ligalign function provides access to a rigid and flexible ligand alignment algorithm, created by Abraham Heifets, and Ryan H. Lilien, that offers solid alignment performance with a few more features.
Here's the abstract from the reference:
Ligand-based active site alignment is a widely adopted technique for the structural analysis of protein–ligand complexes. However, existing tools for ligand alignment treat the ligands as rigid objects even though most biological ligands are flexible. We present LigAlign, an automated system for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.
ligalign command, pivot_object, target_object(s) [, options ]
Valid commands are:
Valid options for the given commands are: