obgrep used to guess the file type based on the extension but it does not seem
to work now.
Chris
On 8 Aug 2013, at 10:30, openbabel-discuss-requ...@lists.sourceforge.net wrote:
> Message: 2
> Date: Thu, 8 Aug 2013 09:59:54 +0200
> From: Pascal Muller <pascal.jm.mul...@gmail.com>
> Subject: Re: [Open Babel] Fwd: obgrep doesn't work on .sdf
> To: babel <openbabel-discuss@lists.sourceforge.net>
> Message-ID:
> <CAJ5AYJvcbru61GaiPEGdgSVGzcdJ=pqmhxtvn1mrboswcdj...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>>>> Usually, I use obgrep (Open Babel 2.3.2) with smiles files, but today I
>>>>> tried with an sdf - and it doesn't work. There is no match, and no
>> error
>>>>> message (e.g.
>>>>> obgrep 'C' methane.sdf
>>>>> gives no output, as if there were no match.
>>
>
> Trying with a "_" in the molecule name raises this error:
>
> *** Open Babel Error in ReadMolecule
> met_hane contained a character '_' which is invalid in SMILES
>
> The sdf file is read as a smiles file by obgrep...
> Well, ok, my mistake, I never paid attention to that, but the default
> format is smiles, and otherwise need to include the -i option...
>
> obgrep -isdf C meth.sdf
> is working.
>
> I thought that obgrep was guessing the file format from the extension, like
> babel and obabel.
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