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This is not an issue, it is more a question/suggestion. Is it possible to parallelize the method run of the class Fingerprint? I was trying to look on the MDanalysis documentation and this is not so straightforward because how MDAnalysis.core.universe.Universe.trajectory is designed. But I also read about PMDanalysis. So, should not be possible to incorporate the parralelization to ProLIF? I think that this feature will really improve the package and the usability.

Issue Analytics

  • State:open
  • Created 2 years ago
  • Reactions:1
  • Comments:5 (2 by maintainers)

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noahharrison64commented, Jun 27, 2022

Something I noticed when trying to create prolif molecules is that the rdkit mol user assigned property ‘map index’ was missing if I used mp.Pool. I imagine this is the case for other user assigned properties, if they exist. I believe this issue arose due to the pickling of the molecule objects when multiprocessing is run. I fixed this by running: Chem.SetDefaultPickleProperties(Chem.PropertyPickleOptions.AllProps) Thought I’d just point this out in case this was something you weren’t aware of!

cbouycommented, Jul 10, 2022

That doesn’t sound right! Thanks for reporting it, I’ll try to have a look soon

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