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protocols::membrane::RotationMover Class Reference

Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors. More...

#include <TranslationRotationMover.hh>

Inheritance diagram for protocols::membrane::RotationMover:
Inheritance graph
[legend]

Public Member Functions

 RotationMover ()
 Constructors ///. More...
 
 RotationMover (core::Vector old_normal, core::Vector new_normal, core::Vector rot_center)
 Custom Constructor. More...
 
 RotationMover (core::Vector old_normal, core::Vector new_normal, core::Vector rot_center, core::Size jumpnum)
 Custom Constructor. More...
 
 RotationMover (RotationMover const &src)
 Copy Constructor. More...
 
 ~RotationMover () override
 Destructor. More...
 
protocols::moves::MoverOP clone () const override
 Rosetta Scripts Methods ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Create a Fresh Instance of this Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Pase Rosetta Scripts Options for this Mover. More...
 
std::string get_name () const override
 Mover Methods ///. More...
 
void apply (core::pose::Pose &pose) override
 Rotate the pose - see above. 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 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 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...
 

Private Member Functions

void register_options ()
 Setup Methods ///. More...
 
void init_from_cmd ()
 Initialize Mover options from the commandline. More...
 

Private Attributes

core::Vector old_normal_
 
core::Vector new_normal_
 
core::Vector rot_center_
 
core::Size jumpnum_
 

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...
 

Detailed Description

Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors.

Constructor & Destructor Documentation

protocols::membrane::RotationMover::RotationMover ( )

Constructors ///.

Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors.

Default Constructor

Uses the -mp:setup center and normal flags

References init_from_cmd(), and register_options().

protocols::membrane::RotationMover::RotationMover ( core::Vector  old_normal,
core::Vector  new_normal,
core::Vector  rot_center 
)

Custom Constructor.

User can specify an old normal, a new normal, and a new center around which the rotation takes place

References init_from_cmd(), and register_options().

protocols::membrane::RotationMover::RotationMover ( core::Vector  old_normal,
core::Vector  new_normal,
core::Vector  rot_center,
core::Size  jumpnum 
)

Custom Constructor.

User can specify an old normal, a new normal, and a new center around which the rotation takes place on this particular jump; operation happens on the downstream stub

References init_from_cmd(), and register_options().

protocols::membrane::RotationMover::RotationMover ( RotationMover const &  src)
default

Copy Constructor.

Create a deep copy of this mover

protocols::membrane::RotationMover::~RotationMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::membrane::RotationMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::membrane::RotationMover::clone ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::membrane::RotationMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

std::string protocols::membrane::RotationMover::get_name ( ) const
overridevirtual

Mover Methods ///.

Get the name of this Mover (RotationMover)

Get the name of this Mover

Implements protocols::moves::Mover.

void protocols::membrane::RotationMover::init_from_cmd ( )
private

Initialize Mover options from the commandline.

Initialize mover settings from the commandline using the mp:setup center and normal flags

Initialize mover settings from the commandline using the mp:setup center flag

References new_normal_, protocols::membrane::read_center_normal_from_cmd(), and rot_center_.

Referenced by RotationMover().

void protocols::membrane::RotationMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References new_normal_, protocols::membrane::read_center_normal_from_tag(), and rot_center_.

void protocols::membrane::RotationMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp:setup options: center and normal

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp:setup options: center

References core::conformation::membrane::center, and core::conformation::membrane::normal.

Referenced by RotationMover().

Member Data Documentation

core::Size protocols::membrane::RotationMover::jumpnum_
private

Referenced by apply().

core::Vector protocols::membrane::RotationMover::new_normal_
private

Referenced by apply(), init_from_cmd(), and parse_my_tag().

core::Vector protocols::membrane::RotationMover::old_normal_
private

Referenced by apply().

core::Vector protocols::membrane::RotationMover::rot_center_
private

Referenced by apply(), init_from_cmd(), and parse_my_tag().


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