/light-matter

The lighter side of the dark side

Primary LanguageRoff

A collection of python tools for matching sequences based on predicted secondary structures.

For definitions of terms, look here.

For an explanation of the database and find parameters, look here.

Developers

You'll need Python 2 or 3, and the corresponding requirements in requirements-2.txt or requirements-3.txt.

To run the performance tools, you'll need BLAST installed (so blastp is available to compute bit scores for comparison).

Creating needed data files

Run

$ make performance-data

Reducing RAM usage of the Aho Corasick based finders

See here.

Installing PyMOL

You need pymol to run the /light/performance/bin/display-structures-in-pymol.py script. To install, run:

$ brew tap homebrew/science
$ brew install pymol