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protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric Class Reference

A string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial. More...

#include <PolarGroupBurialPyMolStringMetric.hh>

Inheritance diagram for protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric:
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Public Member Functions

 PolarGroupBurialPyMolStringMetric ()
 Constructors ///. More...
 
 PolarGroupBurialPyMolStringMetric (PolarGroupBurialPyMolStringMetric const &src)
 Copy constructor (not needed unless you need deep copies) More...
 
 ~PolarGroupBurialPyMolStringMetric () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
std::string calculate (core::pose::Pose const &original_pose) const override
 Metric Methods ///. More...
 
std::string name () const override
 Name of the class. More...
 
std::string metric () const override
 Name (descriptive) of the metric. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Given an XML tag, configure an instance of this class. More...
 
core::simple_metrics::SimpleMetricOP clone () const override
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction. More...
 
void set_verbose (bool const setting)
 Set whether this metric should also output to tracer when evaluated. 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)
 
SimpleMetricoperator= (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::scoring::ScoreFunctionCOP sfxn_
 A scorefunction, from which configurations will be copied. More...
 
bool verbose_
 Should this metric also output to tracer when evaluated? Default false. More...
 

Detailed Description

A string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial.

Constructor & Destructor Documentation

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::PolarGroupBurialPyMolStringMetric ( )

Constructors ///.

Default constructor

Default constructor

Initializes ScoreFunction to nullptr.

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::PolarGroupBurialPyMolStringMetric ( PolarGroupBurialPyMolStringMetric const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

Copies, but does not clone, input scorefunction.

protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::~PolarGroupBurialPyMolStringMetric ( )
override

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

Member Function Documentation

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate ( core::pose::Pose const &  original_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::scoring::EnergiesCacheableDataType::BURIED_UNSAT_HBOND_GRAPH, core::scoring::buried_unsatisfied_penalty, core::pack::create_packer_graph(), core::scoring::Energies::data(), core::pose::Pose::energies(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::is_symmetric(), core::pack::make_new_symmetric_PackerTask_by_requested_method(), sfxn_, core::pose::Pose::total_residue(), protocols::TR(), and verbose_.

core::simple_metrics::SimpleMetricOP protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::clone ( ) const
overridevirtual
std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::metric ( ) const
overridevirtual

Name (descriptive) of the metric.

Implements core::simple_metrics::StringMetric.

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::name ( ) const
overridevirtual

Name of the class.

Calls name_static().

Implements core::simple_metrics::StringMetric.

References name_static().

std::string protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::name_static ( )
static
void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Given an XML tag, configure an instance of this class.

Implements core::simple_metrics::StringMetric.

References core::scoring::parse_score_function(), set_scorefxn(), and set_verbose().

void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction.

Used for definition of burial. Input pointer is copied without cloning.

References sfxn_.

Referenced by parse_my_tag().

void protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::set_verbose ( bool const  setting)

Set whether this metric should also output to tracer when evaluated.

References verbose_.

Referenced by parse_my_tag().

Member Data Documentation

core::scoring::ScoreFunctionCOP protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::sfxn_
private

A scorefunction, from which configurations will be copied.

Referenced by calculate(), and set_scorefxn().

bool protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::verbose_
private

Should this metric also output to tracer when evaluated? Default false.

Referenced by calculate(), and set_verbose().


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