[Molecularmechanics] Recycling CML

[Konrad Hinsen]

On Friday 07 November 2003 22:04, Peter Murray-Rust wrote:

> What I meant was "do the fragments lose hydrogens when they are
> connected?". In your case they don't - your methyl is exactly that - a

I see. I didn't even consider that option, my fragments are exactly the atoms 
that are there, nothing gets modified implicitly when a bond is added.

I think that's the only reasonable approach, because otherwise any program 
handling these files would need a lot of chemical knowledge built in.

> methyl group CH3 with a "free valency".  If this is completely standard
> then there's no problem. It means preparing different fragments for each
> substitution pattern of a molecule. Do you, for example, have alpha- and
> beta- glucosyl?

I don't have any glycosyl at all at the moment, but if I had, yes, I'd need 
different definitions for the two. I suppose that's how everyone works in 
this field, but perhaps not.

Konrad.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------