BALL 1.5.0
Loading...
Searching...
No Matches
BALL::Peptides::PeptideBuilder Class Reference

#include <BALL/STRUCTURE/peptideBuilder.h>

Inheritance diagram for BALL::Peptides::PeptideBuilder:
BALL::VIEW::PeptideDialog

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 StringgetChainName () const
 
void setProteinName (const String &name)
 
const StringgetProteinName () const
 
Proteinconstruct ()
 
void setFragmentDB (const FragmentDB *db)
 
const FragmentDBgetFragmentDB () const
 

Protected Member Functions

ResiduecreateResidue_ (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)
 
PDBAtomgetAtomByName_ (Residue &res, const String &name)
 

Protected Attributes

std::vector< AminoAcidDescriptorsequence_
 
String chainname_
 
String proteinname_
 
bool is_proline_
 The proline flag.
 
FragmentDBfragment_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

◆ PeptideBuilder() [1/4]

BALL::Peptides::PeptideBuilder::PeptideBuilder ( )

Default constructor.

◆ PeptideBuilder() [2/4]

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.

◆ PeptideBuilder() [3/4]

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.

◆ PeptideBuilder() [4/4]

BALL::Peptides::PeptideBuilder::PeptideBuilder ( const PeptideBuilder & pc)

copy constructor

◆ ~PeptideBuilder()

virtual BALL::Peptides::PeptideBuilder::~PeptideBuilder ( )
virtual

Destructor.

Member Function Documentation

◆ addAminoAcid() [1/2]

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

Adds another amino acid to the sequence.

◆ addAminoAcid() [2/2]

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.

◆ construct()

Protein * BALL::Peptides::PeptideBuilder::construct ( )

Constructs the peptide and returns it.

◆ createResidue_()

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

◆ getAtomByName_()

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

◆ getChainName()

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

Returns the name of the chain.

◆ getFragmentDB()

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

◆ getProteinName()

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

Returns the name of the protein.

◆ insert_()

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

◆ peptide_()

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

◆ setChainName()

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

Sets the name of the chain.

◆ setFragmentDB()

void BALL::Peptides::PeptideBuilder::setFragmentDB ( const FragmentDB * db)

◆ setOmega_()

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

◆ setProteinName()

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

Sets the name of the protein.

◆ transform_()

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

Member Data Documentation

◆ chainname_

String BALL::Peptides::PeptideBuilder::chainname_
protected

Definition at line 159 of file peptideBuilder.h.

◆ fragment_db_

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

Definition at line 164 of file peptideBuilder.h.

◆ is_proline_

bool BALL::Peptides::PeptideBuilder::is_proline_
protected

The proline flag.

Definition at line 163 of file peptideBuilder.h.

◆ proteinname_

String BALL::Peptides::PeptideBuilder::proteinname_
protected

Definition at line 160 of file peptideBuilder.h.

◆ sequence_

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

Definition at line 158 of file peptideBuilder.h.