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protocols::canonical_sampling::HamiltonianExchange Class Reference

#include <HamiltonianExchange.hh>

Inheritance diagram for protocols::canonical_sampling::HamiltonianExchange:
Inheritance graph
[legend]

Public Member Functions

 HamiltonianExchange ()
 
 ~HamiltonianExchange () override
 
 HamiltonianExchange (HamiltonianExchange const &)
 
HamiltonianExchangeoperator= (HamiltonianExchange 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
 not possible for HamExchange – exit with ERROR if called More...
 
core::Real temperature_move (core::pose::Pose &pose) override
 execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT. More...
 
void initialize_simulation (core::pose::Pose &pose, MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle) override
 callback executed before any Monte Carlo trials 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 show (std::ostream &) const override
 Outputs details about the Mover, including current settings. More...
 
void next_exchange_schedule ()
 
void set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo) override
 Set the MonteCarlo object to be controlled. More...
 
GridCoord level_2_grid_coord (core::Size level) const override
 
core::Size exchange_grid_dim () const override
 
core::Size nlevels_per_dim (core::Size) const override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::AsyncMPITemperingBase
 AsyncMPITemperingBase ()
 
 AsyncMPITemperingBase (AsyncMPITemperingBase const &)
 
AsyncMPITemperingBaseoperator= (AsyncMPITemperingBase const &)
 
 ~AsyncMPITemperingBase () override
 
void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover) override
 callback executed after all Monte Carlo trials More...
 
bool finished_simulation (core::Size trials, core::Size ntrials) override
 Return true if the simulation has been completed. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::TemperingBase
 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...
 
- Public Member Functions inherited from protocols::canonical_sampling::TemperatureController
 TemperatureController ()
 Default constructor. More...
 
 TemperatureController (TemperatureController const &)
 Copy constructor. More...
 
TemperatureControlleroperator= (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...
 
protocols::moves::MonteCarloCOP monte_carlo () const
 Return const access to the MonteCarlo object being controlled. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
 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...
 
- 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...
 
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 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...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static void register_options ()
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::canonical_sampling::TemperingBase
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...
 
- 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...
 

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 clear ()
 return to uninitialized status More...
 
bool initialize_from_file (std::string const &filename) override
 initialize temperatures and weights from file, return false if IO error occurrs More...
 
virtual bool initialize_exchange_schedule_from_file (std::string const &filename)
 initialize exchange schedule from file, return false if IO error occurrs More...
 
core::Size next_exchange_level () const override
 
- Protected Member Functions inherited from protocols::canonical_sampling::AsyncMPITemperingBase
bool time_for_temp_move () override
 Return true if a temperature move should be made on this iteration. More...
 
int rank ()
 
void find_exchange_partner (int &partner, bool &is_master)
 
- Protected Member Functions inherited from protocols::canonical_sampling::TemperingBase
void set_defaults ()
 Help the constructor initialize the object. More...
 
virtual void write_to_file (std::string const &file_in, std::string const &output_name, utility::vector1< core::Real > const &wcounts)
 Save temperatures and weights to a file. More...
 
bool check_temp_consistency ()
 Assert that the current temperature of the MonteCarlo object agrees with the current temperature level of this object. 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...
 
MultiTemperatureTrialCountertrial_counter ()
 
- Protected Member Functions inherited from protocols::canonical_sampling::TemperatureController
protocols::moves::MonteCarloOP monte_carlo ()
 Return non-const access to the MonteCarlo object being controlled. 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...
 

Private Types

typedef AsyncMPITemperingBase Parent
 
typedef utility::vector1
< GridCoord
Grid
 
typedef utility::vector1
< std::pair< int, int > > 
ExchangeSchedule
 

Private Member Functions

void setup_exchange_schedule ()
 
core::Size coord2key (GridCoord const &coord, GridCoord const &max_coord, core::Size exclude_dim=0)
 small helper function; compute unique key out of (z1, z2, ... , zN) excluding zD More...
 

Private Attributes

utility::vector1
< core::scoring::ScoreFunctionOP
hamiltonians_
 ----------—— member variables --------------------—— More...
 
utility::vector0
< ExchangeSchedule
exchange_schedules_
 
core::Size current_exchange_schedule_
 
Grid exchange_grid_
 
core::Size exchange_grid_dimension_
 
bool successfully_initialized_
 
GridCoord max_coord_
 
std::string exchange_schedule_file_
 
BiasEnergyOP bias_energy_
 

Static Private Attributes

static bool options_registered_
 ---------------— register cmdline options ------------------------— More...
 

Additional Inherited Members

- Public Types inherited from protocols::canonical_sampling::TemperatureController
typedef utility::vector1
< core::Size
GridCoord
 
- 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 Attributes inherited from protocols::canonical_sampling::TemperingBase
utility::vector1< core::Realtemperatures_
 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_
 

Member Typedef Documentation

typedef utility::vector1<std::pair<int, int> > protocols::canonical_sampling::HamiltonianExchange::ExchangeSchedule
private

Constructor & Destructor Documentation

protocols::canonical_sampling::HamiltonianExchange::HamiltonianExchange ( )

References set_defaults().

protocols::canonical_sampling::HamiltonianExchange::~HamiltonianExchange ( )
overridedefault
protocols::canonical_sampling::HamiltonianExchange::HamiltonianExchange ( HamiltonianExchange const &  other)

Member Function Documentation

void protocols::canonical_sampling::HamiltonianExchange::apply ( core::pose::Pose )
inlineoverridevirtual

Main Method.

Reimplemented from protocols::canonical_sampling::AsyncMPITemperingBase.

void protocols::canonical_sampling::HamiltonianExchange::clear ( )
protected
protocols::moves::MoverOP protocols::canonical_sampling::HamiltonianExchange::clone ( ) const
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.

Size protocols::canonical_sampling::HamiltonianExchange::coord2key ( GridCoord const &  coord,
GridCoord const &  max_coord,
core::Size  exclude_dim = 0 
)
private

small helper function; compute unique key out of (z1, z2, ... , zN) excluding zD

Referenced by setup_exchange_schedule().

core::Size protocols::canonical_sampling::HamiltonianExchange::exchange_grid_dim ( ) const
inlineoverridevirtual
protocols::moves::MoverOP protocols::canonical_sampling::HamiltonianExchange::fresh_instance ( ) const
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.

std::string protocols::canonical_sampling::HamiltonianExchange::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::canonical_sampling::HamiltonianExchange::init_from_options ( )
overrideprotectedvirtual

Assigns user specified values to primitive members using command line options.

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::init_from_options().

bool protocols::canonical_sampling::HamiltonianExchange::initialize_exchange_schedule_from_file ( std::string const &  filename)
protectedvirtual

initialize exchange schedule from file, return false if IO error occurrs

brief: when an exchange schedule is given in a file, initialize from the file, instead of generate it by setup_exchange_schedule() each exchange pairs are specified with their temp_level, all pairs in one phase make one line in the input file

References exchange_schedules_, core::conformation::membrane::in, and protocols::canonical_sampling::tr().

Referenced by setup_exchange_schedule().

bool protocols::canonical_sampling::HamiltonianExchange::initialize_from_file ( std::string const &  filename)
overrideprotectedvirtual
void protocols::canonical_sampling::HamiltonianExchange::initialize_simulation ( core::pose::Pose pose,
MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
overridevirtual
void protocols::canonical_sampling::HamiltonianExchange::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  level,
core::Real  temperature,
core::Size  cycle 
)
overridevirtual
GridCoord protocols::canonical_sampling::HamiltonianExchange::level_2_grid_coord ( core::Size  level) const
inlineoverridevirtual
std::string protocols::canonical_sampling::HamiltonianExchange::mover_name ( )
static
Size protocols::canonical_sampling::HamiltonianExchange::next_exchange_level ( ) const
overrideprotectedvirtual
void protocols::canonical_sampling::HamiltonianExchange::next_exchange_schedule ( )
Size protocols::canonical_sampling::HamiltonianExchange::nlevels_per_dim ( core::Size  dim) const
overridevirtual
HamiltonianExchange & protocols::canonical_sampling::HamiltonianExchange::operator= ( HamiltonianExchange const &  other)
void protocols::canonical_sampling::HamiltonianExchange::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
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 exchange_schedule_file_, protocols::canonical_sampling::TemperingBase::parse_my_tag(), and successfully_initialized_.

void protocols::canonical_sampling::HamiltonianExchange::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::canonical_sampling::HamiltonianExchange::register_options ( )
static
void protocols::canonical_sampling::HamiltonianExchange::set_defaults ( )
protected

handling of options including command-line

Referenced by HamiltonianExchange().

void protocols::canonical_sampling::HamiltonianExchange::set_monte_carlo ( protocols::moves::MonteCarloOP  monte_carlo)
overridevirtual
void protocols::canonical_sampling::HamiltonianExchange::setup_exchange_schedule ( )
private
void protocols::canonical_sampling::HamiltonianExchange::show ( std::ostream &  output) const
overridevirtual
core::Real protocols::canonical_sampling::HamiltonianExchange::temperature_move ( core::Real  score)
overridevirtual

not possible for HamExchange – exit with ERROR if called

Implements protocols::canonical_sampling::TemperatureController.

core::Real protocols::canonical_sampling::HamiltonianExchange::temperature_move ( core::pose::Pose pose)
overridevirtual

execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT.

Reimplemented from protocols::canonical_sampling::TemperatureController.

Member Data Documentation

BiasEnergyOP protocols::canonical_sampling::HamiltonianExchange::bias_energy_
private

Referenced by operator=(), and set_monte_carlo().

core::Size protocols::canonical_sampling::HamiltonianExchange::current_exchange_schedule_
private
Grid protocols::canonical_sampling::HamiltonianExchange::exchange_grid_
private
core::Size protocols::canonical_sampling::HamiltonianExchange::exchange_grid_dimension_
private
std::string protocols::canonical_sampling::HamiltonianExchange::exchange_schedule_file_
private
utility::vector0< ExchangeSchedule > protocols::canonical_sampling::HamiltonianExchange::exchange_schedules_
private
utility::vector1< core::scoring::ScoreFunctionOP > protocols::canonical_sampling::HamiltonianExchange::hamiltonians_
private

----------—— member variables --------------------——

the different score-funcitons

Referenced by clear(), HamiltonianExchange(), initialize_from_file(), initialize_simulation(), operator=(), and show().

GridCoord protocols::canonical_sampling::HamiltonianExchange::max_coord_
private
bool protocols::canonical_sampling::HamiltonianExchange::options_registered_
staticprivate

---------------— register cmdline options ------------------------—

Referenced by register_options().

bool protocols::canonical_sampling::HamiltonianExchange::successfully_initialized_
private

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