miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics

miniworld.feature.MiniWorld_featuring_species.MSA_featurize_wo_statistics(msa, insertion, chain_to_idx_dict, params)[source]

I modified RF2 version. (just changed name of variables) Input: full MSA information (after Block deletion if necessary) & full insertion information Output: seed MSA features & extra sequences.

Parameters:

  • msa (torch.LongTensor) – Full MSA tensor.

  • insertion (torch.LongTensor) – Full insertion tensor.

  • chain_to_idx_dict (dict) – Dictionary mapping chain ID to residue indices.

  • params (dict) – Dictionary of parameters.

Seed MSA features:

  • aatype of seed sequence (20 regular aa + 1 gap + 1 unknwon + 1 mask)

  • profile of clustered sequences (23) => removed

  • insertion statistics (2) => removed statistics, only use insertion_clust

  • N-term or C-term? (2)

extra sequence features:

  • aatype of extra sequence (23)

  • insertion info (1)

  • N-term or C-term? (2)