Hi all,
any comments on this?
2011/12/8 Joos Kiener <[email protected]>
> Hi all,
>
> if have a question regarding how it is verified that Fingerprinters
> actually works correctly as well as Universalisomorphism Tester?
>
> The Question is related to the cdk based project I'm working on which I
> will "officially release" once I believe it is usable enough.
>
> I use UIT for Subgraph matching and the ExtendedFingerprinter. I had the
> feeling that the fingerprint wasn't especially great at least for the used
> dataset (Part of Subset 13 of ZINC) and hence I wanted to try out the
> PubchemFingerprinter which I did put now I was getting different amount of
> search hits than before. See below tables. I'm now wondering if it is a bug
> on my part or in the Fingerprints and/or UIT. How can I determine the
> actually correct result? Especially since the reference also disagrees with
> UIT.
>
> PubchemFingerprinter:
>
> SMILES Screening Hits Hits
> CCC(C)C(C)C(C)C 8599 344
> O(C)C(C)C(C)C(C)C 938 28
> CCCCCC(C)CC 9227 1547
> N(C)(C)CC(C)C 15861 8893
> O(CC)C(N(C)C)C 1365 83
> CC(C)C(C)C(C(C)C)C(C)C 8599 0
>
> ExtendedFingerprinter
>
> SMILES Screening Hits Hits
> CCC(C)C(C)C(C)C 22488 429
> O(C)C(C)C(C)C(C)C 9398 77
> CCCCCC(C)CC 3955 1603
> N(C)(C)CC(C)C 88301 10917
> O(CC)C(N(C)C)C 1588 74
> CC(C)C(C)C(C(C)C)C(C)C 22488 0
>
> No Screening, just UIT:
>
> SMILES Hits
> CCC(C)C(C)C(C)C 436
> O(C)C(C)C(C)C(C)C 77
> CCCCCC(C)CC 2171
> N(C)(C)CC(C)C 11412
> O(CC)C(N(C)C)C 139
> CC(C)C(C)C(C(C)C)C(C)C 0
>
> As a Reference the same Searches were done in ChemFinder over the same
> Data Set
>
> SMILES Hits Found in ChemFinder
> CCC(C)C(C)C(C)C 427
> O(C)C(C)C(C)C(C)C 77
> CCCCCC(C)CC 1825
> N(C)(C)CC(C)C 11412
> O(CC)C(N(C)C)C 109
> CC(C)C(C)C(C(C)C)C(C)C 0
>
> Best Regards,
>
> Joos
>
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