#include <RingConformationMover.hh>

Inheritance diagram for protocols::simple_moves::RingConformationMover:

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

	RingConformationMover (RingConformationMover const &object_to_copy)
	Copy constructor. More...

	RingConformationMover (core::kinematics::MoveMapOP input_movemap)
	Constructor with MoveMap input option. More...

RingConformationMover &	operator= (RingConformationMover const &object_to_copy)

	~RingConformationMover () override

void	show (std::ostream &output=std::cout) const override
	Generate string representation of RingConformationMover for debugging purposes. More...

std::string	get_name () const override
	Return the name of the Mover. 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...

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

void	apply (core::pose::Pose &input_pose) override
	Apply the corresponding move to <input_pose>. More...

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

core::kinematics::MoveMapCOP	movemap (core::pose::Pose const &pose)
	Get the current MoveMap, creating it if needed. More...

void	movemap (core::kinematics::MoveMapOP new_movemap)
	Set the MoveMap. More...

void	movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)
	Set the MoveMapFactory. More...

bool	sample_all_conformers () const
	Get whether or not this Mover will sample all ring conformers, regardless of energy. More...

void	sample_all_conformers (bool setting)
	Set whether or not this Mover will sample all ring conformers, regardless of energy. 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 void	register_options ()
	Register options with the option system. More...

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_commandline_options ()

void	init ()

void	copy_data (RingConformationMover &object_to_copy_to, RingConformationMover const &object_to_copy_from)

void	setup_residue_list (core::pose::Pose const &pose)

Private Attributes
core::select::movemap::MoveMapFactoryCOP	movemap_factory_

core::kinematics::MoveMapOP	movemap_

utility::vector1< core::Size >	residue_list_

bool	locked_

bool	sample_all_conformers_

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

Based on a given MoveMap, this mover selects movable cyclic residues and flips their rings to an idealized ring conformer.

Constructor & Destructor Documentation

protocols::simple_moves::RingConformationMover::RingConformationMover ( )

Default constructor.

By default, all rings within a given pose will be allowed to move.

References init().

protocols::simple_moves::RingConformationMover::RingConformationMover ( RingConformationMover const & object_to_copy )

Copy constructor.

References copy_data().

protocols::simple_moves::RingConformationMover::RingConformationMover ( core::kinematics::MoveMapOP input_movemap )

Constructor with MoveMap input option.

Parameters

<input_movemap> a MoveMap with desired nu torsions set to true

Remarks: Movable cyclic residues will generally be a subset of residues in the MoveMap whose nu torsions are set to true.

References init().

protocols::simple_moves::RingConformationMover::~RingConformationMover ( )

overridedefault

Member Function Documentation

void protocols::simple_moves::RingConformationMover::apply ( core::pose::Pose & input_pose )

overridevirtual

Apply the corresponding move to <input_pose>.

The mover will create a list of movable residues based on the given MoveMap and select a residue from the list at random. The torsion angles of a randomly selected ring conformer will be applied to the selected residue.

Parameters

<input_pose> the structure to be moved

Implements protocols::moves::Mover.

References protocols::moves::FAIL_DO_NOT_RETRY, get_name(), locked_, protocols::moves::MS_SUCCESS, core::pose::Pose::residue(), residue_list_, core::scoring::rg, sample_all_conformers_, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_ring_conformation(), setup_residue_list(), show(), core::chemical::rings::RingConformer::specific_name, and protocols::simple_moves::TR().

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

overridevirtual

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.

void protocols::simple_moves::RingConformationMover::copy_data	(	RingConformationMover &	object_to_copy_to,
		RingConformationMover const &	object_to_copy_from
	)

private

References locked_, movemap_, movemap_factory_, residue_list_, and sample_all_conformers_.

Referenced by operator=(), and RingConformationMover().

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

overridevirtual

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.

std::string protocols::simple_moves::RingConformationMover::get_name ( ) const

overridevirtual

Return the name of the Mover.

Implements protocols::moves::Mover.

References mover_name().

Referenced by apply().

void protocols::simple_moves::RingConformationMover::init ( void )

private

References locked_, sample_all_conformers_, set_commandline_options(), and protocols::moves::Mover::type().

Referenced by RingConformationMover().

kinematics::MoveMapCOP protocols::simple_moves::RingConformationMover::movemap ( core::pose::Pose const & pose )

Get the current MoveMap, creating it if needed.

References movemap_, and movemap_factory_.

Referenced by setup_residue_list().

void protocols::simple_moves::RingConformationMover::movemap ( core::kinematics::MoveMapOP new_movemap )

Set the MoveMap.

References movemap_.

void protocols::simple_moves::RingConformationMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP new_movemap_factory )

Set the MoveMapFactory.

References movemap_factory_.

Referenced by parse_my_tag().

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

static

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

RingConformationMover & protocols::simple_moves::RingConformationMover::operator= ( RingConformationMover const & object_to_copy )

References copy_data().

void protocols::simple_moves::RingConformationMover::parse_my_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 movemap_factory(), protocols::rosetta_scripts::parse_movemap_factory_legacy(), and sample_all_conformers_.

void protocols::simple_moves::RingConformationMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::simple_moves::RingConformationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), mover_name(), protocols::moves::Mover::name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::simple_moves::RingConformationMoverCreator::provide_xml_schema().

void protocols::simple_moves::RingConformationMover::register_options ( )

static

Register options with the option system.

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

bool protocols::simple_moves::RingConformationMover::sample_all_conformers ( ) const

inline

Get whether or not this Mover will sample all ring conformers, regardless of energy.

References sample_all_conformers_.

void protocols::simple_moves::RingConformationMover::sample_all_conformers ( bool setting )

inline

Set whether or not this Mover will sample all ring conformers, regardless of energy.

References sample_all_conformers_.

void protocols::simple_moves::RingConformationMover::set_commandline_options ( )

private

References locked_, and sample_all_conformers_.

Referenced by init().

void protocols::simple_moves::RingConformationMover::setup_residue_list ( core::pose::Pose const & pose )

private

References movemap(), core::pose::Pose::residue(), residue_list_, and core::pose::Pose::size().

Referenced by apply().

void protocols::simple_moves::RingConformationMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Generate string representation of RingConformationMover for debugging purposes.

Reimplemented from protocols::moves::Mover.

References locked_, sample_all_conformers_, and protocols::moves::Mover::show().

Referenced by apply(), and protocols::simple_moves::operator<<().

Member Data Documentation

bool protocols::simple_moves::RingConformationMover::locked_

private

Referenced by apply(), copy_data(), init(), set_commandline_options(), and show().

core::kinematics::MoveMapOP protocols::simple_moves::RingConformationMover::movemap_

private

Referenced by copy_data(), and movemap().

core::select::movemap::MoveMapFactoryCOP protocols::simple_moves::RingConformationMover::movemap_factory_

private

Referenced by copy_data(), movemap(), and movemap_factory().

utility::vector1< core::Size > protocols::simple_moves::RingConformationMover::residue_list_

private

Referenced by apply(), copy_data(), and setup_residue_list().

bool protocols::simple_moves::RingConformationMover::sample_all_conformers_

private

Referenced by apply(), copy_data(), init(), parse_my_tag(), sample_all_conformers(), set_commandline_options(), and show().

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

src/protocols/simple_moves/RingConformationMover.hh
src/protocols/simple_moves/RingConformationMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation