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Rosetta 3.5
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Rosetta 3.5
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#include <IndependentLoopMover.hh>
Public Member Functions | |
| IndependentLoopMover () | |
| IndependentLoopMover (LoopsOP loops_in) | |
| IndependentLoopMover (LoopsFileData const &lfd) | |
| IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops) | |
| virtual | ~IndependentLoopMover () |
| void | set_defaults () |
| virtual void | apply (core::pose::Pose &pose) |
| Apply the loop-build protocol to the input pose. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| void | set_build_attempts_ (int value) |
| Accessors: More... | |
| void | set_grow_attempts_ (int value) |
| void | set_accept_aborted_loops_ (bool value) |
| void | set_strict_loops (bool value) |
| void | set_random_order_ (bool value) |
| void | set_build_all_loops_ (bool value) |
| void | set_loop_combine_rate_ (core::Real value) |
| int | get_build_attempts () const |
| int | get_grow_attempts () const |
| bool | get_accept_aborted_loops () const |
| bool | get_strict_loops () const |
| bool | get_random_order () const |
| bool | get_build_all_loops () const |
| bool | get_loop_combine_rate () const |
| bool | get_all_loops_closed () const |
 Public Member Functions inherited from protocols::loops::loop_mover::LoopMover | |
| LoopMover () | |
| LoopMover (protocols::loops::LoopsOP loops_in) | |
| LoopMover (protocols::loops::LoopsFileData const &loops_from_file) | |
| LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops) | |
| LoopMover (LoopMover const &rhs) | |
| copy ctor More... | |
| LoopMover & | operator= (LoopMover const &rhs) |
| assignment operator More... | |
| virtual | ~LoopMover () |
| void | set_guarded_loops_not_in_charge () |
| Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More... | |
| void | set_scorefxn (const core::scoring::ScoreFunctionOP score_in) |
| const core::scoring::ScoreFunctionOP & | scorefxn () const |
| void | loops (protocols::loops::LoopsOP lptr) |
| Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More... | |
| void | loops (LoopsFileData const &loop_file_data) |
| Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More... | |
| void | loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops) |
| Set the guarded_loops pointer. More... | |
| protocols::loops::LoopsCOP | loops () const |
| Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More... | |
| protocols::loops::LoopsOP | loops () |
| non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More... | |
| const utility::vector1 < core::fragment::FragSetOP > & | frag_libs () const |
| std::string | torsion_features_string (core::pose::Pose const &pose) const |
| bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450 generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis More... | |
| virtual void | set_extended_torsions (core::pose::Pose &pose, Loop const &loop) |
| Extend a loop. More... | |
| void | add_fragments (core::fragment::FragSetOP fragset) |
| add a fragment set More... | |
| void | clear_fragments () |
| clear the list of fragment sets More... | |
| MoveMapOP const & | false_movemap () const |
| explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More... | |
| void | false_movemap (MoveMapOP const &mm) |
| explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More... | |
| checkpoint::CheckPointerOP & | get_checkpoints () |
| 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 |
Protected Member Functions | |
| virtual LoopResult | model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop)=0 |
| Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover | |
| Size | enforce_false_movemap (MoveMapOP &mm) const |
| import the false_movemap's explicit False settings into the given MoveMap More... | |
| void | set_loops_from_pose_observer_cache (core::pose::Pose const &pose) |
| allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More... | |
| bool | use_loops_from_observer_cache () const |
| void | set_use_loops_from_observer_cache (bool const loops_from_observer_cache) |
| virtual basic::Tracer & | tr () const =0 |
| void | resolve_loop_indices (core::pose::Pose const &p) |
| Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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... | |
Private Member Functions | |
| void | select_loops (Loops &selected_loops) |
| select loops to be built More... | |
Private Attributes | |
| int | build_attempts_ |
| Try loopbuilding n times before extending. More... | |
| int | grow_attempts_ |
| Try extending n times. More... | |
| bool | accept_aborted_loops_ |
| danger - can lead to infinite loops ! More... | |
| bool | strict_loops_ |
| Grow loops outwards if building fails. More... | |
| bool | random_order_ |
| Randomise loop build order. More... | |
| bool | build_all_loops_ |
| Force to build all loops (i.e. ignore skiprate) More... | |
| bool | all_loops_closed_ |
| core::Real | loop_combine_rate_ |
| Loop combine rate. More... | |
Additional Inherited Members | |
| Public Types inherited from protocols::loops::loop_mover::LoopMover | |
| typedef core::kinematics::MoveMapOP | MoveMapOP |
| 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... | |
| protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover | ( | ) |
References set_defaults().
| protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover | ( | LoopsOP | loops_in) |
References set_defaults().
| protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover | ( | LoopsFileData const & | lfd) |
References set_defaults().
| protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover | ( | GuardedLoopsFromFileOP | guarded_loops) |
References set_defaults().
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Apply the loop-build protocol to the input pose.
Implements protocols::loops::loop_mover::LoopMover.
References accept_aborted_loops_, all_loops_closed_, protocols::loops::Loop::auto_choose_cutpoint(), build_attempts_, protocols::loops::loop_mover::CriticalFailure, core::pack::interaction_graph::debug, core::pose::Pose::dump_pdb(), protocols::loops::loop_mover::ExtendFailure, protocols::loops::loop_mover::Failure, core::pose::Pose::fold_tree(), protocols::loops::loop_mover::LoopMover::get_checkpoints(), protocols::moves::Mover::get_current_tag(), grow_attempts_, protocols::loops::Loop::is_extended(), core::pose::Pose::is_fullatom(), protocols::loops::loop_mover::LoopMover::loops(), model_loop(), protocols::loops::remove_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::resolve_loop_indices(), protocols::loops::loop_mover::LoopMover::scorefxn(), select_loops(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_single_loop_fold_tree(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), strict_loops_, protocols::loops::loop_mover::Success, and protocols::loops::loop_mover::LoopMover::tr().
Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), and protocols::comparative_modeling::LoopRelaxMover::apply().
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References accept_aborted_loops_.
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References all_loops_closed_.
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References build_all_loops_.
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References build_attempts_.
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References grow_attempts_.
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References loop_combine_rate_.
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Each derived class must specify its name. The class name.
Reimplemented from protocols::loops::loop_mover::LoopMover.
Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD, protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD, protocols::loop_build::LoopMover_SlidingWindow, protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC, and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.
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References random_order_.
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References strict_loops_.
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Implemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD, protocols::loop_build::LoopMover_SlidingWindow, protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC, protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD, and protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.
Referenced by apply().
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select loops to be built
References build_all_loops_, core::sequence::end, loop_combine_rate_, protocols::loops::loop_mover::LoopMover::loops(), random_order_, protocols::loops::loop_mover::RG(), core::io::serialization::size(), protocols::loops::skip_rate, protocols::loops::start, and protocols::loops::stop.
Referenced by apply().
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References accept_aborted_loops_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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References build_all_loops_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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Accessors:
References build_attempts_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
| void protocols::loops::loop_mover::IndependentLoopMover::set_defaults | ( | ) |
References accept_aborted_loops_, build_all_loops_, build_attempts_, grow_attempts_, loop_combine_rate_, random_order_, and strict_loops_.
Referenced by IndependentLoopMover().
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References grow_attempts_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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References loop_combine_rate_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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References random_order_.
Referenced by protocols::comparative_modeling::LoopRelaxMover::apply().
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References strict_loops_.
Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::set_default_settings().
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danger - can lead to infinite loops !
Referenced by apply(), get_accept_aborted_loops(), set_accept_aborted_loops_(), and set_defaults().
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determines if all the loops were closed in the last time mover was called.
Referenced by apply(), and get_all_loops_closed().
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Force to build all loops (i.e. ignore skiprate)
Referenced by get_build_all_loops(), select_loops(), set_build_all_loops_(), and set_defaults().
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Try loopbuilding n times before extending.
Referenced by apply(), get_build_attempts(), set_build_attempts_(), and set_defaults().
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Try extending n times.
Referenced by apply(), get_grow_attempts(), set_defaults(), and set_grow_attempts_().
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Loop combine rate.
Referenced by get_loop_combine_rate(), select_loops(), set_defaults(), and set_loop_combine_rate_().
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Randomise loop build order.
Referenced by get_random_order(), select_loops(), set_defaults(), and set_random_order_().
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Grow loops outwards if building fails.
Referenced by apply(), get_strict_loops(), set_defaults(), and set_strict_loops().
1.8.4