sdf-parser

sdf-parser

Allow to parse a SDF file and convert it to an array of objects.

Use of the package

npm install sdf-parser

In node script:

// allows to parse a file test.sdf that would be present in the same directory

var { parse } = require('sdf-parser');

var fs = require('fs');
var sdf = fs.readFileSync('./test.sdf', 'utf-8');

var result = parse(sdf);
console.log(result);

require('sdf-parser') (sdf, options)

options:

• exclude : array of string containing the fields to discard
• include : array of string containing the fields to keep
• modifiers : object of functions that need to be converted during the parsing
• filter : function that allows to filter the result
• mixedEOL : if set to true will try to deal with mixed End Of Line separator
• dynamicTyping : convert fields containing only number to numbers (default: true)

Advanced example with filtering and modifiers

var result = parse(sdf, {
  exclude: ['Number of H-Donors'],
  include: ['Number of H-Donors', 'CLogP', 'Code'],
  modifiers: {
    CLogP: function (field) {
      return {
        low: field * 1 - 0.2,
        high: field * 1 + 0.2,
      };
    },
  },
  filter: (entry) => {
    return entry.CLogP && entry.CLogP.low > 4;
  },
});

Iterator

const { iterator } = require('sdf-parser');
const file = await openAsBlob(join(__dirname, 'test.sdf.gz'));

const decompressionStream = new DecompressionStream('gzip');
const textDecoder = new TextDecoderStream();

const stream = file
  .stream()
  .pipeThrough(decompressionStream)
  .pipeThrough(textDecoder);
const results = [];

for await (const entry of iterator(stream)) {
  results.push(entry);
}

License

MIT

Changelog

7.0.4 (2025-03-05)

Bug Fixes

• do not yield molfile that has less than 40 characters long (dc0b2d7)