#include <BundleReporterFilter.hh>

Inheritance diagram for protocols::helical_bundle::BundleReporterFilter:

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

	BundleReporterFilter (BundleReporterFilter const &src)
	Copy constructor. More...

	~BundleReporterFilter () override
	Destructor. More...

filters::FilterOP	clone () const override
	Returns an owning pointer to a new instance of this filter, with copied variables (a copy of this filter). More...

filters::FilterOP	fresh_instance () const override
	Returns an owning pointer to a new instance of this filter, with default initialization (NOT a copy). More...

void	set_score_type_threshold (core::Real const &val)
	Set the score threshold. More...

core::Real	score_type_threshold () const
	Get the score threshold. More...

void	set_score_type (core::scoring::ScoreType const &type)
	Set the score type. More...

core::scoring::ScoreType	score_type () const
	Get the score type. More...

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn_in)
	Set the scorefunction. More...

core::scoring::ScoreFunctionOP	scorefxn ()
	Get the scorefunction (by owning pointer). More...

void	set_filter_behaviour (std::string const &behaviour_string)
	Set the behaviour by string. More...

void	set_filter_behaviour (BundleReporterFilterBehaviour const behaviour_in)
	Set the behaviour by enum. More...

BundleReporterFilterBehaviour	filter_behaviour () const
	Get the filter behaviour. More...

bool	apply (core::pose::Pose const &pose) const override
	Actually apply the filter to a pose. More...

void	report (std::ostream &out, core::pose::Pose const &pose) const override
	Allows reporting of filter values to a stream. More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	Allows reporting of the filter value to a float. More...

std::string	generate_full_tracer_report (core::Size const jobno, core::Real const &score, core::pose::Pose const &pose) const
	Generates the text of the full report that the filter writes out to the REPORT tracer. More...

core::Real	compute (core::pose::Pose const &pose) const
	Computes the energy of the pose. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Parse XML (RosettaScripts) setup. More...

void	set_report_sequence (bool const val=true)
	Set whether we report sequences. More...

void	set_use_threeletter (bool const val=true)
	Set whether we report three-letter codes. More...

bool	report_sequence () const
	Get whether we report sequences. More...

bool	use_threeletter () const
	Get whether we report three-letter codes. More...

std::string	name () const override

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
core::Real	score_type_threshold_
	If the score is used to filter, what's the cutoff threshold above which the filter returns false? More...

core::scoring::ScoreType	score_type_
	What score term should be reported/used to filter? More...

core::scoring::ScoreFunctionOP	scorefxn_
	What scorefunction should be reported/used to filter? More...

BundleReporterFilterBehaviour	behaviour_
	The behaviour of this filter. More...

bool	report_sequence_
	Report sequence? False by default. More...

bool	report_three_letter_codes_
	Report one- or three-letter codes? False (one-letter codes) by default. More...

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

Constructor & Destructor Documentation

◆ BundleReporterFilter() [1/2]

protocols::helical_bundle::BundleReporterFilter::BundleReporterFilter ( )

Constructor.

◆ BundleReporterFilter() [2/2]

protocols::helical_bundle::BundleReporterFilter::BundleReporterFilter ( BundleReporterFilter const & src )

Copy constructor.

◆ ~BundleReporterFilter()

protocols::helical_bundle::BundleReporterFilter::~BundleReporterFilter ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

bool protocols::helical_bundle::BundleReporterFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Actually apply the filter to a pose.

This scores the pose with the scorefunction, writes out the energy and the bundle parameters (if any) to the REPORT tracer, then applies the selected behaviour of the filter (always true, always false, or actually filtering by score).

Implements protocols::filters::Filter.

References protocols::helical_bundle::brf_always_false, protocols::helical_bundle::brf_always_true, protocols::helical_bundle::brf_filter_by_energy, compute(), protocols::jd2::current_nstruct_index(), filter_behaviour(), generate_full_tracer_report(), protocols::filters::Filter::score(), score_type_threshold(), protocols::helical_bundle::TR(), and protocols::helical_bundle::TRReport().

◆ class_name()

std::string protocols::helical_bundle::BundleReporterFilter::class_name ( )

static

Referenced by protocols::helical_bundle::BundleReporterFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::helical_bundle::BundleReporterFilter::clone ( ) const

inlineoverridevirtual

Returns an owning pointer to a new instance of this filter, with copied variables (a copy of this filter).

Implements protocols::filters::Filter.

Referenced by parse_my_tag().

◆ compute()

core::Real protocols::helical_bundle::BundleReporterFilter::compute ( core::pose::Pose const & pose ) const

Computes the energy of the pose.

the energy function must be suitable for residue type set of the pose, and must be symmetric if this is a symmetric pose.

References protocols::filters::Filter::score(), score_type_, scorefxn_, and core::scoring::total_score.

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

◆ filter_behaviour()

BundleReporterFilterBehaviour protocols::helical_bundle::BundleReporterFilter::filter_behaviour ( ) const

inline

Get the filter behaviour.

References behaviour_.

Referenced by apply(), and parse_my_tag().

◆ fresh_instance()

filters::FilterOP protocols::helical_bundle::BundleReporterFilter::fresh_instance ( ) const

inlineoverridevirtual

Returns an owning pointer to a new instance of this filter, with default initialization (NOT a copy).

Implements protocols::filters::Filter.

◆ generate_full_tracer_report()

std::string protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report	(	core::Size const	jobno,
		core::Real const &	score,
		core::pose::Pose const &	pose
	)		const

Generates the text of the full report that the filter writes out to the REPORT tracer.

Called by the APPLY function. Jobno is the RosettaScripts job number; ignored if set to 0.

Called by the APPLY function.

References core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), core::conformation::Residue::name3(), core::conformation::Conformation::parameters_set(), report_sequence(), core::pose::Pose::residue(), protocols::filters::Filter::score(), core::pose::Pose::sequence(), core::pose::Pose::size(), and use_threeletter().

Referenced by apply().

◆ name()

std::string protocols::helical_bundle::BundleReporterFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::helical_bundle::BundleReporterFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Parse XML (RosettaScripts) setup.

Reimplemented from protocols::filters::Filter.

References protocols::helical_bundle::brf_filter_by_energy, clone(), filter_behaviour(), core::scoring::parse_score_function(), report_sequence(), core::scoring::score_type_from_name(), set_filter_behaviour(), set_report_sequence(), set_score_type(), set_score_type_threshold(), set_scorefxn(), set_use_threeletter(), protocols::helical_bundle::TR(), and use_threeletter().

◆ provide_xml_schema()

void protocols::helical_bundle::BundleReporterFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::helical_bundle::BundleReporterFilterCreator::provide_xml_schema().

◆ report()

void protocols::helical_bundle::BundleReporterFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Allows reporting of filter values to a stream.

Reimplemented from protocols::filters::Filter.

References compute(), core::scoring::ScoreTypeManager::name_from_score_type(), core::conformation::membrane::out, and score_type_.

◆ report_sequence()

bool protocols::helical_bundle::BundleReporterFilter::report_sequence ( ) const

inline

Get whether we report sequences.

References report_sequence_.

Referenced by generate_full_tracer_report(), and parse_my_tag().

◆ report_sm()

core::Real protocols::helical_bundle::BundleReporterFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

Allows reporting of the filter value to a float.

Reimplemented from protocols::filters::Filter.

References compute().

◆ score_type()

core::scoring::ScoreType protocols::helical_bundle::BundleReporterFilter::score_type ( ) const

inline

Get the score type.

References score_type_.

◆ score_type_threshold()

core::Real protocols::helical_bundle::BundleReporterFilter::score_type_threshold ( ) const

inline

Get the score threshold.

References score_type_threshold_.

Referenced by apply().

◆ scorefxn()

core::scoring::ScoreFunctionOP protocols::helical_bundle::BundleReporterFilter::scorefxn ( )

inline

Get the scorefunction (by owning pointer).

Non-const access.

References scorefxn_.

◆ set_filter_behaviour() [1/2]

void protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour ( BundleReporterFilterBehaviour const behaviour_in )

inline

Set the behaviour by enum.

Options are brf_always_true, brf_always_false, or brf_filter_by_energy.

References behaviour_, and protocols::helical_bundle::brf_undefined.

◆ set_filter_behaviour() [2/2]

void protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour ( std::string const & behaviour_string )

Set the behaviour by string.

Options are "ALWAYS_TRUE", "ALWAYS_FALSE", or "FILTER".

References protocols::helical_bundle::brf_always_false, protocols::helical_bundle::brf_always_true, protocols::helical_bundle::brf_filter_by_energy, and protocols::helical_bundle::brf_undefined.

Referenced by parse_my_tag().

◆ set_report_sequence()

void protocols::helical_bundle::BundleReporterFilter::set_report_sequence ( bool const val = true )

inline

Set whether we report sequences.

References report_sequence_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_score_type()

void protocols::helical_bundle::BundleReporterFilter::set_score_type ( core::scoring::ScoreType const & type )

inline

Set the score type.

References score_type_.

Referenced by parse_my_tag().

◆ set_score_type_threshold()

void protocols::helical_bundle::BundleReporterFilter::set_score_type_threshold ( core::Real const & val )

inline

Set the score threshold.

References score_type_threshold_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ set_scorefxn()

void protocols::helical_bundle::BundleReporterFilter::set_scorefxn ( core::scoring::ScoreFunctionOP scorefxn_in )

inline

Set the scorefunction.

References scorefxn_.

Referenced by parse_my_tag().

◆ set_use_threeletter()

void protocols::helical_bundle::BundleReporterFilter::set_use_threeletter ( bool const val = true )

inline

Set whether we report three-letter codes.

References report_three_letter_codes_, and protocols::hybridization::val.

Referenced by parse_my_tag().

◆ use_threeletter()

bool protocols::helical_bundle::BundleReporterFilter::use_threeletter ( ) const

inline

Get whether we report three-letter codes.

References report_three_letter_codes_.

Referenced by generate_full_tracer_report(), and parse_my_tag().

Member Data Documentation

◆ behaviour_

BundleReporterFilterBehaviour protocols::helical_bundle::BundleReporterFilter::behaviour_

private

The behaviour of this filter.

Defaults to always returning true, but can be set to always return false or to filter by energy.

Referenced by filter_behaviour(), and set_filter_behaviour().

◆ report_sequence_

bool protocols::helical_bundle::BundleReporterFilter::report_sequence_

private

Report sequence? False by default.

Referenced by report_sequence(), and set_report_sequence().

◆ report_three_letter_codes_

bool protocols::helical_bundle::BundleReporterFilter::report_three_letter_codes_

private

Report one- or three-letter codes? False (one-letter codes) by default.

Referenced by set_use_threeletter(), and use_threeletter().

◆ score_type_

core::scoring::ScoreType protocols::helical_bundle::BundleReporterFilter::score_type_

private

What score term should be reported/used to filter?

Set to total_score by default.

Referenced by compute(), report(), score_type(), and set_score_type().

◆ score_type_threshold_

core::Real protocols::helical_bundle::BundleReporterFilter::score_type_threshold_

private

If the score is used to filter, what's the cutoff threshold above which the filter returns false?

0.0 by default.

Referenced by score_type_threshold(), and set_score_type_threshold().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::helical_bundle::BundleReporterFilter::scorefxn_

private

What scorefunction should be reported/used to filter?

Must be specified by the user or in the code prior to invoking the filter; defaults to a null pointer.

Referenced by compute(), scorefxn(), and set_scorefxn().

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

src/protocols/helical_bundle/BundleReporterFilter.hh
src/protocols/helical_bundle/BundleReporterFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ BundleReporterFilter() [1/2]

◆ BundleReporterFilter() [2/2]

◆ ~BundleReporterFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ filter_behaviour()

◆ fresh_instance()

◆ generate_full_tracer_report()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sequence()

◆ report_sm()

◆ score_type()

◆ score_type_threshold()

◆ scorefxn()

◆ set_filter_behaviour() [1/2]

◆ set_filter_behaviour() [2/2]

◆ set_report_sequence()

◆ set_score_type()

◆ set_score_type_threshold()

◆ set_scorefxn()

◆ set_use_threeletter()

◆ use_threeletter()

Member Data Documentation

◆ behaviour_

◆ report_sequence_

◆ report_three_letter_codes_

◆ score_type_

◆ score_type_threshold_

◆ scorefxn_