Package edPDB
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Package edPDB

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:mod:`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 :class:`edPDB.cbook.PDB` object (which
can also be accessed as :class:`edPDB.PDB`) and uses the methods
defined on it to write new pdb files.

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

Built on top of :mod:`Bio.PDB` from Biopython_.

.. _Biopython: http://biopython.org

Modules
-------

:mod:`edPDB.cbook`
    Cook-book with short functions that show how to implement basic
    functionality.

:mod:`edPDB.xpdb`
    Extensions to the Bio.PDB class.

:mod:`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.

Submodules [hide private]
  • edPDB.cbook: :mod:`edPDB.cbook` -- Recipes for editing PDB files ===================================================
  • edPDB.log: Configure logging for edPDB analysis.
  • edPDB.selections: Extensions to Bio.PDB, some useful selections.
  • edPDB.utilities: :mod:`edPDB.utilities` -- Helper functions and classes ========================================================
  • edPDB.xpdb: Extensions to Bio.PDB, such as handling of large pdb files and some useful selections (see :mod:`edPDB.selections`).

Classes [hide private]
  NullHandler
  PDB
Class that represents a PDB file and allows extractions of interesting parts.
Variables [hide private]
  logger = log.create()