Quoting Egon Willighagen <[email protected]>: > Hi Vincent, > > On Tue, Feb 24, 2009 at 5:10 PM, Vincent Le Guilloux > <[email protected]> wrote: >> Quoting Egon Willighagen <[email protected]>: >>> On Tue, Feb 24, 2009 at 4:25 PM, Vincent Le Guilloux >>>> I'm currently trying to migrate a JOElib based application to CDK. >>> >>> Integrating the both? >> >> Well the current application is entirely based on JOElib. As JOElib is no >> more developped, I'm thinking about using CDK instead... Besides I want to >> keep some JOElib features (mainly descriptors calculation), that's why I >> need a JOElib/CDK converter. > > A few months ago I talked to Joerg about descriptors in JOELib not > available from the CDK, and he could not think of anything > significant... > > You seem to disagree... if you could mention which JOELib descriptors > you miss in the CDK, I'm sure we can write those for the CDK too. >
You are probably right. I just want to check if there is any major differences in descriptor values calculated by both libraries. >>>> The following link: >>>> http://www.docjar.com/html/api/joelib/util/cdk/CDKTools.java.html >>>> >>>> suggests that at some time, a JOElib/CKD converter was available in >>>> the cdk distribution (org.openscience.cdk.libio.joelib.Convertor). >>> >>> It hasn't been used much lately, but the code is available from: >>> >>> http://cdk.svn.sourceforge.net/viewvc/cdk/cdk-libio/trunk/ >> >> Ok thanks. May I know why it has been removed from the current CDK release? > > Because the bindings depend on JOELib, and therefore are GPL. We > splitted the bindings into a separate library to have the CDK library > LGPL (with a few bits of MIT data), but no GPL code that could make > users of the CDK infected by the GPL (or merely the (psycholical) > risk). > Go back to a standard GPL licence then ;) >>>> I was also wondering if there is any basic example of usage of CDK API >>>> (with source code), e.g. loading a sdf file and displaying molecules >>>> in a 2D or 3D viewer? I've checked documentation available but I >>>> haven't found anything like that. >>> >>> The unit tests in src/test are a good source of code examples... >> >> Yeah I just realized that, I will check this out. > > And just email if you have questions... > >>> Rajarshi, can you point Vincent to your code for 2D rendering of a SD >>> file? >> >> Currently I'm looking at the KNIME cdk pluggin source code. I guess it's a >> good starting point, > > Yes, indeed. > >> but any additional source of documentation will be more than welcome. > > There are some vague plans for writing a CDK book, with code > snippets... but nothing concrete. > A basic developper tutorial on how to import sd/mol and manipulate molecules in java would be OK too I guess ;) I will probably come back very soon for further questions (it seems I already have some trouble with missing function/classes between the two major release versions (1.0.4 and 1.1.5)). We'll see :) Thanks again for your answers! > Egon > > -- > Post-doc @ Uppsala University > http://chem-bla-ics.blogspot.com/ > > -- Vincent Le Guilloux Phd Student - ICOA - UMR CNRS 6005 Div. of chemoinformatic and molecular modeling. University of Orléans Phone: ++33 2 38 49 45 77 Fax : ++33 2 38 41 72 81 ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
