protocols::denovo_design::filters::ExposedHydrophobicsFilter Class Reference

#include <ExposedHydrophobicsFilter.hh>

Inheritance diagram for protocols::denovo_design::filters::ExposedHydrophobicsFilter:

Public Member Functions
	ExposedHydrophobicsFilter ()
	Initialize ExposedHydrophobicsFilter. More...
	~ExposedHydrophobicsFilter () override
	virtual constructor to allow derivation More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the ExposedHydrophobicsFilter 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...
bool	apply (core::pose::Pose const &pose) const override
	Apply the ExposedHydrophobicsFilter. Overloaded apply function from filter base class. More...
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
std::string	name () const override
void	set_threshold (core::Real const threshold)
	Sets the threshold; if the calculated filters core is <= threshold, the filter passes, otherwise it fails. More...
void	set_sasa_cutoff (core::Real const sasa_cutoff)
	Sets the SASA cutoff in order for a residue to be considered buried. If a residue has sasa <= sasa_cutoff, it is considered buried and will be ignored by the filter. 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 Attributes
core::Real	threshold_
	If total calculated filter score is <= theshold_, the filter passes, otherwise it fails. More...
core::Real	sasa_cutoff_
	If a residue has sasa <= sasa_cutoff_, it is considered buried and ignored. More...

Static Private Attributes
static std::string const	hydrophobic_residues_ = "MLIVFAWY"

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

Constructor & Destructor Documentation

protocols::denovo_design::filters::ExposedHydrophobicsFilter::ExposedHydrophobicsFilter

(

)

Initialize ExposedHydrophobicsFilter.

---

ExposedHydrophobicsFilter main code:

protocols::denovo_design::filters::ExposedHydrophobicsFilter::~ExposedHydrophobicsFilter ( )

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::ExposedHydrophobicsFilter::apply ( core::pose::Pose const &  pose ) const

overridevirtual

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

Does the ExposedHydrophobics Filtering.

Implements protocols::filters::Filter.

References compute(), and threshold_.

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

static

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

protocols::filters::FilterOP protocols::denovo_design::filters::ExposedHydrophobicsFilter::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::ExposedHydrophobicsFilter::compute

(

core::pose::Pose const &

pose

)

const

References protocols::moves::DsspMover::apply(), core::select::util::SelectResiduesByLayer::compute(), protocols::simple_filters::dssp(), hydrophobic_residues_, core::select::util::SelectResiduesByLayer::initialize(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::select::util::SelectResiduesByLayer::rsd_sasa(), sasa_cutoff_, core::pose::Pose::secstruct(), core::pose::Pose::size(), core::simple_metrics::metrics::sum, and protocols::TR().

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

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

overridevirtual

Implements protocols::filters::Filter.

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

virtual

Return the name of this mover.

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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

overridevirtual

Parses the ExposedHydrophobicsFilter tags.

Reimplemented from protocols::filters::Filter.

References sasa_cutoff_, set_sasa_cutoff(), set_threshold(), and threshold_.

void protocols::denovo_design::filters::ExposedHydrophobicsFilter::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::ExposedHydrophobicsFilterCreator::provide_xml_schema().

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::denovo_design::filters::ExposedHydrophobicsFilter::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::ExposedHydrophobicsFilter::set_sasa_cutoff ( core::Real const  sasa_cutoff )

inline

Sets the SASA cutoff in order for a residue to be considered buried. If a residue has sasa <= sasa_cutoff, it is considered buried and will be ignored by the filter.

References sasa_cutoff_.

Referenced by parse_my_tag().

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

inline

Sets the threshold; if the calculated filters core is <= threshold, the filter passes, otherwise it fails.

References threshold_.

Referenced by parse_my_tag().

Member Data Documentation

std::string const protocols::denovo_design::filters::ExposedHydrophobicsFilter::hydrophobic_residues_ = "MLIVFAWY"

staticprivate

Referenced by compute().

core::Real protocols::denovo_design::filters::ExposedHydrophobicsFilter::sasa_cutoff_

private

If a residue has sasa <= sasa_cutoff_, it is considered buried and ignored.

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

core::Real protocols::denovo_design::filters::ExposedHydrophobicsFilter::threshold_

private

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

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

---

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

• src/protocols/denovo_design/filters/ExposedHydrophobicsFilter.hh
• src/protocols/denovo_design/filters/ExposedHydrophobicsFilter.cc