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load_hppb() cannot use RawFeaturizer #2350

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jcwomack opened this issue Jan 12, 2021 · 5 comments · May be fixed by #2391
Open

load_hppb() cannot use RawFeaturizer #2350

jcwomack opened this issue Jan 12, 2021 · 5 comments · May be fixed by #2391
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@jcwomack
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Using this featurizer causes an AxisError in numpy originating here:

deepchem/deepchem/molnet/load_function/hppb_datasets.py

Line 21 in 01ea79d

available_rows = X.any(axis=1)

I suspect that this is because RawFeaturizer produces a 1-D X array, so X.any(axis=1) fails. The default "ECFP" featurizer does not have this issue, presumably because it produces an n-D X array.
@rbharath
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@jcwomack Good find! I've marked this as a bug and marked it as open to contribution/bugfix

@minhtriet minhtriet linked a pull request Feb 7, 2021 that will close this issue
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@minhtriet
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I created a pull request #2391.

@jcwomack
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jcwomack commented Feb 8, 2021 •
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Thanks @minhtriet. Making the RawFeaturizer produce a single-column matrix of features rather than modifying remove_missing_entries() to account for the special case of a 1-D array of features looks like a sensible approach.

@minhtriet
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Thank you @jcwomack

@arunppsg arunppsg mentioned this issue Nov 19, 2021
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@0zXD
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0zXD commented Mar 6, 2025

Is the issue still on queue?

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