#include <PreProlineFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::PreProlineFilter:

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_threshold (core::Real const threshold)

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 () 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 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

◆ PreProlineFilter()

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

Initialize PreProlineFilter.

PreProlineFilter main code:

References setup_spline().

◆ ~PreProlineFilter()

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

◆ apply()

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_.

◆ class_name()

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

static

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

◆ clone()

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.

◆ compute()

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

virtual

References compute_simple(), compute_spline(), selector_, core::pose::Pose::size(), and use_statistical_potential_.

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

◆ compute_simple()

core::Real protocols::denovo_design::filters::PreProlineFilter::compute_simple	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	selection
	)		const

References core::pose::motif::a(), protocols::denovo_design::abego_str(), core::sequence::get_abego(), core::pose::is_upper_terminus(), core::conformation::Residue::name(), core::pose::Pose::residue(), core::pose::Pose::sequence(), and protocols::TR().

Referenced by compute().

◆ compute_spline()

core::Real protocols::denovo_design::filters::PreProlineFilter::compute_spline	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	selection
	)		const

References core::pose::is_upper_terminus(), core::conformation::Residue::name1(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::size(), spline_, and protocols::TR().

Referenced by compute().

◆ fresh_instance()

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

overridevirtual

Implements protocols::filters::Filter.

◆ get_name()

std::string protocols::denovo_design::filters::PreProlineFilter::get_name ( ) const

virtual

Return the name of this mover.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::denovo_design::filters::PreProlineFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Parses the PreProlineFilter tags.

Reimplemented from protocols::filters::Filter.

References core::select::residue_selector::parse_residue_selector(), set_selector(), set_threshold(), set_use_statistical_potential(), and threshold_.

◆ provide_xml_schema()

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ report()

void protocols::denovo_design::filters::PreProlineFilter::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::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().

◆ set_selector()

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

References selector_.

Referenced by parse_my_tag().

◆ set_threshold()

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

inline

References threshold_.

Referenced by parse_my_tag().

◆ set_use_statistical_potential()

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

References use_statistical_potential_.

Referenced by parse_my_tag().

◆ setup_spline()

void protocols::denovo_design::filters::PreProlineFilter::setup_spline ( )

References protocols::denovo_design::filters::parse_matrix(), spline_, protocols::loops::start, and protocols::TR().

Referenced by PreProlineFilter().

Member Data Documentation

◆ selector_

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

private

Referenced by compute(), and set_selector().

◆ spline_

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

private

Referenced by compute_spline(), and setup_spline().

◆ threshold_

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(), parse_my_tag(), and set_threshold().

◆ use_statistical_potential_

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(), and set_use_statistical_potential().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PreProlineFilter()

PreProlineFilter main code:

◆ ~PreProlineFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_simple()

◆ compute_spline()

◆ fresh_instance()

◆ get_name()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ set_selector()

◆ set_threshold()

◆ set_use_statistical_potential()

◆ setup_spline()

Member Data Documentation

◆ selector_

◆ spline_

◆ threshold_

◆ use_statistical_potential_