Re: [Open Babel] Compressed pybel.Outputfile output

2015-04-25 Thread Maciek Wójcikowski
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 :

> Hi Stefano,
>
> That worked!  Thanks!
> Matthew
>
> On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli  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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>
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Re: [Open Babel] Compressed pybel.Outputfile output

2015-04-24 Thread Matthew Lardy
Hi Stefano,

That worked!  Thanks!
Matthew

On Fri, Apr 24, 2015 at 3:34 PM, Stefano Forli  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/
>
--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
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Re: [Open Babel] Compressed pybel.Outputfile output

2015-04-24 Thread Stefano Forli
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/

--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
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