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:

[legend]

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 () 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)

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

◆ Sigmoid()

protocols::calc_taskop_filters::Sigmoid::Sigmoid ( )

◆ ~Sigmoid()

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

overridedefault

Member Function Documentation

◆ apply()

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.

◆ attributes()

void protocols::calc_taskop_filters::Sigmoid::attributes ( utility::tag::AttributeList & attlist )

static

Referenced by protocols::calc_taskop_filters::MultipleSigmoids::provide_xml_schema(), and provide_xml_schema().

◆ baseline_checkpointing_filename() [1/2]

std::string protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename ( ) const

inline

References baseline_checkpointing_filename_.

◆ baseline_checkpointing_filename() [2/2]

void protocols::calc_taskop_filters::Sigmoid::baseline_checkpointing_filename ( std::string const & s )

inline

References baseline_checkpointing_filename_.

◆ class_name()

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

static

Referenced by protocols::calc_taskop_filters::SigmoidFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::calc_taskop_filters::Sigmoid::compute ( core::pose::Pose const & pose ) const

References baseline_, filter(), negate(), offset_, report_sm(), steepness_, protocols::calc_taskop_filters::TR(), and protocols::hybridization::val.

Referenced by apply(), report(), and report_sm().

◆ filter() [1/2]

protocols::filters::FilterOP protocols::calc_taskop_filters::Sigmoid::filter ( ) const

References filter_.

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

◆ filter() [2/2]

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

References filter_.

◆ fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ negate() [1/2]

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

inline

References negate_.

Referenced by compute(), and parse_my_tag().

◆ negate() [2/2]

void protocols::calc_taskop_filters::Sigmoid::negate ( bool const b )

inline

References protocols::match::upstream::b, and negate_.

◆ offset() [1/2]

core::Real protocols::calc_taskop_filters::Sigmoid::offset ( )

inline

References offset_.

Referenced by parse_my_tag().

◆ offset() [2/2]

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

inline

References offset_.

◆ parse_my_tag()

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().

◆ provide_xml_schema()

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

static

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

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

◆ report()

void protocols::calc_taskop_filters::Sigmoid::report	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::hybridization::val.

◆ report_sm()

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().

◆ reset_baseline()

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().

◆ steepness() [1/2]

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

inline

References steepness_.

Referenced by parse_my_tag().

◆ steepness() [2/2]

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

inline

References steepness_.

◆ threshold() [1/2]

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().

◆ threshold() [2/2]

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

inline

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

Member Data Documentation

◆ baseline_

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

private

dflt 0

Referenced by compute(), and reset_baseline().

◆ baseline_checkpointing_filename_

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().

◆ filter_

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

private

Referenced by filter().

◆ negate_

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().

◆ offset_

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

private

Referenced by compute(), and offset().

◆ steepness_

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

private

dflt NULL

Referenced by compute(), and steepness().

◆ threshold_

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:

src/protocols/calc_taskop_filters/SigmoidFilter.hh
src/protocols/calc_taskop_filters/SigmoidFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Sigmoid()

◆ ~Sigmoid()

Member Function Documentation

◆ apply()

◆ attributes()

◆ baseline_checkpointing_filename() [1/2]

◆ baseline_checkpointing_filename() [2/2]

◆ class_name()

◆ clone()

◆ compute()

◆ filter() [1/2]

◆ filter() [2/2]

◆ fresh_instance()

◆ name()

◆ negate() [1/2]

◆ negate() [2/2]

◆ offset() [1/2]

◆ offset() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ reset_baseline()

◆ steepness() [1/2]

◆ steepness() [2/2]

◆ threshold() [1/2]

◆ threshold() [2/2]

Member Data Documentation

◆ baseline_

◆ baseline_checkpointing_filename_

◆ filter_

◆ negate_

◆ offset_

◆ steepness_

◆ threshold_