A per-residue metric that will calculate/output per residue total energies or a specific score component. WEIGHTED. Correctly decomposes energies to per-residue. More...

#include <PerResidueEnergyMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric:

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

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

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

std::map< core::Size, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_comparison_pose (pose::PoseCOP pose)
	Set a pose into to calculate/report delta of total energy or the energy term provided. (apply_pose - comparison_pose) More...

void	set_scorefunction (scoring::ScoreFunctionCOP scorefxn)
	Set a scorefunction. Will use default Rosetta scorefunction if not set. More...

void	set_scoretype (scoring::ScoreType scoretype)
	Set the scoretype data that we return. Default is total_score. 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

Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
	PerResidueRealMetric ()

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

PerResidueRealMetric &	operator= (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::Real >	cached_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...

virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const=0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as `label` Must be implemented by derived classes. More...

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...

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...

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
scoring::ScoreFunctionCOP	scorefxn_ = nullptr

pose::PoseCOP	ref_pose_ = nullptr

scoring::ScoreType	scoretype_ = scoring::total_score

Detailed Description

A per-residue metric that will calculate/output per residue total energies or a specific score component. WEIGHTED. Correctly decomposes energies to per-residue.

Constructor & Destructor Documentation

◆ PerResidueEnergyMetric() [1/2]

core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::PerResidueEnergyMetric ( )

Constructors ///.

Default constructor

◆ PerResidueEnergyMetric() [2/2]

core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::PerResidueEnergyMetric ( PerResidueEnergyMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PerResidueEnergyMetric()

core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::~PerResidueEnergyMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::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::pose::Pose::energies(), core::select::get_residues_from_subset(), core::scoring::get_score_function(), core::simple_metrics::PerResidueRealMetric::get_selector(), core::scoring::n_score_types, ref_pose_, core::scoring::Energies::residue_total_energies(), scorefxn_, scoretype_, and core::scoring::total_score.

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

◆ clone()

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

◆ metric()

std::string core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

◆ name()

std::string core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

◆ name_static()

std::string core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::per_residue_metrics::PerResidueEnergyMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::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::PerResidueRealMetric.

References core::simple_metrics::SimpleMetric::get_custom_type(), core::simple_metrics::SimpleMetric::parse_base_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), core::scoring::parse_score_function(), ref_pose_, core::pose::saved_native_pose(), core::pose::saved_reference_pose(), core::scoring::score_type_from_name(), set_scorefunction(), set_scoretype(), and TR().

◆ provide_xml_schema()

void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_get_score_function_name(), core::pose::attributes_for_saved_reference_pose(), core::scoring::n_score_types, core::scoring::name_from_score_type(), name_static(), and core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueEnergyMetricCreator::provide_xml_schema().

◆ set_comparison_pose()

void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::set_comparison_pose ( pose::PoseCOP pose )

Set a pose into to calculate/report delta of total energy or the energy term provided. (apply_pose - comparison_pose)

References ref_pose_.

◆ set_scorefunction()

void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::set_scorefunction ( scoring::ScoreFunctionCOP scorefxn )

Set a scorefunction. Will use default Rosetta scorefunction if not set.

References scorefxn_.

Referenced by core::simple_metrics::metrics::TotalEnergyMetric::calculate(), and parse_my_tag().

◆ set_scoretype()

void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::set_scoretype ( scoring::ScoreType scoretype )

Set the scoretype data that we return. Default is total_score.

References scoretype_.

Referenced by core::simple_metrics::metrics::TotalEnergyMetric::calculate(), and parse_my_tag().

Member Data Documentation

◆ ref_pose_

pose::PoseCOP core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::ref_pose_ = nullptr

private

Referenced by calculate(), parse_my_tag(), and set_comparison_pose().

◆ scorefxn_

scoring::ScoreFunctionCOP core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::scorefxn_ = nullptr

private

Referenced by calculate(), and set_scorefunction().

◆ scoretype_

scoring::ScoreType core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::scoretype_ = scoring::total_score

private

Referenced by calculate(), and set_scoretype().

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

src/core/simple_metrics/per_residue_metrics/PerResidueEnergyMetric.hh
src/core/simple_metrics/per_residue_metrics/PerResidueEnergyMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PerResidueEnergyMetric() [1/2]

◆ PerResidueEnergyMetric() [2/2]

◆ ~PerResidueEnergyMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_comparison_pose()

◆ set_scorefunction()

◆ set_scoretype()

Member Data Documentation

◆ ref_pose_

◆ scorefxn_

◆ scoretype_