Rosetta Protocols  2014.35
Classes | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::canonical_sampling::BiasEnergy Class Referenceabstract

#include <BiasEnergy.hh>

Classes

class  Histogram
 

Public Member Functions

 BiasEnergy ()
 
 BiasEnergy (core::Size stride, core::Real omega, core::Real gamma)
 
virtual ~BiasEnergy ()
 
virtual core::Real evaluate (core::pose::Pose const &) const
 
virtual void add_values_to_job (core::pose::Pose const &pose, protocols::jd2::JobOP) const
 
virtual void update (core::pose::Pose const &)
 
void swap_replicas ()
 
void set_temperature (core::Real setting)
 
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)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual void initialize_simulation (core::pose::Pose &, MetropolisHastingsMover const &, core::Size)
 Callback executed before any Monte Carlo trials are attempted. More...
 
virtual void observe_after_metropolis (MetropolisHastingsMover const &)
 Callback executed after the Metropolis criterion is evaluated. More...
 
virtual void finalize_simulation (core::pose::Pose &, MetropolisHastingsMover const &)
 Callback executed after all Monte Carlo trials are completed. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicObserver
 ThermodynamicObserver ()
 Default constructor. More...
 
virtual ~ThermodynamicObserver ()
 Destructor. More...
 
virtual void apply (core::pose::Pose &)
 Callback executed after each move is made. More...
 
virtual bool restart_simulation (core::pose::Pose &, MetropolisHastingsMover &, core::Size &, core::Size &, core::Real &)
 Attempt to restart the last simulation that was recorded by this observer. 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)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. 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
 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...
 
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...
 

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 Attributes

Histogram< float >::OP bias_grid_
 
Histogram< int >::OP 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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 

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 ( )
virtual

Member Function Documentation

void protocols::canonical_sampling::BiasEnergy::add_values_to_job ( core::pose::Pose const &  pose,
protocols::jd2::JobOP  job 
) const
virtual
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 &   
)
virtual
void protocols::canonical_sampling::BiasEnergy::initialize_simulation ( core::pose::Pose ,
MetropolisHastingsMover const &  ,
core::Size   
)
virtual
virtual void protocols::canonical_sampling::BiasEnergy::observe_after_metropolis ( MetropolisHastingsMover const &  metropolis_hastings_mover)
inlinevirtual

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

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

References deltaT_, gamma_, and temperature_.

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

Member Data Documentation

Histogram<float>::OP protocols::canonical_sampling::BiasEnergy::bias_grid_
private
Histogram<int>::OP 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 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: