Re: [Cdk-user] Building a protein from scratch?

[Martin E. <mar...@fa...>]

Hi,

> 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?

Yup, unfortunately this is the way it has to be done at the moment:

// 	Setup AA templates
	SetOfMolecules aminoAcids = AminoAcids.createAAs();
//	Create protein
	BioPolymer protein = new BioPolymer();
//	Create strand
	Strand strand = new Strand();
//	Strand needs a name
	strand.setStrandName(String.valueOf("A"));
//	Loop over the AAs you want to add
	for(int j = 0; j <= 1; j++)	{
//		Create monomer
		Monomer monomer = new Monomer();
//		Monomer needs a name and a type
		monomer.setMonomerName((String)aminoAcids.getMolecule(j).getProperty("molecule_name") + j);
		monomer.setMonomerType((String)aminoAcids.getMolecule(j).getProperty("molecule_name"));
//		Loop over atoms
		for(int i = 0; i < aminoAcids.getMolecule(j).getAtomCount(); i++)	{
			protein.addAtom(aminoAcids.getMolecule(j).getAtomAt(i), monomer,
strand);
		}
//		Loop over bonds
		for(int i = 0; i < aminoAcids.getMolecule(j).getBondCount(); i++)	{
			protein.addBond(aminoAcids.getMolecule(j).getBondAt(i));
		}

Then after this comes the problem of connecting the two residues to each
other (please see the createBonds method in the PDBReader class for
details how that can be done when looping over residues.		

> Questions:
> - would it be easier of AminoAcids would return Monomers?

Yeah, I think that's a good idea.

> - and to add some helper methods like AminoAcids.getByShortID("G") and
>   AminoAcids.getByID("Gly")?

Yup, that would definitely be good.

> - should Strand/BioPolymer get a method addMonomer(Monomer) ?

I remember thinking about this when I added the Strand class and made my
changes to the PDBReader. However, I decided not to implement such a
method for reasons that seem very obscure to me now (I think it had
something to do with the way it was designed before I made my changes).

> 
> Suggestions?

I think the modifications you suggest seem very reasonable. I can make
those changes as soon as possible.

Cheers!

Martin.

-- 
========================================
Martin Eklund
PhD Student
Department of Pharmaceutical Biosciences
Uppsala University, Sweden
Ph: +46-18-4714281
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