#include <ResidueIEFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueIEFilter:

Public Member Functions
	ResidueIEFilter ()

	ResidueIEFilter (std::string const &resnums, std::string const &restype, core::scoring::ScoreFunctionCOP scorefxn, core::scoring::ScoreType const score_type=core::scoring::total_score, core::Real const threshold=0.0, bool const whole_pose=false, bool const whole_interface=false, core::Size const rb_jump=1, core::Real const interface_distance_cutoff=8.0, core::Real max_penalty=1000.0, core::Real penalty_factor=1.0, bool const report_energy=false)

	ResidueIEFilter (ResidueIEFilter const &init)

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

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	report (std::ostream &out, core::pose::Pose const &pose) const override

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

core::Real	compute (core::pose::Pose const &pose) const

	~ResidueIEFilter () override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

std::string const &	resnums () const

core::scoring::ScoreFunctionOP	scorefxn () const

core::scoring::ScoreType	score_type () const

core::Real	threshold () const

void	resnums (std::string const &resnums_str)

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

void	score_type (core::scoring::ScoreType score_type)

void	threshold (core::Real const th)

std::string	name () const override

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 Member Functions
std::set< core::Size >	compute_resnums (core::pose::Pose const &pose) const

core::Real	penalty_from_score (core::Real const res_intE) const

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

Constructor & Destructor Documentation

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter ( )

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter	(	std::string const &	resnums,
		std::string const &	restype,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::scoring::ScoreType const	score_type = `core::scoring::total_score`,
		core::Real const	threshold = `0.0`,
		bool const	whole_pose = `false`,
		bool const	whole_interface = `false`,
		core::Size const	rb_jump = `1`,
		core::Real const	interface_distance_cutoff = `8.0`,
		core::Real	max_penalty = `1000.0`,
		core::Real	penalty_factor = `1.0`,
		bool const	report_energy = `false`
	)

References score_type_, scorefxn_, core::scoring::total_score, and use_resE_.

protocols::simple_filters::ResidueIEFilter::ResidueIEFilter ( ResidueIEFilter const & init )

References scorefxn_.

protocols::simple_filters::ResidueIEFilter::~ResidueIEFilter ( )

overridedefault

Member Function Documentation

bool protocols::simple_filters::ResidueIEFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

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

Implements protocols::filters::Filter.

References compute(), and max_penalty_.

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

core::Real protocols::simple_filters::ResidueIEFilter::compute ( core::pose::Pose const & pose ) const

References protocols::simple_filters::EnergyPerResidueFilter::compute(), compute_resnums(), core::scoring::EnergyEdge::dot(), core::chemical::ResidueTypeBase::name3(), penalty_factor_, penalty_from_score(), core::pose::Pose::residue_type(), resnums(), restype_, score_type_, scorefxn_, threshold_, protocols::simple_filters::tr(), and use_resE_.

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

std::set< core::Size > protocols::simple_filters::ResidueIEFilter::compute_resnums ( core::pose::Pose const & pose ) const

private

References core::pose::Pose::conformation(), core::pose::get_resnum_list(), interface_distance_cutoff_, core::conformation::Residue::is_protein(), core::chemical::ResidueTypeBase::name3(), core::conformation::Conformation::num_chains(), rb_jump_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), resnum_str_, resnums(), restype_, selector_, core::pose::Pose::size(), protocols::simple_filters::tr(), core::pose::Pose::update_residue_neighbors(), whole_interface_, and whole_pose_.

Referenced by compute().

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

inlineoverridevirtual

Implements protocols::filters::Filter.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::ResidueIEFilter::parse_my_tag	(	utility::tag::TagCOP	,
		basic::datacache::DataMap &
	)

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References core::select::residue_selector::get_residue_selector(), interface_distance_cutoff_, max_penalty_, core::scoring::parse_score_function(), penalty_factor_, rb_jump_, report_energy_, resnum_str_, restype_, score_type_, core::scoring::score_type_from_name(), scorefxn_, selector_, threshold_, protocols::simple_filters::tr(), use_resE_, whole_interface_, and whole_pose_.

core::Real protocols::simple_filters::ResidueIEFilter::penalty_from_score ( core::Real const res_intE ) const

private

References report_energy_, and threshold_.

Referenced by compute().

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

static

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

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

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and restype_.

core::Real protocols::simple_filters::ResidueIEFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

std::string const & protocols::simple_filters::ResidueIEFilter::resnums ( ) const

References resnum_str_.

Referenced by compute(), and compute_resnums().

void protocols::simple_filters::ResidueIEFilter::resnums ( std::string const & resnums_str )

References resnum_str_.

core::scoring::ScoreType protocols::simple_filters::ResidueIEFilter::score_type ( ) const

References score_type_.

Referenced by score_type().

void protocols::simple_filters::ResidueIEFilter::score_type ( core::scoring::ScoreType score_type )

References score_type(), and score_type_.

core::scoring::ScoreFunctionOP protocols::simple_filters::ResidueIEFilter::scorefxn ( ) const

References scorefxn_.

Referenced by scorefxn().

void protocols::simple_filters::ResidueIEFilter::scorefxn ( core::scoring::ScoreFunctionOP scorefxn )

References scorefxn(), and scorefxn_.

core::Real protocols::simple_filters::ResidueIEFilter::threshold ( ) const

References threshold_.

void protocols::simple_filters::ResidueIEFilter::threshold ( core::Real const th )

References threshold_.

Member Data Documentation

core::Real protocols::simple_filters::ResidueIEFilter::interface_distance_cutoff_

private

Referenced by compute_resnums(), and parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::max_penalty_

private

Referenced by apply(), and parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::penalty_factor_

private

Referenced by compute(), and parse_my_tag().

core::Size protocols::simple_filters::ResidueIEFilter::rb_jump_

private

Referenced by compute_resnums(), and parse_my_tag().

bool protocols::simple_filters::ResidueIEFilter::report_energy_

private

Referenced by parse_my_tag(), and penalty_from_score().

std::string protocols::simple_filters::ResidueIEFilter::resnum_str_

private

Referenced by compute_resnums(), parse_my_tag(), and resnums().

std::string protocols::simple_filters::ResidueIEFilter::restype_

private

Referenced by compute(), compute_resnums(), parse_my_tag(), and report().

core::scoring::ScoreType protocols::simple_filters::ResidueIEFilter::score_type_

private

Referenced by compute(), parse_my_tag(), ResidueIEFilter(), and score_type().

core::scoring::ScoreFunctionOP protocols::simple_filters::ResidueIEFilter::scorefxn_

private

Referenced by compute(), parse_my_tag(), ResidueIEFilter(), and scorefxn().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ResidueIEFilter::selector_

private

Referenced by compute_resnums(), and parse_my_tag().

core::Real protocols::simple_filters::ResidueIEFilter::threshold_

private

Referenced by compute(), parse_my_tag(), penalty_from_score(), and threshold().

bool protocols::simple_filters::ResidueIEFilter::use_resE_

private

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

bool protocols::simple_filters::ResidueIEFilter::whole_interface_

private

Referenced by compute_resnums(), and parse_my_tag().

bool protocols::simple_filters::ResidueIEFilter::whole_pose_

private

Referenced by compute_resnums(), and parse_my_tag().

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

src/protocols/simple_filters/ResidueIEFilter.hh
src/protocols/simple_filters/ResidueIEFilter.cc

Private Attributes
std::string	resnum_str_

std::string	restype_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreType	score_type_

core::Real	threshold_

bool	whole_pose_

bool	whole_interface_

core::Size	rb_jump_

core::Real	interface_distance_cutoff_

core::Real	max_penalty_

core::Real	penalty_factor_

bool	report_energy_

bool	use_resE_

core::select::residue_selector::ResidueSelectorCOP	selector_

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation