The -s option is more restricted when used with the fs format. If you type
obabel -L fs
the documentation says:
The search target is the parameter of the ``-s`` option and can be
slightly extended SMILES (with ``[#n]`` atoms and ``~`` bonds) or
the name of a file containing a molecule.
This is
Makes sense, but I guess the documentation needs to be updated, both in the -H
cli help
and online because in the current form it's a bit misleading.
Anyway, this means that fastsearch index can't be used for PAINS filtering, for
example,
which was what I was trying to do.
I'm not sure it
(ccing the list)
That's strange. You might get weird effects if you alter the original
file, or move them around, after creating the .fs file, but if you
just create and use it, then it should work.
If you could file a bug report with a specific test case, we could look into it.
- Noel
On 21
How did you create the .fs file? BTW, there should be no need to
escape if you use double quotation mark, i.e. .
On 21 March 2015 at 21:52, Stefano Forli fo...@scripps.edu wrote:
I think there's an error either in the documentation or in the implementation
of the
filter by pattern in obabel
I think there's an error either in the documentation or in the implementation
of the
filter by pattern in obabel (v2.3.2). The online help says:
$ obabel -H
...
-ssmarts Convert only if match SMARTS or mols in file:
...
as well as the documentation page here:
