Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::backrub::BackrubSidechainMover Class Reference

#include <BackrubSidechainMover.hh>

Public Member Functions

 BackrubSidechainMover ()
 
 BackrubSidechainMover (BackrubSidechainMover const &mover)
 
virtual ~BackrubSidechainMover ()
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
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...
 
void update_segments (core::pose::Pose const &pose)
 
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 are attempted. More...
 
virtual void apply (core::pose::Pose &pose)
 
virtual void observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 callback after the Metropolis criterion is evaluated More...
 
virtual void finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
 Callback executed after all Monte Carlo trials are completed. More...
 
utility::vector1< core::Size >
const & 
pivot_residues () const
 
void set_pivot_residues (utility::vector1< core::Size > const &pivot_residues)
 
core::pack::task::TaskFactoryCOP task_factory () const
 
void set_task_factory (core::pack::task::TaskFactoryOP task_factory)
 
core::Real prob_uniform () const
 get the probability of uniformly sampling chi angles More...
 
void set_prob_uniform (core::Real prob_uniform)
 set the probability of uniformly sampling chi angles More...
 
core::Real prob_withinrot () const
 get the probability of sampling within the same rotamer More...
 
void set_prob_withinrot (core::Real prob_withinrot)
 set the probability of sampling within the same rotamer More...
 
core::Real prob_random_pert_current () const
 
void set_prob_random_pert_current (core::Real prob_pert)
 
virtual bool preserve_detailed_balance () const
 get whether detailed balance is preserved More...
 
virtual void set_preserve_detailed_balance (bool preserve_detailed_balance)
 set whether detailed balance is preserved More...
 
bool require_mm_bend () const
 get whether to exit during initialize_simulation if the mm_bend term isn't turned on More...
 
void set_require_mm_bend (bool require_mm_bend)
 set whether to exit during initialize_simulation if the mm_bend term isn't turned on More...
 
virtual utility::vector1
< core::id::TorsionID_Range
torsion_id_ranges (core::pose::Pose &pose)
 get the TorsionIDs perturbed by the mover during moves, along with their ranges More...
 
bool record_statistics () const
 get whether to record mover statistics or not More...
 
void set_record_statistics (bool record_statistics)
 set whether to record mover statistics or not More...
 
std::string const & statistics_filename () const
 get filename for statistics output More...
 
void set_statistics_filename (std::string const &statistics_filename)
 set filename for statistics output More...
 
void reset_statistics ()
 
void output_statistics (std::ostream &out)
 
- Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
 ThermodynamicMover ()
 Default constructor. More...
 
virtual ~ThermodynamicMover ()
 Default destructor. More...
 
virtual core::Real last_proposal_density_ratio ()
 Return the proposal density ratio for last apply method. More...
 
virtual bool is_multi_trial ()
 Return true if the move performs multiple trials on each apply. More...
 
virtual core::Real last_inner_score_temperature_delta ()
 If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...
 
virtual
protocols::canonical_sampling::MetropolisHastingsMoverAP 
metropolis_hastings_mover ()
 If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...
 
virtual void set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
 If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. More...
 
virtual utility::vector1
< core::id::DOF_ID_Range
dof_id_ranges (core::pose::Pose &pose)
 Return a list specifying which degrees of freedom may be perturbed by apply(), and the in what range each perturbation may be. 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...
 
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)
 
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...
 
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...
 

Private Member Functions

void setup_histograms ()
 
void record_histograms (bool accept)
 
void update_type ()
 

Private Attributes

protocols::backrub::BackrubMoverOP backrub_mover_
 
protocols::simple_moves::sidechain_moves::SidechainMoverOP sidechain_mover_
 
utility::vector1< core::Sizevalid_segments_
 
core::Size last_valid_segment_index_
 
core::Real last_chi1_pre_
 
core::Real last_chi1_post_
 
bool record_statistics_
 
std::string statistics_filename_
 
utility::vector1
< numeric::MultiDimensionalHistogram
proposal_hists_
 
utility::vector1
< numeric::MultiDimensionalHistogram
accept_hists_
 

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...
 
- 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...
 

Constructor & Destructor Documentation

protocols::backrub::BackrubSidechainMover::BackrubSidechainMover ( )
protocols::backrub::BackrubSidechainMover::BackrubSidechainMover ( BackrubSidechainMover const &  mover)
protocols::backrub::BackrubSidechainMover::~BackrubSidechainMover ( )
virtual

Member Function Documentation

void protocols::backrub::BackrubSidechainMover::apply ( core::pose::Pose pose)
virtual
protocols::moves::MoverOP protocols::backrub::BackrubSidechainMover::clone ( ) const
virtual

Return a clone of the Mover object.

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.

void protocols::backrub::BackrubSidechainMover::finalize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover 
)
virtual

Callback executed after all Monte Carlo trials are completed.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References filename(), and protocols::canonical_sampling::MetropolisHastingsMover::output_name().

protocols::moves::MoverOP protocols::backrub::BackrubSidechainMover::fresh_instance ( ) const
virtual

Generates a new Mover object freshly created with the default ctor.

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.

std::string protocols::backrub::BackrubSidechainMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::backrub::BackrubSidechainMover::initialize_simulation ( core::pose::Pose pose,
protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover,
core::Size  cycle 
)
virtual

Callback executed before any Monte Carlo trials are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References core::pose::Pose::fold_tree().

void protocols::backrub::BackrubSidechainMover::observe_after_metropolis ( protocols::canonical_sampling::MetropolisHastingsMover const &  metropolis_hastings_mover)
virtual

callback after the Metropolis criterion is evaluated

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References protocols::canonical_sampling::MetropolisHastingsMover::monte_carlo().

void protocols::backrub::BackrubSidechainMover::output_statistics ( std::ostream &  out)
void protocols::backrub::BackrubSidechainMover::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 end, basic::datacache::DataMap::get(), core::pose::get_resnum_list(), basic::datacache::DataMap::has(), core::pack::task::TaskFactory::push_back(), and utility::string_split().

utility::vector1< core::Size > const & protocols::backrub::BackrubSidechainMover::pivot_residues ( ) const
bool protocols::backrub::BackrubSidechainMover::preserve_detailed_balance ( ) const
virtual

get whether detailed balance is preserved

Implements protocols::canonical_sampling::ThermodynamicMover.

core::Real protocols::backrub::BackrubSidechainMover::prob_random_pert_current ( ) const
core::Real protocols::backrub::BackrubSidechainMover::prob_uniform ( ) const

get the probability of uniformly sampling chi angles

core::Real protocols::backrub::BackrubSidechainMover::prob_withinrot ( ) const

get the probability of sampling within the same rotamer

void protocols::backrub::BackrubSidechainMover::record_histograms ( bool  accept)
private
bool protocols::backrub::BackrubSidechainMover::record_statistics ( ) const

get whether to record mover statistics or not

bool protocols::backrub::BackrubSidechainMover::require_mm_bend ( ) const

get whether to exit during initialize_simulation if the mm_bend term isn't turned on

void protocols::backrub::BackrubSidechainMover::reset_statistics ( )
void protocols::backrub::BackrubSidechainMover::set_pivot_residues ( utility::vector1< core::Size > const &  pivot_residues)
void protocols::backrub::BackrubSidechainMover::set_preserve_detailed_balance ( bool  preserve_detailed_balance)
virtual

set whether detailed balance is preserved

Implements protocols::canonical_sampling::ThermodynamicMover.

void protocols::backrub::BackrubSidechainMover::set_prob_random_pert_current ( core::Real  prob_pert)
void protocols::backrub::BackrubSidechainMover::set_prob_uniform ( core::Real  prob_uniform)

set the probability of uniformly sampling chi angles

void protocols::backrub::BackrubSidechainMover::set_prob_withinrot ( core::Real  prob_withinrot)

set the probability of sampling within the same rotamer

void protocols::backrub::BackrubSidechainMover::set_record_statistics ( bool  record_statistics)

set whether to record mover statistics or not

void protocols::backrub::BackrubSidechainMover::set_require_mm_bend ( bool  require_mm_bend)

set whether to exit during initialize_simulation if the mm_bend term isn't turned on

void protocols::backrub::BackrubSidechainMover::set_statistics_filename ( std::string const &  statistics_filename)

set filename for statistics output

void protocols::backrub::BackrubSidechainMover::set_task_factory ( core::pack::task::TaskFactoryOP  task_factory)
void protocols::backrub::BackrubSidechainMover::setup_histograms ( )
private
std::string const & protocols::backrub::BackrubSidechainMover::statistics_filename ( ) const

get filename for statistics output

core::pack::task::TaskFactoryCOP protocols::backrub::BackrubSidechainMover::task_factory ( ) const
utility::vector1< core::id::TorsionID_Range > protocols::backrub::BackrubSidechainMover::torsion_id_ranges ( core::pose::Pose pose)
virtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.

void protocols::backrub::BackrubSidechainMover::update_segments ( core::pose::Pose const &  pose)
void protocols::backrub::BackrubSidechainMover::update_type ( )
private

Member Data Documentation

utility::vector1<numeric::MultiDimensionalHistogram> protocols::backrub::BackrubSidechainMover::accept_hists_
private
protocols::backrub::BackrubMoverOP protocols::backrub::BackrubSidechainMover::backrub_mover_
private

Referenced by BackrubSidechainMover().

core::Real protocols::backrub::BackrubSidechainMover::last_chi1_post_
private
core::Real protocols::backrub::BackrubSidechainMover::last_chi1_pre_
private
core::Size protocols::backrub::BackrubSidechainMover::last_valid_segment_index_
private
utility::vector1<numeric::MultiDimensionalHistogram> protocols::backrub::BackrubSidechainMover::proposal_hists_
private
bool protocols::backrub::BackrubSidechainMover::record_statistics_
private
protocols::simple_moves::sidechain_moves::SidechainMoverOP protocols::backrub::BackrubSidechainMover::sidechain_mover_
private

Referenced by BackrubSidechainMover().

std::string protocols::backrub::BackrubSidechainMover::statistics_filename_
private
utility::vector1<core::Size> protocols::backrub::BackrubSidechainMover::valid_segments_
private

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