Classes | Public Member Functions | Protected Member Functions | Private Types | Private Attributes | List of all members
protocols::canonical_sampling::BiasEnergy Class Referenceabstract

#include <BiasEnergy.hh>

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


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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
- Public Member Functions inherited from protocols::jd2::JobOutputterObserver
virtual ~JobOutputterObserver ()=default

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

◆ HistogramFloatOP

◆ HistogramIntOP

Constructor & Destructor Documentation

◆ BiasEnergy() [1/2]

protocols::canonical_sampling::BiasEnergy::BiasEnergy ( )

◆ BiasEnergy() [2/2]

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

◆ ~BiasEnergy()

protocols::canonical_sampling::BiasEnergy::~BiasEnergy ( )

Member Function Documentation

◆ add_values_to_job()

void protocols::canonical_sampling::BiasEnergy::add_values_to_job ( core::pose::Pose const &  pose,
protocols::jd2::Job job 
) const

◆ evaluate()

core::Real protocols::canonical_sampling::BiasEnergy::evaluate ( core::pose::Pose const &  pose) const

◆ extract_collective_var()

virtual core::Real protocols::canonical_sampling::BiasEnergy::extract_collective_var ( core::pose::Pose const &  ) const
protectedpure virtual

◆ finalize_simulation()

void protocols::canonical_sampling::BiasEnergy::finalize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &   

◆ initialize_simulation()

void protocols::canonical_sampling::BiasEnergy::initialize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &  ,

◆ observe_after_metropolis()

void protocols::canonical_sampling::BiasEnergy::observe_after_metropolis ( MetropolisHastingsMover const &  metropolis_hastings_mover)

Callback executed after the Metropolis criterion is evaluated.

Implements protocols::canonical_sampling::ThermodynamicObserver.

◆ parse_my_tag()

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

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_.

◆ restart_simulation()

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

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().

◆ set_temperature()

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

◆ swap_replicas()

void protocols::canonical_sampling::BiasEnergy::swap_replicas ( )

References bias_grid_, and count_grid_.

◆ update()

void protocols::canonical_sampling::BiasEnergy::update ( core::pose::Pose const &  pose)

◆ write_to_string()

void protocols::canonical_sampling::BiasEnergy::write_to_string ( std::string &  str) const

Member Data Documentation

◆ bias_grid_

HistogramFloatOP protocols::canonical_sampling::BiasEnergy::bias_grid_

◆ count_grid_

HistogramIntOP protocols::canonical_sampling::BiasEnergy::count_grid_

◆ default_bias_

core::Real protocols::canonical_sampling::BiasEnergy::default_bias_

Referenced by evaluate().

◆ deltaT_

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

Referenced by set_temperature(), and update().

◆ gamma_

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

Referenced by parse_my_tag(), and set_temperature().

◆ grid_output_file_

std::string protocols::canonical_sampling::BiasEnergy::grid_output_file_

◆ omega_

core::Real protocols::canonical_sampling::BiasEnergy::omega_

Referenced by parse_my_tag(), and update().

◆ step_counter_

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

Referenced by restart_simulation(), and update().

◆ stride_

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

Referenced by parse_my_tag(), and update().

◆ temperature_

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

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