#include <SSPredictionFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::SSPredictionFilter:

Public Member Functions
	SSPredictionFilter ()

	SSPredictionFilter (core::Real const threshold, std::string const &cmd, std::string const &blueprint_filename, bool const use_probability, bool const mismatch_probability, bool const use_scratch_dir=false)

	~SSPredictionFilter () override

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

protocols::filters::FilterOP	clone () const override

protocols::filters::FilterOP	fresh_instance () const override

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...

core::Real	compute (core::pose::Pose const &pose) const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data_map) override
	Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...

std::string	name () const override

void	set_secstruct (std::string const secstruct)
	Sets the secondary structure to be compared with the psipred result. If neither this nor the blueprint is set, DSSP will be used to determine the pose secondary structure. More...

void	set_cmd (std::string const &cmd)
	Sets the psipred executable (has no effect if "use_svm" is true) More...

void	set_blueprint (protocols::parser::BluePrintOP blueprint)
	Sets a blueprint object which can be used to determine the desired secondary structure. More...

void	set_blueprint_file (std::string const &blueprint_file)
	Sets a blueprint file which can be used to determine the desired secondary structure. More...

void	set_threshold (core::Real const threshold)
	Sets the threshold. If use_probablility is true, the filter will pass if the calculated value is <= threshold. If use_probability is false, the filter will pass if the calcualted value is >= threshold. More...

void	set_use_probability (bool const use_probability)
	Sets whether or not to use the predicted SS probabilities to compute a value, or to use the predicted secondary structure (match or not matching) for each residue. Values are combined into a boltzmann sum-like-value using the provided temperature, so that poorly predicted residues have a larger impact on the score. More...

void	set_mismatch_probability (bool const mismatch_probability)
	assumes use_probability, if set this will compute the cumulative probability of having correct secondary structure at all residues More...

void	set_use_confidence (bool const use_confidence)
	tells whether to use the psipred pass2 confidence values – overrrides use_probability. More...

void	set_temperature (core::Real const temp)
	Sets the temperature which is used to compute probability-based values. More...

void	set_use_svm (bool const use_svm)
	If set, a trained SVM will be used instead of psipred to predict the secondary structure. More...

void	set_psipred_interface (core::io::external::PsiPredInterfaceOP psipred)
	Sets the psipred interface object that will be used to call psipred. More...

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)

Private Member Functions
core::Real	compute_boltz_sum (utility::vector1< core::Real > const &probabilities) const
	computes the weighted boltzmann sum of the passed vector More...

core::Real	compute_mismatch_prob (utility::vector1< core::Real > const &probabilities) const
	computes one minus the geometric mean of the passed vector More...

void	set_scratch_dir ()
	set the scratch dir to out::path::scratch or error if that's not set More...

Private Attributes
core::Real	threshold_

std::string	cmd_

protocols::parser::BluePrintOP	blueprint_

bool	use_probability_

bool	mismatch_probability_

bool	use_confidence_
	tells whether to use the psipred pass2 confidence values – overrrides use_probability. More...

bool	use_svm_
	should we use svm to estimate secondary structure? More...

core::Real	temp_
	what temperature should we be using doing a boltzmann sum? More...

protocols::ss_prediction::SS_predictorOP	ss_predictor_
	the object which predicts the secondary structure More...

core::io::external::PsiPredInterfaceOP	psipred_interface_
	the object which communicates with psipred and interprets its output More...

std::string	secstruct_

std::string	scratch_dir_
	the scratch folder to use with psipred (or "") More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

◆ SSPredictionFilter() [1/2]

protocols::denovo_design::filters::SSPredictionFilter::SSPredictionFilter ( )

◆ SSPredictionFilter() [2/2]

protocols::denovo_design::filters::SSPredictionFilter::SSPredictionFilter	(	core::Real const	threshold,
		std::string const &	cmd,
		std::string const &	blueprint_filename,
		bool const	use_probability,
		bool const	mismatch_probability,
		bool const	use_scratch_dir = `false`
	)

References scratch_dir_, set_psipred_interface(), and set_scratch_dir().

◆ ~SSPredictionFilter()

protocols::denovo_design::filters::SSPredictionFilter::~SSPredictionFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::denovo_design::filters::SSPredictionFilter::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 use_probability_.

◆ class_name()

std::string protocols::denovo_design::filters::SSPredictionFilter::class_name ( )

static

Referenced by protocols::denovo_design::filters::SSPredictionFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::denovo_design::filters::SSPredictionFilter::clone ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Real protocols::denovo_design::filters::SSPredictionFilter::compute ( core::pose::Pose const & pose ) const

◆ compute_boltz_sum()

core::Real protocols::denovo_design::filters::SSPredictionFilter::compute_boltz_sum ( utility::vector1< core::Real > const & probabilities ) const

private

computes the weighted boltzmann sum of the passed vector

References core::simple_metrics::metrics::sum, temp_, and protocols::TR().

Referenced by compute().

◆ compute_mismatch_prob()

core::Real protocols::denovo_design::filters::SSPredictionFilter::compute_mismatch_prob ( utility::vector1< core::Real > const & probabilities ) const

private

computes one minus the geometric mean of the passed vector

computes the overall probability P as the product of each residue probability p. Then returns the Nth root of P for N residues.

References core::simple_metrics::metrics::sum, and protocols::TR().

Referenced by compute().

◆ fresh_instance()

protocols::filters::FilterOP protocols::denovo_design::filters::SSPredictionFilter::fresh_instance ( ) const

overridevirtual

Implements protocols::filters::Filter.

◆ name()

std::string protocols::denovo_design::filters::SSPredictionFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::denovo_design::filters::SSPredictionFilter::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 cmd_, mismatch_probability_, scratch_dir_, set_blueprint_file(), set_cmd(), set_mismatch_probability(), set_psipred_interface(), set_scratch_dir(), set_secstruct(), set_temperature(), set_threshold(), set_use_confidence(), set_use_probability(), set_use_svm(), ss_predictor_, temp_, threshold_, use_confidence_, use_probability_, and use_svm_.

◆ provide_xml_schema()

void protocols::denovo_design::filters::SSPredictionFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::denovo_design::filters::SSPredictionFilterCreator::provide_xml_schema().

◆ report()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

core::Real protocols::denovo_design::filters::SSPredictionFilter::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().

◆ set_blueprint()

void protocols::denovo_design::filters::SSPredictionFilter::set_blueprint ( protocols::parser::BluePrintOP blueprint )

Sets a blueprint object which can be used to determine the desired secondary structure.

References blueprint_.

Referenced by set_blueprint_file().

◆ set_blueprint_file()

void protocols::denovo_design::filters::SSPredictionFilter::set_blueprint_file ( std::string const & blueprint_file )

Sets a blueprint file which can be used to determine the desired secondary structure.

References blueprint_, set_blueprint(), and protocols::TR().

Referenced by parse_my_tag().

◆ set_cmd()

void protocols::denovo_design::filters::SSPredictionFilter::set_cmd ( std::string const & cmd )

Sets the psipred executable (has no effect if "use_svm" is true)

References cmd_.

Referenced by parse_my_tag().

◆ set_mismatch_probability()

void protocols::denovo_design::filters::SSPredictionFilter::set_mismatch_probability ( bool const mismatch_probability )

assumes use_probability, if set this will compute the cumulative probability of having correct secondary structure at all residues

References mismatch_probability_.

Referenced by parse_my_tag().

◆ set_psipred_interface()

void protocols::denovo_design::filters::SSPredictionFilter::set_psipred_interface ( core::io::external::PsiPredInterfaceOP psipred )

inline

Sets the psipred interface object that will be used to call psipred.

References psipred_interface_.

Referenced by parse_my_tag(), and SSPredictionFilter().

◆ set_scratch_dir()

void protocols::denovo_design::filters::SSPredictionFilter::set_scratch_dir ( )

private

set the scratch dir to out::path::scratch or error if that's not set

References scratch_dir_.

Referenced by parse_my_tag(), and SSPredictionFilter().

◆ set_secstruct()

void protocols::denovo_design::filters::SSPredictionFilter::set_secstruct ( std::string const secstruct )

Sets the secondary structure to be compared with the psipred result. If neither this nor the blueprint is set, DSSP will be used to determine the pose secondary structure.

References secstruct_.

Referenced by parse_my_tag().

◆ set_temperature()

void protocols::denovo_design::filters::SSPredictionFilter::set_temperature ( core::Real const temp )

Sets the temperature which is used to compute probability-based values.

References temp_.

Referenced by parse_my_tag().

◆ set_threshold()

void protocols::denovo_design::filters::SSPredictionFilter::set_threshold ( core::Real const threshold )

Sets the threshold. If use_probablility is true, the filter will pass if the calculated value is <= threshold. If use_probability is false, the filter will pass if the calcualted value is >= threshold.

References threshold_.

Referenced by parse_my_tag().

◆ set_use_confidence()

void protocols::denovo_design::filters::SSPredictionFilter::set_use_confidence ( bool const use_confidence )

tells whether to use the psipred pass2 confidence values – overrrides use_probability.

References use_confidence_.

Referenced by parse_my_tag().

◆ set_use_probability()

void protocols::denovo_design::filters::SSPredictionFilter::set_use_probability ( bool const use_probability )

Sets whether or not to use the predicted SS probabilities to compute a value, or to use the predicted secondary structure (match or not matching) for each residue. Values are combined into a boltzmann sum-like-value using the provided temperature, so that poorly predicted residues have a larger impact on the score.

References use_probability_.

Referenced by parse_my_tag().

◆ set_use_svm()

void protocols::denovo_design::filters::SSPredictionFilter::set_use_svm ( bool const use_svm )

If set, a trained SVM will be used instead of psipred to predict the secondary structure.

References use_svm_.

Referenced by parse_my_tag().

Member Data Documentation

◆ blueprint_

protocols::parser::BluePrintOP protocols::denovo_design::filters::SSPredictionFilter::blueprint_

private

Referenced by compute(), set_blueprint(), and set_blueprint_file().

◆ cmd_

std::string protocols::denovo_design::filters::SSPredictionFilter::cmd_

private

Referenced by parse_my_tag(), and set_cmd().

◆ mismatch_probability_

bool protocols::denovo_design::filters::SSPredictionFilter::mismatch_probability_

private

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

◆ psipred_interface_

core::io::external::PsiPredInterfaceOP protocols::denovo_design::filters::SSPredictionFilter::psipred_interface_

private

the object which communicates with psipred and interprets its output

Referenced by compute(), and set_psipred_interface().

◆ scratch_dir_

std::string protocols::denovo_design::filters::SSPredictionFilter::scratch_dir_

private

the scratch folder to use with psipred (or "")

Referenced by parse_my_tag(), set_scratch_dir(), and SSPredictionFilter().

◆ secstruct_

std::string protocols::denovo_design::filters::SSPredictionFilter::secstruct_

private

Referenced by compute(), and set_secstruct().

◆ ss_predictor_

protocols::ss_prediction::SS_predictorOP protocols::denovo_design::filters::SSPredictionFilter::ss_predictor_

private

the object which predicts the secondary structure

Referenced by compute(), and parse_my_tag().

◆ temp_

core::Real protocols::denovo_design::filters::SSPredictionFilter::temp_

private

what temperature should we be using doing a boltzmann sum?

Referenced by compute_boltz_sum(), parse_my_tag(), and set_temperature().

◆ threshold_

core::Real protocols::denovo_design::filters::SSPredictionFilter::threshold_

private

Referenced by apply(), parse_my_tag(), and set_threshold().

◆ use_confidence_

bool protocols::denovo_design::filters::SSPredictionFilter::use_confidence_

private

tells whether to use the psipred pass2 confidence values – overrrides use_probability.

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

◆ use_probability_

bool protocols::denovo_design::filters::SSPredictionFilter::use_probability_

private

Referenced by apply(), compute(), parse_my_tag(), and set_use_probability().

◆ use_svm_

bool protocols::denovo_design::filters::SSPredictionFilter::use_svm_

private

should we use svm to estimate secondary structure?

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

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

src/protocols/denovo_design/filters/SSPredictionFilter.hh
src/protocols/denovo_design/filters/SSPredictionFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ SSPredictionFilter() [1/2]

◆ SSPredictionFilter() [2/2]

◆ ~SSPredictionFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_boltz_sum()

◆ compute_mismatch_prob()

◆ fresh_instance()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ set_blueprint()

◆ set_blueprint_file()

◆ set_cmd()

◆ set_mismatch_probability()

◆ set_psipred_interface()

◆ set_scratch_dir()

◆ set_secstruct()

◆ set_temperature()

◆ set_threshold()

◆ set_use_confidence()

◆ set_use_probability()

◆ set_use_svm()

Member Data Documentation

◆ blueprint_

◆ cmd_

◆ mismatch_probability_

◆ psipred_interface_

◆ scratch_dir_

◆ secstruct_

◆ ss_predictor_

◆ temp_

◆ threshold_

◆ use_confidence_

◆ use_probability_

◆ use_svm_