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core::simple_metrics::metrics::InteractionEnergyMetric Class Reference

Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions. Pose should be scored! More...

#include <InteractionEnergyMetric.hh>

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

 InteractionEnergyMetric ()
 Constructors ///. More...
 
 InteractionEnergyMetric (select::residue_selector::ResidueSelectorCOP selector1, select::residue_selector::ResidueSelectorCOP selector2)
 
 InteractionEnergyMetric (InteractionEnergyMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~InteractionEnergyMetric () 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_residue_selectors (select::residue_selector::ResidueSelectorCOP selector1, select::residue_selector::ResidueSelectorCOP selector2)
 Set the residue selectors we will use to calculate the interaction energies. More...
 
void set_scorefunction (scoring::ScoreFunctionCOP scorefxn)
 Set a scorefunction. Only used if the pose is not scored. Not recommended, this is our failsafe! More...
 
void set_include_only_scoretypes (utility::vector1< scoring::ScoreType > const &include_only_scoretypes)
 Set this to include only these score types. More...
 
void set_ignore_scoretypes (utility::vector1< scoring::ScoreType > const &ignore_scoretypes)
 Always ignore these scoretypes. More...
 
void set_include_rama_prepro_and_proclose (bool include)
 Include Rama PrePro and ProClose? Default False. 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 This simple metric is unpublished, but can provide citation information for the residue selector that it uses.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 This simple metric is unpublished (returns true).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. 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

select::residue_selector::ResidueSelectorCOP selector1_ = nullptr
 
select::residue_selector::ResidueSelectorCOP selector2_ = nullptr
 
scoring::ScoreFunctionCOP scorefxn_ = nullptr
 
utility::vector1
< scoring::ScoreType
score_types_to_ignore_
 
utility::vector1
< scoring::ScoreType
score_types_to_use_only_
 
bool include_rama_prepro_and_proclose_ = false
 
bool force_rescore_pose_ = false
 

Detailed Description

Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions. Pose should be scored!

By default, we skip rama_prepro and pro_close

Scoretypes from REF:

fa_atr fa_rep fa_sol fa_elec lk_ball_wtd pro_close #ignored by default rama_prepro #ignored by default hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc

Constructor & Destructor Documentation

core::simple_metrics::metrics::InteractionEnergyMetric::InteractionEnergyMetric ( )

Constructors ///.

Default constructor

References core::scoring::get_score_function(), and scorefxn_.

Referenced by clone().

core::simple_metrics::metrics::InteractionEnergyMetric::InteractionEnergyMetric ( select::residue_selector::ResidueSelectorCOP  selector1,
select::residue_selector::ResidueSelectorCOP  selector2 
)
core::simple_metrics::metrics::InteractionEnergyMetric::InteractionEnergyMetric ( InteractionEnergyMetric const &  src)
default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

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

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

Member Function Documentation

core::Real core::simple_metrics::metrics::InteractionEnergyMetric::calculate ( core::pose::Pose const &  pose) const
overridevirtual
core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::InteractionEnergyMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::InteractionEnergyMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

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

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

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(), scorefxn_, selector1_, and selector2_.

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

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 scorefxn_, selector1_, and selector2_.

void core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::InteractionEnergyMetric::set_ignore_scoretypes ( utility::vector1< scoring::ScoreType > const &  ignore_scoretypes)

Always ignore these scoretypes.

References score_types_to_ignore_.

void core::simple_metrics::metrics::InteractionEnergyMetric::set_include_only_scoretypes ( utility::vector1< scoring::ScoreType > const &  include_only_scoretypes)

Set this to include only these score types.

References score_types_to_use_only_.

void core::simple_metrics::metrics::InteractionEnergyMetric::set_include_rama_prepro_and_proclose ( bool  include)

Include Rama PrePro and ProClose? Default False.

References include_rama_prepro_and_proclose_.

Referenced by parse_my_tag().

void core::simple_metrics::metrics::InteractionEnergyMetric::set_residue_selectors ( select::residue_selector::ResidueSelectorCOP  selector1,
select::residue_selector::ResidueSelectorCOP  selector2 
)

Set the residue selectors we will use to calculate the interaction energies.

References selector1_, and selector2_.

Referenced by InteractionEnergyMetric().

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

Set a scorefunction. Only used if the pose is not scored. Not recommended, this is our failsafe!

References scorefxn_.

Referenced by parse_my_tag().

bool core::simple_metrics::metrics::InteractionEnergyMetric::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

bool core::simple_metrics::metrics::InteractionEnergyMetric::force_rescore_pose_ = false
private

Referenced by parse_my_tag().

bool core::simple_metrics::metrics::InteractionEnergyMetric::include_rama_prepro_and_proclose_ = false
private
utility::vector1<scoring::ScoreType> core::simple_metrics::metrics::InteractionEnergyMetric::score_types_to_ignore_
private
utility::vector1<scoring::ScoreType> core::simple_metrics::metrics::InteractionEnergyMetric::score_types_to_use_only_
private
scoring::ScoreFunctionCOP core::simple_metrics::metrics::InteractionEnergyMetric::scorefxn_ = nullptr
private
select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::InteractionEnergyMetric::selector1_ = nullptr
private
select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::InteractionEnergyMetric::selector2_ = nullptr
private

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