joelib-devel — JOELib-Development

[Joelib-devel] Toxicity predictions with lazar and predictive toxicology book

[Christoph H. <he...@in...>]

Apologies if you receive multiple copies of this message!
========================================================

The lazar system for free online predictions of toxic activities is now
available at http://www.predictive-toxicology.org/lazar/! You can use a
webinterface to draw chemical structures and to obtain predictions for
rodent (rat and mice) carcinogenicity and Salmonella mutagenicity. Further
toxicity endpoints will be available in the future.

At the same time I want to take the opportunity to announce the new book
"Predictive Toxicology" that I have edited. It covers state-of-the
art techniques, databases, application areas and the most important
predictive toxicology programs. "Predictive Toxicology" has been published
by Marcel Dekker/CRC Press.

If you are interested in confidential predictions, batch predictions
or the development of modules for new endpoints, please contact
he...@in....

If you want to receive also in the future information about new lazar
developments, please subscribe to the lazar-announce mailinglist at
http://www.predictive-toxicology.org/mailman/listinfo/lazar-announce.

If you have questions or comments concerning the lazar system,
please post them to the lazar-discussion mailinglist at
http://www.predictive-toxicology.org/mailman/listinfo/lazar-discussion.

If you want to discuss predictive toxicology topics in general,
please use the the predictive-toxicology mailinglist at
http://www.predictive-toxicology.org/mailman/listinfo/predictive-toxicology.


Best regards,
Christoph Helma
==
:: in silico toxicology
:: he...@in...
:: www.in-silico.de

Re: [Joelib-devel] Atom mapping in substructure searching

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

At 15:09 30/03/2005, Christoph Steinbeck wrote:
>Sorry for not answering this question comprehensively,
>I just want to point out that we have convenience methods for getting the=
=20
>atom-to-atom mapping in CDK MCSS, not just bond maps.

Thanks - that's great. Wasn't aware that those were now in.

Are there any examples of code so we can get off the ground quickly?

>>(1) which of the tools can be easily configured to output one or more=20
>>substructure mappings (including null) from A=3D>C, A=3D>D, A=3D>E. B=3D>C=
, B=3D>D,=20
>>B=3D>E. And the reverse C=3D>A, C=3D>B, etc. . This only works when one=
 species=20
>>is a precise substructure of another.
>>(2) Maximal common subgraph mapping A<=3D>C, A<=3D>D, etc.
>
>I don't see why the
>org.openscience.cdk.isomorphism.UniversalIsomorphismTester should not be=20
>able to give you exactly what you ask for in (1) and (2), as atom-atom=20
>mappings.

Excellent

>>(3) ditto, but for (A+B) <=3D> (C+D+E) without overlaps.
>
>Don't quite get this one.
>Suppose you put AtomContainer A and B into a new AtomContainer "educts",=20
>which yields a disconnected graph and the same with putting C and D and E=
=20
>into a new AtomContainer "products". You would then do a MCSS of both?!?

Maybe this is rubbish, but consider the reaction:
CCC(=3DO)OCC+ O -> CCC(=3DO)O + CCO
If you do a MCS of O vs CCC(=3DO)OC you will get 2 hits. Only one is=
 "useful"=20
and you don't know which. However if you require that all MCS are=20
simultaneously matched then the O will match what is left after the larger=
=20
fragments have been matched.

In many (not all) reactions we have all the atoms in the reaction so it=20
makes sens to map them all at once - it's a strong constraint.

P.


>Cheers,
>
>Chris
>
>--
>Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...)
>Head of the Research Group for Molecular Informatics
>Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
>Z=FClpicher Str. 47, 50674 Cologne
>Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786
>
>What is man but that lofty spirit - that sense of enterprise.
>... Kirk, "I, Mudd," stardate 4513.3..

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076

Re: [Joelib-devel] Atom mapping in substructure searching

[Christoph S. <c.s...@un...>]

Sorry for not answering this question comprehensively,
I just want to point out that we have convenience methods for getting=20
the atom-to-atom mapping in CDK MCSS, not just bond maps.

> (1) which of the tools can be easily configured to output one or more=20
> substructure mappings (including null) from A=3D>C, A=3D>D, A=3D>E. B=3D=
>C,=20
> B=3D>D, B=3D>E. And the reverse C=3D>A, C=3D>B, etc. . This only works =
when one=20
> species is a precise substructure of another.
> (2) Maximal common subgraph mapping A<=3D>C, A<=3D>D, etc.

I don't see why the
org.openscience.cdk.isomorphism.UniversalIsomorphismTester should not be=20
able to give you exactly what you ask for in (1) and (2), as atom-atom=20
mappings.

> (3) ditto, but for (A+B) <=3D> (C+D+E) without overlaps.

Don't quite get this one.
Suppose you put AtomContainer A and B into a new AtomContainer "educts",=20
which yields a disconnected graph and the same with putting C and D and=20
E into a new AtomContainer "products". You would then do a MCSS of both?!=
?

Cheers,

Chris

--=20
Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...)
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=FClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

Re: [Joelib-devel] Atom mapping in substructure searching

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

At 14:10 30/03/2005, Joerg K. Wegner wrote:
>Hi all,
>
>JOELib has an unpublished extended module for MCS, and the publication is 
>still in the review process for the QSAR&Comb.Sci.

Understood. Of course if we were in any other discipline than chemistry you 
could have posted the preprint...

>We can also deal with physicochemical atom properties, which can make 
>sense for reactions.

Do you mean more than formal charges and isotopes? Ore atom subtyping? Most 
other properties will be doubles so cannot match exactly and there is some 
judgment.

>The method returns all, full combinatorial and/or unique, MCS, so there 
>are a lot of index lists for two molecules.

Looks very useful.


>graph isomorphism(1) is a special case of maximum subgraph isomorphism(2) 
>so this is no problem.

I listed them separately because other implementations might not have MCS

>  I am not sure if I understand (3)

this requires the disjoint graphs in the reactants to be mapped to the 
disjoint graphs in the products. For example a water molecule will probably 
map to all products. However if many of the O atoms have already been 
mapped, then it has less possibilities. IOW it is a mapping of graphLists 
(forests), not just graphs.


>Are there plans for a publication?

Yes, but we cannot promise timescales or the type of publication(s).

>This module is a real developer version and looks also like a developer 
>version and I am ambigious to share it, until it was not published.
>You know GPL, means sharing all or nothing.

Indeed. And probably technically you have to send us the full source and so on.

That is an advantage of WS - you can share the functionality without 
releasing the code.

P.



Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076

Re: [Joelib-devel] Atom mapping in substructure searching

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

Hi all,

JOELib has an unpublished extended module for MCS, and the publication 
is still in the review process for the QSAR&Comb.Sci. We can also deal 
with physicochemical atom properties, which can make sense for 
reactions. The method returns all, full combinatorial and/or unique, 
MCS, so there are a lot of index lists for two molecules.

graph isomorphism(1) is a special case of maximum subgraph 
isomorphism(2) so this is no problem. I am not sure if I understand (3)

Are there plans for a publication? This module is a real developer 
version and looks also like a developer version and I am ambigious to 
share it, until it was not published.
You know GPL, means sharing all or nothing.

Kind regards, Joerg

> Crossposted to 3 lists. Please reply carefully.
> 
> We have a requirement to extract atom-atom mapping from a substructure 
> search (or a maximal common subgraph).  It's because our MACiE database 
> contains reactions without atom-atom maps. We have the complete products 
> and reactions for each step in CMLReact and want to either create a map 
> or relabel the atoms consistently. Since these are multistep reactions 
> the products of step N and usually the reactants of stepN+1 though some 
> components may be missing.
> 
> I've used obgrep (SMARTS) but only to give a boolean answer - which 
> molecules in a list have a given substructure. I used CDK a long time 
> ago for maximal common subgraph, but that was based on bonds, not atoms 
> and I haven't used it since. I haven't used JOELib.
> 
> If I have something like A + B => C + D + E
> (1) which of the tools can be easily configured to output one or more 
> substructure mappings (including null) from A=>C, A=>D, A=>E. B=>C, 
> B=>D, B=>E. And the reverse C=>A, C=>B, etc. . This only works when one 
> species is a precise substructure of another.
> (2) Maximal common subgraph mapping A<=>C, A<=>D, etc.
> (2) ditto, but for (A+B) <=> (C+D+E) without overlaps.
> 
> Performance is not an issue - this only (we hope) has to be done once as 
> then we shall use JChempaint as the entry tool. Even a webservice would 
> do. Nor (in principle) is semistructured output though we'd prefer XML 
> or a clear API. But we'd prefer not to have to write new code if possible.
> 
> Hope this makes sense. The only alternative is to reinput hundreds of 
> reactions by hand :-(
> 
> P.
> 
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069 Fax: +44 1223 763076
> 
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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> _______________________________________________
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> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-devel
> 


-- 
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-devel] Atom mapping in substructure searching

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

Crossposted to 3 lists. Please reply carefully.

We have a requirement to extract atom-atom mapping from a substructure 
search (or a maximal common subgraph).  It's because our MACiE database 
contains reactions without atom-atom maps. We have the complete products 
and reactions for each step in CMLReact and want to either create a map or 
relabel the atoms consistently. Since these are multistep reactions the 
products of step N and usually the reactants of stepN+1 though some 
components may be missing.

I've used obgrep (SMARTS) but only to give a boolean answer - which 
molecules in a list have a given substructure. I used CDK a long time ago 
for maximal common subgraph, but that was based on bonds, not atoms and I 
haven't used it since. I haven't used JOELib.

If I have something like A + B => C + D + E
(1) which of the tools can be easily configured to output one or more 
substructure mappings (including null) from A=>C, A=>D, A=>E. B=>C, B=>D, 
B=>E. And the reverse C=>A, C=>B, etc. . This only works when one species 
is a precise substructure of another.
(2) Maximal common subgraph mapping A<=>C, A<=>D, etc.
(2) ditto, but for (A+B) <=> (C+D+E) without overlaps.

Performance is not an issue - this only (we hope) has to be done once as 
then we shall use JChempaint as the entry tool. Even a webservice would do. 
Nor (in principle) is semistructured output though we'd prefer XML or a 
clear API. But we'd prefer not to have to write new code if possible.

Hope this makes sense. The only alternative is to reinput hundreds of 
reactions by hand :-(

P.



Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076

[Joelib-devel] Publication Update for JOELib

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

Hi all,

I have updated the publication list.

I had a lot of luck with presenting JOELib-QSAR related work at the ACS 
(two lectures), the Rauischholzhausen workshop (one poster), and will 
present  more work at the ICCS conference (one lecture).
http://www-ra.informatik.uni-tuebingen.de/software/joelib/users.html

Kind 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-devel] The Blue Obelisk group

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

Hi all,

as some of us now already, we have had the first non-virtual meeting of 
the most relevant cheminformatics open-source projects, being more exact 
some of their administrators/developers.

BTW, the official name for this group is 'The Blue Obelisk', because we 
have meet at the blue obelisk at the horten plaza in San Diego, California.
So, Peter called the open-source community related to cheminformatics 
the 'The Blue Obelisk'-movement and details can be found in his original 
message below.

And as usuall for our open-source group ... send all comments and critic 
directly to a mailing-list of your choice :-)

Kind regards, Joerg

========================================
Peters original message:
------
Greetings,
On Monday night some of use met at the blue obelisk in Horton Plaza, San
Diego. There was some confusion as Geoff went to the Public Blue Obelisk
(shown in picture) while the others went to the Lesser Public Blue Obelisk.
This is some fragmentary historical record, but as PM-R had to consume
Christoph's beer not all has been captured.
http://wwmm.ch.cam.ac.uk/presentations/acs2005/
(see blueobelisk under menu)

I drafted the following words which everyone seemed happy with:
"

The Blue Obelisk

A diverse Internet group who promote re-usable chemistry

     * Open: Access, Data, Standards, Source
     * consistent and complementary
     * non-divisive and fun
Components include
     * CDK
     * JChempaint
     * Jmol
     * JOELib
     * JUMBO
     * NMRShiftDB
     * Octet
     * Openbabel
     * QSAR
     * WWMM
"
and announced this at the meeting. We can make of it what we like  :-)  I
shall start adding an obelisk logo of some sort to some of our offerings.
There is no commitment but I think that by providing each other with web
services, jars, etc. we should provide a rich and consistent approach.

There is no formal membership but it's not primarily a list of Open source
chemistry - it's people working together on the Internet to make sure their
systems work together. - if anyone else has Open resources that
interoperate with some of the above and provide complementary functionality
feel free to post to one of the lists.

P.

this mail re-usable under CreativeCommons

Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076

-- 
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-devel] Re: [QSAR-devel] Re: [Joelib-help] ACS Meeting

[Christoph S. <c.s...@un...>]

Very good.
I´ll also be there. When do you guys arrive? I´m there for a CIC-CINF 
coordination meeting on Friday and have to leave on Tuesday morning.

Cheers,

Chris

Peter Murray-Rust wrote:
> At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
> 
>> Hi all,
>>
>> i'm presenting two lectures at the ACS meeting and i have seen that 
>> Rajarshi Guha is also there. Anyone else?
> 
> 
> excellent. I and Henry will be there. I shan't stay the whole time so we 
> should plan our timetables. Henry and I are both speaking at the Open 
> Access session.
> 
> This will be a great opportunity to meet each other, find out exactly 
> where we are and to make tentative plans. Today we managed to create 
> some simple but impressive workflows and webservices and would be keen 
> to bind JOELib into them.
> 
> P.
> 
>> Here are the topics of my talks, for both i used JOELib using some 
>> interal source code, still not publicly available until published:
>>
>> Difference in vector-based and graph-based coding for ADME prediction.
>> J. K. Wegner, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: ADME/tox Informatics
>> http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
>> Chair: O. F. Güner
>>
>> Relevance of feature selection for clustering molecules.
>> J. K. Wegner, F. Sieker, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: Applications of Information Theory in Chemistry
>> Chairs: V. Shanmugasundaram and G. M Maggiora
>> http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM
>>
>> And here is the link to the full scientific program:
>> http://oasys2.confex.com/acs/229nm/techprogram/
>>
>> Kind 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)
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF email is sponsored by - The IT Product Guide
>> Read honest & candid reviews on hundreds of IT Products from real users.
>> Discover which products truly live up to the hype. Start reading now.
>> _______________________________________________
>> Joelib-help mailing list
>> Joe...@li...
>> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
> 
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_ide95&alloc_id396&op=click
> _______________________________________________
> Qsar-devel mailing list
> Qsa...@li...
> https://lists.sourceforge.net/lists/listinfo/qsar-devel
> 
> 
> 


-- 
Dr. rer. nat. habil. Christoph Steinbeck (c.s...@un...)
Groupleader Junior Research Group for Applied Bioinformatics
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426   Fax: +49 (0) 221-470-7786

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Joelib-devel] Open data vision - was Re: [Joelib-help] ACS Meeting]

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

At 16:20 24/02/2005 +0100, Joerg K. Wegner wrote:
>Hi Peter,
>
>is this correct:

Yes! We should probably continue the discussion of personal meetings=20
offlist, but we hope to be demoing some exciting stuff. Essentially I want=
=20
to show that **IF** scientific data is freely available then very powerful=
=20
analyses of journals can be made. For example we can now
- read the TOC for acta cryst E
- extract each paper
- extract each CIF
- convert to CML
- create InChI
- look it up in our repository
- if new, compute simple properties (MWt, formula)
- create 2D layout
- run MOPAC/GAMESS

we want to extend that to
- compute JOELib descriptors and we would probably do that through a web=20
service.

So the question is then simply:
- do publishers permit this or do they forbid it?

P.

>session: The Future of Scientific Publishing
>http://oasys2.confex.com/acs/229nm/techprogram/
>chair: Guenter Grethe
>9:05 AM Open access and the Chemical Semantic Web
>         Peter Murray-Rust, Henry S. Rzepa
>9:35 AM RDF-based molecular relationships, the Semantic Web and the future=
=20
>of scientific publishing
>         Henry S. Rzepa, Omer Casher, Peter Murray-Rust
>Convention Center -- Room 33B, Oral
>
>BTW, both of my lectures are in
>Convention Center -- Room 33A, Oral
>
>I will arrive at the weekend, so i hope i will manage to come to your=20
>lecture on monday.
>
>Kind regards, Joerg
>
>>At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
>>
>>>Hi all,
>>>
>>>i'm presenting two lectures at the ACS meeting and i have seen that=20
>>>Rajarshi Guha is also there. Anyone else?
>>
>>excellent. I and Henry will be there. I shan't stay the whole time so we=
=20
>>should plan our timetables. Henry and I are both speaking at the Open=20
>>Access session.
>>This will be a great opportunity to meet each other, find out exactly=20
>>where we are and to make tentative plans. Today we managed to create some=
=20
>>simple but impressive workflows and webservices and would be keen to bind=
=20
>>JOELib into them.
>>P.
>>
>>>Here are the topics of my talks, for both i used JOELib using some=20
>>>interal source code, still not publicly available until published:
>>>
>>>Difference in vector-based and graph-based coding for ADME prediction.
>>>J. K. Wegner, A. Zell
>>>The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>>>Session: ADME/tox Informatics
>>>http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
>>>Chair: O. F. G=FCner
>>>
>>>Relevance of feature selection for clustering molecules.
>>>J. K. Wegner, F. Sieker, A. Zell
>>>The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>>>Session: Applications of Information Theory in Chemistry
>>>Chairs: V. Shanmugasundaram and G. M Maggiora
>>>http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM
>>>
>>>And here is the link to the full scientific program:
>>>http://oasys2.confex.com/acs/229nm/techprogram/
>>>
>>>Kind regards, Joerg
>>>--

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

[Joelib-devel] Re: [Joelib-help] ACS Meeting

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

Hi Peter,

is this correct:
session: The Future of Scientific Publishing
http://oasys2.confex.com/acs/229nm/techprogram/
chair: Guenter Grethe
9:05 AM Open access and the Chemical Semantic Web
         Peter Murray-Rust, Henry S. Rzepa
9:35 AM RDF-based molecular relationships, the Semantic Web and the=20
future of scientific publishing
         Henry S. Rzepa, Omer Casher, Peter Murray-Rust
Convention Center -- Room 33B, Oral

BTW, both of my lectures are in
Convention Center -- Room 33A, Oral

I will arrive at the weekend, so i hope i will manage to come to your=20
lecture on monday.

Kind regards, Joerg

> At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
>=20
>> Hi all,
>>
>> i'm presenting two lectures at the ACS meeting and i have seen that=20
>> Rajarshi Guha is also there. Anyone else?
>=20
>=20
> excellent. I and Henry will be there. I shan't stay the whole time so w=
e=20
> should plan our timetables. Henry and I are both speaking at the Open=20
> Access session.
>=20
> This will be a great opportunity to meet each other, find out exactly=20
> where we are and to make tentative plans. Today we managed to create=20
> some simple but impressive workflows and webservices and would be keen=20
> to bind JOELib into them.
>=20
> P.
>=20
>> Here are the topics of my talks, for both i used JOELib using some=20
>> interal source code, still not publicly available until published:
>>
>> Difference in vector-based and graph-based coding for ADME prediction.
>> J. K. Wegner, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: ADME/tox Informatics
>> http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
>> Chair: O. F. G=FCner
>>
>> Relevance of feature selection for clustering molecules.
>> J. K. Wegner, F. Sieker, A. Zell
>> The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>> Session: Applications of Information Theory in Chemistry
>> Chairs: V. Shanmugasundaram and G. M Maggiora
>> http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM
>>
>> And here is the link to the full scientific program:
>> http://oasys2.confex.com/acs/229nm/techprogram/
>>
>> Kind regards, Joerg
>> --=20
>> 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
>> --=20
>> Never mistake motion for action.
>>                                     (E. Hemingway)
>>
>> Never mistake action for meaningful action.
>>                                (Hugo Kubinyi,2004)
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF email is sponsored by - The IT Product Guide
>> Read honest & candid reviews on hundreds of IT Products from real user=
s.
>> Discover which products truly live up to the hype. Start reading now.
>> _______________________________________________
>> Joelib-help mailing list
>> Joe...@li...
>> https://lists.sourceforge.net/lists/listinfo/joelib-help
>=20
>=20
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
>=20
>=20


--=20
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-devel] Re: [QSAR-devel] Re: [Joelib-help] ACS Meeting

[Rajarshi G. <rx...@ps...>]

On Thu, 2005-02-24 at 15:07 +0000, Peter Murray-Rust wrote:
> At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
> >Hi all,
> >
> >i'm presenting two lectures at the ACS meeting and i have seen that 
> >Rajarshi Guha is also there. Anyone else?
> 
> excellent. I and Henry will be there. I shan't stay the whole time so we 
> should plan our timetables. Henry and I are both speaking at the Open 
> Access session.
> 
> This will be a great opportunity to meet each other, find out exactly where 
> we are and to make tentative plans. Today we managed to create some simple 
> but impressive workflows and webservices and would be keen to bind JOELib 
> into them.

It would certainly be nice to meet everybody - would it be possible to
fix up a day/time?

-------------------------------------------------------------------
Rajarshi Guha <rx...@ps...> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
A committee is a life form with six or more legs and no brain.
-- Lazarus Long, "Time Enough For Love"

[Joelib-devel] Re: [Joelib-help] ACS Meeting

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

At 13:27 24/02/2005 +0100, Joerg K. Wegner wrote:
>Hi all,
>
>i'm presenting two lectures at the ACS meeting and i have seen that=20
>Rajarshi Guha is also there. Anyone else?

excellent. I and Henry will be there. I shan't stay the whole time so we=20
should plan our timetables. Henry and I are both speaking at the Open=20
Access session.

This will be a great opportunity to meet each other, find out exactly where=
=20
we are and to make tentative plans. Today we managed to create some simple=
=20
but impressive workflows and webservices and would be keen to bind JOELib=20
into them.

P.

>Here are the topics of my talks, for both i used JOELib using some interal=
=20
>source code, still not publicly available until published:
>
>Difference in vector-based and graph-based coding for ADME prediction.
>J. K. Wegner, A. Zell
>The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>Session: ADME/tox Informatics
>http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
>Chair: O. F. G=FCner
>
>Relevance of feature selection for clustering molecules.
>J. K. Wegner, F. Sieker, A. Zell
>The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
>Session: Applications of Information Theory in Chemistry
>Chairs: V. Shanmugasundaram and G. M Maggiora
>http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM
>
>And here is the link to the full scientific program:
>http://oasys2.confex.com/acs/229nm/techprogram/
>
>Kind 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)
>
>
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>_______________________________________________
>Joelib-help mailing list
>Joe...@li...
>https://lists.sourceforge.net/lists/listinfo/joelib-help

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

[Joelib-devel] ACS Meeting

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

Hi all,

i'm presenting two lectures at the ACS meeting and i have seen that=20
Rajarshi Guha is also there. Anyone else?

Here are the topics of my talks, for both i used JOELib using some=20
interal source code, still not publicly available until published:

Difference in vector-based and graph-based coding for ADME prediction.
J. K. Wegner, A. Zell
The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
Session: ADME/tox Informatics
http://oasys2.confex.com/acs/229nm/techprogram/S17408.HTM
Chair: O. F. G=FCner

Relevance of feature selection for clustering molecules.
J. K. Wegner, F. Sieker, A. Zell
The 229th ACS National Meeting, in San Diego, CA, March 13-17, 2005.
Session: Applications of Information Theory in Chemistry
Chairs: V. Shanmugasundaram and G. M Maggiora
http://oasys2.confex.com/acs/229nm/techprogram/S16537.HTM

And here is the link to the full scientific program:
http://oasys2.confex.com/acs/229nm/techprogram/

Kind regards, Joerg
--=20
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-devel] Re: [QSAR-devel] Wikipedia (en): Chemical File Format

[Egon W. <eg...@us...>]

On Thursday 17 February 2005 09:47, Joerg K. Wegner wrote:
> After my first short experience with Wikipedia and some troubles i
> wondered if anyone else is interested to add content to:
> http://en.wikipedia.org/wiki/Chemical_file_format

Added some content this morning, among which a link to a page written by Henry 
Rzepa on chemical mimes. That's a good page to get info from.

Egon

-- 
eg...@us...
GPG: 1024D/D6336BA6

[Joelib-devel] Wikipedia (en): Chemical File Format

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

After my first short experience with Wikipedia and some troubles i 
wondered if anyone else is interested to add content to:
http://en.wikipedia.org/wiki/Chemical_file_format

Kind 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)

Re: [Joelib-devel] Libraries and Java versions

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

[crossposted to a smaller set of lists!]

Thanks very much Joerg for quick reply...

At 11:24 15/02/2005 +0100, Joerg K. Wegner wrote:
> > [Crossposted to several lists - suggest we only reply on CDK]
>I suggest QSAR devel.

I am keeping in CDK as it overlaps with the Jmol group.


>>Q. what strategy do the various groups have for this? Do you have any 
>>idea of the rate of take up of J1.5?
>JOELib  is 1.4 (only maintenance, no active development)
>JOELib2 is 1.5 (active development)
That is our own in-house approach. JUMBO4.6 is now maintenance-only and 
Jumbo5 is being developed as fully Java 1.5 (at source level). There are 
additional incompatibilities with XML/JAXP - do you have any insight here?


>>Q does this work?
>Never tried.
>The only thing i found is that 1.5. in server mode caused hard shutdowns 
>of our server. Please use -client to switch of the at the moment instable 
>-server mode, which is used via autodetection.
>
>>Q. have you used and deployed code of this sort?
>No, but internally this should be the same code.

I agree it *should*. I just wanted confirmation!

>>Q is it a good strategy?
>Depends on your requirements, adding additional maintenance tasks should 
>be not too difficult.

We have to be able to support people who are not (very) java-literate so 
version problems must be excluded

>>Q should our community (Jmol, JCP, CDK, QSAR, Octet, JOElib, JUMBO) have 
>>a communal view? If we all do the same thing we are limited by the 
>>slowest. I assume that Jmol, for example, need to retain considerable 
>>backward compatibility
>As you all might know JOELib had not really an interface definition for 
>all relevant classes, this was much improved in the JOELib2 version (see 
>code stability metric).
>So, i think such things should forwarded to the single projects and are an 
>maintenance task, like building and getting a valid distribution. I think 
>those things should be added and consolidated in the ANT build.xml files 
>to do things automatically, then we will see if it works.
>Every project can add specific targets, like
>buildForJDK14, buildForJDK15

Agreed and I think we shall do this. It is a question of what we 
distribute. I don't want to distribute JUMBO5(1.4) and JUMBO5(1.5) for example!

>======================
>>  This can mean 2 or even 3 copies of things like Xerces in the distrib. 
>> The size is bad enough but since Xerces is now in the JVM 1.5 and also 
>> seems to change its signatures with every new moon the chance of 
>> incompatible versions is high. There are also copies of CDK libraries in 
>> JCP and so on.
>I'm aware of this problem and had also some nasty debugging experience 
>with those awfull library dependencies, but i have not really a solution 
>for that. As you know i'm a friend of all-in-one libraries, so i think the 
>guys with binding all those dependecies in one release should create an 
>automatic version for such things, e.g. removing cross-dependencies 
>automatically and release those ANT build-files, then the other projects 
>can decide what to do.

I agree that for specific applications this is a good strategy.

>>We also found that when we installed a recent CDK a method in CDK had 
>>disappeared which led to a compilation problem - we've managed to kludge 
>>round but this will be an ongoing problem.  Whenever there is a new (even 
>>minor) release of any of our libraries we all have to clean and rebuild 
>>in case of these problems.
>That's a code stability metric (interface) problem. Welcome to software 
>engineering problems, thats why i changed the version with a heavily 
>redesign. For JOELib2, which is still alpha, this is also the case, but i 
>can not froze all methods and classes, if a redesign is highly recommended 
>to be more user friendly and more stable for the future.

Understood. It is very difficult to balance flexibility and innovation.

>!!!
>I know that general interfaces are crucial important, but hey ... we are 
>working on that ... and we have still a long way to go ... so use as much 
>automatic testing and deployment as possible. Things like suggested also 
>in the book:
>Pragmatic Project Automation
>http://www.pragmaticprogrammer.com/sk/auto/
>
>Additionally we have still communication problems and different interests 
>with our projects and time slides, so there is no quick-fix for this problem.
>
>We are still focused on single tasks, but there is still a binding element 
>missing, which is an ungrateful job, because you will have a lot of work 
>to understand other projects and to design a common interface with the 
>prospect for being unable to publish one scientific paper.
>!!!

Yes. We have been slightly fortunate in that some of our funding has been 
for infrastructure. But we still have to publish it. (Incidentally JUMBO4.6 
distrib has copies of the papers and presentations that we are allowed to 
distribute - papers in JCICS cannot be redistributed - I am talking on this 
at the ACS)

>>Q How do we manage our libraries? If all of us use everyone else's 
>>libraries then these problems will increase. For example we'd like to use 
>>JOELib but not necessarily as part of our distributed system. If the 
>>performance is not time-critical then we can use web services as a means 
>>of insulating the APIs and libraries. For example we might move to 
>>running a CDK 2Dlayout server. This could be distributed so that 
>>connections to the web wouldn't be needed. However it would necessarily 
>>increase the complexity and is incompatible with, say, lightweight applets.
>1. I know that, that one reason why i decided to include a lot of the 
>functionality as source code dependency into JOELib, too. Especially if i 
>had some relevant changes at the interface or functionality.
>
>2. I do not really like the idea to abuse web-services as a common 
>interface, thats not really helpfull to create a common interface between 
>all projects, this binds only developer resources of several projects to 
>implement web-services.

I understand this view. Each of us will have their own dividing line. For 
example if you want a 3D structure it may be worth making a webservice call 
rather than linking in megabytes of code and data. But if you want to count 
hydrogens you need a local routine.

>So again, this is a software engineering problem, we need exact 
>requirement definitions for an interfaces here, or we will loose a lot of 
>time to implement functionalites, also sometimes twice.
>Not that i have a solution, but we have simply too much code and too much 
>functionality to get here a fast solution.
>And i can speak only for myself, i have absolutely no time to define such 
>an interface at the moment. Maybe an interface-Wiki might help us for the 
>discussion, but i am not too optimistic here.

We are all in the same position! But I think we have made much progress in 
the last 2 years and there is a lot of convergence.

P.


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

Re: [Joelib-devel] Libraries and Java versions

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

 > [Crossposted to several lists - suggest we only reply on CDK]
I suggest QSAR devel.

> Q. what strategy do the various groups have for this? Do you have any 
> idea of the rate of take up of J1.5?
JOELib  is 1.4 (only maintenance, no active development)
JOELib2 is 1.5 (active development)

> Q does this work?
Never tried.
The only thing i found is that 1.5. in server mode caused hard shutdowns 
of our server. Please use -client to switch of the at the moment 
instable -server mode, which is used via autodetection.

> Q. have you used and deployed code of this sort?
No, but internally this should be the same code.

> Q is it a good strategy?
Depends on your requirements, adding additional maintenance tasks should 
be not too difficult.

> Q should our community (Jmol, JCP, CDK, QSAR, Octet, JOElib, JUMBO) have 
> a communal view? If we all do the same thing we are limited by the 
> slowest. I assume that Jmol, for example, need to retain considerable 
> backward compatibility
As you all might know JOELib had not really an interface definition for 
all relevant classes, this was much improved in the JOELib2 version (see 
code stability metric).
So, i think such things should forwarded to the single projects and are 
an maintenance task, like building and getting a valid distribution. I 
think those things should be added and consolidated in the ANT build.xml 
files to do things automatically, then we will see if it works.
Every project can add specific targets, like
buildForJDK14, buildForJDK15

======================
>  This can mean 2 or even 3 copies of things like Xerces in the distrib. 
> The size is bad enough but since Xerces is now in the JVM 1.5 and also 
> seems to change its signatures with every new moon the chance of 
> incompatible versions is high. There are also copies of CDK libraries in 
> JCP and so on.
I'm aware of this problem and had also some nasty debugging experience 
with those awfull library dependencies, but i have not really a solution 
for that. As you know i'm a friend of all-in-one libraries, so i think 
the guys with binding all those dependecies in one release should create 
an automatic version for such things, e.g. removing cross-dependencies 
automatically and release those ANT build-files, then the other projects 
can decide what to do.

> We also found that when we installed a recent CDK a method in CDK had 
> disappeared which led to a compilation problem - we've managed to kludge 
> round but this will be an ongoing problem.  Whenever there is a new 
> (even minor) release of any of our libraries we all have to clean and 
> rebuild in case of these problems.
That's a code stability metric (interface) problem. Welcome to software 
engineering problems, thats why i changed the version with a heavily 
redesign. For JOELib2, which is still alpha, this is also the case, but 
i can not froze all methods and classes, if a redesign is highly 
recommended to be more user friendly and more stable for the future.

!!!
I know that general interfaces are crucial important, but hey ... we are 
working on that ... and we have still a long way to go ... so use as 
much automatic testing and deployment as possible. Things like suggested 
also in the book:
Pragmatic Project Automation
http://www.pragmaticprogrammer.com/sk/auto/

Additionally we have still communication problems and different 
interests with our projects and time slides, so there is no quick-fix 
for this problem.

We are still focused on single tasks, but there is still a binding 
element missing, which is an ungrateful job, because you will have a lot 
of work to understand other projects and to design a common interface 
with the prospect for being unable to publish one scientific paper.
!!!

> Q How do we manage our libraries? If all of us use everyone else's 
> libraries then these problems will increase. For example we'd like to 
> use JOELib but not necessarily as part of our distributed system. If the 
> performance is not time-critical then we can use web services as a means 
> of insulating the APIs and libraries. For example we might move to 
> running a CDK 2Dlayout server. This could be distributed so that 
> connections to the web wouldn't be needed. However it would necessarily 
> increase the complexity and is incompatible with, say, lightweight applets.
1. I know that, that one reason why i decided to include a lot of the 
functionality as source code dependency into JOELib, too. Especially if 
i had some relevant changes at the interface or functionality.

2. I do not really like the idea to abuse web-services as a common 
interface, thats not really helpfull to create a common interface 
between all projects, this binds only developer resources of several 
projects to implement web-services.

So again, this is a software engineering problem, we need exact 
requirement definitions for an interfaces here, or we will loose a lot 
of time to implement functionalites, also sometimes twice.
Not that i have a solution, but we have simply too much code and too 
much functionality to get here a fast solution.
And i can speak only for myself, i have absolutely no time to define 
such an interface at the moment. Maybe an interface-Wiki might help us 
for the discussion, but i am not too optimistic here.

Kind 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-devel] Libraries and Java versions

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

[Crossposted to several lists - suggest we only reply on CDK]

We are about to release JUMBO4.6 - effectively a major release - but came 
across two problems which we think need communal agreement. It affects most 
of the Java Open Source community. I suggest we reply ONLY on CDK to limit 
traffic

We develop on both Java 1.4 and 1.5 and discovered yesterday that byte code 
*compiled on 1.5* will not run on 1.4 systems (even simple programs like 
HelloWorld). It fails with an incompatible version number (actually 
requires version 49.0 (sic) of Java). Therefore if we compiled and released 
JUMBO on 1.5 machines it would fail anywhere with 1.4. [We assume that J1.4 
bytecode runs on 1.5 systems]

Q. what strategy do the various groups have for this? Do you have any idea 
of the rate of take up of J1.5?

javac 1.5 has a switch -target 1.4 which we assume generates byte code 
compatible with J1.4 systems.

Q does this work?

Q. have you used and deployed code of this sort?

Q is it a good strategy?

Q should our community (Jmol, JCP, CDK, QSAR, Octet, JOElib, JUMBO) have a 
communal view? If we all do the same thing we are limited by the slowest. I 
assume that Jmol, for example, need to retain considerable backward 
compatibility

=========================

We have also now developed a large communal library. Thus JUMBO includes 
Jmol, JCP, CDK and therefore all their libraries. (We are delighted with 
this functionality - Billy has a very nice CML document viewer based on 
this) However...
  This can mean 2 or even 3 copies of things like Xerces in the distrib. 
The size is bad enough but since Xerces is now in the JVM 1.5 and also 
seems to change its signatures with every new moon the chance of 
incompatible versions is high. There are also copies of CDK libraries in 
JCP and so on.

We also found that when we installed a recent CDK a method in CDK had 
disappeared which led to a compilation problem - we've managed to kludge 
round but this will be an ongoing problem.  Whenever there is a new (even 
minor) release of any of our libraries we all have to clean and rebuild in 
case of these problems.

Q How do we manage our libraries? If all of us use everyone else's 
libraries then these problems will increase. For example we'd like to use 
JOELib but not necessarily as part of our distributed system. If the 
performance is not time-critical then we can use web services as a means of 
insulating the APIs and libraries. For example we might move to running a 
CDK 2Dlayout server. This could be distributed so that connections to the 
web wouldn't be needed. However it would necessarily increase the 
complexity and is incompatible with, say, lightweight applets.

P.


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

[Joelib-devel] Re: [QSAR-devel] PowerMV license?

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

Hi all,

especially JOELib2 has much more features than Dragon and we are 
transparent at each calculation using the recusrive identifier calculation.
The number of features is a simple calculation: multiply 
atomProperty*transformationFeatures if you want (*bondProperty)
atomProperties=53
bondProperties=6
transformationFeatures=220;RDF(50*4 smoothing parameters),BCUT(10*2 
k-values), you can also apply a PCA before the calculation, so WHIM and 
analogue features are not a big deal.
at least: 53*220=11660

So the bottlenck is not the calculation, but the feature selection 
problem, but hey there is already the Weka interface.

Unfortunately I have no time to update the tutorial. I have two lectures 
at the ACS meeting and going afterwards to the Rauischholzhausen 
workshop (Prof. Klebe), so I have no additional time until end of March.

Being more realistic I will have no time until end of June. Sorry!

Any helping hands are welcome ...

Kind regards, Joerg

> On Wednesday 09 February 2005 06:57 pm, Peter Murray-Rust wrote:
> 
>>Are CDK and or JOELib at the stage where they can generate a reasonable
>>number of descriptors? 
> 
> 
> Yes, they are. 
> 
> 
>>They would have to do a good deal of what, say, 
>>Dragon does. 
> 
> 
> Combined they can surely match Dragon. The latter has about 1600 descriptors, 
> but many of these are basically the same, using just a different parameter 
> setting, such at weighting scheme or cutoff radius for radial distribution 
> kind of things.
> 
> 
>>And we'd need a fairly rapid starting point - do either have tutorials?
> 
> 
> For CDK, have a look at the command line executable
> cdk/src/org/openscience/cdk/applications/DescriptorCalculator.java
> 
> Output is CML2, input is MOL files. Subselection should be supported but the 
> patch of Rajarshi earlier this week.
> 
> Joerg's tutorial for JOELib is available from:
> 
> http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/JOELibPrimer.html
> 
> which has a "Descriptors" and an "Application" section.
> 
> 
>>If this is of interest we'll continue
> 
> 
> There are others too working on setting up webservices for QSAR... ask on the 
> cdk-devel or the qsar ML.
> 
> Egon
> 
> 
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
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> Qsa...@li...
> https://lists.sourceforge.net/lists/listinfo/qsar-devel
> 


-- 
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-devel] Re: [QSAR-devel] RE: Qsar-devel digest, Vol 1 #102 - 1 msg

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

Hi Oleg,

thanks a lot for the details (Matlab is magic and has such a nice Java 
connection) and Trinajstic says:

LeVerrier-Faddev-Frame Modification:
The adjacency matrix is first diagonalized (e.g. Householder-QL 
algorithm \cite[(chapter 5, ref. 81)]{tri92}) and then the recursive 
approach of LeVerrier-Faddev-Frame is applied. However, Balasubramanian 
\cite[(chapter 5, ref. 149)]{tri92} has shown that the 
LeVerrier-Fasseev-Frame method is more universal than this modification 
in its applicability to direct graphs, signed graphs, and complex graphs.

@BOOK{tri92,
   title = {{C}hemical {G}raph {T}heory},
   publisher = {CRC Press, Florida, U.S.A.},
   year = {1992},
   author = {N. Trinajsti\'{c}},
   isbn = {0--8493--4256--2},
   owner = {wegnerj},
}

Kind regards, Joerg


> Hi,
> 
> The problem of finding coeficients of the characteristic polynomial can be
> divided in two parts:
> 
> 1. calculation of eigen values - for symetric matrices one can use QR
> decomposition or other methods available which are very efficient (see
> Numerical Recipes in C by Saul A. Teukolsky, William T. (Unk) Vetterling,
> William H. Press). All these routines are implemented in BLAS (Fortran) or
> LINPACK (C) see www.netlib.org (searching on sourceforge.net could give you
> implementaions of QR in other programing languages including JAVA)
> The adjacency matrices weighted or not are symmetric so the method described
> above holds for any type of them.
> 
> 2. calculation of the coefficients of characteristic polynomial from eigen
> values. The elegant solutions is given in MATLAB the derivation of the
> coefficients from the eigen values. Below is given a fragment from MATLAB's
> help which ilustrates this:
> 
> The algorithms employed for poly and roots illustrate an interesting aspect
> of the modern approach to eigenvalue computation. poly(A) generates the
> characteristic polynomial of A, and roots(poly(A)) finds the roots of that
> polynomial, which are the eigenvalues of A. But both poly and roots use eig,
> which is based on similarity transformations. The classical approach, which
> characterizes eigenvalues as roots of the characteristic polynomial, is
> actually reversed. If A is an n-by-n matrix, poly(A) produces the
> coefficients c(1) through c(n+1), with c(1) = 1, in
> 
> The algorithm is
> z = eig(A);
> c = zeros(n+1,1); c(1) = 1;
> for j = 1:n
>     c(2:j+1) = c(2:j+1)-z(j)*c(1:j);
> end
> 
> This recursion is easily derived by expanding the product.
> 
> It is possible to prove that poly(A) produces the coefficients in the
> characteristic polynomial of a matrix within roundoff error of A. This is
> true even if the eigenvalues of A are badly conditioned. The traditional
> algorithms for obtaining the characteristic polynomial, which do not use the
> eigenvalues, do not have such satisfactory numerical properties.
> 
> Hope this helps, if you have any further questions about this problem I will
> be glad to assist you.
> 
> Oleg Ursu

-- 
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-devel] Re: [QSAR-devel] RE: Qsar-devel digest, Vol 1 #102 - 1 msg

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

Hi Oleg,

please give links and references to literature and any further ideas and 
implemtations ... not that this means i will implement all those things 
... but lets discuss them.

As far as i know there is a faster approach using eigenvalues, but i 
have read it is not as general for all kind of weighted adjacency 
matrices, so do you know if this is correct?

Kind regards, Joerg

> "The characteristic polynomial is calculated by using the Le
> Verrier-Faddeev-Frame method, which uses a framework of recursive matrix
> operations." -- this is prety computationaly demanding method I sugest using
> optimizied eigen values calculation algorithm (BLAS for symetric matrices)
> and with the resulting eigenvalues one can easy calculate coeficients of the
> characteristic polynomial.
> 
> Oleg Ursu,
> 
> 
>  
> 
> -----Original Message-----
> From: qsa...@li...
> [mailto:qsa...@li...] On Behalf Of
> qsa...@li...
> Sent: Monday, February 07, 2005 6:27 AM
> To: qsa...@li...
> Subject: Qsar-devel digest, Vol 1 #102 - 1 msg
> 
> Send Qsar-devel mailing list submissions to
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> 
> Today's Topics:
> 
>    1. New JOELib2 release: bug fix + characteristic polynomials (Joerg
> Wegner)
> 
> --__--__--
> 
> Message: 1
> Date: Sun, 6 Feb 2005 15:48:45 +0100 (MET)
> From: Joerg Wegner <we...@in...>
> To: flo...@st...,
> 	fro...@in...,
> 	joelib <joe...@li...>,
> 	joe...@li..., qsa...@li...
> Cc: chr...@un...
> Subject: [QSAR-devel] New JOELib2 release: bug fix + characteristic
> polynomials
> 
> Hi all,
> 
> minor bug fix release (atom label caching indexing for last atom in a
> molecule, for some properties only) and minor feature enhancement
> (characteristic polynomial).
> 
> After looking for a reasonable interpretation for eigenvalues of the
> adjaceny matrix i have found the analogy to the hueckel matrix.This is
> fantastic, but not really general for all weighted adjaceny matrices, with
> user defined atom and bond labels.
> 
> Nontheless there exists still a much better analytical interpretation of the
> (weighted) adjaceny matrix (with atom and bond labels) which is called the
> characteristic polynomial.
> If the polynomials (their coefficients) of two graphs are identical then
> those graphs are isospectral (spectral theory of graphs).
> 
> Using the Heilbronner theorem, we can check and interpret substructural
> fragments, at least on a linear fragment level.
> 
> Heilbronner theorem:
> P(G)=P(G-eij)-P(G-vi-vj)-2*sum(P(G-Z))
> 
> P(G) is the characteristic polynomial in its general form any edge eij
> G-eij: Graph without this edge
> G-vi-vj: Graph without edge atoms
> sum(P(G-Z)): Sum over ALL rings Z, which contains eij. Please note that this
> means really all rings and not only the SSSR ring set, so this is quite
> nice, but hard to be calculated.
> 
> The characteristic polynomial is calculated by using the Le
> Verrier-Faddeev-Frame method, which uses a framework of recursive matrix
> operations.
> 
> Kind regards, Joerg Kurt Wegner
> 
> 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)                         
> 
> 
> 
> 
> 
> --__--__--
> 
> _______________________________________________
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> Qsa...@li...
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> 
> 
> End of Qsar-devel Digest
> 
> 
> 
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-- 
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-devel] New JOELib2 release: bug fix + characteristic polynomials

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

Hi all,

minor bug fix release (atom label caching indexing for last atom in a
molecule, for some properties only) and
minor feature enhancement (characteristic polynomial).

After looking for a reasonable interpretation for eigenvalues of the
adjaceny matrix i have found the analogy to the hueckel matrix.This is
fantastic, but not really general for all weighted adjaceny matrices, with
user defined atom and bond labels.

Nontheless there exists still a much better analytical interpretation of
the (weighted) adjaceny matrix (with atom and bond labels) which is called
the characteristic polynomial.
If the polynomials (their coefficients) of two graphs are identical then
those graphs are isospectral (spectral theory of graphs).

Using the Heilbronner theorem, we can check and interpret substructural
fragments, at least on a linear fragment level.

Heilbronner theorem:
P(G)=P(G-eij)-P(G-vi-vj)-2*sum(P(G-Z))

P(G) is the characteristic polynomial in its general form
any edge eij
G-eij: Graph without this edge
G-vi-vj: Graph without edge atoms
sum(P(G-Z)): Sum over ALL rings Z, which contains eij. Please note that
this means really all rings and not only the SSSR ring set, so this is
quite nice, but hard to be calculated.

The characteristic polynomial is calculated by using the Le
Verrier-Faddeev-Frame method, which uses a framework of recursive matrix
operations.

Kind regards, Joerg Kurt Wegner

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-devel] JOELib2: New release

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

Hi all,

i've released a new JOELib2 version. This version fixes several minor 
bug fixes for the following topics:
- Wrong atom label caching, when deleting atoms
- Wrong kekulization, use protonation model
- Force aromaticity assignment before checking atom types, otherwise 
aromatic atoms Car will be only recognized as C2.
- Speed-up for loading cached properties from MDLSD import.
- Range checking for atom label cache, to ensure correctness.
- Forcing modification counter checking, to ensure correctness

https://sourceforge.net/project/showfiles.php?group_id=39708&package_id=137589&release_id=300034

Kind 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-devel] Re: Question about JOELib

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

Hi Eakasit Pacharawongsakda,

i forward this message also to the developer and help mailing list.

> 		I 'm developing a web-based chemoinformatics system for searching 2D structure. I'm using JOELib library and JME Molecular Editor. I have some question , like belows
> 		-  I use JME Molecular Editor to create SMILES and using open babel to create SMILES from MOL file , but both didn't create the same SMILES. 
> 		  for example
> 			- In my database using open babel SMILES format, we have Cc1ccc(cc1)S(=O)(=O)N(CC(=O)O)c1cc(ccc1)Cl
> 			- A SMILES query from JME Molecular Editor is Cc2ccc(S(=O)(=O)N(CC(=O)O)c1cccc(Cl)c1)cc2
SMILES is a line notation, which says nothing about the uniqueness of 
such a notation. If you want to grant this you should use a molecule 
canonisation, like the morgan algorithm (available in JOELib with 
several tie resolvers), or any newer algorithm (see JCICS or now JCIM 
Journal).

> 			Can I use any functions of JOELib library to search the SMILES query in my database? If so, please explains .
This is too unspecific. What do you want if you are interested to 
compare only the SMILES entries, you must use a unique SMILES, but this 
will depend on the canonisation algorithm you will use.

You can also try a SMARTS matching (exact matching) or any other 
similarity matching (e.g. atom pair coding, feature subset coding, 
fingerprint coding, name it ...)

> 		   Can you explain or advise me how to deal with this for searching ?
Please contact the developer mailing list for further discussions, then 
i will go into details, this will reduce redundancy. The first thing i 
need is an exact problem definition.

> 		- For the method init( ) in JOESmartsPattern class. What SMILES or SMART pattern string is expected to be a parameter of method ?  
> 		  If it is SMART pattern  string, how can I generate it from SMILES pattern using JOELib ?
SMILES is in some parts a subset of SMARTS, but i'm not sure if you can 
always simply use a SMILES-String for the SMARTS initialization.

Kind regards, Joerg Kurt Wegner

-- 
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)