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Rosetta
2020.50
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#include <SimulatedTempering.hh>
Public Member Functions | |
SimulatedTempering () | |
SimulatedTempering (SimulatedTempering const &) | |
void | apply (core::pose::Pose &) override |
Main Method. More... | |
protocols::moves::MoverOP | clone () const override |
Return a clone of the Mover object. More... | |
protocols::moves::MoverOP | fresh_instance () const override |
Generates a new Mover object freshly created with the default ctor. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
core::Real | temperature_move (core::Real score) override |
execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT. More... | |
void | initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) override |
callback executed before any Monte Carlo trials More... | |
void | finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) override |
callback executed after all Monte Carlo trials More... | |
void | finalize_simulation (std::string const &output_name) |
std::string | get_name () const override |
Each derived class must specify its name. The class name. More... | |
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TemperingBase () | |
Default constructor. More... | |
void | apply (core::pose::Pose &) override |
No-op implemented only to satisfy the Mover interface. More... | |
std::string | get_name () const override |
Return the name of this class. More... | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
void | initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) override |
Callback executed before any Monte Carlo trials are attempted. More... | |
void | initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size level, core::Real temperature, core::Size cycle) override |
void | observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) override |
Callback executed after the Metropolis criterion is evaluated. More... | |
void | finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) override |
Callback executed after all Monte Carlo trials are completed. More... | |
core::Real | temperature () const override |
Return the temperature of the underlying MonteCarlo object. More... | |
core::Real | temperature (core::Size level) const override |
Return the temperature of the given level. More... | |
core::Size | temperature_level () const override |
Return the current temperature level. More... | |
core::Size | n_temp_levels () const override |
Return the number of temperature levels used by this controller. More... | |
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TemperatureController () | |
Default constructor. More... | |
TemperatureController (TemperatureController const &) | |
Copy constructor. More... | |
TemperatureController & | operator= (TemperatureController const &)=default |
This has substantially different behavior than the copy constructor. More... | |
bool | reinitialize_for_each_job () const override |
Return false. This class does not need to be reinitialized for each job. More... | |
bool | reinitialize_for_new_input () const override |
Return false. This class does not need to be reinitialized for new input. More... | |
virtual core::Real | temperature_move (core::pose::Pose &pose) |
Execute a temperature move which depends on the current pose. More... | |
virtual GridCoord | level_2_grid_coord (core::Size level) const |
virtual core::Size | exchange_grid_dim () const |
virtual core::Size | nlevels_per_dim (core::Size) const |
protocols::moves::MonteCarloCOP | monte_carlo () const |
Return const access to the MonteCarlo object being controlled. More... | |
virtual bool | finished_simulation (core::Size trials, core::Size ntrials) |
Return true if the simulation has been completed. More... | |
virtual void | set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo) |
Set the MonteCarlo object to be controlled. More... | |
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ThermodynamicObserver () | |
Default constructor. More... | |
~ThermodynamicObserver () override | |
Destructor. More... | |
void | apply (core::pose::Pose &) override |
Callback executed after each move is made. More... | |
virtual bool | restart_simulation (core::pose::Pose &, MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &) |
Attempt to restart the last simulation that was recorded by this observer. More... | |
virtual bool | requires_pose () |
Return false if this observer does not require a valid pose. TrialCounterObserver is an example of such an observer. More... | |
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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... | |
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 Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
static void | register_options () |
static std::string | mover_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
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static void | attributes_for_tempering_base (utility::tag::AttributeList &, utility::tag::XMLSchemaDefinition &) |
static void | register_options () |
Register the options used by this mover with the global options system. More... | |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
Protected Member Functions | |
void | set_defaults () |
handling of options including command-line More... | |
void | init_from_options () override |
Assigns user specified values to primitive members using command line options. More... | |
void | reweight () |
update weights based on current counts More... | |
void | reset_raw_counter () |
reset the raw counts per state (not the weighted ones) to 0 More... | |
bool | initialize_from_file (std::string const &filename) override |
initialize temperatures and weights from file, return false if IO error occurrs More... | |
void | write_to_file (std::string const &file_in, std::string const &output_name, utility::vector1< core::Real > const &wcounts) override |
Save temperatures and weights to a file. More... | |
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void | set_defaults () |
Help the constructor initialize the object. More... | |
bool | check_temp_consistency () |
Assert that the current temperature of the MonteCarlo object agrees with the current temperature level of this object. More... | |
virtual bool | time_for_temp_move () |
Return true if a temperature move should be made on this iteration. More... | |
void | reset_temp_counter () |
core::Size | current_temp () const |
Return the current temperature level. Identical to temperature_level() as far as I can tell. More... | |
void | clear () |
Forget all temperature levels and return to an uninitialized state. More... | |
void | set_temperatures (utility::vector1< core::Real > const &) |
Explicitly set the temperature levels. More... | |
virtual void | set_current_temp (core::Size new_temp) |
Set the temperature to the given level. More... | |
bool | stats_line_output () const |
Return true if a statistics summary should be written. More... | |
bool | stats_silent_output () const |
Return true if a statistics summary should be inserted into a silent file. More... | |
std::string const & | stats_file () const |
Return the name of the silent file into which statistics should be recorded. More... | |
void | generate_temp_range (core::Real temp_low, core::Real temp_high, core::Size n_levels, InterpolationType interpolation=linear) |
Explicitly set the temperature levels by interpolating the given parameters. More... | |
MultiTemperatureTrialCounter & | trial_counter () |
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protocols::moves::MonteCarloOP | monte_carlo () |
Return non-const access to the MonteCarlo object being controlled. More... | |
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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... | |
Private Types | |
typedef TemperingBase | Parent |
Private Attributes | |
core::Real | score_offset_ |
----------—— member variables --------------------—— More... | |
core::Real | self_transition_ |
bool | temperature_jumps_ |
core::Size | reweight_stride_ |
utility::vector1< core::Real > | weights_ |
-— state --— More... | |
utility::vector1< core::Size > | counts_ |
utility::vector1< core::Real > | weighted_counts_ |
core::Size | total_count_ |
Static Private Attributes | |
static bool | options_registered_ |
---------------— register cmdline options ------------------------— More... | |
Additional Inherited Members | |
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typedef utility::vector1 < core::Size > | GridCoord |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef std::list< std::string > | Strings |
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utility::vector1< core::Real > | temperatures_ |
Temperature levels. More... | |
core::Size | temperature_stride_ |
Frequency for attempting temperature moves (e.g. once every io_stride_ steps). More... | |
core::Size | io_stride_ |
Frequency with which statistics should be written (e.g. once every io_stride_ steps). More... | |
bool | trust_current_temp_ |
If false, look for current temperature in monte_carlo_ before each move. Set to true by default. More... | |
bool | stats_line_output_ |
If true, a statistics summary will be written. More... | |
bool | stats_silent_output_ |
If true, the statistics summary will be inserted in a silent file. More... | |
std::string | stats_file_ |
Name of the silent file used for writing statistics. More... | |
bool | instance_initialized_ |
If false, init_from_options() will be called before the simulation starts. More... | |
core::Size | current_temp_ |
Current temperature level. Not the current temperature! More... | |
core::Size | temp_trial_count_ |
Number of times time_for_temp_move() has been called. This method is meant to be called every time temperature_move() is called. More... | |
MultiTemperatureTrialCounter | trial_counter_ |
The only way to set the temperature range used for simulated annealing is to use the command line. The relevant options are:
protocols::canonical_sampling::SimulatedTempering::SimulatedTempering | ( | ) |
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default |
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inlineoverridevirtual |
Main Method.
Implements protocols::moves::Mover.
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overridevirtual |
Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
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overridevirtual |
callback executed after all Monte Carlo trials
Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.
References protocols::canonical_sampling::MetropolisHastingsMover::output_name().
void protocols::canonical_sampling::SimulatedTempering::finalize_simulation | ( | std::string const & | output_name | ) |
References protocols::simple_filters::write_to_file().
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overridevirtual |
Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
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overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
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overrideprotectedvirtual |
Assigns user specified values to primitive members using command line options.
Reimplemented from protocols::canonical_sampling::TemperingBase.
References protocols::canonical_sampling::tr().
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overrideprotectedvirtual |
initialize temperatures and weights from file, return false if IO error occurrs
Reimplemented from protocols::canonical_sampling::TemperingBase.
References core::conformation::membrane::in, and protocols::canonical_sampling::tr().
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overridevirtual |
callback executed before any Monte Carlo trials
Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.
References protocols::canonical_sampling::tr().
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static |
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overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::parse_my_tag().
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protected |
reset the raw counts per state (not the weighted ones) to 0
callback executed before any Monte Carlo trials use to fill count_ with 0
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update weights based on current counts
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protected |
handling of options including command-line
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overridevirtual |
execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT.
Implements protocols::canonical_sampling::TemperatureController.
References protocols::jd2::current_output_name(), protocols::mean_field::min(), protocols::hybridization::r1, core::scoring::rg, protocols::canonical_sampling::tr(), and protocols::simple_filters::write_to_file().
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overrideprotectedvirtual |
Save temperatures and weights to a file.
Reimplemented from protocols::canonical_sampling::TemperingBase.
References core::conformation::membrane::out.
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private |
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staticprivate |
---------------— register cmdline options ------------------------—
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private |
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----------—— member variables --------------------——
— configurables -—
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private |
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-— state --—