See IMP.domino Overview for more information.

Classes
class	Assignment
	Store a configuration of a subset. More...

class	AssignmentContainer

class	AssignmentsTable

class	BranchAndBoundAssignmentsTable

class	BranchAndBoundSampler
	Sample best solutions using BranchAndBound. More...

class	CappedAssignmentContainer

class	CompoundStates

class	DependencyScoreState
	Add a dependency to the dependency graph. More...

class	DiscreteSampler
	A base class for discrete samplers in Domino2. More...

class	DisjointSetsSubsetFilterTable
	A base class. More...

class	DominoSampler
	Sample best solutions using Domino. More...

class	EqualitySubsetFilterTable
	Do not allow two particles to be in the same state. More...

class	EquivalenceAndExclusionSubsetFilterTable
	Define sets of equivalent and exclusive particles. More...

class	EquivalenceSubsetFilterTable
	Define sets of equivalent particles. More...

class	ExclusionSubsetFilterTable
	Do not allow two particles to be in the same state. More...

class	HeapAssignmentContainer

class	IndexStates

class	ListAssignmentContainer

class	ListAssignmentsTable

class	ListSubsetFilterTable
	Maintain an explicit list of what states each particle is allowed to have. More...

class	MinimumRestraintScoreSubsetFilterTable
	Filter a configuration of the subset using the Model thresholds. More...

class	NestedRigidBodyStates

class	Order
	Store a persistent ordering for a subset based on the list. More...

class	PackedAssignmentContainer

class	PairListSubsetFilterTable

class	ParticlesAdaptor

class	ParticleStates

class	ParticleStatesTable

class	PermutationStates

class	ProbabilisticSubsetFilterTable

class	RangeViewAssignmentContainer

class	ReadAssignmentContainer

class	ReadHDF5AssignmentContainer

class	RecursiveAssignmentsTable

class	RecursiveStates

class	RestraintCache

class	RestraintScoreSubsetFilterTable
	Filter a configuration of the subset using the Model thresholds. More...

class	RigidBodyStates

class	SampleAssignmentContainer

class	SimpleAssignmentsTable

class	Slice
	Store a subset of a subset or assignment. More...

class	Subset
	Represent a subset of the particles being optimized. More...

class	SubsetFilter

class	SubsetFilterTable

class	WriteAssignmentContainer

class	WriteHDF5AssignmentContainer

class	XYZStates

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < AssignmentContainer > >	AssignmentContainers

typedef IMP::base::Vector < Assignment >	Assignments

typedef IMP::base::Vector < IMP::base::Pointer < AssignmentsTable > >	AssignmentsTables

typedef IMP::base::Vector < IMP::base::Pointer < BranchAndBoundSampler > >	BranchAndBoundSamplers

typedef IMP::base::Vector < IMP::base::Pointer < DiscreteSampler > >	DiscreteSamplers

typedef IMP::base::Vector < IMP::base::Pointer < DominoSampler > >	DominoSamplers

typedef IMP::base::Vector < IMP::base::Pointer < EqualitySubsetFilterTable > >	EqualitySubsetFilterTables

typedef IMP::base::Vector < IMP::base::Pointer < EquivalenceAndExclusionSubsetFilterTable > >	EquivalenceAndExclusionSubsetFilterTables

typedef IMP::base::Vector < IMP::base::Pointer < EquivalenceSubsetFilterTable > >	EquivalenceSubsetFilterTables

typedef IMP::base::Vector < IMP::base::Pointer < ExclusionSubsetFilterTable > >	ExclusionSubsetFilterTables

typedef boost::graph	InteractionGraph

typedef InteractionGraph::EdgeNameMap	InteractionGraphConstEdgeName

typedef InteractionGraph::VertexNameMap	InteractionGraphConstVertexName

typedef InteractionGraph::edge_descriptor	InteractionGraphEdge

typedef boost::graph_traits < InteractionGraph >	InteractionGraphTraits

typedef InteractionGraph::vertex_descriptor	InteractionGraphVertex

typedef IMP::base::Vector < IMP::base::Pointer < ListSubsetFilterTable > >	ListSubsetFilterTables

typedef IMP::base::Vector < IMP::base::Pointer < MinimumRestraintScoreSubsetFilterTable > >	MinimumRestraintScoreSubsetFilterTables

typedef IMP::base::Vector< Order >	Orders

typedef IMP::base::Vector < IMP::base::Pointer < PairListSubsetFilterTable > >	PairListSubsetFilterTables

typedef IMP::base::Vector < IMP::base::Pointer < ParticleStates > >	ParticleStatesList

typedef IMP::base::Vector < IMP::base::Pointer < ParticleStatesTable > >	ParticleStatesTables

typedef IMP::base::Vector < IMP::base::Pointer < RestraintScoreSubsetFilterTable > >	RestraintScoreSubsetFilterTables

typedef IMP::base::Vector< Slice >	Slices

typedef IMP::base::Vector < IMP::base::Pointer < SubsetFilter > >	SubsetFilters

typedef IMP::base::Vector < IMP::base::Pointer < SubsetFilterTable > >	SubsetFilterTables

typedef boost::graph	SubsetGraph

typedef SubsetGraph::EdgeNameMap	SubsetGraphConstEdgeName

typedef SubsetGraph::VertexNameMap	SubsetGraphConstVertexName

typedef SubsetGraph::edge_descriptor	SubsetGraphEdge

typedef boost::graph_traits < SubsetGraph >	SubsetGraphTraits

typedef SubsetGraph::vertex_descriptor	SubsetGraphVertex

typedef IMP::base::Vector< Subset >	Subsets

Functions
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...

Subset	get_difference (const Subset &a, const Subset &b)

double	get_distance_if_smaller_than (const Subset &s, const Assignment &a, const Assignment &b, ParticleStatesTable *pst, const statistics::Metrics &metrics, double max)

algebra::VectorKD	get_embedding (const Subset &s, const Assignment &a, ParticleStatesTable *pst)
	Return an embedding for an assignment.

std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Ints	get_index (const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)

Subset	get_intersection (const Subset &a, const Subset &b)

SubsetGraph	get_junction_tree (const InteractionGraph &ig)

Assignment	get_nearest_assignment (const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst)
	Return the nearest assignment from an embedding.

ParticlesTemp	get_order (const Subset &s, const SubsetFilterTables &sft)

Ints	get_partial_index (const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)

ParticlePairsTemp	get_possible_interactions (const ParticlesTemp &ps, double max_distance, ParticleStatesTable *pst)

SubsetGraph	get_restraint_graph (ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)

Slice	get_slice (Subset outer, Subset inner, const Subsets &excluded)

Assignments	get_state_clusters (const Subset &subset, const Assignments &states, ParticleStatesTable *pst, double resolution)

Subsets	get_subsets (const SubsetGraph &g)
	Gets all of the Subsets of a SubsetGraph.

Subset	get_union (const Subset &a, const Subset &b)

void	load_leaf_assignments (const Subset &subset, AssignmentsTable at, AssignmentContainer ac)
	Fill in assignments for a leaf.

void	load_merged_assignments (const Subset &first_subset, AssignmentContainer first, const Subset &second_subset, AssignmentContainer second, const SubsetFilterTablesTemp &filters, AssignmentContainer *ret)
	Fill in assignments for an internal node. More...

void	load_merged_assignments_random_order (const Subset &first_subset, AssignmentContainer first, const Subset &second_subset, AssignmentContainer second, const SubsetFilterTablesTemp &filters, unsigned int maximum_tries, AssignmentContainer *ret)
	Sample from the merged assignments. More...

void	swap (Assignment &a, Assignment &b)

void	swap (Slice &a, Slice &b)

void	swap (Order &a, Order &b)

void	swap (Subset &a, Subset &b)

Standard module methods
All `IMP` modules have a set of standard methods to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

Debugging Junction Trees
typedef boost::graph	CliqueGraph

InteractionGraph	get_triangulated (const InteractionGraph &input)

CliqueGraph	get_clique_graph (const InteractionGraph &input)

SubsetGraph	get_minimum_spanning_tree (const CliqueGraph &input)

typedef boost::graph	MergeTree

typedef MergeTree::VertexNameMap	MergeTreeConstVertexName

typedef MergeTree::EdgeNameMap	MergeTreeConstEdgeName

typedef boost::graph_traits < MergeTree >	MergeTreeTraits

typedef MergeTree::vertex_descriptor	MergeTreeVertex

typedef MergeTree::edge_descriptor	MergeTreeEdge

SubsetGraphVertexIndex	get_vertex_index (const SubsetGraph &g)

InteractionGraph	get_interaction_graph (ScoringFunctionAdaptor rs, const ParticleStatesTable *pst)

InteractionGraph	get_interaction_graph (ScoringFunctionAdaptor rs, const ParticlesTemp &pst)

display::Geometries	get_interaction_graph_geometry (const InteractionGraph &ig)

display::Geometries	get_subset_graph_geometry (const SubsetGraph &ig)

MergeTree	get_merge_tree (ScoringFunctionAdaptor input, const ParticleStatesTable *pst)

MergeTree	get_merge_tree (const SubsetGraph &junction_tree)

MergeTree	get_balanced_merge_tree (const SubsetGraph &junction_tree)

bool	get_is_merge_tree (const MergeTree &tree, Subset all, bool verbose=true)

Read and write merge trees
Merge trees can be written to an read from a text stream. As always, this requires a canonical particles list whose order is the same for the reading and writing.
void	write_merge_tree (const MergeTree &tree, const ParticlesTemp &ps, std::ostream &out)

MergeTree	read_merge_tree (std::istream &input, const ParticlesTemp &ps)

Debug tools
We provide a number of different functions for helpering optimize and understand domino-based sampling. These functions are expose part of the implementation and are liable to change without notice.
void	load_particle_states (const Subset &s, const Assignment &ss, const ParticleStatesTable *pst)

RestraintsTemp	get_restraints (const Subset &s, const ParticleStatesTable pst, const DependencyGraph &dg, RestraintSet rs)

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< AssignmentContainer > > IMP::domino::AssignmentContainers

Store a set of objects.

Definition at line 59 of file assignment_containers.h.

typedef IMP::base::Vector< Assignment > IMP::domino::Assignments

Pass or store a set of Assignment .

Definition at line 45 of file Assignment.h.

typedef IMP::base::Vector<IMP::base::Pointer< AssignmentsTable > > IMP::domino::AssignmentsTables

Store a set of objects.

Definition at line 45 of file assignment_tables.h.

typedef IMP::base::Vector<IMP::base::Pointer< BranchAndBoundSampler > > IMP::domino::BranchAndBoundSamplers

Store a set of objects.

Definition at line 39 of file BranchAndBoundSampler.h.

typedef boost::graph IMP::domino::CliqueGraph

See Graphs for more information.

Definition at line 62 of file subset_graphs.h.

typedef IMP::base::Vector<IMP::base::Pointer< DiscreteSampler > > IMP::domino::DiscreteSamplers

Store a set of objects.

Definition at line 126 of file DiscreteSampler.h.

typedef IMP::base::Vector<IMP::base::Pointer< DominoSampler > > IMP::domino::DominoSamplers

Store a set of objects.

Definition at line 128 of file DominoSampler.h.

typedef IMP::base::Vector<IMP::base::Pointer< EqualitySubsetFilterTable > > IMP::domino::EqualitySubsetFilterTables

Store a set of objects.

Definition at line 238 of file subset_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< EquivalenceAndExclusionSubsetFilterTable > > IMP::domino::EquivalenceAndExclusionSubsetFilterTables

Store a set of objects.

Definition at line 256 of file subset_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< EquivalenceSubsetFilterTable > > IMP::domino::EquivalenceSubsetFilterTables

Store a set of objects.

Definition at line 249 of file subset_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< ExclusionSubsetFilterTable > > IMP::domino::ExclusionSubsetFilterTables

Store a set of objects.

Definition at line 229 of file subset_filters.h.

typedef boost::graph IMP::domino::InteractionGraph

An undirected graph with one vertex per particle of interest. Two particles are connected by an edge if a Restraint or ScoreState creates and interaction between the two particles.

See Graphs in IMP for more information.See Graphs in IMP for more information.

Definition at line 33 of file subset_graphs.h.

typedef IMP::base::Vector<IMP::base::Pointer< ListSubsetFilterTable > > IMP::domino::ListSubsetFilterTables

Store a set of objects.

Definition at line 301 of file subset_filters.h.

typedef boost::graph IMP::domino::MergeTree

A directed graph on subsets of vertices. Each vertex is named with an Subset.See Graphs in IMP for more information.

Definition at line 130 of file subset_graphs.h.

typedef IMP::base::Vector<IMP::base::Pointer< MinimumRestraintScoreSubsetFilterTable > > IMP::domino::MinimumRestraintScoreSubsetFilterTables

Store a set of objects.

Definition at line 152 of file subset_filters.h.

typedef IMP::base::Vector< Order > IMP::domino::Orders

Pass or store a set of Order .

Definition at line 67 of file Order.h.

typedef IMP::base::Vector<IMP::base::Pointer< PairListSubsetFilterTable > > IMP::domino::PairListSubsetFilterTables

Store a set of objects.

Definition at line 326 of file subset_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< ParticleStates > > IMP::domino::ParticleStatesList

Store a set of objects.

Definition at line 63 of file particle_states.h.

typedef IMP::base::Vector<IMP::base::Pointer< ParticleStatesTable > > IMP::domino::ParticleStatesTables

Store a set of objects.

Definition at line 114 of file particle_states.h.

typedef IMP::base::Vector<IMP::base::Pointer< RestraintScoreSubsetFilterTable > > IMP::domino::RestraintScoreSubsetFilterTables

Store a set of objects.

Definition at line 127 of file subset_filters.h.

typedef IMP::base::Vector< Slice > IMP::domino::Slices

Pass or store a set of Slice .

Definition at line 61 of file Slice.h.

typedef IMP::base::Vector<IMP::base::Pointer< SubsetFilter > > IMP::domino::SubsetFilters

Store a set of objects.

Definition at line 67 of file subset_filters.h.

typedef IMP::base::Vector<IMP::base::Pointer< SubsetFilterTable > > IMP::domino::SubsetFilterTables

Store a set of objects.

Definition at line 347 of file subset_filters.h.

typedef boost::graph IMP::domino::SubsetGraph

An undirected graph on subsets of vertices. Each vertex is named with an Subset.See Graphs in IMP for more information.

Definition at line 24 of file subset_graphs.h.

typedef IMP::base::Vector< Subset > IMP::domino::Subsets

Pass or store a set of Subset .

Definition at line 79 of file Subset.h.

Function Documentation

MergeTree IMP::domino::get_balanced_merge_tree ( const SubsetGraph & junction_tree )

See Also: get_merge_tree(RestraintSet*,const ParticleStatesTable*)

Compute the merge tree from a junction tree, attempting to keep it fairly balanced.

Note: the merge tree is not nececessarily deterministic (you can get different answers if you run it different times with the same inputs).

std::string IMP::domino::get_data_path ( std::string file_name )

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

double IMP::domino::get_distance_if_smaller_than	(	const Subset &	s,
		const Assignment &	a,
		const Assignment &	b,
		ParticleStatesTable *	pst,
		const statistics::Metrics &	metrics,
		double	max
	)

Return a distance between two assignments if they are less than a threshold. The distance returned is the l2 norm on the distances between each state as given by the corresponding metric. If no metric is passed, then the l2 norm on the embedding is used.

Warning: get_distance_if_close has not been stabilized and is likely to change without notice.

Definition at line 125 of file domino/utility.h.

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std::string IMP::domino::get_example_path ( std::string file_name )

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

Ints IMP::domino::get_index	(	const ParticlesTemp &	particles,
		const Subset &	subset,
		const Subsets &	excluded
	)

If the passed particles are all contained in the Subset and are not contained any of the Subsets in excluded, then return a a list of indices given the location of each passed particle in the passed subset. That is

particles[i]==subset[returned[i]];

Otherwise return an empty list.

This function is designed to be used for implementing SubsetFilterTable classes.

InteractionGraph IMP::domino::get_interaction_graph	(	ScoringFunctionAdaptor	rs,
		const ParticleStatesTable *	pst
	)

Compute the interaction graph of the restraints and the specified particles. The dependency graph in the model is traversed to determine how the passed particles relate to the actual particles read as input by the model. For example, if particles contains a rigid body, then an restraint which uses a member of the rigid body will have an edge from the rigid body particle.

Note: You may want to create an OptimizeRestraints object before calling this function.; These functions are here to aid in debugging of optimization protocols that use Domino2. As a result, its signature and functionality may change without notice.

display::Geometries IMP::domino::get_interaction_graph_geometry ( const InteractionGraph & ig )

Assuming that all the particles have Cartesian coordinates, output edges corresponding to the edges in the interaction graph. The edges are named by the restraint which induces them.

SubsetGraph IMP::domino::get_junction_tree ( const InteractionGraph & ig )

Compute the exact junction tree for an interaction graph. The resulting graph has the junction tree properties

it is a tree
for any two vertices whose subsets both contain a vertex, that vertex is contained in all subsets along the path connecting those two vertices.

Note: the junction tree is not nececessarily deterministic (you can get different answers if you run it different times with the same inputs).

MergeTree IMP::domino::get_merge_tree	(	ScoringFunctionAdaptor	input,
		const ParticleStatesTable *	pst
	)

See Also: get_merge_tree(const SubsetGraph&)

Compute the merge tree for a given restraint set and particle states table. An OptimizeRestraints object is created to improve the InteractionGraph used internally.

MergeTree IMP::domino::get_merge_tree ( const SubsetGraph & junction_tree )

See Also: get_merge_tree(RestraintSet*,const ParticleStatesTable*)

Compute the merge tree from a junction tree.

Note: the merge tree is not nececessarily deterministic (you can get different answers if you run it different times with the same inputs).

ParticlesTemp IMP::domino::get_order	(	const Subset &	s,
		const SubsetFilterTables &	sft
	)

Return the order computed for the particles in the subset to be used for enumeration. This function is there in order to expose internal functionality for easier testing and should not be depended upon.

Ints IMP::domino::get_partial_index	(	const ParticlesTemp &	particles,
		const Subset &	subset,
		const Subsets &	excluded
	)

All of the passed particles are not contained in an ofthe Subsets in excluded, then return a a list of indices given the location of each passed particle in the passed subset or -1 if it is missing.

This function is designed to be used for implementing SubsetFilterTable classes.

ParticlePairsTemp IMP::domino::get_possible_interactions	(	const ParticlesTemp &	ps,
		double	max_distance,
		ParticleStatesTable *	pst
	)

Return the list of interactions implied by the passed balls given the allowed positions specified by the ParticleStatesTable.

SubsetGraph IMP::domino::get_restraint_graph	(	ScoringFunctionAdaptor	rs,
		const ParticleStatesTable *	pst
	)

The restraint graph is formed by having one node per restraint and an edge connecting two restraints if they share input particles. The associated Subsets are the set of input particles for the restraint, projected onto ps.

Note: The graph for the optimized restraints (after temporary application of OptimizeContainers and OptimizeRestraints) is returned.

RestraintsTemp IMP::domino::get_restraints	(	const Subset &	s,
		const ParticleStatesTable *	pst,
		const DependencyGraph &	dg,
		RestraintSet *	rs
	)

Return a list of all restraints from rs that

do not depend on any particle in pst->get_particles() that is not in s The dependency graph is passed for efficiency.

Slice IMP::domino::get_slice	(	Subset	outer,
		Subset	inner,
		const Subsets &	excluded
	)

Return a slice for the inner subset if it is not contained in any of the excluded subsets, otherwise return the empty slice.

Definition at line 67 of file Slice.h.

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Assignments IMP::domino::get_state_clusters	(	const Subset &	subset,
		const Assignments &	states,
		ParticleStatesTable *	pst,
		double	resolution
	)

Return subset of the passed states which are representative. The states for each particle is clustered and then the passed states are reduced to only be on the centers of that clustering.

The XYZ coordinates are used for clustering, there is not currently a nice mechanism to vary this, but it should be figured out. Probably by subclasses statistics::Embedding to statistics::ParticleEmbedding which has a method which takes a particle.

display::Geometries IMP::domino::get_subset_graph_geometry ( const SubsetGraph & ig )

Display the subsets of a subset graph, superimposed on the 3D coordinates of the particles.

void IMP::domino::load_merged_assignments	(	const Subset &	first_subset,
		AssignmentContainer *	first,
		const Subset &	second_subset,
		AssignmentContainer *	second,
		const SubsetFilterTablesTemp &	filters,
		AssignmentContainer *	ret
	)

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

void IMP::domino::load_merged_assignments_random_order	(	const Subset &	first_subset,
		AssignmentContainer *	first,
		const Subset &	second_subset,
		AssignmentContainer *	second,
		const SubsetFilterTablesTemp &	filters,
		unsigned int	maximum_tries,
		AssignmentContainer *	ret
	)

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

It will try maximum_tries times to merge an assignment from the first set with a randomly chosen assignment from the second. Note that duplicate solutions may be present in the output and the output will never be guaranteed to be complete.

Warning: load_sampled_merged_assignments has not been stabilized and is likely to change without notice.

void IMP::domino::load_particle_states	(	const Subset &	s,
		const Assignment &	ss,
		const ParticleStatesTable *	pst
	)

Load the appropriate state for each particle in a Subset.

Classes

Typedefs

Functions

Standard module methods

Debugging Junction Trees

Read and write merge trees

Debug tools

Typedef Documentation

Function Documentation