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toRDKitMol sanization issues #257
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I think @bbuesser found there is no way to get the flexi-valent N to work in RDKit so resorted to avoiding RDKit (in the context of drawing molecules or making SMILES). The use of RDKit in making symmetry numbers is newer than that (by @enochd?). Not sure if/how we can avoid it or fall back to alternatives? |
One hack could be to not run the cyclic symmetry when nitrogen is in the molecule? Not the best solution however... |
See Issue ReactionMechanismGenerator#257 One thought is to make the aromatic_copy of molecule via aromatic_copy = Molecule() aromatic_copy.fromRDKitMol(molecule.toRDKitMol(), kekulize=False)
The |
Running an ethylnitrite example and it crashes because the new calculateCyclicSymmetryNumber calls molecule.toRDKitMol (https://github.com/GreenGroup/RMG-Py/blob/master/rmgpy/molecule/symmetry.py#L340)
Turns out we generate saturated compounds when calculating thermo for radical species by calling estimateRadicalThermoViaHBI in data/thermo.py. We sometimes produce saturated compounds that are not approved by RDKit. The radical and saturated compound in question are:
Radical:
Saturated Compound:
Which generates an explicit valence > 4 for N error. Any thoughts on how to fix this problem?
Typing the following in the command line:
will lead straight to the problem.
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