Greg- I spend too much time on the RDKit sourceforge and google code pages... so I'm sure I will end up answering questions.
I put in the change to the batch process code... with a max of 1000 iterations, and 10 max attempts. Went through a couple thousand molecules pretty quick. I think there were only a few molecules in this test file that needed multiple attempts for optimization. RDKit has been flying through this stuff so I don't think there will be much of a slowdown. Thanks! -Marshall On Mon, Mar 30, 2009 at 10:43 PM, Greg Landrum <[email protected]> wrote: > 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 >
