IMP::domino::RestraintGraph Class Reference

Detailed Description


Public Member Functions
void	add_edge (unsigned int node1_ind, unsigned int node2_ind)
	Creates an undirected edge between two nodes.
void	add_node (unsigned int node_index, Particles &particles, RestraintEvaluatorI *rstr_eval)
	Creates a new node and add it to the graph.
void	analyse (std::ostream &out=std::cout) const
void	clear ()
CombState *	get_minimum_configuration () const
Float	get_minimum_score () const
JNode *	get_node (const Particles &p)
const CombState *	get_opt_combination (unsigned int i) const
	Get the i'th best combination.
Particles	get_particles () const
	Get the particles that are associated to the graph nodes.
void	infer (unsigned int num_of_solutions=1)
	Find the top solutions.
void	initialize_graph (int number_of_nodes)
	Initialize the graph.
void	initialize_potentials (Restraint r, Particles ps, Float weight)
	Initalize potentials according to the input restraint set.
bool	is_sampling_space_set () const
Float	move_to_configuration (const CombState &comb) const
	Move particles to the input combination and return its score.
void	move_to_global_minimum_configuration () const
	Move particles to the the global minimum combination.
unsigned int	number_of_edges () const
unsigned int	number_of_nodes () const
	RestraintGraph (const JunctionTree &jt, Model mdl, RestraintEvaluatorI r_eval)
	Constructor.
void	set_sampling_space (DiscreteSampler &ds)
void	show (std::ostream &out=std::cout) const
	Show the restraint graph.
void	show_sampling_space (std::ostream &out=std::cout) const
Protected Types
typedef boost::graph_traits < Graph >::edge_descriptor	Edge
typedef boost::graph_traits < Graph >::vertex_descriptor	Vertex
Protected Member Functions
void	clear_infered_data ()
unsigned int	collect_evidence (unsigned int father_ind)
void	dfs_order (unsigned int root_ind)
	Determine a DFS.
void	distribute_evidence (unsigned int father_ind)
void	distribute_minimum (unsigned int father_ind, CombState *min_comb)
	Recursive Distribution of minimum state.
JEdge *	get_edge (unsigned int n1, unsigned int n2) const
Pair	get_edge_key (unsigned int node1_ind, unsigned int node2_ind) const
void	load_data (const JunctionTree &jt, Model mdl, RestraintEvaluatorI r_eval)
	Load junction tree and set the restraint graph.
void	update (unsigned int w, unsigned int v)
	Updates node with index w based on the evidence in the node with index v.
Protected Attributes
std::vector< unsigned int >	discover_time_
std::map< Pair, JEdge * >	edge_data_
Graph	g_
bool	infered_
std::vector< CombState * > *	min_combs_
std::vector< int >	node2particle
std::vector< JNode * >	node_data_
std::map< int, int >	particle2node
unsigned int	root_
bool	sampling_space_set_

Constructor & Destructor Documentation

IMP::domino::RestraintGraph::RestraintGraph	(	const JunctionTree &	jt,
		Model *	mdl,
		RestraintEvaluatorI *	r_eval
	)

Constructor.

Parameters:

`[in]`	jt	Holds the junction tree that represent the system dependencies
`[in]`	mdl	The IMP model
`[in]`	r_eval	evaluator used to evaluate the restraints

Member Function Documentation

void IMP::domino::RestraintGraph::add_edge	(	unsigned int	node1_ind,
		unsigned int	node2_ind
	)

Creates an undirected edge between two nodes.

Parameters:

`[in]`	node1_ind	the index of the first node
`[in]`	node2_ind	the index of the second node

void IMP::domino::RestraintGraph::add_node	(	unsigned int	node_index,
		Particles &	particles,
		RestraintEvaluatorI *	rstr_eval
	)

Creates a new node and add it to the graph.

Parameters:

`[in]`	node_index	the index of the node
`[in]`	particles	the particles that are part of the node
`[in]`	rstr_eval	evaluator used to evaluate the restraints

void IMP::domino::RestraintGraph::analyse ( std::ostream & out = std::cout ) const

Prints the value of each restraint encoded in the graph for a state of the global minimum

unsigned int IMP::domino::RestraintGraph::collect_evidence ( unsigned int father_ind ) [protected]

Recursive Collect Evidence, father is the cluster that invoked CollectEvidence

Parameters:

[in] father_ind the index of the node to start collecting from

void IMP::domino::RestraintGraph::dfs_order ( unsigned int root_ind ) [protected]

Determine a DFS.

Parameters:

[in] root_ind the index of the node from which the DFS starts Stores the discover order of the nodes. discover_time[i] is the discover time in the DFS of node with index i.

void IMP::domino::RestraintGraph::distribute_evidence ( unsigned int father_ind ) [protected]

Recursive Distribution of evidence. father is the cluster that invoked distribute_evidence

Parameters:

[in] father_ind the index of the node to start collecting from

void IMP::domino::RestraintGraph::distribute_minimum	(	unsigned int	father_ind,
		CombState *	min_comb
	)			`[protected]`

Recursive Distribution of minimum state.

Parameters:

`[in]`	father_ind	the index of the node to start the min_dist from
`[in]`	min_comb	the minimum combination so far. Each child node will add the states of its particles.

JNode* IMP::domino::RestraintGraph::get_node ( const Particles & p )

Returns:: a node that contains the input set of particles. It might be that there is more than one such one. The function returns the first it finds.

Parameters:

[in] p the set of particles

Returns:: a node that contains the input set of particles

Exceptions:

IMP

exception if none of the graph nodes contain the given set of particles.

const CombState* IMP::domino::RestraintGraph::get_opt_combination ( unsigned int i ) const

Get the i'th best combination.

Parameters:

[in] i the i'th best combination

Exceptions:

if

no combinations have been infered or if i is out of range.

Returns:: the i'th best combination

Particles IMP::domino::RestraintGraph::get_particles ( ) const

Get the particles that are associated to the graph nodes.

Note:: The function does not consider hierarchies.

void IMP::domino::RestraintGraph::infer ( unsigned int num_of_solutions = 1 )

Find the top solutions.

/param[in] num_of_solutions the number of top solutions to report

void IMP::domino::RestraintGraph::initialize_graph ( int number_of_nodes )

Initialize the graph.

Parameters:

[in] number_of_nodes the number of nodes

void IMP::domino::RestraintGraph::initialize_potentials	(	Restraint *	r,
		Particles *	ps,
		Float	weight
	)

Initalize potentials according to the input restraint set.

Parameters:

`[in]`	r	the restraint
`[in]`	ps	the particles participate in the restraint at the hierarhcy level encoded in the graph
`[in]`	weight	the weight of the restraint

void IMP::domino::RestraintGraph::load_data	(	const JunctionTree &	jt,
		Model *	mdl,
		RestraintEvaluatorI *	r_eval
	)			`[protected]`

Load junction tree and set the restraint graph.

Parameters:

`[in]`	jt	contains the junction tree data
`[in]`	mdl	The model that contains the particles
`[in]`	r_eval	Evaluator to be used to evaluate the restraints

Note:: The function uses the particle name attribute as identifier

void IMP::domino::RestraintGraph::show_sampling_space ( std::ostream & out = std::cout ) const

Sets the optimizable attributes of the optimizable components to the values that build the minimum of the scoring function when the state of the root of the junction tree is of a spcific index.

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

RestraintGraph.h
domino/__init__.py

IMP::domino::RestraintGraph Class Reference

Detailed Description

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation