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biu::OffLatticeProtein Class Reference

#include <OffLatticeProtein.hh>

Inheritance diagram for biu::OffLatticeProtein:

[legend]

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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
LatticeProtein *	approximateToLattice (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)
OffLatticeProtein &	operator= (const OffLatticeProtein &offLatPro2)
void	writePDB (const std::string &pdbFileName)
virtual	~OffLatticeProtein ()
Protected Attributes
const Alphabet *	alphabet
DPointVec *	pData
Sequence *	sequence

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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.

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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.

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Field Documentation

const Alphabet* biu::OffLatticeProtein::alphabet [protected]

the alphabet of the sequence

Definition at line 22 of file OffLatticeProtein.hh.

DPointVec* biu::OffLatticeProtein::pData [protected]

the structure information

Definition at line 21 of file OffLatticeProtein.hh.

Sequence* biu::OffLatticeProtein::sequence [protected]

the sequence of the lattice protein in one letter code

Definition at line 23 of file OffLatticeProtein.hh.

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The documentation for this class was generated from the following files:

• src/biu/OffLatticeProtein.hh
• src/biu/OffLatticeProtein.cc