#include <HolesFilter.hh>

Inheritance diagram for protocols::simple_filters::HolesFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef std::string	String

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	HolesFilter ()

	HolesFilter (HolesFilter const &rval)

	~HolesFilter () override=default

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	filtered_value (Real const &ss)

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	parse xml More...

bool	apply (Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

Real	report_sm (Pose const &pose) const override
	used to report filter internals through a score or silent file More...

void	report (std::ostream &out, Pose const &pose) const override
	used to report score More...

Real	compute (Pose const &pose) const

std::string	name () const override

void	set_residue_selector (core::select::residue_selector::ResidueSelectorOP residue_selector)

void	set_threshold (Real threshold)

void	set_exclude_bb_atoms (bool exclude_bb_atoms)

void	set_normalize_per_atom (bool normalize_per_atom)

void	set_normalize_per_residue (bool normalize_per_residue)

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

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 ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Attributes
Real	filtered_value_

String	cmd_

bool	exclude_bb_atoms_

bool	normalize_per_atom_

bool	normalize_per_residue_

core::select::residue_selector::ResidueSelectorOP	residue_selector_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::simple_filters::HolesFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::simple_filters::HolesFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::simple_filters::HolesFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::simple_filters::HolesFilter::Pose

◆ Real

typedef core::Real protocols::simple_filters::HolesFilter::Real

◆ String

typedef std::string protocols::simple_filters::HolesFilter::String

◆ Super

typedef protocols::filters::Filter protocols::simple_filters::HolesFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::simple_filters::HolesFilter::TagCOP

Constructor & Destructor Documentation

◆ HolesFilter() [1/2]

protocols::simple_filters::HolesFilter::HolesFilter ( )

◆ HolesFilter() [2/2]

protocols::simple_filters::HolesFilter::HolesFilter ( HolesFilter const & rval )

default

◆ ~HolesFilter()

protocols::simple_filters::HolesFilter::~HolesFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::HolesFilter::apply ( Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), filtered_value_, and protocols::simple_filters::tr().

◆ class_name()

std::string protocols::simple_filters::HolesFilter::class_name ( )

static

Referenced by protocols::simple_filters::HolesFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::simple_filters::HolesFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

HolesFilter::Real protocols::simple_filters::HolesFilter::compute ( Pose const & pose ) const

References core::conformation::Residue::atom_is_backbone(), cmd_, core::scoring::packing::compute_holes_score(), exclude_bb_atoms_, core::id::AtomID_Map< T >::n_atom(), normalize_per_atom_, normalize_per_residue_, core::pose::Pose::residue(), residue_selector_, core::pose::Pose::size(), and protocols::simple_filters::tr().

Referenced by apply(), report(), and report_sm().

◆ filtered_value()

void protocols::simple_filters::HolesFilter::filtered_value ( Real const & ss )

References filtered_value_.

◆ fresh_instance()

filters::FilterOP protocols::simple_filters::HolesFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ name()

std::string protocols::simple_filters::HolesFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::HolesFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References cmd_, protocols::pack_daemon::error_message, exclude_bb_atoms_, filtered_value_, core::select::residue_selector::get_residue_selector(), normalize_per_atom_, normalize_per_residue_, residue_selector_, and protocols::simple_filters::tr().

◆ provide_xml_schema()

void protocols::simple_filters::HolesFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_filters::HolesFilterCreator::provide_xml_schema().

◆ report()

void protocols::simple_filters::HolesFilter::report	(	std::ostream &	out,
		Pose const &	pose
	)		const

overridevirtual

used to report score

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

HolesFilter::Real protocols::simple_filters::HolesFilter::report_sm ( Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ set_exclude_bb_atoms()

void protocols::simple_filters::HolesFilter::set_exclude_bb_atoms ( bool exclude_bb_atoms )

inline

References exclude_bb_atoms_.

◆ set_normalize_per_atom()

void protocols::simple_filters::HolesFilter::set_normalize_per_atom ( bool normalize_per_atom )

inline

References normalize_per_atom_.

◆ set_normalize_per_residue()

void protocols::simple_filters::HolesFilter::set_normalize_per_residue ( bool normalize_per_residue )

inline

References normalize_per_residue_.

◆ set_residue_selector()

void protocols::simple_filters::HolesFilter::set_residue_selector ( core::select::residue_selector::ResidueSelectorOP residue_selector )

inline

References residue_selector_.

◆ set_threshold()

void protocols::simple_filters::HolesFilter::set_threshold ( Real threshold )

inline

References filtered_value_.

Member Data Documentation

◆ cmd_

String protocols::simple_filters::HolesFilter::cmd_

private

Referenced by compute(), and parse_my_tag().

◆ exclude_bb_atoms_

bool protocols::simple_filters::HolesFilter::exclude_bb_atoms_

private

Referenced by compute(), parse_my_tag(), and set_exclude_bb_atoms().

◆ filtered_value_

Real protocols::simple_filters::HolesFilter::filtered_value_

private

Referenced by apply(), filtered_value(), parse_my_tag(), and set_threshold().

◆ normalize_per_atom_

bool protocols::simple_filters::HolesFilter::normalize_per_atom_

private

Referenced by compute(), parse_my_tag(), and set_normalize_per_atom().

◆ normalize_per_residue_

bool protocols::simple_filters::HolesFilter::normalize_per_residue_

private

Referenced by compute(), parse_my_tag(), and set_normalize_per_residue().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorOP protocols::simple_filters::HolesFilter::residue_selector_

private

Referenced by compute(), parse_my_tag(), and set_residue_selector().

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

src/protocols/simple_filters/HolesFilter.hh
src/protocols/simple_filters/HolesFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ HolesFilter() [1/2]

◆ HolesFilter() [2/2]

◆ ~HolesFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ filtered_value()

◆ fresh_instance()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ set_exclude_bb_atoms()

◆ set_normalize_per_atom()

◆ set_normalize_per_residue()

◆ set_residue_selector()

◆ set_threshold()

Member Data Documentation

◆ cmd_

◆ exclude_bb_atoms_

◆ filtered_value_

◆ normalize_per_atom_

◆ normalize_per_residue_

◆ residue_selector_