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core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric Class Reference

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::Realcalculate (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)
 
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...
 
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)
 
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...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool simple_metric_is_unpublished () const
 Does this simple metric indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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

Constructors ///.

Default constructor

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

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

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

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

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

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

std::string core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::name_static ( )
static
void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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_.

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 parse_my_tag().

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 parse_my_tag().

Member Data Documentation

pose::PoseCOP core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::ref_pose_ = nullptr
private
scoring::ScoreFunctionCOP core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::scorefxn_ = nullptr
private

Referenced by calculate(), and set_scorefunction().

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: