Hi Joos,
On Thu, Nov 24, 2011 at 7:12 AM, Joos Kiener j...@sunrise.ch wrote:
generators.add(new BasicBondGenerator());
In your code, just before this line, add:
generators.add(new BasicSceneGenerator());
Grtz,
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
On Tue, Nov 22, 2011 at 10:18 AM, Jochen Schreiber
joc...@googlemail.com wrote:
If i try this command i get the following error:
java.lang.NullPointerException
at org.openscience.cdk.io.MDLReader.readMolecule(MDLReader.java:327)
at
On Tue, Nov 22, 2011 at 10:37 AM, Jochen Schreiber
joc...@googlemail.com wrote:
And i don't know how i could say to momsim.jar use the MDLV2000Reader.
Neither do I; I don't know that jar. I suggest contacting the author.
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för
On Tue, Nov 22, 2011 at 3:41 AM, Robert Hanson hans...@stolaf.edu wrote:
We just discovered that Jmol PNG images inserted in Google Documents
preserve their state after saving as zipped HTML.
What state are you referring to here? Does Jmol include a script to
restore the view as metadata in the
On Tue, Nov 15, 2011 at 12:02 PM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
On Tue, Nov 15, 2011 at 12:00 PM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
Hmm, that's bit unfortunate, but not too bad, I will hard-code the
descriptors then.
No need for that.
For the Groovy
Hi all,
I wrote up a blog post this morning with how anyone with just a
browser can make simple fixes, like spelling errors, and get some git
commit fame:
http://chem-bla-ics.blogspot.com/2011/11/simplest-way-to-make-cdk-commits.html
Grtz,
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
On Wed, Nov 2, 2011 at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote:
We have two independent reports of javax.Point3i problems when Jmol Jar
files are compiled on a PC and run on a mac. It seems somehow the Poin3i(int
x, int y, int z) initializer is missing.
It sounds to me that vecmatch is
On Wed, Nov 2, 2011 at 1:28 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Nov 2, 2011 at 1:07 PM, Robert Hanson hans...@stolaf.edu wrote:
We have two independent reports of javax.Point3i problems when Jmol Jar
files are compiled on a PC and run on a mac. It seems somehow
On Wed, Nov 2, 2011 at 1:31 PM, Miguel Howard mig...@jmol.org wrote:
I suggest that you simply rename the rename the 3D math packages that
are used by Jmol. That is, use eclipse and rename from javax.Point3i
to org.jmol.javax.Point3i ... or something like that. We have the
source code included
On Sun, Oct 30, 2011 at 4:04 AM, Robert Hanson hans...@stolaf.edu wrote:
Can that be real?
The CDK is at around 1800 a month, and Jmol has a much wider audience;
so, those numbers look comparable.
Or is mostly robots?
That is a good question. 20% has an unknown OS, so that could very
well be
Hi all,
per an itch caused by this Blue Obelisk eXchange question:
http://blueobelisk.shapado.com/questions/how-can-i-store-cdk-fingerprints-in-a-file
on FPS support, I have written a writer (no reader yet):
https://github.com/egonw/cdk/commit/baf2a383ba07002f97029ff12a2090feca2c2655
I
On Fri, Oct 21, 2011 at 9:47 PM, lochana menikarachchi
locha...@yahoo.com wrote:
The problem was with forgetting to add writer.close()
It fixed the problem.
Ah, happy you found the problem!
I will add a note to make this clear in the book... even developers
like we forgot to close the
On Thu, Oct 20, 2011 at 1:02 PM, Ola Spjuth ola.spj...@farmbio.uu.se wrote:
We have been struggling with using SMSD in the best way as it has several
options for
different use cases. Would it be possible to request from someone (perhaps
Asad?) to
set up a web page outlining the various use
Hej Ola,
On Thu, Oct 20, 2011 at 1:15 PM, Ola Spjuth ola.spj...@farmbio.uu.se wrote:
One thing I think could be improved in CDK is the handling/description of
post-processing after reading in chemical structures from different formats.
Understood. The problem is that formats not always have
On Fri, Oct 14, 2011 at 1:02 AM, Robert Hanson hans...@stolaf.edu wrote:
http://chemapps.stolaf.edu/jmol/docs/examples-12/isomers.htm
What's up with example 4? The MFs don't match... or is that intentional?
Just thought of this idea -- will be developing the page to have more
examples. Note
On Wed, Oct 5, 2011 at 11:55 AM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
just wanted to point you attention to a nice piece of work by Karen Schomburg
in the Rarey group in Hamburg.
She developed a way to visualise SMARTS.
Unfortunately, it is not free as in speech, but it *is* free as
On Wed, Oct 5, 2011 at 1:49 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Oh, there's a patch for this bug?
Not for this bug in the generator... but I was wondering if it was
related to the bug in the *parser*... for the latter I uploaded
patches...
Egon
--
Dr E.L. Willighagen
Postdoctoral
On Tue, Oct 4, 2011 at 2:07 PM, gilleain torrance
gilleain.torra...@gmail.com wrote:
It seems like the problem is with the SMILESReader. Where your code has :
SMILESReader sr = new SMILESReader(new StringReader(structure));
MoleculeSet set = (MoleculeSet) sr.read(builder.newMoleculeSet());
On Tue, Oct 4, 2011 at 2:36 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Tue, Oct 4, 2011 at 2:07 PM, gilleain torrance
parser.setPreservingAromaticity(true);
mol = parser.parseSmiles(structure);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
Ah, a recent
On Wed, Oct 5, 2011 at 2:40 AM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
On a somewhat related note, why does the atom type set aromaticity.
Shouldn't this be done via the perception class?
Is this the same problem with AtomTypeManipulator.configure() ?
In the SMILES parser the new patches
On Tue, Oct 4, 2011 at 9:32 AM, Nicolas Vervelle nverve...@gmail.com wrote:
I made an announcement on launchpad mailing list for the release of Jmol
12.2.
Did the updated for 'Dutch' came through properly?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
On Sun, Oct 2, 2011 at 4:04 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
This could be a problem in the morgan numbering - that was where the
last problem was
Yes, and/or the unique numbering scheme in the CDK based on top of the
non-unique Morgan numbers...
To everyone, we could really
On Mon, Sep 19, 2011 at 9:46 AM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
I think the aromatic bonds not should be matched.
I think the '~' bond should match any bond and ':' aromatic bonds, but
'-' is explicit for single bonds...
Egon
--
Dr E.L. Willighagen
Postdoctoral
Hi MediaWiki-plugin users,
while something like jmolSmilesCC/jmolSmiles works fine, when I
try to use this in a Template environment, like with:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
it does not work... the {{{Has Smiles|}}} is properly set, but the
applet gets not the SMILES
On Wed, Sep 14, 2011 at 10:09 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
jmolSmiles text=3D (Jmol){{{Has Smiles|}}}/jmolSmiles
I think a similar thing is happening with
jmolFile{{{CMLFile|}}}/jmolFile which now gives me this exception:
Catchable fatal error: Argument 1 passed
On Wed, Sep 14, 2011 at 7:05 AM, Brian Salter-Duke
b_d...@bigpond.net.au wrote:
On Wed, Sep 14, 2011 at 12:44:11AM +0200, Angel Herr?ez wrote:
https://wiki.ch.ic.ac.uk/wiki/index.php?title=User_talk:Rzepa1
All applets in there work for me:
That's in Fiirefox 6.0.2, WinXP, Java 1.6.0_27
Hi Martin,
I have not had time to answer earlier; it was on my list, but since
you seem stuck with it...
On Fri, Sep 2, 2011 at 12:12 PM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
IMHO, the problem is that the smiles writer (is there a smarts writer?)
No. What is the data model you
On Thu, Sep 8, 2011 at 9:33 AM, Martin Guetlein
martin.guetl...@googlemail.com wrote:
It might be solved by using SmilesGenerator.setUseAromaticityFlag(true)...
setUseAromaticityFlag(true) is already part of the code, but has no effect
on this example.
This was exactly why I had not replied
On Thu, Sep 1, 2011 at 11:42 PM, Deus, Helena helena.d...@deri.org wrote:
For those of you who haven’t answered and would like to give your 2c about
how provenance should be dealt with on the semantic web, here’s your chance!
Authorization would probably not be considered provenance, but I was
On Tue, Sep 6, 2011 at 11:18 AM, Deus, Helena helena.d...@deri.org wrote:
I will forward you concerns to the provenance workgroup.
Well, authorization is going to be a big thing in our EU project...
various reasons for that, social, contractual, political. That's just
the way it is. I can
On Thu, Sep 1, 2011 at 11:42 PM, Deus, Helena helena.d...@deri.org wrote:
For those of you who haven’t answered and would like to give your 2c about
how provenance should be dealt with on the semantic web, here’s your chance!
Authorization would probably not be considered provenance, but I was
Hi Chris,
On Mon, Aug 8, 2011 at 10:56 AM, Pudney Chris (ext) GBJH
chris.pud...@syngenta.com wrote:
Is this the correct approach or is there a bug to report.
The code had a bug. Your suggest patch fixed it, but I realized when
looking at that code that it should not cache the background color
On Fri, Aug 26, 2011 at 10:54 AM, kevin.law...@syngenta.com wrote:
Following Egon’s request to post on software now using the 1.4 CDK series,
LICSS v2.0 has recently been released ( http://code.google.com/p/excel-cdk/
). This is chemical spreadsheet software based on MS Excel using the CDK
On Mon, Aug 22, 2011 at 10:15 AM, Stephan Beisken beis...@ebi.ac.uk wrote:
I tested the functionality using several KNIME workflows. The nodes function
within the limits of their underlying CDK classes and handle errors without
breaking the workflow.
I am sure it does :)
I was just wondering
Hi all,
as many of us care about Open Source and know that getting the
software used is a primary step to get and maintain critical mass, I
invite you to support JChemPaint in this ChemSpider survey, so that
they will not drop JChemPaint as one of the available editor.
Please show your support
Hi Thorsten, Stephan,
On Fri, Aug 19, 2011 at 2:11 PM, Thorsten Meinl
thorsten.me...@uni-konstanz.de wrote:
Thanks to Stephan Beisken from EBI we now have a working plugin for
KNIME that uses the recent 1.3 version of CDK.
Congratulations with that achievement. Migration is not easy; did you
Hi Alex,
On Thu, Aug 18, 2011 at 2:54 PM, Alex Henderson
blueobelisk4a...@gmail.com wrote:
I'd like to take an InChI string and return an IMolecule that has all the
hydrogens set explicitly. The code I have so far is below. Unfortunately it
doesn't work properly.
Your InChI does not seem to
On Tue, Aug 16, 2011 at 2:05 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Sorry for being slow today - but I looked at the article and you don't
provide an examples of IOSetting usage
Check the 'PropertiesListener' part. The API is the same for reader and writers.
Egon
--
Dr E.L.
On Mon, Aug 15, 2011 at 6:22 AM, Pudney Chris (ext) GBJH
chris.pud...@syngenta.com wrote:
Thanks for looking - it was a while ago now but I think I found that I
got better results doing the add followed by removal.
The atom type perception is best done by passing the full molecule,
rather than
On Mon, Aug 15, 2011 at 9:44 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote:
Hi, using the latest CDK when I write out a molecule using the
SDFWriter I loose all aromaticity (ie no kekule form or aromatic bonds
in the output). Has anybody seen this?
Yes, the MDL molfile format does not have a
Hi Andreas,
On Sun, Jul 31, 2011 at 10:04 AM, Andreas Tille andr...@an3as.eu wrote:
For one moment I was thinking that it is a correct thing to
release scientific data under a license which does not allow changing
the data because - hey, I do not want even myself change the result of
my
Hi Andreas,
On Sun, Jul 31, 2011 at 10:04 AM, Andreas Tille andr...@an3as.eu wrote:
For one moment I was thinking that it is a correct thing to
release scientific data under a license which does not allow changing
the data because - hey, I do not want even myself change the result of
my
Hi Andreas,
On Fri, Aug 12, 2011 at 3:15 PM, Andreas Tille andr...@an3as.eu wrote:
I was refering to
http://lists.debian.org/debian-med/2011/07/msg00146.html
Thanx for the pointer. I strongly, and with me many other scientists,
that this license is not the way forward for science, and that
Hi Peter,
On Wed, Aug 3, 2011 at 1:02 PM, Peter Ansell ansell.pe...@gmail.com wrote:
On your question about Chembl in Bio2RDF, we currently directly use
Egon's sparql endpoint to provide access to it, but we can easily
switch, thanks to the way the server can be configured. If John
Overington
Hi all,
On Sun, Jul 31, 2011 at 2:12 AM, Robert Hanson hans...@stolaf.edu wrote:
On Sat, Jul 30, 2011 at 3:42 PM, Richard Ball r...@ellerbach.com wrote:
Egon, what do you recommend?
R,S stereochemistry is a very complex algorithm. I have a limited
implementation in the CDK of the published
On Sun, Jul 31, 2011 at 10:54 PM, Richard Ball r...@ellerbach.com wrote:
Thanks Mike. The problem I want to provide a solution for (assuming there is
one) is: if someone has/gets a .mol file with a complex multi-stereocenter
molecule how can they get the R/S assignment for the particular atoms
On Mon, Jul 25, 2011 at 9:56 AM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
If you used the code exactly as shown, there is a typo in the oxazone in the
for-loop.
In what way? I double checked, but I don't spot the typo... mind you,
it's Groovy, not Java...
Egon
--
Dr E.L. Willighagen
On Mon, Jul 25, 2011 at 10:16 AM, Christoph Steinbeck
steinb...@ebi.ac.uk wrote:
isn't is oxazole once and then oxazone in the for loop (n versus l)?
Hahaha... OK :)
I'm so happy that all the code in my book is actually run when the PDF
is created :)
Egon
--
Dr E.L. Willighagen
Postdoctoral
On Sat, Jul 23, 2011 at 6:45 PM, gilleain torrance
gilleain.torra...@gmail.com wrote:
No, this is what I would expect from the code, and possibly the
algorithm. Since MN don't take atom symbols or bond order into
account, oxazole is just a 5-cycle.
Ah, it is the CanonicalLabeler that does that
Package: libcdk-java
Version: 1:1.2.10-2
Severity: wishlist
I released the new stable series, and the first update release, 1.4.1, just hit
SourceForge.
Egon
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing'), (300, 'unstable'), (1,
Package: libcdk-java
Version: 1:1.2.10-2
Severity: wishlist
I released the new stable series, and the first update release, 1.4.1, just hit
SourceForge.
Egon
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing'), (300, 'unstable'), (1,
On Thu, Jul 7, 2011 at 6:37 PM, Vincent Le Guilloux
vincent.le-guill...@univ-orleans.fr wrote:
In my experience, I have found both mecanism: some descriptors return NaN
values (while the getException() method returns null), and others throws
exceptions (in particular when they detect missing 3D
Hi developers *and* users,
shall we try to come up with a good Exception design for master?
Currently, the CDK uses a mix of various CDK specific exceptions,
though we officially promote the single use of CDKException. Others
have requested to use more general exceptions, like
On Wed, Jul 6, 2011 at 12:35 PM, Nina Jeliazkova
jeliazkova.n...@gmail.com wrote:
On 6 July 2011 13:06, Egon Willighagen egon.willigha...@gmail.com wrote:
1) and 2) are not mutually exclusive.
My preference would be for 1) CDKException but combined with 2) CDKException
subclasses , e.g
On Wed, Jul 6, 2011 at 12:51 PM, Jules Kerssemakers
jules.kerssemak...@googlemail.com wrote:
One of java's core strengths in general is that the class-hierarchies allow
you a lot of rigid control over program flow and what can and cannot be
done. It would be a waste to throw that away by using
On Wed, Jul 6, 2011 at 2:40 PM, Vincent Le Guilloux
vincent.le-guill...@univ-orleans.fr wrote:
I would also roughly go to the Nina's solution, with a strong
agreement with Rajarshi. Just a few additional word to enrich this
interesting discussion:
Agreed. We'll have to aggregate the common
On Wed, Jul 6, 2011 at 3:26 PM, Christoph Steinbeck steinb...@ebi.ac.uk wrote:
I'm not sure if CDK will give you quick results because of lacking atom types.
You may be interested in this post:
http://chembioinfo.wordpress.com/2011/07/06/improved-atom-typing-cdk/
I do not know when this will
to these four
developers for their hard work on the renderer patch!):
500+ Egon Willighagen
124 Rajarshi Guha
108 Gilleain Torrance
38 Syed Asad Rahman
32 Stefan Kuhn
23 Mark Rynbeek
11 Arvid Berg
8 Jules Kerssemakers
6 Miguel Rojas Cherto
6 Jonathan Alvarsson
4 Andreas Truszkowski
4
On Thu, Jun 30, 2011 at 8:58 AM, Peter Ansell ansell.pe...@gmail.com wrote:
The 1.0.1 version of the Bio2RDF server software has been released on
Sourceforge. The software is designed to be a Linked Data interface to
a range of RDF datasources, with the current examples being Bio2RDF
and
Package: kcharselect
Version: 4:4.6.3-1
Severity: normal
Tags: wheezy
For at least DejaVu Sans and Serif, selecting Latin-1 Supplement from the drop
down box
causes a crash of the application with this crash information:
Thread 1 (Thread 0xb57a1710 (LWP 18454)):
[KCrash Handler]
#7 0xb756cad0
Package: kcharselect
Version: 4:4.6.3-1
Severity: normal
Tags: wheezy
For at least DejaVu Sans and Serif, selecting Latin-1 Supplement from the drop
down box
causes a crash of the application with this crash information:
Thread 1 (Thread 0xb57a1710 (LWP 18454)):
[KCrash Handler]
#7 0xb756cad0
To all who have the cdk-1.4.x series checked out from Git,
there was a long-standing regression in the descriptor specifications
due to the move to Git, causing the $Id$ values not automatically
updated anymore. Git has since a while (but not when we moved away
from SVN) support for this keyword
Hi Eric,
On Sat, Jun 18, 2011 at 11:59 PM, Eric Martz ema...@microbio.umass.edu wrote:
Does anyone know of an animation simulation (atomic coordinates) for
changes in 3D protein conformation (or amino acid conformation) due
to changes in pH?
I took the liberty to cross-post your question on
Asad,
On Tue, Mar 22, 2011 at 10:26 AM, Syed Asad Rahman s9a...@gmail.com wrote:
smiles= C1C(CC(=O)C(C1(CC(CC(CC(=O)S[R])=O)=O)O)C(CC(CC(CC(CC)=O)=O)=O)=O)=O
According to Daylight's Depict, the above is not a SMILES but a SMARTS.
The error message is not too informative, and I filed a bug
On Sun, Jun 19, 2011 at 9:00 AM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Rajarshi already updated his rcdk package to
make use of it [0], and I hope more will follow soon.
0. http://blog.rguha.net/?p=970
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Hi all,
I have not been able to find a way to sit behind a desk right now. I
will have internet access, but an unstable one. I'll join via IRC, via
which I will be available to give an update on ChEMBL-RDF. In short,
it comes down to:
1.http://rdf.farmbio.uu.se/chembl/sparql has ChEMBL 09
2. but
On Tue, Jun 14, 2011 at 1:39 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
The original paper 5 years ago is still being cited and I expect this new
one will also be highly read and act as a reference for those interested in
Open chemistry.
119 times now, according to Web of Science, with 19
Hi Christopher,
On Fri, Jun 3, 2011 at 12:41 PM, Christopher Rogers
cmroge...@verizon.net wrote:
I would like to use CDK (or CDK with JChemPaint) to render a molecule into
SVG programmatically.
Yes, that should be more or less possible. The 'possible' comes in as
the code has probably not been
Hi Christian,
On Fri, Jun 3, 2011 at 4:18 PM, Christian Spiteri
christianspit...@gmail.com wrote:
I'm using Mol2Writer to write a molecule to a file, and it's working
fine until I happen to run into this type of atom:
Atom(860069, S:P, 3D:[(47.423, 10.1752, 27.0577)], AtomType(860069,
N:P.3,
Hi all,
after literally years of work, the main CDK library can draw molecules again:
http://chem-bla-ics.blogspot.com/2011/06/httpchem-bla-icsblogspotcom201106cdk.html
(yeah, the URI is a bit weird)
Just to make clear, only the second blob of CDK-JChemPaint code now
got merged in, but this
. In short, not all functionality you can use yet with purely
CDK 1.3.11.
I should have communicated that more clearly. My apologies. But
really, we are getting there!
Egon
On Sat, Jun 11, 2011 at 5:09 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
Hi all,
after literally years of work
Dear Rudy,
On Tue, Jun 7, 2011 at 3:56 PM, Rudy J. Richardson rjr...@umich.edu wrote:
I do not have a specific algorithm at hand for calculating the van der Waals
molecular volume. However, there is a calculator plugin for ChemAxon Marvin
Sketch that calculates this descriptor.
I implemented
Hi Bob,
I know you (right?) implemented the marching cubes algorithm to
calculate molecular surfaces... does you code also calculate the
molecular volume?
Egon
--
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage:
Hi Miguel!
On Tue, Jun 7, 2011 at 6:18 PM, Miguel Howard mig...@jmol.org wrote:
Actually, I did the original marching cubes implementation.
Oops, sorry! (and cool that you are still listening in!)
My recollection is that it did *not* calculate volume. However, it
seems to me that it would be
Hi all,
On Sun, Jun 5, 2011 at 12:24 PM, Peter Murray-Rust pm...@cam.ac.uk wrote:
Action
=
We need to know what is involved in setting up such a site and running it. I
know that Egon has been heavily involved - who else. I'm guessing that there
would be Quixotans who can get started.
Package: wnpp
Severity: wishlist
Package name: libcmlxom-java
Version : 3.0; reported 2011-06-02
Upstream Author : Peter Murray-Rust Group chem-pmrgr...@lists.cam.ac.uk
URL : https://bitbucket.org/wwmm/cmlxom/overview
License : Artistic License 2.0
On Wed, Jun 1, 2011 at 8:32 AM, Onkar Shinde onkarshi...@gmail.com wrote:
Latest changelog for reference.
cdk (1:1.2.10-1) unstable; urgency=low
- Remove modules which do not contain any class files when built - inchi,
pdbcml, qsarxml.
The latter two need CMLXOM packaged, I guess. The
On Wed, Jun 1, 2011 at 5:31 PM, Egon Willighagen
egon.willigha...@gmail.com wrote:
On Wed, Jun 1, 2011 at 8:32 AM, Onkar Shinde onkarshi...@gmail.com wrote:
Latest changelog for reference.
cdk (1:1.2.10-1) unstable; urgency=low
- Remove modules which do not contain any class files when
Package: wnpp
Severity: wishlist
Package name: libcmlxom-java
Version : 3.0; reported 2011-06-02
Upstream Author : Peter Murray-Rust Group chem-pmrgr...@lists.cam.ac.uk
URL : https://bitbucket.org/wwmm/cmlxom/overview
License : Artistic License 2.0
Hi Andrew,
On Wed, Jun 1, 2011 at 8:45 PM, Andrew Dalke da...@dalkescientific.com wrote:
Also, what does CDK do if there's an error in one of the records? For
example, some of the other toolkits' readers skip bad records and report to
stderr. If CDK ignores bad records, is there a way to get
Hi all,
does the CDK have a descriptor reflecting molecular volume? The below
email asks a bit more though...
Egon
-- Forwarded message --
From: Rudy J. Richardson rjr...@umich.edu
Date: Sun, May 29, 2011 at 5:41 PM
Subject: [Bioclipse-users] Add Molecular Volume Descriptor
To:
Hi all,
I have just submitted another piece of the CDK-JChemPaint code as
patch: the renderbasic module. This module contains all the code to
visualize molecules:
https://sourceforge.net/tracker/?func=detailaid=3309071group_id=20024atid=320024
This patch report has all the detail about the
1.2.10 is now released. So, consider this a request for update to that
version, rather than the (now) older 1.2.9 :)
__
This is the maintainer address of Debian's Java team
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-maintainers.
Please use
debian-j...@lists.debian.org for
The patch by Onkar has been applied, and I released 1.2.10. I have not
had time, unfortunately, to test the inclusion in rebuild .deb
packages.
__
This is the maintainer address of Debian's Java team
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-maintainers.
Please use
1.2.10 is now released. So, consider this a request for update to that
version, rather than the (now) older 1.2.9 :)
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The patch by Onkar has been applied, and I released 1.2.10. I have not
had time, unfortunately, to test the inclusion in rebuild .deb
packages.
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The patch by Onkar has been applied, and I released 1.2.10. I have not
had time, unfortunately, to test the inclusion in rebuild .deb
packages.
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On Wed, May 25, 2011 at 12:56 AM, M. Scott Marshall
mscottmarsh...@gmail.com wrote:
* Egon Willighagen is updating the downloadable RDF version of ChEMBL
to version 9
This download is available from:
https://github.com/egonw/chembl.rdf
(click the Download button)
What I have not done yet
Package: libcdk-java
Version: 1:1.2.8-1
Severity: grave
Justification: renders package unusable
While helping the user who reported bug #627683 with the missing dependencies,
we discovered that xml data files are missing from the resulting jars, or at
least cdk-core.jar, which should give
Package: libcdk-java
Version: 1:1.2.8-1
Severity: wishlist
A quick ping that I released version 1.2.9 yesterday, including the patch from
Onkar.
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing'), (300, 'unstable')
Architecture: i386 (i686)
Package: libcdk-java
Version: 1:1.2.8-1
Severity: normal
The jni-inchi functionality used in the cdk-inchi.jar requires the libstdc++5
package
to be installed, to provide libstdc++.so.5, because you otherwise run into this
exception:
Caused by: java.lang.UnsatisfiedLinkError:
Package: libcdk-java
Version: 1:1.2.8-1
Severity: grave
Justification: renders package unusable
While helping the user who reported bug #627683 with the missing dependencies,
we discovered that xml data files are missing from the resulting jars, or at
least cdk-core.jar, which should give
Package: libcdk-java
Version: 1:1.2.8-1
Severity: grave
Justification: renders package unusable
While helping the user who reported bug #627683 with the missing dependencies,
we discovered that xml data files are missing from the resulting jars, or at
least cdk-core.jar, which should give
Package: libcdk-java
Version: 1:1.2.8-1
Severity: wishlist
A quick ping that I released version 1.2.9 yesterday, including the patch from
Onkar.
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing'), (300, 'unstable')
Architecture: i386 (i686)
Hi all,
I have released a new stable update:
The CDK 1.2.9 release does not contain overly many patches, something
you'd expect from a bug fix only series, and has instead a few atom
type perception patches, and a patch by Onkar simplifying building of
Debian package.
Details at:
Hi all,
I have released a new stable update:
Hot on the heels of the stable update 1.2.9, here is a new developers
release. The 1.4.0 is still waiting for the basic (molecule) rendering
of the CDK-JChemPaint patch to be submitted, but I think I will just
submit it and see what happens. If
Dear Ed,
On Wed, Apr 6, 2011 at 9:53 AM, Ed Barker mredbar...@yahoo.co.uk wrote:
I am a chemist in desperate need of some of the algorithms in cdk for
research purposes.
However, I am brand new to java. I learn best by example but I am having a
difficult time
trying to get a simple program
Hi Nick,
On Thu, Mar 17, 2011 at 4:54 PM, Nick Vandewiele
nickvandewi...@gmail.com wrote:
I found strange behaviour of the CDKConstants.VISITED flag after running the
SMARTSQueryTool on cyclic species.
-Normal behavior for linear alkanes such as n-decane:
snip
The VISITED flag returns
Package: virtuoso-opensource-6.1
Version: 6.1.2+dfsg1-1+b1
Severity: wishlist
Right now, loading of the Virtuoso database upon booting blocks this process. It
would be nicer of the boot process would simply continue when the loading is
initiated but performed in the background.
When the database
Package: libcdk-java
Version: 1:1.2.8-1
Severity: normal
The jni-inchi functionality used in the cdk-inchi.jar requires the libstdc++5
package
to be installed, to provide libstdc++.so.5, because you otherwise run into this
exception:
Caused by: java.lang.UnsatisfiedLinkError:
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