A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP. More...

#include <SecondaryStructureMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SecondaryStructureMetric:

[legend]

Public Member Functions
	SecondaryStructureMetric ()
	Constructors ///. More...

	SecondaryStructureMetric (select::residue_selector::ResidueSelectorCOP selector)

	SecondaryStructureMetric (SecondaryStructureMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~SecondaryStructureMetric () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

std::string	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)

void	set_use_dssp_reduced (bool reduced)
	Set to use the reduced DSSP alphabet or not. Default true. More...

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...

core::simple_metrics::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::StringMetric
	StringMetric ()

	~StringMetric () override

	StringMetric (StringMetric const &other)

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...

std::string	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 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 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
select::residue_selector::ResidueSelectorCOP	selector_ = nullptr

bool	dssp_reduced_ = true

Detailed Description

A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SecondaryStructureMetric::SecondaryStructureMetric ( )

Constructors ///.

Default constructor

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

References set_residue_selector().

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References selector_.

core::simple_metrics::metrics::SecondaryStructureMetric::~SecondaryStructureMetric ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

std::string core::simple_metrics::metrics::SecondaryStructureMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Defined in RealMetric:

Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix.

Score is added through setExtraScorePose and is output into the score tables/file at pose output. Calculate the metric. Return the SS string using DSSP. Reduced, 3 letter alphabet as the default.

Implements core::simple_metrics::StringMetric.

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), dssp_reduced_, core::scoring::dssp::Dssp::get_dssp_secstruct(), core::select::get_residues_from_subset(), selector_, core::pose::Pose::size(), and core::id::to_string().

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

overridevirtual

Implements core::simple_metrics::StringMetric.

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::StringMetric.

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

overridevirtual

Name of the class.

Implements core::simple_metrics::StringMetric.

References name_static().

Referenced by provide_citation_info().

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

static

Name of the class for creator.

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

void core::simple_metrics::metrics::SecondaryStructureMetric::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::StringMetric.

References core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), set_residue_selector(), and set_use_dssp_reduced().

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

static

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

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

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

References selector_.

Referenced by parse_my_tag(), and SecondaryStructureMetric().

void core::simple_metrics::metrics::SecondaryStructureMetric::set_use_dssp_reduced ( bool reduced )

Set to use the reduced DSSP alphabet or not. Default true.

References dssp_reduced_.

Referenced by parse_my_tag().

Member Data Documentation

bool core::simple_metrics::metrics::SecondaryStructureMetric::dssp_reduced_ = true

private

Referenced by calculate(), and set_use_dssp_reduced().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::SecondaryStructureMetric::selector_ = nullptr

private

Referenced by calculate(), provide_citation_info(), SecondaryStructureMetric(), and set_residue_selector().

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

src/core/simple_metrics/metrics/SecondaryStructureMetric.hh
src/core/simple_metrics/metrics/SecondaryStructureMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation