@datagrok/bio 2.25.17 → 2.26.0

package/src/utils/antibody-numbering (WIP)/data/blosum62.ts

@@ -0,0 +1,55 @@
+/**
+ * BLOSUM62 substitution matrix.
+ * Used for scoring amino acid matches/mismatches during alignment.
+ */
+
+const AA_ORDER = 'ARNDCQEGHILKMFPSTWYV';
+
+// BLOSUM62 matrix values in the order of AA_ORDER
+const MATRIX: number[][] = [
+  [ 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0], // A
+  [-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3], // R
+  [-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3], // N
+  [-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3], // D
+  [ 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1], // C
+  [-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2], // Q
+  [-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2], // E
+  [ 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3], // G
+  [-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3], // H
+  [-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3], // I
+  [-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1], // L
+  [-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2], // K
+  [-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1], // M
+  [-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1], // F
+  [-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2], // P
+  [ 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2], // S
+  [ 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0], // T
+  [-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3], // W
+  [-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1], // Y
+  [ 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4], // V
+];
+
+const aaIndex = new Map<string, number>();
+for (let i = 0; i < AA_ORDER.length; i++) {
+  aaIndex.set(AA_ORDER[i], i);
+}
+
+/**
+ * Get BLOSUM62 score for a pair of amino acids.
+ * Returns -4 for unknown amino acids.
+ */
+export function blosum62Score(a: string, b: string): number {
+  const i = aaIndex.get(a);
+  const j = aaIndex.get(b);
+  if (i === undefined || j === undefined) return -4;
+  return MATRIX[i][j];
+}
+
+/**
+ * Get the self-score (diagonal) for an amino acid.
+ */
+export function blosum62Self(a: string): number {
+  const i = aaIndex.get(a);
+  if (i === undefined) return -4;
+  return MATRIX[i][i];
+}

package/src/utils/antibody-numbering (WIP)/data/consensus-aho.ts

@@ -0,0 +1,155 @@
+/**
+ * AHo consensus profiles.
+ */
+
+export const AHO_H: [number, string[]][] = [
+  [1, ['Q', 'E', 'D']], [2, ['V', 'Q']], [3, ['Q', 'K', 'H', 'S', 'T']], [4, ['L', 'V']],
+  [5, ['V', 'Q', 'L', 'E', 'K', 'T']], [6, ['E', 'Q', 'A']], [7, ['S', 'P', 'W']],
+  [8, []], [9, ['G', 'E']], [10, ['G', 'A', 'P', 'S']],
+  [11, ['G', 'E', 'D', 'V']], [12, ['L', 'V']], [13, ['V', 'K', 'L']],
+  [14, ['K', 'Q', 'R']], [15, ['P', 'A']], [16, ['G', 'S', 'T']],
+  [17, ['G', 'A', 'E', 'Q', 'R', 'S', 'D']], [18, ['S', 'T']],
+  [19, ['L', 'V']], [20, ['R', 'K', 'S', 'T']], [21, ['L', 'I', 'V', 'M']],
+  [22, ['S', 'T']], [23, ['C']], [24, ['A', 'K', 'T', 'V', 'S']],
+  [25, ['A', 'V', 'T', 'G', 'I']], [26, ['S', 'T', 'Y']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []], [39, []], [40, []],
+  [41, []], [42, []],
+  [43, ['W']], [44, ['V', 'I', 'F']], [45, ['R', 'K']], [46, ['Q']],
+  [47, ['A', 'P', 'R', 'S', 'T', 'M', 'V']], [48, ['P', 'A', 'H']],
+  [49, ['G', 'E', 'S', 'A']], [50, ['K', 'Q', 'R', 'N']],
+  [51, ['G', 'A', 'R', 'S']], [52, ['L']], [53, ['E', 'Q']],
+  [54, ['W', 'Y']], [55, ['I', 'V', 'K', 'M']],
+  [56, ['A', 'G', 'S']],
+  [57, []], [58, []], [59, []], [60, []], [61, []], [62, []], [63, []],
+  [64, []], [65, []], [66, []], [67, []], [68, []], [69, []],
+  [70, ['Y']], [71, ['A', 'N', 'S', 'P', 'T', 'V', 'G']],
+  [72, ['D', 'E', 'Q', 'A', 'S', 'P']], [73, ['S', 'K', 'A', 'W']],
+  [74, ['F', 'V', 'L', 'A']], [75, ['K', 'Q', 'R', 'E']],
+  [76, ['G', 'S', 'D', 'N']], [77, ['R', 'K', 'Q']],
+  [78, ['F', 'V', 'A', 'L', 'I']], [79, ['T', 'S', 'I']],
+  [80, ['I', 'L', 'M', 'V', 'F']], [81, ['S', 'T', 'N']],
+  [82, ['R', 'V', 'A', 'K', 'L', 'P', 'T']], [83, ['D', 'N', 'E']],
+  [84, ['N', 'T', 'K', 'D', 'E', 'S', 'R']], [85, ['S', 'A', 'P', 'D', 'N']],
+  [86, ['K', 'S', 'T', 'A', 'E', 'I', 'R', 'Q', 'N', 'L']], [87, ['N', 'S', 'D', 'K', 'T']],
+  [88, ['T', 'Q', 'S', 'I', 'M']], [89, ['L', 'A', 'V', 'F']],
+  [90, ['Y', 'S', 'F', 'H', 'T', 'V']], [91, ['L', 'M']],
+  [92, ['Q', 'E', 'K', 'D', 'T']], [93, ['L', 'M', 'I', 'V', 'W']],
+  [94, ['A', 'C', 'D', 'G', 'H', 'K', 'L', 'N', 'R', 'S', 'T']],
+  [95, ['A', 'G', 'H', 'K', 'N', 'R', 'S', 'T']], [96, ['L', 'M', 'P', 'V']],
+  [97, ['R', 'T', 'K']], [98, ['A', 'S', 'T', 'V', 'P']],
+  [99, ['E', 'A', 'D', 'G', 'S', 'V']], [100, ['D']], [101, ['T', 'S']],
+  [102, ['A', 'G']], [103, ['V', 'T', 'I', 'L', 'M']], [104, ['Y']],
+  [105, ['Y', 'F']], [106, ['C']],
+  [107, ['A', 'G', 'S', 'D', 'E', 'N', 'T', 'V', 'I', 'L', 'K', 'R', 'Q', 'P', 'F', 'W', 'Y', 'M', 'H', 'C']], [108, ['A', 'G', 'S', 'D', 'E', 'N', 'T', 'V', 'I', 'L', 'K', 'R', 'Q', 'P', 'F', 'W', 'Y', 'M', 'H', 'C']], [109, []], [110, []], [111, []], [112, []], [113, []],
+  [114, []], [115, []], [116, []], [117, []], [118, []], [119, []], [120, []],
+  [121, []], [122, []], [123, []], [124, []], [125, []], [126, []], [127, []],
+  [128, []], [129, []], [130, []], [131, []], [132, []], [133, []], [134, []],
+  [135, []], [136, []], [137, []], [138, []],
+  [139, ['W']], [140, ['G']], [141, ['Q', 'P', 'R', 'K', 'A', 'T']],
+  [142, ['G']], [143, ['T', 'V', 'A', 'I']], [144, ['L', 'T', 'M', 'S', 'Q', 'P']],
+  [145, ['V', 'L', 'I']], [146, ['T', 'I', 'V']], [147, ['V']],
+  [148, ['S', 'T']], [149, ['S', 'A']],
+];
+
+export const AHO_K: [number, string[]][] = [
+  [1, ['D', 'E', 'Q', 'N', 'A']], [2, ['I', 'V', 'L']], [3, ['V', 'Q', 'L', 'E', 'K']],
+  [4, ['M', 'L', 'V', 'I']], [5, ['T', 'S']], [6, ['Q']],
+  [7, ['S', 'T', 'A', 'I']], [8, ['P', 'Q', 'T', 'A', 'H']],
+  [9, ['S', 'G', 'L', 'A', 'D', 'K', 'F', 'P', 'V']], [10, ['S', 'T', 'F', 'I']],
+  [11, ['L', 'M', 'N', 'Q', 'V']], [12, ['T', 'S', 'A', 'P', 'Y']],
+  [13, ['V', 'L', 'A', 'T', 'M']], [14, ['T', 'S', 'A']],
+  [15, ['A', 'P', 'I', 'V', 'L']], [16, ['G']],
+  [17, ['E', 'Q', 'D', 'G', 'T']], [18, ['K', 'R', 'P', 'T', 'Q', 'S']],
+  [19, ['V', 'A', 'I']], [20, ['T', 'S']], [21, ['M', 'L', 'I', 'F']],
+  [22, ['S', 'T', 'N']], [23, ['C']],
+  [24, ['K', 'R', 'Q', 'S']], [25, ['S', 'A', 'T', 'C']], [26, ['S', 'T', 'G']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []], [39, []], [40, []],
+  [41, ['L', 'M', 'I', 'V', 'F']],
+  [42, ['T', 'A', 'N', 'H', 'E', 'G', 'Q', 'Y', 'S', 'D']],
+  [43, ['W']], [44, ['Y', 'L', 'F']], [45, ['Q', 'L', 'R']],
+  [46, ['Q', 'H', 'E']], [47, ['K', 'R']],
+  [48, ['P', 'Q', 'S', 'T']], [49, ['G', 'E', 'D', 'H', 'N']],
+  [50, ['Q', 'K', 'S', 'T', 'G', 'E', 'R']], [51, ['P', 'A', 'S', 'T', 'V']],
+  [52, ['P', 'I', 'V']], [53, ['K', 'R', 'Q', 'E', 'I', 'T']],
+  [54, ['L', 'R', 'T', 'P', 'V', 'A']], [55, ['L', 'W']],
+  [56, ['I', 'V', 'M']], [57, ['Y', 'K', 'H', 'S', 'F']],
+  [58, []], [59, []], [60, []], [61, []], [62, []], [63, []], [64, []],
+  [65, []], [66, []], [67, []], [68, []], [69, []],
+  [70, ['R', 'L', 'S']],
+  [71, ['E', 'A', 'D', 'Q', 'F', 'R', 'Y', 'H', 'I', 'K', 'P', 'G', 'V']],
+  [72, ['S', 'T', 'D', 'P', 'A', 'E']], [73, ['G']], [74, ['V', 'I']],
+  [75, ['P', 'S', 'A']], [76, ['D', 'S', 'A', 'V', 'K', 'G']],
+  [77, ['R']], [78, ['F']], [79, ['T', 'S', 'I', 'K', 'R']],
+  [80, ['G', 'S', 'A']], [81, ['S', 'G', 'R']], [82, ['G', 'R']],
+  [83, ['S', 'Y']], [84, ['G', 'R', 'A']],
+  [85, ['A', 'F', 'P', 'S', 'Y']], [86, ['A', 'D', 'E', 'G', 'Q', 'R', 'V']],
+  [87, ['T', 'R', 'S', 'Q']], [88, ['D', 'E', 'Q', 'S', 'H', 'Y', 'A']],
+  [89, ['F', 'Y']], [90, ['T', 'S']], [91, ['L', 'F']],
+  [92, ['T', 'K', 'N', 'S', 'R']], [93, ['I', 'V']],
+  [94, ['N', 'S', 'H', 'T', 'D']], [95, ['S', 'R', 'P', 'N', 'G', 'D', 'T']],
+  [96, ['V', 'L', 'M']], [97, ['Q', 'E', 'K']],
+  [98, ['A', 'P', 'E', 'S', 'T', 'Q', 'C', 'Y']], [99, ['E', 'D']],
+  [100, ['D']], [101, ['L', 'F', 'V', 'T', 'A', 'I', 'S', 'M']],
+  [102, ['A', 'G']], [103, ['V', 'T', 'S', 'E', 'D', 'L', 'I', 'M']],
+  [104, ['Y', 'F']], [105, ['Y', 'F', 'H']], [106, ['C']],
+  [107, []], [108, []], [109, []], [110, []], [111, []], [112, []], [113, []],
+  [114, []], [115, []], [116, []], [117, []], [118, []], [119, []], [120, []],
+  [121, []], [122, []], [123, []], [124, []], [125, []], [126, []], [127, []],
+  [128, []], [129, []], [130, []], [131, []], [132, []], [133, []], [134, []],
+  [135, []], [136, []], [137, []], [138, []],
+  [139, ['F']], [140, ['G']], [141, ['A', 'Q', 'S', 'G', 'P']],
+  [142, ['G']], [143, ['T']], [144, ['K', 'R', 'E']],
+  [145, ['L', 'V']], [146, ['E', 'V', 'D']], [147, ['L', 'I', 'V']],
+  [148, ['K', 'R']], [149, ['R', 'G']],
+];
+
+export const AHO_L: [number, string[]][] = [
+  [1, ['Q', 'S']], [2, ['S', 'Y', 'P', 'A', 'L', 'F']], [3, ['A', 'V', 'E']],
+  [4, ['L', 'V']], [5, ['T']], [6, ['Q']], [7, ['P', 'E', 'S']],
+  [8, []], [9, ['A', 'P', 'S', 'R']], [10, ['S', 'A']],
+  [11, ['V', 'L', 'A']], [12, ['S', 'T']],
+  [13, ['G', 'V', 'A', 'T', 'K', 'E', 'F']], [14, ['S', 'A', 'T']],
+  [15, ['P', 'L']], [16, ['G']], [17, ['Q', 'E', 'K', 'A']],
+  [18, ['S', 'T', 'K', 'R']], [19, ['I', 'A', 'V']],
+  [20, ['T', 'R', 'S', 'K']], [21, ['I', 'L']], [22, ['S', 'T']], [23, ['C']],
+  [24, ['T', 'G', 'Q', 'S', 'A', 'N', 'R']], [25, ['G', 'S', 'L', 'R']],
+  [26, ['T', 'N', 'D', 'S']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []], [39, []], [40, []],
+  [41, ['V', 'A', 'I']], [42, ['S', 'H', 'Q', 'C', 'N', 'Y', 'E']],
+  [43, ['W']], [44, ['Y', 'F', 'V']], [45, ['Q']],
+  [46, ['Q', 'H', 'E']], [47, ['H', 'K', 'R', 'L', 'F', 'V', 'Q']],
+  [48, ['P', 'A', 'S']], [49, ['G', 'D', 'L']],
+  [50, ['K', 'Q', 'T', 'R', 'H', 'S', 'A', 'M']], [51, ['A', 'S', 'L', 'P', 'G']],
+  [52, ['P', 'F']], [53, ['K', 'V', 'S', 'R', 'T', 'I']],
+  [54, ['L', 'V', 'G', 'Y', 'T']], [55, ['I', 'V', 'M', 'L']],
+  [56, ['I', 'V', 'L', 'M']], [57, ['F', 'Y', 'G', 'S', 'E']],
+  [58, []], [59, []], [60, []], [61, []], [62, []], [63, []], [64, []],
+  [65, []], [66, []], [67, []], [68, []],
+  [69, ['N', 'D', 'K', 'Q', 'E', 'S', 'H']], [70, ['R', 'T']],
+  [71, ['P', 'A', 'G']], [72, ['S', 'P', 'D']], [73, ['G']],
+  [74, ['I', 'V']], [75, ['S', 'P']], [76, ['N', 'E', 'A', 'D']],
+  [77, ['R']], [78, ['F']], [79, ['S']], [80, ['G']],
+  [81, ['S']], [82, ['K', 'N', 'P', 'L', 'I', 'S']],
+  [83, ['F', 'S', 'I']], [84, ['G', 'A', 'S']],
+  [85, ['A', 'I', 'L', 'S', 'T', 'W']], [86, ['A', 'D', 'E', 'G', 'S', 'T']],
+  [87, ['N', 'T', 'D', 'S', 'A']], [88, ['T', 'K', 'S', 'R']],
+  [89, ['A', 'R']], [90, ['S', 'T', 'A', 'Y']], [91, ['L']],
+  [92, ['T', 'G', 'A', 'S']], [93, ['I', 'V']], [94, ['S', 'T']],
+  [95, ['G', 'R', 'S', 'N']], [96, ['L', 'V', 'T', 'A', 'I']],
+  [97, ['Q', 'E', 'R']], [98, ['A', 'S', 'P', 'T']],
+  [99, ['E', 'G', 'M', 'D']], [100, ['D']], [101, ['E']],
+  [102, ['A', 'G']], [103, ['D', 'I', 'E']], [104, ['Y']],
+  [105, ['Y', 'F', 'I']], [106, ['C']],
+  [107, []], [108, []], [109, []], [110, []], [111, []], [112, []], [113, []],
+  [114, []], [115, []], [116, []], [117, []], [118, []], [119, []], [120, []],
+  [121, []], [122, []], [123, []], [124, []], [125, []], [126, []], [127, []],
+  [128, []], [129, []], [130, []], [131, []], [132, []], [133, []], [134, []],
+  [135, []], [136, []], [137, []], [138, []],
+  [139, ['F']], [140, ['G']], [141, ['G', 'T', 'S']],
+  [142, ['G']], [143, ['T']], [144, ['K', 'T', 'R', 'Q']],
+  [145, ['V', 'L']], [146, ['T']], [147, ['V']],
+  [148, ['L', 'K']], [149, ['R', 'G']],
+];

package/src/utils/antibody-numbering (WIP)/data/consensus-imgt.ts

@@ -0,0 +1,162 @@
+/**
+ * IMGT consensus profiles.
+ * Each entry: position -> array of expected amino acids (most common first).
+ * Gap positions (where CDR insertions can occur) have an empty array.
+ */
+
+export const IMGT_H: [number, string[]][] = [
+  [1, ['Q', 'E', 'D']], [2, ['V', 'Q']], [3, ['Q', 'K', 'H', 'S', 'T']], [4, ['L', 'V']],
+  [5, ['V', 'Q', 'L', 'E', 'K', 'T']], [6, ['E', 'Q', 'A']], [7, ['S', 'P', 'W']],
+  [8, ['G', 'E']], [9, ['G', 'A', 'P', 'S']], [10, []], [11, ['G', 'E', 'D', 'V']],
+  [12, ['L', 'V']], [13, ['V', 'K', 'L']], [14, ['K', 'Q', 'R']], [15, ['P', 'A']],
+  [16, ['G', 'S', 'T']], [17, ['G', 'A', 'E', 'Q', 'R', 'S', 'D']], [18, ['S', 'T']],
+  [19, ['L', 'V']], [20, ['R', 'K', 'S', 'T']], [21, ['L', 'I', 'V', 'M']],
+  [22, ['S', 'T']], [23, ['C']], [24, ['A', 'K', 'T', 'V', 'S']],
+  [25, ['A', 'V', 'T', 'G', 'I']], [26, ['S', 'T', 'Y']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []],
+  [39, []], [40, []], [41, ['W']], [42, ['V', 'I', 'F']], [43, ['R', 'K']],
+  [44, ['Q']], [45, ['A', 'P', 'R', 'S', 'T', 'M', 'V']], [46, ['P', 'A', 'H']],
+  [47, ['G', 'E', 'S', 'A']], [48, ['K', 'Q', 'R', 'N']], [49, ['G', 'A', 'R', 'S']],
+  [50, ['L']], [51, ['E', 'Q']], [52, ['W', 'Y']], [53, ['I', 'V', 'K', 'M']],
+  [54, ['A', 'G', 'S']],
+  [55, ['A', 'G', 'S', 'D', 'E', 'N', 'T', 'V', 'I', 'L', 'K', 'R', 'Q', 'P', 'F', 'W', 'Y', 'M', 'H', 'C']], [56, []], [57, []], [58, []], [59, []], [60, []], [61, []],
+  [62, []], [63, []], [64, []], [65, []],
+  [66, ['Y', 'N', 'K', 'D', 'E', 'F', 'G', 'H', 'R', 'S', 'T']], [67, ['Y', 'F']],
+  [68, ['A', 'N', 'S', 'P', 'T', 'V', 'G']], [69, ['D', 'E', 'Q', 'A', 'S', 'P']],
+  [70, ['S', 'K', 'A', 'W']], [71, ['F', 'V', 'L', 'A']], [72, ['K', 'Q', 'R', 'E']],
+  [73, []], [74, ['G', 'S', 'D', 'N']], [75, ['R', 'K', 'Q']],
+  [76, ['F', 'V', 'A', 'L', 'I']], [77, ['T', 'S', 'I']],
+  [78, ['I', 'L', 'M', 'V', 'F']], [79, ['S', 'T', 'N']],
+  [80, ['R', 'V', 'A', 'K', 'L', 'P', 'T']], [81, ['D', 'N', 'E']],
+  [82, ['N', 'T', 'K', 'D', 'E', 'S', 'R']], [83, ['S', 'A', 'P', 'D', 'N']],
+  [84, ['K', 'S', 'T', 'A', 'E', 'I', 'R', 'Q', 'N', 'L']], [85, ['N', 'S', 'D', 'K', 'T']],
+  [86, ['T', 'Q', 'S', 'I', 'M']], [87, ['L', 'A', 'V', 'F']],
+  [88, ['Y', 'S', 'F', 'H', 'T', 'V']], [89, ['L', 'M']],
+  [90, ['Q', 'E', 'K', 'D', 'T']], [91, ['L', 'M', 'I', 'V', 'W']],
+  [92, ['A', 'C', 'D', 'G', 'H', 'K', 'L', 'N', 'R', 'S', 'T']],
+  [93, ['A', 'G', 'H', 'K', 'N', 'R', 'S', 'T']], [94, ['L', 'M', 'P', 'V']],
+  [95, ['R', 'T', 'K']], [96, ['A', 'S', 'T', 'V', 'P']],
+  [97, ['E', 'A', 'D', 'G', 'S', 'V']], [98, ['D']], [99, ['T', 'S']],
+  [100, ['A', 'G']], [101, ['V', 'T', 'I', 'L', 'M']], [102, ['Y']],
+  [103, ['Y', 'F']], [104, ['C']],
+  [105, []], [106, []], [107, []], [108, []], [109, []], [110, []],
+  [111, []], [112, []], [113, []], [114, []], [115, []], [116, []], [117, []],
+  [118, ['W']], [119, ['G']], [120, ['Q', 'P', 'R', 'K', 'A', 'T']],
+  [121, ['G']], [122, ['T', 'V', 'A', 'I']], [123, ['L', 'T', 'M', 'S', 'Q', 'P']],
+  [124, ['V', 'L', 'I']], [125, ['T', 'I', 'V']], [126, ['V']],
+  [127, ['S', 'T']], [128, ['S', 'A']],
+];
+
+export const IMGT_K: [number, string[]][] = [
+  [1, ['D', 'E', 'Q', 'N', 'A']], [2, ['I', 'V', 'L']], [3, ['V', 'Q', 'L', 'E', 'K']],
+  [4, ['M', 'L', 'V', 'I']], [5, ['T', 'S']], [6, ['Q']],
+  [7, ['S', 'T', 'A', 'I']], [8, ['P', 'Q', 'T', 'A', 'H']],
+  [9, ['S', 'G', 'L', 'A', 'D', 'K', 'F', 'P', 'V']], [10, ['S', 'T', 'F', 'I']],
+  [11, ['L', 'M', 'N', 'Q', 'V']], [12, ['T', 'S', 'A', 'P', 'Y']],
+  [13, ['V', 'L', 'A', 'T', 'M']], [14, ['T', 'S', 'A']],
+  [15, ['A', 'P', 'I', 'V', 'L']], [16, ['G']],
+  [17, ['E', 'Q', 'D', 'G', 'T']], [18, ['K', 'R', 'P', 'T', 'Q', 'S']],
+  [19, ['V', 'A', 'I']], [20, ['T', 'S']], [21, ['M', 'L', 'I', 'F']],
+  [22, ['S', 'T', 'N']], [23, ['C']], [24, ['K', 'R', 'Q', 'S']],
+  [25, ['S', 'A', 'T', 'C']], [26, ['S', 'T', 'G']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []],
+  [39, ['L', 'M', 'I', 'V', 'F']], [40, ['T', 'A', 'N', 'H', 'E', 'G', 'Q', 'Y', 'S', 'D']],
+  [41, ['W']], [42, ['Y', 'L', 'F']], [43, ['Q', 'L', 'R']],
+  [44, ['Q', 'H', 'E']], [45, ['K', 'R']], [46, ['P', 'Q', 'S', 'T']],
+  [47, ['G', 'E', 'D', 'H', 'N']], [48, ['Q', 'K', 'S', 'T', 'G', 'E', 'R']],
+  [49, ['P', 'A', 'S', 'T', 'V']], [50, ['P', 'I', 'V']],
+  [51, ['K', 'R', 'Q', 'E', 'I', 'T']], [52, ['L', 'R', 'T', 'P', 'V', 'A']],
+  [53, ['L', 'W']], [54, ['I', 'V', 'M']], [55, ['Y', 'K', 'H', 'S', 'F']],
+  [56, []], [57, []], [58, []], [59, []], [60, []], [61, []], [62, []],
+  [63, []], [64, []], [65, []],
+  [66, ['T', 'S', 'K', 'N', 'I', 'D', 'R', 'Y', 'Q', 'F']], [67, ['R', 'L', 'S']],
+  [68, ['E', 'A', 'D', 'Q', 'F', 'R', 'Y', 'H', 'I', 'K', 'P', 'G', 'V']],
+  [69, ['S', 'T', 'D', 'P', 'A', 'E']], [70, ['G']], [71, ['V', 'I']],
+  [72, ['P', 'S', 'A']], [73, []],
+  [74, ['D', 'S', 'A', 'V', 'K', 'G']], [75, ['R']], [76, ['F']],
+  [77, ['T', 'S', 'I', 'K', 'R']], [78, ['G', 'S', 'A']],
+  [79, ['S', 'G', 'R']], [80, ['G', 'R']], [81, ['S', 'Y']],
+  [82, ['G', 'R', 'A']], [83, ['A', 'F', 'P', 'S', 'Y']],
+  [84, ['A', 'D', 'E', 'G', 'Q', 'R', 'V']], [85, ['T', 'R', 'S', 'Q']],
+  [86, ['D', 'E', 'Q', 'S', 'H', 'Y', 'A']], [87, ['F', 'Y']],
+  [88, ['T', 'S']], [89, ['L', 'F']], [90, ['T', 'K', 'N', 'S', 'R']],
+  [91, ['I', 'V']], [92, ['N', 'S', 'H', 'T', 'D']],
+  [93, ['S', 'R', 'P', 'N', 'G', 'D', 'T']], [94, ['V', 'L', 'M']],
+  [95, ['Q', 'E', 'K']], [96, ['A', 'P', 'E', 'S', 'T', 'Q', 'C', 'Y']],
+  [97, ['E', 'D']], [98, ['D']],
+  [99, ['L', 'F', 'V', 'T', 'A', 'I', 'S', 'M']], [100, ['A', 'G']],
+  [101, ['V', 'T', 'S', 'E', 'D', 'L', 'I', 'M']], [102, ['Y', 'F']],
+  [103, ['Y', 'F', 'H']], [104, ['C']],
+  [105, []], [106, []], [107, []], [108, []], [109, []], [110, []],
+  [111, []], [112, []], [113, []], [114, []], [115, []], [116, []], [117, []],
+  [118, ['F']], [119, ['G']], [120, ['A', 'Q', 'S', 'G', 'P']],
+  [121, ['G']], [122, ['T']], [123, ['K', 'R', 'E']],
+  [124, ['L', 'V']], [125, ['E', 'V', 'D']], [126, ['L', 'I', 'V']],
+  [127, ['K', 'R']],
+];
+
+export const IMGT_L: [number, string[]][] = [
+  [1, ['Q', 'S']], [2, ['S', 'Y', 'P', 'A', 'L', 'F']], [3, ['A', 'V', 'E']],
+  [4, ['L', 'V']], [5, ['T']], [6, ['Q']], [7, ['P', 'E', 'S']],
+  [8, ['A', 'P', 'S', 'R']], [9, ['S', 'A']], [10, []],
+  [11, ['V', 'L', 'A']], [12, ['S', 'T']],
+  [13, ['G', 'V', 'A', 'T', 'K', 'E', 'F']], [14, ['S', 'A', 'T']],
+  [15, ['P', 'L']], [16, ['G']], [17, ['Q', 'E', 'K', 'A']],
+  [18, ['S', 'T', 'K', 'R']], [19, ['I', 'A', 'V']],
+  [20, ['T', 'R', 'S', 'K']], [21, ['I', 'L']], [22, ['S', 'T']], [23, ['C']],
+  [24, ['T', 'G', 'Q', 'S', 'A', 'N', 'R']], [25, ['G', 'S', 'L', 'R']],
+  [26, ['T', 'N', 'D', 'S']],
+  [27, []], [28, []], [29, []], [30, []], [31, []], [32, []], [33, []],
+  [34, []], [35, []], [36, []], [37, []], [38, []],
+  [39, ['V', 'A', 'I']], [40, ['S', 'H', 'Q', 'C', 'N', 'Y', 'E']],
+  [41, ['W']], [42, ['Y', 'F', 'V']], [43, ['Q']],
+  [44, ['Q', 'H', 'E']], [45, ['H', 'K', 'R', 'L', 'F', 'V', 'Q']],
+  [46, ['P', 'A', 'S']], [47, ['G', 'D', 'L']],
+  [48, ['K', 'Q', 'T', 'R', 'H', 'S', 'A', 'M']], [49, ['A', 'S', 'L', 'P', 'G']],
+  [50, ['P', 'F']], [51, ['K', 'V', 'S', 'R', 'T', 'I']],
+  [52, ['L', 'V', 'G', 'Y', 'T']], [53, ['I', 'V', 'M', 'L']],
+  [54, ['I', 'V', 'L', 'M']], [55, ['F', 'Y', 'G', 'S', 'E']],
+  [56, []], [57, []], [58, []], [59, []], [60, []], [61, []], [62, []],
+  [63, []], [64, []], [65, []],
+  [66, ['N', 'D', 'K', 'Q', 'E', 'S', 'H']], [67, ['R', 'T']],
+  [68, ['P', 'A', 'G']], [69, ['S', 'P', 'D']], [70, ['G']],
+  [71, ['I', 'V']], [72, ['S', 'P']], [73, []],
+  [74, ['N', 'E', 'A', 'D']], [75, ['R']], [76, ['F']], [77, ['S']],
+  [78, ['G']], [79, ['S']], [80, ['K', 'N', 'P', 'L', 'I', 'S']],
+  [81, ['F', 'S', 'I']], [82, ['G', 'A', 'S']],
+  [83, ['A', 'I', 'L', 'S', 'T', 'W']], [84, ['A', 'D', 'E', 'G', 'S', 'T']],
+  [85, ['N', 'T', 'D', 'S', 'A']], [86, ['T', 'K', 'S', 'R']],
+  [87, ['A', 'R']], [88, ['S', 'T', 'A', 'Y']], [89, ['L']],
+  [90, ['T', 'G', 'A', 'S']], [91, ['I', 'V']], [92, ['S', 'T']],
+  [93, ['G', 'R', 'S', 'N']], [94, ['L', 'V', 'T', 'A', 'I']],
+  [95, ['Q', 'E', 'R']], [96, ['A', 'S', 'P', 'T']],
+  [97, ['E', 'G', 'M', 'D']], [98, ['D']], [99, ['E']],
+  [100, ['A', 'G']], [101, ['D', 'I', 'E']], [102, ['Y']],
+  [103, ['Y', 'F', 'I']], [104, ['C']],
+  [105, []], [106, []], [107, []], [108, []], [109, []], [110, []],
+  [111, []], [112, []], [113, []], [114, []], [115, []], [116, []], [117, []],
+  [118, ['F']], [119, ['G']], [120, ['G', 'T', 'S']],
+  [121, ['G']], [122, ['T']], [123, ['K', 'T', 'R', 'Q']],
+  [124, ['V', 'L']], [125, ['T']], [126, ['V']], [127, ['L', 'K']],
+];
+
+/** C-terminal finder consensus profiles */
+export const CTERM_H: [number, string[]][] = [
+  [1, ['W']], [2, ['G']], [3, ['Q', 'P', 'R', 'K', 'A', 'T']], [4, ['G']],
+  [5, ['T', 'V', 'A', 'I']], [6, ['L', 'T', 'M', 'S', 'Q', 'P']],
+  [7, ['V', 'L', 'I']], [8, ['T', 'I', 'V']], [9, ['V']], [10, ['S', 'T']],
+];
+
+export const CTERM_K: [number, string[]][] = [
+  [1, ['F']], [2, ['G']], [3, ['A', 'Q', 'S', 'G', 'P']], [4, ['G']],
+  [5, ['T']], [6, ['K', 'R', 'E']], [7, ['L', 'V']], [8, ['E', 'V', 'D']],
+  [9, ['L', 'I', 'V']], [10, ['K', 'R']],
+];
+
+export const CTERM_L: [number, string[]][] = [
+  [1, ['F']], [2, ['G']], [3, ['G', 'T', 'S']], [4, ['G']],
+  [5, ['T']], [6, ['K', 'T', 'R', 'Q']], [7, ['V', 'L']], [8, ['T']],
+  [9, ['V']], [10, ['L', 'K']],
+];

package/src/utils/antibody-numbering (WIP)/data/consensus-kabat.ts

@@ -0,0 +1,157 @@
+/**
+ * Kabat consensus profiles.
+ */
+
+export const KABAT_H: [number, string[]][] = [
+  [1, ['Q','E','D']], [2, ['V','Q']], [3, ['Q','K','H','S','T']], [4, ['L','V']],
+  [5, ['V','Q','L','E','K','T']], [6, ['E','Q','A']], [7, ['S','P','W']],
+  [8, ['G','E']], [9, ['G','A','P','S']], [10, ['G','E','D','V']],
+  [11, ['L','V']], [12, ['V','K','L']], [13, ['K','Q','R']], [14, ['P','A']],
+  [15, ['G','S','T']], [16, ['G','A','E','Q','R','S','D']], [17, ['S','T']],
+  [18, ['L','V']], [19, ['R','K','S','T']], [20, ['L','I','V','M']],
+  [21, ['S','T']], [22, ['C']], [23, ['A','K','T','V','S']],
+  [24, ['A','V','T','G','I']], [25, ['S','T','Y']],
+  [26, ['G','E']], [27, ['F','Y','G','D','S']], [28, ['T','S','I','N','D','A']],
+  [29, ['F','I','L','S','V']], [30, ['S','T','D','G','N','R']],
+  [31, []], [32, []], [33, []], [34, []], [35, []],
+  [36, ['W']], [37, ['V','I','F']], [38, ['R','K']], [39, ['Q']],
+  [40, ['A','P','R','S','T','M','V']], [41, ['P','A','H']],
+  [42, ['G','E','S','A']], [43, ['K','Q','R','N']],
+  [44, ['G','A','R','S']], [45, ['L']], [46, ['E','Q']],
+  [47, ['W','Y']], [48, ['I','V','K','M']], [49, ['A','G','S']],
+  [50, []],
+  [51, ['I','V','T','M']],
+  [52, ['S','N','Y','D','K','I','H','G','W','R','T']],
+  [53, ['A','D','Y','W','G','H','I','T','S','N','R']],
+  [54, ['A','D','F','G','K','N','T','S']],
+  [55, ['A','D','E','G','S','T','W','Y']],
+  [56, ['A','D','D','G','N','S','T','W','Y']],
+  [57, ['T','A','I','K','N','P','S']],
+  [58, ['Y','N','K','D','E','F','G','H','R','S','T']], [59, ['Y','F']],
+  [60, ['A','N','S','P','T','V','G']], [61, ['D','E','Q','A','S','P']],
+  [62, ['S','K','A','W']], [63, ['F','V','L','A']], [64, ['K','Q','R','E']],
+  [65, ['G','S','D','N']], [66, ['R','K','Q']],
+  [67, ['F','V','A','L','I']], [68, ['T','S','I']],
+  [69, ['I','L','M','V','F']], [70, ['S','T','N']],
+  [71, ['R','V','A','K','L','P','T']], [72, ['D','N','E']],
+  [73, ['N','T','K','D','E','S','R']], [74, ['S','A','P','D','N']],
+  [75, ['K','S','T','A','E','I','R','Q','N','L']], [76, ['N','S','D','K','T']],
+  [77, ['T','Q','S','I','M']], [78, ['L','A','V','F']],
+  [79, ['Y','S','F','H','T','V']], [80, ['L','M']],
+  [81, ['Q','E','K','D','T']], [82, ['L','M','I','V','W']],
+  [83, ['R','T','K']], [84, ['A','S','T','V','P']],
+  [85, ['E','A','D','G','S','V']], [86, ['D']], [87, ['T','S']],
+  [88, ['A','G']], [89, ['V','T','I','L','M']], [90, ['Y']],
+  [91, ['Y','F']], [92, ['C']],
+  [93, ['A','T','V']], [94, ['R','K','S','T','A','G']],
+  [95, []], [96, []], [97, []], [98, []], [99, []], [100, []], [101, []],
+  [102, ['Y','V','I','L','F','P','H','S']],
+  [103, ['W']], [104, ['G']], [105, ['Q','P','R','K','A','T']],
+  [106, ['G']], [107, ['T','V','A','I']], [108, ['L','T','M','S','Q','P']],
+  [109, ['V','L','I']], [110, ['T','I','V']], [111, ['V']],
+  [112, ['S','T']], [113, ['S','A']],
+];
+
+export const KABAT_K: [number, string[]][] = [
+  [1, ['D','E','Q','N','A']], [2, ['I','V','L']], [3, ['V','Q','L','E','K']],
+  [4, ['M','L','V','I']], [5, ['T','S']], [6, ['Q']],
+  [7, ['S','T','A','I']], [8, ['P','Q','T','A','H']],
+  [9, ['S','G','L','A','D','K','F','P','V']], [10, ['S','T','F','I']],
+  [11, ['L','M','N','Q','V']], [12, ['T','S','A','P','Y']],
+  [13, ['V','L','A','T','M']], [14, ['T','S','A']],
+  [15, ['A','P','I','V','L']], [16, ['G']],
+  [17, ['E','Q','D','G','T']], [18, ['K','R','P','T','Q','S']],
+  [19, ['V','A','I']], [20, ['T','S']], [21, ['M','L','I','F']],
+  [22, ['S','T','N']], [23, ['C']],
+  [24, ['K','R','Q','S']], [25, ['S','A','T','C']], [26, ['S','T','G']],
+  [27, []], [28, ['N','V','D','S','I','E','Y','T','G']],
+  [29, ['Q','S','G','I','R','V','N','H','T','D']],
+  [30, ['K','S','H','I','R','Y','N','D','V','G','T','A']],
+  [31, ['N','S','T','K','G','V','R','I','D','Y']],
+  [32, ['Y','W','F','D','R','N','S','K','H','A','G']],
+  [33, ['L','M','I','V','F']],
+  [34, ['T','A','N','H','E','G','Q','Y','S','D']],
+  [35, ['W']], [36, ['Y','L','F']], [37, ['Q','L','R']],
+  [38, ['Q','H','E']], [39, ['K','R']],
+  [40, ['P','Q','S','T']], [41, ['G','E','D','H','N']],
+  [42, ['Q','K','S','T','G','E','R']], [43, ['P','A','S','T','V']],
+  [44, ['P','I','V']], [45, ['K','R','Q','E','I','T']],
+  [46, ['L','R','T','P','V','A']], [47, ['L','W']],
+  [48, ['I','V','M']], [49, ['Y','K','H','S','F']],
+  [50, []], [51, ['A','V','T','S','M','G','I']], [52, ['S','K','T','N']],
+  [53, ['T','S','K','N','I','D','R','Y','Q','F']], [54, ['R','L','S']],
+  [55, ['E','A','D','Q','F','R','Y','H','I','K','P','G','V']],
+  [56, ['S','T','D','P','A','E']], [57, ['G']], [58, ['V','I']],
+  [59, ['P','S','A']],
+  [60, ['D','S','A','V','K','G']], [61, ['R']], [62, ['F']],
+  [63, ['T','S','I','K','R']], [64, ['G','S','A']],
+  [65, ['S','G','R']], [66, ['G','R']], [67, ['S','Y']],
+  [68, ['G','R','A']], [69, ['T','R','S','Q']],
+  [70, ['D','E','Q','S','H','Y','A']], [71, ['F','Y']],
+  [72, ['T','S']], [73, ['L','F']], [74, ['T','K','N','S','R']],
+  [75, ['I','V']], [76, ['N','S','H','T','D']],
+  [77, ['S','R','P','N','G','D','T']], [78, ['V','L','M']],
+  [79, ['Q','E','K']], [80, ['A','P','E','S','T','Q','C','Y']],
+  [81, ['E','D']], [82, ['D']],
+  [83, ['L','F','V','T','A','I','S','M']], [84, ['A','G']],
+  [85, ['V','T','S','E','D','L','I','M']], [86, ['Y','F']],
+  [87, ['Y','F','H']], [88, ['C']],
+  [89, ['Q','W','F','L','H','M','G','A','K','S','V']],
+  [90, ['N','Q','H','G']],
+  [91, ['D','Y','G','F','I','S','W','R','T','A','N','H']],
+  [92, []], [93, []], [94, []], [95, []],
+  [96, ['L','Y','W','F','P','R','A','S','I','V','E','H','T']],
+  [97, ['T','S','F']], [98, ['F']],
+  [99, ['G']], [100, ['A','Q','S','G','P']], [101, ['G']],
+  [102, ['T']], [103, ['K','R','E']], [104, ['L','V']],
+  [105, ['E','V','D']], [106, ['L','I','V']], [107, ['K','R']],
+];
+
+export const KABAT_L: [number, string[]][] = [
+  [1, ['Q','S']], [2, ['S','Y','P','A','L','F']], [3, ['A','V','E']],
+  [4, ['L','V']], [5, ['T']], [6, ['Q']], [7, ['P','E','S']],
+  [8, ['A','P','S','R']], [9, ['S','A']], [10, []],
+  [11, ['V','L','A']], [12, ['S','T']],
+  [13, ['G','V','A','T','K','E','F']], [14, ['S','A','T']],
+  [15, ['P','L']], [16, ['G']], [17, ['Q','E','K','A']],
+  [18, ['S','T','K','R']], [19, ['I','A','V']],
+  [20, ['T','R','S','K']], [21, ['I','L']], [22, ['S','T']], [23, ['C']],
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+  [102, ['T']], [103, ['K','T','R','Q']], [104, ['V','L']],
+  [105, ['T']], [106, ['V']], [107, ['L','K']],
+];