Code written in Python 2.7.

# Clustering scripts

All source datasets are held in the "Data" folder. The Data folder also stores
cached computation results that will be created when the script is run.

Data preprocessing, clustering, and visualization scripts are in the
"Clustering" folder. The main scripts are run through the "calc_po4.py" and
"calc_po4_terminal.py" files. The main scripts use relative paths to the
datasets, therefore it is best to run the script with "Clustering" as the
working directory.

When run for the first time the script should be executed as follows:

python calc_po4.py
python calc_po4_terminal.py

Without any arguments the script:
- removes all previously created clustering results,
- sets up all the required folders
- joins the raw data into a data frame
- recalculates all distance matrices used for clustering
- performs parameter optinization to find the best clustering

Additionally, one can provide a single argument "cached",  and then the script
assumes that all the above actions have already been performed. With the cached
argument the programmer can work on visualizartions and summaries without
recomputing distances and clusterings with each run.

# Re-refinement scripts

Scripts for running re-refinement for multiple sets of parameters are in the
"RefmacRunner" folder. The file "runner.py" runs refmac, whereas "graphs.py"
creates plots based on refmac logs (logs are already in the "data" subfolder).
External restraints for re-refinement can be generated at:
http://achesym.ibch.poznan.pl/restraintlib/.

Questions and comments are welcome at:
dariusz.brzezinski (at) cs.put.poznan.pl