If you need this badly there is na option to write CSV file in ODDT's
virtual screening module. You can choose a delimiter and quotation signs,
but unfortunately it does not write smiles to CSV. If you need it badly i
can add parameter to include smiles in CSV. Sorry for off-OpenBabel mail.
from oddt.virtualscreening import virtualscreening as vs
pipeline = vs()
pipeline.load_ligands('sdf', 'ampc/actives_final.sdf.gz')
pipeline.write_csv('ampc_docked.csv')
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-01-22 14:17 GMT+01:00 Chris Swain <sw...@mac.com>:
> Apologies the title should be sdf export.
>
> A couple of additional comments.
>
> It would be useful to have options for the delimiter. It is possible the
> content may contain commas, so options for tab or pipe might be useful
> and/or putting quotes around text.
>
> Not every record in a sdf will have all fields so the usual strategy is to
> first scan the sdf file to identify all fields and then go back to the
> start to do the export.
>
> Cheers,
>
> Chris
>
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