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protocols::canonical_sampling::BiasEnergy Class Referenceabstract

#include <BiasEnergy.hh>

Inheritance diagram for protocols::canonical_sampling::BiasEnergy:
Inheritance graph
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Classes

class  Histogram
 

Public Member Functions

 BiasEnergy ()
 
 BiasEnergy (core::Size stride, core::Real omega, core::Real gamma)
 
 ~BiasEnergy () override
 
virtual core::Real evaluate (core::pose::Pose const &) const
 
void add_values_to_job (core::pose::Pose const &pose, protocols::jd2::Job &) const override
 
virtual void update (core::pose::Pose const &)
 
void swap_replicas ()
 
void write_to_string (std::string &str) const
 
void set_temperature (core::Real setting)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void initialize_simulation (core::pose::Pose &, MetropolisHastingsMover const &, core::Size) override
 Callback executed before any Monte Carlo trials are attempted. More...
 
void observe_after_metropolis (MetropolisHastingsMover const &) override
 Callback executed after the Metropolis criterion is evaluated. More...
 
void finalize_simulation (core::pose::Pose &, MetropolisHastingsMover const &) override
 Callback executed after all Monte Carlo trials are completed. More...
 
bool restart_simulation (core::pose::Pose &, MetropolisHastingsMover &, core::Size &cycle, core::Size &temp_level, core::Real &temperature) override
 Attempt to restart the last simulation that was recorded by this observer. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
 ThermodynamicObserver ()
 Default constructor. More...
 
 ~ThermodynamicObserver () override
 Destructor. More...
 
void apply (core::pose::Pose &) override
 Callback executed after each move is made. 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 MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Protected Member Functions

virtual core::Real extract_collective_var (core::pose::Pose const &) const =0
 
- 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 Types

typedef Histogram< float >::OP HistogramFloatOP
 
typedef Histogram< int >::OP HistogramIntOP
 

Private Attributes

HistogramFloatOP bias_grid_
 
HistogramIntOP count_grid_
 
core::Size step_counter_
 
core::Size stride_
 
core::Real omega_
 
core::Real gamma_
 
core::Real deltaT_
 
core::Real temperature_
 
core::Real default_bias_
 
std::string grid_output_file_
 

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::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. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::canonical_sampling::BiasEnergy::BiasEnergy ( )
protocols::canonical_sampling::BiasEnergy::BiasEnergy ( core::Size  stride,
core::Real  omega,
core::Real  gamma 
)
protocols::canonical_sampling::BiasEnergy::~BiasEnergy ( )
override

Member Function Documentation

void protocols::canonical_sampling::BiasEnergy::add_values_to_job ( core::pose::Pose const &  pose,
protocols::jd2::Job job 
) const
overridevirtual
core::Real protocols::canonical_sampling::BiasEnergy::evaluate ( core::pose::Pose const &  pose) const
virtual
virtual core::Real protocols::canonical_sampling::BiasEnergy::extract_collective_var ( core::pose::Pose const &  ) const
protectedpure virtual
void protocols::canonical_sampling::BiasEnergy::finalize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &   
)
overridevirtual
void protocols::canonical_sampling::BiasEnergy::initialize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &  ,
core::Size   
)
overridevirtual
void protocols::canonical_sampling::BiasEnergy::observe_after_metropolis ( MetropolisHastingsMover const &  metropolis_hastings_mover)
inlineoverridevirtual

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

void protocols::canonical_sampling::BiasEnergy::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References bias_grid_, count_grid_, gamma_, grid_output_file_, omega_, and stride_.

bool protocols::canonical_sampling::BiasEnergy::restart_simulation ( core::pose::Pose ,
MetropolisHastingsMover ,
core::Size ,
core::Size ,
core::Real  
)
overridevirtual

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 bias_grid_, count_grid_, protocols::canonical_sampling::MetropolisHastingsMover::get_last_checkpoint(), core::conformation::membrane::in, step_counter_, temperature_, and protocols::canonical_sampling::tr().

void protocols::canonical_sampling::BiasEnergy::set_temperature ( core::Real  setting)
void protocols::canonical_sampling::BiasEnergy::swap_replicas ( )

References bias_grid_, and count_grid_.

void protocols::canonical_sampling::BiasEnergy::update ( core::pose::Pose const &  pose)
virtual
void protocols::canonical_sampling::BiasEnergy::write_to_string ( std::string &  str) const

References bias_grid_, and count_grid_.

Member Data Documentation

HistogramFloatOP protocols::canonical_sampling::BiasEnergy::bias_grid_
private
HistogramIntOP protocols::canonical_sampling::BiasEnergy::count_grid_
private
core::Real protocols::canonical_sampling::BiasEnergy::default_bias_
private

Referenced by evaluate().

core::Real protocols::canonical_sampling::BiasEnergy::deltaT_
private

Referenced by set_temperature(), and update().

core::Real protocols::canonical_sampling::BiasEnergy::gamma_
private

Referenced by parse_my_tag(), and set_temperature().

std::string protocols::canonical_sampling::BiasEnergy::grid_output_file_
private
core::Real protocols::canonical_sampling::BiasEnergy::omega_
private

Referenced by parse_my_tag(), and update().

core::Size protocols::canonical_sampling::BiasEnergy::step_counter_
private

Referenced by restart_simulation(), and update().

core::Size protocols::canonical_sampling::BiasEnergy::stride_
private

Referenced by parse_my_tag(), and update().

core::Real protocols::canonical_sampling::BiasEnergy::temperature_
private

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