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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< AndResidueSelectorAndResidueSelectorOP
 
typedef utility::pointer::shared_ptr< AndResidueSelector const > AndResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< AsymmetricUnitSelectorAsymmetricUnitSelectorOP
 
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< BinSelectorBinSelectorOP
 
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< BondedResidueSelectorBondedResidueSelectorOP
 
typedef utility::pointer::shared_ptr< BondedResidueSelector const > BondedResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< CachedResidueSubsetCachedResidueSubsetOP
 
typedef utility::pointer::shared_ptr< CachedResidueSubset const > CachedResidueSubsetCOP
 
typedef utility::pointer::shared_ptr< ChainSelectorChainSelectorOP
 
typedef utility::pointer::shared_ptr< ChainSelector const > ChainSelectorCOP
 
typedef utility::pointer::shared_ptr< CloseContactResidueSelectorCloseContactResidueSelectorOP
 
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< DensityFitResidueSelectorDensityFitResidueSelectorOP
 
typedef utility::pointer::shared_ptr< DensityFitResidueSelector const > DensityFitResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< FalseResidueSelectorFalseResidueSelectorOP
 
typedef utility::pointer::shared_ptr< FalseResidueSelector const > FalseResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< FractionSelectorFractionSelectorOP
 
typedef utility::pointer::shared_ptr< FractionSelector const > FractionSelectorCOP
 
typedef utility::pointer::shared_ptr< GlycanLayerSelectorGlycanLayerSelectorOP
 
typedef utility::pointer::shared_ptr< GlycanLayerSelector const > GlycanLayerSelectorCOP
 
typedef utility::pointer::shared_ptr< GlycanPositionSelectorGlycanPositionSelectorOP
 
typedef utility::pointer::shared_ptr< GlycanPositionSelector const > GlycanPositionSelectorCOP
 
typedef utility::pointer::shared_ptr< GlycanResidueSelectorGlycanResidueSelectorOP
 
typedef utility::pointer::shared_ptr< GlycanResidueSelector const > GlycanResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< GlycanSequonsSelectorGlycanSequonsSelectorOP
 
typedef utility::pointer::shared_ptr< GlycanSequonsSelector const > GlycanSequonsSelectorCOP
 
typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelectorInterGroupInterfaceByVectorSelectorOP
 
typedef utility::pointer::shared_ptr< InterGroupInterfaceByVectorSelector const > InterGroupInterfaceByVectorSelectorCOP
 
typedef utility::pointer::shared_ptr< JumpDownstreamSelectorJumpDownstreamSelectorOP
 
typedef utility::pointer::shared_ptr< JumpDownstreamSelector const > JumpDownstreamSelectorCOP
 
typedef utility::pointer::shared_ptr< JumpUpstreamSelectorJumpUpstreamSelectorOP
 
typedef utility::pointer::shared_ptr< JumpUpstreamSelector const > JumpUpstreamSelectorCOP
 
typedef utility::pointer::shared_ptr< LayerSelectorLayerSelectorOP
 
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< NeighborhoodResidueSelectorNeighborhoodResidueSelectorOP
 
typedef utility::pointer::shared_ptr< NeighborhoodResidueSelector const > NeighborhoodResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< NotResidueSelectorNotResidueSelectorOP
 
typedef utility::pointer::shared_ptr< NotResidueSelector const > NotResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< NumNeighborsSelectorNumNeighborsSelectorOP
 
typedef utility::pointer::shared_ptr< NumNeighborsSelector const > NumNeighborsSelectorCOP
 
typedef utility::pointer::shared_ptr< OrResidueSelectorOrResidueSelectorOP
 
typedef utility::pointer::shared_ptr< OrResidueSelector const > OrResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< PhiSelectorPhiSelectorOP
 
typedef utility::pointer::shared_ptr< PhiSelector const > PhiSelectorCOP
 
typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelectorPrimarySequenceNeighborhoodSelectorOP
 
typedef utility::pointer::shared_ptr< PrimarySequenceNeighborhoodSelector const > PrimarySequenceNeighborhoodSelectorCOP
 
typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelectorRandomGlycanFoliageSelectorOP
 
typedef utility::pointer::shared_ptr< RandomGlycanFoliageSelector const > RandomGlycanFoliageSelectorCOP
 
typedef utility::pointer::shared_ptr< RandomResidueSelectorRandomResidueSelectorOP
 
typedef utility::pointer::shared_ptr< RandomResidueSelector const > RandomResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueIndexSelectorResidueIndexSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueIndexSelector const > ResidueIndexSelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueInMembraneSelectorResidueInMembraneSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueInMembraneSelector const > ResidueInMembraneSelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelectorResidueInSequenceMotifSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueInSequenceMotifSelector const > ResidueInSequenceMotifSelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueNameSelectorResidueNameSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueNameSelector const > ResidueNameSelectorCOP
 
typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelectorResiduePDBInfoHasLabelSelectorOP
 
typedef utility::pointer::shared_ptr< ResiduePDBInfoHasLabelSelector const > ResiduePDBInfoHasLabelSelectorCOP
 
typedef utility::pointer::shared_ptr< ResiduePropertySelectorResiduePropertySelectorOP
 
typedef utility::pointer::shared_ptr< ResiduePropertySelector const > ResiduePropertySelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueRangesResidueRangesOP
 
typedef utility::pointer::shared_ptr< ResidueRanges const > ResidueRangesCOP
 
typedef utility::pointer::weak_ptr< ResidueRangesResidueRangesAP
 
typedef utility::pointer::weak_ptr< ResidueRanges const > ResidueRangesCAP
 
typedef utility::vector1< bool > ResidueSubset
 
typedef utility::pointer::shared_ptr< ResidueSubsetResidueSubsetOP
 
typedef utility::pointer::shared_ptr< ResidueSubset const > ResidueSubsetCOP
 
typedef utility::pointer::weak_ptr< ResidueSubsetResidueSubsetAP
 
typedef utility::pointer::weak_ptr< ResidueSubset const > ResidueSubsetCAP
 
typedef utility::pointer::shared_ptr< ResidueSelectorResidueSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueSelector const > ResidueSelectorCOP
 
typedef utility::pointer::weak_ptr< ResidueSelectorResidueSelectorAP
 
typedef utility::pointer::weak_ptr< ResidueSelector const > ResidueSelectorCAP
 
typedef utility::pointer::shared_ptr< ResidueSelectorCreatorResidueSelectorCreatorOP
 
typedef utility::pointer::shared_ptr< ResidueSelectorCreator const > ResidueSelectorCreatorCOP
 
typedef utility::pointer::shared_ptr< ResidueSpanSelectorResidueSpanSelectorOP
 
typedef utility::pointer::shared_ptr< ResidueSpanSelector const > ResidueSpanSelectorCOP
 
typedef utility::pointer::shared_ptr< ResidueVectorResidueVectorOP
 
typedef utility::pointer::shared_ptr< ResidueVector const > ResidueVectorCOP
 
typedef utility::pointer::weak_ptr< ResidueVectorResidueVectorAP
 
typedef utility::pointer::weak_ptr< ResidueVector const > ResidueVectorCAP
 
typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelectorReturnResidueSubsetSelectorOP
 
typedef utility::pointer::shared_ptr< ReturnResidueSubsetSelector const > ReturnResidueSubsetSelectorCOP
 
typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelectorScoreTermValueBasedSelectorOP
 
typedef utility::pointer::shared_ptr< ScoreTermValueBasedSelector const > ScoreTermValueBasedSelectorCOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureSelectorSecondaryStructureSelectorOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureSelector const > SecondaryStructureSelectorCOP
 
typedef utility::pointer::shared_ptr< SelectorLogicParserSelectorLogicParserOP
 
typedef utility::pointer::shared_ptr< SelectorLogicParser const > SelectorLogicParserCOP
 
typedef utility::pointer::shared_ptr< SimpleMetricSelectorSimpleMetricSelectorOP
 
typedef utility::pointer::shared_ptr< SimpleMetricSelector const > SimpleMetricSelectorCOP
 
typedef utility::pointer::shared_ptr< SliceResidueSelectorSliceResidueSelectorOP
 
typedef utility::pointer::shared_ptr< SliceResidueSelector const > SliceResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< SSElementSelectorSSElementSelectorOP
 
typedef utility::pointer::shared_ptr< SSElementSelector const > SSElementSelectorCOP
 
typedef utility::pointer::shared_ptr< SymmetricalResidueSelectorSymmetricalResidueSelectorOP
 
typedef utility::pointer::shared_ptr< SymmetricalResidueSelector const > SymmetricalResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< TrueResidueSelectorTrueResidueSelectorOP
 
typedef utility::pointer::shared_ptr< TrueResidueSelector const > TrueResidueSelectorCOP
 
typedef utility::pointer::shared_ptr< VirtualResidueSelectorVirtualResidueSelectorOP
 
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_logiclogic_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::Sizeget_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< ResidueSelectorOPget_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::Sizeselection_positions (ResidueSubset const &selection)
 Returns the Rosetta Numbering corresponding to the selected residues. More...
 
utility::vector1< core::Sizeunselection_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::ResidueSubsetidentify_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

◆ AsymmetricUnitSelectorCOP

◆ 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

◆ BondedResidueSelectorOP

◆ CachedResidueSubsetCOP

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

◆ 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

◆ 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

◆ DensityFitResidueSelectorOP

◆ FalseResidueSelectorCOP

◆ FalseResidueSelectorOP

◆ FractionSelectorCOP

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

◆ FractionSelectorOP

◆ GlycanLayerSelectorCOP

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

◆ GlycanLayerSelectorOP

◆ GlycanPositionSelectorCOP

◆ GlycanPositionSelectorOP

◆ GlycanResidueSelectorCOP

◆ GlycanResidueSelectorOP

◆ GlycanSequonsSelectorCOP

◆ GlycanSequonsSelectorOP

◆ InterGroupInterfaceByVectorSelectorCOP

◆ InterGroupInterfaceByVectorSelectorOP

◆ JumpDownstreamSelectorCOP

◆ JumpDownstreamSelectorOP

◆ JumpUpstreamSelectorCOP

◆ 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

◆ NeighborhoodResidueSelectorOP

◆ NotResidueSelectorCOP

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

◆ NotResidueSelectorOP

◆ NumNeighborsSelectorCOP

◆ NumNeighborsSelectorOP

◆ OrResidueSelectorCOP

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

◆ 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

◆ PrimarySequenceNeighborhoodSelectorOP

◆ RandomGlycanFoliageSelectorCOP

◆ RandomGlycanFoliageSelectorOP

◆ RandomResidueSelectorCOP

◆ RandomResidueSelectorOP

◆ ResidueIndexSelectorCOP

◆ ResidueIndexSelectorOP

◆ ResidueInMembraneSelectorCOP

◆ ResidueInMembraneSelectorOP

◆ ResidueInSequenceMotifSelectorCOP

◆ ResidueInSequenceMotifSelectorOP

◆ ResidueNameSelectorCOP

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

◆ ResidueNameSelectorOP

◆ ResiduePDBInfoHasLabelSelectorCOP

◆ ResiduePDBInfoHasLabelSelectorOP

◆ ResiduePropertySelectorCOP

◆ 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

◆ 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

◆ 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

◆ 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

◆ ReturnResidueSubsetSelectorOP

◆ ScoreTermValueBasedSelectorCOP

◆ ScoreTermValueBasedSelectorOP

◆ SecondaryStructureSelectorCOP

◆ SecondaryStructureSelectorOP

◆ SelectorLogicParserCOP

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

◆ SelectorLogicParserOP

◆ SimpleMetricSelectorCOP

◆ SimpleMetricSelectorOP

◆ SliceResidueSelectorCOP

◆ SliceResidueSelectorOP

◆ SSElementSelectorCOP

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

◆ SSElementSelectorOP

◆ SymmetricalResidueSelectorCOP

◆ SymmetricalResidueSelectorOP

◆ TrueResidueSelectorCOP

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

◆ TrueResidueSelectorOP

◆ VirtualResidueSelectorCOP

◆ VirtualResidueSelectorOP

Enumeration Type Documentation

◆ basic_selection_logic

Enumerator
and_logic 
or_logic 

Function Documentation

◆ all_false_selection()

bool core::select::residue_selector::all_false_selection ( ResidueSubset const &  selection)

◆ 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 
)

◆ 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 
)

◆ 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)

◆ 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 
)

◆ 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_Exceptionif 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)

◆ has_option()

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

◆ 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

◆ 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 ( )

◆ regex_usable()

bool core::select::residue_selector::regex_usable ( )

◆ 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 
)

◆ 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 
)

◆ 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 
)