Hi,
On Mon, Jul 23, 2012 at 4:07 PM, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> 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.
The change looks good.
>> 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.
This makes sense.
Thanks,
Tim
> Chris
>
>
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