Hi,
Is there an output format that can be used to convert an sdf file to delimited
text, such that the output contains SMILES, molecule name and any fields within
the sdf? Ideally with the first row of the file being the titles off the fields?
Cheers,
Chris
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Hi Chris,
There is not such thing, as far as I know. Although a hack comes to my
mind: smi + --append in CLI:
obabel -ismi -:'c1c1 title_here' -osmi --append logp
The only issue is that smiles and title is separated by tab (\t) and
properties in title append after spaces. Plus you have to enu
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
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 o
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 applicat
> Apologies the title should be sdf export.
But there is sdf.. do you mean csv (i.e., spreadsheet)?
> 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 ever
