Time evaluation for calculating molecular descriptors using the cdk

To estimate the time needed to calculate molecular descriptors for many molecule (more than 200000) I created a workflow which measured the time needed to calculate each molecular descriptor. This workflow can be found here.

The time needed to calculate different molecular descriptors for 1000 molecules:

Possibly related posts: (automatically generated)

This entry was posted on Sunday, September 7th, 2008 at 10:05 am and is filed under cdk-taverna, myexperiment.org, workflows. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

7 Responses to “Time evaluation for calculating molecular descriptors using the cdk”

  1. Egon Willighagen Says:
    September 9, 2008 at 5:23 am | Reply

    Is the bar plot also made by the workflow? I should adapt it for PubChem and/or ChemSpider…

  2. Thomas Kuhn Says:
    September 9, 2008 at 7:08 am | Reply

    No the bar plot is done manually! But it wouldn’t be such a big deal to create a worker which will do this bar plot! There are already worker which creates bar plots like the CompareART2AClassificationResults worker.

  3. suyog Says:
    March 31, 2009 at 4:50 am | Reply

    Can you please help me out?????

    I am trying to access the neighboring atoms of any functional group(eg. alkane)in a molecule…
    But i am not getting the result right..

    can you please help me to do the same?????
    Or any tips for the same???

  4. suyog Says:
    March 31, 2009 at 4:52 am | Reply

    (I am using JOELIB2-API)

  5. suyog Says:
    March 31, 2009 at 9:12 am | Reply

    hey… thanks for reply…

    but if you explain how to do it in cdk, it will be ok for me..!!!

    Thanks…
    Suyog

    • cdktaverna Says:
      April 6, 2009 at 2:02 pm | Reply

      I would perform substructure searches for the functional groups with contains an AnyAtom as atom to the functional group. After the search I would try to access this atom.

Leave a Reply