Fingerprint SPLIF Issue

[Justine Camilla Williams]

Hello,

 

I've been trying to use the SPLIF function in the fingerprints package. I was able to use the SimpleInteractionFingerprint and InteractionFingerprint functions fine, but I got the following error when using SPLIF:

 

"line 638, in SPLIF

    protein_atom['neighbors'])))

OverflowError: Python int too large to convert to C long"

 

I would really appreciate any help with figuring out what the problem might be! I am using the newest version of python. Here is an example of what I tried to run:

 

import oddt

import oddt.fingerprints as fp

import os

 

proteinpath = 'protein.pdb'

lig1 = 'vina_output_ligand_1.pdb'

lig2 = 'vina_output_ligand_2.pdb'

 

refList = [lig1, lig2]

protein = next(oddt.toolkit.readfile('pdb', proteinpath))

protein.protein = True

ligand = next(oddt.toolkit.readfile('pdb', lig1))

fp_query = fp.SPLIF(ligand, protein)

 

I have attached the ligand/protein files I was using. I really appreciate any help with this,

 

Thank you,

 

Justine

[Maciek Wójcikowski]

Hello Justine,

Thanks for your detailed feedback, I tried your code unfortunately with ODDT 0.7 and python 3.7 I could not reproduce your problem. Could you specify your environment?

The error hints that you might be running 32bit system, is that the case?

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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[Maciek Wójcikowski]

I've googled a bit and it might be Windows/python/numpy issue.

Could you try replacing in fingerprint.py line 612: ('hash', int) to ('hash', np.int64)? It should fix the issue. If it does I will commit that change to the repo. Let me know If you cant edit this file I will try to reproduce the error on some Windows machine.

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl