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ptosco/CanonicalReordering.ipynb

Created August 14, 2020 20:31
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CanonicalReordering
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CanonicalReordering.ipynb
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@JanCBrammer
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Thanks @ptosco, the gist saves the day!

For those who, like me, find it taxing to parse the expression in cells 5 and 6, here's the expression somewhat unpacked:

canon_idx_old_idx = [(j, i) for i, j in enumerate(CanonicalRankAtoms(m))] # [(0, 0), (2, 1), (1, 2)]
old_idcs_sorted_by_canon_idcs = tuple(zip(*sorted(canon_idx_old_idx))) # ((0, 1, 2), (0, 2, 1))
canonical_order = old_idcs_sorted_by_canon_idcs[1] # (0, 2, 1)

@craabreu
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Here's a more compact way using numpy:

m_neworder = tuple(np.argsort(Chem.CanonicalRankAtoms(m)))

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