Detailed Description

A base class for discrete samplers in Domino2.

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 50 of file DiscreteSampler.h.

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)

void	set_restraints (RestraintsAdaptor rs)
	Set the Restraints to use in the RestraintScoreSubsetFilterTable. More...

Public Member Functions inherited from IMP::Sampler
	Sampler (Model *m, std::string name="Sampler %1%")

ConfigurationSet *	create_sample () const

Model *	get_model () const

ScoringFunction *	get_scoring_function () const
	Return the scoring function that is being used. More...

void	set_scoring_function (ScoringFunctionAdaptor sf)

Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

virtual VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

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)

virtual std::string	get_type_name () const

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

RestraintsTemp	get_restraints () const

SubsetFilterTables	get_subset_filter_tables_to_use (const RestraintsTemp &rs, ParticleStatesTable *pst) const

Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

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)

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 128 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 interface.

Definition at line 94 of file DiscreteSampler.h.

void IMP::domino::DiscreteSampler::set_restraints ( RestraintsAdaptor rs )

Set the Restraints to use in the RestraintScoreSubsetFilterTable.

The default RestraintScoreSubsetFilterTable filters based on a set of Restraints, which can be set here.

Definition at line 84 of file DiscreteSampler.h.

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

DiscreteSampler.h

Detailed Description

Public Member Functions

Protected Member Functions

Advanced

Member Function Documentation