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kddg - The Kortemme Lab DDG Database Repository

Database APIs for a database used by our lab to store data about mutageneses, macromolecular complexes, experimental measurements, and computational methods. This database is used primarily for DDG predictions at present.

Note: This code is unsupported and provided as is (see LICENSE).

Dependencies

This repository relies on the klab repository: https://github.com/Kortemme-Lab/klab.

Coding convention

  • 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 : Can be more than 79 characters long. We have widescreen technology.
  • Whitespace : Use spaces instead of tabs, with indents set to 4 spaces.
  • 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 use contractions.
  • Nerdy references : Allowed / encouraged.
  • Shiny? : Shiny! See above.

Versioning

The version of this repository (currently 0.29) follows the internal numbering Shane has used for the database schema versions (currently v2.9).

I plan to change the schema considerably in the near future so the code should be considered in flux and alpha.

Installation

This package can be installed via:

pip install kddg

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

In a virtualenv:

pip install -e git+ssh://[email protected]/Kortemme-Lab/klab.git#egg=klab
pip install -e git+ssh://[email protected]/Kortemme-Lab/kddg.git#egg=kddg

In your user-directory:

pip install --user -e git+ssh://[email protected]/Kortemme-Lab/klab.git#egg=klab
pip install --user -e git+ssh://[email protected]/Kortemme-Lab/kddg.git#egg=kddg

In your user-directory, without using SSH:

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