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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

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

	~RealMetric () override

	RealMetric (RealMetric const &other)

RealMetric &	operator= (RealMetric 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...

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)

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...

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
	)

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

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

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.

Implements core::simple_metrics::RealMetric.

References core::scoring::EMapVector::dot(), core::pose::Pose::energies(), core::scoring::Energies::energies_updated(), core::scoring::Energies::energy_graph(), core::scoring::EnergyEdge::fill_energy_map(), core::select::get_residues_from_subset(), include_rama_prepro_and_proclose_, core::scoring::Energies::long_range_container(), core::scoring::methods::n_long_range_types, core::scoring::n_score_types, core::scoring::name_from_score_type(), core::scoring::pair, core::scoring::pro_close, core::scoring::rama_prepro, score_types_to_ignore_, score_types_to_use_only_, scorefxn_, selector1_, selector2_, TR(), and core::scoring::Energies::weights().

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::InteractionEnergyMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::RealMetric.

References InteractionEnergyMetric().

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_citation_info().

std::string core::simple_metrics::metrics::InteractionEnergyMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::metrics::InteractionEnergyMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::metrics::InteractionEnergyMetric::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::RealMetric.

References force_rescore_pose_, include_rama_prepro_and_proclose_, core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), core::scoring::score_type_from_name(), score_types_to_ignore_, score_types_to_use_only_, selector1_, selector2_, set_include_rama_prepro_and_proclose(), set_scorefunction(), and TR().

void core::simple_metrics::metrics::InteractionEnergyMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), scorefxn_, selector1_, and selector2_.

void core::simple_metrics::metrics::InteractionEnergyMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_get_score_function_name(), core::select::residue_selector::attributes_for_parse_residue_selector(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::metrics::InteractionEnergyMetricCreator::provide_xml_schema().

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().

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

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

utility::vector1<scoring::ScoreType> core::simple_metrics::metrics::InteractionEnergyMetric::score_types_to_ignore_

private

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

utility::vector1<scoring::ScoreType> core::simple_metrics::metrics::InteractionEnergyMetric::score_types_to_use_only_

private

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

scoring::ScoreFunctionCOP core::simple_metrics::metrics::InteractionEnergyMetric::scorefxn_ = nullptr

private

Referenced by calculate(), InteractionEnergyMetric(), provide_citation_info(), and set_scorefunction().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::InteractionEnergyMetric::selector1_ = nullptr

private

Referenced by calculate(), parse_my_tag(), provide_citation_info(), and set_residue_selectors().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::InteractionEnergyMetric::selector2_ = nullptr

private

Referenced by calculate(), parse_my_tag(), provide_citation_info(), and set_residue_selectors().

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

src/core/simple_metrics/metrics/InteractionEnergyMetric.hh
src/core/simple_metrics/metrics/InteractionEnergyMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation