This residue selector takes a selector or residue number of a ligand and returns any residues in contact with metal atoms in the ligand. More...

#include <LigandMetalContactSelector.hh>

Inheritance diagram for protocols::residue_selectors::LigandMetalContactSelector:

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Public Types
typedef core::select::residue_selector::ResidueSelectorOP	ResidueSelectorOP

typedef core::select::residue_selector::ResidueSubset	ResidueSubset

Public Member Functions
	LigandMetalContactSelector ()
	Constructor. More...

core::select::residue_selector::ResidueSelectorOP	clone () const override
	Clone operator. More...

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...

std::string	get_resnum_string () const

void	set_resnum_string (std::string const &)

core::select::residue_selector::ResidueSelectorCOP	get_input_set_selector () const

void	set_input_set_selector (core::select::residue_selector::ResidueSelectorCOP)

bool	get_using_a_resselect () const

void	set_using_a_resselect (bool)

core::Real	get_dist_cutoff_multiplier () const

void	set_dist_cutoff_multiplier (core::Real const)

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. More...

utility::vector1< core::Size >	selection_positions (core::pose::Pose const &pose) const
	Calls apply and returns the Rosetta numbering corresponding to the selected residues. 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, enabling mechanical validation of input XML. More...

Private Member Functions
void	calculate_ligand_resnums (core::pose::Pose const &, std::set< core::Size > &) const

Private Attributes
std::string	resnum_string_ =""

core::select::residue_selector::ResidueSelectorCOP	input_set_selector_ = nullptr

bool	using_a_resselect_ =false

core::Real	dist_cutoff_multiplier_ =1.0

Detailed Description

This residue selector takes a selector or residue number of a ligand and returns any residues in contact with metal atoms in the ligand.

Member Typedef Documentation

◆ ResidueSelectorOP

typedef core::select::residue_selector::ResidueSelectorOP protocols::residue_selectors::LigandMetalContactSelector::ResidueSelectorOP

◆ ResidueSubset

typedef core::select::residue_selector::ResidueSubset protocols::residue_selectors::LigandMetalContactSelector::ResidueSubset

Constructor & Destructor Documentation

◆ LigandMetalContactSelector()

protocols::residue_selectors::LigandMetalContactSelector::LigandMetalContactSelector ( )

Constructor.

Member Function Documentation

◆ apply()

LigandMetalContactSelector::ResidueSubset protocols::residue_selectors::LigandMetalContactSelector::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 calculate_ligand_resnums(), dist_cutoff_multiplier_, core::util::find_metalbinding_atoms_for_complex(), core::scoring::pair, core::pose::Pose::total_residue(), and protocols::residue_selectors::TR().

◆ calculate_ligand_resnums()

void protocols::residue_selectors::LigandMetalContactSelector::calculate_ligand_resnums	(	core::pose::Pose const &	pose,
		std::set< core::Size > &	input_set
	)		const

private

References core::pose::get_resnum_list(), input_set_selector_, resnum_string_, core::pose::Pose::total_residue(), and using_a_resselect_.

Referenced by apply().

◆ class_name()

std::string protocols::residue_selectors::LigandMetalContactSelector::class_name ( )

static

Get the mover class name.

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

◆ clone()

core::select::residue_selector::ResidueSelectorOP protocols::residue_selectors::LigandMetalContactSelector::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.

◆ get_dist_cutoff_multiplier()

core::Real protocols::residue_selectors::LigandMetalContactSelector::get_dist_cutoff_multiplier ( ) const

References dist_cutoff_multiplier_.

◆ get_input_set_selector()

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

References input_set_selector_.

◆ get_name()

std::string protocols::residue_selectors::LigandMetalContactSelector::get_name ( ) const

overridevirtual

Get the mover class name.

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

References class_name().

◆ get_resnum_string()

std::string protocols::residue_selectors::LigandMetalContactSelector::get_resnum_string ( ) const

References resnum_string_.

◆ get_using_a_resselect()

bool protocols::residue_selectors::LigandMetalContactSelector::get_using_a_resselect ( ) const

References using_a_resselect_.

◆ parse_my_tag()

void protocols::residue_selectors::LigandMetalContactSelector::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 dist_cutoff_multiplier_, core::select::residue_selector::get_residue_selector(), set_input_set_selector(), and set_resnum_string().

◆ provide_xml_schema()

void protocols::residue_selectors::LigandMetalContactSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide XSD information, enabling mechanical validation of input XML.

References core::pose::attributes_for_get_resnum_selector(), core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes_and_optional_subselector().

Referenced by protocols::residue_selectors::LigandMetalContactSelectorCreator::provide_xml_schema().

◆ set_dist_cutoff_multiplier()

void protocols::residue_selectors::LigandMetalContactSelector::set_dist_cutoff_multiplier ( core::Real const new_d_c_m )

References dist_cutoff_multiplier_.

◆ set_input_set_selector()

void protocols::residue_selectors::LigandMetalContactSelector::set_input_set_selector ( core::select::residue_selector::ResidueSelectorCOP rs )

References input_set_selector_, and using_a_resselect_.

Referenced by parse_my_tag().

◆ set_resnum_string()

void protocols::residue_selectors::LigandMetalContactSelector::set_resnum_string ( std::string const & input_string )

References resnum_string_, and using_a_resselect_.

Referenced by parse_my_tag().

◆ set_using_a_resselect()

void protocols::residue_selectors::LigandMetalContactSelector::set_using_a_resselect ( bool new_bool )

References using_a_resselect_.

Member Data Documentation

◆ dist_cutoff_multiplier_

core::Real protocols::residue_selectors::LigandMetalContactSelector::dist_cutoff_multiplier_ =1.0

private

Referenced by apply(), get_dist_cutoff_multiplier(), parse_my_tag(), and set_dist_cutoff_multiplier().

◆ input_set_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::residue_selectors::LigandMetalContactSelector::input_set_selector_ = nullptr

private

Referenced by calculate_ligand_resnums(), get_input_set_selector(), and set_input_set_selector().

◆ resnum_string_

std::string protocols::residue_selectors::LigandMetalContactSelector::resnum_string_ =""

private

Referenced by calculate_ligand_resnums(), get_resnum_string(), and set_resnum_string().

◆ using_a_resselect_

bool protocols::residue_selectors::LigandMetalContactSelector::using_a_resselect_ =false

private

Referenced by calculate_ligand_resnums(), get_using_a_resselect(), set_input_set_selector(), set_resnum_string(), and set_using_a_resselect().

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

src/protocols/residue_selectors/LigandMetalContactSelector.hh
src/protocols/residue_selectors/LigandMetalContactSelector.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ResidueSelectorOP

◆ ResidueSubset

Constructor & Destructor Documentation

◆ LigandMetalContactSelector()

Member Function Documentation

◆ apply()

◆ calculate_ligand_resnums()

◆ class_name()

◆ clone()

◆ get_dist_cutoff_multiplier()

◆ get_input_set_selector()

◆ get_name()

◆ get_resnum_string()

◆ get_using_a_resselect()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_dist_cutoff_multiplier()

◆ set_input_set_selector()

◆ set_resnum_string()

◆ set_using_a_resselect()

Member Data Documentation

◆ dist_cutoff_multiplier_

◆ input_set_selector_

◆ resnum_string_

◆ using_a_resselect_