protocols::sparta Namespace Reference

Classes
class	ANN
class	ChemicalShiftEvaluator
class	ChemicalShiftEvaluatorCreator
	creator for the ChemicalShiftsEvaluatorCreator class More...
class	GDB
struct	CORdata
struct	RingData
class	PDB
class	Sparta

Typedefs
typedef boost::unordered_map < std::string, std::string >	GDB_Entry
typedef float	Vec3 [3]
typedef float	Mat3 [3][3]
typedef boost::unordered_map < int, boost::unordered_map < int, double > >	DoubleD2
typedef boost::unordered_map < int, double >	DoubleD1
typedef struct protocols::sparta::CORdata	PDB_Entry
typedef boost::unordered_map < int, PDB_Entry >	Mol
typedef boost::unordered_map < int, Mol >	Mols
typedef utility::vector0 < std::string >	StringList
typedef boost::unordered_map < float, boost::unordered_map < float, float > >	PHIPSI_ERR_SURF

Functions
static basic::Tracer	tr ("protocols.sparta")
static basic::Tracer	tr ("protocols.sparta")
void	calc_per_residue_scores (boost::unordered_map< int, std::string > &atom_names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab, utility::vector1< float > &per_residue_scores)
Real	compareRef_fxn (boost::unordered_map< int, std::string > &names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab)
float	getDiff (float ang1, float ang2)
float	getAVG (utility::vector0< float > &v1)
float	getSTD (utility::vector0< float > &v1)
float	getRMS (utility::vector0< float > &v1, utility::vector0< float > &v2)
char *	itoa (int n, char *buff, int)
char *	ftoa (float n, char *buff, char f, int prec)
int	MKDIR (const char *dirName)
bool	isDirExists (const string &Dir)
std::string	simplifyWhiteSpace (const std::string &str)
int	contains (const std::string &str, const std::string &c)
int	contains (const string &str, const char &c)
bool	isDigit (const char &c)
bool	isSpace (const char &c)
StringList	split (const char sep, const string &str)
StringList	split (const string &sep, const string &str)
StringList	split_WhiteSpace (const string &str)
char *	section (const string &str, const char &sep, char *buff, int start, int end)

Typedef Documentation

typedef boost::unordered_map<int, double> protocols::sparta::DoubleD1

Definition at line 37 of file PDB.hh.

typedef boost::unordered_map<int, boost::unordered_map<int, double> > protocols::sparta::DoubleD2

Definition at line 36 of file PDB.hh.

typedef boost::unordered_map< std::string, std::string > protocols::sparta::GDB_Entry

Definition at line 27 of file GDB.hh.

typedef float protocols::sparta::Mat3[3][3]

Definition at line 35 of file PDB.hh.

typedef boost::unordered_map<int, PDB_Entry> protocols::sparta::Mol

Definition at line 60 of file PDB.hh.

typedef boost::unordered_map<int, Mol> protocols::sparta::Mols

Definition at line 61 of file PDB.hh.

typedef struct protocols::sparta::CORdata protocols::sparta::PDB_Entry

typedef boost::unordered_map<float, boost::unordered_map<float, float> > protocols::sparta::PHIPSI_ERR_SURF

Definition at line 33 of file Sparta.hh.

typedef utility::vector0< std::string > protocols::sparta::StringList

Definition at line 32 of file Sparta.hh.

typedef float protocols::sparta::Vec3[3]

Definition at line 34 of file PDB.hh.

Function Documentation

void protocols::sparta::calc_per_residue_scores	(	boost::unordered_map< int, std::string > &	atom_names,
		GDB &	Pred_Sum,
		GDB &	REF_CS_Tab,
		GDB &	COMP_Tab,
		utility::vector1< float > &	per_residue_scores
	)

Definition at line 63 of file SpartaUtil.cc.

References protocols::sparta::GDB::DATA, protocols::sparta::GDB::Entries, protocols::sparta::GDB::FORMAT_str_parser(), getAVG(), protocols::sparta::GDB::getEntry(), getRMS(), protocols::sparta::GDB::isVarFloat(), protocols::sparta::GDB::REMARKS, protocols::sparta::GDB::showGDB(), tr(), and protocols::sparta::GDB::VARS_str_parser().

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

core::Real protocols::sparta::compareRef_fxn	(	boost::unordered_map< int, std::string > &	names,
		GDB &	Pred_Sum,
		GDB &	REF_CS_Tab,
		GDB &	COMP_Tab
	)

Definition at line 197 of file SpartaUtil.cc.

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

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

int protocols::sparta::contains	(	const std::string &	str,
		const std::string &	c
	)

Definition at line 61 of file util.cc.

Referenced by protocols::sparta::GDB::addVAR(), protocols::sparta::GDB::checkFormat(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::GDB::isVarFloat(), protocols::sparta::GDB::isVarInt(), protocols::sparta::GDB::isVarString(), protocols::sparta::GDB::setVAR(), and protocols::sparta::GDB::showGDB().

int protocols::sparta::contains	(	const string &	str,
		const char &	c
	)

Definition at line 79 of file util.cc.

char * protocols::sparta::ftoa	(	float	n,
		char *	buff,
		char	f,
		int	prec
	)

Definition at line 276 of file SpartaUtil.cc.

Referenced by protocols::sparta::Sparta::SpartaLib::get_ANN_data(), and protocols::sparta::Sparta::SpartaLib::getResInfo().

float protocols::sparta::getAVG

(

utility::vector0< float > &

v1)

Definition at line 228 of file SpartaUtil.cc.

Referenced by calc_per_residue_scores(), and getSTD().

float protocols::sparta::getDiff	(	float	ang1,
		float	ang2
	)

Definition at line 216 of file SpartaUtil.cc.

float protocols::sparta::getRMS	(	utility::vector0< float > &	v1,
		utility::vector0< float > &	v2
	)

Definition at line 253 of file SpartaUtil.cc.

Referenced by calc_per_residue_scores().

float protocols::sparta::getSTD

(

utility::vector0< float > &

v1)

Definition at line 240 of file SpartaUtil.cc.

References getAVG().

bool protocols::sparta::isDigit

(

const char &

c)

Definition at line 92 of file util.cc.

Referenced by protocols::sparta::GDB::checkFormat().

bool protocols::sparta::isDirExists

(

const string &

Dir)

Definition at line 315 of file SpartaUtil.cc.

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

bool protocols::sparta::isSpace

(

const char &

c)

Definition at line 99 of file util.cc.

Referenced by simplifyWhiteSpace().

char * protocols::sparta::itoa	(	int	n,
		char *	buff,
		int
	)

Definition at line 268 of file SpartaUtil.cc.

Referenced by protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::sparta::Sparta::SpartaLib::init_PredErrorSurface(), and protocols::sparta::ANN::loadWeightBias3().

int protocols::sparta::MKDIR

(

const char *

dirName)

Definition at line 303 of file SpartaUtil.cc.

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

char * protocols::sparta::section	(	const string &	str,
		const char &	sep,
		char *	buff,
		int	start,
		int	end
	)

Definition at line 186 of file util.cc.

References core::sequence::end, and split().

Referenced by protocols::sparta::GDB::FORMAT_str_parser(), core::scoring::constraints::ConstraintIO::read_constraints(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), and core::fragment::picking_old::vall::vall_library_from_file().

std::string protocols::sparta::simplifyWhiteSpace

(

const std::string &

str)

Definition at line 32 of file util.cc.

References isSpace().

Referenced by protocols::sparta::GDB::checkFormat(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB_Entry(), main(), and protocols::sparta::GDB::showGDB().

StringList protocols::sparta::split	(	const char	sep,
		const string &	str
	)

Definition at line 106 of file util.cc.

Referenced by section(), and protocols::sparta::GDB::VARS_str_parser().

StringList protocols::sparta::split	(	const string &	sep,
		const string &	str
	)

Definition at line 113 of file util.cc.

StringList protocols::sparta::split_WhiteSpace

(

const string &

str)

Definition at line 135 of file util.cc.

Referenced by protocols::sparta::GDB::loadGDB().

static basic::Tracer protocols::sparta::tr ( "protocols.sparta"  )

static

Referenced by protocols::sparta::GDB::addVAR(), protocols::sparta::ANN::applyANNTransformation(), calc_per_residue_scores(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::sparta::Sparta::SpartaLib::getResInfo(), protocols::sparta::Sparta::SpartaLib::init(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB(), protocols::sparta::ANN::loadWeightBias3(), protocols::sparta::GDB::saveGDB(), protocols::sparta::GDB::setEntry(), protocols::sparta::Sparta::SpartaLib::setup_for_scoring(), and protocols::sparta::GDB::setVAR().

static basic::Tracer protocols::sparta::tr ( "protocols.sparta"  )

static