| import itertools |
|
|
|
|
| aa_set = {"A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"} |
| aa_list = ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y"] |
|
|
| foldseek_seq_vocab = "ACDEFGHIKLMNPQRSTVWY#" |
| foldseek_struc_vocab = "pynwrqhgdlvtmfsaeikc#" |
|
|
| struc_unit = "abcdefghijklmnopqrstuvwxyz" |
|
|
|
|
| def create_vocab(size: int) -> dict: |
| """ |
| |
| Args: |
| size: Size of the vocabulary |
| |
| Returns: |
| vocab: Vocabulary |
| """ |
|
|
| token_len = 1 |
| while size > len(struc_unit) ** token_len: |
| token_len += 1 |
|
|
| vocab = {} |
| for i, token in enumerate(itertools.product(struc_unit, repeat=token_len)): |
| vocab[i] = "".join(token) |
| if len(vocab) == size: |
| vocab[i+1] = "#" |
| return vocab |
|
|
| |
| residue_level = {"Active site", "Binding site", "Site", "DNA binding", "Natural variant", "Mutagenesis", |
| "Transmembrane", "Topological domain", "Intramembrane", "Signal peptide", "Propeptide", |
| "Transit peptide", |
| "Chain", "Peptide", "Modified residue", "Lipidation", "Glycosylation", "Disulfide bond", |
| "Cross-link", |
| "Domain", "Repeat", "Compositional bias", "Region", "Coiled coil", "Motif"} |
|
|
| sequence_level = {"Function", "Miscellaneous", "Caution", "Catalytic activity", "Cofactor", "Activity regulation", |
| "Biophysicochemical properties", "Pathway", "Involvement in disease", "Allergenic properties", |
| "Toxic dose", "Pharmaceutical use", "Disruption phenotype", "Subcellular location", |
| "Post-translational modification", "Subunit", "Domain (non-positional annotation)", |
| "Sequence similarities", "RNA Editing", "Tissue specificity", "Developmental stage", "Induction", |
| "Biotechnology", "Polymorphism", "GO annotation", "Proteomes", "Protein names", "Gene names", |
| "Organism", "Taxonomic lineage", "Virus host"} |
|
|
| raw_text_level = {"Function", "Subunit", "Tissue specificity", "Disruption phenotype", "Post-translational modification", |
| "Induction", "Miscellaneous", "Sequence similarities", "Developmental stage", |
| "Domain (non-positional annotation)", "Activity regulation", "Caution", "Polymorphism", "Toxic dose", |
| "Allergenic properties", "Pharmaceutical use", "Cofactor", "Biophysicochemical properties", |
| "Subcellular location", "RNA Editing"} |
