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Public Member Functions | Public Attributes | Static Public Attributes | Private Attributes | List of all members
protocols::cluster::calibur::PreloadedPDB Class Reference

#include <PreloadedPDB.hh>

Public Member Functions

 PreloadedPDB ()
 
 ~PreloadedPDB ()
 
void loadSilentFile (std::string const &silentfilename)
 
void loadPDBFromList (std::string const &pdblistfilename)
 
SimPDBOP getSimPDB (std::string const &pdbfilename)
 

Public Attributes

int num_residue_
 
int mNumDecoy
 
StringVecOP names_
 
std::map< std::string, SimPDBOPfilename2PDB
 

Static Public Attributes

static unsigned int ADVISED_THRESHOLD = 36000
 

Private Attributes

std::string silentfilename_ = ""
 
std::string pdblistfilename_ = ""
 

Constructor & Destructor Documentation

◆ PreloadedPDB()

protocols::cluster::calibur::PreloadedPDB::PreloadedPDB ( )

◆ ~PreloadedPDB()

protocols::cluster::calibur::PreloadedPDB::~PreloadedPDB ( )
inline

Member Function Documentation

◆ getSimPDB()

SimPDBOP protocols::cluster::calibur::PreloadedPDB::getSimPDB ( std::string const &  pdbfilename)

◆ loadPDBFromList()

void protocols::cluster::calibur::PreloadedPDB::loadPDBFromList ( std::string const &  filename)

Populate the PreloadedPDB with the PDB files specified in a list.

Reading of the PDB files is through SimPDB.

References protocols::abinitio::filename(), filename2PDB, LONGEST_CHAIN, mNumDecoy, names_, num_residue_, and pdblistfilename_.

Referenced by protocols::cluster::calibur::Clustering::readDecoyNames().

◆ loadSilentFile()

void protocols::cluster::calibur::PreloadedPDB::loadSilentFile ( std::string const &  filename)

Member Data Documentation

◆ ADVISED_THRESHOLD

unsigned int protocols::cluster::calibur::PreloadedPDB::ADVISED_THRESHOLD = 36000
static

Reasons for choosing 36,000 as the threshold for using disk access

  1. 36,000 decoys of 100 residues each is about 44MB, which is still acceptable for a workstation PC. If user has less capabled hardware, the "-d" switch may be used.
  2. For more than 36,000 decoys, the bottleneck is probably not in disk.

Referenced by protocols::cluster::calibur::Clustering::readDecoyNames().

◆ filename2PDB

std::map<std::string, SimPDBOP > protocols::cluster::calibur::PreloadedPDB::filename2PDB

◆ mNumDecoy

int protocols::cluster::calibur::PreloadedPDB::mNumDecoy

Referenced by loadPDBFromList(), and loadSilentFile().

◆ names_

StringVecOP protocols::cluster::calibur::PreloadedPDB::names_

◆ num_residue_

int protocols::cluster::calibur::PreloadedPDB::num_residue_

Referenced by loadPDBFromList(), and loadSilentFile().

◆ pdblistfilename_

std::string protocols::cluster::calibur::PreloadedPDB::pdblistfilename_ = ""
private

Referenced by loadPDBFromList().

◆ silentfilename_

std::string protocols::cluster::calibur::PreloadedPDB::silentfilename_ = ""
private

Referenced by loadSilentFile().


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