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Rosetta 3.5
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Rosetta 3.5
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#include <KinematicWrapper.hh>
Public Member Functions | |
| KinematicWrapper (KinematicMoverOP kinmover_in, protocols::loops::Loop loop, core::Size cycles=0) | |
| ctor with Loop More... | |
| KinematicWrapper (KinematicMoverOP kinmover_in, core::Size loop_begin, core::Size loop_end, core::Size cycles=0) | |
| ctor with explicit loop begin/end More... | |
| virtual | ~KinematicWrapper () |
| virtual void | apply (core::pose::Pose &pose) |
| re-applies KinematicMover with different pivots until success More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | respect_this_movemap (core::kinematics::MoveMapCOP mm) |
| this function derives the allowed_positions_ vector from mm and the loop begin/end 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 | |
| void | ctor () |
| two ctors have same functions, just different initialization lists; de-duplicated here More... | |
| void | init_allowed_pos () |
| initializes allowed positions - for constructors and resetting More... | |
Private Attributes | |
| KinematicMoverOP | kinmover_ |
| OP for KinematicMover. More... | |
| core::Size const | loop_begin_ |
| the loop this object-instance remodels More... | |
| core::Size const | loop_end_ |
| the loop this object-instance remodels More... | |
| core::Size const | limit_ |
| a limit on the number of cycles the mover will run More... | |
| utility::vector1< core::Size > | allowed_positions_ |
| vector of positions allowed as pivots More... | |
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 class extends KinematicMover by composition (has-a KinematicMover). The idea is to make KinematicMover useful when ONLY the apply() function is available (as in MoverContainers, etc.). It will reapply KinematicMover until the KinematicMover reports a success. This class uses searches through loop begin/middle/end points while searching for solutions. You can pass a MoveMap; it will refuse to put pivots where the MoveMap is not mobile.
| protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper | ( | KinematicMoverOP | kinmover_in, |
| protocols::loops::Loop | loop, | ||
| core::Size | cycles = 0 |
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| ) |
| protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::KinematicWrapper | ( | KinematicMoverOP | kinmover_in, |
| core::Size | loop_begin, | ||
| core::Size | loop_end, | ||
| core::Size | cycles = 0 |
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| ) |
ctor with explicit loop begin/end
References ctor().
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re-applies KinematicMover with different pivots until success
the responsiblity of apply() is to use the underlying KinematicMover to close the loop, taking care of moving the KinematicMover's begin/middle/end and ensuring that closure does occur.
Implements protocols::moves::Mover.
References allowed_positions_, protocols::moves::FAIL_RETRY, kinmover_, limit_, protocols::moves::MS_SUCCESS, protocols::loops::loop_closure::kinematic_closure::RG(), protocols::moves::Mover::set_last_move_status(), and protocols::loops::loop_closure::kinematic_closure::TR().
Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), and protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().
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two ctors have same functions, just different initialization lists; de-duplicated here
trivial wrapper around stuff needed in two ctors (de-duplicating the code)
References init_allowed_pos(), loop_begin_, and loop_end_.
Referenced by KinematicWrapper().
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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initializes allowed positions - for constructors and resetting
initializes the allowed_positions vector with every position in the loop as an allowed pivot
References allowed_positions_, loop_begin_, and loop_end_.
Referenced by ctor(), and respect_this_movemap().
| void protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::respect_this_movemap | ( | core::kinematics::MoveMapCOP | mm) |
this function derives the allowed_positions_ vector from mm and the loop begin/end
this function compares positions in the allowed_positions vector with the movemap, and removes non-mobile positions
References allowed_positions_, init_allowed_pos(), and protocols::loops::loop_closure::kinematic_closure::TR().
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vector of positions allowed as pivots
Referenced by apply(), init_allowed_pos(), and respect_this_movemap().
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OP for KinematicMover.
Referenced by apply().
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a limit on the number of cycles the mover will run
Referenced by apply().
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the loop this object-instance remodels
Referenced by ctor(), and init_allowed_pos().
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private |
the loop this object-instance remodels
Referenced by ctor(), and init_allowed_pos().
1.8.4