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biu::OffLatticeProtein Class Reference

#include <OffLatticeProtein.hh>

Inheritance diagram for biu::OffLatticeProtein:

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Detailed Description

A representation of an off-lattice backbone protein structure.

It provides a PDB-file interface.

Author:
Martin Mann, Sebastian Will, Andreas Richter

Definition at line 17 of file OffLatticeProtein.hh.

Public Member Functions

LatticeProteinapproximateToLattice (const LatticeModel *const lattice, const ContactEnergyFunction *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)
OffLatticeProteinoperator= (const OffLatticeProtein &offLatPro2)
void writePDB (const std::string &pdbFileName)
virtual ~OffLatticeProtein ()

Protected Attributes

const Alphabetalphabet
DPointVecpData
Sequencesequence


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 6 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 40 of file OffLatticeProtein.cc.

biu::OffLatticeProtein::OffLatticeProtein ( const OffLatticeProtein offLatPro  ) 

Definition at line 51 of file OffLatticeProtein.cc.

biu::OffLatticeProtein::~OffLatticeProtein (  )  [virtual]

Definition at line 61 of file OffLatticeProtein.cc.


Member Function Documentation

LatticeProtein * biu::OffLatticeProtein::approximateToLattice ( const LatticeModel *const  lattice,
const ContactEnergyFunction *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 86 of file OffLatticeProtein.cc.

DPointVec biu::OffLatticeProtein::get3Ddata (  )  const [virtual]

Returns the consecutive point representation of the backbone.

Implements biu::BackboneStructure3D.

Definition at line 94 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 99 of file OffLatticeProtein.cc.

OffLatticeProtein & biu::OffLatticeProtein::operator= ( const OffLatticeProtein offLatPro2  ) 

Definition at line 68 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 81 of file OffLatticeProtein.cc.


Field Documentation

the alphabet of the sequence

Definition at line 22 of file OffLatticeProtein.hh.

the structure information

Definition at line 21 of file OffLatticeProtein.hh.

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: