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 std::map< std::string, ANN::ANN_Matrix > protocols::sparta::Sparta::SpartaLib::Atom2ANN_MatrixMap

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

(

)

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

)

References protocols::sparta::GDB::Entries, protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::ftoa(), protocols::sparta::itoa(), protocols::hybridization::r1, protocols::sparta::GDB::saveGDB(), protocols::sparta::GDB::setData(), protocols::sparta::GDB::setEntry(), protocols::sparta::GDB::showGDB(), 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
	)

References protocols::cluster::calibur::aa.

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

)

References core::sequence::end, protocols::sparta::ftoa(), protocols::sparta::itoa(), protocols::hybridization::r1, and protocols::sparta::tr().

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

void protocols::sparta::Sparta::SpartaLib::init

(

void

)

References protocols::cluster::calibur::aa, protocols::sparta::GDB::Entries, protocols::sparta::GDB::loadGDB(), and protocols::sparta::tr().

void protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface

(

)

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

void protocols::sparta::Sparta::SpartaLib::mkdir_pred

(

const std::string &

d

)

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

void protocols::sparta::Sparta::SpartaLib::setup_defaults

(

)

void protocols::sparta::Sparta::SpartaLib::setup_for_scoring

(

core::pose::Pose const &

pose

)

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

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:

• src/protocols/sparta/Sparta.hh
• src/protocols/sparta/Sparta.cc