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core::select::residue_selector::BondedResidueSelector Class Reference

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...

#include <BondedResidueSelector.hh>

Inheritance diagram for core::select::residue_selector::BondedResidueSelector:
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Public Member Functions

 BondedResidueSelector ()
 
 BondedResidueSelector (std::set< core::Size > const &input_set)
 
 BondedResidueSelector (BondedResidueSelector const &other)
 
 ~BondedResidueSelector () override
 
ResidueSelectorOP clone () const override
 Clone operator. More...
 
ResidueSubset apply (core::pose::Pose const &pose) const override
 Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override
 Initialize any data members of this instance from an input tag and a DataMap object. More...
 
std::string get_name () const override
 
void set_input_set (std::set< core::Size > const &input_set)
 adds a ResidueSelector More...
 
void set_input_set (std::string const &input_set_str)
 
void set_input_set_selector (core::select::residue_selector::ResidueSelectorCOP rs)
 
std::set< core::Sizeinput_set () const
 
core::select::residue_selector::ResidueSelectorCOP input_set_selector () const
 
std::string input_set_string () const
 
bool input_set_defined () const
 
bool input_set_selector_defined () const
 
- Public Member Functions inherited from core::select::residue_selector::ResidueSelector
 ResidueSelector ()
 Constructor. More...
 
 ~ResidueSelector () override
 Destructor. More...
 
virtual bool residue_selector_provides_citation_info () const
 Does this residue selector provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool residue_selector_is_unpublished () const
 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Member Functions

void get_input_set (core::pose::Pose const &, ResidueSubset &, std::set< core::Size > &) const
 Sets subset to be true for values contained in input_set. More...
 

Private Attributes

std::set< core::Sizeinput_set_
 
std::string input_set_str_
 
core::select::residue_selector::ResidueSelectorCOP input_set_selector_
 
bool input_set_defined_
 
bool use_input_set_selector_
 

Detailed Description

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.

Residues in the input_set are included in the final selection.

Constructor & Destructor Documentation

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( )

Referenced by clone().

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( std::set< core::Size > const &  input_set)

References set_input_set().

core::select::residue_selector::BondedResidueSelector::BondedResidueSelector ( BondedResidueSelector const &  other)
core::select::residue_selector::BondedResidueSelector::~BondedResidueSelector ( )
overridedefault

Member Function Documentation

ResidueSubset core::select::residue_selector::BondedResidueSelector::apply ( core::pose::Pose const &  pose) const
overridevirtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

Implements core::select::residue_selector::ResidueSelector.

References core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), get_input_set(), input_set_defined_, core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::select::residue_selector::TR().

std::string core::select::residue_selector::BondedResidueSelector::class_name ( )
static
ResidueSelectorOP core::select::residue_selector::BondedResidueSelector::clone ( ) const
overridevirtual

Clone operator.

All ResidueSelectors must implement a clone() operator. This must create a copy of the object and return a ResidueSelectorOP to the original object.

Implements core::select::residue_selector::ResidueSelector.

References BondedResidueSelector().

void core::select::residue_selector::BondedResidueSelector::get_input_set ( core::pose::Pose const &  pose,
ResidueSubset subset,
std::set< core::Size > &  input_set 
) const
private

Sets subset to be true for values contained in input_set.

References core::pose::get_resnum_list(), input_set_, input_set_selector_, input_set_str_, and use_input_set_selector_.

Referenced by apply().

std::string core::select::residue_selector::BondedResidueSelector::get_name ( ) const
overridevirtual
std::set< core::Size > core::select::residue_selector::BondedResidueSelector::input_set ( ) const

References input_set_.

Referenced by BondedResidueSelector(), and set_input_set().

bool core::select::residue_selector::BondedResidueSelector::input_set_defined ( ) const

References input_set_defined_.

Referenced by BondedResidueSelector().

core::select::residue_selector::ResidueSelectorCOP core::select::residue_selector::BondedResidueSelector::input_set_selector ( ) const

References input_set_selector_.

Referenced by BondedResidueSelector().

bool core::select::residue_selector::BondedResidueSelector::input_set_selector_defined ( ) const
std::string core::select::residue_selector::BondedResidueSelector::input_set_string ( ) const

References input_set_str_.

Referenced by BondedResidueSelector().

void core::select::residue_selector::BondedResidueSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datacache 
)
overridevirtual

Initialize any data members of this instance from an input tag and a DataMap object.

Noop implementation in the base class in the case that a derived class has no need to read data from an input tag

Reimplemented from core::select::residue_selector::ResidueSelector.

References core::select::residue_selector::get_residue_selector(), set_input_set(), and set_input_set_selector().

void core::select::residue_selector::BondedResidueSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::select::residue_selector::BondedResidueSelector::set_input_set ( std::set< core::Size > const &  input_set)
void core::select::residue_selector::BondedResidueSelector::set_input_set ( std::string const &  input_set_str)
void core::select::residue_selector::BondedResidueSelector::set_input_set_selector ( core::select::residue_selector::ResidueSelectorCOP  rs)

Member Data Documentation

std::set< core::Size > core::select::residue_selector::BondedResidueSelector::input_set_
private
bool core::select::residue_selector::BondedResidueSelector::input_set_defined_
private
core::select::residue_selector::ResidueSelectorCOP core::select::residue_selector::BondedResidueSelector::input_set_selector_
private
std::string core::select::residue_selector::BondedResidueSelector::input_set_str_
private
bool core::select::residue_selector::BondedResidueSelector::use_input_set_selector_
private

The documentation for this class was generated from the following files: