Lydia, thanks for your insights!
Egon
On Tue, May 19, 2015 at 3:07 PM, Lydia Pintscher
lydia.pintsc...@wikimedia.de wrote:
On Tue, May 19, 2015 at 2:41 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Dear Lydia,
On Wed, May 13, 2015 at 5:20 PM, Lydia Pintscher
lydia.pintsc
Hi all,
I have picked up an old habit I stopped a while ago (no, not smoking):
I have started checking the papers again that cite the CDK and
recording this information in CiteULike. I am going to try to capture
some 5 papers each week, and that will be a tough call, because
writing such a blog
rajarshi.g...@gmail.com wrote:
Unfortunately, the pharmacophore article is in a 2008 issue. That link only
shows up to 2007
On Wed, Apr 29, 2015 at 8:47 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Apr 29, 2015 at 2:39 PM, Rajarshi Guha rajarshi.g...@gmail.com
wrote:
Egon/Chris
. That link only
shows up to 2007
On Wed, Apr 29, 2015 at 8:47 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Apr 29, 2015 at 2:39 PM, Rajarshi Guha rajarshi.g...@gmail.com
wrote:
Egon/Chris - do we have old versions of CDK News somewhere?
https://sourceforge.net/projects
Congrats!
Egon
On Mon, Apr 13, 2015 at 11:42 PM, Robert Hanson hans...@stolaf.edu wrote:
Just noticed that we are at revision # 20,448.
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
:
http://www.lulu.com/shop/egon-willighagen/groovy-cheminformatics-with-the-chemistry-development-kit/paperback/product-22051359.html
http://www.lulu.com/shop/egon-willighagen/groovy-cheminformatics-with-the-chemistry-development-kit/ebook/product-22051365.html
As a preview, please find attached
On Mon, Jan 19, 2015 at 6:12 PM, Lydia Pintscher
lydia.pintsc...@wikimedia.de wrote:
Apparently a small screwup deleted them all. Jan is working on a fix right
now.
Meanwhile, this torrent of the Jan 12 (last week's) JSON dump is available:
On Sat, Jan 17, 2015 at 11:04 PM, Markus Krötzsch
mar...@semantic-mediawiki.org wrote:
It is easy to fix this (though I will not fix it tonight, but tomorrow) by
just adjusting the HTML strings we parse for.
Sure! I have subscribed to the bug report.
As an intermediate workaround for me, what
Hi all,
I have been trying today to get the Java library Wikidata-Toolkit
going, but about to give up... I keep running with both 0.3.0 and
current master into a NullPointerException... I thought it was how I
called the code, and did add several System.out calls, and in the end
just tried to get
since its release
and it won't read the files anyway). Could you try if the problem occurs
with the current development code at github?
Cheers,
Markus
On 17.01.2015 16:59, Egon Willighagen wrote:
Hi all,
I have been trying today to get the Java library Wikidata-Toolkit
going, but about
OK, thanks! Please let me know if I can test anything on my system.
Egon
On 17 Jan 2015 22:50, Markus Krötzsch mar...@semantic-mediawiki.org
wrote:
On 17.01.2015 22:43, Egon Willighagen wrote:
This last test from the cmd line is already with master from GitHub...
Thanks, we
On Thu, Jan 15, 2015 at 12:39 PM, Tim Dudgeon tdudgeon...@gmail.com wrote:
OK, will use IteratingSMILESReader, but the basic problem of format
detection remains.
FormatFactory.guessFormat() does not seem to recognise smiles, and
presumably wouldn't return IteratingSMILESReader (or
Hi John,
On Tue, Dec 30, 2014 at 1:19 AM, John May john.wilkinson...@gmail.com wrote:
I’m pleased to announce that the CDK is now available on the central maven
repo.
Great work!
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University
On Fri, Dec 19, 2014 at 11:42 PM, Zheng Shi zs...@ualberta.ca wrote:
When I look at these molecules which report exception, I find their z
coordinates are all 0. I just wonder whether this does effect on
calculating TPSA. If so, how can I calculate TPSA for these? Thanks.
Is your input
(Arvid: can you have a glance at this email too, please?)
Scooter,
On Tue, Nov 25, 2014 at 3:15 AM, Scooter Morris scoo...@cgl.ucsf.edu wrote:
I'm really struggling with jni-inchi and OSGi. There are two
problems I keep running into. First, I keep getting a warning:
Yeah, it's an
On Tue, Nov 25, 2014 at 8:41 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I am using CDK-1.4.11.
Can you please try with a version from the CDK 1.5 series, preferably
the latest?
I ran this test against master:
@Test
public void testSubstructureBug20141125() throws
Dear Yannick,
On Thu, Nov 20, 2014 at 5:21 PM, Yannick .Djoumbou y.djoum...@gmail.com wrote:
IAtomContainer molecule = sp.parseSmiles(CSCCSCO);
SMARTSQueryTool smarts_pattern = new SMARTSQueryTool([#6]S[#6]);
OK, that seems to work:
Hi all,
I just had a look a the source package, that but is beyond my
capabilities and available time to learn all the things in this nas
package.
In addition to binNMUs, the problem also shows up for multiarch
environments, like mine. For example, because you have i386 Skype
installed on a
Hi all,
I just had a look a the source package, that but is beyond my
capabilities and available time to learn all the things in this nas
package.
In addition to binNMUs, the problem also shows up for multiarch
environments, like mine. For example, because you have i386 Skype
installed on a
Hi Martin,
since I just have the CDK as project in Eclipse, I do not actually
have experience with this... is that a possible alternative for you?
I would also suggest to file a bug report, so that we don't forget to
look into it... I am, sadly, too busy at right this moment...
Egon
On Wed,
Dear Yannick,
On Wed, Oct 29, 2014 at 10:47 PM, Yannick .Djoumbou
y.djoum...@gmail.com wrote:
I am using IteratingMDLReader to iterate over a SDF file and do some
operations on the molecules. I would like to get the name for each compound,
so that I can easily assign the results of the
On Fri, Aug 29, 2014 at 1:38 PM, John May john...@ebi.ac.uk wrote:
I was thinking we should move off 1.6 since it’s no longer supported. I would
like to hop 1.7 and go straight to 1.8 since it’s been out a while but wanted
some opinions. Would changing the JDK version cause problems for
Hi all,
I had not seen anything about the below contest... but looks interesting!
Egon
-- Forwarded message --
From: Dietrich Rordorf / MDPI rord...@mdpi.com
Date: Tue, Jul 22, 2014 at 3:27 PM
Subject: [CHMINF-L] Prize for best open source cheminformatic tool,
part of the
Dear Zheng,
On Fri, Jul 18, 2014 at 11:20 PM, Zheng Shi zs...@ualberta.ca wrote:
When I want to get information from a SDF file with CDK, my question is how
can I get the additional information in sdf file after the END line. The
data looks like below, I can get all the information about the
On Thu, Jul 10, 2014 at 9:43 AM, Peter Murray-Rust pm...@cam.ac.uk wrote:
. I plan to try pandoc. Egon, does it REQUIRE the BMC stylesheet?
Or can I take the style sheet out of the TeX and just convert it anyhow?
Yes, but I would indeed take the approach you suggest, and remove the
templates,
Interesting use case!
Egon
http://enanomapper.net/
On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com wrote:
Hi,
I have made a silica nanoparticle using Materials Studio and I want to
modify surface chemistry of it, I want to remove unwanted groups from the
surface and
Bob,
On Fri, Jun 20, 2014 at 9:31 AM, Angel Herráez angel.herr...@uah.es wrote:
I do not think that Jmol is your best tool for that, since I am
guessing there will be a lot of (repetitive) silica groups to which
the new groups must be added. Removal of groups is probably easy.
For just one
Kazem,
On Fri, Jun 20, 2014 at 8:37 AM, Kazem Sepehrinia ksepehri...@gmail.com wrote:
I have made a silica nanoparticle using Materials Studio and I want to
modify surface chemistry of it, I want to remove unwanted groups from the
surface and create some new groups on the surface of
On Fri, Jun 20, 2014 at 12:46 PM, Angel Herráez angel.herr...@uah.es wrote:
My concerns are about correct atom position, and also adding more
atoms that were not present and should go in the right positions too.
Understood and agreed... if I think of the nanotox field, however,
they typically
Hi Karol, all,
On Thu, May 22, 2014 at 4:36 PM, Karol M. Langner
karol.lang...@gmail.com wrote:
You could also add cclib:
paper: http://dx.doi.org/10.1002/jcc.20823
repo: https://github.com/cclib/cclib
I added these two, but not the webpage... I have done that only for
the main Blue Obelisk
Hi all,
some weeks ago I started making an ImpactStory profile for the Blue
Obelisk. May service as back pocket material if you promote the Blue
Obelisk. It's hard to say we do not have impact, and I think we
succeeded in making a change.
I have followed Figure 4 from the second Blue Obelisk
On Wed, May 14, 2014 at 12:26 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
I wonder how that might be useful for collaborative applications such as eg
CDK, JSmol and the like? Would all the contributor’s ORCIDs bee needed?
Interesting idea! Passed along to @ImpactStory:
On Wed, May 14, 2014 at 1:29 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
I am giving a keynote on Open Data at the Hinxton Genome Campus tomorrow and
will highlight this.
Ah, that reminds me I still had to upload BODR 10 to FigShare... now done:
Dear Blue Obelisk community,
with great sadness it is that I heard yesterday that Jean-Claude
Bradley passed away yesterday. Please read below more information from
Drexel University below. Jean-Claude received the Blue Obelisk award
in 2007.
I have know Jean-Claude for some years and did some
On Wed, May 14, 2014 at 3:43 PM, Craig James cja...@emolecules.com wrote:
www.opensmiles.org
Yes, checked and website can indeed be listed. Added!
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage:
All,
I think I saw this pass by but cannot find it in my inbox, but how did
I get passed this compile error: Plugin requires Maven version 3.0 ?
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage:
Hi all,
the CDK has code to read CML files with a JMOL-ANIMATION convention
which was one used to store Jmol animations in the Chemical Markup
Language.
Is anyone using this convention or using CML in general for conventions?
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
On Thu, Mar 6, 2014 at 3:49 PM, Robert Hanson hans...@stolaf.edu wrote:
What does that even mean, Jmol-Animation convention?
convention is a concept from the Chemical Markup Language format. A
convention refers to how various CML elements encode particular
content.
And how could you possibly
On Thu, Mar 6, 2014 at 4:00 PM, Robert Hanson hans...@stolaf.edu wrote:
sure. I see. Right. Standard, simple animation. Thank you.
And your questions basically confirm my suspicion :)
Thanks,
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University
Dear Peter,
On Sun, Mar 2, 2014 at 11:09 AM, Peter Murray-Rust pm...@cam.ac.uk wrote:
Is this still possible (I was invited to a phylogenetic project but told
that it wasn't funded). So has the deadline passed?
The deadline for mentoring organizations has passed. I did not have
time to try and
Hi all,
I spotted at least two projects in the Google Summer of Code, which
have links to the CDK:
1. NRNB where Cytoscape and PathVisio are falling under. Cytoscape and
PathVisio both have chemical viewer plugins that use the CDK. They
need upgrading to CDK 1.5 and general improvements.
2.
Hi all,
another year, another Google Summer of Code. And again it is possible
to work on Open Source tools in the area of chemistry.
Below are a few things that I have spotted. What else is out there?
* NRNB mentoring organization [0]
- Cytoscape has a chemical structure viz plugin based on
On Thu, Feb 20, 2014 at 8:07 AM, Wibe de Jong wadej...@lbl.gov wrote:
Please peer review, comment, and apply.
Can you check my comment?
https://github.com/wadejong/bodr/commit/c7917225cad829507bdd4c8c2fe7ebd3d795c021#commitcomment-5447272
Thanks,
Egon
--
E.L. Willighagen
Department of
On Sun, Dec 8, 2013 at 10:57 PM, Hugh Williams hwilli...@openlinksw.com wrote:
No problem, looking back through the thread I presume the query you are
running is:
SELECT DISTINCT ?property
WHERE { [] ?property [] }
ORDER BY ?property
I believe ?
Yeah, but I am starting to believe the
Hi Hugh,
my apologies for the late reply... been busy again...
On Wed, Oct 16, 2013 at 4:19 AM, Hugh Williams hwilli...@openlinksw.com wrote:
What is the current triple count of your Virtuoso Server instance.
129857455
Also when the database is warm can you please provide the output of
Hi Jmol devs,
This JChemInf paper introduces CH5M3D: an HTML5 program for creating
3D molecular structures:
http://www.jcheminf.com/content/5/1/46/abstract
Jmol is cited and compared to.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht
On Mon, Nov 11, 2013 at 4:42 PM, John May john...@ebi.ac.uk wrote:
Yes you need to process the structures separately. It’s not that there is a
good but more likely there is non-covalent bonding - you can see how
toolkits interpret - [Na+].[Cl-].
I have not tried it, but it may be worth trying
Hi all,
our group has three vacancies open. Our group does a lot of open chem-
and bioinformatics, and includes the Open Source projects
WikiPathways, PathVisio, BridgeDb, the CDK, etc.
Two of the three positions (a postdoc and PhD position) are for a EU
FP7 project that I will start early next
Hi all,
are there plans within Debian for the upcoming Java security changes,
which make many unsigned and self-signed applets blocked somewhere in
2014?
Are there options for Debian to become a trusted signer of applets?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of
Hi all,
with a lot of pleasure I can tell you that my very basic, one
afternoon Android hacky app has made it into the F-Droid app store:
https://f-droid.org/repository/browse/?fdid=com.github.egonw.isotopes
It uses the Blue Obelisk Data Repository and the Chemistry Development
Kit. It's GPLv3
Hi all Blue Obelisk-ers,
this just came by on the open-science mailing list of the OKFN...
Interesting questions... crappy survey (not particularly hard to see
what they like as answers; which is Open for a change), I'd say, but
good for the cause...
In fact, it makes me suspicions this is
On Thu, Oct 10, 2013 at 4:54 PM, John May john...@ebi.ac.uk wrote:
Molecule: 13, ChemicalEntity: 6, AtomContainer: 1, AtomAndBondCould: 0 -
Good. Clear, I would say.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University
On Fri, Oct 4, 2013 at 4:32 PM, John May john...@ebi.ac.uk wrote:
There is no more Molecule in new CDK versions only AtomContainer, this could
be confusing - vote here: http://strawpoll.me/501772
Nico Adams suggested on Google+ the obvious thing that I should have
thought of last Friday too...
John,
On Mon, Oct 7, 2013 at 9:59 AM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
On 7 October 2013 10:28, Egon Willighagen egon.willigha...@gmail.com
wrote:
On Fri, Oct 4, 2013 at 4:32 PM, John May john...@ebi.ac.uk wrote:
There is no more Molecule in new CDK versions only
On Mon, Oct 7, 2013 at 10:11 AM, John May john.wilkinson...@gmail.com wrote:
It's much better to do one thing really well then to do many things poorly.
But that is not the same as only doing one thing.
The CDK is really slow and introducing a more complex object model will only
make things
On Mon, Oct 7, 2013 at 10:27 AM, John May john.wilkinson...@gmail.com wrote:
Any projects you know that make heavy use of IPolymer (excluding Bioclipse)?
Is that not enough?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University
On Mon, Oct 7, 2013 at 11:00 AM, John May john.wilkinson...@gmail.com wrote:
We're using proportional representation right? :-)
Molecule 3, ChemicalEntity 3 - http://strawpoll.me/514829/r
Molecule 13, AtomContainer 4 - http://strawpoll.me/501772/r
I'm fine with whatever the community agrees
On Mon, Oct 7, 2013 at 1:19 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
You have to do a better job at convincing me how the CDK is and is not
used...
Every use case of the CDK I have seen involves the use of CDK functionality
to represent core chemical objects (atoms, bonds, molecules)
On Mon, Oct 7, 2013 at 1:21 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
One could argue that if a class is only needed by one external project, then
that project should be maintaining that class, rather than it being pushed
into the core CDK. On the other hand, polymer support would be
On Mon, Oct 7, 2013 at 1:30 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
I have to say though - if a functionality or package is used by one or two
people, I do not see it as sufficiently vital to the CDK that it be included
in the codebase. Why not push those types of things to a contrib
On Fri, Oct 4, 2013 at 4:32 PM, John May john...@ebi.ac.uk wrote:
RDKit: RWMol, ROMol
ChemAxon: Molecule (extends MolGraph)
Open Babel: OBMol
PerlMol:Chemistry::Mol
OUCH:Molecule
Daylight:molecule
Do all of these have crystal support too?
I don't care about the semantics
Hi VOS community,
we have recently upgraded our VOS7 SPARQL end point for the ChEMBL-RDF
data [0]: http://rdf.farmbio.uu.se/chembl/sparql
It's crashed a few times (not sure why; I'm now monitoring it day by
day), but I was originally looking forward to the faster performance.
I started from a
On Fri, Oct 4, 2013 at 11:18 AM, Jerven Bolleman
jerven.bolle...@isb-sib.ch wrote:
This query is very cheap to answer no matter which store is used.
Good point. Because it takes some 2secs on average I did not think of
it as being a cheap call:
Hugh,
On Fri, Oct 4, 2013 at 2:38 PM, Hugh Williams hwilli...@openlinksw.com wrote:
1. The output of running the status(); run from command from the Virtuoso
isql commandline tool
REPORT
VARCHAR
On Tue, Sep 24, 2013 at 10:14 PM, lochana menikarachchi
locha...@yahoo.com wrote:
Is there anyway to get the MDLV2000 representation as a String from
IAtomContainer??
Yes, use the Java StringWriter (pseudo code):
StringWriter strWriter = new StringWriter();
writer =new
On Sun, Sep 22, 2013 at 3:21 PM, lochana menikarachchi
locha...@yahoo.com wrote:
My biggest concern is the charge column. One of our programs uses a
proprietary program that relies on this information.
I need to check on the issue from 2011 you refer too, but charge in
general has been read
to take advantage of that:
http://www.opentox.org/meet/opentoxeu2013/opentox-euro-2013-hotels-1
Please also ping me if you are interested in a Blue Obelisk meeting or
dinner. Looking forward to meet up again with the Open Science
chemistry community!
With kind regards,
Egon Willighagen
0.http
Martin, all,
On Fri, Aug 23, 2013 at 6:23 AM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
On 22 August 2013 23:55, Martin Guetlein martin.guetl...@googlemail.com
if we're talking about mixtures (which is not really the case for a dot
connected representation), there could be various
On Sun, Aug 4, 2013 at 10:21 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I will try to make a BODR 10 release due in a week or two.
BODR 10 is now available from SourceForge for download:
https://sourceforge.net/projects/bodr/files/bodr/10/
Thanks to all that contributed
OSRA 2.0 has been released and Rich Apodaca provides build
instructions for Ubuntu in his blog, which may be useful for packaging
this for Debian too.
http://metamolecular.com/blog/2013/08/07/reading-chemical-structures-from-images-with-osra-2-0/
Egon
--
To UNSUBSCRIBE, email to
OSRA 2.0 has been released and Rich Apodaca provides build
instructions for Ubuntu in his blog, which may be useful for packaging
this for Debian too.
http://metamolecular.com/blog/2013/08/07/reading-chemical-structures-from-images-with-osra-2-0/
Egon
--
To UNSUBSCRIBE, email to
: Barry Hardy (Douglas Connect), Andreas Karwath,
Stefan Kramer (Johannes Gutenberg University of Mainz), Nina Jeliazkova
(Ideaconsult), Egon Willighagen (Maastricht University), and Juergen
Borlak (Hannover Medical School)
Abstract Submission:
https://www.easychair.org/conferences/?conf
On Mon, Aug 5, 2013 at 1:37 PM, John May john...@ebi.ac.uk wrote:
I release 1.5.3 yesterday - quite a few changes which I'm summarised here:
https://github.com/cdk/cdk/wiki/1.5.3-release-notes
Thanx!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Hi all,
I just released an update to the CDK 1.4 stable branch [0]. With the
work in this 19th minor release, CDK 1.4 has become the most stable
CDK version ever (with a big thanx to John for fixing some long
standing regressions) [1].
My comments on this release:
This release is another bug
Hi all,
just a quick ping that I have been working on updating BODR,
addressing outstanding issues, updates for recent element namings, and
going through CDK and Kalzium bug reports to see what is relevant for
the next release.
Please note the following:
1. if your project uses BODR data,
Hi all,
I am preparing a BODR 10 release. Please check the ChangeLog for the changes:
https://sourceforge.net/p/bodr/code/74/tree/trunk/bodr/ChangeLog
I guess the biggest change is the license change (discussed some 1.5
yrs ago) from MIT to CCZero. For the rest, several bug fixes and
updates
On Mon, Jul 1, 2013 at 10:03 AM, nls...@users.sourceforge.net wrote:
I will also be at the OpenTox Meeting. I am a developer of Scaffold Hunter [0]
and we are using the CDK for our project.
Is Scaffold Hunter used for toxicology-related data? If so, how about
an abstract for an oral in my Open
Hi all,
I am going the OpenTox EU 2013 [0] meeting to host a session on Open
Approaches. I know the CDK is used for QSAR like applications,
including those involved in toxicology...
Who else is coming to Mainz, and, should we have an informal CDK
meeting there? There are at least a few CDK
On Thu, Jun 27, 2013 at 12:28 PM, John May john.wilkinson...@gmail.com wrote:
We'll still have the nightly but to link to the docs (i.e. from a blog post)
these new links will be stable (for as long as github keeps gh-pages) and
will document the latest build (e.g. 1.4.18) at the minor version
On Sun, Jun 2, 2013 at 7:18 PM, John May john...@ebi.ac.uk wrote:
... it would say there are only 2 atoms (on the naphthalene) belonging to two
rings. In my mind the correct
answer is 8 which we could easily reach using a different unique ring set.
Why not 10? 2 from the naphtalene and 8 from
On Sat, May 11, 2013 at 9:20 PM, Angel Herráez angel.herr...@uah.es wrote:
Meanwhile, I have uploaded a combined J(S)mol logo-banner to the wiki,
http://wiki.jmol.org/index.php/File:J%28S%29mol_logos13.png
(also attached here)
In find it a bit hard to read the Jmol... as they are less bordered
On Sat, Apr 13, 2013 at 11:52 AM, John May john...@ebi.ac.uk wrote:
I changed the CML reader/writer a while back to be compatible with
MarvinSketch and not depend on everyone using the dictRef. Looks like the
molecule is read correctly though and it's the selection which is messed up?
No,
On Mon, Apr 8, 2013 at 6:50 PM, Michel Dumontier
michel.dumont...@gmail.com wrote:
Charlie, Eric, Kerstin, and others, keep up your good work to communicate
the benefits of Semantic Web technologies in simplifying and improving the
delivery of knowledge across the regulatory and
On Wed, Apr 3, 2013 at 10:35 AM, Noel O'Boyle baoille...@gmail.com wrote:
Sunday after CINF reception?
Yeah, that should work for me too, I think.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
On Wed, Apr 3, 2013 at 10:33 PM, Robert Hanson hans...@stolaf.edu wrote:
Oh my! http://www.chm.bris.ac.uk/jmol/jmol-7/
Nice, but it does not beat Jmol 0.6 from March 2001:
jmol-0.6.1.tar.gz 2001-03-26 2.9 MB
- https://sourceforge.net/projects/jmol/files/OldFiles/
That said, there is not much
On Tue, Apr 2, 2013 at 1:41 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Any suggestions on where and when to meet? My vote is
7:45pm, at the Convention Center
I think I am expected to show up at the Sci-Mix meeting that night
with two posters... I would join around 10pm for a drink.
Egon
On Tue, Mar 12, 2013 at 9:35 PM, Marcus D. Hanwell
marcus.hanw...@kitware.com wrote:
To that end, we would like to know which of our Avogadro contributors
agree to relicensing their contributions under the 3-clause BSD
license, linked below,
http://opensource.org/licenses/BSD-3-Clause
If
Hi all,
who else is going to the ACS meeting in New Orleans in April and like
to join a Blue Obelisk dinner/drink?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
On Fri, Feb 22, 2013 at 5:59 PM, Robert Hanson hans...@stolaf.edu wrote:
A lofty goal. No such plans at this stage.
Understood, and no worries :) There will always be plenty of ideas,
but without the bank account of someone like Gates or Slim, we won't
be able to implement them all :)
Plenty
On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson hans...@stolaf.edu wrote:
Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still
work to be done to ensure faithful rendition, but it's a start.
Nice!
Do you also have in mind of writing such files? That would very nicely
Anyone knows?
-- Forwarded message --
From: Robert Hanson hans...@stolaf.edu
Date: Fri, Jan 18, 2013 at 11:26 PM
Subject: [Jmol-users] PDB - OK, who's the wise guy?
To: jmol-us...@lists.sourceforge.net jmol-us...@lists.sourceforge.net
Where does THIS come from? Hex code in a PDB
Hi all,
I like to not have a CDK hangout today. I have a EC funding meeting in
Brussel next week (my first) about a lot of money, and quite nervous
about it :)
So, the next CDK G+ Hangout is the 18th Jan 4:00 PM CET If you like
to join, follow the G+ page of the CDK and let me know you like to
Hi Oliver,
On Fri, Jan 4, 2013 at 10:44 PM, Oliver Karch
oliver.ka...@merckgroup.com wrote:
Indeed using silent builder fixed the issue! I think debug builder would
also do,
It should... I have not had time to look at it yet, but from your
first post already had the impression that you had hit
On Mon, Dec 17, 2012 at 9:29 PM, John May john...@ebi.ac.uk wrote:
It seems strange this would only happen on OS X but it may well be the case.
Bioclipse use OSGi so it might be worth asking them if they have had any
issues with JNI-InChI and OSGi.
Yeah, Arvid Berg made OSGi bundles for
Hi all (potential) code reviewers,
I have left three small patches for cdk-1.4.x to fix a few further
issues in that branch, addressing a few failing unit tests:
595 Fixed the PDBReader.accepts() to also properly accept interfaces,
fixing 1 testAcceptsAtLeastOneChemObjectClass() unit test
Hi all,
here are the minutes of the monthly CDK G+ Hangout where developers
and users can meet up and discuss things.
* 1.5.x state
- number of fails/errors still too high for recommended use
* patches
- comparator patches: should go into 1.4.x accept patches for master
- query chem object
Hi all,
That sounds like a great idea, but only if the metadata itself is maintained,
which is generally hard as these things fall into disrepair. For example the
HCLS LODD entry for the DrugBank RDF [1] claims that it is updated regularly
when in reality it has not been updated since 17
On Fri, Nov 16, 2012 at 11:16 AM, r...@ark.in-berlin.de wrote:
You would then have to add that the above defined molecule has
nothing to do with CDK's Molecule class which is, fortunately for
your definition, phased out.
Yeah, the CDK 'Molecule' was aimed at fully connected graphs... but
that
Hi Joos,
On Fri, Nov 9, 2012 at 11:19 AM, Joos Kiener j...@sunrise.ch wrote:
The issue is to create and sdf file were all the disconnected structures are
nicely displayed. Running StructureDiagrammGenerator only works for
connected structures and GeometryTools also don't seem to offer a out of
On Wed, Nov 7, 2012 at 9:08 PM, Morten Omholt Alver
mortenal...@gmail.com wrote:
I'll try to start the upgrade tomorrow, unless someone has objections to this.
No objections. What we noticed with the CDK is particularly that the
bug system is quite different (e.g. bugs will be renumbered, but
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