JavaScript

The npm package is the immunum core compiled to WebAssembly, built for Node.js, with TypeScript types. Install with npm install immunum (Getting started); every type and function is in the API reference.

Results use camelCase: queryStart, queryEnd and errorKind are query_start, query_end and error_kind in the other interfaces. Every other field name is the same.

Numbering and segmentation

const { Annotator } = require("immunum");

// Chains, scheme and an optional minimum confidence, as in Python
const annotator = new Annotator(["ig"], "imgt");

const sequence =
  "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS";

const result = annotator.number(sequence);
console.log(result.chain);                       // "H"
console.log(result.numbering.get("111A"));       // "K": a Map, in sequence order
console.log(result.queryStart, result.queryEnd); // 0 121

const segments = annotator.segment(sequence);
console.log(segments.cdr3); // "AREGTTGKPIGAFAH"

annotator.free();

An Annotator holds WebAssembly memory. The garbage collector frees it eventually, but not on any schedule, so free it yourself when you're done: call free(), or declare it with using (explicit resource management: Node.js 24 or newer, or TypeScript 5.2 or newer) to free it at the end of the block:

{
  using kabat = new Annotator(["H"], "kabat");
  kabat.segment(sequence).cdr1; // "TYALS"
}

Chain and scheme names, and what the minimum confidence does, are in Concepts.

Multiple domains

numberDomains and segmentDomains return one result per variable domain, such as both domains of an scFv, in sequence order. Each is what number or segment returns for that domain, and the residues between two domains are the second domain's prefix:

const heavy =
  "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS";
const kappa =
  "DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK";
const scfv = heavy + "GGGGSGGGGSGGGGS" + kappa;

const annotator = new Annotator(["ig"], "imgt");
annotator.numberDomains(scfv).map((d) => d.chain);    // ["H", "K"]
annotator.segmentDomains(scfv).map((s) => s.prefix);  // ["", "GGGGSGGGGSGGGGS"]
annotator.free();

Schemes and regions

schemeSupportsChain(scheme, chain) tells whether a scheme numbers a chain before you build an annotator, e.g. to offer only valid choices in a UI. regionsFor(scheme, chain) returns the scheme's FR/CDR boundaries for the chain, both ends inclusive, without numbering a sequence. version() returns the version of immunum the module was built from:

const { regionsFor, schemeSupportsChain, version } = require("immunum");

schemeSupportsChain("kabat", "H"); // true
schemeSupportsChain("kabat", "B"); // false: only IMGT numbers TCR chains
regionsFor("kabat", "H").cdr1;     // [31, 35]
version();                         // "2.0.0"

Errors

A setup mistake throws an Error with a kind; a sequence that can't be numbered comes back with error and errorKind set and every other field null. See Errors.