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protocols::calc_taskop_filters::Sigmoid Class Reference

transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset More...

#include <SigmoidFilter.hh>

Inheritance diagram for protocols::calc_taskop_filters::Sigmoid:
Inheritance graph
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Public Member Functions

 Sigmoid ()
 
 ~Sigmoid () override
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. 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...
 
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...
 
core::Real compute (core::pose::Pose const &pose) const
 
core::Real steepness () const
 
void steepness (core::Real const s)
 
core::Real offset ()
 
void offset (core::Real const o)
 
bool negate () const
 
void negate (bool const b)
 
protocols::filters::FilterOP filter () const
 
void filter (protocols::filters::FilterOP f)
 
void reset_baseline (core::pose::Pose const &pose, bool const attempt_read_from_checkpoint)
 The first MC trajectory should not read the baseline from the checkpoint file, instead, it should set the baseline attempt_read_from_checkpoint determines whether a read attempt from checkpoint should be attempted. More...
 
core::Real threshold () const
 allows within-trajectory resetting of the baseline. Notice this is nonconst, so can't be called from apply. attempt_read_from_checkpoint should be true for MC trials > 1, but false otherwise More...
 
void threshold (core::Real const t)
 
void baseline_checkpointing_filename (std::string const &s)
 
std::string baseline_checkpointing_filename () 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 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)
 
static void attributes (utility::tag::AttributeList &attlist)
 

Private Attributes

protocols::filters::FilterOP filter_
 
core::Real steepness_
 dflt NULL More...
 
core::Real offset_
 
core::Real baseline_
 dflt 0 More...
 
bool negate_
 dflt 0; this is tricky; used internally to keep track of where the pose started. It is only reset by reset_baseline, and cannot, due to constness, be changed by apply More...
 
core::Real threshold_
 dflt false More...
 
std::string baseline_checkpointing_filename_
 dflt 0 (always accept) More...
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Detailed Description

transform the output from a regular filter into a sigmoid ranging from 0-1 according to: fx = 1/[1 + exp[ ( x - offset ) * steepness ] The function asymptotically reaches 1 at negative values and 0 at positive values. It's 0.5 at the offset and steepness determines its slope at the offset

Constructor & Destructor Documentation

protocols::calc_taskop_filters::Sigmoid::Sigmoid ( )
protocols::calc_taskop_filters::Sigmoid::~Sigmoid ( )
overridedefault

Member Function Documentation

bool protocols::calc_taskop_filters::Sigmoid::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(), threshold(), and protocols::hybridization::val.

void protocols::calc_taskop_filters::Sigmoid::attributes ( utility::tag::AttributeList &  attlist)
static
void protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename ( std::string const &  s)
inline
std::string protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename ( ) const
inline
std::string protocols::calc_taskop_filters::Sigmoid::class_name ( )
static
filters::FilterOP protocols::calc_taskop_filters::Sigmoid::clone ( ) const
inlineoverridevirtual
core::Real protocols::calc_taskop_filters::Sigmoid::compute ( core::pose::Pose const &  pose) const
protocols::filters::FilterOP protocols::calc_taskop_filters::Sigmoid::filter ( ) const

References filter_.

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

void protocols::calc_taskop_filters::Sigmoid::filter ( protocols::filters::FilterOP  f)

References filter_.

filters::FilterOP protocols::calc_taskop_filters::Sigmoid::fresh_instance ( ) const
inlineoverridevirtual
std::string protocols::calc_taskop_filters::Sigmoid::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

bool protocols::calc_taskop_filters::Sigmoid::negate ( ) const
inline

References negate_.

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::Sigmoid::negate ( bool const  b)
inline
core::Real protocols::calc_taskop_filters::Sigmoid::offset ( )
inline

References offset_.

Referenced by parse_my_tag().

void protocols::calc_taskop_filters::Sigmoid::offset ( core::Real const  o)
inline

References offset_.

void protocols::calc_taskop_filters::Sigmoid::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 baseline_checkpointing_filename_, filter(), negate(), offset(), protocols::rosetta_scripts::parse_filter(), steepness(), threshold(), and protocols::calc_taskop_filters::TR().

void protocols::calc_taskop_filters::Sigmoid::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::calc_taskop_filters::Sigmoid::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual
core::Real protocols::calc_taskop_filters::Sigmoid::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::calc_taskop_filters::Sigmoid::reset_baseline ( core::pose::Pose const &  pose,
bool const  attempt_read_from_checkpoint 
)

The first MC trajectory should not read the baseline from the checkpoint file, instead, it should set the baseline attempt_read_from_checkpoint determines whether a read attempt from checkpoint should be attempted.

References baseline_, baseline_checkpointing_filename_, core::sequence::end, filter(), core::conformation::membrane::in, core::conformation::membrane::out, and protocols::calc_taskop_filters::TR().

core::Real protocols::calc_taskop_filters::Sigmoid::steepness ( ) const
inline

References steepness_.

Referenced by parse_my_tag().

void protocols::calc_taskop_filters::Sigmoid::steepness ( core::Real const  s)
inline

References steepness_.

core::Real protocols::calc_taskop_filters::Sigmoid::threshold ( ) const
inline

allows within-trajectory resetting of the baseline. Notice this is nonconst, so can't be called from apply. attempt_read_from_checkpoint should be true for MC trials > 1, but false otherwise

References threshold_.

Referenced by apply(), and parse_my_tag().

void protocols::calc_taskop_filters::Sigmoid::threshold ( core::Real const  t)
inline

Member Data Documentation

core::Real protocols::calc_taskop_filters::Sigmoid::baseline_
private

dflt 0

Referenced by compute(), and reset_baseline().

std::string protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename_
private

dflt 0 (always accept)

Referenced by baseline_checkpointing_filename(), parse_my_tag(), and reset_baseline().

protocols::filters::FilterOP protocols::calc_taskop_filters::Sigmoid::filter_
private

Referenced by filter().

bool protocols::calc_taskop_filters::Sigmoid::negate_
private

dflt 0; this is tricky; used internally to keep track of where the pose started. It is only reset by reset_baseline, and cannot, due to constness, be changed by apply

Referenced by negate().

core::Real protocols::calc_taskop_filters::Sigmoid::offset_
private

Referenced by compute(), and offset().

core::Real protocols::calc_taskop_filters::Sigmoid::steepness_
private

dflt NULL

Referenced by compute(), and steepness().

core::Real protocols::calc_taskop_filters::Sigmoid::threshold_
private

dflt false

Referenced by threshold().


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