BAZOO

So much to do, so little time

Trying to squeeze sense out of chemical data

Updated Versions of R Packages

with 4 comments

New versions of several of my R packages are now available on CRAN. rcdk 2.9.6 goes along with rcdklibs 1.2.3. The latter now uses the most recent cdk-1.2.x branch from Github. The former fixes a number of bugs relating to descriptor calculations, saving molecules in SD format and setting/getting properties on molecules. Unfortunately, because the 1.2.x branch does not have robust depiction code, the visualization methods in rcdk are currently disabled. The fingerprint package has also been updated and now includes a number of unit tests.

Written by Rajarshi Guha

November 6th, 2009 at 1:04 am

Posted in cheminformatics,software

Tagged with ,

4 Responses to 'Updated Versions of R Packages'

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  1. Rajarshi,

    please let me know what rendering functionality you had in an earlier rcdk version, because rendering of molecules is possible with the jchempaint-primary patch already.

  2. In the previous version (based around 1.1.x I think) I was able to bring up a Swing window with a depiction – that’s the extent of rendering I needed.

    Does the jchempaint-primary branch in sync with 1.2.x? (Especially the DescriporEngine fix I provided which was breaking rcdk functionality)

    Rajarshi Guha

    7 Nov 09 at 4:02 am

  3. Rajarshi,

    I tried your rpubchem package and found it very helpful. Unfortunately tag is empty when I download XML for individual cids.
    Is it possible to get en masse all sids for pubchem cids? Even better would be if there was some neat method how to get a list of assay that a compound is active in.
    Thanks for your time.

    Honza Warla

    18 Nov 09 at 10:30 am

  4. Hi Hinza, I just tried using get.cid and it seems to work. What version of rpubchem are you using? It might be easier to follow up via email

    Rajarshi Guha

    19 Nov 09 at 1:09 am

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