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protocols::quantum_annealing::InteractionGraphSummaryMetric Class Reference

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:
Inheritance graph
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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 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 (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...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool simple_metric_is_unpublished () const
 Does this simple metric indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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...
 
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(), 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_, and protocols::TR().

core::simple_metrics::SimpleMetricOP protocols::quantum_annealing::InteractionGraphSummaryMetric::clone ( ) const
overridevirtual
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
void protocols::quantum_annealing::InteractionGraphSummaryMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::quantum_annealing::InteractionGraphSummaryMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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

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: