scripts.data.preprocessing.parseEtab.parseEtab

scripts.data.preprocessing.parseEtab.parseEtab(filename, save=True)

Given an etab file, parse the corresponding Potts model parameters.

This assumes that full chain protein etabs are provided, so it is not designed to work with etabs computed on partial chains.

Parameters:

• filename (str) – path to .etab file

• save ; bool, default=True – whether or not to save the outputs to a file

Returns:

• potts_dict (dict) – Sparse representation of etab that maps pairs of (residue1_id : int, residue2_id : int) to 22 x 22 matrices representing pair energies. Self energies are incorperated into the diagonals of self-interaction matricies, with key (residue_id, residue_id). The dimension is 22 because 0 is used as a padding index and 21 is used to represent X for unknown residues.

• potts_selfE (np.ndarray) – Numpy array specifying self energies. Shape: all_chains_length x 22.

• potts (np.ndarray) – Dense representation of potts model mapping pairs of residue ids (the first two dimensions) to 22 x 22 matricies representing pair energies. Self energies are incorperated into the diagonals of self-interactions matricies. Edges are also duplicated e.g. interaction energies between residues 1 and 2 can be found at both :code`potts[1][2]` and potts[2][1]. Shape: all_chains_length x all_chains_length x 22 x 22