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core::simple_metrics::metrics::SelectedResiduesPyMOLMetric Class Reference

A utility metric to output a string of selected residues from a residue selector as a pymol selection. More...

#include <SelectedResiduesPyMOLMetric.hh>

Inheritance diagram for core::simple_metrics::metrics::SelectedResiduesPyMOLMetric:
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Public Member Functions

 SelectedResiduesPyMOLMetric ()
 Constructors ///. More...
 
 SelectedResiduesPyMOLMetric (select::residue_selector::ResidueSelectorCOP selector)
 
 SelectedResiduesPyMOLMetric (SelectedResiduesPyMOLMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~SelectedResiduesPyMOLMetric () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
std::string calculate (core::pose::Pose const &pose) const override
 Metric Methods ///. More...
 
void set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
 Set the required Residue Selector. 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_use_rosetta_numbering (bool const setting)
 Set whether we use Rosetta numbering in the output. More...
 
bool use_rosetta_numbering () const
 Get whether we use Rosetta numbering in the output. More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation information for the residue selector that it uses. More...
 
bool simple_metric_is_unpublished () const override
 This simple metric is unpublished (returns true). More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This simple metric is unpublished. It returns Jared Adolf-Bryfogle. More...
 
- Public Member Functions inherited from core::simple_metrics::StringMetric
 StringMetric ()
 
 ~StringMetric () override
 
 StringMetric (StringMetric 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...
 
std::string 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...
 
utility::vector1< std::string > get_metric_names () const override
 Get the metric name that this Metric will calculate. 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...
 

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

select::residue_selector::ResidueSelectorCOP selector_ = nullptr
 
bool use_rosetta_numbering_ = false
 By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering. More...
 

Detailed Description

A utility metric to output a string of selected residues from a residue selector as a pymol selection.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::SelectedResiduesPyMOLMetric ( )

Constructors ///.

Default constructor

core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::SelectedResiduesPyMOLMetric ( select::residue_selector::ResidueSelectorCOP  selector)
core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::SelectedResiduesPyMOLMetric ( SelectedResiduesPyMOLMetric const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References selector_.

core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::~SelectedResiduesPyMOLMetric ( )
override

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

Member Function Documentation

std::string core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::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. Output the selected residues froms a ResidueSelector as a PyMol selection string.

Implements core::simple_metrics::StringMetric.

References core::pose::Pose::chain(), core::pose::get_chain_from_chain_id(), core::simple_metrics::SimpleMetric::get_custom_type(), core::select::get_residues_from_subset(), core::pose::Pose::pdb_info(), selector_, core::id::to_string(), and use_rosetta_numbering().

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::StringMetric.

std::string core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::name ( ) const
overridevirtual

Name of the class.

Implements core::simple_metrics::StringMetric.

References name_static().

Referenced by provide_authorship_info_for_unpublished().

std::string core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::name_static ( )
static
void core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This simple metric is unpublished. It returns Jared Adolf-Bryfogle.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), and selector_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_citation_info ( ) const
overridevirtual

This simple metric is unpublished, but can provide citation information for the residue selector that it uses.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

References selector_.

void core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::set_residue_selector ( select::residue_selector::ResidueSelectorCOP  selector)

Set the required Residue Selector.

References selector_.

Referenced by parse_my_tag(), and SelectedResiduesPyMOLMetric().

void core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::set_use_rosetta_numbering ( bool const  setting)
inline

Set whether we use Rosetta numbering in the output.

By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References use_rosetta_numbering_.

Referenced by parse_my_tag().

bool core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::simple_metric_is_unpublished ( ) const
overridevirtual

This simple metric is unpublished (returns true).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from core::simple_metrics::SimpleMetric.

bool core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::use_rosetta_numbering ( ) const
inline

Get whether we use Rosetta numbering in the output.

By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References use_rosetta_numbering_.

Referenced by calculate(), and parse_my_tag().

Member Data Documentation

select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::selector_ = nullptr
private
bool core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::use_rosetta_numbering_ = false
private

By default, we use the PDB numbering in the output. If this is true, we use Rosetta numbering.

Referenced by set_use_rosetta_numbering(), and use_rosetta_numbering().


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