Hi Michael,
On Tuesday, July 14, 2015, Michael Reutlinger <[email protected]> wrote:
> Hi Greg,
>
> thanks for your answer. I also figured that the invariant feature of the
> AtomPair functions should be well suited. Initially, I thought that the
> pi-electron and neighbouring atom count would always be added, but this is
> clearly not the case.
>
It shouldn't be the case for the AP fingerprint. It *does*, however, look
like there will be a problem with the TT fingerprints if you provide your
own invariants (this is based on a skim of the code, so I'm not sure that's
correct).
The definition of the pharmacophoric patterns was initially described in
> the PATTY paper (Bush & Sheridan, J. Chem. Inf. Comput. Sci., 1993) and as
> far as I know the definitions are still valid.
>
> Luckily, there is a SMARTS based version floating around (allegedly based
> on an early OpenBabel version):
> http://tripod.nih.gov/files/patty.rules
>
> I compared those to the original definitions from the paper and they seem
> to match and overall make sense.
>
Thanks for that pointer. That is really helpful! If I manage to make the
time to do so, I will incorporate this into the next RDKit release.
I implemented a quick Typer based on this definition, taking into account
> the fact that only the first atom in the SMARTS is typed.
>
> I attached a ipython notebook containing a small example, including the
> example molecule from the paper.
>
> Btw. is the hashing method used for creating the hashed fingerprint still
> valid / suitable if only a small number of the
> maximal numAtomPairFingerprintBits / codeSize is actually used?
>
The quick read-through I did of the code makes me believe that it should be
fine. I will confirm over the next day or so and let you know.
Best,
-greg
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