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protocols::evolution::EvolutionaryDynamicsMover Class Reference

#include <EvolutionaryDynamicsMover.hh>

Inheritance diagram for protocols::evolution::EvolutionaryDynamicsMover:
Inheritance graph
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Public Types

typedef std::string String
 
typedef core::Size Size
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef
protocols::rosetta_scripts::ParsedProtocolOP 
ParsedProtocolOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- Public Types inherited from protocols::monte_carlo::GenericMonteCarloMover
typedef std::string String
 
typedef core::Size Size
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseOP PoseOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef protocols::moves::MoverOP MoverOP
 
typedef
core::pack::task::PackerTask 
PackerTask
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef
protocols::rosetta_scripts::ParsedProtocolOP 
ParsedProtocolOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 EvolutionaryDynamicsMover ()
 default constructor More...
 
 ~EvolutionaryDynamicsMover () override
 destructor More...
 
MoverOP clone () const override
 create copy constructor More...
 
MoverOP fresh_instance () const override
 create this type of objectt More...
 
void apply (Pose &pose) override
 apply EvolutionaryDynamicsMover (Mover) More...
 
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...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml file More...
 
void population_size (core::Real const s)
 
core::Real population_size () const
 
void disable_fitness_evaluation (bool const d)
 
bool disable_fitness_evaluation () const
 
void n_nucleotide_mut_trials_corrected (core::Real const n)
 
core::Real n_nucleotide_mut_trials_corrected () const
 
void mutation_rate (core::Real const m)
 
core::Real mutation_rate () const
 
void branch_length (core::Real const m)
 
core::Real branch_length () const
 
void total_trials (core::Real const m)
 
core::Real total_trials () const
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
 GenericMonteCarloMover ()
 default constructor More...
 
 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...
 
 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...
 
 ~GenericMonteCarloMover () override
 destructor More...
 
MoverOP clone () const override
 create copy constructor More...
 
MoverOP fresh_instance () const override
 create this type of objectt More...
 
void initialize ()
 initialize object used in constructor More...
 
void apply (Pose &pose) override
 apply GenericMonteCarloMover (Mover) More...
 
void reset (Pose &pose)
 reset MC iterations, with pose used for the last & best structures More...
 
void recover_low (Pose &pose)
 return the simulation state to the lowest energy structure we've seen More...
 
bool boltzmann (Pose &pose)
 core of MC More...
 
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...
 
core::Size num_designable (Pose &pose, PackerTaskOP &task)
 
PoseOP last_accepted_pose () const
 return the last accepted pose More...
 
Real last_accepted_score () const
 return the last accepted score More...
 
PoseOP lowest_score_pose () const
 return the lowest score pose More...
 
Real lowest_score () const
 return the lowest score More...
 
Real current_score () const
 return the lowest score More...
 
protocols::moves::MCA mc_accpeted () const
 return mc_accepted More...
 
ScoreFunctionOP score_function () const
 Return the score function in use. More...
 
core::Size add_trigger (const GenericMonteCarloMoverTrigger &trigger)
 Adds a new trigger, returning its id. More...
 
core::Size num_triggers () const
 Returns the number of triggers. More...
 
core::Size maxtrials () const
 Returns maximum number of trials. More...
 
core::Size max_accepted_trials () const
 Returns maximum number of accepted trials. More...
 
core::Size task_scaling () const
 Returns the task scaling value. More...
 
void remove_trigger (core::Size trigger_id)
 Removes the trigger with the specified id. More...
 
void set_maxtrials (core::Size const ntrial)
 set max trials of MC trials More...
 
void set_max_accepted_trials (core::Size const n_max_accepted_trial)
 set max accepted trials of MC trials More...
 
void set_task_scaling (core::Size const scaling)
 set task multiplier to calculate trials from task More...
 
void set_mover (MoverOP mover) override
 set mover More...
 
void set_scorefxn (ScoreFunctionOP const &sfxn)
 Pose is evaluated by ScoreFunctionOP during MC trials. More...
 
void set_temperature (Real const temp)
 set temperature More...
 
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...
 
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...
 
void set_stop_sampling (bool const stop_sampling)
 if set to true, the MC mover will stop sampling More...
 
void set_preapply (bool const preapply=false)
 if preapply=true, auto-accept the first application of the submover, ignoring boltzman criteria. More...
 
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...
 
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...
 
void show_scores (std::ostream &out) const
 show scores of last_accepted_score and "best_score" ( = flip_sign_ * lowest_score ) More...
 
void show_counters (std::ostream &out) const
 show counters of ntrial and acceptance ratio More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml file More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
 
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...
 
void stopping_condition (protocols::filters::FilterOP filter)
 
protocols::filters::FilterOP stopping_condition () const
 
void adaptive_movers (bool const a)
 
bool adaptive_movers () const
 
void adaptation_period (core::Size const a)
 
core::Size adaptation_period () const
 
std::string saved_accept_file_name () const
 
void saved_accept_file_name (std::string const )
 
std::string saved_trial_number_file () const
 
void saved_trial_number_file (std::string const )
 
core::Size load_trial_number_from_checkpoint (core::pose::Pose &)
 
void save_trial_number_to_checkpoint (core::Size const i) const
 
void reset_baselines (bool const r)
 
bool reset_baselines () const
 
void set_keep_filters (bool const k)
 
bool keep_filters () const
 
void task_factory (core::pack::task::TaskFactoryOP tf)
 
core::pack::task::TaskFactoryOP task_factory () const
 
core::Size trial_counter () const
 
void trial_counter (core::Size const i)
 
core::Size accept_counter () const
 
utility::vector1< Realtemperatures () const
 
void temperatures (utility::vector1< Real > const &temps)
 
bool recover_low () const
 
MoverOP mover () const override
 
utility::vector1< FilterOP >
const & 
filters () const
 
utility::vector1< bool > const & adaptive () const
 
utility::vector1< core::Size >
const & 
num_rejections () const
 
ScoreFunctionOP scorefxn () const
 
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< bool > > 
mover_stopping_condition () const
 
bool preapply () const
 
bool drift () const
 
bool stop_sampling () const
 
bool boltz_rank () const
 
utility::vector1< String > const & sample_types () const
 
utility::vector1< core::Real >
const & 
last_accepted_scores () const
 
void last_accepted_scores (utility::vector1< core::Real > const &scores)
 
utility::vector1< core::Real >
const & 
last_tested_scores () const
 
utility::vector1< core::Real >
const & 
lowest_scores () const
 
void lowest_scores (utility::vector1< core::Real > const &scores)
 
void lowest_score (core::Real const score)
 
void last_accepted_score (core::Real const score)
 
void lowest_score_pose (core::pose::PoseOP pose)
 Set the lowest scoring pose. More...
 
void last_accepted_pose (core::pose::PoseOP pose)
 Set the last pose that was accepted. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. More...
 
- Public Member Functions inherited from protocols::moves::MoverApplyingMover
 MoverApplyingMover (std::string const &name)
 
 MoverApplyingMover (MoverApplyingMover const &)=default
 
 ~MoverApplyingMover () override=default
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
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...
 
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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static
utility::tag::XMLSchemaComplexTypeGeneratorOP 
define_composition_schema (utility::tag::XMLSchemaDefinition &)
 
- 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. More...
 

Private Types

typedef
protocols::monte_carlo::GenericMonteCarloMover 
Super
 

Private Attributes

core::Real population_size_
 
bool disable_fitness_evaluation_
 
core::Real n_nucleotide_mut_trials_corrected_
 
core::Real branch_length_
 
core::Real mutation_rate_
 
core::Real total_trials_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::monte_carlo::GenericMonteCarloMover
Real scoring (Pose &pose)
 evalute pose by ScoreFunctionOP or FilterOP More...
 
void fire_all_triggers (core::Size cycle, core::Size num_cycles, const Pose &pose, ScoreFunctionOP scoring)
 Executes all triggers. The order of trigger execution is undefined. Do not assume, depend, or in any way rely on a particular ordering. More...
 
utility::vector1< core::Realgenerate_random () const
 generate a set of random numbers to accompany the filters or scorefxn More...
 
std::string progress_file () const
 
void progress_file (std::string const &s)
 
void set_mc_accepted (moves::MCA const m)
 Sets mc_accpeted. 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...
 
- Protected Attributes inherited from protocols::monte_carlo::GenericMonteCarloMover
int trial_counter_ = 0
 
utility::vector1< core::Sizenum_rejections_
 Count the number of rejections each filter resulted in. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::evolution::EvolutionaryDynamicsMover::EvolutionaryDynamicsMover ( )
protocols::evolution::EvolutionaryDynamicsMover::~EvolutionaryDynamicsMover ( )
overridedefault

destructor

Member Function Documentation

void protocols::evolution::EvolutionaryDynamicsMover::apply ( Pose pose)
overridevirtual
bool protocols::evolution::EvolutionaryDynamicsMover::boltzmann ( Pose pose,
utility::vector1< core::Real > const &  random_nums 
)
overridevirtual
void protocols::evolution::EvolutionaryDynamicsMover::branch_length ( core::Real const  m)
inline

References branch_length_.

core::Real protocols::evolution::EvolutionaryDynamicsMover::branch_length ( ) const
inline

References branch_length_.

Referenced by parse_my_tag().

EvolutionaryDynamicsMover::MoverOP protocols::evolution::EvolutionaryDynamicsMover::clone ( ) const
overridevirtual

create copy constructor

clone this object

Reimplemented from protocols::moves::Mover.

void protocols::evolution::EvolutionaryDynamicsMover::disable_fitness_evaluation ( bool const  d)
inline
bool protocols::evolution::EvolutionaryDynamicsMover::disable_fitness_evaluation ( ) const
inline

References disable_fitness_evaluation_.

Referenced by parse_my_tag().

EvolutionaryDynamicsMover::MoverOP protocols::evolution::EvolutionaryDynamicsMover::fresh_instance ( ) const
overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::evolution::EvolutionaryDynamicsMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::evolution::EvolutionaryDynamicsMover::mover_name ( )
static
void protocols::evolution::EvolutionaryDynamicsMover::mutation_rate ( core::Real const  m)
inline

References mutation_rate_.

core::Real protocols::evolution::EvolutionaryDynamicsMover::mutation_rate ( ) const
inline

References mutation_rate_.

Referenced by parse_my_tag().

void protocols::evolution::EvolutionaryDynamicsMover::n_nucleotide_mut_trials_corrected ( core::Real const  n)
inline
core::Real protocols::evolution::EvolutionaryDynamicsMover::n_nucleotide_mut_trials_corrected ( ) const
inline
void protocols::evolution::EvolutionaryDynamicsMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::evolution::EvolutionaryDynamicsMover::population_size ( core::Real const  s)
inline

References population_size_.

core::Real protocols::evolution::EvolutionaryDynamicsMover::population_size ( ) const
inline

References population_size_.

Referenced by parse_my_tag().

void protocols::evolution::EvolutionaryDynamicsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::evolution::EvolutionaryDynamicsMover::total_trials ( core::Real const  m)
inline

References total_trials_.

core::Real protocols::evolution::EvolutionaryDynamicsMover::total_trials ( ) const
inline

References total_trials_.

Referenced by parse_my_tag().

Member Data Documentation

core::Real protocols::evolution::EvolutionaryDynamicsMover::branch_length_
private

Referenced by branch_length().

bool protocols::evolution::EvolutionaryDynamicsMover::disable_fitness_evaluation_
private
core::Real protocols::evolution::EvolutionaryDynamicsMover::mutation_rate_
private

Referenced by mutation_rate().

core::Real protocols::evolution::EvolutionaryDynamicsMover::n_nucleotide_mut_trials_corrected_
private
core::Real protocols::evolution::EvolutionaryDynamicsMover::population_size_
private

Referenced by boltzmann(), and population_size().

core::Real protocols::evolution::EvolutionaryDynamicsMover::total_trials_
private

The documentation for this class was generated from the following files: