This filter computes the longest continuous stretch of polar residues within a pose or selection. More...

#include <LongestContinuousPolarSegmentFilter.hh>

Inheritance diagram for protocols::simple_filters::LongestContinuousPolarSegmentFilter:

[legend]

Public Member Functions
	LongestContinuousPolarSegmentFilter ()
	Constructor. More...

	LongestContinuousPolarSegmentFilter (std::string const &filter_name)
	Constructor. More...

	~LongestContinuousPolarSegmentFilter () override
	destructor (important for properly forward-declaring smart-pointer members) More...

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...

void	set_exclude_chain_termini (bool const setting)
	Set whether I should exclude stretches of polars are the N- and C-termini of chains. More...

bool	exclude_chain_termini () const
	Get whether I should exclude stretches of polars are the N- and C-termini of chains. More...

void	set_count_gly_as_polar (bool const setting)
	Set whether glycine is counted as a polar residue type. More...

bool	count_gly_as_polar () const
	Get whether glycine is counted as a polar residue type. More...

void	set_filter_out_high (bool const setting)
	Set whether I should filter out high (true) or low (false) poses. More...

bool	filter_out_high () const
	Get whether I should filter out high (true) or low (false) poses. More...

void	set_cutoff (core::Size const cutoff)
	Set the max (or min) tolerated number of polars. More...

core::Size	cutoff () const
	Get the max (or min) tolerated number of polars. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the residue selector. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the residue selector. 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...

virtual bool	is_counted (core::chemical::ResidueType const &restype) const
	Given a residue type, determine whether it's one of the types that this filter should count. More...

virtual std::string	counted_residue_description () const
	returns type of counted residues (polar) 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
void	compute (core::pose::Pose const &pose, core::select::residue_selector::ResidueSelectorCOP selector, bool const ignore_termini, core::Size &longest_stretch_res_count, core::Size &longest_stretch_start, core::Size &longest_stretch_end) const
	Given a pose, actually compute the number of residues in the longest stretch, and return this value, along with the start and end indices (in Rosetta numbering). More...

Private Attributes
bool	exclude_chain_termini_
	Should I exclude stretches of polars are the N- and C-termini of chains? More...

bool	count_gly_as_polar_
	If true, glycine will be considered "polar". True by default. More...

bool	filter_out_high_
	Should I filter out designs with too many or too few polars in a stretch? More...

core::Size	cutoff_
	The cutoff value for filtering. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_
	An optional residue selector to select a subset of a pose. More...

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

Detailed Description

This filter computes the longest continuous stretch of polar residues within a pose or selection.

Constructor & Destructor Documentation

◆ LongestContinuousPolarSegmentFilter() [1/2]

protocols::simple_filters::LongestContinuousPolarSegmentFilter::LongestContinuousPolarSegmentFilter ( )

Constructor.

this constructor sets count_gly_as_polar to true

◆ LongestContinuousPolarSegmentFilter() [2/2]

protocols::simple_filters::LongestContinuousPolarSegmentFilter::LongestContinuousPolarSegmentFilter ( std::string const & filter_name )

Constructor.

constructor for derived classes to call

this constructor sets count_gly_as_polar to false

◆ ~LongestContinuousPolarSegmentFilter()

protocols::simple_filters::LongestContinuousPolarSegmentFilter::~LongestContinuousPolarSegmentFilter ( )

overridedefault

destructor (important for properly forward-declaring smart-pointer members)

Destructor.

Member Function Documentation

◆ apply()

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

overridevirtual

returns true if the structure passes the filter, false otherwise

Returns true if the structure passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), counted_residue_description(), cutoff_, exclude_chain_termini_, filter_out_high_, core::conformation::Residue::name3(), core::pose::Pose::residue(), residue_selector_, and protocols::simple_filters::TR().

◆ class_name()

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

static

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

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ compute()

void protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSelectorCOP	selector,
		bool const	ignore_termini,
		core::Size &	longest_stretch_res_count,
		core::Size &	longest_stretch_start,
		core::Size &	longest_stretch_end
	)		const

private

Given a pose, actually compute the number of residues in the longest stretch, and return this value, along with the start and end indices (in Rosetta numbering).

Returns 0, 0, 0 if no polar stretch could be found.

Parameters

[in]	pose	The pose to analyse.
[in]	selector	An optional const-owning pointer to a ResidueSelector. If provided, only those stretches that have at least one residue selected by the ResidueSelector will be counted.
[in]	ignore_termini	If true, stretches at the N- and C-termini of chains are ignored. If false, they're counted.
[out]	longest_stretch_res_count	The number of polar residues in the longest polar stretch. Set to 0 if no polar stretch is found.
[out]	longest_stretch_start	The index, in Rosetta numbering, of the first residue of the longest polar stretch. Set to 0 if no polar stretch is found.
[out]	longest_stretch_end	The index, in Rosetta numbering, of the last residue of the longest polar stretch. Set to 0 if no polar stretch is found.

References core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), counted_residue_description(), core::sequence::end, is_counted(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::loops::start, core::pose::Pose::total_residue(), and protocols::simple_filters::TR().

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

◆ count_gly_as_polar()

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::count_gly_as_polar ( ) const

inline

Get whether glycine is counted as a polar residue type.

References count_gly_as_polar_.

Referenced by is_counted(), and parse_my_tag().

◆ counted_residue_description()

std::string protocols::simple_filters::LongestContinuousPolarSegmentFilter::counted_residue_description ( ) const

virtual

returns type of counted residues (polar)

Reimplemented in protocols::simple_filters::LongestContinuousApolarSegmentFilter.

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

◆ cutoff()

core::Size protocols::simple_filters::LongestContinuousPolarSegmentFilter::cutoff ( ) const

inline

Get the max (or min) tolerated number of polars.

References cutoff_.

Referenced by parse_my_tag(), and set_cutoff().

◆ exclude_chain_termini()

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::exclude_chain_termini ( ) const

inline

Get whether I should exclude stretches of polars are the N- and C-termini of chains.

References exclude_chain_termini_.

Referenced by parse_my_tag().

◆ filter_out_high()

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::filter_out_high ( ) const

inline

Get whether I should filter out high (true) or low (false) poses.

References filter_out_high_.

Referenced by parse_my_tag().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ is_counted()

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::is_counted ( core::chemical::ResidueType const & restype ) const

virtual

Given a residue type, determine whether it's one of the types that this filter should count.

Based on whether the residue type has the POLAR property. Special-case exception is made for glycine, depending on whether count_gly_as_polar_ is true.

Reimplemented in protocols::simple_filters::LongestContinuousApolarSegmentFilter.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, count_gly_as_polar(), and core::chemical::ResidueType::is_polar().

Referenced by compute().

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by report().

◆ parse_my_tag()

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

overridevirtual

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

Parse tag to allow RosettaScripts XML to call this mover.

Reimplemented from protocols::filters::Filter.

References count_gly_as_polar(), cutoff(), exclude_chain_termini(), filter_out_high(), core::select::residue_selector::parse_residue_selector(), set_count_gly_as_polar(), set_cutoff(), set_exclude_chain_termini(), set_filter_out_high(), and set_residue_selector().

◆ provide_xml_schema()

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

static

References protocols::rosetta_scripts::attributes_for_parse_residue_selector(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ report()

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

overridevirtual

allows printing data to a stream

Allows printing data to a stream.

Reimplemented from protocols::filters::Filter.

References compute(), counted_residue_description(), exclude_chain_termini_, name(), core::conformation::Residue::name3(), core::pose::Pose::residue(), and residue_selector_.

◆ report_sm()

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

overridevirtual

required for reporting score values

Required for reporting score values.

Reimplemented from protocols::filters::Filter.

References compute(), exclude_chain_termini_, and residue_selector_.

◆ residue_selector()

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

inline

Get the residue selector.

Can be shared, or modified later – this is a true owning pointer to the stored selector, not to a clone.

References residue_selector_.

◆ set_count_gly_as_polar()

void protocols::simple_filters::LongestContinuousPolarSegmentFilter::set_count_gly_as_polar ( bool const setting )

inline

Set whether glycine is counted as a polar residue type.

References count_gly_as_polar_.

Referenced by parse_my_tag().

◆ set_cutoff()

void protocols::simple_filters::LongestContinuousPolarSegmentFilter::set_cutoff ( core::Size const cutoff )

inline

Set the max (or min) tolerated number of polars.

References cutoff(), and cutoff_.

Referenced by parse_my_tag().

◆ set_exclude_chain_termini()

void protocols::simple_filters::LongestContinuousPolarSegmentFilter::set_exclude_chain_termini ( bool const setting )

inline

Set whether I should exclude stretches of polars are the N- and C-termini of chains.

References exclude_chain_termini_.

Referenced by parse_my_tag().

◆ set_filter_out_high()

void protocols::simple_filters::LongestContinuousPolarSegmentFilter::set_filter_out_high ( bool const setting )

inline

Set whether I should filter out high (true) or low (false) poses.

References filter_out_high_.

Referenced by parse_my_tag().

◆ set_residue_selector()

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

Set the residue selector.

Does not clone the input; uses it directly. (Can be shared, or modified later).

References residue_selector_.

Referenced by parse_my_tag().

Member Data Documentation

◆ count_gly_as_polar_

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::count_gly_as_polar_

private

If true, glycine will be considered "polar". True by default.

Referenced by count_gly_as_polar(), and set_count_gly_as_polar().

◆ cutoff_

core::Size protocols::simple_filters::LongestContinuousPolarSegmentFilter::cutoff_

private

The cutoff value for filtering.

Above (or below, if filtering out low) this value, designs are rejected. If the number of polars is equal to or below this value (or equal to or above, if filtering out low), designs are accepted.

Referenced by apply(), cutoff(), and set_cutoff().

◆ exclude_chain_termini_

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::exclude_chain_termini_

private

Should I exclude stretches of polars are the N- and C-termini of chains?

Default true.

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

◆ filter_out_high_

bool protocols::simple_filters::LongestContinuousPolarSegmentFilter::filter_out_high_

private

Should I filter out designs with too many or too few polars in a stretch?

Default is true (filter out designs with too many).

Referenced by apply(), filter_out_high(), and set_filter_out_high().

◆ residue_selector_

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

private

An optional residue selector to select a subset of a pose.

Will be nullptr if not specified.

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

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

src/protocols/simple_filters/LongestContinuousPolarSegmentFilter.hh
src/protocols/simple_filters/LongestContinuousPolarSegmentFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LongestContinuousPolarSegmentFilter() [1/2]

◆ LongestContinuousPolarSegmentFilter() [2/2]

◆ ~LongestContinuousPolarSegmentFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ count_gly_as_polar()

◆ counted_residue_description()

◆ cutoff()

◆ exclude_chain_termini()

◆ filter_out_high()

◆ fresh_instance()

◆ is_counted()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ residue_selector()

◆ set_count_gly_as_polar()

◆ set_cutoff()

◆ set_exclude_chain_termini()

◆ set_filter_out_high()

◆ set_residue_selector()

Member Data Documentation

◆ count_gly_as_polar_

◆ cutoff_

◆ exclude_chain_termini_

◆ filter_out_high_

◆ residue_selector_