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core::select::residue_selector::DensityFitResidueSelector Class Reference

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:
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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 bool residue_selector_provides_citation_info () const
 Does this residue selector provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool residue_selector_is_unpublished () const
 Does this residue selector indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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
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
void core::select::residue_selector::DensityFitResidueSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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
bool core::select::residue_selector::DensityFitResidueSelector::fail_on_missing_cache_ = false
private
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
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
bool core::select::residue_selector::DensityFitResidueSelector::use_cache_ = false
private

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