protein_workshop.constants

Contains project-level constants used to configure paths and wandb logging.

Paths are configured using the .env file in the project root.

proteinworkshop.constants.DATA_PATH = '/Users/jamasba/github/ProteinWorkshop/proteinworkshop/data'

Root path to the data directory.

proteinworkshop.constants.FOLDCOMP_DATASET_NAMES = ['afdb_rep_v4', 'afdb_rep_dark_v4', 'afdb_swissprot', 'afdb_swissprot_v4', 'afdb_uniprot_v4', 'esmatlas', 'highquality_clust30', 'a_thaliana', 'c_albicans', 'c_elegans', 'd_discoideum', 'd_melanogaster', 'd_rerio', 'e_coli', 'g_max', 'h_sapiens', 'm_jannaschii', 'm_musculus', 'o_sativa', 'r_norvegicus', 's_cerevisiae', 's_pombe', 'z_mays']

//github.com/steineggerlab/foldcomp. For an up-to-date list of all datsets see https://foldcomp.steineggerlab.workers.dev.

Type:

List of available foldcomp datasets for download. For documentation see https

proteinworkshop.constants.PROJECT_PATH = Path('/Users/jamasba/github/ProteinWorkshop')

Path to the project root.

proteinworkshop.constants.SRC_PATH = Path('/Users/jamasba/github/ProteinWorkshop/proteinworkshop')

Path to the project source code.

proteinworkshop.constants.WANDB_API_KEY = None

API key for wandb.

proteinworkshop.constants.WANDB_ENTITY = None

Entity for wandb logging.

proteinworkshop.constants.WANDB_PROJECT = None

Project name for wandb logging.

proteinworkshop.constants.ZENODO_DATASET_NAMES = ['antibody_developability', 'cath', 'ccpdb', 'ccpdb_ligands', 'ccpdb_metal', 'ccpdb_nucleic', 'ccpdb_nucleotides', 'deep_sea_proteins', 'ec_reaction', 'fold_classification', 'fold_fold', 'fold_family', 'fold_superfamily', 'go-bp', 'go-cc', 'go-mf', 'masif_site', 'metal_3d', 'ptm']

List of pre-processed datasets for proteinworkshop available on Zenodo. For documentation see https://github.com/a-r-j/ProteinWorkshop/#datasets