Open sevyharris opened 4 months ago
If the atom swapping doesn't work well. I have an julia code sitting around from several years ago that I wrote for going from smiles to a julia equivalent of the molecule class. If someone were interested in transcoding that to cython I think that would make it trivial to add this feature and any other modifications we like to smiles=>molecule in the future.
If the atom swapping doesn't work well. I have an julia code sitting around from several years ago that I wrote for going from smiles to a julia equivalent of the molecule class. If someone were interested in transcoding that to cython I think that would make it trivial to add this feature and any other modifications we like to smiles=>molecule in the future.
I might be interested. It looks like there's some weird recursions going on that are complicating my attempts to implement this at the _rdkit_translator level
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Bug Description
I'm trying to create a rmgpy.molecule.Molecule() using smiles
But it fails from an RDKit error:
Possible Solution
I'm wondering if we can get around RDKit's limitations with the following procedure:
It would look something like adding this to the _rdkit_translator() function in RMG-Py/rmgpy/molecule/translator.py:
Other Possible Solution
One workaround is to just instantiate the molecule using the adjacency list. But sometimes that's annoying- especially since we can use smiles for gas phase molecules without any issue. At the very least, a more descriptive error message is probably required, telling the user that you have to use the adjacency list.