Uranium hexafluoride invalid compound name about avogadrio HOT 5 CLOSED

https://en.wikipedia.org/wiki/Heme also doesn't work ("backup")
https://en.wikipedia.org/wiki/Porphin is displayed rather weirdly (see screenshot)

from avogadrio.

Hi there, thank you very much for making me aware of this. Heme and uranyl nitrate don't seem to be rendering properly because for whatever reason the service at https://cactus.nci.nih.gov/chemical/structure is giving back vertical pipe characters | when converting the compound name to SMILES. For example, uranyl nitrate gives:

O(|[U](|O[N+]([O-])=O)(=O)=O)[N+]([O-])=O

Adding some code to strip vertical pipe characters results a render for both uranyl nitrate and heme, but both are pretty messed up.

I didn't think | appeared in valid SMILES. Any idea what it signifies @sgitkene?

from avogadrio.

Uranium hexafluoride appears to just be straight up missing from the online chemical database. Might be worth just adding a local database full of these exceptional cases or maybe integrating another lookup service to fall back on. Or both.

from avogadrio.

Yep, got an idea about how to proceed with this. Gonna add a chain of responsibility against several compound name-SMILES lookup services until one of them gives us back valid SMILES. I've added one that scrapes SMILES from Wikipedia as a last resort, but hasn't been tested enough to merge in. Efforts ongoing.

from avogadrio.

Alrighty, fix (for most of the issues you described) is live as of #22 merge:

Uranium hexafluoride: https://avogadr.io/?background=000000&foreground=ffffff&compound=uranium%20hexafluoride

Heme B: https://avogadr.io/?background=000000&foreground=ffffff&compound=heme%20b

Uranyl nitrate: https://avogadr.io/?background=000000&foreground=ffffff&compound=uranyl%20nitrate

Porphin is still a bit of a mystery. Seems like something on the rendering side might need a bit of a tweak. I'll pop it in a separate issue.

from avogadrio.