On Sun, Jun 9, 2013 at 12:29 PM, Gonzalo Colmenarejo-Sanchez <
[email protected]> wrote:
> Yes, C++ code examples for preprocessed molecules and fingerprints would
> be extremely helpful too.
>
I'll put one together and send it along. I don't normally do file i/o from
C++, so it's taking me longer than I expected to get it working.
> **
>
> By the way, if the query is a SMARTS like e.g. “c1aaccc1” (representing
> several substructures), what fingerprint is exposed to AllProbeBitsMatch,
> the union of all the possible fingerprints, all the possible fingerprints
> sequentially, etc?
>
It's a single fingerprint. The code essentially doesn't include
substructures in the fingerprint that include query features. This means
that the FPs are not incredibly efficient if you have query molecules that
include a high density of query features.
Here's an example showing what happens with an extremely simple case.
Start with a simple molecule:
In [21]:
list(Chem.PatternFingerprint(Chem.MolFromSmiles('CC')).GetOnBits())
Out[21]: [429, 778, 1022]
This matches one substructure query pattern "[*]~[*]" twice, so it sets
three bits: one bit for each match and one for the fact that the match is
"CC".
Constructing the same molecule from SMARTS gives the same result, the
fingerprinter knows how to deal sensibly with the implicit queries in
SMARTS:
In [22]: list(Chem.PatternFingerprint(Chem.MolFromSmarts('CC')).GetOnBits())
Out[22]: [429, 778, 1022]
But as soon as I add a query feature, I lose a bit:
In [23]:
list(Chem.PatternFingerprint(Chem.MolFromSmarts('C[A]')).GetOnBits())
Out[23]: [429, 1022]
This still matches "[*]~[*]" twice, but since the match involves a query
feature, there's no bit set for the match itself.
If I make the match asymmetric, I get four bits:
In [24]: list(Chem.PatternFingerprint(Chem.MolFromSmarts('CO')).GetOnBits())
Out[24]: [54, 429, 759, 1022]
This matches "[*]~[*]" twice, but "OC" and "CO" generate different bits.
Make sense?
-greg
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