BALL::Peptides::PeptideBuilder Class Reference

#include <BALL/STRUCTURE/peptideBuilder.h>

Inheritance diagram for BALL::Peptides::PeptideBuilder:

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. More...
FragmentDB *	fragment_db_

Detailed Description

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

Definition at line 92 of file peptideBuilder.h.

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.

Member Function Documentation

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.

void BALL::Peptides::PeptideBuilder::addAminoAcid

(

const AminoAcidDescriptor &

aad

)

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

Member Data Documentation

String BALL::Peptides::PeptideBuilder::chainname_

protected

Definition at line 159 of file peptideBuilder.h.

FragmentDB* BALL::Peptides::PeptideBuilder::fragment_db_

protected

Definition at line 164 of file peptideBuilder.h.

bool BALL::Peptides::PeptideBuilder::is_proline_

protected

The proline flag.

Definition at line 163 of file peptideBuilder.h.

String BALL::Peptides::PeptideBuilder::proteinname_

protected

Definition at line 160 of file peptideBuilder.h.

std::vector<AminoAcidDescriptor> BALL::Peptides::PeptideBuilder::sequence_

protected

Definition at line 158 of file peptideBuilder.h.