Re: [Cdk-user] Old versions from Maven?

On 26 September 2016 at 22:53, John M wrote: > Found them - https://nexus.ideaconsult.net/content/repositories/ > thirdparty/org/openscience/cdk/. > Correct, there are CDK artifacts there, but older than 1.5.x The move to the new repo is announced at

Re: [Cdk-user] ICountFingerprint usage question

> > John > > Regards, > John W May > john.wilkinson...@gmail.com > > On 3 February 2016 at 06:39, Nina Jeliazkova <jeliazkova.n...@gmail.com> > wrote: > >> Hello All, >> >> I am wondering what is the intended usage of the ICountFingerprint &g

[Cdk-user] ICountFingerprint usage question

Hello All, I am wondering what is the intended usage of the ICountFingerprint interface, and more specifically, how does one iterates over the available hashes using this interface. The obvious way of using the size() and for loop is impractical in cases as CircularFingerprint, where the size is

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

Excellent ! Thanks, Nina On 30 December 2014 at 02:19, John May john.wilkinson...@gmail.com wrote: HI all, I’m pleased to announce that the CDK is now available on the central maven repo. I’ve just pushed a new release (1.5.10 - will add notes tomorrow) but you can use it right now.

Re: [Cdk-user] how to print SMARTS pattern without hydrogens

Martin, Following John's comments, I've realized you might consider writing SMARTS via SmartsHelper.toSmarts() method from ambit2-smarts package (takes QueryAtomContainer )

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

Hi John, I'm not sure skiping JDK versions is the best approach. It will make installing CDK based tools harder in some environments, where JDK version is not personal choice and update procedures are a bit conservative (read it make take couple of years for the IT department to roll out an

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

On 29 Aug 2014 19:29, John May john...@ebi.ac.uk wrote: So 1.7 would be okay Nina? 1.7 is ok :-) Thanks, Nina J On Aug 29, 2014, at 5:27 PM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Hi John, I'm not sure skiping JDK versions is the best approach. It will make installing CDK

Re: [Cdk-user] [Cdk-devel] can't build latest bundle JAR

John, You could eventually change the way snapshots are deployed, and keep only the latest snapshot, not all of them . Regards, Nina On 15 August 2014 16:56, John May john...@ebi.ac.uk wrote: Hi Rajarshi, For now you’ll have to do a clean build of the whole project.. mvn clean install

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

Change the plugin to an older version. Does it says which one is requiring Maven 3.0 ? Nina On 6 March 2014 16:12, Egon Willighagen egon.willigha...@gmail.com wrote: 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

Re: [Cdk-user] SMILES parsing error

On 7 November 2013 18:26, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: On 7 November 2013 18:18, Rajarshi Guha rajarshi.g...@gmail.com wrote: It seems c4ccc2c(cc1=Nc3n3(Cn12))c4 does not parse using the latest CDK master, but does parse fine using http://apps.ideaconsult.net

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

On 7 October 2013 10:28, Egon Willighagen egon.willigha...@gmail.comwrote: 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

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

On 7 October 2013 11:09, Egon Willighagen egon.willigha...@gmail.comwrote: 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

Re: [Cdk-user] circular fingerprints

Rajarshi, All, You probably recall the blog by Patrik Rydberg http://simply-p450s.blogspot.com/2011/12/circular-fingerprints-in-cdk.html . It is based on my old Ambit code implementation of atom environments (a.k.a. circular fingerprints) with application in

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

, Joos 2013/9/25 Nina Jeliazkova jeliazkova.n...@gmail.com On 25 September 2013 08:03, Joos Kiener j...@sunrise.ch wrote: Since I have played around with this for a fairly long time, here some of my observations: - loading lots (thousands) of molfiles from relation databases is quiet slow

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

On 25 September 2013 08:03, Joos Kiener j...@sunrise.ch wrote: Since I have played around with this for a fairly long time, here some of my observations: - loading lots (thousands) of molfiles from relation databases is quiet slow The slow part is not reading molfile from the database,

Re: [Cdk-user] Reading large SD Files

time for that at the moment. Without checking the cdk-io code, I would say almost all readers in CDK use readline() to read text files (with XML readers perhaps an exception). Best regards, Nina Best Regards, Joos Am 20.09.2013 14:23, schrieb Nina Jeliazkova: Hi Joos, All, On 20

Re: [Cdk-user] Reading large SD Files

The RandomAccessReader mentioned above is exactly such low level indexer - it does not perceive chemistry when building the index. Lochana may have issues if trying to load all these molecules in memory - this is definitely not the way to go. Nina On 19 September 2013 03:07, Andrew Dalke

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

Hi Martin, All, On 22 August 2013 23:55, Martin Guetlein martin.guetl...@googlemail.comwrote: On Thu, Aug 22, 2013 at 6:28 PM, Rajarshi Guha rajarshi.g...@gmail.com wrote: Do you mean dot connected compounds? In that sense, most (if not all) QSAR descriptors should be evaluating

Re: [Cdk-user] [Cdk-devel] Kekulé form of Structure

John, Try this https://ambit.uni-plovdiv.bg:8443/ambit2/compound/108403 It came as exact match of the first SMILES http://tinyurl.com/kexyv5y . The SDF download is a Kekule structure. Nina On 9 August 2013 13:19, John May john...@ebi.ac.uk wrote: Hi all, Debugging some CDK tests and I

Re: [Cdk-user] loosing aromaticity when writing SDF files

Hi Martin, On 27 June 2013 13:27, Martin Guetlein martin.guetl...@googlemail.comwrote: Anyone? Maybe theres a workaround for this? But AFAIK there is no kekulize option in CDK, right? Actually there is - check org.openscience.cdk.smiles.FixBondOrdersTool Regards, Nina On Mon, Jun

Re: [Cdk-user] fingerprints generated differently for same molecules using different methods - smileparser and reading the sdf file using IteratingMDLReader

The differences are most probably due to missing atom type and aromaticity recognition. The SmilesParser does atom typing automatically, the MDL reader does not, before running the fingerprinter you would need to explicitly invoke the atom typing and aromaticity recognition. Best regards, Nina

Re: [Cdk-user] strange exception while generating SMILES

Dear Alberto, On 25 November 2012 10:57, Alberto Manganaro alberto.mangan...@unimib.itwrote: Dear all, I'd just like to report you the test I made. As I said, I'm working with JDK 1.7 and with CDK 1.4.9, I'm using the donwnloaded jar (looking inside it, it seems that the bytecode has been

Re: [Cdk-user] strange exception while generating SMILES

Dear Alberto, All On 24 November 2012 10:06, Alberto Manganaro alberto.mangan...@unimib.itwrote: Dear all, I encountered a strange Exception while using classes for generation of SMILES. For a couple of molecules, I get a Comparison method violates its general contract! message and I really

Re: [Cdk-user] [Cdk-devel] FYI: layout disconnected structures in 1 AtomContainer

On 16 November 2012 16:32, r...@ark.in-berlin.de wrote: On Fri, Nov 16, 2012 at 01:59:33PM +0200, Nina Jeliazkova wrote: On 16 November 2012 13:18, r...@ark.in-berlin.de wrote: There will soon be an additional accessor to the parser returning an AtomContainerSet. This will also make

Re: [Cdk-user] layout disconnected structures in 1 AtomContainer

Hi Joos, I think I have posted this code before on a similar question. https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java It will render any set of disconnected structures inside a single atom container.

Re: [Cdk-user] ALOGP Descriptor

Kevin, Better not use ALogP at all. Back at the list you could find reports it is not performing well. I think it was decided to be removed / deprecated. Best regards, Nina On 1 June 2012 10:58, kevin.law...@syngenta.com wrote: Hi I am getting some strange results from the ALOGP

Re: [Cdk-user] ALOGP Descriptor

model ... http://www.opentox.org/pipermail/development/2011/001575.html -Original Message- From: Nina Jeliazkova [mailto:jeliazkova.n...@gmail.com] Sent: 01 June 2012 09:01 To: Lawson Kevin GBJH Cc: cdk-user@lists.sourceforge.net Subject: Re: [Cdk-user] ALOGP Descriptor Kevin

Re: [Cdk-user] [Bioclipse-devel] Your feedback please: finding double bond locations

On 14 May 2012 13:18, Egon Willighagen egon.willigha...@gmail.com wrote: 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

Re: [Cdk-user] Split multiple Structures in 1 AtomContainer into multiple AtomContainers

On 20 March 2012 09:11, Joos Kiener j...@sunrise.ch wrote: Hi all, when as example reading a mol file (or 1 record of an sd-file) that record can contain multiple unconnected structures. Exampel with SMILES: String smiles = CC1(C)C(C2OC(CO)CO2)CC=C1C.CC3(C)C(C4OCC(O)CO4)CC=C3C;

Re: [Cdk-user] Split multiple Structures in 1 AtomContainer into multiple AtomContainers

On 20 March 2012 09:43, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: On 20 March 2012 09:11, Joos Kiener j...@sunrise.ch wrote: Hi all, when as example reading a mol file (or 1 record of an sd-file) that record can contain multiple unconnected structures. Exampel with SMILES: String

Re: [Cdk-user] aromaticity not detected

On 21 February 2012 14:23, Martin Guetlein martin.guetl...@googlemail.com wrote: Hi Egon, thanks for your answer. Glad to hear that this is a known issue, because it troubles me a lot. The CDK algorithm for aromaticity defines rings with double bonds pointing out of the ring as

Re: [Cdk-user] Fragmenting Molecules based on set of rules

On 9 February 2012 18:19, Rajarshi Guha rajarshi.g...@gmail.com wrote: The CDK doesn't support SMIRKS yet, so you'd basically have to implement the fragmentation rules manually (via atom/bond manipulation) Or you could try the SMIRKS implementation from

Re: [Cdk-user] Rendering H2O results 0x0 image

is the trick... Yes, there is really a single class, should be rather straightforward to put back to CDK. I'll try to. Nina Similarly I have problems with rendering the simple molecule like this InChI=1S/CH3/h1H3 while Ambit behaves OK. Very interesting... On 28.11.2011 16:47, Nina

Re: [Cdk-user] not working: loading descriptor instances with java web start

Hi Martin, This is known not to work, as the class path for JavaWeb start is dynamic and the descriptor engine expects a fixed classpath elsewhere. Regards, Nina On 15 November 2011 12:50, Martin Guetlein martin.guetl...@googlemail.comwrote: Hi all, this is probably more a Java related

Re: [Cdk-user] SMARTS Queries /parametrized Queries and pre-screening

On 13 November 2011 23:24, Rajarshi Guha rajarshi.g...@gmail.com wrote: I don't think it's too difficult. The SMARTS parser generates a parse tree. I suppose walking it and removing the variable portions isn't too difficult. It would be important to take into account the OR and AND operators,

Re: [Cdk-user] Patch for FPS write support in the CDK

On 25 October 2011 13:38, Andrew Dalke da...@dalkescientific.com wrote: On Oct 25, 2011, at 10:27 AM, nls...@users.sourceforge.net wrote: Java Bit-Shifting with bytes is a bit strange. The expression b4 does not always shift zeros into the leftmost position (the value depends on the sign

Re: [Cdk-user] Rendered Bonds in Gray

Hi, Are you using StructureDiagramGenerator before rendering? Please have a look at http://sourceforge.net/tracker/?func=detailaid=3295256group_id=20024atid=120024 Best regards, Nina On 12 October 2011 21:21, lochana menikarachchi locha...@yahoo.com wrote: Hi All, When I render molecules

Re: [Cdk-user] Cdk-user Digest, Vol 64, Issue 5

Best Regards, Joos Am 09.09.2011 16:11, schrieb Nina Jeliazkova: I'm not sure how you differentiate library vs database search? To explain myself: graph matching is not done natively in a relational database so you need somekind of library/add-in/carrtridge anyway? Where

Re: [Cdk-user] Cdk-user Digest, Vol 64, Issue 5

Hi Joos, On 9 September 2011 18:27, Joos Kiener j...@sunrise.ch wrote: Hi Nina, I think we just misunderstood each other. So you meant library = cdk and database = commercial? Then I agree. No, I don't assume, but was not quite clear. In my first reply I was actually sending a link to an

Re: [Cdk-user] print MCS as aromatic smarts

On 8 September 2011 10:33, Martin Guetlein martin.guetl...@googlemail.comwrote: On Thu, Sep 8, 2011 at 9:26 AM, Egon Willighagen egon.willigha...@gmail.com wrote: 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,

Re: [Cdk-user] Rendering disconnected structures (e.g. mixtures)

?msg_id=27010062 Thanks! On 02.06.2011 7:22, Nina Jeliazkova wrote: On 2 June 2011 01:38, Dmitry Katsubo dmitry.kats...@gmail.com wrote: I definitely missed that, but perhaps I've joined just shortly afterwards or it was in jcpempaint maillist (which I need to be subscribed too): https

Re: [Cdk-user] Exceptions again: three designs. What will we use in the next CDK series (1.6 or 2.0)?

Hi Thomas, My 2 cents in this discussion. On 13 July 2011 13:33, Thomas Strunz beginn...@hotmail.de wrote: Hi Egon, the problem with checked exceptions is, that the mostly occur on a very low level, meaning in IO operations. In my usage of CDK when creating molecules from file or

Re: [Cdk-user] Feature and Performance updates reported in blogs: When do they appear in public CDK?

On 11 July 2011 16:28, Thomas Strunz beginn...@hotmail.de wrote: Hi all, I saw these to blog posts: http://chembioinfo.wordpress.com/2011/03/15/benchmarking-substructure-search/ http://chembioinfo.wordpress.com/2011/07/06/improved-atom-typing-cdk/ Both state an important problem for my

Re: [Cdk-user] [Cdk-devel] Exceptions again: three designs. What will we use in the next CDK series (1.6 or 2.0)?

Hello Egon, On 6 July 2011 13:06, Egon Willighagen egon.willigha...@gmail.com wrote: 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

Re: [Cdk-user] [Cdk-devel] Exceptions again: three designs. What will we use in the next CDK series (1.6 or 2.0)?

On 6 July 2011 14:42, Rajarshi Guha rajarshi.g...@gmail.com wrote: I like Jules suggestions - use Java exceptions where possible/ reasonable, but have a hierarchy of CDKExceptions; my worry is that it will be easy to have a proliferation of CDKException subclasses, such that rather than throw

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

On 25 April 2011 09:18, Egon Willighagen egon.willigha...@gmail.com wrote: On Thu, Apr 21, 2011 at 9:27 PM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Use this branch: https://github.com/egonw/cdk/tree/13-unsorted-patches It's CDK 1.3.8 + CDK-JChemPaint 18, with the module

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

Hi Dmitry, On 21 April 2011 15:46, Dmitry Katsubo dmitry.kats...@gmail.com wrote: Hi Nina, Thanks for reply. On 16.04.2011 7:45, Nina Jeliazkova wrote: Egon, On 16 April 2011 08:19, Egon Willighagen egon.willigha...@gmail.com wrote: The single big jar is a much requested feature

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

services application , and neither needs SWT ... How do we start - perhaps a hint from JChemPaint developers where/how the dependencies are defined ? Nina Thanks. On 21.04.2011 17:13, Nina Jeliazkova wrote: We've been are using cdk jars as maven artifacts since almost 3 years

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

Hi Dmitry, On 21 April 2011 20:10, Dmitry Katsubo dmitry.kats...@gmail.com wrote: Hi Nina, Thanks of the information. Everything worked smoothly for me. May I ask you about the following: Could you please deploy the latest JChemPaint to this repo? For example, I am using this one:

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

Egon, On 21 April 2011 21:29, Egon Willighagen egon.willigha...@gmail.com wrote: On Thu, Apr 21, 2011 at 7:25 PM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Accepted - I would really appreciate help of splitting JChemPaint into dependencies. SWT dependency is a good example indeed

Re: [Cdk-user] CDK package contains all dependant libraries, which cause a problem

Dear Dmitry, On 16 April 2011 03:15, Dmitry Katsubo dmitry.kats...@gmail.com wrote: Dear CDK developers, I have run into minor issue with CDK binary releases (1.2.x or 1.3.x - does not matter). The problem is that cdk-1.3.8.jar contains CDK class + the classes from all dependent libraries.

Re: [Cdk-user] Properties not read with MDLV2000Reader ?

On 15 March 2011 15:36, Egon Willighagen egon.willigha...@gmail.com wrote: On Mon, Mar 14, 2011 at 2:55 PM, Vincent Le Guilloux vincent.le-guill...@univ-orleans.fr wrote: Fair enough :) I think it's not so much unusual: when it's time to test your new outstanding chemoinformatics library,

Re: [Cdk-user] Properties not read with MDLV2000Reader ?

Hi Egon, On 15 March 2011 15:52, Egon Willighagen egon.willigha...@gmail.com wrote: Hej Nina, On Tue, Mar 15, 2011 at 2:47 PM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Being aware it might be controversial and / or time consuming redesign, can't help to throw this idea

Re: [Cdk-user] CDK-JMol Adapter

On 9 March 2011 13:31, Egon Willighagen egon.willigha...@gmail.com wrote: On Wed, Mar 9, 2011 at 12:26 PM, Thorsten Meinl thorsten.me...@uni-konstanz.de wrote: Has anyone written an updated version for the CDKJMolAdapter? The ones I find are for very old versions for both CDK and JMol.

Re: [Cdk-user] Isomorhism and MolHandler: removeHydrogen flag issue/bug

On 1 March 2011 10:49, Thomas Strunz beginn...@hotmail.de wrote: Hi all, the Isomorphism class has an init method: public void init(IMolecule reactant, IMolecule product, boolean removeHydrogen, boolean cleanAndConfigureMolecule) throws CDKException { this.removeHydrogen =

Re: [Cdk-user] Cdk-user Digest, Vol 58, Issue 1

On 1 March 2011 12:51, Egon Willighagen egon.willigha...@gmail.com wrote: Hej Asad, On Tue, Mar 1, 2011 at 11:43 AM, Syed Asad Rahman a...@ebi.ac.uk wrote: Can I know which algorithm did you use in the SMSD for substructure search? Algorithm.SubStructure Here is an excerpt of the testing

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

On 25 February 2011 12:30, ma...@ebi.ac.uk wrote: I wonder why I haven't asked this before. How is this done on OrChem? These columns provide a quick way to materialize a basic CDK molecule to be passed into the VF2 algorithm. The data structures used are quite straightforward, for

[Cdk-user] createChiralSmiles()

Dear All, Using createChiralSmiles() on molecules with 2D coordinates results in SMILES with slashes even on aromatic rings - is it expected? Nc\4n\c\n\c\1c\4(n\c\(n/1C/2OC3COP\(=O)(O)O\C\3(C\2(O)))Cl) (The SDF file is example file attached) The code used: SmilesGenerator g = new

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

@lists.sourceforge.net Just a short note to mention that I'm closely following this topic. A major rewrite of our own database system is somewhere in the near future, so this is good reading! Thanks for sharing! ~Jules Kerssemakers On 13 December 2010 08:51, Nina Jeliazkova jeliazkova.n

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

= manager.getMolecule(key); // IMPROVEMENT: only load one molecule at a time! if (searchtarget.isSubgraphOf(mol)) { results.add(mol) } } Hope this helps, Best regards, Jules Kerssemakers On 30 November 2010 21:19, Nina Jeliazkova jeliazkova.n...@gmail.comwrote: Hi Thomas, On 30

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

is somewhere in the near future, so this is good reading! Thanks for sharing! ~Jules Kerssemakers On 13 December 2010 08:51, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Hi Thomas, On 10 December 2010 20:04, Thomas Strunz beginn...@hotmail.de wrote: Sorry for calling

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

Hi Thomas, On 10 December 2010 20:04, Thomas Strunz beginn...@hotmail.de wrote: Sorry for calling you stupid. ;) ;) I just meant if you have like 100'000 Molecules and assuming 25 % are aromatic probably mostly benzene rings = 6 molecules + bonds that leads to 12* 25'000 = 300'000

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

Hi, On 10 December 2010 15:13, Thomas Strunz beginn...@hotmail.de wrote: Hi again, first a short update if anyone is interested: Not very surprisingly Java serialization is quite useless. I tried it (HSQLDB has a special column type for this) but to keep it simple, it is considerably

Re: [Cdk-user] class file has wrong version

Hi, Class file versions differ between Java versions and are only backward compatible. In this case most probably Java 1.6 is not installed on OSX or not the default and you are trying to use Java 1.5.x with CDK jar compiled with Java 1.6 . Hope this helps, Nina On 9 December 2010 18:17, Xin

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

On 30 November 2010 21:19, Nina Jeliazkova jeliazkova.n...@gmail.comwrote: Hi Thomas, On 30 November 2010 21:58, Thomas Strunz beginn...@hotmail.de wrote: Hi Nina, I sure have more than 1 IAtomContainer in memory at time so I agree that might be an issue but if screening lets say returns

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

= manager.getMolecule(key); // IMPROVEMENT: only load one molecule at a time! if (searchtarget.isSubgraphOf(mol)) { results.add(mol) } } Hope this helps, Best regards, Jules Kerssemakers On 30 November 2010 21:19, Nina Jeliazkova jeliazkova.n...@gmail.comwrote: Hi Thomas, On 30 November

Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

Hi Thomas, On 30 November 2010 21:58, Thomas Strunz beginn...@hotmail.de wrote: Hi Nina, I sure have more than 1 IAtomContainer in memory at time so I agree that might be an issue but if screening lets say returns 1000 hits, 1000 subgraph matches must be done and hence all the 1000

[Cdk-user] InChI parsing

Hello All, Attemping to parse this InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2 via org.openscience.cdk.inchi.InChIToStructure (latest stdinchi ) fails with an error: Aux. info suppressed Input format: InChI (plain identifier) Output format: Plain text No timeout; Up to 1024 atoms per

Re: [Cdk-user] InChI parsing

something similar - e.g. extract only a skeleton from available InChI layers ? Thanks, Nina On 9 November 2010 10:13, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Hello All, Attemping to parse this InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2 via

[Cdk-user] Rendering issues

Hi All, I've recently received couple of reports related to the quality of 2D rendering of some compounds in Toxtree, mostly salts. Since Toxtree uses CDK 1.3.3 and JChemPaint 3.0.1 , I would like to ask here - is there any standard way to render salts (and in general an atom container,

Re: [Cdk-user] [Cdk-devel] Problems with IteratingMDLReader

All: any clue for a unit test here? I do not... I think this fix will go into the library without unit test... if someone does come up with one, we can always add that later... Actually, any of the existing IteratingMDLReader tests would do, by emulating broken InputStreamReader : +

Re: [Cdk-user] [Cdk-devel] Problems with IteratingMDLReader

Hi Egon, On 16 October 2010 11:58, Egon Willighagen egon.willigha...@gmail.comwrote: Hi Nina, Tobias, On Sat, Oct 16, 2010 at 10:27 AM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: --- Fixed --- public boolean hasNext() { if (!nextAvailableIsKnown

Re: [Cdk-user] [Cdk-devel] Problems with IteratingMDLReader

I have heard of similar things here... isReady() can indeed mean that the stream does not ended yet, but that there currently is no byte ready... (e.g. network lag)... readLine() is likely blocking, but makes perfect sense. Nina, please convert this into a git patch. Here it is.

Re: [Cdk-user] rendering atom labels

there are a number of font issues! gilleain On Wed, Sep 8, 2010 at 6:27 PM, Nina Jeliazkova jeliazkova.n...@gmail.com wrote: Hi All, A rendering question - is it possible to assign additional labels to (subset) of atoms and have them rendered with different font size? Thanks, Nina

[Cdk-user] rendering atom labels

Hi All, A rendering question - is it possible to assign additional labels to (subset) of atoms and have them rendered with different font size? Thanks, Nina -- This SF.net Dev2Dev email is sponsored by: Show off your

Re: [Cdk-user] JChemPaint embedded in Swing application

Hi Stefan, Stefan Kuhn wrote: On Saturday 10 April 2010 09:15:57 Egon Willighagen wrote: Hi Nina, On Fri, Apr 9, 2010 at 11:47 AM, Nina Jeliazkova n...@acad.bg wrote: Well, rendering does work as per your examples, but I didn't succeed at launching JChemPaintPanel using cdk

Re: [Cdk-user] JChemPaint embedded in Swing application

Hi Egon, Egon Willighagen wrote: Hi Nina, On Fri, Apr 9, 2010 at 11:47 AM, Nina Jeliazkova n...@acad.bg wrote: Well, rendering does work as per your examples, but I didn't succeed at launching JChemPaintPanel using cdk-jchempaint-8 and cdk-1.3.4 due to compile errors. Yes

Re: [Cdk-user] JChemPaint embedded in Swing application

20:31:09 Nina Jeliazkova wrote: Hello All, I am trying to upgrade a Swing application ( http://toxtree.sourceforge.net/ ) to use recent versions of CDK and JChemPaint. An embedded JChemPaint had been used successfully since 2005, but I am having troubles with upgrading to recent

Re: [Cdk-user] JChemPaint embedded in Swing application

Egon Willighagen wrote: On Fri, Apr 9, 2010 at 11:02 AM, Stefan Kuhn stefan.k...@ebi.ac.uk wrote: JCP is working (I just checked) with a checkout of the EBI cdk repository at http://www.ebi.ac.uk/steinbeck-srv/git/cdk. This is cdk master plus some patches. Since JCP is no longer integrated

[Cdk-user] JChemPaint embedded in Swing application

some compile errors. Any recommendation for correct dependencies between CDK and JChemPaint versions, or working examples of embedded JChemPaint will help a lot. Best regards, Nina Jeliazkova -- Download Intel#174

Re: [Cdk-user] Regarding Smarts Matcher Performance.

Egon Willighagen wrote: On Wed, Feb 24, 2010 at 4:08 PM, Mark Rijnbeek ma...@ebi.ac.uk wrote: It'd be interesting to see the examples (pattern and molecule). In my database search toolkit (Orchem) I also implemented SMARTS searching, but the CDK's performance was not good. Sounds

Re: [Cdk-user] Problem with org.openscience.cdk.qsar.DescriptorEngine and Java WebStart

Hi Tobias, Descriptor engine relies on introspection to find classes implementing certain (descriptor) interfaces. Since Java Web Start mechanism for loading classes is a bit different , this behaviour is not quite unexpected. Although I am not an author of it, I've struggled before with

Re: [Cdk-user] Problem with org.openscience.cdk.qsar.DescriptorEngine and Java WebStart

Hi Egon, Egon Willighagen wrote: On Wed, Sep 2, 2009 at 11:52 AM, Tobias Girschicktobias.girsch...@in.tum.de wrote: On Wed, 2009-09-02 at 12:26 +0300, Nina Jeliazkova wrote: Descriptor engine relies on introspection to find classes implementing certain (descriptor) interfaces. Since

Re: [Cdk-user] DescriptorEngine help/bug?

Egon Willighagen wrote: On Fri, Jun 6, 2008 at 12:52 AM, Rajarshi Guha [EMAIL PROTECTED] wrote: On May 23, 2008, at 10:39 AM, Ola Spjuth wrote: I still would like to get an optional AtomContainer or AtomContainerSet back from the descriptorcalculation, in order to be able to

Re: [Cdk-user] DescriptorEngine help/bug?

Rajarshi Guha [EMAIL PROTECTED] wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On May 22, 2008, at 2:08 AM, Nina Jeliazkova wrote: Rajarshi Guha wrote: Hmm, making the top class an array type would be a good idea. But at one point you'd need to know the type of the result

Re: [Cdk-user] DescriptorEngine help/bug?

Rajarshi Guha wrote: I took the source code from your Sourceforge bug report and tried running it. However I cannot get the 3D structure in the first place (it reports that not all ring atoms were placed). So I converted the SMILES to 3D using smi23d and tested it directly with the

Re: [Cdk-user] DescriptorEngine help/bug?

Rajarshi Guha wrote: On May 22, 2008, at 1:12 AM, Nina Jeliazkova wrote: Rajarshi Guha wrote: I took the source code from your Sourceforge bug report and tried running it. However I cannot get the 3D structure in the first place (it reports that not all ring atoms were placed). So

Re: [Cdk-user] DeduceBondSystemTool (was problem with inchi on 64 bit machines)

Hi, Egon Willighagen [EMAIL PROTECTED] wrote: On Feb 8, 2008 1:46 PM, Nina Jeliazkova [EMAIL PROTECTED] wrote: My experience with the latest code says that if you parse an aromatic smiles (as below), all the aromatic bonds will correctly have aromatic flag turned on, but the bond order

Re: [Cdk-user] problem with inchi on 64 bit machines

Hi, My experience with the latest code says that if you parse an aromatic smiles (as below), all the aromatic bonds will correctly have aromatic flag turned on, but the bond order will be single everywhere. This causes lot of confusion for further processing, and could be the reason inchi is

Re: [Cdk-user] [Cdk-devel] restriction of CDKAromaticityDetector vs HueckelAromaticityDetector

Hi Rajarshi, Thanks for the quick response :) Rajarshi Guha wrote: On Dec 7, 2007, at 11:47 AM, Nina Jeliazkova wrote: Since I've received no reply, I am resending this to both user and developers list. I don't feel restricting aromaticity perception only to max two fused rings

Re: [Cdk-user] [Cdk-devel] restriction of CDKAromaticityDetector vs HueckelAromaticityDetector

Since I've received no reply, I am resending this to both user and developers list. I don't feel restricting aromaticity perception only to max two fused rings will be very useful. It will break lot of old code. If there is no workaround I would suggest again to retain both old and new

Re: [Cdk-user] Request for Comments: Cloning of IChemObject.getProperties()

Rajarshi Guha [EMAIL PROTECTED] wrote: It seems that 1) would be a little more involved in terms of coding, but also, by specifying a max depth, one might fail to properly clone an object in some cases (especially if max depth is set to a default). However all this is only relevant when

Re: [Cdk-user] Store molecules in a database

Hi, Just had in mind, that using serialization for this purpose is not very good idea, since the serialized object can change if the definition of e.g. AtomContainer will be changed in future. This will result in errors when trying to read old serialized objects with the new version of

[Cdk-user] cdk 1.0.1 JChemPaint

Hi all, Just discovered JChemPaint classes are not included in cdk 1.0.1 jar (released 26.06.2007) - is this intentional or I am missing something? Best regards, Nina - This SF.net email is sponsored by DB2 Express

Re: [Cdk-user] latest CDKJMolAdapter - error found

Hi all, Egon Willighagen [EMAIL PROTECTED] wrote: Nina wrote: It's the latest JMol from SVN. Not that I absolutely need the latest version, but I've tried to recompile it with a newest version of iText, otherwise there is a conflict of some of my code using iText2.0.4 and JMol using

Re: [Cdk-user] CML and bond orders

Egon, Many thanks! Egon Willighagen [EMAIL PROTECTED] wrote: On Friday 27 April 2007, Nina Jeliazkova wrote: Here is the story. 1) Create (somehow) a structure as IMolecule (e.g. benzene with alternating single/double bonds) 2) Run HueckelAromaticityDetector to perceive aromaticity

[Cdk-user] CML and bond orders

. * @author Nina Jeliazkova br * bModified/b 2005-4-7 */ public class cmlTest extends TestCase { /** * * @return */ protected IMolecule getMolecule() { Molecule mol = new Molecule(); Atom a1 = new Atom(C

Re: [Cdk-user] Google SoC deadline (12 March)

Egon, Rajarshi, A student of mine is interested in participating, one of the topics of interest to us is SMARTS/MQL editor ( e.g. later to be used by Toxtree). What do you think (and what are the next steps)? Best regards, Nina Egon Willighagen [EMAIL PROTECTED] wrote: On Saturday 03 March

Re: [Cdk-user] Google SoC deadline (12 March)

Rajarshi Guha [EMAIL PROTECTED] wrote: On Sun, 2007-03-04 at 14:55 +0200, Nina Jeliazkova wrote: Egon, Rajarshi, A student of mine is interested in participating, one of the topics of interest to us is SMARTS/MQL editor ( e.g. later to be used by Toxtree). What do you think

Re: [Cdk-user] Google SoC deadline (12 March)

Egon Willighagen [EMAIL PROTECTED] wrote: On Sunday 04 March 2007, Rajarshi Guha wrote: On Sun, 2007-03-04 at 14:55 +0200, Nina Jeliazkova wrote: A student of mine is interested in participating, one of the topics of interest to us is SMARTS/MQL editor ( e.g. later to be used by Toxtree

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