I sometimes get this error when trying to visualize molecules via their SMILES strings:
This happens to me for the SMILES string I generated for naphthalene with either openbabel (c1cccc2ccccc12) or RDKit (C1=CC2=CC=CC=C2C=C1). Is this an error with the SMILES strings or is there something wrong with my Avogadro?
Both of those work just fine for me.
Can you launch from the terminal and take a look? For example when I launch my dev copy, it shows:
OBProcess::executeObabel: Running "…/prefix/Avogadro2.app/Contents/MacOS/obabel" "-ismi -ocjson --gen3d"
Error with the SMILES strings: I was producing them with a preceding space…
That should be easy to fix on the Avogadro side - I’ll add a patch to trim initial whitespace.
