nucleotide/lib/src/sequenceToMF.js

Deal with nucleotides and molecular formula

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.sequenceToMF = sequenceToMF;
const chemical_groups_1 = require("chemical-groups");
const mf_utilities_1 = require("mf-utilities");
/**
 * Convert a nucleic sequence to a MF
 * @param {String} sequence
 * @param {object} [options={}]
 * @param {string} [options.kind] - rna, ds-dna or dna. Default if contains U: rna, otherwise ds-dna
 * @param {string} [options.fivePrime=monophosphate] - alcohol, monophosphate, diphosphate, triphosphate
 * @param {string} [options.circular=false]
 */
function sequenceToMF(sequence, options = {}) {
    let fivePrimeTerminal = 'HO';
    let threePrimeTerminal = 'H';
    sequence = sequence.replace(/^HO/, '');
    sequence = sequence.replace(/H$/, '');
    sequence = sequence.trim();
    if (sequence === '')
        return '';
    sequence = (0, mf_utilities_1.ensureUppercaseSequence)(sequence);
    // if the sequence is in lowercase but the parenthesis we should convert it to uppercase
    if (sequence.match(/^[a-z]+$/)) {
        sequence = sequence.toUpperCase();
    }
    let { kind, circular, fivePrime = 'monophosphate' } = options;
    fivePrime = fivePrime.replaceAll(/[^A-Za-z]/g, '').toLowerCase();
    if (!kind) {
        if (sequence.includes('U')) {
            kind = 'rna';
        }
        else {
            kind = 'ds-dna';
        }
    }
    kind = kind.replaceAll(/[^A-Za-z]/g, '').toLowerCase();
    if (sequence.includes('(') && kind === 'dsdna') {
        throw new Error('Nucleotide sequenceToMF: modifications not allowed for ds-DNA');
    }
    let results = [[]];
    if (kind === 'dsdna')
        results.push([]);
    let parenthesisCounter = 0;
    for (let i = 0; i < sequence.length; i++) {
        let currentSymbol = sequence[i];
        while (sequence[i + 1] && sequence[i + 1].match(/[a-z]/)) {
            i++;
            currentSymbol += sequence[i];
        }
        if (currentSymbol.length > 1) {
            results[0].push(currentSymbol);
            continue;
        }
        if (currentSymbol === '(' ||
            currentSymbol === ')' ||
            parenthesisCounter > 0) {
            if (currentSymbol === '(') {
                parenthesisCounter++;
                if (i === 0)
                    fivePrimeTerminal = '';
            }
            if (currentSymbol === ')') {
                parenthesisCounter--;
                if (i === sequence.length - 1)
                    threePrimeTerminal = '';
            }
            switch (kind) {
                case 'dna':
                case 'rna':
                    results[0].push(currentSymbol);
                    break;
                default:
                    // eslint-disable-next-line no-console
                    console.warn(`Nucleotide sequenceToMF with modification: unknown kind: ${kind}`);
            }
            continue;
        }
        let nucleotideType = i === 0 ? fivePrime : 'monophosphate';
        currentSymbol = currentSymbol.replace(/[\t\n\r ]/, '');
        if (!currentSymbol)
            continue;
        switch (kind) {
            case 'dna':
                results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]);
                break;
            case 'rna':
                results[0].push(oxyNucleotides[nucleotideType][currentSymbol]);
                break;
            case 'dsdna':
                results[0].push(desoxyNucleotides[nucleotideType][currentSymbol]);
                results[1].unshift(desoxyNucleotides[nucleotideType][complementary[currentSymbol]]);
                break;
            default:
                // eslint-disable-next-line no-console
                console.warn(`Nucleotide sequenceToMF: unknown kind: ${kind}`);
        }
    }
    if (!circular) {
        for (const result of results)
            result.unshift(fivePrimeTerminal);
        for (const result of results)
            result.push(threePrimeTerminal);
    }
    return results.map((result) => result.join('')).join('.');
}
const complementary = {
    A: 'T',
    T: 'A',
    C: 'G',
    G: 'C',
};
const desoxyNucleotides = {
    alcohol: {},
    monophosphate: {},
    diphosphate: {},
    triphosphate: {},
};
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'DNA')) {
    if (group.oneLetter) {
        desoxyNucleotides.alcohol[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'DNAp')) {
    if (group.oneLetter) {
        desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'NucleotideP')) {
    if (group.oneLetter) {
        desoxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'DNApp')) {
    if (group.oneLetter) {
        desoxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'DNAppp')) {
    if (group.oneLetter) {
        desoxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
    }
}
const oxyNucleotides = {
    alcohol: {},
    monophosphate: {},
    diphosphate: {},
    triphosphate: {},
};
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'RNA')) {
    if (group.oneLetter) {
        oxyNucleotides.alcohol[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'RNAp')) {
    if (group.oneLetter) {
        oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'NucleotideP')) {
    if (group.oneLetter) {
        oxyNucleotides.monophosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'RNApp')) {
    if (group.oneLetter) {
        oxyNucleotides.diphosphate[group.oneLetter] = group.symbol;
    }
}
for (const group of chemical_groups_1.groups.filter(({ kind }) => kind === 'RNAppp')) {
    if (group.oneLetter) {
        oxyNucleotides.triphosphate[group.oneLetter] = group.symbol;
    }
}
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