[Joelib-devel] Re: [QSAR-devel] Data storage API summary -> net.sf.qsar.api.data package

[rich a. <che...@ya...>]

Hello All,
 
Joerg, I appreciate your concerns regarding the implementation of Octet model-level interfaces by JOELib clients, and now I have a much clearer idea of why you think it's a good idea to first solve that problem before moving on to implement qsar functionality. I now agree with your postition on this.
 
I also think I understand how you'll be developing and why you need developer access to Octet. So within a day or so, I'll add you as a developer.
 
If you think it would be helpful, I'd be interested in working with you (and any others...?) to implement the Octet interfaces with JOELib classes. As I posted on the cdk-devel list, I believe the main challenge will be in reconciling Octet's bonding model with those of CDK and JOELib, but I think the problem can be solved. Interestingly, this issue goes beyind CDK or JOELib, and arises from fundamentally different views of how bonding should be modeled computationally.
 
cheers,
rich

"Joerg K. Wegner" <we...@in...> wrote:
Hi,

> I don't want to spend time getting things to compile that I do not
> need to use...
So are we here doing things we like, or things we need ?
But, what if i need them, that's the point. A Octet-CDK interface will 
work and from the actual design there are no problems, but i promise 
that a Octet-JOELib interface will cause problems, also as already the 
CDK-JOELib interface, because we have, as expected, different opinions 
about our requirements, because we have started from different design 
criterias. So kick JOELib and you can proceed as you like, if you want 
to use it, i prefer eventually (not sure at all) Octet interface 
changes, and this causes that you must change the actual Octet-CDK 
interface definition. If you will not complain about this, i'm fine with 
your approach, i would prefer to be a direct Octet developer to try to 
reduce complications for Octet, CDK, Jumbo and JOELib, because i think 
this is much more elegant and more efficient than resolving every 
personal preferred complications.

> I thought that that was what we were working on... a common API???

I don't think we know already what we want and need in common. Everyone 
prefers his already available well-know object structure, that's clear.
And we have different opinions, of how we like to proceed. Let's stop 
this discussion here, and continue in two weeks.
Again, Rick, i would like to be a Octet developer and would like to 
check in the Octet-JOELib interface implementations directly to octet or 
in a new CVS directory at the Octet project. So i can start with 
implementing and filling the stubs and change things i will need 
directly. Then we can discuss things for these implementations, before 
they are taken to Octet and dicuss on the mailing list, how to proceed 
and iterate our consens on the actual interface.
Or we can use the tracking system with upload ability.

> I think that MDL was interested in posting their substructure set
> which is used to calculate their fingerprint... that could be used as
> a standard.
Fine, and:
The expert systems are the main critical step in my opinion. I've also 
heard people saying, 'who is intersted in slight differences?'. At least 
from the scientific standpoint i disagree heavily on such comments.
So what expresses [a;$(#6:#6-N)] if we use another expert system ? 
Surely not a random match, but eventually not what we've expected.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)

Never mistake action for meaningful action.
(Hugo Kubinyi,2004)



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