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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