protocols::sparta Namespace Reference

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

Typedefs
typedef float	Vec3 [3]
typedef float	Mat3 [3][3]
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 thread_local basic::Tracer	tr ("protocols.sparta")
std::ostream &	operator<< (std::ostream &os, PDB_Entry const &pe)
static thread_local basic::Tracer	tr ("protocols.sparta")
void	calc_per_residue_scores (Sparta::SpartaLib::AtomNameList &atom_names, GDB &Pred_Sum, GDB &REF_CS_Tab, GDB &COMP_Tab, utility::vector1< float > &per_residue_scores)
Real	compareRef_fxn (Sparta::SpartaLib::AtomNameList &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 float protocols::sparta::Mat3[3][3]

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

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

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

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

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

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

Function Documentation

void protocols::sparta::calc_per_residue_scores	(	Sparta::SpartaLib::AtomNameList &	atom_names,
		GDB &	Pred_Sum,
		GDB &	REF_CS_Tab,
		GDB &	COMP_Tab,
		utility::vector1< float > &	per_residue_scores
	)

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	(	Sparta::SpartaLib::AtomNameList &	names,
		GDB &	Pred_Sum,
		GDB &	REF_CS_Tab,
		GDB &	COMP_Tab
	)

References calc_per_residue_scores(), 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
	)

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::forge::build::SegmentRebuild::modify_impl(), protocols::match::BumpGrid::occupied(), protocols::sparta::GDB::setVAR(), protocols::sparta::GDB::showGDB(), and protocols::features::BetaTurnDetection::validate_ramachandran_hash().

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

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

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

float protocols::sparta::getAVG

(

utility::vector0< float > &

v1

)

References sum().

Referenced by calc_per_residue_scores(), and getSTD().

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

References a().

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

References sum().

Referenced by calc_per_residue_scores().

float protocols::sparta::getSTD

(

utility::vector0< float > &

v1

)

References getAVG(), and sum().

bool protocols::sparta::isDigit

(

const char &

c

)

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

bool protocols::sparta::isDirExists

(

const string &

Dir

)

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

bool protocols::sparta::isSpace

(

const char &

c

)

Referenced by simplifyWhiteSpace().

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

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

)

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

std::ostream & protocols::sparta::operator<<	(	std::ostream &	os,
		PDB_Entry const &	pe
	)

References protocols::sparta::CORdata::atomName, protocols::sparta::CORdata::atomNum, protocols::sparta::CORdata::resName, and protocols::sparta::CORdata::resNum.

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

References split().

Referenced by protocols::sparta::GDB::FORMAT_str_parser(), and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file().

std::string protocols::sparta::simplifyWhiteSpace

(

const std::string &

str

)

References isSpace(), and runtime_assert.

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
	)

Referenced by protocols::surface_docking::SurfaceVectorLoader::create_resource(), protocols::antibody::clusters::CDRClusterMatcher::load_center_data(), protocols::loophash::MPI_LoopHashRefine_Master::load_sample_weight(), protocols::mpi_refinement::MPI_Refine_Master::load_sample_weight(), protocols::kinematic_closure::perturbers::LogFilePerturber::LogFilePerturber(), main(), protocols::hotspot_hashing::LSMSearchPattern::parse_lsm_spec(), section(), protocols::moves::StructureRestrictor::setup_relevant_chains(), and protocols::sparta::GDB::VARS_str_parser().

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

StringList protocols::sparta::split_WhiteSpace

(

const string &

str

)

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

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

static

Referenced by protocols::sparta::GDB::addVAR(), protocols::sparta::ANN::applyANNTransformation(), calc_per_residue_scores(), protocols::sparta::Sparta::check_pose(), 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 thread_local basic::Tracer protocols::sparta::tr ( "protocols.sparta"  )

static