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protocols::sparta::Sparta::SpartaLib Class Reference

{ most of the original SPARTA class goes into SpartaLib – to be reused between different evaluators... More...

#include <Sparta.hh>

Public Types

typedef std::map< int,
std::string > 
ResidList
 
typedef boost::unordered_map
< int, std::string > 
AtomNameList
 
typedef std::map< std::string,
utility::vector0< float > > 
BlosumMatrix
 
typedef std::map< std::string,
ANN::ANN_Matrix
Atom2ANN_MatrixMap
 
typedef std::map< int, float > AngleMap
 
typedef std::map< int,
std::map< std::string, float > > 
SurfaceExposureMap
 

Public Member Functions

 SpartaLib ()
 
void setup_for_scoring (core::pose::Pose const &pose)
 
void deallocate_arrays ()
 
void init ()
 
GDB get_ANN_data (bool create_output)
 
void getResInfo (bool create_output)
 
float getANN_PredError (float phi, float psi, std::string aa, std::string aName)
 
void init_PredErrorSurface ()
 
float getRC (const std::string &resName, const std::string &aName)
 
float getRCadj (const std::string &resName, const std::string &aName)
 
float getPrevRCadj (const std::string &prev_rName, const std::string &aName)
 
float getNextRCadj (const std::string &next_rName, const std::string &aName)
 
float getWeight (const std::string &Name, const std::string &aName)
 
void setup_defaults ()
 
void mkdir_pred (const std::string &d)
 

Public Attributes

std::string SPARTA_DIR
 
std::string PRED_DIR
 
std::string TAB_DIR
 
std::string SHIFT_DIR
 
std::string PDB_DIR
 
std::string EXCLUDED
 
std::string slash_char
 
char buf [300]
 
char lbuf [1000]
 
std::string inName
 
std::string inNames
 
PDB inPDB
 
GDB inTab
 
std::string sumName
 
std::string sourceName
 
float ** U_ANGLES
 
float ** U_RING_SHIFTS
 
std::string ** U_NAME
 
float * U_HN_HB
 
float * U_HA_HB
 
float * U_CO_HB
 
std::string tripFileName
 
GDB TRIPLET_Tab
 
std::string weightFileName
 
GDB WEIGHT_Tab
 
std::string homoFileName
 
GDB HOMO_Tab
 
std::string rcFileName
 
GDB RC_Tab
 
std::string adjFileName
 
GDB ADJ_Tab
 
std::string prevFileName
 
GDB PREV_Tab
 
std::string nextFileName
 
GDB NEXT_Tab
 
std::string fitFileName
 
GDB FIT_Tab
 
int firstRes
 
int lastRes
 
int r1
 
int rN
 
float tVal
 
ResidList residList
 
std::string sequence
 
AtomNameList aN
 
int matchCount
 
std::string pdbListName
 
std::string AAlist
 
BlosumMatrix BLOSUM_62
 
ANN::ANN_Matrix ANN_IN_MTX
 
Atom2ANN_MatrixMap ANN_CS_OUTPUT_FULL
 
AngleMap CHI2_ANGLES
 
AngleMap OMEGA_ANGLES
 
SurfaceExposureMap SURFACE_EXPOSURE
 
boost::unordered_map
< std::string, ANN
SPARTA_ANN
 
boost::unordered_map
< std::string,
boost::unordered_map
< std::string, PHIPSI_ERR_SURF > > 
SPARTA_ERR_SURF
 

Detailed Description

{ most of the original SPARTA class goes into SpartaLib – to be reused between different evaluators...

Member Typedef Documentation

typedef std::map< int, float > protocols::sparta::Sparta::SpartaLib::AngleMap
typedef boost::unordered_map< int, std::string > protocols::sparta::Sparta::SpartaLib::AtomNameList
typedef std::map< std::string, utility::vector0< float > > protocols::sparta::Sparta::SpartaLib::BlosumMatrix
typedef std::map< int, std::string > protocols::sparta::Sparta::SpartaLib::ResidList
typedef std::map< int, std::map< std::string,float > > protocols::sparta::Sparta::SpartaLib::SurfaceExposureMap

Constructor & Destructor Documentation

protocols::sparta::Sparta::SpartaLib::SpartaLib ( )

References core::init::init().

Member Function Documentation

void protocols::sparta::Sparta::SpartaLib::deallocate_arrays ( )
GDB protocols::sparta::Sparta::SpartaLib::get_ANN_data ( bool  create_output)
float protocols::sparta::Sparta::SpartaLib::getANN_PredError ( float  phi,
float  psi,
std::string  aa,
std::string  aName 
)
float protocols::sparta::Sparta::SpartaLib::getNextRCadj ( const std::string &  next_rName,
const std::string &  aName 
)
float protocols::sparta::Sparta::SpartaLib::getPrevRCadj ( const std::string &  prev_rName,
const std::string &  aName 
)
float protocols::sparta::Sparta::SpartaLib::getRC ( const std::string &  resName,
const std::string &  aName 
)
float protocols::sparta::Sparta::SpartaLib::getRCadj ( const std::string &  resName,
const std::string &  aName 
)
void protocols::sparta::Sparta::SpartaLib::getResInfo ( bool  create_output)
float protocols::sparta::Sparta::SpartaLib::getWeight ( const std::string &  Name,
const std::string &  aName 
)
void protocols::sparta::Sparta::SpartaLib::init ( void  )
void protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface ( )
void protocols::sparta::Sparta::SpartaLib::mkdir_pred ( const std::string &  d)
void protocols::sparta::Sparta::SpartaLib::setup_defaults ( )
void protocols::sparta::Sparta::SpartaLib::setup_for_scoring ( core::pose::Pose const &  pose)

Member Data Documentation

std::string protocols::sparta::Sparta::SpartaLib::AAlist
GDB protocols::sparta::Sparta::SpartaLib::ADJ_Tab
std::string protocols::sparta::Sparta::SpartaLib::adjFileName
AtomNameList protocols::sparta::Sparta::SpartaLib::aN
Atom2ANN_MatrixMap protocols::sparta::Sparta::SpartaLib::ANN_CS_OUTPUT_FULL
ANN::ANN_Matrix protocols::sparta::Sparta::SpartaLib::ANN_IN_MTX
BlosumMatrix protocols::sparta::Sparta::SpartaLib::BLOSUM_62
char protocols::sparta::Sparta::SpartaLib::buf[300]
AngleMap protocols::sparta::Sparta::SpartaLib::CHI2_ANGLES
std::string protocols::sparta::Sparta::SpartaLib::EXCLUDED
int protocols::sparta::Sparta::SpartaLib::firstRes

Referenced by setup_for_scoring().

GDB protocols::sparta::Sparta::SpartaLib::FIT_Tab
std::string protocols::sparta::Sparta::SpartaLib::fitFileName
GDB protocols::sparta::Sparta::SpartaLib::HOMO_Tab
std::string protocols::sparta::Sparta::SpartaLib::homoFileName
std::string protocols::sparta::Sparta::SpartaLib::inName

Referenced by setup_for_scoring().

std::string protocols::sparta::Sparta::SpartaLib::inNames
PDB protocols::sparta::Sparta::SpartaLib::inPDB

Referenced by setup_for_scoring().

GDB protocols::sparta::Sparta::SpartaLib::inTab
int protocols::sparta::Sparta::SpartaLib::lastRes

Referenced by setup_for_scoring().

char protocols::sparta::Sparta::SpartaLib::lbuf[1000]
int protocols::sparta::Sparta::SpartaLib::matchCount
GDB protocols::sparta::Sparta::SpartaLib::NEXT_Tab
std::string protocols::sparta::Sparta::SpartaLib::nextFileName
AngleMap protocols::sparta::Sparta::SpartaLib::OMEGA_ANGLES
std::string protocols::sparta::Sparta::SpartaLib::PDB_DIR
std::string protocols::sparta::Sparta::SpartaLib::pdbListName
std::string protocols::sparta::Sparta::SpartaLib::PRED_DIR
GDB protocols::sparta::Sparta::SpartaLib::PREV_Tab
std::string protocols::sparta::Sparta::SpartaLib::prevFileName
int protocols::sparta::Sparta::SpartaLib::r1

Referenced by setup_for_scoring().

GDB protocols::sparta::Sparta::SpartaLib::RC_Tab
std::string protocols::sparta::Sparta::SpartaLib::rcFileName
ResidList protocols::sparta::Sparta::SpartaLib::residList

Referenced by setup_for_scoring().

int protocols::sparta::Sparta::SpartaLib::rN

Referenced by setup_for_scoring().

std::string protocols::sparta::Sparta::SpartaLib::sequence
std::string protocols::sparta::Sparta::SpartaLib::SHIFT_DIR
std::string protocols::sparta::Sparta::SpartaLib::slash_char
std::string protocols::sparta::Sparta::SpartaLib::sourceName
boost::unordered_map< std::string, ANN> protocols::sparta::Sparta::SpartaLib::SPARTA_ANN
std::string protocols::sparta::Sparta::SpartaLib::SPARTA_DIR
boost::unordered_map< std::string, boost::unordered_map< std::string, PHIPSI_ERR_SURF> > protocols::sparta::Sparta::SpartaLib::SPARTA_ERR_SURF
std::string protocols::sparta::Sparta::SpartaLib::sumName
SurfaceExposureMap protocols::sparta::Sparta::SpartaLib::SURFACE_EXPOSURE
std::string protocols::sparta::Sparta::SpartaLib::TAB_DIR
std::string protocols::sparta::Sparta::SpartaLib::tripFileName
GDB protocols::sparta::Sparta::SpartaLib::TRIPLET_Tab
float protocols::sparta::Sparta::SpartaLib::tVal
float** protocols::sparta::Sparta::SpartaLib::U_ANGLES
float * protocols::sparta::Sparta::SpartaLib::U_CO_HB
float * protocols::sparta::Sparta::SpartaLib::U_HA_HB
float* protocols::sparta::Sparta::SpartaLib::U_HN_HB
std::string** protocols::sparta::Sparta::SpartaLib::U_NAME
float** protocols::sparta::Sparta::SpartaLib::U_RING_SHIFTS
GDB protocols::sparta::Sparta::SpartaLib::WEIGHT_Tab
std::string protocols::sparta::Sparta::SpartaLib::weightFileName

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