cpsp Namespace Reference

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Detailed Description

This namespace includes all classes and functionalities to predict optimal and suboptimal structures for lattice proteins in the HP-modell using the approach introduced by Rolf Backofen and Sebastian Will. The method is known as "Constraint-based Protein Structure Prediction" (CPSP) and published as

"A constraint-based approach to fast and exact structure prediction in three-dimensional protein models", R. Backofen and S. Will, Journal of Constraints, 2005.

Data Structures
class	Exception
class	HCore
class	HCoreDatabase
class	HCoreDatabaseFILE
class	HCoreDatabasePGSQL
class	HPThreadingHandler
class	HPThreadingOptions
Namespaces
namespace	gecode
namespace	scth
Typedefs
typedef std::vector< int >	intVec
typedef std::vector< std::string >	StringVec
Functions
std::string	getTimeString ()
std::ostream &	operator<< (std::ostream &os, const Exception &p)
void	writePDB (const std::string &sourceInfo, const std::vector< std::string > &seq, const biu::DPointVec &points, const biu::LatticeModel &lattice, std::ostream &out, bool hasSideChain, const biu::LatticeModel &sclattice)
void	writePDBconect (const std::vector< std::string > &seq, const biu::DPointVec &points, char chainID, bool hasSideChain, std::ostream &out, size_t firstID)
void	writePDBhetatm (const std::vector< std::string > &seq, const biu::DPointVec &points, char chainID, bool hasSideChain, std::ostream &out, size_t firstID)
void	writePDBseq (const std::vector< std::string > &seq, char chainID, std::ostream &out)
Variables
const std::string	POSTFIX = std::string(".txt")
const std::string	PREF_CUB = std::string("cub.")
const std::string	PREF_FCC = std::string("fcc.")
const std::string	ROOT_CUB = std::string("Cubic/")
const std::string	ROOT_FCC = std::string("Fcc/")

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Typedef Documentation

typedef std::vector<int> cpsp::intVec

Definition at line 32 of file HCoreDatabaseFILE.hh.

typedef std::vector<std::string> cpsp::StringVec

Definition at line 28 of file HPThreadingHandler.hh.

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Function Documentation

std::string cpsp::getTimeString

(

)

Definition at line 17 of file PDBsupport.hh.

std::ostream & cpsp::operator<<	(	std::ostream &	os,
		const Exception &	p
	)

Definition at line 49 of file Exception.cc.

void cpsp::writePDB	(	const std::string &	sourceInfo,
		const std::vector< std::string > &	seq,
		const biu::DPointVec &	points,
		const biu::LatticeModel &	lattice,
		std::ostream &	out,
		bool	hasSideChain,
		const biu::LatticeModel &	sclattice
	)

Definition at line 158 of file PDBsupport.hh.

void cpsp::writePDBconect	(	const std::vector< std::string > &	seq,
		const biu::DPointVec &	points,
		char	chainID,
		bool	hasSideChain,
		std::ostream &	out,
		size_t	firstID
	)

Definition at line 107 of file PDBsupport.hh.

void cpsp::writePDBhetatm	(	const std::vector< std::string > &	seq,
		const biu::DPointVec &	points,
		char	chainID,
		bool	hasSideChain,
		std::ostream &	out,
		size_t	firstID
	)

Definition at line 69 of file PDBsupport.hh.

void cpsp::writePDBseq	(	const std::vector< std::string > &	seq,
		char	chainID,
		std::ostream &	out
	)

Definition at line 52 of file PDBsupport.hh.

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Variable Documentation

const std::string cpsp::POSTFIX = std::string(".txt")

Definition at line 50 of file HCoreDatabaseFILE.cc.

const std::string cpsp::PREF_CUB = std::string("cub.")

Definition at line 47 of file HCoreDatabaseFILE.cc.

const std::string cpsp::PREF_FCC = std::string("fcc.")

Definition at line 48 of file HCoreDatabaseFILE.cc.

const std::string cpsp::ROOT_CUB = std::string("Cubic/")

Definition at line 44 of file HCoreDatabaseFILE.cc.

const std::string cpsp::ROOT_FCC = std::string("Fcc/")

Definition at line 45 of file HCoreDatabaseFILE.cc.