On Mon, Sep 19, 2011 at 11:23 AM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
> On Mon, Sep 19, 2011 at 11:04 AM, Chris Morley <c.mor...@gaseq.co.uk>
> wrote:
> > On 19/09/2011 09:32, Martin Guetlein wrote:
> >> Hi,
> >>
> >> I would like to do smarts matching with OpenBabel, and for some
> >> reasons I am restricted to use the command line interface.
> >> Is there an efficient way to match a range of smarts strings against a
> dataset?
> >>
> >> What I found out is that I could use the "-s" option, but I would have
> >> to call babel once for each smarts, right?
> > If the SMARTS patterns are sufficiently simple to be SMILES, then they
> > can all be put in a file whose name is used with the -s option. The
> > matching is OR - any single match will do. The file could be any any
> > molecular format, but must have the appropriate extension.
>
I would have to run this once for each smarts, right? (This would produce
quite a file parsing overhead.)
> >>
> >> A second option I found would be to edit the patterns.txt file and use
> >> the FP3 fingerprint ("-ofpt -xfFP3 -xs"). I dont like the idea of
> >> editing a file in advance, though (The smarts matching is part of some
> >> software I am working on). Is there a way to provide an own patterns
> >> file?
> >
> > You can make your own fingerprint by making a data file with SMARTS
> > patterns, like patterns.txt (or with a couple of other slightly
> > different formats) and specifying the details by making an entry in a
> > plugindefines.txt. The MACCS fingerprint is defined there in this way.
>
> This looks good, I will give it a try, thanks,
> Martin
>
Hmm, it worked fine in Linux, not for Windows, though. The plugindefines.txt
is in a folder that requires admin rights to be edited (C:\Program
Files\OpenBabel-2.3.0\data).
Is there a way around that?
>
>
> >
> > For extra flexibility you could define a compound filter to be used with
> > the --filter option, where SMARTS tests can be combined with conditions
> > based on other molecular (or SDF type) properties.
>
Same as for the -s option here, I have to run it once for each smarts,
right?
Regards,
Martin
> >
> > Chris
> >
> >
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>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 7633 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> guetl...@informatik.uni-freiburg.de
>
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@informatik.uni-freiburg.de
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