BALL::Peptides::PeptideBuilder Class Reference
[Creation of peptides]

#include <BALL/STRUCTURE/peptideBuilder.h>

Inheritance diagram for BALL::Peptides::PeptideBuilder:

List of all members.

Public Member Functions
	PeptideBuilder ()
	PeptideBuilder (const std::vector< AminoAcidDescriptor > &sequence)
	PeptideBuilder (const String &sequence, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false))
	PeptideBuilder (const PeptideBuilder &pc)
virtual	~PeptideBuilder ()
void	addAminoAcid (const String &type, const Angle &phi=Angle(-47., false), const Angle &psi=Angle(-58., false), const Angle &omega=Angle(180., false))
void	addAminoAcid (const AminoAcidDescriptor &aad)
void	setChainName (const String &name)
const String &	getChainName () const
void	setProteinName (const String &name)
const String &	getProteinName () const
Protein *	construct ()
void	setFragmentDB (const FragmentDB *db)
const FragmentDB *	getFragmentDB () const
Protected Member Functions
Residue *	createResidue_ (const String &type, const int id)
void	insert_ (Residue &resnew, Residue &resold)
void	transform_ (const Angle &phi, const Angle &psi, Residue &resold, Residue &resnew)
void	peptide_ (Residue &resold, Residue &resnew)
void	setOmega_ (Residue &resold, Residue &residue, const Angle &omega)
PDBAtom *	getAtomByName_ (Residue &res, const String &name)
Protected Attributes
std::vector< AminoAcidDescriptor >	sequence_
String	chainname_
String	proteinname_
bool	is_proline_
	The proline flag.
FragmentDB *	fragment_db_

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Detailed Description

Build a Peptide from a sequence and the corresponing angles. Dont forget to call setFragmentDB() before using this class.

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Constructor & Destructor Documentation

BALL::Peptides::PeptideBuilder::PeptideBuilder

(

)

Default constructor.

BALL::Peptides::PeptideBuilder::PeptideBuilder

(

const std::vector< AminoAcidDescriptor > &

sequence

)

Detailed constructor. This constructor takes a vector of AminoAcidDescriptors and prepares everything for the construction process.

BALL::Peptides::PeptideBuilder::PeptideBuilder	(	const String &	sequence,
		const Angle &	phi = Angle(-47., false),
		const Angle &	psi = Angle(-58., false),
		const Angle &	omega = Angle(180., false)
	)

Construct a peptide from a one-letter code sequence.

BALL::Peptides::PeptideBuilder::PeptideBuilder

(

const PeptideBuilder &

pc

)

copy constructor

virtual BALL::Peptides::PeptideBuilder::~PeptideBuilder

(

)

[virtual]

Destructor.

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Member Function Documentation

void BALL::Peptides::PeptideBuilder::addAminoAcid

(

const AminoAcidDescriptor &

aad

)

Adds another amino acid to the sequence.

void BALL::Peptides::PeptideBuilder::addAminoAcid	(	const String &	type,
		const Angle &	phi = Angle(-47., false),
		const Angle &	psi = Angle(-58., false),
		const Angle &	omega = Angle(180., false)
	)

Adds another amino acid to the sequence.

Protein* BALL::Peptides::PeptideBuilder::construct

(

)

Constructs the peptide and returns it.

Residue* BALL::Peptides::PeptideBuilder::createResidue_	(	const String &	type,
		const int	id
	)			[protected]

some helper functions for the construction of the residue; for internal use only omega is not yet implemented

PDBAtom* BALL::Peptides::PeptideBuilder::getAtomByName_	(	Residue &	res,
		const String &	name
	)			[protected]

const String& BALL::Peptides::PeptideBuilder::getChainName

(

)

const

Returns the name of the chain.

const FragmentDB* BALL::Peptides::PeptideBuilder::getFragmentDB

(

)

const

const String& BALL::Peptides::PeptideBuilder::getProteinName

(

)

const

Returns the name of the protein.

void BALL::Peptides::PeptideBuilder::insert_	(	Residue &	resnew,
		Residue &	resold
	)			[protected]

void BALL::Peptides::PeptideBuilder::peptide_	(	Residue &	resold,
		Residue &	resnew
	)			[protected]

void BALL::Peptides::PeptideBuilder::setChainName

(

const String &

name

)

Sets the name of the chain.

void BALL::Peptides::PeptideBuilder::setFragmentDB

(

const FragmentDB *

db

)

void BALL::Peptides::PeptideBuilder::setOmega_	(	Residue &	resold,
		Residue &	residue,
		const Angle &	omega
	)			[protected]

void BALL::Peptides::PeptideBuilder::setProteinName

(

const String &

name

)

Sets the name of the protein.

void BALL::Peptides::PeptideBuilder::transform_	(	const Angle &	phi,
		const Angle &	psi,
		Residue &	resold,
		Residue &	resnew
	)			[protected]

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Member Data Documentation

String BALL::Peptides::PeptideBuilder::chainname_ [protected]

FragmentDB* BALL::Peptides::PeptideBuilder::fragment_db_ [protected]

bool BALL::Peptides::PeptideBuilder::is_proline_ [protected]

The proline flag.

String BALL::Peptides::PeptideBuilder::proteinname_ [protected]

std::vector<AminoAcidDescriptor> BALL::Peptides::PeptideBuilder::sequence_ [protected]