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protocols::canonical_sampling::MetricRecorder Class Reference

#include <MetricRecorder.hh>

Inheritance diagram for protocols::canonical_sampling::MetricRecorder:
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Public Member Functions

 MetricRecorder ()
 Constructor. More...
 
 ~MetricRecorder ()
 Destructor. More...
 
 MetricRecorder (MetricRecorder const &)
 Copy constructor. More...
 
MetricRecorderoperator= (MetricRecorder const &)
 operator= More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::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...
 
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...
 
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...
 
std::string const & file_name () const
 
void file_name (std::string const &file_name)
 
core::Size stride () const
 
void stride (core::Size stride)
 
bool cumulate_jobs () const
 
void cumulate_jobs (bool cumulate_jobs)
 
bool cumulate_replicas () const
 
void cumulate_replicas (bool cumulate_replicas)
 
bool prepend_output_name () const
 
void prepend_output_name (bool prepend_output_name)
 
void add_torsion (core::id::TorsionID const &torsion_id, std::string name="")
 
void add_torsion (core::pose::Pose const &pose, std::string const &rsd, std::string type, core::Size torsion, std::string name="")
 
void reset (core::pose::Pose const &pose, 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)
 
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...
 
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback executed after all Monte Carlo trials 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 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)
 
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_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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void write_model (core::pose::Pose const &pose)
 

Private Attributes

std::string file_name_
 
core::Size stride_
 
bool cumulate_jobs_
 
bool cumulate_replicas_
 
bool prepend_output_name_
 
core::Size step_count_
 
utility::io::ozstream recorder_stream_
 
utility::vector1< std::pair
< core::id::TorsionID,
std::string > > 
torsion_ids_
 
time_t last_flush_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Constructor & Destructor Documentation

protocols::canonical_sampling::MetricRecorder::MetricRecorder ( )

Constructor.

Referenced by fresh_instance().

protocols::canonical_sampling::MetricRecorder::~MetricRecorder ( )

Destructor.

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

Copy constructor.

Member Function Documentation

void protocols::canonical_sampling::MetricRecorder::add_torsion ( core::id::TorsionID const &  torsion_id,
std::string  name = "" 
)
void protocols::canonical_sampling::MetricRecorder::add_torsion ( core::pose::Pose const &  pose,
std::string const &  rsd,
std::string  type,
core::Size  torsion,
std::string  name = "" 
)
void protocols::canonical_sampling::MetricRecorder::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::canonical_sampling::MetricRecorder::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

bool protocols::canonical_sampling::MetricRecorder::cumulate_jobs ( ) const

References cumulate_jobs_.

Referenced by cumulate_jobs().

void protocols::canonical_sampling::MetricRecorder::cumulate_jobs ( bool  cumulate_jobs)

References cumulate_jobs(), and cumulate_jobs_.

bool protocols::canonical_sampling::MetricRecorder::cumulate_replicas ( ) const

References cumulate_replicas_.

Referenced by cumulate_replicas().

void protocols::canonical_sampling::MetricRecorder::cumulate_replicas ( bool  cumulate_replicas)
std::string const & protocols::canonical_sampling::MetricRecorder::file_name ( ) const

References file_name_.

Referenced by file_name(), and initialize_simulation().

void protocols::canonical_sampling::MetricRecorder::file_name ( std::string const &  file_name)

References file_name(), and file_name_.

void protocols::canonical_sampling::MetricRecorder::finalize_simulation ( core::pose::Pose ,
protocols::canonical_sampling::MetropolisHastingsMover const &   
)
virtual

callback executed after all Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicObserver.

References recorder_stream_.

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

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).

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 MetricRecorder().

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

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

Implements protocols::moves::Mover.

void protocols::canonical_sampling::MetricRecorder::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
virtual
void protocols::canonical_sampling::MetricRecorder::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover)
virtual
MetricRecorder & protocols::canonical_sampling::MetricRecorder::operator= ( MetricRecorder const &  )

operator=

void protocols::canonical_sampling::MetricRecorder::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 
)
virtual

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.

References add_torsion(), cumulate_jobs_, cumulate_replicas_, file_name_, protocols::moves::Mover::name(), prepend_output_name_, stride_, and protocols::moves::Mover::type().

bool protocols::canonical_sampling::MetricRecorder::prepend_output_name ( ) const

References prepend_output_name_.

Referenced by prepend_output_name().

void protocols::canonical_sampling::MetricRecorder::prepend_output_name ( bool  prepend_output_name)
virtual bool protocols::canonical_sampling::MetricRecorder::reinitialize_for_each_job ( ) const
inlinevirtual

this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

void protocols::canonical_sampling::MetricRecorder::reset ( core::pose::Pose const &  pose,
protocols::canonical_sampling::MetropolisHastingsMoverCAP  metropolis_hastings_mover = 0 
)
core::Size protocols::canonical_sampling::MetricRecorder::stride ( ) const

References stride_.

Referenced by stride().

void protocols::canonical_sampling::MetricRecorder::stride ( core::Size  stride)

References stride(), and stride_.

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

Member Data Documentation

bool protocols::canonical_sampling::MetricRecorder::cumulate_jobs_
private
bool protocols::canonical_sampling::MetricRecorder::cumulate_replicas_
private
std::string protocols::canonical_sampling::MetricRecorder::file_name_
private
time_t protocols::canonical_sampling::MetricRecorder::last_flush_
private

Referenced by update_after_boltzmann().

bool protocols::canonical_sampling::MetricRecorder::prepend_output_name_
private
utility::io::ozstream protocols::canonical_sampling::MetricRecorder::recorder_stream_
private
core::Size protocols::canonical_sampling::MetricRecorder::step_count_
private

Referenced by reset(), and update_after_boltzmann().

core::Size protocols::canonical_sampling::MetricRecorder::stride_
private
utility::vector1<std::pair<core::id::TorsionID, std::string> > protocols::canonical_sampling::MetricRecorder::torsion_ids_
private

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