@aleph-ai/tinyaleph 1.2.0 → 1.3.0

package/backends/bioinformatics/encoding.js

@@ -0,0 +1,339 @@
+/**
+ * Bioinformatics Prime Encoding
+ * 
+ * Maps biological molecules to prime numbers following the tinyaleph paradigm.
+ * 
+ * Design principles:
+ * - Nucleotides use small primes (2, 3, 5, 7, 11)
+ * - Base pairing has prime product symmetry
+ * - Amino acids map to primes 23-109
+ * - Hydrophobicity correlates with prime magnitude
+ */
+
+// ============================================================================
+// Nucleotide Prime Basis
+// ============================================================================
+
+/**
+ * DNA nucleotide to prime mapping
+ * - Purines (A, G): larger primes (7, 11)
+ * - Pyrimidines (T, C): smaller primes (2, 3)
+ * - Watson-Crick pairs have symmetric products: A-T=14, G-C=33
+ */
+const NUCLEOTIDE_PRIMES = {
+  'A': 7,   // Adenine (purine)
+  'T': 2,   // Thymine (pyrimidine) - pairs with A
+  'G': 11,  // Guanine (purine)
+  'C': 3,   // Cytosine (pyrimidine) - pairs with G
+  'U': 5,   // Uracil (RNA) - replaces Thymine
+  'N': 1,   // Unknown nucleotide (identity element)
+};
+
+/**
+ * Reverse mapping: prime to nucleotide
+ */
+const PRIME_TO_NUCLEOTIDE = {
+  7: 'A',
+  2: 'T',
+  11: 'G',
+  3: 'C',
+  5: 'U',
+  1: 'N',
+};
+
+/**
+ * Complement mapping for DNA
+ */
+const DNA_COMPLEMENTS = {
+  'A': 'T', 'T': 'A', 'G': 'C', 'C': 'G', 'N': 'N'
+};
+
+/**
+ * Complement mapping in prime space
+ */
+const PRIME_COMPLEMENTS = {
+  7: 2,   // A → T
+  2: 7,   // T → A
+  11: 3,  // G → C
+  3: 11,  // C → G
+  5: 7,   // U → A (RNA)
+  1: 1,   // N → N
+};
+
+// ============================================================================
+// Amino Acid Prime Basis
+// ============================================================================
+
+/**
+ * Amino acid to prime mapping
+ * 
+ * Properties encoded by prime magnitude:
+ * - Smaller primes (23-43): Hydrophobic/nonpolar
+ * - Medium primes (47-79): Aromatic/Polar
+ * - Larger primes (83-107): Charged
+ */
+const AMINO_ACID_PRIMES = {
+  // Nonpolar, aliphatic (hydrophobic core formers)
+  'G': 23,  // Glycine - simplest, flexible
+  'A': 29,  // Alanine - small hydrophobic
+  'V': 31,  // Valine - branched hydrophobic
+  'L': 37,  // Leucine - branched hydrophobic
+  'I': 41,  // Isoleucine - branched hydrophobic
+  'M': 43,  // Methionine - sulfur-containing
+  
+  // Aromatic (ring structures)
+  'F': 47,  // Phenylalanine - benzene ring
+  'W': 53,  // Tryptophan - largest, indole ring
+  'Y': 59,  // Tyrosine - phenol ring
+  
+  // Polar, uncharged (hydrogen bonding)
+  'S': 61,  // Serine - hydroxyl group
+  'T': 67,  // Threonine - hydroxyl group
+  'C': 71,  // Cysteine - thiol, disulfide bonds
+  'N': 73,  // Asparagine - amide group
+  'Q': 79,  // Glutamine - amide group
+  
+  // Positively charged (basic)
+  'K': 83,  // Lysine - amino group
+  'R': 89,  // Arginine - guanidinium group
+  'H': 97,  // Histidine - imidazole ring
+  
+  // Negatively charged (acidic)
+  'D': 101, // Aspartic acid - carboxyl
+  'E': 103, // Glutamic acid - carboxyl
+  
+  // Special
+  'P': 107, // Proline - cyclic, helix breaker
+  
+  // Stop codon
+  '*': 109, // Stop signal
+  
+  // Unknown
+  'X': 113, // Unknown amino acid
+};
+
+/**
+ * Reverse mapping: prime to amino acid
+ */
+const PRIME_TO_AMINO_ACID = Object.fromEntries(
+  Object.entries(AMINO_ACID_PRIMES).map(([aa, p]) => [p, aa])
+);
+
+/**
+ * Amino acid properties for physics calculations
+ */
+const AMINO_ACID_PROPERTIES = {
+  'G': { hydrophobicity: 0.0, charge: 0, mass: 57.05, volume: 60.1 },
+  'A': { hydrophobicity: 1.8, charge: 0, mass: 71.08, volume: 88.6 },
+  'V': { hydrophobicity: 4.2, charge: 0, mass: 99.13, volume: 140.0 },
+  'L': { hydrophobicity: 3.8, charge: 0, mass: 113.16, volume: 166.7 },
+  'I': { hydrophobicity: 4.5, charge: 0, mass: 113.16, volume: 166.7 },
+  'M': { hydrophobicity: 1.9, charge: 0, mass: 131.20, volume: 162.9 },
+  'F': { hydrophobicity: 2.8, charge: 0, mass: 147.18, volume: 189.9 },
+  'W': { hydrophobicity: -0.9, charge: 0, mass: 186.21, volume: 227.8 },
+  'Y': { hydrophobicity: -1.3, charge: 0, mass: 163.18, volume: 193.6 },
+  'S': { hydrophobicity: -0.8, charge: 0, mass: 87.08, volume: 89.0 },
+  'T': { hydrophobicity: -0.7, charge: 0, mass: 101.11, volume: 116.1 },
+  'C': { hydrophobicity: 2.5, charge: 0, mass: 103.14, volume: 108.5 },
+  'N': { hydrophobicity: -3.5, charge: 0, mass: 114.10, volume: 114.1 },
+  'Q': { hydrophobicity: -3.5, charge: 0, mass: 128.13, volume: 143.8 },
+  'K': { hydrophobicity: -3.9, charge: 1, mass: 128.17, volume: 168.6 },
+  'R': { hydrophobicity: -4.5, charge: 1, mass: 156.19, volume: 173.4 },
+  'H': { hydrophobicity: -3.2, charge: 0.5, mass: 137.14, volume: 153.2 },
+  'D': { hydrophobicity: -3.5, charge: -1, mass: 115.09, volume: 111.1 },
+  'E': { hydrophobicity: -3.5, charge: -1, mass: 129.12, volume: 138.4 },
+  'P': { hydrophobicity: -1.6, charge: 0, mass: 97.12, volume: 112.7 },
+};
+
+// ============================================================================
+// Codon Encoding
+// ============================================================================
+
+/**
+ * Encode a codon as a unique prime signature
+ * Uses position-weighted scheme: p1 + p2*100 + p3*10000
+ */
+function encodeCodon(codon) {
+  if (codon.length !== 3) {
+    throw new Error(`Codon must be 3 nucleotides, got: ${codon}`);
+  }
+  
+  const n1 = NUCLEOTIDE_PRIMES[codon[0].toUpperCase()];
+  const n2 = NUCLEOTIDE_PRIMES[codon[1].toUpperCase()];
+  const n3 = NUCLEOTIDE_PRIMES[codon[2].toUpperCase()];
+  
+  if (n1 === undefined || n2 === undefined || n3 === undefined) {
+    throw new Error(`Invalid codon: ${codon}`);
+  }
+  
+  return n1 + (n2 * 100) + (n3 * 10000);
+}
+
+/**
+ * Decode a codon prime signature back to nucleotides
+ */
+function decodeCodon(signature) {
+  const n3 = Math.floor(signature / 10000);
+  const remainder = signature % 10000;
+  const n2 = Math.floor(remainder / 100);
+  const n1 = remainder % 100;
+  
+  return (PRIME_TO_NUCLEOTIDE[n1] || '?') +
+         (PRIME_TO_NUCLEOTIDE[n2] || '?') +
+         (PRIME_TO_NUCLEOTIDE[n3] || '?');
+}
+
+// ============================================================================
+// Encoding Functions
+// ============================================================================
+
+/**
+ * Encode DNA sequence to prime array
+ */
+function encodeDNA(sequence) {
+  return sequence.toUpperCase().split('')
+    .filter(c => NUCLEOTIDE_PRIMES[c] !== undefined)
+    .map(c => NUCLEOTIDE_PRIMES[c]);
+}
+
+/**
+ * Decode prime array to DNA sequence
+ */
+function decodeDNA(primes) {
+  return primes.map(p => PRIME_TO_NUCLEOTIDE[p] || '?').join('');
+}
+
+/**
+ * Encode RNA sequence to prime array
+ */
+function encodeRNA(sequence) {
+  return sequence.toUpperCase().split('')
+    .filter(c => c === 'A' || c === 'U' || c === 'G' || c === 'C')
+    .map(c => NUCLEOTIDE_PRIMES[c]);
+}
+
+/**
+ * Decode prime array to RNA sequence
+ */
+function decodeRNA(primes) {
+  return primes.map(p => {
+    if (p === 2) return 'U'; // T in DNA → U in RNA
+    return PRIME_TO_NUCLEOTIDE[p] || '?';
+  }).join('');
+}
+
+/**
+ * Encode protein sequence to prime array
+ */
+function encodeProtein(sequence) {
+  return sequence.toUpperCase().split('')
+    .filter(c => AMINO_ACID_PRIMES[c] !== undefined)
+    .map(c => AMINO_ACID_PRIMES[c]);
+}
+
+/**
+ * Decode prime array to protein sequence
+ */
+function decodeProtein(primes) {
+  return primes.map(p => PRIME_TO_AMINO_ACID[p] || '?').join('');
+}
+
+/**
+ * Detect sequence type from content
+ */
+function detectSequenceType(sequence) {
+  const clean = sequence.replace(/[\s\n>]/g, '').toUpperCase();
+  
+  // Check for FASTA header
+  if (sequence.trim().startsWith('>')) return 'FASTA';
+  
+  // Pure DNA
+  if (/^[ATGCN]+$/.test(clean)) return 'DNA';
+  
+  // RNA (has U)
+  if (/^[AUGCN]+$/.test(clean) && clean.includes('U')) return 'RNA';
+  
+  // Protein (has amino acid letters not in DNA)
+  if (/^[ACDEFGHIKLMNPQRSTVWYX\*]+$/.test(clean)) return 'PROTEIN';
+  
+  // Ambiguous
+  return 'UNKNOWN';
+}
+
+/**
+ * Parse FASTA format
+ */
+function parseFASTA(input) {
+  const lines = input.split('\n');
+  const entries = [];
+  let current = null;
+  
+  for (const line of lines) {
+    if (line.startsWith('>')) {
+      if (current) entries.push(current);
+      current = { header: line.slice(1).trim(), sequence: '' };
+    } else if (current) {
+      current.sequence += line.trim();
+    }
+  }
+  
+  if (current) entries.push(current);
+  return entries;
+}
+
+/**
+ * Get properties for an amino acid
+ */
+function getAminoAcidProperties(aa) {
+  return AMINO_ACID_PROPERTIES[aa.toUpperCase()] || null;
+}
+
+/**
+ * Get charge from amino acid prime
+ */
+function getChargeFromPrime(prime) {
+  const aa = PRIME_TO_AMINO_ACID[prime];
+  if (!aa) return 0;
+  return AMINO_ACID_PROPERTIES[aa]?.charge || 0;
+}
+
+/**
+ * Get hydrophobicity from amino acid prime
+ */
+function getHydrophobicityFromPrime(prime) {
+  const aa = PRIME_TO_AMINO_ACID[prime];
+  if (!aa) return 0;
+  return AMINO_ACID_PROPERTIES[aa]?.hydrophobicity || 0;
+}
+
+module.exports = {
+  // Nucleotide mappings
+  NUCLEOTIDE_PRIMES,
+  PRIME_TO_NUCLEOTIDE,
+  DNA_COMPLEMENTS,
+  PRIME_COMPLEMENTS,
+  
+  // Amino acid mappings
+  AMINO_ACID_PRIMES,
+  PRIME_TO_AMINO_ACID,
+  AMINO_ACID_PROPERTIES,
+  
+  // Codon functions
+  encodeCodon,
+  decodeCodon,
+  
+  // Sequence encoding/decoding
+  encodeDNA,
+  decodeDNA,
+  encodeRNA,
+  decodeRNA,
+  encodeProtein,
+  decodeProtein,
+  
+  // Utilities
+  detectSequenceType,
+  parseFASTA,
+  getAminoAcidProperties,
+  getChargeFromPrime,
+  getHydrophobicityFromPrime,
+};