pdbstruct

pdbstruct - tools for efficient protein analysis in python:

1. pdbstruct hollow - generates hollow atoms for hi-res display of voids, pockets and channels.
2. pdbstruct volume - volume calculator and generator of fake atoms that fill the space.
3. pdstruct asa - calculates and saves atomic ASA to the bfactor column.

This was formerly known as Hollow but was renamed because significant improvements in v2.0 means the package can serve as a general module for efficient protein analysis:

• modern packaging and cli
• mmCIF parsers and writers
• memory efficient representation of protein
• spatial hashing for fast close-pair search
• 3d boolean grid

Quick install

1. If you have uv installed, then for a global install:

   >> uv tool install pdbstruct@latest
   

2. Or you can use ux to run the command in an isolated enviornment:

   >> uvx pdbstruct
   

3. Another alternative is to use pipx to install a gloabl cli:

   >> pipx install pdbstruct
   

4. Or drop into your venv python environment:

   >> pip install pdbstruct
   

Hollow

Hollow was originally developed by Bosco Ho and Franz Gruswitz to solve the problem of displaying protein channels in high resolution. Read more about Hollow.

Change log

• Version 2.0 (Jun 2025). Renamed to pdbstruct. Python 3. Pypi. MmCif. Memory effient representation of protein. Spatial hashing to speed pair-wise search. Removed idle functions.
• Version 1.3 (May 2020). Python 3/2 compatible.
• Version 1.2 (Aug 2011). Changed exceptions to work with Python 2.7 (thanks Joshua Adelman)
• Version 1.1 (Feb 2009). Faster initialization of grid. Works in the IDLE Python interpreter.