> where you want the RMSD without alignment (but still need automorphisms for
> the mapping).
I realized that "obrms" does the mapping...
-Geoff
--
Check out the vibrant tech community on one of the world's most
engaging
I've also got
http://baoilleach.blogspot.co.uk/2012/01/whats-up-dock-calculate-rmsd-between.html
where you want the RMSD without alignment (but still need
automorphisms for the mapping).
I'll see if I get a chance to do this today...
On 1 August 2017 at 16:09, Geoffrey Hutchison wrote:
>> I sho
> I should probably add this feature. In the meanwhile, one way would be to
> generate canonical labels and then shuffle the atoms of both into that order.
Considering this seems to be a common problem, perhaps a Pybel example script
is in order (e.g., read in two molecule files, assign the can
Thanks for the quick reply.
This feature would be extremely useful. I think it is a graph isomorphism
problem.
I’m not following the first method that you proposed. But the second method
you mentioned definitely works. In my case, I need to shuffle the atoms of the
benzene such that they ro
I should probably add this feature. In the meanwhile, one way would be to
generate canonical labels and then shuffle the atoms of both into that
order. Alternatively, if there's a way to get the mapping between two
molecules, you would just need to shuffle the atoms of one of them.
(on my phone so
Hi all,
I'm looking at carbon bonded to benzene. The carbon can bond at all the
equivalent carbon in the benzene, as well as several other places in my
simulation.
I am trying to compare structures by their RMSD, to determine the unique
bonding structures. However, when I use OpenBabel the RMSD
