[Molecularmechanics] Recycling CML

[Peter Murray-Rust]

At 17:39 05/11/2003 +0100, Konrad Hinsen wrote:
>On Tuesday 04 November 2003 22:03, Peter Murray-Rust wrote:
>
>
> > changed do all the others?) CML also has an inheritance mechanism:
> >
> > <molecule ref="ala" mode="inherit">
> >    <atomArray>
> >      <atom ref="calpha" x3="12.3" y3="10.2" z3="2.3"/>
> > ...
>
>What are the modifications that are possible with that mechanism? I am
>thinking of the modifications that David presented in his proposal, for
>defining variants of fragments (e.g. the N-terminal variant of an amino acid
>residue). Such a modification involves adding and removing atoms and bonds.

There are 3 main modes:
- override/overwrite (replace existing values with new ones, but keep those 
without replacement values)
- merge - add in new information where is does not conflict with previous
- replace - replace existing molecule with the new information without 
retaining any of the old info

Therefore bonds could be deleted by using the last mode.

The design was intended to provide different snapshots (for whatever 
reason) of a molecule. The initial impetus was dynamics and conformations - 
things like element type and bonds would be kept constant. But there is no 
reason why bonds should not be changed.

The design was originally to create different instances of the same 
molecule, but there is no reason in principle why it shouldn't be used to 
clone them as well.

This could be promising.

BTW - I may seem overcautious  - feel free to ignore this:-). So long as 
designs are matched by software implementations (especially if they reflect 
existing ones) things are fine. But I have seen too many paper specs that 
were surprisingly hard to implement. There are several early designs in CML 
(admittedly forced by the lack of Schemas rather than DTDs) which have 
caused much more effort than originally expected.

Best

P.


>Konrad.
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