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core::select::residue_selector::BinSelector Class Reference

A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin). More...

#include <BinSelector.hh>

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

 BinSelector ()
 Constructor. More...
 
 BinSelector (BinSelector const &src)
 Copy constructor. More...
 
 ~BinSelector () override
 Destructor. More...
 
core::select::residue_selector::ResidueSelectorOP clone () const override
 Clone operator. More...
 
core::select::residue_selector::ResidueSubset apply (core::pose::Pose const &pose) const override
 "Apply" function. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
 XML parse. More...
 
std::string get_name () const override
 Get the mover class name. More...
 
void set_bin_name (std::string const &bin_name_in)
 Set the name of the bin that the residues that we will select must be in. More...
 
std::string const & bin_name () const
 Get the name of the bin that the residues that we will select must be in. More...
 
void set_bin_params_file_name (std::string const &filename_in)
 Set the name of the bin params file that we'll be using. More...
 
std::string const & bin_params_file_name () const
 Get the name of the bin params file that we'll be using. More...
 
void set_select_only_alpha_aas (bool const setting)
 Set whether we're selecting alpha-amino acids only. More...
 
bool select_only_alpha_aas () const
 Get whether we're selecting alpha-amino acids only. More...
 
void initialize_and_check ()
 Load the bin params file and check that settings are consistent. More...
 
void initialize_from_file_contents_and_check (std::string const &filecontents)
 Load the bin params file baed on a file contents string (instead of loading directly from disk) and check that settings are consistent. More...
 
- 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 ()
 Get the mover class name. More...
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Provide XSD information, allowing automatic evaluation of bad XML. More...
 

Private Member Functions

bool initialized () const
 Has the initialize_and_check() function been called? More...
 

Private Attributes

bool initialized_
 Has the initialize_and_check() function been called? More...
 
core::scoring::bin_transitions::BinTransitionCalculatorOP bin_transition_calculator_
 A BinTransitionCalculatorOP pointing at a BinTransitionCalculator object. More...
 
bool select_only_alpha_aas_
 Should we only select alpha-amino acids? More...
 
std::string bin_name_
 The name of the bin that the residues that we will select will be in. More...
 
std::string bin_params_file_name_
 The name of the bin params file that we'll be using. More...
 

Detailed Description

A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin).

Constructor & Destructor Documentation

core::select::residue_selector::BinSelector::BinSelector ( )

Constructor.

core::select::residue_selector::BinSelector::BinSelector ( BinSelector const &  src)

Copy constructor.

core::select::residue_selector::BinSelector::~BinSelector ( )
overridedefault

Destructor.

Member Function Documentation

ResidueSubset core::select::residue_selector::BinSelector::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string const& core::select::residue_selector::BinSelector::bin_name ( ) const
inline

Get the name of the bin that the residues that we will select must be in.

References bin_name_.

Referenced by apply(), initialize_and_check(), and initialize_from_file_contents_and_check().

std::string const& core::select::residue_selector::BinSelector::bin_params_file_name ( ) const
inline

Get the name of the bin params file that we'll be using.

References bin_params_file_name_.

Referenced by initialize_and_check(), and parse_my_tag().

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

Clone operator.

Clone function.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

Copy this object and return owning pointer to the copy (created on the heap).

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

std::string core::select::residue_selector::BinSelector::get_name ( ) const
overridevirtual

Get the mover class name.

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

References class_name().

void core::select::residue_selector::BinSelector::initialize_and_check ( )

Load the bin params file and check that settings are consistent.

Must be called before apply() function.

References bin_name(), bin_params_file_name(), bin_transition_calculator_, initialized(), initialized_, select_only_alpha_aas(), and core::select::residue_selector::TR().

Referenced by parse_my_tag().

void core::select::residue_selector::BinSelector::initialize_from_file_contents_and_check ( std::string const &  filecontents)

Load the bin params file baed on a file contents string (instead of loading directly from disk) and check that settings are consistent.

Must be called as an alternative to initialize_and_check() before apply() function.

References bin_name(), bin_transition_calculator_, initialized(), initialized_, select_only_alpha_aas(), and core::select::residue_selector::TR().

bool core::select::residue_selector::BinSelector::initialized ( ) const
inlineprivate

Has the initialize_and_check() function been called?

Must be called before calling apply().

References initialized_.

Referenced by apply(), initialize_and_check(), and initialize_from_file_contents_and_check().

void core::select::residue_selector::BinSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void core::select::residue_selector::BinSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Provide XSD information, allowing automatic evaluation of bad XML.

References class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by core::select::residue_selector::BinSelectorCreator::provide_xml_schema().

bool core::select::residue_selector::BinSelector::select_only_alpha_aas ( ) const
inline

Get whether we're selecting alpha-amino acids only.

References select_only_alpha_aas_.

Referenced by apply(), initialize_and_check(), initialize_from_file_contents_and_check(), and parse_my_tag().

void core::select::residue_selector::BinSelector::set_bin_name ( std::string const &  bin_name_in)
inline

Set the name of the bin that the residues that we will select must be in.

References bin_name_.

Referenced by parse_my_tag().

void core::select::residue_selector::BinSelector::set_bin_params_file_name ( std::string const &  filename_in)
inline

Set the name of the bin params file that we'll be using.

References bin_params_file_name_.

Referenced by parse_my_tag().

void core::select::residue_selector::BinSelector::set_select_only_alpha_aas ( bool const  setting)
inline

Set whether we're selecting alpha-amino acids only.

References select_only_alpha_aas_.

Referenced by parse_my_tag().

Member Data Documentation

std::string core::select::residue_selector::BinSelector::bin_name_
private

The name of the bin that the residues that we will select will be in.

Referenced by bin_name(), and set_bin_name().

std::string core::select::residue_selector::BinSelector::bin_params_file_name_
private

The name of the bin params file that we'll be using.

Referenced by bin_params_file_name(), and set_bin_params_file_name().

core::scoring::bin_transitions::BinTransitionCalculatorOP core::select::residue_selector::BinSelector::bin_transition_calculator_
private

A BinTransitionCalculatorOP pointing at a BinTransitionCalculator object.

Object created with the BinSelector; initialized by parse_my_tag() or initialize_bin_transition_calculator() functions.

Referenced by apply(), initialize_and_check(), and initialize_from_file_contents_and_check().

bool core::select::residue_selector::BinSelector::initialized_
private

Has the initialize_and_check() function been called?

Must be called before calling apply().

Referenced by initialize_and_check(), initialize_from_file_contents_and_check(), and initialized().

bool core::select::residue_selector::BinSelector::select_only_alpha_aas_
private

Should we only select alpha-amino acids?

Default true. If false, then all polymeric residues are potentially selected (if they're in the correct bin).

Referenced by select_only_alpha_aas(), and set_select_only_alpha_aas().


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