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protocols::monte_carlo::GenericSimulatedAnnealer Class Reference

GenericSimulatedAnnealer mover for performing simulated annealing trajectories. More...

#include <GenericSimulatedAnnealer.hh>

Inheritance diagram for protocols::monte_carlo::GenericSimulatedAnnealer:
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Public Member Functions

 GenericSimulatedAnnealer ()
 default constructor More...
 
 ~GenericSimulatedAnnealer () override
 destructor More...
 
protocols::moves::MoverOP clone () const override
 create copy constructor More...
 
protocols::moves::MoverOP fresh_instance () const override
 create this type of objectt More...
 
void apply (Pose &pose) override
 apply GenericSimulatedAnnealer (Mover) More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 XML interface to this mover. More...
 
virtual void reset (Pose &pose)
 Clears accepted data and initialize with new pose. More...
 
AcceptedScores score_pose (core::pose::Pose const &pose) const
 given a pose, score the result More...
 
void save_checkpoint_file () const
 Saves the current state of the mover into checkpoint files. More...
 
void remove_checkpoint_file () const
 Deletes the checkpoint files. More...
 
bool checkpoint_exists () const
 tests to see if the checkpoint files exist and have been generated More...
 
AcceptedScores const & accepted_scores (core::Size const i) const
 gets a list of scores for acceptance number i More...
 
core::Size num_accepted_scores () const
 number of acceptances More...
 
core::Real calc_boltz_score (utility::vector1< core::Real > const &scores) const
 if boltz_rank is used, this will calculate the ranking score from a list of filter scores More...
 
std::string create_tag (std::string const &suffix) const
 create a silent struct tag for checkpointing with the given suffix More...
 
void load_checkpoint_file (core::pose::Pose &pose)
 loads checkpoint data and attempts to resume a run with pose as the pose More...
 
void checkpoint_file (std::string const &check_file)
 set the checkpoint file name More...
 
void keep_checkpoint_file (bool const keep_checkpoint)
 sets whether or not to delete checkpoint files when done – useful for debugging More...
 
void scale_temperatures (core::Real const temp_factor)
 scales temperatures by the factor provided More...
 
TrialResult boltzmann_result (core::pose::Pose &pose)
 given a modified pose, determines whether we should accept or not, and updates internal class data accordingly uses randomly generated numbers to assess acceptance of scores with temperatures More...
 
TrialResult boltzmann_result (core::pose::Pose &pose, utility::vector1< core::Real > const &random_nums)
 given a modified pose, determines whether we should accept or not, and updates internal class data accordingly More...
 
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...
 
void initialize ()
 initialize object used in constructor 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...
 
virtual bool boltzmann (Pose &pose, utility::vector1< core::Real > const &random_nums)
 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 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...
 
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...
 
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 Member Functions

TrialResult apply_mover (core::pose::Pose &pose)
 calls a round of monte carlo – basically copied from GenericMonteCarloMover More...
 
void calculate_temps ()
 computes the appropriately scaled temperatures and sets them More...
 
utility::vector1< core::Realcalculate_standardized_scores (core::Size const filterid) const
 
core::Real calc_temp_factor () const
 calculates multiplier for temperatures based on which anneal step we are no More...
 
AcceptedScores read_checkpoint_line (std::istream &is) const
 
void recompute_rank_scores ()
 

Private Attributes

core::Size history_
 counter for how many accepts it takes to reach equilibrium at a given temperature More...
 
protocols::moves::MoverOP periodic_mover_
 mover to be called every eval_period steps More...
 
core::Size eval_period_
 how many steps in between running the periodic mover? More...
 
std::string checkpoint_file_
 what name should be used to store checkpoint information so that the run can be resumed? More...
 
bool keep_checkpoint_file_
 if true, the checkpoint files will not be cleaned up after the apply() terminates. Useful for debugging/gathering statistics More...
 
utility::vector1< AcceptedScoresaccepted_scores_
 a history of accepted scores, used for adapting temperature More...
 
utility::vector1< core::Realstart_temperatures_
 the initial temperatures, used for adapting temperature More...
 
core::Size anneal_step_
 counter that tells which annealing step we are on More...
 
core::Size temp_step_
 which step in this temperature are we on More...
 
core::Size current_trial_
 what is the current trial number More...
 

Additional Inherited Members

- 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
 
- 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...
 

Detailed Description

GenericSimulatedAnnealer mover for performing simulated annealing trajectories.

This class extends GenericMonteCarloMover to provide temperature scaling

Constructor & Destructor Documentation

protocols::monte_carlo::GenericSimulatedAnnealer::GenericSimulatedAnnealer ( )

default constructor

References accepted_scores_, and start_temperatures_.

protocols::monte_carlo::GenericSimulatedAnnealer::~GenericSimulatedAnnealer ( )
overridedefault

destructor

Member Function Documentation

AcceptedScores const& protocols::monte_carlo::GenericSimulatedAnnealer::accepted_scores ( core::Size const  i) const
inline

gets a list of scores for acceptance number i

References accepted_scores_.

void protocols::monte_carlo::GenericSimulatedAnnealer::apply ( Pose pose)
overridevirtual

apply GenericSimulatedAnnealer (Mover)

applies the mover

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

References protocols::monte_carlo::GenericMonteCarloMover::accept(), protocols::monte_carlo::ACCEPTED, apply_mover(), checkpoint_exists(), checkpoint_file_, current_trial_, eval_period_, protocols::moves::FAIL_DO_NOT_RETRY, protocols::monte_carlo::FAILED, protocols::monte_carlo::GenericMonteCarloMover::filters(), protocols::monte_carlo::FINISHED, protocols::moves::Mover::get_additional_output(), keep_checkpoint_file_, protocols::monte_carlo::GenericMonteCarloMover::last_accepted_pose(), load_checkpoint_file(), protocols::monte_carlo::GenericMonteCarloMover::maxtrials(), protocols::moves::MCA_accepted_thermally, protocols::monte_carlo::GenericMonteCarloMover::mover(), protocols::monte_carlo::GenericMonteCarloMover::mover_stopping_condition(), protocols::monte_carlo::GenericMonteCarloMover::num_designable(), periodic_mover_, protocols::monte_carlo::GenericMonteCarloMover::recover_low(), protocols::monte_carlo::REJECTED, remove_checkpoint_file(), reset(), save_checkpoint_file(), score_pose(), protocols::monte_carlo::GenericMonteCarloMover::scorefxn(), protocols::moves::Mover::set_last_move_status(), protocols::monte_carlo::GenericMonteCarloMover::show_counters(), protocols::monte_carlo::GenericMonteCarloMover::show_scores(), start_temperatures_, protocols::monte_carlo::GenericMonteCarloMover::stopping_condition(), protocols::monte_carlo::GenericMonteCarloMover::task_factory(), protocols::monte_carlo::GenericMonteCarloMover::task_scaling(), protocols::monte_carlo::GenericMonteCarloMover::temperatures(), and protocols::TR().

Referenced by boltzmann_result().

TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::apply_mover ( core::pose::Pose pose)
private
TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result ( core::pose::Pose pose)

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly uses randomly generated numbers to assess acceptance of scores with temperatures

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

uses randomly generated numbers to assess acceptance of scores with temperatures

References protocols::monte_carlo::GenericMonteCarloMover::filters(), and core::scoring::rg.

Referenced by apply_mover().

TrialResult protocols::monte_carlo::GenericSimulatedAnnealer::boltzmann_result ( core::pose::Pose pose,
utility::vector1< core::Real > const &  random_nums 
)
core::Real protocols::monte_carlo::GenericSimulatedAnnealer::calc_boltz_score ( utility::vector1< core::Real > const &  scores) const
core::Real protocols::monte_carlo::GenericSimulatedAnnealer::calc_temp_factor ( ) const
private

calculates multiplier for temperatures based on which anneal step we are no

References anneal_step_, and protocols::monte_carlo::GenericMonteCarloMover::filters().

Referenced by calculate_temps(), and load_checkpoint_file().

utility::vector1< core::Real > protocols::monte_carlo::GenericSimulatedAnnealer::calculate_standardized_scores ( core::Size const  filterid) const
private
void protocols::monte_carlo::GenericSimulatedAnnealer::calculate_temps ( )
private
bool protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_exists ( ) const

tests to see if the checkpoint files exist and have been generated

References checkpoint_file_.

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_file ( std::string const &  check_file)
inline

set the checkpoint file name

References checkpoint_file_.

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::clone ( ) const
overridevirtual

create copy constructor

clone this object

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

std::string protocols::monte_carlo::GenericSimulatedAnnealer::create_tag ( std::string const &  suffix) const

create a silent struct tag for checkpointing with the given suffix

References core::pack::dunbrack::c, and checkpoint_file_.

Referenced by load_checkpoint_file(), and save_checkpoint_file().

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::fresh_instance ( ) const
overridevirtual

create this type of objectt

create this type of object

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

std::string protocols::monte_carlo::GenericSimulatedAnnealer::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::monte_carlo::GenericMonteCarloMover.

References mover_name().

void protocols::monte_carlo::GenericSimulatedAnnealer::keep_checkpoint_file ( bool const  keep_checkpoint)
inline

sets whether or not to delete checkpoint files when done – useful for debugging

References keep_checkpoint_file_.

void protocols::monte_carlo::GenericSimulatedAnnealer::load_checkpoint_file ( core::pose::Pose pose)
std::string protocols::monte_carlo::GenericSimulatedAnnealer::mover_name ( )
static
core::Size protocols::monte_carlo::GenericSimulatedAnnealer::num_accepted_scores ( ) const
inline

number of acceptances

References accepted_scores_.

void protocols::monte_carlo::GenericSimulatedAnnealer::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::monte_carlo::GenericSimulatedAnnealer::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
AcceptedScores protocols::monte_carlo::GenericSimulatedAnnealer::read_checkpoint_line ( std::istream &  is) const
private
void protocols::monte_carlo::GenericSimulatedAnnealer::recompute_rank_scores ( )
private

References accepted_scores_, and calc_boltz_score().

Referenced by scale_temperatures().

void protocols::monte_carlo::GenericSimulatedAnnealer::remove_checkpoint_file ( ) const

Deletes the checkpoint files.

References checkpoint_file_, and protocols::TR().

Referenced by apply().

void protocols::monte_carlo::GenericSimulatedAnnealer::reset ( Pose pose)
virtual
void protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file ( ) const
void protocols::monte_carlo::GenericSimulatedAnnealer::scale_temperatures ( core::Real const  temp_factor)
AcceptedScores protocols::monte_carlo::GenericSimulatedAnnealer::score_pose ( core::pose::Pose const &  pose) const

Member Data Documentation

utility::vector1< AcceptedScores > protocols::monte_carlo::GenericSimulatedAnnealer::accepted_scores_
private
core::Size protocols::monte_carlo::GenericSimulatedAnnealer::anneal_step_
private

counter that tells which annealing step we are on

Referenced by calc_temp_factor(), calculate_temps(), load_checkpoint_file(), reset(), and save_checkpoint_file().

std::string protocols::monte_carlo::GenericSimulatedAnnealer::checkpoint_file_
private

what name should be used to store checkpoint information so that the run can be resumed?

Referenced by apply(), checkpoint_exists(), checkpoint_file(), create_tag(), load_checkpoint_file(), parse_my_tag(), remove_checkpoint_file(), and save_checkpoint_file().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::current_trial_
private

what is the current trial number

Referenced by apply(), boltzmann_result(), load_checkpoint_file(), reset(), save_checkpoint_file(), and score_pose().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::eval_period_
private

how many steps in between running the periodic mover?

Referenced by apply(), and parse_my_tag().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::history_
private

counter for how many accepts it takes to reach equilibrium at a given temperature

Referenced by calculate_standardized_scores(), calculate_temps(), and parse_my_tag().

bool protocols::monte_carlo::GenericSimulatedAnnealer::keep_checkpoint_file_
private

if true, the checkpoint files will not be cleaned up after the apply() terminates. Useful for debugging/gathering statistics

Referenced by apply(), keep_checkpoint_file(), and parse_my_tag().

protocols::moves::MoverOP protocols::monte_carlo::GenericSimulatedAnnealer::periodic_mover_
private

mover to be called every eval_period steps

Referenced by apply(), and parse_my_tag().

utility::vector1< core::Real > protocols::monte_carlo::GenericSimulatedAnnealer::start_temperatures_
private

the initial temperatures, used for adapting temperature

Referenced by apply(), GenericSimulatedAnnealer(), reset(), and scale_temperatures().

core::Size protocols::monte_carlo::GenericSimulatedAnnealer::temp_step_
private

which step in this temperature are we on

Referenced by calculate_temps(), load_checkpoint_file(), reset(), and save_checkpoint_file().


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