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hesther / enzymemap

Python package to atom map, correct and suggest enzymatic reactions
MIT License
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Move data folder, add cirpy, add typing #8

Open mengqvist opened 1 year ago

mengqvist commented 1 year ago

I've done three things in this PR:

  1. I've moved the data folder into the package root folder. This allows for the usage of relative paths to the data files. Should make the package more robust to different platforms.
  2. I've added CirPy as another name resolver and it compares favorably to the others.
  3. I've added typing to functions in all the scrips in the enzymemap folder.
hesther commented 1 year ago

Great, I will take a more in-depth look within the next days!

hesther commented 1 year ago

Hi @mengqvist, relocating the data folder will need an update of a few more scripts, so I will have to look through these.

Since adding Cirpy will change the resolved SMILES strings and thus affect some reactions (and trigger a re-mapping), I want to use this update + a fix for some of the reactions you found to make version 2.1 of EnzymeMap, and push all three updates (this PR, the bug fix PR and the new Zenodo release) approximately at the same time to avoid reproducibility issues, and avoid having to run the full mapping pipeline several times (which takes quite a while). However, I currently have no open time slots to do that, so this will probably have to wait for a few weeks (probably mid/end September). I you need this PR to go through sooner, let me know, and I can try to prioritize it