Hmm. Not my favourite solution, but I think that the isomorphism checks can be done in batches, resulting in actual isomorph spaces, like this (for C5H10):
This is a small aside. While reading a paper by Grüner, Laue, and Meringer on generation by homomorphism they mentioned the Gale-Ryser (GR) theorem. As it turns out, this is a nice small theorem closely related to the better known Erdős-Gallai (EG). So, GR says that given two partitions of an integer ( p and q) there exists a (0, 1) matrix A iff p* dominates q such that the row sum vector r(A) = p and the column sum vector c(A) = q . As with most mathematics, that's quite terse and full of terminology like 'dominates' : but it's relatively simple. Here is an example: The partitions p and q are at the top left, they both sum to 10. Next, p is transposed to get p* = [5, 4, 1] and this is compared to q at the bottom left. Since the sum at each point in the sequence is greater (or equal) for p* than q , the former dominates. One possible matrix is at the top left with the row sum vector to the right, and th...
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So, is this the result of a generation for C5H10 or has it already been filtered?
So, what I did was all-v-all check the structures produced from a single fragment combination (a single partition) as I assumed that there would only be duplicates within the children of a partition, and not between partition descendants.
Hmmm. I'll make a diagram..
Maybe there are recognizable patterns?
Eg:
10 = [[4, 4, 1, 1], [4, 3, 2, 1], [4, 2, 2, 2], [3, 3, 3, 1], [3, 3, 2, 2]]
In fact, it is also [[7, 1, 1, 1], [6, 2, 1, 1], [5, 3, 1, 1], [5, 2, 2, 1]] but those are rightly rejected for having valences greater than 4.