Hi Greg and Nadine,
Thanks a lot for your answers and the explanation.
I will have a look at either hashing the invariants to 9 bits or removing the
limitation.
Best,
Sereina
On 24 Jun 2016, at 13:20, Greg Landrum <greg.land...@gmail.com> wrote:
> Hi Sereina,
>
> At the moment, for historical reasons, the atom pair and topological torsion
> fingerprint is limited to invariants that are at most 9 bits long (i.e.
> <512). I think it should be possible to remove the restriction, but it
> requires a bit of rethinking of the way the code works.
>
> What you could do is use "the dictionary trick" and assign small integers to
> the connectivity invariants that you see in your dataset and just pass those
> along. This is a bit of extra book-keeping code that you'd need to deal with,
> but should work.
>
> -greg
>
>
>
> On Fri, Jun 24, 2016 at 12:10 PM, Sereina <sereina.rini...@gmail.com> wrote:
> 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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