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fix pseudo-knots process in secondary structure #662

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Job	Run time
lint	21s
test (3.8)	6m 21s
test (3.9)	5m 17s
test (3.10)	9m 8s
test (3.11)	5m 47s
test (3.12)	6m 44s
develop	16s
release	0s
pages	2m 45s
	36m 39s