georgewatson / pdb_objects

Object-oriented processing of PDB files in Python

PDB Objects

Set of classes for object-oriented processing of records from PDB files

© 2019 George D. Watson, University of York (https://georgewatson.me)

Available under an MIT license. See the LICENSE file.

This package is described in a post on my blog.

Supports the following record types:

• ATOM
• HETATM
• TER
• HELIX
• SHEET

No other record types are currently implemented, but can be implemented upon request.

Exposes the following classes:

• PDBRecord (should not normally be used directly, except to implement another record type)
• Residue
• Coords
• Atom (for ATOM and HETATM records)
• Helix
• Sheet
• Ter

Exposes the following public functions:

• read_atom
• read_helix
• read_sheet
• read_ter
• read_record
• read_pdb

See class, function, and method docstrings for more information.

Installation

Available on PyPI. Use pip3 install pdb-objects to install, then put import pdb_objects at the top of your script.

Alternatively, clone this repository.