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

[Joerg W. <we...@in...>]

Hi Egon,
Example is given at:
http://joelib.sourceforge.net/rss/index.xml
Please use a text viewer, not a browser !

For stereo i've used bondStereo and hope this is standard conform ?
Anyway, if not, i can change to 'correctStereoTag'.

Error in JChempaint, Jmol does not work as mentioned in previous mail:
'Model does not have bonds. Cannot depict contents.'
[Ok-Button]
[virtual mouse-click] :-)

Kind regards, Joerg

On Fri, 19 Mar 2004, E.L. Willighagen wrote:

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> On Friday 19 March 2004 12:33, Joerg K. Wegner wrote:
> > 1. I've again released a new JOELib version with sequential SAX parser
> > for HUGE CML files for uncompressed and compressed (ZIP) files (i've
> > found a workaround)!!!
> 
> Excellent!
> 
> > I think after this 'stable' CML standard support i can switch from SDF
> > to CML2 as standard format, because it can be compressed and is much
> > more verbose, which is recommended for storing descriptors (WITH KERNEL
> > informations).
> > https://sourceforge.net/projects/joelib/
> 
> /me is happy
> 
> > 2. I've added the 'attributearray' CML writer which is conform to the
> > OpenBabel array, only because its better layout in RSS files. I would be
> > happy if you will add a CML generation section for JOELib (analogue to
> > OpenBabel) to your CMLRSS documentation. Two properties in
> > joelib.properties need to be set:
> > joelib.io.types.ChemicalMarkupLanguage.output=attributearray
> > ## a first step to 'reproducable' descriptor calculation algorithms
> > joelib.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=false
> >
> > 3.1. I've published a 'QSAR, LBDD and SBDD'-RSS feed. I plan to release
> > from time to time (monthly) some algorithmic and QSAR, LBDD and SBDD
> > topics with literature references.
> > http://joelib.sourceforge.net/rss/index.xml
> > Please see also attached rssviewer.props
> >
> > 3.2. Two entries in the feed contain structures WITH solubility and
> > activity data taken from the literature ! Because this are the most
> > interesting values for pharmaceutical companies and medicinal research i
> > think such entries could be really interesting for other companies and
> > database supplieres also ! I would it find also interesting if there
> > could be a larger supplier which can offer such an open RSS feed, where
> > others can submit some things.
> > Eventually an open Wiki approach with mathematical equations (latex
> > support exists) AND chemical structures (not that i know) can be set up?
> >
> > 4. CDK CML core wishlist (Egon):
> > 4.1. Please move (from MDL CDO) or add in any form of stereochemistry
> > support to core CML and the RSS plugin. This is important for
> > visualizing drugs!
> 
> Ok, can you give me a CML fragment? That's much easier for me, than finding 
> the source code bits that deal with it...
> 
> > 4.2. Please accept RSS entries without structures without throwing an
> > error. Please crosscheck the GPLed Java RSS viewer on SF.net:
> > https://sourceforge.net/projects/rssview/
> 
> It should, and did... what error do you get?
> 
> > They can also add and edit RSS feed properties and have proxy support,
> > additionally all informations are stored in a XML file.
> 
> Adding is supported in the plugin too... info is taken from the feed itself...
> Proxy support is very easy... do you need it?
> 
> About storing the info... I think we are going to use OPML... which that 
> program might be using too...
> 
> > 4.3. Visualization for activity and ADMET data in this RSS feed example
> > (xsd:string, xsd:double, xsd:integer descriptors).
> 
> Again, can you give me some CML fragment? Is this atom based? Then Jmol can do 
> it with a minor customization...
> 
> Egon
> 
> - -- 
> eg...@sc...
> PhD on Molecular Representation in Chemometrics
> Nijmegen University
> http://www.cac.sci.kun.nl/people/egonw/
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> -------------------------------------------------------
> This SF.Net email is sponsored

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
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