get_cid cannot handle #

[stephanflemming]

Hi,

I try to fetch the pubchem cid of the following smiles N#CC4=C(N1CCCNCC1)N(CC=C(Cl)Cl)C5C(=O)N(Cc3nccc2ccccc23)C=NC4=5 (Pubchem entry https://pubchem.ncbi.nlm.nih.gov/compound/23633624) via

get_cid("N#CC4=C(N1CCCNCC1)N(CC=C(Cl)Cl)C5C(=O)N(Cc3nccc2ccccc23)C=NC4=5", from = "smiles")

and run into the following error

Querying N#CC4=C(N1CCCNCC1)N(CC=C(Cl)Cl)C5C(=O)N(Cc3nccc2ccccc23)C=NC4=5. OK (HTTP 200).
Error: lexical error: invalid char in json text.
                                       <?xml version="1.0"?> <PC-Compo
                     (right here) ------^

Probably it's the # that causes this error.

Thanks,
Stephan

[Aariq]

Hi Stephan,

You're absolutely correct that # was the problem. We fixed this in the development version of webchem, so you can either install it with remotes::install_github("ropensci/webchem") or pass your SMILES query through URLencode().

-Eric

Note: This is a duplicate of #269