edPDB – editing PDB files

A collection of python snippets to quickly edit pdb files. This is typically used for setting up system for MD simulations.

Typically, one instantiates a edPDB.cbook.PDB object (which can also be accessed as edPDB.PDB) and uses the methods defined on it to write new pdb files.

The cook book edPDB.cbook contains some more specialized functions that are not integrated into PDB yet; study the source and use them as examples.

Built on top of Bio.PDB from Biopython.

Modules

edPDB.cbook
Cook-book with short functions that show how to implement basic functionality.
edPDB.xpdb
Extensions to the Bio.PDB class.
edPDB.selections
Selections that can be used to extract parts of a pdb.

Future plans

Eventually using this module should become as intuitive as grep, sed and cat of pdb files.

Table Of Contents

Previous topic

edPDB — Simple processing of PDB files

Next topic

edPDB.cbook – Recipes for editing PDB files

This Page