| """Constants shared across modules in the AlphaFold data pipeline.""" | |
| from flax_model.alphafold3.constants import residue_names | |
| MSA_GAP_IDX = residue_names.PROTEIN_TYPES_ONE_LETTER_WITH_UNKNOWN_AND_GAP.index( | |
| '-' | |
| ) | |
| # Feature groups. | |
| NUM_SEQ_NUM_RES_MSA_FEATURES = ('msa', 'msa_mask', 'deletion_matrix') | |
| NUM_SEQ_MSA_FEATURES = ('msa_species_identifiers',) | |
| TEMPLATE_FEATURES = ( | |
| 'template_aatype', | |
| 'template_atom_positions', | |
| 'template_atom_mask', | |
| ) | |
| MSA_PAD_VALUES = {'msa': MSA_GAP_IDX, 'msa_mask': 1, 'deletion_matrix': 0} | |