I understand that this my question is off topic. Nevertheless I hope that – it being in the same field – it is interesting for others in the forum as well.

Anyhow, a colleague recently showed me GAUSSIAN 09. It comes with GaussView 5 for drawing structures. What impressed me was the snappiness of the Clean function. (menu Edit / Clean)

*Any idea what algorithm may be used for the Clean function?*

*Background:* As part of a project called SAN – Self Aware Network, I have a similar problem, though with additional constraints (chirality among others). To find the distribution of points in space, I implemented a *genetic algorithm*. Unfortunately, with large structures, this algorithm tends to get stuck in local minima. I documented the algorithm in the report SAN: Location Optimizer. A mathematician friend implemented a solution using *gradient descend*. Yesterday, he showed me some nice results, but it’s nowhere as snappy as GaussView.