protocols::enzdes::LigBurialFilter Class Reference

#include <EnzFilters.hh>

Inheritance diagram for protocols::enzdes::LigBurialFilter:

Public Types
typedef protocols::filters::Filter	Filter
typedef protocols::filters::FilterOP	FilterOP
typedef protocols::filters::Filters_map	Filters_map

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 &, Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
std::string	name () const override
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string)
	Filter (Filter 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)

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

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

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

typedef protocols::filters::Filters_map protocols::enzdes::LigBurialFilter::Filters_map

Constructor & Destructor Documentation

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

inline

Referenced by clone(), and fresh_instance().

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

inline

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

overridedefault

Member Function Documentation

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(), neighbors_, and protocols::enzdes::TR().

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

static

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

References LigBurialFilter().

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(), core::kinematics::distance(), distance_threshold_, protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(), lig_id_, core::conformation::Conformation::residue(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::enzdes::TR().

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

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

inlineoverridevirtual

Implements protocols::filters::Filter.

References LigBurialFilter().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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

void protocols::enzdes::LigBurialFilter::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  , Filters_map const &  , protocols::moves::Movers_map const &  , core::pose::Pose const &    )

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

Member Data Documentation

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

private

Referenced by compute(), and parse_my_tag().

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

private

Referenced by compute(), and parse_my_tag().

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

private

Referenced by apply(), and parse_my_tag().

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

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