Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::canonical_sampling::TrajectoryRecorder Class Referenceabstract

Base class for recording a simulation trajectory. More...

#include <TrajectoryRecorder.hh>

Public Member Functions

 TrajectoryRecorder ()
 Default constructor. More...
 
 ~TrajectoryRecorder ()
 Destructor. More...
 
 TrajectoryRecorder (TrajectoryRecorder const &)
 Copy constructor. More...
 
virtual std::string get_name () const
 Return the name of this mover. More...
 
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Configure this mover from a RosettaScripts tag. More...
 
std::string const & file_name () const
 Return the file name for the trajectory. More...
 
void file_name (std::string const &file_name)
 Set the file name for the trajectory. More...
 
core::Size model_count () const
 Return the number of models that have been saved so far. More...
 
core::Size step_count () const
 Return the number of iterations that have occurred so far. More...
 
core::Size stride () const
 Return how often models should be written to the trajectory. More...
 
void stride (core::Size stride)
 Set how often models should be written to the trajectory. More...
 
core::Size cache_limit ()
 Return the number of poses that can be cached. More...
 
void cache_limit (core::Size limit)
 Specify the maximum number of poses that can be cached. More...
 
bool cumulate_jobs () const
 Return true if poses from different jobs will be written to the same trajectory file. More...
 
bool cumulate_replicas () const
 Return true if poses from different replicas will be written to the same trajectory file. More...
 
virtual void reset (protocols::moves::MonteCarlo const &mc, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
 Callback executed whenever the simulation is initialized or reset. More...
 
void update_after_boltzmann (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
 Callback executed after each move is made. More...
 
void update_after_boltzmann (protocols::moves::MonteCarlo const &mc)
 Callback executed after each move is made. More...
 
virtual void apply (core::pose::Pose &pose)
 Callback executed after each move is made. More...
 
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 Callback executed before any Monte Carlo trials are attempted. More...
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after the Metropolis criterion is evaluated. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
 ThermodynamicObserver ()
 Default constructor. More...
 
virtual ~ThermodynamicObserver ()
 Destructor. 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...
 
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...
 

Static Public Member Functions

static void register_options ()
 Associate relevant options with the TemperedDocking class. 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

virtual void write_model (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)=0
 Pure virtual method called to write a model to the output file. 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 Member Functions

TrajectoryRecorderoperator= (TrajectoryRecorder const &)
 Assignment not allowed. More...
 

Private Attributes

core::Size stride_
 
core::Size model_count_
 
core::Size step_count_
 
core::Size cache_limit_
 
std::string file_name_
 
bool cumulate_jobs_
 
bool cumulate_replicas_
 

Static Private Attributes

static bool options_registered_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Detailed Description

Base class for recording a simulation trajectory.

This class seems a little too geared towards file IO, which will make it awkward to create the database trajectory subclass that I want. But I'll get it to work one way or another.

Constructor & Destructor Documentation

protocols::canonical_sampling::TrajectoryRecorder::TrajectoryRecorder ( )
protocols::canonical_sampling::TrajectoryRecorder::~TrajectoryRecorder ( )

Destructor.

protocols::canonical_sampling::TrajectoryRecorder::TrajectoryRecorder ( TrajectoryRecorder const &  other)

Copy constructor.

References canonical_sampling.

Member Function Documentation

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

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.

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References update_after_boltzmann().

core::Size protocols::canonical_sampling::TrajectoryRecorder::cache_limit ( )
inline

Return the number of poses that can be cached.

References cache_limit_.

Referenced by protocols::canonical_sampling::DbTrajectoryRecorder::write_model().

void protocols::canonical_sampling::TrajectoryRecorder::cache_limit ( core::Size  limit)
inline

Specify the maximum number of poses that can be cached.

This option can also be specified on the command line using the -trajectory:cache_limit flag. Note that some recorders don't use a cache at all, and will therefore ignore this option.

References cache_limit_.

bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs ( ) const
inline

Return true if poses from different jobs will be written to the same trajectory file.

I suspect this is only meant to be used in the context of jd2. This option can only be set from the command line using the -trajectory:cumulate_jobs flag.

References cumulate_jobs_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas ( ) const
inline

Return true if poses from different replicas will be written to the same trajectory file.

I suspect this is only meant to be used in the context of jd2. This option can only be set from the command line using the -trajectory:cumulate_replicas flag.

References cumulate_replicas_.

Referenced by protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation(), protocols::canonical_sampling::SilentTrajectoryRecorder::write_model(), and protocols::canonical_sampling::PDBTrajectoryRecorder::write_model().

std::string const& protocols::canonical_sampling::TrajectoryRecorder::file_name ( ) const
inline
void protocols::canonical_sampling::TrajectoryRecorder::file_name ( std::string const &  file_name)
inline

Set the file name for the trajectory.

References file_name(), and file_name_.

std::string protocols::canonical_sampling::TrajectoryRecorder::get_name ( ) const
virtual
void protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
virtual
core::Size protocols::canonical_sampling::TrajectoryRecorder::model_count ( ) const
inline
void protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover)
virtual
TrajectoryRecorder & protocols::canonical_sampling::TrajectoryRecorder::operator= ( TrajectoryRecorder const &  )
private

Assignment not allowed.

References runtime_assert.

void protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual
void protocols::canonical_sampling::TrajectoryRecorder::register_options ( )
static

Associate relevant options with the TemperedDocking class.

References NEW_OPT, and protocols::evaluation::options_registered_.

void protocols::canonical_sampling::TrajectoryRecorder::reset ( protocols::moves::MonteCarlo const &  mc,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
)
virtual

Callback executed whenever the simulation is initialized or reset.

Reimplemented in protocols::canonical_sampling::PDBTrajectoryRecorder.

References model_count_, and step_count_.

Referenced by initialize_simulation(), and protocols::canonical_sampling::PDBTrajectoryRecorder::reset().

core::Size protocols::canonical_sampling::TrajectoryRecorder::step_count ( ) const
inline
core::Size protocols::canonical_sampling::TrajectoryRecorder::stride ( ) const
inline
void protocols::canonical_sampling::TrajectoryRecorder::stride ( core::Size  stride)
inline

Set how often models should be written to the trajectory.

This option can also be specified on the command line using the -trajectory:stride flag.

References stride(), and stride_.

void protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann ( core::pose::Pose const &  pose,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
)

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.

References model_count_, step_count_, stride_, and write_model().

Referenced by apply(), observe_after_metropolis(), and update_after_boltzmann().

void protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann ( protocols::moves::MonteCarlo const &  mc)

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.

References protocols::moves::MonteCarlo::last_accepted_pose(), and update_after_boltzmann().

virtual void protocols::canonical_sampling::TrajectoryRecorder::write_model ( core::pose::Pose const &  pose,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
)
protectedpure virtual

Member Data Documentation

core::Size protocols::canonical_sampling::TrajectoryRecorder::cache_limit_
private
bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs_
private
bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas_
private
std::string protocols::canonical_sampling::TrajectoryRecorder::file_name_
private
core::Size protocols::canonical_sampling::TrajectoryRecorder::model_count_
private
bool protocols::canonical_sampling::TrajectoryRecorder::options_registered_
staticprivate

Referenced by TrajectoryRecorder().

core::Size protocols::canonical_sampling::TrajectoryRecorder::step_count_
private
core::Size protocols::canonical_sampling::TrajectoryRecorder::stride_
private

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