protocols::simple_ddg::DdgFilter Class Reference

#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
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string const &)
	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)
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::Size	rb_jump_
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_
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

protocols::simple_ddg::DdgFilter::DdgFilter

(

)

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

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().

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

overridedefault

Member Function Documentation

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().

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

static

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

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

overridevirtual

Implements protocols::filters::Filter.

core::Real protocols::simple_ddg::DdgFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::simple_ddg::ddG::calculate(), chain_ids_, dump_pdbs(), protocols::simple_ddg::ddG::dump_pdbs(), extreme_value_removal(), filter(), protocols::simple_ddg::ddG::filter(), filter_, core::pose::get_jump_id_from_chain_id(), rb_jump_, relax_bound(), protocols::simple_ddg::ddG::relax_bound(), relax_mover(), protocols::simple_ddg::ddG::relax_mover(), relax_unbound(), protocols::simple_ddg::ddG::relax_unbound(), repack(), repack_bound(), protocols::simple_ddg::ddG::repack_bound(), repeats(), repeats_, protocols::simple_ddg::ddG::report_ddG(), scorefxn_, protocols::stepwise::modeler::split_pose(), protocols::simple_ddg::ddG::sum_ddG(), task_factory(), protocols::simple_ddg::ddG::task_factory(), protocols::simple_ddg::TR(), protocols::toolbox::rigid_body::translate(), translate_by(), protocols::simple_ddg::ddG::translate_by(), translate_by_, use_custom_task(), protocols::simple_ddg::ddG::use_custom_task(), and protocols::hybridization::val.

Referenced by apply(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), 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().

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

inline

References dump_pdbs_.

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

inline

References dump_pdbs_.

Referenced by compute(), and parse_my_tag().

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

inline

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

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

inline

References extreme_value_removal_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::filter

(

protocols::filters::FilterOP

m

)

References filter_.

protocols::filters::FilterOP protocols::simple_ddg::DdgFilter::filter

(

)

const

References filter_.

Referenced by compute(), and parse_my_tag().

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

overridevirtual

Implements protocols::filters::Filter.

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

private

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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::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_, rb_jump_, relax_bound(), relax_mover(), relax_unbound(), repack(), repack_bound(), repack_unbound(), repeats(), scorefxn_, task_factory(), protocols::simple_ddg::TR(), translate_by_, and use_custom_task().

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().

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

inline

References relax_bound_.

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

inline

References relax_bound_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::relax_mover

(

protocols::moves::MoverOP

m

)

References relax_mover_.

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

protocols::moves::MoverOP protocols::simple_ddg::DdgFilter::relax_mover

(

)

const

References relax_mover_.

Referenced by compute(), and parse_my_tag().

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

inline

References relax_unbound_.

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

inline

References relax_unbound_.

Referenced by compute(), and parse_my_tag().

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().

bool protocols::simple_ddg::DdgFilter::repack

(

)

const

References repack_.

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

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

inline

References repack_bound_.

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

inline

References repack_bound_.

Referenced by compute(), and parse_my_tag().

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

inline

References repack_unbound_.

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

inline

References repack_unbound_.

Referenced by parse_my_tag().

core::Size protocols::simple_ddg::DdgFilter::repeats

(

)

const

References repeats_.

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

void protocols::simple_ddg::DdgFilter::repeats

(

core::Size const

repeats

)

References repeats(), and repeats_.

void protocols::simple_ddg::DdgFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

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

inline

References task_factory(), and task_factory_.

Referenced by task_factory().

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

inline

References task_factory_.

Referenced by compute(), and parse_my_tag().

void protocols::simple_ddg::DdgFilter::translate_by

(

core::Real const

translate_by

)

References translate_by(), and translate_by_.

core::Real protocols::simple_ddg::DdgFilter::translate_by

(

)

const

References translate_by_.

Referenced by compute(), and translate_by().

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

inline

References use_custom_task_.

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

inline

References use_custom_task_.

Referenced by compute(), and parse_my_tag().

Member Data Documentation

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

private

Referenced by compute(), and parse_my_tag().

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

private

Referenced by apply(), and parse_my_tag().

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

private

Referenced by apply(), and parse_my_tag().

bool protocols::simple_ddg::DdgFilter::dump_pdbs_

private

Referenced by dump_pdbs().

bool protocols::simple_ddg::DdgFilter::extreme_value_removal_

private

Referenced by extreme_value_removal().

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

private

Referenced by compute(), and filter().

bool protocols::simple_ddg::DdgFilter::pb_enabled_

private

is PB enabled?

Referenced by DdgFilter(), and parse_my_tag().

core::Size protocols::simple_ddg::DdgFilter::rb_jump_

private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_ddg::DdgFilter::relax_bound_

private

Referenced by relax_bound().

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

private

Referenced by relax_mover().

bool protocols::simple_ddg::DdgFilter::relax_unbound_

private

Referenced by relax_unbound().

bool protocols::simple_ddg::DdgFilter::repack_

private

Referenced by repack().

bool protocols::simple_ddg::DdgFilter::repack_bound_

private

Referenced by repack_bound().

bool protocols::simple_ddg::DdgFilter::repack_unbound_

private

Referenced by repack_unbound().

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

private

Referenced by compute(), and repeats().

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

private

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

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

private

Referenced by task_factory().

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

private

translation distance in A

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

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