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