A filter takes any SimpleMetric and applies a set cutoff to filter the model. Set the cutoff type to set the behavior of the metric. More...

#include <SimpleMetricFilter.hh>

Inheritance diagram for protocols::simple_filters::SimpleMetricFilter:

[legend]

Public Member Functions
	SimpleMetricFilter ()

	SimpleMetricFilter (core::simple_metrics::SimpleMetricCOP metric, comparison_type co_type)

	SimpleMetricFilter (core::simple_metrics::SimpleMetricCOP metric, comparison_type co_type, std::string composite_action)

	~SimpleMetricFilter () override

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

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	set_simple_metric (core::simple_metrics::SimpleMetricCOP metric)
	Set the SimpleMetric that we will be using to filter. More...

void	set_use_cached_data (bool use_cache, std::string prefix="", std::string suffix="")
	Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix. More...

void	set_fail_on_missing_cache (bool fail)
	If use_cache is set to false, do we fail if no data is found in the pose? Default True. More...

void	set_cutoff (core::Real cutoff)
	Set the cutoff value for any RealMetric or CompositeRealMetric. More...

void	set_match_string (std::string const &match_string)
	Set the match value for any StringMetric or CompositeStringMetric. More...

void	set_comparison_type (comparison_type co_type)
	Sets the cutoff type - aka eq, ne, etc. Options are: eq, ne, lt, gt, lt_or_eq, gt_or_eq. More...

void	set_composite_action (std::string const &composite_action)
	Set the action we take for a set CompositeMetric. More...

void	set_use_sum_for_per_residue_real (bool use_sum_for_per_residue_real)
	Set the filter to use the SUM of values from a PerResidueRealMetric for filtering. This is instead of using the metric as a Composite Metric for each resnum. Default False. More...

void	set_epsilon (core::Real epsilon)
	Set the sigfigs we will use in our comparisons. Default is .0001;. More...

std::string	name () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

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

	Filter (std::string const &)

	~Filter () override

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

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
template<class T >
bool	compare_composites (std::map< std::string, T > const &values) const
	Takes std::map of std::string - value and returns a boolean if it passes the filter. More...

template<class T >
bool	compare_composites (std::map< core::Size, T > const &values) const
	Takes std::map of std::string - value and returns a boolean if it passes the filter. More...

bool	compare_metric (core::Real value) const

bool	compare_metric (std::string const &value) const

Private Attributes
core::simple_metrics::SimpleMetricCOP	metric_ = nullptr

comparison_type	type_ = bogus

core::Real	cutoff_ = 0

std::string	match_ = ""

core::Real	epsilon_ = .0001

std::string	composite_action_ = ""

bool	sum_per_residue_real_metric_ = false

bool	use_cache_ = false

std::string	cache_prefix_ = ""

std::string	cache_suffix_ = ""

bool	fail_on_missing_cache_ = true

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

Detailed Description

A filter takes any SimpleMetric and applies a set cutoff to filter the model. Set the cutoff type to set the behavior of the metric.

Compares metric_value to cutoff_value or match_value

match_value is used for strings, cutoff is used for numbers.

So, if comparison_type is set to eq, if metric_value eq the cutoff_value we return true.

RMSD example: set to lt, and the filter will pass with a metric value anything less than the cuttoff.

CompositeMetrics take an extra parameter, composite_action. Composite action can be "any", "all", or any specific composite metric value you want to match on.

Any: If any match the set criteria, we return true All: If all match the set criteria, we return true etc: If the particular metric of the composite metric (ex fa_rep for the CompositeEnergyMetric), matches the criteria, we return true.

See Methods: set_comparison_type(), set_composite_action(), set_cutoff_value(), set_match_string()

Constructor & Destructor Documentation

◆ SimpleMetricFilter() [1/3]

protocols::simple_filters::SimpleMetricFilter::SimpleMetricFilter ( )

◆ SimpleMetricFilter() [2/3]

protocols::simple_filters::SimpleMetricFilter::SimpleMetricFilter	(	core::simple_metrics::SimpleMetricCOP	metric,
		comparison_type	co_type
	)

References metric_, and set_comparison_type().

◆ SimpleMetricFilter() [3/3]

protocols::simple_filters::SimpleMetricFilter::SimpleMetricFilter	(	core::simple_metrics::SimpleMetricCOP	metric,
		comparison_type	co_type,
		std::string	composite_action
	)

References metric_, set_comparison_type(), and set_composite_action().

◆ ~SimpleMetricFilter()

protocols::simple_filters::SimpleMetricFilter::~SimpleMetricFilter ( )

override

Member Function Documentation

◆ apply()

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

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References cache_prefix_, cache_suffix_, core::simple_metrics::CompositeRealMetric::cached_calculate(), core::simple_metrics::CompositeStringMetric::cached_calculate(), core::simple_metrics::RealMetric::cached_calculate(), core::simple_metrics::StringMetric::cached_calculate(), core::simple_metrics::PerResidueRealMetric::cached_calculate(), core::simple_metrics::PerResidueStringMetric::cached_calculate(), compare_composites(), compare_metric(), fail_on_missing_cache_, metric_, core::simple_metrics::metrics::sum, sum_per_residue_real_metric_, core::id::to_string(), protocols::simple_filters::TR(), and use_cache_.

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compare_composites() [1/2]

template<class T >

bool protocols::simple_filters::SimpleMetricFilter::compare_composites ( std::map< core::Size, T > const & values ) const

private

Takes std::map of std::string - value and returns a boolean if it passes the filter.

References compare_metric(), composite_action_, cutoff_, metric_, core::id::to_string(), and protocols::simple_filters::TR().

◆ compare_composites() [2/2]

template<class T >

bool protocols::simple_filters::SimpleMetricFilter::compare_composites ( std::map< std::string, T > const & values ) const

private

Takes std::map of std::string - value and returns a boolean if it passes the filter.

References compare_metric(), composite_action_, cutoff_, metric_, and protocols::simple_filters::TR().

Referenced by apply().

◆ compare_metric() [1/2]

bool protocols::simple_filters::SimpleMetricFilter::compare_metric ( core::Real value ) const

private

References protocols::simple_filters::bogus, cutoff_, epsilon_, protocols::simple_filters::eq, protocols::simple_filters::gt, protocols::simple_filters::gt_or_eq, protocols::simple_filters::lt, protocols::simple_filters::lt_or_eq, metric_, protocols::simple_filters::ne, protocols::simple_filters::TR(), and type_.

Referenced by apply(), and compare_composites().

◆ compare_metric() [2/2]

bool protocols::simple_filters::SimpleMetricFilter::compare_metric ( std::string const & value ) const

private

References protocols::simple_filters::bogus, protocols::simple_filters::eq, match_, metric_, protocols::simple_filters::ne, protocols::simple_filters::TR(), and type_.

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References epsilon_, fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), protocols::simple_filters::get_string_comparison_type_map(), set_comparison_type(), set_composite_action(), set_cutoff(), set_epsilon(), set_fail_on_missing_cache(), set_match_string(), set_simple_metric(), set_use_cached_data(), set_use_sum_for_per_residue_real(), and sum_per_residue_real_metric_.

◆ provide_xml_schema()

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

static

References class_name(), protocols::simple_filters::get_string_comparison_type_strings(), core::id::to_string(), and protocols::filters::xsd_type_definition_w_attributes_and_repeatable_subelements().

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

◆ report_sm()

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

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References cache_prefix_, cache_suffix_, core::simple_metrics::RealMetric::cached_calculate(), fail_on_missing_cache_, metric_, protocols::simple_filters::TR(), and use_cache_.

◆ set_comparison_type()

void protocols::simple_filters::SimpleMetricFilter::set_comparison_type ( comparison_type co_type )

Sets the cutoff type - aka eq, ne, etc. Options are: eq, ne, lt, gt, lt_or_eq, gt_or_eq.

If this is a StringMetric, only eq and ne are relevant here. IF value [comparison_type] cutoff_ return True.

References type_.

Referenced by parse_my_tag(), and SimpleMetricFilter().

◆ set_composite_action()

void protocols::simple_filters::SimpleMetricFilter::set_composite_action ( std::string const & composite_action )

Set the action we take for a set CompositeMetric.

Composite action can be "any", "all", or any specific composite metric value you want to match on. See Also: set_comparison_type(), set_cutoff

Any: If any match the set criteria, we return true All: If all match the set criteria, we return true etc: If the particular metric of the composite metric (ex fa_rep for the CompositeEnergyMetric), matches the criteria, we return true.

References composite_action_.

Referenced by parse_my_tag(), and SimpleMetricFilter().

◆ set_cutoff()

void protocols::simple_filters::SimpleMetricFilter::set_cutoff ( core::Real cutoff )

Set the cutoff value for any RealMetric or CompositeRealMetric.

Set the cutoff value.

References cutoff_.

Referenced by parse_my_tag().

◆ set_epsilon()

void protocols::simple_filters::SimpleMetricFilter::set_epsilon ( core::Real epsilon )

Set the sigfigs we will use in our comparisons. Default is .0001;.

Set the sigfigs we will use in our comparisons. Default is .0001.

References epsilon_.

Referenced by parse_my_tag().

◆ set_fail_on_missing_cache()

void protocols::simple_filters::SimpleMetricFilter::set_fail_on_missing_cache ( bool fail )

If use_cache is set to false, do we fail if no data is found in the pose? Default True.

References fail_on_missing_cache_.

Referenced by parse_my_tag().

◆ set_match_string()

void protocols::simple_filters::SimpleMetricFilter::set_match_string ( std::string const & match_string )

Set the match value for any StringMetric or CompositeStringMetric.

References match_.

Referenced by parse_my_tag().

◆ set_simple_metric()

void protocols::simple_filters::SimpleMetricFilter::set_simple_metric ( core::simple_metrics::SimpleMetricCOP metric )

Set the SimpleMetric that we will be using to filter.

Set the SimpleMetric (RealMetric) that we will be using to filter.

References metric_.

Referenced by parse_my_tag().

◆ set_use_cached_data()

void protocols::simple_filters::SimpleMetricFilter::set_use_cached_data	(	bool	use_cache,
		std::string	prefix = `""`,
		std::string	suffix = `""`
	)

Set a boolean to attempt to find cached data matching the name/custom_type of the passed in simple_metric. Optionally pass any set prefix/suffix.

This will allow the filter to re-use previously calculated data.

References cache_prefix_, cache_suffix_, protocols::simple_filters::TR(), and use_cache_.

Referenced by parse_my_tag().

◆ set_use_sum_for_per_residue_real()

void protocols::simple_filters::SimpleMetricFilter::set_use_sum_for_per_residue_real ( bool use_sum_for_per_residue_real )

Set the filter to use the SUM of values from a PerResidueRealMetric for filtering. This is instead of using the metric as a Composite Metric for each resnum. Default False.

References sum_per_residue_real_metric_.

Referenced by parse_my_tag().

Member Data Documentation

◆ cache_prefix_

std::string protocols::simple_filters::SimpleMetricFilter::cache_prefix_ = ""

private

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

◆ cache_suffix_

std::string protocols::simple_filters::SimpleMetricFilter::cache_suffix_ = ""

private

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

◆ composite_action_

std::string protocols::simple_filters::SimpleMetricFilter::composite_action_ = ""

private

Referenced by compare_composites(), and set_composite_action().

◆ cutoff_

core::Real protocols::simple_filters::SimpleMetricFilter::cutoff_ = 0

private

Referenced by compare_composites(), compare_metric(), and set_cutoff().

◆ epsilon_

core::Real protocols::simple_filters::SimpleMetricFilter::epsilon_ = .0001

private

Referenced by compare_metric(), parse_my_tag(), and set_epsilon().

◆ fail_on_missing_cache_

bool protocols::simple_filters::SimpleMetricFilter::fail_on_missing_cache_ = true

private

Referenced by apply(), parse_my_tag(), report_sm(), and set_fail_on_missing_cache().

◆ match_

std::string protocols::simple_filters::SimpleMetricFilter::match_ = ""

private

Referenced by compare_metric(), and set_match_string().

◆ metric_

core::simple_metrics::SimpleMetricCOP protocols::simple_filters::SimpleMetricFilter::metric_ = nullptr

private

Referenced by apply(), compare_composites(), compare_metric(), report_sm(), set_simple_metric(), and SimpleMetricFilter().

◆ sum_per_residue_real_metric_

bool protocols::simple_filters::SimpleMetricFilter::sum_per_residue_real_metric_ = false

private

Referenced by apply(), parse_my_tag(), and set_use_sum_for_per_residue_real().

◆ type_

comparison_type protocols::simple_filters::SimpleMetricFilter::type_ = bogus

private

Referenced by compare_metric(), and set_comparison_type().

◆ use_cache_

bool protocols::simple_filters::SimpleMetricFilter::use_cache_ = false

private

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

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

src/protocols/simple_filters/SimpleMetricFilter.hh
src/protocols/simple_filters/SimpleMetricFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SimpleMetricFilter() [1/3]

◆ SimpleMetricFilter() [2/3]

◆ SimpleMetricFilter() [3/3]

◆ ~SimpleMetricFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compare_composites() [1/2]

◆ compare_composites() [2/2]

◆ compare_metric() [1/2]

◆ compare_metric() [2/2]

◆ fresh_instance()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_sm()

◆ set_comparison_type()

◆ set_composite_action()

◆ set_cutoff()

◆ set_epsilon()

◆ set_fail_on_missing_cache()

◆ set_match_string()

◆ set_simple_metric()

◆ set_use_cached_data()

◆ set_use_sum_for_per_residue_real()

Member Data Documentation

◆ cache_prefix_

◆ cache_suffix_

◆ composite_action_

◆ cutoff_

◆ epsilon_

◆ fail_on_missing_cache_

◆ match_

◆ metric_

◆ sum_per_residue_real_metric_

◆ type_

◆ use_cache_