#include <TaskAwareSASAFilter.hh>

Inheritance diagram for protocols::simple_filters::TaskAwareSASAFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef protocols::filters::FilterOP	FilterOP

typedef core::Real	Real

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	TaskAwareSASAFilter ()

	TaskAwareSASAFilter (core::pack::task::TaskFactoryOP task_factory, core::Real const t, bool const d, bool const s, core::Real const r, core::Size const j)

	TaskAwareSASAFilter (TaskAwareSASAFilter const &rval)

	~TaskAwareSASAFilter () override

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

void	threshold (core::Real const t)

void	designable_only (bool const d)

void	sc_only (bool const s)

void	probe_radius (core::Real const r)

void	jump_id (core::Size const j)

core::pack::task::TaskFactoryOP	task_factory () const

core::Real	threshold () const

bool	designable_only () const

bool	sc_only () const

core::Real	probe_radius () const

core::Size	jump_id () const

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	parse xml More...

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

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

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

core::Real	compute (core::pose::Pose const &pose, bool const verbose) const
	calc oligomeric AverageDegree More...

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::pack::task::TaskFactoryOP	task_factory_

core::Real	threshold_

bool	designable_only_

bool	sc_only_

core::Real	probe_radius_

core::Size	jump_id_

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::simple_filters::TaskAwareSASAFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::simple_filters::TaskAwareSASAFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::simple_filters::TaskAwareSASAFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::simple_filters::TaskAwareSASAFilter::Pose

◆ Real

typedef core::Real protocols::simple_filters::TaskAwareSASAFilter::Real

◆ Super

typedef protocols::filters::Filter protocols::simple_filters::TaskAwareSASAFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::simple_filters::TaskAwareSASAFilter::TagCOP

Constructor & Destructor Documentation

◆ TaskAwareSASAFilter() [1/3]

protocols::simple_filters::TaskAwareSASAFilter::TaskAwareSASAFilter ( )

◆ TaskAwareSASAFilter() [2/3]

protocols::simple_filters::TaskAwareSASAFilter::TaskAwareSASAFilter	(	core::pack::task::TaskFactoryOP	task_factory,
		core::Real const	t,
		bool const	d,
		bool const	s,
		core::Real const	r,
		core::Size const	j
	)

◆ TaskAwareSASAFilter() [3/3]

protocols::simple_filters::TaskAwareSASAFilter::TaskAwareSASAFilter ( TaskAwareSASAFilter const & rval )

default

◆ ~TaskAwareSASAFilter()

protocols::simple_filters::TaskAwareSASAFilter::~TaskAwareSASAFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::TaskAwareSASAFilter::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().

◆ class_name()

std::string protocols::simple_filters::TaskAwareSASAFilter::class_name ( )

static

Referenced by protocols::simple_filters::TaskAwareSASAFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::simple_filters::TaskAwareSASAFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::simple_filters::TaskAwareSASAFilter::compute	(	core::pose::Pose const &	pose,
		bool const	verbose
	)		const

calc oligomeric AverageDegree

References core::scoring::calc_per_atom_sasa(), designable_only(), core::pose::Pose::dump_pdb(), core::pose::symmetry::get_sym_aware_jump_num(), core::pose::initialize_atomid_map(), jump_id(), core::chemical::ResidueTypeBase::name(), core::conformation::Residue::name3(), probe_radius(), core::pose::Pose::residue(), sc_only(), core::pose::Pose::size(), task_factory(), protocols::simple_filters::TR(), protocols::toolbox::rigid_body::translate(), and core::conformation::Residue::type().

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

◆ designable_only() [1/2]

bool protocols::simple_filters::TaskAwareSASAFilter::designable_only ( ) const

References designable_only_.

Referenced by compute(), and parse_my_tag().

◆ designable_only() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::designable_only ( bool const d )

References designable_only_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::simple_filters::TaskAwareSASAFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ jump_id() [1/2]

core::Size protocols::simple_filters::TaskAwareSASAFilter::jump_id ( ) const

References jump_id_.

Referenced by compute(), and parse_my_tag().

◆ jump_id() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::jump_id ( core::Size const j )

References jump_id_.

◆ name()

std::string protocols::simple_filters::TaskAwareSASAFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::TaskAwareSASAFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References designable_only(), jump_id(), core::pack::task::parse_task_operations(), probe_radius(), sc_only(), task_factory(), and threshold().

◆ probe_radius() [1/2]

core::Real protocols::simple_filters::TaskAwareSASAFilter::probe_radius ( ) const

References probe_radius_.

Referenced by compute(), and parse_my_tag().

◆ probe_radius() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::probe_radius ( core::Real const r )

References probe_radius_.

◆ provide_xml_schema()

void protocols::simple_filters::TaskAwareSASAFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::TaskAwareSASAFilterCreator::provide_xml_schema().

◆ report()

void protocols::simple_filters::TaskAwareSASAFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

core::Real protocols::simple_filters::TaskAwareSASAFilter::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().

◆ sc_only() [1/2]

bool protocols::simple_filters::TaskAwareSASAFilter::sc_only ( ) const

References sc_only_.

Referenced by compute(), and parse_my_tag().

◆ sc_only() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::sc_only ( bool const s )

References sc_only_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareSASAFilter::task_factory ( ) const

References task_factory_.

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

◆ task_factory() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::task_factory ( core::pack::task::TaskFactoryOP task_factory )

References task_factory(), and task_factory_.

◆ threshold() [1/2]

core::Real protocols::simple_filters::TaskAwareSASAFilter::threshold ( ) const

References threshold_.

Referenced by apply(), and parse_my_tag().

◆ threshold() [2/2]

void protocols::simple_filters::TaskAwareSASAFilter::threshold ( core::Real const t )

References protocols::hybridization::t, and threshold_.

Member Data Documentation

◆ designable_only_

bool protocols::simple_filters::TaskAwareSASAFilter::designable_only_

private

Referenced by designable_only().

◆ jump_id_

core::Size protocols::simple_filters::TaskAwareSASAFilter::jump_id_

private

Referenced by jump_id().

◆ probe_radius_

core::Real protocols::simple_filters::TaskAwareSASAFilter::probe_radius_

private

Referenced by probe_radius().

◆ sc_only_

bool protocols::simple_filters::TaskAwareSASAFilter::sc_only_

private

Referenced by sc_only().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareSASAFilter::task_factory_

private

Referenced by task_factory().

◆ threshold_

core::Real protocols::simple_filters::TaskAwareSASAFilter::threshold_

private

Referenced by threshold().

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

src/protocols/simple_filters/TaskAwareSASAFilter.hh
src/protocols/simple_filters/TaskAwareSASAFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ Real

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ TaskAwareSASAFilter() [1/3]

◆ TaskAwareSASAFilter() [2/3]

◆ TaskAwareSASAFilter() [3/3]

◆ ~TaskAwareSASAFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ designable_only() [1/2]

◆ designable_only() [2/2]

◆ fresh_instance()

◆ jump_id() [1/2]

◆ jump_id() [2/2]

◆ name()

◆ parse_my_tag()

◆ probe_radius() [1/2]

◆ probe_radius() [2/2]

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ sc_only() [1/2]

◆ sc_only() [2/2]

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ threshold() [1/2]

◆ threshold() [2/2]

Member Data Documentation

◆ designable_only_

◆ jump_id_

◆ probe_radius_

◆ sc_only_

◆ task_factory_

◆ threshold_