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 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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[Open Babel] Compressed pybel.Outputfile output

2015-04-24 Thread Matthew Lardy 
Hi all,

Does anyone have a route to write compressed sdf.gz files that are
compatible with pybel.Outputfile?

Thanks in advance!
Matthew
--
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.
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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
___
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss