#include <ExposedHydrophobicsFilter.hh>

Public Member Functions
	ExposedHydrophobicsFilter ()
	Initialize ExposedHydrophobicsFilter. More...

virtual	~ExposedHydrophobicsFilter ()
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Parses the ExposedHydrophobicsFilter tags. More...

virtual std::string	get_name () const
	Return the name of this mover. More...

virtual protocols::filters::FilterOP	clone () const
	return a fresh instance of this class in an owning pointer More...

virtual bool	apply (core::pose::Pose const &pose) const
	Apply the ExposedHydrophobicsFilter. Overloaded apply function from filter base class. More...

protocols::filters::FilterOP	fresh_instance () const

void	report (std::ostream &out, core::pose::Pose const &pose) const

core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

core::Real	compute (core::pose::Pose const &pose) const

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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 void	apply (core::io::serialization::PipeMap &pmap)

virtual void	score (core::io::serialization::PipeMap &pmap)

virtual core::Real	score (core::pose::Pose &pose)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)

virtual std::string	name () const

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:

Referenced by clone(), and fresh_instance().

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

virtual

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

virtual

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

Does the ExposedHydrophobics Filtering.

Implements protocols::filters::Filter.

References compute(), and threshold_.

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

virtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Implements protocols::filters::Filter.

References ExposedHydrophobicsFilter().

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

References protocols::moves::DsspMover::apply(), protocols::toolbox::SelectResiduesByLayer::compute(), dssp, hydrophobic_residues_, protocols::toolbox::SelectResiduesByLayer::initialize(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::residue(), protocols::toolbox::SelectResiduesByLayer::rsd_sasa(), sasa_cutoff_, core::pose::Pose::secstruct(), sum(), core::pose::Pose::total_residue(), and protocols::TR.

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

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

virtual

Implements protocols::filters::Filter.

References ExposedHydrophobicsFilter().

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

virtual

Return the name of this mover.

void protocols::denovo_design::filters::ExposedHydrophobicsFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)

virtual

Parses the ExposedHydrophobicsFilter tags.

Reimplemented from protocols::filters::Filter.

References sasa_cutoff_, and threshold_.

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

virtual

Reimplemented from protocols::filters::Filter.

References compute().

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

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

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(), and parse_my_tag().

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(), and parse_my_tag().

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

symlinks/rosetta/src/protocols/denovo_design/filters/ExposedHydrophobicsFilter.hh
symlinks/rosetta/src/protocols/denovo_design/filters/ExposedHydrophobicsFilter.cc

Public Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

ExposedHydrophobicsFilter main code:

Member Function Documentation

Member Data Documentation