Re: [Open Babel] Problem with gen3D

[Geoff H. <ge...@ge...>]

> 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