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Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::denovo_design::filters::PreProlineFilter Class Reference

#include <PreProlineFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::PreProlineFilter:
Inheritance graph
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Public Member Functions

 PreProlineFilter ()
 Initialize PreProlineFilter. More...
 
 ~PreProlineFilter () override
 virtual constructor to allow derivation More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parses the PreProlineFilter tags. More...
 
virtual std::string get_name () const
 Return the name of this mover. More...
 
protocols::filters::FilterOP clone () const override
 return a fresh instance of this class in an owning pointer More...
 
protocols::filters::FilterOP fresh_instance () const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 Apply the PreProlineFilter. Overloaded apply function from filter base class. More...
 
virtual core::Real compute (core::pose::Pose const &pose) const
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
bool apply (core::pose::Pose const &pose) const override
 Does the PreProline Filtering. More...
 
void set_use_statistical_potential (bool const use_stat)
 
void set_selector (core::select::residue_selector::ResidueSelectorCOP selector)
 
void setup_spline ()
 
core::Real compute_simple (core::pose::Pose const &pose, utility::vector1< bool > const &selection) const
 
core::Real compute_spline (core::pose::Pose const &pose, utility::vector1< bool > const &selection) const
 
std::string name () const override
 
- 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 Attributes

core::Real threshold_
 If total calculated filter score is <= theshold_, the filter passes, otherwise it fails. More...
 
bool use_statistical_potential_
 If set, spline based on statistical potential will be used, otherwise only preproline residues not in beta conformation will be counted (default = True) More...
 
core::select::residue_selector::ResidueSelectorCOP selector_
 
numeric::interpolation::spline::BicubicSpline spline_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Constructor & Destructor Documentation

protocols::denovo_design::filters::PreProlineFilter::PreProlineFilter ( )

Initialize PreProlineFilter.


PreProlineFilter main code:

References setup_spline().

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

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Member Function Documentation

bool protocols::denovo_design::filters::PreProlineFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Does the PreProline Filtering.

Implements protocols::filters::Filter.

References compute(), and threshold_.

std::string protocols::denovo_design::filters::PreProlineFilter::class_name ( )
static
protocols::filters::FilterOP protocols::denovo_design::filters::PreProlineFilter::clone ( ) const
overridevirtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Implements protocols::filters::Filter.

core::Real protocols::denovo_design::filters::PreProlineFilter::compute ( core::pose::Pose const &  pose) const
virtual
core::Real protocols::denovo_design::filters::PreProlineFilter::compute_simple ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  selection 
) const
core::Real protocols::denovo_design::filters::PreProlineFilter::compute_spline ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  selection 
) const
protocols::filters::FilterOP protocols::denovo_design::filters::PreProlineFilter::fresh_instance ( ) const
overridevirtual
std::string protocols::denovo_design::filters::PreProlineFilter::get_name ( ) const
virtual

Return the name of this mover.

std::string protocols::denovo_design::filters::PreProlineFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::denovo_design::filters::PreProlineFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

Apply the PreProlineFilter. Overloaded apply function from filter base class.

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::denovo_design::filters::PreProlineFilter::set_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

References selector_.

void protocols::denovo_design::filters::PreProlineFilter::set_use_statistical_potential ( bool const  use_stat)
void protocols::denovo_design::filters::PreProlineFilter::setup_spline ( )

Member Data Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::denovo_design::filters::PreProlineFilter::selector_
private

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

numeric::interpolation::spline::BicubicSpline protocols::denovo_design::filters::PreProlineFilter::spline_
private

Referenced by compute_spline(), and setup_spline().

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

If total calculated filter score is <= theshold_, the filter passes, otherwise it fails.

Referenced by apply(), and parse_my_tag().

bool protocols::denovo_design::filters::PreProlineFilter::use_statistical_potential_
private

If set, spline based on statistical potential will be used, otherwise only preproline residues not in beta conformation will be counted (default = True)

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


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