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protocols::sparta::GDB Class Reference

#include <GDB.hh>

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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
 
boost::unordered_map< int,
std::string > 		residList
 
utility::vector0< std::string > REMARKS
 
utility::vector0< std::string > DATA
 
boost::unordered_map< int,
std::string > 		VARS
 
boost::unordered_map< int,
std::string > 		FORMAT
 
boost::unordered_map< int,
GDB_Entry > 		Entries
 

Private Attributes

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

Detailed Description

Definition at line 30 of file GDB.hh.

Constructor & Destructor Documentation

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

Definition at line 39 of file GDB.cc.

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

Definition at line 46 of file GDB.cc.

Member Function Documentation

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

Definition at line 289 of file GDB.cc.

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

Definition at line 351 of file GDB.cc.

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

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

Definition at line 297 of file GDB.cc.

References protocols::sparta::contains(), core::io::serialization::size(), and protocols::sparta::tr().

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

Definition at line 452 of file GDB.cc.

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)

Definition at line 488 of file GDB.cc.

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)

Definition at line 365 of file GDB.cc.

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

Definition at line 201 of file GDB.cc.

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

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

Definition at line 208 of file GDB.cc.

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

Definition at line 229 of file GDB.cc.

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

Definition at line 258 of file GDB.cc.

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

Definition at line 251 of file GDB.cc.

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

Definition at line 382 of file GDB.cc.

References protocols::sparta::contains().

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

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

Definition at line 391 of file GDB.cc.

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

Definition at line 405 of file GDB.cc.

References protocols::sparta::contains().

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

Definition at line 414 of file GDB.cc.

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

Definition at line 428 of file GDB.cc.

References protocols::sparta::contains().

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

Definition at line 437 of file GDB.cc.

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

Definition at line 57 of file GDB.cc.

References protocols::fldsgn::topology::compare(), 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)

Definition at line 512 of file GDB.cc.

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

Definition at line 130 of file GDB.cc.

References 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 ( )

Definition at line 529 of file GDB.cc.

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

Definition at line 358 of file GDB.cc.

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

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

Definition at line 266 of file GDB.cc.

References 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 
)

Definition at line 329 of file GDB.cc.

References protocols::sparta::contains(), core::io::serialization::size(), and protocols::sparta::tr().

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

Definition at line 140 of file GDB.cc.

References protocols::sparta::contains(), 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)

Definition at line 474 of file GDB.cc.

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

Definition at line 34 of file GDB.hh.

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

Definition at line 32 of file GDB.hh.

utility::vector0< std::string > protocols::sparta::GDB::DATA

Definition at line 49 of file GDB.hh.

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

GDB_Entry protocols::sparta::GDB::EMPTY

Definition at line 44 of file GDB.hh.

boost::unordered_map< int, GDB_Entry > protocols::sparta::GDB::Entries

Definition at line 53 of file GDB.hh.

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

Definition at line 42 of file GDB.hh.

boost::unordered_map<int, std::string> protocols::sparta::GDB::FORMAT

Definition at line 51 of file GDB.hh.

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

Definition at line 40 of file GDB.hh.

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

Definition at line 38 of file GDB.hh.

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

Definition at line 33 of file GDB.hh.

utility::vector0< std::string > protocols::sparta::GDB::REMARKS

Definition at line 48 of file GDB.hh.

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

boost::unordered_map<int, std::string> protocols::sparta::GDB::residList

Definition at line 46 of file GDB.hh.

boost::unordered_map<int, std::string> protocols::sparta::GDB::VARS

Definition at line 50 of file GDB.hh.

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

Definition at line 40 of file GDB.hh.

int protocols::sparta::GDB::VarsNumber

Definition at line 41 of file GDB.hh.

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