[Molecularmechanics] Recycling CML

[Konrad Hinsen]

On Wednesday 05 November 2003 16:38, Peter Murray-Rust wrote:

> If you are prepared to expand this *internally* into a connection table
> then there probably isn't a problem. If you wish to hold the higher level
> formalism as the internal data structure it may be more difficult.

Yes, internally this will be expanded (at least in my code). I don't think 
it's a good idea to base exchange formats on particular internal data 
structures.

> If you are only ever dealing with linear peptides it isn't a problem. If
> you are dealing with a variety of small fragments which may be joined in a
> variety of ways you need to think about the grammar. Crystallographers have
> a dictionary of fragments - I hear regular moans about the hassle of
> creating new fragments.

What are the difficulties? I am using a rather similar approach in my code, 
and haven't had any difficulties in defining new fragments, nor have others 
who have worked on very different systems. In my approach, a fragment can 
include any other fragment and then add bonds to any atoms inside that 
fragment by using explicit paths to refer to them. There is no limit to the 
number or kind of links that can be created.

In the context of the representation we are discussing here, all that is 
required is a notation to refer to a sequence of elements defining ultimately 
one atom. This could be a list of ids, for example.

> >I am not aware of any force field that requires such information as
> >input. Moreover, the rare program that does need the information can
> > figure it out for itself.
>
> To do this it probably has to expand the complete connection table.

Yes, certainly. But that is not difficult to do.

> >I'd rather have something more compact for that, some array notation for
> >positions for example.
>
> you can use the array format
>   <molecule ref="ala" mode="inherit">
>      <atomArray ref="calpha cbeta" x3="12.3 4.7 ..." y3="10.2 9.2 ..."
> z3="2.3 -1.6 ..."/>
> </molecule>

That looks fine.

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
-------------------------------------------------------------------------------