Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::moves::CanonicalSamplingMover Class Reference

#include <CanonicalSamplingMover.hh>

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
 
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)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
 
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...
 

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_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::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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)
virtual
void protocols::moves::CanonicalSamplingMover::detailed_balance ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::detailed_balance ( ) const
inline
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 
)
private
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
virtual

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

Implements protocols::moves::Mover.

core::Real protocols::moves::CanonicalSamplingMover::get_temp ( )
inline
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 
)
private
static void protocols::moves::CanonicalSamplingMover::register_options ( )
static
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)
private
core::Real protocols::moves::CanonicalSamplingMover::transition_threshold ( ) const
inline
void protocols::moves::CanonicalSamplingMover::use_hierarchical_clustering ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_hierarchical_clustering ( ) const
inline
void protocols::moves::CanonicalSamplingMover::use_MPI_bcast ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_MPI_bcast ( ) const
inline
void protocols::moves::CanonicalSamplingMover::use_MPI_sync_pools ( bool  truefalse)
bool protocols::moves::CanonicalSamplingMover::use_MPI_sync_pools ( ) const
inline

Member Data Documentation

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

Referenced by OPT_1GRP_KEY().

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

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