I've been having trouble with the 3D coordinate generation in Open Babel. The generator hangs on particular molecules with complicated bonding, and my guess is that the code gets stuck in an infinite loop when it can't satisfy all the constraints while building a 3D structure.
For example the following molecule fragment, consisting of two merged Boron icosahedrons, appears to run forever. obabel -:"[Pd]1234567[B]89%10%11%12%13[B]%14%15%16%17%181[B]1%192[B]2%203[B]348[B]48%20[B]%20%192[B]2%151[B]19%14([B]%1034[B]8%2021)[B]12%12%17[B]34%13[B]85%11[B]596[B]67%16[B]7%109[B]385[B]24%10[B]%18167" -o sdf -O temp.sdf --gen3D I've tried working around this problem by running gen3D on each molecule as it's own subprocess, but this has become annoying. My next step is to modify the source code to avoid this problem, or at least add a timeout option so that the code returns. I was wondering if anyone else on this list was having the same problems, and if anyone had any ideas. ------------------------------------------------------------------------------ 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
