Hi all,
congratulations all! The CDK has existed for 25 years.
I hope to read more reflections on social media, but wrote up mine in
https://doi.org/10.59350/4ce2c-fxh02
Posted on LinkedIn here:
https://www.linkedin.com/posts/egon-willighagen_25-years-of-the-chemistry-development-kit-activity-73
many (vega)
lunches need to be ordered).
The form allows you to indicate if you want to present on the first day
your own CDK-using work and on which days you will participate (both, I
hope).
Please contact me if you have any questions,
with kind regards,
Egon
On Sun, 3 Nov 2024 at 20:20, Egon
Hi John, all,
I am playing with SMIRKS but it's pretty new to me.
Transform neutralAcid = Smirks.compile("[O-:1]>>[O:1]");
IAtomContainer cdkStruct = parser.parseSmiles("CC(=O)[O-]");
Iterable iterable = neutralAcid.apply(cdkStruct,
Transform.Mode.Exclusive);
for (IAtomContainer neutral : iterabl
Hi everyone,
mark your calendar: 10-11 March 2025 in Maastricht, The Netherlands we will
hold a Chemistry Development Kit User Group Meeting. One day will have
presentations from CDK developers and CDK users, while the second day is
unconference/hackathon style.
Please email me if you are interes
Thanks for posting!
I have reshared an announcement based on this on Mastodon:
https://fosstodon.org/@blueobelisk/113055702502809492 (I decided from the
Blue Obelisk account, since this is not just for the CDK)
Egon
On Mon, 5 Aug 2024 at 10:44, Andrew Dalke wrote:
> Hi everyone,
>
> I have rel
his is causing me problems when handling 2D or 3D molfiles.
> I find I can work around it by doing IAtomContainer -> SMILES ->
> IAtomContainer, which works for now.
> I'll need to look more deeply at the code to work out better options.
> There's a lot going on like MCS a
roject.ext.set('cdkVersion', '2.2')
>
> It's likely just updating will fix the issue. It should be relatively
> seamless but let me know if there are any issues and I'll tell you how to
> fix it.
>
> On Sat, 23 Sept 2023 at 06:38, Egon Willighagen
Tim,
I guess you are referring to
https://github.com/InformaticsMatters/squonk/blob/master/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMolDepict.java
I also looked at the molfile reading in CDKMoleculeIOUtils and it looks
correct to me, but the hydrogen adding may be a conflicting iss
Sorry, this was probably a duplicate. See the other thread.
Egon
On Sat, 2 Sept 2023 at 10:27, Chong Kim San Allen via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:
> Dear Helpdesk,
>
>
>
> I have used CDK to generate the Extended Fingerprints for a couple of
> compounds and I found that cer
Dear Allen,
On Wed, 30 Aug 2023 at 01:24, Chong Kim San Allen via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:
> I am wondering if you can tell me which fingerprints generate unfolded
> features and if there is a table of the subgraphs that represents these
> features for these fingerprints?
The code in legacy was an academic project, but has limited functionality.
There are nowadays a few open source tools that can predict the IUPAC name.
By using OPSIN you can check if that prediction makes sense: OPSIN
generated a chemical structure from the IUPAC name and if that is the same
as the
I have never really used this and generally not up to date with JavaDoc
sounds worth figuring out.
Egon
On Fri, 11 Nov 2022 at 05:41, Uli Fechner wrote:
> Hi,
>
> I would like to do some serious javadoc documentation for the
> soon-to-come RInChI functionality in CDK.
>
> I could either put
On Thu, 10 Nov 2022 at 14:02, John Mayfield
wrote:
> Can you to open a GitHub issue, thanks. It's likely harmless but should be
> silent so something we can tweak.
>
Set aside the issue, it *should* be silent... this is the code:
https://github.com/cdk/cdk/blob/40b552eb70d2eafce9540b424f22bd0f7
Hi all,
John is working on SMIRKS support in the main Chemistry Development Kit
code base:
https://github.com/cdk/cdk/pull/916
Feedback is welcome.
Egon
--
FAIR needs global, unique identifiers. We started the European Registry of
Material to provide identifiers to link biological data
Dear Woon Yee,
you can use the getFingerprint() method instead.
Egon
On Mon, 25 Jul 2022 at 10:59, #NG WOON YEE# via Cdk-user <
cdk-user@lists.sourceforge.net> wrote:
> Dear Helpdesk,
>
>
>
> I was using CDK (version 2.7) to generate FCFP4 and 6 for the compound
> butyramide (
> https://www.ebi
Thanks for the reminder!
Egon
On Wed, 19 Jan 2022 at 11:30, Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:
> Dear all,
>
> as announced last November on this list, the CDK 20th anniversary workshop
> will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.
>
> We
All the ingredients are there. The thing is, however, that there are
multiple ways to do the standardization. Check what Ola did in Bioclipse-DS
/ Bioclipse-QSAR.
Egon
On Mon, Sep 27, 2021 at 9:24 PM Staffan Arvidsson McShane <
staffan.arvids...@gmail.com> wrote:
> I'm looking for a good way to
Hi all,
just a quick note that a recent Twitter discussion led to a Python wrapper
for Bacting [0,1] which is a Maven-ized version of (subset of, but growing)
Bioclipse, called pybacting [2] which is available from PyPI and with that
easy to use. Bacting/pybacting is using CDK 2.5.
So, you can ac
On Wed, Jan 20, 2021 at 10:31 AM Andrew Dalke
wrote:
> So I'm leaving the supported CDK formats in chemfp to SMILES, SDF, and
> InChI. And if no one asks for other formats then I don't need to do
> anything.
>
I understand that supporting XYZ and PDB here is a "when asked".
Regarding unused for
at 8:19 AM Andrew Dalke
wrote:
> On Jan 20, 2021, at 07:37, Egon Willighagen
> wrote:
> > Jmol had code to deduce bonds (for files which only have coordinates and
> no bond info, like XYZ), which was ported at some point to the CDK. Here's
> some example code:
> https://
On Tue, Jan 19, 2021 at 11:50 PM Andrew Dalke
wrote:
> BTW, I had to drop support for some of the formats, like XYZ and PDB,
> because I couldn't figure out how to use them to read a structure into a
> form that could be use to generate fingerprints. If anyone needs them and
> can tell me how to
Dear Winod,
On Wed, Dec 30, 2020 at 11:24 AM Winod Dhamnekar
wrote:
> What should be the contents of pom.xml file in cdk directory?
The pom.xml is the file Maven uses to see how the source code needs to
be compiled. It often also contains metadata about the project, such
as authors, license, etc
Yes, half yearly releases would be nice. I second the usefulness of being
able to cite a specific version, ideally one on Zenodo with DOI, and that
-SNAPSHOT is not something I would like in a paper either.
That said, making a release takes a couple of hours and as release manager
I also always ha
Dear Fleming,
while the methods are different, the CDK does have descriptors for some of
the properties you mention. Some are based on the 3D structure, but not all.
When it comes to interactions, less so. The CDK does not have a lot of
functionality to calculate or map properties onto the molecu
Mmm... time to update my book to discuss this :)
Egon
On Fri, Feb 21, 2020 at 10:35 AM John Mayfield
wrote:
> Hi Maria,
>
> Not all fingerprint support the "RAW" option and Count options.
>
> John
>
> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina
> wrote:
>
>> Dear community,
>>
>> It is decide
Hi everyone,
with great pleasure I can let you know that in the past two month Debian
developers have updated the CDK version in the Debian distribution, and you
can download CDK 2.3 from Debian unstable [0].
Grtz and happy new year,
Egon
0.https://packages.debian.org/search?keywords=libcdk-jav
On Fri, Aug 2, 2019 at 11:28 AM John Mayfield
wrote:
> Other option You can also use the old *BasicAtomGenerator* which never
> puts hydrogens on anything...
>
Documentation on the old generator stack can be found in this copy of the
Groovy CDK book, "Depiction" chapter:
https://figshare.com/ar
Thanks, Syed!
Egon
On Sat, Oct 13, 2018 at 3:55 PM Syed Asad Rahman wrote:
> Dear All,
>
> A quick update- in the past few months I have received several request
> from the CDK community to upgrade SMSD and RDT by making it compatible to
> the CDK v2.0 version.
>
> Finally, I have updated both
Oh, very happy to hear that! Are you going to put it up on DockerHub?
Egon
On Thu, Sep 13, 2018 at 10:42 PM Maria Sorokina
wrote:
> I managed to make my app function.
>
> The problem comes from the way a Spring Boot application packages the jar
> - internally, the jar is different from plain ol
m
with metadata (bioschemas, bio.tools, etc...) so that these services are
FAIR too... that I had in mind of this fork of the Docker discussion...
Egon
On Tue, Sep 11, 2018 at 5:50 PM John Mayfield
wrote:
> It doesn't use InChI :-).
>
> On Tue, 11 Sep 2018 at 16:43, Egon Willighag
Anyway, I'm quite excited about the idea of a Docker for CDK
functionality... (well, excited it triggered here not so much I am entirely
sure this is a fantastic platform, but in our OpenRiskNet we use it for
workflows, and being able to replace some stuff with CDK functionality in
that cloud *is*
Maybe a temporary glitch?
https://cactus.nci.nih.gov/chemical/structure/CCC/sdf works for me right
now...
Egon
On Sun, May 20, 2018 at 4:20 PM Xuan Cao wrote:
> Hi John,
>
> Thank you for your reply! I will look into that!
>
> BTW, the link is not working (404).
>
> Xuan
>
> On 20 May 2018 at 0
Hi all,
this weekend I installed Java9 and did a bit of initial testing... for
the CDK the following seems to have changed:
1. it compiles without issues
2. the compiling seems faster (N=3): 19 seconds instead of the old 66 seconds
3. the tests seem to run *slower* (N=3)... 134 seconds instead of
Hi Staffan,
some years ago we looked at exactly this with AZ (Lars) and Gilleain
(EBI)... I need to look up that code...
Egon
On Fri, Jul 21, 2017 at 10:39 AM, Staffan Arvidsson <
staffan.arvids...@gmail.com> wrote:
> Hi all,
>
> I wonder if there is any way of producing atom signatures with
>
Hi Yannick,
I don't think we have a LogD model.
Egon
On Sun, Jul 9, 2017 at 11:08 PM, Yannick .Djoumbou wrote:
> Hey all,
>
> I am looking for a tool to compute the LogD for various compounds. I could
> not find any function/module that computes this property. Is there one? If
> not, what woul
Mmm... I'd consider that a regression, as that was the intended behavior...
John, do you agree we should restore that behavior, or do you have a
better solution?
Egon
On Sat, Jun 24, 2017 at 4:23 PM, Tim Dudgeon wrote:
> Hi All,
>
> I'm needing to write the title line (the first line in the re
Hi all,
https://jcheminf.springeropen.com/articles/10.1186/s13321-017-0220-4
Thanks to everyone who contributed to the project, both (part-time)
developers but also all users, for whom we are doing this.
Happy reading!
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht
On Thu, Apr 27, 2017 at 11:04 AM, John Mayfield wrote:
> It's a chicken and egg problem... people don't use it, and even can't use
>> it, because there are no good tools yet; not making good tools also ensures
>> no one uses it.
>
>
> I somewhat agree but MDL/ChemDraw support it and it's still no
On Thu, Apr 27, 2017 at 9:54 AM, John Mayfield
wrote:
> I was wondering does anyone use n-way bonds in CDK (a bond with more than
> two atoms)?
>
> IAtom atom1 = object.getBuilder().newInstance(IAtom.class, "C");
>> IAtom atom2 = object.getBuilder().newInstance(IAtom.class, "O");
>> IAtom atom3 =
Mol?
> Is there an example anywhere?
>
> Tim
>
>
>
> On 07/03/2017 16:42, Egon Willighagen wrote:
>>
>> On Tue, Mar 7, 2017 at 5:31 PM, Tim Dudgeon wrote:
>>>
>>> What's the state of play with rendering 3D structures with CDK?
>>> I
On Tue, Mar 7, 2017 at 5:31 PM, Tim Dudgeon wrote:
> What's the state of play with rendering 3D structures with CDK?
> I see some mention of this in the 2006 paper, but it seems to say that
> 3D rendering is done using JMol?
Yes, correct. We have had 3D viz in the CDK, with Java3D, but Jmol was b
15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(2
>>> 5)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H
>>> ,30,31)(H2,17,18,19)/
>>>
>>> You'd also be surprised how far a very simple approach gets you:
>>> Neutralize.java
>>>
John suggest this list of SMARTS recently:
http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html
And Nina mentioned code in AMBIT for SMIRKS to do the job...
Egon
On Fri, Feb 17, 2017 at 2:51 PM, Rajarshi Guha
wrote:
> Hi, I have a situtation where I start from an InChI for a molec
On Tue, Jan 3, 2017 at 3:50 PM, Martin Gütlein wrote:
>> Does this have an API?
>
> Yes, a REST API, as described here http://coffer.informatik.uni-mainz.de/doc
> (The API is also compatible to the OpenTox standard).
Please consider adopting OpenAPI :) (Which I will push at the
OpenRiskNet meetin
Moving this to cdk-user mailing list...
On Wed, Dec 28, 2016 at 7:54 PM, Rajarshi Guha wrote:
> On Wed, Dec 28, 2016 at 10:56 AM, Tomas Pluskal wrote:
>>
>> +1 for establishing a simple website at cdk.github.io (it takes five
>> minutes using GitHub Pages).
>
> +1
John, you have had ideas about
Dear Todd,
On Tue, Aug 16, 2016 at 9:05 PM, Martin, Todd wrote:
> The web link is fine for referencing T.E.S.T. I still use 1.0 release of CDK
> so not to break the JChemPaint linkage. In the web services version we will
> probably use a newer CDK version since we wont need JChemPaint for that. I
Hi all,
over the last few months we have been working on finalizing a third
paper about the CDK library. You can find the result here:
https://github.com/cdk/cdk-paper-3 (including a PDF) This paper picks
out a number of changes in the library and describes changes in the
development model, since
John,
how do I create wedge bond info for 2D depiction after starting with a
(chiral) SMILES?
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: h
Dear Steve,
On Mon, Aug 15, 2016 at 7:32 PM, Steve Roy wrote:
> [Cu+].CC#N.CC#N.CC#N.CC#N.F[P-](F)(F)(F)(F)F
>
with the latest CDK version (1.5.x) I get something that more resembles
what you expect:
https://cdkdepict-openchem.rhcloud.com/depict/bow/svg?smi=[Cu%2B].CC%23N.CC%23N.CC%23N.CC%23N.
No objections.
Egon
On Sat, Aug 13, 2016 at 5:20 PM, John M wrote:
> Hi All,
>
> Lots of the ReactionManipulator methods don't consider agents. Guessing they
> may have been written before an API change.
>
> Is there any objection to me updating the semantics such that
> getAllMolecules and getA
On Sun, Jun 5, 2016 at 2:11 PM, John M wrote:
> Does anyone use this method (generateExperimentalCoordinates) over the other
> one (generateCoordinates), and if so why?
It was added at the time to not break previous behavior. But your
layout is superior, and if removing the method breaks code, th
On Thu, May 12, 2016 at 5:54 PM, John M wrote:
>
> Thoughts?
>
Yes, this is very useful indeed! And it looks so much better than that
stuff I did when with Peter and Janet Thornthon (OK, that was only 3
months)! That double arrow would be very cool, but doing this from SMILES
is just brilliant! W
Something like this (in Groovy, from my CDK book)?
import org.openscience.cdk.tools.*;
crambin = ProteinBuilderTool.createProtein(
"TTCCPSIVARSNFNVCRLPGTPEA" +
"ICATYTGCIIIPGATCPGDYAN"
);
println "Crambin has " + crambin.atomCount +
" atoms."
Grtz,
Egon
On Thu, Apr 28, 2016 at 1:24 AM, Jo
On Mon, Apr 25, 2016 at 11:23 AM, John M wrote:
> Also, I'm planning on removing the front page link to CDK 1.4.19 from
> SourceForge (https://sourceforge.net/projects/cdk/). I understand this is
> the most recent "stable" version but I think it would be better to simply
> not have a default. It's
tracker too, so that students can
see the ideas too!
Egon
On Tue, Mar 1, 2016 at 7:06 PM, Greg Landrum wrote:
> I can probably help with that Egon, at least as far as the RDKit bit is
> concerned.
>
>
> On Tuesday, 1 March 2016, Egon Willighagen
> wrote:
>>
>> Geoff
Geoff,
thanks for the suggestions. I need to look at the HTML code that uses
$foo.js and create an SVG image... emscripting looks nice, but also
harder to easily integrate... I need to see how much you can rip out,
to just have the core content...
Egon
On Tue, Mar 1, 2016 at 4:55 PM, Geoffrey Hu
Hi all,
the NRNB is an USA-based organization around Cytoscape and
WikiPathways, the latter involving PathVisio. You may know that
Cytoscape has a plugin that used the CDK (by Scooter Morris et al.,
UCSF) and here in Maastricht we have been working on PathVisio plugins
for metabolites also using t
On Wed, Jan 20, 2016 at 10:44 AM, John M wrote:
> Ultimately it's silly that V2000 and V3000 are considered different but
> haven't had time to put them in a single 'MolfileReader' yet.
The formats *are* different, but that does not mean the readers must be too!
The MDL formats for reaction list
Dear Yu,
On Wed, Dec 16, 2015 at 1:19 PM, 杜宇 wrote:
> I just achieved a ligand-based model with ChEMBL data. Is there any standard
> data set to evaluate models against other models?
> By comparison, I could depict a ROC curve to validate my model and convince
> others. But as far as I know, alth
let me know if you have upgrade questions,
happy new year, and may the CDK be with you!
Egon
0.http://www.lulu.com/shop/egon-willighagen/groovy-cheminformatics-with-the-chemistry-development-kit/paperback/product-22051359.html
(CDK 1.5.10, 240 pages)
1.https://figshare.com/articles
On Thu, Dec 31, 2015 at 8:16 PM, Rajarshi Guha wrote:
> On Thu, Dec 31, 2015 at 6:21 AM, John M wrote:
> As to Egons concern regarding maintenance burden - I think it's a safe to
> state that deprecated API's will not be maintained.
That does not sound consistent... one one hand you want to keep
John, all,
On Thu, Dec 31, 2015 at 12:21 PM, John M wrote:
> Is the approach of adding new API and deprecate the old sound acceptable? Or
> are public API changes acceptable?
In general I think keeping APIs is a good thing, also for development
branches. I think APIs should be kept, unless there
Hi all,
excuse me my x-mas spam, but I just wanted to let everyone know that I
have placed an 2011 copy of the "Groovy Cheminformatics with the CDK"
book as CC-BY on Figshare (that's edition 1.4.1-0).
https://dx.doi.org/10.6084/m9.figshare.2057790.v1
Please grab a copy!
Egon
--
E.L. Willighag
On Tue, Nov 10, 2015 at 4:23 PM, Till Schäfer
wrote:
> Long story short: Thank you for the good work!
I'm happy to hear John's work is working out well for you!
Grtz,
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage
ifferent CDK versions would produce the same
> fingerprint for the same molecule.
>
> Regards,
> Till
>
> Am Mittwoch, 4. November 2015, 14:37:03 schrieb Till Schäfer:
>> thx for the fast answer.
>>
>> Viele Grüße
>> Till
>>
>> Am Mittwoch, 4. No
Oh, sorry the CDK 1.4 identical to 1.5... No, they are typically
not, as they depend on an aromaticity model. This is why I introduced
the SP2-based fingerprinter, which also takes into account
hybridization, but does not depend on definitions of aromaticity...
and should be more stable.
(But
Dear Till,
neither. The default (oldest) CDK fingerprint is like the Daylight
fingerprint (using the same approach), but is not meant to be
identical.
Grtz,
Egon
On Wed, Nov 4, 2015 at 2:05 PM, Till Schäfer
wrote:
> Hi,
> i would like to know if the daylight fingerprint should be identical for
On Sun, Oct 25, 2015 at 5:02 PM, John May wrote:
> GitHub can attach binaries to releases, we do it already:
> https://github.com/cdk/cdk/releases/tag/cdk-1.5.11. Given the whole
> SourceForge Gimp fiasco I’m wary of using it.
Oh, nice! I seem to have missed/overlooked that... yeah, well, go for
On Sat, Oct 24, 2015 at 8:26 PM, John M wrote:
> Anyways, just deployed one to OpenShift running the latest CDK SnapShot with
> some improvements to layout: http://cdkdepict-openchem.rhcloud.com/depict.html
Nice!
> Are there any objections to distributing source/war via github
> ('/cdk/depict')
John, Siva, all,
I would not worry too much about these questions (see also [0]).
1. in the end you need to check individual molecules, study the 3D
structure, bond lengths, etc. That's how you determine if they are "really"
aromatic. Some of this you can predict with QM approaches, but even then
Tue, Jul 7, 2015 at 5:03 PM, Egon Willighagen
> wrote:
>>
>> Dear Zheng Shi,
>>
>> I think what you are looking for is "isomorphism checking". If the
>> chemical graph of two structures is the same, they are called
>> isomorphic. The foll
Dear Zheng Shi,
I think what you are looking for is "isomorphism checking". If the
chemical graph of two structures is the same, they are called
isomorphic. The following Groovy code shows a very basic example:
butane = MoleculeFactory.makeAlkane(4);
isomorphismTester = new UniversalIsomorphismTe
Dear Siva,
It was renamed to "IteratingSDFReader". See
http://chem-bla-ics.blogspot.com/2014/04/changes-in-cdk-16-2-iteratingmdlreader.html
Grtz.
Egon
On Mon, Jun 29, 2015 at 4:59 PM, T. V. Siva Kumar wrote:
> I was porting my code from Cdk1.4 to Cdk1.5. The class IteratingMDLReader is
> missi
Hi all,
I'm attending the Metabolomics 2015 meeting starting today, and already
noted some CDK uses. Anyone else at this conference?
Maybe meet up? We could discuss CDK 1.5, or I could help with upgrading to
this version? I already had one question about stability of 1.5. At this
moment, that mos
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 po
uha 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
> wrote:
>>
>> On Wed, Apr 29, 2015 at 2:39 PM, Rajarshi Guha
>> wrote:
>> > Egon/C
nly
> shows up to 2007
>
> On Wed, Apr 29, 2015 at 8:47 AM, Egon Willighagen
> wrote:
>>
>> On Wed, Apr 29, 2015 at 2:39 PM, Rajarshi Guha
>> wrote:
>> > Egon/Chris - do we have old versions of CDK News somewhere?
>>
>> https://sourceforge.net/pro
On Wed, Apr 29, 2015 at 2:39 PM, Rajarshi Guha wrote:
> Egon/Chris - do we have old versions of CDK News somewhere?
https://sourceforge.net/projects/cdk/files/CDK%20News/
That was an easy one :)
Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.b
and as PDF:
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 at
On Thu, Jan 15, 2015 at 12:39 PM, Tim Dudgeon 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 IteratingSDFReader)
> anyway.
Dear Tim,
On Tue, Jan 6, 2015 at 7:32 PM, Tim Dudgeon wrote:
> Is this expected?
Yes, that is expected. You can see what our build server says here:
https://jenkins.bigcat.unimaas.nl/job/cdk/lastCompletedBuild/testReport/
The README gives instructions on how to run Maven without stopping
when
Hi John,
On Tue, Dec 30, 2014 at 1:19 AM, John May 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 (http://www.bigcat.unimaas.nl/)
Homepage: http://ego
On Fri, Dec 19, 2014 at 11:42 PM, Zheng Shi 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 perhaps from a MDL mo
On Tue, Nov 25, 2014 at 8:41 AM, Egon Willighagen
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 Exceptio
(Arvid: can you have a glance at this email too, please?)
Scooter,
On Tue, Nov 25, 2014 at 3:15 AM, Scooter Morris 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 annoying combination...
Dear Yannick,
On Thu, Nov 20, 2014 at 5:21 PM, Yannick .Djoumbou wrote:
> IAtomContainer molecule = sp.parseSmiles("CSCCSCO");
> SMARTSQueryTool smarts_pattern = new SMARTSQueryTool("[#6]S[#6]");
OK, that seems to work:
http://apps.ideaconsult.net:8080/ambit2/depict/cdk?search=CSCCSCO&smarts=%5
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, Nov
Dear Yannick,
On Wed, Oct 29, 2014 at 10:47 PM, Yannick .Djoumbou
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 operations. Is there a wa
On Fri, Aug 29, 2014 at 1:38 PM, John May 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 anyone?
I have ping
Dear Zheng,
On Fri, Jul 18, 2014 at 11:20 PM, Zheng Shi 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 molecules
> with
On Tue, Apr 8, 2014 at 9:32 AM, Martin Guetlein
wrote:
> jep, its quite an effort to move from 1.4 to 1.5. I will report back
> how it went..
Please let me know if you have questions. I am trying to record all
bits, but don't have much yet (see PDF).
If you let me know your questions, I will hel
On Mon, Apr 7, 2014 at 8:44 PM, Martin Guetlein
wrote:
> Are there any plans already to integrate this?
It already is in master:
8f48540 Fixed bug in CircularFingerprint/biotypes (for FCFP)
8ef313f Use MDLV2000Reader for tests
a11b89d Minor tidying of comments
40c9854 CircularFingerprinter recyc
Hi Lochana,
On Fri, Mar 28, 2014 at 3:43 AM, lochana menikarachchi
wrote:
> Is there any reason to distribute CDK under LGPL license?
CDK was licensed LGPL because it was based on CompChem, Jmol, and
JChemPaint were LGPL.
> Why not apache license?
I do not remember the reasons why those tools
Dear Saulius,
> On Thu, Mar 27, 2014 at 1:21 PM, Saulius Gražulis wrote:
>> In addition, CDK, being a library, is not directly usable in
>> Perl/Shell/Unix environment. Someone some day has to build a set of Unix
>> executables for CDK to be usable in our context... Like ones you have
>> build in
On Thu, Mar 13, 2014 at 5:15 AM, Vaibhav wrote:
> How to calculate the lower bound distance and upper bound distance between
> two atoms?
I am not sure what upper and lower bounds you are thinking of here...
based no VdW radii, or based on the fact that molecules have
conformers?
Egon
--
E.L.
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: http://egonw.github.c
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. Scaf
Dear CDK users and developers,
today I received the sad news that Patrik Rydberg passed away in
November last year [0]. Patrik was a long time user of the CDK, e.g.
with his SMARTCyp work of which you can find some papers at [1]. An
more complete overview of his work can be found at Google Scholar
On Tue, Nov 19, 2013 at 9:30 PM, bjoern.gruen...@googlemail.com
wrote:
> ChemcialToolBox: A Galaxy of cheminformatic tools in a web browser
>
> I am very happy to finally announce the first release of ChemicalToolBox!
Nice! That makes a third major workflow environment with CDK support, thanks!
On Mon, Nov 11, 2013 at 4:42 PM, John May 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 this:
- add a
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