#include <RigidBodyMotionMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyMotionMover:

Collaboration diagram for protocols::rigid::RigidBodyMotionMover:

Public Member Functions
	RigidBodyMotionMover (const core::kinematics::FoldTree &tree)

void	apply (core::pose::Pose &pose)
	Randomly selects a chunk and perturbs its rigid body transformation. More...

double	magnitude_translation () const
	Returns the magnitude of translation. More...

double	magnitude_rotation () const
	Returns the magnitude of rotation. More...

double	chainbreak_bias () const
	Returns the strength of the chainbreak bias. More...

const core::kinematics::FoldTree &	fold_tree () const
	Returns the input fold tree. More...

void	set_magnitude_translation (double mag_trans)
	Updates the magnitude of translation. More...

void	set_magnitude_rotation (double mag_rot)
	Updates the magnitude of rotation. More...

void	set_chainbreak_bias (double cb_bias)
	Updates the strength of the chainbreak bias. More...

void	set_fold_tree (const core::kinematics::FoldTree &tree)
	Updates the input fold tree and regenerates chunks. More...

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

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	update_chunks ()
	Derives chunk definitions from input fold tree. More...

void	compute_bias (unsigned i, const core::pose::Pose &pose, numeric::xyzVector< double > *cb_deltas) const
	Having selected chunk i, compute the chainbreak-biased translation vector. More...

Private Attributes
core::kinematics::FoldTree	tree_
	Input fold tree. More...

protocols::loops::Loops	chunks_
	Chunks derived from input fold tree. Stored in increasing order of start position. More...

double	mag_rot_
	Magnitude of rotation. Unless otherwise specified, equal to -rigid:rotation. More...

double	mag_trans_
	Magnitude of translation. Unless otherwise specified, equal to -rigid:translation. More...

double	cb_bias_
	Value on [0..1] that controls the strength of the chainbreak bias in translation moves. More...

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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

Definition at line 35 of file RigidBodyMotionMover.hh.

Constructor & Destructor Documentation

protocols::rigid::RigidBodyMotionMover::RigidBodyMotionMover ( const core::kinematics::FoldTree & tree)

explicit

Definition at line 59 of file RigidBodyMotionMover.cc.

References set_chainbreak_bias(), set_fold_tree(), set_magnitude_rotation(), and set_magnitude_translation().

Member Function Documentation

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

virtual

Randomly selects a chunk and perturbs its rigid body transformation.

Implements protocols::moves::Mover.

Definition at line 72 of file RigidBodyMotionMover.cc.

References chunks_, compute_bias(), fold_tree(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), magnitude_rotation(), magnitude_translation(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rb_delta(), protocols::loops::Loops::size(), and protocols::rigid::TR().

double protocols::rigid::RigidBodyMotionMover::chainbreak_bias ( ) const

Returns the strength of the chainbreak bias.

Definition at line 172 of file RigidBodyMotionMover.cc.

References cb_bias_.

Referenced by compute_bias().

void protocols::rigid::RigidBodyMotionMover::compute_bias	(	unsigned	i,
		const core::pose::Pose &	pose,
		numeric::xyzVector< double > *	cb_deltas
	)		const

private

Having selected chunk i, compute the chainbreak-biased translation vector.

Definition at line 112 of file RigidBodyMotionMover.cc.

References protocols::rigid::angle_between(), protocols::match::upstream::b, chainbreak_bias(), chunks_, protocols::loops::Loops::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::xyz().

Referenced by apply().

const core::kinematics::FoldTree & protocols::rigid::RigidBodyMotionMover::fold_tree ( ) const

Returns the input fold tree.

Definition at line 176 of file RigidBodyMotionMover.cc.

References tree_.

Referenced by apply().

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

virtual

Returns the name of this mover.

Implements protocols::moves::Mover.

Definition at line 202 of file RigidBodyMotionMover.cc.

double protocols::rigid::RigidBodyMotionMover::magnitude_rotation ( ) const

Returns the magnitude of rotation.

Definition at line 164 of file RigidBodyMotionMover.cc.

References mag_rot_.

Referenced by apply().

double protocols::rigid::RigidBodyMotionMover::magnitude_translation ( ) const

Returns the magnitude of translation.

Definition at line 168 of file RigidBodyMotionMover.cc.

References mag_trans_.

Referenced by apply().

void protocols::rigid::RigidBodyMotionMover::set_chainbreak_bias ( double cb_bias)

Updates the strength of the chainbreak bias.

Definition at line 190 of file RigidBodyMotionMover.cc.

References cb_bias_.

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::set_fold_tree ( const core::kinematics::FoldTree & tree)

Updates the input fold tree and regenerates chunks.

Definition at line 196 of file RigidBodyMotionMover.cc.

References core::kinematics::FoldTree::check_fold_tree(), tree_, and update_chunks().

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::set_magnitude_rotation ( double mag_rot)

Updates the magnitude of rotation.

Definition at line 180 of file RigidBodyMotionMover.cc.

References mag_rot_.

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::set_magnitude_translation ( double mag_trans)

Updates the magnitude of translation.

Definition at line 185 of file RigidBodyMotionMover.cc.

References mag_trans_.

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::update_chunks ( )

private

Derives chunk definitions from input fold tree.

Definition at line 151 of file RigidBodyMotionMover.cc.

References protocols::loops::Loops::add_loop(), chunks_, protocols::loops::Loops::clear(), core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::num_cutpoint(), protocols::loops::Loops::sequential_order(), protocols::loops::start, protocols::loops::stop, and tree_.

Referenced by set_fold_tree().

Member Data Documentation

double protocols::rigid::RigidBodyMotionMover::cb_bias_

private

Value on [0..1] that controls the strength of the chainbreak bias in translation moves.

Definition at line 89 of file RigidBodyMotionMover.hh.

Referenced by chainbreak_bias(), and set_chainbreak_bias().

protocols::loops::Loops protocols::rigid::RigidBodyMotionMover::chunks_

private

Chunks derived from input fold tree. Stored in increasing order of start position.

Definition at line 80 of file RigidBodyMotionMover.hh.

Referenced by apply(), compute_bias(), and update_chunks().

double protocols::rigid::RigidBodyMotionMover::mag_rot_

private

Magnitude of rotation. Unless otherwise specified, equal to -rigid:rotation.

Definition at line 83 of file RigidBodyMotionMover.hh.

Referenced by magnitude_rotation(), and set_magnitude_rotation().

double protocols::rigid::RigidBodyMotionMover::mag_trans_

private

Magnitude of translation. Unless otherwise specified, equal to -rigid:translation.

Definition at line 86 of file RigidBodyMotionMover.hh.

Referenced by magnitude_translation(), and set_magnitude_translation().

core::kinematics::FoldTree protocols::rigid::RigidBodyMotionMover::tree_

private

Input fold tree.

Definition at line 77 of file RigidBodyMotionMover.hh.

Referenced by fold_tree(), set_fold_tree(), and update_chunks().

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

src/protocols/rigid/RigidBodyMotionMover.hh
src/protocols/rigid/RigidBodyMotionMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation