Re: [Open Babel] Compressed pybel.Outputfile output
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/ >> > > > > -- > 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 > > -- 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
Re: [Open Babel] Compressed pybel.Outputfile output
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___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Compressed pybel.Outputfile output
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