sdf-parser/lib/MolfileStream.js

SDF parser

import { normaliseChunk } from "./normaliseChunk.js";
const SNIFF_LENGTH = 10_000;
/**
 * A `TransformStream` that splits an incoming SDF text stream on the `$$$$`
 * record delimiter and emits individual molfile strings.
 *
 * Handles CRLF, LF, and mixed line endings. By default (`mixedEOL: undefined`)
 * the stream sniffs the first 10 000 characters to detect `\r` and activates
 * normalisation only when needed — zero overhead for pure-LF files.
 *
 * Entries shorter than 40 characters are discarded.
 * @example
 * ```ts
 * const stream = readStream.pipeThrough(new MolfileStream());
 * for await (const molfile of stream) {
 *   console.log(molfile);
 * }
 * ```
 */
export class MolfileStream extends TransformStream {
    constructor({ mixedEOL } = {}) {
        let splitBuffer = '';
        const crState = { pendingCR: false };
        // auto-detection state
        let sniffBuffer = '';
        let decided = mixedEOL !== undefined;
        let normalise = mixedEOL === true;
        function splitRecords(text, controller) {
            const combined = splitBuffer + text;
            splitBuffer = '';
            let begin = 0;
            let index = 0;
            while ((index = combined.indexOf('$$$$', index)) !== -1) {
                const endOfDelimiter = combined.indexOf('\n', index);
                if (endOfDelimiter === -1) {
                    index = begin;
                    break;
                }
                const eolLength = combined[endOfDelimiter - 1] === '\r' ? 2 : 1;
                if (index - eolLength - begin > 40) {
                    controller.enqueue(combined.slice(begin, index - eolLength));
                }
                index = endOfDelimiter + 1;
                begin = index;
            }
            if (begin < combined.length) {
                splitBuffer = combined.slice(begin);
            }
        }
        super({
            transform(chunk, controller) {
                if (decided) {
                    splitRecords(normalise ? normaliseChunk(chunk, crState) : chunk, controller);
                    return;
                }
                sniffBuffer += chunk;
                if (sniffBuffer.length < SNIFF_LENGTH)
                    return;
                decided = true;
                normalise = sniffBuffer.includes('\r');
                const text = normalise
                    ? normaliseChunk(sniffBuffer, crState)
                    : sniffBuffer;
                sniffBuffer = '';
                splitRecords(text, controller);
            },
            flush(controller) {
                if (!decided) {
                    // Stream ended before SNIFF_LENGTH chars were seen.
                    normalise = sniffBuffer.includes('\r');
                    const text = normalise
                        ? normaliseChunk(sniffBuffer, crState)
                        : sniffBuffer;
                    splitRecords(text, controller);
                }
                if (normalise && crState.pendingCR) {
                    splitBuffer += '\r';
                    crState.pendingCR = false;
                }
                if (splitBuffer.length > 40) {
                    controller.enqueue(splitBuffer);
                }
            },
        });
    }
}
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