I figured as much, and I guess in my case the pandas side will be useful enough for this, thanks.
On Mon, 10 Jan 2022 at 14:05, Greg Landrum <greg.land...@gmail.com> wrote: > Hi James, > > The RDKit does not have a full-featured CSV parser, writing such a thing > is a non-trivial task. If you need to support general CSV, I'd suggest > using pandas or python's builtin csv module... it seems like overkill, but > dealing with all the oddness that can show up in CSVs is really not easy. > > Best, > -greg > > > On Mon, Jan 10, 2022 at 11:15 AM James Wallace <jeawall...@gmail.com> > wrote: > >> As the subject suggests, I'm trying to find a universal solution for >> reading CSVs via the SmilesMolSupplier (as the input setup could be single >> column or multiple column, using the pandas tools for interconversion is >> overkill) >> >> The general structure I use for analysing the CSV is: >> >> >> with open(chem_file_name, "r") as csv_upload_file: >> first_line = csv_upload_file.readline() >> dialect = sniffer.sniff(first_line) >> has_header = sniffer.has_header(first_line) >> csv_upload_file.close() >> >> supplier = Chem.SmilesMolSupplier(chem_file_name, >> delimiter=str(dialect.delimiter), smilesColumn=smi_col_header, >> nameColumn=-1, titleLine=has_header) >> >> If I use a CSV without quoted data,, this is fine, I can autodetect the >> delimiter, the column header is loaded in by the rest of my workflow, >> everything else is worked out through the CSV sniffer. However, where it is >> quoted data, the actual parsing will fail because of the quotemarks. >> >> [10:09:56] SMILES Parse Error: syntax error for input: '"C1=CC=CC=C1"' >> [10:09:56] ERROR: Smiles parse error on line 1 >> >> Is there some easy way of handling this, or do I have to mandate not >> using quoting of data in the CSV generation? >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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