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Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::residue_selectors::HBondSelector Class Reference

#include <HBondSelector.hh>

Inheritance diagram for protocols::residue_selectors::HBondSelector:
Inheritance graph
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Public Member Functions

 HBondSelector ()
 Constructor. More...
 
 HBondSelector (HBondSelector const &src)
 
 ~HBondSelector () override
 Destructor. More...
 
core::select::residue_selector::ResidueSelectorOP clone () const override
 Clone function. 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_hbond_energy_cutoff (core::Real input_value)
 Set the threshold for considering something to be a hydrogen bond. More...
 
core::Real get_hbond_energy_cutoff () const
 Get the threshold for considering something to be a hydrogen bond. More...
 
void set_include_bb_bb (bool const input_setting)
 Set whether backbone-backbone hydrogen bonds are included. More...
 
bool get_include_bb_bb () const
 Get whether backbone-backbone hydrogen bonds are included. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction. More...
 
core::scoring::ScoreFunctionCOP get_scorefxn () const
 Get the scorefunction. More...
 
std::string get_input_set_str () const
 
void set_input_set_str (std::string)
 
core::select::residue_selector::ResidueSelectorCOP get_input_set_selector () const
 
void set_input_set_selector (core::select::residue_selector::ResidueSelectorCOP)
 
bool get_input_set_defined () const
 
bool get_use_input_set_selector () 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 ()
 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

void compute_input_set (core::pose::Pose const &, std::set< core::Size > &) const
 

Private Attributes

core::Real hbond_energy_cutoff_
 The energy cutoff for considering something to be a hydrogen. More...
 
bool include_bb_bb_
 Should backbone-backbone hydrogen bonds be included? Default false. More...
 
core::scoring::ScoreFunctionOP scorefxn_
 The scorefunction to use for hydrogen bond scoring. More...
 
core::select::residue_selector::ResidueSelectorCOP input_set_selector_
 Ways of specifying for which residues we'll be searching for hydrogen bond partners. More...
 
std::string input_set_str_
 
bool input_set_defined_
 
bool use_input_set_selector_
 

Constructor & Destructor Documentation

protocols::residue_selectors::HBondSelector::HBondSelector ( )
protocols::residue_selectors::HBondSelector::HBondSelector ( HBondSelector const &  src)
protocols::residue_selectors::HBondSelector::~HBondSelector ( )
overridedefault

Destructor.

Member Function Documentation

core::select::residue_selector::ResidueSubset protocols::residue_selectors::HBondSelector::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::residue_selectors::HBondSelector::class_name ( )
static

Get the mover class name.

Static function to return class name; anything else returning the class name should call this function to avoid discrepancies

Referenced by get_name(), protocols::residue_selectors::HBondSelectorCreator::keyname(), and provide_xml_schema().

core::select::residue_selector::ResidueSelectorOP protocols::residue_selectors::HBondSelector::clone ( ) const
overridevirtual

Clone function.

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

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

void protocols::residue_selectors::HBondSelector::compute_input_set ( core::pose::Pose const &  pose,
std::set< core::Size > &  input_set 
) const
private
core::Real protocols::residue_selectors::HBondSelector::get_hbond_energy_cutoff ( ) const

Get the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by HBondSelector().

bool protocols::residue_selectors::HBondSelector::get_include_bb_bb ( ) const

Get whether backbone-backbone hydrogen bonds are included.

References include_bb_bb_.

Referenced by HBondSelector().

bool protocols::residue_selectors::HBondSelector::get_input_set_defined ( ) const

References input_set_defined_.

Referenced by HBondSelector().

core::select::residue_selector::ResidueSelectorCOP protocols::residue_selectors::HBondSelector::get_input_set_selector ( ) const

References input_set_selector_.

Referenced by HBondSelector().

std::string protocols::residue_selectors::HBondSelector::get_input_set_str ( ) const

References input_set_str_.

Referenced by HBondSelector().

std::string protocols::residue_selectors::HBondSelector::get_name ( ) const
overridevirtual

Get the mover class name.

Non-static function to return class name

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

References class_name().

core::scoring::ScoreFunctionCOP protocols::residue_selectors::HBondSelector::get_scorefxn ( ) const

Get the scorefunction.

References scorefxn_.

Referenced by HBondSelector().

bool protocols::residue_selectors::HBondSelector::get_use_input_set_selector ( ) const

References use_input_set_selector_.

Referenced by HBondSelector().

void protocols::residue_selectors::HBondSelector::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::residue_selectors::HBondSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::residue_selectors::HBondSelector::set_hbond_energy_cutoff ( core::Real  input_value)

Set the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by HBondSelector().

void protocols::residue_selectors::HBondSelector::set_include_bb_bb ( bool const  input_setting)

Set whether backbone-backbone hydrogen bonds are included.

References include_bb_bb_.

Referenced by HBondSelector().

void protocols::residue_selectors::HBondSelector::set_input_set_selector ( core::select::residue_selector::ResidueSelectorCOP  select)
void protocols::residue_selectors::HBondSelector::set_input_set_str ( std::string  input)
void protocols::residue_selectors::HBondSelector::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction.

Clones the input.

References scorefxn_.

Referenced by HBondSelector(), and parse_my_tag().

Member Data Documentation

core::Real protocols::residue_selectors::HBondSelector::hbond_energy_cutoff_
private

The energy cutoff for considering something to be a hydrogen.

Defaults to -0.5.

Referenced by apply(), get_hbond_energy_cutoff(), parse_my_tag(), and set_hbond_energy_cutoff().

bool protocols::residue_selectors::HBondSelector::include_bb_bb_
private

Should backbone-backbone hydrogen bonds be included? Default false.

Referenced by apply(), get_include_bb_bb(), parse_my_tag(), and set_include_bb_bb().

bool protocols::residue_selectors::HBondSelector::input_set_defined_
private
core::select::residue_selector::ResidueSelectorCOP protocols::residue_selectors::HBondSelector::input_set_selector_
private

Ways of specifying for which residues we'll be searching for hydrogen bond partners.

If none are provided, all residues in the pose forming hydrogen bonds will be selected.

Referenced by compute_input_set(), get_input_set_selector(), HBondSelector(), parse_my_tag(), and set_input_set_selector().

std::string protocols::residue_selectors::HBondSelector::input_set_str_
private
core::scoring::ScoreFunctionOP protocols::residue_selectors::HBondSelector::scorefxn_
private

The scorefunction to use for hydrogen bond scoring.

If no scorefunction is provided, then the default scorefunction is used.

Referenced by apply(), get_scorefxn(), HBondSelector(), and set_scorefxn().

bool protocols::residue_selectors::HBondSelector::use_input_set_selector_
private

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