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| KinematicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy) |
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| KinematicAbinitio (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap) |
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| ~KinematicAbinitio () |
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virtual moves::MoverOP | clone () const |
| ... More...
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virtual void | apply (core::pose::Pose &pose) |
| run the protocol More...
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virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More...
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virtual void | set_max_seq_sep (core::pose::Pose &pose, Size setting) |
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virtual bool | prepare_stage1 (core::pose::Pose &pose) |
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virtual bool | prepare_stage2 (core::pose::Pose &pose) |
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virtual bool | prepare_stage3 (core::pose::Pose &pose) |
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virtual bool | prepare_loop_in_stage3 (core::pose::Pose &, Size, Size) |
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virtual bool | prepare_loop_in_stage4 (core::pose::Pose &, Size, Size) |
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virtual moves::TrialMoverOP | stage1_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) |
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virtual moves::TrialMoverOP | stage2_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) |
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virtual moves::TrialMoverOP | stage3_mover (core::pose::Pose &pose, int lct1, int lct2, moves::TrialMoverOP trials_in) |
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virtual moves::TrialMoverOP | stage4_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) |
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void | closure_protocol (loops::loop_closure::ccd::SlidingWindowLoopClosureOP closure_protocol) |
| set the closure_protocol... if not set no closure... More...
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| FoldConstraints (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int dummy) |
| c'stor from Movers More...
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| FoldConstraints (core::fragment::FragSetCOP fragset3mer, core::fragment::FragSetCOP fragset9mer, core::kinematics::MoveMapCOP movemap) |
| c'stor from FragSets — ClassicFragmentMover and SmoothFragmentMover will be created More...
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| FoldConstraints (FoldConstraints const &src) |
| Explicit copy constructor to handle OPs. More...
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| ~FoldConstraints () |
| Explicit destructor to handle OPs. More...
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void | set_constraint_weight (core::Real setting) |
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void | set_show_viol_level (core::Size setting) |
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| ClassicAbinitio (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small, int) |
| This constructor does not work – Fix it before using it. More...
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| ClassicAbinitio (core::fragment::FragSetCOP fragset_small, core::fragment::FragSetCOP fragset_large, core::kinematics::MoveMapCOP movemap) |
| constructor: supply fragsets for large and small fragment moves More...
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| ClassicAbinitio (ClassicAbinitio const &src) |
| Explicit copy constructor since this class contains OPs of other classes. More...
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| ~ClassicAbinitio () |
| Explicit destructor since this class contains OPs of other classes. More...
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virtual void | init (core::pose::Pose const &pose) |
| setup moves, mc-object, scores More...
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simple_moves::FragmentMoverOP | smooth_move_small () |
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simple_moves::FragmentMoverOP | brute_move_small () |
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simple_moves::FragmentMoverOP | brute_move_large () |
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core::kinematics::MoveMapCOP | movemap () |
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void | set_moves (simple_moves::FragmentMoverOP brute_move_small, simple_moves::FragmentMoverOP brute_move_large, simple_moves::FragmentMoverOP smooth_move_small) |
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void | set_mc (moves::MonteCarloOP) |
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moves::MonteCarlo & | mc () |
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moves::MonteCarlo const & | mc () const |
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virtual void | set_cycles (core::Real increase_cycles=1.0) |
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Size | total_trials () const |
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virtual void | set_score_weight (core::scoring::ScoreType, core::Real setting, StageID stage=ALL_STAGES) |
| for debugging, one wants to have access to the native pose. More...
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bool | just_smooth_cycles () const |
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Size | stage1_cycles () const |
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Size | stage2_cycles () const |
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Size | stage3_cycles () const |
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void | set_stage4_cycles (Size stage4_cycles_new) |
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Size | stage4_cycles () const |
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Size | stage5_cycles () const |
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bool | bQuickTest () const |
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void | set_skip_stage1 (bool setting) |
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void | set_skip_stage2 (bool setting) |
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| Protocol () |
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| ~Protocol () |
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void | set_evaluation (evaluation::MetaPoseEvaluatorOP ev) |
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void | add_evaluation (evaluation::PoseEvaluatorOP ev) |
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void | evaluate_pose (core::pose::Pose &pose, std::string tag, core::io::silent::SilentStruct &pss) const |
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evaluation::MetaPoseEvaluatorOP | evaluator () |
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void | set_kinematics (abinitio::KinematicControlOP kc) |
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abinitio::KinematicControl const & | kinematics () |
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virtual bool | start_from_centroid () const |
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virtual bool | return_centroid () const |
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virtual void | return_centroid (bool setting) |
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void | set_fullatom_scorefxn (core::scoring::ScoreFunctionOP sfxn) |
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void | set_centroid_scorefxn (core::scoring::ScoreFunctionOP sfxn) |
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void | set_silentout_file_name (std::string str) |
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core::scoring::ScoreFunctionOP | fullatom_scorefxn () |
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core::scoring::ScoreFunctionOP | centroid_scorefxn () |
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virtual checkpoint::CheckPointer & | get_checkpoints () |
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| Mover () |
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virtual | ~Mover () |
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virtual MoverSP | create () |
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MoverCOP | get_self_ptr () const |
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MoverOP | get_self_ptr () |
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MoverCAP | get_self_weak_ptr () const |
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MoverAP | get_self_weak_ptr () |
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virtual void | apply (core::io::serialization::PipeMap &pmap) |
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virtual void | parse_state (SerializableState const &state) |
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virtual void | parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache) |
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virtual void | save_state (SerializableState &state) |
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| Mover (std::string const &type_name) |
| sets the type for a mover; name_ has been removed (2010/05/14) More...
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| Mover (Mover const &other) |
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Mover & | operator= (Mover const &other) |
| assignment operator More...
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virtual core::Real | last_proposal_density_ratio () |
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std::string const & | type () const |
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void | set_type (std::string const &setting) |
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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...
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virtual void | set_current_tag (std::string const &new_tag) |
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virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More...
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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...
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PoseCOP | get_input_pose () const |
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PoseCOP | get_native_pose () const |
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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...
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void | type (const std::string &type_in) |
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virtual void | parse_my_tag (TagCOP tag, basic::datacache::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...
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std::string | get_type () const |
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MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More...
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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...
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virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More...
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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...
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virtual Strings & | info () |
| non-const accessor More...
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virtual Strings const & | info () const |
| const accessor More...
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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...
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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...
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virtual MoverOP | fresh_instance () const |
| Generates a new Mover object freshly created with the default ctor. More...
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void | set_current_job (protocols::jobdist::BasicJobCOP job) |
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jobdist::BasicJobCOP | get_current_job () const |
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virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More...
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virtual void | set_default_scores () |
| sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0 More...
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virtual void | set_default_options () |
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virtual void | replace_scorefxn (core::pose::Pose &pose, StageID, core::Real intra_stage_progress) |
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bool | prepare_stage4 (core::pose::Pose &pose) |
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bool | do_stage1_cycles (core::pose::Pose &pose) |
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bool | do_stage2_cycles (core::pose::Pose &pose) |
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virtual void | setup_default_min_move () |
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virtual void | set_movemap (core::kinematics::MoveMapCOP mm) |
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void | set_min_move (protocols::simple_moves::MinMoverOP mm) |
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protocols::simple_moves::MinMover & | min_move () |
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void | min_trial (core::pose::Pose &pose) |
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core::Real | max_seq_sep_fudge () const |
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void | max_seq_sep_fudge (core::Real setting) |
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constraints_additional::MaxSeqSepConstraintSet
const & | constraints () |
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void | bIgnoreSequenceSeparation (bool setting) |
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bool | bIgnoreSequenceSeparation () |
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Size | total_res (core::pose::Pose const &pose) const |
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void | set_seq_sep_stage1 (core::Real setting) |
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void | set_seq_sep_stage3 (core::Real setting) |
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virtual void | update_moves () |
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virtual void | set_defaults (core::pose::Pose const &pose) |
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virtual void | set_default_mc (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn) |
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core::scoring::ScoreFunction
const & | current_scorefxn () const |
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void | current_scorefxn (core::scoring::ScoreFunction const &scorefxn) |
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void | recover_low (core::pose::Pose &pose, StageID stage) |
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void | set_current_weight (core::scoring::ScoreType type, core::Real setting) |
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virtual bool | do_stage3_cycles (core::pose::Pose &pose) |
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virtual bool | do_stage4_cycles (core::pose::Pose &pose) |
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virtual bool | do_stage5_cycles (core::pose::Pose &pose) |
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virtual moves::TrialMoverOP | stage4rot_mover (core::pose::Pose &pose, int kk, moves::TrialMoverOP trials_in) |
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virtual moves::TrialMoverOP | stage5_mover (core::pose::Pose &pose, moves::TrialMoverOP trials_in) |
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virtual void | set_trials () |
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moves::TrialMoverOP | trial_large () |
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moves::TrialMoverOP | trial_small () |
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moves::TrialMoverOP | trial_smooth () |
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virtual bool | prepare_stage5 (core::pose::Pose &pose) |
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void | output_debug_structure (core::pose::Pose &pose, std::string prefix) |
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moves::MonteCarloOP | mc_ptr () |
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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...
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