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protocols::denovo_design::filters::SSPredictionFilter Class Reference

#include <SSPredictionFilter.hh>

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

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

Member Function Documentation

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_.

std::string protocols::denovo_design::filters::SSPredictionFilter::class_name ( )
static
protocols::filters::FilterOP protocols::denovo_design::filters::SSPredictionFilter::clone ( ) const
overridevirtual
core::Real protocols::denovo_design::filters::SSPredictionFilter::compute ( core::pose::Pose const &  pose) const
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().

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().

protocols::filters::FilterOP protocols::denovo_design::filters::SSPredictionFilter::fresh_instance ( ) const
overridevirtual
std::string protocols::denovo_design::filters::SSPredictionFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::denovo_design::filters::SSPredictionFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::denovo_design::filters::SSPredictionFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::denovo_design::filters::SSPredictionFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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().

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

protocols::parser::BluePrintOP protocols::denovo_design::filters::SSPredictionFilter::blueprint_
private
std::string protocols::denovo_design::filters::SSPredictionFilter::cmd_
private

Referenced by parse_my_tag(), and set_cmd().

bool protocols::denovo_design::filters::SSPredictionFilter::mismatch_probability_
private
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().

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().

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

Referenced by compute(), and set_secstruct().

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().

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().

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

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

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().

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