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).
This repository relies on the klab repository: https://github.com/Kortemme-Lab/klab.
- 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.
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.
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://git@github.com/Kortemme-Lab/klab.git#egg=klab pip install -e git+ssh://git@github.com/Kortemme-Lab/kddg.git#egg=kddg
In your user-directory: :: pip install --user -e git+ssh://git@github.com/Kortemme-Lab/klab.git#egg=klab pip install --user -e git+ssh://git@github.com/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