele2)
	Combine two residue ssubsets with OR logic. More...
ResidueSelectorOP	parse_residue_selector_logic_string (basic::datacache::DataMap const &dm, utility::tag::TagCOP const &tag, std::string const &selector_logic_attribute_name="selector_logic")
	Read a string from the input tag with the indicated attribute name and interpret it as boolean logical operations on a set of existing ResidueSelectors that are already stored in the DataMap. More...
void	attributes_for_parse_residue_selector_logic_string (utility::tag::XMLSchemaDefinition &xsd, utility::tag::AttributeList &attributes, std::string const &selector_logic_attribute_name="selector_logic")
	Append an (optional) attribute that will be used in the call to parse_residue_selector_logic_string. More...
bool	regex_usable ()
	test regex support More...
utility::vector1< core::select::residue_selector::ResidueSubset >	identify_ss_blocks_vec (utility::vector1< bool > const &subset)
	Will eventually replace standard function. More...
bool	all_L_dssp (core::pose::Pose const &pose)
	Is the DSSP all loop? A pose unfortunately starts with all L as the DSSP when creating a pose from seq and inserting residues as is done for segments. More...

Typedef Documentation

AndResidueSelectorCOP

typedef utility::pointer::shared_ptr< AndResidueSelector const > core::select::residue_selector::AndResidueSelectorCOP

AndResidueSelectorOP

typedef utility::pointer::shared_ptr< AndResidueSelector > core::select::residue_selector::AndResidueSelectorOP

AsymmetricUnitSelectorCOP

typedef utility::pointer::shared_ptr< AsymmetricUnitSelector const > core::select::residue_selector::AsymmetricUnitSelectorCOP

AsymmetricUnitSelectorOP

typedef utility::pointer::shared_ptr< AsymmetricUnitSelector > core::select::residue_selector::AsymmetricUnitSelectorOP

BFactorSelectorCOP

using core::select::residue_selector::BFactorSelectorCOP = typedef utility::pointer::shared_ptr< BFactorSelector const >

BFactorSelectorOP

using core::select::residue_selector::BFactorSelectorOP = typedef utility::pointer::shared_ptr< BFactorSelector >

BinSelectorCOP

typedef utility::pointer::shared_ptr< BinSelector const > core::select::residue_selector::BinSelectorCOP

BinSelectorOP

typedef utility::pointer::shared_ptr< BinSelector > core::select::residue_selector::BinSelectorOP

BlockSelectorCOP

using core::select::residue_selector::BlockSelectorCOP = typedef utility::pointer::shared_ptr< BlockSelector const >

BlockSelectorOP

using core::select::residue_selector::BlockSelectorOP = typedef utility::pointer::shared_ptr< BlockSelector >

BondedResidueSelectorCOP

typedef utility::pointer::shared_ptr< BondedResidueSelector const > core::select::residue_selector::BondedResidueSelectorCOP

BondedResidueSelectorOP

typedef utility::pointer::shared_ptr< BondedResidueSelector > core::select::residue_selector::BondedResidueSelectorOP

CachedResidueSubsetCOP

typedef utility::pointer::shared_ptr< CachedResidueSubset const > core::select::residue_selector::CachedResidueSubsetCOP

CachedResidueSubsetOP

typedef utility::pointer::shared_ptr< CachedResidueSubset > core::select::residue_selector::CachedResidueSubsetOP

ChainSelectorCOP

typedef utility::pointer::shared_ptr< ChainSelector const > core::select::residue_selector::ChainSelectorCOP

ChainSelectorOP

typedef utility::pointer::shared_ptr< ChainSelector > core::select::residue_selector::ChainSelectorOP

CloseContactResidueSelectorCOP

typedef utility::pointer::shared_ptr< CloseContactResidueSelector const > core::select::residue_selector::CloseContactResidueSelectorCOP

CloseContactResidueSelectorOP

typedef utility::pointer::shared_ptr< CloseContactResidueSelector > core::select::residue_selector::CloseContactResidueSelectorOP

ConfluentSelectorCOP

using core::select::residue_selector::ConfluentSelectorCOP = typedef utility::pointer::shared_ptr< ConfluentSelector const >

ConfluentSelectorOP

using core::select::residue_selector::ConfluentSelectorOP = typedef utility::pointer::shared_ptr< ConfluentSelector >

DensityFitResidueSelectorCOP

typedef utility::pointer::shared_ptr< DensityFitResidueSelector const > core::select::residue_selector::DensityFitResidueSelectorCOP

DensityFitResidueSelectorOP

typedef utility::pointer::shared_ptr< DensityFitResidueSelector > core::select::residue_selector::DensityFitResidueSelectorOP

FalseResidueSelectorCOP

typedef utility::pointer::shared_ptr< FalseResidueSelector const > core::select::residue_selector::FalseResidueSelectorCOP

FalseResidueSelectorOP

typedef utility::pointer::shared_ptr< FalseResidueSelector > core::select::residue_selector::FalseResidueSelectorOP

FractionSelectorCOP

typedef utility::pointer::shared_ptr< FractionSelector const > core::select::residue_selector::FractionSelectorCOP

FractionSelectorOP

typedef utility::pointer::shared_ptr< FractionSelector > core::select::residue_selector::FractionSelectorOP

GlycanLayerSelectorCOP

typedef utility::pointer::shared_ptr< GlycanLayerSelector const > core::select::residue_selector::GlycanLayerSelectorCOP

GlycanLayerSelectorOP

typedef utility::pointer::shared_ptr< GlycanLayerSelector > core::select::residue_selector::GlycanLayerSelectorOP

GlycanPositionSelectorCOP

typedef utility::pointer::shared_ptr< GlycanPositionSelector const > core::select::residue_selector::GlycanPositionSelectorCOP

GlycanPositionSelectorOP

typedef utility::pointer::shared_ptr< GlycanPositionSelector > core::select::residue_selector::GlycanPositionSelectorOP

GlycanResidueSelectorCOP

typedef utility::pointer::shared_ptr< GlycanResidueSelector const > core::select::residue_selector::GlycanResidueSelectorCOP

GlycanResidueSelectorOP

typedef utility::pointer::shared_ptr< GlycanResidueSelector > core::select::residue_selector::GlycanResidueSelectorOP

GlycanSequonsSelectorCOP

typedef utility::pointer::shared_ptr< GlycanSequonsSelector const > core::select::residue_selector::GlycanSequonsSelectorCOP

GlycanSequonsSelectorOP

typedef utility::pointer::shared_ptr< GlycanSequonsSelector > core::select::residue_selector::GlycanSequonsSelectorOP

InterGroupInterfaceByVectorSelectorCOP

typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelector const > core::select::residue_selector::InterGroupInterfaceByVectorSelectorCOP

InterGroupInterfaceByVectorSelectorOP

typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelector > core::select::residue_selector::InterGroupInterfaceByVectorSelectorOP

JumpDownstreamSelectorCOP

typedef utility::pointer::shared_ptr< JumpDownstreamSelector const > core::select::residue_selector::JumpDownstreamSelectorCOP

JumpDownstreamSelectorOP

typedef utility::pointer::shared_ptr< JumpDownstreamSelector > core::select::residue_selector::JumpDownstreamSelectorOP

JumpUpstreamSelectorCOP

typedef utility::pointer::shared_ptr< JumpUpstreamSelector const > core::select::residue_selector::JumpUpstreamSelectorCOP

JumpUpstreamSelectorOP

typedef utility::pointer::shared_ptr< JumpUpstreamSelector > core::select::residue_selector::JumpUpstreamSelectorOP

LayerSelectorCOP

typedef utility::pointer::shared_ptr< LayerSelector const > core::select::residue_selector::LayerSelectorCOP

LayerSelectorOP

typedef utility::pointer::shared_ptr< LayerSelector > core::select::residue_selector::LayerSelectorOP

LogicResidueSelectorCOP

using core::select::residue_selector::LogicResidueSelectorCOP = typedef utility::pointer::shared_ptr< LogicResidueSelector const >

LogicResidueSelectorOP

using core::select::residue_selector::LogicResidueSelectorOP = typedef utility::pointer::shared_ptr< LogicResidueSelector >

NeighborhoodResidueSelectorCOP

typedef utility::pointer::shared_ptr< NeighborhoodResidueSelector const > core::select::residue_selector::NeighborhoodResidueSelectorCOP

NeighborhoodResidueSelectorOP

typedef utility::pointer::shared_ptr< NeighborhoodResidueSelector > core::select::residue_selector::NeighborhoodResidueSelectorOP

NotResidueSelectorCOP

typedef utility::pointer::shared_ptr< NotResidueSelector const > core::select::residue_selector::NotResidueSelectorCOP

NotResidueSelectorOP

typedef utility::pointer::shared_ptr< NotResidueSelector > core::select::residue_selector::NotResidueSelectorOP

NumNeighborsSelectorCOP

typedef utility::pointer::shared_ptr< NumNeighborsSelector const > core::select::residue_selector::NumNeighborsSelectorCOP

NumNeighborsSelectorOP

typedef utility::pointer::shared_ptr< NumNeighborsSelector > core::select::residue_selector::NumNeighborsSelectorOP

OrResidueSelectorCOP

typedef utility::pointer::shared_ptr< OrResidueSelector const > core::select::residue_selector::OrResidueSelectorCOP

OrResidueSelectorOP

typedef utility::pointer::shared_ptr< OrResidueSelector > core::select::residue_selector::OrResidueSelectorOP

PhiSelectorCOP

typedef utility::pointer::shared_ptr< PhiSelector const > core::select::residue_selector::PhiSelectorCOP

PhiSelectorOP

typedef utility::pointer::shared_ptr< PhiSelector > core::select::residue_selector::PhiSelectorOP

PrimarySequenceNeighborhoodSelectorCOP

typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelector const > core::select::residue_selector::PrimarySequenceNeighborhoodSelectorCOP

PrimarySequenceNeighborhoodSelectorOP

typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelector > core::select::residue_selector::PrimarySequenceNeighborhoodSelectorOP

RandomGlycanFoliageSelectorCOP

typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelector const > core::select::residue_selector::RandomGlycanFoliageSelectorCOP

RandomGlycanFoliageSelectorOP

typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelector > core::select::residue_selector::RandomGlycanFoliageSelectorOP

RandomResidueSelectorCOP

typedef utility::pointer::shared_ptr< RandomResidueSelector const > core::select::residue_selector::RandomResidueSelectorCOP

RandomResidueSelectorOP

typedef utility::pointer::shared_ptr< RandomResidueSelector > core::select::residue_selector::RandomResidueSelectorOP

ResidueIndexSelectorCOP

typedef utility::pointer::shared_ptr< ResidueIndexSelector const > core::select::residue_selector::ResidueIndexSelectorCOP

ResidueIndexSelectorOP

typedef utility::pointer::shared_ptr< ResidueIndexSelector > core::select::residue_selector::ResidueIndexSelectorOP

ResidueInMembraneSelectorCOP

typedef utility::pointer::shared_ptr< ResidueInMembraneSelector const > core::select::residue_selector::ResidueInMembraneSelectorCOP

ResidueInMembraneSelectorOP

typedef utility::pointer::shared_ptr< ResidueInMembraneSelector > core::select::residue_selector::ResidueInMembraneSelectorOP

ResidueInSequenceMotifSelectorCOP

typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelector const > core::select::residue_selector::ResidueInSequenceMotifSelectorCOP

ResidueInSequenceMotifSelectorOP

typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelector > core::select::residue_selector::ResidueInSequenceMotifSelectorOP

ResidueNameSelectorCOP

typedef utility::pointer::shared_ptr< ResidueNameSelector const > core::select::residue_selector::ResidueNameSelectorCOP

ResidueNameSelectorOP

typedef utility::pointer::shared_ptr< ResidueNameSelector > core::select::residue_selector::ResidueNameSelectorOP

ResiduePDBInfoHasLabelSelectorCOP

typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelector const > core::select::residue_selector::ResiduePDBInfoHasLabelSelectorCOP

ResiduePDBInfoHasLabelSelectorOP

typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelector > core::select::residue_selector::ResiduePDBInfoHasLabelSelectorOP

ResiduePropertySelectorCOP

typedef utility::pointer::shared_ptr< ResiduePropertySelector const > core::select::residue_selector::ResiduePropertySelectorCOP

ResiduePropertySelectorOP

typedef utility::pointer::shared_ptr< ResiduePropertySelector > core::select::residue_selector::ResiduePropertySelectorOP

ResidueRangesAP

typedef utility::pointer::weak_ptr< ResidueRanges > core::select::residue_selector::ResidueRangesAP

ResidueRangesCAP

typedef utility::pointer::weak_ptr< ResidueRanges const > core::select::residue_selector::ResidueRangesCAP

ResidueRangesCOP

typedef utility::pointer::shared_ptr< ResidueRanges const > core::select::residue_selector::ResidueRangesCOP

ResidueRangesOP

typedef utility::pointer::shared_ptr< ResidueRanges > core::select::residue_selector::ResidueRangesOP

ResidueSelectorAP

typedef utility::pointer::weak_ptr< ResidueSelector > core::select::residue_selector::ResidueSelectorAP

ResidueSelectorCAP

typedef utility::pointer::weak_ptr< ResidueSelector const > core::select::residue_selector::ResidueSelectorCAP

ResidueSelectorCOP

typedef utility::pointer::shared_ptr< ResidueSelector const > core::select::residue_selector::ResidueSelectorCOP

ResidueSelectorCreatorCOP

typedef utility::pointer::shared_ptr< ResidueSelectorCreator const > core::select::residue_selector::ResidueSelectorCreatorCOP

ResidueSelectorCreatorOP

typedef utility::pointer::shared_ptr< ResidueSelectorCreator > core::select::residue_selector::ResidueSelectorCreatorOP

ResidueSelectorOP

typedef utility::pointer::shared_ptr< ResidueSelector > core::select::residue_selector::ResidueSelectorOP

ResidueSpanSelectorCOP

typedef utility::pointer::shared_ptr< ResidueSpanSelector const > core::select::residue_selector::ResidueSpanSelectorCOP

ResidueSpanSelectorOP

typedef utility::pointer::shared_ptr< ResidueSpanSelector > core::select::residue_selector::ResidueSpanSelectorOP

ResidueSubset

typedef utility::vector1< bool > core::select::residue_selector::ResidueSubset

ResidueSubsetAP

typedef utility::pointer::weak_ptr< ResidueSubset > core::select::residue_selector::ResidueSubsetAP

ResidueSubsetCAP

typedef utility::pointer::weak_ptr< ResidueSubset const > core::select::residue_selector::ResidueSubsetCAP

ResidueSubsetCOP

typedef utility::pointer::shared_ptr< ResidueSubset const > core::select::residue_selector::ResidueSubsetCOP

ResidueSubsetOP

typedef utility::pointer::shared_ptr< ResidueSubset > core::select::residue_selector::ResidueSubsetOP

ResidueVectorAP

typedef utility::pointer::weak_ptr< ResidueVector > core::select::residue_selector::ResidueVectorAP

ResidueVectorCAP

typedef utility::pointer::weak_ptr< ResidueVector const > core::select::residue_selector::ResidueVectorCAP

ResidueVectorCOP

typedef utility::pointer::shared_ptr< ResidueVector const > core::select::residue_selector::ResidueVectorCOP

ResidueVectorOP

typedef utility::pointer::shared_ptr< ResidueVector > core::select::residue_selector::ResidueVectorOP

ReturnResidueSubsetSelectorCOP

typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelector const > core::select::residue_selector::ReturnResidueSubsetSelectorCOP

ReturnResidueSubsetSelectorOP

typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelector > core::select::residue_selector::ReturnResidueSubsetSelectorOP

ScoreTermValueBasedSelectorCOP

typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelector const > core::select::residue_selector::ScoreTermValueBasedSelectorCOP

ScoreTermValueBasedSelectorOP

typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelector > core::select::residue_selector::ScoreTermValueBasedSelectorOP

SecondaryStructureSelectorCOP

typedef utility::pointer::shared_ptr< SecondaryStructureSelector const > core::select::residue_selector::SecondaryStructureSelectorCOP

SecondaryStructureSelectorOP

typedef utility::pointer::shared_ptr< SecondaryStructureSelector > core::select::residue_selector::SecondaryStructureSelectorOP

SelectorLogicParserCOP

typedef utility::pointer::shared_ptr< SelectorLogicParser const > core::select::residue_selector::SelectorLogicParserCOP

SelectorLogicParserOP

typedef utility::pointer::shared_ptr< SelectorLogicParser > core::select::residue_selector::SelectorLogicParserOP

SimpleMetricSelectorCOP

typedef utility::pointer::shared_ptr< SimpleMetricSelector const > core::select::residue_selector::SimpleMetricSelectorCOP

SimpleMetricSelectorOP

typedef utility::pointer::shared_ptr< SimpleMetricSelector > core::select::residue_selector::SimpleMetricSelectorOP

SliceResidueSelectorCOP

typedef utility::pointer::shared_ptr< SliceResidueSelector const > core::select::residue_selector::SliceResidueSelectorCOP

SliceResidueSelectorOP

typedef utility::pointer::shared_ptr< SliceResidueSelector > core::select::residue_selector::SliceResidueSelectorOP

SSElementSelectorCOP

typedef utility::pointer::shared_ptr< SSElementSelector const > core::select::residue_selector::SSElementSelectorCOP

SSElementSelectorOP

typedef utility::pointer::shared_ptr< SSElementSelector > core::select::residue_selector::SSElementSelectorOP

SymmetricalResidueSelectorCOP

typedef utility::pointer::shared_ptr< SymmetricalResidueSelector const > core::select::residue_selector::SymmetricalResidueSelectorCOP

SymmetricalResidueSelectorOP

typedef utility::pointer::shared_ptr< SymmetricalResidueSelector > core::select::residue_selector::SymmetricalResidueSelectorOP

TrueResidueSelectorCOP

typedef utility::pointer::shared_ptr< TrueResidueSelector const > core::select::residue_selector::TrueResidueSelectorCOP

TrueResidueSelectorOP

typedef utility::pointer::shared_ptr< TrueResidueSelector > core::select::residue_selector::TrueResidueSelectorOP

VirtualResidueSelectorCOP

typedef utility::pointer::shared_ptr< VirtualResidueSelector const > core::select::residue_selector::VirtualResidueSelectorCOP

VirtualResidueSelectorOP

typedef utility::pointer::shared_ptr< VirtualResidueSelector > core::select::residue_selector::VirtualResidueSelectorOP

Enumeration Type Documentation

basic_selection_logic

enum core::select::residue_selector::basic_selection_logic

Enumerator
and_logic
or_logic

Function Documentation

all_false_selection()

bool core::select::residue_selector::all_false_selection

(

ResidueSubset const &

selection

)

Returns True if all the positions in the ResidueSubset are False.

References core::sequence::end.

Referenced by protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::apply(), protocols::glycan_docking::GlycanDockProtocol::apply(), and protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::apply_no_remarks().

all_L_dssp()

bool core::select::residue_selector::all_L_dssp

(

core::pose::Pose const &

pose

)

Is the DSSP all loop? A pose unfortunately starts with all L as the DSSP when creating a pose from seq and inserting residues as is done for segments.

References core::pose::Pose::secstruct(), and core::pose::Pose::size().

all_true_selection()

bool core::select::residue_selector::all_true_selection

(

ResidueSubset const &

selection

)

Returns True if all the positions in the ResidueSubset are True.

References core::sequence::end.

AND_combine() [1/2]

ResidueSelectorOP core::select::residue_selector::AND_combine	(	ResidueSelectorOP	sele1,
		ResidueSelectorOP	sele2
	)

If sele1 is already an AndResidueSelector, add sele2 to it. If not, return a new AndResidueSelector which combines the two.

If either of the selectors are a nullptr, just return the other.

AND_combine() [2/2]

ResidueSubset core::select::residue_selector::AND_combine	(	ResidueSubset const &	sele1,
		ResidueSubset const &	sele2
	)

Combine two residue ssubsets with OR logic.

Referenced by protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two().

are_selections_equal()

bool core::select::residue_selector::are_selections_equal	(	ResidueSubset const &	selection1,
		ResidueSubset const &	selection2
	)

Evaluate if two ResidueSubsets are equal.

Referenced by protocols::fold_from_loops::utils::map_by_residue_subsets().

attributes_for_parse_residue_selector()

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

Companion function for parse_residue_selector.

References parse_residue_selector_xsd_documentation().

Referenced by core::simple_metrics::add_per_residue_simple_metric_schema(), protocols::sewing::hashing::AlignmentFileGeneratorMover::append_ligands_subelement(), protocols::sewing::movers::AppendAssemblyMover::attributes_for_append_assembly_mover(), protocols::hbnet::HBNet::attributes_for_hbnet(), attributes_for_parse_residue_selector_default_option_name(), protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(), protocols::kinematic_closure::BalancedKicMover::complex_type_generator_for_balancedKIC_mover(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements(), protocols::fold_from_loops::utils::Nub::provide_xml_definition(), core::select::residue_selector::ScoreTermValueBasedSelector::provide_xml_schema(), core::pack::task::operation::OperateOnResidueSubset::provide_xml_schema(), core::select::jump_selector::ExclusivelySharedJumpSelector::provide_xml_schema(), core::select::jump_selector::JumpForResidue::provide_xml_schema(), core::select::residue_selector::AndResidueSelector::provide_xml_schema(), core::select::residue_selector::BFactorSelector::provide_xml_schema(), core::select::residue_selector::BlockSelector::provide_xml_schema(), core::select::residue_selector::BondedResidueSelector::provide_xml_schema(), core::select::residue_selector::CloseContactResidueSelector::provide_xml_schema(), core::select::residue_selector::ConfluentSelector::provide_xml_schema(), core::select::residue_selector::FractionSelector::provide_xml_schema(), core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema(), core::select::residue_selector::NeighborhoodResidueSelector::provide_xml_schema(), core::select::residue_selector::NotResidueSelector::provide_xml_schema(), core::select::residue_selector::OrResidueSelector::provide_xml_schema(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema(), core::select::residue_selector::RandomGlycanFoliageSelector::provide_xml_schema(), core::select::residue_selector::RandomResidueSelector::provide_xml_schema(), core::select::residue_selector::SliceResidueSelector::provide_xml_schema(), core::select::residue_selector::SymmetricalResidueSelector::provide_xml_schema(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(), core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), core::simple_metrics::metrics::SecondaryStructureMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResidueCountMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesMetric::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceMetric::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::HbondMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::provide_xml_schema(), protocols::aa_composition::AddCompositionConstraintMover::provide_xml_schema(), protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema(), protocols::aa_composition::AddMHCEpitopeConstraintMover::provide_xml_schema(), protocols::aa_composition::AddNetChargeConstraintMover::provide_xml_schema(), protocols::abinitio::abscript::AbscriptLoopCloserCM::provide_xml_schema(), protocols::abinitio::abscript::FragmentJumpCM::provide_xml_schema(), protocols::abinitio::abscript::RigidChunkCM::provide_xml_schema(), protocols::analysis::simple_metrics::ConstraintsMetric::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), protocols::backbone_moves::RandomizeBBByRamaPrePro::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::provide_xml_schema(), protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::provide_xml_schema(), protocols::constraint_generator::AtomPairConstraintGenerator::provide_xml_schema(), protocols::constraint_generator::CoordinateConstraintGenerator::provide_xml_schema(), protocols::constraint_generator::MetalContactsConstraintGenerator::provide_xml_schema(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema(), protocols::cyclic_peptide::CrankshaftFlipMover::provide_xml_schema(), protocols::cyclic_peptide::FlipChiralityMover::provide_xml_schema(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema(), protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema(), protocols::cyclic_peptide::TryDisulfPermutations::provide_xml_schema(), protocols::denovo_design::architects::PoseArchitect::provide_xml_schema(), protocols::denovo_design::filters::CavityVolumeFilter::provide_xml_schema(), protocols::denovo_design::filters::PreProlineFilter::provide_xml_schema(), protocols::denovo_design::filters::SSShapeComplementarityFilter::provide_xml_schema(), protocols::docking::EnsureExclusivelySharedJumpMover::provide_xml_schema(), protocols::drug_design::RDKitMetric::provide_xml_schema(), protocols::environment::claims::TorsionClaim::provide_xml_schema(), protocols::environment::claims::XYZClaim::provide_xml_schema(), protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::provide_xml_schema(), protocols::fldsgn::filters::SecondaryStructureFilter::provide_xml_schema(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::provide_xml_schema(), protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema(), protocols::match::MatcherMover::provide_xml_schema(), protocols::metal_interface::RemoveMetalConnectionsMover::provide_xml_schema(), protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric::provide_xml_schema(), protocols::pose_creation::MakePolyXMover::provide_xml_schema(), protocols::pose_creation::SliceToMiniProteinMover::provide_xml_schema(), protocols::pose_sewing::filters::CoreScorer::provide_xml_schema(), protocols::pose_sewing::filters::HasDisulfideFilter::provide_xml_schema(), protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::provide_xml_schema(), protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::provide_xml_schema(), protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::provide_xml_schema(), protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema(), protocols::ptm_prediction::PTMPredictionMetric::provide_xml_schema(), protocols::residue_selectors::HBondSelector::provide_xml_schema(), protocols::residue_selectors::LigandMetalContactSelector::provide_xml_schema(), protocols::residue_selectors::NativeSelector::provide_xml_schema(), protocols::residue_selectors::StoreResidueSubsetMover::provide_xml_schema(), protocols::rna::movers::ERRASER2Protocol::provide_xml_schema(), protocols::score_filters::GeometryFilter::provide_xml_schema(), protocols::sewing::hashing::AlignmentFileGeneratorMover::provide_xml_schema(), protocols::simple_filters::AtomicDistanceFilter::provide_xml_schema(), protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema(), protocols::simple_filters::HolesFilter::provide_xml_schema(), protocols::simple_filters::ResidueCountFilter::provide_xml_schema(), protocols::simple_filters::ResidueIEFilter::provide_xml_schema(), protocols::simple_filters::ResidueSelectionDistanceFilter::provide_xml_schema(), protocols::simple_filters::SSElementLengthFilter::provide_xml_schema(), protocols::simple_moves::DeclareBond::provide_xml_schema(), protocols::simple_moves::FoldTreeFromMotif::provide_xml_schema(), protocols::simple_moves::ModifyVariantTypeMover::provide_xml_schema(), protocols::simple_moves::MutateResidue::provide_xml_schema(), protocols::simple_moves::SetupMetalsMover::provide_xml_schema(), protocols::simple_moves::SixDoFGridDockMover::provide_xml_schema(), protocols::switches::GraftSwitchMover::provide_xml_schema(), protocols::task_operations::ConservativeDesignOperation::provide_xml_schema(), protocols::task_operations::ReadResfileFromDB::provide_xml_schema(), protocols::task_operations::ResfileCommandOperation::provide_xml_schema(), protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema(), protocols::simple_moves::AddResidueLabelMoverCreator::provide_xml_schema(), core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema_attributes(), and core::pack::task::operation::ReadResfile::xml_schema_attributes().

attributes_for_parse_residue_selector_default_option_name()

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

Companion function for parse_residue_selector.

This assumes the default residue selector option name ("residue_selector").

References attributes_for_parse_residue_selector().

Referenced by protocols::rosetta_scripts::attributes_for_parse_residue_selector(), core::pack::task::operation::DesignRestrictions::provide_xml_schema(), core::select::residue_selector::DensityFitResidueSelector::provide_xml_schema(), core::simple_metrics::metrics::SasaMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema(), protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema(), protocols::constraint_generator::ResidueTypeConstraintGenerator::provide_xml_schema(), protocols::cyclic_peptide::CycpepSymmetryFilter::provide_xml_schema(), protocols::drug_design::ApplyChemistryMover::provide_xml_schema(), protocols::farnesyl::InstallFarnesylMover::provide_xml_schema(), protocols::minimization_packing::DisulfideOptimizationMover::provide_xml_schema(), and protocols::simple_filters::BuriedSurfaceAreaFilter::provide_xml_schema().

attributes_for_parse_residue_selector_logic_string()

void core::select::residue_selector::attributes_for_parse_residue_selector_logic_string	(	utility::tag::XMLSchemaDefinition &	,
		utility::tag::AttributeList &	attributes,
		std::string const &	selector_logic_attribute_name
	)

Append an (optional) attribute that will be used in the call to parse_residue_selector_logic_string.

Referenced by core::pack::task::operation::DesignRestrictions::provide_xml_schema(), and core::pack::task::operation::OperateOnResidueSubset::provide_xml_schema().

attributes_for_parse_residue_selector_when_required()

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

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

References parse_residue_selector_xsd_documentation().

Referenced by protocols::fold_from_loops::utils::Nub::provide_xml_definition(), core::select::movemap::MoveMapFactory::provide_xml_schema(), protocols::cyclic_peptide::CrosslinkerMover::provide_xml_schema(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::provide_xml_schema(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::provide_xml_schema(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::provide_xml_schema(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::provide_xml_schema(), protocols::fold_from_loops::NubInitioMover::provide_xml_schema(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::provide_xml_schema(), and protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema().

complex_type_name_for_residue_selector()

std::string core::select::residue_selector::complex_type_name_for_residue_selector

(

std::string const &

rs_type

)

Used to name the xs:complexType for a residue selector that is created with the "rs_type" tag-name. Does so by prepending "rs_" and appending "Type" to the "rs_type". E.g., "rs_AndType" would be the name given to the complexType to describe the format of the AndResidueSelector.

Referenced by core::select::residue_selector::ResidueSelectorFactory::define_residue_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().

count_selected()

core::Size core::select::residue_selector::count_selected

(

ResidueSubset const &

selection

)

Returns the number of selected residues in the ResidueSubset.

References core::sequence::end.

Referenced by protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::glycan_docking::GlycanDockProtocol::apply(), protocols::glycan_docking::calc_GlycanDock_intf_metrics(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::fold_from_loops::NubInitioMover::count_contacts(), protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two(), protocols::carbohydrates::GlycanSampler::init_objects(), protocols::fold_from_loops::NubInitioMover::sanity_check(), protocols::carbohydrates::GlycanSampler::setup_movers(), protocols::fold_from_loops::NubInitioMover::template_insertion_ranges(), and protocols::fold_from_loops::NubInitioMover::used_template_ranges().

get_cyclic_pose_residue_mappings_from_selectors()

std::vector< std::map< core::Size, core::Size > > core::select::residue_selector::get_cyclic_pose_residue_mappings_from_selectors	(	select::residue_selector::ResidueSelectorCOP	residue_selector,
		select::residue_selector::ResidueSelectorCOP	residue_selector_ref,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		bool	desymmetrize_selectors
	)

References core::select::get_master_subunit_selection(), core::select::get_residues_from_subset(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by core::simple_metrics::metrics::RMSDMetric::calculate().

get_embedded_residue_selector()

ResidueSelectorOP core::select::residue_selector::get_embedded_residue_selector	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

returns a residue selector embeded in a tag. for example, the Chain selector in the example below:

Example: RESIDUE_SELECTORS> <Neighborhood name="chAB_neighbors"> <Chain chains="A,B"> </Neighborhood> /RESIDUE_SELECTORS>

@thorws utility::excn::EXCN_Msg_Exception if selector is not embedded ( ! tag->size() > 1)

Referenced by core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), and core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag().

get_embedded_residue_selectors()

utility::vector1< ResidueSelectorOP > core::select::residue_selector::get_embedded_residue_selectors	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

returns residue selectors embeded in a tag. for example, the Chain selector in the example below:

Example: RESIDUE_SELECTORS> <Neighborhood name="chAB_neighbors"> <Chain chains="A,B"> <Glycan > </Neighborhood> /RESIDUE_SELECTORS>

@thorws utility::excn::EXCN_Msg_Exception if no embedded selectors (tag->size() <= 1)

get_residue_mapping_from_selectors()

std::map< core::Size, core::Size > core::select::residue_selector::get_residue_mapping_from_selectors	(	select::residue_selector::ResidueSelectorCOP	selector,
		select::residue_selector::ResidueSelectorCOP	selector_ref,
		core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		bool	desymmetrize_selectors = true
	)

Determine the residue mapping by residue selector and the reference selector. If both are null, will get a map of all residues. De-symmetrizes both residue selectors.

By default, we only get a mapping of the master subunit. IE - ALL residues NOT in the asymmetric unit will be false

References core::select::get_master_subunit_selection(), core::select::get_residues_from_subset(), core::pose::symmetry::is_symmetric(), and core::pose::Pose::size().

Referenced by core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), and core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map().

get_residue_selector()

ResidueSelectorCOP core::select::residue_selector::get_residue_selector	(	std::string const &	selector_name,
		basic::datacache::DataMap const &	data
	)

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

Looks for selector in the datamap, if not found, will attempt to parse logicals using SelectorLogicParser. (AND/OR/NOT separated by spaces). Not gets priority. Returns a const ptr to the selector

Exceptions

utility::excn::EXCN_Msg_Exception

if selector is not found in datamap

References core::select::residue_selector::SelectorLogicParser::parse_string_to_residue_selector(), and TR().

Referenced by protocols::denovo_design::get_residue_selector(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag(), protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric::parse_my_tag(), protocols::fldsgn::filters::SecondaryStructureCountFilter::parse_my_tag(), protocols::match::MatcherMover::parse_my_tag(), protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::simple_filters::ContactMolecularSurfaceFilter::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), protocols::aa_composition::AddCompositionConstraintMover::parse_my_tag(), protocols::aa_composition::AddMHCEpitopeConstraintMover::parse_my_tag(), protocols::aa_composition::AddNetChargeConstraintMover::parse_my_tag(), protocols::switches::GraftSwitchMover::parse_my_tag(), core::select::jump_selector::ExclusivelySharedJumpSelector::parse_my_tag(), core::select::jump_selector::JumpForResidue::parse_my_tag(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(), protocols::docking::EnsureExclusivelySharedJumpMover::parse_my_tag(), protocols::hbnet::HBNet::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), core::select::residue_selector::RandomResidueSelector::parse_my_tag(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::parse_my_tag(), core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::abinitio::abscript::FragmentCM::parse_my_tag(), protocols::abinitio::abscript::FragmentJumpCM::parse_my_tag(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::parse_my_tag(), protocols::denovo_design::filters::CavityVolumeFilter::parse_my_tag(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::parse_my_tag(), protocols::pose_creation::MergePDBMover::parse_my_tag(), protocols::pose_sewing::filters::CoreScorer::parse_my_tag(), protocols::pose_sewing::filters::HasDisulfideFilter::parse_my_tag(), protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::parse_my_tag(), protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::parse_my_tag(), protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::parse_my_tag(), protocols::pose_sewing::simple_metrics::MinimumInterAlphaDistanceMetric::parse_my_tag(), protocols::pose_sewing::simple_metrics::WindowPoseCompMotifMetric::parse_my_tag(), protocols::protein_mpnn::ProteinMPNNMover::parse_my_tag(), protocols::rbsegment_relax::ConfChangeMover::parse_my_tag(), protocols::rna::movers::ERRASER2Protocol::parse_my_tag(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::symmetry::SetupForSequenceSymmetryMover::parse_my_tag(), core::simple_metrics::metrics::ShapeSimilarityMetric::parse_my_tag(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::parse_my_tag(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::parse_my_tag(), core::select::residue_selector::BondedResidueSelector::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), core::select::residue_selector::AndResidueSelector::parse_my_tag(), core::select::residue_selector::BFactorSelector::parse_my_tag(), core::select::residue_selector::BlockSelector::parse_my_tag(), core::select::residue_selector::CloseContactResidueSelector::parse_my_tag(), core::select::residue_selector::ConfluentSelector::parse_my_tag(), core::select::residue_selector::FractionSelector::parse_my_tag(), core::select::residue_selector::InterGroupInterfaceByVectorSelector::parse_my_tag(), core::select::residue_selector::LogicResidueSelector::parse_my_tag(), core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag(), core::select::residue_selector::NotResidueSelector::parse_my_tag(), core::select::residue_selector::OrResidueSelector::parse_my_tag(), core::select::residue_selector::SliceResidueSelector::parse_my_tag(), protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag(), protocols::residue_selectors::HBondSelector::parse_my_tag(), protocols::residue_selectors::LigandMetalContactSelector::parse_my_tag(), protocols::residue_selectors::NativeSelector::parse_my_tag(), parse_residue_selector(), protocols::denovo_design::movers::parse_residue_selectors(), protocols::jd3::parse_single_residue_selector(), core::pack::task::operation::OperateOnResidueSubset::parse_tag(), core::pack::task::operation::ReadResfile::parse_tag(), protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag(), protocols::constraint_generator::DistanceConstraintGenerator::parse_tag(), protocols::constraint_generator::HydrogenBondConstraintGenerator::parse_tag(), protocols::constraint_generator::MetalContactsConstraintGenerator::parse_tag(), protocols::task_operations::ConservativeDesignOperation::parse_tag(), protocols::task_operations::ReadResfileFromDB::parse_tag(), protocols::environment::claims::TorsionClaim::TorsionClaim(), and protocols::environment::claims::XYZClaim::XYZClaim().

has_any_false_selection()

bool core::select::residue_selector::has_any_false_selection

(

ResidueSubset const &

selection

)

Returns True if at least one position in the ResidueSubset is False.

References core::sequence::end.

has_any_true_selection()

bool core::select::residue_selector::has_any_true_selection

(

ResidueSubset const &

selection

)

Returns True if at least one position in the ResidueSubset is True.

References core::sequence::end.

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::constraint_generator::AtomPairConstraintGenerator::generate_atom_pair_constraints(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::has_cutpoints(), and protocols::fold_from_loops::movers::NubInitioLoopClosureMover::has_movable_residues().

has_option()

bool core::select::residue_selector::has_option	(	utility::tag::TagCOP const &	tag,
		std::string const &	key
	)

Referenced by core::select::residue_selector::SimpleMetricSelector::parse_my_tag().

identify_ss_blocks_vec()

utility::vector1< core::select::residue_selector::ResidueSubset > core::select::residue_selector::identify_ss_blocks_vec

(

core::select::residue_selector::ResidueSubset const &

selection

)

Will eventually replace standard function.

Referenced by core::select::residue_selector::BlockSelector::apply().

logic_map()

static const std::map< std::string, basic_selection_logic > core::select::residue_selector::logic_map ( { { "or_logic", or_logic }, { "and_logic", and_logic } }  )

static

References and_logic, and or_logic.

Referenced by core::select::residue_selector::ResiduePropertySelector::parse_my_tag(), and core::select::residue_selector::ResiduePropertySelector::provide_xml_schema().

OR_combine() [1/2]

ResidueSelectorOP core::select::residue_selector::OR_combine	(	ResidueSelectorOP	sele1,
		ResidueSelectorOP	sele2
	)

If sele1 is already an OrResidueSelector, add sele2 to it. If not, return a new OrResidueSelector which combines the two.

If either of the selectors are a nullptr, just return the other.

Referenced by protocols::protein_interface_design::filters::RmsdFilter::add_selector(), protocols::protein_interface_design::movers::BackrubDDMover::add_selector(), and protocols::calc_taskop_movers::DesignRepackMover::parse_my_tag().

OR_combine() [2/2]

ResidueSubset core::select::residue_selector::OR_combine	(	ResidueSubset const &	sele1,
		ResidueSubset const &	sele2
	)

Combine two residue subsets with OR logic.

parse_residue_selector()

ResidueSelectorCOP core::select::residue_selector::parse_residue_selector	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap const &	data,
		std::string const &	option_name = "residue_selector"
	)

returns a residue selector given a tag and datamap

Looks for "residue_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_residue_selector()

References get_residue_selector(), and TR().

Referenced by protocols::cyclic_peptide::PeptideInternalHbondsMetric::configure_from_filter_tag(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag(), protocols::simple_filters::Worst9merFilter::parse_my_tag(), protocols::simple_moves::FoldTreeFromMotif::parse_my_tag(), protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(), protocols::carbohydrates::TautomerizeAnomerMover::parse_my_tag(), protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag(), protocols::simple_filters::SSElementLengthFilter::parse_my_tag(), protocols::residue_selectors::StoreResidueSubsetMover::parse_my_tag(), protocols::simple_moves::AddResidueLabelMover::parse_my_tag(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::simple_moves::SetupMetalsMover::parse_my_tag(), protocols::pose_creation::MakePolyXMover::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), protocols::score_filters::GeometryFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::simple_moves::AddSapConstraintMover::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::simple_moves::MutateResidue::parse_my_tag(), core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::parse_my_tag(), core::pack::guidance_scoreterms::sap::SapScoreMetric::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), core::simple_metrics::metrics::RMSDMetric::parse_my_tag(), core::simple_metrics::metrics::SasaMetric::parse_my_tag(), core::simple_metrics::metrics::SecondaryStructureMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResidueCountMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesMetric::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::parse_my_tag(), core::simple_metrics::metrics::SequenceMetric::parse_my_tag(), core::simple_metrics::metrics::SequenceSimilarityMetric::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::HbondMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::parse_my_tag(), protocols::aa_composition::AddHelixSequenceConstraintsMover::parse_my_tag(), protocols::analysis::simple_metrics::ConstraintsMetric::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), protocols::backbone_moves::RandomizeBBByRamaPrePro::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::parse_my_tag(), protocols::calc_taskop_movers::CreateSequenceMotifMover::parse_my_tag(), protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag(), protocols::carbohydrates::GlycanSampler::parse_my_tag(), protocols::carbohydrates::GlycanTreeMinMover::parse_my_tag(), protocols::carbohydrates::GlycanTreeModeler::parse_my_tag(), protocols::carbohydrates::LinkageConformerMover::parse_my_tag(), protocols::carbohydrates::SimpleGlycosylateMover::parse_my_tag(), protocols::cyclic_peptide::CrankshaftFlipMover::parse_my_tag(), protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::parse_my_tag(), protocols::cyclic_peptide::CycpepSymmetryFilter::parse_my_tag(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag(), protocols::denovo_design::filters::PreProlineFilter::parse_my_tag(), protocols::denovo_design::filters::SSShapeComplementarityFilter::parse_my_tag(), protocols::drug_design::ApplyChemistryMover::parse_my_tag(), protocols::drug_design::RDKitMetric::parse_my_tag(), protocols::esm_perplexity::PerResidueEsmProbabilitiesMetric::parse_my_tag(), protocols::farnesyl::InstallFarnesylMover::parse_my_tag(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::parse_my_tag(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::parse_my_tag(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::parse_my_tag(), protocols::fold_from_loops::NubInitioMover::parse_my_tag(), protocols::kinematic_closure::BalancedKicMover::parse_my_tag(), protocols::metal_interface::RemoveMetalConnectionsMover::parse_my_tag(), protocols::minimization_packing::DisulfideOptimizationMover::parse_my_tag(), protocols::minimization_packing::PertMinMover::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_my_tag(), protocols::ptm_prediction::PTMPredictionMetric::parse_my_tag(), protocols::simple_filters::BuriedSurfaceAreaFilter::parse_my_tag(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::parse_my_tag(), protocols::simple_filters::ResidueSelectionDistanceFilter::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::simple_moves::ConvertRealToVirtualMover::parse_my_tag(), protocols::simple_moves::ConvertVirtualToRealMover::parse_my_tag(), protocols::simple_moves::SixDoFGridDockMover::parse_my_tag(), core::select::movemap::MoveMapFactory::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(), core::select::residue_selector::RandomGlycanFoliageSelector::parse_my_tag(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::parse_my_tag(), protocols::simple_moves::StructProfileMover::parse_my_tag(), protocols::cyclic_peptide::FlipChiralityMover::parse_my_tag(), protocols::cyclic_peptide::PeptideCyclizeMover::parse_my_tag(), protocols::cyclic_peptide::PeptideStubMover::parse_my_tag(), protocols::simple_moves::DeclareBond::parse_my_tag(), core::simple_metrics::PerResidueProbabilitiesMetric::parse_per_residue_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), core::simple_metrics::PerResidueStringMetric::parse_per_residue_tag(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::task_operations::ResfileCommandOperation::parse_tag(), protocols::task_operations::SequenceMotifTaskOperation::parse_tag(), protocols::fold_from_loops::utils::Nub::parse_tag(), protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag(), protocols::constraint_generator::CoordinateConstraintGenerator::parse_tag(), protocols::constraint_generator::DihedralConstraintGenerator::parse_tag(), protocols::constraint_generator::ResidueTypeConstraintGenerator::parse_tag(), protocols::denovo_design::architects::PoseArchitect::parse_tag(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::parse_tag(), and protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::parse_tag().

parse_residue_selector_logic_string()

ResidueSelectorOP core::select::residue_selector::parse_residue_selector_logic_string	(	basic::datacache::DataMap const &	dm,
		utility::tag::TagCOP const &	tag,
		std::string const &	atname
	)

Read a string from the input tag with the indicated attribute name and interpret it as boolean logical operations on a set of existing ResidueSelectors that are already stored in the DataMap.

References core::select::residue_selector::SelectorLogicParser::parse_string_to_residue_selector().

Referenced by core::pack::task::operation::OperateOnResidueSubset::parse_tag(), and core::pack::task::operation::DesignRestrictions::parse_tag().

parse_residue_selector_xsd_documentation()

std::string core::select::residue_selector::parse_residue_selector_xsd_documentation

(

)

Referenced by attributes_for_parse_residue_selector(), and attributes_for_parse_residue_selector_when_required().

regex_usable()

bool core::select::residue_selector::regex_usable

(

)

test regex support

Referenced by core::select::residue_selector::ResidueInSequenceMotifSelector::apply().

represent_residue_selector()

std::string core::select::residue_selector::represent_residue_selector	(	ResidueSubset const &	selection,
		std::string const &	is_true,
		std::string const &	is_false
	)

Returns a string representing the ResidueSubset (· for non selected, * for selected)

Returns a string representing the ResidueSubset (- for non selected, * for selected)

Referenced by protocols::fold_from_loops::movers::AlignByResidueSelectorMover::apply(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::fold_from_loops::NubInitioMover::count_contacts(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::find_labels(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::print_task_operators(), protocols::fold_from_loops::utils::report_unfolded(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::show_cutpoints(), and protocols::fold_from_loops::NubInitioMover::used_template_ranges().

selection_positions()

utility::vector1< core::Size > core::select::residue_selector::selection_positions

(

ResidueSubset const &

selection

)

Returns the Rosetta Numbering corresponding to the selected residues.

References protocols::mpi_refinement::distance(), and core::sequence::end.

Referenced by protocols::docking::EnsureExclusivelySharedJumpMover::apply(), protocols::carbohydrates::GlycanTreeMinMover::apply(), protocols::carbohydrates::LinkageConformerMover::apply(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::apply(), protocols::protein_mpnn::ProteinMPNNMover::apply(), protocols::simple_moves::BBDihedralSamplerMover::apply(), core::select::jump_selector::JumpForResidue::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), protocols::task_operations::ResfileCommandOperation::apply(), protocols::task_operations::SequenceMotifTaskOperation::apply(), protocols::fold_from_loops::utils::Nub::assign_disulfides(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds(), protocols::pose_creation::MergePDBMover::determine_overlap(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::find_labels2(), protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects(), protocols::protein_mpnn::ProteinMPNNMover::residue_selectors_to_indices(), core::select::jump_selector::JumpSelector::selection_jumps(), core::select::residue_selector::ResidueSelector::selection_positions(), protocols::simple_moves::BBDihedralSamplerMover::setup_all_bb_residues(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::show_cutpoints(), and protocols::protein_mpnn::ProteinMPNNMover::validate_residue_selectors().

set_pose_secstruct()

void core::select::residue_selector::set_pose_secstruct

(

std::string const &

ss

)

TR()

static basic::Tracer core::select::residue_selector::TR ( "core.select.residue_selector.CachedResidueSubset"  )

static

Referenced by core::select::residue_selector::SecondaryStructureSelector::add_overlap(), core::select::residue_selector::DensityFitResidueSelector::apply(), core::select::residue_selector::BFactorSelector::apply(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::BlockSelector::apply(), core::select::residue_selector::BondedResidueSelector::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), core::select::residue_selector::GlycanLayerSelector::apply(), core::select::residue_selector::GlycanPositionSelector::apply(), core::select::residue_selector::LayerSelector::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), core::select::residue_selector::RandomGlycanFoliageSelector::apply(), core::select::residue_selector::ResidueIndexSelector::apply(), core::select::residue_selector::ResidueInSequenceMotifSelector::apply(), core::select::residue_selector::ResiduePDBInfoHasLabelSelector::apply(), core::select::residue_selector::ResidueSpanSelector::apply(), core::select::residue_selector::ScoreTermValueBasedSelector::apply(), core::select::residue_selector::SecondaryStructureSelector::apply(), core::select::residue_selector::SliceResidueSelector::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), core::select::residue_selector::SecondaryStructureSelector::fix_secstruct_definition(), get_cyclic_pose_residue_mappings_from_selectors(), get_residue_selector(), core::select::residue_selector::SecondaryStructureSelector::get_secstruct(), core::select::residue_selector::BinSelector::initialize_and_check(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), core::select::residue_selector::ResidueIndexSelector::parse_my_tag(), core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(), core::select::residue_selector::RandomResidueSelector::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), core::select::residue_selector::BFactorSelector::parse_my_tag(), core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(), core::select::residue_selector::LogicResidueSelector::parse_my_tag(), core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag(), core::select::residue_selector::PhiSelector::parse_my_tag(), parse_residue_selector(), core::select::residue_selector::SSElementSelector::parse_ss(), core::select::residue_selector::LayerSelector::set_angle_exponent(), core::select::residue_selector::LayerSelector::set_angle_shift_factor(), core::select::residue_selector::LayerSelector::set_ball_radius(), core::select::residue_selector::LayerSelector::set_cutoffs(), core::select::residue_selector::LayerSelector::set_dist_exponent(), core::select::residue_selector::LayerSelector::set_layers(), core::select::residue_selector::LayerSelector::set_sc_neighbor_denominator(), core::select::residue_selector::LayerSelector::set_sc_neighbor_dist_midpoint(), core::select::residue_selector::LayerSelector::set_use_sc_neighbors(), core::select::residue_selector::SliceResidueSelector::show_selection_logic(), and core::select::residue_selector::RandomResidueSelector::subset_from_randomized_vector().

unselection_positions()

utility::vector1< core::Size > core::select::residue_selector::unselection_positions

(

ResidueSubset const &

selection

)

Returns the Rosetta Numbering corresponding to the unselected residues.

References protocols::mpi_refinement::distance(), and core::sequence::end.

Referenced by protocols::docking::EnsureExclusivelySharedJumpMover::apply().

xsd_type_definition_w_attributes()

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

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

References complex_type_name_for_residue_selector().

Referenced by protocols::residue_selectors::StoredResidueSubsetSelector::provide_xml_schema(), protocols::residue_selectors::TaskSelector::provide_xml_schema(), core::select::residue_selector::AsymmetricUnitSelector::provide_xml_schema(), core::select::residue_selector::BFactorSelector::provide_xml_schema(), core::select::residue_selector::BinSelector::provide_xml_schema(), core::select::residue_selector::BlockSelector::provide_xml_schema(), core::select::residue_selector::ChainSelector::provide_xml_schema(), core::select::residue_selector::ConfluentSelector::provide_xml_schema(), core::select::residue_selector::DensityFitResidueSelector::provide_xml_schema(), core::select::residue_selector::FalseResidueSelector::provide_xml_schema(), core::select::residue_selector::FractionSelector::provide_xml_schema(), core::select::residue_selector::GlycanLayerSelector::provide_xml_schema(), core::select::residue_selector::GlycanPositionSelector::provide_xml_schema(), core::select::residue_selector::GlycanResidueSelector::provide_xml_schema(), core::select::residue_selector::GlycanSequonsSelector::provide_xml_schema(), core::select::residue_selector::JumpDownstreamSelector::provide_xml_schema(), core::select::residue_selector::JumpUpstreamSelector::provide_xml_schema(), core::select::residue_selector::LayerSelector::provide_xml_schema(), core::select::residue_selector::LogicResidueSelector::provide_xml_schema(), core::select::residue_selector::NumNeighborsSelector::provide_xml_schema(), core::select::residue_selector::PhiSelector::provide_xml_schema(), core::select::residue_selector::ResidueIndexSelector::provide_xml_schema(), core::select::residue_selector::ResidueInMembraneSelector::provide_xml_schema(), core::select::residue_selector::ResidueInSequenceMotifSelector::provide_xml_schema(), core::select::residue_selector::ResidueNameSelector::provide_xml_schema(), core::select::residue_selector::ResiduePDBInfoHasLabelSelector::provide_xml_schema(), core::select::residue_selector::ResiduePropertySelector::provide_xml_schema(), core::select::residue_selector::ResidueSpanSelector::provide_xml_schema(), core::select::residue_selector::SecondaryStructureSelector::provide_xml_schema(), core::select::residue_selector::SSElementSelector::provide_xml_schema(), core::select::residue_selector::TrueResidueSelector::provide_xml_schema(), core::select::residue_selector::VirtualResidueSelector::provide_xml_schema(), protocols::cyclic_peptide::RamaMutationSelector::provide_xml_schema(), protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::provide_xml_schema(), protocols::fold_from_loops::selectors::ConstraintResidueSelector::provide_xml_schema(), protocols::fold_from_loops::selectors::CutpointResidueSelector::provide_xml_schema(), protocols::fold_from_loops::selectors::ProteinResidueSelector::provide_xml_schema(), and protocols::hbnet::UnsatSelector::provide_xml_schema().

xsd_type_definition_w_attributes_and_optional_subselector()

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

Define the XML schema definition for a ResidueSelector that contains a single ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

References complex_type_name_for_residue_selector(), and core::select::residue_selector::ResidueSelectorFactory::residue_selector_xml_schema_group_name().

Referenced by core::select::residue_selector::ScoreTermValueBasedSelector::provide_xml_schema(), core::select::residue_selector::BondedResidueSelector::provide_xml_schema(), core::select::residue_selector::CloseContactResidueSelector::provide_xml_schema(), core::select::residue_selector::NeighborhoodResidueSelector::provide_xml_schema(), core::select::residue_selector::NotResidueSelector::provide_xml_schema(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema(), core::select::residue_selector::RandomGlycanFoliageSelector::provide_xml_schema(), core::select::residue_selector::RandomResidueSelector::provide_xml_schema(), core::select::residue_selector::SimpleMetricSelector::provide_xml_schema(), core::select::residue_selector::SliceResidueSelector::provide_xml_schema(), core::select::residue_selector::SymmetricalResidueSelector::provide_xml_schema(), protocols::residue_selectors::HBondSelector::provide_xml_schema(), protocols::residue_selectors::LigandMetalContactSelector::provide_xml_schema(), and protocols::residue_selectors::NativeSelector::provide_xml_schema().

xsd_type_definition_w_attributes_and_optional_subselectors() [1/2]

void core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselectors	(	utility::tag::XMLSchemaDefinition &	xsd,
		std::string const &	rs_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 ResidueSelector that contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

References complex_type_name_for_residue_selector(), and core::select::residue_selector::ResidueSelectorFactory::residue_selector_xml_schema_group_name().

xsd_type_definition_w_attributes_and_optional_subselectors() [2/2]

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

Define the XML schema definition for a ResidueSelector that contains more than one ResidueSelector in its set of sub-elements (aka sub-tags) and may contain some number of attributes (aka options).

References complex_type_name_for_residue_selector(), and core::select::residue_selector::ResidueSelectorFactory::residue_selector_xml_schema_group_name().

Referenced by core::select::residue_selector::AndResidueSelector::provide_xml_schema(), core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema(), and core::select::residue_selector::OrResidueSelector::provide_xml_schema().