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Public Types | Public Member Functions | Public Attributes | List of all members
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_MatrixAtom2ANN_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, ANNSPARTA_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

◆ AngleMap

typedef std::map< int, float > protocols::sparta::Sparta::SpartaLib::AngleMap

◆ Atom2ANN_MatrixMap

◆ AtomNameList

typedef boost::unordered_map< int, std::string > protocols::sparta::Sparta::SpartaLib::AtomNameList

◆ BlosumMatrix

typedef std::map< std::string, utility::vector0< float > > protocols::sparta::Sparta::SpartaLib::BlosumMatrix

◆ ResidList

typedef std::map< int, std::string > protocols::sparta::Sparta::SpartaLib::ResidList

◆ SurfaceExposureMap

typedef std::map< int, std::map< std::string,float > > protocols::sparta::Sparta::SpartaLib::SurfaceExposureMap

Constructor & Destructor Documentation

◆ SpartaLib()

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

References core::init::init().

Member Function Documentation

◆ deallocate_arrays()

void protocols::sparta::Sparta::SpartaLib::deallocate_arrays ( )

◆ get_ANN_data()

GDB protocols::sparta::Sparta::SpartaLib::get_ANN_data ( bool  create_output)

◆ getANN_PredError()

float protocols::sparta::Sparta::SpartaLib::getANN_PredError ( float  phi,
float  psi,
std::string  aa,
std::string  aName 
)

◆ getNextRCadj()

float protocols::sparta::Sparta::SpartaLib::getNextRCadj ( const std::string &  next_rName,
const std::string &  aName 
)

◆ getPrevRCadj()

float protocols::sparta::Sparta::SpartaLib::getPrevRCadj ( const std::string &  prev_rName,
const std::string &  aName 
)

◆ getRC()

float protocols::sparta::Sparta::SpartaLib::getRC ( const std::string &  resName,
const std::string &  aName 
)

◆ getRCadj()

float protocols::sparta::Sparta::SpartaLib::getRCadj ( const std::string &  resName,
const std::string &  aName 
)

◆ getResInfo()

void protocols::sparta::Sparta::SpartaLib::getResInfo ( bool  create_output)

◆ getWeight()

float protocols::sparta::Sparta::SpartaLib::getWeight ( const std::string &  Name,
const std::string &  aName 
)

◆ init()

void protocols::sparta::Sparta::SpartaLib::init ( void  )

◆ init_PredErrorSurface()

void protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface ( )

◆ mkdir_pred()

void protocols::sparta::Sparta::SpartaLib::mkdir_pred ( const std::string &  d)

◆ setup_defaults()

void protocols::sparta::Sparta::SpartaLib::setup_defaults ( )

◆ setup_for_scoring()

void protocols::sparta::Sparta::SpartaLib::setup_for_scoring ( core::pose::Pose const &  pose)

Member Data Documentation

◆ AAlist

std::string protocols::sparta::Sparta::SpartaLib::AAlist

◆ ADJ_Tab

GDB protocols::sparta::Sparta::SpartaLib::ADJ_Tab

◆ adjFileName

std::string protocols::sparta::Sparta::SpartaLib::adjFileName

◆ aN

AtomNameList protocols::sparta::Sparta::SpartaLib::aN

◆ ANN_CS_OUTPUT_FULL

Atom2ANN_MatrixMap protocols::sparta::Sparta::SpartaLib::ANN_CS_OUTPUT_FULL

◆ ANN_IN_MTX

ANN::ANN_Matrix protocols::sparta::Sparta::SpartaLib::ANN_IN_MTX

◆ BLOSUM_62

BlosumMatrix protocols::sparta::Sparta::SpartaLib::BLOSUM_62

◆ buf

char protocols::sparta::Sparta::SpartaLib::buf[300]

◆ CHI2_ANGLES

AngleMap protocols::sparta::Sparta::SpartaLib::CHI2_ANGLES

◆ EXCLUDED

std::string protocols::sparta::Sparta::SpartaLib::EXCLUDED

◆ firstRes

int protocols::sparta::Sparta::SpartaLib::firstRes

Referenced by setup_for_scoring().

◆ FIT_Tab

GDB protocols::sparta::Sparta::SpartaLib::FIT_Tab

◆ fitFileName

std::string protocols::sparta::Sparta::SpartaLib::fitFileName

◆ HOMO_Tab

GDB protocols::sparta::Sparta::SpartaLib::HOMO_Tab

◆ homoFileName

std::string protocols::sparta::Sparta::SpartaLib::homoFileName

◆ inName

std::string protocols::sparta::Sparta::SpartaLib::inName

Referenced by setup_for_scoring().

◆ inNames

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

◆ inPDB

PDB protocols::sparta::Sparta::SpartaLib::inPDB

Referenced by setup_for_scoring().

◆ inTab

GDB protocols::sparta::Sparta::SpartaLib::inTab

◆ lastRes

int protocols::sparta::Sparta::SpartaLib::lastRes

Referenced by setup_for_scoring().

◆ lbuf

char protocols::sparta::Sparta::SpartaLib::lbuf[1000]

◆ matchCount

int protocols::sparta::Sparta::SpartaLib::matchCount

◆ NEXT_Tab

GDB protocols::sparta::Sparta::SpartaLib::NEXT_Tab

◆ nextFileName

std::string protocols::sparta::Sparta::SpartaLib::nextFileName

◆ OMEGA_ANGLES

AngleMap protocols::sparta::Sparta::SpartaLib::OMEGA_ANGLES

◆ PDB_DIR

std::string protocols::sparta::Sparta::SpartaLib::PDB_DIR

◆ pdbListName

std::string protocols::sparta::Sparta::SpartaLib::pdbListName

◆ PRED_DIR

std::string protocols::sparta::Sparta::SpartaLib::PRED_DIR

◆ PREV_Tab

GDB protocols::sparta::Sparta::SpartaLib::PREV_Tab

◆ prevFileName

std::string protocols::sparta::Sparta::SpartaLib::prevFileName

◆ r1

int protocols::sparta::Sparta::SpartaLib::r1

Referenced by setup_for_scoring().

◆ RC_Tab

GDB protocols::sparta::Sparta::SpartaLib::RC_Tab

◆ rcFileName

std::string protocols::sparta::Sparta::SpartaLib::rcFileName

◆ residList

ResidList protocols::sparta::Sparta::SpartaLib::residList

Referenced by setup_for_scoring().

◆ rN

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

Referenced by setup_for_scoring().

◆ sequence

std::string protocols::sparta::Sparta::SpartaLib::sequence

◆ SHIFT_DIR

std::string protocols::sparta::Sparta::SpartaLib::SHIFT_DIR

◆ slash_char

std::string protocols::sparta::Sparta::SpartaLib::slash_char

◆ sourceName

std::string protocols::sparta::Sparta::SpartaLib::sourceName

◆ SPARTA_ANN

boost::unordered_map< std::string, ANN> protocols::sparta::Sparta::SpartaLib::SPARTA_ANN

◆ SPARTA_DIR

std::string protocols::sparta::Sparta::SpartaLib::SPARTA_DIR

◆ SPARTA_ERR_SURF

boost::unordered_map< std::string, boost::unordered_map< std::string, PHIPSI_ERR_SURF> > protocols::sparta::Sparta::SpartaLib::SPARTA_ERR_SURF

◆ sumName

std::string protocols::sparta::Sparta::SpartaLib::sumName

◆ SURFACE_EXPOSURE

SurfaceExposureMap protocols::sparta::Sparta::SpartaLib::SURFACE_EXPOSURE

◆ TAB_DIR

std::string protocols::sparta::Sparta::SpartaLib::TAB_DIR

◆ tripFileName

std::string protocols::sparta::Sparta::SpartaLib::tripFileName

◆ TRIPLET_Tab

GDB protocols::sparta::Sparta::SpartaLib::TRIPLET_Tab

◆ tVal

float protocols::sparta::Sparta::SpartaLib::tVal

◆ U_ANGLES

float** protocols::sparta::Sparta::SpartaLib::U_ANGLES

◆ U_CO_HB

float * protocols::sparta::Sparta::SpartaLib::U_CO_HB

◆ U_HA_HB

float * protocols::sparta::Sparta::SpartaLib::U_HA_HB

◆ U_HN_HB

float* protocols::sparta::Sparta::SpartaLib::U_HN_HB

◆ U_NAME

std::string** protocols::sparta::Sparta::SpartaLib::U_NAME

◆ U_RING_SHIFTS

float** protocols::sparta::Sparta::SpartaLib::U_RING_SHIFTS

◆ WEIGHT_Tab

GDB protocols::sparta::Sparta::SpartaLib::WEIGHT_Tab

◆ weightFileName

std::string protocols::sparta::Sparta::SpartaLib::weightFileName

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