PubChemPy
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Is there a way to get all the SMILES for an assay?
Right now I am downloading the smiles one by one, from a compound ID with
mycp = pcp.Compound.from_cid(myCid) canSmiles = mycp.canonical_smiles
After a while, however, I get
urllib2.URLError: <urlopen error [Errno 110] Connection timed out>
And I suspect that pubchem gets (rightfully) upset and blacklists me for a while.
Is there any other way to get all the smiles for an assay?