On Friday 12 March 2004 11:07, Peter Murray-Rust wrote: > At 10:39 12/03/2004 +0100, Joerg K. Wegner wrote: > >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?)
I'm not that clear with the blog concept: a website of someone keeping a diary?, or a wiki like communal website? Anyway, I agree that it is time to organize all chemistry open source initiative and come up with solutions which many projects deal with, e.g. atom typing and interoperability... > >>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. CDK has libio to JOELib... so without the need to write anything (except the getJOELibMolecule() wrapper), you can already do: joelibMol = getJOELibMolecule(getCDKMolecule(cmlMolecule)) joelibMol.doSomeCalc() newCMLMol = getCMLMolecule(getCDKMolecule(joelibMol)) merge(cmlMolecule, newCMLMolecule) BTW, Joerg, it would be very nice if you could have a CMLRSS set up that takes all current other feeds, calculates properties and puts that only as CMLRSS again. Egon ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
