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::simple_filters::Sigmoid:

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Collaboration diagram for protocols::simple_filters::Sigmoid:

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Public Member Functions
	Sigmoid ()

virtual	~Sigmoid ()

filters::FilterOP	clone () const

filters::FilterOP	fresh_instance () const

virtual bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...

virtual void	report (std::ostream &out, core::pose::Pose const &pose) const

virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

void	parse_my_tag (utility::tag::TagPtr const tag, moves::DataMap &, filters::Filters_map const &filters, moves::Movers_map const &, core::pose::Pose const &)

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

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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 void	apply (core::io::serialization::PipeMap &pmap)

virtual void	score (core::io::serialization::PipeMap &pmap)

virtual core::Real	score (core::pose::Pose &pose)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)

virtual std::string	name () const

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

Definition at line 31 of file SigmoidFilter.hh.

Constructor & Destructor Documentation

protocols::simple_filters::Sigmoid::Sigmoid ( )

Definition at line 39 of file SigmoidFilter.cc.

Referenced by clone(), and fresh_instance().

protocols::simple_filters::Sigmoid::~Sigmoid ( )

virtual

Definition at line 51 of file SigmoidFilter.cc.

Member Function Documentation

bool protocols::simple_filters::Sigmoid::apply ( core::pose::Pose const & pose) const

virtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

Definition at line 114 of file SigmoidFilter.cc.

References compute(), and threshold().

void protocols::simple_filters::Sigmoid::baseline_checkpointing_filename ( std::string const s)

inline

Definition at line 59 of file SigmoidFilter.hh.

References baseline_checkpointing_filename_.

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

inline

Definition at line 60 of file SigmoidFilter.hh.

References baseline_checkpointing_filename_.

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

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 36 of file SigmoidFilter.hh.

References Sigmoid().

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

Definition at line 131 of file SigmoidFilter.cc.

References baseline_, filter(), negate(), offset_, report_sm(), steepness_, and protocols::simple_filters::TR().

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

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

Definition at line 143 of file SigmoidFilter.cc.

References filter_.

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

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

Definition at line 146 of file SigmoidFilter.cc.

References filter_.

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

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 39 of file SigmoidFilter.hh.

References Sigmoid().

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

inline

Definition at line 52 of file SigmoidFilter.hh.

References negate_.

Referenced by compute(), and parse_my_tag().

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

inline

Definition at line 53 of file SigmoidFilter.hh.

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

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

inline

Definition at line 50 of file SigmoidFilter.hh.

References offset_.

Referenced by parse_my_tag().

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

inline

Definition at line 51 of file SigmoidFilter.hh.

References offset_.

void protocols::simple_filters::Sigmoid::parse_my_tag	(	utility::tag::TagPtr const	tag,
		moves::DataMap &	,
		filters::Filters_map const &	filters,
		moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 102 of file SigmoidFilter.cc.

References baseline_checkpointing_filename_, filter(), negate(), offset(), protocols::rosetta_scripts::parse_filter(), steepness(), threshold(), and protocols::simple_filters::TR().

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

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 120 of file SigmoidFilter.cc.

References compute().

core::Real protocols::simple_filters::Sigmoid::report_sm ( core::pose::Pose const & ) const

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 126 of file SigmoidFilter.cc.

References compute().

Referenced by compute().

void protocols::simple_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.

Definition at line 56 of file SigmoidFilter.cc.

References baseline_, baseline_checkpointing_filename_, core::sequence::end, filter(), and protocols::simple_filters::TR().

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

inline

Definition at line 48 of file SigmoidFilter.hh.

References steepness_.

Referenced by parse_my_tag().

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

inline

Definition at line 49 of file SigmoidFilter.hh.

References steepness_.

core::Real protocols::simple_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

Definition at line 57 of file SigmoidFilter.hh.

References threshold_.

Referenced by apply(), and parse_my_tag().

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

inline

Definition at line 58 of file SigmoidFilter.hh.

References core::scoring::hbonds::t(), and threshold_.

Member Data Documentation

core::Real protocols::simple_filters::Sigmoid::baseline_

private

dflt 0

Definition at line 65 of file SigmoidFilter.hh.

Referenced by compute(), and reset_baseline().

std::string protocols::simple_filters::Sigmoid::baseline_checkpointing_filename_

private

dflt 0 (always accept)

Definition at line 68 of file SigmoidFilter.hh.

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

protocols::filters::FilterOP protocols::simple_filters::Sigmoid::filter_

private

Definition at line 62 of file SigmoidFilter.hh.

Referenced by filter().

bool protocols::simple_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

Definition at line 66 of file SigmoidFilter.hh.

Referenced by negate().

core::Real protocols::simple_filters::Sigmoid::offset_

private

Definition at line 64 of file SigmoidFilter.hh.

Referenced by compute(), and offset().

core::Real protocols::simple_filters::Sigmoid::steepness_

private

dflt NULL

Definition at line 63 of file SigmoidFilter.hh.

Referenced by compute(), and steepness().

core::Real protocols::simple_filters::Sigmoid::threshold_

private

dflt false

Definition at line 67 of file SigmoidFilter.hh.

Referenced by threshold().

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

src/protocols/simple_filters/SigmoidFilter.hh
src/protocols/simple_filters/SigmoidFilter.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation