[Cdk-user] Building a protein from scratch?

[Egon W. <e.w...@sc...>]

Hi all,

how can I create (no 3D coords, just connectivity) create protein from 
scratch, with say two strands? Let's assume that I'm not doing anything other 
than connecting a few amino acids... Say, GAGA and VAVA...

It needs to start with something like:

# setup AA templates
SetOfMolecules aminoAcids = cdk.templates.AminoAcids.createAAs();
# create a protein
BioPolymer protein = new BioPolymer();
# But then?
Strand = new Strand(); # strand 1
# There does not some a addMonomer(), so a loop over all atoms and bonds?

Questions:
- would it be easier of AminoAcids would return Monomers?
- and to add some helper methods like AminoAcids.getByShortID("G") and
  AminoAcids.getByID("Gly")?
- should Strand/BioPolymer get a method addMonomer(Monomer) ?

Suggestions?

Egon