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:[EMAIL PROTECTED] 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
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