[Cdk-devel] [ cdk-Patches-3074735 ] Implementation of Acidic and Basic group count descriptors

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Patches item #3074735, was opened at 2010-09-24 13:03
Message generated for change (Comment added) made by egonw
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>Category: cdk-1.4.x
>Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Egon Willighagen (egonw)
>Assigned to: Rajarshi Guha (rajarshi)
Summary: Implementation of Acidic and Basic group count descriptors

Initial Comment:
For feature request #3056330.

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>Comment By: Egon Willighagen (egonw)
Date: 2010-10-17 16:48

Message:
Rebased on top of cdk-1.4.x and with these fixes:

- fixed compiling by adding missing @cdk.module annotation for test
classes
- added info in JavaDoc on the source of the SMARTS
- fixed unit tests to reflect that symmetrical SMARTS can be found twice
(though not unique, but the SMARTSTool does not correct for that)
- added one unit test for a larger molecule, with two different acidic
groups

I think in due time this descriptor can be replaced by a better one, but
for now it does implement the feature request.

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Comment By: Rajarshi Guha (rajarshi)
Date: 2010-10-16 22:20

Message:
Any udates on this?

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Comment By: Egon Willighagen (egonw)
Date: 2010-10-05 07:39

Message:
Halfway through the updates, but got a bit distracted with finishing up in
Uppsala...

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Comment By: Rajarshi Guha (rajarshi)
Date: 2010-10-05 06:43

Message:
has the patch been updated?

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Comment By: Rajarshi Guha (rajarshi)
Date: 2010-09-26 15:01

Message:
wrt sources, I see. Well if we can determine the sources that's fine.

For the test case, yes, I was just thinking of a few bigger molecules -
not necessarily a large curated set. Just something more meaty than HCN :)

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Comment By: Egon Willighagen (egonw)
Date: 2010-09-26 10:08

Message:
Rajarshi, thanx for your review. The SMARTS are derived from JOELib, per
the feature request, but will add that information. I also left a question
on BOx [0]. Unfortunately, the JOELib JavaDoc is not more informative about
the source of those SMARTS. I assume those two ring system are corner
cases, and will fix the JavaDoc.

Regarding the larger molecule, I can add a e.g. this:

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=151489&loc=ec_rcs

Is that what you have a in mind? A larger, curated test set would of
course be ideal, but I am not aware of such.



0.http://blueobelisk.shapado.com/questions/paper-with-smarts-based-acidic-and-basic-group-counts

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Comment By: Rajarshi Guha (rajarshi)
Date: 2010-09-26 00:14

Message:
Please include sources (if any) for the SMARTS patterns

In the acidic groups descriptor it's not clear what $(n1nnnc1) and
$(n1nncn1) are supposed to match. Could you include an example in the
Javadocs (or bring the Javadocs in sync with the code as these are
commented out)

A few more comprehensive (ie bigger target SMILES) tests would be useful

otherwise looks good

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