On 12 Feb 2013, at 07:32, openbabel-discuss-requ...@lists.sourceforge.net wrote:
> Message: 3
> Date: Sun, 10 Feb 2013 19:40:53 +0000
> From: Chris Morley <c.mor...@gaseq.co.uk>
> Subject: Re: [Open Babel] 2.3.2
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <5117f7c5.9000...@gaseq.co.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 09/02/2013 20:04, Chris Swain wrote:
>> Hi
>> My main machine has OpenBabel 2.3.1 installed and this command works fine.
>>
>> ChrisMacbookPro:~ swain$ /usr/local/bin/obgrep -v -c "NNNN"
>> /Users/swain/Desktop/ChemicalStructures/acetophenones.sdf
>> 665
>> The number being the number of molecules in the sdf file.
>>
>>
>> I've been playing around with OpenBabel 2.3.2 from SVN and I now get an
>> error, it seems I now need to explicitly include the input file type.
>>
>> ChrisMacbookPro:~ swain$ /usr/local/bin/obgrep -v -c "NNNN"
>> /Users/swain/Desktop/ChemicalStructures/acetophenones.sdf
>>
>> Does not work but if I include -isdf it does work.
>>
>> SMILES files work with or without the input file defined.
>>
>> I'm not sure if this is something I have done or if it is a bug?
>
> It does that for me too, apparently as a result of a change made last
> summer.
>
> As an alternative, you could use obabel with the -v option and a nul
> output format:
>
> obabel 10dataset.sdf -onul -v "C1CCCCC1"
> 8 molecules converted
>
> This has the extension in that, instead of a SMARTS pattern, the
> parameter of -v can be the name of a file containing several structures
> (in any format) you want to exclude (or, with the -s option, include).
>
> There is currently no obabel equivalent of obgrep's -t NUM option which
> restricts to molecules with exactly NUM matches - but I've just
> rectified that in the development code.
>
> Chris
Am I correct in thinking the output is written to stand error not standard
output?
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