Automated molecule alignment script from 2D structure sdf files. The 3D coordinates of XYZ files will be generated.
Prepare a <mols>.sdf file containing all molecules to be aligned and <ref>.sdf as an alignment reference.
Run the command : python3 align.py --ref <ref>.sdf --mols <mols>.sdf --type mmff
This is a great blog that talks a lot about RdKit applications.
https://iwatobipen.wordpress.com/2018/09/26/3d-alignment-function-of-rdkit-rdkit/