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, SimPDBOP >	filename2PDB

Static Public Attributes
static unsigned int	ADVISED_THRESHOLD = 36000

Private Attributes
std::string	silentfilename_ = ""
std::string	pdblistfilename_ = ""

Constructor & Destructor Documentation

protocols::cluster::calibur::PreloadedPDB::PreloadedPDB

(

)

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

inline

Member Function Documentation

SimPDBOP protocols::cluster::calibur::PreloadedPDB::getSimPDB

(

std::string const &

pdbfilename

)

References protocols::abinitio::filename(), and filename2PDB.

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().

void protocols::cluster::calibur::PreloadedPDB::loadSilentFile

(

std::string const &

filename

)

Populate the PreloadedPDB with a silentfile

References protocols::cluster::calibur::center_residues(), protocols::abinitio::filename(), filename2PDB, mNumDecoy, names_, num_residue_, silentfilename_, protocols::cluster::calibur::toFloat(), and protocols::cluster::calibur::toInt().

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

Member Data Documentation

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().

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

Referenced by getSimPDB(), loadPDBFromList(), loadSilentFile(), and protocols::cluster::calibur::SimPDB::SimPDB().

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

Referenced by loadPDBFromList(), and loadSilentFile().

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

Referenced by loadPDBFromList(), loadSilentFile(), and protocols::cluster::calibur::Clustering::readDecoyNames().

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

Referenced by loadPDBFromList(), and loadSilentFile().

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

private

Referenced by loadPDBFromList().

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

private

Referenced by loadSilentFile().

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

• src/protocols/cluster/calibur/PreloadedPDB.hh
• src/protocols/cluster/calibur/PreloadedPDB.cc