protocols::simple_filters::HolesFilter Class Reference

#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 (Filter 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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

protocols::simple_filters::HolesFilter::HolesFilter

(

)

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

default

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

overridedefault

Member Function Documentation

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().

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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().

void protocols::simple_filters::HolesFilter::filtered_value

(

Real const &

ss

)

References filtered_value_.

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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().

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().

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().

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().

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

inline

References exclude_bb_atoms_.

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

inline

References normalize_per_atom_.

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

inline

References normalize_per_residue_.

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

inline

References residue_selector_.

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

inline

References filtered_value_.

Member Data Documentation

String protocols::simple_filters::HolesFilter::cmd_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::HolesFilter::exclude_bb_atoms_

private

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

Real protocols::simple_filters::HolesFilter::filtered_value_

private

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

bool protocols::simple_filters::HolesFilter::normalize_per_atom_

private

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

bool protocols::simple_filters::HolesFilter::normalize_per_residue_

private

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

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

private

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

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

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