Separate environment for T018 #416
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The utility used in OpenCADD (i.e. `opencadd.structure.core.Structure`) is just a wrapper around `MDAnalysis.Universe` with no added functionalities. Therefore, the `opencadd` dependency was removed and `MDAnalysis` was used directly instead, in order to avoid version pinning problems in `opencadd`.
plip has not updated its code with regard to new numpy versions, and thus the explicit casting `np.uint32(i)` in line 361 of `plip.basic.supplemental` (function `int32_to_negative`) throws thousands of warnings. These are suppressed here, as the warning suppression in our `util.__init__` is not catching these, probably due to setting of the logging level at the top of this module.
The nootebook is re-run with the added environment. This caused some slight (numerical) changes (e.g. calculated binding affinities by `smina`, calculated interactions by `plip`) in the outputs, which were mentioned in the text. Therefore, the text was also edited to reflect the new results.
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mbackenkoehler
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volkamerlab:separate-environments
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A separate environment is added to T018:
major.minor.patch) to their latest working versions.pandas, this version is the latest version resolved byconda.pandasis pinned to2.1.4(i.e., the latest2.1.xversion) instead of2.2.0(i.e., the latest resolvable version) because the latestRDKitversion (i.e.,2023.09.5) does not work withpandas 2.2.0. I fixed the issue inRDKitand submitted a PR. Once a newRDKitrelease with this fix is released, we can update thepandasdependency to the latest version.In addition, the following changes are applied to the
utilssubpackage in T018 (i.e., the backend of T018):DeprecationWarningandFutureWarningnotifications are suppressed to not show up in notebook outputs. These are all due to our dependencies not having updated their codes to adopt to newer versions of their own dependencies.opencadddependency is removed, and replaced withMDAnalysis: The utility we used in OpenCADD (i.e.opencadd.structure.core.Structure) is just a wrapper aroundMDAnalysis.Universewith no added functionalities. Therefore, theopencadddependency was removed andMDAnalysiswas used directly instead, in order to avoid version pinning problems inopencadd.Lastly the notebook is rerun:
smina, calculated interactions byplip) in the outputs, which were mentioned in the text. Therefore, the text was also edited to reflect the new results.