A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry. More...

#include <CycpepSymmetryFilter.hh>

Inheritance diagram for protocols::cyclic_peptide::CycpepSymmetryFilter:

[legend]

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

	~CycpepSymmetryFilter () 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...

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...

void	set_symm_repeats (core::Size const repeats_in)
	Sets the repeats in the symmetry that we're looking for (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.). More...

void	set_mirror_symm (bool const symm_in)
	Sets whether we're considering mirror (e.g. s4, s6) or non-mirror (e.g. c4, c6) symmetry. More...

void	set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Sets the residue selector. More...

void	set_angle_threshold (core::Real const &setting)
	Set the cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom. More...

core::Size	symm_repeats () const
	Gets the repeats in the symmetry that we're looking for (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.). More...

bool	mirror_symm () const
	Gets whether we're considering mirror (e.g. s4, s6) or non-mirror (e.g. c4, c6) symmetry. More...

core::Real const &	angle_threshold () const
	The cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom. More...

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

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	get_residues (core::pose::Pose const &pose, core::select::residue_selector::ResidueSelectorCOP selector, utility::vector1< core::Size > &reslist_out) const
	Given a pose and an optional ResidueSelector, get a list of residues. More...

bool	is_cyclic_peptide (core::pose::Pose const &pose, utility::vector1< core::Size > const &residues) const
	Checks that the geometry to which we're applying this filter is actually a cyclic peptide. More...

bool	mainchain_torsions_differ (core::pose::Pose const &pose, core::Size const res1, core::Size const res2, bool const flip) const
	Returns TRUE if the number of mainchain torsions differs, or if the values differ; FALSE otherwise. More...

Private Attributes
core::Size	symm_repeats_
	The number of symmetry repeats (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.). More...

bool	mirror_symm_
	Are we considing mirror symmetry? More...

core::select::residue_selector::ResidueSelectorCOP	selector_
	A ResidueSelector to select a cyclic peptide part of a pose. More...

core::Real	angle_threshold_
	The cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom. More...

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

Detailed Description

A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry.

Constructor & Destructor Documentation

◆ CycpepSymmetryFilter()

protocols::cyclic_peptide::CycpepSymmetryFilter::CycpepSymmetryFilter ( )

Constructor.

◆ ~CycpepSymmetryFilter()

protocols::cyclic_peptide::CycpepSymmetryFilter::~CycpepSymmetryFilter ( )

overridedefault

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

Member Function Documentation

◆ angle_threshold()

core::Real const& protocols::cyclic_peptide::CycpepSymmetryFilter::angle_threshold ( ) const

inline

The cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom.

References angle_threshold_.

Referenced by mainchain_torsions_differ(), and parse_my_tag().

◆ apply()

bool protocols::cyclic_peptide::CycpepSymmetryFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References get_residues(), is_cyclic_peptide(), mainchain_torsions_differ(), mirror_symm(), selector(), symm_repeats(), and protocols::cyclic_peptide::TR().

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), report(), and report_sm().

◆ class_name()

std::string protocols::cyclic_peptide::CycpepSymmetryFilter::class_name ( )

static

Referenced by protocols::cyclic_peptide::CycpepSymmetryFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

protocols::filters::FilterOP protocols::cyclic_peptide::CycpepSymmetryFilter::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ fresh_instance()

protocols::filters::FilterOP protocols::cyclic_peptide::CycpepSymmetryFilter::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

◆ get_residues()

void protocols::cyclic_peptide::CycpepSymmetryFilter::get_residues	(	core::pose::Pose const &	pose,
		core::select::residue_selector::ResidueSelectorCOP	selector,
		utility::vector1< core::Size > &	reslist_out
	)		const

private

Given a pose and an optional ResidueSelector, get a list of residues.

References selector(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ is_cyclic_peptide()

bool protocols::cyclic_peptide::CycpepSymmetryFilter::is_cyclic_peptide	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residues
	)		const

private

Checks that the geometry to which we're applying this filter is actually a cyclic peptide.

References core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_gamma_aa(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::lower_connect_id(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::chemical::ResidueType::upper_connect_id().

Referenced by apply().

◆ mainchain_torsions_differ()

bool protocols::cyclic_peptide::CycpepSymmetryFilter::mainchain_torsions_differ	(	core::pose::Pose const &	pose,
		core::Size const	res1,
		core::Size const	res2,
		bool const	flip
	)		const

private

Returns TRUE if the number of mainchain torsions differs, or if the values differ; FALSE otherwise.

If flip is true, then torsion values are inverted prior to comparison.

References angle_threshold(), core::conformation::Residue::mainchain_torsions(), and core::pose::Pose::residue().

Referenced by apply().

◆ mirror_symm()

bool protocols::cyclic_peptide::CycpepSymmetryFilter::mirror_symm ( ) const

inline

Gets whether we're considering mirror (e.g. s4, s6) or non-mirror (e.g. c4, c6) symmetry.

References mirror_symm_.

Referenced by apply(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), parse_my_tag(), and report().

◆ name()

std::string protocols::cyclic_peptide::CycpepSymmetryFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::cyclic_peptide::CycpepSymmetryFilter::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 angle_threshold(), mirror_symm(), core::select::residue_selector::parse_residue_selector(), selector(), set_angle_threshold(), set_mirror_symm(), set_selector(), set_symm_repeats(), and symm_repeats().

◆ provide_xml_schema()

void protocols::cyclic_peptide::CycpepSymmetryFilter::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::cyclic_peptide::CycpepSymmetryFilterCreator::provide_xml_schema().

◆ report()

void protocols::cyclic_peptide::CycpepSymmetryFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References apply(), mirror_symm(), and symm_repeats().

◆ report_sm()

core::Real protocols::cyclic_peptide::CycpepSymmetryFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References apply().

◆ selector()

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CycpepSymmetryFilter::selector ( ) const

inline

Gets the residue selector.

References selector_.

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

◆ set_angle_threshold()

void protocols::cyclic_peptide::CycpepSymmetryFilter::set_angle_threshold ( core::Real const & setting )

Set the cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom.

References angle_threshold_.

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and parse_my_tag().

◆ set_mirror_symm()

void protocols::cyclic_peptide::CycpepSymmetryFilter::set_mirror_symm ( bool const symm_in )

inline

Sets whether we're considering mirror (e.g. s4, s6) or non-mirror (e.g. c4, c6) symmetry.

References mirror_symm_.

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and parse_my_tag().

◆ set_selector()

void protocols::cyclic_peptide::CycpepSymmetryFilter::set_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Sets the residue selector.

Note that the selector is NOT cloned.

References selector_.

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), and parse_my_tag().

◆ set_symm_repeats()

void protocols::cyclic_peptide::CycpepSymmetryFilter::set_symm_repeats ( core::Size const repeats_in )

Sets the repeats in the symmetry that we're looking for (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.).

References symm_repeats_.

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and parse_my_tag().

◆ symm_repeats()

core::Size protocols::cyclic_peptide::CycpepSymmetryFilter::symm_repeats ( ) const

inline

Gets the repeats in the symmetry that we're looking for (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.).

References symm_repeats_.

Referenced by apply(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry(), parse_my_tag(), and report().

Member Data Documentation

◆ angle_threshold_

core::Real protocols::cyclic_peptide::CycpepSymmetryFilter::angle_threshold_

private

The cutoff, in degrees, that two mainchain dihedral values must lie within in order for two residues to be considered to have the "same" value for that mainchain degree of freedom.

Defaults to 10 degrees.

Referenced by angle_threshold(), and set_angle_threshold().

◆ mirror_symm_

bool protocols::cyclic_peptide::CycpepSymmetryFilter::mirror_symm_

private

Are we considing mirror symmetry?

False by default; can only be true if symm_repeats_ is even.

Referenced by mirror_symm(), and set_mirror_symm().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CycpepSymmetryFilter::selector_

private

A ResidueSelector to select a cyclic peptide part of a pose.

Unused if left null. (In this case, the filter is applied to the whole pose).

Referenced by selector(), and set_selector().

◆ symm_repeats_

core::Size protocols::cyclic_peptide::CycpepSymmetryFilter::symm_repeats_

private

The number of symmetry repeats (e.g. 2 for c2 or s2 symmetry, 3 for c3, etc.).

Defaults to 2.

Referenced by set_symm_repeats(), and symm_repeats().

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

src/protocols/cyclic_peptide/CycpepSymmetryFilter.hh
src/protocols/cyclic_peptide/CycpepSymmetryFilter.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CycpepSymmetryFilter()

◆ ~CycpepSymmetryFilter()

Member Function Documentation

◆ angle_threshold()

◆ apply()

◆ class_name()

◆ clone()

◆ fresh_instance()

◆ get_residues()

◆ is_cyclic_peptide()

◆ mainchain_torsions_differ()

◆ mirror_symm()

◆ name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ selector()

◆ set_angle_threshold()

◆ set_mirror_symm()

◆ set_selector()

◆ set_symm_repeats()

◆ symm_repeats()

Member Data Documentation

◆ angle_threshold_

◆ mirror_symm_

◆ selector_

◆ symm_repeats_