nbehrnd

Already an input like ```bash obabel -:"c1ccncc1" -O py*.smi ``` will not create `py*.smi`, but `py1.smi`. In other cases, the file names will require an escape to access them (e.g.,...

May you share a MWE yielding this problem? With a minimal ``` import pubchempy as pcp def retrieve_similar(structure=""): """Retrieve PubChem entries of similar structure.""" similars = pcp.get_compounds(structure, 'smiles', searchtype='similarity', threshold=0.7,...

E.g. `obabel -:"c1ccncn1" -O test.png --append MW`

@fredrikw Ah *this one*. In parlance of Jmol, it is a `.pngj` to retain the model and adjustments of visualization in one container which enables later interaction in Jmol, too...

@kkempfer The inclusion of a Molfile into a `.png` is mentioned in section 18.8.2 / Image formats - png. On-line on readthedocs, it is [here](https://open-babel.readthedocs.io/en/latest/FileFormats/PNG_2D_depiction.html); in case you use the...

You want to annotate the SMILES, don't you? If there is only one datum, then the SMILES has to be enclosed by the quotation marks (either single, or double) as...

The provision of multiple SMILES including an optional title as in the example by the documentation indeed was new for me; I did not spot this when `openbabel` transitioned to...

For the purpose of replication, may you share a MWE of the script you use which yields the warning? Though in a different operating system (Linux Debian 11, yet equally...

Out of curiosity, may you name the new feature / the improved functionality of OpenBabel which is not present (yet) in the repackaged version available from the repositories? For comparison,...

Rewording your post, you identified a detail *to improve* OpenBabel, didn't you? Well in this case, I suggest to 1) check out a current snap shot of OpenBabel as a...