I've committed couple of ops to allow the commandline (and GUI) to do some more simple tasks.
The --align op uses the first molecule as a reference and then aligns the rest (probably conformers) to it using the OBAlign class. Each is given a property rmsd, measuring how close the fit is, which can be added to the title: obabel refmol.xxx dataset.yyy - O outset.zzz --align --append rmsd The atoms in each molecule need to be in the same order. If used with an -s option, only the atoms which match a SMARTS pattern are used as reference, and the atoms in the molecules can be in any order. An application for this is to align a substructure when a set of molecules is depicted in 2D, to make them easier to appreciate. See http://openbabel.org/docs/2.3.0/Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure The standalone program obfit has similar functionality, but is less versatile. The other op is --largest (aka --smallest) for use with sets of molecules: obabel dataset.xxx -O outset.yyy --largest 5 MW which would convert only the 5 molecules with the the largest molecular weight. Any numeric descriptor or property can be used and the parameters on --largest can be in either order, so that you don't have to remember. A + after the descriptor/property adds its value to the title. The coding of these was trickier than the functionality would suggest... which I suppose is telling us something. Chris ------------------------------------------------------------------------------ Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
