@datagrok/bio 2.25.16 → 2.26.0

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

@@ -0,0 +1,152 @@
+/**
+ * Martin (enhanced Chothia) consensus profiles.
+ */
+
+export const MARTIN_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, []], [27, []], [28, []], [29, []], [30, []], [31, []], [32, []],
+  [33, ['A', 'G', 'W', 'Y', 'D', 'L', 'S', 'T', 'V', 'F']],
+  [34, ['M', 'I', 'W', 'V', 'L']], [35, ['A', 'G', 'H', 'N', 'S', 'T', 'Y']],
+  [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']], [43, ['K', 'Q', 'R', 'N']],
+  [44, ['G', 'A', 'R', 'S']], [45, ['L']], [46, ['E', 'Q']],
+  [47, ['W', 'Y', 'F', 'L']], [48, ['I', 'V', 'K', 'M']], [49, ['A', 'G', 'S']],
+  [50, ['A', 'G', 'S', 'D', 'E', 'N', 'T', 'V', 'I', 'L', 'K', 'R', 'Q', 'P', 'F', 'W', 'Y', 'M', 'H', 'C']], [51, ['A', 'G', 'S', 'D', 'E', 'N', 'T', 'V', 'I', 'L', 'K', 'R', 'Q', 'P', 'F', 'W', 'Y', 'M', 'H', 'C']], [52, []], [53, []],
+  [54, ['S', 'I', 'T', 'D', 'G', 'R', 'N', 'L', 'A', 'Y', 'F', 'E']],
+  [55, ['G', 'S', 'R', 'D', 'W', 'A', 'Y', 'F', 'V', 'N', 'T', 'E', 'L', 'H']],
+  [56, ['S', 'E', 'D', 'I', 'R', 'G', 'Y', 'T', 'V', 'N', 'A', 'H', 'K']],
+  [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', 'S', 'D', 'K', 'T']], [74, ['T', 'Q', 'S', 'I', 'M']],
+  [75, ['L', 'A', 'V', 'F']], [76, ['Y', 'S', 'F', 'H', 'T', 'V']],
+  [77, ['L', 'M']], [78, ['Q', 'E', 'K', 'D', 'T']],
+  [79, ['L', 'M', 'I', 'V', 'W']],
+  [80, ['S', 'N', 'D', 'T', 'R', 'A', 'H', 'K']], [81, ['S', 'N', 'R', 'T', 'A', 'K', 'G']],
+  [82, ['L', 'M', 'V', 'P']], [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 MARTIN_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, ['Q', 'G', 'E', 'S', 'K', 'H']], [28, ['S', 'N', 'D', 'E', 'R', 'T', 'G']],
+  [29, []], [30, []], [31, []], [32, []],
+  [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, ['W', 'G', 'L', 'K', 'N', 'A', 'D', 'Y', 'S', 'E', 'T', 'R', 'Q', 'F', 'V']],
+  [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', 'V', 'I', 'A', 'S', 'F', 'L']], [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 MARTIN_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, ['Q', 'T', 'N', 'S', 'K', 'A', 'R']], [28, ['S', 'I', 'L', 'N', 'G', 'Q']],
+  [29, ['S', 'D', 'G', 'N', 'A', 'R', 'H']],
+  [30, []], [31, ['N', 'K', 'D', 'R', 'Y']],
+  [32, ['F', 'S', 'L', 'A', 'Y', 'T', 'D', 'G', 'N']],
+  [33, ['V', 'A', 'I']], [34, ['S', 'H', 'Q', 'C', 'N', 'Y', 'E']],
+  [35, ['W']], [36, ['Y', 'F', 'V']], [37, ['Q']],
+  [38, ['Q', 'H', 'E']], [39, ['H', 'K', 'R', 'L', 'F', 'V', 'Q']],
+  [40, ['P', 'A', 'S']], [41, ['G', 'D', 'L']],
+  [42, ['K', 'Q', 'T', 'R', 'H', 'S', 'A', 'M']], [43, ['A', 'S', 'L', 'P', 'G']],
+  [44, ['P', 'F']], [45, ['K', 'V', 'S', 'R', 'T', 'I']],
+  [46, ['L', 'V', 'G', 'Y', 'T']], [47, ['I', 'V', 'M', 'L']],
+  [48, ['I', 'V', 'L', 'M']], [49, ['F', 'Y', 'G', 'S', 'E']],
+  [50, ['D', 'A', 'N', 'E', 'Q', 'Y', 'G', 'V', 'R', 'L', 'K']],
+  [51, ['V', 'D', 'N', 'T', 'K']], [52, ['T', 'S', 'Q', 'N', 'D', 'K']],
+  [53, ['N', 'D', 'K', 'Q', 'E', 'S', 'H']], [54, ['R', 'T']],
+  [55, ['P', 'A', 'G']], [56, ['S', 'P', 'D']], [57, ['G']],
+  [58, ['I', 'V']], [59, ['S', 'P']],
+  [60, ['N', 'E', 'A', 'D']], [61, ['R']], [62, ['F']], [63, ['S']],
+  [64, ['G']], [65, ['S']], [66, ['K', 'N', 'P', 'L', 'I', 'S']],
+  [67, ['S', 'D', 'I']], [68, ['G', 'A']],
+  [69, ['N', 'T', 'D', 'S', 'A']], [70, ['T', 'K', 'S', 'R']],
+  [71, ['A', 'R']], [72, ['S', 'T', 'A', 'Y']], [73, ['L']],
+  [74, ['T', 'G', 'A', 'S']], [75, ['I', 'V']], [76, ['S', 'T']],
+  [77, ['G', 'R', 'S', 'N']], [78, ['L', 'V', 'T', 'A', 'I']],
+  [79, ['Q', 'E', 'R']], [80, ['A', 'S', 'P', 'T']],
+  [81, ['E', 'G', 'M', 'D']], [82, ['D']], [83, ['E']],
+  [84, ['A', 'G']], [85, ['D', 'I', 'E']], [86, ['Y']],
+  [87, ['Y', 'F', 'I']], [88, ['C']],
+  [89, ['A', 'Q', 'C', 'H', 'G', 'S']], [90, ['A', 'V', 'L', 'S', 'T', 'M']],
+  [91, ['Y', 'W', 'L', 'R', 'G']],
+  [92, []], [93, []], [94, []], [95, []],
+  [96, ['L', 'V', 'W', 'R', 'P', 'Y', 'S', 'F', 'A']],
+  [97, ['L', 'T', 'V', 'I', 'A', 'F', 'S']], [98, ['F']],
+  [99, ['G']], [100, ['G', 'T', 'S']], [101, ['G']],
+  [102, ['T']], [103, ['K', 'T', 'R', 'Q']], [104, ['V', 'L']],
+  [105, ['T']], [106, ['V']], [107, ['L', 'K']],
+];

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

@@ -0,0 +1,36 @@
+/**
+ * Central consensus profile registry.
+ * Maps (scheme, chainType) -> profile data.
+ */
+import type { Scheme, ChainType } from '../types';
+import { IMGT_H, IMGT_K, IMGT_L, CTERM_H, CTERM_K, CTERM_L } from './consensus-imgt';
+import { KABAT_H, KABAT_K, KABAT_L } from './consensus-kabat';
+import { MARTIN_H, MARTIN_K, MARTIN_L } from './consensus-martin';
+import { AHO_H, AHO_K, AHO_L } from './consensus-aho';
+
+export type ProfileData = [number, string[]][];
+
+/** Get the consensus profile for a given scheme and chain type */
+export function getConsensusProfile(scheme: Scheme, chain: ChainType): ProfileData {
+  const key = `${scheme}_${chain}`;
+  const profiles: Record<string, ProfileData> = {
+    imgt_H: IMGT_H, imgt_K: IMGT_K, imgt_L: IMGT_L,
+    kabat_H: KABAT_H, kabat_K: KABAT_K, kabat_L: KABAT_L,
+    chothia_H: MARTIN_H, chothia_K: MARTIN_K, chothia_L: MARTIN_L,
+    aho_H: AHO_H, aho_K: AHO_K, aho_L: AHO_L,
+  };
+  return profiles[key] ?? IMGT_H;
+}
+
+/** Get the C-terminal finder profile for a chain type */
+export function getCtermProfile(chain: ChainType): ProfileData {
+  const profiles: Record<ChainType, ProfileData> = {
+    H: CTERM_H, K: CTERM_K, L: CTERM_L,
+  };
+  return profiles[chain];
+}
+
+export { IMGT_H, IMGT_K, IMGT_L, CTERM_H, CTERM_K, CTERM_L };
+export { KABAT_H, KABAT_K, KABAT_L };
+export { MARTIN_H, MARTIN_K, MARTIN_L };
+export { AHO_H, AHO_K, AHO_L };

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

@@ -0,0 +1,63 @@
+/**
+ * Region definitions per scheme, keyed by chain group.
+ * Each region: [name, startPosition, endPosition].
+ * Mirrors the Python number_antibody.py definitions.
+ */
+import type { Scheme, ChainGroup } from '../types';
+
+export type RegionDef = [name: string, start: number, end: number];
+
+const IMGT_REGIONS: Record<ChainGroup, RegionDef[]> = {
+  Heavy: [
+    ['FR1', 1, 26], ['CDR1', 27, 38], ['FR2', 39, 55],
+    ['CDR2', 56, 65], ['FR3', 66, 104], ['CDR3', 105, 117], ['FR4', 118, 128],
+  ],
+  Light: [
+    ['FR1', 1, 26], ['CDR1', 27, 38], ['FR2', 39, 55],
+    ['CDR2', 56, 65], ['FR3', 66, 104], ['CDR3', 105, 117], ['FR4', 118, 127],
+  ],
+};
+
+const KABAT_REGIONS: Record<ChainGroup, RegionDef[]> = {
+  Heavy: [
+    ['FR1', 1, 30], ['CDR1', 31, 35], ['FR2', 36, 49],
+    ['CDR2', 50, 65], ['FR3', 66, 94], ['CDR3', 95, 102], ['FR4', 103, 113],
+  ],
+  Light: [
+    ['FR1', 1, 23], ['CDR1', 24, 34], ['FR2', 35, 49],
+    ['CDR2', 50, 56], ['FR3', 57, 88], ['CDR3', 89, 97], ['FR4', 98, 107],
+  ],
+};
+
+const CHOTHIA_REGIONS: Record<ChainGroup, RegionDef[]> = {
+  Heavy: [
+    ['FR1', 1, 25], ['CDR1', 26, 32], ['FR2', 33, 51],
+    ['CDR2', 52, 56], ['FR3', 57, 94], ['CDR3', 95, 102], ['FR4', 103, 113],
+  ],
+  Light: [
+    ['FR1', 1, 25], ['CDR1', 26, 32], ['FR2', 33, 49],
+    ['CDR2', 50, 52], ['FR3', 53, 90], ['CDR3', 91, 96], ['FR4', 97, 107],
+  ],
+};
+
+const AHO_REGIONS: Record<ChainGroup, RegionDef[]> = {
+  Heavy: [
+    ['FR1', 1, 24], ['CDR1', 25, 40], ['FR2', 41, 55],
+    ['CDR2', 56, 78], ['FR3', 79, 108], ['CDR3', 109, 138], ['FR4', 139, 149],
+  ],
+  Light: [
+    ['FR1', 1, 24], ['CDR1', 25, 40], ['FR2', 41, 55],
+    ['CDR2', 56, 78], ['FR3', 79, 108], ['CDR3', 109, 138], ['FR4', 139, 149],
+  ],
+};
+
+const SCHEME_REGIONS: Record<Scheme, Record<ChainGroup, RegionDef[]>> = {
+  imgt: IMGT_REGIONS,
+  kabat: KABAT_REGIONS,
+  chothia: CHOTHIA_REGIONS,
+  aho: AHO_REGIONS,
+};
+
+export function getRegions(scheme: Scheme, chainGroup: ChainGroup): RegionDef[] {
+  return SCHEME_REGIONS[scheme]?.[chainGroup] ?? IMGT_REGIONS.Heavy;
+}

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

@@ -0,0 +1,31 @@
+/**
+ * antibody-numbering - Browser-compatible antibody sequence numbering library.
+ *
+ * Assigns antibody numbering (IMGT/Kabat/Chothia/AHo) to amino acid sequences
+ * using profile-based alignment against consensus sequences.
+ *
+ * @example
+ * ```ts
+ * import { numberSequence } from 'antibody-numbering';
+ *
+ * const result = numberSequence(
+ *   'QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCAR',
+ *   'imgt'
+ * );
+ *
+ * console.log(result.chainType);        // 'Heavy'
+ * console.log(result.numberingDetail);  // [{ position: '1', aa: 'Q' }, ...]
+ * console.log(result.annotations);      // [{ name: 'FR1', ... }, ...]
+ * ```
+ */
+
+export { numberSequence, numberSequences, extractSequence } from './annotator';
+export type {
+  Scheme,
+  ChainType,
+  ChainGroup,
+  NumberingResult,
+  NumberingEntry,
+  RegionAnnotation,
+  AlignmentResult,
+} from './types';