Moin all,
I downloaded the Taverna 2.2.0 zip file with source code [0], and
imported this into Eclipse. Most works fine, except some code in the
plugins-api module. In particular, the
net.sf.taverna.raven.plugins.Plugin.java has these compile errors, due
to a missing package:
import
On Sat, Oct 23, 2010 at 3:27 PM, Alan R Williams ala...@cs.man.ac.uk wrote:
Do you have the problem if you run mvn install ?
I will try... I also downloaded from SVN and will try that too...
Egon
--
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
Homepage:
On Sat, Oct 23, 2010 at 4:39 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Sat, Oct 23, 2010 at 3:27 PM, Alan R Williams ala...@cs.man.ac.uk wrote:
Do you have the problem if you run mvn install ?
I will try...
That seems to work, and only reports a few failing unit tests:
[INFO
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
that is ported by Apple, and that ships with Mac OS X, is
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html
That expresses future aspirations, rather than testable reality. There is
nothing for
OS X at http://openjdk.java.net/
You can find instructions
On Fri, Oct 22, 2010 at 12:16 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://www.theregister.co.uk/2010/10/21/apple_threatens_to_kill_java_on_the_mac/
As of the release of Java for Mac OS X 10.6 Update 3, the version of Java
that is ported by Apple, and that ships with Mac OS X, is
On Fri, Oct 22, 2010 at 12:33 PM, Rzepa, Henry h.rz...@imperial.ac.uk wrote:
http://lists.apple.com/archives/Java-dev/2010/Oct/msg00248.html
That expresses future aspirations, rather than testable reality. There is
nothing for
OS X at http://openjdk.java.net/
You can find instructions
On Thu, Oct 21, 2010 at 3:17 PM, Philip Bays pb...@saintmarys.edu wrote:
Anyone apply the Java update released yesterday? If so, did it break
anything?
Somewhat related, but also somewhat OT... have people been using
OpenJDK on OS/X? Is that possible yet, as it seems Java will phase out
their
On Wed, Oct 20, 2010 at 3:25 PM, Alan R Williams ala...@cs.man.ac.uk wrote:
On 19/10/2010 19:07, Jason Reilly wrote:
I look forward to the OSGi version to be release (I have some experience
with Felix/Karaf).
The engine (which runs the workflows) will be framework-agnostic
although we are
On Wed, Oct 20, 2010 at 11:22 AM, Alan R Williams ala...@cs.man.ac.uk wrote:
I am not sure why. However, you could try
callback.partialResults(results);
rather than do it for each service.
That was the first option I tried... does not work either... this is
what I originally had:
Hi Stian,
On Wed, Oct 20, 2010 at 12:29 PM, Stian Soiland-Reyes
soiland-re...@cs.manchester.ac.uk wrote:
You need to implement this method:
protected List? extends Object getIdentifyingData() {
// FIXME: Use your fields instead of example fields
return
On Wed, Oct 20, 2010 at 2:49 PM, Stian Soiland-Reyes
soiland-re...@cs.manchester.ac.uk wrote:
On Wed, Oct 20, 2010 at 12:17, Egon Willighagen egon.willigha...@gmail.com
wrote:
We should probably make it a fault to return [] from getIdentifyingData().
Yes, please consider that a feature
Hi all,
with thanx to David and Stian, I managed to set up a plugin site
(http://pele.farmbio.uu.se/oscar4-taverna/), and I can successfully
install the plugin (and it is listed as installed, and listed in
$HOME/.taverna-2.2.0/)...
However, the activities do not show up in the workbench GUI. I
On Mon, Oct 18, 2010 at 7:50 PM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
Actually, any of the existing IteratingMDLReader tests would do, by
emulating broken InputStreamReader :
Nice! I had no idea that creating a custom inputstream was so easy!
Got a git patch?
Egon
--
Dr E.L.
Hi Nina, Tobias,
On Sat, Oct 16, 2010 at 10:27 AM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
--- Fixed ---
public boolean hasNext() {
if (!nextAvailableIsKnown) {
hasNext = false;
// now try to parse the next Molecule
try
Hi all,
what should we do with 'old', 'unreviewed' patches? Those patches that
have been in the tracker for a long time, and have not seen any
comment by reviewers, and as such, patches that are not requested to
be revised?
Should we create a time out of, say, three months? So that patches
that
On Sat, Oct 16, 2010 at 3:30 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
That is nice - but we're possibly going to get lots of merge failures
if the patches have been lying around too long. In such a case I
suspect that a patch will, by default, never get applied :)
Good point.
So, we
Andreas,
On Thu, Oct 14, 2010 at 4:51 PM, Stian Soiland-Reyes
soiland-re...@cs.manchester.ac.uk wrote:
So whoever made
http://www.ts-concepts.de/cdk-taverna2/maven/repository/org/openscience/reactionenumerator/reactionenumerator/1.1.3/reactionenumerator-1.1.3.pom
would have to update it - the
Hi all,
thanx to the new tutorial, creating a plugin from scratch is very
easy! Well done!
Now, there also is a stub tutorial for creating a plugin site, so that
people can easily install a plugin?
For the XMPP plugin I wrote for 2.0, I wrote up how to do it manually
[0], but I rather have a
On Wed, Oct 13, 2010 at 11:34 AM, Andreas Truszkowski
atruszkow...@gmx.de wrote:
Do you know what Java exception is being thrown which is then converted
to a CDKTavernaException?
ERROR 2010-10-13 12:31:29,474 (System.err:139) -
java.lang.ClassCastException: cannot assign instance of
On Wed, Oct 6, 2010 at 9:10 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Hi, what is the preferred way to check whether a bond is in a ring?
The SpanningTree.
Egon
--
Dr E.L. Willighagen
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog:
Hi all,
On Fri, Oct 1, 2010 at 9:04 AM, Pascal Muller
pascal.jm.mul...@gmail.com wrote:
If I remember correctly the Murcko framework code in the CDK is broken.
I would be *very* useful if the people interested in this
functionality could set up (e.g. in the wiki) a set if molecules with
the
On Fri, Oct 1, 2010 at 11:47 AM, Nick Price
n...@technologyforgrowth.co.uk wrote:
I have been trying to install the CDK plugin to TAVERERNA 1.7.2 as I
understand it does not work with TAVERNA 2. On a Windows Vista system
the plugin appears to install correctly and the plugin manager shows it
Hi Adel,
On Thu, Sep 30, 2010 at 4:23 PM, Adel Golovin golo...@ebi.ac.uk wrote:
Thank you for an excellent opensource chemical package.
However I write to report an issue :(
I have come across a problem with fingerprints.
The fingerprints depend on the order of atoms in the MDL file.
The
On Thu, Sep 30, 2010 at 5:08 PM, Adel Golovin golo...@ebi.ac.uk wrote:
cdk-1.3.4
Good. On the bus home I wrote four new unit tests for the
fingerprinter, and using the AtomContainerAtomPermutor and
AtomContainerBondPermutor on two molecules, and that showed no
problems. If you send me your file
Hi all,
tomorrow, September 27-29, it is exactly 10 years ago that Dan
Gezelter (the Jmol inventor) hosted a meeting at Notre Dame (South
Bend) where he, Christoph Steinbeck (the CompChem and JChemPaint
inventor), and me founded the Chemistry Development Kit, loosely named
after the 'Java
Public bug reported:
Binary package hint: dh-make-perl
To reproduce:
$ cd /tmp
$ sudo dh-make-perl --install --cpan PatchReader
Output (last, relevant lines only):
dpkg-deb: building package `libpatchreader-perl' in
`../libpatchreader-perl_0.9.5-1_all.deb'.
make: Leaving directory
The bug was reported via my maverick system, but the problem was found
on lucid instead.
--
dh_make_perl fails to install the create .deb
https://bugs.launchpad.net/bugs/646662
You received this bug notification because you are a member of Debian
Perl Group, which is subscribed to dh-make-perl
On Thu, Sep 23, 2010 at 10:10 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
With the 1.3.6 jar and the jchempaint 15 jar I can't compile
Correct. The CDK-JChemPaint patch 15 is for CDK 1.3.5...
Are there any plans to finally get the rendering in sync with the CDK
so that one could actually
Same here. Sept 24. :(
--
Upgrade from 2.2.14-5ubuntu6 to 2.2.14-5ubuntu7 results in syntax error,
missing module
https://bugs.launchpad.net/bugs/562370
You received this bug notification because you are a member of Ubuntu
Server Team, which is subscribed to apache2 in ubuntu.
--
Same here. Sept 24. :(
--
Upgrade from 2.2.14-5ubuntu6 to 2.2.14-5ubuntu7 results in syntax error,
missing module
https://bugs.launchpad.net/bugs/562370
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
--
ubuntu-bugs mailing list
Public bug reported:
Binary package hint: dh-make-perl
To reproduce:
$ cd /tmp
$ sudo dh-make-perl --install --cpan PatchReader
Output (last, relevant lines only):
dpkg-deb: building package `libpatchreader-perl' in
`../libpatchreader-perl_0.9.5-1_all.deb'.
make: Leaving directory
The bug was reported via my maverick system, but the problem was found
on lucid instead.
--
dh_make_perl fails to install the create .deb
https://bugs.launchpad.net/bugs/646662
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
--
On Wed, Sep 22, 2010 at 10:52 PM, Richard Cyganiak rich...@cyganiak.de wrote:
On 22 Sep 2010, at 20:41, Egon Willighagen wrote:
If you want to see ChEMBL in the next issue, better get started on those
links ;-)
I am on the road right now, but there is low hanging fruit... however,
at the same
On Wed, Sep 22, 2010 at 8:50 PM, Anja Jentzsch a...@anjeve.de wrote:
215 data sets have been entered into CKAN and added to the lodcloud group.
203 of those form a connected cloud of data sets, and are shown in the
picture. The data sets consist of over 25 billion RDF triples, which are
On Wed, Sep 15, 2010 at 7:38 PM, Jonathan Gutow gu...@uwosh.edu wrote:
On Sep 15, 2010, at 10:41 AM, Robert Hanson wrote:
-- proposing a NEW DEFAULT for Jmol for 12.1 and 12.0:
double bonds in the plane of the atoms, not twisty with
orientation.
This is the default I always expected,
On Thu, Sep 16, 2010 at 8:24 AM, Thomas G. Kristensen t...@cs.au.dk wrote:
On Wed, Sep 15, 2010 at 12:43 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
You can file a feature request... best to add an example file that we
can use as test data, so LGPL licensed... a small demo file
. Kristensen t...@cs.au.dk wrote:
On Thu, Sep 16, 2010 at 8:28 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Thu, Sep 16, 2010 at 8:24 AM, Thomas G. Kristensen t...@cs.au.dk wrote:
On Wed, Sep 15, 2010 at 12:43 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
You can file a feature
On Wed, Sep 15, 2010 at 12:30 PM, Thomas G. Kristensen t...@cs.au.dk wrote:
I'm trying to parse molecules with formal charges from a mol2 file,
but no matter what I try it seems the formal charges are ignored when
using the Mol2Reader. Inspecting the source code I discovered that mol
type,
Hi again,
I have just released a new CDK *development* version. Details and full
changelog is available:
http://chem-bla-ics.blogspot.com/2010/09/cdk-137-changes-authors-and-reviewers.html
Users of the 1.3.x development releases are encouraged to upgrade;
users of 1.2.x are advised to wait
Hi Sebastian,
On Mon, Sep 13, 2010 at 2:44 PM, Sebastian Wolf sw...@ipb-halle.de wrote:
When I profile my project I saw that the method
org.openscience.cdk.AtomContainer.addAtom(IAtom) calls
org.openscience.cdk.ChemObject.addListener(IChemObjectListener). In this
method contains
I still have this problem; it happens when recovering from suspend but
also sometimes upon booting... booting in recovery mode and then resume
and manually booting *kdm* seems to work as workaround...
I'll try to attach that apport output...
** Tags added: apport-collected
--
[maverick] System
AlsaVersion: Advanced Linux Sound Architecture Driver Version 1.0.23.
Architecture: amd64
ArecordDevices:
List of CAPTURE Hardware Devices
card 0: Intel [HDA Intel], device 0: STAC92xx Analog [STAC92xx Analog]
Subdevices: 2/2
Subdevice #0: subdevice #0
Subdevice #1: subdevice
apport information
** Attachment added: AcpiTables.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581424/+files/AcpiTables.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: AlsaDevices.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581425/+files/AlsaDevices.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: AplayDevices.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581426/+files/AplayDevices.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: BootDmesg.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581427/+files/BootDmesg.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: Card0.Amixer.values.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581428/+files/Card0.Amixer.values.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: Card0.Codecs.codec.2.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581430/+files/Card0.Codecs.codec.2.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: Lsusb.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581442/+files/Lsusb.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: Card0.Codecs.codec.0.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581429/+files/Card0.Codecs.codec.0.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: IwConfig.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581440/+files/IwConfig.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: Lspci.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581441/+files/Lspci.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: CurrentDmesg.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581439/+files/CurrentDmesg.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: ProcInterrupts.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581445/+files/ProcInterrupts.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: ProcModules.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581446/+files/ProcModules.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: PciMultimedia.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581443/+files/PciMultimedia.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: ProcCpuinfo.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581444/+files/ProcCpuinfo.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: RfKill.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581447/+files/RfKill.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: UdevDb.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581448/+files/UdevDb.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
apport information
** Attachment added: WifiSyslog.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581450/+files/WifiSyslog.txt
** Changed in: linux (Ubuntu)
Status: Invalid = New
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
apport information
** Attachment added: UdevLog.txt
https://bugs.edge.launchpad.net/bugs/612275/+attachment/1581449/+files/UdevLog.txt
--
[maverick] System crashes after login with (process:268): GLib-WARNING **:
getpwuid_r(): failed due to unknown user id (0)
On Thu, Sep 9, 2010 at 11:33 AM, gilleain torrance
gilleain.torra...@gmail.com wrote:
double w = bounds.getWidth()*zoomfactor + widthPad;
double h = bounds.getHeight()*zoomfactor + heightPad;
Well, this is one good example why I want to get rid of zoomfactor...
right now it is applied to the
On Thu, Sep 9, 2010 at 6:27 PM, Susie Stephens susie.steph...@gmail.com wrote:
Chem2bio2rdf might have some data that they could share with you. Dave Wild
is the PI for the project.
And he was one of the speakers...
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until
Hi all,
here's another list of patches that remain to be reviewed. The patch
reviewing system is holding pretty well, and the throughput is
increasing (18 patches were reviewed in August). But we are still
short on patch reviewers, and I like to stress once more that you do
not have to be an
online [0].
With kind regards,
Egon Willighagen
0.http://egonw.github.com/acsrdf2010/
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Hi all,
I just ran into this interesting video:
http://www.drumbeat.org/content/popcorn-js-semantic-video-demo
Should be able to make video's and podcasts less hamburger-like...
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse
On Thu, Sep 2, 2010 at 8:55 PM, Robert Hanson hans...@stolaf.edu wrote:
Oh, yeah. I forgot to update them. And I don't have that laptop here. Well,
they are all from http://stolaf.edu/depts/chemistry/mo/struc -- lots of
examples there.
Ah, OK.
Thanx once again!
Egon
--
Dr E.L. Willighagen
On Wed, Sep 1, 2010 at 11:05 PM, Robert Hanson hans...@stolaf.edu wrote:
done. I retro-added it to 12.0, just because.
Jmol 12.1.9 and 12.0.11 will have sp3d and sp3d2 hybridizations. See
documentation for details.
Yeah, I saw it in the changelog yesterday! Cool!
I will blog about this
On Thu, Sep 2, 2010 at 9:21 PM, Robert Hanson hans...@stolaf.edu wrote:
This just in!
Congrats!
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
LinkedIn:
Hi Bob,
I'm writing up a short tutorial on orbital drawing, as I want to
visualize the kind of thing I represent in my ODK project [0]... Up to
sp3 everything is fine, but I was hoping you could also add sp3d and
sp3d2 hybridizations, see the nice slides at [1], and slides 21-22 in
particular.
On Fri, Aug 27, 2010 at 4:44 PM, Robert Hanson hans...@stolaf.edu wrote:
sp3d2 and sp3d are really just combinations of sp2 or p orbitals and lobes,
right? So it's the same thing. Just direct them where you want them -- or is
that the problem, you haven't figured out how to direct the lobes
Hi all,
on behalf of Peter, Christoph awarded Nina Jeliazkova the Blue Obelisk
Award for her contributions to ODOSOS cheminformatics at the Blue
Obelisk dinner tonight at the ACS meeting in Boston.
Egon
PS. the award is not for any particular achievement, but I do like to
mention some of Nina's
Hi all,
the ESW wiki is running MediaWiki, but not Semantic MW, right? Could
it be an option to actually get that installed and, umm... eat our own
dog food? Samuel (my former student) working on RDFIO during his
Google Summer of Code project, and it should even be possible to get a
SPARQL end
On Fri, Aug 20, 2010 at 5:53 AM, Robert Hanson hans...@stolaf.edu wrote:
Thank you, Paul, for contacting us about this error. Looks like we had a bug
that only appears for first-time users.
Ah, so it was a folder that did not exist?
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University
Cheminformatics should have special
interest in these three sessions, and I am very much looking forward
to seeing you all next Sunday and/or Monday!
The full program can be found at:
http://egonw.github.com/acsrdf2010/
(please retweet and share with friends otherwise)
with kind regards,
Egon
Hi all (and Peter's team in particular),
Converting PDF back into text is a somewhat tricky exercise, as words
can actually be characters rendered in approximately word format...
Strigi [0] does a decent but not perfect recovery of text... is there
someone here who has experience with PDF 2 text
On Sat, Aug 14, 2010 at 4:26 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
On Sat, Aug 14, 2010 at 11:41 AM, Egon Willighagen
Converting PDF back into text is a somewhat tricky exercise, as words
can actually be characters rendered in approximately word format...
This understates the problem
Hi Paul,
On Fri, Aug 13, 2010 at 3:01 PM, Paul A Craig pac8...@rit.edu wrote:
I am trying to run Jmol on my LInux 9.10 computer and keep getting this error
message. I am new to Linux and am not a java programmer. I see the same
problem on my Mac.
I am running Ubuntu 10.04 with Java
Hi all,
a Request for Comments (RFC):
Rename IAtom.getHydrogenCount to getImplicitHydrogenCount
See:
http://sourceforge.net/tracker/?func=detailaid=3020065group_id=20024atid=120024
This is a major API change, to only a method renamed... Comments? Or
should we just rename the method?
Egon
--
Hi all,
I'll be in the Boston area during the ACS conference... please send me
an email if you like to talk about the CDK or about Bioclipse!
Egon
--
Dr E.L. Willighagen
Post-doc @ Uppsala University (only until 2010-09-30)
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage:
Hi Mark,
On Thu, Aug 12, 2010 at 6:07 PM, Mark Rijnbeek ma...@ebi.ac.uk wrote:
I was wondering: if the structure has explicit aromaticity bonds, would
it not be better to preserve this in the container? Rather than
overruling it with the CDK's aromaticity detection.
AFAIK the SMILES
All,
On Thu, Aug 12, 2010 at 6:43 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
AFAIK the SMILES specification dictates that the parser detects the
aromaticity...
For example... the parser needs to decide if something is aromatic or
anti-aromatic... both are validly encoded with lower
On Thu, Aug 12, 2010 at 8:50 PM, ma...@ebi.ac.uk wrote:
One more thing, in the example I sent, the one ring that does not get
aromaticity detected thus ends up as a ring with only single bonds. I
though that in particular was not a desirable effect.
Yes, that was discussed this week.
On Wed, Aug 11, 2010 at 6:08 PM, Philip Bays pb...@saintmarys.edu wrote:
I just got this response from the author of the Java Embedding Plugin that
the Mozilla browsers use to implement Java applets on the Mac. A solution
may be in sight:=)
Great! Thanx for getting in contact with them!
Egon
On Fri, Jul 30, 2010 at 4:38 PM, Geoffrey Hutchison
ge...@geoffhutchison.net wrote:
Maybe we can come up with something for CDK, and maybe an overview sheet with
a list of open source chemistry packages (courtesy of the Blue Obelisk)? Then
we'd have three little piles of sheets to compete
I think there recently was a discussion on reaction balancing... did
not have time to tune in on that yet... perhaps someone can reply to
the Blue Obelisk mailing list?
E.
-- Forwarded message --
From: Peter Murray-Rust pm...@cam.ac.uk
Date: Sun, Aug 8, 2010 at 2:07 PM
Subject:
Hi all,
I saw some interesting emails lately on the scripts and sorts... has
anyone yet considered using MyExperiment.org for sharing useful Jmol
scripts?
Would that be an interesting platform to share Jmol scripts like:
Show the heme groups in protein X.
Demonstrate the hydrogen bonding
On Thu, Aug 5, 2010 at 12:29 PM, Nick Vandewiele
nick.vandewi...@ugent.be wrote:
Thanks for the answer. Thus, the bottomline is that those missing source
files are just bugs, and not deliberately left out.
No, there are not left out deliberately... data moved around over
time, and I think I
On Thu, Aug 5, 2010 at 12:44 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Will try to fix this asap; the bug is already reported.
I am uploading CDK 1.2.6.1 which fixes the problem of the missing templates.
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group
Dear Gert,
On Wed, Aug 4, 2010 at 10:00 AM, Gert Thijs gert.th...@silicos.com wrote:
Silicos is pleased to announce the release of version 3 of its
molecular filtering software Sieve.
Thank you for another contribution to the community!
• Selection criteria by means of smarts patterns;
Hi all,
(Jules, thanx for this detailed answer!)
On Mon, Aug 2, 2010 at 12:28 PM, Jules Kerssemakers
j.kerssemak...@cmbi.ru.nl wrote:
You may get a few ClassNotFoundExceptions in the beginning when you
try to run your program, this means you missed a jar file that needs
to be included, such
On Sun, Aug 1, 2010 at 5:00 AM, Andrew Dalke da...@dalkescientific.com wrote:
On Jul 31, 2010, at 12:30 AM, Egon Willighagen wrote:
some legal framework kicks in to overcome this problem...
I'm pretty sure it works something like that with
copyright on books too... not?
Not.
Orphan works
Hi Nick,
On Sat, Jul 31, 2010 at 4:46 PM, Nick Vandewiele
nick.vandewi...@ugent.be wrote:
Newbie question: Could somebody explain why 2 separate versions (cdk 1.2.x
and 1.3.x) of the CDK are developed and maintained?
CDK uses a version numbering scheme were odd minor numbers indicate
On Wed, Jul 28, 2010 at 4:10 PM, Robert Hanson hans...@stolaf.edu wrote:
Here's a listing of all the new capabilities of Jmol 12.0, categorized:
http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm
Congrats, Bob!
Egon
--
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse
On Wed, Jul 28, 2010 at 7:40 PM, Stian Soiland-Reyes
soiland-re...@cs.manchester.ac.uk wrote:
We got a question if Taverna's LGPL license allows it to be used
commercially. The short answer is Yes, but I've written some details
here:
http://www.mygrid.org.uk/dev/wiki/display/tav/Licensing
On Mon, Jul 26, 2010 at 7:29 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
IteratorIAtom atoms = methane.atoms();
The idiom to iterate over atoms is
for (IAtom atom : methane.atoms=()) {
}
Alternatively, you could do:
IteratorIAtom atoms = methane.atoms().iterator();
Egon
--
Post-doc
On Tue, Jul 27, 2010 at 10:39 AM, Nicolas Vervelle nverve...@gmail.com wrote:
Adding @Deprecated and @Override annotations (boring, but easy)
Starting to use Generics (that won't be simple and it will take time)
And optimizations when I see some (for example, I have cleaned up the
Profiling
On Tue, Jul 27, 2010 at 1:58 PM, Robert Hanson hans...@stolaf.edu wrote:
we just need to have someone with a Mac use their Java Preferences App to
set the preference for applets to Java 1.5 and see if it fixes the problem.
I think it will. If so, then clearly it IS a Java 1.6 issue.
I would
Hi Mark,
On Sun, Jul 25, 2010 at 9:02 PM, xyz mjf xyz...@gmail.com wrote:
A colleague of mine has recently developed useful functionality such as
(2D) structure visualisation and sub structure searching, by linking MS
Excel to CDK.
Is there online info available on this product? Perhaps
601 - 700 of 2668 matches
Mail list logo
