precomputed_data_HLA-EpiCheck

This file contains precomputed data used in the HLA-Epicheck project (see https://gitlab.inria.fr/capsid.public_codes/hla-epicheck). This data can be re-used to run the notebook 'dataset_gen_al_radius_15.ipynb'.

Data is organized by locus and antigen. In each antigen folder, four types of data can be found :

patchs : prepatches computed with the script compute_prepatches.tcl. Each file contains the prepatches for a given residue and patch radius (see file name). The format used in each file is as follows: each line corresponds to a prepatch and contains two colon-separated entries. The first one corresponds to a space-separated list of the residues that compose the prepatch and the second one corresponds to the PDB frame from which the prepatch was extracted.

PDBs : PDB files used for computing the prepatches and SASA data.

SASAs_out : SASA values computed for each PDB frame (i.e. one SASA file per frame). The format used in each file is as follows: each line corresponds to an AA and contains the AA number (numbering starts at 0) and the corresponding SASA value.

RSASA_median.txt : median RSASA computed for each AA along the trajectory. The format used in each file is as follows: each line corresponds to an AA and contains the AA number (numbering starts at 0) and the corresponding RSASA value.