https://github.com/justinmc/parse-pdb

A small utility for parsing PDB files into useable JSON
https://github.com/justinmc/parse-pdb

json molecular-data molecule pdb

Last synced: 2 months ago
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A small utility for parsing PDB files into useable JSON

• Host: GitHub
• URL: https://github.com/justinmc/parse-pdb
• Owner: justinmc
• License: mit
• Created: 2017-12-16T20:24:55.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2023-01-25T01:53:00.000Z (almost 2 years ago)
• Last Synced: 2024-09-26T20:47:59.659Z (3 months ago)
• Topics: json, molecular-data, molecule, pdb
• Language: JavaScript
• Size: 106 KB
• Stars: 9
• Watchers: 2
• Forks: 5
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# parse-pdb

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

See also [parse-pdb-rust](https://github.com/justinmc/parse-pdb-rust).

## 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](http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html).

```

  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.