Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::rbsegment_relax::HelicalGaussianMover Class Reference

#include <RBSegmentMover.hh>

Public Member Functions

 HelicalGaussianMover (RBSegment const &seg, core::Real sigAxisR=0.0, core::Real sigAxisT=0.0, core::Real sigOffAxisR=0.0, core::Real sigOffAxisT=0.0)
 constructor: More...
 
 HelicalGaussianMover (core::Real sigAxisR=0.0, core::Real sigAxisT=0.0, core::Real sigOffAxisR=0.0, core::Real sigOffAxisT=0.0)
 constructor: More...
 
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
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose)
 Apply a +1 or -1 residue "shift" to this helix. 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_segment (RBSegment const &seg)
 Set the segment this mover is working on. 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
 
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)
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Attributes

core::Real sigAxisT_
 
core::Real sigAxisR_
 
core::Real sigOffAxisT_
 
core::Real sigOffAxisR_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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::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...
 
- 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...
 
- 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

Random movements wrt the helical axis

Constructor & Destructor Documentation

protocols::rbsegment_relax::HelicalGaussianMover::HelicalGaussianMover ( RBSegment const &  seg,
core::Real  sigAxisR = 0.0,
core::Real  sigAxisT = 0.0,
core::Real  sigOffAxisR = 0.0,
core::Real  sigOffAxisT = 0.0 
)
inline

constructor:

  • sigAxisR: the stdev of rotation along the helical axis
  • sigAxisT: the stdev of movement along the helical axis
  • sigOffAxisR: the stdev of rotation normal to the helical axis
  • sigOffAxisT: the stdev of movement normal to the helical axis

Referenced by clone().

protocols::rbsegment_relax::HelicalGaussianMover::HelicalGaussianMover ( core::Real  sigAxisR = 0.0,
core::Real  sigAxisT = 0.0,
core::Real  sigOffAxisR = 0.0,
core::Real  sigOffAxisT = 0.0 
)
inline

constructor:

  • sigAxisR: the stdev of rotation along the helical axis
  • sigAxisT: the stdev of movement along the helical axis
  • sigOffAxisR: the stdev of rotation normal to the helical axis
  • sigOffAxisT: the stdev of movement normal to the helical axis

Member Function Documentation

void protocols::rbsegment_relax::HelicalGaussianMover::apply ( core::pose::Pose pose)
virtual

Apply a +1 or -1 residue "shift" to this helix.

Helical-axis segment movers.

Implements protocols::rbsegment_relax::RBSegmentMover.

References numeric::random::RandomGenerator::gaussian(), protocols::rbsegment_relax::rbseg_RG, protocols::rbsegment_relax::TR, and trans().

virtual protocols::moves::MoverOP protocols::rbsegment_relax::HelicalGaussianMover::clone ( ) const
inlinevirtual

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 HelicalGaussianMover().

std::string protocols::rbsegment_relax::HelicalGaussianMover::get_name ( ) const
virtual

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

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

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

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.

References numeric::xyzMatrix< class >::clear(), exit, nres, core::pose::Pose::residue(), protocols::rbsegment_relax::TR, numeric::xyzMatrix< class >::xx(), core::conformation::Residue::xyz(), numeric::xyzMatrix< class >::yy(), and numeric::xyzMatrix< class >::zz().

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

set movement parameters

  • sigAxisR: the stdev of rotation along the helical axis
  • sigAxisT: the stdev of movement along the helical axis
  • sigOffAxisR: the stdev of rotation normal to the helical axis
  • sigOffAxisT: the stdev of movement normal to the helical axis

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

References sigAxisR_, sigAxisT_, sigOffAxisR_, and sigOffAxisT_.

Member Data Documentation

core::Real protocols::rbsegment_relax::HelicalGaussianMover::sigAxisR_
private

Referenced by set_movement().

core::Real protocols::rbsegment_relax::HelicalGaussianMover::sigAxisT_
private

Referenced by set_movement().

core::Real protocols::rbsegment_relax::HelicalGaussianMover::sigOffAxisR_
private

Referenced by set_movement().

core::Real protocols::rbsegment_relax::HelicalGaussianMover::sigOffAxisT_
private

Referenced by set_movement().


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