A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read. More...

#include <InteractionGraphSummaryMetric.hh>

Inheritance diagram for protocols::quantum_annealing::InteractionGraphSummaryMetric:

[legend]

Public Member Functions
	InteractionGraphSummaryMetric ()
	Constructors ///. More...

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

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

std::string	calculate (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	set_task_factory (core::pack::task::TaskFactoryCOP task_factory_in)
	Set the task factory to be used for interaxction graph setup. More...

void	set_scorefunction (core::scoring::ScoreFunctionCOP sfxn_in)
	Set the scorefunction used for scoring. More...

void	set_short_version (bool const setting)
	Set whether we're storing a short summary, or a long one. More...

bool	short_version () const
	Get whether we're storing a short summary, or a long one. More...

void	set_filename (std::string const &str)
	If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results. More...

std::string const &	filename () const
	If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results. 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

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...

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
core::pack::task::TaskFactoryCOP	task_factory_
	The task factory that we'll use to set up the packing. We won't actually DO the packing, mind you. We'll just use this to set up the interaction graph. More...

core::scoring::ScoreFunctionCOP	scorefxn_
	The scorefunction that we'll use. More...

std::string	filename_ = ""
	If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results. More...

bool	short_version_
	If true, then only the interaction graph summary is printed. If false, then the interaction graph summary plus the full information needed to reconstruct the pose is included. More...

Detailed Description

A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read.

Constructor & Destructor Documentation

protocols::quantum_annealing::InteractionGraphSummaryMetric::InteractionGraphSummaryMetric ( )

Constructors ///.

Default constructor

protocols::quantum_annealing::InteractionGraphSummaryMetric::InteractionGraphSummaryMetric ( InteractionGraphSummaryMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

protocols::quantum_annealing::InteractionGraphSummaryMetric::~InteractionGraphSummaryMetric ( )

override

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

Member Function Documentation

std::string protocols::quantum_annealing::InteractionGraphSummaryMetric::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::pose::Pose::clone(), core::pack::task::TaskFactory::create_packer_task(), core::pack::rotamer_set::RotamerSetsFactory::create_rotamer_sets(), filename(), filename_, core::pack::interaction_graph::get_annealable_graph_summary(), core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_task(), core::pack::pack_rotamers_setup(), scorefxn_, short_version(), task_factory_, core::id::to_string(), and protocols::TR().

core::simple_metrics::SimpleMetricOP protocols::quantum_annealing::InteractionGraphSummaryMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::StringMetric.

std::string const& protocols::quantum_annealing::InteractionGraphSummaryMetric::filename ( ) const

inline

If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results.

References filename_.

Referenced by calculate().

std::string protocols::quantum_annealing::InteractionGraphSummaryMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::StringMetric.

std::string protocols::quantum_annealing::InteractionGraphSummaryMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::StringMetric.

References name_static().

std::string protocols::quantum_annealing::InteractionGraphSummaryMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::quantum_annealing::InteractionGraphSummaryMetricCreator::keyname(), name(), and provide_xml_schema().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::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 core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), set_filename(), set_scorefunction(), set_short_version(), and set_task_factory().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::quantum_annealing::InteractionGraphSummaryMetricCreator::provide_xml_schema().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::set_filename ( std::string const & str )

inline

If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results.

References filename_, and protocols::kinmatch::str().

Referenced by parse_my_tag().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::set_scorefunction ( core::scoring::ScoreFunctionCOP sfxn_in )

Set the scorefunction used for scoring.

Copied, not cloned.

References scorefxn_.

Referenced by parse_my_tag().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::set_short_version ( bool const setting )

inline

Set whether we're storing a short summary, or a long one.

If true, then only the interaction graph summary is printed. If false, then the interaction graph summary plus the full information needed to reconstruct the pose is included.

False by default.

References short_version_.

Referenced by parse_my_tag().

void protocols::quantum_annealing::InteractionGraphSummaryMetric::set_task_factory ( core::pack::task::TaskFactoryCOP task_factory_in )

Set the task factory to be used for interaxction graph setup.

Doesn't clone input.

References task_factory_.

Referenced by parse_my_tag().

bool protocols::quantum_annealing::InteractionGraphSummaryMetric::short_version ( ) const

inline

Get whether we're storing a short summary, or a long one.

If true, then only the interaction graph summary is printed. If false, then the interaction graph summary plus the full information needed to reconstruct the pose is included.

False by default.

References short_version_.

Referenced by calculate().

Member Data Documentation

std::string protocols::quantum_annealing::InteractionGraphSummaryMetric::filename_ = ""

private

If this value is not empty, we will dump the IG summary to a file during calculation and simply return the filename as the return string. this will perform variable substituion on the "{rand}" substring such that "path/to/{rand}.txt" will result in something like "path/to/5748295.txt". The number will be different for each call so you can re-use the same metric without overwriting previous results.

Referenced by calculate(), filename(), and set_filename().

core::scoring::ScoreFunctionCOP protocols::quantum_annealing::InteractionGraphSummaryMetric::scorefxn_

private

The scorefunction that we'll use.

Referenced by calculate(), and set_scorefunction().

bool protocols::quantum_annealing::InteractionGraphSummaryMetric::short_version_

private

If true, then only the interaction graph summary is printed. If false, then the interaction graph summary plus the full information needed to reconstruct the pose is included.

False by default.

Referenced by set_short_version(), and short_version().

core::pack::task::TaskFactoryCOP protocols::quantum_annealing::InteractionGraphSummaryMetric::task_factory_

private

The task factory that we'll use to set up the packing. We won't actually DO the packing, mind you. We'll just use this to set up the interaction graph.

Referenced by calculate(), and set_task_factory().

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

src/protocols/quantum_annealing/InteractionGraphSummaryMetric.hh
src/protocols/quantum_annealing/InteractionGraphSummaryMetric.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation