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cpsp Namespace Reference


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/")


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.


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.


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.