Hi Thomas, CDK developers and users, I have just submitted the patch for the atom type enrichment int he CDK.
Best wishes, Asad On 12 Jul 2011, at 13:03, cdk-user-requ...@lists.sourceforge.net wrote: > Send Cdk-user mailing list submissions to > cdk-user@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cdk-user > or, via email, send a message with subject or body 'help' to > cdk-user-requ...@lists.sourceforge.net > > You can reach the person managing the list at > cdk-user-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cdk-user digest..." > > > Today's Topics: > > 1. Feature and Performance updates reported in blogs: When do > they appear in "public CDK"? (Thomas Strunz) > 2. Re: Feature and Performance updates reported in blogs: When > do they appear in "public CDK"? (Nina Jeliazkova) > 3. Re: Feature and Performance updates reported in blogs: When > do they appear in "public CDK"? (Egon Willighagen) > 4. Re: Exceptions again: three designs. What will we use in the > next CDK series (1.6 or 2.0)? (Egon Willighagen) > 5. New free CDK software (Vincent Le Guilloux) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 11 Jul 2011 15:28:53 +0200 > From: Thomas Strunz <beginn...@hotmail.de> > Subject: [Cdk-user] Feature and Performance updates reported in blogs: > When do they appear in "public CDK"? > To: <cdk-user@lists.sourceforge.net> > Message-ID: <dub103-w15f88cf035e075b28cc91dee...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > 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 usage of CDK. > > My Question is, when (if not already) are such improvements inserted into the > public release of cdk? > > And where could I actually see if they where already included? > > > Best regards, > > Thomas > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Mon, 11 Jul 2011 17:45:06 +0300 > From: Nina Jeliazkova <jeliazkova.n...@gmail.com> > Subject: Re: [Cdk-user] Feature and Performance updates reported in > blogs: When do they appear in "public CDK"? > To: Thomas Strunz <beginn...@hotmail.de> > Cc: cdk-user@lists.sourceforge.net > Message-ID: > <cae5qdd11gfm86f0j4lxiaju_bcdku_lqmbww3i+-tidwq8f...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 usage of CDK. >> >> My Question is, when (if not already) are such improvements inserted into >> the public release of cdk? >> > > >> And where could I actually see if they where already included? >> >> > I guess the release change logs could tell this. > > Best regards, > Nina > > P.S. I was not aware of the second link, adding 90 atom types is indeed a > huge improvement. > > >> Best regards, >> >> Thomas >> >> >> ------------------------------------------------------------------------------ >> All of the data generated in your IT infrastructure is seriously valuable. >> Why? It contains a definitive record of application performance, security >> threats, fraudulent activity, and more. Splunk takes this data and makes >> sense of it. IT sense. And common sense. >> http://p.sf.net/sfu/splunk-d2d-c2 >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> >> > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 3 > Date: Mon, 11 Jul 2011 18:10:07 +0200 > From: Egon Willighagen <egon.willigha...@gmail.com> > Subject: Re: [Cdk-user] Feature and Performance updates reported in > blogs: When do they appear in "public CDK"? > To: Thomas Strunz <beginn...@hotmail.de> > Cc: cdk-user@lists.sourceforge.net > Message-ID: > <campqvy-l6chbzdxmrgpinhylamc99ozhqxxfh5pda5mzimc...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Thomas, > > On Mon, Jul 11, 2011 at 3:28 PM, Thomas Strunz <beginn...@hotmail.de> wrote: >> My Question is, when (if not already) are such improvements inserted into >> the public release of cdk? > > As soon as I we get to see patches and they have been reviewed and > approved. Gilleain is looking at the patches above, if not mistaken, > so contact him to ask him about that state, and perhaps if you can > contribute. > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet f?r milj?medicin > Karolinska Institutet (http://ki.se/imm) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > > ------------------------------ > > Message: 4 > Date: Tue, 12 Jul 2011 08:56:08 +0200 > From: Egon Willighagen <egon.willigha...@gmail.com> > Subject: Re: [Cdk-user] Exceptions again: three designs. What will we > use in the next CDK series (1.6 or 2.0)? > To: Thomas Strunz <beginn...@hotmail.de> > Cc: cdk-u...@lists.sf.net, cdk-de...@lists.sf.net > Message-ID: > <CAMPqvY8y8kRPxy7WCnjfLUY34eKFX2ZVv=kbhvcsosuzucz...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Thu, Jul 7, 2011 at 3:17 PM, Thomas Strunz <beginn...@hotmail.de> wrote: >> IMHO it must get more granular and also I really don't like the fact that >> CDKException is a checked exception. In most of the cases it is just >> annoying and useless. > > I think I disagree. You can get any Runtime exception and never know > what to expect. > > Invalid input is very common here, and your software needs to recover > from that, and differently from other situations. I think a Runtime > exception should only happen when something *unexpected* happened, > like OutOfMemory or so... > >> I know, endless debate and maybe you have had it several times but for me as >> user as it is now: annoying like hell. Just like pure JDBC. >> >> other frameworks that use Runtime exceptions are IMHO a lot more friendlier >> to work with. > > Why do you find it annoying? And useless? Why do you find Runtime > exceptions from user friendly? > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet f?r milj?medicin > Karolinska Institutet (http://ki.se/imm) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > > ------------------------------ > > Message: 5 > Date: Tue, 12 Jul 2011 12:23:39 +0200 > From: Vincent Le Guilloux <vincent.le-guill...@univ-orleans.fr> > Subject: [Cdk-user] New free CDK software > To: "cdk-user@lists.sourceforge.net" <cdk-user@lists.sourceforge.net> > Message-ID: > <20110712122339.61291zmxh1xhh...@webmailper.univ-orleans.fr> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > > Dear all, > > Just to inform everyone about a new free software that makes use of the CDK: > http://sa2.sourceforge.net/ > > This software is basically able to manage small to very large chemical > libraries (we have millions of compounds in our in-house database), > and any sets of properties associated with each molecules, through a > MySQL database. Various chemoinformatics analysis can then be > performed on top of the database. > > It makes uses of the CDK-jcp nightly built picked up here (as I need > depiction too): > http://pele.farmbio.uu.se/nightly-jcp/ > > It uses various CDK functionalities, including descriptors / > fingerprints calculation, substructure search, 2D depiction, SMART > macthing... > > From a developer point of view, it is based on the NetBeans Platform, > and is therefore quite modular. > > The software will be licensed under the GPL v2 license. Currently, the > sources are not available yet, as I want to stabilize and document the > API before releasing it. > > FYI, and as asked by Egon, I've encountered various problems using the > CDK during the development of the software, some of which are listed > here: > - Atom types not recognized > - Various problems with SDF reader / writer, which have been fixed now > for most of them I think. > - SMART matching problems, mainly a performance issue (I've run very > basic tests comparing CDK, JOELib and Indigo for those who are > interested in the details). > - Invalid SMILES reading (fixed now I guess) > > An article is on its way too, but not submitted yet. > > Cheers :) > > -- > Vincent Le Guilloux > > Phd Student - ICOA - UMR CNRS 6005 > Div. of chemoinformatic and molecular modeling. > University of Orl?ans > Phone: ++33 2 38 49 45 77 > Fax : ++33 2 38 41 72 81 > > > > > > > ------------------------------ > > ------------------------------------------------------------------------------ > All of the data generated in your IT infrastructure is seriously valuable. > Why? It contains a definitive record of application performance, security > threats, fraudulent activity, and more. Splunk takes this data and makes > sense of it. IT sense. And common sense. > http://p.sf.net/sfu/splunk-d2d-c2 > > ------------------------------ > > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > End of Cdk-user Digest, Vol 62, Issue 11 > **************************************** ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
