Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

[Visvaldas K. <coy...@ya...>]

Dear Noel,


Thank you for your answers!

For my 1st question, I had in mind something along the lines of openbabel python bindings. However, a "standalone" version of the rmsd calculation could be probably useful for quite a few people.

Vis




________________________________
From: Noel O'Boyle <bao...@gm...>
To: Visvaldas K. <coy...@ya...> 
Sent: Tuesday, January 17, 2012 11:40 AM
Subject: Re: [OpenBabel-scripting] [Open Babel] pybel - (howto) calculation of RMSD for two molecules (but different conformers)

Regarding (2), it does handle what you call "local symmetry" (automorphisms).

Regarding (1), it wouldn't take long to write a C++ program (not sure
about Python) that used Open Babel to calculate the RMSD in the way
you describe. But I guess you are asking for an option to obabel,
right?

- Noel

On 16 January 2012 20:25, Visvaldas K. <coy...@ya...> wrote:
> 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,
>
> Vis
>
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