Hi Sereina
I had the same problem a while ago :). I think the reason is that the AP
fingerprint invariant only allows hashes for atoms up to an integer value
of 511 (9 bits) and the Morgan connectivity invariant returns 32 bit codes,
therefore you get this error "larger than allowed value".
What you can do is write your own version of the invariant and hash it to a
9 bit integer. This might however lead to some collisions :(.
Hope that helps and best,
Nadine
2016-06-24 12:10 GMT+02:00 Sereina <sereina.rini...@gmail.com>:
> Hi RDKitters,
>
> Is there a way to use the Morgan (connectivity) atom invariants in the
> atom pairs fingerprint?
> I tried naively the following:
>
> inv = AllChem.GetConnectivityInvariants(m)
> AllChem.GetHashedAtomPairFingerprintAsBitVect(m, atomInvariants=inv)
>
> but it gives me the error “ValueError: list element larger than allowed
> value"
>
> Any ideas would be greatly appreciated.
>
> Best,
> Sereina
>
>
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