Dear Kirk, On Fri, Nov 21, 2008 at 12:38 AM, Robert DeLisle <rkdeli...@gmail.com> 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
