compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62. More...

#include <SequenceSimilarityMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SequenceSimilarityMetric:

[legend]

Public Member Functions
	SequenceSimilarityMetric ()

	SequenceSimilarityMetric (select::residue_selector::ResidueSelectorCOP selector)

	SequenceSimilarityMetric (SequenceSimilarityMetric const &src)

	~SequenceSimilarityMetric () override

core::Real	calculate (pose::Pose const &pose) const override
	Calculate the metric. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	the selector will decide which positions will be scored More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector, bool apply_selector_to_native)

void	set_native_pose (core::pose::PoseCOP setting)

void	set_apply_selector_to_native (bool setting)

void	set_native_pose (core::pose::PoseCOP setting, bool apply_selector_to_native)

void	set_normalize (bool setting)

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

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

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

SimpleMetricOP	clone () const override

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from core::simple_metrics::RealMetric
	RealMetric ()

	~RealMetric () override

	RealMetric (RealMetric const &other)

RealMetric &	operator= (RealMetric 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...

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

utility::vector1< std::string >	get_metric_names () const override
	Get the metric name(s) that this Metric will calculate. 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...

Static Public Member Functions
static core::Real	score (std::string const &seq1, std::string const &seq2, bool normalize)

static std::string	name_static ()
	Name of the class for creator. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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
core::select::residue_selector::ResidueSelectorCOP	selector_

core::pose::PoseCOP	native_pose_

bool	apply_selector_to_native_

bool	normalize_

Detailed Description

compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( )

core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( select::residue_selector::ResidueSelectorCOP selector )

core::simple_metrics::metrics::SequenceSimilarityMetric::SequenceSimilarityMetric ( SequenceSimilarityMetric const & src )

References apply_selector_to_native_, native_pose_, normalize_, and selector_.

core::simple_metrics::metrics::SequenceSimilarityMetric::~SequenceSimilarityMetric ( )

override

Member Function Documentation

core::Real core::simple_metrics::metrics::SequenceSimilarityMetric::calculate ( pose::Pose const & pose ) const

overridevirtual

Calculate the metric.

Calculate and return the value. This function can not store the value. Use the apply function to store the value in the pose.

Implements core::simple_metrics::RealMetric.

References apply_selector_to_native_, native_pose_, normalize_, core::pose::Pose::pdb_info(), score(), selector_, core::pose::Pose::sequence(), and core::pose::Pose::size().

SimpleMetricOP core::simple_metrics::metrics::SequenceSimilarityMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::RealMetric.

std::string core::simple_metrics::metrics::SequenceSimilarityMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

std::string core::simple_metrics::metrics::SequenceSimilarityMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

Referenced by provide_citation_info().

std::string core::simple_metrics::metrics::SequenceSimilarityMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::metrics::SequenceSimilarityMetricCreator::keyname(), name(), and provide_xml_schema().

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

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::RealMetric.

References native_pose_, core::select::residue_selector::parse_residue_selector(), core::pose::saved_native_pose(), set_apply_selector_to_native(), set_normalize(), and set_residue_selector().

void core::simple_metrics::metrics::SequenceSimilarityMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), and selector_.

void core::simple_metrics::metrics::SequenceSimilarityMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::metrics::SequenceSimilarityMetricCreator::provide_xml_schema().

core::Real core::simple_metrics::metrics::SequenceSimilarityMetric::score	(	std::string const &	seq1,
		std::string const &	seq2,
		bool	normalize
	)

static

References protocols::mean_field::num_elements().

Referenced by calculate().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_apply_selector_to_native ( bool setting )

inline

References apply_selector_to_native_.

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

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose ( core::pose::PoseCOP setting )

inline

References native_pose_.

Referenced by set_native_pose().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_native_pose	(	core::pose::PoseCOP	setting,
		bool	apply_selector_to_native
	)

inline

References set_apply_selector_to_native(), and set_native_pose().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_normalize ( bool setting )

inline

References normalize_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

inline

the selector will decide which positions will be scored

References selector_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::SequenceSimilarityMetric::set_residue_selector	(	core::select::residue_selector::ResidueSelectorCOP	selector,
		bool	apply_selector_to_native
	)