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protocols::toolbox::KClusterData Class Reference

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

#include <KCluster.hh>

Inheritance diagram for protocols::toolbox::KClusterData:
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Collaboration diagram for protocols::toolbox::KClusterData:
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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< 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 (string, Size)
 
Size get_ndata () const
 
Size get_natom () const
 
std::string get_tag (core::Size i)
 
std::string source_filename (core::Size i)
 
FA3Pd coords ()
 
void mark_tags (KClusterElementOP, string)
 
void save_all_in_one ()
 
void save_cluster_tree ()
 
Real dist_square (FA2d &, FA2d &)
 
Real dist_square (Size, Size)
 
void show_cluster_assignments ()
 

Private Attributes

protocols::toolbox::DecoySetEvaluation dataset_
 
Size ndata_
 
Size natom_
 
Size n_ca_atom_
 
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

Definition at line 205 of file KCluster.hh.

Member Typedef Documentation

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

Definition at line 210 of file KCluster.hh.

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

Definition at line 212 of file KCluster.hh.

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

Definition at line 211 of file KCluster.hh.

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

Definition at line 213 of file KCluster.hh.

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

Definition at line 214 of file KCluster.hh.

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

Definition at line 215 of file KCluster.hh.

Constructor & Destructor Documentation

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

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 59 of file KCluster.cc.

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

Definition at line 185 of file KCluster.cc.

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

Member Function Documentation

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

Definition at line 240 of file KCluster.hh.

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

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

Definition at line 219 of file KCluster.cc.

References protocols::toolbox::fit_centered_coords(), and natom_.

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

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

Definition at line 242 of file KCluster.cc.

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

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

Definition at line 227 of file KCluster.hh.

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

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

Definition at line 223 of file KCluster.hh.

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

Definition at line 232 of file KCluster.hh.

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

Definition at line 289 of file KCluster.cc.

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().

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

Definition at line 249 of file KCluster.cc.

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

Referenced by KClusterData().

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

Definition at line 358 of file KCluster.cc.

References tags_.

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

Definition at line 379 of file KCluster.cc.

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

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

Definition at line 425 of file KCluster.cc.

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_, core::io::silent::SilentFileData::read_file(), core::io::serialization::size(), and tags_.

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

Definition at line 489 of file KCluster.cc.

References tags_.

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

Definition at line 236 of file KCluster.hh.

Member Data Documentation

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

Definition at line 256 of file KCluster.hh.

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

Size protocols::toolbox::KClusterData::n_ca_atom_
private

Definition at line 259 of file KCluster.hh.

Referenced by KClusterData(), and load_silent_file().

Size protocols::toolbox::KClusterData::natom_
private

Definition at line 258 of file KCluster.hh.

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

Size protocols::toolbox::KClusterData::ndata_
private

Definition at line 257 of file KCluster.hh.

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

Size protocols::toolbox::KClusterData::nfile_
private

Definition at line 260 of file KCluster.hh.

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

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

Definition at line 263 of file KCluster.hh.

Referenced by load_silent_file().

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

Definition at line 262 of file KCluster.hh.

Referenced by load_silent_file().

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

Definition at line 264 of file KCluster.hh.

Referenced by KClusterData(), and load_silent_file().

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

Definition at line 261 of file KCluster.hh.

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:
Generated on Sat Jun 1 2013 12:57:43 for Rosetta 3.5 by   doxygen 1.8.4