This mover performs a cyclic-aware crankshaft flip at a residue position. More...

#include <CrankshaftFlipMover.hh>

Inheritance diagram for protocols::cyclic_peptide::CrankshaftFlipMover:

[legend]

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

	CrankshaftFlipMover (core::select::residue_selector::ResidueSelectorCOP selector_in, bool allow_peptoid_flip_in, bool allow_peptide_flip_in, bool allow_pre_gly_flip_in, core::Real tolerance_in)
	Constructor. More...

	CrankshaftFlipMover (CrankshaftFlipMover const &src)
	Copy Constructor. More...

	~CrankshaftFlipMover () 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...

bool	try_peptoid_flip (core::pose::Pose &pose, core::Size res1_index, core::Size res2_index)
	Check if peptoid flip can be done at position, if it can flip poistion and return true else return false. More...

bool	try_peptide_flip (core::pose::Pose &pose, core::Size res1_index, core::Size res2_index)
	Check if peptide flip can be done at position, if it can flip poistion and return true else return false. More...

bool	try_pre_gly_flip (core::pose::Pose &pose, core::Size res1_index, core::Size res2_index)
	Check if pre-gly flip can be done at position, if it can flip poistion and return true else return false. More...

void	allow_peptoid_flips (bool af)
	Setters and Getters. More...

void	allow_peptide_flips (bool af)

void	allow_pre_gly_flips (bool af)

bool	allow_peptoid_flips ()

bool	allow_peptide_flips ()

bool	allow_pre_gly_flips ()

bool	angle_degrees_in_range (core::Real angle, core::Real target)
	returns true if the angle is close to the target withing some tolerance More...

void	selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Setter for selector. More...

core::select::residue_selector::ResidueSelectorCOP	selector ()

core::Real	tolerance () const

void	tolerance (core::Real tolerance)

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

CrankshaftFlipMover &	operator= (CrankshaftFlipMover const &src)
	Mover Methods ///. 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
	Sets up the citation info. 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 Attributes
bool	allow_peptoid_flips_

bool	allow_peptide_flips_

bool	allow_pre_gly_flips_

core::Real	tolerance_

core::select::residue_selector::ResidueSelectorCOP	selector_

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

This mover performs a cyclic-aware crankshaft flip at a residue position.

In lattice-based polymer simulations, crankshaft flips are moves that involve two adjacent monomers in a loop moving together (http://aip.scitation.org/doi/abs/10.1063/1.431297). In peptides, the equivalent is two backbone atoms, C_i and N_(i+1) moving by correlated rotations in psi_i, phi_(i+1). This move has been observed in several experimental contexts, including in crystal structures of antibody loops(http://doi.org/10.1016/j.jmb.2010.10.030) and in simulations of cyclic peptides (https://pubs.acs.org/doi/10.1021/acs.jctc.6b00193) and in simulations of cyclic peptoids (https://pubs.acs.org/doi/full/10.1021/acs.jpcb.2c01669). It should be useful in loop modeling and cyclic-peptides/peptoids/hybrids. Depending on the residue type different rules are uswed to flip the backbone, outlined in the table below. This mover is designed to be general and compatible with both homo- and hetero-polymers of the following type: peptides (not Gly or Pro), peptoids, glycine, proline, and N-methylated amino acids. The purtubations that are allowed for different combinations at the i and i+1 positions and compatible conformations are described in the table below.

Constructor & Destructor Documentation

◆ CrankshaftFlipMover() [1/3]

protocols::cyclic_peptide::CrankshaftFlipMover::CrankshaftFlipMover ( )

Constructors ///.

Default constructor

References allow_peptide_flips_, allow_peptoid_flips_, allow_pre_gly_flips_, and tolerance_.

◆ CrankshaftFlipMover() [2/3]

protocols::cyclic_peptide::CrankshaftFlipMover::CrankshaftFlipMover	(	core::select::residue_selector::ResidueSelectorCOP	selector_in,
		bool	allow_peptoid_flip_in = `true`,
		bool	allow_peptide_flip_in = `true`,
		bool	allow_pre_gly_flip_in = `true`,
		core::Real	tolerance_in = `20.0`
	)

Constructor.

References selector_.

◆ CrankshaftFlipMover() [3/3]

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

Copy Constructor.

Copy constructor.

References selector_.

◆ ~CrankshaftFlipMover()

protocols::cyclic_peptide::CrankshaftFlipMover::~CrankshaftFlipMover ( )

override

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

Member Function Documentation

◆ allow_peptide_flips() [1/2]

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptide_flips ( )

inline

References allow_peptide_flips_.

◆ allow_peptide_flips() [2/2]

void protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptide_flips ( bool af )

inline

References allow_peptide_flips_.

◆ allow_peptoid_flips() [1/2]

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptoid_flips ( )

inline

References allow_peptoid_flips_.

◆ allow_peptoid_flips() [2/2]

void protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptoid_flips ( bool af )

inline

Setters and Getters.

References allow_peptoid_flips_.

◆ allow_pre_gly_flips() [1/2]

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_pre_gly_flips ( )

inline

References allow_pre_gly_flips_.

◆ allow_pre_gly_flips() [2/2]

void protocols::cyclic_peptide::CrankshaftFlipMover::allow_pre_gly_flips ( bool af )

inline

References allow_pre_gly_flips_.

◆ angle_degrees_in_range()

bool protocols::cyclic_peptide::CrankshaftFlipMover::angle_degrees_in_range	(	core::Real	angle,
		core::Real	target
	)

returns true if the angle is close to the target withing some tolerance

References tolerance_.

Referenced by try_peptide_flip(), and try_pre_gly_flip().

◆ apply()

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

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

Implements protocols::moves::Mover.

References allow_peptide_flips_, allow_peptoid_flips_, allow_pre_gly_flips_, core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::has_upper_connect(), core::pose::Pose::residue(), selector_, core::pose::Pose::size(), protocols::cyclic_peptide::TR(), try_peptide_flip(), try_peptoid_flip(), try_pre_gly_flip(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::cyclic_peptide::CrankshaftFlipMover::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::CrankshaftFlipMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

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

static

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

◆ operator=()

CrankshaftFlipMover & protocols::cyclic_peptide::CrankshaftFlipMover::operator= ( CrankshaftFlipMover const & src )

Mover Methods ///.

copy assignment operator

References allow_peptide_flips_, allow_peptoid_flips_, allow_pre_gly_flips_, selector_, and tolerance_.

◆ parse_my_tag()

void protocols::cyclic_peptide::CrankshaftFlipMover::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 allow_peptide_flips_, allow_peptoid_flips_, allow_pre_gly_flips_, core::select::residue_selector::parse_residue_selector(), selector_, and tolerance_.

◆ provide_citation_info()

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

overridevirtual

Sets up the citation info.

This mover is unpublished. It returns P. Douglas Renfrew as its author.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

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

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::CrankshaftFlipMover::selector ( )

inline

References selector_.

Referenced by selector().

◆ selector() [2/2]

void protocols::cyclic_peptide::CrankshaftFlipMover::selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Setter for selector.

References selector(), and selector_.

◆ show()

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

◆ tolerance() [1/2]

core::Real protocols::cyclic_peptide::CrankshaftFlipMover::tolerance ( ) const

inline

References tolerance_.

◆ tolerance() [2/2]

void protocols::cyclic_peptide::CrankshaftFlipMover::tolerance ( core::Real tolerance )

inline

References tolerance(), and tolerance_.

Referenced by tolerance().

◆ try_peptide_flip()

bool protocols::cyclic_peptide::CrankshaftFlipMover::try_peptide_flip	(	core::pose::Pose &	pose,
		core::Size	res1_index,
		core::Size	res2_index
	)

Check if peptide flip can be done at position, if it can flip poistion and return true else return false.

returns true if res1 is Peptide and res2 is Peptide (not P) and both positions have correct dihedrals

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_pro, angle_degrees_in_range(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::cyclic_peptide::TR(), and core::conformation::Residue::type().

Referenced by apply().

◆ try_peptoid_flip()

bool protocols::cyclic_peptide::CrankshaftFlipMover::try_peptoid_flip	(	core::pose::Pose &	pose,
		core::Size	res1_index,
		core::Size	res2_index
	)

Check if peptoid flip can be done at position, if it can flip poistion and return true else return false.

returns true if res1 is Peptoid or Gly and res2 is Peptoid, Pro, or N-Methyl

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::ResidueType::is_N_substituted(), core::chemical::ResidueTypeBase::is_peptoid(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::conformation::Residue::type().

Referenced by apply().

◆ try_pre_gly_flip()

bool protocols::cyclic_peptide::CrankshaftFlipMover::try_pre_gly_flip	(	core::pose::Pose &	pose,
		core::Size	res1_index,
		core::Size	res2_index
	)

Check if pre-gly flip can be done at position, if it can flip poistion and return true else return false.

returns true if res1 is Peptoid or Peptide and res2 is Gly and both positions have correct dihedrals

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, angle_degrees_in_range(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::cyclic_peptide::TR(), and core::conformation::Residue::type().

Referenced by apply().

Member Data Documentation

◆ allow_peptide_flips_

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptide_flips_

private

Referenced by allow_peptide_flips(), apply(), CrankshaftFlipMover(), operator=(), and parse_my_tag().

◆ allow_peptoid_flips_

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_peptoid_flips_

private

Referenced by allow_peptoid_flips(), apply(), CrankshaftFlipMover(), operator=(), and parse_my_tag().

◆ allow_pre_gly_flips_

bool protocols::cyclic_peptide::CrankshaftFlipMover::allow_pre_gly_flips_

private

Referenced by allow_pre_gly_flips(), apply(), CrankshaftFlipMover(), operator=(), and parse_my_tag().

◆ selector_

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

private

Referenced by apply(), CrankshaftFlipMover(), operator=(), parse_my_tag(), and selector().

◆ tolerance_

core::Real protocols::cyclic_peptide::CrankshaftFlipMover::tolerance_

private

Referenced by angle_degrees_in_range(), CrankshaftFlipMover(), operator=(), parse_my_tag(), and tolerance().

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

src/protocols/cyclic_peptide/CrankshaftFlipMover.hh
src/protocols/cyclic_peptide/CrankshaftFlipMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CrankshaftFlipMover() [1/3]

◆ CrankshaftFlipMover() [2/3]

◆ CrankshaftFlipMover() [3/3]

◆ ~CrankshaftFlipMover()

Member Function Documentation

◆ allow_peptide_flips() [1/2]

◆ allow_peptide_flips() [2/2]

◆ allow_peptoid_flips() [1/2]

◆ allow_peptoid_flips() [2/2]

◆ allow_pre_gly_flips() [1/2]

◆ allow_pre_gly_flips() [2/2]

◆ angle_degrees_in_range()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ operator=()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ selector() [1/2]

◆ selector() [2/2]

◆ show()

◆ tolerance() [1/2]

◆ tolerance() [2/2]

◆ try_peptide_flip()

◆ try_peptoid_flip()

◆ try_pre_gly_flip()

Member Data Documentation

◆ allow_peptide_flips_

◆ allow_peptoid_flips_

◆ allow_pre_gly_flips_

◆ selector_

◆ tolerance_