Re: [Cdk-user] Is the StructureDiagramGenerator algorithm deterministic?

[Egon W. <ego...@gm...>]

Hi Jean Marc,

On Mon, Mar 22, 2010 at 9:41 PM, JEAN MARC NUZILLARD
<jm....@un...> wrote:
> I created two identical molecules by calling addAtoms and addBonds
> in the same order with the same arguments and then I generated coordinates
> using a StructureDiagramGenerator.
> Looking with Jmol at the molecules in the corresponding SD file,
> it appeared that the graphs were different.
> Repeting the whole process, I sometimes get the same graphs,
> but sometimes different ones.

I guess, the chemical graphs were identical but the graphics different?

> The molecule is camphor. I am usign CDK-1.2.5.

Can you perhaps share your code?

> Is there a non-deterministic part in the SDG algorithm?

Yes, I think there is.

> Is there a way to purposely get different graphs for the same molecule,
> thus allowing the user to choose the best looking one?

I am not aware of that option, other than just repeating it. The
suggestion by Gilleain of permuting the atom order might help here
increase the change of a different diagram.

I can also suggest to have a look at the template functionality...
perhaps for your applications there are common structures that you
always want to get the same coordinates. In that case, you could add
templates for those common substructures.

Egon


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