biu::OffLatticeProtein Class Reference
#include <OffLatticeProtein.hh>
Inheritance diagram for biu::OffLatticeProtein:
Detailed Description
A representation of an off-lattice backbone protein structure.It provides a PDB-file interface.
Definition at line 17 of file OffLatticeProtein.hh.
Public Member Functions | |
LatticeProtein * | approximateToLattice (const LatticeModel *const lattice, const DistanceEnergyFunction *const energy) const |
virtual DPointVec | get3Ddata () const |
virtual double | getDRMSD (const BackboneStructure3D &other) const |
OffLatticeProtein (const OffLatticeProtein &offLatPro) | |
OffLatticeProtein (const DPointVec &data3D, const Alphabet *const _alphabet, const std::string &seqStr) | |
OffLatticeProtein (const std::string &coordinatesFileName, const Alphabet *const _alphabet) | |
OffLatticeProtein & | operator= (const OffLatticeProtein &offLatPro2) |
void | writePDB (const std::string &pdbFileName) |
virtual | ~OffLatticeProtein () |
Protected Attributes | |
const Alphabet * | alphabet |
DPointVec * | pData |
Sequence * | sequence |
Constructor & Destructor Documentation
biu::OffLatticeProtein::OffLatticeProtein | ( | const std::string & | coordinatesFileName, | |
const Alphabet *const | _alphabet | |||
) |
Constructs a new off lattice protein.
- Parameters:
-
coordinatesFileName Inputfile in the format "aa x y z \n" in which aa is the amino acid in one letter code and x, y and z specify the coordinates of the amino acid. _alphabet The alphabet of the protein sequence.
Definition at line 8 of file OffLatticeProtein.cc.
biu::OffLatticeProtein::OffLatticeProtein | ( | const DPointVec & | data3D, | |
const Alphabet *const | _alphabet, | |||
const std::string & | seqStr | |||
) |
Constructs a new off lattice protein.
- Parameters:
-
data3D 3D double coordinates of the lattice protein. _alphabet The alphabet of the protein sequence. seqStr The sequence of the lattice protein. data3D 3D-position data of the protein.
Definition at line 42 of file OffLatticeProtein.cc.
biu::OffLatticeProtein::OffLatticeProtein | ( | const OffLatticeProtein & | offLatPro | ) |
Definition at line 53 of file OffLatticeProtein.cc.
biu::OffLatticeProtein::~OffLatticeProtein | ( | ) | [virtual] |
Definition at line 63 of file OffLatticeProtein.cc.
Member Function Documentation
LatticeProtein * biu::OffLatticeProtein::approximateToLattice | ( | const LatticeModel *const | lattice, | |
const DistanceEnergyFunction *const | energy | |||
) | const |
Approximates an off lattice backbone protein to a given lattice using a brute force build-up algorithm described in Park B. H., Levitt M. (1995). The complexity and accuracy of discrete state models of protein structure. Journal of Molecular Biology, 249(2), 493-507.
- Returns:
- The returned object was allocated with NEW and has to be destroyed by the calling function via DELETE!
Definition at line 88 of file OffLatticeProtein.cc.
DPointVec biu::OffLatticeProtein::get3Ddata | ( | ) | const [virtual] |
Returns the consecutive point representation of the backbone.
Implements biu::BackboneStructure3D.
Definition at line 96 of file OffLatticeProtein.cc.
double biu::OffLatticeProtein::getDRMSD | ( | const BackboneStructure3D & | other | ) | const [virtual] |
Returns the distance root mean square deviation (DRMSD) to an other BackboneStructure3D
Implements biu::BackboneStructure3D.
Definition at line 101 of file OffLatticeProtein.cc.
OffLatticeProtein & biu::OffLatticeProtein::operator= | ( | const OffLatticeProtein & | offLatPro2 | ) |
Definition at line 70 of file OffLatticeProtein.cc.
void biu::OffLatticeProtein::writePDB | ( | const std::string & | pdbFileName | ) |
Converts the Structure to PDB-output and writes to file.
Definition at line 83 of file OffLatticeProtein.cc.
Field Documentation
const Alphabet* biu::OffLatticeProtein::alphabet [protected] |
DPointVec* biu::OffLatticeProtein::pData [protected] |
Sequence* biu::OffLatticeProtein::sequence [protected] |
the sequence of the lattice protein in one letter code
Definition at line 23 of file OffLatticeProtein.hh.
The documentation for this class was generated from the following files:
- src/biu/OffLatticeProtein.hh
- src/biu/OffLatticeProtein.cc