#include <BoltzmannFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::BoltzmannFilter:

Public Member Functions
	BoltzmannFilter ()
	default ctor More...

bool	apply (core::pose::Pose const &pose) const override
	Constructor with a single target residue. 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...

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

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

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

	~BoltzmannFilter () 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	add_positive_filter (protocols::filters::FilterOP f)

void	add_negative_filter (protocols::filters::FilterOP f)

void	anchors (utility::vector1< core::Real > const &anchors)

utility::vector1< core::Real >	anchors () const

utility::vector1< protocols::filters::FilterOP >	get_positive_filters () const

utility::vector1< protocols::filters::FilterOP >	get_negative_filters () const

void	temperature (core::Real const temp)

core::Real	temperature () const

void	triage_threshold (core::Real const t)

core::Real	triage_threshold () const

core::Real	fitness_threshold () const

void	fitness_threshold (core::Real const f)

bool	norm_neg () const

void	norm_neg (bool const n)

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 Types
typedef protocols::filters::Filter	parent

Private Attributes
utility::vector1< protocols::filters::FilterOP >	positive_filters_

utility::vector1< protocols::filters::FilterOP >	negative_filters_

utility::vector1< core::Real >	anchors_

core::Real	temperature_

core::Real	fitness_threshold_

core::Real	triage_threshold_

bool	norm_neg_

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

Member Typedef Documentation

◆ parent

typedef protocols::filters::Filter protocols::protein_interface_design::filters::BoltzmannFilter::parent

private

Constructor & Destructor Documentation

◆ BoltzmannFilter()

protocols::protein_interface_design::filters::BoltzmannFilter::BoltzmannFilter ( )

default ctor

References anchors_, negative_filters_, and positive_filters_.

◆ ~BoltzmannFilter()

protocols::protein_interface_design::filters::BoltzmannFilter::~BoltzmannFilter ( )

overridedefault

Member Function Documentation

◆ add_negative_filter()

void protocols::protein_interface_design::filters::BoltzmannFilter::add_negative_filter ( protocols::filters::FilterOP f )

References negative_filters_.

Referenced by parse_my_tag().

◆ add_positive_filter()

void protocols::protein_interface_design::filters::BoltzmannFilter::add_positive_filter ( protocols::filters::FilterOP f )

References positive_filters_.

Referenced by parse_my_tag().

◆ anchors() [1/2]

utility::vector1< core::Real > protocols::protein_interface_design::filters::BoltzmannFilter::anchors ( ) const

References anchors_.

Referenced by anchors(), and parse_my_tag().

◆ anchors() [2/2]

void protocols::protein_interface_design::filters::BoltzmannFilter::anchors ( utility::vector1< core::Real > const & anchors )

References anchors(), and anchors_.

◆ apply()

bool protocols::protein_interface_design::filters::BoltzmannFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

References compute(), and fitness_threshold().

◆ class_name()

std::string protocols::protein_interface_design::filters::BoltzmannFilter::class_name ( )

static

Referenced by protocols::protein_interface_design::filters::BoltzmannFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::compute ( core::pose::Pose const & pose ) const

NOTICE that this returns -Fitness [-1:0] for use in optimization F = Sum_{+}( -E/T ) / [ Sum_{-}( -E/T ) + Sum_{+} ( -E/T ) + Sum_{+}(( E - anchor )/T) ] This is the standard fitness function, except for anchor. Anchor can be (but doesn't have to be) defined for each positive state and sets a threshold above which energy increases in the positive state substantially reduce fitness, irrespective of what happened to all negative states. Can be used to ensure that the stability of a target state is not compromised during design. Set this to a very large number (99999) to eliminate the effects of the anchor, or specify no anchors at all

References anchors_, core::chemical::element::F, get_negative_filters(), get_positive_filters(), norm_neg(), report_sm(), temperature(), protocols::protein_interface_design::filters::TR(), and triage_threshold().

Referenced by apply(), and report_sm().

◆ fitness_threshold() [1/2]

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold ( ) const

References fitness_threshold_.

Referenced by apply(), and parse_my_tag().

◆ fitness_threshold() [2/2]

void protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold ( core::Real const f )

References fitness_threshold_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ get_negative_filters()

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_negative_filters ( ) const

References negative_filters_.

Referenced by compute(), and parse_my_tag().

◆ get_positive_filters()

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::get_positive_filters ( ) const

References positive_filters_.

Referenced by compute(), and parse_my_tag().

◆ name()

std::string protocols::protein_interface_design::filters::BoltzmannFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ norm_neg() [1/2]

bool protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg ( ) const

References norm_neg_.

Referenced by compute(), and parse_my_tag().

◆ norm_neg() [2/2]

void protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg ( bool const n )

References norm_neg_.

◆ parse_my_tag()

void protocols::protein_interface_design::filters::BoltzmannFilter::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 add_negative_filter(), add_positive_filter(), anchors(), anchors_, fitness_threshold(), get_negative_filters(), get_positive_filters(), norm_neg(), protocols::rosetta_scripts::parse_filter(), temperature(), protocols::protein_interface_design::filters::TR(), and triage_threshold().

◆ provide_xml_schema()

void protocols::protein_interface_design::filters::BoltzmannFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::protein_interface_design::filters::BoltzmannFilterCreator::provide_xml_schema().

◆ report()

void protocols::protein_interface_design::filters::BoltzmannFilter::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

◆ report_sm()

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::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().

Referenced by compute().

◆ temperature() [1/2]

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature ( ) const

References temperature_.

Referenced by compute(), and parse_my_tag().

◆ temperature() [2/2]

void protocols::protein_interface_design::filters::BoltzmannFilter::temperature ( core::Real const temp )

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

◆ triage_threshold() [1/2]

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold ( ) const

References triage_threshold_.

Referenced by compute(), and parse_my_tag().

◆ triage_threshold() [2/2]

void protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold ( core::Real const t )

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

Member Data Documentation

◆ anchors_

utility::vector1< core::Real > protocols::protein_interface_design::filters::BoltzmannFilter::anchors_

private

Referenced by anchors(), BoltzmannFilter(), compute(), and parse_my_tag().

◆ fitness_threshold_

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold_

private

Referenced by fitness_threshold().

◆ negative_filters_

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::negative_filters_

private

Referenced by add_negative_filter(), BoltzmannFilter(), and get_negative_filters().

◆ norm_neg_

bool protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg_

private

Referenced by norm_neg().

◆ positive_filters_

utility::vector1< protocols::filters::FilterOP > protocols::protein_interface_design::filters::BoltzmannFilter::positive_filters_

private

Referenced by add_positive_filter(), BoltzmannFilter(), and get_positive_filters().

◆ temperature_

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature_

private

Referenced by temperature().

◆ triage_threshold_

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold_

private

Referenced by triage_threshold().

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

src/protocols/protein_interface_design/filters/BoltzmannFilter.hh
src/protocols/protein_interface_design/filters/BoltzmannFilter.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ BoltzmannFilter()

◆ ~BoltzmannFilter()

Member Function Documentation

◆ add_negative_filter()

◆ add_positive_filter()

◆ anchors() [1/2]

◆ anchors() [2/2]

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ fitness_threshold() [1/2]

◆ fitness_threshold() [2/2]

◆ fresh_instance()

◆ get_negative_filters()

◆ get_positive_filters()

◆ name()

◆ norm_neg() [1/2]

◆ norm_neg() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ temperature() [1/2]

◆ temperature() [2/2]

◆ triage_threshold() [1/2]

◆ triage_threshold() [2/2]

Member Data Documentation

◆ anchors_

◆ fitness_threshold_

◆ negative_filters_

◆ norm_neg_

◆ positive_filters_

◆ temperature_

◆ triage_threshold_