Rerun code base with new data and new use cases - Githubissues

volkamerlab / KinaseFocusedFragmentLibrary

Subpocket-based fragmentation and recombination of kinase inhibitors

MIT License

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Rerun code base with new data and new use cases #28

Closed dominiquesydow closed 1 year ago

dominiquesydow commented 1 year ago

Description

Update code base to fix deprecations or add enhancements addressing

run fragmentation and recombination based on the latest KLIFS dataset
- https://github.com/volkamerlab/KinFragLib/issues/52
run fragmentation and recombination based on a subset of fragments (including empty subpockets)
- https://github.com/volkamerlab/KinFragLib/issues/47
- https://github.com/volkamerlab/KinFragLib/issues/50

Todos

[x] Fix deprecated pandas usage (append method)
[x] Allow for empty subpocket SDF files (OSError try-catch)
[x] Continue preprocessing with the next structure in case a ligand or pocket KLIFS file cannot be read into the rdkit

Status

[x] Ready to go

dominiquesydow commented 1 year ago

@mbackenkoehler, as a follow-up on our conversation earlier, I am merging this PR only just now, which includes a couple of fixes that I had to make in order to run the 2022 dataset (so I recommend a git pull from master after this merge).