mutcleaner.core.constants

Alphabet and genetic-code constants used across mutcleaner.

This module collects IUPAC alphabets for DNA/RNA/amino acids, base-complement mappings, 1↔3 letter amino-acid code conversions, and the standard genetic code (codon → amino acid) for DNA and RNA.

Examples

Validate a DNA sequence contains only standard bases:

all(b in STANDARD_DNA_BASES for b in "ATGCGT")

Translate a DNA codon:

AA = STANDARD_GENETIC_CODE_DNA["ATG"]   # 'M'

Get the 1-letter code from a PDB-style residue name:

AA1 = AA3_TO_1["ASP"]    # 'D'
AA3 = AA1_TO_3["D"]      # 'Asp'

Attributes

STANDARD_DNA_BASESset of str

Canonical DNA bases ({'A','T','C','G'}).

AMBIGUOUS_DNA_BASESset of str

IUPAC ambiguous DNA symbols (e.g. 'R','Y','S','W','K','M','B','D','H','V','N').

STANDARD_RNA_BASESset of str

Canonical RNA bases ({'A','U','C','G'}).

AMBIGUOUS_RNA_BASESset of str

IUPAC ambiguous RNA symbols.

STANDARD_AMINO_ACIDSset of str

20 standard amino-acid one-letter codes.

AMBIGUOUS_AMINO_ACIDSset of str

Ambiguous/non-standard amino-acid symbols (e.g. 'B','Z','X','J','U','O').

DNA_BASE_COMPLEMENTSdict[str, str]

DNA Watson-Crick complements.

RNA_BASE_COMPLEMENTSdict[str, str]

RNA Watson-Crick complements.

AA3_TO_1dict[str, str]

Amino-acid 3-letter → 1-letter code map (case-tolerant; includes 'TER' → '*').

AA1_TO_3dict[str, str]

Amino-acid 1-letter → 3-letter code map (includes stop '*' → 'TER').

STANDARD_GENETIC_CODE_DNAdict[str, str]

DNA codon table (triplet of ATCG → ACDEFGHIKLMNPQRSTVWY*).

STANDARD_START_CODONS_DNAset[str]

DNA start codons (default {'ATG'}).

STANDARD_GENETIC_CODE_RNAdict[str, str]

RNA codon table (triplet of AUCG → ACDEFGHIKLMNPQRSTVWY*).

STANDARD_START_CODONS_RNAset[str]

RNA start codon set (default {'AUG'}).