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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  AndResidueSelectorCreator
 
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  BinSelector
 A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin). More...
 
class  BinSelectorCreator
 
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  BondedResidueSelectorCreator
 
class  CachedResidueSubset
 
class  ChainSelector
 
class  ChainSelectorCreator
 
class  CloseContactResidueSelector
 A class that finds the neighboring residues for a particular residue by looking at atom-atom distances. More...
 
class  CloseContactResidueSelectorCreator
 
class  DensityFitResidueSelector
 Selects residues that are considered 'error' region with respect to the density resolution. More...
 
class  DensityFitResidueSelectorCreator
 
class  FalseResidueSelector
 
class  FalseResidueSelectorCreator
 
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  GlycanPositionSelectorCreator
 
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  GlycanResidueSelectorCreator
 
class  GlycanSequonsSelector
 Find glycosylation sequons in pose 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  GlycanSequonsSelectorCreator
 
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  InterGroupInterfaceByVectorSelectorCreator
 
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  JumpDownstreamSelectorCreator
 
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  JumpUpstreamSelectorCreator
 
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  LayerSelectorCreator
 
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  NeighborhoodResidueSelectorCreator
 
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  NotResidueSelectorCreator
 
class  NumNeighborsSelector
 
class  NumNeighborsSelectorCreator
 
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  OrResidueSelectorCreator
 
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  PhiSelectorCreator
 
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  RandomGlycanFoliageSelectorCreator
 
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  RandomResidueSelectorCreator
 
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  ResidueIndexSelectorCreator
 
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  ResidueInMembraneSelectorCreator
 
class  ResidueInSequenceMotifSelector
 Select residues by motif search 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  ResidueInSequenceMotifSelectorCreator
 
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  ResidueNameSelectorCreator
 
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  ResiduePDBInfoHasLabelSelectorCreator
 
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  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  ResidueSpanSelectorCreator
 
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  ScoreTermValueBasedSelectorCreator
 
class  SecondaryStructureSelector
 
class  SecondaryStructureSelectorCreator
 
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  SliceResidueSelector
 The SliceResidueSelector allows slicing of the returned values of other residue selectors. More...
 
class  SliceResidueSelectorCreator
 
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  SSElementSelectorCreator
 
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  TrueResidueSelectorCreator
 

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
 
typedef
utility::pointer::shared_ptr
< BinSelector
BinSelectorOP
 
typedef
utility::pointer::shared_ptr
< BinSelector const > 
BinSelectorCOP
 
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
 
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
< 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
 
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< boolResidueSubset
 
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
< 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
 

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)
 
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::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::Sizeselection_positions (ResidueSubset const &selection)
 Returns the Rosetta Numbering corresponding to the selected 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...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AndResidueSelector const > core::select::residue_selector::AndResidueSelectorCOP
typedef utility::pointer::shared_ptr< BinSelector const > core::select::residue_selector::BinSelectorCOP
typedef utility::pointer::shared_ptr< BinSelector > core::select::residue_selector::BinSelectorOP
typedef utility::pointer::shared_ptr< CachedResidueSubset const > core::select::residue_selector::CachedResidueSubsetCOP
typedef utility::pointer::shared_ptr< ChainSelector const > core::select::residue_selector::ChainSelectorCOP
typedef utility::pointer::shared_ptr< ChainSelector > core::select::residue_selector::ChainSelectorOP
typedef utility::pointer::shared_ptr< GlycanLayerSelector const > core::select::residue_selector::GlycanLayerSelectorCOP
typedef utility::pointer::shared_ptr< LayerSelector const > core::select::residue_selector::LayerSelectorCOP
typedef utility::pointer::shared_ptr< LayerSelector > core::select::residue_selector::LayerSelectorOP
typedef utility::pointer::shared_ptr< NotResidueSelector const > core::select::residue_selector::NotResidueSelectorCOP
typedef utility::pointer::shared_ptr< OrResidueSelector const > core::select::residue_selector::OrResidueSelectorCOP
typedef utility::pointer::shared_ptr< PhiSelector const > core::select::residue_selector::PhiSelectorCOP
typedef utility::pointer::shared_ptr< PhiSelector > core::select::residue_selector::PhiSelectorOP
typedef utility::pointer::shared_ptr< ResidueNameSelector const > core::select::residue_selector::ResidueNameSelectorCOP
typedef utility::pointer::weak_ptr< ResidueRanges > core::select::residue_selector::ResidueRangesAP
typedef utility::pointer::weak_ptr< ResidueRanges const > core::select::residue_selector::ResidueRangesCAP
typedef utility::pointer::shared_ptr< ResidueRanges const > core::select::residue_selector::ResidueRangesCOP
typedef utility::pointer::shared_ptr< ResidueRanges > core::select::residue_selector::ResidueRangesOP
typedef utility::pointer::weak_ptr< ResidueSelector const > core::select::residue_selector::ResidueSelectorCAP
typedef utility::pointer::shared_ptr< ResidueSelector const > core::select::residue_selector::ResidueSelectorCOP
typedef utility::pointer::shared_ptr< ResidueSelector > core::select::residue_selector::ResidueSelectorOP
typedef utility::pointer::shared_ptr< ResidueSpanSelector const > core::select::residue_selector::ResidueSpanSelectorCOP
typedef utility::pointer::weak_ptr< ResidueSubset > core::select::residue_selector::ResidueSubsetAP
typedef utility::pointer::weak_ptr< ResidueSubset const > core::select::residue_selector::ResidueSubsetCAP
typedef utility::pointer::shared_ptr< ResidueSubset const > core::select::residue_selector::ResidueSubsetCOP
typedef utility::pointer::shared_ptr< ResidueSubset > core::select::residue_selector::ResidueSubsetOP
typedef utility::pointer::weak_ptr< ResidueVector > core::select::residue_selector::ResidueVectorAP
typedef utility::pointer::weak_ptr< ResidueVector const > core::select::residue_selector::ResidueVectorCAP
typedef utility::pointer::shared_ptr< ResidueVector const > core::select::residue_selector::ResidueVectorCOP
typedef utility::pointer::shared_ptr< ResidueVector > core::select::residue_selector::ResidueVectorOP
typedef utility::pointer::shared_ptr< SelectorLogicParser const > core::select::residue_selector::SelectorLogicParserCOP
typedef utility::pointer::shared_ptr< SSElementSelector const > core::select::residue_selector::SSElementSelectorCOP
typedef utility::pointer::shared_ptr< TrueResidueSelector const > core::select::residue_selector::TrueResidueSelectorCOP

Enumeration Type Documentation

Enumerator
and_logic 
or_logic 

Function Documentation

bool core::select::residue_selector::all_false_selection ( ResidueSubset const &  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.

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.

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().

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().

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::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements(), protocols::fold_from_loops::utils::Nub::provide_xml_definition(), protocols::simple_moves::AddResidueLabelMoverCreator::provide_xml_schema(), protocols::denovo_design::architects::PoseArchitect::provide_xml_schema(), protocols::constraint_generator::MetalContactsConstraintGenerator::provide_xml_schema(), protocols::simple_filters::ResidueSelectionDistanceFilter::provide_xml_schema(), protocols::simple_moves::FoldTreeFromMotif::provide_xml_schema(), protocols::task_operations::ReadResfileFromDB::provide_xml_schema(), protocols::cyclic_peptide::DeclareBond::provide_xml_schema(), protocols::task_operations::ConservativeDesignOperation::provide_xml_schema(), core::select::residue_selector::ScoreTermValueBasedSelector::provide_xml_schema(), protocols::simple_moves::SetupMetalsMover::provide_xml_schema(), protocols::residue_selectors::StoreResidueSubsetMover::provide_xml_schema(), protocols::score_filters::GeometryFilter::provide_xml_schema(), protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric::provide_xml_schema(), protocols::simple_moves::ModifyVariantTypeMover::provide_xml_schema(), protocols::cyclic_peptide::FlipChiralityMover::provide_xml_schema(), protocols::simple_filters::AtomicDistanceFilter::provide_xml_schema(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::provide_xml_schema(), core::select::residue_selector::SymmetricalResidueSelector::provide_xml_schema(), protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema(), core::select::residue_selector::RandomResidueSelector::provide_xml_schema(), core::select::residue_selector::NotResidueSelector::provide_xml_schema(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::provide_xml_schema(), core::select::residue_selector::OrResidueSelector::provide_xml_schema(), core::select::residue_selector::AndResidueSelector::provide_xml_schema(), protocols::pose_creation::MakePolyXMover::provide_xml_schema(), protocols::residue_selectors::NativeSelector::provide_xml_schema(), core::select::residue_selector::BondedResidueSelector::provide_xml_schema(), protocols::task_operations::ResfileCommandOperation::provide_xml_schema(), protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema(), protocols::simple_filters::ResidueIEFilter::provide_xml_schema(), protocols::residue_selectors::LigandMetalContactSelector::provide_xml_schema(), protocols::abinitio::abscript::AbscriptLoopCloserCM::provide_xml_schema(), protocols::abinitio::abscript::FragmentJumpCM::provide_xml_schema(), protocols::simple_filters::BuriedUnsatHbondFilter::provide_xml_schema(), protocols::constraint_generator::CoordinateConstraintGenerator::provide_xml_schema(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::provide_xml_schema(), protocols::residue_selectors::HBondSelector::provide_xml_schema(), protocols::denovo_design::filters::PreProlineFilter::provide_xml_schema(), core::select::residue_selector::SliceResidueSelector::provide_xml_schema(), core::pack::task::operation::OperateOnResidueSubset::provide_xml_schema(), core::simple_metrics::metrics::SelectedResidueCountMetric::provide_xml_schema(), protocols::denovo_design::filters::CavityVolumeFilter::provide_xml_schema(), protocols::abinitio::abscript::RigidChunkCM::provide_xml_schema(), core::select::residue_selector::CloseContactResidueSelector::provide_xml_schema(), protocols::aa_composition::AddHelixSequenceConstraintsMover::provide_xml_schema(), protocols::aa_composition::AddNetChargeConstraintMover::provide_xml_schema(), protocols::environment::claims::XYZClaim::provide_xml_schema(), protocols::task_operations::SequenceMotifTaskOperation::provide_xml_schema(), protocols::backbone_moves::RandomizeBBByRamaPrePro::provide_xml_schema(), protocols::aa_composition::AddCompositionConstraintMover::provide_xml_schema(), protocols::denovo_design::filters::SSShapeComplementarityFilter::provide_xml_schema(), protocols::aa_composition::AddMHCEpitopeConstraintMover::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_xml_schema(), protocols::constraint_generator::AtomPairConstraintGenerator::provide_xml_schema(), protocols::environment::claims::TorsionClaim::provide_xml_schema(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::provide_xml_schema(), core::select::residue_selector::InterGroupInterfaceByVectorSelector::provide_xml_schema(), protocols::rna::movers::ERRASER2Protocol::provide_xml_schema(), core::simple_metrics::metrics::SecondaryStructureMetric::provide_xml_schema(), core::select::residue_selector::RandomGlycanFoliageSelector::provide_xml_schema(), protocols::pose_creation::SliceToMiniProteinMover::provide_xml_schema(), protocols::cyclic_peptide::TryDisulfPermutations::provide_xml_schema(), protocols::match::MatcherMover::provide_xml_schema(), protocols::simple_filters::SSElementLengthFilter::provide_xml_schema(), protocols::switches::GraftSwitchMover::provide_xml_schema(), core::select::residue_selector::NeighborhoodResidueSelector::provide_xml_schema(), core::simple_metrics::metrics::SelectedResiduesMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::provide_xml_schema(), protocols::simple_filters::HolesFilter::provide_xml_schema(), core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema(), protocols::fldsgn::filters::SecondaryStructureFilter::provide_xml_schema(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::provide_xml_schema(), protocols::simple_moves::MutateResidue::provide_xml_schema(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::HbondMetric::provide_xml_schema(), core::simple_metrics::metrics::DihedralDistanceMetric::provide_xml_schema(), core::simple_metrics::metrics::SequenceMetric::provide_xml_schema(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema(), core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::provide_xml_schema(), protocols::sewing::hashing::AlignmentFileGeneratorMover::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), protocols::calc_taskop_movers::CreateSequenceMotifMover::provide_xml_schema(), protocols::simple_filters::ResidueCountFilter::provide_xml_schema(), protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::provide_xml_schema(), core::pack::task::residue_selector::ClashBasedShellSelector::provide_xml_schema_attributes(), and core::pack::task::operation::ReadResfile::xml_schema_attributes().

void core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name ( utility::tag::AttributeList &  attlist,
std::string const &  documentation_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::OperateOnResidueSubset::provide_xml_schema(), and core::pack::task::operation::DesignRestrictions::provide_xml_schema().

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 
)
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().

core::Size core::select::residue_selector::count_selected ( ResidueSubset const &  selection)
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>

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

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

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>

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

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

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::fold_from_loops::movers::AlignByResidueSelectorMover::parse_my_tag(), protocols::symmetry::SetupForSequenceSymmetryMover::parse_my_tag(), protocols::abinitio::abscript::FragmentCM::parse_my_tag(), core::select::residue_selector::BondedResidueSelector::parse_my_tag(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(), core::select::residue_selector::RandomResidueSelector::parse_my_tag(), core::select::residue_selector::NotResidueSelector::parse_my_tag(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::parse_my_tag(), protocols::denovo_design::filters::CavityVolumeFilter::parse_my_tag(), core::select::residue_selector::OrResidueSelector::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), core::select::residue_selector::AndResidueSelector::parse_my_tag(), protocols::cyclic_peptide::TryDisulfPermutations::parse_my_tag(), protocols::residue_selectors::NativeSelector::parse_my_tag(), protocols::abinitio::abscript::FragmentJumpCM::parse_my_tag(), protocols::multistage_rosetta_scripts::cluster::metrics::SequenceMetric::parse_my_tag(), protocols::aa_composition::AddMHCEpitopeConstraintMover::parse_my_tag(), protocols::aa_composition::AddNetChargeConstraintMover::parse_my_tag(), protocols::residue_selectors::LigandMetalContactSelector::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), core::select::residue_selector::InterGroupInterfaceByVectorSelector::parse_my_tag(), protocols::aa_composition::AddCompositionConstraintMover::parse_my_tag(), protocols::simple_filters::BuriedUnsatHbondFilter::parse_my_tag(), protocols::residue_selectors::HBondSelector::parse_my_tag(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::parse_my_tag(), protocols::match::MatcherMover::parse_my_tag(), protocols::switches::GraftSwitchMover::parse_my_tag(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::parse_my_tag(), core::select::residue_selector::SliceResidueSelector::parse_my_tag(), core::select::residue_selector::CloseContactResidueSelector::parse_my_tag(), protocols::rna::movers::ERRASER2Protocol::parse_my_tag(), protocols::simple_filters::ContactMolecularSurfaceFilter::parse_my_tag(), protocols::fldsgn::filters::SecondaryStructureCountFilter::parse_my_tag(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::parse_my_tag(), protocols::simple_filters::HolesFilter::parse_my_tag(), protocols::simple_filters::ShapeComplementarityFilter::parse_my_tag(), core::select::residue_selector::NeighborhoodResidueSelector::parse_my_tag(), protocols::sewing::movers::AppendAssemblyMover::parse_my_tag(), protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_my_tag(), protocols::hbnet::HBNet::parse_my_tag(), parse_residue_selector(), protocols::denovo_design::movers::parse_residue_selectors(), protocols::jd3::parse_single_residue_selector(), protocols::constraint_generator::DistanceConstraintGenerator::parse_tag(), protocols::task_operations::ConservativeDesignOperation::parse_tag(), protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag(), protocols::task_operations::ReadResfileFromDB::parse_tag(), core::pack::task::operation::OperateOnResidueSubset::parse_tag(), protocols::constraint_generator::HydrogenBondConstraintGenerator::parse_tag(), protocols::constraint_generator::MetalContactsConstraintGenerator::parse_tag(), core::pack::task::operation::ReadResfile::parse_tag(), protocols::environment::claims::TorsionClaim::TorsionClaim(), and protocols::environment::claims::XYZClaim::XYZClaim().

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.

bool core::select::residue_selector::has_any_true_selection ( ResidueSubset const &  selection)
static const std::map< std::string, basic_selection_logic > core::select::residue_selector::logic_map ( {{"or_logic", or_logic},{"and_logic", and_logic}}  )
static
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().

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

Combine two residue subsets with OR logic.

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::cyclic_peptide::DeclareBond::parse_my_tag(), protocols::simple_moves::FoldTreeFromMotif::parse_my_tag(), protocols::simple_moves::AddResidueLabelMover::parse_my_tag(), protocols::simple_filters::ResidueSelectionDistanceFilter::parse_my_tag(), protocols::cyclic_peptide::PeptideCyclizeMover::parse_my_tag(), protocols::denovo_design::filters::PreProlineFilter::parse_my_tag(), protocols::residue_selectors::StoreResidueSubsetMover::parse_my_tag(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::parse_my_tag(), protocols::fold_from_loops::movers::ReleaseConstraintFromResidueMover::parse_my_tag(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::cyclic_peptide::FlipChiralityMover::parse_my_tag(), protocols::score_filters::GeometryFilter::parse_my_tag(), protocols::simple_filters::AtomicDistanceFilter::parse_my_tag(), protocols::simple_moves::SetupMetalsMover::parse_my_tag(), protocols::cyclic_peptide::PeptideStubMover::parse_my_tag(), protocols::denovo_design::filters::SSShapeComplementarityFilter::parse_my_tag(), protocols::simple_moves::StructProfileMover::parse_my_tag(), protocols::simple_moves::MutateResidue::parse_my_tag(), protocols::pose_creation::MakePolyXMover::parse_my_tag(), protocols::cyclic_peptide::CycpepSymmetryFilter::parse_my_tag(), protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag(), protocols::backbone_moves::RandomizeBBByRamaPrePro::parse_my_tag(), protocols::aa_composition::AddHelixSequenceConstraintsMover::parse_my_tag(), protocols::minimization_packing::DisulfideOptimizationMover::parse_my_tag(), protocols::simple_filters::BuriedSurfaceAreaFilter::parse_my_tag(), protocols::carbohydrates::GlycanTreeMinMover::parse_my_tag(), protocols::simple_filters::LeastNativeLike9merFilter::parse_my_tag(), protocols::farnesyl::InstallFarnesylMover::parse_my_tag(), protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(), protocols::carbohydrates::TautomerizeAnomerMover::parse_my_tag(), protocols::minimization_packing::PertMinMover::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag(), core::simple_metrics::metrics::SelectedResidueCountMetric::parse_my_tag(), protocols::simple_moves::ConvertVirtualToRealMover::parse_my_tag(), protocols::simple_moves::ConvertRealToVirtualMover::parse_my_tag(), core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(), protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag(), core::select::residue_selector::RandomGlycanFoliageSelector::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::parse_my_tag(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::parse_my_tag(), protocols::simple_filters::SSElementLengthFilter::parse_my_tag(), core::simple_metrics::metrics::SecondaryStructureMetric::parse_my_tag(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::parse_my_tag(), core::simple_metrics::metrics::SasaMetric::parse_my_tag(), core::simple_metrics::metrics::SequenceSimilarityMetric::parse_my_tag(), protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::parse_my_tag(), core::select::movemap::MoveMapFactory::parse_my_tag(), core::simple_metrics::metrics::SelectedResiduesMetric::parse_my_tag(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::parse_my_tag(), protocols::cyclic_peptide::CrosslinkerMover::parse_my_tag(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::parse_my_tag(), core::simple_metrics::metrics::TotalEnergyMetric::parse_my_tag(), core::simple_metrics::per_residue_metrics::HbondMetric::parse_my_tag(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::parse_my_tag(), core::simple_metrics::metrics::DihedralDistanceMetric::parse_my_tag(), protocols::carbohydrates::LinkageConformerMover::parse_my_tag(), core::simple_metrics::metrics::SequenceMetric::parse_my_tag(), protocols::calc_taskop_movers::CreateSequenceMotifMover::parse_my_tag(), core::simple_metrics::metrics::InteractionEnergyMetric::parse_my_tag(), protocols::carbohydrates::SimpleGlycosylateMover::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::parse_my_tag(), core::pack::task::residue_selector::ClashBasedShellSelector::parse_my_tag(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::parse_my_tag(), core::simple_metrics::metrics::RMSDMetric::parse_my_tag(), protocols::carbohydrates::GlycanSampler::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::parse_my_tag(), protocols::carbohydrates::GlycanTreeModeler::parse_my_tag(), protocols::fold_from_loops::NubInitioMover::parse_my_tag(), core::simple_metrics::PerResidueStringMetric::parse_per_residue_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), protocols::task_operations::ResfileCommandOperation::parse_tag(), protocols::denovo_design::architects::PoseArchitect::parse_tag(), protocols::constraint_generator::CoordinateConstraintGenerator::parse_tag(), protocols::constraint_generator::ResidueTypeConstraintGenerator::parse_tag(), protocols::task_operations::SequenceMotifTaskOperation::parse_tag(), protocols::constraint_generator::AtomPairConstraintGenerator::parse_tag(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::parse_tag(), protocols::constraint_generator::DihedralConstraintGenerator::parse_tag(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::fold_from_loops::utils::Nub::parse_tag(), and protocols::denovo_design::task_operations::ConsensusLoopDesignOperation::parse_tag().

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().

std::string core::select::residue_selector::parse_residue_selector_xsd_documentation ( )
bool core::select::residue_selector::regex_usable ( )
std::string core::select::residue_selector::represent_residue_selector ( ResidueSubset const &  selection,
std::string const &  is_true,
std::string const &  is_false 
)
utility::vector1< core::Size > core::select::residue_selector::selection_positions ( ResidueSubset const &  selection)
void core::select::residue_selector::set_pose_secstruct ( std::string const &  ss)
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::ScoreTermValueBasedSelector::apply(), core::select::residue_selector::SecondaryStructureSelector::apply(), core::select::residue_selector::BondedResidueSelector::apply(), core::select::residue_selector::ResiduePDBInfoHasLabelSelector::apply(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::apply(), core::select::residue_selector::SymmetricalResidueSelector::apply(), core::select::residue_selector::PhiSelector::apply(), core::select::residue_selector::BinSelector::apply(), core::select::residue_selector::LayerSelector::apply(), core::select::residue_selector::ResidueSpanSelector::apply(), core::select::residue_selector::ResidueIndexSelector::apply(), core::select::residue_selector::ResidueInSequenceMotifSelector::apply(), core::select::residue_selector::CloseContactResidueSelector::apply(), core::select::residue_selector::GlycanLayerSelector::apply(), core::select::residue_selector::SliceResidueSelector::apply(), core::select::residue_selector::DensityFitResidueSelector::apply(), core::select::residue_selector::RandomGlycanFoliageSelector::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::select::residue_selector::GlycanPositionSelector::apply(), core::select::residue_selector::SecondaryStructureSelector::fix_secstruct_definition(), get_residue_selector(), core::select::residue_selector::SecondaryStructureSelector::get_secstruct(), core::select::residue_selector::BinSelector::initialize_and_check(), core::select::residue_selector::BinSelector::initialize_from_file_contents_and_check(), core::select::residue_selector::ScoreTermValueBasedSelector::parse_my_tag(), core::select::residue_selector::PrimarySequenceNeighborhoodSelector::parse_my_tag(), core::select::residue_selector::SymmetricalResidueSelector::parse_my_tag(), core::select::residue_selector::RandomResidueSelector::parse_my_tag(), core::select::residue_selector::PhiSelector::parse_my_tag(), core::select::residue_selector::ResidueIndexSelector::parse_my_tag(), core::select::residue_selector::DensityFitResidueSelector::parse_my_tag(), core::select::residue_selector::NeighborhoodResidueSelector::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().

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

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 
)
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 
)
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().