A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore. More...

#include <PerResidueDensityFitMetric.hh>

Inheritance diagram for core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric:

[legend]

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

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

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

std::map< core::Size, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. 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	set_match_mode (bool match_mode)
	Use density correlation instead of a zscore to fit to density Default False. Useful for comparison to other densities of different resolution. More...

void	set_use_selector_as_zscore_mask (bool selector_as_mask)
	Use the selector as true mask to calculate the Zscore. Otherwise, use it just as a selection for result. Default true. More...

void	set_sliding_window_size (core::Size window_size)
	Set the sliding window size. Default is 3. If you have anything other than protein, you probably want 1. Only used for Z-score mode. More...

void	set_mixed_sliding_window (bool mixed_sliding_window)
	Set the code to use a mixed sliding window depending on the residue. 3 for protein, 1 for everything else. Only used for Z-score mode. More...

bool	match_res_mode () const
	Is this match res mode? More...

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

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

PerResidueRealMetric &	operator= (PerResidueRealMetric 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...

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::Real >	cached_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...

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::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 Member Functions
void	compute_scores (pose::Pose &pose, std::map< Size, Real > &per_rsd_dens, std::map< Size, Real > &per_rsd_nbrdens, std::map< Size, Real > &per_rsd_rama, std::map< Size, Real > &per_rsd_geometry) const
	Compute All per-residue scores. More...

Private Attributes
Size	sliding_window_size_ = 1

bool	mixed_sliding_window_ = false

bool	match_res_ = false

bool	use_selector_as_zscore_mask_ = true

Detailed Description

A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore.

Zscore Uses weighted sum of density, density-compared-to-neighbors, rama (where applicable) and cart_bonded to compute

Constructor & Destructor Documentation

◆ PerResidueDensityFitMetric() [1/2]

core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::PerResidueDensityFitMetric ( )

Constructors ///.

Default constructor

◆ PerResidueDensityFitMetric() [2/2]

core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::PerResidueDensityFitMetric ( PerResidueDensityFitMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PerResidueDensityFitMetric()

core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::~PerResidueDensityFitMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::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.

Implements core::simple_metrics::PerResidueRealMetric.

References compute_scores(), core::pose::Pose::conformation(), core::scoring::elec_dens_window, core::simple_metrics::PerResidueRealMetric::get_selector(), core::scoring::electron_density::getDensityMap(), core::pose::symmetry::is_symmetric(), match_res_, core::scoring::electron_density::ElectronDensity::matchRes(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::hybridization::score, core::scoring::electron_density::ElectronDensity::setScoreWindowContext(), core::scoring::electron_density::ElectronDensity::setWindow(), core::pose::Pose::size(), and TR().

◆ clone()

core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

◆ compute_scores()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::compute_scores	(	pose::Pose &	pose,
		std::map< Size, Real > &	per_rsd_dens,
		std::map< Size, Real > &	per_rsd_nbrdens,
		std::map< Size, Real > &	per_rsd_rama,
		std::map< Size, Real > &	per_rsd_geometry
	)		const

private

Compute All per-residue scores.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::electron_density::calculate_density_nbr(), core::scoring::electron_density::calculate_geometry(), core::scoring::electron_density::calculate_rama(), core::pose::Pose::conformation(), core::simple_metrics::PerResidueRealMetric::get_selector(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::is_virtual_residue(), mixed_sliding_window_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), sliding_window_size_, and use_selector_as_zscore_mask_.

Referenced by calculate().

◆ match_res_mode()

bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::match_res_mode ( ) const

inline

Is this match res mode?

References match_res_.

◆ metric()

std::string core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

◆ name()

std::string core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

◆ name_static()

std::string core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCreator::keyname(), name(), and provide_xml_schema().

◆ parse_my_tag()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::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::PerResidueRealMetric.

References match_res_, mixed_sliding_window_, core::simple_metrics::SimpleMetric::parse_base_tag(), core::simple_metrics::PerResidueRealMetric::parse_per_residue_tag(), set_match_mode(), set_mixed_sliding_window(), set_sliding_window_size(), set_use_selector_as_zscore_mask(), sliding_window_size_, and use_selector_as_zscore_mask_.

◆ provide_xml_schema()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References name_static(), and core::simple_metrics::xsd_per_residue_real_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCreator::provide_xml_schema().

◆ set_match_mode()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_match_mode ( bool match_mode )

Use density correlation instead of a zscore to fit to density Default False. Useful for comparison to other densities of different resolution.

References match_res_.

Referenced by parse_my_tag().

◆ set_mixed_sliding_window()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_mixed_sliding_window ( bool mixed_sliding_window )

Set the code to use a mixed sliding window depending on the residue. 3 for protein, 1 for everything else. Only used for Z-score mode.

References mixed_sliding_window_.

Referenced by parse_my_tag().

◆ set_sliding_window_size()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_sliding_window_size ( core::Size window_size )

Set the sliding window size. Default is 3. If you have anything other than protein, you probably want 1. Only used for Z-score mode.

References sliding_window_size_.

Referenced by parse_my_tag().

◆ set_use_selector_as_zscore_mask()

void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::set_use_selector_as_zscore_mask ( bool selector_as_mask )

Use the selector as true mask to calculate the Zscore. Otherwise, use it just as a selection for result. Default true.

References use_selector_as_zscore_mask_.

Referenced by parse_my_tag().

Member Data Documentation

◆ match_res_

bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::match_res_ = false

private

Referenced by calculate(), match_res_mode(), parse_my_tag(), and set_match_mode().

◆ mixed_sliding_window_

bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::mixed_sliding_window_ = false

private

Referenced by compute_scores(), parse_my_tag(), and set_mixed_sliding_window().

◆ sliding_window_size_

Size core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::sliding_window_size_ = 1

private

Referenced by compute_scores(), parse_my_tag(), and set_sliding_window_size().

◆ use_selector_as_zscore_mask_

bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::use_selector_as_zscore_mask_ = true

private

Referenced by compute_scores(), parse_my_tag(), and set_use_selector_as_zscore_mask().

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

src/core/simple_metrics/per_residue_metrics/PerResidueDensityFitMetric.hh
src/core/simple_metrics/per_residue_metrics/PerResidueDensityFitMetric.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PerResidueDensityFitMetric() [1/2]

◆ PerResidueDensityFitMetric() [2/2]

◆ ~PerResidueDensityFitMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ compute_scores()

◆ match_res_mode()

◆ metric()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_match_mode()

◆ set_mixed_sliding_window()

◆ set_sliding_window_size()

◆ set_use_selector_as_zscore_mask()

Member Data Documentation

◆ match_res_

◆ mixed_sliding_window_

◆ sliding_window_size_

◆ use_selector_as_zscore_mask_