ALOGP has been behaving weirdly for some time now
On Thu, May 31, 2012 at 6:10 AM, Kevin Lawson <[email protected]> wrote:
> Hi
>
> I am getting some strange results from the ALOGP descriptor algorithm.
> LICSS uses the following code to prep molecules for descriptor calculation:
>
> atomContainer = sp.parseSmiles(s);
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);
>
> CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
> CDKHydrogenAdder ha =
> CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
> ha.addImplicitHydrogens(atomContainer);
>
> AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer);
>
> With this preparation the ALOGP descriptor returns 0.0 for both the Smiles
> c1ccccc1 and for c1ncccc1 (benzene and pyridine)
> I also ran the first 1000 compounds from the Wellcome AntiMalarial dataset
> through the calculation. As you can see from the attachment,
> the values are usually much lower than the quoted values in the data set
> (~4 log units on average) and are, indeed usually obviously too low.
>
> To check that I wasn't making a mistake with the submission code, I ran
> all 1000 compounds through Rajarshi's CDK Descriptor calculator:
> http://rguha.net/code/java/cdkdesc.html with identical results
> (Rajarshi's calculator also returns 0.0 for benzene). I have also
> converted the
> compounds to Kekule form using the FixBondOrdersTool. Results are
> different, but no better! (also in the attached file). I have tried
> changing the
> order of the preparation steps but it doesn't make any difference to the
> results.
>
> Any thoughts?
>
> Best wishes
>
> Kevin
>
>
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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