jandom/SEAnalysis — Issue #3: plugin vs one-block
Author: jandom
Created: 2011-11-12 10:09:45+00:00
State: open

Now, the SEAnalysis is written as a single python module. However, inside it we can separate out two parts: the protein-related stuff and the Markov/Uniformization related code; these are largely independent.

The protein part contains the code for reading a pdb file, converting it to a distance matrix, handling secondary structure information and interpreting/presenting paths. The Markov-part has the Energy, Q- and R- Matrices and the Uniformization code.

We should separate the biology from maths: it is conceivable that somebody will need the markov part only; also, it is good for content separation (the parts _are_ fundamentally independent)