Hi Noel,
Thanks a lot for your suggestion.
For structures with different position of double bond apparently it
results different orders.
Here is how I tested: https://bitbucket.org/snippets/deeenes/peGEnG
Do you think the mapping to a reference molecule could work?
Best,
Denes
2018-03-12 14:
Good points, all. Yes - the mapping to a reference molecule should work.
The following blogpost should help:
https://baoilleach.blogspot.co.uk/2010/11/automorphisms-isomorphisms-symmetry.html
Have a look at that, and I'll talk you through the details if you have
questions. OBMol.RenumberAtoms will
> 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
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
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
Dear All,
I would like to export multiple 3D structures into PDB to use them as
ensembles in docking.
I get constitutions from databases in MOL format or as SMILEs and via pybel
I use Open Babel's `make3D()` method to generate 3D. Then I export them one
by one into PDB and subsequently I merge the
