Hi all,
the last weeks have been really busy for me, with my full time Open
PHACTS position, and writing for a EU call on the side. And I am on
holiday right now, and had actually hoped to finish a my book on the
CDK API Groovy Cheminformatics ...
I have received various patches in good order,
Hi all,
I know some of you are festing in Helsinki, but I'm in Cambridge and
up for a pub drink tonight.
Feel free to join! Of course, discussions will be about the Blue
Obelisk and Blue Obelisk projects...
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics -
On Tue, Sep 18, 2012 at 2:15 PM, Noel O'Boyle baoille...@gmail.com wrote:
Excellent. Count me in in spirit. Unfortunately, actually getting
there will involve working around other things which I don't know the
details of right now. Can you email me a phone number off-list and I
can text closer
On Thu, Aug 2, 2012 at 10:49 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
here is a kind reminder to fill out the Doodle to indicate what hours
in a week you could join an online monthly CDK meeting.
Thanx to all who filled out the Doodle.
The monthly meeting is now set to Fridays
On Wed, Sep 5, 2012 at 9:14 AM, Rianne Fijten riannefij...@gmail.com wrote:
InChIGeneratorFactory factory = null;
InChIGenerator generator = null;
try {
generator = factory.getInChIGenerator(molecule);
I think you forgot to instantiate the factory here :)
factory =
On Thu, Aug 30, 2012 at 9:36 AM, Peter Murray-Rust pm...@cam.ac.uk wrote:
On Thu, Aug 30, 2012 at 2:08 AM, Andrew Dalke da...@dalkescientific.com
wrote:
On Aug 29, 2012, at 4:02 PM, Peter Murray-Rust wrote:
[Please note that I personally do not have write access to the BO
pages].
So, umm,
Dear Andrew,
On Mon, Aug 27, 2012 at 12:14 PM, Andrew Dalke
da...@dalkescientific.com wrote:
3) SMARTS from Ehrlich and Rarey's recent J. Cheminformatics paper
Ehrlich and Rarey published a list of 1235 SMARTS in
Systematic benchmark of substructure search in molecular graphs -
From
On Mon, Aug 27, 2012 at 7:12 PM, lochana menikarachchi
locha...@yahoo.com wrote:
Is it possible to create a custom fingerprint using CDK?
Yes. An example is actually given in my book...
Two options:
1. implement the IFingerprinter interface
2. use a list of predefined substructures...
Which
Hi Niels, Onkar,
On Thu, May 24, 2012 at 9:54 AM, Niels Thykier ni...@thykier.net wrote:
Personally I have no issues with targetting this for experimental; in
fact I think it makes perfect sense to use experimental for possible
API/ABI issues[1].
Daniel Leidert and I met up in Utrecht along
Hi Niels, Onkar,
On Sun, Aug 5, 2012 at 10:02 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I will have a look the JavaDoc cleaning thing now...
I quickly figured out that that would take me more effort, to properly
hook that in the Debian build systems...
I did have a look
CDK 1.4.13 is released now. I have checked the debian/ folder on Alioth,
and have the attached patch to simplify compiling by reducing the amount
of needed patching.
** Patch added:
0001-Refresh-patch-as-per-latest-upstream-source-use-ant..patch
Hi all,
here is a kind reminder to fill out the Doodle to indicate what hours
in a week you could join an online monthly CDK meeting.
Egon
On Sun, Jul 15, 2012 at 12:39 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Dear all,
On Sun, Jul 15, 2012 at 12:29 PM, Egon Willighagen
Dear Andrey Paramonov,
I am cleaning up my email inbox these days, and just ran into your
email to cdk-user@...
On Tue, May 1, 2012 at 9:57 PM, Андрей Парамонов cmr.p...@gmail.com wrote:
I'm trying to implement a simple MOL-to-SVG renderer using CDK 1.4.7.
The source code, input and output
On Sun, Jul 29, 2012 at 11:06 AM, Андрей Парамонов cmr.p...@gmail.com wrote:
Also, I want to point you to the option of creating SVG via the
JChemPaint stack? There is activity in that area:
https://github.com/JChemPaint/jchempaint/wiki/The-svg-font-problem-and-its-solution
I've looked
Hi Stephan,
On Sun, Jul 22, 2012 at 9:46 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
I'm trying to find GPL retorsynthesis software, such as LHASA or WODCA. As
it seems all of the freeware I knew from 2002 is gone, and only 1 commercial
version I could find cost several thousand dollars, I
Hi all,
I have just written up an introduction into code review with Nightly
(and the Ant build system) in my blog:
http://chem-bla-ics.blogspot.nl/2012/07/cace-computer-aided-code-evaluation-of.html
I hope you find it useful,
with kind regards,
Egon
--
Dr E.L. Willighagen
Postdoctoral
On Sun, Jul 22, 2012 at 10:13 AM, Rzepa Henry h.rz...@imperial.ac.uk wrote:
I would love to sprinkle QR codes in lecture notes, and have students
acquire the molecule on their mobile device seconds later?
QR codes basically encode a random string. Commonly, URLs, e.g. with
QRate.me for
On Wed, Jul 18, 2012 at 11:47 PM, John May john.wilkinson...@gmail.com wrote:
It would be good to unify the 'has2DCoordinates' and 'has3DCoordinates'
Absolutely. This is what 'master' is about.
to behave the same way. Personally I would opt to change 'has2DCoordinates' as
I can see the use
Dear CDK users and developers,
last Friday the project had a first online teleconference (using
Google+ Hangout), which we plan to repeat. While the purpose of these
meetings is CDK development, both developers *and* users can find
interest in joining these meetings. To the developers user
Dear all,
On Sun, Jul 15, 2012 at 12:29 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
We agreed on having monthly meetings from now on, and I will set up a
Doodle to find a good time slot.
I have set up this Doodle at: http://www.doodle.com/9ss2ywb2hbgbdfpq
Please use it to indicate
Hi Lochana,
On Mon, Jun 25, 2012 at 5:47 PM, lochana menikarachchi
locha...@yahoo.com wrote:
What is the boolean[] doubleBondConfiguration in chiralSMILES generator??
If not mistaken, this indicates whether the bond is E/Z or not...
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
While I was looking for another bugreport I made, I saw this one
again, and while now about 17 months old, it was easy to reproduce:
$ reportbug
/usr/lib/pymodules/python2.7/reportbug/ui/gtk2_ui.py:453:
PangoWarning: pango_layout_set_width: assertion `layout != NULL'
failed
gtk.main ()
Package: oss4
Version: 4.2-build2004-1
Severity: normal
The release on Date: Tue, 14 Jun 2011 10:06:56 -0500 closed the wrong bug. The
below is a snippet from the changelog:
Closes: 589127 595298 604679 619272 627149 628879
and
* debian/control: adjust linux-headers dependencies (Closes:
Kevin, Nina,
a unit test to show it is no good would be useful...
On Fri, Jun 1, 2012 at 10:27 AM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
P.S. unfortunately nobody picked up my last year challenge for a good
open source LogP model ...
Package: calligrasheets
Version: 1:2.4.1-1
Severity: normal
I cannot start the program from the command line:
$ calligrasheets
sheets(365)/kdecore (services) KServiceFactory::findServiceByDesktopPath:
sheetspart.desktop not found
sheets(365)/kdecore (services)
On Tue, May 29, 2012 at 4:42 PM, Bernadette Hyland
bhyl...@3roundstones.com wrote:
Perhaps use a mail filter rule that includes CfP or other subject tags so
you aren't flooded. I for one find the calls useful and not much of any
annoyance.
If only that was consistently used... I find a list,
Hi all,
my inbox is flooded with call for papers for the many SemWeb
conferences, meetings, special issues, ...
This is silly: can we please use SemWeb technologies for this instead,
so that when I have something to submit, I can just query for upcoming
meetings, issues, etc?
Egon
--
Dr E.L.
Package: python-cinfony
Version: 1.0-1
Severity: wishlist
Tags: upstream
Cinfony 1.1 has been released and supports CDK 1.4.x, which is requested to be
sponsored for unstable, but blocked by being binary incompatible with Cinfony
1.0.
-- System Information:
Debian Release: wheezy/sid
APT
NIels,
On Wed, May 23, 2012 at 10:04 AM, Niels Thykier ni...@thykier.net wrote:
On 2012-05-19 14:56, Onkar Shinde wrote:
It seems that some public methods are changing signature and also that
some public constants are disappearing in this release (compared to our
current version).
Which ones
Hi Niels,
On Wed, May 23, 2012 at 2:45 PM, Niels Thykier ni...@thykier.net wrote:
I just read the diff between our current version (1.2.10) and the RFS
version 1.4.9. Actually, thanks you just made me realize that it FTBFS
when built twice in a row!
Ah, right! Yes, from 1.2 to 1.4 there are
On Wed, May 23, 2012 at 4:15 PM, Niels Thykier ni...@thykier.net wrote:
The issue is that it fails to clean properly - at least some (java)doc
files are not cleaned, but also some non-text files (can't remember - I
didn't pay too much attention to it). I haven't actually investigated
the
On Thu, May 17, 2012 at 4:22 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
Some feedback; it's a nice read:
Drat. Now I can't use you as a reviewer. ;-)
:)
- in the reference section, many of the cited webpage do not author(s)
yet. Those should be added. E.g. 55. OpenSMILES 2012,
Hi Geoff,
On Wed, May 16, 2012 at 9:07 PM, Geoffrey Hutchison geo...@pitt.edu wrote:
We're currently finishing up a manuscript on Avogadro, to be submitted as
part of an upcoming special topic issue of J. Cheminformatics. I realized
last night, that in submitting to an open access journal,
On Wed, May 16, 2012 at 11:00 PM, Robert Hanson hans...@stolaf.edu wrote:
Thank you, Nico, for releasing Jmol 12.3.25. This version of Jmol is very
special. It includes
set forcefield MMFF
Well done!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Dear CDK and Bioclipse users,
with this email I would like to ask 2 minutes of your time (no, I'm
not going to offer 1M euro via Mr. Williams :). One of the standing
issues in the CDK was the lack of a general-purpose implementation of
an algorithm to find the location of double bonds in
On Mon, May 14, 2012 at 10:58 AM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
c1ccc(C[C@@H](C(N[C@H](Cc2c3c3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H]
Mmm... if I try the indole bit, it seems to work fine:
Cc2c3c3[nH]c2
I also note that Daylight fails on the
Hi all,
On Fri, May 4, 2012 at 1:44 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I'm moving forward with this, and write a patch against CDK 1.4.x,
because we'll need it for Bioclipse 2.6 (though Bioclipse can always
'fork' in case in mainstream CDK we decide to put it only
On Fri, May 4, 2012 at 3:36 PM, Syed Asad Rahman a...@ebi.ac.uk wrote:
Hi Egon, I am just curious about the impact or regression it might have. I
support the idea but in my past experience, playing with CDK atom types was a
challenging task!
I am giving this careful consideration, and is the
On Thu, Apr 26, 2012 at 5:21 PM, kevin.law...@syngenta.com wrote:
BTW I am using cdk-1.4.8. Have also tried the Iterating MDL Reader. This
also fails for V3000 files but works for V2000 files. However, if I use
cdk-1.4.2 then the iterating reader works fine for both V3000 and v2000
files
Some comments regarding updating the package for CDK 1.4.x ...
- r-cran-rjava no longer needed, as R interaction code has been removed (*)
- SVN is replaced with Git, with the main Git repos at
https://github.com/cdk/cdk/
- the Suggests: should be removed
- CDK 1.4 no longer has CLI tools, so the
Some comments regarding updating the package for CDK 1.4.x ...
- r-cran-rjava no longer needed, as R interaction code has been removed (*)
- SVN is replaced with Git, with the main Git repos at
https://github.com/cdk/cdk/
- the Suggests: should be removed
- CDK 1.4 no longer has CLI tools, so the
Hi all,
those who have seen my slides from the NBIC meeting [0], saw that the
journal with the highest journal impact factor [1] with new work where
the CDK is used is Nature Chemical Biology [2].
And today I saw this JACS paper where the CDK is used [3]. The
describes work on virtual generation
On Thu, Apr 26, 2012 at 11:07 AM, Noel O'Boyle baoille...@gmail.com wrote:
Maybe you can give that talk online sometime as part of a BBB conference.
Hint hint.
Sure, it was just 10 minutes :)
Regarding the Python stuff
(1) There's no numpy port to Jython. So to access the CDK and numpy
On Sun, Apr 22, 2012 at 10:40 PM, Eric Martz ema...@microbio.umass.edu wrote:
This is the first I've heard about PWF. There are some slides by
Helen Berman about it here:
http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf
Listening to a talk from Gerard
Hi all,
the Bioclipse team is looking for someone with good semweb skills to
be used in predictive toxicoloy, for a two year postdoc position.
See the announcement below, or follow this link:
http://www.uu.se/jobb/others/annonsvisning?tarContentId=186211languageId=1
Egon
-- Forwarded
Hi all,
thanx to Peter Maas, Chemical blogspace is still up and running:
http://cb.openmolecules.net/
While I was looking for citations of OpenMolecule RDF
(http://rdf.openmolecules.net/) I noted that Cb was cited a few months
ago in this paper:
Buchanan, Robert A. (2011) Beyond the Chemistry
On Sun, Apr 15, 2012 at 12:15 PM, Alan R Williams ala...@cs.man.ac.uk wrote:
2.4 is very nearly ready to go, so this has just squeaked in :-)
I have signed the contributor agreement, but do not think I currently
have write access to the Google code SVN repository.
Do you want me to add you?
cc: cdk-tave...@lists.sourceforge.net
2012/4/10 Kleo Achilleos kleoachill...@gmail.com:
I have tried connecting the ouput to some other CDK processor like
SMILES_File_Writer but it fails. That is why I thought the data wasn't read
properly.
I just tried a simple workflow: input .smi file,
2012/4/14 Kleo Achilleos kleoachill...@gmail.com:
Forgive my english. I only meant that I wasn't doing any obvious mistakes.
Nothing about CDK.
Same here! I only meant that I am not sure you are doing something
wrong; if you do, I am doing the same thing wrong :) But Andreas will
be able to
: Egon Willighagen egon.willigha...@gmail.com
Date: Sat Apr 14 17:04:12 2012 +0200
Fixed Jmol casing (JMol is a different project; no joke)
diff --git
a/ui/net.sf.taverna.t2.ui-exts/tags/ui-exts-1.3/renderers-exts/src/main/java/net/sf/taverna/t2/renderers/JMolRenderer.java
b/ui
On Fri, Apr 13, 2012 at 7:03 AM, Robert Hanson hans...@stolaf.edu wrote:
OK. Please test!
http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
Very nice!
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University
On Sun, Apr 8, 2012 at 6:02 PM, Donal K. Fellows
donal.k.fell...@manchester.ac.uk wrote:
On 08/04/2012 15:29, Kleo Achilleos wrote:
I am trying to run a CDK tool SMILES_File_Reader but the output is of
the form
[...]
I have Windows 7 - 64, Java 6, Taverna 2.3.0 and just installed CDK.
That they do not do these things yet, sounds like a there are a lot of
opportunities...
Egon
Op 5 apr. 2012 17:41 schreef Michel Dumontier michel.dumont...@gmail.com
het volgende:
In case you haven't seen, Nature PG now has LOD and a SPARQL endpoint :
On Wed, Apr 4, 2012 at 9:12 AM, Joos Kiener j...@sunrise.ch wrote:
I can generate images (png) however the issue I have is that the Molecule is
rendered too close to the boarder of the picture. It doesn't look nice at
all and sometimes something is cut-off.
Use the BasicSceneGenerator.Margin
On Wed, Apr 4, 2012 at 10:24 AM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
Still even without the border nothing should be cut off. That sound like a
scaling bug.
It is a know problem; the current bounds are calculated based on atom positions.
There are scaling problems, too, which is
On Mon, Apr 2, 2012 at 2:55 PM, M. Scott Marshall
mscottmarsh...@gmail.com wrote:
Having the next LODD/BioRDF telcon next week (NOT TODAY).
I will send an agenda for next week's call in the next few days.
Next week Monday is easter?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
On Mon, Apr 2, 2012 at 3:48 PM, M. Scott Marshall
mscottmarsh...@gmail.com wrote:
In the Netherlands it is a day off, yes. In Europe as well, I believe, but
not in the U.S. I was hoping that we wouldn't lose too many people.. We can
try for another day if that's the case.
OK, I'll try to be
On Thu, Mar 29, 2012 at 11:11 AM, Peter Murray-Rust pm...@cam.ac.uk wrote:
If you write a section on your code then this will generally mean that you
are listed as an author. We only want descriptions of the CML
interface/API/coverage - not the greater functionality of the program/library
I
Hi Jonathan,
On Fri, Mar 23, 2012 at 11:46 PM, Jonathan Gutow gu...@uwosh.edu wrote:
This suggests that there is a workaround for getting Jmol to work with the
IcedTea plugin. I thought from reading it that IcedTea couldn't handle the
segmented loading.
The applet loads for me nowadays in
On Thu, Mar 29, 2012 at 3:08 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
1. Do you want a QA controlled (by Apple) environment, or the more
advertising-oriented environment of Android?
I do have several Android apps installed without advertisement... I do
not think the above choice is
Dear Henry,
On Fri, Mar 30, 2012 at 11:01 AM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry,
All,
On Fri, Mar 30, 2012 at 10:29 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
I find it very disturbing that educators are even considering creating
a learning environment where students are restricted in their
learning! That is just another step back to the middle ages... Henry
On Thu, Mar 29, 2012 at 4:19 AM, Craig T Martin cmar...@chem.umass.edu wrote:
I don't yet have an iPad personally, but it's on my list of things to buy
next and I have a number of colleagues who are absolutely fanatical.
Tomorrow we go to the Dean to pitch an idea that will involve the purchase
Vance,
On Fri, Mar 23, 2012 at 10:01 PM, Vance - vance0...@gmail.com wrote:
Is it possible to render an image of a chemical, as well as to highlight or
mark certain elements within the image?
Depending on the version of the rendering code base you are using, you
can also look at these
Hi all,
to make your patches easier portable between master and cdk-1.4.x,
please do not use Molecule or IMolecule, only IAtomContainer...
because we removed the 'IMolecule' completely from master.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
On Wed, Mar 21, 2012 at 4:48 PM, Vance - vance0...@gmail.com wrote:
Where can I find some sample code that shows how to do this?
http://pele.farmbio.uu.se/nightly/api/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.html
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of
Dear Horacio,
-- Forwarded message --
From: Horacio Pérez-Sánchez
Date: 2012/3/23
Subject: Molecular flexibility analysis
I wonder whether Chemistry Development kit tools can be used for, given a
database with thousands of ligands, analyzing each ligand and reporting
which
On Fri, Mar 23, 2012 at 8:33 PM, Eric Martz ema...@microbio.umass.edu wrote:
I just heard a segment on NPR about hundreds of high schools that are
abandoning textbooks and giving every student an iPad instead.
This is so sad... we're not even over the MS vendor lock-in, and ready
to buy into
Hi Kevin, Rajarshi,
On Sat, Mar 17, 2012 at 7:27 PM, kevin.law...@syngenta.com wrote:
Here's a copy of what I posted originally but slightly recoded to have the
functions return
values instead of having them change passed objects as Rajarshi suggests. No
other
changes made (I hope!). I
On Mon, Mar 19, 2012 at 12:21 PM, kevin.law...@syngenta.com wrote:
As a quick test, I ran the first 1000 molecules in the Wellcome antimalarials
dataset through. Each Smiles string was parsed
and then subjected to CDKHueckelAromaticityDetector.detectAromaticity before
fixAromaticBondOrders
Scott,
On Mon, Mar 19, 2012 at 12:19 AM, M. Scott Marshall
mscottmarsh...@gmail.com wrote:
Tomorrow, a teleconference to discuss efforts to employ RDF for
expression studies (hoping for a short tour of code from a few
contributors) and follow up for LODD emerging practices note.
I have
On Sat, Mar 17, 2012 at 3:04 AM, kevin.law...@syngenta.com wrote:
O=C1Oc6c6(C(O)C1C5c2c2CC(c3ccc(cc3)c4c4)C5)
OK, I updated the unit test for that one.
Btw - fun to try your code (either with the modified algorithm or the
original CDK version) on the Smiles for
Acridine:
On Sat, Mar 17, 2012 at 8:46 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Kevin, it has your patch, and two unit tests.
Rajarshi made a few comments:
https://github.com/egonw/cdk/commit/aaaca27a2655d876c07296bd9e008914bef7858a
Kevin, could you please have a look at those? Particularly
Hi Kevin,
On Thu, Mar 15, 2012 at 7:12 PM, kevin.law...@syngenta.com wrote:
Conclusions:
1. I think the modified algorithm I originally attached will generate the
same results as the original CDK 1.4.2 algorithm but much faster for
molecules containing multiple, but mostly unconnected
Hi Martin,
On Tue, Feb 21, 2012 at 11:39 AM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
I found another example ( O=C1C=CNC(=O)N1 ) that is not aromatic
according to CDK, but according to daylight
(http://www.daylight.com/daycgi/depict?4f3d4331433d434e43283d4f294e31)
and OpenBabel.
Nina, Martin,
On Tue, Feb 21, 2012 at 1:23 PM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
Yes, it would be great to have some compatibility mode towards
OpenBabel. I am working on a piece of software that uses OpenBabel,
CDK and Jmol, and aromaticity causes a lot of problems.
can
Hi all,
I noticed a few recent questions about where to find what CDK class,
about the difference between the cdk-1.4.x.jar and jars like
cdk-core.jar... I will summarize things a bit. Some further contains
can also be found in my blog:
Hi all (for those not on the CDK Google+ page),
this may be interesting to you... they are specifically inviting
abstract submissions for talks that used Open Data, Open Source, and
Open Standards...
Egon
-- Forwarded message --
From: Uko Maran u...@theor.chem.ut.ee
Date: Thu,
Hi Joos,
On Sun, Feb 5, 2012 at 6:34 PM, Joos Kiener j...@sunrise.ch wrote:
for my Master Thesis in computer science (Master of Advanced Studies) I have
created a simple framework based on the CDK for storing and searching
chemical structures in a relational database.
How does it optimize
HI devs,
On Sun, Feb 5, 2012 at 9:02 PM, Marcus D. Hanwell (Code Review)
rev...@kitware.com wrote:
I'd like you to do a code review. Please visit
http://review.source.kitware.com/4169
to review the following change.
OK, I left my review comment... how does a reviewer sign off the
patch,
On Sat, Feb 4, 2012 at 1:57 PM, Nick Vandewiele
nick.vandewi...@ugent.be wrote:
The SMARTS string would not contain the entire SMARTS string and be cut-off
after [#1] sequence, probably due to the .asCharacters() method.
Another aspect to keep in mind is that in the XML parser world
character
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es:
Everything you describe sounds like the regular and proper way to do. It may
be your browser, but I would not expect it.
Any modern browsers now behave, and Iceweasel is Gecko-based, right?
Iceweasel is just Firefox, but the name 'firefox'
2012/1/29 Herráez Sánchez Ángel angel.herr...@uah.es:
I recollect other people reporting problems with IcedTea, may be that.
...
jmolInitialize(.., JmolApplet.jar)
Yeah, I'd found that too and using the signed full jar... and that
works in Konqueror, Icedweasel, and Chrome.
So, I think we
Lochana,
On Tue, Jan 17, 2012 at 6:08 PM, lochana menikarachchi
locha...@yahoo.com wrote:
I have a sdf file with abbreviated amino acids..The CDK SDF readers seem to
read this molecule but fails to write it back in SDF format..Is there anyway
to expand these abbreviations?? Any other library
Rajarshi,
do you have ideas?
On Mon, Dec 19, 2011 at 3:05 PM, Jochen Schreiber
jschr...@smail.inf.fh-brs.de wrote:
i have a question. I have updatet my ubuntu and now i am getting the
following error:
E.
--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
On Sun, Jan 22, 2012 at 4:37 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
On Sun, Jan 22, 2012 at 2:25 PM, Karol M. Langner karol.lang...@gmail.com
They sure are independent, if that's what you mean by orthogonal,
but many people would claim they are correlated (at least statistically).
Yes -
cc:jmol-user
Hi Peter,
2012/1/16 Peter Sahlin peter.sah...@akademi.bastad.se:
Hope you can read my swedish, otherwise tell me and I will translate.
Yeah, I could read it :) I'm not a native speaker, but in the past
three years up picked it up a bit.
Hämtade Jmol 12.3.12 igår, men där fick
On Mon, Dec 5, 2011 at 2:49 PM, Robert Hanson hans...@stolaf.edu wrote:
https://market.android.com/search?q=jmolso=1
Cool! And now that I actually have an android, even cooler!
Q: is it possible to create a URL or so, that would auto load the app
with a particular protein? Or better: with a
On Sun, Jan 8, 2012 at 12:05 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
Does anyone know what the current state of the Open Source JCAMP parsing
library at http://sourceforge.net/projects/jcamp-dx is?
Peter, since you are one of the three project leaders of that project,
I guess the most
Hi Eric,
On Wed, Dec 21, 2011 at 9:30 PM, Eric Jang ericjang2...@gmail.com wrote:
How are formal charges calculated for atom containers in CDK? Where can I
find the iterative algorithm?
At this moment, not really... practically, the atom type perception
takes care of that, but not quite...
Hi Martin,
On Mon, Nov 28, 2011 at 9:53 PM, Martin Riese
martin.ri...@googlemail.com wrote:
When I draw the single oxygen in the JChemPaint Applet
(http://www.ebi.ac.uk/steinbeck-srv/jchempaint-nightly/EditorApplet.html),
it automatically adds the implicit H2. I would like to do this as
well,
Hi Joos,
a short, quick reply... I will not have time to look in detail into
the issue in the next two weeks...
On Thu, Dec 8, 2011 at 12:47 PM, Joos Kiener j...@sunrise.ch wrote:
The Question is related to the cdk based project I'm working on which I will
officially release once I believe it
Lochana,
On Sun, Dec 18, 2011 at 1:24 AM, lochana menikarachchi
locha...@yahoo.com wrote:
I have noticed either cdk MDLV2000 reader or sdf writer looses some
information in the sdf file. (column 7) This breaks compatibility with other
programs that rely on this information.
Can you create a
Hi Dmitry,
On Mon, Nov 28, 2011 at 4:39 PM, Dmitry Katsubo
dmitry.kats...@gmail.com wrote:
When I try to render the molecule from InChI=1S/H2O/h1H2, the renderer
generates image with zero height/width. Is there any limitation in CDK
preventing this molecule from being rendered? Is it somehow
Dear all,
Andreas and Kalai worked on the new version of CDK-Taverna, compatible
and taking advantage of Taverna2, and the paper describing their work
has just been published (disclaimer: I am co-author):
New developments on the cheminformatics open workflow environment CDK-Taverna
Andreas
Hi all,
in the next two weeks I will not be online much, because of holidays
and moving to my next position, at Maastricht University... more on
that in my blog later.
I have quite a few email about the CDK in my inbox, and ask everyone
to be patient... I will reply. Moreover, there are also a
On Sun, Dec 11, 2011 at 7:47 PM, ngn
reply+c-785329-7e1f5b1fa10827fd4496e81c1df74439165f41d5-26...@reply.github.com
wrote:
Very good move to make readers implement IteratorT extend IChemObject !
But why dropping the interface from DefaultIteratingChemObjectReader ? It
could still be
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With kind regards,
Egon Willighagen
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm
Scott,
On Tue, Nov 22, 2011 at 12:36 PM, M. Scott Marshall
mscottmarsh...@gmail.com wrote:
We are wrapping up a Google Doc version of the W3C note. Please call
in to discuss it. We will be requesting comments from HCLS after this
last iteration of edits.
On Thu, Nov 24, 2011 at 9:47 AM, Joos Kiener j...@sunrise.ch wrote:
which seems to be a bit outdated (and for non-java-api-experts tedious to
find all the references).
I added the line for BasicSceneGenerator...
I have a repository with current scripts here:
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