sdf-parser/lib/util/getMolecule.js

SDF parser

/**
 * Parse a single SDF entry string into a molecule object.
 * @param sdfPart - A single SDF record (everything before the `$$$$` line).
 * @param labels - Shared label tracking object, mutated in place.
 * @param currentLabels - Array to collect label names found in this entry.
 * @param options - Resolved parse options.
 * @returns The molecule object, or `undefined` if the entry is too short.
 */
export function getMolecule(sdfPart, labels, currentLabels, options) {
    const { eol, dynamicTyping, include, exclude, modifiers, forEach } = options;
    const parts = sdfPart.split(`${eol}>`);
    if (parts.length === 0 || parts[0].length <= 5)
        return undefined;
    const molecule = { molfile: parts[0] + eol };
    for (let j = 1; j < parts.length; j++) {
        const lines = parts[j].split(eol);
        const from = lines[0].indexOf('<');
        const to = lines[0].indexOf('>');
        const label = lines[0].slice(from + 1, to);
        currentLabels.push(label);
        if (!labels[label]) {
            labels[label] = {
                counter: 0,
                isNumeric: dynamicTyping,
                keep: false,
            };
            if (!exclude?.includes(label) && (!include || include.includes(label))) {
                labels[label].keep = true;
                if (modifiers[label])
                    labels[label].modifier = modifiers[label];
                if (forEach[label])
                    labels[label].forEach = forEach[label];
            }
        }
        if (labels[label].keep) {
            for (let k = 1; k < lines.length - 1; k++) {
                if (molecule[label]) {
                    molecule[label] = `${molecule[label]}${eol}${lines[k]}`;
                }
                else {
                    molecule[label] = lines[k];
                }
            }
            if (labels[label].modifier) {
                const modifiedValue = labels[label].modifier(molecule[label]);
                if (modifiedValue === undefined || modifiedValue === null) {
                    // eslint-disable-next-line @typescript-eslint/no-dynamic-delete
                    delete molecule[label];
                }
                else {
                    molecule[label] = modifiedValue;
                }
            }
            if (labels[label].isNumeric &&
                (!Number.isFinite(+molecule[label]) ||
                    molecule[label].match(/^0[0-9]/))) {
                labels[label].isNumeric = false;
            }
        }
    }
    return molecule;
}
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