protocols::toolbox::KClusterData Class Reference

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

#include <KCluster.hh>

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
virtual	~KClusterData ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. 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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::toolbox::KClusterData::KClusterData

(

)

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

Member Function Documentation

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

inline

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

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

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

References protocols::toolbox::fit_centered_coords(), cluster::K_not_fit_xyz, natom_, option, sum(), and weights.

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

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

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

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

inline

References ndata_.

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

inline

References original_tags_.

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(), list, 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_, runtime_assert, core::io::silent::SilentFileData::size(), tag, and tags_.

Referenced by load_silent_files().

void protocols::toolbox::KClusterData::load_silent_files

(

)

References protocols::toolbox::DecoySetEvaluation::coords(), dataset_, cluster::K_not_fit_xyz, load_silent_file(), natom_, ndata_, option, protocols::toolbox::reset_x(), in::file::silent, in::file::silent_list, size(), protocols::TR, user, utility_exit_with_message, and weights.

Referenced by KClusterData().

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

References tag, and tags_.

void protocols::toolbox::KClusterData::save_all_in_one

(

)

References core::io::silent::SilentFileData::begin(), core::io::silent::SilentFileData::end(), ndata_, nfile_, option, core::io::silent::SilentFileData::read_file(), in::file::silent, out::file::silent, in::file::silent_list, size(), tags_, and user.

void protocols::toolbox::KClusterData::save_cluster_tree

(

)

References core::io::silent::SilentFileData::begin(), utility::file::create_directory_recursive(), core::io::silent::SilentFileData::end(), protocols::toolbox::file_full_path(), filename(), protocols::toolbox::fix_tag_suffix(), cluster::K_redundant, cluster::K_save_headers, ndata_, nfile_, option, path, core::io::silent::SilentFileData::read_file(), in::file::silent, in::file::silent_list, size(), tags_, and user.

void protocols::toolbox::KClusterData::show_cluster_assignments

(

)

References tags_.

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

inline

References original_filenames_.

Member Data Documentation

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

private

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

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

private

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

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

private

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

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().

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

private

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

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

private

Referenced by load_silent_file(), and source_filename().

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

private

Referenced by get_tag(), and load_silent_file().

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

private

Referenced by KClusterData(), and load_silent_file().

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