IMP::multifit::RMSDClustering< TransT > Class Template Reference

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Detailed Description

template<class TransT>
class IMP::multifit::RMSDClustering< TransT >

RMSD clustering.

/note Iteratively joins pairs of close transformatins. The algorithm first clusters transformations for which the transformed centroids are close (fall into the same bin in a hash. Then, all clusters are globally reclustered. /note TransT should implement the functions: join_into() add a transformation to the current cluster and possibly updates the representative transformation for the cluster get_score() that returns the score (higher score is better) update_score() that updates the score of the cluster according to a new member get_representative_transformation() a function that returns the the representative transformation for a cluster

List of all members.

Public Types
typedef boost::property < boost::edge_weight_t, short >	ClusEdgeWeightProperty
typedef boost::property < boost::vertex_index_t, int >	ClusVertexIndexProperty
typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS, ClusVertexIndexProperty, ClusEdgeWeightProperty >	Graph
typedef GeometricHash< int, 3 >	Hash3
typedef RCGTraits::edge_descriptor	RCEdge
typedef RCGTraits::edge_iterator	RCEdgeIt
typedef boost::graph_traits < Graph >	RCGTraits
typedef RCGTraits::vertex_descriptor	RCVertex
typedef RCGTraits::vertex_iterator	RCVertexIt

Public Member Functions
	RMSDClustering (float bin_size=3.)
void	cluster (float max_dist, const std::vector< TransT > &input_trans, std::vector< TransT > &output_trans)
	cluster transformations
void	prepare (const ParticlesTemp &ps)
	prepare for clustering
void	set_bin_size (float bin_size)

Protected Member Functions
void	build_full_graph (const Hash3 &h, const std::vector< TransformationRecord * > &recs, float max_dist, Graph &g)
void	build_graph (const Hash3::PointList &inds, const std::vector< TransformationRecord * > &recs, float max_dist, Graph &g)
virtual void	clean (std::vector< TransformationRecord * > *&records)
	Remove transformations which are not valid.
int	cluster_graph (Graph &g, const std::vector< TransformationRecord * > &recs, float max_dist)
virtual int	exhaustive_clustering (float max_dist, std::vector< TransformationRecord * > &recs)
int	fast_clustering (float max_dist, std::vector< TransformationRecord * > &recs)
virtual float	get_squared_distance (const TransT &trans1, const TransT &trans2)

Protected Attributes
float	bin_size_
algebra::Vector3D	centroid_
bool	is_fast_
bool	is_ready_
Particles	ps_
atom::RMSDCalculator	rmsd_calc_
core::XYZs	xyzs_

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Constructor & Destructor Documentation

template<class TransT >

IMP::multifit::RMSDClustering< TransT >::RMSDClustering

(

float

bin_size = 3.

)

Parameters:

[in]

bin_size

the radius of the bins of the hash differ with at most this value

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Member Function Documentation

template<class TransT >

void IMP::multifit::RMSDClustering< TransT >::clean ( std::vector< TransformationRecord * > *&  records )

protectedvirtual

Remove transformations which are not valid.

template<class TransT >

void IMP::multifit::RMSDClustering< TransT >::cluster	(	float	max_dist,
		const std::vector< TransT > &	input_trans,
		std::vector< TransT > &	output_trans
	)

cluster transformations

template<class TransT >

float IMP::multifit::RMSDClustering< TransT >::get_squared_distance ( const TransT &  trans1, const TransT &  trans2  )

protectedvirtual

returns the RMSD between two transformations with respect to the stored points

template<class TransT >

void IMP::multifit::RMSDClustering< TransT >::prepare

(

const ParticlesTemp &

ps

)

prepare for clustering

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

• RMSDClustering.h