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protocols::rigid::RigidBodyMotionMover Class Reference

#include <RigidBodyMotionMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyMotionMover:
Inheritance graph
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Public Member Functions

 RigidBodyMotionMover (const core::kinematics::FoldTree &tree)
 
void apply (core::pose::Pose &pose) override
 Randomly selects a chunk and perturbs its rigid body transformation. More...
 
core::Real magnitude_translation () const
 Returns the magnitude of translation. More...
 
core::Real magnitude_rotation () const
 Returns the magnitude of rotation. More...
 
core::Real chainbreak_bias () const
 Returns the strength of the chainbreak bias. More...
 
const core::kinematics::FoldTreefold_tree () const
 Returns the input fold tree. More...
 
void set_magnitude_translation (core::Real mag_trans)
 Updates the magnitude of translation. More...
 
void set_magnitude_rotation (core::Real mag_rot)
 Updates the magnitude of rotation. More...
 
void set_chainbreak_bias (core::Real 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 override
 Returns the name of this mover. 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void update_chunks ()
 Derives chunk definitions from input fold tree. More...
 
void compute_bias (core::Size i, const core::pose::Pose &pose, numeric::xyzVector< core::Real > *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...
 
core::Real mag_rot_
 Magnitude of rotation. Unless otherwise specified, equal to -rigid:rotation. More...
 
core::Real mag_trans_
 Magnitude of translation. Unless otherwise specified, equal to -rigid:translation. More...
 
core::Real 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::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
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...
 

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::rigid::RigidBodyMotionMover::apply ( core::pose::Pose pose)
overridevirtual
core::Real protocols::rigid::RigidBodyMotionMover::chainbreak_bias ( ) const

Returns the strength of the chainbreak bias.

References cb_bias_.

Referenced by compute_bias().

void protocols::rigid::RigidBodyMotionMover::compute_bias ( core::Size  i,
const core::pose::Pose pose,
numeric::xyzVector< core::Real > *  cb_deltas 
) const
private
const core::kinematics::FoldTree & protocols::rigid::RigidBodyMotionMover::fold_tree ( ) const

Returns the input fold tree.

References tree_.

Referenced by apply().

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

Returns the name of this mover.

Implements protocols::moves::Mover.

core::Real protocols::rigid::RigidBodyMotionMover::magnitude_rotation ( ) const

Returns the magnitude of rotation.

References mag_rot_.

Referenced by apply().

core::Real protocols::rigid::RigidBodyMotionMover::magnitude_translation ( ) const

Returns the magnitude of translation.

References mag_trans_.

Referenced by apply().

void protocols::rigid::RigidBodyMotionMover::set_chainbreak_bias ( core::Real  cb_bias)

Updates the strength of the chainbreak bias.

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.

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

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::set_magnitude_rotation ( core::Real  mag_rot)

Updates the magnitude of rotation.

References mag_rot_.

Referenced by RigidBodyMotionMover().

void protocols::rigid::RigidBodyMotionMover::set_magnitude_translation ( core::Real  mag_trans)

Updates the magnitude of translation.

References mag_trans_.

Referenced by RigidBodyMotionMover().

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

Member Data Documentation

core::Real protocols::rigid::RigidBodyMotionMover::cb_bias_
private

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

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.

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

core::Real protocols::rigid::RigidBodyMotionMover::mag_rot_
private

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

Referenced by magnitude_rotation(), and set_magnitude_rotation().

core::Real protocols::rigid::RigidBodyMotionMover::mag_trans_
private

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

Referenced by magnitude_translation(), and set_magnitude_translation().

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

Input fold tree.

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


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