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@dominiquesydow dominiquesydow released this 14 Sep 10:24
· 214 commits to master since this release
d824ecc

Updates the opencadd.databases.klifs module w.r.t. to changes and updates in the KLIFS database

  • Update KLIFS Swagger URL to development version https://dev.klifs.net/swagger_v2/
  • Move many globals in schema module that touch KLIFS field names/types to a new fields.Fields class (there was a bit too much redundancy here and the old setup was hard to maintain when new fields come in because we had to touch too many different globals in sync)
    • Cavet: Rename existing kinase.hgnc_name>kinase.gene_name
    • Cavet: Rename existing kinase.class > kinase.subfamily
    • Cavet: Change existing signature Kinases.all_kinase_families(group, species) to Kinases.all_kinase_families(groups, species)
    • Cavet: Change existing signature Kinases.all_kinases(group, family, species) to Kinases.all_kinases(groups, families, species) --- KLIFS allows for multiple inputs now
    • Update schema for kinases: Add kinase.klifs_name and kinase.uniprot
    • Update schema for bioactivities: Add kinase.chembl_id and ligand.chembl_id
    • Update schema for structures: Add ligand.klifs_id
  • Rerun opencadd.databases.klifs tutorial notebook!
  • Rerun notebook that saves all KLIFS IDs locally (after KLIFS fixed the "Some ligand PDB IDs mapped to mulitple ligand KLIFS IDs" problem)
  • Escape HTML encoding for all output DataFrames: #67
  • Add test that syncs the KLIFS fields (remote) with the opencadd fields (if new fields available in KLIFS, CI will fail)