does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump. More...

#include <RigidBodyMover.hh>

Public Member Functions
	RigidBodyPerturbNoCenterMover ()

	RigidBodyPerturbNoCenterMover (int const rb_jump_in, core::Real const rot_mag_in, core::Real const trans_mag_in)

	RigidBodyPerturbNoCenterMover (core::pose::Pose const &pose_in, core::kinematics::MoveMap const &mm, core::Real const rot_mag_in, core::Real const trans_mag_in, Direction dir_in)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

	RigidBodyPerturbNoCenterMover (RigidBodyPerturbNoCenterMover const &src)

virtual	~RigidBodyPerturbNoCenterMover ()

virtual void	apply (core::pose::Pose &pose)

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

void	rot_magnitude (core::Real const magnitude)

void	trans_magnitude (core::Real const magnitude)

void	add_jump (core::Size)

void	clear_jumps ()

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

Public Member Functions inherited from protocols::rigid::RigidBodyMover
	RigidBodyMover ()

	RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)

	RigidBodyMover (RigidBodyMover const &src)

virtual	~RigidBodyMover ()

void	rot_center (core::Vector const rot_center_in)
	Manual override of rotation center. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual bool	preserve_detailed_balance () const
	Return true if detailed balance is being preserved (i.e. no branch angle optimization). More...

virtual void	set_preserve_detailed_balance (bool)
	set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

int	rb_jump () const

void	rb_jump (int jump_id)

void	unfreeze ()

void	freeze ()

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()
	Default constructor. More...

virtual	~ThermodynamicMover ()
	Default destructor. More...

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	Callback executed before any Monte Carlo trials are attempted. More...

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after the Metropolis criterion is evaluated. More...

virtual core::Real	last_proposal_density_ratio ()
	Return the proposal density ratio for last apply method. More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	Callback executed after all Monte Carlo trials are completed. More...

virtual bool	is_multi_trial ()
	Return true if the move performs multiple trials on each apply. More...

virtual core::Real	last_inner_score_temperature_delta ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Attributes
core::Real	rot_mag_
	perturbation magnitudes (rotational and translational) More...

core::Real	trans_mag_

Protected Attributes inherited from protocols::rigid::RigidBodyMover
int	rb_jump_

Direction	dir_
	direction of folding (n-term to c-term) More...

core::Vector	rot_center_
	center of rotation More...

bool	freeze_

Private Types
typedef RigidBodyMover	Parent

typedef utility::vector1 < core::Size >	JumpList

Private Attributes
JumpList	movable_jumps_

Additional Inherited Members
Public Types inherited from protocols::rigid::RigidBodyMover
typedef ThermodynamicMover	parent

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

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...

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

does a perturbation defined by the rotational and translational magnitudes without setting up the center Can be defined through a move map or with rb_jump Defining through a movemap with multiple jumps leads to a random jump being chosen at apply time, NOT at construction time! This is done to simplify docking with more than one active jump.

Member Typedef Documentation

typedef utility::vector1< core::Size > protocols::rigid::RigidBodyPerturbNoCenterMover::JumpList

private

typedef RigidBodyMover protocols::rigid::RigidBodyPerturbNoCenterMover::Parent

private

Constructor & Destructor Documentation

protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover ( )

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

Referenced by clone().

protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover	(	int const	rb_jump_in,
		core::Real const	rot_mag_in,
		core::Real const	trans_mag_in
	)

References movable_jumps_, and protocols::moves::Mover::type().

protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover	(	core::pose::Pose const &	pose_in,
		core::kinematics::MoveMap const &	mm,
		core::Real const	rot_mag_in,
		core::Real const	trans_mag_in,
		Direction	dir_in
	)

constructor for the rbm that doesn't set a center

References protocols::rigid::RigidBodyMover::dir_, core::kinematics::MoveMap::get_jump(), movable_jumps_, core::pose::Pose::num_jump(), protocols::rigid::TRBM, and protocols::moves::Mover::type().

protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover ( RigidBodyPerturbNoCenterMover const & src )

protocols::rigid::RigidBodyPerturbNoCenterMover::~RigidBodyPerturbNoCenterMover ( )

virtual

Member Function Documentation

void protocols::rigid::RigidBodyPerturbNoCenterMover::add_jump ( core::Size jump_id )

References movable_jumps_.

void protocols::rigid::RigidBodyPerturbNoCenterMover::apply ( core::pose::Pose & pose )

virtual

Implements protocols::rigid::RigidBodyMover.

References protocols::rigid::RigidBodyMover::dir_, core::kinematics::Jump::gaussian_move(), core::pose::Pose::jump(), movable_jumps_, numeric::random::RandomGenerator::random_element(), protocols::rigid::RigidBodyMover::rb_jump_, protocols::rigid::RG, rot_mag_, core::pose::Pose::set_jump(), protocols::rigid::TR, and trans_mag_.

void protocols::rigid::RigidBodyPerturbNoCenterMover::clear_jumps ( )

References movable_jumps_.

moves::MoverOP protocols::rigid::RigidBodyPerturbNoCenterMover::clone ( ) const

virtual

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.

References RigidBodyPerturbNoCenterMover().

std::string protocols::rigid::RigidBodyPerturbNoCenterMover::get_name ( ) const

virtual

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

Reimplemented from protocols::rigid::RigidBodyMover.

void protocols::rigid::RigidBodyPerturbNoCenterMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References rot_mag_, and trans_mag_.

void protocols::rigid::RigidBodyPerturbNoCenterMover::rot_magnitude ( core::Real const magnitude )

inline

References rot_mag_.

void protocols::rigid::RigidBodyPerturbNoCenterMover::trans_magnitude ( core::Real const magnitude )

inline

References trans_mag_.