Peptides::PeptideBuilder Class Reference
[Creation of peptides]

Build a Peptide from a sequence and the corresponing angles. More...

#include <peptideBuilder.h>

Inheritance diagram for Peptides::PeptideBuilder:

List of all members.

Public Member Functions
	PeptideBuilder ()
	Default constructor.
	PeptideBuilder (const std::vector< AminoAcidDescriptor > &sequence)
	Detailed constructor.
	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.
	PeptideBuilder (const PeptideBuilder &pc)
	copy constructor
virtual	~PeptideBuilder ()
	Destructor.
void	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	addAminoAcid (const AminoAcidDescriptor &aad)
	Adds another amino acid to the sequence.
void	setChainName (const String &name)
	Sets the name of the chain.
const String &	getChainName () const
	Returns the name of the chain.
void	setProteinName (const String &name)
	Sets the name of the protein.
const String &	getProteinName () const
	Returns the name of the protein.
Protein *	construct ()
	Constructs the peptide and returns it.
void	setFragmentDB (const FragmentDB *db) throw ()
const FragmentDB *	getFragmentDB () const throw ()
Protected Member Functions
Residue *	createResidue_ (const String &type, const int id)
	some helper functions for the construction of the residue; for internal use only omega is not yet implemented
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

Peptides::PeptideBuilder::PeptideBuilder (   )

Default constructor.

Peptides::PeptideBuilder::PeptideBuilder (  const std::vector< AminoAcidDescriptor > &  sequence  )

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

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.

virtual Peptides::PeptideBuilder::~PeptideBuilder (   )  [virtual]

Destructor.

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Member Function Documentation

void Peptides::PeptideBuilder::addAminoAcid (  const AminoAcidDescriptor &  aad  )

Adds another amino acid to the sequence.

void 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* Peptides::PeptideBuilder::construct (   )

Constructs the peptide and returns it.

const String& Peptides::PeptideBuilder::getChainName (   )  const

Returns the name of the chain.

const String& Peptides::PeptideBuilder::getProteinName (   )  const

Returns the name of the protein.

void Peptides::PeptideBuilder::setChainName (  const String &  name  )

Sets the name of the chain.

void Peptides::PeptideBuilder::setProteinName (  const String &  name  )

Sets the name of the protein.