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Published 20 hours ago • verified publisher icon choderalab

KeyError in HYBRIDIZATION_RDKIT

Open nezix opened this issue 1 year ago • 7 comments

I get a dictionary KeyError when calling espaloma_charge -i "GPC_1RDS.mol2":

"espaloma_charge/utils.py", line 55, in fp_rdkit
HYBRIDIZATION_RDKIT[atom.GetHybridization()]
KeyError: rdkit.Chem.rdchem.HybridizationType.SP2D

It looks like SP2D is indeed not in the HYBRIDIZATION_RDKIT.

https://github.com/choderalab/espaloma_charge/blob/59c6bccb9c86e15434dfeff280e6d79845ba5c89/espaloma_charge/utils.py#L11 GPC_1RDS.zip

nezix avatar Oct 13 '23 20:10 nezix