Rosetta: protocols::drug_design::SAScoreFilter Class Reference

Rosetta

#include <SAScoreFilter.hh>

Inheritance diagram for protocols::drug_design::SAScoreFilter:

Inheritance graph

[legend]

Public Member Functions
	SAScoreFilter ()

	SAScoreFilter (std::string const &residue)

core::Real	threshold () const

void	threshold (core::Real setting)

bool	apply (core::pose::Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

filters::FilterOP	clone () const override

filters::FilterOP	fresh_instance () const override

void	report (std::ostream &out, core::pose::Pose const &pose) const override

core::Real	report_sm (core::pose::Pose const &pose) const override
	used to report filter internals through a score or silent file More...

core::Real	compute (core::pose::Pose const &pose) const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

core::Real	calculate_rdkit (RDKit::ROMol &mol) const

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

virtual std::string	name () const

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	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
core::Size	num_spiro (RDKit::ROMol const &mol) const

core::Size	num_bridgeheads (RDKit::ROMol const &mol) const

core::Size	num_chiral (RDKit::ROMol &mol, bool includeUnassigned=false) const

RDKit::SparseIntVect< boost::uint32_t > *	get_morgan_fingerprint (RDKit::ROMol const &mol, int radius) const

Private Attributes
std::string	residue_
	Which residue to calculate the score for. More...

core::Real	threshold_
	Threshold (maximum) for truth value context. More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

◆ SAScoreFilter() [1/2]

protocols::drug_design::SAScoreFilter::SAScoreFilter ( )

inline

Referenced by clone(), and fresh_instance().

◆ SAScoreFilter() [2/2]

protocols::drug_design::SAScoreFilter::SAScoreFilter ( std::string const & residue )

inline

Member Function Documentation

◆ apply()

bool protocols::drug_design::SAScoreFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), and threshold_.

◆ calculate_rdkit()

core::Real protocols::drug_design::SAScoreFilter::calculate_rdkit ( RDKit::ROMol & mol ) const

References get_morgan_fingerprint(), protocols::mean_field::max(), protocols::mean_field::min(), num_bridgeheads(), num_chiral(), and num_spiro().

Referenced by compute().

◆ class_name()

std::string protocols::drug_design::SAScoreFilter::class_name ( )

static

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

◆ clone()

filters::FilterOP protocols::drug_design::SAScoreFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References SAScoreFilter().

◆ compute()

core::Real protocols::drug_design::SAScoreFilter::compute ( core::pose::Pose const & pose ) const

References calculate_rdkit(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::pose::parse_resnum(), core::pose::Pose::residue(), residue_, core::pose::Pose::total_residue(), protocols::drug_design::TR(), and core::conformation::Residue::type().

Referenced by apply(), report(), and report_sm().

◆ fresh_instance()

filters::FilterOP protocols::drug_design::SAScoreFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References SAScoreFilter().

◆ get_morgan_fingerprint()

RDKit::SparseIntVect< boost::uint32_t > * protocols::drug_design::SAScoreFilter::get_morgan_fingerprint	(	RDKit::ROMol const &	mol,
		int	radius
	)		const

private

The caller takes ownership of the returned item

Referenced by calculate_rdkit().

◆ num_bridgeheads()

core::Size protocols::drug_design::SAScoreFilter::num_bridgeheads ( RDKit::ROMol const & mol ) const

private

References protocols::mean_field::min(), and core::conformation::membrane::out.

Referenced by calculate_rdkit().

◆ num_chiral()

core::Size protocols::drug_design::SAScoreFilter::num_chiral	(	RDKit::ROMol &	mol,
		bool	includeUnassigned = `false`
	)		const

private

nonconst mol as it recalculates annotations

Referenced by calculate_rdkit().

◆ num_spiro()

core::Size protocols::drug_design::SAScoreFilter::num_spiro ( RDKit::ROMol const & mol ) const

private

References protocols::mean_field::min(), and core::conformation::membrane::out.

Referenced by calculate_rdkit().

◆ parse_my_tag()

void protocols::drug_design::SAScoreFilter::parse_my_tag	(	utility::tag::TagCOP	,
		basic::datacache::DataMap &
	)

overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References residue_, threshold_, and protocols::drug_design::TR().

◆ provide_xml_schema()

void protocols::drug_design::SAScoreFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ report()

void protocols::drug_design::SAScoreFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::Residue::name(), core::conformation::membrane::out, core::pose::parse_resnum(), core::pose::Pose::residue(), residue_, and protocols::drug_design::TR().

◆ report_sm()

core::Real protocols::drug_design::SAScoreFilter::report_sm ( core::pose::Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ threshold() [1/2]

core::Real protocols::drug_design::SAScoreFilter::threshold ( ) const

inline

References threshold_.

◆ threshold() [2/2]

void protocols::drug_design::SAScoreFilter::threshold ( core::Real setting )

inline

References threshold_.

Member Data Documentation

◆ residue_

std::string protocols::drug_design::SAScoreFilter::residue_

private

Which residue to calculate the score for.

Referenced by compute(), parse_my_tag(), and report().

◆ threshold_

core::Real protocols::drug_design::SAScoreFilter::threshold_

private

Threshold (maximum) for truth value context.

Referenced by apply(), parse_my_tag(), and threshold().

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

src/protocols/drug_design/SAScoreFilter.hh
src/protocols/drug_design/SAScoreFilter.cc