BALL::Peptides::PeptideBuilder Class Reference
[Creation of
peptides]
Build
a Peptide from a sequence and the corresponing angles. More...
#include <peptideBuilder.h>
Inheritance diagram for BALL::Peptides::PeptideBuilder:
[legend]
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 |
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| virtual | ~PeptideBuilder () |
| Destructor. |
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| 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. |
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| 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) |
| const FragmentDB * | getFragmentDB () const |
Protected Member Functions |
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| 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_ |
Detailed Description
Build a Peptide from a sequence and the corresponing angles.Dont forget to call setFragmentDB() before using this class.
Constructor & Destructor Documentation
| 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.
