joelib-help

[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)

[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

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[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:

> -----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=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/
> GPG: 1024D/D6336BA6
> 
> -----BEGIN PGP SIGNATURE-----
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> 
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> =yvea
> -----END PGP SIGNATURE-----
> 
> 
> 
> -------------------------------------------------------
> 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
--
Never mistake motion for action.
                                    (E. Hemingway)
                         
Never mistake action for meaningful action.
                               (Hugo Kubinyi,2004)                         

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

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

Greetings all,
I have been away from my mail for 24 hours and this all seems to be 
exploding! Fantastic. This is written before reading everything...

At 14:03 19/03/2004 +0100, E.L. Willighagen wrote:
>-----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

This sounds great. We are happy to explore how CML can support these type 
of applications. The challenge is not to write CML (which is easy) but to 
create a structure which is usable by others. So imagine that you got a CML 
file from someone you hadn't talked to - could you use it?

A good example is properties. Let's say Joerg creates something that looks 
like:
<molecule xmlns:joerg="http://de.uni-tuebingen.informatik/wegner/dict">
   <atomsSnipped/>
   <propertyList>
     <property>
       <scalar type="xsd:float" dictRef="joerg:clogp" 
title="cLogP>1.23</scalar>
     </property>
   </propertyList>
</molecule>

what should RssViewer do? Options might be
  1 display the molecule and omit the propertyList completely
  2 notify the user that there were properties but that RSS viewer couldn't 
view them
  3 list the values along with the dictRef, title *and* the xmlns. This 
identifies the property but doesn't explain it
  4 visit joerg's website and retrieve the dictionary entry.

I would suggest we aim for at least 2. However we are going into completely 
fresh semantic web territory - very exciting.

> > 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.

This is wonderful. Joerg, please liaise with YY so that (a) we notify 
people and (b) can include your name in the RSS providers at our ACS 
presentation. [This applies to any other list members - if you have a 
CMLRSS feed and let YY/Henry know in the next 2-3 days we will promote it.)

Again, we are promoting CMLRSS at the NeSC meeting - as announced earlier. 
Egon - please can you liaise with YY - within the next 3-4 days as to what 
version we can put on. (We can always announce a later one at the meeting).

Hope to post more later

P.

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069

[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:
> 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!

Elaborate... MDL style wedge bonds are read from CML... what are you referi=
ng=20
too? CML fragment please...

> 4.2. Please accept RSS entries without structures without throwing an
> error.=20

Cannot reproduce that behaviour. I don't have that problem. Can you tell me=
=20
how to reproduce the bug?

> 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.

Thanx for the ideas... this does not have a high priority ...

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

Yes, that is being worked out... Will report later...

Egon


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

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