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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)
 
- 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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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)
 

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

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References blueprint_, cmd_, mismatch_probability_, psipred_interface_, scratch_dir_, set_scratch_dir(), set_secstruct(), ss_predictor_, temp_, threshold_, protocols::TR(), use_confidence_, use_probability_, and use_svm_.

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_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)

References secstruct_.

Referenced by parse_my_tag().

Member Data Documentation

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

Referenced by compute(), and parse_my_tag().

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

Referenced by parse_my_tag().

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

Referenced by compute(), and parse_my_tag().

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(), parse_my_tag(), and SSPredictionFilter().

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(), and parse_my_tag().

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

Referenced by apply(), and parse_my_tag().

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

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

Referenced by compute(), and parse_my_tag().

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

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

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

should we use svm to estimate secondary structure?

Referenced by compute(), and parse_my_tag().


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