Fantastic! Thanks, Greg! After I got things working I've been able to generate a database and do some preliminary searches. I'm impressed at how quickly I can search ~100,000 compounds with SMARTS patterns. I have a feeling this one is going to get a lot of use.
-Kirk On Mon, Nov 24, 2008 at 12:45 AM, Greg Landrum <[email protected]>wrote: > Dear Kirk, > > On Fri, Nov 21, 2008 at 12:38 AM, Robert DeLisle <[email protected]> > wrote: > > > > After running through the process with exception handling in place I was > > able to isolate 10 structures that were being problematic. All of them > had > > at least one bond designated as 0 order in the SD file - much as you > found > > for some of the other structures previously. I assume that these passed > the > > initial import step but are failing upon descriptor generation for > obvious > > reasons. > > > > I suppose the only request that I have is for more graceful error > handling. > > I've attached my (admittedly sloppy) version of CreateDB.py showing what > I > > did to isolate the errors. > > The problem here was in the mol file parser: it was not correctly > setting up bonds that have order 0. Now it generates a warning (order > 0 isn't technically allowed by the ctab spec) and sets the bond up > correctly. I also added some error checking to handle other bogus bond > orders. > > This was entered as issue 2337369 > ( > https://sourceforge.net/tracker2/?func=detail&aid=2337369&group_id=160139&atid=814650 > ) > and fixed in rev892. > > -greg >
