How many times to reorder atoms during normalisation?

Question

How many times to reorder atoms during normalisation?

js-ojus opened this issue 12 years ago · 1 comments

When a molecule is being normalised, an initial reordering of atoms is performed based on descending secondary hash. Normalised IDs are assigned. A reordering is performed to take into account the order of neighbours. Normalised IDs are assigned, again.

Question: is this enough? Wouldn't it sort once per neighbour, effectively requiring more iterations (probably up to a maximum of 6, practically)?

Answer 1 · 2013-07-30T12:59:29.000Z

Beyond 3 iterations, there seems to be a trivial swapping occurring, leading to an infinite loop. So, I have limited the number of iterations to 3. This can be re-looked at, should there arise a need.