Very helpful - thanks. I think incorporating this functionality in future OpenBabel releases would be very useful... Found a number of posts online of people (e.g. http://blueobelisk.shapado.com/questions/how-to-split-large-sdf-files-into-series-of-smaller-files) of people wanting to do this...
On 3 June 2011 19:02, Craig A. James <cja...@emolecules.com> wrote: > On 6/3/11 12:56 AM, JP wrote: >> >> Hi there, >> >> Using OpenBabel 2.3.0, is there a way how to split a molecule file >> (e.g. sdf) into chunks? >> >> I can imagine two different modes of action: >> >> 0) split molecule file in n chunks >> 1) split molecule file in chunks of (at most) n molecules >> >> The use case for this is that sometimes you want to work with smaller >> files (e.g. when submitting multiple jobs on a cluster), or for >> testing of products. > > Attached is a Perl program that we developed for this. We find it pretty > useful. > > Usage: split_sdf.pl [N] [-skip N] [-do N] [file.sdf] > N is number of SD records per file > -skip N Skip N records before starting output > -do N Do N records and then quit > -zap_extra_lf Zap extra linefeed between records > > Files will be named with numeric suffix, e.g. "split_sdf.pl foo.sdf" > will generate files like these: > foo_1.sdf > foo_2.sdf > ... etc. > > Craig > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Discover what all the cheering's about. > Get your free trial download today. > http://p.sf.net/sfu/quest-dev2dev2 > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Simplify data backup and recovery for your virtual environment with vRanger. Installation's a snap, and flexible recovery options mean your data is safe, secure and there when you need it. Discover what all the cheering's about. Get your free trial download today. http://p.sf.net/sfu/quest-dev2dev2 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
