protocols::cluster::calibur::SimPDB Class Reference

#include <SimPDB.hh>

Public Member Functions
void	read ()
	SimPDB (std::string const &aProteinFileName)
	SimPDB (std::string const &aProteinFileName, int const len)
	~SimPDB ()
	SimPDB ()
	SimPDB (int len)

Public Attributes
std::string	protein_file_name_
int	num_residue_
std::vector< core::Real >	calpha_vector_

Static Public Attributes
static int	s_residue = 1
static int	e_residue = LONGEST_CHAIN
static char *	chains = strdup("AC ")
static PreloadedPDB *	preloadedPDB = nullptr
static bool	preloadPDB = true

Constructor & Destructor Documentation

SimPDB() [1/4]

protocols::cluster::calibur::SimPDB::SimPDB

(

std::string const &

aProteinFileName

)

References calpha_vector_, protocols::cluster::calibur::PreloadedPDB::filename2PDB, LONGEST_CHAIN, num_residue_, preloadedPDB, preloadPDB, protein_file_name_, and read().

SimPDB() [2/4]

protocols::cluster::calibur::SimPDB::SimPDB	(	std::string const &	aProteinFileName,
		int const	len
	)

References calpha_vector_, protocols::cluster::calibur::PreloadedPDB::filename2PDB, num_residue_, preloadedPDB, preloadPDB, protein_file_name_, and read().

~SimPDB()

protocols::cluster::calibur::SimPDB::~SimPDB ( )

default

SimPDB() [3/4]

protocols::cluster::calibur::SimPDB::SimPDB ( )

default

SimPDB() [4/4]

protocols::cluster::calibur::SimPDB::SimPDB

(

int

len

)

References calpha_vector_, and num_residue_.

Member Function Documentation

read()

void protocols::cluster::calibur::SimPDB::read

(

)

Reads a PDB file from disk. Do not read from PDB files anywhere else.

References calpha_vector_, protocols::cluster::calibur::center_residues(), chains, e_residue, num_residue_, protein_file_name_, s_residue, protocols::cluster::calibur::toFloat(), and protocols::cluster::calibur::toInt().

Referenced by SimPDB().

Member Data Documentation

calpha_vector_

std::vector<core::Real> protocols::cluster::calibur::SimPDB::calpha_vector_

Referenced by read(), and SimPDB().

chains

char * protocols::cluster::calibur::SimPDB::chains = strdup("AC ")

static

Referenced by protocols::cluster::calibur::Clustering::initialize(), and read().

e_residue

int protocols::cluster::calibur::SimPDB::e_residue = LONGEST_CHAIN

static

Referenced by read().

num_residue_

int protocols::cluster::calibur::SimPDB::num_residue_

Referenced by read(), and SimPDB().

preloadedPDB

PreloadedPDB * protocols::cluster::calibur::SimPDB::preloadedPDB = nullptr

static

This feature allows the preloading of SimPDB objects. SimPDB will then be obtained from preloadedPDB instead of from disk.

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

preloadPDB

bool protocols::cluster::calibur::SimPDB::preloadPDB = true

static

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

protein_file_name_

std::string protocols::cluster::calibur::SimPDB::protein_file_name_

Referenced by read(), and SimPDB().

s_residue

int protocols::cluster::calibur::SimPDB::s_residue = 1

static

These parameters control how PDB files are to be loaded. They do not apply to silent file, which are assumed to be pre-processed.

Referenced by read().

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

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