composite metric returning motif scores that pass per block More...

#include <BlockwisePoseCompMotifMetric.hh>

Inheritance diagram for protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric:

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

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

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

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

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector)

void	set_normalize_by_residues (bool in)

void	set_drop_best (bool in)

void	set_distance_mode (bool in)

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name of the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. 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::CompositeRealMetric
	CompositeRealMetric ()

	~CompositeRealMetric () override

	CompositeRealMetric (CompositeRealMetric const &other)

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 SimpleMetricData cache in the pose. labeled as out_label. More...

std::map< std::string, 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...

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::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	selector_

bool	normalize_by_residues_ = false

bool	drop_best_ = true

bool	distance_mode_ = false

Detailed Description

composite metric returning motif scores that pass per block

Constructor & Destructor Documentation

◆ BlockwisePoseCompMotifMetric() [1/2]

protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::BlockwisePoseCompMotifMetric ( )

Constructors ///.

Default constructor

◆ BlockwisePoseCompMotifMetric() [2/2]

protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::BlockwisePoseCompMotifMetric ( BlockwisePoseCompMotifMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~BlockwisePoseCompMotifMetric()

protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::~BlockwisePoseCompMotifMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< std::string, core::Real > protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::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::CompositeRealMetric.

References protocols::pose_sewing::calculate_bw_pose_compat_motifs(), distance_mode_, drop_best_, protocols::pose_sewing::identify_ss_blocks(), normalize_by_residues_, core::conformation::membrane::out, selector_, and protocols::TR().

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::CompositeRealMetric.

◆ get_metric_names()

utility::vector1< std::string > protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::get_metric_names ( ) const

overridevirtual

Get the submetric names that this Metric will calculate.

Implements core::simple_metrics::CompositeRealMetric.

◆ metric()

std::string protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::CompositeRealMetric.

◆ name()

std::string protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::CompositeRealMetric.

References name_static().

◆ name_static()

std::string protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::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::CompositeRealMetric.

References distance_mode_, drop_best_, core::select::residue_selector::get_residue_selector(), normalize_by_residues_, core::simple_metrics::SimpleMetric::parse_base_tag(), and selector_.

◆ provide_xml_schema()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetricCreator::provide_xml_schema().

◆ set_distance_mode()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_distance_mode ( bool in )

References distance_mode_, and core::conformation::membrane::in.

◆ set_drop_best()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_drop_best ( bool in )

References drop_best_, and core::conformation::membrane::in.

◆ set_normalize_by_residues()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_normalize_by_residues ( bool in )

References core::conformation::membrane::in, and normalize_by_residues_.

◆ set_selector()

void protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References selector_.

Member Data Documentation

◆ distance_mode_

bool protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::distance_mode_ = false

private

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

◆ drop_best_

bool protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::drop_best_ = true

private

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

◆ normalize_by_residues_

bool protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::normalize_by_residues_ = false

private

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

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::pose_sewing::simple_metrics::BlockwisePoseCompMotifMetric::selector_

private

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

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

src/protocols/pose_sewing/simple_metrics/BlockwisePoseCompMotifMetric.hh
src/protocols/pose_sewing/simple_metrics/BlockwisePoseCompMotifMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BlockwisePoseCompMotifMetric() [1/2]

◆ BlockwisePoseCompMotifMetric() [2/2]

◆ ~BlockwisePoseCompMotifMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ get_metric_names()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_distance_mode()

◆ set_drop_best()

◆ set_normalize_by_residues()

◆ set_selector()

Member Data Documentation

◆ distance_mode_

◆ drop_best_

◆ normalize_by_residues_

◆ selector_