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protocols::canonical_sampling::CanonicalSamplingMover Class Reference

#include <CanonicalSamplingMover.hh>

Inheritance diagram for protocols::canonical_sampling::CanonicalSamplingMover:
Inheritance graph
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Public Member Functions

 CanonicalSamplingMover ()
 
 CanonicalSamplingMover (core::scoring::ScoreFunctionOP sfxn, protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP ptr, int ntrial)
 
void add_mover (protocols::moves::MoverOP m, core::Real weight)
 
std::string get_ABGEO_string (core::pose::Pose &pose, protocols::loops::Loops &loop)
 
void ntrials (int ntrial)
 
void set_defaults_from_cmdline ()
 
void set_temp (core::Real temperature)
 
core::Real get_temp ()
 
void set_interval_pose_dump (int p_interval)
 
void set_interval_data_dump (int d_interval)
 
void set_scorefunction (core::scoring::ScoreFunctionOP sfxn)
 
void detailed_balance (bool truefalse)
 
bool detailed_balance () const
 
core::Real transition_threshold () const
 
void use_MPI_sync_pools (bool truefalse)
 
bool use_MPI_sync_pools () const
 
void use_MPI_bcast (bool truefalse)
 
bool use_MPI_bcast () const
 
void use_hierarchical_clustering (bool truefalse)
 
bool use_hierarchical_clustering () const
 
void output_only_cluster_transitions (bool truefalse)
 
void set_poolrmsd (protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP ptr)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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 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...
 

Static Public Member Functions

static void register_options ()
 
- 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...
 

Private Member Functions

core::Real periodic_range (core::Real a, core::Real x)
 
void dump_xtc_format_decoy (std::ostream &os, core::pose::Pose const &pose, loops::Loops const &loop_to_dump)
 
void dump_decoy_or_score (std::ostream &os, core::pose::Pose const &pose, core::Size i_trial, std::string const &jobname, loops::Loops const &loop_to_dump, bool score_only=false)
 
void setup_constraints (core::pose::Pose &pose)
 

Private Attributes

protocols::moves::MonteCarloOP mc_
 
core::scoring::ScoreFunctionOP sfxn_
 
moves::RandomMoverOP randmove_
 
protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP pool_rms_
 
core::Size interval_posedump_
 
core::Size interval_transitiondump_
 
core::Size ntrials_
 
bool detailed_balance_
 
bool MPI_synchronize_pools_
 
bool MPI_bcast_
 
bool use_hierarchical_clustering_
 
bool save_loops_only_
 
bool dump_loops_only_
 
bool output_only_cluster_transition_
 
core::Real transition_threshold_
 
core::Real temperature_
 
bool ramp_temperature_
 
bool boinc_mode_
 

Static Private Attributes

static bool options_registered_
 

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
 
- 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::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover ( )
protocols::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover ( core::scoring::ScoreFunctionOP  sfxn,
protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP  ptr,
int  ntrial 
)

Member Function Documentation

void protocols::canonical_sampling::CanonicalSamplingMover::add_mover ( protocols::moves::MoverOP  m,
core::Real  weight 
)

References randmove_.

void protocols::canonical_sampling::CanonicalSamplingMover::apply ( core::pose::Pose )
overridevirtual
void protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance ( bool  truefalse)

References detailed_balance_.

bool protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance ( ) const
inline

References detailed_balance_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::dump_decoy_or_score ( std::ostream &  os,
core::pose::Pose const &  pose,
core::Size  i_trial,
std::string const &  jobname,
loops::Loops const &  loop_to_dump,
bool  score_only = false 
)
private
void protocols::canonical_sampling::CanonicalSamplingMover::dump_xtc_format_decoy ( std::ostream &  os,
core::pose::Pose const &  pose,
loops::Loops const &  loop_to_dump 
)
private
std::string protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string ( core::pose::Pose pose,
protocols::loops::Loops loop 
)
std::string protocols::canonical_sampling::CanonicalSamplingMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::canonical_sampling::CanonicalSamplingMover::get_temp ( )
inline

References temperature_.

void protocols::canonical_sampling::CanonicalSamplingMover::ntrials ( int  ntrial)

References ntrials_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transitions ( bool  truefalse)
core::Real protocols::canonical_sampling::CanonicalSamplingMover::periodic_range ( core::Real  a,
core::Real  x 
)
private

Referenced by get_ABGEO_string().

void protocols::canonical_sampling::CanonicalSamplingMover::register_options ( )
static
void protocols::canonical_sampling::CanonicalSamplingMover::set_defaults_from_cmdline ( )
void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_data_dump ( int  d_interval)
void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_pose_dump ( int  p_interval)

References interval_posedump_.

Referenced by set_defaults_from_cmdline().

void protocols::canonical_sampling::CanonicalSamplingMover::set_poolrmsd ( protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP  ptr)

References pool_rms_.

void protocols::canonical_sampling::CanonicalSamplingMover::set_scorefunction ( core::scoring::ScoreFunctionOP  sfxn)

References sfxn_.

void protocols::canonical_sampling::CanonicalSamplingMover::set_temp ( core::Real  temperature)

References mc_, sfxn_, and temperature_.

void protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints ( core::pose::Pose pose)
private
core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold ( ) const
inline

References transition_threshold_.

void protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( bool  truefalse)
bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( ) const
inline
void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast ( bool  truefalse)

References MPI_bcast_.

bool protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast ( ) const
inline

References MPI_bcast_.

void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools ( bool  truefalse)
bool protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools ( ) const
inline

Member Data Documentation

bool protocols::canonical_sampling::CanonicalSamplingMover::boinc_mode_
private
bool protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance_
private

Referenced by apply(), and detailed_balance().

bool protocols::canonical_sampling::CanonicalSamplingMover::dump_loops_only_
private
core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_posedump_
private
core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_transitiondump_
private
protocols::moves::MonteCarloOP protocols::canonical_sampling::CanonicalSamplingMover::mc_
private

Referenced by apply(), and set_temp().

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_bcast_
private

Referenced by apply(), and use_MPI_bcast().

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_synchronize_pools_
private

Referenced by apply(), and use_MPI_sync_pools().

core::Size protocols::canonical_sampling::CanonicalSamplingMover::ntrials_
private

Referenced by apply(), and ntrials().

bool protocols::canonical_sampling::CanonicalSamplingMover::options_registered_
staticprivate
bool protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transition_
private
protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP protocols::canonical_sampling::CanonicalSamplingMover::pool_rms_
private

Referenced by apply(), and set_poolrmsd().

bool protocols::canonical_sampling::CanonicalSamplingMover::ramp_temperature_
private

Referenced by apply(), and set_defaults_from_cmdline().

moves::RandomMoverOP protocols::canonical_sampling::CanonicalSamplingMover::randmove_
private

Referenced by add_mover(), and apply().

bool protocols::canonical_sampling::CanonicalSamplingMover::save_loops_only_
private

Referenced by apply(), and set_defaults_from_cmdline().

core::scoring::ScoreFunctionOP protocols::canonical_sampling::CanonicalSamplingMover::sfxn_
private

Referenced by apply(), set_scorefunction(), and set_temp().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::temperature_
private

Referenced by get_temp(), and set_temp().

core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold_
private
bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering_
private

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