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core::simple_metrics::metrics::SequenceMetric Class Reference

A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector. More...

#include <SequenceMetric.hh>

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

 SequenceMetric ()
 Constructors ///. More...
 
 SequenceMetric (select::residue_selector::ResidueSelectorCOP selector)
 
 SequenceMetric (SequenceMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~SequenceMetric () 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)
 
void set_output_mode (SequenceMetricMode const mode_in)
 Set the output mode – one-letter code (e.g. Y), three-letter code (e.g. DTY), residue base name (e.g. DTYR), or full residue name (e.g. DTYR:CtermProteinFull). More...
 
void set_output_mode (std::string const &mode_in)
 Set the output mode using the string corresponding to the output mode. 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
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 This simple metric is unpublished, but can provide citation informatino for the residue selector that it uses.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 This simple metric is unpublished (returns true).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 This simple metric is unpublished.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 (original author) and Vikram K. Mulligan (expanded funcitionality) as authors. 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 std::string allowed_output_modes ()
 Returns all allowed output modes. More...
 
static utility::vector1
< std::string > 
allowed_output_modes_as_vector ()
 Returns all allowed output modes as a vector of strings. More...
 
static std::string const & mode_name_from_enum (SequenceMetricMode const mode_enum)
 Given an output mode enum, get its string representation. More...
 
static SequenceMetricMode mode_enum_from_name (std::string const &mode_string)
 Given an output mode string, get its enum. 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
 
SequenceMetricMode output_mode_
 The output mode – one-letter code (e.g. Y), three-letter code (e.g. DTY), residue base name (e.g. DTYR), or full residue name (e.g. DTYR:CtermProteinFull). More...
 

Detailed Description

A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector.

Constructor & Destructor Documentation

core::simple_metrics::metrics::SequenceMetric::SequenceMetric ( )

Constructors ///.

Default constructor

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

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References selector_.

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

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

Member Function Documentation

std::string core::simple_metrics::metrics::SequenceMetric::allowed_output_modes ( )
static
utility::vector1< std::string > core::simple_metrics::metrics::SequenceMetric::allowed_output_modes_as_vector ( )
static

Returns all allowed output modes as a vector of strings.

Note that this is a bit inefficient. It generates the vector each time, and returns it by copy. Not intended for repeated calls.

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

References mode_name_from_enum(), and core::simple_metrics::metrics::SMM_END_OF_LIST.

Referenced by provide_xml_schema().

std::string core::simple_metrics::metrics::SequenceMetric::calculate ( core::pose::Pose const &  pose) const
overridevirtual
core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::SequenceMetric::clone ( ) const
overridevirtual
std::string core::simple_metrics::metrics::SequenceMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::StringMetric.

SequenceMetricMode core::simple_metrics::metrics::SequenceMetric::mode_enum_from_name ( std::string const &  mode_string)
static

Given an output mode string, get its enum.

Returns SMM_INVALID_MODE if invalid.

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

References mode_name_from_enum(), core::simple_metrics::metrics::SMM_END_OF_LIST, and core::simple_metrics::metrics::SMM_INVALID_MODE.

Referenced by set_output_mode().

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

This simple metric is unpublished. It returns Jared Adolf-Bryfogle (original author) and Vikram K. Mulligan (expanded funcitionality) as authors.

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::SequenceMetric::provide_citation_info ( ) const
overridevirtual

This simple metric is unpublished, but can provide citation informatino 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::SequenceMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void core::simple_metrics::metrics::SequenceMetric::set_output_mode ( SequenceMetricMode const  mode_in)

Set the output mode – one-letter code (e.g. Y), three-letter code (e.g. DTY), residue base name (e.g. DTYR), or full residue name (e.g. DTYR:CtermProteinFull).

Throws an error if invalid enum provided.

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

References output_mode_, and core::simple_metrics::metrics::SMM_END_OF_LIST.

Referenced by parse_my_tag(), and set_output_mode().

void core::simple_metrics::metrics::SequenceMetric::set_output_mode ( std::string const &  mode_in)

Set the output mode using the string corresponding to the output mode.

Throws an error if string is invalid.

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

References mode_enum_from_name(), and set_output_mode().

void core::simple_metrics::metrics::SequenceMetric::set_residue_selector ( select::residue_selector::ResidueSelectorCOP  selector)

References selector_.

Referenced by parse_my_tag(), and SequenceMetric().

bool core::simple_metrics::metrics::SequenceMetric::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.

Member Data Documentation

SequenceMetricMode core::simple_metrics::metrics::SequenceMetric::output_mode_
private

The output mode – one-letter code (e.g. Y), three-letter code (e.g. DTY), residue base name (e.g. DTYR), or full residue name (e.g. DTYR:CtermProteinFull).

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

Referenced by calculate(), and set_output_mode().

select::residue_selector::ResidueSelectorCOP core::simple_metrics::metrics::SequenceMetric::selector_ = nullptr
private

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