Hi,
Thanks for this very kind offer.
I actually have tools to do this, I use Vortex or MOE. However I am asked about
this occasionally and I just thought it might be a useful addition to have an
Open-Source tool available. Usually people just want to import the data into a
spreadsheet application.
Cheers,
Chris
> On 22 Jan 2016, at 13:33, Maciek Wójcikowski <mac...@wojcikowski.pl> wrote:
>
> 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 <mailto:mac...@wojcikowski.pl>
>
> 2016-01-22 14:17 GMT+01:00 Chris Swain <sw...@mac.com <mailto: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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