protocols::protein_interface_design::filters::BoltzmannFilter Class Reference

#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 (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 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

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

private

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::BoltzmannFilter::BoltzmannFilter

(

)

default ctor

References anchors_, negative_filters_, and positive_filters_.

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

overridedefault

Member Function Documentation

void protocols::protein_interface_design::filters::BoltzmannFilter::add_negative_filter

(

protocols::filters::FilterOP

f

)

References negative_filters_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::add_positive_filter

(

protocols::filters::FilterOP

f

)

References positive_filters_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::anchors

(

utility::vector1< core::Real > const &

anchors

)

References anchors(), and anchors_.

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

(

)

const

References anchors_.

Referenced by anchors(), and parse_my_tag().

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().

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().

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

overridevirtual

Implements protocols::filters::Filter.

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().

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold

(

)

const

References fitness_threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold

(

core::Real const

f

)

References fitness_threshold_.

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

overridevirtual

Implements protocols::filters::Filter.

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

bool protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg

(

)

const

References norm_neg_.

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::norm_neg

(

bool const

n

)

References norm_neg_.

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().

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().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

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().

void protocols::protein_interface_design::filters::BoltzmannFilter::temperature

(

core::Real const

temp

)

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

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::temperature

(

)

const

References temperature_.

Referenced by compute(), and parse_my_tag().

void protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold

(

core::Real const

t

)

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

core::Real protocols::protein_interface_design::filters::BoltzmannFilter::triage_threshold

(

)

const

References triage_threshold_.

Referenced by compute(), and parse_my_tag().

Member Data Documentation

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

private

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

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

private

Referenced by fitness_threshold().

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

private

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

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

private

Referenced by norm_neg().

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

private

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

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

private

Referenced by temperature().

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

private

Referenced by triage_threshold().

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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