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util.hh File Reference

Utility functions for the residue selector classes, primarily, in constructing XML-Schema type definitions. More...

#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <basic/datacache/DataMap.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/tag/XMLSchemaGeneration.fwd.hh>
#include <string>
#include <list>
#include <algorithm>
#include <map>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::select
 
 core::select::residue_selector
 

Functions

std::map< core::Size, core::Sizecore::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. More...
 
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)
 
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. More...
 
void core::select::residue_selector::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 core::select::residue_selector::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 core::select::residue_selector::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 core::select::residue_selector::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 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 More...
 
void core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name (utility::tag::AttributeList &attlist, std::string const &documentation_string)
 Companion function for parse_residue_selector. More...
 
void core::select::residue_selector::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 core::select::residue_selector::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 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 More...
 
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: More...
 
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: More...
 
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. More...
 
ResidueSubset core::select::residue_selector::OR_combine (ResidueSubset const &sele1, ResidueSubset const &sele2)
 Combine two residue subsets with OR logic. More...
 
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. More...
 
ResidueSubset core::select::residue_selector::AND_combine (ResidueSubset const &sele1, ResidueSubset const &sele2)
 Combine two residue ssubsets with OR logic. More...
 
bool core::select::residue_selector::all_false_selection (ResidueSubset const &selection)
 Returns True if all the positions in the ResidueSubset are False. More...
 
bool core::select::residue_selector::all_true_selection (ResidueSubset const &selection)
 Returns True if all the positions in the ResidueSubset are True. More...
 
bool core::select::residue_selector::has_any_false_selection (ResidueSubset const &selection)
 Returns True if at least one position in the ResidueSubset is False. More...
 
bool core::select::residue_selector::has_any_true_selection (ResidueSubset const &selection)
 Returns True if at least one position in the ResidueSubset is True. More...
 
core::Size core::select::residue_selector::count_selected (ResidueSubset const &selection)
 Returns the number of selected residues in the ResidueSubset. More...
 
utility::vector1< core::Sizecore::select::residue_selector::selection_positions (ResidueSubset const &selection)
 Returns the Rosetta Numbering corresponding to the selected residues. More...
 
bool core::select::residue_selector::are_selections_equal (ResidueSubset const &selection1, ResidueSubset const &selection2)
 Evaluate if two ResidueSubsets are equal. More...
 
std::string core::select::residue_selector::represent_residue_selector (ResidueSubset const &selection, std::string const &is_true, std::string const &is_false)
 Returns a string representing the ResidueSubset (ยท for non selected, * for selected) More...
 
ResidueSelectorOP core::select::residue_selector::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 core::select::residue_selector::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 core::select::residue_selector::regex_usable ()
 test regex support More...
 

Detailed Description

Utility functions for the residue selector classes, primarily, in constructing XML-Schema type definitions.

Author
Andrew Leaver-Fay (leave.nosp@m.rfa@.nosp@m.email.nosp@m..unc.nosp@m..edu)