[Molecularmechanics] Recommendations for object oriented approaches / UML models

[Marc Baaden]

Dear Peter and David,

thanks for your comments and suggestions. I was aware of CML and of the
Gromacs developers' endeavour to use XML-based data formats in the
future.

However it is not clear in my mind how equivalent an XML-based description
like CML and a more application/implementation oriented UML model are
related. I had the impression that although a CML description of eg trajectory
data might be very difficult (and maybe overkill), a UML description would
be more straighforward (somehow abstracting from existing classes in MD code
for example).

>> Peter Murray-Rust
[..]
>> We have developed an OO approach to many of the static aspects of
>> small molecular systems with CML and by translating the XSD schema
>> automatically to Java. There are ca 100 significant object classes.
[..]
>> My personal feeling is that extending OO to dynamics and trajectories
>> may be more effort than it is worth unless we can standardise our
>> communal representation of the systems
[..]

Could this be addressed via a minimium common denominator? Eg extending
static structures by saying that there might be various sets (evtl. time
dependent) of their coordinates. (Maybe that's already implemented, I haven't
checked the CML schema yet, sorry).

>> David van der Spoel
>> We are still considering doing something like this for GROMACS, but
>> at a
>>    minimum-effort kind of way. Design criteria
>> - simplicity: for developers and users
>> - compatibility: we can not expect our users to write XSLT files so
>> we
>> have to built in compatibility with older (GROMACS) formats and other
>> "Industry Standard" formats such as pdb.
[..]

I agreee. That's why I was thinking that UML could be more "user friendly"
in the sense that it uses graphical views of the object model that might be
easier to approach and comprehend by the common user (ok, some very optimistic
speculation here).

>> Although we should be able to use some of the CML stuff, much of the
>> MD
>> trajectories etc. is too specific to add into a CML itself.

I also think UML would leave an option to use binary formats or high-level
data formats like HDF or netCDF for the data that is better suited by these
models.

Thank you very much for your input.

>> I welcome a discussion just before we start coding...

In the (again optimistic) case that I'll get up to speed with UML until then,
I'd be glad to participate in the discussion :)

Cheers,
Marc