On 22/07/2012 23:35, Tim Vandermeersch wrote:
> Hi,
>
> The problem seems to be in src/fingerprints/finger3.cpp:
>
> //Each bit represents a single substructure; no need for
> confirmation when substructure searching
> virtual unsigned int Flags() { return FPT_UNIQUEBITS;};
>
> This confuses me. It's not because a the substructures are present in
> the queried molecule that the queried molecule is a superstructure of
> the query. So an isomorphism search is still needed to confirm the
> hit.
This code comment (and the implementation of it in fastsearchformat) is
clearly wrong and has been for a long time. The flag means that the bit
represents only one substructure feature and is not a hash as in FP2. I
have corrected in trunk code in fastsearchformat and the comment in
finger3.cpp.
> When I change the Flags() function to return 0, I still don't get the
> expected results though. With my query there should be 46 hits but FP3
> gives 26, FP4 25 and MACCS only 12. Is there something I'm missing
> here. If the bits simply represent a substructure, the fingerprint
> screening should return all possible molecules containing the query.
I think that this is because a structure as a pattern is not being
distinguished sufficiently from a structure as a molecule. A SMILES
input of OC will match any ether when it is used as SMARTS or in a FP2
substructure search. With FP4 or MACCS, it is seen as methanol and a bit
corresponding to an alcohol is set. This prevents a match to an ordinary
ether.
obabel -:"OC" -ofpt -xfFP4 -xs
>
Alcohol C_ONS_bond
1 molecule converted
obabel -:"COC" -ofpt -xfFP4 -xs
>
Dialkylether C_ONS_bond
1 molecule converted
obabel -:"OC" -ofpt -xfMACCS -xs
>
93: QCH3 139: OH 157: C-O 160: CH3 164: O
1 molecule converted
obabel -:"COC" -ofpt -xfMACCS -xs
>
74: CH3ACH3 86: CH2QCH2 93: QCH3 126: A!O!A 149: CH3
> 1*2
157: C-O 160: CH3 164: O
1 molecule converted
I guess structure-key fingerprints should not be used for substructure
searches, at least until we have a way round this. But they may be
better for similarity comparisons. For example, in the above, the
presence of an alcohol is more chemically significant than any old O
bonded to C.
Chris
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