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:

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

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

References bin_name(), bin_transition_calculator_, core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), initialized(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::lower_connect_id(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), select_only_alpha_aas(), core::pose::Pose::size(), core::select::residue_selector::TR(), and core::chemical::ResidueType::upper_connect_id().

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

Get the mover class name.

Referenced by get_name(), core::select::residue_selector::BinSelectorCreator::keyname(), and provide_xml_schema().

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

XML parse.

Parse RosettaScripts tags and set up this mover.

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

References bin_params_file_name(), initialize_and_check(), select_only_alpha_aas(), set_bin_name(), set_bin_params_file_name(), and set_select_only_alpha_aas().

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:

src/core/select/residue_selector/BinSelector.hh
src/core/select/residue_selector/BinSelector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation