Comments inline below. On Mon, May 14, 2012 at 11:46 PM, My Th <[email protected]> wrote: > You could try to align the molecules and then get the coordinates which > are close enough. Or if the bond perception works correctly and there > are only those Cl bonded to Rh which have to go away, then you could > iterate trough the bonded neighbors of Rh to find the atoms to remove > (Hint, OBAtomAtomIter).
Oooo, I'll have to run that by my group. I don't know anything about bond perception yet, but I do know bonds are built when the molecules are loaded into pybel. I'm also pretty certain from earlier conversations that the metal will not be found in the ligand we're binding to which means I should be able to reliably find at least that starting point. > > Anyway, final structure will have to be checked to make sure that > everything went as expected. > > If you have to remove just four atoms then it would also not be > unthinkable to just provide atom indexes to the script and remove those > atoms. The chemists I'm working with said that they could promise me that the first N molecules of each complex would be the metal which is why I was considering stripping them out prior to loading the into openbabel. I'd hoped not to do that as I was worried it wouldn't be general enough to cover all the input formats we might want to use in the future. Sounds Molecule.atoms is always in the order loaded in from the file though? If that's the case, a simple slice will do it instead. This sounds like the simplest way to get it working right now, but I like the sound of your first suggestion as a more general approach. > > And if it is just one structure you have to edit, then the easiest way > probably is to open it in Avogadro, delete the atoms you want to go away > and save the new structure. Added bonus for this is that you directly > see which atoms you are removing. Large dataset so I definitely need to do it programatically. Any thoughts on why pybel.formula is not updating when I use the underlying OBMol.DeleteAtom? Greg ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
