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fix pseudo-knots process in secondary structure #664

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Job	Run time
test (3.8)	4m 47s
lint	24s
test (3.9)	6m 23s
test (3.10)	6m 47s
test (3.11)	4m 54s
test (3.12)	5m 22s
develop	20s
release	0s
pages	1s
	28m 58s