Reproducible CSD analysis accompanying the paper "Conformation-dependent restraints for polynucleotides: The sugar moiety."

The repository contains experimental source code, PDB validation data, image generation scripts, and detailed results of the analyses discussed in "Conformation-dependent restraints for polynucleotides: The sugar moiety." by Kowiel et al. The repository is divided into the following folders:

• the main folder contains the main soruce code files; to start the experiments run sugar_analyses.py
• sugar_queries contains CONQUEST queries used to retrieve structures with sugar fragments from the CSD
• sugar_results contains cached experiment results (these can be recreated by running sugar_analyses.py)
• sugar_terminal_results contains cached experiment results for terminal sugars
• validation experiments contains all the validation experiments, such as contains NDB validation data and script for calculating differences between bond lengths and angles, as well as additional code and results concerning (re-)refinements of structures with the use of the proposed restraints

To run the experiments the following software has to be installed:

• experiments were run using Python 2.7
• the main Python modules used were: numpy, pandas, scipy, matplotlib, seaborn, plotnine, json, scikit-learn
• CSD queries were run using the CSD Python API version 2.1.0 and the ccdc module

If you have trouble reproducing the experiments or have any comments/suggestions, feel free to write at dariusz.brzezinski (at) cs.put.poznan.pl