Rosetta  2020.37
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protocols::protein_interface_design::filters::BoltzmannFilter Class Reference

#include <BoltzmannFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::BoltzmannFilter:
Inheritance graph
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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::Realanchors () 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 bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Realanchors_
 
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

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
protocols::filters::FilterOP protocols::protein_interface_design::filters::BoltzmannFilter::clone ( ) const
overridevirtual
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
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
void protocols::protein_interface_design::filters::BoltzmannFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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)
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)
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
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
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
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().


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