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protocols::rbsegment_relax::SequenceShiftMover Class Reference

#include <RBSegmentMover.hh>

Inheritance diagram for protocols::rbsegment_relax::SequenceShiftMover:
Inheritance graph
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Public Member Functions

 SequenceShiftMover (RBSegment const &seg, core::Size magnitude=4)
 constructor More...
 
 SequenceShiftMover (core::pose::Pose const &pose_in, RBSegment const &seg, core::Size magnitude=4)
 constructor More...
 
 SequenceShiftMover (RBResidueRange const &rb, core::Size magnitude=4)
 constructor More...
 
 SequenceShiftMover ()
 
protocols::moves::MoverOP clone () const override
 clone this object More...
 
void set_movement (core::Real, core::Real, core::Real, core::Real) override
 set movement parameters. ignore all input args More...
 
void apply (core::pose::Pose &pose) override
 Apply a + or - residue "shift" to this helix. More...
 
void apply (core::pose::Pose &pose, int shift)
 Apply a + or - residue "shift" to this helix. More...
 
void set_extra_penalty (utility::vector1< bool > const &penalty_res)
 Set an extra block-shift penalty at certain residues. More...
 
void trigger_accept ()
 Last move accepted; update offsets_. More...
 
int score (bool step_fn=false)
 Return a score: the minimum number of block shifts accumulated. More...
 
void set_verbose (bool inval)
 
loops::LoopsOP get_residues_to_rebuild ()
 IF ref_pose is given, get a list of residues to rebuild via fragment insertion. 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 getCoordinateTransformation (core::pose::Pose const &, numeric::xyzVector< core::Real > &rotationCenter, numeric::xyzMatrix< core::Real > &coordinateTransform)
 Returns: (a) the matrix that rotates global coordinates into local fragment coordinates and (b) the center of rotation of the fragment. Default implementation sets them to global coords. 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 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...
 
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 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

std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 

Private Attributes

core::Size magnitude_
 
int last_move_
 
core::pose::Pose ref_pose_
 
utility::vector1< int > offsets_
 
utility::vector1< boolpenalty_res_
 
bool verbose_
 

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::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

"Register shift" a segment by one amino-acid Works in both centroid and all-atom

Constructor & Destructor Documentation

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover ( RBSegment const &  seg,
core::Size  magnitude = 4 
)
inline

constructor

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover ( core::pose::Pose const &  pose_in,
RBSegment const &  seg,
core::Size  magnitude = 4 
)
inline
protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover ( RBResidueRange const &  rb,
core::Size  magnitude = 4 
)
inline

constructor

protocols::rbsegment_relax::SequenceShiftMover::SequenceShiftMover ( )
inline

Member Function Documentation

void protocols::rbsegment_relax::SequenceShiftMover::apply ( core::pose::Pose pose)
overridevirtual

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

Apply a "register shift" move to this fragment.

Implements protocols::rbsegment_relax::RBSegmentMover.

References core::scoring::rg.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

void protocols::rbsegment_relax::SequenceShiftMover::apply ( core::pose::Pose pose,
int  shift 
)
protocols::moves::MoverOP protocols::rbsegment_relax::SequenceShiftMover::clone ( ) const
inlineoverridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

std::string protocols::rbsegment_relax::SequenceShiftMover::get_name ( ) const
overrideprivatevirtual

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

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

loops::LoopsOP protocols::rbsegment_relax::SequenceShiftMover::get_residues_to_rebuild ( )

IF ref_pose is given, get a list of residues to rebuild via fragment insertion.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

int protocols::rbsegment_relax::SequenceShiftMover::score ( bool  step_fn = false)

Return a score: the minimum number of block shifts accumulated.

References protocols::loops::start.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

void protocols::rbsegment_relax::SequenceShiftMover::set_extra_penalty ( utility::vector1< bool > const &  penalty_res)
inline

Set an extra block-shift penalty at certain residues.

References penalty_res_.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

void protocols::rbsegment_relax::SequenceShiftMover::set_movement ( core::Real  ,
core::Real  ,
core::Real  ,
core::Real   
)
inlineoverridevirtual

set movement parameters. ignore all input args

Reimplemented from protocols::rbsegment_relax::RBSegmentMover.

void protocols::rbsegment_relax::SequenceShiftMover::set_verbose ( bool  inval)
inline

References verbose_.

void protocols::rbsegment_relax::SequenceShiftMover::trigger_accept ( )

Last move accepted; update offsets_.

References protocols::loops::start.

Referenced by protocols::rbsegment_relax::OptimizeThreadingMover::apply().

Member Data Documentation

int protocols::rbsegment_relax::SequenceShiftMover::last_move_
private
core::Size protocols::rbsegment_relax::SequenceShiftMover::magnitude_
private
utility::vector1< int > protocols::rbsegment_relax::SequenceShiftMover::offsets_
private

Referenced by SequenceShiftMover().

utility::vector1< bool > protocols::rbsegment_relax::SequenceShiftMover::penalty_res_
private

Referenced by set_extra_penalty().

core::pose::Pose protocols::rbsegment_relax::SequenceShiftMover::ref_pose_
private
bool protocols::rbsegment_relax::SequenceShiftMover::verbose_
private

Referenced by set_verbose().


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