Hi Matthew,
In latest version of OB (master branch on github) automatically detects .gz
extensions and compresses the output - adds "-z" option to converter.
https://github.com/openbabel/openbabel/blob/master/scripts/python/pybel.py#L253
If you're using newest OB it should work out of the box. Otherwise
Stefano's solution is the one you go for.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2015-04-25 0:45 GMT+02:00 Matthew Lardy <mla...@gmail.com>:
> Hi Stefano,
>
> That worked! Thanks!
> Matthew
>
> On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli <fo...@scripps.edu> wrote:
>
>> Hi Matthew,
>> I guess something like this could do the trick:
>> -------------------------
>> import gzip
>> import pybel
>>
>> mol = pybel.readfile('sdf', 'filename.sdf').next()
>> outfilename = 'example.sdf.gz'
>> output = gzip.open(outfilename, 'wb')
>> molString = mol.write(format='sdf')
>> output.write(molString)
>> output.close()
>> -------------------------
>> I didn't tested but I don't see why it shouldn't work(TM)
>>
>> S
>>
>>
>>
>> On 04/24/2015 03:12 PM, Matthew Lardy wrote:
>>
>>> Hi all,
>>>
>>> Does anyone have a route to write compressed sdf.gz files that are
>>> compatible with
>>> pybel.Outputfile?
>>>
>>> Thanks in advance!
>>> Matthew
>>>
>>
>> --
>> Stefano Forli, PhD
>>
>> Staff Scientist
>> Molecular Graphics Laboratory
>> Dept. of Integrative Structural
>> and Computational Biology, MB-112F
>> The Scripps Research Institute
>> 10550 North Torrey Pines Road
>> La Jolla, CA 92037-1000, USA.
>>
>> tel: +1 (858)784-2055
>> fax: +1 (858)784-2860
>> email: fo...@scripps.edu
>> http://www.scripps.edu/~forli/
>>
>
>
>
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