#include <DdgFilter.hh>

Inheritance diagram for protocols::simple_ddg::DdgFilter:

Public Member Functions
	DdgFilter ()

	DdgFilter (core::Real const ddg_threshold, core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1, core::Size const repeats=1)

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

core::Size	repeats () const

void	repeats (core::Size const repeats)

void	repack (bool const repack)

bool	repack () const

void	repack_bound (bool const rpb)

bool	repack_bound () const

void	repack_unbound (bool const rpu)

bool	repack_unbound () const

void	relax_bound (bool const rlb)

bool	relax_bound () const

void	relax_unbound (bool const rlu)

bool	relax_unbound () const

void	translate_by (core::Real const translate_by)

core::Real	translate_by () const

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

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

void	use_custom_task (bool uct)

bool	use_custom_task () const

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

	~DdgFilter () override

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...

void	relax_mover (protocols::moves::MoverOP m)

protocols::moves::MoverOP	relax_mover () const

void	filter (protocols::filters::FilterOP m)

protocols::filters::FilterOP	filter () const

void	extreme_value_removal (bool const b)

bool	extreme_value_removal () const

void	dump_pdbs (bool const dp)

bool	dump_pdbs () const

std::string	name () const override

void	set_rb_jump (core::Size const setting)

void	set_jump_selector (core::select::jump_selector::JumpSelectorCOP sele)

core::select::jump_selector::JumpSelectorCOP	get_jump_selector () 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 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
void	initPB ()

Private Attributes
core::Real	ddg_threshold_

core::Real	ddg_threshold_min_

core::scoring::ScoreFunctionOP	scorefxn_

core::pack::task::TaskFactoryOP	task_factory_

bool	use_custom_task_

bool	repack_bound_

bool	repack_unbound_

bool	relax_bound_

bool	relax_unbound_

utility::vector1< core::Size >	chain_ids_

core::Size	repeats_

bool	repack_

protocols::moves::MoverOP	relax_mover_

protocols::filters::FilterOP	filter_

core::Size	rb_jump_ = 1

core::select::jump_selector::JumpSelectorCOP	jump_selector_ = nullptr

bool	pb_enabled_
	is PB enabled? More...

core::Real	translate_by_
	translation distance in A More...

bool	extreme_value_removal_

bool	dump_pdbs_

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

Constructor & Destructor Documentation

◆ DdgFilter() [1/2]

protocols::simple_ddg::DdgFilter::DdgFilter ( )

References protocols::filters::Filter::scorename_.

◆ DdgFilter() [2/2]

protocols::simple_ddg::DdgFilter::DdgFilter	(	core::Real const	ddg_threshold,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	rb_jump = `1`,
		core::Size const	repeats = `1`
	)

References core::scoring::PB_elec, pb_enabled_, scorefxn_, and protocols::simple_ddg::TR().

◆ ~DdgFilter()

protocols::simple_ddg::DdgFilter::~DdgFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_ddg::DdgFilter::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(), ddg_threshold_, ddg_threshold_min_, and protocols::simple_ddg::TR().

◆ class_name()

std::string protocols::simple_ddg::DdgFilter::class_name ( )

static

Referenced by protocols::simple_ddg::DdgFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

filters::FilterOP protocols::simple_ddg::DdgFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::simple_ddg::DdgFilter::compute ( core::pose::Pose const & pose ) const

Referenced by apply(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_ddg(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::simple_ddg::AlaScan::report(), report(), report_sm(), and protocols::simple_ddg::AlaScan::report_symmetry().

◆ dump_pdbs() [1/2]

bool protocols::simple_ddg::DdgFilter::dump_pdbs ( ) const

inline

References dump_pdbs_.

Referenced by compute(), and parse_my_tag().

◆ dump_pdbs() [2/2]

void protocols::simple_ddg::DdgFilter::dump_pdbs ( bool const dp )

inline

References dump_pdbs_.

◆ extreme_value_removal() [1/2]

bool protocols::simple_ddg::DdgFilter::extreme_value_removal ( ) const

inline

References extreme_value_removal_.

Referenced by compute(), and parse_my_tag().

◆ extreme_value_removal() [2/2]

void protocols::simple_ddg::DdgFilter::extreme_value_removal ( bool const b )

inline

References protocols::match::upstream::b, and extreme_value_removal_.

◆ filter() [1/2]

protocols::filters::FilterOP protocols::simple_ddg::DdgFilter::filter ( ) const

References filter_.

Referenced by compute(), and parse_my_tag().

◆ filter() [2/2]

void protocols::simple_ddg::DdgFilter::filter ( protocols::filters::FilterOP m )

References filter_.

◆ fresh_instance()

filters::FilterOP protocols::simple_ddg::DdgFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ get_jump_selector()

core::select::jump_selector::JumpSelectorCOP protocols::simple_ddg::DdgFilter::get_jump_selector ( ) const

inline

References jump_selector_.

◆ initPB()

void protocols::simple_ddg::DdgFilter::initPB ( )

private

◆ name()

std::string protocols::simple_ddg::DdgFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_ddg::DdgFilter::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 chain_ids_, ddg_threshold_, ddg_threshold_min_, dump_pdbs(), extreme_value_removal(), filter(), core::select::jump_selector::get_jump_selector(), core::scoring::get_score_function_name(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, relax_bound(), relax_mover(), relax_unbound(), repack(), repack_bound(), repack_unbound(), repeats(), scorefxn_, set_jump_selector(), set_rb_jump(), task_factory(), protocols::simple_ddg::TR(), translate_by_, and use_custom_task().

◆ provide_xml_schema()

void protocols::simple_ddg::DdgFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_ddg::DdgFilterCreator::provide_xml_schema().

◆ relax_bound() [1/2]

bool protocols::simple_ddg::DdgFilter::relax_bound ( ) const

inline

References relax_bound_.

Referenced by compute(), and parse_my_tag().

◆ relax_bound() [2/2]

void protocols::simple_ddg::DdgFilter::relax_bound ( bool const rlb )

inline

References relax_bound_.

◆ relax_mover() [1/2]

protocols::moves::MoverOP protocols::simple_ddg::DdgFilter::relax_mover ( ) const

References relax_mover_.

Referenced by compute(), and parse_my_tag().

◆ relax_mover() [2/2]

void protocols::simple_ddg::DdgFilter::relax_mover ( protocols::moves::MoverOP m )

References relax_mover_.

Referenced by protocols::simple_ddg::SSElementBisectddGFilter::get_ddg_bisect_score().

◆ relax_unbound() [1/2]

bool protocols::simple_ddg::DdgFilter::relax_unbound ( ) const

inline

References relax_unbound_.

Referenced by compute(), and parse_my_tag().

◆ relax_unbound() [2/2]

void protocols::simple_ddg::DdgFilter::relax_unbound ( bool const rlu )

inline

References relax_unbound_.

◆ repack() [1/2]

bool protocols::simple_ddg::DdgFilter::repack ( ) const

References repack_.

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

◆ repack() [2/2]

void protocols::simple_ddg::DdgFilter::repack ( bool const repack )

References repack(), and repack_.

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_ddg(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

◆ repack_bound() [1/2]

bool protocols::simple_ddg::DdgFilter::repack_bound ( ) const

inline

References repack_bound_.

Referenced by compute(), and parse_my_tag().

◆ repack_bound() [2/2]

void protocols::simple_ddg::DdgFilter::repack_bound ( bool const rpb )

inline

References repack_bound_.

◆ repack_unbound() [1/2]

bool protocols::simple_ddg::DdgFilter::repack_unbound ( ) const

inline

References repack_unbound_.

Referenced by parse_my_tag().

◆ repack_unbound() [2/2]

void protocols::simple_ddg::DdgFilter::repack_unbound ( bool const rpu )

inline

References repack_unbound_.

◆ repeats() [1/2]

core::Size protocols::simple_ddg::DdgFilter::repeats ( ) const

References repeats_.

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

◆ repeats() [2/2]

void protocols::simple_ddg::DdgFilter::repeats ( core::Size const repeats )

References repeats(), and repeats_.

◆ report()

void protocols::simple_ddg::DdgFilter::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_ddg::DdgFilter::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().

◆ set_jump_selector()

void protocols::simple_ddg::DdgFilter::set_jump_selector ( core::select::jump_selector::JumpSelectorCOP sele )

inline

References jump_selector_.

Referenced by parse_my_tag().

◆ set_rb_jump()

void protocols::simple_ddg::DdgFilter::set_rb_jump ( core::Size const setting )

inline

References rb_jump_.

Referenced by parse_my_tag().

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdgFilter::task_factory ( ) const

inline

References task_factory_.

Referenced by compute(), and parse_my_tag().

◆ task_factory() [2/2]

void protocols::simple_ddg::DdgFilter::task_factory ( core::pack::task::TaskFactoryOP task_factory )

inline

References task_factory(), and task_factory_.

Referenced by task_factory().

◆ translate_by() [1/2]

core::Real protocols::simple_ddg::DdgFilter::translate_by ( ) const

References translate_by_.

Referenced by compute(), and translate_by().

◆ translate_by() [2/2]

void protocols::simple_ddg::DdgFilter::translate_by ( core::Real const translate_by )

References translate_by(), and translate_by_.

◆ use_custom_task() [1/2]

bool protocols::simple_ddg::DdgFilter::use_custom_task ( ) const

inline

References use_custom_task_.

Referenced by compute(), and parse_my_tag().

◆ use_custom_task() [2/2]

void protocols::simple_ddg::DdgFilter::use_custom_task ( bool uct )

inline

References use_custom_task_.

Member Data Documentation

◆ chain_ids_

utility::vector1<core::Size> protocols::simple_ddg::DdgFilter::chain_ids_

private

Referenced by compute(), and parse_my_tag().

◆ ddg_threshold_

core::Real protocols::simple_ddg::DdgFilter::ddg_threshold_

private

Referenced by apply(), and parse_my_tag().

◆ ddg_threshold_min_

core::Real protocols::simple_ddg::DdgFilter::ddg_threshold_min_

private

Referenced by apply(), and parse_my_tag().

◆ dump_pdbs_

bool protocols::simple_ddg::DdgFilter::dump_pdbs_

private

Referenced by dump_pdbs().

◆ extreme_value_removal_

bool protocols::simple_ddg::DdgFilter::extreme_value_removal_

private

Referenced by extreme_value_removal().

◆ filter_

protocols::filters::FilterOP protocols::simple_ddg::DdgFilter::filter_

private

Referenced by compute(), and filter().

◆ jump_selector_

core::select::jump_selector::JumpSelectorCOP protocols::simple_ddg::DdgFilter::jump_selector_ = nullptr

private

Referenced by compute(), get_jump_selector(), and set_jump_selector().

◆ pb_enabled_

bool protocols::simple_ddg::DdgFilter::pb_enabled_

private

is PB enabled?

Referenced by DdgFilter(), and parse_my_tag().

◆ rb_jump_

core::Size protocols::simple_ddg::DdgFilter::rb_jump_ = 1

private

Referenced by compute(), and set_rb_jump().

◆ relax_bound_

bool protocols::simple_ddg::DdgFilter::relax_bound_

private

Referenced by relax_bound().

◆ relax_mover_

protocols::moves::MoverOP protocols::simple_ddg::DdgFilter::relax_mover_

private

Referenced by relax_mover().

◆ relax_unbound_

bool protocols::simple_ddg::DdgFilter::relax_unbound_

private

Referenced by relax_unbound().

◆ repack_

bool protocols::simple_ddg::DdgFilter::repack_

private

Referenced by repack().

◆ repack_bound_

bool protocols::simple_ddg::DdgFilter::repack_bound_

private

Referenced by repack_bound().

◆ repack_unbound_

bool protocols::simple_ddg::DdgFilter::repack_unbound_

private

Referenced by repack_unbound().

◆ repeats_

core::Size protocols::simple_ddg::DdgFilter::repeats_

private

Referenced by compute(), and repeats().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_ddg::DdgFilter::scorefxn_

private

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

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdgFilter::task_factory_

private

Referenced by task_factory().

◆ translate_by_

core::Real protocols::simple_ddg::DdgFilter::translate_by_

private

translation distance in A

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

◆ use_custom_task_

bool protocols::simple_ddg::DdgFilter::use_custom_task_

private

Referenced by use_custom_task().

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

src/protocols/simple_ddg/DdgFilter.hh
src/protocols/simple_ddg/DdgFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DdgFilter() [1/2]

◆ DdgFilter() [2/2]

◆ ~DdgFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ dump_pdbs() [1/2]

◆ dump_pdbs() [2/2]

◆ extreme_value_removal() [1/2]

◆ extreme_value_removal() [2/2]

◆ filter() [1/2]

◆ filter() [2/2]

◆ fresh_instance()

◆ get_jump_selector()

◆ initPB()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ relax_bound() [1/2]

◆ relax_bound() [2/2]

◆ relax_mover() [1/2]

◆ relax_mover() [2/2]

◆ relax_unbound() [1/2]

◆ relax_unbound() [2/2]

◆ repack() [1/2]

◆ repack() [2/2]

◆ repack_bound() [1/2]

◆ repack_bound() [2/2]

◆ repack_unbound() [1/2]

◆ repack_unbound() [2/2]

◆ repeats() [1/2]

◆ repeats() [2/2]

◆ report()

◆ report_sm()

◆ set_jump_selector()

◆ set_rb_jump()

◆ task_factory() [1/2]

◆ task_factory() [2/2]

◆ translate_by() [1/2]

◆ translate_by() [2/2]

◆ use_custom_task() [1/2]

◆ use_custom_task() [2/2]

Member Data Documentation

◆ chain_ids_

◆ ddg_threshold_

◆ ddg_threshold_min_

◆ dump_pdbs_

◆ extreme_value_removal_

◆ filter_

◆ jump_selector_

◆ pb_enabled_

◆ rb_jump_

◆ relax_bound_

◆ relax_mover_

◆ relax_unbound_

◆ repack_

◆ repack_bound_

◆ repack_unbound_

◆ repeats_

◆ scorefxn_

◆ task_factory_

◆ translate_by_

◆ use_custom_task_