[Joelib-help] JOELib and CMLRSS and WWMM and OpenMolecules

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

Hi all,

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)!!!
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/

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!

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/
They can also add and edit RSS feed properties and have proxy support, 
additionally all informations are stored in a XML file.

4.3. Visualization for activity and ADMET data in this RSS feed example 
(xsd:string, xsd:double, xsd:integer descriptors).

Kind CML2, RSS and developer 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)