#include <SecondaryStructureFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::SecondaryStructureFilter:

Public Types
typedef protocols::filters::Filter	Super

typedef protocols::filters::Filter	Filter

typedef std::string	String

typedef protocols::filters::FilterOP	FilterOP

typedef core::pose::Pose	Pose

typedef utility::tag::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

Public Member Functions
	SecondaryStructureFilter ()

	SecondaryStructureFilter (String const &ss)

	~SecondaryStructureFilter () override

FilterOP	clone () const override

FilterOP	fresh_instance () const override

void	filtered_ss (String const &s)

void	filtered_abego (String const &s)

void	set_use_dssp (bool const use_ss)
	Should we use the secstruct in the pose (false), or compute via dssp (true)? default=false for historical reasons. More...

void	set_strand_pairings (String const &s)
	Sets sheet topology string. More...

void	set_blueprint (std::string const &blueprint_file)
	sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelector const &selector)
	sets the residue selector used to choose which residues to scan. Default is all protein residues More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
	parse xml More...

bool	apply (Pose const &pose) const override
	Returns true if the given pose passes the filter, false otherwise. More...

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

std::string	name () const override

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

	Filter (std::string const &)

	~Filter () override

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

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)

Protected Member Functions
std::string	get_filtered_secstruct (core::pose::Pose const &pose) const
	Returns the desired secondary structure. More...

std::string	get_strand_pairings (core::pose::Pose const &pose) const
	returns the strand pairing string to be used in computation More...

void	correct_for_incomplete_strand_pairings (core::pose::Pose const &pose, std::string &secstruct) const
	If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match. More...

core::Size	compute (Pose const &pose, core::select::residue_selector::ResidueSubset const &subset) const
	returns the number of residues in the protein that have matching secondary structure More...

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	selector_

String	filtered_ss_

utility::vector1< String >	filtered_abego_

String	strand_pairings_

bool	use_abego_

bool	use_dssp_

core::Real	threshold_

bool	treat_L_as_D_

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

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::fldsgn::filters::SecondaryStructureFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::SecondaryStructureFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::fldsgn::filters::SecondaryStructureFilter::Pose

◆ String

typedef std::string protocols::fldsgn::filters::SecondaryStructureFilter::String

◆ Super

typedef protocols::filters::Filter protocols::fldsgn::filters::SecondaryStructureFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::filters::SecondaryStructureFilter::TagCOP

Constructor & Destructor Documentation

◆ SecondaryStructureFilter() [1/2]

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter ( )

◆ SecondaryStructureFilter() [2/2]

protocols::fldsgn::filters::SecondaryStructureFilter::SecondaryStructureFilter ( String const & ss )

◆ ~SecondaryStructureFilter()

protocols::fldsgn::filters::SecondaryStructureFilter::~SecondaryStructureFilter ( )

inlineoverride

Member Function Documentation

◆ apply()

bool protocols::fldsgn::filters::SecondaryStructureFilter::apply ( Pose const & pose ) const

overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References report_sm(), protocols::filters::Filter::score(), threshold_, and tr().

◆ class_name()

std::string protocols::fldsgn::filters::SecondaryStructureFilter::class_name ( )

static

Referenced by protocols::fldsgn::filters::SecondaryStructureFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute()

core::Size protocols::fldsgn::filters::SecondaryStructureFilter::compute	(	Pose const &	pose,
		core::select::residue_selector::ResidueSubset const &	subset
	)		const

protected

returns the number of residues in the protein that have matching secondary structure

Parameters

[in]	pose	Pose to be analyzed
[in]	subset	Subset of the pose to be analyzed. Only residues that are true in the subset will be included in the computation.

Returns: Number of protein residues in the residue subset that match the desired secondary structure WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match

If impossible strand pairings exist (i.e a two-strand pose where one strand has 6 residues and the other has 5), either 'E' or 'L' will be allowed at the unpaired position

Parameters

[in]	pose	Pose to be analyzed
[in]	subset	Subset of the pose to be analyzed. Only residues that are true in the subset will be included in the computation. WARNING: ignores abegos for now, since abegomanager only returns a bool The filter score will report only secondary structures, but if you specify abego, the 'apply' function will return false if abegos don't match

If impossible strand pairings exist (i.e a two-strand pose where one strand has 6 residues and the other has 5), either 'E' or 'L' will be allowed at the unpaired position

References core::scoring::abego, core::sequence::ABEGOManager::check_rama(), correct_for_incomplete_strand_pairings(), protocols::simple_filters::dssp(), filtered_abego_, core::sequence::ABEGOManager::get_abego_string(), get_filtered_secstruct(), core::conformation::Residue::is_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), core::pose::Pose::size(), tr(), treat_L_as_D_, use_abego_, and use_dssp_.

Referenced by report_sm().

◆ correct_for_incomplete_strand_pairings()

void protocols::fldsgn::filters::SecondaryStructureFilter::correct_for_incomplete_strand_pairings	(	core::pose::Pose const &	pose,
		std::string &	secstruct
	)		const

protected

If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.

Parameters

[in]	pose	Input pose to be tested.
	[in/out]	secstruct Desired secondary structure. It will be modified in-place
[in]	strand_pairings	Strand pairings to be used for modification

If strand_pairings_ is user-specified, the specific residue pairings will be computed based on it. If strand_pairings_ is empty, residue pairings will be taken from the cached StructureData in the pose, if present. If strand_pairings is empty and no cached StructureData was found, this will do nothing. Any unpaired residues found in the sheet topology with 'E' secondary structure will be changed to 'h' (to allow either loop or strand)

Parameters

[in]	pose	Input pose to be tested.
	[in/out]	secstruct Desired secondary structure. It will be modified in-place
[in]	strand_pairings	Strand pairings to be used for modification

If strand_pairings is user-specified, the specific residue pairings will be computed based on it. If strand_pairings is empty, residue pairings will be taken from the cached StructureData in the pose, if present. If strand_pairings_ is empty and no cached StructureData was found, this will do nothing. Any unpaired residues found in the sheet topology with 'E' secondary structure will be changed to 'h' (to allow either loop or strand)

References protocols::denovo_design::residue_selectors::PairedSheetResidueSelector::set_secstruct(), core::pose::Pose::size(), strand_pairings_, and tr().

Referenced by compute().

◆ filtered_abego()

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego ( String const & s )

References filtered_abego_, and use_abego_.

◆ filtered_ss()

void protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss ( String const & s )

References filtered_ss_.

◆ fresh_instance()

FilterOP protocols::fldsgn::filters::SecondaryStructureFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

◆ get_filtered_secstruct()

std::string protocols::fldsgn::filters::SecondaryStructureFilter::get_filtered_secstruct ( core::pose::Pose const & pose ) const

protected

Returns the desired secondary structure.

Rules for selecting this seconary structure:

If a user-specified filtered_ss_ is set, return that
If StructureData is cached in the pose, use the secondary structure of that
Use pose secondary structure, throwing and error if use_dssp is false

References filtered_ss_, protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), protocols::denovo_design::components::StructureDataFactory::has_cached_data(), core::pose::Pose::secstruct(), protocols::denovo_design::components::StructureData::ss(), tr(), and use_dssp_.

Referenced by compute().

◆ get_strand_pairings()

std::string protocols::fldsgn::filters::SecondaryStructureFilter::get_strand_pairings ( core::pose::Pose const & pose ) const

protected

returns the strand pairing string to be used in computation

Parameters

[in] pose Pose to be analyzed

If strand_pairings_ is non-empty, it will be returned Otherwise, the strand pairings will be computed from the Pose's StructureData If StructureData is not present and strand_pairings_ are not specified, quit

◆ name()

std::string protocols::fldsgn::filters::SecondaryStructureFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::fldsgn::filters::SecondaryStructureFilter::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References core::scoring::abego, filtered_abego_, filtered_ss_, core::sequence::ABEGOManager::get_abego_string(), core::select::residue_selector::parse_residue_selector(), set_blueprint(), set_residue_selector(), set_use_dssp(), threshold_, tr(), treat_L_as_D_, use_abego_, and use_dssp_.

◆ provide_xml_schema()

void protocols::fldsgn::filters::SecondaryStructureFilter::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::fldsgn::filters::SecondaryStructureFilterCreator::provide_xml_schema().

◆ report_sm()

core::Real protocols::fldsgn::filters::SecondaryStructureFilter::report_sm ( Pose const & ) const

overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), selector_, and core::pose::Pose::size().

Referenced by apply().

◆ set_blueprint()

void protocols::fldsgn::filters::SecondaryStructureFilter::set_blueprint ( std::string const & blueprint_file )

sets the blueprint file based on filename. If a strand pairing is impossible (i.e. the structure has two strands, 5 and 6 residues, respectively, it sets the unpaired residues to 'h' so that they still match.

Sets the filtered_ss, filtered_abego, and strand_pairings from the blueprint file given.

References filtered_abego_, filtered_ss_, and strand_pairings_.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::fldsgn::filters::SecondaryStructureFilter::set_residue_selector ( core::select::residue_selector::ResidueSelector const & selector )

sets the residue selector used to choose which residues to scan. Default is all protein residues

References core::select::residue_selector::ResidueSelector::clone(), and selector_.

Referenced by parse_my_tag().

◆ set_strand_pairings()

void protocols::fldsgn::filters::SecondaryStructureFilter::set_strand_pairings ( String const & s )

Sets sheet topology string.

References strand_pairings_.

◆ set_use_dssp()

void protocols::fldsgn::filters::SecondaryStructureFilter::set_use_dssp ( bool const use_ss )

Should we use the secstruct in the pose (false), or compute via dssp (true)? default=false for historical reasons.

References use_dssp_.

Referenced by parse_my_tag().

Member Data Documentation

◆ filtered_abego_

utility::vector1< String > protocols::fldsgn::filters::SecondaryStructureFilter::filtered_abego_

private

Referenced by compute(), filtered_abego(), parse_my_tag(), and set_blueprint().

◆ filtered_ss_

String protocols::fldsgn::filters::SecondaryStructureFilter::filtered_ss_

private

Referenced by filtered_ss(), get_filtered_secstruct(), parse_my_tag(), and set_blueprint().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::fldsgn::filters::SecondaryStructureFilter::selector_

private

Referenced by report_sm(), and set_residue_selector().

◆ strand_pairings_

String protocols::fldsgn::filters::SecondaryStructureFilter::strand_pairings_

private

Referenced by correct_for_incomplete_strand_pairings(), set_blueprint(), and set_strand_pairings().

◆ threshold_

core::Real protocols::fldsgn::filters::SecondaryStructureFilter::threshold_

private

Referenced by apply(), and parse_my_tag().

◆ treat_L_as_D_

bool protocols::fldsgn::filters::SecondaryStructureFilter::treat_L_as_D_

private

Referenced by compute(), and parse_my_tag().

◆ use_abego_

bool protocols::fldsgn::filters::SecondaryStructureFilter::use_abego_

private

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

◆ use_dssp_

bool protocols::fldsgn::filters::SecondaryStructureFilter::use_dssp_

private

Referenced by compute(), get_filtered_secstruct(), parse_my_tag(), and set_use_dssp().

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

src/protocols/fldsgn/filters/SecondaryStructureFilter.hh
src/protocols/fldsgn/filters/SecondaryStructureFilter.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ DataMap

◆ Filter

◆ FilterOP

◆ Pose

◆ String

◆ Super

◆ TagCOP

Constructor & Destructor Documentation

◆ SecondaryStructureFilter() [1/2]

◆ SecondaryStructureFilter() [2/2]

◆ ~SecondaryStructureFilter()

Member Function Documentation

◆ apply()

◆ class_name()

◆ clone()

◆ compute()

◆ correct_for_incomplete_strand_pairings()

◆ filtered_abego()

◆ filtered_ss()

◆ fresh_instance()

◆ get_filtered_secstruct()

◆ get_strand_pairings()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report_sm()

◆ set_blueprint()

◆ set_residue_selector()

◆ set_strand_pairings()

◆ set_use_dssp()

Member Data Documentation

◆ filtered_abego_

◆ filtered_ss_

◆ selector_

◆ strand_pairings_

◆ threshold_

◆ treat_L_as_D_

◆ use_abego_

◆ use_dssp_