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

[E.L. W. <eg...@sc...>]

=2D----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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=3Dattributearray
> ## a first step to 'reproducable' descriptor calculation algorithms
> joelib.io.types.ChemicalMarkupLanguage.output.storeChemistryKernelInfo=3D=
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=
=20
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=
=2E..
Proxy support is very easy... do you need it?

About storing the info... I think we are going to use OPML... which that=20
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=20
it with a minor customization...

Egon

=2D --=20
eg...@sc...
PhD on Molecular Representation in Chemometrics
Nijmegen University
http://www.cac.sci.kun.nl/people/egonw/
GPG: 1024D/D6336BA6

=2D----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.0.7 (SunOS)

iD8DBQFAWu+Nd9R8I9Yza6YRAgHxAKCIEjwjqsvbtX4vLubFfQwJmJvKmQCeNo0L
RrVgzdM5aUMJKyO4UgqzMZI=3D
=3Dyvea
=2D----END PGP SIGNATURE-----