Hi Wandré,

  The easiest way to avoid recalculating the fingerprints is to keep the FPS 
file around. The rdkit2fps program calculates the AtomPair fingerprint and 
converts the resulting DataStructs fingerprint object into a hex-encoded 
fingerprint, which is stored as text in the FPS file.

One difference that I just realized, however, is that it uses 
"GetHashedAtomPairFingerprintAsBitVect" while you use "GetAtomPairFingerprint". 
The example I gave generates a dense fingerprint rather than a sparse one. This 
difference probably isn't a lot, but it may make my proposed solution unusable 
for your needs.

Regarding a database, I didn't realize you were using a database. Your original 
email showed a script that didn't make use of a database.

The details of how to import/export data from a database are database- and 
schema-specific. I don't have any experience with the RDKit Postgres cartridge 
to be able to offer any advice, if that's what you are using.

Chemfp includes a programming API, with documentation at 
http://chemfp.readthedocs.io/en/chemfp-1.3/ , which may help with any data 
import/export . Depending on your needs, you may find that the FPS file by 
itself is enough.

RDKit also supports adapters from the hex-encoded fingerprint used in the FPS 
format a dense bit vector using:


Again, note that this is for an ExplicitBitVect and not an IntSparseIntVect.

Best regards,


> On Jan 11, 2018, at 18:49, Wandré <wandrevel...@gmail.com> wrote:
> Thanks Andrew, I will try this steps.
> So, to avoid recalculate fingerprints, how can I calculate them and store in 
> database?
> When I calculate AtomPair fingerprint, returns a 
> rdkit.DataStructs.cDataStructs.IntSparseIntVect object
> How to store this rdkit Python object in a database and how to read them 
> again?
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e Inteligência 
> Computacional - UNIFEI
> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG

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