A mover that takes a cyclic peptide and alters its position (rigid-body transform), superimposing it on a cyclic permutation or reverse cyclic permutation of itself. More...

#include <CycpepRigidBodyPermutationMover.hh>

Inheritance diagram for protocols::cyclic_peptide::CycpepRigidBodyPermutationMover:

[legend]

Public Member Functions
	CycpepRigidBodyPermutationMover ()
	Default constructor. More...

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

void	apply (core::pose::Pose &pose) override
	Apply the mover. 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
	parse XML tag (to use this Mover in Rosetta Scripts) 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...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	This mover is unpublished. It returns Vikram K. Mulligan as its author. More...

void	set_mover_mode (std::string const &setting)
	Set how we will permute the peptide, by string: setting its permutation or randomizing it. More...

void	set_mover_mode (CycpepRigidBodyPermutationMoverMode const setting)
	Set how we will permute the peptide, by enum: setting its permutation or randomizing it. More...

void	set_permutation_setting (signed long int const offset)
	Set how much we are permuting the peptide in setting mode. If inversion_setting is false, this is residues in the forward direction; if it is true, this is residues in the reverse direction. More...

void	set_inversion_setting (bool const inversion_setting)
	Set whether we are overlaying the peptide on a permuted version of itself (false) or on a permuted version of the reverse sequence (true). Only used in setting mode. More...

void	set_inversion_random (bool const inversion_random)
	Set whether we are only overlaying the peptide on a permuted version of itself (false) or whether we are allowed to consider overlays on a permuted version of the reverse sequence (true). Only used in randomization mode. More...

void	set_random_position_offset (core::Real const offset)
	Set whether we should add a small random offset to the peptide's position. More...

void	set_random_orientation_perturbation (core::Real const perturbation)
	Set whether we should add a small random perturbation to the peptide's orientation. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set a residue selector to select a cyclic peptide that is a part of a pose. More...

CycpepRigidBodyPermutationMoverMode	mover_mode () const
	Get how we will permute the peptide, by enum: setting its permutation or randomizing it. More...

signed long int	permutation_setting () const
	Get how much we are permuting the peptide in setting mode. If inversion_setting is false, this is residues in the forward direction; if it is true, this is residues in the reverse direction. More...

bool	inversion_setting () const
	Set whether we are overlaying the peptide on a permuted version of itself (false) or on a permuted version of the reverse sequence (true). Only used in setting mode. More...

bool	inversion_random () const
	Get whether we are only overlaying the peptide on a permuted version of itself (false) or whether we are allowed to consider overlays on a permuted version of the reverse sequence (true). Only used in randomization mode. More...

core::Real	random_position_offset () const
	Get whether we should add a small random offset to the peptide's position. More...

core::Real	random_orientation_perturbation () const
	Get whether we should add a small random perturbation to the peptide's orientation. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the residue selector to select a cyclic peptide that is a part of a pose. 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)
	Describe the XML interface for this mover, in a machine-readable way that permits automatic checking of user inputs. More...

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	confirm_is_cyclic_peptide (core::pose::Pose const &pose, utility::vector1< core::Size > const &selected_residues) const
	Check that the pose or selection is a cyclic peptide, and throw with an informative error message if it is not. More...

utility::vector1< core::Size >	generate_residue_index_map (utility::vector1< core::Size > const &selected_residues) const
	Given a selection of residues, plus the current configuration of this mover, generate a vector of residue indices that has been suitably circularly permuted or inverse circular permuted. More...

core::pose::PoseOP	generate_cycpep_pose_copy (core::pose::Pose const &pose, utility::vector1< core::Size > const &selected_residues) const
	Given a pose, cut out selected residues. More...

void	align_cycpep_pose_to_original_pose (core::pose::Pose &cycpep_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_index_map) const
	Align the cyclic peptide pose to the original. More...

void	perturb_cycpep_pose_position (core::pose::Pose &pose) const
	Perturb the cyclic peptide pose position. More...

void	perturb_cycpep_pose_orientation (core::pose::Pose &pose) const
	Perturb the cyclic peptide pose orientation. More...

void	copy_cycpep_pose_coordinates_to_original_pose (core::pose::Pose const &cycpep_pose, core::pose::Pose &pose, utility::vector1< core::Size > const &selected_residues) const
	Copy the cyclic peptide pose coordinates to the original. More...

Private Attributes
CycpepRigidBodyPermutationMoverMode	mode_ = CycpepRigidBodyPermutationMoverMode::RANDOM_PERMUTATION
	How we will permute the peptide: setting its permutation or randomizing it. More...

signed long int	permutation_setting_ = 0
	If we are setting the permutation, what is the setting? Zero by default (no permutation). More...

bool	inversion_setting_ = false
	If we are setting the permutation, are we setting this to overlay on the forward or backwards sequence? False by default (overlaying on forward sequence). More...

bool	inversion_random_ = true
	If we are randomizing the permutation, do we also allow overlay on the backwards sequence? True by default. More...

core::Real	random_position_offset_ = 0.0
	Should we add a small random offset to the peptide's position? More...

core::Real	random_orientation_perturbation_ = 0.0
	Should we add a small random perturbation to the peptide's orientation? More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_
	An optional residue selector, used to select a cyclic peptide in a pose. 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

A mover that takes a cyclic peptide and alters its position (rigid-body transform), superimposing it on a cyclic permutation or reverse cyclic permutation of itself.

Constructor & Destructor Documentation

◆ CycpepRigidBodyPermutationMover()

protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::CycpepRigidBodyPermutationMover ( )

Default constructor.

◆ ~CycpepRigidBodyPermutationMover()

protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::~CycpepRigidBodyPermutationMover ( )

overridedefault

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

Member Function Documentation

◆ align_cycpep_pose_to_original_pose()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::align_cycpep_pose_to_original_pose	(	core::pose::Pose &	cycpep_pose,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	residue_index_map
	)		const

private

Align the cyclic peptide pose to the original.

The offset in the residue index map is used. N, CA, C, O, CB, CM (beta-aas), and CA1 (peptoids) atoms are used, provided that pairs of residues have both.

Parameters

[in,out]	cycpep_pose	The pose whose coordinates are updated by this operation.
[in]	pose	The pose that we're aligning TO. This is unaltered by this operation.
[in]	residue_index_map	A vector of residue indices in pose, where the index in the vector is the residue index in cycpep_pose.

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_peptoid(), core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ apply()

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

overridevirtual

Apply the mover.

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References align_cycpep_pose_to_original_pose(), confirm_is_cyclic_peptide(), copy_cycpep_pose_coordinates_to_original_pose(), generate_cycpep_pose_copy(), generate_residue_index_map(), perturb_cycpep_pose_orientation(), perturb_cycpep_pose_position(), residue_selector_, core::select::residue_selector::selection_positions(), and core::pose::Pose::total_residue().

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ confirm_is_cyclic_peptide()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	selected_residues
	)		const

private

Check that the pose or selection is a cyclic peptide, and throw with an informative error message if it is not.

The checks are:

Does each residue have a lower connect and an upper connect?
Is the upper of each connected to the lower of the next?
Is there a connection from the last to the first?
Note
This is general enough for peptides with other cyclization chemistries, but NOT general enough for lariats or peptides with tails. (Though this function and generate_residue_index_map could be generalized to allow that in the future.)

References core::chemical::ResidueTypeBase::base_name(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), core::conformation::Residue::is_bonded(), core::chemical::ResidueType::lower_connect_id(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::to_string(), and core::chemical::ResidueType::upper_connect_id().

Referenced by apply().

◆ copy_cycpep_pose_coordinates_to_original_pose()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::copy_cycpep_pose_coordinates_to_original_pose	(	core::pose::Pose const &	cycpep_pose,
		core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	selected_residues
	)		const

private

Copy the cyclic peptide pose coordinates to the original.

Parameters

[in]	cycpep_pose	The cyclic peptide pose, the pose that we are copying FROM.
[in,out]	pose	The original pose, the pose whose coordinates we are UPDATING.
[in]	selected_residues	A vector of indices of the residues of the cyclic peptide.

References core::chemical::ResidueTypeBase::base_name(), core::pose::Pose::batch_get_xyz(), core::pose::Pose::batch_set_xyz(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::id::to_string(), core::pose::Pose::total_residue(), protocols::cyclic_peptide::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ generate_cycpep_pose_copy()

core::pose::PoseOP protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_cycpep_pose_copy	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	selected_residues
	)		const

private

Given a pose, cut out selected residues.

Assumes that we've got a cyclic peptide.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueTypeBase::base_name(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connected_residue_at_upper(), core::pose::Pose::empty(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::n_possible_residue_connections(), core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ generate_residue_index_map()

utility::vector1< core::Size > protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::generate_residue_index_map ( utility::vector1< core::Size > const & selected_residues ) const

private

Given a selection of residues, plus the current configuration of this mover, generate a vector of residue indices that has been suitably circularly permuted or inverse circular permuted.

References inversion_setting_, mode_, permutation_setting_, protocols::cyclic_peptide::SET_PERMUTATION, protocols::cyclic_peptide::string_from_cycpep_rigid_body_permutation_mover_mode(), and protocols::cyclic_peptide::TR().

Referenced by apply().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ inversion_random()

bool protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::inversion_random ( ) const

Get whether we are only overlaying the peptide on a permuted version of itself (false) or whether we are allowed to consider overlays on a permuted version of the reverse sequence (true). Only used in randomization mode.

References inversion_random_.

Referenced by set_inversion_random().

◆ inversion_setting()

bool protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::inversion_setting ( ) const

Set whether we are overlaying the peptide on a permuted version of itself (false) or on a permuted version of the reverse sequence (true). Only used in setting mode.

References inversion_setting_.

Referenced by set_inversion_setting().

◆ mover_mode()

CycpepRigidBodyPermutationMoverMode protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::mover_mode ( ) const

Get how we will permute the peptide, by enum: setting its permutation or randomizing it.

References mode_.

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

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

Rosetta Scripts Support ///.

Parse XML tag (to use this Mover in RosettaScripts).

Reimplemented from protocols::moves::Mover.

References mode_, core::select::residue_selector::parse_residue_selector(), protocols::cyclic_peptide::RANDOM_PERMUTATION, set_inversion_random(), set_inversion_setting(), set_mover_mode(), protocols::cyclic_peptide::SET_PERMUTATION, set_permutation_setting(), set_random_orientation_perturbation(), set_random_position_offset(), and set_residue_selector().

◆ permutation_setting()

signed long int protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::permutation_setting ( ) const

Get how much we are permuting the peptide in setting mode. If inversion_setting is false, this is residues in the forward direction; if it is true, this is residues in the reverse direction.

Note: Deliberately signed.

References permutation_setting_.

◆ perturb_cycpep_pose_orientation()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::perturb_cycpep_pose_orientation ( core::pose::Pose & pose ) const

private

Perturb the cyclic peptide pose orientation.

Does nothing if random_orientation_perturbation_ == 0.0. Otherwise, generates a random unit vector from a spherically-symmetric distribution, and rotates by X degrees about this vector, where X is drawn from a Gaussian distribution of standard deviation random_orientation_perturbation_ degrees. The centre of rotation is the centroid of the N, C, CA, O, CB (if present), CM (if beta-aa), and CA1 (if peptoid) atoms.

Parameters

[in,out] pose The pose whose orientation we're perturbing. Altered by this operation.

References core::chemical::ResidueType::atom_index(), core::pose::Pose::batch_get_xyz(), core::pose::Pose::batch_set_xyz(), protocols::simple_filters::coords(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::natoms(), random_orientation_perturbation_, core::pose::Pose::residue_type(), core::pose::Pose::total_atoms(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by apply().

◆ perturb_cycpep_pose_position()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::perturb_cycpep_pose_position ( core::pose::Pose & pose ) const

private

Perturb the cyclic peptide pose position.

Does nothing if random_position_offset_ == 0.0. Otherwise, generates a random vector from a Gaussian distribution with mean length random_position_offset_ and adds this to the coordinates of the pose.

Parameters

[in,out] pose The pose whose position we're offsetting. Altered by this operation.

References core::pose::Pose::batch_get_xyz(), core::pose::Pose::batch_set_xyz(), core::chemical::ResidueType::natoms(), random_position_offset_, core::pose::Pose::residue_type(), core::pose::Pose::total_atoms(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ provide_citation_info()

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

overridevirtual

This mover is unpublished. It returns Vikram K. Mulligan as its author.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

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

static

Describe the XML interface for this mover, in a machine-readable way that permits automatic checking of user inputs.

References protocols::rosetta_scripts::attributes_for_parse_residue_selector(), protocols::cyclic_peptide::list_cycpep_rigid_body_permutation_mover_modes(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ random_orientation_perturbation()

core::Real protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::random_orientation_perturbation ( ) const

Get whether we should add a small random perturbation to the peptide's orientation.

The default, 0.0, means no perturbation. Larger values set the magnitude of the random roll, in degrees. The roll is about the peptide centroid.

References random_orientation_perturbation_.

◆ random_position_offset()

core::Real protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::random_position_offset ( ) const

Get whether we should add a small random offset to the peptide's position.

The default, 0.0, means no offset. Larger values set the magnitude of the random displacement, in Angstroms.

References random_position_offset_.

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::residue_selector ( ) const

Get the residue selector to select a cyclic peptide that is a part of a pose.

Could be nullptr if no selector is set.

References residue_selector_.

◆ set_inversion_random()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_inversion_random ( bool const inversion_random )

Set whether we are only overlaying the peptide on a permuted version of itself (false) or whether we are allowed to consider overlays on a permuted version of the reverse sequence (true). Only used in randomization mode.

References inversion_random(), inversion_random_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

◆ set_inversion_setting()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_inversion_setting ( bool const inversion_setting )

Set whether we are overlaying the peptide on a permuted version of itself (false) or on a permuted version of the reverse sequence (true). Only used in setting mode.

References inversion_setting(), inversion_setting_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

◆ set_mover_mode() [1/2]

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode ( CycpepRigidBodyPermutationMoverMode const setting )

Set how we will permute the peptide, by enum: setting its permutation or randomizing it.

Set how we will permute the peptide: setting its permutation or randomizing it.

References mode_, protocols::cyclic_peptide::N_MODES, protocols::cyclic_peptide::string_from_cycpep_rigid_body_permutation_mover_mode(), and protocols::cyclic_peptide::TR().

◆ set_mover_mode() [2/2]

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_mover_mode ( std::string const & setting )

Set how we will permute the peptide, by string: setting its permutation or randomizing it.

Throws if string not recognized.

References protocols::cyclic_peptide::cycpep_rigid_body_permutation_mover_mode_from_string(), protocols::cyclic_peptide::list_cycpep_rigid_body_permutation_mover_modes(), and protocols::cyclic_peptide::UNKNOWN_MODE.

Referenced by parse_my_tag().

◆ set_permutation_setting()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_permutation_setting ( signed long int const offset )

Set how much we are permuting the peptide in setting mode. If inversion_setting is false, this is residues in the forward direction; if it is true, this is residues in the reverse direction.

Note: Deliberately signed.

References permutation_setting_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

◆ set_random_orientation_perturbation()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_random_orientation_perturbation ( core::Real const perturbation )

Set whether we should add a small random perturbation to the peptide's orientation.

The default, 0.0, means no perturbation. Larger values set the magnitude of the random roll, in degrees. The roll is about the peptide centroid.

References random_orientation_perturbation_.

Referenced by parse_my_tag().

◆ set_random_position_offset()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_random_position_offset ( core::Real const offset )

Set whether we should add a small random offset to the peptide's position.

The default, 0.0, means no offset. Larger values set the magnitude of the random displacement, in Angstroms.

References random_position_offset_.

Referenced by parse_my_tag().

◆ set_residue_selector()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set a residue selector to select a cyclic peptide that is a part of a pose.

Input selector is used directly, not cloned. Pass nullptr to disable.

References residue_selector_, and protocols::cyclic_peptide::TR().

Referenced by parse_my_tag().

◆ show()

void protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::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<<().

Member Data Documentation

◆ inversion_random_

bool protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::inversion_random_ = true

private

If we are randomizing the permutation, do we also allow overlay on the backwards sequence? True by default.

Referenced by inversion_random(), and set_inversion_random().

◆ inversion_setting_

bool protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::inversion_setting_ = false

private

If we are setting the permutation, are we setting this to overlay on the forward or backwards sequence? False by default (overlaying on forward sequence).

Referenced by generate_residue_index_map(), inversion_setting(), and set_inversion_setting().

◆ mode_

CycpepRigidBodyPermutationMoverMode protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::mode_ = CycpepRigidBodyPermutationMoverMode::RANDOM_PERMUTATION

private

How we will permute the peptide: setting its permutation or randomizing it.

Referenced by generate_residue_index_map(), mover_mode(), parse_my_tag(), and set_mover_mode().

◆ permutation_setting_

signed long int protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::permutation_setting_ = 0

private

If we are setting the permutation, what is the setting? Zero by default (no permutation).

Note: Deliberately signed.

Referenced by generate_residue_index_map(), permutation_setting(), and set_permutation_setting().

◆ random_orientation_perturbation_

core::Real protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::random_orientation_perturbation_ = 0.0

private

Should we add a small random perturbation to the peptide's orientation?

The default, 0.0, means no perturbation. Larger values set the magnitude of the random roll, in degrees. The roll is about the peptide centroid.

Referenced by perturb_cycpep_pose_orientation(), random_orientation_perturbation(), and set_random_orientation_perturbation().

◆ random_position_offset_

core::Real protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::random_position_offset_ = 0.0

private

Should we add a small random offset to the peptide's position?

The default, 0.0, means no offset. Larger values set the magnitude of the random displacement, in Angstroms.

Referenced by perturb_cycpep_pose_position(), random_position_offset(), and set_random_position_offset().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::residue_selector_

private

An optional residue selector, used to select a cyclic peptide in a pose.

Not used if nullptr.

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

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

src/protocols/cyclic_peptide/CycpepRigidBodyPermutationMover.hh
src/protocols/cyclic_peptide/CycpepRigidBodyPermutationMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CycpepRigidBodyPermutationMover()

◆ ~CycpepRigidBodyPermutationMover()

Member Function Documentation

◆ align_cycpep_pose_to_original_pose()

◆ apply()

◆ clone()

◆ confirm_is_cyclic_peptide()

◆ copy_cycpep_pose_coordinates_to_original_pose()

◆ fresh_instance()

◆ generate_cycpep_pose_copy()

◆ generate_residue_index_map()

◆ get_name()

◆ inversion_random()

◆ inversion_setting()

◆ mover_mode()

◆ mover_name()

◆ parse_my_tag()

◆ permutation_setting()

◆ perturb_cycpep_pose_orientation()

◆ perturb_cycpep_pose_position()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ random_orientation_perturbation()

◆ random_position_offset()

◆ residue_selector()

◆ set_inversion_random()

◆ set_inversion_setting()

◆ set_mover_mode() [1/2]

◆ set_mover_mode() [2/2]

◆ set_permutation_setting()

◆ set_random_orientation_perturbation()

◆ set_random_position_offset()

◆ set_residue_selector()

◆ show()

Member Data Documentation

◆ inversion_random_

◆ inversion_setting_

◆ mode_

◆ permutation_setting_

◆ random_orientation_perturbation_

◆ random_position_offset_

◆ residue_selector_