This repository can perform a Kernel-based similarity clustering approach to group crystals by their packing similarity.
(Works hand in hand with motiffinder21/ another project)
For every molecule there are many different ways it can pack in space. Every possible stable solid form of a molecular material is called a polymorph. This code was written to try and analyse and quantify the diversity of those polymorphs for three different molecules carbohelicene (carbo), diethynylhelicene (ethynyl) and dicyanohelicene (cyano).
To cluster the polymorphs by similarity. Each molecular crystal is first transformed into a graph representation. Then a pyramid-match kernel is used to quantify the similarity of the graphs.
The code can be found in the scripts folder.