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core::simple_metrics::metrics::SasaMetric Class Reference

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

#include <SasaMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SasaMetric:
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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
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation information for the residue selector that it uses. More...
 
bool simple_metric_is_unpublished () const override
 This simple metric is unpublished (returns true). More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This simple metric is unpublished. It returns Jared Adolf-Bryfogle and Vikram K. Mulligan. More...
 
- Public Member Functions inherited from core::simple_metrics::RealMetric
 RealMetric ()
 
 ~RealMetric () override
 
 RealMetric (RealMetric const &other)
 
void apply (pose::Pose &pose, std::string prefix="", std::string suffix="", bool override_existing_data=false) const override
 Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix. 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)
 
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 bool simple_metric_provides_citation_info () const
 Does this simple metric provide information about how to cite it? 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 
)
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
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_authorship_info_for_unpublished().

std::string core::simple_metrics::metrics::SasaMetric::name_static ( )
static
void core::simple_metrics::metrics::SasaMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::simple_metrics::metrics::SasaMetric::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This simple metric is unpublished. It returns Jared Adolf-Bryfogle and Vikram K. Mulligan.

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

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::simple_metrics::metrics::SasaMetric::provide_citation_info ( ) const
overridevirtual

This simple metric is unpublished, but can provide citation information for the residue selector that it uses.

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

Reimplemented from core::simple_metrics::SimpleMetric.

References selector_.

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

bool core::simple_metrics::metrics::SasaMetric::simple_metric_is_unpublished ( ) const
overridevirtual

This simple metric is unpublished (returns true).

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

Reimplemented from core::simple_metrics::SimpleMetric.

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

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