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openforcefield / cmiles

Generate canonical molecule identifiers for quantum chemistry database
https://cmiles.readthedocs.io
MIT License
23 stars 7 forks source link

Add examples that start with oemol/rdmol/qcschema #18

Open bannanc opened 5 years ago

bannanc commented 5 years ago

I wanted to use cmiles to store molecules so I can reliably store the molecules I'm using to test chemper and return to them. It turns out all I needed was cmiles.utils.mol_to_smiles(m). However, it took me a while to find that function.

The Jupyter notebooks in the "notebooks" folder seem to have complex corner cases, which are also important to be documented. When time allows I think it would be valuable to make an "example" notebook that has the more straight forward example that people might want to use this for. Or just still a couple of python snippets in the README. I started by trying to use the How to use cmiles section in the README, but I couldn't even find the function it mentions, to_molecule_id.

ChayaSt commented 5 years ago

Since cmiles is still pre-alpha, the documentation is not extensive yet. But I agree, I need to add a better How to use cmiles ASAP.

bannanc commented 5 years ago

That's totally fair, downside of making me excited about it as an option for testing chemper haha.

You could stick a bold pre-alpha at the top too, I just thought I'd put the issue here so it was documented.