protocols::toolbox::KMedoid Class Reference

Typical K-Medoids Clustering Algorithm. More...

#include <KCluster.hh>

Inheritance diagram for protocols::toolbox::KMedoid:

Collaboration diagram for protocols::toolbox::KMedoid:

Public Member Functions
	KMedoid ()
bool	whoami ()
Real	get_threshold ()
void	init (KClusterElementOP, Size first=0)
Real	assign (KClusterElementOP, KClusterData &)
void	update (KClusterElementOP, KClusterData &)
void	set_threshold (Real)
Public Member Functions inherited from protocols::toolbox::KCluster
	KCluster ()
virtual	~KCluster ()
void	cluster (KClusterElementOP, KClusterData &, Size first=0)
void	set_ncluster (Size nc)

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

Protected Attributes
Size	cur_ncluster_
Real	threshold_
Protected Attributes inherited from protocols::toolbox::KCluster
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.

Definition at line 296 of file KCluster.hh.

Constructor & Destructor Documentation

protocols::toolbox::KMedoid::KMedoid

(

)

Definition at line 555 of file KCluster.cc.

References threshold_.

Member Function Documentation

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 634 of file KCluster.cc.

References protocols::toolbox::KClusterData::coords(), copy_coord(), cur_ncluster_, protocols::toolbox::KClusterData::dist_square(), and protocols::toolbox::KClusterData::get_natom().

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

protected

Definition at line 623 of file KCluster.cc.

Referenced by assign().

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 563 of file KCluster.cc.

References threshold_.

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 579 of file KCluster.cc.

References cur_ncluster_, protocols::toolbox::KCluster::n_cluster_, protocols::RG(), and protocols::TR().

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 568 of file KCluster.cc.

References core::scoring::hbonds::t(), and threshold_.

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 720 of file KCluster.cc.

References protocols::toolbox::KClusterData::coords(), cur_ncluster_, protocols::toolbox::KClusterData::dist_square(), and protocols::toolbox::KClusterData::get_natom().

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

virtual

Implements protocols::toolbox::KCluster.

Definition at line 573 of file KCluster.cc.

References protocols::TR().

Member Data Documentation

Size protocols::toolbox::KMedoid::cur_ncluster_

protected

Definition at line 308 of file KCluster.hh.

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

Real protocols::toolbox::KMedoid::threshold_

protected

Definition at line 309 of file KCluster.hh.

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

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

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