JW notes | Reviewed the notebooks+instructions on the train. VERY nice work! Thanks for remembering to post the materials and announce the workshop on general. Conda solve for the first env takes a long time - Maybe even make 3 envs (mamba, 0.10.6, and 0.11.1) It was smart to use a tagged version of the protein ligand benchmark set “launching the bespoke executoror” You should show how to start the executor on binder Including OE in the conda envs is making bespoke caching machinery try to run oe variants of some molecule processing steps, which is causing my local build to crash JM – I can’t reproduce this (JW reproduces on binder) JM – I’ll remove OE from the environments and say “optionally, you can install OE if you have a license”.
The protein.pdb file isn’t readable by rdkittoolkitwrapper (but t4 has a proline? This is weird) JM – I can reproduce this and have an awesome one-liner to fix it JW – I’m still curious about the root cause - Optimally we could make a small change to the input PDB, and then raise an issue once we understand what’s going wrong.
The toolkit notebook doesn’t load the bespoke force field JM – No, it does, you should read better JW – I should read better
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