Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover. More...

#include <SymmetricCycpepAlign.hh>

Inheritance diagram for protocols::cyclic_peptide::SymmetricCycpepAlign:

[legend]

Public Member Functions
	SymmetricCycpepAlign ()
	Constructors ///. More...

	SymmetricCycpepAlign (SymmetricCycpepAlign const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~SymmetricCycpepAlign () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

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

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

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

core::Size	symmetry_repeats () const
	Get the number of symmetry repeats. For example, for c4 or s4 symmetry, this would be "4". Defaults to "2". More...

bool	mirror_symmetry () const
	Get whether we're using mirror symmetry (e.g. s2 symmetry vs. c2 symmetry). More...

bool	auto_detect_symmetry () const
	Get whether we're auto-detecting symmetry. More...

core::Real const &	angle_threshold () const
	Get the angle threshold for counting poses as symmetric. More...

bool	trim_to_single_repeat () const
	Get whether all geometry that is not the protein backbone of a single symmetry repeat will be deleted. (This includes any crosslinkers.) More...

core::Size	repeat_to_preserve () const
	If trim_to_single_repeat_ is true, this is the symmetry repeat to preserve. More...

core::Size	last_symmetry_repeats () const
	Report the symmetry of the last auto-detected peptide. More...

bool	last_symmetry_mirror () const
	Report whether the symmetry of the last auto-detected peptide was mirror symmetry. More...

bool	invert () const
	Are we aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true)? More...

void	set_symmetry (core::Size const repeats_in, bool const mirror_in)
	Set the number of symmetry repeats and whether we're using mirror symmetry. For example, for c4 symmetry, inputs are "4", "false". For s4, they'd be "4", "true". More...

void	set_auto_detect_symmetry (bool const setting)
	Set whether we're auto-detecting symmetry. More...

void	set_angle_threshold (core::Real const &setting)
	Set the angle threshold for counting poses as symmetric. More...

void	set_trim_info (bool const do_trim, core::Size const repeat_to_preserve=1)
	Set whether we're going to delete all geometry that isn't the protein backbone of a single symmetry repeat, and which repeat to preserve. More...

void	set_invert (bool const setting)
	Set whether we're aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true). More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Member Functions
void	set_last_symmetry (core::Size const last_symm_in, bool const last_symm_mirror_in)
	Set the symmetry of the last auto-detected peptide symmetry. More...

bool	do_auto_detection_of_symmetry (core::pose::Pose const &pose, core::Size &symmrepeats, bool &mirrorsymm) const
	Given a quasi-symmetric pose, figure out its symmetry. More...

bool	do_symmetry_checks (core::pose::Pose const &pose, core::Size const symmrepeats, bool const mirrorsymm) const
	Given a quasi-symmetric pose, confirm that it has the specified symmetry. More...

core::Size	count_protein_residues (core::pose::Pose const &pose) const
	Given a pose, count the protein residues in it. More...

core::select::residue_selector::ResidueSelectorCOP	select_protein_residues (core::pose::Pose const &pose) const
	Given a pose, return a ResidueSelector that selects all the protein residues in the pose. More...

void	align_to_origin (core::pose::Pose &pose) const
	Given a pose, center it on the origin. More...

void	align_to_zaxis (core::pose::Pose &pose, core::Size const symmrepeats, bool const mirrorsymm) const
	Given a pose centered on the origin, align it to the z-axis based on its symmetry. More...

void	do_trim_to_single_repeat (core::pose::Pose &pose, core::Size const symmrepeats, core::Size const repeat_to_preserve) const
	Given a pose that has been properly centered on the origin and aligned to the z-axis, delete all but a single symmetry repeat. More...

Private Attributes
core::Size	symmetry_repeats_
	The number of symmetry repeats. For example, for c4 or s4 symmetry, this would be "4". Defaults to "2". More...

bool	mirror_symmetry_
	Does this peptide have mirror symmetry? Default "false". More...

bool	auto_detect_symmetry_
	Should the mover auto-detect symmetry? Default "false". More...

core::Real	angle_threshold_
	The angle threshold for detecting symmetry. More...

bool	trim_to_single_repeat_
	If true, all geometry that is not the protein backbone of a single symmetry repeat will be deleted. (This includes any crosslinkers.) False by default. More...

core::Size	repeat_to_preserve_
	If trim_to_single_repeat_ is true, this is the symmetry repeat to preserve. Default 1. More...

core::Size	last_symmetry_repeats_
	The symmetry of the last auto-detected peptide. More...

bool	last_symmetry_mirror_
	The mirror status of the symmetry of the last auto-detected peptide. More...

bool	invert_
	Aligns the peptide normal with the inverse Z-axis instead of with the Z-axis. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover.

Constructor & Destructor Documentation

◆ SymmetricCycpepAlign() [1/2]

protocols::cyclic_peptide::SymmetricCycpepAlign::SymmetricCycpepAlign ( )

Constructors ///.

Default constructor

◆ SymmetricCycpepAlign() [2/2]

protocols::cyclic_peptide::SymmetricCycpepAlign::SymmetricCycpepAlign ( SymmetricCycpepAlign const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~SymmetricCycpepAlign()

protocols::cyclic_peptide::SymmetricCycpepAlign::~SymmetricCycpepAlign ( )

overridedefault

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

Member Function Documentation

◆ align_to_origin()

void protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin ( core::pose::Pose & pose ) const

private

Given a pose, center it on the origin.

References core::pose::Pose::apply_transform_Rx_plus_v(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ align_to_zaxis()

void protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis	(	core::pose::Pose &	pose,
		core::Size const	symmrepeats,
		bool const	mirrorsymm
	)		const

private

Given a pose centered on the origin, align it to the z-axis based on its symmetry.

References core::pose::Pose::apply_transform_Rx_plus_v(), count_protein_residues(), invert(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ angle_threshold()

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

inline

Get the angle threshold for counting poses as symmetric.

Two dihedral values from different residues must fall within this cutoff, in degrees, for them to be considered the "same". Default 10 degrees.

References angle_threshold_.

Referenced by do_auto_detection_of_symmetry(), do_symmetry_checks(), and parse_my_tag().

◆ apply()

void protocols::cyclic_peptide::SymmetricCycpepAlign::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References align_to_origin(), align_to_zaxis(), auto_detect_symmetry(), do_auto_detection_of_symmetry(), do_symmetry_checks(), do_trim_to_single_repeat(), protocols::moves::FAIL_DO_NOT_RETRY, mirror_symmetry(), protocols::moves::MS_SUCCESS, repeat_to_preserve(), protocols::moves::Mover::set_last_move_status(), set_last_symmetry(), symmetry_repeats(), and trim_to_single_repeat().

◆ auto_detect_symmetry()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::auto_detect_symmetry ( ) const

inline

Get whether we're auto-detecting symmetry.

References auto_detect_symmetry_.

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::cyclic_peptide::SymmetricCycpepAlign::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ count_protein_residues()

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::count_protein_residues ( core::pose::Pose const & pose ) const

private

Given a pose, count the protein residues in it.

References core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by align_to_zaxis(), do_auto_detection_of_symmetry(), do_symmetry_checks(), and do_trim_to_single_repeat().

◆ do_auto_detection_of_symmetry()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::do_auto_detection_of_symmetry	(	core::pose::Pose const &	pose,
		core::Size &	symmrepeats,
		bool &	mirrorsymm
	)		const

private

Given a quasi-symmetric pose, figure out its symmetry.

Starts with the maximum possible, and tries every possible symmetry type, favouring mirror symmetry over non-mirror symmetry.

Parameters

[in]	pose	The quasi-symmetric pose.
[out]	symmrepeats	The number of symmetry repeats.
[out]	mirrorsymm	Is this a mirror symmetry type (sN) or not (cN)?

References angle_threshold(), protocols::cyclic_peptide::CycpepSymmetryFilter::apply(), count_protein_residues(), protocols::cyclic_peptide::CycpepSymmetryFilter::mirror_symm(), select_protein_residues(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_angle_threshold(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_mirror_symm(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_selector(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_symm_repeats(), protocols::cyclic_peptide::CycpepSymmetryFilter::symm_repeats(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ do_symmetry_checks()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::do_symmetry_checks	(	core::pose::Pose const &	pose,
		core::Size const	symmrepeats,
		bool const	mirrorsymm
	)		const

private

Given a quasi-symmetric pose, confirm that it has the specified symmetry.

References angle_threshold(), protocols::cyclic_peptide::CycpepSymmetryFilter::apply(), count_protein_residues(), select_protein_residues(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_angle_threshold(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_mirror_symm(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_selector(), protocols::cyclic_peptide::CycpepSymmetryFilter::set_symm_repeats(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ do_trim_to_single_repeat()

void protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat	(	core::pose::Pose &	pose,
		core::Size const	symmrepeats,
		core::Size const	repeat_to_preserve
	)		const

private

Given a pose that has been properly centered on the origin and aligned to the z-axis, delete all but a single symmetry repeat.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), count_protein_residues(), core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::is_protein(), repeat_to_preserve(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ fresh_instance()

moves::MoverOP protocols::cyclic_peptide::SymmetricCycpepAlign::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::cyclic_peptide::SymmetricCycpepAlign::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

◆ invert()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::invert ( ) const

inline

Are we aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true)?

References invert_.

Referenced by align_to_zaxis(), and parse_my_tag().

◆ last_symmetry_mirror()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_mirror ( ) const

inline

Report whether the symmetry of the last auto-detected peptide was mirror symmetry.

Returns false always if auto-detection is not enabled.

References auto_detect_symmetry_, and last_symmetry_mirror_.

◆ last_symmetry_repeats()

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_repeats ( ) const

inline

Report the symmetry of the last auto-detected peptide.

Returns 0 if auto-detection is not enabled.

References auto_detect_symmetry_, and last_symmetry_repeats_.

◆ mirror_symmetry()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::mirror_symmetry ( ) const

inline

Get whether we're using mirror symmetry (e.g. s2 symmetry vs. c2 symmetry).

References mirror_symmetry_.

Referenced by apply(), and parse_my_tag().

◆ mover_name()

std::string protocols::cyclic_peptide::SymmetricCycpepAlign::mover_name ( )

static

Referenced by get_name(), protocols::cyclic_peptide::SymmetricCycpepAlignCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::cyclic_peptide::SymmetricCycpepAlign::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

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

Reimplemented from protocols::moves::Mover.

References angle_threshold(), invert(), mirror_symmetry(), repeat_to_preserve(), set_angle_threshold(), set_auto_detect_symmetry(), set_invert(), set_symmetry(), set_trim_info(), symmetry_repeats(), and trim_to_single_repeat().

◆ provide_citation_info()

void protocols::cyclic_peptide::SymmetricCycpepAlign::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::cyclic_peptide::SymmetricCycpepAlign::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::cyclic_peptide::SymmetricCycpepAlignCreator::provide_xml_schema().

◆ repeat_to_preserve()

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::repeat_to_preserve ( ) const

inline

If trim_to_single_repeat_ is true, this is the symmetry repeat to preserve.

References repeat_to_preserve_.

Referenced by apply(), do_trim_to_single_repeat(), parse_my_tag(), and set_trim_info().

◆ select_protein_residues()

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::SymmetricCycpepAlign::select_protein_residues ( core::pose::Pose const & pose ) const

private

Given a pose, return a ResidueSelector that selects all the protein residues in the pose.

Uses Jared's ReturnResidueSubetSelector, which was a good idea. Thanks, Jared!

References core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by do_auto_detection_of_symmetry(), and do_symmetry_checks().

◆ set_angle_threshold()

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

Set the angle threshold for counting poses as symmetric.

Two dihedral values from different residues must fall within this cutoff, in degrees, for them to be considered the "same". Default 10 degrees.

References angle_threshold_.

Referenced by parse_my_tag().

◆ set_auto_detect_symmetry()

void protocols::cyclic_peptide::SymmetricCycpepAlign::set_auto_detect_symmetry ( bool const setting )

Set whether we're auto-detecting symmetry.

References auto_detect_symmetry_.

Referenced by parse_my_tag().

◆ set_invert()

void protocols::cyclic_peptide::SymmetricCycpepAlign::set_invert ( bool const setting )

inline

Set whether we're aligning the peptide normal with the Z-axis (false) or the inverse Z-axis (true).

References invert_.

Referenced by parse_my_tag().

◆ set_last_symmetry()

void protocols::cyclic_peptide::SymmetricCycpepAlign::set_last_symmetry	(	core::Size const	last_symm_in,
		bool const	last_symm_mirror_in
	)

private

Set the symmetry of the last auto-detected peptide symmetry.

References last_symmetry_mirror_, and last_symmetry_repeats_.

Referenced by apply().

◆ set_symmetry()

void protocols::cyclic_peptide::SymmetricCycpepAlign::set_symmetry	(	core::Size const	repeats_in,
		bool const	mirror_in
	)

Set the number of symmetry repeats and whether we're using mirror symmetry. For example, for c4 symmetry, inputs are "4", "false". For s4, they'd be "4", "true".

References mirror_symmetry_, and symmetry_repeats_.

Referenced by parse_my_tag().

◆ set_trim_info()

void protocols::cyclic_peptide::SymmetricCycpepAlign::set_trim_info	(	bool const	do_trim,
		core::Size const	repeat_to_preserve = `1`
	)

Set whether we're going to delete all geometry that isn't the protein backbone of a single symmetry repeat, and which repeat to preserve.

Parameters

[in]	do_trim	If set to true, the peptide will be trimmed down to a single repeat. False by default (no trimming).
[in]	repeat_to_preserve	If do_trim is set to true, this is the repeat that should be preserved. 1 by default.

References repeat_to_preserve(), repeat_to_preserve_, and trim_to_single_repeat_.

Referenced by parse_my_tag().

◆ show()

void protocols::cyclic_peptide::SymmetricCycpepAlign::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::cyclic_peptide::operator<<().

◆ symmetry_repeats()

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::symmetry_repeats ( ) const

inline

Get the number of symmetry repeats. For example, for c4 or s4 symmetry, this would be "4". Defaults to "2".

References symmetry_repeats_.

Referenced by apply(), and parse_my_tag().

◆ trim_to_single_repeat()

bool protocols::cyclic_peptide::SymmetricCycpepAlign::trim_to_single_repeat ( ) const

inline

Get whether all geometry that is not the protein backbone of a single symmetry repeat will be deleted. (This includes any crosslinkers.)

References trim_to_single_repeat_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

◆ angle_threshold_

core::Real protocols::cyclic_peptide::SymmetricCycpepAlign::angle_threshold_

private

The angle threshold for detecting symmetry.

Two dihedral values from different residues must fall within this cutoff, in degrees, for them to be considered the "same". Default 10 degrees.

Referenced by angle_threshold(), and set_angle_threshold().

◆ auto_detect_symmetry_

bool protocols::cyclic_peptide::SymmetricCycpepAlign::auto_detect_symmetry_

private

Should the mover auto-detect symmetry? Default "false".

Starts with the highets-fold allowed and works down, testing mirror symmetry before non-mirror symmetry. Only based on backbone.

Referenced by auto_detect_symmetry(), last_symmetry_mirror(), last_symmetry_repeats(), and set_auto_detect_symmetry().

◆ invert_

bool protocols::cyclic_peptide::SymmetricCycpepAlign::invert_

private

Aligns the peptide normal with the inverse Z-axis instead of with the Z-axis.

Referenced by invert(), and set_invert().

◆ last_symmetry_mirror_

bool protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_mirror_

private

The mirror status of the symmetry of the last auto-detected peptide.

Initialized to false; only set if auto-detection is used.

Referenced by last_symmetry_mirror(), and set_last_symmetry().

◆ last_symmetry_repeats_

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::last_symmetry_repeats_

private

The symmetry of the last auto-detected peptide.

Initialized to 0; only set if auto-detection is used.

Referenced by last_symmetry_repeats(), and set_last_symmetry().

◆ mirror_symmetry_

bool protocols::cyclic_peptide::SymmetricCycpepAlign::mirror_symmetry_

private

Does this peptide have mirror symmetry? Default "false".

Referenced by mirror_symmetry(), and set_symmetry().

◆ repeat_to_preserve_

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::repeat_to_preserve_

private

If trim_to_single_repeat_ is true, this is the symmetry repeat to preserve. Default 1.

Does nothing if trim_to_single_repeat_ is false.

Referenced by repeat_to_preserve(), and set_trim_info().

◆ symmetry_repeats_

core::Size protocols::cyclic_peptide::SymmetricCycpepAlign::symmetry_repeats_

private

The number of symmetry repeats. For example, for c4 or s4 symmetry, this would be "4". Defaults to "2".

Referenced by set_symmetry(), and symmetry_repeats().

◆ trim_to_single_repeat_

bool protocols::cyclic_peptide::SymmetricCycpepAlign::trim_to_single_repeat_

private

If true, all geometry that is not the protein backbone of a single symmetry repeat will be deleted. (This includes any crosslinkers.) False by default.

Referenced by set_trim_info(), and trim_to_single_repeat().

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

src/protocols/cyclic_peptide/SymmetricCycpepAlign.hh
src/protocols/cyclic_peptide/SymmetricCycpepAlign.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SymmetricCycpepAlign() [1/2]

◆ SymmetricCycpepAlign() [2/2]

◆ ~SymmetricCycpepAlign()

Member Function Documentation

◆ align_to_origin()

◆ align_to_zaxis()

◆ angle_threshold()

◆ apply()

◆ auto_detect_symmetry()

◆ clone()

◆ count_protein_residues()

◆ do_auto_detection_of_symmetry()

◆ do_symmetry_checks()

◆ do_trim_to_single_repeat()

◆ fresh_instance()

◆ get_name()

◆ invert()

◆ last_symmetry_mirror()

◆ last_symmetry_repeats()

◆ mirror_symmetry()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ repeat_to_preserve()

◆ select_protein_residues()

◆ set_angle_threshold()

◆ set_auto_detect_symmetry()

◆ set_invert()

◆ set_last_symmetry()

◆ set_symmetry()

◆ set_trim_info()

◆ show()

◆ symmetry_repeats()

◆ trim_to_single_repeat()

Member Data Documentation

◆ angle_threshold_

◆ auto_detect_symmetry_

◆ invert_

◆ last_symmetry_mirror_

◆ last_symmetry_repeats_

◆ mirror_symmetry_

◆ repeat_to_preserve_

◆ symmetry_repeats_

◆ trim_to_single_repeat_