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.
>
> 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.
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.
Chris
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