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core::simple_metrics::metrics::TotalEnergyMetric Class Reference

A metric to report the total energy of the system or the delta total energy between another input pose. More...

#include <TotalEnergyMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::TotalEnergyMetric:
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Public Member Functions

 TotalEnergyMetric ()
 Constructors ///. More...
 
 TotalEnergyMetric (core::select::residue_selector::ResidueSelectorCOP selector)
 
 TotalEnergyMetric (core::select::residue_selector::ResidueSelectorCOP selector, core::scoring::ScoreFunctionCOP scorefxn)
 
 TotalEnergyMetric (TotalEnergyMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~TotalEnergyMetric () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
core::Real calculate (core::pose::Pose const &pose) const override
 Metric Methods ///. More...
 
void set_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
 Set a scorefunction. Will use default Rosetta scorefunction if not set. More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP residue_selector)
 Set a residue selector to calculate total energy of a subset of residues. More...
 
void set_comparison_pose (core::pose::PoseCOP pose)
 Set a pose into to calculate/report delta of total energy. (apply_pose - comparison_pose) More...
 
void set_scoretype (scoring::ScoreType scoretype)
 Set a specific scoretype to report 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
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation informatino for the residue selector and scorefunction that it uses.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 This simple metric is unpublished (returns true).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 This simple metric is unpublished.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 as the author. 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::scoring::ScoreFunctionCOP scorefxn_ = nullptr
 
core::select::residue_selector::ResidueSelectorCOP residue_selector_ = nullptr
 
core::pose::PoseCOP ref_pose_ = nullptr
 
scoring::ScoreType scoretype_ = scoring::total_score
 

Detailed Description

A metric to report the total energy of the system or the delta total energy between another input pose.

Constructor & Destructor Documentation

core::simple_metrics::metrics::TotalEnergyMetric::TotalEnergyMetric ( )

Constructors ///.

Default constructor

core::simple_metrics::metrics::TotalEnergyMetric::TotalEnergyMetric ( core::select::residue_selector::ResidueSelectorCOP  selector)
core::simple_metrics::metrics::TotalEnergyMetric::TotalEnergyMetric ( core::select::residue_selector::ResidueSelectorCOP  selector,
core::scoring::ScoreFunctionCOP  scorefxn 
)
core::simple_metrics::metrics::TotalEnergyMetric::TotalEnergyMetric ( TotalEnergyMetric const &  src)
default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::metrics::TotalEnergyMetric::~TotalEnergyMetric ( )
override

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

Member Function Documentation

core::Real core::simple_metrics::metrics::TotalEnergyMetric::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. Calculate the metric. Returns the total score from the scorefunction or the total score of each residue in the residue selector.

If a comparison pose is given, will calculate the delta between them (pose - comparison_pose).

Implements core::simple_metrics::RealMetric.

References ref_pose_, residue_selector_, scorefxn_, and scoretype_.

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::TotalEnergyMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::TotalEnergyMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

This simple metric is unpublished. It returns Jared Adolf-Bryfogle as the author.

This simple metric is unpublished. It returns Jared Adolf-Bryfogle (original author) and Vikram K. Mulligan (expanded funcitionality) as authors.

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(), residue_selector_, and scorefxn_.

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

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

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 residue_selector_, and scorefxn_.

void core::simple_metrics::metrics::TotalEnergyMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::TotalEnergyMetric::set_comparison_pose ( core::pose::PoseCOP  pose)

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

References ref_pose_.

void core::simple_metrics::metrics::TotalEnergyMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  residue_selector)

Set a residue selector to calculate total energy of a subset of residues.

References residue_selector_.

Referenced by parse_my_tag(), and TotalEnergyMetric().

void core::simple_metrics::metrics::TotalEnergyMetric::set_scorefunction ( core::scoring::ScoreFunctionCOP  scorefxn)

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

References scorefxn_.

Referenced by parse_my_tag(), and TotalEnergyMetric().

void core::simple_metrics::metrics::TotalEnergyMetric::set_scoretype ( scoring::ScoreType  scoretype)

Set a specific scoretype to report Default is total_score.

References scoretype_.

Referenced by parse_my_tag().

bool core::simple_metrics::metrics::TotalEnergyMetric::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::pose::PoseCOP core::simple_metrics::metrics::TotalEnergyMetric::ref_pose_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::TotalEnergyMetric::residue_selector_ = nullptr
private
core::scoring::ScoreFunctionCOP core::simple_metrics::metrics::TotalEnergyMetric::scorefxn_ = nullptr
private
scoring::ScoreType core::simple_metrics::metrics::TotalEnergyMetric::scoretype_ = scoring::total_score
private

Referenced by calculate(), and set_scoretype().


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