Rosetta: protocols::toolbox::KMedoid Class Reference

Typical K-Medoids Clustering Algorithm. More...

#include <KCluster.hh>

Inheritance diagram for protocols::toolbox::KMedoid:

Inheritance graph

Public Member Functions
	KMedoid ()

bool	whoami () override

core::Real	get_threshold () override

void	init (KClusterElementOP, core::Size first=0) override

core::Real	assign (KClusterElementOP, KClusterData &) override

void	update (KClusterElementOP, KClusterData &) override

void	set_threshold (core::Real) override

Public Member Functions inherited from protocols::toolbox::KCluster
	KCluster ()

	~KCluster () override

void	cluster (KClusterElementOP, KClusterData &, core::Size first=0)

void	set_ncluster (core::Size nc)

Protected Member Functions
void	copy_coord (core::Size, FA2d &, FA2d &)

Protected Attributes
core::Size	cur_ncluster_

core::Real	threshold_

Protected Attributes inherited from protocols::toolbox::KCluster
core::Size	n_cluster_

Additional Inherited Members
Public Types inherited from protocols::toolbox::KCluster
typedef ObjexxFCL::FArray2_double	FA2d

typedef ObjexxFCL::FArray2P_double	FA2Pd

typedef ObjexxFCL::FArray2D_double	FA2Dd

Detailed Description

Typical K-Medoids Clustering Algorithm.

Constructor & Destructor Documentation

protocols::toolbox::KMedoid::KMedoid ( )

References threshold_.

Member Function Documentation

Real protocols::toolbox::KMedoid::assign	(	KClusterElementOP	c,
		KClusterData &	d
	)

overridevirtual

Implements protocols::toolbox::KCluster.

References protocols::toolbox::KClusterData::coords(), copy_coord(), cur_ncluster_, protocols::toolbox::KClusterData::dist_square(), protocols::toolbox::KClusterData::get_natom(), and core::simple_metrics::metrics::sum.

void protocols::toolbox::KMedoid::copy_coord	(	core::Size	len,
		FA2d &	src,
		FA2d &	dst
	)

protected

Referenced by assign().

Real protocols::toolbox::KMedoid::get_threshold ( )

overridevirtual

Implements protocols::toolbox::KCluster.

References threshold_.

void protocols::toolbox::KMedoid::init	(	KClusterElementOP	c,
		core::Size	first = `0`
	)

overridevirtual

Implements protocols::toolbox::KCluster.

References cur_ncluster_, protocols::mean_field::min(), protocols::toolbox::KCluster::n_cluster_, core::scoring::rg, and protocols::TR().

void protocols::toolbox::KMedoid::set_threshold ( core::Real t )

overridevirtual

Implements protocols::toolbox::KCluster.

References protocols::hybridization::t, and threshold_.

void protocols::toolbox::KMedoid::update	(	KClusterElementOP	c,
		KClusterData &	d
	)

overridevirtual

Implements protocols::toolbox::KCluster.

References protocols::toolbox::KClusterData::coords(), cur_ncluster_, protocols::toolbox::KClusterData::dist_square(), protocols::toolbox::KClusterData::get_natom(), and core::simple_metrics::metrics::sum.

bool protocols::toolbox::KMedoid::whoami ( )

overridevirtual

Implements protocols::toolbox::KCluster.

References protocols::TR().

Member Data Documentation

core::Size protocols::toolbox::KMedoid::cur_ncluster_

protected

Referenced by assign(), init(), and update().

core::Real protocols::toolbox::KMedoid::threshold_

protected

Referenced by get_threshold(), KMedoid(), and set_threshold().

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

src/protocols/toolbox/KCluster.hh
src/protocols/toolbox/KCluster.cc