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core::simple_metrics::per_residue_metrics::PerResidueSasaMetric Class Reference

A per-residue metric that will calculate SASA for each residue given in a selector. More...

#include <PerResidueSasaMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueSasaMetric:
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Public Member Functions

 PerResidueSasaMetric ()=default
 Constructors ///. More...
 
 PerResidueSasaMetric (core::scoring::sasa::SasaMethodHPMode const mode)
 Mode constructor. More...
 
 PerResidueSasaMetric (PerResidueSasaMetric const &)=default
 Copy constructor (not needed unless you need deep copies) More...
 
 ~PerResidueSasaMetric () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
std::map< core::Size, core::Realcalculate (core::pose::Pose const &pose) const override
 Metric Methods ///. 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 set_mode (core::scoring::sasa::SasaMethodHPMode const mode_in)
 Set the SASA mode (all SASA, polar only, hydrophobic only, etc.). More...
 
void set_mode (std::string const &mode_in)
 Set the SASA mode (all SASA, polar only, hydrophobic only, etc.). More...
 
core::scoring::sasa::SasaMethodHPMode mode () const
 Get the SASA mode (all SASA, polar only, hydrophobic only, etc.). More...
 
- Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
 PerResidueRealMetric ()
 
 ~PerResidueRealMetric () override
 
 PerResidueRealMetric (PerResidueRealMetric const &other)
 
PerResidueRealMetricoperator= (PerResidueRealMetric 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...
 
void set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
 Set a ResidueSelector for which we will calculate values over. More...
 
void set_output_as_pdb_nums (bool output_as_pdb_nums)
 Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...
 
std::map< core::Size, core::Realcached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_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 submetric names that this Metric will calculate. More...
 
select::residue_selector::ResidueSelectorCOP get_selector () const
 Get the set residue selector of this class. More...
 
virtual void parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
 Parse the base class tag. Keep required interface for parse_my_tag. 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...
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::PerResidueRealMetric
static void add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
 Add options to the schema from this base class. More...
 
- 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::scoring::sasa::SasaMethodHPMode mode_ = core::scoring::sasa::SasaMethodHPMode::ALL_SASA
 The SASA mode (all SASA, polar only, hydrophobic only, etc.). More...
 

Detailed Description

A per-residue metric that will calculate SASA for each residue given in a selector.

Virtual atoms are skipped completely.

Constructor & Destructor Documentation

core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::PerResidueSasaMetric ( )
default

Constructors ///.

Default constructor

core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::PerResidueSasaMetric ( core::scoring::sasa::SasaMethodHPMode const  mode)

Mode constructor.

Constructors ///.

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

Mode constructor.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::PerResidueSasaMetric ( PerResidueSasaMetric const &  )
default

Copy constructor (not needed unless you need deep copies)

core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::~PerResidueSasaMetric ( )
override

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

Member Function Documentation

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::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. Defined in PerResidueRealMetric Calculate the metric. This map is Rosetta Resnum->value and includes only those residues selected.

Return by value as this function can not STORE the result, it only calculates. Store the result in the pose by using the apply method, which calls this method and stores the result in the pose as ExtraScoreValues.

Implements core::simple_metrics::PerResidueRealMetric.

References core::scoring::sasa::SasaCalc::calculate(), core::scoring::sasa::SasaCalc::get_residue_sasa(), core::select::get_residues_from_subset(), and core::scoring::sasa::SasaCalc::set_sasa_method_hp_mode().

Referenced by core::simple_metrics::metrics::SasaMetric::calculate().

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

core::scoring::sasa::SasaMethodHPMode core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::mode ( ) const
inline

Get the SASA mode (all SASA, polar only, hydrophobic only, etc.).

Note
The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References mode_.

std::string core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::name ( ) const
overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

std::string core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::name_static ( )
static
void core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::set_mode ( core::scoring::sasa::SasaMethodHPMode const  mode_in)

Set the SASA mode (all SASA, polar only, hydrophobic only, etc.).

Note
The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).
void core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::set_mode ( std::string const &  mode_in)

Set the SASA mode (all SASA, polar only, hydrophobic only, etc.).

Note
The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.
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::SasaMethod::sasa_metric_mode_from_name().

Member Data Documentation

core::scoring::sasa::SasaMethodHPMode core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::mode_ = core::scoring::sasa::SasaMethodHPMode::ALL_SASA
private

The SASA mode (all SASA, polar only, hydrophobic only, etc.).

Note
The enum class is defined in core/simple_metrics/metrics/SasaMetric.hh.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Referenced by mode().


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