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| | EvolutionaryDynamicsMover () |
| | default constructor More...
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| | ~EvolutionaryDynamicsMover () override |
| | destructor More...
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| MoverOP | clone () const override |
| | create copy constructor More...
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| MoverOP | fresh_instance () const override |
| | create this type of objectt More...
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| void | apply (Pose &pose) override |
| | apply EvolutionaryDynamicsMover (Mover) More...
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| bool | boltzmann (Pose &pose, utility::vector1< core::Real > const &random_nums) override |
| | core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria More...
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| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
| | parse xml file More...
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| void | population_size (core::Real const s) |
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| core::Real | population_size () const |
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| void | disable_fitness_evaluation (bool const d) |
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| bool | disable_fitness_evaluation () const |
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| void | n_nucleotide_mut_trials_corrected (core::Real const n) |
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| core::Real | n_nucleotide_mut_trials_corrected () const |
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| void | mutation_rate (core::Real const m) |
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| core::Real | mutation_rate () const |
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| void | branch_length (core::Real const m) |
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| core::Real | branch_length () const |
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| void | total_trials (core::Real const m) |
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| core::Real | total_trials () const |
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| std::string | get_name () const override |
| | Each derived class must specify its name. The class name. More...
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| |
| | GenericMonteCarloMover () |
| | default constructor More...
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| | GenericMonteCarloMover (core::Size const maxtrials, core::Size const max_accepted_trials, core::Size const task_scaling, MoverOP const &mover, Real const temperature=0.0, String const &sample_type="low", bool const drift=true) |
| | value constructor without score function More...
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| | GenericMonteCarloMover (core::Size const maxtrials, core::Size const max_accepted_trials, core::Size const task_scaling, MoverOP const &mover, TaskFactoryOP factory_in, Real const temperature=0.0, String const &sample_type="low", bool const drift=true) |
| | value constructor with score function More...
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| | ~GenericMonteCarloMover () override |
| | destructor More...
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| MoverOP | clone () const override |
| | create copy constructor More...
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| MoverOP | fresh_instance () const override |
| | create this type of objectt More...
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| void | initialize () |
| | initialize object used in constructor More...
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| void | apply (Pose &pose) override |
| | apply GenericMonteCarloMover (Mover) More...
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| void | reset (Pose &pose) |
| | reset MC iterations, with pose used for the last & best structures More...
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| void | recover_low (Pose &pose) |
| | return the simulation state to the lowest energy structure we've seen More...
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| bool | boltzmann (Pose &pose) |
| | core of MC More...
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| void | accept (Pose &pose, utility::vector1< core::Real > const &provisional_scores, protocols::moves::MCA const mca_status) |
| | Does what the mover needs to do when a pose is accepted, given a pose and scores. More...
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| core::Size | num_designable (Pose &pose, PackerTaskOP &task) |
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| PoseOP | last_accepted_pose () const |
| | return the last accepted pose More...
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| Real | last_accepted_score () const |
| | return the last accepted score More...
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| PoseOP | lowest_score_pose () const |
| | return the lowest score pose More...
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| Real | lowest_score () const |
| | return the lowest score More...
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| Real | current_score () const |
| | return the lowest score More...
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| protocols::moves::MCA | mc_accpeted () const |
| | return mc_accepted More...
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| ScoreFunctionOP | score_function () const |
| | Return the score function in use. More...
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| core::Size | add_trigger (const GenericMonteCarloMoverTrigger &trigger) |
| | Adds a new trigger, returning its id. More...
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| core::Size | num_triggers () const |
| | Returns the number of triggers. More...
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| core::Size | maxtrials () const |
| | Returns maximum number of trials. More...
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| core::Size | max_accepted_trials () const |
| | Returns maximum number of accepted trials. More...
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| core::Size | task_scaling () const |
| | Returns the task scaling value. More...
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| void | remove_trigger (core::Size trigger_id) |
| | Removes the trigger with the specified id. More...
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| void | set_maxtrials (core::Size const ntrial) |
| | set max trials of MC trials More...
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| void | set_max_accepted_trials (core::Size const n_max_accepted_trial) |
| | set max accepted trials of MC trials More...
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| void | set_task_scaling (core::Size const scaling) |
| | set task multiplier to calculate trials from task More...
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| void | set_mover (MoverOP mover) override |
| | set mover More...
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| void | set_scorefxn (ScoreFunctionOP const &sfxn) |
| | Pose is evaluated by ScoreFunctionOP during MC trials. More...
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| void | set_temperature (Real const temp) |
| | set temperature More...
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| void | set_sampletype (String const &type) |
| | set sample type, max or min when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score More...
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| void | set_drift (bool const drift) |
| | if drift=false, the pose is set back to the initial pose at each MC trial Of course, this is not MC sampling. More...
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| void | set_stop_sampling (bool const stop_sampling) |
| | if set to true, the MC mover will stop sampling More...
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| void | set_preapply (bool const preapply=false) |
| | if preapply=true, auto-accept the first application of the submover, ignoring boltzman criteria. More...
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| void | set_recover_low (bool const recover_low) |
| | if recover_low=true, after apply() the structure is the lowest energy structure, rather than the last accepted structure. More...
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| void | set_boltz_rank (bool const boltz_rank) |
| | if boltz_rank=true, rank structures by the temperature-weighted sum of scores, rather than a single filter More...
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| void | show_scores (std::ostream &out) const |
| | show scores of last_accepted_score and "best_score" ( = flip_sign_ * lowest_score ) More...
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| void | show_counters (std::ostream &out) const |
| | show counters of ntrial and acceptance ratio More...
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| void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override |
| | parse xml file More...
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| virtual void | parse_task_operations (TagCOP, basic::datacache::DataMap const &) |
| | parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
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| void | add_filter (FilterOP filter, bool const adaptive, Real const temp, String const &sample_type, bool rank_by=false) |
| | set filter Pose is evaluated by FilterOP which can do report_sm() or ScoreFunctionOP during MC trials You can choose either way FilterOP or ScoreFunction. More...
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| void | stopping_condition (protocols::filters::FilterOP filter) |
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| protocols::filters::FilterOP | stopping_condition () const |
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| void | adaptive_movers (bool const a) |
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| bool | adaptive_movers () const |
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| void | adaptation_period (core::Size const a) |
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| core::Size | adaptation_period () const |
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| std::string | saved_accept_file_name () const |
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| void | saved_accept_file_name (std::string const) |
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| std::string | saved_trial_number_file () const |
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| void | saved_trial_number_file (std::string const) |
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| core::Size | load_trial_number_from_checkpoint (core::pose::Pose &) |
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| void | save_trial_number_to_checkpoint (core::Size const i) const |
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| void | reset_baselines (bool const r) |
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| bool | reset_baselines () const |
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| void | set_keep_filters (bool const k) |
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| bool | keep_filters () const |
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| void | task_factory (core::pack::task::TaskFactoryOP tf) |
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| core::pack::task::TaskFactoryOP | task_factory () const |
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| core::Size | trial_counter () const |
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| void | trial_counter (core::Size const i) |
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| core::Size | accept_counter () const |
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| utility::vector1< Real > | temperatures () const |
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| void | temperatures (utility::vector1< Real > const &temps) |
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| bool | recover_low () const |
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| MoverOP | mover () const override |
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| utility::vector1< FilterOP > const & | filters () const |
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| utility::vector1< bool > const & | adaptive () const |
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| utility::vector1< core::Size > const & | num_rejections () const |
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| ScoreFunctionOP | scorefxn () const |
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| utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > | mover_stopping_condition () const |
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| bool | preapply () const |
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| bool | drift () const |
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| bool | stop_sampling () const |
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| bool | boltz_rank () const |
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| utility::vector1< String > const & | sample_types () const |
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| utility::vector1< core::Real > const & | last_accepted_scores () const |
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| void | last_accepted_scores (utility::vector1< core::Real > const &scores) |
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| utility::vector1< core::Real > const & | last_tested_scores () const |
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| utility::vector1< core::Real > const & | lowest_scores () const |
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| void | lowest_scores (utility::vector1< core::Real > const &scores) |
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| void | lowest_score (core::Real const score) |
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| void | last_accepted_score (core::Real const score) |
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| void | lowest_score_pose (core::pose::PoseOP pose) |
| | Set the lowest scoring pose. More...
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| void | last_accepted_pose (core::pose::PoseOP pose) |
| | Set the last pose that was accepted. More...
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| std::string | get_name () const override |
| | Each derived class must specify its name. The class name. More...
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| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| | Provide the citation. More...
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| | MoverApplyingMover (std::string const &name) |
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| | MoverApplyingMover (MoverApplyingMover const &)=default |
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| | ~MoverApplyingMover () override=default |
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| | Mover () |
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| virtual MoverOP | 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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| | Mover (std::string const &type_name) |
| | sets the type for a mover; name_ has been removed (2010/05/14) More...
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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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| 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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| 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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| void | set_type (std::string const &setting) |
| | Set the 'type' string. More...
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| std::string | get_type () const |
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| void | type (const std::string &type_in) |
| | Set the 'type' string. More...
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| std::string const & | type () const |
| | Get the set 'type' string. More...
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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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| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
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| jobdist::BasicJobCOP | get_current_job () const |
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| virtual void | set_current_tag (std::string const &new_tag) |
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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 | show (std::ostream &output=std::cout) const |
| | Outputs details about the Mover, including current settings. More...
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| virtual core::Real | last_proposal_density_ratio () |
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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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Public Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover