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Rosetta 3.5
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Rosetta 3.5
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#include <RotateJumpAxisMover.hh>
Public Member Functions | |
| RotateJumpAxisMover (core::Size const rb_jump_num) | |
| constructor for random distribution (just needs rb_jump_num) More... | |
| RotateJumpAxisMover (core::Size const rb_jump_num, core::Angle const upper, core::Angle const lower) | |
| constructor for range - these angles are in degrees, not radians! More... | |
| RotateJumpAxisMover (core::Size const rb_jump_num, core::Angle const angle) | |
| constructor for single value - these angles are in degrees, not radians! More... | |
| virtual | ~RotateJumpAxisMover () |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. 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) | |
| Mover & | operator= (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 MoverOP | clone () const |
| clone has to be overridden only if clone invocation is expected. More... | |
| 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 Strings & | info () |
| 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 Member Functions | |
| core::Angle | calc_angle () |
Private Attributes | |
| core::Size const | rb_jump_num_ |
| core::Angle const | upper_angle_ |
| core::Angle const | lower_angle_ |
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 protocols::filters::Filters_map | Filters_map |
| 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::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... | |
This mover rotates a jump transform. Its original use was to rotate a freely rotateable zinc-histidine bond as emulated by an atom-to-atom fixed-length jump. It recalculates the Stubs for the jump and applies the new jump, resulting in an N degree rotation of one partner about the axis between the histidine nitrogen and the zinc. It will work for any jump but is intended for atom-atom jumps (not residue-residue jumps). It will choose an angle from the uniform random distribution bounded by inputs (defaults to (-180,180]); if you want a particular value then set the limits equal.
Definition at line 34 of file RotateJumpAxisMover.hh.
| protocols::rigid::RotateJumpAxisMover::RotateJumpAxisMover | ( | core::Size const | rb_jump_num) |
constructor for random distribution (just needs rb_jump_num)
random angle constructor. rb_jump_num is the number of the jump. Magic numbers 180 and -179.9999999... maintain the uniform range. I'm sure there's a better way to get [180, -180) but I can't figure out what it is.
Definition at line 102 of file RotateJumpAxisMover.cc.
| protocols::rigid::RotateJumpAxisMover::RotateJumpAxisMover | ( | core::Size const | rb_jump_num, |
| core::Angle const | upper, | ||
| core::Angle const | lower | ||
| ) |
constructor for range - these angles are in degrees, not radians!
range of angles constructor - takes DEGREES not RADIANS. rb_jump_num is the number of the jump.
Definition at line 107 of file RotateJumpAxisMover.cc.
| protocols::rigid::RotateJumpAxisMover::RotateJumpAxisMover | ( | core::Size const | rb_jump_num, |
| core::Angle const | angle | ||
| ) |
constructor for single value - these angles are in degrees, not radians!
particular angle constructor - takes DEGREES not RADIANS. rb_jump_num is the number of the jump.
Definition at line 112 of file RotateJumpAxisMover.cc.
References protocols::moves::Mover::type().
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virtual |
Definition at line 116 of file RotateJumpAxisMover.cc.
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Implements protocols::moves::Mover.
Definition at line 54 of file RotateJumpAxisMover.cc.
References calc_angle(), core::pose::Pose::conformation(), core::conformation::Conformation::downstream_jump_stub(), core::pose::Pose::fold_tree(), core::conformation::get_anchor_and_root_atoms(), core::kinematics::FoldTree::jump_edge(), rb_jump_num_, core::pose::Pose::residue(), core::pose::Pose::set_jump(), protocols::rigid::TR(), and core::conformation::Conformation::upstream_jump_stub().
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private |
Definition at line 98 of file RotateJumpAxisMover.cc.
References lower_angle_, protocols::rigid::RG(), and upper_angle_.
Referenced by apply().
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virtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 94 of file RotateJumpAxisMover.cc.
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private |
Definition at line 57 of file RotateJumpAxisMover.hh.
Referenced by calc_angle().
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private |
Definition at line 55 of file RotateJumpAxisMover.hh.
Referenced by apply().
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private |
Definition at line 56 of file RotateJumpAxisMover.hh.
Referenced by calc_angle().
1.8.4