The point of doing this (I thought) was that you can number a molecule in such a way that the adjacency matrix is PVR-numbered, and that this is canonical. So my cunning plan was to generate all sequences of n numbers that are partially ordered, choosing them from [1, 2n] to give all non-redundant (simple) graphs with n vertices.
Unfortunately, it seems like this can't work:
This image shows all adjacency matrices for n = 3 which are PVR-numbered. They are made by backtracking through all sequences of integers with a partial order, pruning the solutions using the symmetry of the matrix as a constraint.
Anyway, the point is that the first two graphs are clearly isomorphic! More simply, they both represent propane. Maybe this is well known, but it's a surprise to me...

1 comments:
The method used by the previous deterministic structure generator used a similar approach... If just looking at rows may not be enough... what happens if you would look at the ordering of the columns too?
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