Rosetta 3.4
Public Member Functions | Static Public Member Functions | Protected Member Functions
protocols::canonical_sampling::SimulatedTempering Class Reference

#include <SimulatedTempering.hh>

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List of all members.

Public Member Functions

 SimulatedTempering ()
 SimulatedTempering (SimulatedTempering const &)
virtual void apply (core::pose::Pose &)
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected.
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).
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.
core::Real temperature_move (core::Real score)
 execute the temperatur move ( called by observer_after_metropolis ) returns the current temperatur in kT.
virtual void initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
 callback executed before any Monte Carlo trials
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback executed after all Monte Carlo trials
void finalize_simulation (std::string const &output_name)

Static Public Member Functions

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.

Protected Member Functions

void set_defaults ()
 handling of options including command-line
virtual void init_from_options ()
 Assigns user specified values to primitive members using command line options.
void reweight ()
 update weights based on current counts
void reset_raw_counter ()
 reset the raw counts per state (not the weighted ones) to 0
virtual bool initialize_from_file (std::string const &filename)
 initialize temperatures and weights from file, return false if IO error occurrs
virtual void write_to_file (std::string const &file_in, std::string const &output_name, utility::vector1< core::Real > const &wcounts)

Constructor & Destructor Documentation

protocols::canonical_sampling::SimulatedTempering::SimulatedTempering ( )

Referenced by clone(), and fresh_instance().

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

Member Function Documentation

virtual void protocols::canonical_sampling::SimulatedTempering::apply ( core::pose::Pose ) [inline, virtual]
protocols::moves::MoverOP protocols::canonical_sampling::SimulatedTempering::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.

References SimulatedTempering().

void protocols::canonical_sampling::SimulatedTempering::finalize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover 
) [virtual]
void protocols::canonical_sampling::SimulatedTempering::finalize_simulation ( std::string const &  output_name)
protocols::moves::MoverOP protocols::canonical_sampling::SimulatedTempering::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 SimulatedTempering().

std::string protocols::canonical_sampling::SimulatedTempering::get_name ( ) const [virtual]

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

Reimplemented from protocols::canonical_sampling::TemperingBase.

void protocols::canonical_sampling::SimulatedTempering::init_from_options ( ) [protected, virtual]

Assigns user specified values to primitive members using command line options.

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::tr().

bool protocols::canonical_sampling::SimulatedTempering::initialize_from_file ( std::string const &  filename) [protected, virtual]

initialize temperatures and weights from file, return false if IO error occurrs

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::set_temperatures(), and protocols::canonical_sampling::tr().

void protocols::canonical_sampling::SimulatedTempering::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
) [virtual]
void protocols::canonical_sampling::SimulatedTempering::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::canonical_sampling::TemperingBase.

References protocols::canonical_sampling::TemperingBase::parse_my_tag().

void protocols::canonical_sampling::SimulatedTempering::register_options ( ) [static]

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.

Reimplemented from protocols::canonical_sampling::TemperingBase.

References protocols::evaluation::options_registered_, and protocols::evaluation::register_options().

void protocols::canonical_sampling::SimulatedTempering::reset_raw_counter ( ) [protected]

reset the raw counts per state (not the weighted ones) to 0

callback executed before any Monte Carlo trials use to fill count_ with 0

References protocols::canonical_sampling::TemperingBase::n_temp_levels().

Referenced by finalize_simulation(), initialize_simulation(), and temperature_move().

void protocols::canonical_sampling::SimulatedTempering::reweight ( ) [protected]

update weights based on current counts

Referenced by finalize_simulation(), and temperature_move().

void protocols::canonical_sampling::SimulatedTempering::set_defaults ( ) [protected]

handling of options including command-line

Reimplemented from protocols::canonical_sampling::TemperingBase.

core::Real protocols::canonical_sampling::SimulatedTempering::temperature_move ( core::Real  score) [virtual]
void protocols::canonical_sampling::SimulatedTempering::write_to_file ( std::string const &  file_in,
std::string const &  output_name,
utility::vector1< core::Real > const &  wcounts 
) [protected, virtual]

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