# Align molecules by clique match¶

A program that aligns a database of molecules with a reference molecule based on the clique of matches between the reference and each query. Clique detection is the process of finding all possible correspondences between two graphs within a set of bounds, the upper bound being the MCS, and in the this example, the lower bound is up to five atoms different to the MCS.

## Example¶

prompt > cliquealign.py ligand.pdb dbase.oeb.gz output.oeb.gz