Fetching the data

To manually fetch the latest KinActive datasets, please navigate to the Zenodo repository.

The CLI implements a convenient way to download all data and separate datasets. To view the available options, execute kinactive fetch

Usage: kinactive fetch [OPTIONS]

A simple utility to fetch related data.

All options except `out_dir` are flags.

Usage example: `kinactive fetch --pdb_struc_pred --sp_seq_pred -vru` will
fetch ML model predictions for SwissProt sequences and PDB structures,
unpack fetched archives, remove them, and output basic logging info.

To fetch the data manually, navigate to
https://zenodo.org/doi/10.5281/zenodo.10256947

Options:
--db                     lXtractor data collection of PK sequences and
                       structures.
--pdb_struc_pred         DFG and active/inactive predictions for all
                       structural domains in the lXt-PK data collection
                       produced by DFGclassifier and KinActive models.
--pdb_struc_features     Default feature set for all structural domains in
                       the lXt-PK data collection.
--pdb_lig_features       Default feature set of ligand variables for all
                       structural domain in the lXt-PK data collection.
--pdb_seq_features       Default feature set for all domain structure
                       sequences in the lXt-PK data collection.
--pdb_can_seq_features   Default feature set for domains of all canonical
                       UniProt sequences encompassed by the lXt-PK data
                       collection.
--sp_seq_pred            Predictions of DFG-in/DFG-out conformational
                       propensities for all PK domains found in SwissProt.
--sp_model_seq_features  A set of sequence variables necessary to run all
                       sequence-based models for all PK domains in
                       SwissProt.
-a, --all_data           Download all available data.
-u, --unpack             Unpack each downloaded tar.gz archive.
-r, --rm_unpacked        Remove fetched archive after unpacking.
-l, --links              Display data links.
-o, --out_dir TEXT       A path to a directory where to save files. If not
                       provided, the current working directory will be
                       used.
-v, --verbose            Output basic logging information to stdout.
-h, --help               Show this message and exit.