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protocols::drug_design::RDKitMetric Class Reference

A SimpleMetric which measures properties calcualted by RDKit on a ligand. More...

#include <RDKitMetric.hh>

Inheritance diagram for protocols::drug_design::RDKitMetric:
Inheritance graph
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Public Member Functions

 RDKitMetric ()
 Constructors ///. More...
 
 RDKitMetric (core::select::residue_selector::ResidueSelectorCOP residue, std::string const &metric_name)
 
void residue_selector (core::select::residue_selector::ResidueSelectorCOP residue)
 
core::select::residue_selector::ResidueSelectorCOP residue_selector () const
 
void rdkit_metric (std::string const &setting)
 
std::string const & rdkit_metric () const
 
core::Real 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 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::RealMetric
 RealMetric ()
 
 ~RealMetric () override
 
 RealMetric (RealMetric const &other)
 
RealMetricoperator= (RealMetric const &)
 
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...
 
core::Real 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(s) 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::select::residue_selector::ResidueSelectorCOP residue_
 
std::string rdkit_metric_
 

Detailed Description

A SimpleMetric which measures properties calcualted by RDKit on a ligand.

Constructor & Destructor Documentation

protocols::drug_design::RDKitMetric::RDKitMetric ( )

Constructors ///.

Default constructor

protocols::drug_design::RDKitMetric::RDKitMetric ( core::select::residue_selector::ResidueSelectorCOP  residue,
std::string const &  metric_name 
)

References rdkit_metric().

Member Function Documentation

core::Real protocols::drug_design::RDKitMetric::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::RealMetric.

References core::select::get_residues_from_subset(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::rdkit::rdkit_metric(), rdkit_metric_, core::pose::Pose::residue(), residue_, protocols::drug_design::TR(), and core::conformation::Residue::type().

core::simple_metrics::SimpleMetricOP protocols::drug_design::RDKitMetric::clone ( ) const
overridevirtual
std::string protocols::drug_design::RDKitMetric::metric ( ) const
overridevirtual

Name of the metric.

Implements core::simple_metrics::RealMetric.

References rdkit_metric_.

std::string protocols::drug_design::RDKitMetric::name ( ) const
overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

std::string protocols::drug_design::RDKitMetric::name_static ( )
static

Name of the class for creator.

Referenced by protocols::drug_design::RDKitMetricCreator::keyname(), name(), and provide_xml_schema().

void protocols::drug_design::RDKitMetric::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::RealMetric.

References core::select::residue_selector::parse_residue_selector(), rdkit_metric(), and residue_selector().

void protocols::drug_design::RDKitMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::drug_design::RDKitMetric::rdkit_metric ( std::string const &  setting)
std::string const& protocols::drug_design::RDKitMetric::rdkit_metric ( ) const
inline

References rdkit_metric_.

Referenced by parse_my_tag(), and RDKitMetric().

void protocols::drug_design::RDKitMetric::residue_selector ( core::select::residue_selector::ResidueSelectorCOP  residue)
inline

References residue_.

core::select::residue_selector::ResidueSelectorCOP protocols::drug_design::RDKitMetric::residue_selector ( ) const
inline

References residue_.

Referenced by parse_my_tag().

Member Data Documentation

std::string protocols::drug_design::RDKitMetric::rdkit_metric_
private

Referenced by calculate(), metric(), and rdkit_metric().

core::select::residue_selector::ResidueSelectorCOP protocols::drug_design::RDKitMetric::residue_
private

Referenced by calculate(), and residue_selector().


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