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.