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:

[legend]

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from core::simple_metrics::StringMetric
	StringMetric ()

	~StringMetric () override

	StringMetric (StringMetric const &other)

void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as out_label. 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)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

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...

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 )

References set_residue_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

Returns all allowed output modes.

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

References core::simple_metrics::metrics::SMM_END_OF_LIST.

Referenced by provide_xml_schema().

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

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. Calculate the metric.

Implements core::simple_metrics::StringMetric.

References core::chemical::ResidueTypeBase::base_name(), core::select::get_residues_from_subset(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), output_mode_, core::pose::Pose::residue_type(), selector_, core::pose::Pose::size(), core::simple_metrics::metrics::SMM_BASE_NAME, core::simple_metrics::metrics::SMM_FULL_NAME, core::simple_metrics::metrics::SMM_INVALID_MODE, core::simple_metrics::metrics::SMM_ONELETTER_CODE, and core::simple_metrics::metrics::SMM_THREELETTER_CODE.

core::simple_metrics::SimpleMetricOP core::simple_metrics::metrics::SequenceMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::StringMetric.

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

Given an output mode enum, get its string representation.

Returns "INVALID" 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 core::simple_metrics::metrics::mode_to_name_map_(), core::simple_metrics::metrics::SMM_END_OF_LIST, and core::simple_metrics::metrics::SMM_INVALID_MODE.

Referenced by allowed_output_modes_as_vector(), mode_enum_from_name(), parse_my_tag(), and provide_xml_schema().

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_citation_info().

std::string core::simple_metrics::metrics::SequenceMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::metrics::SequenceMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::metrics::SequenceMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::StringMetric.

References mode_name_from_enum(), core::simple_metrics::SimpleMetric::parse_base_tag(), core::select::residue_selector::parse_residue_selector(), set_output_mode(), set_residue_selector(), and core::simple_metrics::metrics::SMM_ONELETTER_CODE.

void core::simple_metrics::metrics::SequenceMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References name(), and selector_.

void core::simple_metrics::metrics::SequenceMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References allowed_output_modes(), allowed_output_modes_as_vector(), core::select::residue_selector::attributes_for_parse_residue_selector(), mode_name_from_enum(), name_static(), core::simple_metrics::metrics::SMM_ONELETTER_CODE, and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::metrics::SequenceMetricCreator::provide_xml_schema().

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().

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

Referenced by calculate(), provide_citation_info(), SequenceMetric(), and set_residue_selector().

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

src/core/simple_metrics/metrics/SequenceMetric.hh
src/core/simple_metrics/metrics/SequenceMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation