Detailed Description

Sample best solutions using Domino.

Note that if there are many solutions, the ConfigurationSet returned by get_sample() might be huge (in terms of memory usage) and slow to generate. The Assignments returned by get_sample_assignments() can be a lot smaller and faster.

Definition at line 32 of file DominoSampler.h.

Public Member Functions
	DominoSampler (kernel::Model *m, std::string name="DominoSampler %1%")

	DominoSampler (kernel::Model m, ParticleStatesTable pst, std::string name="DominoSampler %1%")

Assignments	do_get_sample_assignments (const IMP::domino::Subset &known) const

virtual std::string	get_type_name () const

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

void	set_use_cross_subset_filtering (bool tf)

Public Member Functions inherited from IMP::domino::DiscreteSampler
	DiscreteSampler (kernel::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 (kernel::Particle p, ParticleStates se)

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)

Public Member Functions inherited from IMP::kernel::Sampler
	Sampler (kernel::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 ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

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)

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_merge_tree (const MergeTree &mt)
	Specify the merge tree directly. More...

Statistics
If you specify the merge tree explicitly, you can query for statistics about particular nodes in the merge tree.
unsigned int	get_number_of_assignments_for_vertex (unsigned int tree_vertex) const
	Get the number of states found for the merge at that vertex of the tree. More...

Assignments	get_sample_assignments_for_vertex (unsigned int tree_vertex) const
	Return a few subset states from that merge. More...

Interactive mode
Once a merge tree is specified, one can interactively perform the sampling by requesting that domino fill in the Assignments for a given node of the merge tree from the assignments for the children. This can be useful for debugging Domino as well as for providing a distributed implementation. For each method, you can pass max_states to limit how many states are generated. You might want to just use load_leaf_assignments() and load_merged_assignments() instead.
Assignments	get_vertex_assignments (unsigned int node_index, unsigned int max_states=std::numeric_limits< int >::max()) const
	Fill in assignments for a leaf. More...

Assignments	get_vertex_assignments (unsigned int node_index, const Assignments &first, const Assignments &second, unsigned int max_states=std::numeric_limits< int >::max()) const
	Fill in assignments for an internal node. More...

void	load_vertex_assignments (unsigned int node_index, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const
	Fill in assignments for a leaf. More...

void	load_vertex_assignments (unsigned int node_index, AssignmentContainer first, AssignmentContainer second, AssignmentContainer *ac, unsigned int max_states=std::numeric_limits< int >::max()) const
	Fill in assignments for an internal node. More...

Additional Inherited Members
Protected Member Functions inherited from IMP::domino::DiscreteSampler
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 kernel::RestraintsTemp &rs, ParticleStatesTable *pst) const

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

virtual void	do_destroy ()

Member Function Documentation

unsigned int IMP::domino::DominoSampler::get_number_of_assignments_for_vertex ( unsigned int tree_vertex ) const

Get the number of states found for the merge at that vertex of the tree.

Assignments IMP::domino::DominoSampler::get_sample_assignments_for_vertex ( unsigned int tree_vertex ) const

Return a few subset states from that merge.

virtual ::IMP::base::VersionInfo IMP::domino::DominoSampler::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 46 of file DominoSampler.h.

Assignments IMP::domino::DominoSampler::get_vertex_assignments	(	unsigned int	node_index,
		unsigned int	max_states = `std::numeric_limits< int >::max()`
	)		const

Fill in assignments for a leaf.

Assignments IMP::domino::DominoSampler::get_vertex_assignments	(	unsigned int	node_index,
		const Assignments &	first,
		const Assignments &	second,
		unsigned int	max_states = `std::numeric_limits< int >::max()`
	)		const

Fill in assignments for an internal node.

The passed assignments, the ordering for the children is the node index for the children.

void IMP::domino::DominoSampler::load_vertex_assignments	(	unsigned int	node_index,
		AssignmentContainer *	ac,
		unsigned int	max_states = `std::numeric_limits< int >::max()`
	)		const

Fill in assignments for a leaf.

void IMP::domino::DominoSampler::load_vertex_assignments	(	unsigned int	node_index,
		AssignmentContainer *	first,
		AssignmentContainer *	second,
		AssignmentContainer *	ac,
		unsigned int	max_states = `std::numeric_limits< int >::max()`
	)		const

Fill in assignments for an internal node.

The passed assignments, the ordering for the children is that of the node indexes for the children.

void IMP::domino::DominoSampler::set_merge_tree ( const MergeTree & mt )

Specify the merge tree directly.

void IMP::domino::DominoSampler::set_use_cross_subset_filtering ( bool tf )

perform filtering between subsets based by eliminating states that cannot be realized in a subset.

Definition at line 62 of file DominoSampler.h.

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

DominoSampler.h

Detailed Description

Public Member Functions

Advanced

Statistics

Interactive mode

Additional Inherited Members

Member Function Documentation