Rosetta Protocols  2014.35
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes | Private Attributes | List of all members
protocols::canonical_sampling::SilentTrajectoryRecorder Class Reference

Record a trajectory to the rosetta-specific silent file format. More...

#include <SilentTrajectoryRecorder.hh>

Public Types

typedef TrajectoryRecorder Parent
 
- 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
 

Public Member Functions

 SilentTrajectoryRecorder ()
 Default constructor. More...
 
 SilentTrajectoryRecorder (SilentTrajectoryRecorder const &)
 Copy constructor. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 
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...
 
virtual bool restart_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover &metropolis_hastings_mover, core::Size &cycle, core::Size &temp_level, core::Real &temperature)
 Attempt to restart the last simulation that was recorded by this observer. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::TrajectoryRecorder
 TrajectoryRecorder ()
 Default constructor. More...
 
 ~TrajectoryRecorder ()
 Destructor. More...
 
 TrajectoryRecorder (TrajectoryRecorder const &)
 Copy constructor. 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...
 
- 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 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)
 
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...
 
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 ()
 Associates relevant options with the TemperedDocking class. More...
 
- Static Public Member Functions inherited from protocols::canonical_sampling::TrajectoryRecorder
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)
 Append the given model to the silent file trajectory being written. 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

core::Size score_stride_
 

Static Protected Attributes

static bool options_registered_
 

Private Attributes

protocols::jd2::JobOutputterOP job_outputter_
 

Detailed Description

Record a trajectory to the rosetta-specific silent file format.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::canonical_sampling::SilentTrajectoryRecorder::SilentTrajectoryRecorder ( )

Default constructor.

References basic::options::option, and protocols::evaluation::options_registered_.

Referenced by fresh_instance().

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

Copy constructor.

Member Function Documentation

protocols::moves::MoverOP protocols::canonical_sampling::SilentTrajectoryRecorder::clone ( ) const
virtual

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.

protocols::moves::MoverOP protocols::canonical_sampling::SilentTrajectoryRecorder::fresh_instance ( ) const
virtual

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.

References SilentTrajectoryRecorder().

std::string protocols::canonical_sampling::SilentTrajectoryRecorder::get_name ( ) const
virtual

Return the name of this mover.

Reimplemented from protocols::canonical_sampling::TrajectoryRecorder.

void protocols::canonical_sampling::SilentTrajectoryRecorder::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
virtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::TrajectoryRecorder.

References protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation(), and protocols::canonical_sampling::tr.

void protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover)
virtual
void protocols::canonical_sampling::SilentTrajectoryRecorder::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::SilentTrajectoryRecorder::register_options ( )
static

Associates relevant options with the TemperedDocking class.

References NEW_OPT, protocols::evaluation::options_registered_, and protocols::moves::Mover::register_options().

Referenced by protocols::docking::TemperedDocking::register_options().

bool protocols::canonical_sampling::SilentTrajectoryRecorder::restart_simulation ( core::pose::Pose ,
protocols::canonical_sampling::MetropolisHastingsMover ,
core::Size ,
core::Size ,
core::Real  
)
virtual

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 from protocols::canonical_sampling::ThermodynamicObserver.

References core::pose::Pose::add_constraints(), utility::file::FileName::base(), core::io::silent::SilentFileData::begin(), basic::datacache::BasicDataCache::clear(), core::pose::Pose::constraint_set(), protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs(), protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas(), protocols::jd2::current_output_filename(), protocols::jd2::current_output_name(), protocols::jd2::current_replica(), core::pose::Pose::data(), protocols::canonical_sampling::TrajectoryRecorder::file_name(), filename(), core::io::silent::SilentFileData::filename(), core::io::silent::SilentFileData::matched_tags(), protocols::canonical_sampling::MetropolisHastingsMover::output_file_name(), core::io::silent::SilentFileData::read_file(), runtime_assert, core::io::silent::SilentFileData::size(), protocols::canonical_sampling::TrajectoryRecorder::stride(), utility::string2int(), tag, and protocols::canonical_sampling::tr.

void protocols::canonical_sampling::SilentTrajectoryRecorder::write_model ( core::pose::Pose const &  pose,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
)
protectedvirtual

Member Data Documentation

protocols::jd2::JobOutputterOP protocols::canonical_sampling::SilentTrajectoryRecorder::job_outputter_
private

Referenced by parse_my_tag(), and write_model().

bool protocols::canonical_sampling::SilentTrajectoryRecorder::options_registered_
staticprotected
core::Size protocols::canonical_sampling::SilentTrajectoryRecorder::score_stride_
protected

Referenced by parse_my_tag(), and write_model().


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