Rosetta: protocols::toolbox::KClusterData Class Reference

Rosetta

database of a K-style Clustering algorithm More...

#include <KCluster.hh>

Inheritance diagram for protocols::toolbox::KClusterData:

Inheritance graph

[legend]

Public Types
typedef ObjexxFCL::FArray1D_double	FA1Dd

typedef ObjexxFCL::FArray2D_double	FA2Dd

typedef ObjexxFCL::FArray2_double	FA2d

typedef ObjexxFCL::FArray2P_double	FA2Pd

typedef ObjexxFCL::FArray3P_double	FA3Pd

typedef utility::vector1< std::string >	TagList

Public Member Functions
	~KClusterData () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...

	KClusterData ()

void	load_silent_files ()

void	load_silent_file (std::string, core::Size)

core::Size	get_ndata () const

core::Size	get_natom () const

std::string	get_tag (core::Size i)

std::string	source_filename (core::Size i)

FA3Pd	coords ()

void	mark_tags (KClusterElementOP, std::string)

void	save_all_in_one ()

void	save_cluster_tree ()

core::Real	dist_square (FA2d &, FA2d &)

core::Real	dist_square (core::Size, core::Size)

void	show_cluster_assignments ()

Private Attributes
protocols::toolbox::DecoySetEvaluation	dataset_

core::Size	ndata_

core::Size	natom_

core::Size	n_ca_atom_

core::Size	nfile_

utility::vector1< TagList >	tags_

utility::vector1< TagList >	original_tags_

utility::vector1< std::string >	original_filenames_

utility::vector1< core::Size >	rmsd_ca_list_

Detailed Description

database of a K-style Clustering algorithm

Member Typedef Documentation

◆ FA1Dd

typedef ObjexxFCL::FArray1D_double protocols::toolbox::KClusterData::FA1Dd

◆ FA2d

typedef ObjexxFCL::FArray2_double protocols::toolbox::KClusterData::FA2d

◆ FA2Dd

typedef ObjexxFCL::FArray2D_double protocols::toolbox::KClusterData::FA2Dd

◆ FA2Pd

typedef ObjexxFCL::FArray2P_double protocols::toolbox::KClusterData::FA2Pd

◆ FA3Pd

typedef ObjexxFCL::FArray3P_double protocols::toolbox::KClusterData::FA3Pd

◆ TagList

typedef utility::vector1< std::string > protocols::toolbox::KClusterData::TagList

Constructor & Destructor Documentation

◆ ~KClusterData()

protocols::toolbox::KClusterData::~KClusterData ( )

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ KClusterData()

protocols::toolbox::KClusterData::KClusterData ( )

References core::sequence::end, load_silent_files(), protocols::loops::Loops::loop_size(), n_ca_atom_, natom_, ndata_, nfile_, rmsd_ca_list_, and protocols::TR().

Member Function Documentation

◆ coords()

FA3Pd protocols::toolbox::KClusterData::coords ( )

inline

References protocols::toolbox::DecoySetEvaluation::coords(), and dataset_.

Referenced by protocols::toolbox::KMedoid::assign(), and protocols::toolbox::KMedoid::update().

◆ dist_square() [1/2]

Real protocols::toolbox::KClusterData::dist_square	(	core::Size	ndx1,
		core::Size	ndx2
	)

References protocols::toolbox::DecoySetEvaluation::coords(), dataset_, dist_square(), and natom_.

◆ dist_square() [2/2]

Real protocols::toolbox::KClusterData::dist_square	(	FA2d &	conf1,
		FA2d &	conf2
	)

References protocols::toolbox::fit_centered_coords(), natom_, and core::simple_metrics::metrics::sum.

Referenced by protocols::toolbox::KMedoid::assign(), protocols::toolbox::GreedyKCenter::assign(), dist_square(), and protocols::toolbox::KMedoid::update().

◆ get_natom()

core::Size protocols::toolbox::KClusterData::get_natom ( ) const

inline

References n_ca_atom_.

Referenced by protocols::toolbox::KMedoid::assign(), and protocols::toolbox::KMedoid::update().

◆ get_ndata()

core::Size protocols::toolbox::KClusterData::get_ndata ( ) const

inline

References ndata_.

◆ get_tag()

std::string protocols::toolbox::KClusterData::get_tag ( core::Size i )

inline

References original_tags_.

◆ load_silent_file()

void protocols::toolbox::KClusterData::load_silent_file	(	std::string	silent_file,
		core::Size	nfile
	)

References core::io::silent::SilentFileData::begin(), dataset_, core::io::silent::SilentFileData::end(), protocols::toolbox::DecoySetEvaluation::n_atoms(), n_ca_atom_, protocols::toolbox::DecoySetEvaluation::n_decoys(), protocols::toolbox::DecoySetEvaluation::n_decoys_max(), natom_, ndata_, nfile_, original_filenames_, original_tags_, protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), core::io::silent::SilentFileData::read_file(), protocols::toolbox::DecoySetEvaluation::reserve(), rmsd_ca_list_, core::io::silent::SilentFileData::size(), and tags_.

Referenced by load_silent_files().

◆ load_silent_files()

void protocols::toolbox::KClusterData::load_silent_files ( )

References protocols::toolbox::DecoySetEvaluation::coords(), dataset_, load_silent_file(), natom_, ndata_, protocols::toolbox::reset_x(), and protocols::TR().

Referenced by KClusterData().

◆ mark_tags()

void protocols::toolbox::KClusterData::mark_tags	(	KClusterElementOP	c,
		std::string	t
	)

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

◆ save_all_in_one()

void protocols::toolbox::KClusterData::save_all_in_one ( )

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), ndata_, nfile_, core::io::silent::SilentFileData::read_file(), tags_, and core::io::silent::SilentFileData::write_silent_struct().

◆ save_cluster_tree()

void protocols::toolbox::KClusterData::save_cluster_tree ( )

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), protocols::toolbox::file_full_path(), protocols::abinitio::filename(), protocols::toolbox::fix_tag_suffix(), ndata_, nfile_, protocols::hybridization::path, core::io::silent::SilentFileData::read_file(), tags_, and core::io::silent::SilentFileData::write_silent_struct().

◆ show_cluster_assignments()

void protocols::toolbox::KClusterData::show_cluster_assignments ( )

References tags_.

◆ source_filename()

std::string protocols::toolbox::KClusterData::source_filename ( core::Size i )

inline

References original_filenames_.

Member Data Documentation

◆ dataset_

protocols::toolbox::DecoySetEvaluation protocols::toolbox::KClusterData::dataset_

private

Referenced by coords(), dist_square(), load_silent_file(), and load_silent_files().

◆ n_ca_atom_

core::Size protocols::toolbox::KClusterData::n_ca_atom_

private

Referenced by get_natom(), KClusterData(), and load_silent_file().

◆ natom_

core::Size protocols::toolbox::KClusterData::natom_

private

Referenced by dist_square(), KClusterData(), load_silent_file(), and load_silent_files().

◆ ndata_

core::Size protocols::toolbox::KClusterData::ndata_

private

Referenced by get_ndata(), KClusterData(), load_silent_file(), load_silent_files(), save_all_in_one(), and save_cluster_tree().

◆ nfile_

core::Size protocols::toolbox::KClusterData::nfile_

private

Referenced by KClusterData(), load_silent_file(), save_all_in_one(), and save_cluster_tree().

◆ original_filenames_

utility::vector1< std::string > protocols::toolbox::KClusterData::original_filenames_

private

Referenced by load_silent_file(), and source_filename().

◆ original_tags_

utility::vector1< TagList > protocols::toolbox::KClusterData::original_tags_

private

Referenced by get_tag(), and load_silent_file().

◆ rmsd_ca_list_

utility::vector1< core::Size > protocols::toolbox::KClusterData::rmsd_ca_list_

private

Referenced by KClusterData(), and load_silent_file().

◆ tags_

utility::vector1< TagList > protocols::toolbox::KClusterData::tags_

private

Referenced by load_silent_file(), mark_tags(), save_all_in_one(), save_cluster_tree(), and show_cluster_assignments().

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

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