pdbmine v1.2.3

pdbmine

A Node.js API for the RCSB Protein Data Bank (PDB)

Installation

npm install pdbmine

If you plan on using pdbmine in your research/project please cite us at https://arxiv.org/abs/1904.03801

Usage

Just require the package.

var miner = require('pdbmine');

You can query the PDB with a string, and a callback function. The result will be an array of PDB ID strings.

miner.query('ribozyme', function(result){
  console.log(result);
});

You can also just get a list of all the PDB IDs:

miner.get_all_ids(function(result){
  console.log(result);
});

You can download a pdb or cif format file of the structure of interest:

miner.download('5k7c', 'pdb', function(data){
  fs = require('fs');
  fs.writeFileSync('5k7c.pdb', data);
});

You can also get info on certain structures by calling the following function. You pass in either a single PDB-ID or a list, a single parameter or a list of parameters, and a callback function.

miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
  console.log(result);
});

Valid parameters can be accessed via miner.fields. They are also listed at the bottom of this README

You can filter the results from describe_pdb() using the standard Array filtering method:

miner.describe_pdb(['100D','4OJI'], ['depositionDate', 'macromoleculeType'], function(result){
  filtered_result = result.filter(obj => obj.macromoleculeType == 'Protein');
  console.log(filtered_result);
});

Don't like callback functions? You can avoid passing in callback functions and instead use Promises as follows:

miner.query('ribozyme')
	 .then(results => miner.describe_pdb(results, ['macromoleculeType']))
	 .then(descriptions => descriptions.filter(obj => obj.macromoleculeType == 'RNA'))
	 .then(rnas => {
	 	console.log(rnas);
	 });

Parameters