Rosetta Protocols  2014.35
Public Member Functions | List of all members
protocols::canonical_sampling::ThermodynamicObserver Class Referenceabstract

Base class for reporting and recording data from a simulation. More...

#include <ThermodynamicObserver.hh>

Public Member Functions

 ThermodynamicObserver ()
 Default constructor. More...
virtual ~ThermodynamicObserver ()
 Destructor. More...
virtual void apply (core::pose::Pose &)
 Callback executed after each move is made. More...
virtual void initialize_simulation (core::pose::Pose &, MetropolisHastingsMover const &, core::Size)
 Callback executed before any Monte Carlo trials are attempted. More...
virtual void observe_after_metropolis (MetropolisHastingsMover const &metropolis_hastings_mover)=0
 Callback executed after the Metropolis criterion is evaluated. More...
virtual void finalize_simulation (core::pose::Pose &, MetropolisHastingsMover const &)
 Callback executed after all Monte Carlo trials are completed. 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 ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
void set_type (std::string const &setting)
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...
void set_current_tag (std::string const &new_tag)
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
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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
std::string get_type () const
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...
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 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...

Additional Inherited Members

- 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::stringStrings
- 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 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...

Detailed Description

Base class for reporting and recording data from a simulation.

Constructor & Destructor Documentation

protocols::canonical_sampling::ThermodynamicObserver::ThermodynamicObserver ( )

Default constructor.

protocols::canonical_sampling::ThermodynamicObserver::~ThermodynamicObserver ( )


Member Function Documentation

virtual void protocols::canonical_sampling::ThermodynamicObserver::apply ( core::pose::Pose )

Callback executed after each move is made.

Even though the argument is a reference to a non-const pose, this method should not make any changes to the pose. Making changes to the pose is the role of the ThermodynamicMover class. The role of this class is to simply observe the poses being generated.

Implements protocols::moves::Mover.

Reimplemented in protocols::canonical_sampling::MetricRecorder, protocols::canonical_sampling::TrajectoryRecorder, protocols::canonical_sampling::TemperatureController, protocols::canonical_sampling::AsyncMPITemperingBase, protocols::canonical_sampling::ParallelTempering, protocols::canonical_sampling::TemperingBase, protocols::canonical_sampling::HamiltonianExchange, and protocols::canonical_sampling::SimulatedTempering.

virtual void protocols::canonical_sampling::ThermodynamicObserver::finalize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &   
virtual void protocols::canonical_sampling::ThermodynamicObserver::initialize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &  ,
virtual void protocols::canonical_sampling::ThermodynamicObserver::observe_after_metropolis ( MetropolisHastingsMover const &  metropolis_hastings_mover)
pure virtual
virtual bool protocols::canonical_sampling::ThermodynamicObserver::requires_pose ( )

Return false if this observer does not require a valid pose. TrialCounterObserver is an example of such an observer.

Reimplemented in protocols::canonical_sampling::TrialCounterObserver, and protocols::canonical_sampling::ProgressBarObserver.

virtual bool protocols::canonical_sampling::ThermodynamicObserver::restart_simulation ( core::pose::Pose ,
MetropolisHastingsMover ,
core::Size ,
core::Size ,

Attempt to restart the last simulation that was recorded by this observer.

For example, consider an observer that records trajectories. This method should open the file that was going to be written, read out the last pose in that trajectory, and assign it to the given pose reference so that the current trajectory can start from the same place. Other observers may help setup other parts of the simulation.

This is not a particularly robust system, because it may require several unrelated observers working in concert to properly reconstitute the simulation. In fact, the restart feature in MetropolisHastingsMover is currently commented out, so this method is never actually invoked. I would advise reimplementing this method to utility_exit_with_message() in any subclasses you write, so that you don't waste time writing an unused method but so you don't confuse anyone if this feature gets revived in the future.

Reimplemented in protocols::canonical_sampling::DbTrajectoryRecorder, and protocols::canonical_sampling::SilentTrajectoryRecorder.

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