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:

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)
RealMetric &	operator= (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)
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::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

Implements core::simple_metrics::RealMetric.

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

References core::select::residue_selector::attributes_for_parse_residue_selector(), name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::drug_design::RDKitMetricCreator::provide_xml_schema().

void protocols::drug_design::RDKitMetric::rdkit_metric

(

std::string const &

setting

)

References core::chemical::rdkit::get_metric_names(), rdkit_metric_, and protocols::drug_design::TR().

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().

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

• src/protocols/drug_design/RDKitMetric.hh
• src/protocols/drug_design/RDKitMetric.cc