@squonk/sdf-parser

SDF Parser with Streaming Support

This parser parses a sdf file, supporting web streams, and returns a collection of records. Each record has the following type

``typescript
export type SDFRecord = {
molText: string | undefined;
properties: Record;
};
`

Example 1

`typescript
import { parser } from "@squonk/sdf-parser";

const content = C8H10N4O2
...
M END
>
Caffeine

>
C8H10N4O2

>
194.19

$$$$;

const records = parser(content);
`

records:

`typescript
[
{
molText: "C8H10N4O2\r\n...\r\nM END\r\n",
properties: {
"Compound Name": "Caffeine",
Formula: "C8H10N4O2",
Molweight: "194.19",
},
},
];
`

Example 2: Web Streams

Using web streams, that are now available in most browsers, we create a readable stream with, for example, a fetch request. We can pipe this through the required decoding transformers before parsing it with the provided SDF StreamTransformer.

`typescript
const response = fetch("/some/sdf-file.sdf.gz");
const stream = response.body;
if (stream) {
stream
.pipeThrough(new DecompressionStream("gzip")) // if file is gzipped
.pipeThrough(new TextDecoderStream()) // decode Uint8Array to a string
.pipeThrough(createSDFTransformer()); // parse each chunk into records
}
`

You can then .pipeTo a WriteableStream and do what you wish with each chunk which will be a record object.

Example 3: NodeJS Streams

If you can't rely on the availability of web streams APIs, and can instead parse on a server then you can use this NodeJS implementation.

`typescript
const response = fetch("/some/sdf-file.sdf.gz");
const stream = response.body;
if (stream) {
stream
.pipe(createGunzip()) // if file is gzipped
.pipe(decoderTransform) // wrap a TextDecoder
.pipe(new NodeSDFTransformer()) // parse the SDF record stream
}
``