A Metric to cacluate overall sasa of a pose. More...

#include <SasaMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SasaMetric:

Public Member Functions
	SasaMetric ()=default
	Default constructor. More...

	SasaMetric (select::residue_selector::ResidueSelectorCOP selector, core::scoring::sasa::SasaMethodHPMode const mode=core::scoring::sasa::SasaMethodHPMode::ALL_SASA)

	SasaMetric (SasaMetric const &)=default

	~SasaMetric () override

core::Real	calculate (pose::Pose const &pose) const override
	Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set a residue selector to calculate total sasa of residues in the selector. More...

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

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

void	set_sasa_metric_mode (core::scoring::sasa::SasaMethodHPMode const mode_in)
	Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.). More...

void	set_sasa_metric_mode (std::string const &mode_in)
	Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.). More...

core::scoring::sasa::SasaMethodHPMode	sasa_metric_mode () const
	Get the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.). 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 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::scoring::sasa::SasaMethodHPMode	sasa_metric_mode_ = core::scoring::sasa::SasaMethodHPMode::ALL_SASA
	The mode for this metric. Default is to count all solvent-accessible surface area. More...

Detailed Description

A Metric to cacluate overall sasa of a pose.

Use the Apply method to calculate and add the metric to the pose score to be written Virtual atoms are skipped completely.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SasaMetric::SasaMetric ( )

default

Default constructor.

core::simple_metrics::metrics::SasaMetric::SasaMetric	(	select::residue_selector::ResidueSelectorCOP	selector,
		core::scoring::sasa::SasaMethodHPMode const	mode = `core::scoring::sasa::SasaMethodHPMode::ALL_SASA`
	)

References set_residue_selector(), and set_sasa_metric_mode().

core::simple_metrics::metrics::SasaMetric::SasaMetric ( SasaMetric const & )

default

core::simple_metrics::metrics::SasaMetric::~SasaMetric ( )

override

Member Function Documentation

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

overridevirtual

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

Base Class Interface:

Score is added through setExtraScorePose and is output into the score tables/file at pose output. Calculate The total sasa of the pose or the SASA of the residues given in a residue selector.

Implements core::simple_metrics::RealMetric.

References core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::calculate(), sasa_metric_mode_, selector_, and core::simple_metrics::PerResidueRealMetric::set_residue_selector().

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

overridevirtual

Implements core::simple_metrics::RealMetric.

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

overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

static

Name of the class for creator.

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

void core::simple_metrics::metrics::SasaMetric::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 core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), set_residue_selector(), and set_sasa_metric_mode().

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), core::scoring::sasa::SasaMethod::list_sasa_method_hp_modes(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

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

core::scoring::sasa::SasaMethodHPMode core::simple_metrics::metrics::SasaMetric::sasa_metric_mode ( ) const

inline

Get the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References sasa_metric_mode_.

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

Set a residue selector to calculate total sasa of residues in the selector.

References selector_.

Referenced by parse_my_tag(), and SasaMetric().

void core::simple_metrics::metrics::SasaMetric::set_sasa_metric_mode ( core::scoring::sasa::SasaMethodHPMode const mode_in )

Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::sasa::END_OF_LIST, and sasa_metric_mode_.

Referenced by parse_my_tag(), SasaMetric(), and set_sasa_metric_mode().

void core::simple_metrics::metrics::SasaMetric::set_sasa_metric_mode ( std::string const & mode_in )

Set the behaviour of this metric (count all SASA, count polar SASA, count hydrophobic SASA, etc.).

Default is to compute all SASA.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References core::scoring::sasa::INVALID_MODE, core::scoring::sasa::SasaMethod::sasa_metric_mode_from_name(), and set_sasa_metric_mode().

Member Data Documentation

core::scoring::sasa::SasaMethodHPMode core::simple_metrics::metrics::SasaMetric::sasa_metric_mode_ = core::scoring::sasa::SasaMethodHPMode::ALL_SASA

private

The mode for this metric. Default is to count all solvent-accessible surface area.

Referenced by calculate(), sasa_metric_mode(), and set_sasa_metric_mode().

core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::SasaMetric::selector_

private

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

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation