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protocols::canonical_sampling::TrajectoryRecorder Class Referenceabstract

#include <TrajectoryRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::TrajectoryRecorder:
Inheritance graph
Collaboration diagram for protocols::canonical_sampling::TrajectoryRecorder:
Collaboration graph

Public Member Functions

 TrajectoryRecorder ()
 Constructor. More...
 ~TrajectoryRecorder ()
 Destructor. More...
 TrajectoryRecorder (TrajectoryRecorder const &)
 Copy constructor. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string const & file_name () const
void file_name (std::string const &file_name)
core::Size model_count () const
core::Size step_count () const
core::Size stride () const
bool cumulate_jobs () const
bool cumulate_replicas () const
void stride (core::Size stride)
virtual void reset (protocols::moves::MonteCarlo const &mc, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
void update_after_boltzmann (core::pose::Pose const &pose, protocols::canonical_sampling::MetropolisHastingsMoverCAP metropolis_hastings_mover=0)
void update_after_boltzmann (protocols::moves::MonteCarlo const &mc)
virtual void apply (core::pose::Pose &pose)
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
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 ()
virtual ~ThermodynamicObserver ()
virtual bool restart_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
 callback executed before any Monte Carlo trials More...
virtual void finalize_simulation (core::pose::Pose &, protocols::canonical_sampling::MetropolisHastingsMover const &)
 callback executed after all Monte Carlo trials More...
virtual bool requires_pose ()
 return false here if a valid pose is not required for "observe" i.e. a trialcounter 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
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
 clone has to be overridden only if clone invocation is expected. 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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Static Public Member Functions

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

Protected Member Functions

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

Private Member Functions

TrajectoryRecorderoperator= (TrajectoryRecorder const &)

Private Attributes

core::Size stride_
core::Size model_count_
core::Size step_count_
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::TagPtr TagPtr
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Constructor & Destructor Documentation

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


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

Copy constructor.

Member Function Documentation

void protocols::canonical_sampling::TrajectoryRecorder::apply ( core::pose::Pose pose)
bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_jobs ( ) const
bool protocols::canonical_sampling::TrajectoryRecorder::cumulate_replicas ( ) const
std::string const& protocols::canonical_sampling::TrajectoryRecorder::file_name ( ) const
void protocols::canonical_sampling::TrajectoryRecorder::file_name ( std::string const &  file_name)

References file_name(), and file_name_.

std::string protocols::canonical_sampling::TrajectoryRecorder::get_name ( ) const

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

Implements protocols::moves::Mover.

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

void protocols::canonical_sampling::TrajectoryRecorder::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
core::Size protocols::canonical_sampling::TrajectoryRecorder::model_count ( ) const
void protocols::canonical_sampling::TrajectoryRecorder::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover)
TrajectoryRecorder & protocols::canonical_sampling::TrajectoryRecorder::operator= ( TrajectoryRecorder const &  )
void protocols::canonical_sampling::TrajectoryRecorder::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

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

References cumulate_jobs_, cumulate_replicas_, file_name_, and stride_.

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

void protocols::canonical_sampling::TrajectoryRecorder::register_options ( )

Associates relevant options with the TemperedDocking class.

References protocols::evaluation::options_registered_.

void protocols::canonical_sampling::TrajectoryRecorder::reset ( protocols::moves::MonteCarlo const &  mc,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
core::Size protocols::canonical_sampling::TrajectoryRecorder::step_count ( ) const
core::Size protocols::canonical_sampling::TrajectoryRecorder::stride ( ) const
void protocols::canonical_sampling::TrajectoryRecorder::stride ( core::Size  stride)

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

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

Referenced by TrajectoryRecorder().

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

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