bool OEOverlayConfsByRMSD(OEMCMolBase& mol, const unsigned maxTermHeavyAtoms = 25u)

This method overlays the all conformers of the molecule, onto the first conformer, such that the RSMD between the conformers are minimized. The automorphisms of the molecule graph is taken into consideration during the RMSD calculations.

Molecule whose conformers are to be overlayed.
Maximum number of terminal heavy atoms that should be considered in assessing automorphisms in the molecule graphs. If the number of terminal heavy atoms exceeds this limit, they are ignored for assessing automorphisms.