[Molecularmechanics] Recycling CML

[Peter Murray-Rust]

At 20:14 07/11/2003 +0100, Konrad Hinsen wrote:
>On Friday 07 November 2003 20:05, Peter Murray-Rust wrote:
>
> > This is where you have to be very clear about the semantics. Konrad's
> > proposal omitted H in the example. Many people use H atoms and remove them
>
>All hydrogens are there (I just checked). But I could indeed have made a file
>without the hydrogens.

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 
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?

P.