Re: [Joelib-help] CMLRSS and WWMM and OpenMolecules

[Peter Murray-R. <pm...@ca...>]

At 10:39 12/03/2004 +0100, Joerg K. Wegner wrote:
>Hi all,
>
>very fine !
>
>>[crossposted, so please be considerate in replies]
>So, do we need a cross-platform mailing list ?:-}

It could be that we need a chemical developers blog.

>Can a RSS channel used for such things ?

Yes. In general RSS is read-only so it would be coupled to a mailing list 
of some sort (Henry?)

>>We already have proof of concept for molecules, properties, spectra (no 
>>viewer yet) and crystallography.
>For a Java based visualization i would recommend the complex SGT:
>http://www.epic.noaa.gov/java/sgt/
>
>I've already used it for the primitive visualization of the JCAMP-DX 
>format in JOELib (only developer interface for uncompressed formats !). No 
>JCAMP-CS support, which could be something for OpenBabel/JOELib.

Christoph, Stefan and I are working on a CMLSpect viewer. We already have 
JCAMP2CML. We want to avoid the posting of JCAMP as it breaks the XML 
model. However it would be possible to convert CMLSpect to JCAMP

>>For example the output of one feed could be input to another service such 
>>as JOELib which computes properties and descriptors. This is still under 
>>construction (V0.2)
>Great !

... mainly at the design stage:-) The main technical question is how one 
merges new properties into an old molecule. This is a middleware problem. I 
think it's most like to be relevant to servers at present. "Add your CML 
molecule and get some more properties. We already do this for MOPAC. I 
think that JOELib could easily be factored in - best if someone already had 
a running protocol. Thus if you had a clogp module already running as 
something like:

JOEMol j = new JOEMOl(cmlMolecule);
double logp = j.getLogP();

then it would be easy to incorporate. I haven't had time to look at how to 
code JOELib and it is easiest if we have high-level routines at this level, 
especially cml2JOE and joe2CML. I have done this for CDK by passing XML 
strings. I know this is inefficient but ultimately we need to work at this 
API level. I therefore have just two calls:

cdkMolecule = getCDKMolecule(cmlMolecule)
cdkMolecule.doSomCalculation()
newCmlMolecule = getCMLMolecule(cdkMolecule)
merge(cmlMolecule, newCMLMolecule)

and we could do the same for JOELIB.


>>the purpose of this email to invite people if they wish, to join in to 
>>this "virtual laboratory", and hence "participate" in the ACS session.
>I've not the money to join :-( But i'm going to the
>1. Chemoinformatics Conference in Sheffield, U.K., 21-23 April ...
>2. Analytica Conference Munich, Germany, 12-14 May ...
>... if anyone of you will be there i would be happy to discuss any 
>chemoinformatics topics in more detail.

YY will be presenting WWMM at Munich

P.


>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)

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069