protocols::sparta::GDB Class Reference

#include <GDB.hh>

Public Types
typedef boost::unordered_map < std::string, std::string >	GDB_Entry
typedef std::map< int, std::string >	ResidueList
typedef utility::vector0 < std::string >	StringList
typedef std::map< int, std::string >	VarList
typedef std::map< int, std::string >	FormatList
typedef std::map< int, GDB_Entry >	EntryList

Public Member Functions
	GDB ()
	GDB (const std::string &fileName)
void	loadGDB (const std::string &fileName)
void	saveGDB (const std::string &fileName)
void	showGDB (std::ostream &os)
void	addVAR (const std::string &VAR_Name, const std::string &FORMAT_Name)
void	setVAR (int index, const std::string &VAR_Name, const std::string &FORMAT_Name)
void	setData (const std::string &DataName, const std::string &DataVal)
std::string	getData (const std::string &DataName)
GDB_Entry	getEntry (int number)
GDB_Entry	getEntry (const std::string &VName, const std::string &VVal, int index)
GDB_Entry	getEntry (const std::string &VName1, const std::string &VVal1, const std::string &VName2, const std::string &VVal2, int index)
void	setEntry (int index, const std::string &VarName, const std::string &VarVal)
void	addEntry (const std::string &VarName, const std::string &VarVal)
void	addRemark (const std::string &str)
std::string	getResidName (int rNum)
int	getEntryCount ()
void	presetClass (const std::string &ClassName)
bool	checkFormat (const std::string &f)
bool	isVarFloat (int index)
bool	isVarInt (int index)
bool	isVarString (int index)
bool	isVarFloat (const std::string &VarName)
bool	isVarInt (const std::string &VarName)
bool	isVarString (const std::string &VarName)
void	VARS_str_parser (const std::string &str)
void	FORMAT_str_parser (const std::string &str)
void	set_plaintext ()

Public Attributes
std::string	GDBfileName
std::string	FORMAT_str
std::string	VARS_str
int	VarsNumber
int	firstResID
GDB_Entry	EMPTY
ResidueList	residList
StringList	REMARKS
StringList	DATA
VarList	VARS
FormatList	FORMAT
EntryList	Entries

Private Attributes
std::string	ClassType
bool	plain_text
char	buf [5000]

Member Typedef Documentation

typedef std::map< int, GDB_Entry > protocols::sparta::GDB::EntryList

typedef std::map<int, std::string> protocols::sparta::GDB::FormatList

typedef boost::unordered_map< std::string, std::string > protocols::sparta::GDB::GDB_Entry

typedef std::map<int, std::string> protocols::sparta::GDB::ResidueList

typedef utility::vector0< std::string > protocols::sparta::GDB::StringList

typedef std::map<int, std::string> protocols::sparta::GDB::VarList

Constructor & Destructor Documentation

protocols::sparta::GDB::GDB

(

)

protocols::sparta::GDB::GDB

(

const std::string &

fileName

)

Member Function Documentation

void protocols::sparta::GDB::addEntry	(	const std::string &	VarName,
		const std::string &	VarVal
	)

void protocols::sparta::GDB::addRemark

(

const std::string &

str

)

Referenced by protocols::sparta::Sparta::run_A_ANN_Prediction().

void protocols::sparta::GDB::addVAR	(	const std::string &	VAR_Name,
		const std::string &	FORMAT_Name
	)

References protocols::sparta::contains(), and protocols::sparta::tr().

bool protocols::sparta::GDB::checkFormat

(

const std::string &

f

)

References protocols::sparta::contains(), protocols::sparta::isDigit(), protocols::sparta::simplifyWhiteSpace(), and protocols::kinmatch::str().

void protocols::sparta::GDB::FORMAT_str_parser

(

const std::string &

str

)

References protocols::sparta::contains(), protocols::sparta::section(), protocols::kinmatch::str(), and protocols::sparta::tr().

Referenced by protocols::sparta::calc_per_residue_scores(), and protocols::sparta::Sparta::SpartaLib::get_ANN_data().

string protocols::sparta::GDB::getData

(

const std::string &

DataName

)

Referenced by protocols::sparta::Sparta::check_pose().

GDB::GDB_Entry protocols::sparta::GDB::getEntry

(

int

number

)

Referenced by protocols::sparta::calc_per_residue_scores().

GDB::GDB_Entry protocols::sparta::GDB::getEntry	(	const std::string &	VName,
		const std::string &	VVal,
		int	index
	)

References core::sequence::end.

GDB::GDB_Entry protocols::sparta::GDB::getEntry	(	const std::string &	VName1,
		const std::string &	VVal1,
		const std::string &	VName2,
		const std::string &	VVal2,
		int	index
	)

References core::sequence::end.

int protocols::sparta::GDB::getEntryCount

(

)

string protocols::sparta::GDB::getResidName

(

int

rNum

)

bool protocols::sparta::GDB::isVarFloat

(

int

index

)

References protocols::sparta::contains().

Referenced by protocols::sparta::calc_per_residue_scores().

bool protocols::sparta::GDB::isVarFloat

(

const std::string &

VarName

)

References core::sequence::end.

bool protocols::sparta::GDB::isVarInt

(

int

index

)

References protocols::sparta::contains().

bool protocols::sparta::GDB::isVarInt

(

const std::string &

VarName

)

References core::sequence::end.

bool protocols::sparta::GDB::isVarString

(

int

index

)

References protocols::sparta::contains().

bool protocols::sparta::GDB::isVarString

(

const std::string &

VarName

)

References core::sequence::end.

void protocols::sparta::GDB::loadGDB

(

const std::string &

fileName

)

References protocols::sparta::simplifyWhiteSpace(), protocols::sparta::split_WhiteSpace(), protocols::kinmatch::str(), and protocols::sparta::tr().

Referenced by protocols::sparta::Sparta::SpartaLib::init().

void protocols::sparta::GDB::presetClass

(

const std::string &

ClassName

)

void protocols::sparta::GDB::saveGDB

(

const std::string &

fileName

)

References core::conformation::membrane::out, and protocols::sparta::tr().

Referenced by protocols::sparta::Sparta::SpartaLib::get_ANN_data(), and protocols::sparta::Sparta::run_A_ANN_Prediction().

void protocols::sparta::GDB::set_plaintext

(

)

void protocols::sparta::GDB::setData	(	const std::string &	DataName,
		const std::string &	DataVal
	)

Referenced by protocols::sparta::Sparta::SpartaLib::get_ANN_data().

void protocols::sparta::GDB::setEntry	(	int	index,
		const std::string &	VarName,
		const std::string &	VarVal
	)

References core::sequence::end, and protocols::sparta::tr().

Referenced by protocols::sparta::Sparta::SpartaLib::get_ANN_data().

void protocols::sparta::GDB::setVAR	(	int	index,
		const std::string &	VAR_Name,
		const std::string &	FORMAT_Name
	)

References protocols::sparta::contains(), and protocols::sparta::tr().

void protocols::sparta::GDB::showGDB

(

std::ostream &

os

)

References protocols::sparta::contains(), core::sequence::end, and protocols::sparta::simplifyWhiteSpace().

Referenced by protocols::sparta::calc_per_residue_scores(), and protocols::sparta::Sparta::SpartaLib::get_ANN_data().

void protocols::sparta::GDB::VARS_str_parser

(

const std::string &

str

)

References protocols::sparta::split().

Referenced by protocols::sparta::calc_per_residue_scores(), and protocols::sparta::Sparta::SpartaLib::get_ANN_data().

Member Data Documentation

char protocols::sparta::GDB::buf[5000]

private

std::string protocols::sparta::GDB::ClassType

private

StringList protocols::sparta::GDB::DATA

Referenced by protocols::sparta::calc_per_residue_scores().

GDB_Entry protocols::sparta::GDB::EMPTY

EntryList protocols::sparta::GDB::Entries

Referenced by protocols::sparta::calc_per_residue_scores(), protocols::sparta::compareRef_fxn(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::sparta::Sparta::SpartaLib::init(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), and protocols::sparta::ANN::loadWeightBias3().

int protocols::sparta::GDB::firstResID

FormatList protocols::sparta::GDB::FORMAT

std::string protocols::sparta::GDB::FORMAT_str

std::string protocols::sparta::GDB::GDBfileName

bool protocols::sparta::GDB::plain_text

private

StringList protocols::sparta::GDB::REMARKS

Referenced by protocols::sparta::calc_per_residue_scores().

ResidueList protocols::sparta::GDB::residList

VarList protocols::sparta::GDB::VARS

std::string protocols::sparta::GDB::VARS_str

int protocols::sparta::GDB::VarsNumber

---

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

• src/protocols/sparta/GDB.hh
• src/protocols/sparta/GDB.cc