A class that is derived to calculate a set of core::Real values for each Residue. Apply(pose) method calculates this metric and adds it to the pose score for output. More...

#include <PerResidueRealMetric.hh>

Inheritance diagram for core::simple_metrics::PerResidueRealMetric:

[legend]

Public Member Functions
	PerResidueRealMetric ()

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

PerResidueRealMetric &	operator= (PerResidueRealMetric const &)

void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as out_label. More...

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for which we will calculate values over. More...

void	set_output_as_pdb_nums (bool output_as_pdb_nums)
	Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...

virtual std::map< core::Size, core::Real >	calculate (pose::Pose const &pose) const =0
	Calculate the metric. This map is Rosetta Resnum->value and includes only those residues selected. More...

std::map< core::Size, core::Real >	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_cache=true) const
	Grab the data from the pose if it exists or calculate the metric. More...

std::string	name () const override=0
	Name of the class. More...

std::string	metric () const override=0
	Name of the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. More...

select::residue_selector::ResidueSelectorCOP	get_selector () const
	Get the set residue selector of this class. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override=0
	called by parse_my_tag – should not be used directly More...

SimpleMetricOP	clone () const override=0

virtual void	parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

Public Member Functions inherited from core::simple_metrics::SimpleMetric
	SimpleMetric (std::string const &simple_metric_type)

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

void	set_custom_type (std::string const &custom_type)

std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...

virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

std::string	simple_metric_type () const

std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...

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 void	add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
	Add options to the schema from this base class. More...

Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
select::residue_selector::ResidueSelectorCOP	selector_

bool	output_as_pdb_nums_ = false

Detailed Description

A class that is derived to calculate a set of core::Real values for each Residue. Apply(pose) method calculates this metric and adds it to the pose score for output.

Calculate(pose) method calculates core::Real values and returns them as a map<Size, Real> Resnum:Value

Constructor & Destructor Documentation

core::simple_metrics::PerResidueRealMetric::PerResidueRealMetric ( )

References selector_.

core::simple_metrics::PerResidueRealMetric::~PerResidueRealMetric ( )

overridedefault

core::simple_metrics::PerResidueRealMetric::PerResidueRealMetric ( PerResidueRealMetric const & other )

References selector_.

Member Function Documentation

void core::simple_metrics::PerResidueRealMetric::add_schema ( utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema )

static

Add options to the schema from this base class.

References core::simple_metrics::add_per_residue_simple_metric_schema().

Referenced by core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

void core::simple_metrics::PerResidueRealMetric::apply	(	std::string const &	out_label,
		pose::Pose &	pose,
		bool	override_existing_data = `false`
	)		const

overridevirtual

Calculate the metric and add it to the pose as a score. labeled as out_label.

Score is added to the SimpleMetricData cache in the pose A ReferencePose is created with out_label as a name for further access. Data is output to the final scorefile.

Implements core::simple_metrics::SimpleMetric.

References calculate(), core::simple_metrics::get_sm_data(), name(), output_as_pdb_nums_, and core::simple_metrics::throw_sm_override_error().

Referenced by core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::calculate(), core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::calculate(), and core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate().

std::map< core::Size, core::Real > core::simple_metrics::PerResidueRealMetric::cached_calculate	(	pose::Pose const &	pose,
		bool	use_cache,
		std::string	prefix = `""`,
		std::string	suffix = `""`,
		bool	fail_on_missing_cache = `true`,
		bool	use_ref_pose_for_cache = `true`
	)		const

Grab the data from the pose if it exists or calculate the metric.

If use_cache is true, we will attempt to pull the data from the pose. If fail_on_missing_cache is true, we will fail, otherwise, we will calculate the metric.

This function is meant to support caching metrics, so values do not need to be calculated twice, for example in SimpleMetricFilter/Features or code-wise where data takes a while to calculate and can be reused.

If we cached the data, we have created a ref-pose and can match the current resnums with our refpose resnums using the use_ref_pose_for_cache option. This allows us to delete residues and still retain the given data to match.

References calculate(), core::simple_metrics::SimpleMetric::get_final_sm_type(), core::simple_metrics::get_sm_data(), core::simple_metrics::has_sm_data(), and name().

Referenced by protocols::simple_filters::SimpleMetricFilter::apply(), and protocols::features::SimpleMetricFeatures::report_per_residue_features().

virtual std::map< core::Size, core::Real > core::simple_metrics::PerResidueRealMetric::calculate ( pose::Pose const & pose ) const

pure virtual

Calculate the metric. This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

Referenced by apply(), and cached_calculate().

SimpleMetricOP core::simple_metrics::PerResidueRealMetric::clone ( ) const

overridepure virtual

Implements core::simple_metrics::SimpleMetric.

utility::vector1< std::string > core::simple_metrics::PerResidueRealMetric::get_metric_names ( ) const

overridevirtual

Get the submetric names that this Metric will calculate.

Implements core::simple_metrics::SimpleMetric.

References metric().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::PerResidueRealMetric::get_selector ( ) const

Get the set residue selector of this class.

References selector_.

std::string core::simple_metrics::PerResidueRealMetric::metric ( ) const

overridepure virtual

Name of the metric.

Implements core::simple_metrics::SimpleMetric.

Referenced by get_metric_names(), and protocols::features::SimpleMetricFeatures::report_per_residue_features().

std::string core::simple_metrics::PerResidueRealMetric::name ( ) const

overridepure virtual

Name of the class.

Implements core::simple_metrics::SimpleMetric.

Referenced by apply(), and cached_calculate().

PerResidueRealMetric & core::simple_metrics::PerResidueRealMetric::operator= ( PerResidueRealMetric const & ot )

References core::simple_metrics::SimpleMetric::operator=(), output_as_pdb_nums_, and selector_.

Referenced by core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::operator=().

void core::simple_metrics::PerResidueRealMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridepure virtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::SimpleMetric.

void core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

virtual

Parse the base class tag. Keep required interface for parse_my_tag.

References core::select::residue_selector::parse_residue_selector(), set_output_as_pdb_nums(), and set_residue_selector().

void core::simple_metrics::PerResidueRealMetric::set_output_as_pdb_nums ( bool output_as_pdb_nums )

Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores.

References output_as_pdb_nums_.

Referenced by parse_per_residue_tag().

void core::simple_metrics::PerResidueRealMetric::set_residue_selector ( select::residue_selector::ResidueSelectorCOP selector )

Set a ResidueSelector for which we will calculate values over.

References selector_.

Referenced by core::simple_metrics::metrics::SasaMetric::calculate(), core::simple_metrics::metrics::RMSDMetric::calculate(), parse_per_residue_tag(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::PerResidueClashMetric(), and protocols::features::SimpleMetricFeatures::report_per_residue_features().

Member Data Documentation

bool core::simple_metrics::PerResidueRealMetric::output_as_pdb_nums_ = false

private

Referenced by apply(), operator=(), and set_output_as_pdb_nums().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::PerResidueRealMetric::selector_

private

Referenced by get_selector(), operator=(), PerResidueRealMetric(), and set_residue_selector().

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

src/core/simple_metrics/PerResidueRealMetric.hh
src/core/simple_metrics/PerResidueRealMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation