coFeatures/config.yaml at main · ESPhoenix/coFeatures · GitHub

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pathInfo:
  inputDir: "/home/esp/Machine_Learning/11_pdb_dataset/013_bio_unit_pdbs_clean"
  outDir: "/home/esp/Machine_Learning/11_pdb_dataset/02_features/01_biounits"
  aminoAcidTable: "/home/esp/Machine_Learning/11_pdb_dataset/00_scripts/cofeatures/amino_acid_properties.txt"

cofactorInfo:
  FMN:
    keyAtoms: ["N1","N3","N5", "O2", "O4", "C7M", "C8M"]
    orbAtoms: ["N10","C10","C4A","N5","C5A","C9A"]
    cloudAtoms: ["N10","C9A","C9","C8","C8M","C7","C7M","C6","C5A","N5","C4A","C4","O4","N3","HN3","C2","O2","N1","C10"]
  FAD:
    keyAtoms: ["N1","N3","N5", "O2", "O4", "C7M", "C8M"]
    orbAtoms: ["N10","C10","C4X","N5","C5X","C9A"]
    cloudAtoms: ["N10","C9A","C9","C8","C8M","C7","C7M","C6","C5X","N5","C4X","C4","O4","N3","HN3","C2","O2","N1","C10"]

optionsInfo:
  orbRange: [14]
  cloudRange: [4]
  genAminoAcidCategories: True
  keepIndividualCounts: False
  normaliseCounts: True
  keepTotalCounts: False