This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables. More...

#include <ProtocolSettingsMetric.hh>

Inheritance diagram for core::simple_metrics::composite_metrics::ProtocolSettingsMetric:

[legend]

Public Member Functions
	ProtocolSettingsMetric (bool base_name_option_only=true, bool get_script_vars=true, bool get_user_options=true, bool skip_corrections=true)
	Constructors ///. More...

	ProtocolSettingsMetric (utility::options::OptionCollection const &options, bool base_name_option_only=true, bool get_script_vars=true, bool get_user_options=true, bool skip_corrections=true)
	Parse the Local Options Collection. More...

	ProtocolSettingsMetric (ProtocolSettingsMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~ProtocolSettingsMetric () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

std::map< std::string, std::string >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

void	set_only_report_these_options (utility::vector1< std::string > const &select_opts)
	Only return these options. If not getting full namespaces, these are ONLY the base names. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name of the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. More...

void	set_job_tag (std::string const &job_tag)
	Set a specific job tag that will be output as job_tag for this particular run. Used for benchmarking. 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	parse_options (utility::options::OptionCollection const &options, bool base_name_option_only=true, bool get_script_vars=true, bool get_user_options=true, bool skip_corrections=true)
	Parse an options collection into a set of string-string pairs. More...

void	split_script_vars (std::string const &script_vars_option_string, std::map< std::string, std::string > &options_values) const
	Split the script_vars string into individual options and place them into options_values map. More...

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

	~CompositeStringMetric () override

	CompositeStringMetric (CompositeStringMetric 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 within the SimpleMetricData cache. labeled as out_label. More...

std::map< std::string, 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...

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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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
std::map< std::string, std::string >	options_values_

utility::vector1< std::string >	limit_reporting_to_these_options_

std::string	job_tag_ = ""

Detailed Description

This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables.

Constructor & Destructor Documentation

core::simple_metrics::composite_metrics::ProtocolSettingsMetric::ProtocolSettingsMetric	(	bool	base_name_option_only = `true`,
		bool	get_script_vars = `true`,
		bool	get_user_options = `true`,
		bool	skip_corrections = `true`
	)

Constructors ///.

Parse the Global Options Collections

Default constructor

References parse_options().

core::simple_metrics::composite_metrics::ProtocolSettingsMetric::ProtocolSettingsMetric	(	utility::options::OptionCollection const &	options,
		bool	base_name_option_only = `true`,
		bool	get_script_vars = `true`,
		bool	get_user_options = `true`,
		bool	skip_corrections = `true`
	)

Parse the Local Options Collection.

References parse_options().

core::simple_metrics::composite_metrics::ProtocolSettingsMetric::ProtocolSettingsMetric ( ProtocolSettingsMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

core::simple_metrics::composite_metrics::ProtocolSettingsMetric::~ProtocolSettingsMetric ( )

override

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

Member Function Documentation

std::map< std::string, std::string > core::simple_metrics::composite_metrics::ProtocolSettingsMetric::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::CompositeStringMetric.

References job_tag_, limit_reporting_to_these_options_, options_values_, and core::scoring::pair.

core::simple_metrics::SimpleMetricOP core::simple_metrics::composite_metrics::ProtocolSettingsMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::CompositeStringMetric.

utility::vector1< std::string > core::simple_metrics::composite_metrics::ProtocolSettingsMetric::get_metric_names ( ) const

overridevirtual

Get the submetric names that this Metric will calculate.

Implements core::simple_metrics::CompositeStringMetric.

References limit_reporting_to_these_options_, options_values_, and core::scoring::pair.

std::string core::simple_metrics::composite_metrics::ProtocolSettingsMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::CompositeStringMetric.

std::string core::simple_metrics::composite_metrics::ProtocolSettingsMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::CompositeStringMetric.

References name_static().

std::string core::simple_metrics::composite_metrics::ProtocolSettingsMetric::name_static ( )

static

Name of the class for creator.

Referenced by core::simple_metrics::composite_metrics::ProtocolSettingsMetricCreator::keyname(), name(), and provide_xml_schema().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::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::CompositeStringMetric.

References job_tag_, core::simple_metrics::SimpleMetric::parse_base_tag(), parse_options(), set_job_tag(), and set_only_report_these_options().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::parse_options	(	utility::options::OptionCollection const &	options,
		bool	base_name_option_only = `true`,
		bool	get_script_vars = `true`,
		bool	get_user_options = `true`,
		bool	skip_corrections = `true`
	)

Parse an options collection into a set of string-string pairs.

References protocols::sparta::contains(), core::sequence::end, options_values_, split_script_vars(), and TR().

Referenced by parse_my_tag(), and ProtocolSettingsMetric().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by core::simple_metrics::composite_metrics::ProtocolSettingsMetricCreator::provide_xml_schema().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::set_job_tag ( std::string const & job_tag )

Set a specific job tag that will be output as job_tag for this particular run. Used for benchmarking.

References job_tag_.

Referenced by parse_my_tag().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::set_only_report_these_options ( utility::vector1< std::string > const & select_opts )

Only return these options. If not getting full namespaces, these are ONLY the base names.

References limit_reporting_to_these_options_.

Referenced by parse_my_tag().

void core::simple_metrics::composite_metrics::ProtocolSettingsMetric::split_script_vars	(	std::string const &	script_vars_option_string,
		std::map< std::string, std::string > &	options_values
	)		const

Split the script_vars string into individual options and place them into options_values map.

Referenced by parse_options().

Member Data Documentation

std::string core::simple_metrics::composite_metrics::ProtocolSettingsMetric::job_tag_ = ""

private

Referenced by calculate(), parse_my_tag(), and set_job_tag().

utility::vector1< std::string > core::simple_metrics::composite_metrics::ProtocolSettingsMetric::limit_reporting_to_these_options_

private

Referenced by calculate(), get_metric_names(), and set_only_report_these_options().

std::map< std::string, std::string > core::simple_metrics::composite_metrics::ProtocolSettingsMetric::options_values_

private

Referenced by calculate(), get_metric_names(), and parse_options().

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

src/core/simple_metrics/composite_metrics/ProtocolSettingsMetric.hh
src/core/simple_metrics/composite_metrics/ProtocolSettingsMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation