I definitely agree. Perhaps a modification of the -m option, e.g. "-m 50" would be chunks of 50 molecules, and "-m 50p" would be 50 parts. In this way, "-m" on its own would be equivalent to "-m 1". The only problem would be if someone wrote "-m 2" by accident, instead of "-m 2p".
- Noel On 4 June 2011 10:55, JP <jeanpaul.ebe...@inhibox.com> wrote: > 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 > ------------------------------------------------------------------------------ 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
