#include <PerturbBundleHelix.hh>

Inheritance diagram for protocols::helical_bundle::PerturbBundleHelix:

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Public Types
typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParameters	BundleParameters

typedef protocols::helical_bundle::parameters::BundleParametersOP	BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP	BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersSet	BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSetOP	BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP	BundleParametersSetCOP

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

Public Member Functions
	PerturbBundleHelix ()
	Creator for PerturbBundleHelix mover. More...

	~PerturbBundleHelix () override
	Destructor for PerturbBundleHelix mover. More...

protocols::moves::MoverOP	clone () const override
	Clone operator to create a pointer to a fresh PerturbBundleHelix object that copies this one. More...

protocols::moves::MoverOP	fresh_instance () const override
	Fresh_instance operator to create a pointer to a fresh PerturbBundleHelix object that does NOT copy this one. More...

void	apply (core::pose::Pose &pose) override
	Actually apply the mover to the pose. More...

void	set_parameters_set_index (core::Size const index)
	Sets the index of the ParametersSet object in the pose that's being perturbed. More...

void	set_parameters_index (core::Size const index)
	Sets the index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...

core::Size	parameters_set_index () const
	Returns the index of the ParametersSet object in the pose that's being perturbed. More...

core::Size	parameters_index () const
	Returns the index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...

bool	last_apply_failed () const

std::string	get_name () const override
	Returns the name of this mover ("PerturbBundleHelix"). 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

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

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 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_apply_failed (bool const status)

Private Attributes
core::Size	parameters_set_index_
	The index of the ParametersSet object in the pose that's being perturbed. More...

core::Size	parameters_index_
	The index of the Parameters object in the ParametersSet object in the pose that's being perturbed. More...

bool	last_apply_failed_
	Stores whether the last apply attempt failed. More...

Additional Inherited Members
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...

Member Typedef Documentation

◆ BundleParameters

typedef protocols::helical_bundle::parameters::BundleParameters protocols::helical_bundle::PerturbBundleHelix::BundleParameters

◆ BundleParametersCOP

typedef protocols::helical_bundle::parameters::BundleParametersCOP protocols::helical_bundle::PerturbBundleHelix::BundleParametersCOP

◆ BundleParametersOP

typedef protocols::helical_bundle::parameters::BundleParametersOP protocols::helical_bundle::PerturbBundleHelix::BundleParametersOP

◆ BundleParametersSet

typedef protocols::helical_bundle::parameters::BundleParametersSet protocols::helical_bundle::PerturbBundleHelix::BundleParametersSet

◆ BundleParametersSetCOP

typedef protocols::helical_bundle::parameters::BundleParametersSetCOP protocols::helical_bundle::PerturbBundleHelix::BundleParametersSetCOP

◆ BundleParametersSetOP

typedef protocols::helical_bundle::parameters::BundleParametersSetOP protocols::helical_bundle::PerturbBundleHelix::BundleParametersSetOP

◆ Parameters

typedef core::conformation::parametric::Parameters protocols::helical_bundle::PerturbBundleHelix::Parameters

◆ ParametersOP

typedef core::conformation::parametric::ParametersOP protocols::helical_bundle::PerturbBundleHelix::ParametersOP

◆ ParametersSet

typedef core::conformation::parametric::ParametersSet protocols::helical_bundle::PerturbBundleHelix::ParametersSet

◆ ParametersSetOP

typedef core::conformation::parametric::ParametersSetOP protocols::helical_bundle::PerturbBundleHelix::ParametersSetOP

Constructor & Destructor Documentation

◆ PerturbBundleHelix()

protocols::helical_bundle::PerturbBundleHelix::PerturbBundleHelix ( )

Creator for PerturbBundleHelix mover.

◆ ~PerturbBundleHelix()

protocols::helical_bundle::PerturbBundleHelix::~PerturbBundleHelix ( )

overridedefault

Destructor for PerturbBundleHelix mover.

Member Function Documentation

◆ apply()

void protocols::helical_bundle::PerturbBundleHelix::apply ( core::pose::Pose & pose )

overridevirtual

Actually apply the mover to the pose.

Implements protocols::moves::Mover.

References protocols::helical_bundle::BundleParametrizationCalculator::build_helix(), core::pose::Pose::conformation(), core::conformation::Conformation::n_parameters_sets(), parameters_index(), core::conformation::Conformation::parameters_set(), parameters_set_index(), set_last_apply_failed(), and protocols::helical_bundle::TR().

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

◆ clone()

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundleHelix::clone ( ) const

overridevirtual

Clone operator to create a pointer to a fresh PerturbBundleHelix object that copies this one.

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::helical_bundle::PerturbBundleHelix::fresh_instance ( ) const

overridevirtual

Fresh_instance operator to create a pointer to a fresh PerturbBundleHelix object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::helical_bundle::PerturbBundleHelix::get_name ( ) const

overridevirtual

Returns the name of this mover ("PerturbBundleHelix").

Implements protocols::moves::Mover.

References mover_name().

◆ last_apply_failed()

bool protocols::helical_bundle::PerturbBundleHelix::last_apply_failed ( ) const

inline

References last_apply_failed_.

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

◆ mover_name()

std::string protocols::helical_bundle::PerturbBundleHelix::mover_name ( )

static

Referenced by get_name(), protocols::helical_bundle::PerturbBundleHelixCreator::keyname(), and provide_xml_schema().

◆ parameters_index()

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_index ( ) const

inline

Returns the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

References parameters_index_.

Referenced by apply().

◆ parameters_set_index()

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_set_index ( ) const

inline

Returns the index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

References parameters_set_index_.

Referenced by apply().

◆ provide_xml_schema()

void protocols::helical_bundle::PerturbBundleHelix::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::helical_bundle::PerturbBundleHelixCreator::provide_xml_schema().

◆ set_last_apply_failed()

void protocols::helical_bundle::PerturbBundleHelix::set_last_apply_failed ( bool const status )

inlineprivate

References last_apply_failed_.

Referenced by apply().

◆ set_parameters_index()

void protocols::helical_bundle::PerturbBundleHelix::set_parameters_index ( core::Size const index )

inline

Sets the index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

References parameters_index_.

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

◆ set_parameters_set_index()

void protocols::helical_bundle::PerturbBundleHelix::set_parameters_set_index ( core::Size const index )

inline

Sets the index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

References parameters_set_index_.

Referenced by protocols::helical_bundle::PerturbBundle::rebuild_conformation().

Member Data Documentation

◆ last_apply_failed_

bool protocols::helical_bundle::PerturbBundleHelix::last_apply_failed_

private

Stores whether the last apply attempt failed.

Referenced by last_apply_failed(), and set_last_apply_failed().

◆ parameters_index_

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_index_

private

The index of the Parameters object in the ParametersSet object in the pose that's being perturbed.

This Parameters object contains the Crick parameters that define the helix that's being perturbed.

Referenced by parameters_index(), and set_parameters_index().

◆ parameters_set_index_

core::Size protocols::helical_bundle::PerturbBundleHelix::parameters_set_index_

private

The index of the ParametersSet object in the pose that's being perturbed.

This ParametersSet contains the Parameters object that defines the helix that's being perturbed.

Referenced by parameters_set_index(), and set_parameters_set_index().

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

src/protocols/helical_bundle/PerturbBundleHelix.hh
src/protocols/helical_bundle/PerturbBundleHelix.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BundleParameters

◆ BundleParametersCOP

◆ BundleParametersOP

◆ BundleParametersSet

◆ BundleParametersSetCOP

◆ BundleParametersSetOP

◆ Parameters

◆ ParametersOP

◆ ParametersSet

◆ ParametersSetOP

Constructor & Destructor Documentation

◆ PerturbBundleHelix()

◆ ~PerturbBundleHelix()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ last_apply_failed()

◆ mover_name()

◆ parameters_index()

◆ parameters_set_index()

◆ provide_xml_schema()

◆ set_last_apply_failed()

◆ set_parameters_index()

◆ set_parameters_set_index()

Member Data Documentation

◆ last_apply_failed_

◆ parameters_index_

◆ parameters_set_index_