This directory contains key scripts involved in construction of the adapted and average kernels

The scripts are:
reindexing_script.py for reindexing structures to ensure consistent atom indexing

group_of_mappings_script.py for obtaining a mathematical group of atom-atom mappings appropriate for a set of conformations

adapted_kernel_script.py construction of an adapted kernel, kpca projection, and running of the GCH

average_kernel_script.py construction of an average kernel, kpca projection, and running of the GCH

please note: some scripts take arguments from a command line but others may have 'hardcoded' variables such as file names that must be edited for each run of the script. 

Kernel based scripts incorporate some code adapted from other sources (The original gch libraries: https://github.com/andreanelli/GCH
and the DirectionalConvexHull code in: https://github.com/scikit-learn-contrib/scikit-matter/blob/main/src/skmatter/sample_selection/_base.py), as referenced in the scripts.

