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:

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

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

  2. Thomas Kuhn says:

    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:

    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:

    (I am using JOELIB2-API)

  5. suyog says:

    hey… thanks for reply…

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

    Thanks…
    Suyog

    • cdktaverna says:

      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.

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