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Public Types | Public Member Functions | Public Attributes | Private Attributes | List of all members
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

◆ EntryList

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

◆ FormatList

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

◆ GDB_Entry

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

◆ ResidueList

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

◆ StringList

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

◆ VarList

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

Constructor & Destructor Documentation

◆ GDB() [1/2]

protocols::sparta::GDB::GDB ( )

◆ GDB() [2/2]

protocols::sparta::GDB::GDB ( const std::string &  fileName)

Member Function Documentation

◆ addEntry()

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

◆ addRemark()

void protocols::sparta::GDB::addRemark ( const std::string &  str)

References protocols::kinmatch::str().

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

◆ addVAR()

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

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

◆ checkFormat()

bool protocols::sparta::GDB::checkFormat ( const std::string &  f)

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

◆ FORMAT_str_parser()

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().

◆ getData()

string protocols::sparta::GDB::getData ( const std::string &  DataName)

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

◆ getEntry() [1/3]

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

References core::sequence::end.

◆ getEntry() [2/3]

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.

◆ getEntry() [3/3]

GDB::GDB_Entry protocols::sparta::GDB::getEntry ( int  number)

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

◆ getEntryCount()

int protocols::sparta::GDB::getEntryCount ( )

◆ getResidName()

string protocols::sparta::GDB::getResidName ( int  rNum)

◆ isVarFloat() [1/2]

bool protocols::sparta::GDB::isVarFloat ( const std::string &  VarName)

References core::sequence::end.

◆ isVarFloat() [2/2]

bool protocols::sparta::GDB::isVarFloat ( int  index)

References protocols::sparta::contains().

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

◆ isVarInt() [1/2]

bool protocols::sparta::GDB::isVarInt ( const std::string &  VarName)

References core::sequence::end.

◆ isVarInt() [2/2]

bool protocols::sparta::GDB::isVarInt ( int  index)

References protocols::sparta::contains().

◆ isVarString() [1/2]

bool protocols::sparta::GDB::isVarString ( const std::string &  VarName)

References core::sequence::end.

◆ isVarString() [2/2]

bool protocols::sparta::GDB::isVarString ( int  index)

References protocols::sparta::contains().

◆ loadGDB()

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().

◆ presetClass()

void protocols::sparta::GDB::presetClass ( const std::string &  ClassName)

◆ saveGDB()

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().

◆ set_plaintext()

void protocols::sparta::GDB::set_plaintext ( )

◆ setData()

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

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

◆ setEntry()

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().

◆ setVAR()

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().

◆ showGDB()

void protocols::sparta::GDB::showGDB ( std::ostream &  os)

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

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

◆ VARS_str_parser()

void protocols::sparta::GDB::VARS_str_parser ( const std::string &  str)

References protocols::sparta::split(), and protocols::kinmatch::str().

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

Member Data Documentation

◆ buf

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

◆ ClassType

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

◆ DATA

StringList protocols::sparta::GDB::DATA

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

◆ EMPTY

GDB_Entry protocols::sparta::GDB::EMPTY

◆ Entries

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().

◆ firstResID

int protocols::sparta::GDB::firstResID

◆ FORMAT

FormatList protocols::sparta::GDB::FORMAT

◆ FORMAT_str

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

◆ GDBfileName

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

◆ plain_text

bool protocols::sparta::GDB::plain_text
private

◆ REMARKS

StringList protocols::sparta::GDB::REMARKS

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

◆ residList

ResidueList protocols::sparta::GDB::residList

◆ VARS

VarList protocols::sparta::GDB::VARS

◆ VARS_str

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

◆ VarsNumber

int protocols::sparta::GDB::VarsNumber
The documentation for this class was generated from the following files:
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