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core::simple_metrics::metrics::SecondaryStructureMetric Class Reference

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:
Inheritance graph

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)
SimpleMetricoperator= (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
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)
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 ( )

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

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

Name of the metric.

Implements core::simple_metrics::StringMetric.

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

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 ( )
void core::simple_metrics::metrics::SecondaryStructureMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
void core::simple_metrics::metrics::SecondaryStructureMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const

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)
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

Referenced by calculate(), and set_use_dssp_reduced().

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

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