[Cdk-devel] Re: [cml/ccml-discuss] JUMBO4.6 and implications for communal libraries (chemjars)

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

OK - I'm guessing that CDK might be the best place for a chemjars 
discussion... This is not just about XML

At 13:18 17/02/2005 +0100, Egon Willighagen wrote:
>On Thursday 17 February 2005 11:15, Peter Murray-Rust wrote:
> > [crossposted to several lists; be thoughtful in replying]
> > My suggestion is that our community try to rationalise at least some of
> > this. Suppose we had a site
> > chemjars.sf.net
> > whose primary role was to offer the best selection of stable jars for our
> > projects. If our distrib required (say) vecmath we would copy it from
> > chemjars, rather than include it in the distrib. (The bioscience community,
> > e.g. myGrid/taverna does this, I think). There could be a standard ant file
> > on chemjars that was simply called for each function.
>
>I think CDK would support such an initiative...

Excellent. We just need someone to thing about setting up such a site. It's 
probably not too difficult.

> > Current distributions would be smaller, robuster, etc. There would be a
> > greater communal knowledge of problems.
>
>Sharing best practices would be most interesting to me...

Good.

> > The major remaining problem seems to be XML. This continues to drive us
> > wild. So far it seems:
> > - XML is OS dependent. Am I right that Jmol requires gnujaxp if it is to
> > run XML on Mac, for example
>
>Correct. XML is not available from pre1.4 JVMs. So anything like 1.3 or
>earlier *requires* a XML parsing library. GNUJAXP is a good one then, because
>it's only 70kB. But Xerces is theoretically possibly too :)
>
> > - Xerces (at least) has a new version every new moon. They are all
> > incompatible AFAICS. I can no longer run validation on XML - the last tool
> > (ASBuilder) disappeared and the new XML validation language in Java 1.5
> > tells us that it doesn't understand the XML Schema namespace!!!
> > - Xerces is now embedded in Java 1.5 and causes additional interactions
> > with any Xerces in the distrib. (I think JUMBO has at least two if not 3
> > xerces from other thirdparties!).
> >
> > Any of you checking out JUMBO will see the problem. I'd be grateful for
> > - Jmol (Miguel)
> > - how does Jmol parse XML (CML) - what parser does it use etc?
>
>Jmol 10 does not officially support CML for pre1.4 JVMs, i.e. Miguel knows 
>too
>little of alternatives and want to focus on the rendering (I'm with him on
>that)... However, I do provide CML support for Jmol 10 using
>gnujaxp-saxonly.jar...

OK - we need to know if anyone else does and reconcile them

>
> > JCP (Egon) - same for JCP
>
>JCP only supports 1.4.x JVM (or better), so will use JAXP that comes with the
>Sun JVM by default. No gnujaxp/xerces required for CML reading.
>
> > Also I think CDK had some hardcoded XML parsers (e.g. if you can't find
> > Xerces use Aelfred).
>
>No hard-coded XML parsers. No xerces/gnujaxp required on runtime if 1.4.x or
>better is used. As said, J1.3 does not have a XML parser, so then Xerces or
>gnujaxp *is* required.

I do not intend for JUMBO to support 1.3 . So we can remove all pre-1.4 jars


> > I think this causes prob elms which chemjars would
> > overcome. Everyone would be able to know what they should use.
>
>I will start a discussion wether CDK wants to keep supporting J1.3. Last time
>I asked (quite some time ago) there was at least one user on a platform which
>did not have a 1.4 yet, but that should no longer be the case I think...

Excellent.

 From an operational viewpoint a developer needs to know:
- what do I need to *build* my system. That could include fop, saxon, tidy, 
batik, doxygen, etc. It should be possible to run much of that with loose 
coupling
- what is the first level of ThirdParty jars. e.g. I want "jchempaint" or 
"jmol" or "cdk". I don't want to have to know about whether they use 
xerces, vecmath, etc.
- do any of the ThirdParty tools call *my* stuff! For example a display 
program might use JUMBO for reading, jumbo might use the  display program

P.


>Egon
>
>--
>e.w...@sc...
>PhD student on Molecular Representation in Chemometrics
>Radboud University Nijmegen
>http://www.cac.science.ru.nl/people/egonw/
>GPG: 1024D/D6336BA6
>
>
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Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069