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protocols::moves::CanonicalSamplingMover Class Reference

#include <CanonicalSamplingMover.hh>

Inheritance diagram for protocols::moves::CanonicalSamplingMover:
Inheritance graph
Collaboration diagram for protocols::moves::CanonicalSamplingMover:
Collaboration graph

Public Member Functions

 CanonicalSamplingMover ()
 CanonicalSamplingMover (core::scoring::ScoreFunctionOP sfxn, mc_convergence_checks::Pool_RMSD_OP ptr, int ntrial)
void add_mover (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 (mc_convergence_checks::Pool_RMSD_OP ptr)
virtual void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. 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
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
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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
 this function informs 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
 this function informs 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
 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). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

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. 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. More...

Private Member Functions

core::Real periodic_range (core::Real a, core::Real x)
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

MonteCarloOP mc_
core::scoring::ScoreFunctionOP sfxn_
moves::RandomMoverOP randmove_
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_

Static Private Attributes

static bool options_registered_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
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::moves::CanonicalSamplingMover::CanonicalSamplingMover ( )
protocols::moves::CanonicalSamplingMover::CanonicalSamplingMover ( core::scoring::ScoreFunctionOP  sfxn,
mc_convergence_checks::Pool_RMSD_OP  ptr,
int  ntrial 

Member Function Documentation

void protocols::moves::CanonicalSamplingMover::add_mover ( MoverOP  m,
core::Real  weight 
virtual void protocols::moves::CanonicalSamplingMover::apply ( core::pose::Pose pose)
void protocols::moves::CanonicalSamplingMover::detailed_balance ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::detailed_balance ( ) const
void protocols::moves::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 
std::string protocols::moves::CanonicalSamplingMover::get_ABGEO_string ( core::pose::Pose pose,
protocols::loops::Loops loop 
virtual std::string protocols::moves::CanonicalSamplingMover::get_name ( ) const

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

Implements protocols::moves::Mover.

core::Real protocols::moves::CanonicalSamplingMover::get_temp ( )
void protocols::moves::CanonicalSamplingMover::ntrials ( int  ntrial)
void protocols::moves::CanonicalSamplingMover::output_only_cluster_transitions ( bool  truefalse)
core::Real protocols::moves::CanonicalSamplingMover::periodic_range ( core::Real  a,
core::Real  x 
static void protocols::moves::CanonicalSamplingMover::register_options ( )
void protocols::moves::CanonicalSamplingMover::set_defaults_from_cmdline ( )
void protocols::moves::CanonicalSamplingMover::set_interval_data_dump ( int  d_interval)
void protocols::moves::CanonicalSamplingMover::set_interval_pose_dump ( int  p_interval)
void protocols::moves::CanonicalSamplingMover::set_poolrmsd ( mc_convergence_checks::Pool_RMSD_OP  ptr)
void protocols::moves::CanonicalSamplingMover::set_scorefunction ( core::scoring::ScoreFunctionOP  sfxn)
void protocols::moves::CanonicalSamplingMover::set_temp ( core::Real  temperature)
void protocols::moves::CanonicalSamplingMover::setup_constraints ( core::pose::Pose pose)
core::Real protocols::moves::CanonicalSamplingMover::transition_threshold ( ) const
void protocols::moves::CanonicalSamplingMover::use_hierarchical_clustering ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_hierarchical_clustering ( ) const
void protocols::moves::CanonicalSamplingMover::use_MPI_bcast ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_MPI_bcast ( ) const
void protocols::moves::CanonicalSamplingMover::use_MPI_sync_pools ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_MPI_sync_pools ( ) const

Member Data Documentation

bool protocols::moves::CanonicalSamplingMover::detailed_balance_
bool protocols::moves::CanonicalSamplingMover::dump_loops_only_
core::Size protocols::moves::CanonicalSamplingMover::interval_posedump_
core::Size protocols::moves::CanonicalSamplingMover::interval_transitiondump_
MonteCarloOP protocols::moves::CanonicalSamplingMover::mc_
bool protocols::moves::CanonicalSamplingMover::MPI_bcast_
bool protocols::moves::CanonicalSamplingMover::MPI_synchronize_pools_
core::Size protocols::moves::CanonicalSamplingMover::ntrials_
bool protocols::moves::CanonicalSamplingMover::options_registered_

Referenced by OPT_1GRP_KEY().

bool protocols::moves::CanonicalSamplingMover::output_only_cluster_transition_
mc_convergence_checks::Pool_RMSD_OP protocols::moves::CanonicalSamplingMover::pool_rms_
bool protocols::moves::CanonicalSamplingMover::ramp_temperature_
moves::RandomMoverOP protocols::moves::CanonicalSamplingMover::randmove_
bool protocols::moves::CanonicalSamplingMover::save_loops_only_
core::scoring::ScoreFunctionOP protocols::moves::CanonicalSamplingMover::sfxn_
core::Real protocols::moves::CanonicalSamplingMover::temperature_
core::Real protocols::moves::CanonicalSamplingMover::transition_threshold_
bool protocols::moves::CanonicalSamplingMover::use_hierarchical_clustering_

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