Next-generation RotamerBoltzmannWeight filter. More...

#include <RotamerBoltzmannWeight2.hh>

Inheritance diagram for protocols::calc_taskop_filters::RotamerBoltzmannWeight2:

Public Types
enum	ScoreType { MEAN_PROBABILITY , MAX_PROBABILITY , MODIFIED_DDG , PROBABILITY , MIN_PROBABILITY }

typedef std::map< core::Size, core::Real >	ResidueDDGs

Public Member Functions
	RotamerBoltzmannWeight2 ()

	RotamerBoltzmannWeight2 (RotamerBoltzmannWeight2 const &rval)
	copy constructor – required because each instance should have unique calculator id More...

	~RotamerBoltzmannWeight2 () override

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

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...

virtual std::string	get_name () const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)

void	set_energy_landscape_evaluator (protocols::toolbox::EnergyLandscapeEvaluatorCOP evaluator)

void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)

void	set_score_type (ScoreType const scoretype)

std::string const &	calculator_id () const

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 Member Functions
core::Real	compute_score (core::pose::Pose const &pose, pose_metric_calculators::RotamerProbabilities const &probabilities) const

void	register_calculator () const

void	unregister_calculator ()

core::Real	compute_modified_ddg (core::pose::Pose const &pose, pose_metric_calculators::RotamerProbabilities const &probs) const

core::Real	compute_ddg (core::pose::Pose const &pose) const

core::Real	compute_modified_residue_energy (pose_metric_calculators::RotamerProbability const &probability) const

Static Private Member Functions
static std::string	new_calculator_id ()

Private Attributes
ScoreType	score_type_

std::string	calculator_id_

core::scoring::ScoreFunctionCOP	scorefxn_

protocols::pose_metric_calculators::RotamerBoltzCalculatorOP	calculator_

Static Private Attributes
static core::Real const	default_temperature_ = 0.8

static core::Real const	default_lambda_ = 0.5

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

Detailed Description

Next-generation RotamerBoltzmannWeight filter.

Member Typedef Documentation

◆ ResidueDDGs

typedef std::map< core::Size, core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight2::ResidueDDGs

Member Enumeration Documentation

◆ ScoreType

enum protocols::calc_taskop_filters::RotamerBoltzmannWeight2::ScoreType

Enumerator
MEAN_PROBABILITY
MAX_PROBABILITY
MODIFIED_DDG
PROBABILITY
MIN_PROBABILITY

Constructor & Destructor Documentation

◆ RotamerBoltzmannWeight2() [1/2]

protocols::calc_taskop_filters::RotamerBoltzmannWeight2::RotamerBoltzmannWeight2 ( )

References calculator_, calculator_id_, and protocols::calc_taskop_filters::TR().

◆ RotamerBoltzmannWeight2() [2/2]

protocols::calc_taskop_filters::RotamerBoltzmannWeight2::RotamerBoltzmannWeight2 ( RotamerBoltzmannWeight2 const & rval )

copy constructor – required because each instance should have unique calculator id

References calculator_id_, and protocols::calc_taskop_filters::TR().

◆ ~RotamerBoltzmannWeight2()

protocols::calc_taskop_filters::RotamerBoltzmannWeight2::~RotamerBoltzmannWeight2 ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight2::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

◆ calculator_id()

std::string const & protocols::calc_taskop_filters::RotamerBoltzmannWeight2::calculator_id ( ) const

References calculator_id_.

◆ class_name()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight2::class_name ( )

static

Referenced by get_name(), protocols::calc_taskop_filters::RotamerBoltzmannWeight2Creator::keyname(), name(), new_calculator_id(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight2::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compute_ddg()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_ddg ( core::pose::Pose const & pose ) const

private

References protocols::simple_ddg::DdgFilter::compute(), protocols::simple_ddg::DdgFilter::repack(), and scorefxn_.

Referenced by compute_modified_ddg().

◆ compute_modified_ddg()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_modified_ddg	(	core::pose::Pose const &	pose,
		pose_metric_calculators::RotamerProbabilities const &	probs
	)		const

private

References compute_ddg(), compute_modified_residue_energy(), protocols::buns::energy, core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and protocols::calc_taskop_filters::TR().

Referenced by compute_score().

◆ compute_modified_residue_energy()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_modified_residue_energy ( pose_metric_calculators::RotamerProbability const & probability ) const

private

References default_temperature_, and protocols::simple_moves::bb_sampler::probability.

Referenced by compute_modified_ddg(), and report().

◆ compute_score()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight2::compute_score	(	core::pose::Pose const &	pose,
		pose_metric_calculators::RotamerProbabilities const &	probabilities
	)		const

private

References protocols::calc_taskop_filters::compute_max_probability(), protocols::calc_taskop_filters::compute_mean_probability(), protocols::calc_taskop_filters::compute_min_probability(), compute_modified_ddg(), protocols::calc_taskop_filters::compute_probability(), MAX_PROBABILITY, MEAN_PROBABILITY, MIN_PROBABILITY, MODIFIED_DDG, PROBABILITY, and score_type_.

Referenced by report(), and report_sm().

◆ fresh_instance()

protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight2::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ get_name()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight2::get_name ( ) const

virtual

References class_name().

◆ name()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight2::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ new_calculator_id()

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight2::new_calculator_id ( )

staticprivate

References class_name(), and protocols::calc_taskop_filters::IdManager< T >::register_new_id().

Referenced by unregister_calculator().

◆ parse_my_tag()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References default_lambda_, default_temperature_, protocols::antibody::lambda, MAX_PROBABILITY, MEAN_PROBABILITY, MIN_PROBABILITY, MODIFIED_DDG, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), PROBABILITY, set_energy_landscape_evaluator(), set_residue_selector(), set_score_type(), and set_scorefxn().

◆ provide_xml_schema()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::calc_taskop_filters::RotamerBoltzmannWeight2Creator::provide_xml_schema().

◆ register_calculator()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::register_calculator ( ) const

private

References calculator_, calculator_id_, core::pose::metrics::CalculatorFactory::Instance(), core::pose::metrics::CalculatorFactory::register_calculator(), and protocols::calc_taskop_filters::TR().

Referenced by report(), and report_sm().

◆ report()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References calculator_id_, compute_modified_residue_energy(), compute_score(), core::pose::Pose::metric(), core::conformation::Residue::name(), core::conformation::membrane::out, register_calculator(), and core::pose::Pose::residue().

◆ report_sm()

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight2::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References calculator_, calculator_id_, compute_score(), core::pose::Pose::metric(), and register_calculator().

◆ set_energy_landscape_evaluator()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_energy_landscape_evaluator ( protocols::toolbox::EnergyLandscapeEvaluatorCOP evaluator )

References calculator_, and unregister_calculator().

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

References calculator_, and unregister_calculator().

Referenced by parse_my_tag().

◆ set_score_type()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_score_type ( ScoreType const scoretype )

References score_type_.

Referenced by parse_my_tag().

◆ set_scorefxn()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References calculator_, scorefxn_, and unregister_calculator().

Referenced by parse_my_tag().

◆ unregister_calculator()

void protocols::calc_taskop_filters::RotamerBoltzmannWeight2::unregister_calculator ( )

private

References calculator_id_, core::pose::metrics::CalculatorFactory::Instance(), new_calculator_id(), core::pose::metrics::CalculatorFactory::remove_calculator(), and protocols::calc_taskop_filters::TR().

Referenced by set_energy_landscape_evaluator(), set_residue_selector(), and set_scorefxn().

Member Data Documentation

◆ calculator_

protocols::pose_metric_calculators::RotamerBoltzCalculatorOP protocols::calc_taskop_filters::RotamerBoltzmannWeight2::calculator_

private

Referenced by register_calculator(), report_sm(), RotamerBoltzmannWeight2(), set_energy_landscape_evaluator(), set_residue_selector(), and set_scorefxn().

◆ calculator_id_

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight2::calculator_id_

private

Referenced by calculator_id(), register_calculator(), report(), report_sm(), RotamerBoltzmannWeight2(), and unregister_calculator().

◆ default_lambda_

core::Real const protocols::calc_taskop_filters::RotamerBoltzmannWeight2::default_lambda_ = 0.5

staticprivate

Referenced by parse_my_tag().

◆ default_temperature_

core::Real const protocols::calc_taskop_filters::RotamerBoltzmannWeight2::default_temperature_ = 0.8

staticprivate

Referenced by compute_modified_residue_energy(), and parse_my_tag().

◆ score_type_

ScoreType protocols::calc_taskop_filters::RotamerBoltzmannWeight2::score_type_

private

Referenced by compute_score(), and set_score_type().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::calc_taskop_filters::RotamerBoltzmannWeight2::scorefxn_

private

Referenced by compute_ddg(), and set_scorefxn().

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

src/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.hh
src/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ResidueDDGs

Member Enumeration Documentation

◆ ScoreType

Constructor & Destructor Documentation

◆ RotamerBoltzmannWeight2() [1/2]

◆ RotamerBoltzmannWeight2() [2/2]

◆ ~RotamerBoltzmannWeight2()

Member Function Documentation

◆ apply()

◆ calculator_id()

◆ class_name()

◆ clone()

◆ compute_ddg()

◆ compute_modified_ddg()

◆ compute_modified_residue_energy()

◆ compute_score()

◆ fresh_instance()

◆ get_name()

◆ name()

◆ new_calculator_id()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_calculator()

◆ report()

◆ report_sm()

◆ set_energy_landscape_evaluator()

◆ set_residue_selector()

◆ set_score_type()

◆ set_scorefxn()

◆ unregister_calculator()

Member Data Documentation

◆ calculator_

◆ calculator_id_

◆ default_lambda_

◆ default_temperature_

◆ score_type_

◆ scorefxn_