BAZOO

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Trying to squeeze sense out of chemical data

CDKDescUI Update

with 8 comments

Version 1.0.5 of the CDK descriptor calculator is now available. This version updates the command line batch mode to allow one to calculate a specific set of descriptors (as opposed to all or say, topological). The selected descriptors are specified using an XML file, which can be generated in the GUI mode – fire up the calculator in GUI mode, check the selected descriptors and then save the selection. You can then specify the selection file via the -s option.

Written by Rajarshi Guha

June 27th, 2010 at 10:06 pm

Posted in cheminformatics,software

Tagged with , ,

8 Responses to 'CDKDescUI Update'

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  1. Real cool and usefull feature, thanks.
    By the way, I found that when calculating Kier and Hall descriptors it will stop with an error when a structure contains a covalent bound metal (Usually Zn, Pt, Cu ). I assume this is a bug in CDK?

    Peter Maas

    28 Jun 10 at 7:35 am

  2. Hi Rajarshi,
    thanks for the update. Command line and batch mode is very useful.

    Just a quick note, the Ionization Potential is buggy, it never finishes with 3D optimized molecules. The other bottleneck are the topological indices (I suspect all the path indices, but did not benchmark them alone, should be doable with the batch mode :-) .

    Cheers
    Tobias

    Tobias Kind

    28 Jun 10 at 8:33 am

  3. @Peter, thanks. Yes, sounds like a bug in the CDK. Can you send me an example file (or better, file a bug report with an example file and assign to me)

    Rajarshi Guha

    28 Jun 10 at 1:55 pm

  4. @Tobias, regarding IP, I know :(

    But the code is so convoluted I can’t exactly see how to fix it without rewriting it. As for the topo indices – yes, the extensives substructure searching is killing it. Trying to make the SMARTS searcher use the new SMSD code, but just can’t get enough time

    Rajarshi Guha

    28 Jun 10 at 1:56 pm

  5. OK, I’ll file a bug report. Not sure if I can assign it but I’ll give it a shot.

    Peter Maas

    30 Jun 10 at 11:16 am

  6. Hi Rajarshi, I ran into another issue running this over larger SD-files. When the program hangs on a problamitic entry like I reported above (btw, it also hangs on just Ar or He entry), I’ve to press cancel. In this case, none of the calculated values have been written and I’ve to start again. (As stated above, Kier Hall Descriptors are a pain in the x here.

    Cheers,

    Peter

    Peter Maas

    7 Jul 10 at 8:33 am

  7. Peter, thanks for pointing that out. Should be easy to fix

    Rajarshi Guha

    12 Jul 10 at 1:42 am

  8. Peter, the latest version (1.1.1) now saves all data upto the point of cancellation

    Rajarshi Guha

    24 Jul 10 at 10:58 pm

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