Thierry, only just saw your question. Will look at this ASAP.
--
Wishlist: include the scomp command line util
https://bugs.launchpad.net/bugs/342349
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Please find the scomp.debdiff attached.
** Attachment added: Result of: debdiff xmlbeans_2.4.0-0ubuntu2.dsc
xmlbeans_2.4.0-0ubuntu3~ppa1.dsc scomp.debdiff
http://launchpadlibrarian.net/33293610/scomp.debdiff
--
Wishlist: include the scomp command line util
Thierry, only just saw your question. Will look at this ASAP.
--
Wishlist: include the scomp command line util
https://bugs.launchpad.net/bugs/342349
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Please find the scomp.debdiff attached.
** Attachment added: Result of: debdiff xmlbeans_2.4.0-0ubuntu2.dsc
xmlbeans_2.4.0-0ubuntu3~ppa1.dsc scomp.debdiff
http://launchpadlibrarian.net/33293610/scomp.debdiff
--
Wishlist: include the scomp command line util
Available as Debian package: http://packages.debian.org/sid/ant-contrib
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ant-contrib is not packaged
https://bugs.launchpad.net/bugs/273107
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On Thu, Oct 8, 2009 at 9:36 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Mon, Oct 5, 2009 at 11:27 AM, Alan Williams ala...@cs.man.ac.uk wrote:
At the moment Taverna is still using Java 1.5 because of lack of support
for Java 1.6 on 32bit Macs. I was wondering what people's
Hi Remy,
On Wed, Oct 7, 2009 at 1:23 PM, remy d1 remy...@gmail.com wrote:
I try to make substructure search with jchempaint applet and a MySQL
database. I use MyChem ( http://mychem.sourceforge.net ) to generate
SMILES in my database.
Good. This is very useful functionality, and we have been
On Wed, Oct 7, 2009 at 1:53 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
On Wed, Oct 7, 2009 at 7:36 AM, Egon Willighagen
Apart from the rendering issues, why make a QueryAtomContainer by hand? The
SMARTSQueryTool will accept a SMILES as the query pattern
Sure, but SMILES cannot express
Dear Mannie,
On Tue, Oct 6, 2009 at 4:57 PM, Mannie Tagarira
mannie.t...@googlemail.com wrote:
A new plugin is now available for Taverna 2.1 beta 2 to integrate it
with myExperiment (visit http://www.myexperiment.org). This work
builds on the Taverna 1.7 plugin, and provides similar
Hi all,
I just got this message, and I am pretty sure the CDK does this wrong
too... the original problem was that InChI generation failed, because
a SDF was read wrongly...
So, I was wondering how many CDK users are relying on MDL molfile bond
order 4 = aromatic?
Some time ago, the CDK
Hi all,
unless you have not read any news in the last two days, you will have
seen that Google is rolling out a second batch of Google Wave
accounts... I have one invite for someone who wants to co-develop the
CDKitty robot, which adds CDK-based functionality to Google Wave...
The code is at:
Hi all,
experimenting a bit... got a headache, so difficult to focus on
something serious.
Ran into this idea/voting forum thingy, and wondering what it can mean
to the CDK. We already have a Feature Request tracker, but that is
mostly used for rather well defined ideas... and not wild ideas.
Hi Pedro,
On Thu, Sep 10, 2009 at 11:00 PM, Pedro Melo m...@simplicidade.org wrote:
Example 5 of XEP-0244 introduces a xs: namespace prefix without a proper
declaration. Are the authors assuming that the declaration is going to be in
the stream top level header? What happens when this stanza
On Mon, Sep 7, 2009 at 12:54 PM, Syed Asad Rahmana...@ebi.ac.uk wrote:
I am unable to compile SMARTSParser.jjt
The get the following error
javacc-5.0/bin/javacc SMARTSParser.jjt
It seems the syntax has changed...the JavaCC the CDK is using is still
from 2003...
Please file a bug report
Hi Anja!
On Sun, Sep 6, 2009 at 12:05 AM, Anja Jentzscha...@anjeve.de wrote:
the Linking Open Drug Data Task Force just won the first prize of the
Linking Open Data Triplification Challenge [1] which took place at the
I-Semantics in Graz. The paper we submitted can be found online [2] as well
Hi Duncan,
On Mon, Sep 7, 2009 at 1:22 PM, Duncan Hullduncan.h...@cs.man.ac.uk wrote:
The XML summer school which returns this year at St. Edmund Hall,
Oxford from 20th-25th September 2009. As always, it's packed with
high quality technical XML training for every level of expertise,
from the
Hi Guillaume,
please use the cdk-jchempaint or cdk-user mailing list next time.
On Mon, Aug 31, 2009 at 3:24 PM, Guillaume Durieugdur...@... wrote:
I have trouble with a peculiar molecule that I cannot render well using
CDK (tried all versions...)
For instance, the smile C(=O)c1cnn2c12
Dear Wasaq,
On Sun, Sep 6, 2009 at 8:28 PM, Waqas Hussainwaqa...@gmail.com wrote:
Some problems with the XEP:
1. The XEP basically allows a service to expose a set of global functions.
There is no possibility for function namespaces. This is similar to the SOAP
over XMPP XEP, where you can
On Fri, Sep 4, 2009 at 3:23 PM, Jonathan Gutowgu...@uwosh.edu wrote:
I may be able to make this work. It will be in a new fiscal year so
I can probably get travel funding. I'd be willing to help with either
workshop. Is workshop 1 appropriate for the webexport function or do
we want
On Wed, Sep 2, 2009 at 8:11 PM, N David Brownhubd...@googlemail.com wrote:
Given the 677 compounds tested and the proximity to the TSAR values, I
think that's an odd comment. It's an approximation, true, but for the
drop in computational cost I find the accuracy astounding.
So, just out of
2009/9/1 Thorsten Meinl thorsten.me...@uni-konstanz.de:
There is the CDKHydrogenAdder for adding implicit and explicit hydrogens to
molecules. But is there a class or method to *remove* explicit hydrogens? I
suppose just removing all hydrogens from an AtomContainer won't do the trick,
will it?
Hi all,
I'm giving a presentation at the GDCh meeting in Frankfurt on Monday
morning, and have time in the afternoon to talk about CDK, Bioclipse
and/or the Blue Obelisk movement. Or about Open Data, Open Standards
and Open Source in chemoinformatics.
If you happen to be around the Frankfurt
Hi all,
I'm giving a presentation at the GDCh meeting in Frankfurt on Monday
morning, and have time in the afternoon to talk about CDK, Bioclipse
and/or the Blue Obelisk movement. Or about Open Data, Open Standards
and Open Source in chemoinformatics.
If you happen to be around the Frankfurt
Dear Aquina,
On Thu, Aug 27, 2009 at 5:50 AM, Aquinaaqu...@tron-delta.org wrote:
I don't want to file a new bug report so I'm gonna post here what I
have.
Executing /usr/lib/kde4/bin/kbuildsycoca4 --noincremental puts out
some warnings...
kbuildsycoca4 running...
kbuildsycoca4(16860)
Dear Aquina,
On Thu, Aug 27, 2009 at 5:50 AM, Aquinaaqu...@tron-delta.org wrote:
I don't want to file a new bug report so I'm gonna post here what I
have.
Executing /usr/lib/kde4/bin/kbuildsycoca4 --noincremental puts out
some warnings...
kbuildsycoca4 running...
kbuildsycoca4(16860)
Hi Rajarshi,
On Mon, Aug 24, 2009 at 3:42 AM, Rajarshi Guharajarshi.g...@gmail.com wrote:
Hi, previously I could write SD properties in MDLWriter using the
setSdFields() method. In the latest cdk-1.2.x branch that seems to
have disappeared. How does one output properties now?
Use the
redirected: cdk-user
On Thu, Aug 20, 2009 at 5:46 PM, Stefan Kuhnstefan.k...@ebi.ac.uk wrote:
does cdk have a possibility to model atom valences? Can e.g. a Nitrogen be
declared to be of valence X?
What atomic property are you particularly interested in?
The CDK atom typing environment
On Mon, Aug 24, 2009 at 6:27 PM, Stefan Kuhnstefan.k...@ebi.ac.uk wrote:
On Monday 24 August 2009 09:14:28 Egon Willighagen wrote:
Hm, ok. What I would need is something much more simple, namely the
possibility for the user in JCP to set something called valence to an int
value, which would
Dear Fred and Richard,
On Wed, Aug 12, 2009 at 7:40 PM, Richard Cyganiakrich...@cyganiak.de wrote:
the Jena framework [1] includes
a SPARQL query library called ARQ [2], which includes APIs for
querying remote SPARQL stores. So you can use it to send SPARQL
queries to DBpedia from your Java
Public bug reported:
Please add the new rdfindexer command line utility to the strigi-utils
deb pacakge, which is the RDF equivalent of the xmlindexer.
** Affects: strigi (Ubuntu)
Importance: Undecided
Status: New
** Tags: wishlist
--
add rdfindexer to strigi-utils command line
Public bug reported:
Please add the new rdfindexer command line utility to the strigi-utils
deb pacakge, which is the RDF equivalent of the xmlindexer.
** Affects: strigi (Ubuntu)
Importance: Undecided
Status: New
** Tags: wishlist
--
add rdfindexer to strigi-utils command line
Hi Bob,
while translating 11.8 into Dutch (updating, really), I noticed
Executing script 1... and Executing script 2... ... can you update
that make it use {0} ? Otherwise, I will early next week...
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
Hi all,
not sure I am supposed to reply to this as author of the XEP, but here
goes... I hope it will trigger more replies to the call.
On Wed, Aug 12, 2009 at 11:33 PM, XMPP Extensions Editoredi...@xmpp.org wrote:
1. Is this specification needed to fill gaps in the XMPP protocol stack or to
On Thu, Aug 13, 2009 at 12:57 PM, Robert Hansonhans...@stolaf.edu wrote:
I think we're probably ready for 11.8. The only things I have going are
major ideas that I don't want to get started on prior to that. How about a
release on Tuesday?
Bioclipse 2.1 (a development series) is using RC4, and
On Wed, Aug 12, 2009 at 11:53 AM, Jan-Pascal van
Bestjanpas...@vanbest.org wrote:
Torsten Werner wrote:
On Tue, Aug 11, 2009 at 12:53 PM, Vincent Fourmondfourm...@debian.org
wrote:
I'm wondering: would it be a good idea to remove everything but to
leave a dummy file in pkg-java/trunk/solr
Hi Suyog,
On Wed, Aug 12, 2009 at 8:23 AM, suyogsuyog@gmail.com wrote:
I am trying to access the CDK API on line, but I am not able to do
it.
I have tried on bellow link :
http://pele.farmbio.uu.se/nightly/api/
But it was giving an error as : The requested URL /nightly/api/ was
On Thu, Aug 6, 2009 at 8:38 AM, Robert Hansonhans...@stolaf.edu wrote:
This is a human-readable format that can be transformed into the binary U3D
format that then can be inserted into PDB files
using a simple command-line utility IDFConverter.exe (Windows only). The end
result is a stunning
On Thu, Aug 6, 2009 at 9:04 AM, Robert Hansonhans...@stolaf.edu wrote:
It's possible to embed the Jmol state script in the U3D file, so one can
load the PDF file itself or the U3D file itself back into Jmol:
script filename.pdf
or
script filename.u3d
(although I did not do that with the
On Sun, Aug 2, 2009 at 9:06 AM, Robert Hansonhans...@stolaf.edu wrote:
Can someone help here?
I think he registered after my reply.
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
--
Let
Hi Bob!
On Sat, Aug 1, 2009 at 7:46 AM, Robert Hansonhans...@stolaf.edu wrote:
The 2009 Gordon Research Conference on Visualization in Science and
Education is over. It was unbelievably cool. It's strict policy not to
discuss anything that was at that meeting, so please don't ask me to do
Hi all,
I have just uploaded the first release in a new development cycle: CDK
1.3.0. When this development cycle has finished, it will end up as a
new stable 1.4.0 release, replacing the current stable 1.2.x release.
But no ETA [0] for that release.
Due to changes in the SourceForge website
Hi Peter,
it looks like the SDFWriter does not accept IAtomContainerSet, which
IRingSet extends... can you file a bug report please?
On Mon, Jul 27, 2009 at 10:20 AM, Peter Maaspeter.m...@specs.net wrote:
I'm try to write ringSets to a SD-file.
Strangly enough I can write them to a molfile
Hi Monika,
On Sun, Jul 26, 2009 at 5:17 PM, Monika
Machunikmonika.machu...@gmail.com wrote:
I am renewing my question about Taverna plugin. How to make an existing
plugin work with Taverna (version 2.1b2)?
Sorry for having been silent after my first replies... I have not yet
tried my code
Hi all,
JabRef is not comming out as good as it can, as I think JabRef has
more to offer then now is visible from:
http://www.flickr.com/photos/mfenner/3742253794/
Such as copying formated references into OpenOffice...
Martin Fenner is taking this to the life sciences community, and I'm
sure
Hi Monika,
On Sat, Jul 18, 2009 at 11:13 AM, Monika
Machunikmonika.machu...@gmail.com wrote:
Could you advise me what to start with? Do I have to download some sources
from svn? Which ones?
How to write plugins for Taverna?
Are you aiming at Taverna2 or Taverna1? If the former, you could look
Miguel,
can you comment on what to use instead of getImplicitLonePairCount()
as described below?
-- Forwarded message --
From: Mark Rijnbeek
Date: Thu, Jul 16, 2009 at 2:06 PM
Subject: Re: [Cdk-jchempaint] Two questions on class changes
To: cdk-jchempa...@lists.sourceforge.net
Hi all,
I just uploaded Release Candidate 3 for Jmol 11.8 with the following changes:
# code: more efficient VRML export
# new feature: set helixStep 1,2,3,... sets step for quaternion-based
analysis of structure -- see 1C4D
# bug fix: 1C4D has [FOR] -- not accepted
# bug fix: color
On Fri, Jul 10, 2009 at 10:37 AM, Noel O'Boylebaoille...@gmail.com wrote:
With cdk-1.2.3.jar, I have:
cdk.readstring(smi, ).calcfp().bits
[130, 527, 619, 748]
cdk.readstring(smi, CCCN).calcfp().bits
[130, 527, 619, 748, 918, 934, 1023]
This is very bad indeed... I'm in the middle in the
On Fri, Jul 10, 2009 at 1:37 PM, Noel O'Boylebaoille...@gmail.com wrote:
Meanwhile, I would very much appreciate if you could file a bug report...
Done.
Thanx!
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
On Fri, Jul 10, 2009 at 1:37 PM, Stefan Kuhnstefan.k...@ebi.ac.uk wrote:
According to this, is a substructure of CCCN (it could be a
coincidence of course, but like I said, this is my only test case so I
am suspicious).
Just one remark: It does not mean that is a substructure of
Hi Chris,
On Fri, Jul 10, 2009 at 12:44 PM, Christoph
Steinbecksteinb...@ebi.ac.uk wrote:
Not sure why this happened and who did it but that should be easy to
find out.
'git bisect' is your friend...
In principle, I think that Fingerprints can easily change from release
to release
On Wed, Jul 8, 2009 at 5:01 PM, Noel O'Boylebaoille...@gmail.com wrote:
Shurely there's some mistake. There's no reference to the CDK in the article.
Yes, I'm noting that too... I'm now looking at the source code...
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
On Wed, Jul 8, 2009 at 5:13 PM, Egon
Willighagenegon.willigha...@gmail.com wrote:
On Wed, Jul 8, 2009 at 5:01 PM, Noel O'Boylebaoille...@gmail.com wrote:
Shurely there's some mistake. There's no reference to the CDK in the article.
Yes, I'm noting that too... I'm now looking at the source
On Wed, Jul 8, 2009 at 5:15 PM, Rajarshi Guharajarshi.g...@gmail.com wrote:
On Wed, Jul 8, 2009 at 11:01 AM, Noel O'Boyle baoille...@gmail.com wrote:
Yes, unfortunately no citation. But if you look in the jar files, the CDK
is there
Why did they not cite the CDK?? We're not even in the
On Wed, Jul 8, 2009 at 3:38 PM, Rajarshi Guharajarshi.g...@gmail.com wrote:
http://www.nature.com/nchembio/journal/vaop/ncurrent/suppinfo/nchembio.187_S1.html
One would almost forget:
Congrats to the Stefan Wentzel and the co-authors for this interesting paper!
Really looking forward to mining
Hi Xin,
On Fri, Jun 12, 2009 at 7:50 PM, Xin Gongxg...@galenea.com wrote:
1, Here is my rcdk code:
….
mol -
parse.smiles(CC(C)C1=C2C(=NC(=NC2=O)CC3=CC=C(C=C3)OCCO)N(N1)C4=C(C=CC=C4Cl)Cl)
do.aromaticity(mol)
do.typing(mol)
convert.implicit.to.explicit(mol)
alogp = round(get.alogp(mol),2)
On Fri, Jul 3, 2009 at 10:14 AM, Egon
Willighagenegon.willigha...@gmail.com wrote:
Rich asks in his blog:
http://depth-first.com/articles/2009/07/02/dear-lazyweb-does-jmol-support-output-for-use-with-3d-glasses
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
On Thu, Jun 4, 2009 at 7:12 PM, Andrzej Jan Taraminaandr...@chaeron.com wrote:
1) Pros/cons of using XMPP for distributed query?
Asynchronous.
2) How would this be an improvement over using plain REST (XML over HTTP)
between the different nodes?
Semantics inherit in the protocol.
3)
On Tue, Jun 30, 2009 at 5:59 PM, Robert Hansonhans...@stolaf.edu wrote:
I have gettext installed; it is running. But when it tries to do use javac
it says:
[echo] Updating messages_pt_BR.class file for JmolApplet ...
[exec]
On Wed, Jul 1, 2009 at 6:25 PM, sebisebastian.kl...@hispeed.ch wrote:
On Mit, 2009-07-01 at 18:20 +0200, sebi wrote:
On Mit, 2009-07-01 at 11:06 +0200, Egon Willighagen wrote:
# these are RCDK methods to build the molecule instance
@mol = Lang.read_molfile(molfile)
# or
@mol
Hi all,
bug fix release 11.6.25 for the stable Jmol series has just been made
available on SourceForge with the following changes:
# bug fix: select model=1 does not work (since 11.6.RC17!)
# bug fix: dipole offsetside not working for molecular dipole (EVER!)
# bug fix: 2 pixels off in y for
Hi all,
a new Jmol prerelease has been uploaded to SourceForge, bringing these
changes as listed in the changelog:
# bug fix: select model=1 does not work (since 11.6.RC17!)
# new application: JmolData.jar
# This application completely disallows any display -- it is totally formless
# There are
...@users.sf.net
* 2001-2007,2009 Egon Willighagen eg...@users.sf.net
*
* Contact: cdk-de...@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free
On Tue, Jun 30, 2009 at 1:59 PM, sebisebastian.kl...@hispeed.ch wrote:
Are the latest fixes included in the jchempaint-primary branch?
Or is the renderer now included in the 1.2.x/master branch from git
repos?
I would like to update RCDK, but I'm not sure which branch is latest
with the
Hi all,
not too long after the .44 release the changes are piling up again;
see below. Downloads from:
http://sourceforge.net/project/showfiles.php?group_id=23629package_id=142353release_id=693156
# bug fix: load trajectory XXX.cif not applying fractional coordinates.
# bug fix: load trajectory
On Mon, Jun 29, 2009 at 5:06 AM, Robert Hansonhans...@stolaf.edu wrote:
In case there is anyone in the London/Oxford/Lancaster areas or
Berlin/Frankfurt areas who would like to get together and talk about Jmol
(or let me give a presentation!), here is my itinerary for July/Aug:
July 22 -
On Wed, Jun 24, 2009 at 11:41 AM, Jan H. Jensenjhjen...@kemi.ku.dk wrote:
The GAMESS reader sounds very interesting, but I haven't been able to
find any documentation on the web?
Usually, Bob puts up demos of new features at:
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
But I do
On Tue, Jun 23, 2009 at 11:20 AM, Rick Jellifferjelli...@allette.com.au wrote:
I am working on improving the semweb markup on an Australian government
Department of Health and Aging website, which has HTML and XML versions of
the medicines allowed for prescription and the amount the government
On Tue, Jun 23, 2009 at 11:49 AM, Rick Jellifferjelli...@allette.com.au wrote:
So there is still no convenient way to mark up existing XML as RDF? It was
a showstopper 10 years ago but I kind of expected there would have been some
progresssigh
Define 'markup'... you can just embed your
On Tue, Jun 23, 2009 at 12:15 PM, Rick Jellifferjelli...@allette.com.au wrote:
Markup = annotation. Taking existing data and adding stuff to make it more
useful, without disrupting existing uses of that data (and without creating
the size/maintenance issues you get from duplication.)
One of
On Tue, Jun 23, 2009 at 2:48 PM, Rick Jellifferjelli...@allette.com.au wrote:
I see that the 2008 draft
http://www.w3.org/2006/07/SWD/RDFa/rdfa-overview
says
RDFa itself is intended to be a technique that allows for adding metadata
to any (XML) markup document, including SMIL, RSS, SVG,
Hi all,
with Nico on holiday, I got to honour to make a Jmol release again,
after a very long time of not doing releases :)
I'm pleased to announce the Jmol Prerelease 11.7.44 with the following
changes by the every amazingly productive Bob:
# bug fix: write FRAMES also for trajectories
# new
Public bug reported:
Binary package hint: sun-java6-jdk
Today, I was compiling from SVN commit 164 of jni-inchi.sf.net, which
uses maven...
During the process I got this message:
[INFO] mkdir -p ../../../target/native/o/LINUX-AMD64/jni
[INFO]
Public bug reported:
Binary package hint: sun-java6-jdk
Today, I was compiling from SVN commit 164 of jni-inchi.sf.net, which
uses maven...
During the process I got this message:
[INFO] mkdir -p ../../../target/native/o/LINUX-AMD64/jni
[INFO]
On Wed, Jun 3, 2009 at 7:58 AM, Robert Hanson hans...@stolaf.edu wrote:
Well, wouldn't you know it? What started out as a simple idea turned into
quite a challenge. But I think I'm done, and I am very interested in
extensive testing. Sorry, Angel -- you may have to rewrite your book!
Argh...
On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote:
see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Check it out!
Nice !
Egon
--
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/
On Thu, Jun 4, 2009 at 9:52 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Jun 3, 2009 at 10:20 PM, Robert Hanson hans...@stolaf.edu wrote:
see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
Check it out!
Nice !
BTW, I get an unexpected exception in step 2 of 17
On Tue, Jun 2, 2009 at 1:15 AM, Brian Salter-Duke b_d...@bigpond.net.au wrote:
On quality, I think that is a different and general concern. We try to
not use poor quality images, so we would try to use only good quality
Jmol data files. I am happy that we restrict the type of jmol files to a
On Wed, May 27, 2009 at 5:19 AM, Pudney Chris GBJH
chris.pud...@syngenta.com wrote:
Assuming these listeners are unnecessary for the purposes of rendering
structures I'd like to empty the ChemObjectListeners lists (or avoid
them being populated in the first place).
This is why the
Hi all,
as I write, CDK 1.2.3, also know as the 'Don't use this Renderer'
release is finally being uploaded to SourceForge... it fixes a few
things (see below), but most importantly, it removes a few Renderer
classes which should have been removed before the 1.2.0 release.
As you might know, the
Hi Angel,
2009/5/21 Angel Herráez angel.herr...@uah.es:
I guess this is trivial for you, but just in case it is contributing
to your problem I will say it:
JChemPaint 2.4 is JCP2, while JChemPaint 2.5 is really JCP3beta. The
code is totally rewritten for JCP3.
Yes, thanx for pointing this
On Thu, May 21, 2009 at 9:48 AM, Gerard Meijssen
gerard.meijs...@gmail.com wrote:
I am really pleased that you are willing to follow the WMF in this but as I
have argued on this list in the past, DBpedia is a collection of facts..
Yes, people keep repeating that... yet EU law, at least in NL,
On Mon, May 18, 2009 at 10:11 AM, Noel O'Boyle baoille...@gmail.com wrote:
Not to discourage you, but several (if not the majority) of the
references to the BO paper are by people trying to find a citation for
OpenBabel. I am hoping that this problem will eventually be resolved
:-)
Sure. But
On Fri, May 8, 2009 at 5:36 PM, Loren Lenzen loren.len...@sial.com wrote:
My fault, I did not mean ID tags. I was referring to the data fields that
come after the structural information. For example:
Vendor
Sigma
I know I can get them by looking for the regex, but I assumed that the
On Thu, May 7, 2009 at 9:07 PM, Loren Lenzen loren.len...@sial.com wrote:
3) It appears that the SMILES parser doesn't recognize the heavier metals
(e.g. Eu). How much of the periodic table is left out? Is there a way to
capture these atoms without them returning a CDKexception.
SMILES
On Mon, May 4, 2009 at 10:24 AM, Chris Pudney
ch...@focal-technologies.com wrote:
I'm migrating some CDK code from 1.0.1 to 1.2.1 - the code performs two
main functions:
1. 2D structure diagram generation
2. structure diagram rendering
Please use the CDKAtomTypeMatcher to perceive atom
On Mon, May 4, 2009 at 3:49 PM, Vincent Le Guilloux
vincent.le-guill...@univ-orleans.fr wrote:
Quoting Rajarshi Guha rg...@indiana.edu:
The parser is misreading the Sc part as scandium rather than a sulphur
followed by an sp2 carbon. So it's a CDK issue. Can yuo file this as a
big report?
On Mon, May 4, 2009 at 1:43 AM, Robert Hanson hans...@stolaf.edu wrote:
The page doesn't work at all for me. I get a Java error for all the applets.
It works for me: FF 3.0.10, Ubuntu Jaunty, libnpjp2.so Java plugin,
which seems to link to Sun JVM 1.6.0_13.
Egon
--
Post-doc @ Uppsala
Hi Marco,
while not an official plugin...
On Wed, Apr 29, 2009 at 3:39 PM, Marco Roos m.ro...@uva.nl wrote:
Ultimately, I prefer to use the plugin in Taverna 2. Therefore, I have
these questions:
* If you have created a T2 plugin: would you share your code to serve as
a template for others?
Just was told about this:
http://sideeffects.embl.de/
Rather permissively licensed.
SIDER contains information on marketed medicines and their recorded
adverse drug reactions. The information is extracted from public
documents and package inserts. The available information include side
effect
Hi all,
per Miguel's request I have set up a Planet CDK with CDK-dedicated blogs:
http://pele.farmbio.uu.se/planetcdk/
If you like to be listed there, please send me your blog feed... If
you blog about the CDK but other things too, please provide a feed URL
for the CDK subcategory, tag, or
Hi Tuomas,
On Fri, Apr 17, 2009 at 4:55 PM, Tuomas Koski koski.tuo...@gmail.com wrote:
I have created a www.lobstermonster.org to host my experiments with
XMPP and web service based on XMPP.
At the moment I have implemented two web services using XMPP :
- Contact form and chat
On Tue, Apr 7, 2009 at 11:00 PM, Dean Collins d...@cognation.net wrote:
Basically it is an ajax/xmpp site with 2430 chat rooms set up over the
next 6 months for people to talk about specific Baseball games.
Interesting... I have been thinking about making a web front end for
IO-DATA services,
On Tue, Apr 7, 2009 at 11:50 AM, Stefan Kuhn stefan.k...@ebi.ac.uk wrote:
If you mean potential stereocentres in a molecule without stereo specification
(ie. without wedges): No, this is an open issue.
Stefan, did you have a look at the patch by Todd Martin on symmetry?
Would that do the job?
Chris,
On Tue, Apr 7, 2009 at 1:45 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Tue, Apr 7, 2009 at 1:25 PM, Nina Jeliazkova n...@acad.bg wrote:
Trying to reply to this thread,
https://sourceforge.net/mailarchive/message.php?msg_name=49C96659.2090401%40ebi.ac.uk
,I have to say
On Tue, Apr 7, 2009 at 1:25 PM, Nina Jeliazkova n...@acad.bg wrote:
Trying to reply to this thread,
https://sourceforge.net/mailarchive/message.php?msg_name=49C96659.2090401%40ebi.ac.uk
,I have to say SmilesGenerator generates different smiles, depending on
how the molecule was created (e.g.
On Tue, Apr 7, 2009 at 12:46 PM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
Naively, I would also say that if a 4-bonded carbon has substituents
with 4 different Morgan numbers, it could be considered a stereo center.
Mmmm... aren't Morgan number supposed to make ties in such cases?
But,
On Tue, Apr 7, 2009 at 5:26 PM, gilleain torrance
gilleain.torra...@gmail.com wrote:
On Tue, Apr 7, 2009 at 3:57 PM, Aidar Mahmutov aida...@mail.ru wrote:
Is it real to take Jmol as a basis for editor? Add, delete, create atoms.
Construct multiatomic structures, manipulate them. Fill some
Hi Aidar,
2009/4/4 Aidar Mahmutov aida...@mail.ru:
I have problem with Jmol and cdk integration. I'm using Jmol SVN(11.6.20) and
CDK SVN(1.20). I've proceeded instruction how to integrate it, also read
article Jmol as 3D viewer for CDK, visited cdk cite, downloaded
CDKIntegration.java.
Hi Scott (and others),
On Thu, Apr 2, 2009 at 12:42 AM, M. Scott Marshall
marsh...@science.uva.nl wrote:
Here's the reminder for Thursday's HCLS call.
I will not be able to make it today.
And I think I found which telcon's are most interesting to me (LODD
and BioRDF), though several others
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