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protocols::rbsegment_relax::GaussianRBSegmentMover Class Reference

#include <RBSegmentMover.hh>

Inheritance diagram for protocols::rbsegment_relax::GaussianRBSegmentMover:
Inheritance graph
Collaboration diagram for protocols::rbsegment_relax::GaussianRBSegmentMover:
Collaboration graph

Public Member Functions

 GaussianRBSegmentMover (RBSegment const &seg, core::Real sigR=0.0, core::Real sigT=0.0)
 constructor More...
 GaussianRBSegmentMover (core::Real sigR=0.0, core::Real sigT=0.0)
virtual void set_movement (core::Real sigAxisR=0.0, core::Real sigAxisT=0.0, core::Real sigOffAxisR=0.0, core::Real sigOffAxisT=0.0)
 set movement parameters More...
virtual protocols::moves::MoverOP clone () const
 clone this object More...
void apply (core::pose::Pose &pose)
 Randomly perturb the segment. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void getCoordinateTransformation (core::pose::Pose const &pose, numeric::xyzVector< core::Real > &rotationCenter, numeric::xyzMatrix< core::Real > &coordinateTransform)
 Get the fragment center / matrix that rotates global coordinates into local fragment coordinates. Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue. More...
- Public Member Functions inherited from protocols::rbsegment_relax::RBSegmentMover
 RBSegmentMover ()
 constructor More...
 RBSegmentMover (RBSegment const &seg)
 constructor More...
virtual void set_movement (RBSegment const &rb)
 steal movement params from a segment definition More...
void applyRotation (core::pose::Pose &pose, core::Real alpha, core::Real beta, core::Real gamma)
 Apply an arbitrary rotation specified by Euler angles (in degrees!) More...
void applyRotation (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > rotation)
 Apply an arbitrary rotation specified by a rotation matrix. More...
void applyTranslation (core::pose::Pose &pose, numeric::xyzVector< core::Real > translation)
 Apply an arbitrary translation. More...
void applyTransformation (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > rotation, numeric::xyzVector< core::Real > translation)
 Apply a rotation followed by a translation (does not recompute coordinate transformation between the two!) More...
void applySpin (core::pose::Pose &pose, numeric::xyzVector< core::Real > rotationAxis, core::Real degrees)
 Apply a spin of the specified angle (in degrees) about arbitrary axis. More...
void setResidueRange (RBSegment const &seg)
 (re)set the starting and ending residues of this transform More...
RBSegment const & getResidueRange ()
 Get the the starting and ending residues of transform. More...
void print ()
 Print debugging info. 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)
Moveroperator= (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 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 Stringsinfo ()
 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 Attributes

core::Real sigma_rot
core::Real sigma_trans

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 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::rbsegment_relax::RBSegmentMover
numeric::xyzVector< core::RealgetCoM (core::pose::Pose const &pose)
 Helper function computes center of mass of the segment in the pose. More...
- Static Protected Member Functions inherited from protocols::rbsegment_relax::RBSegmentMover
static numeric::xyzMatrix
< core::Real
coordTransformFromThreePoints (numeric::xyzVector< core::Real > ori, numeric::xyzVector< core::Real > zAxis, numeric::xyzVector< core::Real > xzPlane)
 Helper function to get a coordinate transformation from 3 points: the origin, a point specifying the +z axis, and a point specifying the x-z plane. More...
- Protected Attributes inherited from protocols::rbsegment_relax::RBSegmentMover
RBSegment segment_

Detailed Description

Generic random segment mover

Constructor & Destructor Documentation

protocols::rbsegment_relax::GaussianRBSegmentMover::GaussianRBSegmentMover ( RBSegment const &  seg,
core::Real  sigR = 0.0,
core::Real  sigT = 0.0 


  • sigT: the stdev of movement along the helical axis
  • sigR: the stdev of rotation along the helical axis

Referenced by clone().

protocols::rbsegment_relax::GaussianRBSegmentMover::GaussianRBSegmentMover ( core::Real  sigR = 0.0,
core::Real  sigT = 0.0 

Member Function Documentation

void protocols::rbsegment_relax::GaussianRBSegmentMover::apply ( core::pose::Pose pose)

Randomly perturb the segment.

Apply a random rigid-body transformation to an arbitrary segment.

Implements protocols::rbsegment_relax::RBSegmentMover.

References protocols::rbsegment_relax::rbseg_RG(), and trans().

virtual protocols::moves::MoverOP protocols::rbsegment_relax::GaussianRBSegmentMover::clone ( ) const

clone this object

Reimplemented from protocols::moves::Mover.

References GaussianRBSegmentMover().

std::string protocols::rbsegment_relax::GaussianRBSegmentMover::get_name ( ) const

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

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

void protocols::rbsegment_relax::GaussianRBSegmentMover::getCoordinateTransformation ( core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > &  rotationCenter,
numeric::xyzMatrix< core::Real > &  coordinateTransform 

Get the fragment center / matrix that rotates global coordinates into local fragment coordinates. Defined such that +z points to the C-terminal end of the helix axis, +x from the helix axis to the N-terminal residue.

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

virtual void protocols::rbsegment_relax::GaussianRBSegmentMover::set_movement ( core::Real  sigAxisR = 0.0,
core::Real  sigAxisT = 0.0,
core::Real  sigOffAxisR = 0.0,
core::Real  sigOffAxisT = 0.0 

set movement parameters

  • sigR: the stdev of rotation
  • sigT: the stdev of movement

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

References sigma_rot, and sigma_trans.

Member Data Documentation

core::Real protocols::rbsegment_relax::GaussianRBSegmentMover::sigma_rot

Referenced by set_movement().

core::Real protocols::rbsegment_relax::GaussianRBSegmentMover::sigma_trans

Referenced by set_movement().

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