sequaljs/dist/__test__/proforma_2_1_custom_monosaccharides.test.js

JavaScript/TypeScript library for parsing and manipulating ProForma peptide sequence notation

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
const sequence_1 = require("../sequence");
describe("ProForma 2.1: Custom Monosaccharides in Glycans (Section 10.2)", () => {
    test("should parse single custom monosaccharide", () => {
        const seq = sequence_1.Sequence.fromProforma("SEQUEN[Glycan:{C8H13N1O5}1Hex2]CE");
        expect(seq.seq[5].mods.length).toBe(1);
        const mod = seq.seq[5].mods[0];
        expect(mod.source).toBe("Glycan");
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5}1Hex2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse custom monosaccharide with isotopes", () => {
        const seq = sequence_1.Sequence.fromProforma("SEQUEN[Glycan:{C8H13[15N1]O5}1Hex2]CE");
        const mod = seq.seq[5].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13[15N1]O5}1Hex2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse charged custom monosaccharide", () => {
        const seq = sequence_1.Sequence.fromProforma("SEQUEN[Glycan:{C8H13N1O5Na1:z+1}1Hex2]CE");
        const mod = seq.seq[5].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5Na1:z+1}1Hex2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse charged custom monosaccharide with negative charge", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C6H10O8S1:z-1}1Hex2]PEPTIDE");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C6H10O8S1:z-1}1Hex2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse multiple custom monosaccharides", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C8H13N1O5}1{C6H10O5}2]PEPTIDE");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5}1{C6H10O5}2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse mixed standard and custom monosaccharides", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:HexNAc2{C9H15N1O7}1Hex3]PEPTIDE");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("HexNAc2{C9H15N1O7}1Hex3");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse mixed custom and standard with charge", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C8H13N1O5Na1:z+1}2Hex1HexNAc1]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5Na1:z+1}2Hex1HexNAc1");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse labile custom monosaccharide", () => {
        const seq = sequence_1.Sequence.fromProforma("{Glycan:{C8H13N1O5}1Hex2}PEPTIDE");
        const labileMods = seq.mods.get(-3);
        expect(labileMods).toBeDefined();
        expect(labileMods.length).toBe(1);
        expect(labileMods[0].modValue.pipeValues[0].value).toBe("{C8H13N1O5}1Hex2");
        expect(labileMods[0].modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should parse labile charged custom monosaccharide", () => {
        const seq = sequence_1.Sequence.fromProforma("{Glycan:{C8H13N1O5Na1:z+1}1}PEPTIDE");
        const labileMods = seq.mods.get(-3);
        expect(labileMods).toBeDefined();
        expect(labileMods[0].modValue.pipeValues[0].value).toBe("{C8H13N1O5Na1:z+1}1");
        expect(labileMods[0].modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should serialize custom monosaccharide", () => {
        const original = "SEQUEN[Glycan:{C8H13N1O5}1Hex2]CE";
        const seq = sequence_1.Sequence.fromProforma(original);
        const proforma = seq.toProforma();
        expect(proforma).toBe(original);
    });
    test("should serialize charged custom monosaccharide", () => {
        const original = "SEQUEN[Glycan:{C8H13N1O5Na1:z+1}1Hex2]CE";
        const seq = sequence_1.Sequence.fromProforma(original);
        const proforma = seq.toProforma();
        expect(proforma).toBe(original);
    });
    test("should serialize custom with isotopes", () => {
        const original = "SEQUEN[Glycan:{C8H13[15N1]O5}1Hex2]CE";
        const seq = sequence_1.Sequence.fromProforma(original);
        const proforma = seq.toProforma();
        expect(proforma).toBe(original);
    });
    test("should round-trip custom monosaccharides", () => {
        const testCases = [
            "SEQUEN[Glycan:{C8H13N1O5}1Hex2]CE",
            "SEQUEN[Glycan:{C8H13[15N1]O5}1Hex2]CE",
            "SEQUEN[Glycan:{C8H13N1O5Na1:z+1}1Hex2]CE",
            "N[Glycan:{C6H10O8S1:z-1}1Hex2]PEPTIDE",
            "N[Glycan:HexNAc2{C9H15N1O7}1Hex3]PEPTIDE",
            "{Glycan:{C8H13N1O5}1Hex2}PEPTIDE",
        ];
        for (const original of testCases) {
            const seq = sequence_1.Sequence.fromProforma(original);
            const proforma = seq.toProforma();
            const seq2 = sequence_1.Sequence.fromProforma(proforma);
            const proforma2 = seq2.toProforma();
            expect(proforma).toBe(original);
            expect(proforma2).toBe(original);
        }
    });
    test("should validate standard monosaccharides", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:HexNAc2Hex3NeuAc1]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should validate mixed standard and custom", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:Hex1{C8H13N1O5}1HexNAc2]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should handle custom monosaccharide with parenthetical occurrence", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C8H13N1O5}(1)Hex(2)]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5}(1)Hex(2)");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should handle complex custom formula", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C11H17N1O9}1]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C11H17N1O9}1");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should handle multiple occurrences of same custom monosaccharide", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C8H13N1O5}3]K");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5}3");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
    });
    test("should handle custom monosaccharide with charge state on sequence", () => {
        const seq = sequence_1.Sequence.fromProforma("N[Glycan:{C8H13N1O5Na1:z+1}1Hex2]PEPTIDE/2");
        const mod = seq.seq[0].mods[0];
        expect(mod.modValue.pipeValues[0].value).toBe("{C8H13N1O5Na1:z+1}1Hex2");
        expect(mod.modValue.pipeValues[0].isValidGlycan).toBe(true);
        expect(seq.charge).toBe(2);
    });
    test("should validate glycan count requirements", () => {
        const validCases = [
            { glycan: "HexNAc", reason: "at end, count 1 implied" },
            { glycan: "HexNAc2Hex", reason: "HexNAc has count 2, Hex at end" },
            { glycan: "Hex(3)HexNAc2", reason: "explicit counts" },
            { glycan: "{C8H13N1O5}1Hex2", reason: "custom with count, Hex with count" },
        ];
        validCases.forEach(({ glycan, reason }) => {
            const seq = sequence_1.Sequence.fromProforma(`N[Glycan:${glycan}]K`);
            expect(seq.seq[0].mods[0].modValue.pipeValues[0].isValidGlycan).toBe(true);
        });
    });
    test("should reject invalid glycan counts", () => {
        const invalidCases = [
            { glycan: "HexNAcHex", reason: "HexNAc not at end, missing count" },
            { glycan: "HexNAc0", reason: "zero count not allowed" },
            { glycan: "{C8H13N1O5}Hex2", reason: "custom not at end, missing count" },
        ];
        invalidCases.forEach(({ glycan, reason }) => {
            const seq = sequence_1.Sequence.fromProforma(`N[Glycan:${glycan}]K`);
            expect(seq.seq[0].mods[0].modValue.pipeValues[0].isValidGlycan).toBe(false);
        });
    });
});