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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...

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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
 
std::map< int, std::string > residList
 
std::string sequence
 
boost::unordered_map< int,
std::string > 		aN
 
int matchCount
 
std::string pdbListName
 
boost::unordered_map
< std::string,
boost::unordered_map
< std::string, float > > 		Fitting
 
std::string AAlist
 
boost::unordered_map
< std::string,
utility::vector0< float > > 		BLOSUM_62
 
boost::unordered_map< int,
utility::vector0< float > > 		ANN_IN_MTX
 
boost::unordered_map
< std::string,
boost::unordered_map< int,
utility::vector0< float > > > 		ANN_CS_OUTPUT_FULL
 
boost::unordered_map< int, float > CHI2_ANGLES
 
boost::unordered_map< int, float > OMEGA_ANGLES
 
boost::unordered_map< int,
boost::unordered_map
< std::string, float > > 		SURFACE_EXPOSURE
 
boost::unordered_map< int,
std::string >::iterator 		itN
 
boost::unordered_map< int,
boost::unordered_map
< std::string, std::string >
>::iterator 		it
 
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...

Definition at line 60 of file Sparta.hh.

Constructor & Destructor Documentation

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

Definition at line 95 of file Sparta.cc.

References core::init().

Member Function Documentation

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

Definition at line 638 of file Sparta.cc.

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

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

Definition at line 651 of file Sparta.cc.

References protocols::sparta::GDB::Entries, protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::ftoa(), protocols::sparta::itoa(), protocols::sparta::GDB::saveGDB(), protocols::sparta::GDB::setData(), protocols::sparta::GDB::setEntry(), protocols::sparta::GDB::showGDB(), core::io::serialization::size(), SPARTA_MAX_NUM, protocols::kinmatch::str(), protocols::sparta::tr(), and protocols::sparta::GDB::VARS_str_parser().

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

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

Definition at line 893 of file Sparta.cc.

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

Definition at line 934 of file Sparta.cc.

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

Definition at line 923 of file Sparta.cc.

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

Definition at line 901 of file Sparta.cc.

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

Definition at line 912 of file Sparta.cc.

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

Definition at line 272 of file Sparta.cc.

References protocols::sparta::ftoa(), protocols::sparta::itoa(), protocols::swa::phi(), protocols::swa::psi(), and protocols::sparta::tr().

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

Definition at line 943 of file Sparta.cc.

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

Definition at line 232 of file Sparta.cc.

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

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

Definition at line 862 of file Sparta.cc.

References protocols::sparta::GDB::Entries, protocols::sparta::itoa(), protocols::swa::phi(), and protocols::swa::psi().

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

Definition at line 953 of file Sparta.cc.

References protocols::sparta::isDirExists(), and protocols::sparta::MKDIR().

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

Definition at line 182 of file Sparta.cc.

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

Definition at line 140 of file Sparta.cc.

References firstRes, inName, inPDB, lastRes, protocols::sparta::PDB::loadPDB(), protocols::sparta::PDB::r1, r1, residList, protocols::sparta::PDB::residListOne, protocols::sparta::PDB::rN, rN, and protocols::sparta::tr().

Referenced by protocols::sparta::Sparta::score_pose(), and protocols::sparta::Sparta::score_pose_per_residue().

Member Data Documentation

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

Definition at line 145 of file Sparta.hh.

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

Definition at line 115 of file Sparta.hh.

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

Definition at line 114 of file Sparta.hh.

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

Definition at line 137 of file Sparta.hh.

boost::unordered_map< std::string, boost::unordered_map< int, utility::vector0< float > > > protocols::sparta::Sparta::SpartaLib::ANN_CS_OUTPUT_FULL

Definition at line 148 of file Sparta.hh.

boost::unordered_map< int, utility::vector0< float > > protocols::sparta::Sparta::SpartaLib::ANN_IN_MTX

Definition at line 147 of file Sparta.hh.

boost::unordered_map< std::string, utility::vector0< float > > protocols::sparta::Sparta::SpartaLib::BLOSUM_62

Definition at line 146 of file Sparta.hh.

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

Definition at line 87 of file Sparta.hh.

boost::unordered_map< int, float > protocols::sparta::Sparta::SpartaLib::CHI2_ANGLES

Definition at line 149 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 128 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 124 of file Sparta.hh.

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

Definition at line 123 of file Sparta.hh.

boost::unordered_map<std::string, boost::unordered_map<std::string, float> > protocols::sparta::Sparta::SpartaLib::Fitting

Definition at line 143 of file Sparta.hh.

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

Definition at line 109 of file Sparta.hh.

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

Definition at line 108 of file Sparta.hh.

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

Definition at line 89 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 90 of file Sparta.hh.

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

Definition at line 91 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 92 of file Sparta.hh.

boost::unordered_map< int, boost::unordered_map< std::string, std::string > >::iterator protocols::sparta::Sparta::SpartaLib::it

Definition at line 154 of file Sparta.hh.

boost::unordered_map< int, std::string >::iterator protocols::sparta::Sparta::SpartaLib::itN

Definition at line 153 of file Sparta.hh.

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

Definition at line 128 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 87 of file Sparta.hh.

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

Definition at line 139 of file Sparta.hh.

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

Definition at line 121 of file Sparta.hh.

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

Definition at line 120 of file Sparta.hh.

boost::unordered_map< int, float > protocols::sparta::Sparta::SpartaLib::OMEGA_ANGLES

Definition at line 149 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 141 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 118 of file Sparta.hh.

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

Definition at line 117 of file Sparta.hh.

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

Definition at line 130 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 112 of file Sparta.hh.

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

Definition at line 111 of file Sparta.hh.

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

Definition at line 134 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 130 of file Sparta.hh.

Referenced by setup_for_scoring().

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

Definition at line 135 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 86 of file Sparta.hh.

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

Definition at line 95 of file Sparta.hh.

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

Definition at line 156 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 157 of file Sparta.hh.

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

Definition at line 94 of file Sparta.hh.

boost::unordered_map< int, boost::unordered_map< std::string,float > > protocols::sparta::Sparta::SpartaLib::SURFACE_EXPOSURE

Definition at line 151 of file Sparta.hh.

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

Definition at line 85 of file Sparta.hh.

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

Definition at line 102 of file Sparta.hh.

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

Definition at line 103 of file Sparta.hh.

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

Definition at line 132 of file Sparta.hh.

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

Definition at line 97 of file Sparta.hh.

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

Definition at line 100 of file Sparta.hh.

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

Definition at line 100 of file Sparta.hh.

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

Definition at line 100 of file Sparta.hh.

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

Definition at line 99 of file Sparta.hh.

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

Definition at line 98 of file Sparta.hh.

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

Definition at line 106 of file Sparta.hh.

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

Definition at line 105 of file Sparta.hh.

The documentation for this class was generated from the following files:
Generated on Sat Jun 1 2013 12:56:12 for Rosetta 3.5 by   doxygen 1.8.4