Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::canonical_sampling::CanonicalSamplingMover Class Reference

#include <CanonicalSamplingMover.hh>

Inheritance diagram for protocols::canonical_sampling::CanonicalSamplingMover:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ CanonicalSamplingMover() [1/2]

protocols::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover ( )

◆ CanonicalSamplingMover() [2/2]

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

Member Function Documentation

◆ add_mover()

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

◆ apply()

void protocols::canonical_sampling::CanonicalSamplingMover::apply ( core::pose::Pose )

◆ detailed_balance() [1/2]

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

References detailed_balance_.

Referenced by set_defaults_from_cmdline().

◆ detailed_balance() [2/2]

void protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance ( bool  truefalse)

References detailed_balance_.

◆ dump_decoy_or_score()

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 

◆ dump_xtc_format_decoy()

void protocols::canonical_sampling::CanonicalSamplingMover::dump_xtc_format_decoy ( std::ostream &  os,
core::pose::Pose const &  pose,
loops::Loops const &  loop_to_dump 

◆ get_ABGEO_string()

std::string protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string ( core::pose::Pose pose,
protocols::loops::Loops loop 

◆ get_name()

std::string protocols::canonical_sampling::CanonicalSamplingMover::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ get_temp()

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

References temperature_.

◆ ntrials()

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

References ntrials_.

Referenced by set_defaults_from_cmdline().

◆ output_only_cluster_transitions()

void protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transitions ( bool  truefalse)

◆ periodic_range()

core::Real protocols::canonical_sampling::CanonicalSamplingMover::periodic_range ( core::Real  a,
core::Real  x 

References core::pose::motif::a().

Referenced by get_ABGEO_string().

◆ register_options()

void protocols::canonical_sampling::CanonicalSamplingMover::register_options ( )

◆ set_defaults_from_cmdline()

void protocols::canonical_sampling::CanonicalSamplingMover::set_defaults_from_cmdline ( )

◆ set_interval_data_dump()

void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_data_dump ( int  d_interval)

◆ set_interval_pose_dump()

void protocols::canonical_sampling::CanonicalSamplingMover::set_interval_pose_dump ( int  p_interval)

References interval_posedump_.

Referenced by set_defaults_from_cmdline().

◆ set_poolrmsd()

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

References pool_rms_.

◆ set_scorefunction()

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

References sfxn_.

◆ set_temp()

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

References mc_, sfxn_, and temperature_.

◆ setup_constraints()

void protocols::canonical_sampling::CanonicalSamplingMover::setup_constraints ( core::pose::Pose pose)

◆ transition_threshold()

core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold ( ) const

References transition_threshold_.

◆ use_hierarchical_clustering() [1/2]

bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( ) const

◆ use_hierarchical_clustering() [2/2]

void protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering ( bool  truefalse)

◆ use_MPI_bcast() [1/2]

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

References MPI_bcast_.

◆ use_MPI_bcast() [2/2]

void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_bcast ( bool  truefalse)

References MPI_bcast_.

◆ use_MPI_sync_pools() [1/2]

bool protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools ( ) const

◆ use_MPI_sync_pools() [2/2]

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

Member Data Documentation

◆ boinc_mode_

bool protocols::canonical_sampling::CanonicalSamplingMover::boinc_mode_

◆ detailed_balance_

bool protocols::canonical_sampling::CanonicalSamplingMover::detailed_balance_

Referenced by apply(), and detailed_balance().

◆ dump_loops_only_

bool protocols::canonical_sampling::CanonicalSamplingMover::dump_loops_only_

◆ interval_posedump_

core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_posedump_

◆ interval_transitiondump_

core::Size protocols::canonical_sampling::CanonicalSamplingMover::interval_transitiondump_

◆ mc_

protocols::moves::MonteCarloOP protocols::canonical_sampling::CanonicalSamplingMover::mc_

Referenced by apply(), and set_temp().

◆ MPI_bcast_

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_bcast_

Referenced by apply(), and use_MPI_bcast().

◆ MPI_synchronize_pools_

bool protocols::canonical_sampling::CanonicalSamplingMover::MPI_synchronize_pools_

Referenced by apply(), and use_MPI_sync_pools().

◆ ntrials_

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

Referenced by apply(), and ntrials().

◆ options_registered_

bool protocols::canonical_sampling::CanonicalSamplingMover::options_registered_

◆ output_only_cluster_transition_

bool protocols::canonical_sampling::CanonicalSamplingMover::output_only_cluster_transition_

◆ pool_rms_

protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP protocols::canonical_sampling::CanonicalSamplingMover::pool_rms_

Referenced by apply(), and set_poolrmsd().

◆ ramp_temperature_

bool protocols::canonical_sampling::CanonicalSamplingMover::ramp_temperature_

Referenced by apply(), and set_defaults_from_cmdline().

◆ randmove_

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

Referenced by add_mover(), and apply().

◆ save_loops_only_

bool protocols::canonical_sampling::CanonicalSamplingMover::save_loops_only_

Referenced by apply(), and set_defaults_from_cmdline().

◆ sfxn_

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

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

◆ temperature_

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

Referenced by get_temp(), and set_temp().

◆ transition_threshold_

core::Real protocols::canonical_sampling::CanonicalSamplingMover::transition_threshold_

◆ use_hierarchical_clustering_

bool protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering_

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