Re: [Rdkit-discuss] 64 bit Morgan Fingerpronts

[Gareth J. <jav...@gm...>]

Wojtek,

You can use GetNonzeroelements() to convert the sparse fingerprint to a 
Python Dict of hash to count.

Cheers,
Gareth


In [7]: mol = Chem.MolFromSmiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12')

In [8]: fp = AllChem.GetMorganFingerprint(mol, 2)

In [9]: elements = fp.GetNonzeroElements();

In [10]: elements
Out[10]:
{10565946: 2,
  348155210: 1,
  476388586: 1,
  540046244: 1,
  553412256: 1,
  864942730: 2,
  909857231: 1,
  1100037548: 1,
  1333761024: 1,
  1512818157: 1,
  1981181107: 1,
  2030573601: 1,
  2041434490: 1,
  2092489639: 3,
  2246728737: 3,
  2370996728: 1,
  2877515035: 1,
  2971716993: 1,
  2975126068: 2,
  3140581776: 1,
  3217380708: 4,
  3218693969: 1,
  3462333187: 1,
  3657471097: 3,
  3796970912: 1}

In [11]:

On 4/21/2021 5:44 AM, Wojtek Plonka wrote:
> Dear All
>
> Do any of you have a working example of getting Morgan Fingerprints, 
> as sparse bit vector (non-hashed) in the 64 bit version using Python?
> I'm looking into the issue of collisions on the "main hash" on large 
> (100+ million molecules) data
> Thank you very much!
> Kindest regards,
>
> Wojtek Plonka
> +48885756652
> wojtekplonka.com <http://www.wojtekplonka.com>
> fb.com/wojtek.plonka <https://fb.com/wojtek.plonka>
>
>
>
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