Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Private Attributes | List of all members
protocols::canonical_sampling::SidechainMetropolisHastingsMover Class Reference

Run a sidechain-only canonical Monte Carlo simulation. More...

#include <SidechainMetropolisHastingsMover.hh>

Inheritance diagram for protocols::canonical_sampling::SidechainMetropolisHastingsMover:
Inheritance graph
[legend]

Public Types

typedef MetropolisHastingsMover Parent
 
- 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
 

Public Member Functions

 SidechainMetropolisHastingsMover ()
 Default constructor. More...
 
 SidechainMetropolisHastingsMover (core::Size stride)
 Constructor with stride parameter. More...
 
 SidechainMetropolisHastingsMover (SidechainMetropolisHastingsMover const &metropolis_hastings_mover)
 Copy constructor. More...
 
 ~SidechainMetropolisHastingsMover () override
 Default destructor. More...
 
void apply (core::pose::Pose &pose) override
 Run the sidechain-only simulation. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const override
 Return the name of this mover. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Return a newly instantiated mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Use a RosettaScripts tag to configure this mover. More...
 
bool pass_metropolis (core::Real delta_energy, core::Real last_proposal_density_ratio) const
 Return true if a move should be accepted, given delta_energy and proposal_density_ratio. More...
 
core::Size output_count (core::Size ct) const
 Return non-zero if the observers should be invoked on this iteration. More...
 
void set_stride (core::Size setting)
 Set the frequency with which the observers should be invoked. More...
 
- Public Member Functions inherited from protocols::canonical_sampling::MetropolisHastingsMover
 MetropolisHastingsMover ()
 Default constructor. More...
 
 MetropolisHastingsMover (MetropolisHastingsMover const &metropolis_hastings_mover)
 Copy constructor. More...
 
 ~MetropolisHastingsMover () override
 Destructor. More...
 
bool reinitialize_for_each_job () const override
 Return false. This mover does not need to be reinitialized for each job. More...
 
bool reinitialize_for_new_input () const override
 Return false. This mover does not need to be reinitialized for new input. More...
 
protocols::moves::MonteCarloCOP monte_carlo () const
 Return the MonteCarlo object being used by this simulation. More...
 
void set_monte_carlo (protocols::moves::MonteCarloOP monte_carlo)
 Provide a MonteCarlo object to use for this simulation. More...
 
TemperatureControllerCOP tempering () const
 Return the TemperatureController being used by this simulation. More...
 
void set_tempering (TemperatureControllerOP)
 Provide a TemperatureController to use for this simulation. More...
 
core::Size ntrials () const
 Return the number of iterations used by this simulation. More...
 
void set_ntrials (core::Size ntrials)
 Set the number of iterations to use for this simulation. More...
 
core::Size current_trial () const
 Return the iteration currently being processed by the simulation. More...
 
std::string const & output_name () const
 Return the file name used by some of the observers to output data. More...
 
void set_output_name (std::string const &output_name)
 Set the file name used by some of the observers to output data. More...
 
std::string output_file_name (std::string const &suffix, bool cumulate_jobs=false, bool cumulate_replicas=false) const
 Return a file name that is consistent with the given options. More...
 
virtual ThermodynamicMoverOP random_mover () const
 Return true if the simulation has been completed. More...
 
virtual void add_mover (ThermodynamicMoverOP mover, core::Real weight, utility::tag::TagCOP const &subtag)
 Add the given mover to the simulation. More...
 
virtual void add_mover (ThermodynamicMoverOP mover, core::Real weight)
 Add the given mover to the simulation. More...
 
void add_backrub_mover (core::Real weight)
 Convenience method to add a backrub move to the simulation. More...
 
void add_kic_mover (core::Real weight, protocols::loops::Loop const &loop)
 Convenience method to add a kinematic closure move to the simulation. More...
 
void add_small_mover (core::Real weight)
 Convenience method to add a small move to the simulation. More...
 
void add_shear_mover (core::Real weight)
 Convenience method to add a shear move to the simulation. More...
 
void add_sidechain_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta)
 Convenience method to add a sidechain move to the simulation. More...
 
void add_sidechain_mc_mover (core::Real weight, core::Real prob_uniform, core::Real prob_withinrot, bool preserve_cbeta, core::Size ntrials)
 Convenience method to add a Monte Carlo sidechain move to the simulation. This move uses an internal Monte Carlo loop to generate a whole new set of sidechain conformations. More...
 
void add_observer (ThermodynamicObserverOP observer)
 Add the given observer to this simulation. More...
 
ThermodynamicMover const & last_move () const
 Return the most recently used ThermodynamicMover. More...
 
bool last_accepted () const
 Return true if the last attempted move was accepted. More...
 
std::string get_last_checkpoint () const
 
- 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...
 
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
 
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...
 

Private Attributes

core::Size stride_
 

Additional Inherited Members

- Static Public Member Functions inherited from protocols::canonical_sampling::MetropolisHastingsMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string mover_or_add_group_name ()
 
static std::string add_ct_name (std::string)
 
- 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...
 
- Protected Member Functions inherited from protocols::canonical_sampling::MetropolisHastingsMover
TemperatureControllerOP const & tempering ()
 Protected non-const access to the TemperatureController. More...
 
ThermodynamicMoverOP mover_by_index (numeric::Size idx) const
 Return the mover that was added at the given index. More...
 
void write_checkpoint (core::pose::Pose const &pose)
 write checkpoint snapshots for restarting More...
 
bool get_checkpoints ()
 get checkpoint_id for restarting More...
 
void wind_down_simulation (core::pose::Pose &pose)
 Finalize all the movers and observers used in this simulation, and write some debrief statistics to the tracer. More...
 
core::Size prepare_simulation (core::pose::Pose &pose)
 Initialize all the movers and observers to be used in this simulation. More...
 
void set_last_accepted (bool setting)
 Indicate whether or not the last attempted move was accepted. More...
 
void set_last_move (ThermodynamicMoverOP setting)
 Indicate what type of move was last attempted. More...
 
utility::vector1
< ThermodynamicObserverOP >
const & 
observers ()
 Return a list of all observers attached to this simulation. More...
 
protocols::moves::MonteCarlononconst_monte_carlo ()
 Protected non-const access to the MonteCarlo object. 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...
 

Detailed Description

Run a sidechain-only canonical Monte Carlo simulation.

The Monte Carlo algorithm present in apply() has been optimized for the case where only the sidechains can moves. This makes it possible speed up score function evaluation by either precalculating and/or caching residue pair energies. In this specific case, however, I'm not exactly sure how the algorithm is doing its optimization.

Warning
Although this class inherits from MetropolisHastingsMover, it doesn't support all of its parent's interface. In particular, since the algorithm is customized for a particular sidechain move, movers added via add_mover() or its related methods are ignored. However, observers added via add_observer() can still be used to report on the state of the simulation.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( )

Default constructor.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( core::Size  stride)

Constructor with stride parameter.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::SidechainMetropolisHastingsMover ( SidechainMetropolisHastingsMover const &  metropolis_hastings_mover)
default

Copy constructor.

protocols::canonical_sampling::SidechainMetropolisHastingsMover::~SidechainMetropolisHastingsMover ( )
overridedefault

Default destructor.

Member Function Documentation

void protocols::canonical_sampling::SidechainMetropolisHastingsMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::canonical_sampling::SidechainMetropolisHastingsMover::clone ( ) const
overridevirtual

Return the name of this mover.

Return a copy of this mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

protocols::moves::MoverOP protocols::canonical_sampling::SidechainMetropolisHastingsMover::fresh_instance ( ) const
overridevirtual

Return a newly instantiated mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

std::string protocols::canonical_sampling::SidechainMetropolisHastingsMover::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

core::Size protocols::canonical_sampling::SidechainMetropolisHastingsMover::output_count ( core::Size  ct) const

Return non-zero if the observers should be invoked on this iteration.

See also
set_stride()

References stride_.

Referenced by apply().

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

Use a RosettaScripts tag to configure this mover.

Reimplemented from protocols::canonical_sampling::MetropolisHastingsMover.

References protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), and stride_.

bool protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis ( core::Real  delta_energy,
core::Real  last_proposal_density_ratio 
) const
void protocols::canonical_sampling::SidechainMetropolisHastingsMover::set_stride ( core::Size  setting)
inline

Set the frequency with which the observers should be invoked.

See also
output_count()

Member Data Documentation

core::Size protocols::canonical_sampling::SidechainMetropolisHastingsMover::stride_
private

Referenced by output_count(), and parse_my_tag().


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