Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered. More...

#include <BuriedSurfaceAreaFilter.hh>

Inheritance diagram for protocols::simple_filters::BuriedSurfaceAreaFilter:

[legend]

Public Member Functions
	BuriedSurfaceAreaFilter ()

	~BuriedSurfaceAreaFilter () override

bool	apply (core::pose::Pose const &pose) const override
	returns true if the structure passes the filter, false otherwise More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	required for reporting score values More...

void	report (std::ostream &os, core::pose::Pose const &pose) const override
	allows printing data to a stream More...

std::string	name () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Filter in Rosetta Scripts) More...

protocols::filters::FilterOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::filters::FilterOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Sets the residue selector to use to select a subset of residues for which to calculate buried surface area. More...

void	set_select_only_FAMILYVW (bool const setting)
	Set whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...

void	set_cutoff_buried_surface_area (core::Real const &setting)
	Set the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...

void	set_filter_out_low (bool const setting)
	Set whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded. More...

void	set_atom_mode (std::string const &setting)
	Set the atom mode (the subset of atoms to use for the calculation) by string. More...

void	set_atom_mode (BSAF_mode const setting)
	Set the atom mode (the subset of atoms to use for the calculation). More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Gets the residue selector to use to select a subset of residues for which to calculate buried surface area. More...

bool	select_only_FAMILYVW () const
	Get whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...

core::Real const &	cutoff_buried_surface_area () const
	Get the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...

bool	filter_out_low () const
	Get whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded. More...

BSAF_mode	atom_mode () const
	Get the atom mode (the subset of atoms to use). More...

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 Member Functions
bool	compute (std::ostream &os, core::pose::Pose const &pose, core::Real &buried_surf_area) const
	Common function called by apply(), report(), and report_sm(). More...

bool	is_allowed_type (char const oneletter_code) const
	Is this a residue type for which we can calculate a total SASA value? More...

bool	is_FAMILYVW (char const oneletter_code) const
	Is this a hydrophobic residue type (FAMILYVW)? More...

void	compute_residue_selection (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset &selection) const
	Given a pose (input) and a ResidueSubset (output), compute the residues that should be operated on. More...

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	residue_selector_
	A residue selector to use to select a subset of residues for which to calculate buried surface area. Unused if not specified (i.e. all residues are used by default). More...

bool	select_only_FAMILYVW_
	If true, only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...

BSAF_mode	atom_mode_
	The subset of atoms to consider. Default is all atoms, but only hydrophobic atoms or only polar atoms are both possible, too. More...

core::Real	cutoff_area_
	The cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...

bool	filter_out_low_
	If true, structures with less than the cutoff buried area are discrded. More...

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

Detailed Description

Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered.

Constructor & Destructor Documentation

◆ BuriedSurfaceAreaFilter()

protocols::simple_filters::BuriedSurfaceAreaFilter::BuriedSurfaceAreaFilter ( )

◆ ~BuriedSurfaceAreaFilter()

protocols::simple_filters::BuriedSurfaceAreaFilter::~BuriedSurfaceAreaFilter ( )

overridedefault

Member Function Documentation

◆ apply()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References compute(), and protocols::simple_filters::TR().

◆ atom_mode()

BSAF_mode protocols::simple_filters::BuriedSurfaceAreaFilter::atom_mode ( ) const

inline

Get the atom mode (the subset of atoms to use).

References atom_mode_.

Referenced by compute().

◆ class_name()

std::string protocols::simple_filters::BuriedSurfaceAreaFilter::class_name ( )

static

Referenced by protocols::simple_filters::BuriedSurfaceAreaFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::simple_filters::BuriedSurfaceAreaFilter::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compute()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::compute	(	std::ostream &	os,
		core::pose::Pose const &	pose,
		core::Real &	buried_surf_area
	)		const

private

Common function called by apply(), report(), and report_sm().

Does the actual computation. Returns true if the filter passes and false if it fails.

Does the actual computation.

References atom_mode(), core::conformation::Residue::atom_type(), protocols::simple_filters::BSAF_all_atoms, protocols::simple_filters::BSAF_hydrophobic_atoms, protocols::simple_filters::BSAF_polar_atoms, compute_residue_selection(), cutoff_buried_surface_area(), filter_out_low(), core::chemical::AtomType::is_acceptor(), is_allowed_type(), core::chemical::AtomType::is_donor(), core::chemical::AtomType::is_polar_hydrogen(), core::pose::Pose::metric(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::scoring::normalizing_area_total_hydrophobic_atoms_only(), core::scoring::normalizing_area_total_polar_atoms_only(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and protocols::simple_filters::TR().

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

◆ compute_residue_selection()

void protocols::simple_filters::BuriedSurfaceAreaFilter::compute_residue_selection	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSubset &	selection
	)		const

private

Given a pose (input) and a ResidueSubset (output), compute the residues that should be operated on.

References is_allowed_type(), is_FAMILYVW(), core::chemical::ResidueTypeBase::name1(), residue_selector(), core::pose::Pose::residue_type(), select_only_FAMILYVW(), and core::pose::Pose::total_residue().

Referenced by compute().

◆ cutoff_buried_surface_area()

core::Real const& protocols::simple_filters::BuriedSurfaceAreaFilter::cutoff_buried_surface_area ( ) const

inline

Get the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

References cutoff_area_.

Referenced by compute(), and parse_my_tag().

◆ filter_out_low()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::filter_out_low ( ) const

inline

Get whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded.

If true, structures with less than the cutoff buried area are discrded.

References filter_out_low_.

Referenced by compute(), and parse_my_tag().

◆ fresh_instance()

protocols::filters::FilterOP protocols::simple_filters::BuriedSurfaceAreaFilter::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ is_allowed_type()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::is_allowed_type ( char const oneletter_code ) const

private

Is this a residue type for which we can calculate a total SASA value?

Referenced by compute(), and compute_residue_selection().

◆ is_FAMILYVW()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::is_FAMILYVW ( char const oneletter_code ) const

private

Is this a hydrophobic residue type (FAMILYVW)?

Referenced by compute_residue_selection().

◆ name()

std::string protocols::simple_filters::BuriedSurfaceAreaFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::simple_filters::BuriedSurfaceAreaFilter::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Filter in Rosetta Scripts)

Reimplemented from protocols::filters::Filter.

References cutoff_buried_surface_area(), filter_out_low(), core::select::residue_selector::parse_residue_selector(), select_only_FAMILYVW(), set_atom_mode(), set_cutoff_buried_surface_area(), set_filter_out_low(), set_residue_selector(), and set_select_only_FAMILYVW().

◆ provide_xml_schema()

void protocols::simple_filters::BuriedSurfaceAreaFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::simple_filters::BuriedSurfaceAreaFilterCreator::provide_xml_schema().

◆ report()

void protocols::simple_filters::BuriedSurfaceAreaFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References compute().

◆ report_sm()

core::Real protocols::simple_filters::BuriedSurfaceAreaFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::simple_filters::TR().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::BuriedSurfaceAreaFilter::residue_selector ( ) const

inline

Gets the residue selector to use to select a subset of residues for which to calculate buried surface area.

References residue_selector_.

Referenced by compute_residue_selection().

◆ select_only_FAMILYVW()

bool protocols::simple_filters::BuriedSurfaceAreaFilter::select_only_FAMILYVW ( ) const

inline

Get whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

References select_only_FAMILYVW_.

Referenced by compute_residue_selection(), and parse_my_tag().

◆ set_atom_mode() [1/2]

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_atom_mode ( BSAF_mode const setting )

Set the atom mode (the subset of atoms to use for the calculation).

References atom_mode_, and protocols::simple_filters::BSAF_end_of_list.

◆ set_atom_mode() [2/2]

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_atom_mode ( std::string const & setting )

Set the atom mode (the subset of atoms to use for the calculation) by string.

References protocols::simple_filters::BSAF_all_atoms, protocols::simple_filters::BSAF_hydrophobic_atoms, and protocols::simple_filters::BSAF_polar_atoms.

Referenced by parse_my_tag().

◆ set_cutoff_buried_surface_area()

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_cutoff_buried_surface_area ( core::Real const & setting )

Set the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

References cutoff_area_.

Referenced by parse_my_tag().

◆ set_filter_out_low()

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_filter_out_low ( bool const setting )

Set whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded.

If true, structures with less than the cutoff buried area are discrded.

References filter_out_low_.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Sets the residue selector to use to select a subset of residues for which to calculate buried surface area.

Copies the input owning pointer; does not clone. This means that residue selectors could be shared with other Rosetta modules.

References residue_selector_.

Referenced by parse_my_tag().

◆ set_select_only_FAMILYVW()

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_select_only_FAMILYVW ( bool const setting )

Set whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

References select_only_FAMILYVW_.

Referenced by parse_my_tag().

Member Data Documentation

◆ atom_mode_

BSAF_mode protocols::simple_filters::BuriedSurfaceAreaFilter::atom_mode_

private

The subset of atoms to consider. Default is all atoms, but only hydrophobic atoms or only polar atoms are both possible, too.

Referenced by atom_mode(), and set_atom_mode().

◆ cutoff_area_

core::Real protocols::simple_filters::BuriedSurfaceAreaFilter::cutoff_area_

private

The cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

Defaults to 500 square Angstroms (arbitrarily chosen).

Referenced by cutoff_buried_surface_area(), and set_cutoff_buried_surface_area().

◆ filter_out_low_

bool protocols::simple_filters::BuriedSurfaceAreaFilter::filter_out_low_

private

If true, structures with less than the cutoff buried area are discrded.

True by default.

Referenced by filter_out_low(), and set_filter_out_low().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::BuriedSurfaceAreaFilter::residue_selector_

private

A residue selector to use to select a subset of residues for which to calculate buried surface area. Unused if not specified (i.e. all residues are used by default).

Referenced by residue_selector(), and set_residue_selector().

◆ select_only_FAMILYVW_

bool protocols::simple_filters::BuriedSurfaceAreaFilter::select_only_FAMILYVW_

private

If true, only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

Referenced by select_only_FAMILYVW(), and set_select_only_FAMILYVW().

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

src/protocols/simple_filters/BuriedSurfaceAreaFilter.hh
src/protocols/simple_filters/BuriedSurfaceAreaFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BuriedSurfaceAreaFilter()

◆ ~BuriedSurfaceAreaFilter()

Member Function Documentation

◆ apply()

◆ atom_mode()

◆ class_name()

◆ clone()

◆ compute()

◆ compute_residue_selection()

◆ cutoff_buried_surface_area()

◆ filter_out_low()

◆ fresh_instance()

◆ is_allowed_type()

◆ is_FAMILYVW()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ residue_selector()

◆ select_only_FAMILYVW()

◆ set_atom_mode() [1/2]

◆ set_atom_mode() [2/2]

◆ set_cutoff_buried_surface_area()

◆ set_filter_out_low()

◆ set_residue_selector()

◆ set_select_only_FAMILYVW()

Member Data Documentation

◆ atom_mode_

◆ cutoff_area_

◆ filter_out_low_

◆ residue_selector_

◆ select_only_FAMILYVW_