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.
>>
>> 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
>
> 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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Dipl-Inf. Martin Gütlein
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