On 12/04/2011 20:31, carlos ortega wrote: > Thank you, > > this line work fine. > > But, is not possible put the name for each molecule that appear in the sdf > file? > > I have about one million of molecules in the sdf file, > > each one have its name in the sdf file, and is some tedious search one name in > one million of files, because the conversion puts other name.
I can see that this would be useful, but at present the molecule title cannot be used as the output file name with babel or obabel. It would probably be possible using a simple Python script. Chris > > ________________________________ > From: Chris Morley<c.mor...@gaseq.co.uk> > To: carlos ortega<cao...@yahoo.es> > Sent: Tue, April 12, 2011 3:18:45 PM > Subject: Re: [Open Babel] info about how convert from SDF multifile to mol2 > > On 12/04/2011 20:00, carlos ortega wrote: >> Greetings, >> >> I used the line >> >> babel *.sdf .mol2 -m >> >> But, does not work. >> >> It put one file mol2 and the name is the same for the file SDF. > > Sorry, I misunderstood what you were doing. Use > babel mymultifile.sdf out.mol2 -m > which will produce a mol2 file for every molecule in the sdf file, > starting with out1.mol2, out2.mol2 ... > > Chris > >> >> I use red hat 5.3 and i download the DAG packages for Red Hat Linux el5 > x86_64, >> openbabel-2.1.1-1.el5.rf.x86_64.rpmHere >> http://rpmfind.net/linux/rpm2html/search.php?query=openbabel&submit=Search+... >> >> Can you help me? >> >> Thank you! >> >> >> Carlos Alberto Ortega Zuñiga >> >> >> >> >> >> >> ________________________________ >> From: Chris Morley<c.mor...@gaseq.co.uk> >> To: openbabel-discuss@lists.sourceforge.net >> Sent: Tue, April 12, 2011 2:50:09 PM >> Subject: Re: [Open Babel] info about how convert from SDF multifile to mol2 >> >> On 12/04/2011 17:58, carlos ortega wrote: >>> Greetings, >>> I try to use babel to convert a multifile SDF to several files MOL2, >>> >>> I use this line: >>> >>> babel -isdf *.sdf -omol2 *.mol2 -m >>> >>> But the conversion put other name for the giles MOL2, and the file SDF has > the >>> name for each file MOL2. >>> >>> How I do to put the name? >>> My file SDF has a lot of files, one million or more. >> >> If you are using Windows >> babel *.sdf *.mol2 >> would convert each sdf file to a mol2 file with the same name. >> >> With Linux, the shell replaces the second * character and you have to >> use instead >> babel *.sdf .mol2 -m >> >> The newer, slightly different obabel interface is now recommended, so >> that the last command becomes >> obabel *.sdf -O .mol2 -m >> >> Chris >> >> ------------------------------------------------------------------------------ >> Forrester Wave Report - Recovery time is now measured in hours and minutes >> not days. Key insights are discussed in the 2010 Forrester Wave Report as >> part of an in-depth evaluation of disaster recovery service providers. >> Forrester found the best-in-class provider in terms of services and vision. >> Read this report now! http://p.sf.net/sfu/ibm-webcastpromo >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> ------------------------------------------------------------------------------ Forrester Wave Report - Recovery time is now measured in hours and minutes not days. Key insights are discussed in the 2010 Forrester Wave Report as part of an in-depth evaluation of disaster recovery service providers. Forrester found the best-in-class provider in terms of services and vision. Read this report now! http://p.sf.net/sfu/ibm-webcastpromo _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
