On 12/11/2010 18:05, Chris Swain wrote: > I've been experimenting with switching some of my scripts from babel to > obabel and I've come across a few unexpected results. > > /usr/local/bin/obabel -ismiles '/Users/swain/Desktop/output.smiles' -f 1 > -l 20 -osdf '/Users/swain/Desktop/output3.sdf' --gen3D > > returns the output to the Terminal and does not create the file. > > In the documentation there is mention of issues with concatenated > single-character options > but is "-f 1 -l 20" is regarded as such?
With obabel you need -O before an output file name. So your example should be: /usr/local/bin/obabel -ismiles '/Users/swain/Desktop/output.smiles' -f 1 -l 20 -osdf -O '/Users/swain/Desktop/output3.sdf' --gen3D Requiring -O is supposed to make it less likely that input file get written over. You could do without -ismiles and -osdf because the file names have appropriate extensions. "-f 1 -l 20" could be "f1 l20" but not "f1l20". (I don't think it can in babel either.) There is less to go wrong if you structure the command as: (as you have) obabel inputfile outputfile options although -i -o -f -l -m options can go anywhere. Chris ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
