Selects residues that are considered 'error' region with respect to the density resolution. More...

#include <DensityFitResidueSelector.hh>

Inheritance diagram for core::select::residue_selector::DensityFitResidueSelector:

Public Types
typedef core::select::residue_selector::ResidueSelectorOP	ResidueSelectorOP

typedef core::select::residue_selector::ResidueSubset	ResidueSubset

Public Member Functions
	DensityFitResidueSelector ()
	Constructor. More...

	DensityFitResidueSelector (simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCOP den_fit_metric)

	DensityFitResidueSelector (DensityFitResidueSelector const &src)
	Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs) More...

	~DensityFitResidueSelector () override
	Destructor. More...

ResidueSelectorOP	clone () const override
	Clone operator. More...

ResidueSubset	apply (core::pose::Pose const &input_pose) const override
	"Apply" function. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	XML parse. More...

std::string	get_name () const override
	Get the mover class name. More...

void	set_den_fit_metric (simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCOP den_fit_metric)
	Set the density fit metric that will be used to do the calculation in this class. Clones into this class. More...

simple_metrics::per_residue_metrics::PerResidueDensityFitMetricOP	get_den_fit_metric ()
	Edit the density fit metric used to do the calculation in this class. More...

void	set_score_cut (Real score_cut)
	Set the scorecut to use. From -3 up. -.5 is default. Anything higher, is deemed 'good' for zscore. This is also the correlation for match_mode. Correlation of 1.0 fits density completely. .7 is a good cutoff. More...

void	set_invert (bool invert)
	Set to invert - IE select BAD density instead of GOOD. More...

void	set_cache_options (bool use_sm_cache, std::string const &prefix="", std::string const &suffix="", bool fail_on_missing_cache=false)
	Set up options to use any data already stored in the SM cache through its apply method. More...

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. 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	class_name ()
	Get the mover class name. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Provide XSD information, enabling mechanical validation of input XML. More...

Private Attributes
core::Real	score_cut_ = -.5

bool	invert_ = false

core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricOP	den_fit_metric_

bool	use_cache_ = false

std::string	prefix_ = ""

std::string	suffix_ = ""

bool	fail_on_missing_cache_ = false

Detailed Description

Selects residues that are considered 'error' region with respect to the density resolution.

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

Member Typedef Documentation

typedef core::select::residue_selector::ResidueSelectorOP core::select::residue_selector::DensityFitResidueSelector::ResidueSelectorOP

typedef core::select::residue_selector::ResidueSubset core::select::residue_selector::DensityFitResidueSelector::ResidueSubset

Constructor & Destructor Documentation

core::select::residue_selector::DensityFitResidueSelector::DensityFitResidueSelector ( )

Constructor.

References den_fit_metric_.

core::select::residue_selector::DensityFitResidueSelector::DensityFitResidueSelector ( simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCOP den_fit_metric )

References den_fit_metric_.

core::select::residue_selector::DensityFitResidueSelector::DensityFitResidueSelector ( DensityFitResidueSelector const & src )

Copy Constructor. Usually not necessary unless you need deep copying (e.g. OPs)

Copy Constructor.

References den_fit_metric_.

core::select::residue_selector::DensityFitResidueSelector::~DensityFitResidueSelector ( )

override

Destructor.

Member Function Documentation

DensityFitResidueSelector::ResidueSubset core::select::residue_selector::DensityFitResidueSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

"Apply" function.

Given the pose, generate a vector of bools with entries for every residue in the pose indicating whether each residue is selected ("true") or not ("false").

Implements core::select::residue_selector::ResidueSelector.

References core::pose::Pose::conformation(), den_fit_metric_, fail_on_missing_cache_, invert_, core::pose::symmetry::is_symmetric(), core::pose::Pose::pdb_info(), prefix_, score_cut_, core::pose::Pose::size(), suffix_, core::select::residue_selector::TR(), and use_cache_.

std::string core::select::residue_selector::DensityFitResidueSelector::class_name ( )

static

Get the mover class name.

Referenced by get_name(), core::select::residue_selector::DensityFitResidueSelectorCreator::keyname(), and provide_xml_schema().

core::select::residue_selector::ResidueSelectorOP core::select::residue_selector::DensityFitResidueSelector::clone ( ) const

overridevirtual

Clone operator.

Clone function.

Copy the current object (creating the copy on the heap) and return an owning pointer to the copy. All ResidueSelectors must implement this.

Copy this object and return owning pointer to the copy (created on the heap).

Implements core::select::residue_selector::ResidueSelector.

PerResidueDensityFitMetricOP core::select::residue_selector::DensityFitResidueSelector::get_den_fit_metric ( )

Edit the density fit metric used to do the calculation in this class.

References den_fit_metric_.

std::string core::select::residue_selector::DensityFitResidueSelector::get_name ( ) const

overridevirtual

Get the mover class name.

Implements core::select::residue_selector::ResidueSelector.

References class_name().

void core::select::residue_selector::DensityFitResidueSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

XML parse.

Parse RosettaScripts tags and set up this mover.

Reimplemented from core::select::residue_selector::ResidueSelector.

References den_fit_metric_, fail_on_missing_cache_, core::simple_metrics::get_metric_from_datamap_and_subtags(), invert_, core::select::residue_selector::parse_residue_selector(), prefix_, score_cut_, set_cache_options(), set_invert(), set_score_cut(), suffix_, core::select::residue_selector::TR(), and use_cache_.

void core::select::residue_selector::DensityFitResidueSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide XSD information, enabling mechanical validation of input XML.

References core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by core::select::residue_selector::DensityFitResidueSelectorCreator::provide_xml_schema().

void core::select::residue_selector::DensityFitResidueSelector::set_cache_options	(	bool	use_sm_cache,
		std::string const &	prefix = `""`,
		std::string const &	suffix = `""`,
		bool	fail_on_missing_cache = `false`
	)

Set up options to use any data already stored in the SM cache through its apply method.

References fail_on_missing_cache_, prefix_, suffix_, and use_cache_.

Referenced by parse_my_tag().

void core::select::residue_selector::DensityFitResidueSelector::set_den_fit_metric ( simple_metrics::per_residue_metrics::PerResidueDensityFitMetricCOP den_fit_metric )

Set the density fit metric that will be used to do the calculation in this class. Clones into this class.

References den_fit_metric_.

void core::select::residue_selector::DensityFitResidueSelector::set_invert ( bool invert )

Set to invert - IE select BAD density instead of GOOD.

References invert_.

Referenced by parse_my_tag().

void core::select::residue_selector::DensityFitResidueSelector::set_score_cut ( Real score_cut )

Set the scorecut to use. From -3 up. -.5 is default. Anything higher, is deemed 'good' for zscore. This is also the correlation for match_mode. Correlation of 1.0 fits density completely. .7 is a good cutoff.

References score_cut_.

Referenced by parse_my_tag().

Member Data Documentation

core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetricOP core::select::residue_selector::DensityFitResidueSelector::den_fit_metric_

private

Referenced by apply(), DensityFitResidueSelector(), get_den_fit_metric(), parse_my_tag(), and set_den_fit_metric().

bool core::select::residue_selector::DensityFitResidueSelector::fail_on_missing_cache_ = false

private

Referenced by apply(), parse_my_tag(), and set_cache_options().

bool core::select::residue_selector::DensityFitResidueSelector::invert_ = false

private

Referenced by apply(), parse_my_tag(), and set_invert().

std::string core::select::residue_selector::DensityFitResidueSelector::prefix_ = ""

private

Referenced by apply(), parse_my_tag(), and set_cache_options().

core::Real core::select::residue_selector::DensityFitResidueSelector::score_cut_ = -.5

private

Referenced by apply(), parse_my_tag(), and set_score_cut().

std::string core::select::residue_selector::DensityFitResidueSelector::suffix_ = ""

private

Referenced by apply(), parse_my_tag(), and set_cache_options().

bool core::select::residue_selector::DensityFitResidueSelector::use_cache_ = false

private

Referenced by apply(), parse_my_tag(), and set_cache_options().

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

src/core/select/residue_selector/DensityFitResidueSelector.hh
src/core/select/residue_selector/DensityFitResidueSelector.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation