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;
  },
});

Streams

This API is only available on Node.js.

molecules(options)

Transform an input text stream to a stream of molecule objects.

options

• fullResult: true to emit the full result of parse instead of just the molecules.
• All other options from the parse function.

const { stream } = require('sdf-parser');
fs.createReadStream('test.sdf')
  .pipe(stream.molecules())
  .on('data', (molecule) => {
    console.log(molecule.molfile);
  });

entries()

Transform an input text stream to a stream of sdf entries.

const { stream } = require('sdf-parser');
fs.createReadStream('test.sdf')
  .pipe(stream.entries())
  .on('data', (entry) => {
    // sdf entry as a string
  });

License

MIT

Changelog

5.0.2 (2022-08-17)

Bug Fixes

• infinite loop with files without EOL in the EOF (#7) (9266761)