A mover to change one torsion angle. More...

#include <SetTorsion.hh>

Inheritance diagram for protocols::simple_moves::SetTorsion:

[legend]

Public Member Functions
	SetTorsion ()
	default ctor More...

	~SetTorsion () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

core::Size	n_torsion_sets () const

utility::vector1< core::Size >	residue_list (core::Size iset, core::pose::Pose const &pose)

core::Real	angle (core::Size const iset, core::Real const &old_angle) const
	Actually get the value that the torsion will be set to. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	torsion_name (core::Size const iset)

void	set_fold_tree_root (core::Size const root)
	Sets a residue index that will serve as the root of the FoldTree for the SetTorsion operation. More...

core::Size	get_fold_tree_root () const
	Returns the residue index that will serve as the root of the FoldTree for the SetTorsion operation. More...

void	add_perturbation_type (std::string const &type_in)
	Add a perturbation type to the list of perturbation types. More...

TorsionPerturbType	perturbation_type (core::Size const index) const
	Get a perturbation type. More...

void	add_perturbation_magnitude (core::Real const &mag_in)
	Add a perturbation magnitude to the list of perturbation magnitudes. More...

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

core::Real	perturbation_magnitude (core::Size const index) const
	Get a perturbation magnitude. 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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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...

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	mover_name ()

static std::string	torsion_ct_name (std::string)

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 Types
typedef protocols::moves::Mover	parent

Private Attributes
bool	random_set_

utility::vector1< std::string >	angle_

utility::vector1< std::string >	residues_

utility::vector1< std::string >	torsion_name_

utility::vector1< std::string >	custom_rama_map_
	Used for custom rama sampling. One entry per <Torsion> block; defaults to "". More...

utility::vector1< core::Size >	extending_

utility::vector1< utility::vector1< core::id::NamedAtomID > >	torsion_atoms_

utility::vector1< TorsionPerturbType >	perturbation_type_
	The type of perturbation, if the "perturb" option is used. More...

utility::vector1< core::Real >	perturbation_magnitude_
	The perturbation magnitude, if the "perturb" option is used. More...

core::Size	fold_tree_root_
	The root for the FoldTree during the operation. If 0, the default FoldTree is used. The FoldTree is reset to the input FoldTree after the operation. 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 to change one torsion angle.

Member Typedef Documentation

◆ parent

typedef protocols::moves::Mover protocols::simple_moves::SetTorsion::parent

private

Constructor & Destructor Documentation

◆ SetTorsion()

protocols::simple_moves::SetTorsion::SetTorsion ( )

default ctor

◆ ~SetTorsion()

protocols::simple_moves::SetTorsion::~SetTorsion ( )

overridedefault

Member Function Documentation

◆ add_perturbation_magnitude()

void protocols::simple_moves::SetTorsion::add_perturbation_magnitude ( core::Real const & mag_in )

inline

Add a perturbation magnitude to the list of perturbation magnitudes.

Checks for non-negative magnitude. After this operation, the perturbation_magnitude_ vector is one entry longer.

References perturbation_magnitude_.

Referenced by parse_my_tag().

◆ add_perturbation_type()

void protocols::simple_moves::SetTorsion::add_perturbation_type ( std::string const & type_in )

inline

Add a perturbation type to the list of perturbation types.

Currently only allows "uniform" or "gaussian". Checks for proper input. After this operation, the perturbation_type_ vector is one entry longer.

References perturbation_type_, protocols::simple_moves::perturbtorsion_gaussian, and protocols::simple_moves::perturbtorsion_uniform.

Referenced by parse_my_tag().

◆ angle()

core::Real protocols::simple_moves::SetTorsion::angle	(	core::Size const	iset,
		core::Real const &	old_angle
	)		const

Actually get the value that the torsion will be set to.

Depending on settings, this will look up a value, generate a random value, or perturb an input value.

References angle_, perturbation_magnitude(), perturbation_type(), protocols::simple_moves::perturbtorsion_gaussian, protocols::simple_moves::perturbtorsion_uniform, and core::scoring::rg.

Referenced by apply().

◆ apply()

void protocols::simple_moves::SetTorsion::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ clone()

protocols::moves::MoverOP protocols::simple_moves::SetTorsion::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::simple_moves::SetTorsion::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_fold_tree_root()

core::Size protocols::simple_moves::SetTorsion::get_fold_tree_root ( ) const

inline

Returns the residue index that will serve as the root of the FoldTree for the SetTorsion operation.

References fold_tree_root_.

◆ get_name()

std::string protocols::simple_moves::SetTorsion::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::simple_moves::SetTorsion::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::SetTorsionCreator::keyname(), and provide_xml_schema().

◆ n_torsion_sets()

core::Size protocols::simple_moves::SetTorsion::n_torsion_sets ( ) const

inline

References residues_.

Referenced by apply().

◆ parse_my_tag()

void protocols::simple_moves::SetTorsion::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_perturbation_magnitude(), add_perturbation_type(), angle_, custom_rama_map_, extending_, fold_tree_root_, random_set_, residues_, torsion_atoms_, and torsion_name_.