Re: [Cdk-user] Clearing 3D coordinates before depiction

dling 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 alignment and highlighting. > > Thanks f

Re: [Cdk-user] Clearing 3D coordinates before depiction

t.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 < > egon.willigha...@gma

Re: [Cdk-user] Clearing 3D coordinates before depiction

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

Re: [Cdk-user] Extended Fingerprint: what do the features represent?

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

Re: [Cdk-user] Extended Fingerprint: what do the features represent?

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

Re: [Cdk-user] IUPAC name generation

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

Re: [Cdk-user] package-info.java

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

Re: [Cdk-user] Getting warning from AminoAcidCountDescriptor

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:

Re: [Cdk-user] Generation of FCFP Fingerprint

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 ( >

Re: [Cdk-user] [Cdk-devel] Registration ending soon for CDK 20th anniversary symposium on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022.

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. > >

Re: [Cdk-user] Support for chemical standardization

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

[Cdk-user] CDK via Bioclipse/Bacting in Python and on Google Collab with pybacting

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

Re: [Cdk-user] CDK support in chemfp 3.5b1

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

Re: [Cdk-user] CDK support in chemfp 3.5b1

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://egonw

Re: [Cdk-user] CDK support in chemfp 3.5b1

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

Re: [Cdk-user] What are the contents of pom.xml file to install cdk-2.0.jar after installing apache maven?

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,

Re: [Cdk-user] CDK 2.4 release date?

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

Re: [Cdk-user] VolSurf-like molecular descriptors

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

Re: [Cdk-user] Raw fingerprints impossible to calculate

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

[Cdk-user] CDK 2.3 now in Debian Unstable

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

Re: [Cdk-user] controlling hydrogen display with DepictionGenerator

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:

Re: [Cdk-user] SMSD and RDT with CDK v 2.x released

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

Re: [Cdk-user] InChi and Docker [solved]

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

Re: [Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

(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 Willighagen > wrote: >

[Cdk-user] CDK functionality in Docker images (was: InChi and Docker)

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*

Re: [Cdk-user] Question about 3D SDF file from SMILES string

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). > >

[Cdk-user] initial Java9 observations

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

Re: [Cdk-user] Atom Signatures with stereo-info

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

Re: [Cdk-user] Computing the LogD

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

Re: [Cdk-user] Title line for MDL formats

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

[Cdk-user] Third CDK paper is out

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

Re: [Cdk-user] n way-bonds

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 =

Re: [Cdk-user] Rendering 3D mols

> Pass the molfile to what? To JMol? > 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 <tdudgeon...@gmail.com> wrote: >>> >>> What's the state of

Re: [Cdk-user] Rendering 3D mols

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,

Re: [Cdk-user] 'neutralizing' a molecule

;>> 1(26)9(24)6(33-15)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 &g

Re: [Cdk-user] [Cdk-devel] CDK III paper: software using CDK 1.4 or 1.5?

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

[Cdk-user] CDK v1.5.15 and v2.0-SNAPSHOT

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

[Cdk-user] wedge bonds from SMILES?

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:

Re: [Cdk-user] Complex Molecule Rendering

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:

Re: [Cdk-user] [Cdk-devel] Reaction Agents

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

Re: [Cdk-user] Interest in metabolic reaction depictions.

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

Re: [Cdk-user] create amino acide

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,

Re: [Cdk-user] [Cdk-devel] CDK Release 1.5.14

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

Re: [Cdk-user] [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

that students can see the ideas too! Egon On Tue, Mar 1, 2016 at 7:06 PM, Greg Landrum <greg.land...@gmail.com> 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 <egon.willig

Re: [Cdk-user] [BlueObelisk-discuss] Two Google Summer of Code projects related to the CDK

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

Re: [Cdk-user] inconsistency in ready molfiles

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

Re: [Cdk-user] Dear CDK, QUESTIONS of standard data set to evaluate ligand-based models

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.

[Cdk-user] CDK code migration guides

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

Re: [Cdk-user] [Cdk-devel] Preserving public API

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

Re: [Cdk-user] [Cdk-devel] Preserving public API

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

[Cdk-user] Free (old) copy of Groovy Cheminformatics with the CDK

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.

Re: [Cdk-user] Feedback about CDK 1.4 to 1.5 Migration

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

Re: [Cdk-user] Fingerprints in 1.4 und 1.5

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

Re: [Cdk-user] Fingerprints in 1.4 und 1.5

ing for > something else: if the different 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

Re: [Cdk-user] CDK Depict

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

Re: [Cdk-user] CDK Depict

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

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

. On Tue, Jul 7, 2015 at 5:03 PM, Egon Willighagen egon.willigha...@gmail.com 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 following Groovy code shows a very basic example

Re: [Cdk-user] puzzles about how to compare two molecules to check whether they are the same in cdk

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

[Cdk-user] Metabolomics 2015

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

Re: [Cdk-user] Regarding IteratingMDLReader in Cdk1.5

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 tvsivaku...@gmail.com wrote: I was porting my code from Cdk1.4 to Cdk1.5. The class

[Cdk-user] CDK Literature #6

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

Re: [Cdk-user] Fwd: CDKPsearch speed

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

Re: [Cdk-user] Fwd: CDKPsearch speed

. 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

[Cdk-user] 1.5.10 version of my Groovy Cheminformatics with the CDK book

: 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

Re: [Cdk-user] First property missing from SD file

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

Re: [Cdk-user] [Cdk-devel] CDK 1.5.10 available on Maven Central

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

Re: [Cdk-user] problems with calculating TPSA in cdk

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

Re: [Cdk-user] jni-inchi and OSGi

(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

Re: [Cdk-user] Weird problem with CDK smarts pattern matching

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

Re: [Cdk-user] Weird problem with CDK smarts pattern matching

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:

Re: [Cdk-user] cdk-jar including java sources

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,

Re: [Cdk-user] Iterating over SDF files

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

Re: [Cdk-user] [Cdk-devel] New JDK version

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

Re: [Cdk-user] Get associated information from SDF file with CDK

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

[Cdk-user] how to solve this compile error: Plugin requires Maven version 3.0

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:

[Cdk-user] ScaffoldHunter and NRNB are in the Google Summer of Code 2014

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.

Re: [Cdk-user] [Cdk-devel] Inchi to structure

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

Re: [Cdk-user] [Cdk-devel] AtomContainer - Poll Results

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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...

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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)

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] [Cdk-devel] Important: Your vote needed on some API re-naming

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

Re: [Cdk-user] Storing IAtomContainers in a Database

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

Re: [Cdk-user] Charge and Stereo Columns in SD Files

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

Re: [Cdk-user] descriptors for multi-compound molecules

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

Re: [Cdk-user] [Cdk-devel] CDK 1.5.3 Released (development)

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

[Cdk-user] release CDK 1.4.19

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

Re: [Cdk-user] CDK for toxicology?

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

[Cdk-user] CDK for toxicology?

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

Re: [Cdk-user] [Cdk-devel] Stable API Documentation

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

Re: [Cdk-user] [Cdk-devel] How many atoms of quinine belong to two rings?

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

Re: [Cdk-user] CML wedge bond info reading regression?

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,

[Cdk-user] CDK hangout (postponed)

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

Re: [Cdk-user] SmileParser fails with

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

Re: [Cdk-user] Problems with jni-inchi on MacOSX

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

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