joelib-help — JOELib-Help

[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-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-----
> Version: GnuPG v1.0.7 (SunOS)
> 
> iD8DBQFAWu+Nd9R8I9Yza6YRAgHxAKCIEjwjqsvbtX4vLubFfQwJmJvKmQCeNo0L
> RrVgzdM5aUMJKyO4UgqzMZI=
> =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

[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-----

[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)

Re: [Joelib-help] CML2 and (solved?) AtomTyperProblem

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

At 10:46 16/03/2004 +0100, Joerg K. Wegner wrote:
>Hi Geoff,
>
>I've used Egon's code to establish CML2 support for JOELib. (Thank's again 
>!!!). This includes full stereochemistry support, also for MDL SD were the 
>missing lines were added to the writer (see attachments)!
>pipe: original.sdf -> test.cml -> test.sdf
>
>As already discussed, this can be a step to 'reproducible' 
>conversion/descriptorCalculation results.
>
>CML (metainformations) and SDF (comment) contains now both the ID for the 
>used chemistry kernel (expert systems).
>This number is the hash code for all hard- and soft-coded expert system 
>informations.
>I've modified the JOEGlobalDataBase and all text file definitions. They 
>contain now all CVS tags:
>
>VENDOR:          http://joelib.sf.net
>RELEASE_VERSION: $Revision: 1.4 $
>RELEASE_DATE:    $Date: 2004/03/15 13:33:42 $
>
>So this is not platform independant, BUT if we can find a way to assign 
>the same vendor, version and date tag (independent standard organization 
>or just a combined standard web page for JOELib/OpenBabel!!!) we can get 
>the same hash codes !
>BTW, the hash code uses the standard hash code calculation for string in Java.

This looks very exciting - haven't worked through the details.

>So descriptors contain now also a reference to the used kernel, e.g.:
>
><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
>title="Number_of_HBD_2">0</cml:scalar>
Yes - apart from the dictRef - this is great. At present it is required to 
add integer if you wish to inform a generic processing engine that this is 
an integer. Otherwise it defaults to an xsd:string. JOElib itself knows the 
implied semantics and could omit it. The title is optional - it is for 
humans - machines simply replicate it. So if you are happy to refer to this 
by joelib:kernel:715333816 you have everything.

The string joelib:kernel:715333816 is an XML QName, so it can't have two 
colons. The prefix has no semantic value and maps to a URI. So the full 
spec could be:

<cml:cml xmlns:cml="http://www.xml-cml.org/schema/cml2/core" 
xmlns:jk="http:joelib.sf.net/joelib/kernel/dict">
<cml:scalar dataType="xsd:integer" dictRef="jk:a715333816" 
title="Number_of_HBD_2">0</cml:scalar>
</cml:cml>

Note that a QNname must have both components starting with a letter, hence: 
a715333816

>Peter, is this now correct ?
>
>I will release a new JOELib version the next hours, then i'm going home, 
>i'm sick.

Hope you get better soon.

Best wishes

P.

MORE comments below:


>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)
>
>
>
><?xml version="1.0" encoding="ISO-8859-1"?>
><!DOCTYPE molecule SYSTEM "cml.dtd" []>
><cml:molecule xmlns:cml="http://www.xml-cml.org/schema/cml2/core" 
>title="Gonan derivate with stereochemistry" id="-2114331329">

IDs must start with a letter

><cml:metadataList title="generated automatically from JOELib">
><cml:metadata name="dc:creator" content="Used JOELib chemistry kernel ID 
>is 715333816 and the used CML writer is 
>joelib.io.types.cml.MoleculeHuge(version 1.2)"></cml:metadata>
><cml:metadata name="dc:description" content="Conversion of legacy filetype 
>to CML"></cml:metadata>
><cml:metadata name="dc:identifier" content="unknown"></cml:metadata>
><cml:metadata name="dc:content"></cml:metadata>
><cml:metadata name="dc:rights" content="unknown"></cml:metadata>
><cml:metadata name="dc:type" content="chemistry"></cml:metadata>
><cml:metadata name="dc:contributor" content="see http://joelib.sf.net for 
>a full list of contributors"></cml:metadata>
><cml:metadata name="dc:date" content="16 Mar 2004 08:53:52 
>GMT"></cml:metadata>
><cml:metadata name="cmlm:structure" content="yes"></cml:metadata>

Looks great

></cml:metadataList>
><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" 
>title="joelib:kernel:715333816:softCoded:joelib.data.JOEAromaticTyper" 
>id="joelib:kernel:single:1345017519">joelib.data.JOEAromaticTyper 
>http://joelib.sf.net joelib/data/plain/aromatic.txt 1.4 
>2004-03-15_13-33-42</cml:scalar>

This is a compound data field. We are working on how dictionaries can 
support this. The fields are, I think:
classname
URI
id
datetime

XSD can support complexContent which describes and validates these. We are 
looking at how the dictionaries can support this

><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" 
>title="joelib:kernel:715333816:softCoded:joelib.data.JOEAtomTyper" 
>id="joelib:kernel:single:331687181">joelib.data.JOEAtomTyper 
>http://joelib.sf.net joelib/data/plain/atomtype.txt 1.8 
>2004-03-15_13-33-42</cml:scalar>
><cml:scalar dataType="xsd:string" dictRef="joelib:kernel" 
>title="joelib:kernel:715333816" 
>id="joelib:kernel:715333816">joelib:kernel:single:1345017519, 
>joelib:kernel:single:331687181, joelib:kernel:single:-349822152, 
>joelib:kernel:single:1305056389, joelib:kernel:single:2066602532, 
>joelib:kernel:single:1443728660, joelib:kernel:single:2056739992, 
>joelib:kernel:single:-465953241, joelib:kernel:single:-752030822, 
>joelib:kernel:single:-647783807, joelib:kernel:single:1562896312, 
>joelib:kernel:single:1380529384, joelib:kernel:single:2132350161, 
>joelib:kernel:single:-1630937171, joelib:kernel:single:862707252, 
>joelib:kernel:single:-94117937</cml:scalar>

I would make this an array and use prefixes:
><cml:array dataType="xsd:QName dictRef="joelib:kernel" 
>title="joelib:kernel:715333816" id="joelib:kernel:715333816">

jks:a1345017519 jks:331687181 ...</cml:array>

But it looks messy. Do you actually want to process these as integers? If 
so it can be redesigned

>joelib:kernel:single:1345017519, joelib:kernel:single:331687181, 
>joelib:kernel:single:-349822152, joelib:kernel:single:1305056389, 
>joelib:kernel:single:2066602532, joelib:kernel:single:1443728660, 
>joelib:kernel:single:2056739992, joelib:kernel:single:-465953241, 
>joelib:kernel:single:-752030822, joelib:kernel:single:-647783807, 
>joelib:kernel:single:1562896312, joelib:kernel:single:1380529384, 
>joelib:kernel:single:2132350161, joelib:kernel:single:-1630937171, 
>joelib:kernel:single:862707252, joelib:kernel:single:-94117937</cml:scalar>



><cml:atom id="-2114331329:a1">
><cml:string builtin="elementType">C</cml:string>
><cml:float builtin="x2">13.916500091552734</cml:float>
><cml:float builtin="y2">-7.770199775695801</cml:float>

Looks good
This is CML1 - I assume you can now use CML2

><cml:scalar units="units:electron" dataType="xsd:float" 
>dictRef="joelib:partialCharge">-0.022420638985526313</cml:scalar>

Yes. this is great. I am hoping to get some hierarchy for units so they 
don't need constant reiteration. And if space matters you can use CML2array

><cml:integer builtin="hydrogenCount">5</cml:integer>
></cml:atom>



><cml:atom id="-2114331329:a2">
><cml:string builtin="elementType">C</cml:string>
><cml:float builtin="x2">13.916500091552734</cml:float>



><cml:name convention="trivial">Gonan derivate with stereochemistry</cml:name>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="Fraction_of_rotatable_bonds">4.3478260869565216E-2</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="Geometrical_shape_coefficient">9.202824265150003</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="Molecular_weight">2.452599936723709E2</cml:scalar>



><cml:scalar dataType="xsd:string" title="RDF"><![CDATA[Gasteiger_Marsili
>50<1.5940199183282508E-16,3.5320351902369007E-12,1.0787560326377212E-8,4.562926679481138E-6,2.6872124085373483E-4,2.2069047752468125E-3,2.303245111884276E-3,-5.436356512771221E-4,-3.2478281395112424E-4,4.918651334382971E-5,1.536251324560617E-3,2.277435169742313E-3,1.300816511980075E-3,6.126140107135232E-4,-4.1824716100300705E-4,-1.368863814540861E-3,-8.208339192751625E-4,5.3376461771753E-4,1.534072562138197E-3,1.7908914501277423E-3,5.507175720486667E-6,-5.763211262243748E-4,1.4132473231521047E-4,8.686437677244833E-4,1.5090055350379477E-3,1.6546296948737362E-3,8.647678978194836E-4,2.500403657505191E-4,-8.328990776669339E-5,3.4797339389094526E-4,1.0482630671704465E-3,3.57933385516601E-4,-9.243630247315901E-5,-1.6374118268106688E-4,-6.744686206966648E-4,-7.3563670708480915E-6,1.0783852781926621E-3,1.1659437942465932E-3,5.3669116363927E-4,-1.1314694263345528E-4,-6.928623677582942E-4,-4.119554183357553E-4,2.042136965559031E-5,2.119917715225437E-4,2.94531451807724E-4,-6.505797814441567
E 
>-4,-2.9527826356305804E-4,6.187696472975766E-5,1.1298076477827559E-4,9.012712526200434E-5>]]></cml:scalar>

You could use array and xsd:float for this. CDATA isn't needed unless you 
expect < or & in your content

><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
>title="Number_of_rotatable_bonds">1</cml:scalar>
><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
>title="Number_of_HBD_2">0</cml:scalar>
><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
>title="Number_of_HBD_1">0</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="MolarRefractivity">9.199900000000002E1</cml:scalar>
><cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
>title="Number_of_aromatic_bonds">0</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="Zagreb_group_index_2">1.8E2</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="Zagreb_group_index_1">1.47E2</cml:scalar>
><cml:scalar dataType="xsd:double" dictRef="joelib:kernel:715333816" 
>title="PolarSurfaceArea">0.0</cml:scalar>

This needs structuring...

><cml:scalar dataType="xsd:string" title="Topological_atom_pair"><![CDATA[42
>1
>Atom_valence
>C
>1.0
>5.0
>C
>3.0
>2
>C
>2.0

I have deleted the rest for convenience but will be happy to help with the 
design. Much of this can be made compact and semantically rich with array 
and table.

It's somewhat inconvenient working in email - would be better to have 
attachments. This is actually an excellent thing for a Wiki

Best

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] New release with ZIP import/export available

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

Hi all,

a new JOELib release with ZIP import/export is available.

This accepts also multiple files in one ZIP file, except multiple CML 
files, because the SAX parser closes the stream after the first CML file 
. If anyone finds a workaround i would be happy if you will tell me.

So, this a really GREAT (or SMALL :-) possibility to save disk space for 
SDF descriptor files !

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-help] CML2 and (solved?) AtomTyperProblem

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

Hi Geoff,

I've used Egon's code to establish CML2 support for JOELib. (Thank's 
again !!!). This includes full stereochemistry support, also for MDL SD 
were the missing lines were added to the writer (see attachments)!
pipe: original.sdf -> test.cml -> test.sdf

As already discussed, this can be a step to 'reproducible' 
conversion/descriptorCalculation results.

CML (metainformations) and SDF (comment) contains now both the ID for 
the used chemistry kernel (expert systems).
This number is the hash code for all hard- and soft-coded expert system 
informations.
I've modified the JOEGlobalDataBase and all text file definitions. They 
contain now all CVS tags:

VENDOR:          http://joelib.sf.net
RELEASE_VERSION: $Revision: 1.4 $
RELEASE_DATE:    $Date: 2004/03/15 13:33:42 $

So this is not platform independant, BUT if we can find a way to assign 
the same vendor, version and date tag (independent standard organization 
or just a combined standard web page for JOELib/OpenBabel!!!) we can get 
the same hash codes !
BTW, the hash code uses the standard hash code calculation for string in 
Java.

So descriptors contain now also a reference to the used kernel, e.g.:

<cml:scalar dataType="xsd:integer" dictRef="joelib:kernel:715333816" 
title="Number_of_HBD_2">0</cml:scalar>

Peter, is this now correct ?

I will release a new JOELib version the next hours, then i'm going home, 
i'm sick.

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: [Jmol-developers] Re: [Joelib-help] CMLRSS and WWMM and OpenMolecules

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

> >
> > Yes. In general RSS is read-only so it would be coupled to a mailing list
> > of some sort (Henry?)
>
>I'm not that clear with the blog concept: a website of someone keeping a
>diary?, or a wiki like communal website?

Yes and yes. It's a writable website with standard HTTP tools and often 
open to all. RSS is the common way of aggregating them. I haven't looked 
recently but I expect that Slashdot would be regarded as a blog.

>Anyway, I agree that it is time to organize all chemistry open source
>initiative and come up with solutions which many projects deal with, e.g.
>atom typing and interoperability...

I think the NeSC meeting will help us a great 
deal.http://www.nesc.ac.uk/esi/events/394/


> > cdkMolecule = getCDKMolecule(cmlMolecule)
> > cdkMolecule.doSomCalculation()
> > newCmlMolecule = getCMLMolecule(cdkMolecule)
> > merge(cmlMolecule, newCMLMolecule)
> >
> > and we could do the same for JOELIB.
>
>CDK has libio to JOELib... so without the need to write anything (except the
>getJOELibMolecule() wrapper), you can already do:
>
>joelibMol = getJOELibMolecule(getCDKMolecule(cmlMolecule))
>joelibMol.doSomeCalc()
>newCMLMol = getCMLMolecule(getCDKMolecule(joelibMol))
>merge(cmlMolecule, newCMLMolecule)

Excellent. For myself it would be very useful to have these examples as 
simple standalone example programs (I have to admit I get lost looking for 
functionality in libraries, including my own!). So it's a excellent 
opportunity for volunteers to write sample programs. As an example I 
haven't used JOELib to calculate cLogp simply because I haven't had the 
time to explore it.

>BTW, Joerg, it would be very nice if you could have a CMLRSS set up that 
>takes
>all current other feeds, calculates properties and puts that only as CMLRSS
>again.

This would be fantastic. Note - at this stage I recommend that all 
aggregation should be manual. This is to avoid robots out of control which 
create denial of service, loops etc. We can move to automatic in V0.2. So 
it might work like this:

JoergW reads a list of sites.
foreach week
         foreach site
                 read new molecules (date < lastdate)
                 calculate properties
                 add to JWProperty feed
         set lastdate

At this stage I don't think Joerg should be required to merge molecules 
although you are welcome to try! This would mean the same property might be 
calculated twice. A specialist aggregator could deal with that.

I am also keen to see bitscreens being distributed. I think we could set a 
standard here


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

Re: [Jmol-developers] Re: [Joelib-help] CMLRSS and WWMM and OpenMolecules

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

On Friday 12 March 2004 11:07, Peter Murray-Rust wrote:
> At 10:39 12/03/2004 +0100, Joerg K. Wegner wrote:
> >very fine !
> >
> >>[crossposted, so please be considerate in replies]
> >
> >So, do we need a cross-platform mailing list ?:-}
>
> It could be that we need a chemical developers blog.
>
> >Can a RSS channel used for such things ?
>
> Yes. In general RSS is read-only so it would be coupled to a mailing list
> of some sort (Henry?)

I'm not that clear with the blog concept: a website of someone keeping a 
diary?, or a wiki like communal website?

Anyway, I agree that it is time to organize all chemistry open source 
initiative and come up with solutions which many projects deal with, e.g. 
atom typing and interoperability...

> >>We already have proof of concept for molecules, properties, spectra (no
> >>viewer yet) and crystallography.
> >
> >For a Java based visualization i would recommend the complex SGT:
> >http://www.epic.noaa.gov/java/sgt/
> >
> >I've already used it for the primitive visualization of the JCAMP-DX
> >format in JOELib (only developer interface for uncompressed formats !). No
> >JCAMP-CS support, which could be something for OpenBabel/JOELib.
>
> Christoph, Stefan and I are working on a CMLSpect viewer. We already have
> JCAMP2CML. We want to avoid the posting of JCAMP as it breaks the XML
> model. However it would be possible to convert CMLSpect to JCAMP
>
> >>For example the output of one feed could be input to another service such
> >>as JOELib which computes properties and descriptors. This is still under
> >>construction (V0.2)
> >
> >Great !
>
> ... mainly at the design stage:-) The main technical question is how one
> merges new properties into an old molecule. This is a middleware problem. I
> think it's most like to be relevant to servers at present. "Add your CML
> molecule and get some more properties. We already do this for MOPAC. I
> think that JOELib could easily be factored in - best if someone already had
> a running protocol. Thus if you had a clogp module already running as
> something like:
>
> JOEMol j = new JOEMOl(cmlMolecule);
> double logp = j.getLogP();
>
> then it would be easy to incorporate. I haven't had time to look at how to
> code JOELib and it is easiest if we have high-level routines at this level,
> especially cml2JOE and joe2CML. I have done this for CDK by passing XML
> strings. I know this is inefficient but ultimately we need to work at this
> API level. I therefore have just two calls:
>
> cdkMolecule = getCDKMolecule(cmlMolecule)
> cdkMolecule.doSomCalculation()
> newCmlMolecule = getCMLMolecule(cdkMolecule)
> merge(cmlMolecule, newCMLMolecule)
>
> and we could do the same for JOELIB.

CDK has libio to JOELib... so without the need to write anything (except the 
getJOELibMolecule() wrapper), you can already do:

joelibMol = getJOELibMolecule(getCDKMolecule(cmlMolecule))
joelibMol.doSomeCalc()
newCMLMol = getCMLMolecule(getCDKMolecule(joelibMol))
merge(cmlMolecule, newCMLMolecule)

BTW, Joerg, it would be very nice if you could have a CMLRSS set up that takes 
all current other feeds, calculates properties and puts that only as CMLRSS 
again.

Egon

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

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

At 10:39 12/03/2004 +0100, Joerg K. Wegner wrote:
>Hi all,
>
>very fine !
>
>>[crossposted, so please be considerate in replies]
>So, do we need a cross-platform mailing list ?:-}

It could be that we need a chemical developers blog.

>Can a RSS channel used for such things ?

Yes. In general RSS is read-only so it would be coupled to a mailing list 
of some sort (Henry?)

>>We already have proof of concept for molecules, properties, spectra (no 
>>viewer yet) and crystallography.
>For a Java based visualization i would recommend the complex SGT:
>http://www.epic.noaa.gov/java/sgt/
>
>I've already used it for the primitive visualization of the JCAMP-DX 
>format in JOELib (only developer interface for uncompressed formats !). No 
>JCAMP-CS support, which could be something for OpenBabel/JOELib.

Christoph, Stefan and I are working on a CMLSpect viewer. We already have 
JCAMP2CML. We want to avoid the posting of JCAMP as it breaks the XML 
model. However it would be possible to convert CMLSpect to JCAMP

>>For example the output of one feed could be input to another service such 
>>as JOELib which computes properties and descriptors. This is still under 
>>construction (V0.2)
>Great !

... mainly at the design stage:-) The main technical question is how one 
merges new properties into an old molecule. This is a middleware problem. I 
think it's most like to be relevant to servers at present. "Add your CML 
molecule and get some more properties. We already do this for MOPAC. I 
think that JOELib could easily be factored in - best if someone already had 
a running protocol. Thus if you had a clogp module already running as 
something like:

JOEMol j = new JOEMOl(cmlMolecule);
double logp = j.getLogP();

then it would be easy to incorporate. I haven't had time to look at how to 
code JOELib and it is easiest if we have high-level routines at this level, 
especially cml2JOE and joe2CML. I have done this for CDK by passing XML 
strings. I know this is inefficient but ultimately we need to work at this 
API level. I therefore have just two calls:

cdkMolecule = getCDKMolecule(cmlMolecule)
cdkMolecule.doSomCalculation()
newCmlMolecule = getCMLMolecule(cdkMolecule)
merge(cmlMolecule, newCMLMolecule)

and we could do the same for JOELIB.


>>the purpose of this email to invite people if they wish, to join in to 
>>this "virtual laboratory", and hence "participate" in the ACS session.
>I've not the money to join :-( But i'm going to the
>1. Chemoinformatics Conference in Sheffield, U.K., 21-23 April ...
>2. Analytica Conference Munich, Germany, 12-14 May ...
>... if anyone of you will be there i would be happy to discuss any 
>chemoinformatics topics in more detail.

YY will be presenting WWMM at Munich

P.


>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)

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

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

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

Hi all,

very fine !

> [crossposted, so please be considerate in replies]
So, do we need a cross-platform mailing list ?:-}
Can a RSS channel used for such things ?

> We already have proof of concept for molecules, properties, spectra (no 
> viewer yet) and crystallography.
For a Java based visualization i would recommend the complex SGT:
http://www.epic.noaa.gov/java/sgt/

I've already used it for the primitive visualization of the JCAMP-DX 
format in JOELib (only developer interface for uncompressed formats !). 
No JCAMP-CS support, which could be something for OpenBabel/JOELib.

> For example the output of one feed 
> could be input to another service such as JOELib which computes 
> properties and descriptors. This is still under construction (V0.2)
Great !

> the purpose of this email to invite people if they wish, to join in to 
> this "virtual laboratory", and hence "participate" in the ACS session.
I've not the money to join :-( But i'm going to the
1. Chemoinformatics Conference in Sheffield, U.K., 21-23 April ...
2. Analytica Conference Munich, Germany, 12-14 May ...
... if anyone of you will be there i would be happy to discuss any 
chemoinformatics topics in more detail.

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] CMLRSS and WWMM and OpenMolecules

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

[crossposted, so please be considerate in replies]

Greetings to the OpenSource chemistry community,

We have recently developed a method for publishing molecules on an RSS 
feed, CMLRSS and hope this may be of interest.  CMLRSS consists of a 
standard RSS news feed with CML embedded in those items which contain 
chemistry. When viewed with a CML-aware client such as Jmol or JChempaint 
with the rssviewer plugin the molecule appears in appropriate form (2D or 
3D). This is a simple method to provide an Open feed of molecules of all 
types. Details are at http://wwmm.ch.cam.ac.uk/moin/CmlRss

We would first like to thank the OpenSource chemistry community for 
contributing much to this. The viewers (Jmol/JChempaint) are in Java, and 
many of the molecules have been converted using OpenBabel and/or CDK. The 
WorldWideMolecularMatrix and CMLRSS are being presented at the ACS meeting 
in Anaheim http://oasys2.confex.com/acs/227nm/techprogram/P725453.HTM. We 
append details below.

We invite members of the OpenSource chemistry community and others to 
contribute feeds of Open molecules. Tools to create feeds are available on 
our site and we intend to add CMLRSS output to CDK, OpenBabel, etc. (If you 
can write CML then it's easy to add the <item> information for CMLRSS). If 
you have molecules, with or without ancillary information, you wish to make 
available see http://wwmm.ch.cam.ac.uk/moin/CmlRss.
We already have proof of concept for molecules, properties, spectra (no 
viewer yet) and crystallography. The feeds do not have to be large - but 
the entries should be interesting or useful in some way. Note that 2D, 3D, 
5D (2D+3D) and 8D (2D, 3D +fractional) coordinate systems are all allowable.

The system is designed to allow aggregation of molecules (e.g. in a Xindice 
database) and to be re-used. For example the output of one feed could be 
input to another service such as JOELib which computes properties and 
descriptors. This is still under construction (V0.2)

PeterMR

Announcement
===========

As part of a session on "Research Collaboratories, Virtual laboratories and 
Grid Computing" at the
forthcoming ACS meeting (http://oasys2.confex.com/acs/227nm/techprogram/ )
we are presenting on "Semantic Grid computing - the WorldWideMolecularMatrix"
Part of this will focus on the theme of RSS which I posted about last year. We
have now developed a chemical component to this, now christened CMLRSS, and 
it is
the purpose of this email to invite people if they wish, to join in to this 
"virtual laboratory",
and hence "participate" in the ACS session.
The procedure is as follows
a) For an introduction to the concept, see eg 
http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/
or http://wwmm.ch.cam.ac.uk/moin/CmlRss
b)We have prepared a distribution kit available either from 
http://www.ch.ic.ac.uk/rzepa/cmlrss_distrib/
or from http://wwmm.ch.cam.ac.uk/moin/RssClient We emphasize that whilst we 
believe this to
function correctly, it has not yet been comprehensively tested on all 
platforms, and some
components are still at the "late alpha", or "early beta" stage. Needless 
to say, we welcome
comments and reports of bugs!
c) You can view the existing CMLRSS grid by installing either Jmol (a 3D 
molecule viewer)
or JChempaint (a 2D editor) as provided, along with the CMLRSS plugin in 
the kit
(these are Java programs so you will have to have Java installed). By
running this, you will open around 8 existing RSS "Channels" and hence 
subscribe to chemical
feeds from these sites. You can if you wish aggregate these feeds into one, 
then filter them
down by (e.g. element). You will notice several themes in the existing 
channels,
including an aggregation of the long running "Molecules of the Month" 
sites, several
database sites (NMR, X-Ray, ChemStock) and the World-Wide Molecular Matrix.
d) You are also welcome to follow the instructions in the above 
distribution to
create your own CMLRSS channel (I might add that several of the sites 
mentioned above
were our beta testers for this kit; it took only one or two days to get up 
and running).
If you do so, please let us know so that we can add you to the list (one of 
the many
"todo" items is to organise the addition of further channels in a better way).
I should end with the observation that as far as we know, this is the 
furthest that the
RSS concept has been pushed into a science field, and another step towards the
"semantic web" espoused by Sir Tim Berners-Lee. We would of course love to 
hear
about your experiences with this system.
-- 
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 
2AZ, UK.


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

[Joelib-help] JOELib under Mac OS

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

Hi all,

 >I did look at JOELib a while back, do you know if anyone has installed 
 >it under MacOSX, if so do I need to install ANT first?
has anyone tried ?

Ant is optional, but from the developer standpoint of view highly 
recommended, you can simply use the huge amount of shell scripts if 
these work under MacOSX ?

If not you are forced to write your own command line scripts, which 
forces you to add all required libraries under joelib/lib and 
joelib/build (if source code version) to your Java CLASSPATH.

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-help] Force-Field and/or MD simulations using web services

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

Hi all,

just for informations purpose !

Re: [Joelib-help] how to read smiles from db instead of file for descriptor calculation?

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

Hi,

i recommend to enhance:
joelib.util.database.AbstractDatabase
or
(joelib.util.database.SimpleJOELibDatabase)
(copy required methods to your class)
especially to avoid different maintenance problems and inconsistencies, 
if i change something in SimpleJOELibDatabase. This is only a simple 
implementation to check also for duplicates compounds by using a hash 
code based on molecules.

===
Database connection:
The connection is established by using wsi.ra.database.DatabaseConnection

Required properties must be defined in src/joelib.properties or you 
should add an instance method to set these properties by hand.

wsi.ra.database.DatabaseConnection.location=jdbc:mysql://localhost/test
wsi.ra.database.DatabaseConnection.password=
wsi.ra.database.DatabaseConnection.username=
wsi.ra.database.DatabaseConnection.driver=org.gjt.mm.mysql.Driver

===
You should implement in your sources:

An access method, e.g. using:

The AbstractDatabase supports contains a method
ResultSet selectBy(String tableName, String select, String by, 
String value)

ResultSet rs=null;
String smiles;
try {
   rs=myDBConnection.selectBy("test","SMILES","ID","myIDnumber");
   //rs.next(); // depends on your JDBC driver !
   smiles = rs.getString("SMILES");
   rs.close();
catch (SQLException e) {
   // TODO: catch errors
   e.printStackTrace();
}
\\TODO: handle SMILES result


Please have a look at all classes/sources in
joelib.util.database
wsi.ra.database
so you can eventually avoid rewritting functionality, but i recommend to 
  use your own DB access class with or without using already available 
code used by inheritance or simple copy/paste mechanisms !

All required methods are there already available, and it's not too much 
code to go through.

Regards, Joerg

> Regarding: Reading SMILES from Database;
> 
> a) What is the method or procedure to read smiles with title
> (SMILES|TITLES) from DB (e.g., default:  jdbc:mysql://localhost/test)
> compute descriptors (selected options) and write to another table in the
> database (default: test)?
> 
> if the DB table format (input)
> 
> ID | SMILES | MOLWT | MOLFORMULA
> 
> Result options: (output table to db)
> 
> ID | SMILES | SELECTED DESC1 | SELECTED DESCRIPTOR 2|
> 
> regards
> 
> 
> 
> --
> M. Karthikeyan, Ph.D., Scientist
>  _|      _|    _|_|_|  _|
>  _|_|    _|  _|        _|
>  _|  _|  _|  _|        _|
>  _|    _|_|  _|        _|
>  _|      _| o  _|_|_|o _|_|_|_|
>  National    Chemical  Laboratory
>  Pune - 411 008, INDIA
>  Ph: +91-(0)20-5893 457  FAX: 5893 973
>  http://www.ncl-india.org/
> 
> 
> 
> 
> -------------------------------------------------------
> SF.Net is sponsored by: Speed Start Your Linux Apps Now.
> Build and deploy apps & Web services for Linux with
> a free DVD software kit from IBM. Click Now!
> http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 


-- 
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

[Joelib-help] Re: [Joelib-devel] MolConnZ, import and batch files under windows

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

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

On Thursday 19 February 2004 12:17, Joerg K. Wegner wrote:
> sorry EGON ! I was focused on the technical question.
> Would be great !!! I've also some time ago also used the commercial
> Marvin as interface for testing purpose, but never really needed this
> functionality, because i used other tools.
>
> If you have an actual JMol package, which uses the JOELib import/export
> from GUI i will be glad to add this as optional package to the file
> downloads, additional to Ghemical, Weka and the Software design libraries.
> http://sourceforge.net/project/showfiles.php?group_id=3D39708

(Jmol with a lower case m... :)

What I would love to see, is a JOELib plugin for Jmol... I'm not sure what =
the=20
main funtion of JOELib is (descriptor calculation, I guess...), but it is=20
relatively easy to put that into a Jmol plugin... but, second uncertainty..=
=2E=20
I'm not sure what the best way would be to interact with JOELib...=20

In other words, what would be most interesting for Jmol to depict?

Anyway, I'm seeing a plugin that would calculate the JOELib descriptors for=
=20
the shown structure... more ideas? Have a look at=20
http://cdk.sf.net/plugins.html to see what the plugins are about...

> If such things are already available i can add a short description to
> the XML DocBook tutorial or you can add it and your name as author ...
> as you like. In fact im using SGML not XML, ...
>
> But this does not change my time priorities, so i would be really happy
> to add any interfaces, but i'm not able to maintain they actively,
> because my actual focus lies on our interal JCompChem cheminformatics
> library with data mining and maximum common substructure search
> algoritms.=20

Sure. I have your two recent articles on my desk, but have not found time y=
et=20
to read them...

BTW, CDK already provides MCSS code... why not use that? It has the best=20
algorithm available at this moment... unless you're interesting in finding =
a=20
better one...

> These things are really alpha, because the packages are
> refactored yet, because we have found some blind alleys, which restricts
> further algorithm development, so ... in progress. Eventually these
> things will be publicly available in the future, too ... as part of
> JOELib ... and after (hopefully) publishing some nice combinations ...
>
> Regards, Joerg
>
> P.S.: This reminds me to update the CDK installation instruction ... and
> add some more instructions to the tutorial ... my actual deprecated CDK
> version has some problems in 2D layout ...

Yes, please do keep up... where gaining momentum every month...=20

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)

iD8DBQFANJ3zd9R8I9Yza6YRAqljAJwLuwh44ehn/Ew6PWNMYU3m7IPXawCaAyDY
xNHnzDaLo7nWwVYbcDoqi1Y=3D
=3D/HaH
=2D----END PGP SIGNATURE-----

[Joelib-help] Re: [Joelib-devel] MolConnZ, import and batch files under windows

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

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

On Thursday 19 February 2004 10:12, Joerg K. Wegner wrote:
> > 1) thank you for your immediate response. I can wait till I can see the
> > atom symbols in 3D (i feel it is very much required for chemist to
> > understand the molecule in 3D view)
> > I will try the 2D technique suggested by you.
>
> I agree, but it the priority is still very low for me :-)

Hi karthikeyan,

Jmol (jmol.sf.net) is an excellent 3D viewer which can label atoms by eleme=
nt=20
and by number ... it's not based on Java3D and has excellent performance. I=
t=20
shares at least the CML formats with JOELib, so it should interoperate=20
without much trouble....

Joerg, have you considered distributing Jmol with JOELib? It's not based on=
=20
Java3D (a plus or minus, does not really matter), but is still actively=20
developed...

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)

iD8DBQFANIfsd9R8I9Yza6YRAraNAJ9xOo/cuB4vQOTiBj3h+Zp0Ydd8bgCguaEG
aVqzT18LxiE2FWxRQ/E136M=3D
=3D21oG
=2D----END PGP SIGNATURE-----

[Joelib-help] how to read smiles from db instead of file for descriptor calculation?

[karthikeyan <ka...@em...>]

Regarding: Reading SMILES from Database;

a) What is the method or procedure to read smiles with title
(SMILES|TITLES) from DB (e.g., default:  jdbc:mysql://localhost/test)
compute descriptors (selected options) and write to another table in the
database (default: test)?

if the DB table format (input)

ID | SMILES | MOLWT | MOLFORMULA

Result options: (output table to db)

ID | SMILES | SELECTED DESC1 | SELECTED DESCRIPTOR 2|

regards



--
M. Karthikeyan, Ph.D., Scientist
 _|      _|    _|_|_|  _|
 _|_|    _|  _|        _|
 _|  _|  _|  _|        _|
 _|    _|_|  _|        _|
 _|      _| o  _|_|_|o _|_|_|_|
 National    Chemical  Laboratory
 Pune - 411 008, INDIA
 Ph: +91-(0)20-5893 457  FAX: 5893 973
 http://www.ncl-india.org/

[Joelib-help] Zoom in 3D view with 2 button mouse

[karthikeyan <ka...@em...>]

I just want to add comment :  for viewing in 3D mode

Since two button mouse is most common,
Hold alt- key and 'click Left-button and drag' forward /backward
should Zoom (+ / -) dynamically.

regards


--
M. Karthikeyan, Ph.D., Scientist
 _|      _|    _|_|_|  _|
 _|_|    _|  _|        _|
 _|  _|  _|  _|        _|
 _|    _|_|  _|        _|
 _|      _| o  _|_|_|o _|_|_|_|
 National    Chemical  Laboratory
 Pune - 411 008, INDIA
 Ph: +91-(0)20-5893 457  FAX: 5893 973
 http://www.ncl-india.org/

[Joelib-help] Re: weka : protected vs public

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

Hi,

i'm not a 'Dr.' but i'm working on that :-)

if you like you can subscribe to the help mailing list, because i'm 
sending the aswers to this list also, to avoid answer redundancy !
http://lists.sourceforge.net/lists/listinfo/joelib-help

> I recompiled with ant, and followed your suggestion
> to create pdf.
> Excellent, PDF created with structures (along with
> atom lables). all the atoms (default c) are highlighted
> with 'square',
> a) How to keep the 'square' off from atoms?
> May be I am demanding too much?
Who cares, much more interesting is, who will implement things :-)
I've added an option to joelib.properties (next release or CVS in the 
next days):
joelib.gui.render.Renderer2DModel.drawCarbonAtoms=false
You can also use:
joelib.gui.render.Renderer2DModel.useKekuleStructure=true
which forces atom labels:

> b) How to suppress the [warning] and [info] messages?
change joelib/src/log4j.properties then recompile.
Switch 'INFO' and 'WARN' to 'ERROR' for the classes you want to suppress 
info's. For debugging you can switch to 'DEBUG', e.g. in JOEMol and you 
will get a HUGE amount of debugging messages.

> c) With smiles I could not see the structures in PDF files
> (obvious: no atom co-ordinates in smiles)
correct, you will need a layout algorithm, e.g.
- CDK, Marvin (commercial) for 2D layout
- Ghemical (force-field), Corina (expert system with torsion angles, 
commercial) for 3D layout. For Corina i've written a external JOELib 
task (or plugin) which a can publish if you want to explicitely use that 
one.

> d) how to create 'csv' files of descriptors for the molecules
> in smiles/sdf format?
Tricky and why ?
If you convert SDF->SDF JOELib will add all descriptors.
This will not work so easily for the SMILES and FLAT format.
Why ?
We need to define the output format !!!
Two solutions and SMILES (only for SMILES output) and TITLE are 
predefined key words:
1. joelib.properties:
joelib.io.types.Smiles.lineStructure=SMILES|TITLE|DESC1|DESC3
joelib.io.types.Flat.lineStructure=TITLE|DESC_WHAT_YOU_LIKE|ONE_MORE

It is clear that you can should not use atom properties, matrices and 
arrays in these formats, which can be handled by SDF, CTX and CML.

2. sh convertSkip.sh command line (more usefull for batch mode). Do not 
forget to quote these entries !!!
[+f<lineStructure>]
[+ff<lineStructureFile>]
[+s<lineStructure>]

e.g.: '+fTITLE|DESC_WHAT_YOU_LIKE|ONE_MORE'
For the flat file you can also define a file, e.g.
myDescs1.flat.txt
TITLE
DESC_WHAT_YOU_LIKE
ONE_MORE

and use
+ffmyDescs1.flat.txt


> Finally regarding weka:
> how to compile entire code?
You can dowload the Weka4JOELib weka.jar binary distribution directly from:
http://sourceforge.net/project/showfiles.php?group_id=39708&package_id=92211
If you want to use the source code you are on your own, please contact 
the Weka mailing list or read their manual or add the source to 
joelib/src and use compile (do not forget to copy the required 
properties file)
http://www.cs.waikato.ac.nz/ml/weka/

With friendly regards, Joerg

> 
> --
> M. Karthikeyan, Ph.D., Scientist
>  _|      _|    _|_|_|  _|
>  _|_|    _|  _|        _|
>  _|  _|  _|  _|        _|
>  _|    _|_|  _|        _|
>  _|      _| o  _|_|_|o _|_|_|_|
>  National    Chemical  Laboratory
>  Pune - 411 008, INDIA
>  Ph: +91-(0)20-5893 457  FAX: 5893 973
>  http://www.ncl-india.org/
> 
> 
> 


-- 
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

[Joelib-help] Re: [Joelib-devel] MolConnZ, import and batch files under windows

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

Hi Egon,

first: if the e-mail of C. Steinbeck is not correct, please feel free to 
forward this message. Eventually he could be interested in such things 
also. I've read his actual JCICS-CASE paper.

> (Jmol with a lower case m... :)
Jmol :-)

> In other words, what would be most interesting for Jmol to depict?
Import&Export and descriptors, as you surely know i use the OELib 
kernel, also OpenBebl kernel, so we can easily add all supported types 
of them, if anyone can find to port the C++ to Java, which is VERY easy 
... but costs still time ... the important point are the atom types, and 
these are available.

> Anyway, I'm seeing a plugin that would calculate the JOELib descriptors for 
> the shown structure... more ideas? Have a look at 
> http://cdk.sf.net/plugins.html to see what the plugins are about...
I'll have a short look ... and again ...

>>But this does not change my time priorities, so i would be really happy
>>to add any interfaces, but i'm not able to maintain they actively,
>>because my actual focus lies on our interal JCompChem cheminformatics
>>library with data mining and maximum common substructure search
>>algoritms.
> Sure. I have your two recent articles on my desk, but have not found time yet 
> to read them...
Machine learning and algorithm stuff ...

> BTW, CDK already provides MCSS code... why not use that? It has the best 
> algorithm available at this moment... unless you're interesting in finding a 
> better one...
I'm not interested in finding a better one ... i'm interested in using 
them with a general defined approach, so that we can adapt the algorithm 
to our cheminformatics requirements.
The CDK implementation uses, if i'm understanding this correctly the 
association graph method, so i use the same association matrix method 
with a generalized atomType assignment, which contains also the ESTATE 
or my improved CESTATE one ... which works already great using some 
Hashing ...
The association graph is not the problem, but the missing atom types and 
atom properties (descriptors) in CDK.
The relevant clique detection algorithm in my implementation is just an 
interface and can be replaced by any other implementation ... depends on 
your needs, because fast implementations uses, of course, heuristic 
approaches !
BTW, the original reference for this kind of MCS was 1976 !

The performance depends on the used Clique detection algorithm, 
references can be also found in my papers, because i use already two 
implementations, ...there exists a lot of them ... but i do not believe 
that it is possible to improve the performance easily, because there was 
a lot of work already done by graph experts.

We are working on a multiple interpretation and reimplementing three 
other literature approaches, to be able for multiple MCS which is much 
more interesting if you are interested in finding a pharmacophore based 
description based on ligands ... so this is in progress ... or if you 
like some CASE relevant analysing stuff ... at the moment we have 
reached the pre-alpha, so we are testing, testing and testing ... to 
find suitable combinations and parameters ...

Regards, Joerg


> 
> 
>>These things are really alpha, because the packages are
>>refactored yet, because we have found some blind alleys, which restricts
>>further algorithm development, so ... in progress. Eventually these
>>things will be publicly available in the future, too ... as part of
>>JOELib ... and after (hopefully) publishing some nice combinations ...
>>
>>Regards, Joerg
>>
>>P.S.: This reminds me to update the CDK installation instruction ... and
>>add some more instructions to the tutorial ... my actual deprecated CDK
>>version has some problems in 2D layout ...
> 
> 
> Yes, please do keep up... where gaining momentum every month... 
> 
> 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-----
> Version: GnuPG v1.0.7 (SunOS)
> 
> iD8DBQFANJ3zd9R8I9Yza6YRAqljAJwLuwh44ehn/Ew6PWNMYU3m7IPXawCaAyDY
> xNHnzDaLo7nWwVYbcDoqi1Y=
> =/HaH
> -----END PGP SIGNATURE-----
> 
> 


-- 
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

[Joelib-help] Re: [Joelib-devel] MolConnZ, import and batch files under windows

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

Hi,

sorry EGON ! I was focused on the technical question.
Would be great !!! I've also some time ago also used the commercial 
Marvin as interface for testing purpose, but never really needed this 
functionality, because i used other tools.

If you have an actual JMol package, which uses the JOELib import/export 
from GUI i will be glad to add this as optional package to the file 
downloads, additional to Ghemical, Weka and the Software design libraries.
http://sourceforge.net/project/showfiles.php?group_id=39708

If such things are already available i can add a short description to 
the XML DocBook tutorial or you can add it and your name as author ... 
as you like. In fact im using SGML not XML, ...

But this does not change my time priorities, so i would be really happy 
to add any interfaces, but i'm not able to maintain they actively, 
because my actual focus lies on our interal JCompChem cheminformatics 
library with data mining and maximum common substructure search 
algoritms. These things are really alpha, because the packages are 
refactored yet, because we have found some blind alleys, which restricts 
further algorithm development, so ... in progress. Eventually these 
things will be publicly available in the future, too ... as part of 
JOELib ... and after (hopefully) publishing some nice combinations ...

Regards, Joerg

P.S.: This reminds me to update the CDK installation instruction ... and 
add some more instructions to the tutorial ... my actual deprecated CDK 
version has some problems in 2D layout ...




E.L. Willighagen wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On Thursday 19 February 2004 10:12, Joerg K. Wegner wrote:
> 
>>>1) thank you for your immediate response. I can wait till I can see the
>>>atom symbols in 3D (i feel it is very much required for chemist to
>>>understand the molecule in 3D view)
>>>I will try the 2D technique suggested by you.
>>
>>I agree, but it the priority is still very low for me :-)
> 
> 
> Hi karthikeyan,
> 
> Jmol (jmol.sf.net) is an excellent 3D viewer which can label atoms by element 
> and by number ... it's not based on Java3D and has excellent performance. It 
> shares at least the CML formats with JOELib, so it should interoperate 
> without much trouble....
> 
> Joerg, have you considered distributing Jmol with JOELib? It's not based on 
> Java3D (a plus or minus, does not really matter), but is still actively 
> developed...
> 
> 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-----
> Version: GnuPG v1.0.7 (SunOS)
> 
> iD8DBQFANIfsd9R8I9Yza6YRAraNAJ9xOo/cuB4vQOTiBj3h+Zp0Ydd8bgCguaEG
> aVqzT18LxiE2FWxRQ/E136M=
> =21oG
> -----END PGP SIGNATURE-----
> 
> 


-- 
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

[Joelib-help] MolConnZ, import and batch files under windows

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

Hi karthikeyan,

> 1) thank you for your immediate response. I can wait till I can see the
> atom symbols in 3D (i feel it is very much required for chemist to understand the
> molecule in 3D view)
> I will try the 2D technique suggested by you.
I agree, but it the priority is still very low for me :-)

> 2) Second query:  (pl.)
> I have problem in reading Molconnz (.s) file in Joelib. I get an error:
> Molecule entry (#1) skipped: .. io.MoleculeIOexception: Line 14(1)
> should contain 7
> descriptor not 11: 2.828427 2.00000 1.4142 1.000 0.0000 etc.,
> I am using the molconnz output directly
This depends on your MolConnZ version ! The supported format is defined in
joelib\src\joelib\data\plain\molconnz350.txt
and the first lines should contain:
id nvx nrings ncirc nelem fw aname
...

so if you are using any other version you must supply your file 
definition, e.g. molconnz400.txt and define these descriptors in
joelib\src\joelib\data\plain\knownResults.txt
where you must define if your descriptors are double, integer, boolean, 
or whatever.

If you do not define these things JOELib can still of course load the 
entries and select them, but always as string !
So if you plan to normalize your data or filters, or something else i 
recommend the definition in knownResults.txt.

> or should I convert into some format before submitting to joelib?
Is possible also, e.g. SDF which is my preffered format, but still not 
the best one, because you must still define the descriptors in 
knownResults.txt.
The CML in JOELib is the most verbose format, because the descriptors 
obtains already a format (after defined in knownResults.txt )! Then they 
can be loaded without any definitions !
Furthermore the CML reader/writer is consistent in JOELib, but 
eventually not up-to-date with the Murray-Rust CML2 implementation in 
his Java library and OpenBabel, because he develops a huge amount of 
code i'm not able to follow so fast. And i'm not sure about their 
descriptor abilities, because OpenBabel has no descriptor storing 
facility. Please correct me anybody if this is not true.
The conversion of XML files should be not to difficult, so ...

> The final objective is: to read all molconnz descriptor and 'optionally'
> write in a clean format (col/row)
> 
> mol1 d1 d2 d3 d4..
> mol2 d1 d2 d3 d4..
SMILES/Flat file format is supported also in
sh convertSkip.sh
where the flat file format should be defined in a separate file
format.txt with
mol1-ID
d1
d2
d3
d4

or in joelib.properties for the SMILES, but i think i've added a command 
line switch also!!!

> 3) finally... regarding compiling using ant, the output is directed to
> build directory
> and how to run from main *.bat files if the output is in build
> directory?
> as a shortcut I copied all the *.bat files to build directory.. and it
> is working ok
As already discussed i do not like the bat-files and they are not really 
supported and up-to-date.
If possible in any way, i recommend cygwin !!! A unix shell for windows, 
so you can use the shell scripts !!!
Of course the bat files will work if all required libraries are added to 
the classpath (classes in build-directory and all lib/*jar files), but 
that's a boring work and changes often ...
The shell scripts or ant will resolve the dependencies automatically !

Regards, Joerg

> 
> regards
> 
> 
> 
> --
> M. Karthikeyan, Ph.D., Scientist
>  _|      _|    _|_|_|  _|
>  _|_|    _|  _|        _|
>  _|  _|  _|  _|        _|
>  _|    _|_|  _|        _|
>  _|      _| o  _|_|_|o _|_|_|_|
>  National    Chemical  Laboratory
>  Pune - 411 008, INDIA
>  Ph: +91-(0)20-5893 457  FAX: 5893 973
>  http://www.ncl-india.org/
> 
> 
> 


-- 
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

[Joelib-help] Atom symbols in JOELib visualization ?

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

Dear Dr. Karthikeyan,

> Is there any provision to see atom symbols in molecule viewer especially
I assume that you are using the 3D viewer.

1. You can see atom symbols in the 2D viewer (not directly accessible 
from a testing method), but you can e.g. simply use the PDF output, 
which uses the 2D viewer funcionality:
sh convert.sh test.sdf test.pdf

There is a huge amount of properties for this visualization in the 
joelib.properties-file available:
joelib.gui.render.Renderer2DModel.*
joelib.gui.render.Mol2Image.*
joelib.io.types.PDF.*

The most relevant will be:
joelib.gui.render.Renderer2DModel.drawNumbers=false
joelib.gui.render.Renderer2DModel.useKekuleStructure=false
joelib.gui.render.Renderer2DModel.showEndCarbons=true
joelib.gui.render.Renderer2DModel.atomColoring=false

joelib.gui.render.Mol2Image.defaultWidth=500
joelib.gui.render.Mol2Image.defaultHeight=400

!!! First additional remark !!! The PDF output MUST store all molecules 
in the memory, so it can be used only for a small number of molecules, 
especially if they have a huge amount of descriptors, because they are 
printed to PDF also.
!!! Second additional remark !!! There is no 2D layout algorithm 
directly available but the CDK interface supports such things, but this 
is not available directly, because this is an optional functionality.

2. In the Java3D viewer are until now no atom symbols available.

Kind regards, Joerg

> 
> in the 'wire' mode?
> 
> regards
> 
> --
> M. Karthikeyan, Ph.D., Scientist
>  _|      _|    _|_|_|  _|
>  _|_|    _|  _|        _|
>  _|  _|  _|  _|        _|
>  _|    _|_|  _|        _|
>  _|      _| o  _|_|_|o _|_|_|_|
>  National    Chemical  Laboratory
>  Pune - 411 008, INDIA
>  Ph: +91-(0)20-5893 457  FAX: 5893 973
>  http://www.ncl-india.org/
> 
> 
> 


-- 
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

[Joelib-help] QSAR-JOELib paper are now online available

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

Hi all,

if you are interested in QSAR, here we go. All mentioned descriptor 
calculation methods are part of the actual JOELib distribution. So 
decide on your own if you like them.

Part I - Data preparation and feature selection:
http://dx.doi.org/10.1021/ci0342324

Part II - Human Intestinal Absorption:
http://dx.doi.org/10.1021/ci034233w

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