parse-pdb

A simple utility for parsing PDB files into an easily useable JSON format that handles atoms ,residues, and chains.

Getting Started

npm install --save parse-pdb

``
const parsePdb = require('parse-pdb');
const { readFileSync } = require('fs');

const pdbString = readFileSync('./3aid.pdb', 'utf8');

const parsed = parsePdb(pdbString);

console.log(parsed.atoms);
/*
[ { serial: 1,
name: 'N',
altLoc: '',
resName: 'PRO',
chainID: 'A',
resSeq: 1,
iCode: '',
x: -2.555,
y: 9.253,
z: 34.411,
occupancy: 1,
tempFactor: 30.6,
element: 'N',
charge: '' },
...1845 others
]
*/
`

JSON Format

The output json is an object containing arrays of each structure keyed on record name, according to the pdb spec.

`
atoms:
serial: integer
name: string
altLoc: string
resName: string
chainID: string
resSeq: integer
iCode: string
x: float
y: float
z: float
occupancy: float
tempFactor: float
element: string
charge: string
seqRes:
serNum: integer
chainID: string
numRes: integer
resNames: array of strings
residues:
id: integer (count)
serNum: integer
chainID: string
resName: string
atoms: array of atoms
chains: Map
key: chainID
value:
id: integer (count)
chainID: string
residues: array of residues
``

License

MIT. See LICENSE file.