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@florian-huber florian-huber commented Jan 8, 2026

Changed the fingerprint computation code quite a bit.
It now can run with rdkit as well as scikit-fingerprints type generators.

Some inconsistency between both packages is the use of the term sparse, which means unfolded fingerprints in rdkit, but scipy.csr formated versions of folded fingerpritns for scikit-fingerprints.

Here, I now switched to a general distinction of three categories:

  • count: True / False --> either counting occurences or simple binary presence/absence
  • return_csr: True / False --> when True will return the folded fingerprints in csr format
  • folded: True / False --> when False, will not output fixed-sized fingerprints but arrays of integer bits

@florian-huber florian-huber merged commit e7defe1 into main Jan 16, 2026
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@florian-huber florian-huber deleted the scikit_fingerprints branch January 16, 2026 12:04
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