Rosetta: protocols::enzdes::LigBurialFilter Class Reference

Rosetta

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::LigBurialFilter:

Inheritance graph

[legend]

Public Types
typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

Public Member Functions
	LigBurialFilter ()

	LigBurialFilter (core::Size lig_id, core::Size const numneighbors, core::Real const distance_threshold)

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

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

FilterOP	clone () const override

FilterOP	fresh_instance () const override

	~LigBurialFilter () override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override

std::string	name () const override

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 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 Attributes
core::Size	lig_id_

core::Size	neighbors_

core::Real	distance_threshold_

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

Member Typedef Documentation

◆ Filter

typedef protocols::filters::Filter protocols::enzdes::LigBurialFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::enzdes::LigBurialFilter::FilterOP

Constructor & Destructor Documentation

◆ LigBurialFilter() [1/2]

protocols::enzdes::LigBurialFilter::LigBurialFilter ( )

inline

◆ LigBurialFilter() [2/2]

protocols::enzdes::LigBurialFilter::LigBurialFilter	(	core::Size	lig_id,
		core::Size const	numneighbors,
		core::Real const	distance_threshold
	)

inline

◆ ~LigBurialFilter()

protocols::enzdes::LigBurialFilter::~LigBurialFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::enzdes::LigBurialFilter::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(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), neighbors_, and protocols::enzdes::TR().

◆ class_name()

std::string protocols::enzdes::LigBurialFilter::class_name ( )

static

Referenced by protocols::enzdes::LigBurialFilterCreator::keyname().

◆ clone()

FilterOP protocols::enzdes::LigBurialFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Size protocols::enzdes::LigBurialFilter::compute ( core::pose::Pose const & pose ) const

counts the number of residues contacting the ligand

References core::pose::Pose::conformation(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::kinematics::distance(), distance_threshold_, protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), lig_id_, core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::conformation::Conformation::residue(), core::pose::Pose::size(), protocols::enzdes::TR(), and core::conformation::Residue::xyz().

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

◆ fresh_instance()

FilterOP protocols::enzdes::LigBurialFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ name()

std::string protocols::enzdes::LigBurialFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References protocols::enzdes::DiffAtomSasaFilter::class_name().

◆ parse_my_tag()

void protocols::enzdes::LigBurialFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

: this filter basically works exactly as ResidueBurialFilter, but with the advantage that it has the capability to

: figure out resid of the ligand

Reimplemented from protocols::filters::Filter.

References distance_threshold_, lig_id_, neighbors_, and protocols::enzdes::TR().

◆ provide_xml_schema()

void protocols::enzdes::LigBurialFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::enzdes::LigBurialFilterCreator::provide_xml_schema().

◆ report()

void protocols::enzdes::LigBurialFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), protocols::ligand_docking::ga_ligand_dock::count_neighbors(), and core::conformation::membrane::out.

◆ report_sm()

core::Real protocols::enzdes::LigBurialFilter::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(), and protocols::ligand_docking::ga_ligand_dock::count_neighbors().

Member Data Documentation

◆ distance_threshold_

core::Real protocols::enzdes::LigBurialFilter::distance_threshold_

private

Referenced by compute(), and parse_my_tag().

◆ lig_id_

core::Size protocols::enzdes::LigBurialFilter::lig_id_

private

Referenced by compute(), and parse_my_tag().

◆ neighbors_

core::Size protocols::enzdes::LigBurialFilter::neighbors_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/enzdes/EnzFilters.hh
src/protocols/enzdes/EnzFilters.cc