Re: [Cdk-user] CDK cmd line utilities (was: About the detection of identical entries)
You can script the CDK in python using - http://baoilleach.blogspot.co.uk/2011/12/cinfony-11-released.html There is also: R http://cran.r-project.org/web/packages/rcdk/index.html ABCL https://github.com/slyrus/abcl-cdk J On 28 Mar 2014, at 05:37, Egon Willighagen egon.willigha...@gmail.com wrote: Dear Saulius, On Thu, Mar 27, 2014 at 1:21 PM, Saulius Gražulis grazulis@... 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 Vilnius for Jumbo, for instance. We used to have those, but since they were not used a lot at the time (years and years ago), we stopped maintaining them. This weekend, during the #blueobelisk hackathon in Cambridge, we discussed it again, as there is now a simple framework that takes away much of the work... I am tempted to introduce the cmd line apps for the CDK again (in a separate project)... So, what would you need? Please file needs here: https://github.com/egonw/cdkcmd/issues Another approach would be to try to call CDK directly from the Perl using Inline::Java module, but then again we need to build objects suitable for CDK. Interesting idea... the command line utils I have an idea about how I would do that... for this, I am not sure, but I can imagine they share the wrapping command classes... 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: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
Re: [Cdk-user] CDK License
I thought companies might be more interested in contributing to CDK if it is under apache 2.0.. http://www.getchef.com/blog/2009/08/11/why-we-chose-the-apache-license/ On Friday, March 28, 2014 1:07 PM, John May john...@ebi.ac.uk wrote: +1 I choose BSD for new projects but it would be a lot of work to track down and get confirmation from everyone. Java is a bit of an odd ball since, almost everything is dynamically linked, the only exception being static variables. GNU’s official stance with Java is that Applications which link to LGPL libraries need not be released under the LGPL - https://www.gnu.org/licenses/lgpl-java.html. I might add that to the README actually. J On 28 Mar 2014, at 06:17, Egon Willighagen egon.willigha...@gmail.com wrote: Hi Lochana, On Fri, Mar 28, 2014 at 3:43 AM, lochana menikarachchi locha...@yahoo.com 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 had that license. If I had to (chance to) change the license of the CDK (which involves getting in contact with a lot of people and getting approval) is to move to BSD or MIT, not Apache... What would it add? People already can embed the CDK in proprietary software; I know the linking is always a bit unclear, but to me (personally), anything not changing the CDK classes itself, is *linking*. Why would you not choose LGPL? Also, did you guys thought about incubating CDK as an apache project?? What would that add? I sounds to me we would get a lot more formal meeting if we would, distracting us from the work... ? My 2 cents... 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: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: -0001-7542-0286 -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user -- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user-- ___ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
