Perhaps this should have gone a to a new thread...
I have a couple of questions about RMSD. Maybe they could lead to "requested
features":)
1) from the documentation, it seems that rmsd calc _always_ does superposition
of the molecules before calculating RMSD. From some older (2007) openbabel
thread it seams there is no way to compute RMSD without superposition. This
would be very useful, say, in ligand-protein docking calculations.
2) The computed RMSDs are "symmetry corrected". There is a global symmetry and
a local symmetry. Is the local symmetry also calculated for the purposes of
symmetry correction when doing RMSD? Actually, it's not a trivial problem; one
way to tackle it is to permute rotations around all rotatable dihedrals in a
reference molecule, and to try to obtain a nearly identical molecule ("nearly"
because of imperfections). Perhaps other algorithms exist. An example would be
a local symmetry of the phenyl ring in phenylalanine: phenylalanine is
non-symmetric, but phenyl inside it has two pairs of equivalent carbons.
Best regards,
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