protocols::cluster::DataPoint Class Reference

Data structure for one input data point for affinity propagation clustering. More...

#include <APCluster.hh>

Public Member Functions
	DataPoint (core::Size i_in)
	~DataPoint ()=default
void	add_similarity (core::Size k, core::Real s_ik, core::Size max_sims)
	Set similarity s(i,k), the suitability of point k to be an exemplar for this point. More...
bool	is_set_s_kk () const

Public Attributes
core::Size	i
core::Real	s_kk
core::Real	r_kk
core::Real	a_kk
core::Real	sum
core::Size	curr_exemplar
core::Size	best_exemplar
utility::vector1< Exemplar >	candidates
utility::vector1< Exemplar * >	candidate_for

Detailed Description

Data structure for one input data point for affinity propagation clustering.

There should be one instance of this class for each input point. Fields are public because it's a glorified struct – clients shouldn't use this directly.

Constructor & Destructor Documentation

protocols::cluster::DataPoint::DataPoint ( core::Size  i_in )

inline

protocols::cluster::DataPoint::~DataPoint ( )

default

Member Function Documentation

void protocols::cluster::DataPoint::add_similarity	(	core::Size	k,
		core::Real	s_ik,
		core::Size	max_sims
	)

Set similarity s(i,k), the suitability of point k to be an exemplar for this point.

If this point has more than max_sims similarities already stored, the lowest one (most negative) will be discarded.

There is currently no protection against adding s(i,k) twice, which will not be caught and will screw up the computation royally.

References candidates, curr_exemplar, i, protocols::cluster::Exemplar::min_heap(), and s_kk.

bool protocols::cluster::DataPoint::is_set_s_kk ( ) const

inline

References curr_exemplar.

Member Data Documentation

core::Real protocols::cluster::DataPoint::a_kk

Referenced by protocols::cluster::APCluster::assign_exemplars(), protocols::cluster::APCluster::reinitialize(), protocols::cluster::APCluster::update_a_ik(), and protocols::cluster::APCluster::update_r_ik().

core::Size protocols::cluster::DataPoint::best_exemplar

Referenced by protocols::cluster::APCluster::reinitialize(), protocols::cluster::APCluster::restore_best_exemplars(), and protocols::cluster::APCluster::save_best_exemplars().

utility::vector1< Exemplar* > protocols::cluster::DataPoint::candidate_for

Referenced by protocols::cluster::APCluster::freeze(), and protocols::cluster::APCluster::update_a_ik().

utility::vector1< Exemplar > protocols::cluster::DataPoint::candidates

Referenced by add_similarity(), protocols::cluster::APCluster::assign_exemplars(), protocols::cluster::APCluster::freeze(), protocols::cluster::APCluster::get_net_sim(), protocols::cluster::APCluster::load_binary(), protocols::cluster::APCluster::reinitialize(), protocols::cluster::APCluster::save_binary(), protocols::cluster::APCluster::update_a_ik(), and protocols::cluster::APCluster::update_r_ik().

core::Size protocols::cluster::DataPoint::curr_exemplar

Referenced by add_similarity(), protocols::cluster::APCluster::assign_exemplars(), protocols::cluster::APCluster::get_all_exemplars(), protocols::cluster::APCluster::get_cluster_for(), protocols::cluster::APCluster::get_net_sim(), protocols::cluster::APCluster::get_num_exemplars(), is_set_s_kk(), protocols::cluster::APCluster::load_binary(), protocols::cluster::APCluster::reinitialize(), protocols::cluster::APCluster::restore_best_exemplars(), protocols::cluster::APCluster::save_best_exemplars(), and protocols::cluster::APCluster::save_binary().

core::Size protocols::cluster::DataPoint::i

Referenced by add_similarity(), protocols::cluster::APCluster::assign_exemplars(), protocols::cluster::APCluster::get_all_exemplars(), protocols::cluster::APCluster::get_num_exemplars(), protocols::cluster::APCluster::load_binary(), and protocols::cluster::APCluster::save_binary().

core::Real protocols::cluster::DataPoint::r_kk

Referenced by protocols::cluster::APCluster::assign_exemplars(), protocols::cluster::APCluster::reinitialize(), protocols::cluster::APCluster::update_a_ik(), and protocols::cluster::APCluster::update_r_ik().

core::Real protocols::cluster::DataPoint::s_kk

Referenced by add_similarity(), protocols::cluster::APCluster::get_net_sim(), protocols::cluster::APCluster::load_binary(), protocols::cluster::APCluster::save_binary(), and protocols::cluster::APCluster::update_r_ik().

core::Real protocols::cluster::DataPoint::sum

Referenced by protocols::cluster::APCluster::update_a_ik().

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

• src/protocols/cluster/APCluster.hh
• src/protocols/cluster/APCluster.cc