Kortemme Lab tools repository
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klab - The Kortemme Lab Tools Repository

A collection of utilities used by our lab for computational biophysics, including PDB parsing, SGE cluster submission scripts, and interfaces with the Rosetta macromolecular software suite.

Coding convention

Besides the whitespace convention (spaces, not tabs), contributors can / generally do use their own preferences. However, code within a module should follow a consistent convention. Finally, please do not reformat modules created by other developers to your preferences.

Here are some semi-standard guidelines:

  • General rules : The PEP 8 conventions (https://www.python.org/dev/peps/pep-0008/) are mostly sensible.
  • Blank lines : See "Blank Lines" in PEP 8. Particularly, surround top-level function and class definitions with two blank lines.
  • Line length : Up to the module creator programmer.
  • Whitespace : Use spaces instead of tabs, with indents set to 4 spaces. Feel free to nuke any tabbed indents with prejudice.
  • Import order : Import standard Python packages first (sys, os) then higher-level/add-on packages (sqlalchemy, numpy), then our other packages (klab), then this package (kddg). Put a line break between each section of imports.
  • Natural language : Please do not introduce contractions into alien modules unless that is the usual for that module.


This package can be installed via:

pip install klab

To install via pip and allow git push/pulling, use:

In a virtualenv:

pip install -e git+ssh://git@github.com/Kortemme-Lab/klab.git#egg=klab

In your user-directory:

pip install --user -e git+ssh://git@github.com/Kortemme-Lab/klab.git#egg=klab

In your user-directory, without using SSH:

pip install --user -e git+https://github.com/Kortemme-Lab/klab.git#egg=klab