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

License

MIT