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Rosetta 3.5
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Rosetta 3.5
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a mover that packs the side-chains using a rotamer library in a lazy fashion. More...
#include <PackRotamersMoverLazy.hh>
Public Member Functions | |
| PackRotamersMoverLazy (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1) | |
| default constructor More... | |
| PackRotamersMoverLazy () | |
| virtual | ~PackRotamersMoverLazy () |
| constructor with typename More... | |
| virtual void | call_setup (Pose &pose) |
| virtual void | apply_to_rotpack (Pose &pose, utility::vector0< int > rot_to_pack) |
| virtual void | parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) |
| allow non-const access to the internal minimizer options object More... | |
 Public Member Functions inherited from protocols::simple_moves::PackRotamersMover | |
| PackRotamersMover () | |
| default constructor More... | |
| PackRotamersMover (std::string const &) | |
| constructor with typename More... | |
| PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1) | |
| Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More... | |
| virtual | ~PackRotamersMover () |
| PackRotamersMover (PackRotamersMover const &other) | |
| virtual void | apply (Pose &pose) |
| Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More... | |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| bool | task_is_valid (Pose const &pose) const |
| when the PackerTask was not generated locally, verify compatibility with pose More... | |
| virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache) |
| virtual void | parse_score_function (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) |
| parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More... | |
| virtual void | parse_task_operations (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) |
| parse "task_operations" XML option (can be employed virtually by derived Packing movers) More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
| required in the context of the parser/scripting scheme More... | |
| virtual protocols::moves::MoverOP | clone () const |
| required in the context of the parser/scripting scheme More... | |
| void | score_function (ScoreFunctionCOP sf) |
| Sets the ScoreFunction to <sf> More... | |
| void | task_factory (TaskFactoryCOP tf) |
| Sets the TaskFactory to <tf> More... | |
| void | task (PackerTaskCOP t) |
| Sets the PackerTask to <t> More... | |
| void | nloop (core::Size nloop_in) |
| ScoreFunctionCOP | score_function () const |
| Returns the ScoreFunction. More... | |
| PackerTaskCOP | task () const |
| Returns the PackerTask. More... | |
| core::Size | nloop () const |
| TaskFactoryCOP | task_factory () const |
| Returns the TaskFactory. More... | |
| RotamerSetsCOP | rotamer_sets () const |
| InteractionGraphBaseCOP | ig () const |
| 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 | 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) |
| 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
Additional Inherited Members | |
| Public Types inherited from protocols::simple_moves::PackRotamersMover | |
| typedef core::pack::interaction_graph::InteractionGraphBaseOP | InteractionGraphBaseOP |
| please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here! More... | |
| typedef core::pack::interaction_graph::InteractionGraphBaseCOP | InteractionGraphBaseCOP |
| typedef core::pack::rotamer_set::RotamerSetsOP | RotamerSetsOP |
| typedef core::pack::rotamer_set::RotamerSetsCOP | RotamerSetsCOP |
| typedef core::pack::task::PackerTaskCOP | PackerTaskCOP |
| typedef core::pack::task::TaskFactoryCOP | TaskFactoryCOP |
| typedef core::scoring::ScoreFunctionCOP | ScoreFunctionCOP |
| 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::simple_moves::PackRotamersMover | |
| virtual void | setup (Pose &pose) |
| get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More... | |
| virtual core::PackerEnergy | run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const |
| virtual void | note_packertask_settings (Pose const &) |
| note PackerTask's packable and designable residues as string info More... | |
a mover that packs the side-chains using a rotamer library in a lazy fashion.
| protocols::simple_moves::PackRotamersMoverLazy::PackRotamersMoverLazy | ( | ScoreFunctionCOP | scorefxn, |
| PackerTaskCOP | task = 0, |
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| core::Size | nloop = 1 |
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| ) |
default constructor
| protocols::simple_moves::PackRotamersMoverLazy::PackRotamersMoverLazy | ( | ) |
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constructor with typename
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References protocols::simple_moves::PackRotamersMover::nloop(), protocols::simple_moves::PackRotamersMover::run(), protocols::simple_moves::PackRotamersMover::score_function(), and protocols::simple_moves::PackRotamersMover::scorefxn_.
Referenced by protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight().
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allow non-const access to the internal minimizer options object
parse XML (specifically in the context of the parser/scripting scheme)
Reimplemented from protocols::simple_moves::PackRotamersMover.
References protocols::simple_moves::PackRotamersMover::nloop(), protocols::simple_moves::PackRotamersMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), and protocols::simple_moves::TR().
1.8.4