#include <CanonicalSamplingMover.hh>
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 Strings & | info () |
| 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) |
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 | ( | ) |
References set_defaults_from_cmdline().
◆ CanonicalSamplingMover() [2/2]
| protocols::canonical_sampling::CanonicalSamplingMover::CanonicalSamplingMover | ( | core::scoring::ScoreFunctionOP | sfxn, |
| protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD_OP | ptr, | ||
| int | ntrial | ||
| ) |
References set_defaults_from_cmdline().
Member Function Documentation
◆ add_mover()
| void protocols::canonical_sampling::CanonicalSamplingMover::add_mover | ( | protocols::moves::MoverOP | m, |
| core::Real | weight | ||
| ) |
References protocols::simple_moves::bb_sampler::probability, and randmove_.
◆ apply()
|
overridevirtual |
Main Method.
Implements protocols::moves::Mover.
References protocols::viewer::add_conformation_viewer(), core::scoring::constraints::add_constraints_from_cmdline(), core::scoring::atom_pair_constraint, protocols::loops::Loops::begin(), boinc_mode_, core::scoring::CA_rmsd(), core::energy_methods::RG_Energy_Fast::calculate_rg_score(), core::pose::Pose::conformation(), protocols::jd2::JobDistributor::current_job(), protocols::jd2::current_output_name(), detailed_balance_, dump_decoy_or_score(), core::sequence::end, protocols::loops::Loops::end(), core::chemical::element::F, get_ABGEO_string(), protocols::jd2::JobDistributor::get_instance(), core::io::silent::gzip(), core::init::init(), interval_posedump_, interval_transitiondump_, protocols::jd2::JobDistributor::job_outputter(), protocols::canonical_sampling::jobname_dirhash(), mc_, MPI_bcast_, MPI_synchronize_pools_, protocols::moves::Mover::name(), ntrials_, protocols::loops::Loops::num_loop(), output_only_cluster_transition_, pool_rms_, core::io::raw_data::precision(), ramp_temperature_, randmove_, core::io::silent::SilentFileData::read_file(), core::io::silent::SilentFileData::read_tags_fast(), core::pose::Pose::remove_constraints(), save_loops_only_, core::io::silent::SilentFileData::set_filename(), setup_constraints(), sfxn_, core::pose::Pose::size(), protocols::canonical_sampling::tr(), transition_threshold_, and use_hierarchical_clustering_.
◆ detailed_balance() [1/2]
|
inline |
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()
|
private |
void CanonicalSamplingMover::dump_xtc_format_decoy( std::ostream& os, core::pose::Pose const& pose, loops::Loops const& loop_to_dump ) {
}
References boinc_mode_, dump_loops_only_, interval_posedump_, interval_transitiondump_, protocols::loops::Loops::num_loop(), and core::io::silent::SilentFileData::write_silent_struct().
Referenced by apply().
◆ dump_xtc_format_decoy()
|
private |
◆ get_ABGEO_string()
| std::string protocols::canonical_sampling::CanonicalSamplingMover::get_ABGEO_string | ( | core::pose::Pose & | pose, |
| protocols::loops::Loops & | loop | ||
| ) |
References core::pose::Pose::omega(), core::scoring::omega, periodic_range(), core::pose::Pose::phi(), and core::pose::Pose::psi().
Referenced by apply().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_temp()
|
inline |
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 | ) |
References output_only_cluster_transition_.
Referenced by set_defaults_from_cmdline().
◆ periodic_range()
|
private |
References core::pose::motif::a().
Referenced by get_ABGEO_string().
◆ register_options()
|
static |
References protocols::evaluation::options_registered_, and protocols::hybridization::path.
◆ 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 | ) |
References interval_transitiondump_.
Referenced by set_defaults_from_cmdline().
◆ 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()
|
private |
◆ transition_threshold()
|
inline |
References transition_threshold_.
◆ use_hierarchical_clustering() [1/2]
|
inline |
References use_hierarchical_clustering_.
◆ use_hierarchical_clustering() [2/2]
| void protocols::canonical_sampling::CanonicalSamplingMover::use_hierarchical_clustering | ( | bool | truefalse | ) |
References use_hierarchical_clustering_.
◆ use_MPI_bcast() [1/2]
|
inline |
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]
|
inline |
References MPI_synchronize_pools_.
◆ use_MPI_sync_pools() [2/2]
| void protocols::canonical_sampling::CanonicalSamplingMover::use_MPI_sync_pools | ( | bool | truefalse | ) |
References MPI_synchronize_pools_.
Member Data Documentation
◆ boinc_mode_
|
private |
Referenced by apply(), dump_decoy_or_score(), and set_defaults_from_cmdline().
◆ detailed_balance_
|
private |
Referenced by apply(), and detailed_balance().
◆ dump_loops_only_
|
private |
Referenced by dump_decoy_or_score(), and set_defaults_from_cmdline().
◆ interval_posedump_
|
private |
Referenced by apply(), dump_decoy_or_score(), and set_interval_pose_dump().
◆ interval_transitiondump_
|
private |
Referenced by apply(), dump_decoy_or_score(), and set_interval_data_dump().
◆ mc_
|
private |
Referenced by apply(), and set_temp().
◆ MPI_bcast_
|
private |
Referenced by apply(), and use_MPI_bcast().
◆ MPI_synchronize_pools_
|
private |
Referenced by apply(), and use_MPI_sync_pools().
◆ ntrials_
|
private |
◆ options_registered_
|
staticprivate |
Referenced by set_defaults_from_cmdline().
◆ output_only_cluster_transition_
|
private |
Referenced by apply(), and output_only_cluster_transitions().
◆ pool_rms_
|
private |
Referenced by apply(), and set_poolrmsd().
◆ ramp_temperature_
|
private |
Referenced by apply(), and set_defaults_from_cmdline().
◆ randmove_
|
private |
Referenced by add_mover(), and apply().
◆ save_loops_only_
|
private |
Referenced by apply(), and set_defaults_from_cmdline().
◆ sfxn_
|
private |
Referenced by apply(), set_scorefunction(), and set_temp().
◆ temperature_
|
private |
Referenced by get_temp(), and set_temp().
◆ transition_threshold_
|
private |
Referenced by apply(), set_defaults_from_cmdline(), and transition_threshold().
◆ use_hierarchical_clustering_
|
private |
Referenced by apply(), and use_hierarchical_clustering().
The documentation for this class was generated from the following files:
- src/protocols/canonical_sampling/CanonicalSamplingMover.hh
- src/protocols/canonical_sampling/CanonicalSamplingMover.cc
