Hi Denes,
It's not quite clear to me whether you are saying that Open Babel is
rearranging the atom order (and want us to fix that) or you are asking how
to rearrange the atom order in two molecules such that corresponding atoms
are in the same order? Can you clarify?
Regards,
- Noel
On 9 March
The "--canonical" option of obabel can reorder atoms into a canonical
order. This can also be accessed through the API, e.g. through Pybel, via
_operations["canonical"].
An alternative approach would be to take a particular reference molecule,
find the mapping of a query molecule onto this, and th
> The "--canonical" option of obabel can reorder atoms into a canonical order.
> This can also be accessed through the API, e.g. through Pybel, via
> _operations["canonical"].
Actually, I think the concern is that the atoms are not grouped by residue,
e.g., all the hydrogens will end up at the
