A base class for discrete samplers in Domino2. More...
#include <IMP/domino/DiscreteSampler.h>
Inheritance diagram for IMP::domino::DiscreteSampler:Public Member Functions | |
| DiscreteSampler (Model *m, ParticleStatesTable *pst, std::string name) | |
| unsigned int | get_maximum_number_of_assignments () const |
| Assignments | get_sample_assignments (const Subset &s) const |
| void | set_maximum_number_of_assignments (unsigned int mx) |
| void | set_particle_states (Particle *p, ParticleStates *se) |
| Public Member Functions inherited from IMP::kernel::Sampler | |
| Sampler (Model *m, std::string name="Sampler %1%") | |
| ConfigurationSet * | create_sample () const |
| Model * | get_model () const |
| ScoringFunction * | get_scoring_function () const |
| void | set_scoring_function (ScoringFunctionAdaptor sf) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Protected Member Functions | |
| virtual Assignments | do_get_sample_assignments (const Subset &all) const =0 |
| virtual ConfigurationSet * | do_sample () const |
| AssignmentsTable * | get_assignments_table_to_use (const SubsetFilterTables &sfts, unsigned int max=std::numeric_limits< int >::max()) const |
| SubsetFilterTables | get_subset_filter_tables_to_use (const RestraintsTemp &rs, ParticleStatesTable *pst) const |
Related Functions | |
(Note that these are not member functions.) | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < DiscreteSampler > > | DiscreteSamplersTemp |
| Related Functions inherited from IMP::kernel::Sampler | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Sampler > > | SamplersTemp |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Advanced | |
Default values are provided, you only need to replace these if you want to do something special. See the overview of the module for a general description. | |
| void | set_particle_states_table (ParticleStatesTable *cse) |
| void | set_assignments_table (AssignmentsTable *sst) |
| ParticleStatesTable * | get_particle_states_table () const |
| void | remove_subset_filter_table (SubsetFilterTable *d) |
| void | remove_subset_filter_tables (const SubsetFilterTables &d) |
| void | set_subset_filter_tables (const SubsetFilterTables &ps) |
| void | set_subset_filter_tables_order (const SubsetFilterTables &objs) |
| unsigned int | add_subset_filter_table (SubsetFilterTable *obj) |
| void | add_subset_filter_tables (const SubsetFilterTables &objs) |
| void | clear_subset_filter_tables () |
| unsigned int | get_number_of_subset_filter_tables () const |
| bool | get_has_subset_filter_tables () |
| SubsetFilterTable * | get_subset_filter_table (unsigned int i) const |
| SubsetFilterTables | get_subset_filter_tables () const |
| void | reserve_subset_filter_tables (unsigned int sz) |
Detailed Description
All the samplers derived from it share some common properties:
- each particle is allowed to have one of a discrete set of conformations, as stored in a ParticleStatesTable
- there is, optionally, one scoring function, accessed through the SubsetEvaluatorTable
- there can be many SubsetFilterTable objects which are used to prune the discrete space.
Defaults are provided for all the parameters:
- if no SubsetFilterTables are provided, then the ExclusionSubsetFilterTable and the RestraintScoreSubsetFilterTable are used.
- Note
- the restraint scores must be non-negative in general. If you are using restraints which can produce negative values, we can provide a restraint which wraps another and makes it non-negative. Ping us.
- The discrete samplers enumerate all acceptable conformations. As a result, users should take care to remove uninteresting degrees of freedom (for example, remove rigid transformations of a complex). Techniques to do this can involve pinning one or more particles (by locking them to a single conformation or to a few degrees of freedom).
Definition at line 51 of file DiscreteSampler.h.
Member Function Documentation
| Assignments IMP::domino::DiscreteSampler::get_sample_assignments | ( | const Subset & | s | ) | const |
Return the Assignment objects describing the subsets fitting the description.
- Note
- At the moment, Subset must be equal to Subset(ParticleStatesTable::get_particles()).
| void IMP::domino::DiscreteSampler::set_maximum_number_of_assignments | ( | unsigned int | mx | ) |
Limit the number of states that is ever produced for any set of particles.
Doing this can be useful to get some feedback when too many states would otherwise be produced. A warning will be emitted whenever the limit eliminates states.
Definition at line 117 of file DiscreteSampler.h.
| void IMP::domino::DiscreteSampler::set_particle_states | ( | Particle * | p, |
| ParticleStates * | se | ||
| ) |
Particle states can be set either using this method, or equivalently, by accessing the table itself using get_particle_states_table(). This method is provided for users who want to use the default values and want a simple inferface.
Definition at line 77 of file DiscreteSampler.h.
Friends And Related Function Documentation
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related |
Pass a set of objects.
Definition at line 126 of file DiscreteSampler.h.
The documentation for this class was generated from the following file: