valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/sequence_alphabets.py

@@ -0,0 +1,449 @@
+"""
+Biological Sequence Alphabet Value Sets
+
+Alphabets for biological sequences including DNA, RNA, and protein sequences. Includes standard alphabets and extended versions with ambiguity codes following IUPAC nomenclature and common bioinformatics standards.
+
+
+Generated from: bio/sequence_alphabets.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class DNABaseEnum(RichEnum):
+    """
+    Standard DNA nucleotide bases (canonical)
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    G = "G"
+    T = "T"
+
+# Set metadata after class creation
+DNABaseEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16708', 'annotations': {'complement': 'T', 'purine': 'true', 'chemical_formula': 'C5H5N5'}, 'aliases': ['adenine']},
+    "C": {'meaning': 'CHEBI:16040', 'annotations': {'complement': 'G', 'pyrimidine': 'true', 'chemical_formula': 'C4H5N3O'}, 'aliases': ['cytosine']},
+    "G": {'meaning': 'CHEBI:16235', 'annotations': {'complement': 'C', 'purine': 'true', 'chemical_formula': 'C5H5N5O'}, 'aliases': ['guanine']},
+    "T": {'meaning': 'CHEBI:17821', 'annotations': {'complement': 'A', 'pyrimidine': 'true', 'chemical_formula': 'C5H6N2O2'}, 'aliases': ['thymine']},
+}
+
+class DNABaseExtendedEnum(RichEnum):
+    """
+    Extended DNA alphabet with IUPAC ambiguity codes
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    G = "G"
+    T = "T"
+    R = "R"
+    Y = "Y"
+    S = "S"
+    W = "W"
+    K = "K"
+    M = "M"
+    B = "B"
+    D = "D"
+    H = "H"
+    V = "V"
+    N = "N"
+    GAP = "GAP"
+
+# Set metadata after class creation
+DNABaseExtendedEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16708', 'annotations': {'represents': 'A'}, 'aliases': ['adenine']},
+    "C": {'meaning': 'CHEBI:16040', 'annotations': {'represents': 'C'}, 'aliases': ['cytosine']},
+    "G": {'meaning': 'CHEBI:16235', 'annotations': {'represents': 'G'}, 'aliases': ['guanine']},
+    "T": {'meaning': 'CHEBI:17821', 'annotations': {'represents': 'T'}, 'aliases': ['thymine']},
+    "R": {'annotations': {'represents': 'A,G', 'iupac': 'true'}},
+    "Y": {'annotations': {'represents': 'C,T', 'iupac': 'true'}},
+    "S": {'annotations': {'represents': 'G,C', 'iupac': 'true', 'bond_strength': 'strong (3 H-bonds)'}},
+    "W": {'annotations': {'represents': 'A,T', 'iupac': 'true', 'bond_strength': 'weak (2 H-bonds)'}},
+    "K": {'annotations': {'represents': 'G,T', 'iupac': 'true'}},
+    "M": {'annotations': {'represents': 'A,C', 'iupac': 'true'}},
+    "B": {'annotations': {'represents': 'C,G,T', 'iupac': 'true'}},
+    "D": {'annotations': {'represents': 'A,G,T', 'iupac': 'true'}},
+    "H": {'annotations': {'represents': 'A,C,T', 'iupac': 'true'}},
+    "V": {'annotations': {'represents': 'A,C,G', 'iupac': 'true'}},
+    "N": {'annotations': {'represents': 'A,C,G,T', 'iupac': 'true'}},
+    "GAP": {'annotations': {'symbol': '-', 'represents': 'gap'}},
+}
+
+class RNABaseEnum(RichEnum):
+    """
+    Standard RNA nucleotide bases (canonical)
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    G = "G"
+    U = "U"
+
+# Set metadata after class creation
+RNABaseEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16708', 'annotations': {'complement': 'U', 'purine': 'true', 'chemical_formula': 'C5H5N5'}, 'aliases': ['adenine']},
+    "C": {'meaning': 'CHEBI:16040', 'annotations': {'complement': 'G', 'pyrimidine': 'true', 'chemical_formula': 'C4H5N3O'}, 'aliases': ['cytosine']},
+    "G": {'meaning': 'CHEBI:16235', 'annotations': {'complement': 'C', 'purine': 'true', 'chemical_formula': 'C5H5N5O'}, 'aliases': ['guanine']},
+    "U": {'meaning': 'CHEBI:17568', 'annotations': {'complement': 'A', 'pyrimidine': 'true', 'chemical_formula': 'C4H4N2O2'}, 'aliases': ['uracil']},
+}
+
+class RNABaseExtendedEnum(RichEnum):
+    """
+    Extended RNA alphabet with IUPAC ambiguity codes
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    G = "G"
+    U = "U"
+    R = "R"
+    Y = "Y"
+    S = "S"
+    W = "W"
+    K = "K"
+    M = "M"
+    B = "B"
+    D = "D"
+    H = "H"
+    V = "V"
+    N = "N"
+    GAP = "GAP"
+
+# Set metadata after class creation
+RNABaseExtendedEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16708', 'annotations': {'represents': 'A'}, 'aliases': ['adenine']},
+    "C": {'meaning': 'CHEBI:16040', 'annotations': {'represents': 'C'}, 'aliases': ['cytosine']},
+    "G": {'meaning': 'CHEBI:16235', 'annotations': {'represents': 'G'}, 'aliases': ['guanine']},
+    "U": {'meaning': 'CHEBI:17568', 'annotations': {'represents': 'U'}, 'aliases': ['uracil']},
+    "R": {'annotations': {'represents': 'A,G', 'iupac': 'true'}},
+    "Y": {'annotations': {'represents': 'C,U', 'iupac': 'true'}},
+    "S": {'annotations': {'represents': 'G,C', 'iupac': 'true'}},
+    "W": {'annotations': {'represents': 'A,U', 'iupac': 'true'}},
+    "K": {'annotations': {'represents': 'G,U', 'iupac': 'true'}},
+    "M": {'annotations': {'represents': 'A,C', 'iupac': 'true'}},
+    "B": {'annotations': {'represents': 'C,G,U', 'iupac': 'true'}},
+    "D": {'annotations': {'represents': 'A,G,U', 'iupac': 'true'}},
+    "H": {'annotations': {'represents': 'A,C,U', 'iupac': 'true'}},
+    "V": {'annotations': {'represents': 'A,C,G', 'iupac': 'true'}},
+    "N": {'annotations': {'represents': 'A,C,G,U', 'iupac': 'true'}},
+    "GAP": {'annotations': {'symbol': '-', 'represents': 'gap'}},
+}
+
+class AminoAcidEnum(RichEnum):
+    """
+    Standard amino acid single letter codes
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    D = "D"
+    E = "E"
+    F = "F"
+    G = "G"
+    H = "H"
+    I = "I"
+    K = "K"
+    L = "L"
+    M = "M"
+    N = "N"
+    P = "P"
+    Q = "Q"
+    R = "R"
+    S = "S"
+    T = "T"
+    V = "V"
+    W = "W"
+    Y = "Y"
+
+# Set metadata after class creation
+AminoAcidEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16449', 'annotations': {'three_letter': 'Ala', 'polarity': 'nonpolar', 'essential': 'false', 'molecular_weight': '89.09'}, 'aliases': ['alanine']},
+    "C": {'meaning': 'CHEBI:17561', 'annotations': {'three_letter': 'Cys', 'polarity': 'polar', 'essential': 'false', 'molecular_weight': '121.15', 'special': 'forms disulfide bonds'}, 'aliases': ['L-cysteine']},
+    "D": {'meaning': 'CHEBI:17053', 'annotations': {'three_letter': 'Asp', 'polarity': 'acidic', 'essential': 'false', 'molecular_weight': '133.10', 'charge': 'negative'}, 'aliases': ['L-aspartic acid']},
+    "E": {'meaning': 'CHEBI:16015', 'annotations': {'three_letter': 'Glu', 'polarity': 'acidic', 'essential': 'false', 'molecular_weight': '147.13', 'charge': 'negative'}, 'aliases': ['L-glutamic acid']},
+    "F": {'meaning': 'CHEBI:17295', 'annotations': {'three_letter': 'Phe', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '165.19', 'aromatic': 'true'}, 'aliases': ['L-phenylalanine']},
+    "G": {'meaning': 'CHEBI:15428', 'annotations': {'three_letter': 'Gly', 'polarity': 'nonpolar', 'essential': 'false', 'molecular_weight': '75.07', 'special': 'smallest, most flexible'}, 'aliases': ['glycine']},
+    "H": {'meaning': 'CHEBI:15971', 'annotations': {'three_letter': 'His', 'polarity': 'basic', 'essential': 'true', 'molecular_weight': '155.16', 'charge': 'positive'}, 'aliases': ['L-histidine']},
+    "I": {'meaning': 'CHEBI:17191', 'annotations': {'three_letter': 'Ile', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '131.17', 'branched': 'true'}, 'aliases': ['L-isoleucine']},
+    "K": {'meaning': 'CHEBI:18019', 'annotations': {'three_letter': 'Lys', 'polarity': 'basic', 'essential': 'true', 'molecular_weight': '146.19', 'charge': 'positive'}, 'aliases': ['L-lysine']},
+    "L": {'meaning': 'CHEBI:15603', 'annotations': {'three_letter': 'Leu', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '131.17', 'branched': 'true'}, 'aliases': ['L-leucine']},
+    "M": {'meaning': 'CHEBI:16643', 'annotations': {'three_letter': 'Met', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '149.21', 'special': 'start codon'}, 'aliases': ['L-methionine']},
+    "N": {'meaning': 'CHEBI:17196', 'annotations': {'three_letter': 'Asn', 'polarity': 'polar', 'essential': 'false', 'molecular_weight': '132.12'}, 'aliases': ['L-asparagine']},
+    "P": {'meaning': 'CHEBI:17203', 'annotations': {'three_letter': 'Pro', 'polarity': 'nonpolar', 'essential': 'false', 'molecular_weight': '115.13', 'special': 'helix breaker, rigid'}, 'aliases': ['L-proline']},
+    "Q": {'meaning': 'CHEBI:18050', 'annotations': {'three_letter': 'Gln', 'polarity': 'polar', 'essential': 'false', 'molecular_weight': '146.15'}, 'aliases': ['L-glutamine']},
+    "R": {'meaning': 'CHEBI:16467', 'annotations': {'three_letter': 'Arg', 'polarity': 'basic', 'essential': 'false', 'molecular_weight': '174.20', 'charge': 'positive'}, 'aliases': ['L-arginine']},
+    "S": {'meaning': 'CHEBI:17115', 'annotations': {'three_letter': 'Ser', 'polarity': 'polar', 'essential': 'false', 'molecular_weight': '105.09', 'hydroxyl': 'true'}, 'aliases': ['L-serine']},
+    "T": {'meaning': 'CHEBI:16857', 'annotations': {'three_letter': 'Thr', 'polarity': 'polar', 'essential': 'true', 'molecular_weight': '119.12', 'hydroxyl': 'true'}, 'aliases': ['L-threonine']},
+    "V": {'meaning': 'CHEBI:16414', 'annotations': {'three_letter': 'Val', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '117.15', 'branched': 'true'}, 'aliases': ['L-valine']},
+    "W": {'meaning': 'CHEBI:16828', 'annotations': {'three_letter': 'Trp', 'polarity': 'nonpolar', 'essential': 'true', 'molecular_weight': '204.23', 'aromatic': 'true', 'special': 'largest'}, 'aliases': ['L-tryptophan']},
+    "Y": {'meaning': 'CHEBI:17895', 'annotations': {'three_letter': 'Tyr', 'polarity': 'polar', 'essential': 'false', 'molecular_weight': '181.19', 'aromatic': 'true', 'hydroxyl': 'true'}, 'aliases': ['L-tyrosine']},
+}
+
+class AminoAcidExtendedEnum(RichEnum):
+    """
+    Extended amino acid alphabet with ambiguity codes and special characters
+    """
+    # Enum members
+    A = "A"
+    C = "C"
+    D = "D"
+    E = "E"
+    F = "F"
+    G = "G"
+    H = "H"
+    I = "I"
+    K = "K"
+    L = "L"
+    M = "M"
+    N = "N"
+    P = "P"
+    Q = "Q"
+    R = "R"
+    S = "S"
+    T = "T"
+    V = "V"
+    W = "W"
+    Y = "Y"
+    B = "B"
+    Z = "Z"
+    J = "J"
+    X = "X"
+    STOP = "STOP"
+    GAP = "GAP"
+    U = "U"
+    O = "O"
+
+# Set metadata after class creation
+AminoAcidExtendedEnum._metadata = {
+    "A": {'meaning': 'CHEBI:16449', 'annotations': {'three_letter': 'Ala'}, 'aliases': ['alanine']},
+    "C": {'meaning': 'CHEBI:17561', 'annotations': {'three_letter': 'Cys'}, 'aliases': ['L-cysteine']},
+    "D": {'meaning': 'CHEBI:17053', 'annotations': {'three_letter': 'Asp'}, 'aliases': ['L-aspartic acid']},
+    "E": {'meaning': 'CHEBI:16015', 'annotations': {'three_letter': 'Glu'}, 'aliases': ['L-glutamic acid']},
+    "F": {'meaning': 'CHEBI:17295', 'annotations': {'three_letter': 'Phe'}, 'aliases': ['L-phenylalanine']},
+    "G": {'meaning': 'CHEBI:15428', 'annotations': {'three_letter': 'Gly'}, 'aliases': ['glycine']},
+    "H": {'meaning': 'CHEBI:15971', 'annotations': {'three_letter': 'His'}, 'aliases': ['L-histidine']},
+    "I": {'meaning': 'CHEBI:17191', 'annotations': {'three_letter': 'Ile'}, 'aliases': ['L-isoleucine']},
+    "K": {'meaning': 'CHEBI:18019', 'annotations': {'three_letter': 'Lys'}, 'aliases': ['L-lysine']},
+    "L": {'meaning': 'CHEBI:15603', 'annotations': {'three_letter': 'Leu'}, 'aliases': ['L-leucine']},
+    "M": {'meaning': 'CHEBI:16643', 'annotations': {'three_letter': 'Met'}, 'aliases': ['L-methionine']},
+    "N": {'meaning': 'CHEBI:17196', 'annotations': {'three_letter': 'Asn'}, 'aliases': ['L-asparagine']},
+    "P": {'meaning': 'CHEBI:17203', 'annotations': {'three_letter': 'Pro'}, 'aliases': ['L-proline']},
+    "Q": {'meaning': 'CHEBI:18050', 'annotations': {'three_letter': 'Gln'}, 'aliases': ['L-glutamine']},
+    "R": {'meaning': 'CHEBI:16467', 'annotations': {'three_letter': 'Arg'}, 'aliases': ['L-arginine']},
+    "S": {'meaning': 'CHEBI:17115', 'annotations': {'three_letter': 'Ser'}, 'aliases': ['L-serine']},
+    "T": {'meaning': 'CHEBI:16857', 'annotations': {'three_letter': 'Thr'}, 'aliases': ['L-threonine']},
+    "V": {'meaning': 'CHEBI:16414', 'annotations': {'three_letter': 'Val'}, 'aliases': ['L-valine']},
+    "W": {'meaning': 'CHEBI:16828', 'annotations': {'three_letter': 'Trp'}, 'aliases': ['L-tryptophan']},
+    "Y": {'meaning': 'CHEBI:17895', 'annotations': {'three_letter': 'Tyr'}, 'aliases': ['L-tyrosine']},
+    "B": {'annotations': {'three_letter': 'Asx', 'represents': 'D,N', 'ambiguity': 'true'}, 'aliases': ['L-aspartic acid or Asparagine (D or N)']},
+    "Z": {'annotations': {'three_letter': 'Glx', 'represents': 'E,Q', 'ambiguity': 'true'}, 'aliases': ['L-glutamic acid or Glutamine (E or Q)']},
+    "J": {'annotations': {'three_letter': 'Xle', 'represents': 'L,I', 'ambiguity': 'true'}, 'aliases': ['L-leucine or Isoleucine (L or I)']},
+    "X": {'annotations': {'three_letter': 'Xaa', 'represents': 'any', 'ambiguity': 'true'}},
+    "STOP": {'annotations': {'symbol': '*', 'three_letter': 'Ter', 'represents': 'stop codon'}},
+    "GAP": {'annotations': {'symbol': '-', 'represents': 'gap'}},
+    "U": {'meaning': 'CHEBI:16633', 'annotations': {'three_letter': 'Sec', 'special': '21st amino acid', 'codon': 'UGA with SECIS element'}, 'aliases': ['L-selenocysteine']},
+    "O": {'meaning': 'CHEBI:21860', 'annotations': {'three_letter': 'Pyl', 'special': '22nd amino acid', 'codon': 'UAG in certain archaea/bacteria'}, 'aliases': ['L-pyrrolysine']},
+}
+
+class CodonEnum(RichEnum):
+    """
+    Standard genetic code codons (DNA)
+    """
+    # Enum members
+    TTT = "TTT"
+    TTC = "TTC"
+    TTA = "TTA"
+    TTG = "TTG"
+    CTT = "CTT"
+    CTC = "CTC"
+    CTA = "CTA"
+    CTG = "CTG"
+    ATT = "ATT"
+    ATC = "ATC"
+    ATA = "ATA"
+    ATG = "ATG"
+    GTT = "GTT"
+    GTC = "GTC"
+    GTA = "GTA"
+    GTG = "GTG"
+    TCT = "TCT"
+    TCC = "TCC"
+    TCA = "TCA"
+    TCG = "TCG"
+    AGT = "AGT"
+    AGC = "AGC"
+    CCT = "CCT"
+    CCC = "CCC"
+    CCA = "CCA"
+    CCG = "CCG"
+    ACT = "ACT"
+    ACC = "ACC"
+    ACA = "ACA"
+    ACG = "ACG"
+    GCT = "GCT"
+    GCC = "GCC"
+    GCA = "GCA"
+    GCG = "GCG"
+    TAT = "TAT"
+    TAC = "TAC"
+    TAA = "TAA"
+    TAG = "TAG"
+    TGA = "TGA"
+    CAT = "CAT"
+    CAC = "CAC"
+    CAA = "CAA"
+    CAG = "CAG"
+    AAT = "AAT"
+    AAC = "AAC"
+    AAA = "AAA"
+    AAG = "AAG"
+    GAT = "GAT"
+    GAC = "GAC"
+    GAA = "GAA"
+    GAG = "GAG"
+    TGT = "TGT"
+    TGC = "TGC"
+    TGG = "TGG"
+    CGT = "CGT"
+    CGC = "CGC"
+    CGA = "CGA"
+    CGG = "CGG"
+    AGA = "AGA"
+    AGG = "AGG"
+    GGT = "GGT"
+    GGC = "GGC"
+    GGA = "GGA"
+    GGG = "GGG"
+
+# Set metadata after class creation
+CodonEnum._metadata = {
+    "TTT": {'annotations': {'amino_acid': 'F', 'amino_acid_name': 'Phenylalanine'}},
+    "TTC": {'annotations': {'amino_acid': 'F', 'amino_acid_name': 'Phenylalanine'}},
+    "TTA": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "TTG": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "CTT": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "CTC": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "CTA": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "CTG": {'annotations': {'amino_acid': 'L', 'amino_acid_name': 'Leucine'}},
+    "ATT": {'annotations': {'amino_acid': 'I', 'amino_acid_name': 'Isoleucine'}},
+    "ATC": {'annotations': {'amino_acid': 'I', 'amino_acid_name': 'Isoleucine'}},
+    "ATA": {'annotations': {'amino_acid': 'I', 'amino_acid_name': 'Isoleucine'}},
+    "ATG": {'annotations': {'amino_acid': 'M', 'amino_acid_name': 'Methionine', 'special': 'start codon'}},
+    "GTT": {'annotations': {'amino_acid': 'V', 'amino_acid_name': 'Valine'}},
+    "GTC": {'annotations': {'amino_acid': 'V', 'amino_acid_name': 'Valine'}},
+    "GTA": {'annotations': {'amino_acid': 'V', 'amino_acid_name': 'Valine'}},
+    "GTG": {'annotations': {'amino_acid': 'V', 'amino_acid_name': 'Valine'}},
+    "TCT": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "TCC": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "TCA": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "TCG": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "AGT": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "AGC": {'annotations': {'amino_acid': 'S', 'amino_acid_name': 'Serine'}},
+    "CCT": {'annotations': {'amino_acid': 'P', 'amino_acid_name': 'Proline'}},
+    "CCC": {'annotations': {'amino_acid': 'P', 'amino_acid_name': 'Proline'}},
+    "CCA": {'annotations': {'amino_acid': 'P', 'amino_acid_name': 'Proline'}},
+    "CCG": {'annotations': {'amino_acid': 'P', 'amino_acid_name': 'Proline'}},
+    "ACT": {'annotations': {'amino_acid': 'T', 'amino_acid_name': 'Threonine'}},
+    "ACC": {'annotations': {'amino_acid': 'T', 'amino_acid_name': 'Threonine'}},
+    "ACA": {'annotations': {'amino_acid': 'T', 'amino_acid_name': 'Threonine'}},
+    "ACG": {'annotations': {'amino_acid': 'T', 'amino_acid_name': 'Threonine'}},
+    "GCT": {'annotations': {'amino_acid': 'A', 'amino_acid_name': 'Alanine'}},
+    "GCC": {'annotations': {'amino_acid': 'A', 'amino_acid_name': 'Alanine'}},
+    "GCA": {'annotations': {'amino_acid': 'A', 'amino_acid_name': 'Alanine'}},
+    "GCG": {'annotations': {'amino_acid': 'A', 'amino_acid_name': 'Alanine'}},
+    "TAT": {'annotations': {'amino_acid': 'Y', 'amino_acid_name': 'Tyrosine'}},
+    "TAC": {'annotations': {'amino_acid': 'Y', 'amino_acid_name': 'Tyrosine'}},
+    "TAA": {'annotations': {'amino_acid': '*', 'name': 'ochre', 'special': 'stop codon'}},
+    "TAG": {'annotations': {'amino_acid': '*', 'name': 'amber', 'special': 'stop codon'}},
+    "TGA": {'annotations': {'amino_acid': '*', 'name': 'opal', 'special': 'stop codon or selenocysteine'}},
+    "CAT": {'annotations': {'amino_acid': 'H', 'amino_acid_name': 'Histidine'}},
+    "CAC": {'annotations': {'amino_acid': 'H', 'amino_acid_name': 'Histidine'}},
+    "CAA": {'annotations': {'amino_acid': 'Q', 'amino_acid_name': 'Glutamine'}},
+    "CAG": {'annotations': {'amino_acid': 'Q', 'amino_acid_name': 'Glutamine'}},
+    "AAT": {'annotations': {'amino_acid': 'N', 'amino_acid_name': 'Asparagine'}},
+    "AAC": {'annotations': {'amino_acid': 'N', 'amino_acid_name': 'Asparagine'}},
+    "AAA": {'annotations': {'amino_acid': 'K', 'amino_acid_name': 'Lysine'}},
+    "AAG": {'annotations': {'amino_acid': 'K', 'amino_acid_name': 'Lysine'}},
+    "GAT": {'annotations': {'amino_acid': 'D', 'amino_acid_name': 'Aspartic acid'}},
+    "GAC": {'annotations': {'amino_acid': 'D', 'amino_acid_name': 'Aspartic acid'}},
+    "GAA": {'annotations': {'amino_acid': 'E', 'amino_acid_name': 'Glutamic acid'}},
+    "GAG": {'annotations': {'amino_acid': 'E', 'amino_acid_name': 'Glutamic acid'}},
+    "TGT": {'annotations': {'amino_acid': 'C', 'amino_acid_name': 'Cysteine'}},
+    "TGC": {'annotations': {'amino_acid': 'C', 'amino_acid_name': 'Cysteine'}},
+    "TGG": {'annotations': {'amino_acid': 'W', 'amino_acid_name': 'Tryptophan'}},
+    "CGT": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "CGC": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "CGA": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "CGG": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "AGA": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "AGG": {'annotations': {'amino_acid': 'R', 'amino_acid_name': 'Arginine'}},
+    "GGT": {'annotations': {'amino_acid': 'G', 'amino_acid_name': 'Glycine'}},
+    "GGC": {'annotations': {'amino_acid': 'G', 'amino_acid_name': 'Glycine'}},
+    "GGA": {'annotations': {'amino_acid': 'G', 'amino_acid_name': 'Glycine'}},
+    "GGG": {'annotations': {'amino_acid': 'G', 'amino_acid_name': 'Glycine'}},
+}
+
+class NucleotideModificationEnum(RichEnum):
+    """
+    Common nucleotide modifications
+    """
+    # Enum members
+    FIVE_METHYL_C = "FIVE_METHYL_C"
+    SIX_METHYL_A = "SIX_METHYL_A"
+    PSEUDOURIDINE = "PSEUDOURIDINE"
+    INOSINE = "INOSINE"
+    DIHYDROURIDINE = "DIHYDROURIDINE"
+    SEVEN_METHYL_G = "SEVEN_METHYL_G"
+    FIVE_HYDROXY_METHYL_C = "FIVE_HYDROXY_METHYL_C"
+    EIGHT_OXO_G = "EIGHT_OXO_G"
+
+# Set metadata after class creation
+NucleotideModificationEnum._metadata = {
+    "FIVE_METHYL_C": {'description': '5-methylcytosine', 'meaning': 'CHEBI:27551', 'annotations': {'symbol': 'm5C', 'type': 'DNA methylation', 'function': 'gene regulation'}},
+    "SIX_METHYL_A": {'description': 'N6-methyladenosine', 'meaning': 'CHEBI:21891', 'annotations': {'symbol': 'm6A', 'type': 'RNA modification', 'function': 'RNA stability, translation'}},
+    "PSEUDOURIDINE": {'description': 'Pseudouridine', 'meaning': 'CHEBI:17802', 'annotations': {'symbol': 'Ψ', 'type': 'RNA modification', 'function': 'RNA stability'}},
+    "INOSINE": {'description': 'Inosine', 'meaning': 'CHEBI:17596', 'annotations': {'symbol': 'I', 'type': 'RNA editing', 'pairs_with': 'A, C, U'}},
+    "DIHYDROURIDINE": {'description': 'Dihydrouridine', 'meaning': 'CHEBI:23774', 'annotations': {'symbol': 'D', 'type': 'tRNA modification'}},
+    "SEVEN_METHYL_G": {'description': '7-methylguanosine', 'meaning': 'CHEBI:20794', 'annotations': {'symbol': 'm7G', 'type': 'mRNA cap', 'function': 'translation initiation'}},
+    "FIVE_HYDROXY_METHYL_C": {'description': '5-hydroxymethylcytosine', 'meaning': 'CHEBI:76792', 'annotations': {'symbol': 'hmC', 'type': 'DNA modification', 'function': 'demethylation intermediate'}},
+    "EIGHT_OXO_G": {'description': '8-oxoguanine', 'meaning': 'CHEBI:44605', 'annotations': {'symbol': '8-oxoG', 'type': 'oxidative damage', 'pairs_with': 'A or C'}},
+}
+
+class SequenceQualityEnum(RichEnum):
+    """
+    Sequence quality indicators (Phred scores)
+    """
+    # Enum members
+    Q0 = "Q0"
+    Q10 = "Q10"
+    Q20 = "Q20"
+    Q30 = "Q30"
+    Q40 = "Q40"
+    Q50 = "Q50"
+    Q60 = "Q60"
+
+# Set metadata after class creation
+SequenceQualityEnum._metadata = {
+    "Q0": {'description': 'Phred quality 0 (100% error probability)', 'annotations': {'phred_score': '0', 'error_probability': '1.0', 'ascii_char': '!'}},
+    "Q10": {'description': 'Phred quality 10 (10% error probability)', 'annotations': {'phred_score': '10', 'error_probability': '0.1', 'ascii_char': '+'}},
+    "Q20": {'description': 'Phred quality 20 (1% error probability)', 'annotations': {'phred_score': '20', 'error_probability': '0.01', 'ascii_char': '5'}},
+    "Q30": {'description': 'Phred quality 30 (0.1% error probability)', 'annotations': {'phred_score': '30', 'error_probability': '0.001', 'ascii_char': '?'}},
+    "Q40": {'description': 'Phred quality 40 (0.01% error probability)', 'annotations': {'phred_score': '40', 'error_probability': '0.0001', 'ascii_char': 'I'}},
+    "Q50": {'description': 'Phred quality 50 (0.001% error probability)', 'annotations': {'phred_score': '50', 'error_probability': '0.00001', 'ascii_char': 'S'}},
+    "Q60": {'description': 'Phred quality 60 (0.0001% error probability)', 'annotations': {'phred_score': '60', 'error_probability': '0.000001', 'ascii_char': ']'}},
+}
+
+__all__ = [
+    "DNABaseEnum",
+    "DNABaseExtendedEnum",
+    "RNABaseEnum",
+    "RNABaseExtendedEnum",
+    "AminoAcidEnum",
+    "AminoAcidExtendedEnum",
+    "CodonEnum",
+    "NucleotideModificationEnum",
+    "SequenceQualityEnum",
+]