Thanks Geoff, I have some distance geometry code in python and I'm playing with that, but not all distance geometry implementations are of equal quality. I'm working with large numbers of small and medium sized molecules derived from messy crystallography data, so my main goal is a robust function that doesn't get stuck on complex or incorrect structures. I am definitely interested in any developments to the 3D structure builder.
Cheers, -Peter On Fri, Jul 20, 2012 at 11:02 AM, Geoff Hutchison <ge...@geoffhutchison.net> wrote: >> Thanks for the reply - this problem occurs in the builder.Build method >> before the force field optimization, where initial coordinates are >> given to each atom. > > It's not so much an issue of the "constraints" as the fact that you have a > messy fused-ring system. The ring perception and particularly aromatization > routines perform very poorly on systems with large numbers of fused rings. > > I'm currently coding a distance-geometry 3D coordinate generation algorithm, > but it will probably be another few days before I have anything particularly > useful. I'm saving your e-mail as an example that should work quickly and > I'll send you a message if you'd like to try out the development code. > > -Geoff ------------------------------------------------------------------------------ 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 OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
