Separate environment for T018

AAriam commented 7 months ago

A separate environment is added to T018:

all dependencies are pinned exactly (i.e., major.minor.patch) to their latest working versions.
For all dependencies except pandas, this version is the latest version resolved by conda.
pandas is pinned to 2.1.4 (i.e., the latest 2.1.x version) instead of 2.2.0 (i.e., the latest resolvable version) because the latest RDKit version (i.e., 2023.09.5) does not work with pandas 2.2.0. I fixed the issue in RDKit and submitted a PR. Once a new RDKit release with this fix is released, we can update the pandas dependency to the latest version.

In addition, the following changes are applied to the utils subpackage in T018 (i.e., the backend of T018):

DeprecationWarning and FutureWarning notifications 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.
The opencadd dependency is removed, and replaced with MDAnalysis: The utility we 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.

Lastly the notebook is rerun:

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 commented 7 months ago

Thank you, great work!

volkamerlab / teachopencadd