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 hard to provide details)
- Noel
On 22 Jul 2017 3:48 p.m., "CodyA" <cral...@umich.edu> wrote:
> 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 values I get are
> large for visually identical structures.
>
> This is because "When aligning molecules, the atoms of the two molecules
> must be in the same order"
>
> In my case, the carbon-carbon bond is between Carbon 1 and carbon 13,
> Carbon
> 2 and carbon 13, etc. all of which are different order but result in the
> same visually identical structure.
>
> Is there any way to programmatically put the atoms of the target in the
> same
> order as reference?
>
>
>
>
>
> --
> View this message in context: http://forums.openbabel.org/
> Put-atoms-of-target-molecule-in-same-order-as-reference-tp4660120.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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