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core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric Class Reference

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:
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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::Realcalculate (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)
 
void apply (pose::Pose &pose, std::string prefix="", std::string suffix="", bool override_existing_data=false) const override
 Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix. 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::Realcached_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...
 
- Public Member Functions inherited from core::simple_metrics::SimpleMetric
 SimpleMetric (std::string const &simple_metric_type)
 
 ~SimpleMetric () override
 
 SimpleMetric (SimpleMetric const &other)
 
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 bool simple_metric_provides_citation_info () const
 Does this simple metric 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 simple_metric_is_unpublished () const
 Does this simple metric 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 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

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

Constructors ///.

Default constructor

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

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

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

Member Function Documentation

std::map< core::Size, core::Real > core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::calculate ( core::pose::Pose const &  pose) const
overridevirtual
core::simple_metrics::SimpleMetricOP core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::clone ( ) const
overridevirtual
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
bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::match_res_mode ( ) const
inline

Is this match res mode?

References match_res_.

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

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

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

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

std::string core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::name_static ( )
static
void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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().

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().

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().

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

bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::match_res_ = false
private
bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::mixed_sliding_window_ = false
private
Size core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::sliding_window_size_ = 1
private
bool core::simple_metrics::per_residue_metrics::PerResidueDensityFitMetric::use_selector_as_zscore_mask_ = true
private

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