On Tue, Mar 31, 2009 at 7:26 AM, Marshall Levesque <[email protected]> wrote: > Greg- > > I gotta say that the "RDKit Tech Support Team" is phenomenal at > getting questions answered!
yeah, well, the theory is that after a while other people will be able to answer questions as well. hint, hint. :-) > The previous spiderweb of a 3D structure made it not at all obvious to > me that a little more optimization would do the trick. > > I will look into adding the additional UFFOptimizeMolecule calls. > > Is there a rough estimate you have for the MAX number of attempts one > would make with a 'screening compound' sized molecule in Optimizing > via RDKit? Not really. This isn't something I have spent much time investigating. It's probably also true that the defaults are not particularly well chosen. You may want to increase maxIters to 500 when calling UFFOptimizeMolecule and only try once or twice. There is a slight speed penalty in calling UFFOptimizeMolecule repeatedly instead of doing it once with maxIters increased, but there may also be a win because doing so resets the optimizer (which is neither clever nor massively robust). I'm afraid you'll have to experiment. -greg
